Index
Date: 2019-10-22

$ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

## $

$(String) - Static method in class org.jmol.i18n.GT

## A

a - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
a - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
a - Variable in class org.jmol.adapter.readers.xtal.CastepReader
a - Variable in class org.jmol.adapter.readers.xtal.GulpReader
a - Variable in class org.jmol.dssx.Bridge
a - Variable in class org.jmol.g3d.PrecisionRenderer
a - Variable in class org.jmol.jvxl.readers.MapFileReader
a - Variable in class org.jmol.minimize.forcefield.Calculation
a - Variable in class org.jmol.render.SticksRenderer
a - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
a - Variable in class org.jmol.util.SimpleUnitCell
A0 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
a1 - Variable in class org.jmol.g3d.HermiteRenderer
a1 - Variable in class org.jmol.util.Modulation
a2 - Variable in class org.jmol.g3d.HermiteRenderer
a2 - Variable in class org.jmol.util.Modulation
a4 - Variable in class org.jmol.render.SticksRenderer
A4_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
A4_CHRG - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
A4_SB - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
A4_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
A4_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
a_ - Variable in class org.jmol.util.SimpleUnitCell
A_WINS - Static variable in class org.jmol.symmetry.CIPChirality
aa - Variable in class org.jmol.g3d.TriangleRenderer
aa - Variable in class org.jmol.renderbio.BioMeshRenderer
aabb - Variable in class org.jmol.adapter.readers.more.AFLOWReader
aaLen - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
aaPlus - Static variable in class org.jmol.modelsetbio.BioExt
aaRet - Variable in class org.jmol.modelset.AtomCollection
aaSp2 - Static variable in class org.jmol.modelsetbio.BioExt
aaSp21 - Static variable in class org.jmol.modelsetbio.BioExt
aaStep - Variable in class org.jmol.thread.MoveToThread
aaStepCenter - Variable in class org.jmol.navigate.Navigator
aaStepCenter - Variable in class org.jmol.thread.MoveToThread
aaStepNavCenter - Variable in class org.jmol.thread.MoveToThread
aaT - Variable in class org.jmol.render.MeasuresRenderer
aaTest1 - Variable in class org.jmol.viewer.TransformManager
aatoken - Variable in class org.jmol.script.ScriptContext
aatoken - Variable in class org.jmol.script.ScriptEval
aatoken - Variable in class org.jmol.script.ScriptFunction
aatokenCompiled - Variable in class org.jmol.script.ScriptCompiler
aaTotal - Variable in class org.jmol.thread.MoveToThread
ab - Variable in class org.jmol.awt.AwtSwingComponent
abc - Variable in class org.jmol.adapter.readers.xtal.CastepReader
ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
abinitContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
AbinitReader - Class in org.jmol.adapter.readers.xtal
AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
abNo - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
AboutDialog - Class in org.openscience.jmol.app.jmolpanel
AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
abs - Static variable in class org.jmol.script.T
absolute - Static variable in class org.jmol.script.T
ABSOLUTE_MIN_MESH_SIZE - Static variable in class org.jmol.renderbio.BioMeshRenderer
absoluteButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
AbstractButton - Class in org.jmol.awtjs.swing
AbstractButton(String) - Constructor for class org.jmol.awtjs.swing.AbstractButton
AbstractTableModel - Interface in org.jmol.awtjs.swing
abYes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
ac - Variable in class org.jmol.adapter.readers.cif.CifReader
ac - Variable in class org.jmol.adapter.readers.cif.MSRdr
ac - Variable in class org.jmol.adapter.readers.more.MdTopReader
ac - Variable in class org.jmol.adapter.readers.more.Mol2Reader
ac - Variable in class org.jmol.adapter.readers.pdb.PdbReader
ac - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
ac - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
ac - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
ac - Variable in class org.jmol.adapter.readers.simple.AmpacReader
ac - Variable in class org.jmol.adapter.readers.simple.CubeReader
ac - Variable in class org.jmol.adapter.readers.simple.InputReader
ac - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
ac - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
ac - Variable in class org.jmol.adapter.readers.xtal.CastepReader
ac - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
ac - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
ac - Variable in class org.jmol.adapter.smarter.AtomIterator
ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
ac - Variable in class org.jmol.atomdata.AtomData
ac - Variable in class org.jmol.geodesic.EnvelopeCalculation
ac - Variable in class org.jmol.jvxl.readers.AtomDataReader
ac - Variable in class org.jmol.jvxl.readers.VolumeFileReader
ac - Variable in class org.jmol.minimize.forcefield.Calculations
ac - Variable in class org.jmol.minimize.Minimizer
ac - Variable in class org.jmol.modelset.AtomCollection
ac - Variable in class org.jmol.popup.JmolPopup
ac - Variable in class org.jmol.shape.AtomShape
ac - Variable in class org.jmol.shapesurface.Contact
ac - Variable in class org.jmol.smiles.SmilesGenerator
ac - Variable in class org.jmol.util.JmolMolecule
ac0 - Variable in class org.jmol.adapter.readers.cif.MMTFReader
ac0 - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
accept(File, String) - Method in class org.jmol.console.JmolConsole.FileChecker
accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
access - Variable in class org.jmol.viewer.Viewer
ACCESS() - Constructor for enum org.jmol.viewer.Viewer.ACCESS
acdAssignments - Variable in class org.jmol.adapter.readers.more.JcampdxReader
acdMolFile - Variable in class org.jmol.adapter.readers.more.JcampdxReader
ACF_ANG - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
ACF_BOHR - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
ACF_M - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
ACF_NM - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
acfFactor - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
acfUnits - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
acm - Variable in class org.jmol.viewer.Viewer
acos - Static variable in class org.jmol.script.T
acr - Variable in class org.jmol.adapter.smarter.XtalSymmetry
act - Variable in class org.jmol.modelset.Model
action(String) - Method in interface org.jmol.api.JmolAudioPlayer
action(String) - Method in class org.jmol.util.JmolAudio
  Execute an action from load audio "xxxxx.wav" filter "id=a1 action=xxx"
action - Variable in class org.jmol.viewer.Gesture
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
ACTION_center - Static variable in class org.jmol.viewer.ActionManager
ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
ACTION_count - Static variable in class org.jmol.viewer.ActionManager
ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
ACTION_select - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
actionCommand - Variable in class org.jmol.awtjs.swing.JComponent
actionInfo - Static variable in class org.jmol.viewer.ActionManager
actionListener - Variable in class org.jmol.awtjs.swing.JComponent
actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
actionManager - Variable in class org.jmol.thread.HoverWatcherThread
ActionManager - Class in org.jmol.viewer
ActionManager() - Constructor for class org.jmol.viewer.ActionManager
ActionManagerMT - Class in org.jmol.multitouch
ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
actionNames - Static variable in class org.jmol.viewer.ActionManager
actionPerformed(ActionEvent) - Method in class org.jmol.awt.AwtPopupHelper
actionPerformed(ActionEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
actionPerformed(ActionEvent) - Method in class org.jmol.console.ImageDialog
actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
actionRotateBond(int, int, int, int, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
  Actually rotate the bond.
actionStates - Variable in class org.jmol.viewer.Viewer
actionStatesRedo - Variable in class org.jmol.viewer.Viewer
activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
active - Variable in class org.jmol.dialog.FilePreview
active_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
activeMenu - Variable in class org.jmol.modelkit.ModelKitPopup
actualID - Variable in class org.jmol.shapesurface.Isosurface
adapter - Variable in class org.jmol.multitouch.ActionManagerMT
adapterModelCount - Variable in class org.jmol.modelset.ModelLoader
adapterTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
add(String) - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
add(SC) - Method in interface org.jmol.api.SC
add(SC) - Method in class org.jmol.awt.AwtSwingComponent
add(SC) - Method in class org.jmol.awtjs.swing.AbstractButton
add(SC) - Method in class org.jmol.awtjs.swing.ButtonGroup
add(Component) - Method in class org.jmol.awtjs.swing.Container
add(JComponent, GridBagConstraints) - Method in class org.jmol.awtjs.swing.Grid
add(JComponent, Object) - Method in class org.jmol.awtjs.swing.JPanel
add(Container, JmolAbstractButton) - Method in class org.jmol.console.AppletConsole
add(Map<String, Object>, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
add - Static variable in class org.jmol.script.T
add(int, int, int, long) - Method in class org.jmol.viewer.Gesture
ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
addActionListener(Object) - Method in interface org.jmol.api.SC
addActionListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
addActionListener(Object) - Method in class org.jmol.awtjs.swing.JComponent
  Note that it will be the job of the JavaScript on the page to do with actionListener what is desired.
addAllCheckboxItems(SC, String[]) - Method in class org.jmol.modelkit.ModelKitPopup
addAlleneLonePair(SmilesAtom, Node[], int) - Method in class org.jmol.smiles.SmilesStereo
  for allenes, we must check for missing atoms
addAllLists(Lst<SV>, Lst<SV>) - Method in class org.jmol.scriptext.MathExt
addAllTriangles() - Method in class org.jmol.jvxl.calc.MarchingSquares
addAssembly(String[]) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addAtom(Lst<Object>, int, byte[], int[], String[], int, Lst<Object>, float[], Lst<Object>, float[], BS, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
addAtom(Atom) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
addAtom() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addAtom(boolean, BS, int, Object, int, String, int, float, Lst<Object>, float, float, P3, boolean, int, int, String, V3, char, float) - Method in class org.jmol.modelset.ModelLoader
addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst<Object>, boolean, byte, BS) - Method in class org.jmol.modelset.ModelSet
addAtom() - Method in class org.jmol.smiles.SmilesSearch
addAtom(int, SimpleNode, boolean, boolean, boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Add a new atom or return null
addAtomComment - Variable in class org.jmol.smiles.SmilesGenerator
addAtomModulation(String, char, char, double[], String, double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Create a list of modulations for each atom type (atom name).
addAtomProp(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
  turns this into a SPHERICAL iterator for "within Distance" measures
addAtoms(int) - Method in class org.jmol.modelset.Group
addAtoms(BS) - Method in class org.jmol.symmetry.UnitCellIterator
addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addAttr() - Method in class org.jmol.export._MayaExporter
addAttrib(Lst<String[]>, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
addAxis(int, V3) - Method in class org.jmol.symmetry.PointGroup
addAzacyclicN(int) - Method in class org.jmol.symmetry.CIPData
addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
addBasis(Map<String, Object>) - Method in class org.jmol.adapter.writers.QCJSONWriter
  Add a basis to the associative array moBases keyed on its hashcode
addBetaSet - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
addBinding(String, Object) - Method in class org.jmol.viewer.binding.Binding
addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
addBioPolymer(BioPolymer) - Method in class org.jmol.modelsetbio.BioModel
addBond(Bond) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
addBond(SmilesBond) - Method in class org.jmol.smiles.SmilesAtom
  Add a bond to the atom.
addBondOr() - Method in class org.jmol.smiles.SmilesBond
addBonds(Lst<Bond>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
addBonds(String, int) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
addBondToAtom(Atom, Bond) - Method in class org.jmol.modelset.BondCollection
addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
addBrace(T) - Method in class org.jmol.script.ScriptCompiler
addBracketedBioName(SB, Node, String, boolean) - Method in class org.jmol.smiles.SmilesGenerator
addBridge(Bridge, Map<int[][], Boolean>) - Method in class org.jmol.dssx.Bridge
addBs(SB, String, BS) - Method in class org.jmol.viewer.StateCreator
addBundle(Viewer, String, String) - Method in class org.jmol.i18n.GT
addBundles(Viewer, String, String, String, String) - Method in class org.jmol.i18n.GT
addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
addButton(JPanel, String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
addBZ(Lst<P4>, Lst<P3>, Lst<P4>, Lst<P3>, int) - Method in class org.jmol.util.BZone
addCellType(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
addCGO(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addChiralAtoms(Lst<CIPChirality.CIPAtom>, int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Create an ASCII string that allows the list of descriptors to be generated in order.
addCoef(Map<String, Object>, float[], String, float, float, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
addColix(short, boolean) - Method in class org.jmol.export._IdtfExporter
addColix(int) - Method in class org.jmol.shapecgo.CGOMesh
addColor(Integer, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
addColors(Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Add new colors from the main "colors" map object.
addColorToMap(Map<String, BS>, String, BS) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
  adds a set of specifically-colored vertices to the map, ensuring that no vertex is in two maps.
addCommand(String) - Method in class org.jmol.util.CommandHistory
  Adds any number of lines to the command history
addCommand(String) - Method in class org.jmol.viewer.Viewer
  Adds one or more commands to the command history
addCommandLine(String) - Method in class org.jmol.util.CommandHistory
  Adds a single line to the bottom of the list, resets list position.
addCompare(T, T) - Method in class org.jmol.script.ScriptTokenParser
addComponent(Component) - Method in class org.jmol.awtjs.swing.Container
addConnect() - Method in class org.jmol.export._MayaExporter
addConnection(int[]) - Method in class org.jmol.adapter.readers.pdb.PdbReader
addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
addConstraint(Object[]) - Method in class org.jmol.minimize.Minimizer
addContextVariable(Map<String, SV>, String) - Static method in class org.jmol.script.ScriptCompiler
addContourPoints(Lst<Object>, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
addCount - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
addData(String, Object) - Method in class org.jmol.modelkit.ModelKitPopup
addData(MOCalculation, boolean) - Method in interface org.jmol.quantum.mo.DataAdder
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder11H
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder13I
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder7F
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder9G
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderF
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderG
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderH
addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderI
addData5D() - Method in class org.jmol.quantum.MOCalculation
addData6D() - Method in class org.jmol.quantum.MOCalculation
addDataP() - Method in class org.jmol.quantum.MOCalculation
addDataS() - Method in class org.jmol.quantum.MOCalculation
addDataSP() - Method in class org.jmol.quantum.MOCalculation
addDirectory(String, String) - Static method in class org.jmol.viewer.FileManager
addDisplayedBackbone(Atom, boolean) - Method in class org.jmol.shapebio.Backbone
addDisplayedBond(int, boolean) - Method in class org.jmol.modelset.Atom
addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
addEdge(Lst<int[]>, Map<String, Object>, Integer, int[], int, P3[]) - Method in class org.jmol.shapespecial.Polyhedra
  Check each edge to see that (a) it has not been used before (b) it does not have vertex points on both sides of it (c) if it runs opposite another edge, then both edge masks are set properly
addEdge(int, int, int) - Method in class org.jmol.util.MeshCapper
  Input method from MeshSlicer.
addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
addEdges(Hashtable<String, SmilesRingSet>) - Method in class org.jmol.smiles.SmilesRing
addExplicitLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
addFacet(int, int, int, P3, P3[], V3[], int[][], int, int, boolean, V3) - Method in class org.jmol.shapespecial.Polyhedra
  Add one of the three "facets" that compose the planes of a "collapsed" polyhedron.
addFile(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
  Adds this file to the history.
addFilterAttribute(Map<String, Object>, String, String) - Method in class org.jmol.script.ScriptEval
addFlags(int, String) - Static method in class org.jmol.smiles.SmilesSearch
addForce(V3d, int, double) - Method in class org.jmol.minimize.forcefield.Calculations
addForces(Calculation, int) - Method in class org.jmol.minimize.forcefield.Calculations
addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
addFunctions(SB, Map<String, JmolScriptFunction>, String, boolean, boolean) - Method in class org.jmol.viewer.StateCreator
addGroup(Lst<Object>, String, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Create a hierarchical list of named groups as generally seen on the PyMOL app's right-hand object menu.
addGroup(Chain, Group) - Method in class org.jmol.modelset.ModelLoader
addGroup3Name(String) - Static method in class org.jmol.modelsetbio.BioResolver
  These can overrun 3 characters; that is not significant.
addGroupAtoms(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
addHbond(Monomer, Monomer, int, int, Map<String, Boolean>) - Method in class org.jmol.dssx.DSSP
addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
addHeader() - Method in class org.jmol.adapter.readers.cif.CifReader
addHeader() - Method in class org.jmol.adapter.readers.cif.MMTFReader
addHelpItems(JMenu, String, String) - Method in class org.jmol.console.AppletConsole
addHelpMenuBar(JMenuBar) - Method in class org.jmol.console.AppletConsole
addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addHetero(String, String, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addHighL(int) - Method in class org.jmol.quantum.MOCalculation
  modular loading of high-L data adders
addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
addHydrogenBond(Lst<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
addHydrogens - Variable in class org.jmol.jvxl.readers.Parameters
addHydrogens(Lst<Atom>, P3[]) - Method in class org.jmol.modelset.ModelSet
  these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
addHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
addhydrogens - Static variable in class org.jmol.script.T
addHydrogens(BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
addHydrogensInline(BS, Lst<Atom>, P3[]) - Method in interface org.jmol.api.JmolScriptManager
addHydrogensInline(BS, Lst<Atom>, P3[]) - Method in class org.jmol.script.ScriptManager
addHydrogensInline(BS, Lst<Atom>, P3[]) - Method in class org.jmol.viewer.Viewer
addImagePixel(byte, int, int, int, int, int) - Method in class org.jmol.g3d.Pixelator
addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.BioResolver
addIncompleteFaces(BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
addIndex - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
addInfo(SB, String[], String, String) - Method in class org.jmol.viewer.binding.Binding
addInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
addIntersectionVertex(T3, float, int, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSlicer
addIsosurface(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addItemListener(Object) - Method in interface org.jmol.api.SC
addItemListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
addItemListener(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
addItems(String[][]) - Method in class org.jmol.popup.PopupResource
addItems(int, T[], int, Lst<Object>, Viewer) - Static method in class org.jmol.shapecgo.CGOMesh
addItemText(SB, char, int, String, String, String, String) - Static method in class org.jmol.popup.GenericPopup
addJmolDataProperties(Model, Map<String, float[]>) - Method in class org.jmol.modelset.ModelLoader
addJmolObject(int, BS, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addKey(Lst<Object>, String) - Static method in class org.jmol.shapecgo.CGOMesh
addKeyBuffer(char) - Method in class org.jmol.awt.Mouse
addKeyBuffer(char) - Method in class org.jmol.awtjs2d.Mouse
addLabel(int, int, int, float[], String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addLadder(Map<int[][], Boolean>) - Method in class org.jmol.dssx.Bridge
addLatticeVector(Lst<float[]>, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
addLatticeVector(Lst<float[]>, String) - Method in interface org.jmol.adapter.smarter.MSInterface
addLatticeVectors() - Method in class org.jmol.adapter.readers.cif.CifReader
addLatticeVectors(Lst<float[]>) - Method in interface org.jmol.api.SymmetryInterface
addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.SpaceGroup
addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.Symmetry
addLine - Variable in class org.jmol.script.ScriptFlowContext
addList(PyMOLGroup) - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
addListener(JmolSelectionListener) - Method in class org.jmol.viewer.SelectionManager
addListSelectionListener(Object) - Method in class org.jmol.awtjs.swing.JTable
  It will be the function of the JavaScript on the page to do with selectionListener what is desired.
addListSelectionListener(Object) - Method in interface org.jmol.awtjs.swing.ListSelectionModel
addLoadData(SB, String, Map<String, Object>, int) - Method in class org.jmol.script.ScriptEval
addMacrosMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addMatrix(String, M4, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addMeasurements(MeasurementData[], int, Lst<Object>, BS, int, Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addMenuItem(SC, String) - Method in class org.jmol.popup.GenericPopup
addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericPopup
addMesh(int, Lst<Object>, String, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addMesh(String, MeshSurface, M4, M4, short, int[], BS) - Method in class org.jmol.export._ObjExporter
  Adds a new mesh using the given data (faces, vertices, and normals) and colix after transforming it via the given affine transform matrix.
addMeshData(String, int, int, int, int, SB, SB, SB, SB, SB, SB) - Method in class org.jmol.export._IdtfExporter
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
addMMTFBonds(int[], int[], int, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMTFReader
addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
addMod(String, String, double[]) - Method in class org.jmol.adapter.readers.cif.MSCifParser
addMOData(int, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
addModel() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
addModelTitle(String) - Method in class org.jmol.adapter.readers.cif.CifReader
addModulation(Map<String, double[]>, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
addModulation(Map<String, double[]>, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
addMolFile(int, SB, BS, BS, boolean, boolean, boolean, Quat) - Method in class org.jmol.util.MolWriter
addMolSS(String, STR) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Secondary structure definition.
addMolStructures() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
addMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
  Note that this method does not check to see that there are no overlapping protein structures.
addMore() - Method in class org.jmol.adapter.readers.cif.CifReader
addMouseListener(Object) - Method in interface org.jmol.api.SC
addMouseListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
addMouseListener(Object) - Method in class org.jmol.awtjs.swing.Component
addName(String) - Method in class org.jmol.script.ContextToken
addNeighboringVertexes(short[], short, short) - Static method in class org.jmol.util.Geodesic
addNested(String) - Method in class org.jmol.smiles.SmilesSearch
addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNewBond(int, int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
  add the bond and mark it for molecular processing
addNewBond(String, String, int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addNextToken() - Method in class org.jmol.script.ScriptTokenParser
addNextTokenIf(int) - Method in class org.jmol.script.ScriptTokenParser
addNormal(V3, V3, float) - Static method in class org.jmol.smiles.SmilesAromatic
  adds a normal if similarity is within limits
addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addNormix(int) - Method in class org.jmol.shapecgo.CGOMesh
addNumber(int, int, Object) - Method in class org.jmol.script.ScriptCompiler
addObject(JmolObject) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addOp(String, Matrix, Matrix, Matrix) - Method in interface org.jmol.api.SymmetryInterface
addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
  addOp The primary driver of the Reverse Polish Notation evaluation engine.
addOp(SymmetryOperation, String, boolean) - Method in class org.jmol.symmetry.SpaceGroup
addOp(String, Matrix, Matrix, Matrix) - Method in class org.jmol.symmetry.Symmetry
addOpAllowMath(T, boolean, int) - Method in class org.jmol.script.ScriptMathProcessor
addOperation(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
addPixel(int, int, int) - Method in class org.jmol.g3d.Pixelator
addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorScreened
addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorShaded
addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorT
addPluginMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
addPngFileBytes(String, byte[], int, Hashtable<Object, String>, boolean, String, int, Lst<Object>) - Method in class org.jmol.viewer.OutputManager
addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
addPoint(T3, int) - Method in class org.jmol.shapespecial.Draw
addPoint(int) - Method in class org.jmol.smiles.SmilesMeasure
addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
addPoint(int, int) - Method in class org.jmol.util.MeshCapper
  The MeshSlicer class manages all introduction of vertices; we must pass on to it the subset of vertices from the original Jmol isosurface being capped.
addPoints(int, Object) - Method in class org.jmol.shapespecial.Draw
addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
addPolygonV3(int, int, int, int, int, int, BS) - Method in class org.jmol.util.MeshSurface
addPolyhedron(Polyhedron) - Method in class org.jmol.shapespecial.Polyhedra
addPrimitive() - Method in class org.jmol.smiles.SmilesBond
addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
addProcess(Lst<T[]>, int, int) - Method in class org.jmol.script.ScriptEval
addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the given properties to the history.
addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the given property to the history.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
addRenderer(int) - Method in class org.jmol.export.Export3D
addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
  allows core JavaScript loading to not involve these classes
addRenderer(int) - Method in class org.jmol.util.GData
addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
addResidueHydrogenBond(Atom, Atom, int, int, float, Lst<Bond>) - Method in class org.jmol.modelsetbio.AminoPolymer
addReturnPath(CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Add the path back to the root for an auxiliary center.
addRing(SmilesRing) - Method in class org.jmol.smiles.SmilesRingSet
addRotatedTensor(Atom, Tensor, int, boolean, SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
addScr(String, String, String, boolean) - Method in class org.jmol.script.ScriptManager
addScript(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
addScript(String, boolean) - Method in class org.jmol.script.ScriptManager
addSecondaryStructure(STR, String, int, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
addSet(SmilesRingSet, Hashtable<String, SmilesRingSet>) - Method in class org.jmol.smiles.SmilesRingSet
addSetting(int, int, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
addShader(String, short) - Method in class org.jmol.export._IdtfExporter
addShapeProperty(Lst<Object[]>, String, Object) - Method in class org.jmol.scriptext.IsoExt
addSinCos(int, String, String, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Add x, y, and z modulations as [ csin, ccos, 0 ] or, possibly Legendre [ coef, order, 0 ]
addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
addSlater(int, int, int, int, int, double, float) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
addSpaceGroupOperation(String, boolean) - Method in class org.jmol.adapter.smarter.XtalSymmetry
addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
addStereoCheck(int, int, SimpleNode, String, BS) - Method in class org.jmol.smiles.SmilesGenerator
  checks a group and either adds a new group to the growing check string or returns null
addString(Atom, int, String, String) - Method in class org.jmol.shape.Labels
addStructure(Structure) - Method in class org.jmol.adapter.readers.cif.MMCifReader
addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addStructure(STR, String, int, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
addStructureByBS(int, int, STR, BS) - Method in class org.jmol.modelsetbio.BioModel
addStructureProtected(STR, String, int, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
addStructuresFromTags(STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
addStructureSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
  We must add groups to the proper bsStructure element
addSubAtom(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
addSubstituteTokenIf(int, T) - Method in class org.jmol.script.ScriptTokenParser
addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
addSymmetrySM(String, M4) - Method in class org.jmol.symmetry.SpaceGroup
addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
addTexture(short, String) - Method in class org.jmol.export._ObjExporter
  Adds a texture to the .mtl file if it is a new texture.
addTickInfo(SB, TickInfo, boolean) - Static method in class org.jmol.viewer.StateCreator
addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
addTo(T3, float) - Method in class org.jmol.util.ModulationSet
addToBonds(Bond, Bond[]) - Method in class org.jmol.modelset.BondCollection
addToken(String, T) - Static method in class org.jmol.script.T
addTokenToPostfix(int, Object) - Method in class org.jmol.script.ScriptTokenParser
addTokenToPostfixInt(int, int, Object) - Method in class org.jmol.script.ScriptTokenParser
addTokenToPostfixToken(T) - Method in class org.jmol.script.ScriptTokenParser
addTokenToPrefix(T) - Method in class org.jmol.script.ScriptCompiler
addToMeasurement(int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
addTracePt(int, Point3fi) - Method in class org.jmol.util.Vibration
addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
addTriangle(MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex, String) - Method in class org.jmol.util.MeshCapper
  Add the triangle and remove v1 from the chain.
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSlicer
  from MeshCapper
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
  addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
addTuple(int, P3) - Method in class org.jmol.bspt.Bspf
addTuple(T3) - Method in class org.jmol.bspt.Bspt
  Iterate through all of your data points, calling addTuple
addTuple(int, T3) - Method in class org.jmol.bspt.Element
addTuple(int, T3) - Method in class org.jmol.bspt.Leaf
addTuple(int, T3) - Method in class org.jmol.bspt.Node
addType(int, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
  sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
addTypeStr(String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
addUnit(int, String, BS, Map<String, BS>) - Method in class org.jmol.modelsetbio.BioModelSet
  Repetitively AND unit components to get the final set of atoms
addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
addUStr(Atom, String, float) - Method in class org.jmol.adapter.readers.cif.MSRdr
addUTens(String, float) - Method in class org.jmol.util.ModulationSet
addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
addValue(Map<String, Object>, String, String, Object) - Method in class org.jmol.applet.Jmol
addValuesSquared(float) - Method in class org.jmol.quantum.MOCalculation
addVariable(String, boolean) - Method in class org.jmol.script.ScriptFunction
addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
addVertexCopy(T3, float, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
  addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
addVertexCopy(T3, float, int, boolean, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
addWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
addWindowBorder(String, Point) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the window border to the history.
addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the window informations to the history.
addWindowListener() - Method in class org.jmol.console.JmolConsole
addWindowPosition(String, Point) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the window position to the history.
addWindowSize(String, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the window size to the history.
addWindowVisibility(String, boolean) - Method in class org.openscience.jmol.app.HistoryFile
  Adds the window visibility to the history.
addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
addXList(Lst<?>) - Method in class org.jmol.script.ScriptMathProcessor
addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
addXMap(Map<String, ?>) - Method in class org.jmol.script.ScriptMathProcessor
addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
addXtalHydrogens - Variable in class org.jmol.modelkit.ModelKitPopup
  when TRUE, add H atoms to C when added to the modelSet.
addZoomTranslationNavigationText(SB) - Method in class org.jmol.viewer.TransformManager
adfContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
AdfReader - Class in org.jmol.adapter.readers.quantum
  TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
adjust - Static variable in class org.jmol.script.T
adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
adjustCartoonSeamNormals(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
  Matches normals for adjacent mesh sections to create a seamless overall mesh.
adjustForWindow - Variable in class org.jmol.modelset.Text
adjustM40Occupancies() - Method in class org.jmol.adapter.readers.xtal.JanaReader
  M40 occupancies are divided by the site multiplicity; here we factor that back in.
adjustRangeMinMax(T3[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry
aDOMNode - Variable in class org.jmol.io.DOMReader
ADP_FACTOR - Static variable in class org.jmol.util.Tensor
ADP_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
adpmax - Static variable in class org.jmol.script.T
adpmin - Static variable in class org.jmol.script.T
adpMode - Variable in class org.jmol.atomdata.AtomData
aflowContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
AFLOWReader - Class in org.jmol.adapter.readers.more
  A reader for various AFLOW file types.
AFLOWReader() - Constructor for class org.jmol.adapter.readers.more.AFLOWReader
afterMath - Variable in class org.jmol.script.ScriptCompiler
afterWhite - Variable in class org.jmol.script.ScriptCompiler
AimsReader - Class in org.jmol.adapter.readers.xtal
  FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
AlchemyReader - Class in org.jmol.adapter.readers.simple
  TRIPOS simple Alchemy reader.
AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
alert(String) - Method in class org.jmol.viewer.Viewer
alertedNoEdit - Variable in class org.jmol.modelkit.ModelKitPopup
align - Variable in class org.jmol.modelset.Text
align - Static variable in class org.jmol.script.T
align1 - Variable in class org.jmol.smiles.PolyhedronStereoSorter
align2 - Variable in class org.jmol.smiles.PolyhedronStereoSorter
alignLeft - Variable in class org.jmol.modelset.LabelToken
alignment_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
alignUnitCells() - Method in class org.jmol.adapter.readers.more.AFLOWReader
alignZX(P3, P3, P3) - Method in class org.jmol.navigate.Navigator
  brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
alkeneChild - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  last atom of an alkene or cumulene atom
alkeneParent - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  first atom of an alkene or cumulene atom
all - Static variable in class org.jmol.script.T
ALL_BONDS - Static variable in class org.jmol.smiles.SmilesBond
ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
all_states - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
allCarbohydrates - Static variable in class org.jmol.modelsetbio.BioResolver
  this form is used for counting groups in ModelSet GLX added for 13.1.16
allconnected - Static variable in class org.jmol.script.T
allEmptyString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
ALLENE - Static variable in class org.jmol.smiles.SmilesStereo
alleneStereo - Variable in class org.jmol.smiles.SmilesGenerator
allfloat - Static variable in class org.jmol.script.T
allFractionalRelative - Variable in class org.jmol.symmetry.UnitCell
  this flag TRUE causes an update of matrixCtoFNoOffset each time an offset is changed so that it is updated and the two stay the same; set true only for JmolData, tensors, and isosurfaceMesh it is no longer clear to me exactly why this is necessary, and perhaps it is not for some of these
allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
allInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
allNaN() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
allNull() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
allocateArray(JmolMolecule[], int) - Static method in class org.jmol.util.JmolMolecule
allocateBioPolymer(Group[], int, boolean, int) - Static method in class org.jmol.modelsetbio.BioResolver
allocateBuffers(int, int, boolean, boolean) - Method in class org.jmol.g3d.Platform3D
allocateColix(int, boolean) - Static method in class org.jmol.util.C
allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Platform3D
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in interface org.jmol.api.GenericPlatform
allocateRgbImage(int, int, int[], int, boolean) - Static method in class org.jmol.awt.Image
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
allocateRgbImage(int, int, int[], int, boolean, Object) - Static method in class org.jmol.awtjs2d.Image
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
  Create an "image" that is either a canvas with width/height/buf32 (from g3d.Platform32) or just an associative array with those (image writing
allocateTBuffers(boolean) - Method in class org.jmol.g3d.Platform3D
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
  This is the older main access point for creating an application or applet vwr.
allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
  a simpler option
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
  legacy only
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
  old way...
allocDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
allocMesh(String, Mesh) - Method in class org.jmol.shapecgo.CGO
allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
allocRaster(boolean, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
allocTempEnum(int) - Method in class org.jmol.util.TempArray
allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
allocTempPoints(int) - Method in class org.jmol.util.TempArray
allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
allocTempScreens(int) - Method in class org.jmol.util.TempArray
allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
allocVertexColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
allOperators - Variable in class org.jmol.modelkit.ModelKitPopup
allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
allowAromaticBond(Bond) - Method in class org.jmol.modelset.BondCollection
allowArrayDotNotation - Variable in class org.jmol.viewer.Viewer
allowAtomName(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
allowaudio - Static variable in class org.jmol.script.T
allowAudio - Variable in class org.jmol.viewer.GlobalSettings
allowCapture() - Method in class org.jmol.viewer.Viewer
allowDebug - Static variable in class org.jmol.i18n.GT
allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
allowembeddedscripts - Static variable in class org.jmol.script.T
allowEmbeddedScripts - Variable in class org.jmol.viewer.GlobalSettings
allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
allowgestures - Static variable in class org.jmol.script.T
allowGestures - Variable in class org.jmol.viewer.GlobalSettings
allowHighPrecision - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
allowJSEval - Variable in class org.jmol.applet.Jmol
allowJSThreads - Variable in class org.jmol.script.ScriptContext
allowJSThreads - Variable in class org.jmol.script.ScriptEval
allowkeystrokes - Static variable in class org.jmol.script.T
allowKeyStrokes - Variable in class org.jmol.viewer.GlobalSettings
allowMapData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
allowMesh - Variable in class org.jmol.shapesurface.Isosurface
allowMissingEnd - Variable in class org.jmol.script.ScriptCompiler
allowmodelkit - Static variable in class org.jmol.script.T
allowModelkit - Variable in class org.jmol.viewer.GlobalSettings
allowmoveatoms - Static variable in class org.jmol.script.T
allowMoveAtoms - Variable in class org.jmol.viewer.GlobalSettings
allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
allowmultitouch - Static variable in class org.jmol.script.T
allowMultiTouch - Variable in class org.jmol.viewer.GlobalSettings
allowNegative - Variable in class org.jmol.jvxl.readers.IsoShapeReader
allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
allowrotateselected - Static variable in class org.jmol.script.T
allowRotateSelected - Variable in class org.jmol.viewer.GlobalSettings
allowRotations - Variable in class org.jmol.adapter.readers.cif.CifReader
allowScripting - Variable in class org.jmol.viewer.Viewer
allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
allowSignedFeatures - Variable in class org.jmol.popup.GenericPopup
allowSmilesUnbracketed(String) - Static method in class org.jmol.smiles.SmilesAtom
allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
allowSurface - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
allowUnderflow - Variable in class org.jmol.script.ScriptMathProcessor
allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
allPositive - Variable in class org.jmol.symmetry.HallRotationTerm
allSame() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
allSelectedWidgets() - Method in class org.openscience.jmol.app.webexport.WebPanel
allStates - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
allTypes - Variable in class org.jmol.adapter.readers.more.JcampdxReader
allZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
almost180 - Static variable in class org.jmol.modelset.AtomCollection
alpha - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
alpha - Variable in class org.jmol.adapter.readers.xtal.CastepReader
alpha - Variable in class org.jmol.adapter.readers.xtal.GulpReader
alpha - Variable in class org.jmol.jvxl.readers.MapFileReader
ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
alpha - Variable in class org.jmol.util.SimpleUnitCell
ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
ALPHA_SHIFT - Static variable in class org.jmol.util.C
ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
AlphaMonomer - Class in org.jmol.modelsetbio
AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets - Static variable in class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets - Static variable in class org.jmol.modelsetbio.CarbohydrateMonomer
alphaOnly - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
AlphaPolymer - Class in org.jmol.modelsetbio
AlphaPolymer(Monomer[], int) - Constructor for class org.jmol.modelsetbio.AlphaPolymer
AlphaPolymer.Code - Enum in org.jmol.modelsetbio
alphas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
ALT - Static variable in class org.jmol.util.ColorEncoder
ALT - Static variable in class org.jmol.viewer.binding.Binding
ALT_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
ALT_MASK - Static variable in class org.jmol.awtjs.Event
altArgbsCpk - Variable in class org.jmol.viewer.ColorManager
altArgbsCpk - Static variable in class org.jmol.viewer.JC
altElementCounts - Variable in class org.jmol.util.JmolMolecule
altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
altElementMax - Static variable in class org.jmol.util.Elements
  length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementMax - Variable in class org.jmol.util.JmolMolecule
altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
altElementNames - Static variable in class org.jmol.util.Elements
altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
altElementNumbers - Static variable in class org.jmol.util.Elements
altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
altElementSymbols - Static variable in class org.jmol.util.Elements
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
ALTLOC - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
altLoc - Variable in class org.jmol.adapter.smarter.Atom
altloc - Variable in class org.jmol.modelset.Atom
altloc - Static variable in class org.jmol.script.T
altLocCount - Variable in class org.jmol.modelset.Model
altlocs - Variable in class org.jmol.popup.JmolPopup
altNames - Variable in class org.jmol.adapter.readers.pdb.P2nReader
altType - Variable in class org.jmol.util.Tensor
altVertices - Variable in class org.jmol.util.MeshSurface
am - Variable in class org.jmol.modelset.ModelSet
am - Variable in class org.jmol.thread.AnimationThread
am - Variable in class org.jmol.viewer.Viewer
ambient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ambient_occlusion_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ambient_occlusion_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ambient_occlusion_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ambientFraction - Variable in class org.jmol.util.Shader
ambientocclusion - Static variable in class org.jmol.script.T
ambientOcclusion - Variable in class org.jmol.util.GData
ambientpercent - Static variable in class org.jmol.script.T
ambientPercent - Variable in class org.jmol.util.Shader
ambiguityType - Variable in class org.jmol.symmetry.SpaceGroup
ambiguousNames - Static variable in class org.jmol.symmetry.SpaceGroup
amino - Static variable in class org.jmol.script.T
AMINO - Static variable in class org.jmol.util.ColorEncoder
AminoMonomer - Class in org.jmol.modelsetbio
AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
AminoPolymer - Class in org.jmol.modelsetbio
AminoPolymer(Monomer[], int) - Constructor for class org.jmol.modelsetbio.AminoPolymer
ampacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
AmpacReader - Class in org.jmol.adapter.readers.simple
  A reader for AMPAC output.
AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
AMPLITUDE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Maximum value for vibration scale.
AMPLITUDE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Precision of the vibration scale slider
AMPLITUDE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Initial value of vibration scale.
amplitudeSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
anaglyph_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
anaglyphChannelBytes - Variable in class org.jmol.g3d.Graphics3D
anaglyphLength - Variable in class org.jmol.g3d.Graphics3D
anchor - Variable in class org.jmol.awtjs.swing.GridBagConstraints
andBitSet(BS) - Method in class org.jmol.shapespecial.Polyhedra
andequals - Static variable in class org.jmol.script.T
andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
angle - Static variable in class org.jmol.script.T
angle - Variable in class org.jmol.thread.SpinThread
angle_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
angle_label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
angle_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
angleCount - Variable in class org.jmol.minimize.forcefield.Calculations
anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.Slice
anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
angleUnits - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
angleUnitsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
angleXY - Variable in class org.openscience.jmol.app.surfacetool.Slice
angleXY - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
angleXYSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
angleZSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
angMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
angstroms - Static variable in class org.jmol.script.T
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.Parameters
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.SurfaceReader
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
angstromsToPixels(float) - Method in class org.jmol.viewer.TransformManager
angularPart(double, double, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
animation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
animation - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
animation - Static variable in class org.jmol.script.T
animation(boolean) - Method in class org.jmol.viewer.AnimationManager
animation_duration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
animationDirection - Variable in class org.jmol.viewer.AnimationManager
animationfps - Static variable in class org.jmol.script.T
animationFps - Variable in class org.jmol.viewer.AnimationManager
animationFps - Variable in class org.jmol.viewer.GlobalSettings
animationFrames - Variable in class org.jmol.viewer.AnimationManager
AnimationManager - Class in org.jmol.viewer
AnimationManager(Viewer) - Constructor for class org.jmol.viewer.AnimationManager
animationmode - Static variable in class org.jmol.script.T
animationOn - Variable in class org.jmol.viewer.AnimationManager
animationPaused - Variable in class org.jmol.viewer.AnimationManager
animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
animationStep - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
AnimationThread - Class in org.jmol.thread
AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
animationThread - Variable in class org.jmol.viewer.AnimationManager
AnimationWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
animThread - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
anionLookupTable - Static variable in class org.jmol.util.Elements
aniosU - Variable in class org.jmol.jvxl.readers.Parameters
ANISO_B11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_B12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_B13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_B22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_B23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_B33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_BETA_11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_BETA_12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_BETA_13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_BETA_22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_BETA_23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_BETA_33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_U11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_U12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_U13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_U22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_U23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_MMCIF_U33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_U11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_U12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_U13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_U22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_U23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
ANISO_U33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
anisoB - Variable in class org.jmol.jvxl.readers.Parameters
anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
anisotropy - Variable in class org.jmol.jvxl.readers.Parameters
anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
anisotropy - Static variable in class org.jmol.script.T
anisotropy() - Method in class org.jmol.util.Tensor
  anisotropy = directed distance from (center of two closest) to (the furthest)
anisou() - Method in class org.jmol.adapter.readers.pdb.PdbReader
ANISOU - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
Annotation - Class in org.jmol.modelsetbio
Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
AnnotationParser - Class in org.jmol.dssx
  A parser for output from 3DNA web service.
AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
annotationParser - Variable in class org.jmol.viewer.Viewer
antialias - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
antialias - Variable in class org.jmol.render.MeshRenderer
antialias - Variable in class org.jmol.viewer.TransformManager
antialias2 - Variable in class org.jmol.g3d.Graphics3D
antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
antialiasdisplay - Static variable in class org.jmol.script.T
antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
antialiased - Variable in class org.jmol.viewer.Viewer
antialiasEnabled - Variable in class org.jmol.util.GData
antialiasimages - Static variable in class org.jmol.script.T
antialiasImages - Variable in class org.jmol.viewer.GlobalSettings
antialiasThisFrame - Variable in class org.jmol.util.GData
antialiastranslucent - Static variable in class org.jmol.script.T
antialiasTranslucent - Variable in class org.jmol.viewer.GlobalSettings
ANUM - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
AO_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
aobuf - Variable in class org.jmol.g3d.Graphics3D
aoMax - Variable in class org.jmol.jvxl.readers.IsoShapeReader
aoMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
aPar - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
ApbsReader - Class in org.jmol.jvxl.readers
ApbsReader() - Constructor for class org.jmol.jvxl.readers.ApbsReader
aperatureAngle - Variable in class org.jmol.viewer.TransformManager
apertureAngle - Variable in class org.jmol.export.___Exporter
apiPlatform - Variable in class org.jmol.api.JmolViewer
apiPlatform - Variable in class org.jmol.g3d.Platform3D
apiPlatform - Variable in class org.jmol.util.GData
apm - Variable in class org.jmol.viewer.ActionManager
  picking modes set picking....
apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
app(SB, String) - Method in class org.jmol.viewer.GlobalSettings
app(SB, String) - Method in class org.jmol.viewer.StateCreator
appCheckItem(String, SC) - Method in class org.jmol.popup.GenericPopup
  Opportunity to do something special with an item.
appCheckItem(String, SC) - Method in class org.jmol.popup.JmolPopup
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericPopup
  Opportunity to do something special with a given submenu is created
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolPopup
AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
appConsole - Variable in class org.jmol.viewer.Viewer
AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
  general entry point
AppConsole.ConsoleDocument - Class in org.openscience.jmol.app.jmolpanel.console
AppConsole.ConsoleTextPane - Class in org.openscience.jmol.app.jmolpanel.console
AppConsole.ExecuteCommandThread - Class in org.openscience.jmol.app.jmolpanel.console
APPEND - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
append(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
append(String) - Method in class org.jmol.console.AppletConsole.GenericTextPane
append(String) - Method in interface org.jmol.console.GenericTextArea
append - Variable in class org.jmol.dialog.FilePreview
append - Static variable in class org.jmol.script.T
append(String) - Method in class org.jmol.util.JSONWriter
appendAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesSearch
appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Appends an AtomSetCollection
appendAtomSetCollectionList(Lst<?>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
appendAtomTokenValue(Viewer, Atom, LabelToken, SB, int[], P3) - Static method in class org.jmol.modelset.LabelToken
appendBuffer(String, boolean) - Method in class org.jmol.script.ScriptEval
appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
appendContourTriangleIntersection(int, float, float, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
  appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
appendedData - Variable in class org.jmol.adapter.readers.cif.CifReader
appendEncodedBitSetTag(SB, String, BS, int, Object[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
appendFontCmd(SB) - Method in class org.jmol.modelset.Text
appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
appendLoadStates(SB) - Method in class org.jmol.viewer.StateCreator
appendLogData(String) - Method in class org.jmol.minimize.forcefield.Calculations
appendNew - Variable in class org.jmol.modelset.ModelLoader
appendnew - Static variable in class org.jmol.script.T
appendNew - Variable in class org.jmol.viewer.GlobalSettings
appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
APPENDS - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
appendTickInfo(String, SB, TickInfo) - Method in class org.jmol.viewer.StateCreator
appendUunitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
appendXmlColorData(SB, String, boolean, boolean, float, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
appendXmlEdgeData(SB, JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
appendXmlTriangleData(SB, int[][], int, BS, int[], boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
  encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ...
appendXmlVertexData(SB, JvxlData, int[], T3[], float[], int, String, int, BS, int[], boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
  encode the vertex data.
appendXmlVertexOnlyData(SB, JvxlData, MeshData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
appFixLabel(String) - Method in class org.jmol.popup.GenericPopup
appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
appGetBooleanProperty(String) - Method in class org.jmol.modelkit.ModelKitPopup
appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericPopup
appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
appGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
appGetMenuAsString(String) - Method in class org.jmol.popup.JmolPopup
applet - Variable in class org.jmol.applet.Jmol
applet - Variable in class org.jmol.applet.TickerThread
applet - Variable in class org.jmol.applet.WrappedAppletLoader
applet - Variable in class org.jmol.awtjs.swing.AbstractButton
appletCodeBase - Static variable in class org.jmol.viewer.Viewer
AppletConsole - Class in org.jmol.console
AppletConsole() - Constructor for class org.jmol.console.AppletConsole
AppletConsole - Class in org.jmol.consolejs
  An interface to Jmol.Console.
AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
AppletConsole.ControlEnterTextArea - Class in org.jmol.console
AppletConsole.GenericTextPane - Class in org.jmol.console
appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
appletDocumentBaseURL - Variable in class org.jmol.viewer.FileManager
appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
appletInfoDivs - Variable in class org.openscience.jmol.app.webexport.WebPanel
appletName - Variable in class org.jmol.viewer.Viewer
appletObject - Variable in class org.jmol.util.GenericApplet
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.PopInJmol
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.ScriptButtons
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.WebPanel
appletPath - Variable in class org.openscience.jmol.app.webexport.Test
appletproxy - Static variable in class org.jmol.script.T
appletProxy - Variable in class org.jmol.viewer.FileManager
appletProxy - Variable in class org.jmol.viewer.GlobalSettings
appletSizeSpinnerH - Variable in class org.openscience.jmol.app.webexport.WebPanel
appletSizeSpinnerP - Variable in class org.openscience.jmol.app.webexport.WebPanel
appletSizeSpinnerW - Variable in class org.openscience.jmol.app.webexport.WebPanel
AppletWrapper - Class in org.jmol.applet
  Using Applet only because originally there was the possibility of non-Swing versions of the JRE being used.
AppletWrapper(String, int, String[]) - Constructor for class org.jmol.applet.AppletWrapper
appletWrapper - Variable in class org.jmol.applet.ClassPreloader
apply(ModulationSet, double[][]) - Method in class org.jmol.util.Modulation
apply() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
applyAllSymmetry(MSInterface, BS) - Method in class org.jmol.adapter.smarter.XtalSymmetry
applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
applyButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
applyColorScale() - Method in class org.jmol.jvxl.readers.SurfaceReader
applyEmpiricalRules(MinObject, double[], int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
applyLeftMouse(int) - Static method in class org.jmol.awt.Mouse
applyLeftMouse(int) - Static method in class org.jmol.awtjs2d.Mouse
applyPerspective(T3, T3) - Method in class org.jmol.viewer.TransformManager
  adjusts the temporary point for perspective and offsets
applyRotation(M3, boolean, BS, V3, boolean, M4) - Method in class org.jmol.viewer.TransformManager
applyStereochemistry() - Method in class org.jmol.modelset.ModelLoader
applySymmetry - Variable in class org.jmol.adapter.readers.pdb.PdbReader
applySymmetry() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.MMTFReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
applySymmetryBio(Map<String, Object>, boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
applySymmetryFromReader(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
applySymmetryLattice() - Method in class org.jmol.adapter.smarter.XtalSymmetry
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.XtalSymmetry
applysymmetrytobonds - Static variable in class org.jmol.script.T
applySymmetryToBonds - Variable in class org.jmol.viewer.GlobalSettings
applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
appRestorePopupMenu() - Method in class org.jmol.popup.GenericPopup
appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
appRestorePopupMenu() - Method in class org.jmol.popup.JmolPopup
approx(T3) - Static method in class org.jmol.symmetry.SymmetryDesc
approx0(T3) - Static method in class org.jmol.symmetry.SymmetryDesc
approxF(float) - Static method in class org.jmol.symmetry.SymmetryOperation
approxInt(float) - Method in class org.jmol.adapter.readers.cif.MSRdr
appRunScript(String) - Method in class org.jmol.popup.GenericPopup
appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
appUpdateForShow() - Method in class org.jmol.modelkit.ModelKitPopup
appUpdateForShow() - Method in class org.jmol.popup.GenericPopup
appUpdateForShow() - Method in class org.jmol.popup.JmolPopup
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
  Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
  (1) setOption --> set setOption true or set setOption false
arc - Static variable in class org.jmol.script.T
area - Static variable in class org.jmol.script.T
areas - Variable in class org.jmol.util.BZone
areAxesTainted() - Method in class org.jmol.viewer.Viewer
areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
areEqual(SV, SV) - Static method in class org.jmol.script.SV
  For legacy reasons, "x" == "X" but see isLike()
areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
areEqualTest(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
  for JUnit test, mainly
argb - Variable in class org.jmol.adapter.readers.pymol.JmolObject
argb - Variable in class org.jmol.awtjs.swing.Color
argb - Variable in class org.jmol.g3d.TextString
argbCurrent - Variable in class org.jmol.util.GData
argbEndcap - Variable in class org.jmol.g3d.CylinderRenderer
argbNoisyDn - Variable in class org.jmol.util.GData
argbNoisyUp - Variable in class org.jmol.util.GData
argbs - Static variable in class org.jmol.util.C
argbsAmino - Static variable in class org.jmol.modelsetbio.BioResolver
argbsAmino - Variable in class org.jmol.util.ColorEncoder
argbsChainAtom - Static variable in class org.jmol.modelsetbio.BioResolver
  some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
argbsChainHetero - Static variable in class org.jmol.modelsetbio.BioResolver
argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
argbsCpk - Static variable in enum org.jmol.c.PAL
  Default table of CPK atom colors.
argbsCpk - Variable in class org.jmol.util.ColorEncoder
argbsCpk - Variable in class org.jmol.viewer.ColorManager
argbsCpkRasmol - Static variable in enum org.jmol.c.PAL
argbsFormalCharge - Static variable in class org.jmol.viewer.JC
argbsGreyscale - Static variable in class org.jmol.util.C
argbsHbondType - Static variable in class org.jmol.util.Edge
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
argbsNucleic - Static variable in class org.jmol.modelsetbio.BioResolver
argbsNucleic - Variable in class org.jmol.util.ColorEncoder
argbsRoygb - Variable in class org.jmol.util.ColorEncoder
argbsRoygbScale - Static variable in class org.jmol.viewer.JC
argbsRwb - Variable in class org.jmol.util.ColorEncoder
argbsRwbScale - Static variable in class org.jmol.viewer.JC
argbsShapely - Static variable in class org.jmol.modelsetbio.BioResolver
argbsShapely - Variable in class org.jmol.util.ColorEncoder
arom - Variable in class org.jmol.minimize.forcefield.AtomType
aromatic - Static variable in class org.jmol.script.T
aromaticAmbiguous - Variable in class org.jmol.smiles.SmilesAtom
aromaticDefined - Variable in class org.jmol.smiles.SmilesSearch
aromaticDouble - Variable in class org.jmol.smiles.SmilesGenerator
aromaticDouble - Variable in class org.jmol.smiles.SmilesSearch
aromaticMMFF94 - Variable in class org.jmol.smiles.SmilesSearch
aromaticOpen - Variable in class org.jmol.smiles.SmilesSearch
aromaticPlanar - Variable in class org.jmol.smiles.SmilesSearch
aromaticRings - Variable in class org.jmol.smiles.SmilesGenerator
aromaticStrict - Variable in class org.jmol.smiles.SmilesSearch
aromaticUnknown - Variable in class org.jmol.smiles.SmilesSearch
array - Static variable in class org.jmol.script.T
arrayAdd(Object) - Method in class org.jmol.util.JSONWriter
arrayClose(boolean) - Method in class org.jmol.util.JSONWriter
arrayListHandler - Variable in class org.openscience.jmol.app.webexport.Test
ArrayListTransferable(Lst<String>) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
ArrayListTransferHandler - Class in org.openscience.jmol.app.webexport
ArrayListTransferHandler(WebPanel) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler
ArrayListTransferHandler.ArrayListTransferable - Class in org.openscience.jmol.app.webexport
arrayOpen(boolean) - Method in class org.jmol.util.JSONWriter
arrayPt - Variable in class org.jmol.script.SV.Sort
arrow - Static variable in class org.jmol.script.T
arrowHeadBase - Static variable in class org.jmol.renderspecial.DipolesRenderer
arrowHeadFaces - Static variable in class org.jmol.renderbio.RocketRenderer
arrowHeadOffset - Static variable in class org.jmol.renderspecial.DipolesRenderer
arrowHeadOffset - Static variable in class org.jmol.renderspecial.VectorsRenderer
arrowHeadTip - Static variable in class org.jmol.renderspecial.DipolesRenderer
arrowHeadWidthFactor - Static variable in class org.jmol.renderspecial.DipolesRenderer
as - Static variable in class org.jmol.script.T
asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
asBoolean() - Method in class org.jmol.script.SV
asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
asc - Variable in class org.jmol.adapter.smarter.XtalSymmetry
ASCENDER - Static variable in class org.jmol.util.MeshCapper
ascent - Variable in class org.jmol.g3d.TextRenderer
ascent - Variable in class org.jmol.modelset.Text
ascent - Variable in class org.jmol.render.LabelsRenderer
ascent - Variable in class org.jmol.util.Font
asFloat() - Method in class org.jmol.script.SV
ashades - Variable in class org.jmol.util.Shader
ashadesGreyscale - Variable in class org.jmol.util.Shader
asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
asInt() - Method in class org.jmol.script.SV
asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
aspectRatio - Variable in class org.jmol.renderbio.BioShapeRenderer
asQuads - Variable in class org.jmol.jvxl.readers.Ras3DReader
asResidues - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
ASSEM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
ASSEM_LIST - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
ASSEM_OPERS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
assemblyFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
assemblyIdAtoms - Variable in class org.jmol.adapter.readers.cif.MMCifReader
assign - Static variable in class org.jmol.script.T
assign(int) - Method in class org.jmol.scriptext.CmdExt
assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
  algorithm discussed above.
assignAromaticDouble(Bond) - Method in class org.jmol.modelset.BondCollection
  try to assign AROMATICDOUBLE to this bond.
assignAromaticDoubleForAtom(Atom) - Method in class org.jmol.modelset.BondCollection
  N atoms with 3 bonds cannot also have a double bond; other atoms need one and only one double bond; the rest must be single bonds.
assignAromaticMustBeSingle(Atom) - Method in class org.jmol.modelset.BondCollection
assignAromaticNandO(BS) - Method in class org.jmol.modelset.BondCollection
assignAromaticSingle(Bond) - Method in class org.jmol.modelset.BondCollection
  try to assign AROMATICSINGLE to this bond.
assignAromaticSingleForAtom(Atom, int) - Method in class org.jmol.modelset.BondCollection
  N atoms with 3 bonds cannot also have a double bond; other atoms needs all single bonds, because the bond leading up to it is double.
assignAtom(int, String, boolean, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
  Original ModelKitPopup functionality -- assign an atom.
assignAtom(int, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
assignAtom(int, P3, String) - Method in class org.jmol.scriptext.CmdExt
assignAtom(int, String, P3) - Method in class org.jmol.viewer.Viewer
assignBond(int, int) - Method in class org.jmol.modelkit.ModelKitPopup
  Original ModelKit functionality -- assign a bond.
assignBond(int, char) - Method in class org.jmol.modelset.BondCollection
assignBond(int, char) - Method in class org.jmol.scriptext.CmdExt
assignConnect(int, int) - Method in class org.jmol.scriptext.CmdExt
assignLeft - Variable in class org.jmol.script.ScriptMathProcessor
assignNew(int, int) - Method in class org.jmol.viewer.ActionManager
assignPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
assignValueFromGapColorForKin(String) - Method in class org.jmol.jvxl.readers.KinemageReader
  C++ code gives these as " value > x.x ? "xxxxx", etc.
assocCutoff - Variable in class org.jmol.jvxl.readers.Parameters
assocCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
assocGridPointMap - Variable in class org.jmol.shapesurface.IsosurfaceMesh
assocGridPointNormals - Variable in class org.jmol.shapesurface.IsosurfaceMesh
associatedAtoms - Variable in class org.jmol.modelset.BondSet
associateNormals - Variable in class org.jmol.shapesurface.Isosurface
ASSOCIATION - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
asString() - Method in class org.jmol.script.SV
assumeAtomRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
astrType - Static variable in class org.jmol.script.T
asVector - Variable in class org.jmol.script.ScriptMathProcessor
asVector - Variable in class org.jmol.smiles.SmilesSearch
ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
asymMatrix - Variable in class org.jmol.util.Tensor
asymmetry() - Method in class org.jmol.util.Tensor
  asymmetry = deviation from a symmetric tensor
async - Static variable in class org.jmol.script.T
async - Variable in class org.jmol.viewer.Viewer
async_builds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
at - Variable in class org.jmol.modelset.AtomCollection
aTemp - Variable in class org.jmol.adapter.readers.pymol.PickleReader
aTemp - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
atemp - Variable in class org.jmol.smiles.SmilesGenerator
ati_bugs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
atModel - Variable in class org.jmol.adapter.readers.cif.MSRdr
atokenInfix - Variable in class org.jmol.script.ScriptTokenParser
atom() - Method in class org.jmol.adapter.readers.pdb.PdbReader
ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
atom() - Method in class org.jmol.adapter.readers.xtal.CgdReader
Atom - Class in org.jmol.adapter.smarter
Atom() - Constructor for class org.jmol.adapter.smarter.Atom
atom - Variable in class org.jmol.adapter.smarter.AtomIterator
atom - Variable in class org.jmol.minimize.MinAtom
Atom - Class in org.jmol.modelset
Atom() - Constructor for class org.jmol.modelset.Atom
atom - Variable in class org.jmol.quantum.QMAtom
atom - Variable in class org.jmol.render.LabelsRenderer
atom - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  the associated Jmol (or otherwise) atom; use of the SimpleNode interface allows us to implement this in SMILES or Jmol as well as providing an interface other programs could use if implementing this code
atom1 - Variable in class org.jmol.modelset.Bond
atom1 - Variable in class org.jmol.smiles.SmilesBond
atom2 - Variable in class org.jmol.modelset.Bond
atom2 - Variable in class org.jmol.smiles.SmilesBond
ATOM_COUNT_MAX - Static variable in class org.jmol.symmetry.PointGroup
ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
ATOM_INFRAME - Static variable in class org.jmol.modelset.Atom
ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
atom_name_wildcard - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ATOM_NOFLAGS - Static variable in class org.jmol.modelset.Atom
ATOM_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.modelset.Atom
atom_type_format - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ATOM_TYPE_OXIDATION_NUMBER - Static variable in class org.jmol.adapter.readers.cif.CifReader
ATOM_TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cif.CifReader
ATOM_VISIBLE - Static variable in class org.jmol.modelset.Atom
ATOM_VISSET - Static variable in class org.jmol.modelset.Atom
atomArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
atomBool(byte[], int, int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
atomCapacity - Variable in class org.jmol.modelset.AtomCollection
atomCenterOrCoordinateParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
atomCharges - Variable in class org.jmol.adapter.readers.xtal.GulpReader
atomClass - Variable in class org.jmol.smiles.SmilesAtom
AtomCollection - Class in org.jmol.modelset
AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
AtomCollection.AtomSorter - Class in org.jmol.modelset
atomColorList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
atomCoordAngstroms - Variable in class org.jmol.quantum.MepCalculation
atomCount - Variable in class org.jmol.adapter.readers.molxyz.MolReader
atomCount - Variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
atomCount - Variable in class org.jmol.smiles.SmilesStereo
atomData - Variable in class org.jmol.adapter.readers.molxyz.MolReader
AtomData - Class in org.jmol.atomdata
AtomData() - Constructor for class org.jmol.atomdata.AtomData
atomData - Variable in class org.jmol.geodesic.EnvelopeCalculation
atomData - Variable in class org.jmol.jvxl.readers.AtomDataReader
AtomDataReader - Class in org.jmol.jvxl.readers
AtomDataReader() - Constructor for class org.jmol.jvxl.readers.AtomDataReader
AtomDataServer - Interface in org.jmol.atomdata
atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
atomExpression(T[], int, int, boolean, boolean, Object[], boolean) - Method in class org.jmol.script.ScriptExpr
atomExpression - Static variable in class org.jmol.viewer.PropertyManager
atomExpressionAt(int) - Method in class org.jmol.script.ScriptExpr
atomExpressionAt(int) - Method in class org.jmol.scriptext.ScriptExt
atomExpressionCommand - Static variable in class org.jmol.script.T
atomFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
atomFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
atomFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
atomFloat(byte[], int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
atomFormats - Variable in class org.jmol.shape.Hover
atomFrag - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
atomGroup - Variable in class org.jmol.adapter.readers.cif.MMTFReader
atomHighlighted - Variable in class org.jmol.viewer.Viewer
atomHoverLabel - Variable in class org.jmol.modelkit.ModelKitPopup
ATOMIC_ORBITAL_ZERO_CUT_OFF - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
atomicAndIsotopeNumber - Variable in class org.jmol.modelset.Atom
atomicMass - Variable in class org.jmol.smiles.SmilesAtom
atomicMass - Static variable in class org.jmol.util.Elements
atomicNumber - Variable in class org.jmol.atomdata.AtomData
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
atomicorbital - Static variable in class org.jmol.script.T
atomID - Variable in class org.jmol.modelset.Atom
atomid - Static variable in class org.jmol.script.T
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C2 - Static variable in class org.jmol.viewer.JC
ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C4 - Static variable in class org.jmol.viewer.JC
ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C5 - Static variable in class org.jmol.viewer.JC
ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_C5M - Static variable in class org.jmol.viewer.JC
ATOMID_C6 - Static variable in class org.jmol.viewer.JC
ATOMID_C7 - Static variable in class org.jmol.viewer.JC
ATOMID_C8 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_MAX - Static variable in class org.jmol.modelsetbio.BioResolver
ATOMID_N1 - Static variable in class org.jmol.viewer.JC
ATOMID_N2 - Static variable in class org.jmol.viewer.JC
ATOMID_N3 - Static variable in class org.jmol.viewer.JC
ATOMID_N4 - Static variable in class org.jmol.viewer.JC
ATOMID_N6 - Static variable in class org.jmol.viewer.JC
ATOMID_N7 - Static variable in class org.jmol.viewer.JC
ATOMID_N9 - Static variable in class org.jmol.viewer.JC
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
ATOMID_O1 - Static variable in class org.jmol.viewer.JC
ATOMID_O1P - Static variable in class org.jmol.viewer.JC
ATOMID_O2 - Static variable in class org.jmol.viewer.JC
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O2P - Static variable in class org.jmol.viewer.JC
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O4 - Static variable in class org.jmol.viewer.JC
ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
ATOMID_O6 - Static variable in class org.jmol.viewer.JC
ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
ATOMID_S4 - Static variable in class org.jmol.viewer.JC
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
atomIdNames - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
atomIndex - Variable in class org.jmol.adapter.readers.simple.HyperChemReader
atomIndex - Variable in class org.jmol.atomdata.AtomData
atomIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
atomIndex - Variable in class org.jmol.jvxl.readers.Parameters
atomIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
atomindex - Static variable in class org.jmol.script.T
atomIndex - Variable in class org.jmol.shape.Hover
atomIndex - Variable in class org.jmol.shape.Mesh
atomIndex - Variable in class org.jmol.shapesurface.Isosurface
atomIndex - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  the application-assigned unique atom index for this atom; used in updating lstSmallRings
atomIndex0 - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
atomIndex1 - Variable in class org.jmol.shapespecial.Dipoles
atomIndex1 - Variable in class org.jmol.util.Tensor
atomIndex1 - Variable in class org.jmol.viewer.Connection
atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
atomIndex2 - Variable in class org.jmol.shapespecial.Dipoles
atomIndex2 - Variable in class org.jmol.util.Tensor
atomIndex2 - Variable in class org.jmol.viewer.Connection
AtomIndexIterator - Interface in org.jmol.api
  note: YOU MUST RELEASE THE ITERATOR
atomIndexLast - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
atomIndexSphere - Variable in class org.jmol.modelkit.ModelKitPopup
atomInt(byte[], int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
AtomIterator - Class in org.jmol.adapter.smarter
AtomIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.AtomIterator
AtomIteratorWithinModel - Class in org.jmol.modelset
AtomIteratorWithinModel() - Constructor for class org.jmol.modelset.AtomIteratorWithinModel
AtomIteratorWithinModelSet - Class in org.jmol.modelset
AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
atomLabels - Variable in class org.jmol.shape.Labels
atomList - Variable in class org.jmol.util.JmolMolecule
atomMap - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
atomMap - Variable in class org.jmol.adapter.readers.cif.MMTFReader
atomMap - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
atomMap - Variable in class org.jmol.adapter.readers.simple.InputReader
atomMap - Variable in class org.jmol.minimize.Minimizer
atomMap - Variable in class org.jmol.symmetry.PointGroup
atomMolecule - Variable in class org.jmol.atomdata.AtomData
atomName - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
atomName - Variable in class org.jmol.adapter.smarter.Atom
atomname - Static variable in class org.jmol.script.T
atomName1 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
atomName2 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
atomNames - Variable in class org.jmol.adapter.readers.pdb.JmolDataReader
atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
atomNames - Variable in class org.jmol.adapter.readers.quantum.PsiReader
atomNames - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
atomNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
atomNames - Variable in class org.jmol.modelset.AtomCollection
atomNo - Variable in class org.jmol.jvxl.readers.AtomDataReader
atomNo - Variable in class org.jmol.quantum.SlaterData
atomno - Static variable in class org.jmol.script.T
atomNumber - Variable in class org.jmol.smiles.SmilesAtom
atomOrPointPicked(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
atomPicked(int) - Method in class org.jmol.jsv.JSpecView
atompicking - Static variable in class org.jmol.script.T
atomPicking - Variable in class org.jmol.viewer.GlobalSettings
atomPositions - Variable in class org.jmol.adapter.readers.simple.AmpacReader
atomProp - Variable in class org.jmol.jvxl.readers.AtomDataReader
atomproperty - Static variable in class org.jmol.script.T
atomPropertyFloat(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
  called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyInt(int) - Method in class org.jmol.modelset.Atom
  called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
AtomPropertyMapper - Class in org.jmol.jvxl.readers
  maps property data
AtomPropertyMapper() - Constructor for class org.jmol.jvxl.readers.AtomPropertyMapper
atomPropertyString(Viewer, int) - Method in class org.jmol.modelset.Atom
atomPropertyTuple(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
atomPt - Variable in class org.jmol.render.LabelsRenderer
atomPts - Variable in class org.jmol.adapter.readers.xtal.CastepReader
atomRadius - Variable in class org.jmol.adapter.readers.cif.CifReader
atomRadius - Variable in class org.jmol.atomdata.AtomData
atomRadius - Variable in class org.jmol.jvxl.readers.AtomDataReader
atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
atomResnos - Variable in class org.jmol.modelset.AtomCollection
atoms - Variable in class org.jmol.adapter.readers.cif.CifReader
atoms - Variable in class org.jmol.adapter.readers.cif.MSRdr
atoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
atoms - Variable in class org.jmol.adapter.smarter.AtomIterator
atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atoms - Variable in class org.jmol.atomdata.AtomData
atoms - Variable in class org.jmol.minimize.Minimizer
atoms - Variable in class org.jmol.modelset.AtomIteratorWithinModel
atoms - Variable in class org.jmol.modelset.MeasurementData
atoms - Static variable in class org.jmol.script.T
atoms - Variable in class org.jmol.shape.AtomShape
atoms - Variable in class org.jmol.shapebio.BioShapeCollection
atoms - Variable in class org.jmol.shapespecial.Dipole
atoms - Variable in class org.jmol.shapesurface.Contact
atoms - Variable in class org.jmol.smiles.SmilesGenerator
atoms - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  the substituents -- up to four supported here at this time
atoms - Variable in class org.jmol.symmetry.CIPData
  all application atoms referenced by bit sets
atoms - Variable in class org.jmol.symmetry.UnitCellIterator
atomSeqIDs - Variable in class org.jmol.modelset.AtomCollection
atomSerial - Variable in class org.jmol.adapter.smarter.Atom
atomSerials - Variable in class org.jmol.modelset.AtomCollection
AtomSet(int, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
atomSetAtomCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetAtomIndexes - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetBondCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
  A JFrame that allows for choosing an Atomset to view.
AtomSetChooser(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
AtomSetChooser.AtomSet - Class in org.openscience.jmol.app.jmolpanel
  Objects in the AtomSetChooser tree
atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
AtomSetCollection - Class in org.jmol.adapter.smarter
AtomSetCollection(String, AtomSetCollectionReader, AtomSetCollection[], Lst<?>) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
atomSetCollection - Variable in class org.jmol.io.DOMReader
atomSetCollection - Variable in class org.jmol.io.FileReader
atomSetCollection - Variable in class org.jmol.io.FilesReader
AtomSetCollectionReader - Class in org.jmol.adapter.smarter
AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
atomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetObject
atomSetIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
  The index of that AtomSet
atomSetInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSetName - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
  The name of the AtomSet
atomSetNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollection
AtomSetObject - Class in org.jmol.adapter.smarter
AtomSetObject() - Constructor for class org.jmol.adapter.smarter.AtomSetObject
AtomShape - Class in org.jmol.shape
AtomShape() - Constructor for class org.jmol.shape.AtomShape
atomSite - Variable in class org.jmol.adapter.smarter.Atom
atomSite - Variable in class org.jmol.modelset.Atom
atomSite - Variable in class org.jmol.smiles.SmilesAtom
atomsLabeledInline - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
atomStartEnd - Variable in class org.jmol.adapter.smarter.Structure
atomStr(byte[], int, int, String[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
atomSym - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
atomSymmetry - Variable in class org.jmol.modelset.Atom
atomSyms - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
atomTensorList - Variable in class org.jmol.modelset.AtomCollection
atomTensors - Variable in class org.jmol.modelset.AtomCollection
atomTest - Static variable in class org.jmol.symmetry.SymmetryOperation
AtomType - Class in org.jmol.minimize.forcefield
AtomType(int, int, int, float, int, String, String) - Constructor for class org.jmol.minimize.forcefield.AtomType
atomtype - Static variable in class org.jmol.script.T
atomType - Variable in class org.jmol.smiles.SmilesAtom
atomTypeFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
atomTypeLen - Variable in class org.jmol.adapter.readers.pdb.PdbReader
atomTypePt0 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
atomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
atomTypes - Variable in class org.jmol.adapter.readers.more.MdTopReader
atomTypes - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
atomTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
atomTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
atomTypes - Variable in class org.jmol.modelset.AtomCollection
atomtypes - Static variable in class org.jmol.script.T
atomTypes - Variable in class org.jmol.viewer.GlobalSettings
atomX - Variable in class org.jmol.modelset.Text
atomx - Static variable in class org.jmol.script.T
atomXyzTruncated - Variable in class org.jmol.jvxl.readers.AtomDataReader
atomY - Variable in class org.jmol.modelset.Text
atomy - Static variable in class org.jmol.script.T
atomZ - Variable in class org.jmol.modelset.Text
atomz - Static variable in class org.jmol.script.T
ATROPISOMER_SHIFT - Static variable in class org.jmol.util.Edge
atropKeys - Variable in class org.jmol.smiles.SmilesSearch
atropType - Variable in class org.jmol.smiles.SmilesBond
attArgs - Variable in class org.jmol.adapter.readers.xml.XmlReader
attEcho - Variable in class org.jmol.console.ScriptEditor
attEcho - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
attError - Variable in class org.jmol.console.ScriptEditor
attError - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
attHighlight - Variable in class org.jmol.console.ScriptEditor
attPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
attribs - Variable in class org.jmol.adapter.readers.xml.XmlReader
atts - Variable in class org.jmol.adapter.readers.xml.XmlReader
attStatus - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
attUserInput - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
audio - Static variable in class org.jmol.script.T
audios - Variable in class org.jmol.viewer.StatusManager
auditBlockCode - Variable in class org.jmol.adapter.readers.cif.CifReader
augmentGroup3List(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
AUTH_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
AUTH_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
AUTH_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
auto - Static variable in class org.jmol.script.T
auto_classify_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_color_next - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_copy_images - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_defer_atom_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_defer_builds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_dss - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_hide_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_indicate_flags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_number_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_remove_hydrogens - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_rename_duplicate_objects - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_sculpt - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_show_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_show_nonbonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_show_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_show_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
auto_zoom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
autoAnimationDelay - Variable in class org.openscience.jmol.app.JmolApp
autobond - Static variable in class org.jmol.script.T
autoBond - Variable in class org.jmol.viewer.GlobalSettings
autoBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
autoBond_Pre_11_9_24(BS, BS, BS, BS, short) - Method in class org.jmol.modelset.ModelSet
autoBondBs4(BS, BS, BS, BS, short, boolean) - Method in class org.jmol.modelset.ModelSet
autoBondCheck(Atom, Atom, int, short, BS) - Method in class org.jmol.modelset.ModelSet
autoCalculate(int, String) - Method in class org.jmol.viewer.Viewer
autoClose - Variable in class org.jmol.util.JmolAudio
autoclose_dialogs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
autoExit - Variable in class org.jmol.viewer.Viewer
autofps - Static variable in class org.jmol.script.T
autoFps - Variable in class org.jmol.viewer.GlobalSettings
autoHbond(BS, BS, boolean) - Method in class org.jmol.modelset.ModelSet
  a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
autoHbond(BS, BS, boolean) - Method in class org.jmol.viewer.Viewer
autoplaymovie - Static variable in class org.jmol.script.T
autoplayMovie - Variable in class org.jmol.viewer.GlobalSettings
autoScaleOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
autoScrolls - Variable in class org.jmol.awtjs.swing.JComponent
auxChirality - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  auxiliary chirality as determined in createAuxiliaryRule4Data; possibilities include R/S, r/s, M/P, m/p, C/T (but not c/t), or ~ (ASCII 126, no stereochemistry); for sorting purposes C=M=R < p=r=s < ~
auxEZ - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  auxiliary chirality E/Z for this atom node
auxiliaryInfo - Variable in class org.jmol.modelset.Model
auxSort(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Sort by a given rule, preserving currentRule, which could be 4 or 5
average - Static variable in class org.jmol.script.T
average(P3[]) - Method in class org.jmol.util.BZone
AviCreator - Class in org.jmol.image
AviCreator() - Constructor for class org.jmol.image.AviCreator
AwtClipboard - Class in org.jmol.awt
  This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtClipboard(Object) - Constructor for class org.jmol.awt.AwtClipboard
AwtColor - Class in org.jmol.awt
AwtColor(int) - Constructor for class org.jmol.awt.AwtColor
AwtColor(int, int, int) - Constructor for class org.jmol.awt.AwtColor
AwtColor(int, int, int, int) - Constructor for class org.jmol.awt.AwtColor
AwtFile - Class in org.jmol.awt
  a subclass of File allowing extension to JavaScript private to org.jmol.awt
AwtFile(String) - Constructor for class org.jmol.awt.AwtFile
AwtFont - Class in org.jmol.awt
  methods required by Jmol that access java.awt.Font private to org.jmol.awt
AwtFont() - Constructor for class org.jmol.awt.AwtFont
AwtG2D - Class in org.jmol.awt
  generic 2D drawing methods -- AWT version
AwtG2D() - Constructor for class org.jmol.awt.AwtG2D
AwtJmolPopup - Class in org.jmol.awt
AwtJmolPopup() - Constructor for class org.jmol.awt.AwtJmolPopup
AwtModelKitPopup - Class in org.jmol.awt
AwtModelKitPopup() - Constructor for class org.jmol.awt.AwtModelKitPopup
AwtPopupHelper - Class in org.jmol.awt
  all popup-related awt/swing class references are in this file.
AwtPopupHelper(GenericPopup) - Constructor for class org.jmol.awt.AwtPopupHelper
AwtSwingComponent - Class in org.jmol.awt
  A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.
AwtSwingComponent() - Constructor for class org.jmol.awt.AwtSwingComponent
ax - Variable in class org.jmol.g3d.TriangleRenderer
axE - Variable in class org.jmol.g3d.TriangleRenderer
axes - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
axes - Static variable in class org.jmol.script.T
Axes - Class in org.jmol.shape
Axes() - Constructor for class org.jmol.shape.Axes
axes - Variable in class org.jmol.shapespecial.DrawMesh
axes - Variable in class org.jmol.symmetry.PointGroup
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
axesAreTainted - Variable in class org.jmol.viewer.Viewer
axescolor - Static variable in class org.jmol.script.T
axesLengths - Variable in class org.jmol.util.ModulationSet
  unit cell axes -- used in Modulation for calculating magnetic modulations
axesMaxN - Static variable in class org.jmol.symmetry.PointGroup
axesmode - Static variable in class org.jmol.script.T
axesMode - Variable in class org.jmol.viewer.GlobalSettings
axesmolecular - Static variable in class org.jmol.script.T
axesoffset - Static variable in class org.jmol.script.T
axesOffset - Variable in class org.jmol.viewer.GlobalSettings
axesorientationrasmol - Static variable in class org.jmol.script.T
axesOrientationRasmol - Variable in class org.jmol.viewer.GlobalSettings
axesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
AxesRenderer - Class in org.jmol.render
AxesRenderer() - Constructor for class org.jmol.render.AxesRenderer
axesscale - Static variable in class org.jmol.script.T
axesScale - Variable in class org.jmol.viewer.GlobalSettings
axesTypes - Static variable in class org.jmol.render.AxesRenderer
axesunitcell - Static variable in class org.jmol.script.T
axeswindow - Static variable in class org.jmol.script.T
axis - Variable in class org.jmol.navigate.Navigator
axis - Static variable in class org.jmol.script.T
axis - Variable in class org.jmol.shapespecial.DrawMesh
axis - Variable in class org.jmol.util.Modulation
axis1color - Static variable in class org.jmol.script.T
axis2color - Static variable in class org.jmol.script.T
axis3color - Static variable in class org.jmol.script.T
axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
axisangle - Static variable in class org.jmol.script.T
axisangleT - Variable in class org.jmol.viewer.TransformManager
axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
axisChoice - Variable in class org.jmol.symmetry.SpaceGroup
axisLabels - Static variable in class org.jmol.render.AxesRenderer
axisNX - Static variable in class org.jmol.viewer.JC
axisNY - Static variable in class org.jmol.viewer.JC
axisNZ - Static variable in class org.jmol.viewer.JC
axisPoints - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
axisPoints - Variable in class org.jmol.shape.Axes
  [x, y, z, -x, -y, -z] or [a, b, c, -a, -b, -c]
axisType - Variable in class org.jmol.shape.Axes
axisType - Variable in class org.jmol.symmetry.HallRotationTerm
axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
axisX - Static variable in class org.jmol.viewer.JC
axisXY - Variable in class org.jmol.shape.Axes
axisY - Static variable in class org.jmol.viewer.JC
axisZ - Static variable in class org.jmol.viewer.JC
axW - Variable in class org.jmol.g3d.TriangleRenderer
ay - Variable in class org.jmol.g3d.TriangleRenderer
az - Variable in class org.jmol.g3d.TriangleRenderer
azE - Variable in class org.jmol.g3d.TriangleRenderer
azW - Variable in class org.jmol.g3d.TriangleRenderer

## B

b - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
b - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
b - Variable in class org.jmol.adapter.readers.xtal.CastepReader
b - Variable in class org.jmol.adapter.readers.xtal.GulpReader
b - Variable in class org.jmol.dssx.Bridge
b - Variable in class org.jmol.g3d.PrecisionRenderer
b - Variable in class org.jmol.jvxl.readers.MapFileReader
b - Variable in class org.jmol.minimize.forcefield.Calculation
b - Variable in class org.jmol.render.SticksRenderer
b - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
b - Variable in class org.jmol.util.Rgb16
b - Variable in class org.jmol.util.SimpleUnitCell
b - Variable in class org.jmol.viewer.ActionManager
b1 - Variable in class org.jmol.g3d.HermiteRenderer
b2 - Variable in class org.jmol.g3d.HermiteRenderer
b8 - Static variable in class org.jmol.jvxl.readers.MrcBinaryReader
b_ - Variable in class org.jmol.util.SimpleUnitCell
B_ISO - Static variable in class org.jmol.adapter.readers.cif.CifReader
B_WINS - Static variable in class org.jmol.symmetry.CIPChirality
babel - Static variable in class org.jmol.script.T
babel21 - Static variable in class org.jmol.script.T
back - Static variable in class org.jmol.script.T
backbone - Static variable in class org.jmol.script.T
Backbone - Class in org.jmol.shapebio
Backbone() - Constructor for class org.jmol.shapebio.Backbone
backboneBlockVis - Variable in class org.jmol.modelsetbio.Monomer
backbonePt - Variable in class org.jmol.renderbio.NucleicRenderer
BackboneRenderer - Class in org.jmol.renderbio
BackboneRenderer() - Constructor for class org.jmol.renderbio.BackboneRenderer
backboneScreen - Variable in class org.jmol.renderbio.NucleicRenderer
backface_cull - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
background - Static variable in class org.jmol.script.T
backgroundColix - Variable in class org.jmol.export.___Exporter
backgroundColix - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
backgroundcolor - Static variable in class org.jmol.script.T
BackgroundColorWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
backgroundImage - Variable in class org.jmol.util.GData
backgroundImageFileName - Variable in class org.jmol.viewer.GlobalSettings
backgroundmodel - Static variable in class org.jmol.script.T
backgroundModelIndex - Variable in class org.jmol.viewer.AnimationManager
backgroundTransparent - Static variable in class org.jmol.g3d.Platform3D
backlit - Static variable in class org.jmol.script.T
backshell - Static variable in class org.jmol.script.T
bad() - Method in class org.jmol.script.ScriptError
balls - Static variable in class org.jmol.script.T
Balls - Class in org.jmol.shape
Balls() - Constructor for class org.jmol.shape.Balls
BallsRenderer - Class in org.jmol.render
BallsRenderer() - Constructor for class org.jmol.render.BallsRenderer
bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
BannerFrame - Class in org.openscience.jmol.app.jsonkiosk
  A simple class that throws up a white rectangle that has a single centered label.
BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jsonkiosk.BannerFrame
bannerLabel - Variable in class org.openscience.jmol.app.jsonkiosk.BannerFrame
barb - Static variable in class org.jmol.script.T
barray - Static variable in class org.jmol.script.T
baseAtomIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
baseAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
baseBondIndex - Variable in class org.jmol.modelsetbio.BioResolver
baseCenter - Variable in class org.jmol.modelsetbio.NucleicMonomer
baseColor - Variable in class org.jmol.jvxl.data.JvxlData
baseFont3d - Variable in class org.jmol.shape.Frank
baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
baseModel - Variable in class org.jmol.jsv.JDXMOLParser
basemodel - Static variable in class org.jmol.script.T
baseModelCount - Variable in class org.jmol.modelset.ModelLoader
baseModelIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
baseModelIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
BasePair - Class in org.jmol.modelsetbio
BasePair() - Constructor for class org.jmol.modelsetbio.BasePair
basepair - Static variable in class org.jmol.script.T
basePt - Variable in class org.jmol.renderbio.NucleicRenderer
baseScreen - Variable in class org.jmol.renderbio.NucleicRenderer
baseStrandOffset - Variable in class org.jmol.renderbio.StrandsRenderer
baseSymmetry - Variable in class org.jmol.adapter.smarter.XtalSymmetry
baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
baseTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
baseUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
BASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
basisAtoms - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
basisBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
basisData - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter - Class in org.jmol.adapter.readers.quantum
basisFunctions - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
basisId - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
basisID - Variable in class org.jmol.adapter.writers.QCJSONWriter
basisIds - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
batch_prefix - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
BATOM1 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
BATOM2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bb - Variable in class org.jmol.g3d.TriangleRenderer
Bbcage - Class in org.jmol.shape
Bbcage() - Constructor for class org.jmol.shape.Bbcage
BbcageRenderer - Class in org.jmol.render
BbcageRenderer() - Constructor for class org.jmol.render.BbcageRenderer
bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
bbCenter - Variable in class org.jmol.util.BoxInfo
bbCorner0 - Variable in class org.jmol.util.BoxInfo
bbCorner1 - Variable in class org.jmol.util.BoxInfo
bboxAtoms - Variable in class org.jmol.modelset.ModelSet
bboxModels - Variable in class org.jmol.modelset.ModelSet
bButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
bbVector - Variable in class org.jmol.util.BoxInfo
bbVertices - Variable in class org.jmol.util.BoxInfo
  The ordering of these vertices is given below.
BCifDensityReader - Class in org.jmol.jvxl.readers
  Binary CIF density reader.
BCifDensityReader() - Constructor for class org.jmol.jvxl.readers.BCifDensityReader
bdSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
beenSliced - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
BEG_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
BEG_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
BEG_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
BEGIN - Static variable in class org.jmol.shapecgo.CGOMesh
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.util.GData
beginRendering(boolean, boolean) - Method in class org.jmol.viewer.Viewer
best - Static variable in class org.jmol.script.T
beta - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
beta - Variable in class org.jmol.adapter.readers.xtal.CastepReader
beta - Variable in class org.jmol.adapter.readers.xtal.GulpReader
beta - Variable in class org.jmol.jvxl.readers.MapFileReader
beta - Static variable in class org.jmol.modelsetbio.AminoMonomer
beta - Static variable in class org.jmol.script.T
beta - Variable in class org.jmol.util.SimpleUnitCell
betaOnly - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
betas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
BFACTOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bfactor - Variable in class org.jmol.adapter.smarter.Atom
bfactor100Hi - Variable in class org.jmol.modelset.AtomCollection
bfactor100Lo - Variable in class org.jmol.modelset.AtomCollection
bfactor100s - Variable in class org.jmol.modelset.AtomCollection
bfactorMax - Variable in class org.jmol.shapebio.BioShape
bfactorMin - Variable in class org.jmol.shapebio.BioShape
BFXN_ANGL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
bg_gradient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_image_filename - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_image_linear - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_image_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_image_tilesize - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_rgb - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_rgb_bottom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bg_rgb_top - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bgargb - Variable in class org.jmol.g3d.TextString
bgcolix - Variable in class org.jmol.modelset.Text
bgcolix - Variable in class org.jmol.render.LabelsRenderer
bgcolixes - Variable in class org.jmol.shape.Labels
bgcolor - Variable in class org.jmol.applet.AppletWrapper
bgcolor - Variable in class org.jmol.awtjs.swing.Component
bgcolor - Variable in class org.jmol.g3d.Pixelator
bgcolor - Variable in class org.jmol.util.GData
bgColor - Variable in class org.openscience.jmol.app.webexport.JmolInstance
bGlobals - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
bgRgb - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bgRGB - Variable in class org.jmol.g3d.PixelatorShaded
BGYOR - Static variable in class org.jmol.util.ColorEncoder
BHASSETTING - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
BID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bilbaoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
BilbaoReader - Class in org.jmol.adapter.readers.xtal
  Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.
BilbaoReader() - Constructor for class org.jmol.adapter.readers.xtal.BilbaoReader
bin - Static variable in class org.jmol.script.T
binary - Static variable in class org.jmol.script.T
BinaryDcdReader - Class in org.jmol.adapter.readers.more
  DCD binary trajectory file reader.
BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
binaryDoc - Variable in class org.jmol.adapter.readers.pymol.PickleReader
binaryDoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
binarydoc - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
binaryOp(T, SV, SV) - Method in class org.jmol.script.ScriptMathProcessor
bind - Static variable in class org.jmol.script.T
bind(String, String) - Method in class org.jmol.viewer.ActionManager
bindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
bindAction(String, String) - Method in class org.jmol.viewer.Viewer
Binding - Class in org.jmol.viewer.binding
Binding() - Constructor for class org.jmol.viewer.binding.Binding
bindings - Variable in class org.jmol.viewer.binding.Binding
bindName(int, String) - Method in class org.jmol.viewer.binding.Binding
BINFLOAT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BINGET - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BININT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BININT1 - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BININT2 - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BINPUT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BINSTRING - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
BINUNICODE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
bioAtomName - Variable in class org.jmol.smiles.SmilesAtom
BioExt - Class in org.jmol.modelsetbio
BioExt() - Constructor for class org.jmol.modelsetbio.BioExt
BioMeshRenderer - Class in org.jmol.renderbio
BioMeshRenderer() - Constructor for class org.jmol.renderbio.BioMeshRenderer
BioModel - Class in org.jmol.modelsetbio
BioModel(ModelSet, int, int, String, Properties, Map<String, Object>) - Constructor for class org.jmol.modelsetbio.BioModel
bioModelset - Variable in class org.jmol.modelset.AtomCollection
  If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning
BioModelSet - Class in org.jmol.modelsetbio
BioModelSet() - Constructor for class org.jmol.modelsetbio.BioModelSet
biomtChainAtomCounts - Variable in class org.jmol.adapter.readers.pdb.PdbReader
BioPolymer - Class in org.jmol.modelsetbio
  A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers", which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone), Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
BioPolymer() - Constructor for class org.jmol.modelsetbio.BioPolymer
bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
bioPolymer - Variable in class org.jmol.shapebio.BioShape
bioPolymerCount - Variable in class org.jmol.dssx.DSSP
bioPolymerCount - Variable in class org.jmol.modelsetbio.BioModel
bioPolymerIndexInModel - Variable in class org.jmol.modelsetbio.BioPolymer
bioPolymers - Variable in class org.jmol.dssx.DSSP
bioPolymers - Variable in class org.jmol.modelsetbio.BioModel
BioResolver - Class in org.jmol.modelsetbio
  a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
BioResolver() - Constructor for class org.jmol.modelsetbio.BioResolver
bioShape - Variable in class org.jmol.renderbio.BioShapeRenderer
BioShape - Class in org.jmol.shapebio
BioShape(BioShapeCollection, int, BioPolymer) - Constructor for class org.jmol.shapebio.BioShape
BioShapeCollection - Class in org.jmol.shapebio
  Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set.
BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
BioShapeRenderer - Class in org.jmol.renderbio
BioShapeRenderer() - Constructor for class org.jmol.renderbio.BioShapeRenderer
bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
biosymmetry - Variable in class org.jmol.modelset.Model
biosymmetryCount - Variable in class org.jmol.modelset.Model
bioType - Variable in class org.jmol.smiles.SmilesAtom
bioType - Variable in class org.jmol.smiles.SmilesParser
BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
bitset - Static variable in class org.jmol.script.T
bitSetForModelFileNumber(int) - Method in class org.jmol.script.ScriptExpr
BLACK - Static variable in class org.jmol.util.C
BLOCK_ATOMS - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
BLOCK_CALC - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
BLOCK_MAGRES - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
BLOCK_NEW - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
BLOCK_NONE - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
blockCubeData - Variable in class org.jmol.jvxl.readers.Parameters
blockdata - Static variable in class org.jmol.script.T
blockHeight - Variable in class org.jmol.renderbio.NucleicRenderer
BLUE - Static variable in class org.jmol.util.C
bnd(int, int...) - Method in class org.jmol.viewer.ActionManager
bo - Variable in class org.jmol.modelset.BondCollection
bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
BOND - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
bond - Variable in class org.jmol.adapter.readers.xml.XmlReader
Bond - Class in org.jmol.adapter.smarter
Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
bond - Variable in class org.jmol.adapter.smarter.BondIterator
Bond - Class in org.jmol.modelset
Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
bond - Variable in class org.jmol.render.SticksRenderer
bond - Variable in class org.jmol.shapespecial.Dipole
BOND_AROMATIC - Static variable in class org.jmol.util.Edge
BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
BOND_AROMATIC_MASK - Static variable in class org.jmol.util.Edge
BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_MASK - Static variable in class org.jmol.util.Edge
BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_QUINTUPLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_sextuple - Static variable in class org.jmol.util.Edge
BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.Edge
BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.Edge
BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
BOND_H_CALC - Static variable in class org.jmol.util.Edge
BOND_H_CALC_MASK - Static variable in class org.jmol.util.Edge
BOND_H_MINUS_3 - Static variable in class org.jmol.util.Edge
BOND_H_MINUS_4 - Static variable in class org.jmol.util.Edge
BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_2 - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_3 - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_4 - Static variable in class org.jmol.util.Edge
BOND_H_PLUS_5 - Static variable in class org.jmol.util.Edge
BOND_H_REGULAR - Static variable in class org.jmol.util.Edge
BOND_HBOND_SHIFT - Static variable in class org.jmol.util.Edge
BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.Edge
BOND_NEW - Static variable in class org.jmol.util.Edge
BOND_ORDER_ANY - Static variable in class org.jmol.util.Edge
BOND_ORDER_NULL - Static variable in class org.jmol.util.Edge
BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.Edge
BOND_PARTIAL01 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL12 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL23 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL32 - Static variable in class org.jmol.util.Edge
BOND_PARTIAL_MASK - Static variable in class org.jmol.util.Edge
BOND_PYMOL_MULT - Static variable in class org.jmol.util.Edge
BOND_PYMOL_NOMULT - Static variable in class org.jmol.util.Edge
BOND_RENDER_SINGLE - Static variable in class org.jmol.util.Edge
  Extended Bond Definition Types Originally these were short 16-bit values
BOND_STEREO_FAR - Static variable in class org.jmol.util.Edge
BOND_STEREO_MASK - Static variable in class org.jmol.util.Edge
BOND_STEREO_NEAR - Static variable in class org.jmol.util.Edge
BOND_STRUT - Static variable in class org.jmol.util.Edge
BOND_SULFUR_MASK - Static variable in class org.jmol.util.Edge
bondArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
bondAtomIndex1 - Variable in class org.jmol.modelkit.ModelKitPopup
bondAtomIndex2 - Variable in class org.jmol.modelkit.ModelKitPopup
bondAtoms(Atom, Atom, int, short, BS, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
bondAtoms(Object, Object, short) - Method in class org.jmol.modelset.ModelLoader
bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
BondCollection - Class in org.jmol.modelset
BondCollection() - Constructor for class org.jmol.modelset.BondCollection
bondCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
bondCount - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
bondCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bondCount - Variable in class org.jmol.adapter.smarter.BondIterator
bondCount - Variable in class org.jmol.minimize.forcefield.Calculations
bondCount - Variable in class org.jmol.minimize.Minimizer
bondCount - Variable in class org.jmol.modelset.BondCollection
bondCount - Variable in class org.jmol.modelset.BondIteratorSelected
bondCount - Variable in class org.jmol.modelset.Model
bondcount - Static variable in class org.jmol.script.T
bondCount - Variable in class org.jmol.smiles.SmilesAtom
bondCount - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  true atom covalent bond count; cached for better performance
bondCount - Variable in class org.jmol.viewer.Connections
bondCount0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
bondDirectionPaired - Variable in class org.jmol.smiles.SmilesParser
BONDED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bonded - Static variable in class org.jmol.script.T
bondedAtoms - Variable in class org.jmol.minimize.MinAtom
bondedOnly - Variable in class org.jmol.shapespecial.Polyhedra
bondFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
bondFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
bondHoverLabel - Variable in class org.jmol.modelkit.ModelKitPopup
bondIndex - Variable in class org.jmol.modelkit.ModelKitPopup
bondIndex0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bonding_vdw_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
bondingRadii - Variable in class org.jmol.modelset.AtomCollection
bondingradius - Static variable in class org.jmol.script.T
bondingversion - Static variable in class org.jmol.script.T
bondingVersion - Static variable in class org.jmol.util.Elements
bondingVersion - Variable in class org.jmol.viewer.GlobalSettings
bondingVersion - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
BondIterator - Class in org.jmol.adapter.smarter
BondIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.BondIterator
BondIterator - Interface in org.jmol.modelset
BondIteratorSelected - Class in org.jmol.modelset
BondIteratorSelected(Bond[], int, int, BS, boolean) - Constructor for class org.jmol.modelset.BondIteratorSelected
bondmode - Static variable in class org.jmol.script.T
bondmodeor - Static variable in class org.jmol.script.T
bondModeOr - Variable in class org.jmol.viewer.GlobalSettings
bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
bondOrder - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
bondOrder - Variable in class org.jmol.render.SticksRenderer
bondorder - Static variable in class org.jmol.script.T
bondPicked(int) - Method in class org.jmol.viewer.ActionManager
bondpicking - Static variable in class org.jmol.script.T
bondPicking - Variable in class org.jmol.viewer.GlobalSettings
bondPickingMode - Variable in class org.jmol.viewer.ActionManager
bondradiusmilliangstroms - Static variable in class org.jmol.script.T
bondRadiusMilliAngstroms - Variable in class org.jmol.viewer.GlobalSettings
bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bonds - Variable in class org.jmol.adapter.smarter.BondIterator
bonds - Variable in class org.jmol.minimize.MinAtom
bonds - Variable in class org.jmol.minimize.Minimizer
bonds - Variable in class org.jmol.modelset.Atom
  MAY BE NULL
bonds - Variable in class org.jmol.modelset.BondIteratorSelected
bonds - Static variable in class org.jmol.script.T
bonds - Variable in class org.jmol.smiles.SmilesAtom
bondsBackbone - Variable in class org.jmol.render.SticksRenderer
bondSelectionModeOr - Variable in class org.jmol.modelset.BondIteratorSelected
BondSet - Class in org.jmol.modelset
BondSet() - Constructor for class org.jmol.modelset.BondSet
bondset - Static variable in class org.jmol.script.T
bondsOr - Variable in class org.jmol.smiles.SmilesBond
bondsPerp - Variable in class org.jmol.render.SticksRenderer
bondtolerance - Static variable in class org.jmol.script.T
bondTolerance - Variable in class org.jmol.viewer.GlobalSettings
bondTolerance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
bondType - Variable in class org.jmol.modelset.BondIteratorSelected
bondTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
BONMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
BOOLEAN_OPTIONS - Static variable in class org.jmol.modelkit.ModelKitPopup
booleanparam - Static variable in class org.jmol.script.T
booleanSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
bOptions - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
BORDER - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
border - Variable in class org.openscience.jmol.app.JmolApp
border - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
BORDERCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
BorderLayout - Class in org.jmol.awtjs.swing
BorderLayout() - Constructor for class org.jmol.awtjs.swing.BorderLayout
BORDERSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
bos - Variable in class org.jmol.export._StlExporter
bottom - Variable in class org.jmol.awtjs.swing.Insets
bottom - Static variable in class org.jmol.script.T
bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
boundaryPlaneCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
boundbox - Static variable in class org.jmol.script.T
boundBox - Variable in class org.jmol.shapespecial.Draw
boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
boundBoxCenter - Variable in class org.openscience.jmol.app.surfacetool.Slice
boundboxcolor - Static variable in class org.jmol.script.T
boundBoxNegCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
boundBoxPosCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
boundingBox - Variable in class org.jmol.jvxl.readers.VolumeFileReader
Box(String) - Static method in class org.jmol.popup.MainPopupResourceBundle
boxFaces - Static variable in class org.jmol.renderbio.RocketRenderer
boxHeight - Variable in class org.jmol.modelset.Text
boxInfo - Variable in class org.jmol.modelset.ModelSet
BoxInfo - Class in org.jmol.util
  The BoxInfo class holds critical information about boundboxes.
BoxInfo() - Constructor for class org.jmol.util.BoxInfo
boxVec - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
boxWidth - Variable in class org.jmol.modelset.Text
boxX - Variable in class org.jmol.modelset.Text
boxXY - Variable in class org.jmol.modelset.Text
boxXY - Variable in class org.jmol.render.LabelsRenderer
boxY - Variable in class org.jmol.modelset.Text
boxYoff2 - Variable in class org.jmol.modelset.Text
bps - Variable in class org.jmol.modelsetbio.NucleicMonomer
br - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
br - Variable in class org.jmol.jvxl.readers.XmlReader
braceCount - Variable in class org.jmol.script.ScriptCompiler
braceCount - Variable in class org.jmol.script.ScriptMathProcessor
braceCount - Variable in class org.jmol.smiles.SmilesParser
bracketCount - Variable in class org.jmol.script.ScriptCompiler
branch - Static variable in class org.jmol.script.T
branchAtomIndex - Variable in class org.jmol.modelkit.ModelKitPopup
branchLevel - Variable in class org.jmol.smiles.SmilesParser
breakAt(int) - Method in class org.jmol.script.ScriptEval
breakcmd - Static variable in class org.jmol.script.T
breakOutAtomTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
breakOutBondTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
breakOutTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
breakTie(CIPChirality.CIPAtom, int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Break a tie at any level in the iteration between to atoms that otherwise are the same by sorting their substituents.
brickLayer - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
brickLayerByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
brickLayerVoxelCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
brickRowByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
Bridge - Class in org.jmol.dssx
  A class for cataloging ladder bridges in a DSSP calculation
Bridge(Atom, Atom, Map<int[][], Boolean>) - Constructor for class org.jmol.dssx.Bridge
bridgesA - Variable in class org.jmol.dssx.DSSP
bridgesP - Variable in class org.jmol.dssx.DSSP
brillouin - Static variable in class org.jmol.script.T
bs - Variable in class org.jmol.jvxl.data.MeshData.SSet
bs - Variable in class org.jmol.smiles.SmilesRingSet
bs14 - Variable in class org.jmol.minimize.MinAtom
bsa - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
bsA() - Method in class org.jmol.viewer.Viewer
bsAdded - Variable in class org.jmol.modelset.Group
bsAddedHydrogens - Variable in class org.jmol.modelsetbio.BioResolver
bsAddedMask - Variable in class org.jmol.modelsetbio.BioResolver
bsAll - Variable in class org.jmol.adapter.smarter.Structure
bsAll - Variable in class org.jmol.modelset.ModelSet
bsAllModels - Variable in class org.jmol.shapespecial.Draw
bsAnions - Static variable in class org.jmol.util.Elements
bsAromatic - Variable in class org.jmol.minimize.forcefield.ForceFieldUFF
bsAromatic - Variable in class org.jmol.modelset.BondCollection
bsAromatic - Variable in class org.jmol.smiles.SmilesGenerator
bsAromatic - Variable in class org.jmol.smiles.SmilesSearch
bsAromatic - Variable in class org.jmol.symmetry.CIPData
  Jmol's definition of aromatic
bsAromatic5 - Variable in class org.jmol.smiles.SmilesSearch
bsAromatic6 - Variable in class org.jmol.smiles.SmilesSearch
bsAromaticDouble - Variable in class org.jmol.modelset.BondCollection
bsAromaticRings - Variable in class org.jmol.smiles.SmilesSearch
bsAromaticSingle - Variable in class org.jmol.modelset.BondCollection
bsAssigned - Variable in class org.jmol.modelsetbio.BioResolver
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoSolventReader
bsAtomOK - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
bsAtoms - Variable in class org.jmol.adapter.readers.pymol.JmolObject
bsAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
bsAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomIterator
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bsAtoms - Variable in class org.jmol.adapter.smarter.BondIterator
bsAtoms - Variable in class org.jmol.minimize.Minimizer
bsAtoms - Variable in class org.jmol.modelset.Model
bsAtoms - Variable in class org.jmol.symmetry.CIPData
  bit set of all atoms to process
bsAtoms - Variable in class org.jmol.symmetry.PointGroup
bsAtoms - Variable in class org.jmol.thread.SpinThread
bsAtoms1 - Variable in class org.jmol.modelset.StateScript
bsAtoms2 - Variable in class org.jmol.modelset.StateScript
bsAtomsDeleted - Variable in class org.jmol.modelset.Model
bsAtomsForHs - Variable in class org.jmol.modelsetbio.BioResolver
bsAtropisomeric - Variable in class org.jmol.symmetry.CIPData
  bit set of all biphenyl-like connections "[!H](.t1:-20,20)a{a(.t2:-20,20)-a}a[!H]"
bsAzacyclic - Variable in class org.jmol.symmetry.CIPData
  all N atoms that are sp3-hybridized and at small ring fusions
bsb - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
bsBackbone - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
bsBad - Variable in class org.jmol.dssx.DSSP
bsBadIndex - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
bsBgColixSet - Variable in class org.jmol.shape.Labels
bsBondDuplicates - Variable in class org.jmol.adapter.readers.cif.CifReader
bsBonds - Variable in class org.jmol.modelset.StateScript
bsBondsDn - Variable in class org.jmol.smiles.SmilesGenerator
bsBondsUp - Variable in class org.jmol.smiles.SmilesGenerator
bsBranches - Variable in class org.jmol.thread.SpinThread
bsBytesExcluded - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
bsCartoon - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsCarve - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsCations - Static variable in class org.jmol.util.Elements
bsCheck - Variable in class org.jmol.modelset.Model
bsCheck - Variable in class org.jmol.smiles.SmilesSearch
bsClickable - Variable in class org.jmol.modelset.AtomCollection
bsColixSet - Variable in class org.jmol.shape.Shape
bsConnected - Variable in class org.jmol.adapter.readers.cif.CifReader
bsDeleted - Variable in class org.jmol.viewer.SelectionManager
bsDisplay - Variable in class org.jmol.shape.MeshCollection
bsDisplay - Variable in class org.jmol.util.MeshSurface
bsDisplay - Variable in class org.jmol.viewer.AnimationManager
bsEdgesToCheck - Variable in class org.jmol.smiles.SmilesRing
bsEnes - Variable in class org.jmol.symmetry.CIPData
  all sp2-hybridized atoms that are not Kekule-ambiguous
bsExclude - Variable in class org.jmol.adapter.readers.cif.CifReader
bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
bsFixed - Variable in class org.jmol.minimize.forcefield.ForceField
bsFixed - Variable in class org.jmol.minimize.Minimizer
bsFixed - Variable in class org.jmol.viewer.SelectionManager
bsFixedDefault - Variable in class org.jmol.minimize.Minimizer
bsFlat - Variable in class org.jmol.shapespecial.Polyhedron
bsFontSet - Variable in class org.jmol.shape.Labels
bsForPass2 - Variable in class org.jmol.render.SticksRenderer
bsFound - Variable in class org.jmol.smiles.SmilesSearch
bsFrameOffsets - Variable in class org.jmol.viewer.TransformManager
bsFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
bsHandles - Variable in class org.jmol.renderspecial.DrawRenderer
bsHelixM - Variable in class org.jmol.symmetry.CIPData
  aromatic atoms at the end of a negative helical turn "A{a}(.t:-10,-40)a(.t:-10,-40)aaa"
bsHelixP - Variable in class org.jmol.symmetry.CIPData
  aromatic atoms at the end of a positive helical turn "A{a}(.t:10,40)a(.t:10,40)aaa"
bsHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsHidden - Variable in class org.jmol.modelset.AtomCollection
bsHidden - Variable in class org.jmol.viewer.SelectionManager
bsHighlight - Variable in class org.jmol.modelkit.ModelKitPopup
bsHighlight - Variable in class org.jmol.shape.Halos
bsHydrogen - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsIgnore - Variable in class org.jmol.geodesic.EnvelopeCalculation
bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
bsIgnore - Variable in class org.jmol.shapespecial.Dots
bsIgnored - Variable in class org.jmol.atomdata.AtomData
bsIncludingH - Variable in class org.jmol.smiles.SmilesGenerator
bsKekuleAmbiguous - Variable in class org.jmol.symmetry.CIPData
  atoms that need specially-calculated element number in Rule 1a
bsLabeled - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsLineBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsLocale - Variable in class org.jmol.jvxl.readers.IsoSolventReader
bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
bsMinFixed - Variable in class org.jmol.minimize.Minimizer
bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
bsModels - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
bsModelsDefined - Variable in class org.jmol.adapter.smarter.StructureIterator
bsModulated - Variable in class org.jmol.modelset.AtomCollection
bsMolecule - Variable in class org.jmol.adapter.readers.cif.CifReader
bsMolecule - Variable in class org.jmol.shapespecial.Dipole
bsMolecule - Variable in class org.jmol.symmetry.CIPData
  atoms in all molecules containing the atoms of interest
bsMolecules - Variable in class org.jmol.atomdata.AtomData
bsMyIgnored - Variable in class org.jmol.jvxl.readers.AtomDataReader
bsMySelected - Variable in class org.jmol.geodesic.EnvelopeCalculation
bsMySelected - Variable in class org.jmol.jvxl.readers.AtomDataReader
bsNearby - Variable in class org.jmol.jvxl.readers.AtomDataReader
bsNeedRule - Variable in class org.jmol.symmetry.CIPChirality
  set bits RULE_1a - RULE_6 to indicate a need for that rule based on what is in the model
bsNegativeAromatic - Variable in class org.jmol.symmetry.CIPData
  [a-]
bsNonbonded - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsNoSurface - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsNucleic - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsOK - Variable in class org.jmol.quantum.NciCalculation
bsOn - Variable in class org.jmol.shapespecial.Dots
bsOrderSet - Variable in class org.jmol.shape.Sticks
bsPartialCharges - Variable in class org.jmol.modelset.AtomCollection
bsPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  bitset of indices of the associated atoms in the path to this atom node from the root; used to keep track of the path to this atom in order to prevent infinite cycling; the last atom in the path when cyclic is a duplicate atom.
Bspf - Class in org.jmol.bspt
  A Binary Space Partitioning Forest
Bspf(int) - Constructor for class org.jmol.bspt.Bspf
bspf - Variable in class org.jmol.modelset.AtomCollection
  Binary Space Partitioning Forest
bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
bsPolygons - Variable in class org.jmol.render.MeshRenderer
bsPolygons - Variable in class org.jmol.shapesurface.PMeshWriter
bsPolygons - Variable in class org.jmol.util.MeshSurface
bsPolygonsToExport - Variable in class org.jmol.render.MeshRenderer
bsPolys - Variable in class org.jmol.shapespecial.Polyhedra
Bspt - Class in org.jmol.bspt
  a Binary Space Partitioning Tree
Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
  Create a bspt with the specified number of dimensions.
bspt - Variable in class org.jmol.bspt.CubeIterator
bspt - Variable in class org.jmol.bspt.Element
bspts - Variable in class org.jmol.bspt.Bspf
bsptsValid - Variable in class org.jmol.bspt.Bspf
bsr - Variable in class org.jmol.renderbio.BioMeshRenderer
bsr - Variable in class org.jmol.renderbio.NucleicRenderer
bsRenderableAtoms - Variable in class org.jmol.viewer.ShapeManager
bsRenderMesh - Variable in class org.jmol.renderbio.BioMeshRenderer
bsReturn - Variable in class org.jmol.smiles.SmilesSearch
bsRingKeys - Variable in class org.jmol.smiles.SmilesGenerator
bsRotateBranch - Variable in class org.jmol.modelkit.ModelKitPopup
bsRule6Subs - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a list of only the undifferentiated ligands in Rule 6 -- root atom only
bsSelected - Variable in class org.jmol.atomdata.AtomData
bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
bsSelected - Variable in class org.jmol.minimize.Minimizer
bsSelected - Variable in class org.jmol.modelset.AtomIteratorWithinModel
bsSelected - Variable in class org.jmol.modelset.BondIteratorSelected
bsSelected - Variable in class org.jmol.quantum.MepCalculation
bsSelected - Variable in class org.jmol.renderspecial.PolyhedraRenderer
bsSelected - Variable in class org.jmol.shape.Measures
bsSelected - Variable in class org.jmol.shapebio.Backbone
bsSelected - Variable in class org.jmol.shapespecial.Dots
bsSelected - Variable in class org.jmol.smiles.SmilesGenerator
bsSelected - Variable in class org.jmol.smiles.SmilesSearch
bsSelectedAtoms - Variable in class org.jmol.viewer.TransformManager
bsSelectedCells - Variable in class org.jmol.awtjs.swing.JTable
bsSelectedMonomers - Variable in class org.jmol.modelsetbio.BioPolymer
bsSelectedRows - Variable in class org.jmol.awtjs.swing.JTable
bsSelection - Variable in class org.jmol.viewer.SelectionManager
bsSelectRange(T, int) - Static method in class org.jmol.script.SV
bsSelectToken(T) - Static method in class org.jmol.script.SV
bsSets - Variable in class org.jmol.adapter.readers.cif.CifReader
bsSizeDefault - Variable in class org.jmol.shape.AtomShape
bsSizeSet - Variable in class org.jmol.shape.Shape
bsSlabbedInternal - Variable in class org.jmol.viewer.ShapeManager
bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
bsSlabGhost - Variable in class org.jmol.util.MeshSurface
bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
bsStickBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsStructureDefined - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
bsStructuredModels - Variable in class org.jmol.adapter.smarter.AtomSetCollection
bsStructures - Variable in class org.jmol.adapter.readers.cif.MMTFReader
bsSubset - Variable in class org.jmol.viewer.SelectionManager
bsSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
bsSurface - Variable in class org.jmol.modelset.AtomCollection
bsSurfaceDone - Variable in class org.jmol.jvxl.readers.IsoSolventReader
bsSurfacePoints - Variable in class org.jmol.jvxl.readers.IsoSolventReader
bsSurfaceVoxels - Variable in class org.jmol.jvxl.readers.AtomDataReader
bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
bsSymmetry - Variable in class org.jmol.modelset.ModelSet
bsTaint - Variable in class org.jmol.minimize.Minimizer
bsTemp - Variable in class org.jmol.geodesic.EnvelopeCalculation
bsTemp - Variable in class org.jmol.renderbio.BioMeshRenderer
bsTemp - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
bsTemp - Variable in class org.jmol.shape.Mesh
bsTemp - Variable in class org.jmol.smiles.VTemp
bsTemp - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  used to count the number of priorities
bsTemp - Variable in class org.jmol.viewer.SelectionManager
bsToDo - Variable in class org.jmol.smiles.SmilesGenerator
bsTranslucent - Variable in class org.jmol.render.RepaintManager
bsUniqueBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
bsUserVdws - Variable in class org.jmol.viewer.Viewer
BSUtil - Class in org.jmol.util
BSUtil() - Constructor for class org.jmol.util.BSUtil
bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
bsVdw - Variable in class org.jmol.minimize.MinAtom
bsVdw - Variable in class org.jmol.shapesurface.IsosurfaceMesh
bsVertexCount - Variable in class org.jmol.shapespecial.Polyhedra
bsVertices - Variable in class org.jmol.shapespecial.Polyhedra
bsVisible - Variable in class org.jmol.modelset.AtomCollection
bsVisible - Variable in class org.jmol.renderbio.BioShapeRenderer
bsVisibleModels - Variable in class org.jmol.viewer.AnimationManager
bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
bsXAromatic - Variable in class org.jmol.symmetry.CIPData
  excluded aromatics [r5d3n+0,r5d2o+0]
bTest - Variable in class org.jmol.adapter.readers.xtal.GulpReader
btnType - Variable in class org.jmol.awtjs.swing.JMenuItem
btSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
BTYPE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
BUFF - Static variable in class org.jmol.minimize.forcefield.MMFFESCalc
buffer - Variable in class org.openscience.jmol.app.InputScannerThread
bufferedImage - Variable in class org.jmol.g3d.Platform3D
bufferHeight - Variable in class org.jmol.g3d.Platform3D
bufferSize - Variable in class org.jmol.g3d.Platform3D
bufferSize - Variable in class org.jmol.util.GData
bufferSizeT - Variable in class org.jmol.g3d.Platform3D
bufferWidth - Variable in class org.jmol.g3d.Platform3D
build - Variable in class org.jmol.adapter.readers.pymol.PickleReader
BUILD - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
buildAdvancedPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
buildBasicPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
buildBox(P3, V3, V3, V3) - Method in class org.jmol.renderbio.RocketRenderer
buildButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
buildFilePanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
buildPolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
buildScene(String, Lst<Object>, Map<String, Lst<Object>>, Map<String, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Build a scene at file reading time.
buildSlaters() - Method in class org.jmol.adapter.readers.xml.XmlMOReader
buildSpaceGroup(String) - Method in class org.jmol.symmetry.SpaceGroup
buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
buildStructure(String) - Method in class org.jmol.popup.PopupResource
bundle - Static variable in class org.jmol.modelkit.ModelKitPopup
BUNIQUEID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
button - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
BUTTON_MASK - Static variable in class org.jmol.awtjs.Event
BUTTON_MASK - Static variable in class org.jmol.viewer.binding.Binding
button_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
button_mode_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
buttonGroup - Variable in class org.jmol.awt.AwtPopupHelper
ButtonGroup - Class in org.jmol.awtjs.swing
ButtonGroup() - Constructor for class org.jmol.awtjs.swing.ButtonGroup
buttonGroup - Variable in class org.jmol.awtjs2d.JSPopupHelper
buttonGroup - Variable in class org.jmol.popup.GenericPopup
buttonModelkit - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
buttonPanel - Variable in class org.jmol.console.ScriptEditor
buttonPanel - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
buttonRotate - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
bValue(T) - Static method in class org.jmol.script.SV
BW - Static variable in class org.jmol.util.ColorEncoder
BWR - Static variable in class org.jmol.util.ColorEncoder
bwSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
byChain - Variable in class org.jmol.adapter.readers.cif.MMCifReader
BYELEMENT_JMOL - Static variable in class org.jmol.util.ColorEncoder
BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
BYELEMENT_RASMOL - Static variable in class org.jmol.util.ColorEncoder
BYRESIDUE_AMINO - Static variable in class org.jmol.util.ColorEncoder
BYRESIDUE_NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
BYRESIDUE_SHAPELY - Static variable in class org.jmol.util.ColorEncoder
bySymop - Variable in class org.jmol.adapter.readers.cif.MMCifReader
byteArrayOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
byteFactor - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
bytesOrStream - Variable in class org.jmol.io.FileReader
bytesToString(Object) - Method in class org.jmol.adapter.readers.pymol.PickleReader
bytesToString(Object) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
bzColor(int) - Method in class org.jmol.util.BZone
  give each Brillouin zone a new color
bzColors - Static variable in class org.jmol.util.BZone
bzDrawPointsAndEdges - Variable in class org.jmol.util.BZone
bzFaceCenters - Variable in class org.jmol.util.BZone
bzGamma - Variable in class org.jmol.util.BZone
bzLatticePts - Variable in class org.jmol.util.BZone
bzLatticePtsAll - Variable in class org.jmol.util.BZone
BZone - Class in org.jmol.util
  class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells based on https://chemapps.stolaf.edu/jmol/jsmol/spt/ext/xtal/bz.spt
BZone() - Constructor for class org.jmol.util.BZone
bzones - Variable in class org.jmol.util.BZone
bzPlanePts - Variable in class org.jmol.util.BZone
bzSavePmeshes - Variable in class org.jmol.util.BZone

## C

c - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
c - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
c - Variable in class org.jmol.adapter.readers.xtal.CastepReader
c - Variable in class org.jmol.adapter.readers.xtal.GulpReader
c - Variable in class org.jmol.awtjs.swing.Cell
c - Variable in class org.jmol.jvxl.readers.MapFileReader
c - Variable in class org.jmol.minimize.forcefield.Calculation
C - Static variable in class org.jmol.modelsetbio.AminoMonomer
c - Static variable in class org.jmol.quantum.NciCalculation
C - Class in org.jmol.util
  Note: Color table is now in javajs/util/CU.java
C() - Constructor for class org.jmol.util.C
c - Variable in class org.jmol.util.SimpleUnitCell
c0_xxz_yyz - Static variable in class org.jmol.quantum.mo.DataAdder7F
c1 - Variable in class org.jmol.g3d.HermiteRenderer
c1n_xxy - Static variable in class org.jmol.quantum.mo.DataAdder7F
c1n_yyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
c1n_yzz - Static variable in class org.jmol.quantum.mo.DataAdder7F
C1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c1p_xxx - Static variable in class org.jmol.quantum.mo.DataAdder7F
c1p_xyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
c1p_xzz - Static variable in class org.jmol.quantum.mo.DataAdder7F
c2 - Variable in class org.jmol.g3d.HermiteRenderer
C2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c2 - Static variable in class org.jmol.symmetry.PointGroup
C2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c2p_xxz_yyz - Static variable in class org.jmol.quantum.mo.DataAdder7F
c3 - Static variable in class org.jmol.symmetry.PointGroup
c3n_xxy - Static variable in class org.jmol.quantum.mo.DataAdder7F
c3n_yyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
C3P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c3p_xxx - Static variable in class org.jmol.quantum.mo.DataAdder7F
c3p_xyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
C4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c4 - Static variable in class org.jmol.symmetry.PointGroup
C4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
C5 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c5 - Static variable in class org.jmol.symmetry.PointGroup
C5P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
C6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c6 - Static variable in class org.jmol.symmetry.PointGroup
C8 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
c8 - Static variable in class org.jmol.symmetry.PointGroup
c_ - Variable in class org.jmol.util.SimpleUnitCell
CA - Static variable in class org.jmol.modelsetbio.AminoMonomer
cA_ - Variable in class org.jmol.util.SimpleUnitCell
cache - Static variable in class org.jmol.script.T
cache() - Method in class org.jmol.scriptext.CmdExt
cache - Variable in class org.jmol.viewer.FileManager
cache_display - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cache_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cache_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cache_memory - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cache_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cacheClear() - Method in class org.jmol.viewer.FileManager
cacheClear() - Method in class org.jmol.viewer.Viewer
cacheFileByName(String, boolean) - Method in class org.jmol.appletjs.Jmol
cacheFileByName(String, boolean) - Method in class org.jmol.viewer.Viewer
cacheFileByNameAdd(String, boolean) - Method in class org.jmol.viewer.FileManager
cacheGet(String, boolean) - Method in class org.jmol.viewer.FileManager
cacheID - Variable in class org.jmol.adapter.readers.pymol.JmolObject
cacheList() - Method in class org.jmol.viewer.FileManager
cacheName - Variable in class org.jmol.script.FileLoadThread
cachePut(String, Object) - Method in class org.jmol.appletjs.Jmol
cachePut(String, Object) - Method in class org.jmol.viewer.FileManager
cachePut(String, Object) - Method in class org.jmol.viewer.Viewer
  JSInterface -- allows saving files in memory for later retrieval
CACTUS_FILE_TYPES - Static variable in class org.jmol.viewer.JC
caf - Variable in class org.jmol.viewer.AnimationManager
  current animation frame
CageRenderer - Class in org.jmol.render
CageRenderer() - Constructor for class org.jmol.render.CageRenderer
cai - Variable in class org.jmol.viewer.AnimationManager
calc(int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
calc - Variable in class org.jmol.minimize.forcefield.ForceField
calc1Screen(P3, V3, short, float, P3) - Method in class org.jmol.renderbio.BioShapeRenderer
CALC_ANGLE - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_DISTANCE - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_ES - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_MAX - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_OOP - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_STRETCH_BEND - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_TORSION - Static variable in class org.jmol.minimize.forcefield.Calculations
CALC_VDW - Static variable in class org.jmol.minimize.forcefield.Calculations
calcAllRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
  only for base models, not trajectories
calcArgbEndcap(boolean, boolean) - Method in class org.jmol.g3d.CylinderRenderer
calcArgbsGreyscale() - Static method in class org.jmol.util.C
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.api.JmolViewer
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.modelset.ModelSet
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.viewer.Viewer
calcAxis() - Method in class org.jmol.modelsetbio.Helix
calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
calcAxis() - Method in class org.jmol.modelsetbio.Sheet
calcBfactorRange(BS) - Method in class org.jmol.modelset.AtomCollection
calcBfactorRange() - Method in class org.jmol.shapebio.BioShape
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.modelset.ModelSet
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.viewer.Viewer
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
  sets all camera and scale factors needed by the specific perspective model instantiated
calcContourPoint(float, float, float, P3) - Method in class org.jmol.jvxl.calc.MarchingSquares
calcConvexBits() - Method in class org.jmol.geodesic.EnvelopeCalculation
calcConvexMap(boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
calcCosSin(float, float, float) - Method in class org.jmol.g3d.CylinderRenderer
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
calcFactors(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
calcHbondEnergy(P3, P3, AminoMonomer, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
  based on RasMol 2.7.2.1.1 model checkDistances: When we are seriously looking for H bonds, we want to also check that distCN > distCH and that the OH distance is less than 3 Angstroms.
calcLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
calcLegendre(int) - Method in class org.jmol.util.Modulation
calcMeanPositionalDisplacement(int) - Method in class org.jmol.shapebio.BioShape
  Calculates the mean positional displacement in milliAngstroms.
calcMetrics() - Method in class org.jmol.shape.Frank
calcNavCameraFactors(float) - Method in class org.jmol.viewer.TransformManager
calcNavigationDepthPercent() - Method in class org.jmol.navigate.Navigator
calcNavigationPoint() - Method in interface org.jmol.api.JmolNavigatorInterface
calcNavigationPoint() - Method in class org.jmol.navigate.Navigator
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
  All the magic happens here.
calcNavSlabAndDepthValues() - Method in class org.jmol.navigate.Navigator
calcOptions - Variable in class org.jmol.adapter.readers.quantum.GamessReader
calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
calcPhiPsiAngles2(AminoMonomer, AminoMonomer) - Method in class org.jmol.modelsetbio.AminoPolymer
calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
  For reduced density only; coloring is done point by point.
calcPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Fill this plane with data based on the current set of raw data planes.
calcPoints(int, boolean) - Method in class org.jmol.g3d.CylinderRenderer
calcRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
  These are not actual hydrogen bonds.
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
calcRectRubberBand() - Method in class org.jmol.viewer.ActionManager
calcRopeMidPoints() - Method in class org.jmol.renderbio.RocketsRenderer
calcRotatedPoint(float, int, boolean, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
calcRotationRadius(int, P3, boolean) - Method in class org.jmol.modelset.ModelSet
calcRotationRadiusBs(BS) - Method in class org.jmol.modelset.ModelSet
calcs - Variable in class org.jmol.minimize.forcefield.Calculation
calcScreenControlPoints() - Method in class org.jmol.renderbio.BioShapeRenderer
calcScreens(float, short[]) - Method in class org.jmol.renderbio.BioShapeRenderer
  calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
calcSelectedGroupsCount(BS) - Method in class org.jmol.modelset.Chain
  prior to coloring by group, we need the chain count per chain that is selected
calcSelectedGroupsCount(BS) - Method in class org.jmol.modelset.Model
calcSelectedGroupsCount() - Method in class org.jmol.modelset.ModelSet
calcSelectedMoleculesCount() - Method in class org.jmol.modelset.ModelSet
calcSelectedMonomersCount() - Method in class org.jmol.modelset.ModelSet
calcSelectedMonomersCount() - Method in class org.jmol.modelsetbio.BioModelSet
calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioPolymer
calcSheetUnitVectors() - Method in class org.jmol.modelsetbio.Sheet
calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
  sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
calcSP(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
calcSphereShading() - Method in class org.jmol.util.Shader
calcSurfaceDistances() - Method in class org.jmol.modelset.AtomCollection
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager4D
calcType - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
calcType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolEnvCalc
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
calculate(VolumeData, BS, P3[], Atom[], float[], int) - Method in class org.jmol.quantum.MepCalculation
calculate - Static variable in class org.jmol.script.T
calculate() - Method in class org.jmol.scriptext.CmdExt
calculate(T3, boolean) - Method in class org.jmol.util.ModulationSet
  Calculate r_I internal d-space coordinate of an atom.
calculateAllPolymers(Group[], int, int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
calculateAllStructuresExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
calculateAllstruts(Viewer, ModelSet, BS, BS) - Method in class org.jmol.modelsetbio.BioExt
calculateAllStuctures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
calculateAnglesInDegrees() - Method in class org.jmol.modelsetbio.AlphaPolymer
calculateChirality(BS) - Method in class org.jmol.viewer.Viewer
calculateChiralityForAtoms(BS, boolean) - Method in class org.jmol.modelset.ModelSet
calculateChiralityForSmiles(String) - Method in class org.jmol.viewer.Viewer
calculateCIPChiralityForAtoms(Viewer, BS) - Method in interface org.jmol.api.SymmetryInterface
calculateCIPChiralityForAtoms(Viewer, BS) - Method in class org.jmol.symmetry.Symmetry
calculateCIPChiralityForSmiles(Viewer, String) - Method in interface org.jmol.api.SymmetryInterface
calculateCIPChiralityForSmiles(Viewer, String) - Method in class org.jmol.symmetry.Symmetry
calculateCodes(float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
calculateCutoff() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
calculatedArea - Variable in class org.jmol.shapesurface.IsosurfaceMesh
calculatedArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
calculatedDipole - Variable in class org.jmol.shapespecial.Dipoles
calculateDssp(Object[], int, Object, boolean, boolean, boolean, int) - Method in class org.jmol.dssx.DSSP
calculateDssrProperty(String) - Method in class org.jmol.modelset.ModelSet
calculateDSSRStructure(Viewer, BS) - Method in interface org.jmol.api.JmolAnnotationParser
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.AnnotationParser
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.DSSR1
calculateDssx(Lst<Bond>, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModel
calculatedVolume - Variable in class org.jmol.shapesurface.IsosurfaceMesh
calculatedVolume - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
calculateFormalCharges(BS) - Method in class org.jmol.viewer.Viewer
calculateFractionalPoint(float, P3, P3, float, float, P3) - Method in class org.jmol.jvxl.data.VolumeData
calculateGeodesicSurface(BS, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
calculateGeodesicSurface(BS, float) - Method in class org.jmol.shapesurface.Isosurface
calculateHydrogens(BS, int[], boolean, boolean, Lst<Atom>) - Method in class org.jmol.modelset.AtomCollection
  get a list of potential H atom positions based on elemental valence and formal charge
calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
calculateMolecularDipole(int, BS) - Method in class org.jmol.modelset.ModelSet
calculateMolecularDipole(BS) - Method in class org.jmol.viewer.Viewer
calculatePartialCharges(Bond[], int[], Atom[], int[], BS, boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
  assign partial charges ala MMFF94
calculatePartialCharges(ModelSet, BS, BS) - Method in class org.jmol.minimize.Minimizer
calculatePartialCharges(BS) - Method in class org.jmol.viewer.Viewer
calculatePointGroup(BS) - Method in class org.jmol.modelset.ModelSet
calculatePointGroupForFirstModel(BS, boolean, boolean, String, int, float, T3[], P3, String) - Method in class org.jmol.modelset.ModelSet
calculatePolymers(Group[], int, int, BS) - Method in class org.jmol.modelset.ModelSet
calculateQCoefs(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
  determine simple linear combination assuming simple -3 to 3 no more than two dimensions.
calculateR0(double, double, double, double, double) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
calculateRunsFourOrMore(AlphaPolymer.Code[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
calculateStraightness() - Method in class org.jmol.viewer.Viewer
calculateStraightnessAll() - Method in class org.jmol.modelset.ModelSet
calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioExt
calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioModelSet
calculateStructures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
  Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
calculateStructures(boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModel
calculateStructures(BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
calculateStructuresAllExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
  allows rebuilding of PDB structures; also accessed by ModelManager from Eval
calculateStruts(BS, BS) - Method in class org.jmol.modelset.ModelSet
  see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
calculateStruts(ModelSet, BS, BS, Lst<Atom>, float, int, boolean) - Static method in class org.jmol.modelsetbio.BioExt
  Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous).
calculateStruts(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
calculateStruts(BS, BS) - Method in class org.jmol.viewer.Viewer
calculateSurface(BS, float) - Method in class org.jmol.modelset.AtomCollection
calculateSurface(BS, float) - Method in class org.jmol.viewer.Viewer
calculateVolume(BS, VDW) - Method in class org.jmol.modelset.AtomCollection
calculateVolumeOrArea(MeshData, int, boolean, boolean) - Static method in class org.jmol.jvxl.data.MeshData
calculateVolumeOrArea(IsosurfaceMesh, boolean) - Method in class org.jmol.shapesurface.Isosurface
Calculation - Class in org.jmol.minimize.forcefield
Calculation() - Constructor for class org.jmol.minimize.forcefield.Calculation
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
  The number of the calculation being interpreted.
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.QchemReader
  The number of the job being interpreted.
Calculations - Class in org.jmol.minimize.forcefield
Calculations(ForceField, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<MMConstraint>) - Constructor for class org.jmol.minimize.forcefield.Calculations
calculations - Variable in class org.jmol.minimize.forcefield.Calculations
CalculationsMMFF - Class in org.jmol.minimize.forcefield
CalculationsMMFF(ForceField, Map<Object, Object>, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<MMConstraint>) - Constructor for class org.jmol.minimize.forcefield.CalculationsMMFF
CalculationsUFF - Class in org.jmol.minimize.forcefield
CalculationsUFF(ForceField, Map<Object, Object>, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<MMConstraint>) - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF
calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
calculationType - Variable in class org.jmol.jvxl.readers.Parameters
calculationType - Variable in class org.jmol.quantum.MOCalculation
calcUnitCell(double[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
calcUnitCellMinMax() - Method in class org.jmol.modelset.ModelSet
calcVertexPoint(int, int, int, int, P3) - Method in class org.jmol.jvxl.calc.MarchingCubes
calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
callbacks - Variable in class org.jmol.util.GenericApplet
camera - Variable in class org.jmol.viewer.TransformManager
cameraDepth - Variable in class org.jmol.modelset.Orientation
cameradepth - Static variable in class org.jmol.script.T
cameraDepth - Variable in class org.jmol.thread.MoveToThread
cameraDepth - Variable in class org.jmol.viewer.TransformManager
cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
cameraDistance - Variable in class org.jmol.export.___Exporter
cameraDistance - Variable in class org.jmol.viewer.TransformManager
cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
cameraPosition - Variable in class org.jmol.export.___Exporter
cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
cameraSetting - Variable in class org.jmol.viewer.TransformManager
cameraX - Variable in class org.jmol.modelset.Orientation
cameraX - Variable in class org.jmol.thread.MoveToThread
cameraY - Variable in class org.jmol.modelset.Orientation
cameraY - Variable in class org.jmol.thread.MoveToThread
canAdd(Bridge) - Method in class org.jmol.dssx.Bridge
canBeNormalized(V3d) - Static method in class org.jmol.minimize.Util
canBeSquared(double) - Static method in class org.jmol.minimize.Util
canCapCylinders - Variable in class org.jmol.export.__CartesianExporter
cancel - Static variable in class org.jmol.script.T
cancel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cancel() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
cancelPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Responds to cancel being press- or equivalent eg window closed.
canDoLineTo() - Method in interface org.jmol.api.GenericGraphics
canDoLineTo() - Method in class org.jmol.awt.AwtG2D
canDoLineTo() - Method in class org.jmol.awtjs2d.JsG2D
canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
canDownsample - Variable in class org.jmol.jvxl.readers.VolumeFileReader
canImport(JComponent, DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
canIncrement() - Method in class org.jmol.script.SV
CANONICAL_DC_LIST - Static variable in class org.jmol.quantum.QS
CANONICAL_DS_LIST - Static variable in class org.jmol.quantum.QS
CANONICAL_FC_LIST - Static variable in class org.jmol.quantum.QS
CANONICAL_FS_LIST - Static variable in class org.jmol.quantum.QS
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalSeitzList - Static variable in class org.jmol.symmetry.SpaceGroup
canonizeAlphaDigit(char) - Static method in class org.jmol.api.JmolAdapter
canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
canSkipLoad - Variable in class org.jmol.modelset.AtomCollection
canvas - Variable in class org.jmol.awtjs2d.Platform
canvas - Variable in class org.jmol.console.ImageDialog
cap - Static variable in class org.jmol.script.T
capCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
capData(P4, float) - Method in class org.jmol.jvxl.data.VolumeData
capMap - Variable in class org.jmol.util.MeshCapper
  initialization only
capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
capper - Variable in class org.jmol.util.MeshSlicer
cappingObject - Variable in class org.jmol.shape.Mesh
cappingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
capPlanesPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
capture - Static variable in class org.jmol.script.T
capture() - Method in class org.jmol.scriptext.CmdExt
captureParams - Variable in class org.jmol.viewer.Viewer
CapVertex(T3, int) - Constructor for class org.jmol.util.MeshCapper.CapVertex
carbohydrate - Static variable in class org.jmol.script.T
CarbohydrateMonomer - Class in org.jmol.modelsetbio
CarbohydrateMonomer() - Constructor for class org.jmol.modelsetbio.CarbohydrateMonomer
CarbohydratePolymer - Class in org.jmol.modelsetbio
CarbohydratePolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.CarbohydratePolymer
cardinalityOf(BS) - Static method in class org.jmol.util.BSUtil
  cardinality = "total number of set bits"
cartesianOffset - Variable in class org.jmol.symmetry.UnitCell
cartesianProduct(T3, T3) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  dual-purpose function for cross products, proper rotations, and improper rotations
CARTN_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
CARTN_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
CARTN_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
CARTOON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon - Static variable in class org.jmol.script.T
Cartoon - Class in org.jmol.shapebio
Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
cartoon_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_cylindrical_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_discrete_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_dumbbell_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_dumbbell_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_dumbbell_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_fancy_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_fancy_sheets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_flat_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_flat_sheets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_helix_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_highlight_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ladder_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ladder_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ladder_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_loop_cap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_loop_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_loop_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_nucleic_acid_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_nucleic_acid_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_nucleic_acid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_oval_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_oval_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_oval_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_scale_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_scale_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_scale_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_putty_transform - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_rect_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_rect_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_refine - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_refine_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_refine_tips - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ring_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ring_finder - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ring_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ring_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ring_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_ring_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_round_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_sampling - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_side_chain_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_smooth_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_smooth_first - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_smooth_last - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_smooth_loops - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_throw - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_trace_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_tube_cap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_tube_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_tube_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoon_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cartoonBaseEdges - Variable in class org.jmol.renderbio.NucleicRenderer
cartoonbaseedges - Static variable in class org.jmol.script.T
cartoonBaseEdges - Variable in class org.jmol.viewer.GlobalSettings
cartoonblockheight - Static variable in class org.jmol.script.T
cartoonBlockHeight - Variable in class org.jmol.viewer.GlobalSettings
cartoonBlocks - Variable in class org.jmol.renderbio.NucleicRenderer
cartoonblocks - Static variable in class org.jmol.script.T
cartoonBlocks - Variable in class org.jmol.viewer.GlobalSettings
cartoonColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
cartoonFancy - Variable in class org.jmol.viewer.GlobalSettings
cartoonLadderMode - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
cartoonLadders - Variable in class org.jmol.renderbio.NucleicRenderer
cartoonladders - Static variable in class org.jmol.script.T
cartoonLadders - Variable in class org.jmol.viewer.GlobalSettings
CartoonRenderer - Class in org.jmol.renderbio
CartoonRenderer() - Constructor for class org.jmol.renderbio.CartoonRenderer
cartoonRibose - Variable in class org.jmol.renderbio.NucleicRenderer
cartoonribose - Static variable in class org.jmol.script.T
cartoonRibose - Variable in class org.jmol.viewer.GlobalSettings
cartoonRockets - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
cartoonrockets - Static variable in class org.jmol.script.T
cartoonRockets - Variable in class org.jmol.viewer.GlobalSettings
cartoons - Variable in class org.jmol.dialog.FilePreview
cartoonsFancy - Variable in class org.jmol.renderbio.BioShapeRenderer
cartoonsfancy - Static variable in class org.jmol.script.T
cartoonSteps - Variable in class org.jmol.renderbio.NucleicRenderer
cartoonsteps - Static variable in class org.jmol.script.T
cartoonSteps - Variable in class org.jmol.viewer.GlobalSettings
cartoonTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
cartoonTypes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
casecmd - Static variable in class org.jmol.script.T
CastepDensityReader - Class in org.jmol.jvxl.readers
CastepDensityReader() - Constructor for class org.jmol.jvxl.readers.CastepDensityReader
CastepReader - Class in org.jmol.adapter.readers.xtal
  CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.
CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
catalogUnit(Viewer, float[][], String, float, BS, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
  Carried out for each unit
catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
  Returns a Lst
catchcmd - Static variable in class org.jmol.script.T
cationLookupTable - Static variable in class org.jmol.util.Elements
cavity - Static variable in class org.jmol.script.T
cavity_cull - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cavityRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
cavityRadius - Variable in class org.jmol.jvxl.readers.Parameters
cb - Variable in class org.jmol.dialog.Dialog
CB - Static variable in class org.jmol.minimize.forcefield.MMFFAngleCalc
cB_ - Variable in class org.jmol.util.SimpleUnitCell
cbAxesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cbClearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
CBK - Enum in org.jmol.c
CBK() - Constructor for enum org.jmol.c.CBK
cbl - Variable in class org.jmol.viewer.StatusManager
cbOpenFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cbPerspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cbShowAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cbShowBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
CC_ATOM_CHARGE - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_SYM - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_X_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_Y_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_ATOM_Z_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
CC_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
CCDC_GEOM_BOND_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
cchScript - Variable in class org.jmol.script.ScriptCompiler
cchToken - Variable in class org.jmol.script.ScriptCompiler
cd - Static variable in class org.jmol.script.T
cd(String) - Method in class org.jmol.viewer.Viewer
ce - Variable in class org.jmol.util.ColorEncoder
ce - Variable in class org.jmol.viewer.ColorManager
CELL - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
cell() - Method in class org.jmol.adapter.readers.xtal.JanaReader
cell() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
Cell - Class in org.jmol.awtjs.swing
Cell(JComponent, GridBagConstraints) - Constructor for class org.jmol.awtjs.swing.Cell
cell - Static variable in class org.jmol.script.T
cell0 - Variable in class org.jmol.render.UccageRenderer
cell1 - Variable in class org.jmol.render.UccageRenderer
cellLattice - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
cellParameterType - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
cellParamNames - Static variable in class org.jmol.api.JmolAdapter
cellParams - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
cellParams - Variable in class org.jmol.adapter.readers.xtal.MagresReader
cellRange - Variable in class org.jmol.symmetry.SymmetryInfo
cellSelectionEnabled - Variable in class org.jmol.awtjs.swing.JTable
celOn - Variable in class org.jmol.util.Shader
celPower - Variable in class org.jmol.util.Shader
celRGB - Variable in class org.jmol.util.Shader
celshading - Static variable in class org.jmol.script.T
celshadingpower - Static variable in class org.jmol.script.T
celZ - Variable in class org.jmol.util.Shader
CENTER - Static variable in class org.jmol.awtjs.swing.BorderLayout
CENTER - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
CENTER - Static variable in class org.jmol.awtjs.swing.SwingConstants
center - Variable in class org.jmol.export.___Exporter
center - Variable in class org.jmol.jvxl.readers.Parameters
center - Variable in class org.jmol.jvxl.readers.SurfaceReader
center - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
center - Variable in class org.jmol.modelset.Orientation
center - Variable in class org.jmol.navigate.Navigator
center - Static variable in class org.jmol.renderspecial.DipolesRenderer
center - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
center - Static variable in class org.jmol.script.T
center - Variable in class org.jmol.shapespecial.Dipole
center - Variable in class org.jmol.shapespecial.Ellipsoid
center - Variable in class org.jmol.shapespecial.Polyhedra
center - Variable in class org.jmol.shapespecial.Polyhedron
center - Variable in class org.jmol.shapesurface.Isosurface
center - Variable in class org.jmol.symmetry.PointGroup
center - Variable in class org.jmol.symmetry.UnitCellIterator
center - Variable in class org.jmol.thread.MoveToThread
center - Variable in class org.jmol.util.BZone
center - Variable in class org.jmol.util.Modulation
center - Static variable in class org.jmol.viewer.JC
center - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
centerat - Static variable in class org.jmol.script.T
centerAt() - Method in class org.jmol.scriptext.CmdExt
centerAt(int, int, P3) - Method in class org.jmol.viewer.TransformManager
centerAtomIndex - Variable in class org.jmol.modelkit.ModelKitPopup
centerAtomIndex - Variable in class org.jmol.symmetry.PointGroup
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
centerDipole() - Method in class org.jmol.shapespecial.Dipole
centerDistance - Variable in class org.jmol.modelkit.ModelKitPopup
centerI - Variable in class org.jmol.geodesic.EnvelopeCalculation
centering - Variable in class org.jmol.symmetry.SymmetryOperation
centerParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
centerParameter(int) - Method in class org.jmol.scriptext.ScriptExt
centerParameterForModel(int, int, Object[]) - Method in class org.jmol.script.ScriptParam
centerPoint - Variable in class org.jmol.modelkit.ModelKitPopup
centers - Variable in class org.jmol.shapespecial.Polyhedra
centers - Variable in class org.jmol.shapesurface.IsosurfaceMesh
centerStart - Variable in class org.jmol.navigate.Navigator
centerT - Variable in class org.jmol.geodesic.EnvelopeCalculation
centralAtom - Variable in class org.jmol.shapespecial.Polyhedron
centralize() - Method in class org.jmol.adapter.smarter.AtomSetCollection
centroid - Static variable in class org.jmol.script.T
centroidPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
centroidPacked - Variable in class org.jmol.adapter.smarter.XtalSymmetry
cfiStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
cgdLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
CgdReader - Class in org.jmol.adapter.readers.xtal
  A reader for TOPOS systre file Crystal Graph Data format.
CgdReader() - Constructor for class org.jmol.adapter.readers.xtal.CgdReader
cgo - Static variable in class org.jmol.script.T
cgo() - Method in class org.jmol.scriptext.IsoExt
CGO - Class in org.jmol.shapecgo
CGO() - Constructor for class org.jmol.shapecgo.CGO
cgo_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_dot_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_dot_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_ellipsoid_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_line_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_line_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_ray_width_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_shader_ub_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_shader_ub_flags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_shader_ub_normal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_sphere_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgo_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cgoMesh - Variable in class org.jmol.rendercgo.CGORenderer
cgoMesh - Variable in class org.jmol.shapecgo.CGO
CGOMesh - Class in org.jmol.shapecgo
CGOMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapecgo.CGOMesh
CGORenderer - Class in org.jmol.rendercgo
  Something like a PyMOL Compiled Graphical Object, but more interesting!
CGORenderer() - Constructor for class org.jmol.rendercgo.CGORenderer
cH - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
ch1 - Variable in class org.jmol.modelset.LabelToken
CHAIN - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
Chain - Class in org.jmol.modelset
  A Model is a collection of Chains of Groups of Atoms.
Chain(Model, int, int) - Constructor for class org.jmol.modelset.Chain
chain - Variable in class org.jmol.modelset.Group
  required
chain - Static variable in class org.jmol.script.T
chainAtomCount - Variable in class org.jmol.adapter.readers.cif.MMCifReader
chainAtomCounts - Variable in class org.jmol.adapter.readers.cif.MMCifReader
chainAtomMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
chaincasesensitive - Static variable in class org.jmol.script.T
chainCaseSensitive - Variable in class org.jmol.viewer.GlobalSettings
chainCaseSpecified - Variable in class org.jmol.viewer.Viewer
chainCheck - Variable in class org.jmol.smiles.SmilesGenerator
chainCount - Variable in class org.jmol.modelset.Model
chainID - Variable in class org.jmol.adapter.readers.more.Mol2Reader
chainID - Variable in class org.jmol.adapter.smarter.Atom
chainID - Variable in class org.jmol.modelset.Chain
  chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
chainList - Variable in class org.jmol.viewer.Viewer
chainMap - Variable in class org.jmol.viewer.Viewer
chainNo - Variable in class org.jmol.modelset.Chain
  chainNo is for information purposes only; retrieved by {atoms}.chainNo
chainno - Static variable in class org.jmol.script.T
chainOf - Variable in class org.jmol.modelset.ModelLoader
chains - Variable in class org.jmol.modelset.Model
chainSum - Variable in class org.jmol.adapter.readers.cif.MMCifReader
chainToUpper(int) - Method in class org.jmol.modelset.AtomCollection
CHANGEABLE_MASK - Static variable in class org.jmol.util.C
changeableColixMap - Variable in class org.jmol.util.GData
changeColixArgb(int, int) - Method in class org.jmol.util.GData
CHAR - Static variable in class org.jmol.shapecgo.CGOMesh
characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlHandler
charAt(int) - Method in class org.jmol.script.ScriptCompiler
charge - Variable in class org.jmol.smiles.SmilesAtom
charge - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
CHARGE_OFFSET - Static variable in class org.jmol.modelset.Atom
chargesFound - Variable in class org.jmol.adapter.readers.simple.MopacReader
ChargesOnly - Variable in class org.jmol.popup.JmolPopup
chargeSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
chargeType - Variable in class org.jmol.adapter.readers.xtal.CastepReader
chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
check - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
check(boolean, boolean) - Method in class org.jmol.renderbio.BioMeshRenderer
check - Static variable in class org.jmol.script.T
check() - Method in class org.jmol.smiles.SmilesMeasure
check(int, int, int, int, long, long) - Method in class org.jmol.viewer.MouseState
check - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
CHECK1 - Static variable in class org.jmol.thread.JmolThread
CHECK2 - Static variable in class org.jmol.thread.JmolThread
CHECK3 - Static variable in class org.jmol.thread.JmolThread
checkAction(ActionEvent) - Method in class org.jmol.console.ScriptEditor
checkAims(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkAlchemy(String) - Static method in class org.jmol.adapter.smarter.Resolver
checkAll - Variable in class org.jmol.adapter.smarter.XtalSymmetry
checkAllFieldsPresent(String[], int, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
checkAllocColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
checkAndRemoveFilterKey(String) - Method in class org.jmol.adapter.readers.quantum.MOReader
  Prior to filterMO all extraneous filter keys must be removed.
checkAromaticDefined(Node[], BS, BS) - Static method in class org.jmol.smiles.SmilesAromatic
  Set aromatic atoms based on predefined BOND_AROMATIC definitions.
checkAtomArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.VolumeFileReader
  checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAxisOrder(int, V3, T3) - Method in class org.jmol.symmetry.PointGroup
checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[], float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
checkBgColixLength(short, int) - Method in class org.jmol.shape.Labels
checkBinary(String) - Method in class org.jmol.jvxl.readers.PmeshReader
checkBioType(String, int) - Method in class org.jmol.smiles.SmilesParser
checkBlock() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  looking for tags here.
checkBondArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
checkBondDistance(Atom, Atom, float, float) - Method in class org.jmol.adapter.readers.cif.CifReader
checkBondToR(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
  Checks to see if we have a bond to R and, if so, adds this R atom as a key to its attached atom
checkBoolean(String) - Method in class org.jmol.popup.JmolPopup
checkBoundsMinMax(P3, P3) - Method in class org.jmol.shape.Shape
checkBoxListener - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
checkBrace(SmilesSearch, char, char) - Method in class org.jmol.smiles.SmilesParser
checkBridge(Bridge, boolean, int, int) - Method in class org.jmol.dssx.DSSP
  check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge
checkBridges(Lst<?>, BS, Lst<?>, BS, BS) - Static method in class org.jmol.smiles.SmilesAromatic
checkBulge(Bridge, boolean, int) - Method in class org.jmol.dssx.DSSP
checkButton - Variable in class org.jmol.console.ScriptEditor
checkButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
checkByteCount - Variable in class org.jmol.shape.Mesh
checkCalculationType() - Method in class org.jmol.quantum.MOCalculation
checkCarbohydrate(String) - Static method in class org.jmol.modelsetbio.BioResolver
checkCastepVaspSiesta(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkCharge(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
checkChirality(SmilesSearch, String, int, SmilesAtom) - Static method in class org.jmol.smiles.SmilesStereo
checkClick(TouchPoint, List<Event>, boolean) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
checkClickAction(int, int, long, int) - Method in class org.jmol.viewer.ActionManager
checkColixLength(short, int) - Method in class org.jmol.shape.AtomShape
checkCommand() - Method in class org.openscience.jmol.app.InputScannerThread
checkCommand() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
checkComment() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
checkContinue() - Method in class org.jmol.script.ScriptEval
  checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.
checkContour(MarchingSquares.Triangle, int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
checkCoordinatesChanged() - Method in class org.jmol.viewer.Viewer
checkCp(ContactPair, ContactPair, int, int) - Static method in class org.jmol.shapesurface.Contact
checkCrystal(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkCube(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkCurrentLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkCurrentRule(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Check this atom "A" vs a challenger "B" against the current rule.
checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
checkDiameter(int) - Method in class org.jmol.renderbio.BioMeshRenderer
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.UnitCell
checkDragWheelAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
checkedSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
checkElementSelected(char) - Method in class org.jmol.awt.Mouse
checkEne(BS, BS, int, int, int, BS) - Method in class org.jmol.symmetry.CIPData
  Look for a path that contains this ene in a fully conjugated pattern
checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
checkExtension(int) - Method in class org.jmol.script.ScriptEval
checkFacet(P3[], int, int[], int, V3, P4, V3, V3, Map<Integer, Object[]>, Map<String, Object>, float, BS, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
  Clean out overlapping triangles based on normals and cross products.
checkField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
checkFileExists(String, boolean, String, int, boolean) - Method in class org.jmol.script.ScriptEval
checkFileStart(String) - Static method in class org.jmol.adapter.smarter.Resolver
checkFilter(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkFilterAssembly(String, Map<String, Object>) - Method in class org.jmol.adapter.readers.cif.MMCifReader
checkFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkFloatRange(float, float, float) - Static method in class org.jmol.viewer.Viewer
checkFlowCommand(String) - Method in class org.jmol.script.ScriptCompiler
checkFlowEnd(int, String, int, boolean) - Method in class org.jmol.script.ScriptCompiler
checkFlowEndBrace() - Method in class org.jmol.script.ScriptCompiler
  process a pending explicit right brace }
checkFlowStartBrace(boolean) - Method in class org.jmol.script.ScriptCompiler
checkFoldingXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkForceEndIf(int) - Method in class org.jmol.script.ScriptFlowContext
checkForCoordinate(boolean) - Method in class org.jmol.script.ScriptTokenParser
checkForFreq() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
checkForItemSelector(boolean) - Method in class org.jmol.script.ScriptTokenParser
checkForResidualBFactors(SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkFrankclicked(int, int) - Method in class org.jmol.viewer.ShapeManager
checkFront(short, short, short) - Method in class org.jmol.render.MeshRenderer
checkFusedRings(Lst<SmilesRing>, int[], Lst<BS>) - Static method in class org.jmol.smiles.SmilesAromatic
  Add fused rings based on the Hueckel 4n+2 rule.
checkGenNBO(String[], String) - Static method in class org.jmol.adapter.smarter.Resolver
checkGouraud(short, short, short, short, short, short) - Method in class org.jmol.g3d.Graphics3D
checkGreater - Variable in class org.jmol.modelset.AtomIteratorWithinModel
checkGromacs(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkHalt(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
checkHalt(String, boolean) - Method in class org.jmol.script.ScriptManager
checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
checkHandedness(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
  Determine the ordered CIP winding of this atom.
checkHaveXMLUtil() - Static method in class org.jmol.jvxl.data.JvxlCoder
checkHeaderContains(String) - Static method in class org.jmol.adapter.smarter.Resolver
checkHover() - Method in class org.jmol.viewer.ActionManager
checkHueckelAromatic(int, Node[], BS, BS, int, int[]) - Static method in class org.jmol.smiles.SmilesAromatic
  For each atom in the ring, look up a unique combination of covalent bond count, valence, and charge for each atom and use that as a key into the PI_COUNTS array.
checkID(String) - Method in class org.jmol.shapespecial.Ellipsoids
checkID(String) - Method in class org.jmol.shapespecial.Polyhedra
checkImpliedScriptCmd - Variable in class org.jmol.script.ScriptCompiler
checkIn(String, Object) - Static method in class org.jmol.util.GenericApplet
checking - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
checking - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
checkInheritedShapes() - Method in class org.jmol.viewer.ShapeManager
  starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms.
checkInMotion(int) - Method in class org.jmol.viewer.Viewer
checkInsideOut(int, int, int) - Method in class org.jmol.jvxl.readers.MapFileReader
checkInterrupted(JmolThread) - Method in class org.jmol.thread.JmolThread
checkIntRange(int, int, int) - Static method in class org.jmol.viewer.Viewer
checkJSpecView(boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
checkKey(String, boolean) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Filter keys only for this model.
checkKey(String) - Method in class org.jmol.popup.GenericPopup
checkKey(String, String, String) - Method in class org.jmol.viewer.PropertyManager
checkLast(int) - Method in class org.jmol.script.ScriptParam
checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  sets continuing and doProcessLines
checkLatticeOnly - Variable in class org.jmol.adapter.smarter.AtomSetCollection
checkLength(int) - Method in class org.jmol.script.ScriptParam
checkLength(int) - Method in class org.jmol.scriptext.ScriptExt
checkLength23() - Method in class org.jmol.script.ScriptParam
checkLength34() - Method in class org.jmol.script.ScriptParam
checkLengthErrorPt(int, int) - Method in class org.jmol.script.ScriptParam
checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
checkLine() - Method in class org.jmol.adapter.readers.more.AFLOWReader
checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
checkLine() - Method in class org.jmol.adapter.readers.more.JcampdxReader
checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
checkLine() - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Reads a Collection of AtomSets from a BufferedReader.
checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
checkLine() - Method in class org.jmol.adapter.readers.simple.InputReader
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
checkLine() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.CgdReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.JanaReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.
checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
checkLine() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkLineContinuation() - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkLineStarts(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkLogic(SmilesSearch, String, SmilesAtom, SmilesBond, SmilesAtom, boolean, boolean, int[]) - Method in class org.jmol.smiles.SmilesParser
checkM2() - Method in class org.jmol.viewer.TransformManager4D
checkMap(Map<String, BS>, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
  Ensure that if two models have the same name or number, we appropriately OR their bitsets.
checkMap(Map<String, ?>, String, boolean, Lst<Object>, Object, int, boolean) - Method in class org.jmol.viewer.PropertyManager
checkMatchBond(SmilesAtom, SmilesAtom, SmilesBond, int, int, Edge) - Method in class org.jmol.smiles.SmilesSearch
checkMemory() - Static method in class org.jmol.util.Logger
checkMenuUpdate() - Method in class org.jmol.viewer.Viewer
checkMesh(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
checkMeshBB(Shape[], int, BoxInfo) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
checkMinAttachedAngle(Atom, float, V3, V3, boolean) - Static method in class org.jmol.modelset.ModelSet
checkMinimization() - Method in class org.jmol.viewer.Viewer
checkMinZ(Atom, int[]) - Method in class org.jmol.modelset.Group
checkModelTrigger - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
checkMol(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkMopacGraphf(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkMOs() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
checkMotionRendering(int) - Method in class org.jmol.viewer.Viewer
  check motion for rendering during mouse movement, spin, vibration, and animation
checkMotionRotateZoom(int, int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
checkNested(SmilesSearch, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesParser
checkNewDotsArray() - Method in class org.jmol.geodesic.EnvelopeCalculation
checkNewGroup(JmolAdapter, int, String, int, char, boolean, boolean) - Method in class org.jmol.modelset.ModelLoader
checkNewSetCommand() - Method in class org.jmol.script.ScriptCompiler
checkNoEmptyModel() - Method in class org.jmol.adapter.smarter.AtomSetCollection
checkNotPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkNucleicObject(BS, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
checkObject(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
checkObjectClicked(boolean, int, int, BS) - Method in class org.jmol.modelset.Text
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Labels
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Shape
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Sticks
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.TextShape
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Draw
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Ellipsoids
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapesurface.Isosurface
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.viewer.ShapeManager
checkObjectClicked(int, int, int) - Method in class org.jmol.viewer.Viewer
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Labels
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Shape
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shapespecial.Draw
checkObjectDragged(int, int, int, int, int, BS, int) - Method in class org.jmol.viewer.ShapeManager
checkObjectDragged(int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Frank
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Shape
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Sticks
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.TextShape
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Draw
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapesurface.Isosurface
checkObjectHovered(int, int, BS, boolean) - Method in class org.jmol.viewer.ShapeManager
checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
checkOdyssey(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkOperation(Quat, T3, int) - Method in class org.jmol.symmetry.PointGroup
checkOption(Object) - Static method in class org.openscience.jmol.app.webexport.WebPanel
checkOption2(String, String) - Method in class org.jmol.viewer.Viewer
checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
checkOptions(CommandLine, Options) - Method in class org.openscience.jmol.app.JmolApp
checkOrbitalType(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
checkOut(String) - Static method in class org.jmol.util.GenericApplet
checkPacked(int, Map<String, Object>, SB) - Method in class org.jmol.scriptext.CmdExt
  Process FILL and PACKED and all their variants.
checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
checkPhiPsi(float[], float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
checkPoint(T3) - Method in class org.jmol.export._IdtfExporter
checkPoint(Point3fi) - Method in class org.jmol.modelset.MeasurementPending
checkPoints(BS) - Method in class org.jmol.shapesurface.PMeshWriter
checkPressedAction(int, int, long) - Method in class org.jmol.viewer.ActionManager
checkPrimitiveAtom(SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
checkPrimitiveBond(SmilesBond, int, int, Edge) - Method in class org.jmol.smiles.SmilesSearch
checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
  Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
checkPropertyParameter(String) - Method in interface org.jmol.api.JmolPropertyManager
checkPropertyParameter(String) - Method in class org.jmol.viewer.PropertyManager
checkPropertyParameter(String) - Method in class org.jmol.viewer.Viewer
checkPt(float[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
  two values -- v1, and v2, which need not be ordered v1 < v2.
checkRasmolHydrogenBond(AminoMonomer, BioPolymer, int, P3, BS, Lst<Bond>, int[][], boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
checkReleaseAction(int, int, long, boolean) - Method in class org.jmol.viewer.ActionManager
checkRemark() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
checkRemark() - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkResume(String) - Method in class org.jmol.script.ScriptManager
checkRings(Lst<BS>, int[], int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
checkScript() - Method in class org.jmol.console.ScriptEditor
checkScriptExecution(String, boolean) - Method in class org.jmol.script.ScriptManager
checkScriptSilent(String) - Method in interface org.jmol.api.JmolScriptEvaluator
checkScriptSilent(String) - Method in class org.jmol.script.ScriptEval
  a method for just checking a script
checkSecurity(String) - Method in class org.jmol.viewer.FileManager
checkSelect(Map<String, SV>, T[]) - Method in interface org.jmol.api.JmolScriptEvaluator
checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
  Check a map for a WHERE phrase
checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.viewer.Viewer
checkShades(int) - Method in class org.jmol.util.Shader
checkSkip(T, int) - Method in class org.jmol.script.ScriptMathProcessor
checkSlab(int, T3, float, float, BS) - Method in class org.jmol.util.MeshSlicer
checkSpecial - Variable in class org.jmol.adapter.smarter.AtomSetCollection
checkSpecial1(int, String[], String) - Static method in class org.jmol.adapter.smarter.Resolver
checkSpecial2(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkSpecialParameterSyntax() - Method in class org.jmol.script.ScriptCompiler
  Check for special parameters, including: +, -, \, *, /, &, |, =, period, or [, single or double quote, command-specific parameters, $....
checkSpecialVoxel(P3, P3, P3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
checkStandardDeviation(V3[], V3, int, float) - Static method in class org.jmol.smiles.SmilesAromatic
  calculates a dot-product standard deviation and reports if it is below a cutoff
checkStepping(String) - Method in class org.jmol.script.ScriptManager
checkStereochemistry() - Method in class org.jmol.smiles.SmilesSearch
checkStereoChemistry(SmilesSearch, VTemp) - Method in class org.jmol.smiles.SmilesStereo
checkStereochemistryAll(boolean, SimpleNode, int, int, SimpleNode, SimpleNode, SimpleNode, SimpleNode, SimpleNode, SimpleNode, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
checkStereoForAtom(SmilesAtom, Node, boolean, boolean) - Method in class org.jmol.smiles.SmilesStereo
checkStereoPairs(SimpleNode, int, SimpleNode[], int) - Method in class org.jmol.smiles.SmilesGenerator
checkStringLength(int) - Method in class org.jmol.shape.Labels
checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
checkSum - Variable in class org.jmol.jvxl.readers.BCifDensityReader
checkSymmetry() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
checkTickTemps() - Method in class org.jmol.render.FontLineShapeRenderer
checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
checkToken(int) - Method in class org.jmol.script.ScriptParam
checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
checkTriangles(boolean, BS, BS) - Method in class org.jmol.shapesurface.PMeshWriter
checkTwoAtomAction(Point3fi, int) - Method in class org.jmol.viewer.ActionManager
checkType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
checkUnitCell(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkUnitCell(SymmetryInterface, P3, P3, boolean) - Method in interface org.jmol.api.SymmetryInterface
checkUnitCell(SymmetryInterface, P3, P3, boolean) - Method in class org.jmol.symmetry.Symmetry
checkUnitCellItem(String[], String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
checkUnitCellOffset() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
checkUnitCellParams() - Method in class org.jmol.adapter.readers.pdb.PdbReader
checkUnquotedFileName() - Method in class org.jmol.script.ScriptCompiler
checkUpdateSymmetryInfo() - Method in class org.jmol.modelkit.ModelKitPopup
checkUserAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
checkVisible() - Method in class org.jmol.modelset.Atom
checkWien2k(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkWinding(MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  Check for CCW winding.
checkWithin(T3, Lst<P3>, float, boolean) - Static method in class org.jmol.shape.Mesh
checkXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
checkXYZlist(String) - Method in class org.jmol.symmetry.SpaceGroup
CHEM_COMP_BOND_AROMATIC_FLAG - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CHEM_COMP_BOND_ATOM_ID_1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CHEM_COMP_BOND_ATOM_ID_2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CHEM_COMP_BOND_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CHEM_COMP_BOND_VALUE_ORDER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CHEM_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
CHEM_COMP_NAME - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
chemappsPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
chemCompBondFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
chemCompFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
chemFileProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CHEMFLAG - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
chemical - Static variable in class org.jmol.script.T
chemicalName - Variable in class org.jmol.adapter.readers.cif.CifReader
chemicalshift - Static variable in class org.jmol.script.T
chFirst - Variable in class org.jmol.script.ScriptCompiler
ChimeMessenger - Class in org.jmol.viewer
  A legacy Chime-compatible messenger.
ChimeMessenger() - Constructor for class org.jmol.viewer.ChimeMessenger
chiralClass - Variable in class org.jmol.smiles.SmilesStereo
chirality - Static variable in class org.jmol.script.T
chiralOrder - Variable in class org.jmol.smiles.SmilesStereo
chiralPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  ASCII-encoded priority string
chk - Variable in class org.jmol.script.ScriptContext
chk - Variable in class org.jmol.script.ScriptError
chk - Variable in class org.jmol.script.ScriptMathProcessor
chk - Variable in class org.jmol.scriptext.ScriptExt
choice - Variable in class org.jmol.dialog.Dialog
chooseBestBoundBox() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
chooser - Variable in class org.jmol.dialog.FilePreview
chop(String) - Static method in class org.jmol.viewer.StateCreator
chord - Variable in class org.jmol.util.ContactPair
chpt0 - Variable in class org.jmol.script.ScriptFunction
CHRG - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
Cif2DataParser - Class in org.jmol.adapter.readers.cif
  Fully implemented 2016.12.1 see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html Will deliver JSON versions of the data while file reading and Java List/Map structures when called by x = getProperty("cifInfo", filename) Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org) found at https://github.com/COMCIFS/cif_api
Cif2DataParser() - Constructor for class org.jmol.adapter.readers.cif.Cif2DataParser
Cif2Reader - Class in org.jmol.adapter.readers.cif
  Preliminary Cif2 reader.
Cif2Reader() - Constructor for class org.jmol.adapter.readers.cif.Cif2Reader
cif2StartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
cifData - Variable in class org.jmol.jvxl.readers.BCifDensityReader
CifDensityReader - Class in org.jmol.jvxl.readers
  CIF density reader.
CifDensityReader() - Constructor for class org.jmol.jvxl.readers.CifDensityReader
cifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
CifReader - Class in org.jmol.adapter.readers.cif
  A true line-free CIF file reader for CIF files.
CifReader() - Constructor for class org.jmol.adapter.readers.cif.CifReader
cip - Variable in class org.jmol.symmetry.Symmetry
CIP_CHIRALITY_AXIAL_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_CANTDETERMINE - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_EZ_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_M_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_m_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_MASK - Static variable in class org.jmol.modelset.Atom
CIP_CHIRALITY_NAME_MASK - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_NAME_OFFSET - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_NONE - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_OFFSET - Static variable in class org.jmol.modelset.Atom
CIP_CHIRALITY_P_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_p_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_PSEUDO_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_R_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_r_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_RULE_MASK - Static variable in class org.jmol.modelset.Atom
CIP_CHIRALITY_RULE_OFFSET - Static variable in class org.jmol.modelset.Atom
CIP_CHIRALITY_S_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_s_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqCis_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqcis_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqTrans_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_seqtrans_FLAG - Static variable in class org.jmol.viewer.JC
CIP_CHIRALITY_UNKNOWN - Static variable in class org.jmol.viewer.JC
CIP_MASK - Static variable in class org.jmol.modelset.Atom
CIPAtom() - Constructor for class org.jmol.symmetry.CIPChirality.CIPAtom
cipChirality - Variable in class org.jmol.smiles.SmilesAtom
CIPChirality - Class in org.jmol.symmetry
  A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
CIPChirality() - Constructor for class org.jmol.symmetry.CIPChirality
CIPChirality.CIPAtom - Class in org.jmol.symmetry
CIPData - Class in org.jmol.symmetry
  A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.
CIPData() - Constructor for class org.jmol.symmetry.CIPData
CIPDataSmiles - Class in org.jmol.symmetry
  A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
CIPDataSmiles() - Constructor for class org.jmol.symmetry.CIPDataSmiles
CIPDataTracker - Class in org.jmol.symmetry
  An optional class to track digraph paths to decisions.
CIPDataTracker() - Constructor for class org.jmol.symmetry.CIPDataTracker
CIPDataTracker.CIPTracker - Class in org.jmol.symmetry
ciprule - Static variable in class org.jmol.script.T
ciprule6full - Static variable in class org.jmol.script.T
cipRule6Full - Variable in class org.jmol.viewer.GlobalSettings
CIPTracker(int, CIPChirality.CIPAtom, CIPChirality.CIPAtom, int, int, boolean) - Constructor for class org.jmol.symmetry.CIPDataTracker.CIPTracker
circle - Static variable in class org.jmol.script.T
circle3d - Variable in class org.jmol.g3d.Graphics3D
CIRCLE_FRACTION - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
circleNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
CircleRenderer - Class in org.jmol.g3d
  Implements flat circle drawing/filling routines.
CircleRenderer() - Constructor for class org.jmol.g3d.CircleRenderer
CITATION_TITLE - Static variable in class org.jmol.adapter.readers.cif.CifReader
citationFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
clamp_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
clash - Static variable in class org.jmol.script.T
classBase - Static variable in class org.jmol.adapter.smarter.Resolver
ClassPreloader - Class in org.jmol.applet
ClassPreloader(AppletWrapper) - Constructor for class org.jmol.applet.ClassPreloader
clauseAlternateSpec() - Method in class org.jmol.script.ScriptTokenParser
  check for %x or % (null alternate)
clauseAnd() - Method in class org.jmol.script.ScriptTokenParser
clauseAtomSpec() - Method in class org.jmol.script.ScriptTokenParser
clauseCell(int) - Method in class org.jmol.script.ScriptTokenParser
clauseChainSpec(int) - Method in class org.jmol.script.ScriptTokenParser
  [:] [chars] [:] ["chars"] [:] [*] [:] [0-9] [:] [?] [:] (empty chain)
clauseComparator(boolean) - Method in class org.jmol.script.ScriptTokenParser
clauseConnected(boolean) - Method in class org.jmol.script.ScriptTokenParser
clauseDefine(boolean, boolean) - Method in class org.jmol.script.ScriptTokenParser
clauseItemSelector() - Method in class org.jmol.script.ScriptTokenParser
clauseModelSpec() - Method in class org.jmol.script.ScriptTokenParser
  process /1 /1.1 / * or just /
clauseNot() - Method in class org.jmol.script.ScriptTokenParser
clauseOr(boolean) - Method in class org.jmol.script.ScriptTokenParser
clausePrimitive() - Method in class org.jmol.script.ScriptTokenParser
clauseResidueSpec() - Method in class org.jmol.script.ScriptTokenParser
clauseResNameSpec() - Method in class org.jmol.script.ScriptTokenParser
  [a] or just a
clauseSequenceSpec() - Method in class org.jmol.script.ScriptTokenParser
clauseSubstructure() - Method in class org.jmol.script.ScriptTokenParser
clauseWithin(boolean) - Method in class org.jmol.script.ScriptTokenParser
clean() - Method in class org.jmol.shape.MeshCollection
clean() - Method in class org.jmol.shapecgo.CGO
clean() - Method in class org.jmol.shapespecial.Draw
clean_electro_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cleanFace(P3[]) - Method in class org.jmol.util.BZone
cleanKey(String) - Method in class org.jmol.adapter.readers.more.AFLOWReader
  cleans key to just letters and digits
cleanLine() - Method in class org.jmol.adapter.readers.simple.InputReader
cleanPattern(String) - Static method in class org.jmol.smiles.SmilesParser
cleanRegistry() - Static method in class org.jmol.applet.Jmol
cleanScriptComments(String) - Method in class org.jmol.script.ScriptCompiler
  allows for three kinds of comments.
cleanSingletons(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  PyMOL does not display cartoons or traces for single-residue runs.
cleanSmiles(String) - Method in interface org.jmol.api.SmilesMatcherInterface
cleanSmiles(String) - Method in class org.jmol.smiles.SmilesMatcher
cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
clear() - Method in interface org.jmol.api.GenericMouseInterface
clear() - Method in interface org.jmol.api.JmolDataManager
clear(int) - Method in interface org.jmol.api.JmolRepaintManager
clear(boolean) - Method in interface org.jmol.api.JmolScriptManager
clear() - Method in class org.jmol.awt.Mouse
clear() - Method in class org.jmol.awtjs2d.Mouse
clear() - Method in class org.jmol.g3d.Graphics3D
clear() - Method in class org.jmol.jvxl.data.JvxlData
clear() - Method in class org.jmol.minimize.forcefield.ForceField
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
clear() - Method in class org.jmol.minimize.Minimizer
clear(BS, Atom, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
clear() - Method in class org.jmol.multitouch.ActionManagerMT
clear(int) - Method in class org.jmol.render.RepaintManager
clear(boolean) - Method in class org.jmol.script.ScriptManager
clear - Static variable in class org.jmol.script.T
clear() - Method in class org.jmol.shape.Measures
clear(String) - Method in class org.jmol.shape.Mesh
clear(String) - Method in class org.jmol.shapecgo.CGOMesh
clear(boolean) - Method in class org.jmol.shapespecial.Dipoles
clear(String) - Method in class org.jmol.shapespecial.DrawMesh
clear() - Static method in exception org.jmol.smiles.InvalidSmilesException
clear() - Method in class org.jmol.smiles.SmilesSearch
clear(Map<String, Object>) - Static method in class org.jmol.thread.TimeoutThread
clear() - Method in class org.jmol.util.CommandHistory
  clears the history.
clear() - Method in class org.jmol.util.GData
clear() - Method in class org.jmol.util.MeshCapper.CapVertex
  Free all links.
clear() - Method in class org.jmol.util.MeshCapper
clear() - Method in class org.jmol.util.TempArray
clear() - Method in class org.jmol.viewer.ActionManager
clear() - Method in class org.jmol.viewer.AnimationManager
clear() - Method in class org.jmol.viewer.DataManager
clear() - Method in class org.jmol.viewer.FileManager
clear() - Method in class org.jmol.viewer.GlobalSettings
clear() - Method in class org.jmol.viewer.SelectionManager
clear(GlobalSettings) - Method in class org.jmol.viewer.StateManager
clear() - Method in class org.jmol.viewer.TransformManager
clear() - Method in class org.openscience.jmol.app.HistoryFile
clear() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
clear() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
clearAndCachePngjFile(FileManager, String[]) - Method in class org.jmol.io.JmolUtil
clearAtomSets() - Method in class org.jmol.viewer.Viewer
clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
clearBindings() - Method in class org.jmol.viewer.ActionManager
clearBioPolymers() - Method in class org.jmol.modelsetbio.BioModel
clearBsFound(int) - Method in class org.jmol.smiles.SmilesSearch
clearBuffer() - Method in class org.jmol.g3d.Platform3D
clearButton - Variable in class org.jmol.console.ScriptEditor
clearButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
clearButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
clearCache() - Method in class org.jmol.modelset.ModelSet
clearClickCount() - Method in class org.jmol.viewer.Viewer
clearCommandWatcherThread() - Method in class org.jmol.script.ScriptManager
clearConsole() - Method in class org.jmol.viewer.StatusManager
clearContent(String) - Method in class org.jmol.console.GenericConsole
clearContent() - Method in class org.jmol.console.ScriptEditor.EditorDocument
  Removes all content of the script window, and add a new prompt.
clearContent() - Method in class org.jmol.console.ScriptEditor.EditorTextPane
clearContent(String) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
clearContent() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
  Removes all content of the script window, and add a new prompt.
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelSet
clearDB(int) - Method in class org.jmol.modelset.ModelSet
clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEval
clearFontCache() - Method in class org.jmol.g3d.Graphics3D
clearFontCache() - Static method in class org.jmol.g3d.TextRenderer
clearFontCache() - Method in class org.jmol.util.GData
clearForces() - Method in class org.jmol.minimize.forcefield.ForceField
clearFunctions() - Method in class org.jmol.viewer.Viewer
clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
clearHighlight() - Method in class org.jmol.console.ScriptEditor.EditorDocument
clearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
clearInButton - Variable in class org.jmol.console.GenericConsole
clearKeyBuffer() - Method in class org.jmol.awt.Mouse
clearKeyBuffer() - Method in class org.jmol.awtjs2d.Mouse
clearLineCache() - Method in class org.jmol.g3d.LineRenderer
clearListener(AbstractButton) - Method in class org.jmol.awt.AwtPopupHelper
clearListeners(Object[]) - Method in class org.jmol.awt.AwtPopupHelper
clearMeasurements() - Method in class org.jmol.api.JmolViewer
clearMeasurements() - Method in class org.jmol.viewer.Viewer
clearMesh(String) - Method in class org.jmol.shape.Mesh
clearMinimization() - Method in class org.jmol.viewer.Viewer
clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
clearOrbitals() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
clearOutButton - Variable in class org.jmol.console.GenericConsole
clearPixel(int, int) - Method in class org.jmol.g3d.Pixelator
clearPixel(int, int) - Method in class org.jmol.g3d.PixelatorT
clearQueue() - Method in interface org.jmol.api.JmolScriptManager
clearQueue() - Method in class org.jmol.script.ScriptManager
clearReaderData() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
clearRepaintManager(int) - Method in class org.jmol.viewer.Viewer
clearRule4Lists() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Clear Rule 4b information if Rule-5 pseudochiral centers have been found, as that could change the order of descriptors in the Mata list.
clearScreenBuffer() - Method in class org.jmol.g3d.Platform3D
clearScreenBufferThreaded() - Method in class org.jmol.g3d.Platform3D
clearScriptQueue() - Method in class org.jmol.viewer.Viewer
clearSelection() - Method in class org.jmol.api.JmolViewer
clearSelection() - Method in class org.jmol.awtjs.swing.JTable
clearSelection(boolean) - Method in class org.jmol.viewer.SelectionManager
clearSelection() - Method in class org.jmol.viewer.Viewer
clearSg() - Method in class org.jmol.shapesurface.Isosurface
clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
clearShapeManager(Error) - Method in class org.jmol.script.ScriptParallelProcessor
clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
clearSmallRingEZ(SimpleNode[], Lst<int[]>) - Method in class org.jmol.symmetry.CIPChirality
  Remove E/Z designations for small-rings double bonds (IUPAC 2013.P-93.5.1.4.1).
clearSpin() - Method in class org.jmol.viewer.TransformManager
clearState(boolean) - Method in class org.jmol.script.ScriptEval
clearStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
clearTBuffer() - Method in class org.jmol.g3d.Platform3D
clearTemp() - Method in class org.jmol.viewer.StateCreator
clearTempPoints() - Method in class org.jmol.util.TempArray
clearTempScreens() - Method in class org.jmol.util.TempArray
clearThreads() - Method in class org.jmol.viewer.TransformManager
clearThreads() - Method in class org.jmol.viewer.Viewer
clearTimeout(String) - Method in class org.jmol.viewer.Viewer
clearTimeouts() - Method in class org.jmol.viewer.Viewer
clearType(String, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
clearV(MeshCapper.CapVertex) - Static method in class org.jmol.util.MeshCapper
clearVibration() - Method in class org.jmol.viewer.TransformManager
clearVisibleSets() - Method in class org.jmol.modelset.AtomCollection
click(HTMLElement, HTMLWindowEvent) - Method in interface org.jmol.awtjs.swing.SwingController
  Fired from clicking an element such as a button or check box or table entry, or from entering text in a text box.
CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
CLICK - Static variable in class org.jmol.viewer.binding.Binding
CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
clickabilityFlags - Variable in class org.jmol.modelset.Atom
clickable - Static variable in class org.jmol.script.T
clickableMax - Static variable in class org.jmol.viewer.ShapeManager
clickAction - Variable in class org.jmol.viewer.ActionManager
CLICKED - Static variable in class org.jmol.awtjs.Event
clicked(long, int, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
clicked - Variable in class org.jmol.viewer.ActionManager
clickedCount - Variable in class org.jmol.viewer.ActionManager
clickToSetElement - Variable in class org.jmol.modelkit.ModelKitPopup
  Except for H atoms, do not allow changes to elements just by clicking them.
client - Variable in class org.jmol.modelset.MeasurementData
client - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
clipboard - Static variable in class org.jmol.script.T
clipCode(int, int, int) - Method in class org.jmol.export.Export3D
clipCode(int) - Method in class org.jmol.util.GData
clipCode3(int, int, int) - Method in class org.jmol.util.GData
clipImageOrPasteText(String) - Method in class org.jmol.api.JmolViewer
clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManager
clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManagerAwt
clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManagerJS
clipImageOrPasteText(String) - Method in class org.jmol.viewer.Viewer
clipped - Variable in class org.jmol.g3d.CylinderRenderer
cList - Variable in class org.jmol.awtjs.swing.Container
cList - Variable in class org.jmol.shapecgo.CGOMesh
clockBaseline - Variable in class org.jmol.applet.AppletWrapper
clockWidth - Variable in class org.jmol.applet.AppletWrapper
clockX - Variable in class org.jmol.applet.AppletWrapper
clone() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
clone() - Method in class org.jmol.util.Vibration
cloneAtomSetWithBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneLastAtomSet(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
cloneLastAtomSetFromPoints(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
cloneUnitCell(UnitCell) - Static method in class org.jmol.symmetry.UnitCell
cloneV() - Method in class org.jmol.util.MeshCapper.CapVertex
close(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
close() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
close() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
close() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
closeButton - Variable in class org.jmol.console.ScriptEditor
closeButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
closeButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
closeMe() - Method in interface org.jmol.api.GenericImageDialog
closeMe() - Method in class org.jmol.console.ImageDialog
closePreview() - Method in class org.jmol.dialog.Dialog
closeReader() - Method in class org.jmol.jvxl.readers.BCifDensityReader
closeReader() - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
closeReader() - Method in class org.jmol.jvxl.readers.VolumeDataReader
closeReader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
closeReaderSFR() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
closeSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
closest - Variable in class org.jmol.modelset.ModelSet
closest(P3, P3[]) - Method in class org.jmol.util.BZone
closestAtom - Variable in class org.jmol.shape.Sticks
closeStream() - Method in class org.jmol.util.JSONWriter
cm - Variable in class org.jmol.viewer.Viewer
cM - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
cMapSourceBRIX - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceCCP4 - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceChempyBrick - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceCrystallographic - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceDesc - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceFLD - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceGeneralPurpose - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceGRD - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceObsolete - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cMapSourceVMDPlugin - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
cmd(String) - Method in class org.jmol.util.BZone
cmdAnimation() - Method in class org.jmol.script.ScriptEval
cmdAxes(int) - Method in class org.jmol.script.ScriptEval
cmdBackground(int) - Method in class org.jmol.script.ScriptEval
cmdBind() - Method in class org.jmol.script.ScriptEval
cmdBondorder() - Method in class org.jmol.script.ScriptEval
cmdBoundbox(int) - Method in class org.jmol.script.ScriptEval
cmdCD() - Method in class org.jmol.script.ScriptEval
cmdCenter(int) - Method in class org.jmol.script.ScriptEval
cmdColor() - Method in class org.jmol.script.ScriptEval
cmdDefine() - Method in class org.jmol.script.ScriptEval
cmdDelay() - Method in class org.jmol.script.ScriptEval
cmdDelete() - Method in class org.jmol.script.ScriptEval
cmdDisplay(boolean) - Method in class org.jmol.script.ScriptEval
cmdDots(int) - Method in class org.jmol.script.ScriptEval
cmdEcho(int) - Method in class org.jmol.script.ScriptEval
cmdExt - Variable in class org.jmol.script.ScriptExpr
CmdExt - Class in org.jmol.scriptext
CmdExt() - Constructor for class org.jmol.scriptext.CmdExt
cmdFile() - Method in class org.jmol.script.ScriptEval
cmdFixed() - Method in class org.jmol.script.ScriptEval
cmdFlow(int, boolean, Lst<T[]>) - Method in class org.jmol.script.ScriptEval
cmdFlowSwitch(ContextToken, int) - Method in class org.jmol.script.ScriptEval
cmdFont(int, float) - Method in class org.jmol.script.ScriptEval
cmdFor(int, boolean) - Method in class org.jmol.script.ScriptEval
cmdFrank(int) - Method in class org.jmol.script.ScriptEval
cmdFunc() - Method in class org.jmol.script.ScriptEval
cmdGetProperty() - Method in class org.jmol.script.ScriptEval
cmdGoto(boolean) - Method in class org.jmol.script.ScriptEval
cmdHbond() - Method in class org.jmol.script.ScriptEval
cmdHelp() - Method in class org.jmol.script.ScriptEval
cmdHistory(int) - Method in class org.jmol.script.ScriptEval
cmdHover() - Method in class org.jmol.script.ScriptEval
cmdLabel(int, BS) - Method in class org.jmol.script.ScriptEval
cmdLoad() - Method in class org.jmol.script.ScriptEval
cmdLog() - Method in class org.jmol.script.ScriptEval
cmdLoop() - Method in class org.jmol.script.ScriptEval
cmdMessage() - Method in class org.jmol.script.ScriptEval
cmdModel(int) - Method in class org.jmol.script.ScriptEval
  ONE difference between FRAME and MODEL: model 1 sets model NAMED one in the case of PDB frame 1 always sets the first model
cmdMove() - Method in class org.jmol.script.ScriptEval
cmdMoveto() - Method in class org.jmol.script.ScriptEval
cmdPause() - Method in class org.jmol.script.ScriptEval
cmdPrint() - Method in class org.jmol.script.ScriptEval
cmdPrompt() - Method in class org.jmol.script.ScriptEval
cmdpt0 - Variable in class org.jmol.script.ScriptFunction
cmdReset() - Method in class org.jmol.script.ScriptEval
cmdRestore() - Method in class org.jmol.script.ScriptEval
cmdRestrict() - Method in class org.jmol.script.ScriptEval
cmdReturn(SV) - Method in class org.jmol.script.ScriptEval
cmdRotate(boolean, boolean) - Method in class org.jmol.script.ScriptEval
cmds - Variable in class org.jmol.rendercgo.CGORenderer
cmds - Variable in class org.jmol.shapecgo.CGOMesh
cmdSave() - Method in class org.jmol.script.ScriptEval
cmdScript(int, String, String) - Method in class org.jmol.script.ScriptEval
cmdSelect(int) - Method in class org.jmol.script.ScriptEval
cmdSelectionHalos(int) - Method in class org.jmol.script.ScriptEval
cmdSet() - Method in class org.jmol.script.ScriptEval
cmdSetEcho() - Method in class org.jmol.script.ScriptEval
cmdSetLabel(String) - Method in class org.jmol.script.ScriptEval
cmdSetPicking() - Method in class org.jmol.script.ScriptEval
cmdSetPickingStyle() - Method in class org.jmol.script.ScriptEval
cmdSlab(boolean) - Method in class org.jmol.script.ScriptEval
cmdSsbond() - Method in class org.jmol.script.ScriptEval
cmdStructure() - Method in class org.jmol.script.ScriptEval
cmdSubset() - Method in class org.jmol.script.ScriptEval
cmdSync() - Method in class org.jmol.script.ScriptEval
cmdThrow() - Method in class org.jmol.script.ScriptEval
cmdTimeout(int) - Method in class org.jmol.script.ScriptEval
cmdTranslate(boolean) - Method in class org.jmol.script.ScriptEval
cmdUnbind() - Method in class org.jmol.script.ScriptEval
cmdUndoRedoMove() - Method in class org.jmol.script.ScriptEval
cmdUnitcell(int) - Method in class org.jmol.script.ScriptEval
cmdVector() - Method in class org.jmol.script.ScriptEval
cmdVibration() - Method in class org.jmol.script.ScriptEval
cmdWireframe() - Method in class org.jmol.script.ScriptEval
cmdZap(boolean) - Method in class org.jmol.script.ScriptEval
cmdZoom(boolean) - Method in class org.jmol.script.ScriptEval
cmeshes - Variable in class org.jmol.shapecgo.CGO
cmi - Variable in class org.jmol.viewer.AnimationManager
  current model index
CML - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CML_NAMESPACE_URI - Static variable in class org.jmol.adapter.smarter.Resolver
cnmrPeaks - Variable in class org.jmol.popup.JmolPopup
code - Variable in class org.jmol.adapter.readers.cif.Subsystem
code - Variable in enum org.jmol.c.FIL
code - Variable in class org.jmol.i18n.Language
Code() - Constructor for enum org.jmol.modelsetbio.AlphaPolymer.Code
code - Variable in enum org.jmol.util.Edge.EnumBondOrder
codeBase - Variable in class org.jmol.util.GenericApplet
codePath - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
coef - Variable in class org.jmol.g3d.SphereRenderer
coef - Variable in class org.jmol.jvxl.readers.IsoMOReader
coef - Variable in class org.jmol.quantum.SlaterData
coef1 - Static variable in class org.jmol.quantum.NciCalculation
coef2 - Static variable in class org.jmol.quantum.NciCalculation
coef3 - Static variable in class org.jmol.quantum.NciCalculation
COEF_INDICES - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
coefCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
coefCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
coeffs - Variable in class org.jmol.quantum.MOCalculation
coefs - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
coefs - Variable in class org.jmol.jvxl.readers.IsoMOReader
coefs - Variable in class org.jmol.quantum.MOCalculation
coefs - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
col - Static variable in class org.jmol.script.T
col2key - Variable in class org.jmol.adapter.readers.cif.CifReader
colix - Variable in class org.jmol.adapter.smarter.Bond
colix - Variable in class org.jmol.export.Export3D
colix - Variable in class org.jmol.modelset.Bond
colix - Variable in class org.jmol.modelset.Measurement
colix - Variable in class org.jmol.modelset.MeasurementData
colix - Variable in class org.jmol.modelset.Text
colix - Variable in class org.jmol.render.ShapeRenderer
colix - Variable in class org.jmol.renderbio.NucleicRenderer
colix - Variable in class org.jmol.renderbio.RocketRenderer
colix - Variable in class org.jmol.shape.Measures
colix - Variable in class org.jmol.shape.MeshCollection
colix - Variable in class org.jmol.shapespecial.Dipole
colix - Variable in class org.jmol.shapespecial.Dipoles
colix - Variable in class org.jmol.shapespecial.Ellipsoid
colix - Variable in class org.jmol.shapespecial.Polyhedron
colix - Variable in class org.jmol.util.MeshSurface
colix - Variable in class org.jmol.viewer.Connection
colix0 - Variable in class org.jmol.rendercgo.CGORenderer
colix1 - Variable in class org.jmol.rendercgo.CGORenderer
colix2 - Variable in class org.jmol.rendercgo.CGORenderer
colixA - Variable in class org.jmol.g3d.CylinderRenderer
colixA - Variable in class org.jmol.render.FontLineShapeRenderer
colixA - Variable in class org.jmol.renderspecial.DipolesRenderer
colixAtom - Variable in class org.jmol.modelset.Atom
colixB - Variable in class org.jmol.g3d.CylinderRenderer
colixB - Variable in class org.jmol.render.FontLineShapeRenderer
colixB - Variable in class org.jmol.renderspecial.DipolesRenderer
colixBack - Variable in class org.jmol.renderbio.BioShapeRenderer
colixBack - Variable in class org.jmol.util.MeshSurface
colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
colixCurrent - Variable in class org.jmol.util.GData
colixEdge - Variable in class org.jmol.shapespecial.Polyhedron
colixEndcap - Variable in class org.jmol.g3d.CylinderRenderer
colixes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
colixes - Variable in class org.jmol.render.AxesRenderer
colixes - Variable in class org.jmol.renderbio.BioShapeRenderer
colixes - Variable in class org.jmol.shape.AtomShape
colixesBack - Variable in class org.jmol.renderbio.BioShapeRenderer
colixesBack - Variable in class org.jmol.shapebio.BioShape
colixHash - Static variable in class org.jmol.util.C
colixHighlight - Variable in class org.jmol.shape.Halos
colixMax - Static variable in class org.jmol.util.C
colixRubberband - Variable in class org.jmol.viewer.ColorManager
colixSelection - Variable in class org.jmol.shape.Halos
collapsed - Static variable in class org.jmol.script.T
collapsed - Variable in class org.jmol.shapespecial.Polyhedron
COLLECTION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  String for prefix/resource identifier for the collection area.
collectionName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
colon - Static variable in class org.jmol.script.T
COLOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
Color - Class in org.jmol.awtjs.swing
Color() - Constructor for class org.jmol.awtjs.swing.Color
color - Variable in enum org.jmol.c.STR
color - Variable in class org.jmol.jvxl.data.JvxlData
color - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
color - Static variable in class org.jmol.script.T
COLOR - Static variable in class org.jmol.shape.Echo
color - Variable in class org.jmol.shape.Mesh
color - Variable in class org.jmol.shape.MeshCollection
COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
color - Variable in class org.jmol.util.BZone
color - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
color4(short) - Method in class org.jmol.export._PovrayExporter
COLOR_BACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
COLOR_BLACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
COLOR_FRONT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
colorArrayed - Variable in class org.jmol.shapesurface.PMeshWriter
colorByPhase - Variable in class org.jmol.jvxl.readers.Parameters
colorBySets - Variable in class org.jmol.jvxl.readers.Parameters
colorBySign - Variable in class org.jmol.jvxl.readers.Parameters
colorCommand - Variable in class org.jmol.shape.Mesh
colorCommand(SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
colorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
colorData - Variable in class org.jmol.viewer.ColorManager
colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
colorDensity - Variable in class org.jmol.shape.Mesh
colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
ColorEncoder - Class in org.jmol.util
ColorEncoder(ColorEncoder, Viewer) - Constructor for class org.jmol.util.ColorEncoder
colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
colorIndex(float, int) - Static method in class org.jmol.util.ColorEncoder
colorIndexRepeat(float, int) - Static method in class org.jmol.util.ColorEncoder
colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
ColorManager - Class in org.jmol.viewer
ColorManager(Viewer, GData) - Constructor for class org.jmol.viewer.ColorManager
colorNames - Static variable in class org.jmol.applet.AppletWrapper
colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
colorNegLCAO - Variable in class org.jmol.jvxl.readers.Parameters
colorPhase - Variable in class org.jmol.jvxl.readers.Parameters
colorPhased - Variable in class org.jmol.shapesurface.IsosurfaceMesh
colorPhases - Static variable in class org.jmol.jvxl.readers.SurfaceReader
colorPos - Variable in class org.jmol.jvxl.readers.Parameters
colorPosLCAO - Variable in class org.jmol.jvxl.readers.Parameters
colorPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
colorPtr - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
colorrasmol - Static variable in class org.jmol.script.T
colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
colors - Variable in class org.jmol.adapter.readers.pymol.JmolObject
colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
colors - Static variable in class org.jmol.applet.AppletWrapper
colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
colorscheme - Static variable in class org.jmol.script.T
colorSchemes - Static variable in class org.jmol.util.ColorEncoder
colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
colorSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
colorSettingClamped(Lst<Object>, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
colorsExplicit - Variable in class org.jmol.util.MeshSurface
colorShape(int, int, boolean) - Method in class org.jmol.script.ScriptEval
colorSolid - Variable in class org.jmol.shapesurface.PMeshWriter
colorType - Variable in class org.jmol.shape.Mesh
colorType - Variable in class org.jmol.shapesurface.Isosurface
colorVertices(short, BS, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
  color a specific set of vertices a specific color
colspan - Variable in class org.jmol.awtjs.swing.Cell
ColumnSelectionModel - Interface in org.jmol.awtjs.swing
combineModulation(String, float, float) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Retrieve cataloged displacement and add in this component, returning a new double[3].
combineSurfaces(Lst<ContactPair>, int, int, float[], Object, boolean, boolean) - Method in class org.jmol.shapesurface.Contact
comma - Static variable in class org.jmol.script.T
command - Static variable in class org.jmol.script.T
commandDelay - Static variable in class org.jmol.script.CommandWatcherThread
commandExpected() - Method in class org.jmol.script.ScriptTokenParser
CommandHistory - Class in org.jmol.util
  Implements a queue for a bash-like command history.
CommandHistory() - Constructor for class org.jmol.util.CommandHistory
  Creates a new instance using the default size (100)
commandHistory - Variable in class org.jmol.viewer.Viewer
commandHistoryLevelMax - Static variable in class org.jmol.script.ScriptEval
commandLineOptions - Variable in class org.jmol.export.___Exporter
commandList - Variable in class org.jmol.util.CommandHistory
  Array of commands.
commandLoop(boolean) - Method in class org.jmol.script.ScriptEval
commandOptions - Variable in class org.jmol.viewer.Viewer
commands - Static variable in class org.jmol.script.T
commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
commands - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
commandStart - Variable in class org.jmol.script.ScriptFlowContext
CommandWatcherThread - Class in org.jmol.script
CommandWatcherThread() - Constructor for class org.jmol.script.CommandWatcherThread
commandWatcherThread - Variable in class org.jmol.script.ScriptManager
commensurateSection1 - Variable in class org.jmol.adapter.readers.cif.MSRdr
comment - Variable in class org.jmol.script.ScriptCompiler
commentChar - Variable in class org.jmol.export.___Exporter
COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
comparator - Static variable in class org.jmol.script.T
compare(Object, Object) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
compare(Map<String, Object>, Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
compare(SlaterData, SlaterData) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
compare(TextString, TextString) - Method in class org.jmol.g3d.TextString
compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
compare(String[], String[]) - Method in class org.jmol.modelsetbio.BioResolver
compare(SV, SV) - Method in class org.jmol.script.SV.Sort
compare - Static variable in class org.jmol.script.T
compare() - Method in class org.jmol.scriptext.CmdExt
compare(Object[], Object[]) - Method in class org.jmol.shapespecial.Polyhedra
compare(Object[], Object[]) - Method in class org.jmol.smiles.PolyhedronStereoSorter
  Comparison is by torsion angle, as set previously and passed in as Float a[1] and b[1].
compare(Object, Object) - Method in class org.jmol.util.EigenSort
compare(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.MeshCapperSorter
compare(Option, Option) - Method in class org.openscience.jmol.app.JmolApp.OptSort
compareAtoms(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
compareAtoms(int, int) - Method in interface org.jmol.api.PymolAtomReader
compareFloat(int, float, float) - Method in class org.jmol.script.ScriptExpr
compareFloatData(int, float[], int, float) - Method in class org.jmol.script.ScriptExpr
compareInt(int, int, int) - Method in class org.jmol.script.ScriptExpr
compareLikeUnlike(BS, BS) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
compareRule1a(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Looking for phantom atom (atom number 0) or element number
compareRule1b(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Looking for root distance -- duplicate atoms only.
compareRule2(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Chapter 9 Rule 2.
compareRule3(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Chapter 9 Rule 3.
compareRule4b5(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Compare the better R-ref or S-ref list for A with the same for B.
compareRule6(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Just look for match with the Rule 6 reference atom index
compareRules4ac(CIPChirality.CIPAtom, String) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Chapter 9 Rules 4a and 4c.
compareString(int, int, String) - Method in class org.jmol.script.ScriptExpr
compareStringValues(int, String, String) - Method in class org.jmol.script.ScriptExpr
compareTo(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Used in Array.sort when an atom is set and Collection.sort when determining the Mata like/unlike sequence for Rules 4b and 5.
compile(String, boolean) - Method in interface org.jmol.api.JmolPatternMatcher
compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
  Compiles a set of tokens for each primitive element of a label.
compile(String, String, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
compile(String, boolean) - Method in class org.jmol.util.PatternMatcher
compile0(boolean) - Method in class org.jmol.script.ScriptCompiler
compileCommand() - Method in class org.jmol.script.ScriptCompiler
compileExpr(String) - Method in class org.jmol.viewer.Viewer
compileExpression() - Method in class org.jmol.script.ScriptTokenParser
compileExpressions() - Method in class org.jmol.script.ScriptTokenParser
compiler - Variable in class org.jmol.script.ScriptEval
compiler - Variable in class org.jmol.script.ScriptFlowContext
compiler - Variable in class org.jmol.viewer.Viewer
compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEval
compileScriptFile(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEval
compileScriptFileInternal(String, String, String, String) - Method in class org.jmol.script.ScriptEval
compileScriptString(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEval
compileSelect(SV[]) - Method in class org.jmol.viewer.PropertyManager
completeCommand(String) - Method in class org.jmol.console.GenericConsole
completeCommand(Map<String, ?>, boolean, boolean, String, int) - Static method in class org.jmol.script.T
completeInitialization(Graphics, Dimension) - Method in class org.jmol.applet.AppletWrapper
compnd - Variable in class org.jmol.adapter.readers.pdb.PdbReader
compnd(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
component - Variable in class org.jmol.awtjs.swing.Cell
Component - Class in org.jmol.awtjs.swing
Component(String) - Constructor for class org.jmol.awtjs.swing.Component
component - Variable in class org.jmol.smiles.SmilesAtom
componentCount - Variable in class org.jmol.smiles.SmilesParser
componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
componentParenCount - Variable in class org.jmol.smiles.SmilesParser
componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
compositions - Variable in class org.jmol.adapter.readers.more.AFLOWReader
compute(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.Calculations
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFAngleCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFDistanceCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFESCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFOOPCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFSBCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFTorsionCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFVDWCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFAngleCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFDistanceCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFOOPCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFTorsionCalc
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFVDWCalc
comSSMat - Variable in class org.jmol.adapter.readers.cif.MSCifParser
concatList(SV, SV, boolean) - Static method in class org.jmol.script.SV
CONE - Static variable in class org.jmol.shapecgo.CGOMesh
cone_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
conect() - Method in class org.jmol.adapter.readers.pdb.PdbReader
coneNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
CONF_TYPE_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
configuration - Static variable in class org.jmol.script.T
configuration() - Method in class org.jmol.scriptext.CmdExt
configurationPtr - Variable in class org.jmol.adapter.readers.cif.CifReader
configurationPtr - Variable in class org.jmol.adapter.readers.pdb.PdbReader
configurationSelected - Variable in class org.jmol.popup.JmolPopup
conformationIndex - Variable in class org.jmol.adapter.readers.cif.CifReader
conformationIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
connect(float[][]) - Method in class org.jmol.modelset.ModelSet
connect - Static variable in class org.jmol.script.T
connect(int) - Method in class org.jmol.scriptext.CmdExt
connect_bonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
connect_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
connect_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
connectAll(int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
connectAllBad(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
connected - Static variable in class org.jmol.script.T
connectedAtoms - Variable in class org.jmol.shape.Mesh
Connection - Class in org.jmol.viewer
Connection(int, int, short, short, int, float, int) - Constructor for class org.jmol.viewer.Connection
connections - Variable in class org.jmol.shape.MeshCollection
connections - Variable in class org.jmol.smiles.SmilesParser
connections - Variable in class org.jmol.util.MolWriter
Connections - Class in org.jmol.viewer
Connections(Viewer) - Constructor for class org.jmol.viewer.Connections
connections - Variable in class org.jmol.viewer.Connections
connectivity - Variable in class org.jmol.smiles.SmilesAtom
connectLast - Variable in class org.jmol.adapter.readers.pdb.PdbReader
connectNBO(int, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
connectNBO(String) - Method in class org.jmol.viewer.Viewer
connectNextAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
connectNextAtomSet - Variable in class org.jmol.adapter.readers.pdb.PdbReader
connectorFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
connectorFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
connectors - Variable in class org.jmol.adapter.readers.quantum.CsfReader
console - Variable in class org.jmol.console.ImageDialog
console - Static variable in class org.jmol.script.T
console() - Method in class org.jmol.scriptext.CmdExt
console - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
consoleButton - Variable in class org.jmol.console.ScriptEditor
consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
ConsoleDocument() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
consoleGetImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
consoleMessage(String) - Method in class org.jmol.util.GenericApplet
ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel.console
ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
consoleTextPane - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
ConsoleTextPane(AppConsole) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
ConsoleWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
constrainQuadratic(double, double, double, int) - Method in class org.jmol.minimize.forcefield.Calculations
Constraint - Class in org.jmol.modelkit
Constraint(int, Object...) - Constructor for class org.jmol.modelkit.Constraint
constraint - Static variable in class org.jmol.script.T
constraintEnergy(int) - Method in class org.jmol.minimize.forcefield.Calculations
constraintMap - Variable in class org.jmol.minimize.Minimizer
constraints - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
constraints - Variable in class org.jmol.minimize.Minimizer
constraintsByType - Variable in class org.jmol.minimize.forcefield.Calculations
constructBitSetPolyhedron(Atom) - Method in class org.jmol.shapespecial.Polyhedra
constructBondsPolyhedron(Atom, int) - Method in class org.jmol.shapespecial.Polyhedra
constructDismissButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
constructMeasurementButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
constructMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
constructRadiusPolyhedron(Atom, AtomIndexIterator) - Method in class org.jmol.shapespecial.Polyhedra
constructUnitCellPolygon(Atom, boolean) - Method in class org.jmol.shapespecial.Polyhedra
contact - Static variable in class org.jmol.script.T
contact() - Method in class org.jmol.scriptext.IsoExt
Contact - Class in org.jmol.shapesurface
Contact() - Constructor for class org.jmol.shapesurface.Contact
contactPair - Variable in class org.jmol.jvxl.readers.AtomDataReader
contactPair - Variable in class org.jmol.jvxl.readers.Parameters
ContactPair - Class in org.jmol.util
ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
ContactRenderer - Class in org.jmol.rendersurface
ContactRenderer() - Constructor for class org.jmol.rendersurface.ContactRenderer
contactType - Variable in class org.jmol.util.ContactPair
Container - Class in org.jmol.awtjs.swing
Container(String) - Constructor for class org.jmol.awtjs.swing.Container
container - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
contains(int, int) - Method in class org.jmol.util.Rectangle
contentDisabled - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
contentPane - Variable in class org.jmol.awtjs.swing.JDialog
contentPath - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
context - Variable in class org.jmol.awtjs2d.Platform
context - Variable in class org.jmol.script.ScriptProcess
context - Static variable in class org.jmol.script.T
contextCount - Static variable in class org.jmol.script.ScriptContext
contextDepthMax - Static variable in class org.jmol.script.ScriptEval
contextdepthmax - Static variable in class org.jmol.script.T
contextPath - Variable in class org.jmol.script.ScriptContext
contextPath - Variable in class org.jmol.script.ScriptEval
ContextToken - Class in org.jmol.script
ContextToken() - Constructor for class org.jmol.script.ContextToken
contextVariables - Variable in class org.jmol.script.ContextToken
contextVariables - Variable in class org.jmol.script.ScriptCompiler
contextVariables - Variable in class org.jmol.script.ScriptParam
CONTINUE - Static variable in class org.jmol.script.ScriptCompiler
continuecmd - Static variable in class org.jmol.script.T
continueWith(String) - Method in class org.jmol.adapter.readers.cif.CifReader
continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
contour - Static variable in class org.jmol.script.T
CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
contourColixes - Variable in class org.jmol.shapesurface.IsosurfaceMesh
contourColixes - Variable in class org.jmol.shapesurface.PMeshWriter
contourColors - Variable in class org.jmol.jvxl.data.JvxlData
contourFromZero - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourFromZero - Variable in class org.jmol.jvxl.readers.Parameters
contourIncrements - Variable in class org.jmol.jvxl.readers.Parameters
contourIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
contourlines - Static variable in class org.jmol.script.T
contourPlaneMaximumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourPlaneMinimumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
contours - Static variable in class org.jmol.script.T
contoursDiscrete - Variable in class org.jmol.jvxl.calc.MarchingSquares
contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourType - Variable in class org.jmol.jvxl.readers.Parameters
contourValues - Variable in class org.jmol.jvxl.data.JvxlData
contourValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
ContourVertex(P3) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
contourVertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares
CONTRACTIONS - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
ControlEnterTextArea() - Constructor for class org.jmol.console.AppletConsole.ControlEnterTextArea
controlHermites - Variable in class org.jmol.renderbio.BioMeshRenderer
controlHermites - Variable in class org.jmol.renderspecial.DrawRenderer
controlPoints - Variable in class org.jmol.modelsetbio.BioPolymer
controlPoints - Variable in class org.jmol.renderbio.BioShapeRenderer
controlPointScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
converged - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
convertPointFromScreen(Object, P3) - Method in interface org.jmol.api.GenericPlatform
convertPointFromScreen(Object, P3) - Static method in class org.jmol.awt.Display
convertPointFromScreen(Object, P3) - Method in class org.jmol.awt.Platform
convertPointFromScreen(Object, P3) - Static method in class org.jmol.awtjs2d.Display
convertPointFromScreen(Object, P3) - Method in class org.jmol.awtjs2d.Platform
convertToMegabytes(long) - Static method in class org.jmol.popup.GenericPopup
CONVEX_HULL_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
coord - Variable in class org.jmol.minimize.MinAtom
coord - Static variable in class org.jmol.script.T
coordinateInRange(int, int, T3, int, P3i) - Method in class org.jmol.shape.Shape
coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
  Get the boolean whether coordinates are fractional.
coordinatesAreFractional - Variable in class org.jmol.script.ScriptParam
coordinatesAreFractional - Variable in class org.jmol.symmetry.SymmetryInfo
coordinatesArePrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
coords - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
coords - Variable in class org.jmol.shapespecial.Dipole
coordSaved - Variable in class org.jmol.minimize.forcefield.ForceField
coordSaved - Variable in class org.jmol.minimize.Minimizer
copy(BS) - Static method in class org.jmol.util.BSUtil
copy() - Method in class org.jmol.util.Point3fi
copy2(BS, BS) - Static method in class org.jmol.util.BSUtil
copyandUnzip(String, String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
  Based on code available at Java2s.com
copyBinaryFile(String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
copyColixTranslucency(short, short) - Static method in class org.jmol.util.C
copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
copyInvert(BS, int) - Static method in class org.jmol.util.BSUtil
copyModulations(String, String) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Create a new catalog entry for an atom's modulation components.
copyright - Static variable in class org.jmol.viewer.JC
copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
copyTensor() - Method in class org.jmol.util.Tensor
cordMidPoints - Variable in class org.jmol.renderbio.RocketsRenderer
corner - Variable in class org.jmol.shape.Axes
corners - Variable in class org.jmol.renderbio.RocketRenderer
corners - Static variable in class org.jmol.script.T
cos - Static variable in class org.jmol.script.T
cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
cosASB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
cosBeta - Variable in class org.jmol.util.SimpleUnitCell
cosGamma - Variable in class org.jmol.util.SimpleUnitCell
cosPhi - Variable in class org.jmol.g3d.CylinderRenderer
cossin - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
cosTheta - Variable in class org.jmol.g3d.CylinderRenderer
cosTolerance - Variable in class org.jmol.symmetry.PointGroup
couldBeChiralAlkene(SimpleNode, SimpleEdge) - Method in class org.jmol.symmetry.CIPData
  Allow double bonds only if trivalent and first-row atom.
couldBeChiralAtom(SimpleNode) - Method in class org.jmol.symmetry.CIPData
  Determine whether an atom is one we need to consider.
coulomb_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
coulomb_dielectric - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
coulomb_units_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
count - Variable in class org.jmol.bspt.Element
count - Variable in class org.jmol.modelset.Measurement
count - Variable in class org.jmol.render.MeasuresRenderer
count - Static variable in class org.jmol.script.T
COUNT_MASK - Static variable in class org.jmol.viewer.binding.Binding
countAuxDuplicates(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Get a count of the number of duplicate nodes to the auxiliary atom.
countData(String) - Method in class org.jmol.jvxl.readers.JvxlReader
countData(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
counter - Variable in class org.jmol.script.ScriptParallelProcessor
countGroup(int, String, String) - Method in class org.jmol.modelset.ModelLoader
countPlusIndices - Variable in class org.jmol.modelset.Measurement
countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
covalentHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
covalentradius - Static variable in class org.jmol.script.T
covalentVersion - Static variable in class org.jmol.util.Elements
cpno - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
cr - Variable in class org.jmol.adapter.readers.cif.MSRdr
create - Static variable in class org.jmol.script.T
create(SimpleNode, CIPChirality.CIPAtom, boolean, boolean, boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
createActions() - Method in class org.jmol.viewer.ActionManager
createAllBZs(int, boolean, String, float) - Method in class org.jmol.util.BZone
  Starting with 1, build the Brillouin zones as polyhedra, optionally discarding the previous as we go.
createAndShowGUI(Viewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
createAtomDataSet(Viewer, ModelSet, int, Object, BS) - Static method in class org.jmol.modelset.ModelLoader
createAtomDataSet(Object, int) - Method in class org.jmol.viewer.ModelManager
createAtomSeCollectionFromArrayData(Lst<Object>, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
createAtomSeCollectionFromStrings(String[], SB, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
createAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
createAtomSetCollectionFromFile(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
createAtomSetCollectionFromFiles(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
createAtomSetCollectionFromReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
  not used in Jmol project -- will close reader
createAtomSetCollectionFromString(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
createAuxiliaryDescriptors(CIPChirality.CIPAtom, CIPChirality.CIPAtom[]) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  By far the most complex of the methods, this method creates a list of downstream (higher-sphere) auxiliary chirality designators, starting with those furthest from the root and moving in, toward the root.
createBonds(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
  Use the site bitset to check for atoms that are within +/-dx Angstroms of the specified distances in GEOM_BOND where dx is determined by the uncertainty (dx) in the record.
createBZ(int, Object[], boolean, String, float) - Method in class org.jmol.util.BZone
  Create a Brillouin zone.
createCap(V3) - Method in class org.jmol.util.MeshCapper
  Entry point when finished generating edges.
createCartoonObject(String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
createColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
createContours(float, float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
createCube() - Method in class org.jmol.quantum.MepCalculation
createCube() - Method in class org.jmol.quantum.MOCalculation
createCube() - Method in class org.jmol.quantum.NciCalculation
createCube() - Method in class org.jmol.quantum.QuantumCalculation
createDFMap(int[], String, String, int) - Static method in class org.jmol.quantum.QS
createDialog(Component) - Method in class org.jmol.dialog.FileChooser
createDomNodeJS(String, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
  totally untested, probably useless
createEllipsoidShades() - Method in class org.jmol.util.Shader
createExportPanel(String[], String[], String) - Method in class org.jmol.dialog.Dialog
createFileData(String) - Method in interface org.jmol.api.JmolDataManager
createFileData(String) - Method in class org.jmol.viewer.DataManager
createFont3D(int, int, float, float, FontManager, Object) - Static method in class org.jmol.util.Font
createFunction(String, String, String) - Method in class org.jmol.scriptext.IsoExt
  for the ISOSURFACE command
createGeodesic() - Method in class org.jmol.jvxl.readers.IsoShapeReader
createGeodesic(int) - Static method in class org.jmol.util.Geodesic
createImage(Object) - Method in interface org.jmol.api.GenericPlatform
  can be ignored (return null) if platform cannot save images
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
  Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
createImage(Object, PlatformViewer) - Static method in class org.jmol.awt.Image
createImage(Object) - Method in class org.jmol.awt.Platform
  could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in class org.jmol.awtjs2d.Platform
createImage(String, String, Object, int) - Method in class org.jmol.util.GenericApplet
createImage(String, String, String, byte[], int) - Method in class org.jmol.viewer.StatusManager
  offer to let application do the image creation.
createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
createImageStatus(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Starting with Jmol 11.8.RC5, this is just informational if type == null and null is returned, then it means "Jmol, you handle it"
createInfoArray(SymmetryOperation, SymmetryInterface, P3, P3, String, float, int) - Method in class org.jmol.symmetry.SymmetryDesc
createIsosurface(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
createLadders(Lst<Bridge>, boolean) - Method in class org.jmol.dssx.DSSP
  "ladder =: one or more consecutive bridges of identical type" (p.
createLanguageList() - Method in class org.jmol.i18n.GT
createLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
createLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
createLcaoLobe(V3, float, int) - Method in class org.jmol.shapesurface.Isosurface
createMenu() - Method in class org.jmol.console.ImageDialog
createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create a menu for the app.
createMenubar() - Method in class org.jmol.console.AppletConsole
createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create the menubar for the app.
createMenuItem(String) - Method in class org.jmol.console.AppletConsole
createMenuItem(String) - Method in class org.jmol.console.ImageDialog
createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  This is the hook through which all menu items are created.
createMesh() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
createMesh(int, int, int, int, float, int) - Method in class org.jmol.renderbio.BioMeshRenderer
  Cartoon meshes are triangulated objects.
createModels(int) - Method in class org.jmol.modelset.ModelSet
createModelSet(JmolAdapter, Object, BS) - Method in class org.jmol.modelset.ModelLoader
createModelSet(String, String, SB, Object, BS, boolean) - Method in class org.jmol.viewer.ModelManager
createModelSetAndReturnError(Object, boolean, SB, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
  finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint
createMonteCarloOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
  create a movie from a set of image files
createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.image.AviCreator
createNewAtomSet() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
createNextBZ(BZone, BZone, String) - Method in class org.jmol.util.BZone
createOrbital() - Method in class org.jmol.jvxl.readers.IsoMOReader
createParticle(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
createPdfDocument(OC, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
createPuttyObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  "Putty" shapes scaled in a variety of ways.
createRibbonObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  PyMOL "ribbons" could be Jmol backbone or trace, depending upon the value of PyMOL.ribbon_sampling.
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManager
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerAwt
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerJS
createSet(int, int, int) - Method in class org.jmol.jvxl.data.MeshData
createSGFromList(String, Lst<?>) - Static method in class org.jmol.symmetry.SpaceGroup
createShapeObject(int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Create JmolObjects for each shape.
createShapeObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create JmolObjects for all the molecular shapes; not executed for a state script.
createShapeObjects(BS[], boolean, int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  create all objects for a given molecule or scene
createSlaterData(int, String, String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
createSpacefillObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Create a BALLS JmolObject for each radius.
createSpaceGroup(int, String, Object, int) - Method in interface org.jmol.api.SymmetryInterface
createSpaceGroup(int, String, Object, int) - Static method in class org.jmol.symmetry.SpaceGroup
createSpaceGroup(int, String, Object, int) - Method in class org.jmol.symmetry.Symmetry
createSpaceGroupN(String) - Static method in class org.jmol.symmetry.SpaceGroup
createSpaceGroups() - Static method in class org.jmol.symmetry.SpaceGroup
createSphericalSlaterByType(int, int, String, float, float) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
  We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSubzonePolyhedron(BZone, String) - Method in class org.jmol.util.BZone
  Generate the polyhedra.
createSurfaceTool() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
createTextureFile(String, MeshSurface, int[]) - Method in class org.jmol.export._ObjExporter
  Writes a texture file with the colors in the colixes array in a way that it can be mapped by the texture coordinates vt.
createTheImage(Object, String, OC, Map<String, Object>, String[]) - Method in class org.jmol.viewer.OutputManager
createTool(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Hook through which every toolbar item is created.
createToolbar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create the toolbar.
createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Create a button to go inside of the toolbar.
createTopoMap(BS) - Method in class org.jmol.smiles.SmilesSearch
createTraceObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  trace, or cartoon in the case of cartoon ladders.
createTransferable(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
createTreeModel() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Creates the treeModel of the AtomSets available in the JmolViewer
createVCRController(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Creates a VCR type set of controller inside a JPanel.
createVoxelData() - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
  Developer must customize this method
createWebExport() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
createWS(String) - Method in class org.jmol.util.BZone
  Create a Wigner-Seitz unitcell centered on {0 0 0}.
createZip(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
createZipSet(String, String[], boolean, OC, String) - Method in class org.jmol.viewer.OutputManager
creatingImage - Variable in class org.jmol.viewer.Viewer
creditsAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
CreditsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
CreditsDialog - Class in org.openscience.jmol.app.jmolpanel
CreditsDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.CreditsDialog
crit - Variable in class org.jmol.minimize.Minimizer
criterion - Variable in class org.jmol.minimize.forcefield.ForceField
criterion - Static variable in class org.jmol.script.T
cross - Static variable in class org.jmol.renderspecial.DipolesRenderer
cross - Static variable in class org.jmol.script.T
cross0 - Variable in class org.jmol.renderspecial.DipolesRenderer
cross1 - Variable in class org.jmol.renderspecial.DipolesRenderer
crossBinary(String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
crossed - Static variable in class org.jmol.script.T
crossEnd - Static variable in class org.jmol.renderspecial.DipolesRenderer
crossOffset - Static variable in class org.jmol.renderspecial.DipolesRenderer
crossWidth - Static variable in class org.jmol.renderspecial.DipolesRenderer
crossWidthPixels - Variable in class org.jmol.renderspecial.DipolesRenderer
crtval - Static variable in class org.jmol.shapespecial.Ellipsoid
crtypes - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
cryst1 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
cryst1() - Method in class org.jmol.adapter.readers.pdb.PdbReader
CRYSTAL - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CRYSTAL_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CRYSTAL_SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
CRYSTAL_SYMMETRY_TRANSFORM3 - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
crystalClass - Variable in class org.jmol.symmetry.SpaceGroup
crystalContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
CrystalReader - Class in org.jmol.adapter.readers.xtal
  A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
crystGroup - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
CS - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
CS2 - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
csfLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
CsfReader - Class in org.jmol.adapter.readers.quantum
  CSF file reader based on CIF idea -- fluid property fields.
CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
CTRL - Static variable in class org.jmol.viewer.binding.Binding
CTRL_ALT - Static variable in class org.jmol.awtjs.Event
CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
CTRL_MASK - Static variable in class org.jmol.awtjs.Event
CTRL_SHIFT - Static variable in class org.jmol.awtjs.Event
CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
cubeFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
CubeIterator - Class in org.jmol.bspt
  Iterator used for finding all points within a box or a hemi-box
CubeIterator(Bspt) - Constructor for class org.jmol.bspt.CubeIterator
cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
cubeIterators - Variable in class org.jmol.bspt.Bspf
CubeReader - Class in org.jmol.adapter.readers.simple
  Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
CubeReader - Class in org.jmol.jvxl.readers
CubeReader() - Constructor for class org.jmol.jvxl.readers.CubeReader
cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
cull_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
current - Variable in class org.jmol.thread.HoverWatcherThread
current - Variable in class org.jmol.viewer.ActionManager
currentAtomSetIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
currentBgColor - Variable in class org.jmol.shape.TextShape
currentBgTranslucentLevel - Variable in class org.jmol.shape.TextShape
currentBlock - Variable in class org.jmol.adapter.readers.xtal.MagresReader
currentChain - Variable in class org.jmol.modelset.ModelLoader
currentChainID - Variable in class org.jmol.modelset.ModelLoader
currentColor - Variable in class org.jmol.shape.TextShape
currentCompnd - Variable in class org.jmol.adapter.readers.pdb.PdbReader
currentCursor - Variable in class org.jmol.viewer.Viewer
currentDipole - Variable in class org.jmol.shapespecial.Dipoles
currentDirection - Variable in class org.jmol.viewer.AnimationManager
currentFont - Variable in class org.jmol.shape.TextShape
currentFont - Variable in class org.jmol.util.GData
currentFrameIs(int) - Method in class org.jmol.viewer.AnimationManager
currentFrankId - Variable in class org.jmol.popup.JmolPopup
currentGroup3 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
currentGroup3 - Variable in class org.jmol.modelset.ModelLoader
currentGroupInsertionCode - Variable in class org.jmol.modelset.ModelLoader
currentGroupSequenceNumber - Variable in class org.jmol.modelset.ModelLoader
currentIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
currentIsLast() - Method in class org.jmol.viewer.AnimationManager
currentKey - Variable in class org.jmol.adapter.readers.pdb.PdbReader
currentLevel - Static variable in class org.jmol.util.Geodesic
currentlocalpath - Static variable in class org.jmol.script.T
currentlyRendering - Variable in class org.jmol.util.GData
currentMenuItemId - Variable in class org.jmol.popup.GenericPopup
currentMesh - Variable in class org.jmol.shape.MeshCollection
currentMetricsFont3d - Variable in class org.jmol.shape.Frank
currentModelIndex - Variable in class org.jmol.modelkit.ModelKitPopup
currentMorphModel - Variable in class org.jmol.viewer.AnimationManager
currentNormalOrigin - Variable in class org.jmol.export._ObjExporter
  Wavefront OBJ refers to vertices and normals and textures by their location in the file.
currentObject - Variable in class org.jmol.shape.TextShape
currentPalette - Variable in class org.jmol.util.ColorEncoder
currentPoints - Variable in class org.jmol.geodesic.EnvelopeCalculation
currentProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
currentResno - Variable in class org.jmol.adapter.readers.pdb.PdbReader
currentRule - Variable in class org.jmol.symmetry.CIPChirality
  the current rule being applied exhaustively
currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
currentShadeIndex - Variable in class org.jmol.g3d.Graphics3D
currentShapeID - Variable in class org.jmol.viewer.Viewer
currentShapeState - Variable in class org.jmol.viewer.Viewer
currentSize - Variable in class org.jmol.dialog.FilePreview.FPPanel
currentStep - Variable in class org.jmol.minimize.forcefield.ForceField
currentTextureOrigin - Variable in class org.jmol.export._ObjExporter
  Wavefront OBJ refers to vertices and normals and textures by their location in the file.
currentThread - Variable in class org.jmol.script.ScriptEval
currentTime - Variable in class org.jmol.thread.JmolThread
currentTranslucentLevel - Variable in class org.jmol.shape.TextShape
currentVertexOrigin - Variable in class org.jmol.export._ObjExporter
  Wavefront OBJ refers to vertices and normals and textures by their location in the file.
cursor - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
CURSOR_CROSSHAIR - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_DEFAULT - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_HAND - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_MOVE - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_WAIT - Static variable in interface org.jmol.api.GenericPlatform
CURSOR_ZOOM - Static variable in interface org.jmol.api.GenericPlatform
cursorPos - Variable in class org.jmol.util.CommandHistory
  Current position of the cursor;
curve - Static variable in class org.jmol.script.T
CUSTOM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
CUSTOM - Static variable in class org.jmol.util.ColorEncoder
CUSTOM_CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
CUSTOMTYPE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
CUT - Static variable in class org.jmol.quantum.MOCalculation
cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
cutoff - Variable in class org.jmol.jvxl.data.JvxlData
cutoff - Variable in class org.jmol.jvxl.readers.Parameters
cutoff - Static variable in class org.jmol.script.T
cutoffAutomatic - Variable in class org.jmol.jvxl.readers.Parameters
cutoffRange - Variable in class org.jmol.shapesurface.Isosurface
cx - Variable in class org.jmol.bspt.CubeIterator
CX - Variable in class org.jmol.quantum.MOCalculation
cx - Variable in class org.jmol.shapesurface.PMeshWriter
cxyz - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
cy - Variable in class org.jmol.bspt.CubeIterator
CY - Variable in class org.jmol.quantum.MOCalculation
CYAN - Static variable in class org.jmol.util.C
cyclicFlag - Variable in class org.jmol.modelsetbio.BioPolymer
cylinder - Static variable in class org.jmol.script.T
CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
cylinder3d - Variable in class org.jmol.g3d.Graphics3D
cylinder_shader_ff_workaround - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cylinderBase - Static variable in class org.jmol.renderspecial.DipolesRenderer
cylinderMatrix - Variable in class org.jmol.export._IdtfExporter
cylinderNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
CylinderRenderer - Class in org.jmol.g3d
  Draws shaded cylinders in 3D.
CylinderRenderer(Graphics3D) - Constructor for class org.jmol.g3d.CylinderRenderer
cylinders_shader_filter_faces - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
cz - Variable in class org.jmol.bspt.CubeIterator
CZ - Variable in class org.jmol.quantum.MOCalculation

## D

d - Variable in class org.jmol.adapter.readers.cif.Subsystem
d - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
d - Variable in class org.jmol.minimize.forcefield.Calculation
d - Variable in class org.jmol.util.ContactPair
d1 - Variable in class org.jmol.g3d.HermiteRenderer
d2 - Variable in class org.jmol.g3d.HermiteRenderer
d2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
da - Variable in class org.jmol.minimize.forcefield.Calculations
DA_D - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
DA_DA - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
dAB - Variable in class org.jmol.jvxl.readers.IsoSolventReader
dAB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
dash_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_gap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_round_ends - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dash_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dashDots - Variable in class org.jmol.render.FontLineShapeRenderer
dashes - Static variable in class org.jmol.render.FontLineShapeRenderer
data - Variable in class org.jmol.adapter.readers.cif.CifReader
data - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
data - Variable in class org.jmol.jvxl.readers.DelPhiBinaryReader
data - Variable in class org.jmol.jvxl.readers.IsoFxyReader
data - Variable in class org.jmol.jvxl.readers.IsoFxyzReader
data - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
data - Variable in class org.jmol.minimize.MinObject
data - Variable in class org.jmol.modelset.LabelToken
data - Static variable in class org.jmol.script.T
data() - Method in class org.jmol.scriptext.CmdExt
data - Variable in class org.jmol.symmetry.CIPChirality
  collected bitsets and more specialized SMILES/SMARTS searches and vwr references
data - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
DATA_LABEL - Static variable in interface org.jmol.api.JmolDataManager
DATA_SAVE_IN_STATE - Static variable in interface org.jmol.api.JmolDataManager
DATA_SELECTION - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_AF - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_AFF - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_AFFF - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_LAST - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_STRING - Static variable in interface org.jmol.api.JmolDataManager
DATA_TYPE_UNKNOWN - Static variable in interface org.jmol.api.JmolDataManager
DATA_VALUE - Static variable in interface org.jmol.api.JmolDataManager
DataAdder - Interface in org.jmol.quantum.mo
DataAdder11H - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributions
DataAdder11H() - Constructor for class org.jmol.quantum.mo.DataAdder11H
DataAdder13I - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributions
DataAdder13I() - Constructor for class org.jmol.quantum.mo.DataAdder13I
DataAdder7F - Class in org.jmol.quantum.mo
  adds 7 spherical F orbital contributions
DataAdder7F() - Constructor for class org.jmol.quantum.mo.DataAdder7F
DataAdder9G - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributions
DataAdder9G() - Constructor for class org.jmol.quantum.mo.DataAdder9G
DataAdderF - Class in org.jmol.quantum.mo
  adds 10 cartesian F orbital contributions
DataAdderF() - Constructor for class org.jmol.quantum.mo.DataAdderF
DataAdderG - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributions
DataAdderG() - Constructor for class org.jmol.quantum.mo.DataAdderG
DataAdderH - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributions
DataAdderH() - Constructor for class org.jmol.quantum.mo.DataAdderH
DataAdderI - Class in org.jmol.quantum.mo
  change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributions
DataAdderI() - Constructor for class org.jmol.quantum.mo.DataAdderI
dataAdderOK - Variable in class org.jmol.quantum.MOCalculation
dataAdders - Variable in class org.jmol.quantum.MOCalculation
databaseArray - Static variable in class org.jmol.viewer.JC
databases - Static variable in class org.jmol.viewer.JC
dataFrames - Variable in class org.jmol.modelset.Model
dataIsReducedDensity - Variable in class org.jmol.quantum.NciCalculation
DataManager - Class in org.jmol.viewer
DataManager() - Constructor for class org.jmol.viewer.DataManager
dataMax - Variable in class org.jmol.jvxl.data.JvxlData
dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
dataMin - Variable in class org.jmol.jvxl.data.JvxlData
dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
dataOnly - Variable in class org.jmol.util.MeshSurface
dataOnly - Variable in class org.jmol.viewer.Viewer
dataReaders - Variable in class org.jmol.io.FilesReader
dataScaling - Variable in class org.jmol.quantum.NciCalculation
dataseparator - Static variable in class org.jmol.script.T
dataSeparator - Variable in class org.jmol.viewer.GlobalSettings
dataSourceFrame - Variable in class org.jmol.modelset.Model
dataT - Variable in class org.jmol.adapter.readers.pdb.PdbReader
dataType - Variable in class org.jmol.jvxl.readers.Parameters
dataType - Variable in class org.jmol.jvxl.readers.VolumeDataReader
dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
dataValues - Variable in class org.jmol.viewer.DataManager
dataXYReversed - Variable in class org.jmol.jvxl.readers.Parameters
date - Static variable in class org.jmol.viewer.JC
db - Variable in class org.jmol.minimize.forcefield.Calculations
dBb(BS, boolean) - Method in class org.jmol.modelset.BondCollection
DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
dBm(BS, boolean) - Method in class org.jmol.modelset.BondCollection
  send request up to ModelCollection level.
dc - Variable in class org.jmol.minimize.forcefield.Calculations
DC - Static variable in class org.jmol.quantum.QS
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
dcdFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
dclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
dd - Variable in class org.jmol.minimize.forcefield.Calculations
dData - Variable in class org.jmol.minimize.forcefield.Calculation
ddata - Variable in class org.jmol.minimize.MinObject
dE - Variable in class org.jmol.minimize.forcefield.Calculation
dE - Variable in class org.jmol.minimize.forcefield.ForceField
DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
debug - Static variable in class org.jmol.export._ObjExporter
  Flag to cause debugging output to stdout.
debug - Static variable in class org.jmol.script.T
debug(String) - Method in class org.jmol.util.DefaultLogger
debug(String) - Static method in class org.jmol.util.Logger
  Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at DEBUG level.
debug_pick - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
debugContext - Variable in class org.jmol.adapter.readers.xml.XmlHandler
debugging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
debugging - Static variable in class org.jmol.util.Logger
debuggingHigh - Static variable in class org.jmol.util.Logger
debugHigh - Variable in class org.jmol.script.ScriptExpr
debugHigh - Variable in class org.jmol.script.ScriptMathProcessor
debughigh - Static variable in class org.jmol.script.T
debugPrint(String) - Method in class org.jmol.export._ObjExporter
  Debug print utility.
debugScript - Variable in class org.jmol.script.ScriptEval
debugscript - Static variable in class org.jmol.script.T
debugScript - Variable in class org.jmol.viewer.GlobalSettings
decimal - Static variable in class org.jmol.script.T
decode(String) - Method in class org.jmol.adapter.readers.cif.MMTFReader
decodeAssemblyOperators(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
decodeKey(Integer) - Static method in class org.jmol.minimize.MinObject
deduceElementSymbol(String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
  The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
deepCopy(Object, boolean, boolean) - Static method in class org.jmol.script.SV
  Copies a hash or array deeply; invoked by Jmol script x = @a where a.type == "hash" or a.type == "varray"
deepCopySV(SV) - Static method in class org.jmol.script.SV
DEFAULT - Static variable in class org.jmol.g3d.TriangleRenderer
DEFAULT - Static variable in class org.jmol.smiles.SmilesStereo
default_2fofc_map_rep - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
DEFAULT_BASIS - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JC
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JC
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JC
default_buster_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
DEFAULT_CAMERA_DEPTH - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_CHARGE - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
DEFAULT_DRAG_DROP_SCRIPT - Static variable in class org.jmol.viewer.JC
DEFAULT_FACECENTEROFFSET - Static variable in class org.jmol.shapespecial.Polyhedra
default_fofc_map_rep - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JC
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JC
DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JC
DEFAULT_MAD - Static variable in class org.jmol.shapespecial.Dipoles
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
DEFAULT_MAX_SIZE - Static variable in class org.jmol.util.CommandHistory
DEFAULT_METHOD - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JC
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
DEFAULT_MULT - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
DEFAULT_NAV_FPS - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_OFFSETSIDE - Static variable in class org.jmol.shapespecial.Dipoles
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JC
DEFAULT_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_PERSPECTIVE_MODEL - Static variable in class org.jmol.viewer.TransformManager
default_phenix_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
default_phenix_no_fill_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
DEFAULT_PLANAR_PARAM - Static variable in class org.jmol.shapespecial.Polyhedra
  a dot product comparison term
default_refmac_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
DEFAULT_RHOPARAM - Variable in class org.jmol.quantum.NciCalculation
DEFAULT_RHOPLOT_PRO - Variable in class org.jmol.quantum.NciCalculation
DEFAULT_RHOPLOT_SCF - Variable in class org.jmol.quantum.NciCalculation
DEFAULT_SPIN_FPS - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_SPIN_Y - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JC
DEFAULT_VISUAL_RANGE - Static variable in class org.jmol.viewer.TransformManager
defaultActions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Actions defined by the Jmol class
defaultAlignment - Variable in class org.jmol.shape.Labels
defaultanglelabel - Static variable in class org.jmol.script.T
defaultAngleLabel - Variable in class org.jmol.viewer.GlobalSettings
defaultBBox - Variable in class org.jmol.modelset.ModelSet
defaultBgcolix - Variable in class org.jmol.shape.Labels
defaultBondingMars - Static variable in class org.jmol.util.Elements
  Default table of bonding radii stored as a short mar ...
defaultChoice - Static variable in class org.jmol.dialog.Dialog
defaultcmd - Static variable in class org.jmol.script.T
defaultColix - Variable in class org.jmol.shape.Labels
defaultColix - Variable in class org.jmol.shapesurface.Isosurface
defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultColorFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultColorFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
defaultColorNegative - Static variable in class org.jmol.jvxl.readers.Parameters
defaultColorNegativeLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
defaultColorPositive - Static variable in class org.jmol.jvxl.readers.Parameters
defaultColorPositiveLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
defaultcolorscheme - Static variable in class org.jmol.script.T
defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
defaultContourCount - Static variable in class org.jmol.jvxl.readers.Parameters
defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
defaultCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
defaultCutoff - Static variable in class org.jmol.jvxl.readers.SurfaceReader
defaultdirectory - Static variable in class org.jmol.script.T
defaultDirectory - Variable in class org.jmol.viewer.GlobalSettings
defaultdistancelabel - Static variable in class org.jmol.script.T
defaultDistanceLabel - Variable in class org.jmol.viewer.GlobalSettings
defaultdrawarrowscale - Static variable in class org.jmol.script.T
defaultDrawArrowScale - Variable in class org.jmol.viewer.GlobalSettings
defaultdropscript - Static variable in class org.jmol.script.T
defaultDropScript - Variable in class org.jmol.viewer.GlobalSettings
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
defaultFontId - Variable in class org.jmol.shape.Labels
defaultFontName - Static variable in class org.jmol.shape.Frank
defaultFontSize - Static variable in class org.jmol.shape.Frank
defaultFontStyle - Static variable in class org.jmol.shape.Frank
defaultGroupCount - Static variable in class org.jmol.modelset.ModelLoader
defaultHeight - Variable in class org.jmol.awtjs.swing.JDialog
defaultlabelpdb - Static variable in class org.jmol.script.T
defaultLabelPDB - Variable in class org.jmol.viewer.GlobalSettings
defaultLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
defaultlabelxyz - Static variable in class org.jmol.script.T
defaultLabelXYZ - Variable in class org.jmol.viewer.GlobalSettings
defaultlattice - Static variable in class org.jmol.script.T
defaultloadfilter - Static variable in class org.jmol.script.T
defaultLoadFilter - Variable in class org.jmol.viewer.GlobalSettings
defaultloadscript - Static variable in class org.jmol.script.T
defaultLoadScript - Variable in class org.jmol.viewer.GlobalSettings
defaultLobeCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
DefaultLogger - Class in org.jmol.util
  Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
defaultMacroDirectory - Static variable in class org.jmol.viewer.JC
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.Parameters
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.SurfaceReader
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.Parameters
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.SurfaceReader
defaultMepCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
defaultMepMax - Static variable in class org.jmol.jvxl.readers.Parameters
defaultMepMin - Static variable in class org.jmol.jvxl.readers.Parameters
defaultMessage - Variable in class org.jmol.console.GenericConsole
defaultMode - Variable in class org.jmol.viewer.TransformManager
defaultOffset - Variable in class org.jmol.shape.Labels
defaultON - Static variable in class org.jmol.script.T
defaultOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
defaultOrbitalCutoffOld - Static variable in class org.jmol.jvxl.readers.Parameters
defaultPaletteID - Variable in class org.jmol.shape.Labels
defaultPointer - Variable in class org.jmol.shape.Labels
defaultQMElectronDensityCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
defaultRotationRadius - Variable in class org.jmol.modelset.Model
defaults - Static variable in class org.jmol.script.T
defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
defaultSolventRadius - Static variable in class org.jmol.jvxl.readers.Parameters
defaultsOnlyForNone - Variable in class org.jmol.shape.Labels
defaultStructure - Variable in class org.jmol.modelsetbio.BioModel
defaultstructuredssp - Static variable in class org.jmol.script.T
defaultStructureDSSP - Variable in class org.jmol.viewer.GlobalSettings
defaultTickInfo - Variable in class org.jmol.shape.Measures
defaulttorsionlabel - Static variable in class org.jmol.script.T
defaultTorsionLabel - Variable in class org.jmol.viewer.GlobalSettings
defaulttranslucent - Static variable in class org.jmol.script.T
defaultTranslucent - Variable in class org.jmol.viewer.GlobalSettings
defaultvdw - Static variable in class org.jmol.script.T
defaultVdw - Variable in class org.jmol.viewer.Viewer
defaultWidth - Variable in class org.jmol.awtjs.swing.JDialog
defaultZPos - Variable in class org.jmol.shape.Labels
defer_builds_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
defer_updates - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
  called by the client to generate a set of measurements
define - Static variable in class org.jmol.script.T
define(MeasurementData, int) - Method in class org.jmol.shape.Measures
defineAll(int, Measurement, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
defineAtoms(String, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
defineAtomSet(String) - Method in class org.jmol.script.ScriptEval
defineAtomSets(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
DefineCenterAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
definedAtomSets - Variable in class org.jmol.viewer.Viewer
defineMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.Measures
defineSets() - Method in class org.jmol.script.ScriptEval
  support for @xxx or define xxx commands
DEG_TO_RAD - Static variable in class org.jmol.minimize.forcefield.Calculations
DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
degree - Variable in class org.jmol.smiles.SmilesAtom
degrees - Variable in class org.jmol.navigate.Navigator
DEGREES - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
degreesPerRadian - Static variable in class org.jmol.export.___Exporter
degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
degreeStep - Variable in class org.jmol.navigate.Navigator
delay - Static variable in class org.jmol.script.T
delaymaximumms - Static variable in class org.jmol.script.T
delayMaximumMs - Variable in class org.jmol.viewer.GlobalSettings
delayScript(int) - Method in class org.jmol.script.ScriptEval
delete(BS) - Method in class org.jmol.modelset.Atom
delete - Static variable in class org.jmol.script.T
delete() - Method in class org.openscience.jmol.app.webexport.JmolInstance
deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
deleteAllBonds2() - Method in class org.jmol.modelset.BondCollection
deleteAllButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
deleteAtomReferences() - Method in class org.jmol.modelset.Bond
deleteAtoms - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
deleteAtoms(BS) - Method in class org.jmol.modelset.ModelSet
deleteAtoms(int, BS, BS) - Method in class org.jmol.modelset.StateScript
deleteAtoms(BS) - Method in class org.jmol.modelsetbio.BioResolver
  called from org.jmol.modelsetbio.resolver when adding hydrogens.
deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
deleteAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
deleteAtoms(BS, boolean) - Method in class org.jmol.viewer.Viewer
deleteAtomsInVariables(BS) - Method in interface org.jmol.api.JmolScriptEvaluator
deleteAtomsInVariables(BS) - Method in class org.jmol.script.ScriptEval
deleteAtomTensors(BS) - Method in class org.jmol.modelset.AtomCollection
deleteBits(BS, BS) - Static method in class org.jmol.util.BSUtil
  this one slides deleted bits out of a pattern.
deleteBond(Bond) - Method in class org.jmol.modelset.Atom
deleteBondAt(int) - Method in class org.jmol.modelset.Atom
deleteBonds(BS, boolean) - Method in class org.jmol.modelset.ModelSet
deleteBonds(BS) - Method in class org.jmol.viewer.Viewer
deleteButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
deleteConnections(float, float, int, BS, BS, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
deleteContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
deleteDipole(Dipole) - Method in class org.jmol.shapespecial.Dipoles
deleteI(int) - Method in class org.jmol.shape.Measures
deleteInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
deleteLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
deleteLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
deleteM(Measurement) - Method in class org.jmol.shape.Measures
deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
deleteMesh() - Method in class org.jmol.shape.MeshCollection
deleteMeshElement(int) - Method in class org.jmol.shapecgo.CGO
deleteMeshElement(int) - Method in class org.jmol.shapespecial.Draw
deleteMeshI(int) - Method in class org.jmol.shape.MeshCollection
deleteMeshKey(String) - Method in class org.jmol.shape.MeshCollection
deleteModel(int, int, int, BS, BS) - Method in class org.jmol.modelset.ModelSet
deleteModelAtoms(int, int, BS) - Method in interface org.jmol.api.JmolDataManager
deleteModelAtoms(int, int, BS) - Method in class org.jmol.modelset.AtomCollection
deleteModelAtoms(int, int, BS) - Method in class org.jmol.viewer.DataManager
deleteModelAtoms(int, int, int, BS) - Method in class org.jmol.viewer.Viewer
deleteModelBonds(int) - Method in class org.jmol.modelset.ModelSet
deleteModels(BS) - Method in class org.jmol.modelset.ModelSet
deleteModels(int) - Method in class org.jmol.shapecgo.CGO
deleteModels(int) - Method in class org.jmol.shapespecial.Draw
deleteModels(int, BS) - Method in class org.jmol.viewer.Viewer
  called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
deleteO(Object) - Method in class org.jmol.shape.Measures
deletePolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
deleteSaved(String) - Method in class org.jmol.viewer.StateManager
deleteSavedType(String) - Method in class org.jmol.viewer.StateManager
deleteShapeAtoms(Object[], BS) - Method in class org.jmol.viewer.ShapeManager
deleteUnneededAtoms() - Method in class org.jmol.modelsetbio.BioResolver
  Delete hydrogen atoms that are still in bsAddedHydrogens, because they were not actually added.
deleteVdwDependentShapes(BS) - Method in class org.jmol.viewer.ShapeManager
deleteWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
DELPHI_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
DelPhiBinaryReader - Class in org.jmol.jvxl.readers
DelPhiBinaryReader() - Constructor for class org.jmol.jvxl.readers.DelPhiBinaryReader
delta - Variable in class org.jmol.minimize.forcefield.Calculation
delta - Variable in class org.jmol.thread.MoveToThread.Slider
delta2 - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
delta2 - Variable in class org.jmol.util.Modulation
demoBZ(Object[], boolean) - Method in class org.jmol.util.BZone
density - Static variable in class org.jmol.script.T
DEPR_FD_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DEPR_FD_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DEPR_FO_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DEPR_FO_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DEPR_FU_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DEPR_FU_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
deprecatedparam - Static variable in class org.jmol.script.T
depth - Variable in class org.jmol.export.Export3D
depth - Variable in class org.jmol.g3d.SphereRenderer
depth - Static variable in class org.jmol.script.T
depth - Variable in class org.jmol.util.GData
depth1 - Variable in class org.jmol.g3d.HermiteRenderer
depth_cue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
depthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
depthByPixels(int) - Method in class org.jmol.viewer.Viewer
depthDelta - Variable in class org.jmol.navigate.Navigator
depthPercent - Variable in class org.jmol.navigate.Navigator
depthPercentSetting - Variable in class org.jmol.viewer.TransformManager
depthPlane - Variable in class org.jmol.viewer.TransformManager
depthStart - Variable in class org.jmol.navigate.Navigator
depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
depthValue - Variable in class org.jmol.viewer.TransformManager
depthZ - Variable in class org.jmol.export.___Exporter
desc - Variable in class org.jmol.symmetry.Symmetry
DESCENDER - Static variable in class org.jmol.util.MeshCapper
descent - Variable in class org.jmol.modelset.Text
descent - Variable in class org.jmol.render.LabelsRenderer
descent - Variable in class org.jmol.util.Font
descr - Variable in class org.jmol.minimize.forcefield.AtomType
desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
desiredQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
desiredQpt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
destroy() - Method in interface org.jmol.api.JmolAppletInterface
destroy() - Method in class org.jmol.applet.AppletWrapper
destroy() - Method in class org.jmol.applet.Jmol
destroy() - Method in class org.jmol.g3d.Graphics3D
destroy() - Method in class org.jmol.util.GData
destroy() - Method in class org.jmol.util.GenericApplet
destroy() - Method in interface org.openscience.jmol.app.JmolPlugin
destroyConsole() - Method in class org.jmol.console.GenericConsole
details - Variable in class org.jmol.smiles.SmilesStereo
detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
determineAtomSetCollectionReader(Object, boolean) - Static method in class org.jmol.adapter.smarter.Resolver
  the main resolver method.
determineSpaceGroup(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
determineSpaceGroupIndex(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
determineSpaceGroupN(String) - Static method in class org.jmol.symmetry.SpaceGroup
determineSpaceGroupNA(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
determineSpaceGroupNS(String, SpaceGroup) - Static method in class org.jmol.symmetry.SpaceGroup
determineSurfaceFileType(BufferedReader) - Static method in class org.jmol.viewer.FileManager
determineSurfaceTypeIs(InputStream) - Static method in class org.jmol.viewer.FileManager
determineUniqueAxis(float, float, float, float, float, float) - Static method in class org.jmol.symmetry.SpaceGroup
DF_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
dfact2 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
dfBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
dfCoefMaps - Variable in class org.jmol.adapter.writers.QCJSONWriter
dfCoefMaps - Variable in class org.jmol.jvxl.readers.IsoMOReader
dfCoefMaps - Variable in class org.jmol.quantum.MOCalculation
dFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
DFT_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
dgridContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
DgridReader - Class in org.jmol.adapter.readers.quantum
  A reader for Dgrid BASISFILE data.
DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
diagonal - Variable in class org.openscience.jmol.app.surfacetool.Slice
diagonalReferenceAxis - Variable in class org.jmol.symmetry.HallRotationTerm
Dialog - Class in org.jmol.dialog
Dialog() - Constructor for class org.jmol.dialog.Dialog
dialog - Variable in class org.jmol.dialog.FileChooser
Dialog.ExportChoiceListener - Class in org.jmol.dialog
Dialog.QualityListener - Class in org.jmol.dialog
Dialog.TypeFilter - Class in org.jmol.dialog
dialogAsk(String, String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
dialogAsk(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
  Ask for new file name when opening a file
dialogLocation - Variable in class org.jmol.dialog.FileChooser
dialogSize - Variable in class org.jmol.dialog.FileChooser
dialogType - Variable in class org.jmol.dialog.Dialog
diameter - Variable in class org.jmol.g3d.CylinderRenderer
diameter - Variable in class org.jmol.jvxl.data.JvxlData
diameter - Variable in class org.jmol.render.MeshRenderer
diameter - Variable in class org.jmol.renderspecial.DipolesRenderer
diameter - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
diameter - Variable in class org.jmol.renderspecial.VectorsRenderer
diameter - Static variable in class org.jmol.script.T
diameter - Variable in class org.jmol.shape.Mesh
diameter - Variable in class org.jmol.shapespecial.Draw
diameter0 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
diameterBeg - Variable in class org.jmol.renderbio.BioShapeRenderer
diameterEnd - Variable in class org.jmol.renderbio.BioShapeRenderer
diameterMid - Variable in class org.jmol.renderbio.BioShapeRenderer
diameterP - Variable in class org.jmol.geodesic.EnvelopeCalculation
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
diffuseFactor - Variable in class org.jmol.util.Shader
diffusepercent - Static variable in class org.jmol.script.T
diffusePercent - Variable in class org.jmol.util.Shader
dihedral_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dihedral_label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dihedral_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dihedralList - Variable in class org.jmol.thread.SpinThread
dim - Variable in class org.jmol.bspt.Node
Dimension - Class in org.jmol.awtjs.swing
Dimension(int, int) - Constructor for class org.jmol.awtjs.swing.Dimension
dimension - Variable in class org.jmol.util.SimpleUnitCell
dimMax - Variable in class org.jmol.bspt.Bspf
dimMax - Variable in class org.jmol.bspt.Bspt
dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
DIPOLAR_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
DIPOLE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
dipole - Static variable in class org.jmol.script.T
dipole() - Method in class org.jmol.scriptext.IsoExt
Dipole - Class in org.jmol.shapespecial
Dipole() - Constructor for class org.jmol.shapespecial.Dipole
DIPOLE_TYPE_ATOMS - Static variable in class org.jmol.shapespecial.Dipole
DIPOLE_TYPE_BOND - Static variable in class org.jmol.shapespecial.Dipole
DIPOLE_TYPE_MOLECULAR - Static variable in class org.jmol.shapespecial.Dipole
DIPOLE_TYPE_POINTS - Static variable in class org.jmol.shapespecial.Dipole
DIPOLE_TYPE_POINTVECTOR - Static variable in class org.jmol.shapespecial.Dipole
DIPOLE_TYPE_UNKNOWN - Static variable in class org.jmol.shapespecial.Dipole
dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
dipoleInfo - Variable in class org.jmol.shapespecial.Dipole
Dipoles - Class in org.jmol.shapespecial
Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
dipoles - Variable in class org.jmol.shapespecial.Dipoles
dipolescale - Static variable in class org.jmol.script.T
dipoleScale - Variable in class org.jmol.viewer.GlobalSettings
DipolesRenderer - Class in org.jmol.renderspecial
DipolesRenderer() - Constructor for class org.jmol.renderspecial.DipolesRenderer
dipoleValue - Variable in class org.jmol.shapespecial.Dipole
dipoleValue - Variable in class org.jmol.shapespecial.Dipoles
dipoleVectorScale - Variable in class org.jmol.renderspecial.DipolesRenderer
direct - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
direction - Static variable in class org.jmol.script.T
directives - Variable in class org.jmol.smiles.SmilesStereo
directLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
directLatticeVectorsFirst - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
  CRYSTAL 17 moves directLatticeVectors before LATTICE PARAMETERS
DISABLE - Static variable in class org.jmol.shapecgo.CGOMesh
disableField(int) - Method in class org.jmol.adapter.readers.cif.CifReader
  used for turning off fractional or nonfractional coord.
disablepopupmenu - Static variable in class org.jmol.script.T
disablePopupMenu - Variable in class org.jmol.viewer.GlobalSettings
discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilContains(String) - Method in interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilContains2(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilContains2(String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardLinesUntilNonBlank() - Method in interface org.jmol.api.JmolJDXMOLReader
discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardPreviousAtoms() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
discardTempDataSR(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
discrete - Static variable in class org.jmol.script.T
DISCRETESTATE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
DISORDER_ASSEMBLY - Static variable in class org.jmol.adapter.readers.cif.CifReader
DISORDER_GROUP - Static variable in class org.jmol.adapter.readers.cif.CifReader
disorderAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
DISP_SAW_AX - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DISP_SAW_AY - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DISP_SAW_AZ - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DISP_SAW_C - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DISP_SAW_W - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
DISP_SPEC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.CmdExt
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.IsoExt
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.ScriptExt
dispatchCommands(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
displacement - Static variable in class org.jmol.script.T
Display - Class in org.jmol.awt
  methods required by Jmol that access java.awt.Component private to org.jmol.awt
Display() - Constructor for class org.jmol.awt.Display
Display - Class in org.jmol.awtjs2d
  methods required by Jmol that access java.awt.Component private to org.jmol.awt
Display() - Constructor for class org.jmol.awtjs2d.Display
display - Variable in class org.jmol.dialog.FilePreview
display - Variable in class org.jmol.i18n.Language
display - Static variable in class org.jmol.script.T
display(ModelSet, BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
display - Variable in class org.jmol.viewer.Viewer
display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
display - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
displayAtoms(BS, boolean, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
displayBonds(BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
displaycellparameters - Static variable in class org.jmol.script.T
displayCellParameters - Variable in class org.jmol.viewer.GlobalSettings
displayConsole() - Method in class org.jmol.console.GenericConsole
displayed - Static variable in class org.jmol.script.T
displayLoadErrors - Variable in class org.jmol.viewer.Viewer
displayLoadErrorsSave - Variable in class org.jmol.script.ScriptContext
displayMaxX - Variable in class org.jmol.util.GData
displayMaxX2 - Variable in class org.jmol.util.GData
displayMaxY - Variable in class org.jmol.util.GData
displayMaxY2 - Variable in class org.jmol.util.GData
displayMinX - Variable in class org.jmol.util.GData
displayMinX2 - Variable in class org.jmol.util.GData
displayMinY - Variable in class org.jmol.util.GData
displayMinY2 - Variable in class org.jmol.util.GData
DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
  Action calling evalStringQuiet(<action> + CheckBoxState)
DisplayPanel.DefineCenterAction - Class in org.openscience.jmol.app.jmolpanel
DisplayPanel.HomeAction - Class in org.openscience.jmol.app.jmolpanel
DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
  Action calling moveTo()
DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
  Action calling setStatus()
displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
displayType - Variable in class org.jmol.shapesurface.Contact
displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
dispose() - Method in interface org.jmol.api.GenericMouseInterface
dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
dispose() - Method in class org.jmol.api.JmolViewer
dispose() - Method in class org.jmol.awt.FileDropper
dispose() - Method in class org.jmol.awt.Mouse
dispose() - Method in class org.jmol.awtjs.swing.JDialog
dispose(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Remove this component's HTML5 equivalent and clear references to it.
dispose() - Method in class org.jmol.awtjs2d.Mouse
dispose() - Method in class org.jmol.console.GenericConsole
dispose() - Method in class org.jmol.console.JmolConsole
dispose() - Method in class org.jmol.console.ScriptEditor
dispose() - Method in class org.jmol.consolejs.AppletConsole
dispose() - Method in class org.jmol.multitouch.ActionManagerMT
dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
dispose() - Method in class org.jmol.viewer.ActionManager
dispose() - Method in class org.jmol.viewer.Viewer
  end of life for this viewer
dispose() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
dispose(JFrame, boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
disposeGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
disposeGraphics(Object) - Static method in class org.jmol.awt.Image
disposeGraphics(Object) - Method in class org.jmol.awt.Platform
disposeGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
disposeMenu() - Method in class org.jmol.awtjs.swing.JPopupMenu
disregardNeighbors - Variable in class org.jmol.geodesic.EnvelopeCalculation
dist_counter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
distance - Variable in class org.jmol.jvxl.readers.Parameters
distance - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
distance - Static variable in class org.jmol.script.T
distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
distance2 - Variable in class org.jmol.symmetry.UnitCellIterator
distance2V(V3d, V3d) - Static method in class org.jmol.minimize.Util
distance_exclusion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
distancefactor - Static variable in class org.jmol.script.T
distanceMode - Variable in class org.jmol.quantum.MepCalculation
distancePointToPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
distanceRef - Variable in class org.jmol.shapespecial.Polyhedra
distanceRef - Variable in class org.jmol.shapespecial.Polyhedron
distanceSquared - Variable in class org.jmol.modelset.AtomIteratorWithinModel
distanceTolerance - Variable in class org.jmol.symmetry.PointGroup
distanceTolerance2 - Variable in class org.jmol.symmetry.PointGroup
distanceToMappingPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
distanceVerticalToPlane(float, float, P3, P3, P3) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
distinguishAndPropagateGroup(int, Chain, String, int, int, int) - Method in class org.jmol.modelset.ModelLoader
distinguishAndPropagateGroup(Chain, String, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.BioResolver
div - Static variable in class org.jmol.script.T
div12(M4) - Static method in class org.jmol.symmetry.SymmetryOperation
divide - Static variable in class org.jmol.script.T
dList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
dm - Variable in class org.jmol.viewer.Viewer
dmax - Variable in class org.jmol.jvxl.readers.MapFileReader
dMax - Static variable in class org.jmol.quantum.NciCalculation
dmean - Variable in class org.jmol.jvxl.readers.MapFileReader
dmesh - Variable in class org.jmol.renderspecial.DrawRenderer
dmeshes - Variable in class org.jmol.shapespecial.Draw
dmin - Variable in class org.jmol.jvxl.readers.MapFileReader
dmolContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
DmolReader - Class in org.jmol.adapter.readers.xtal
DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
dna - Static variable in class org.jmol.script.T
DNA_MASK - Static variable in class org.jmol.viewer.JC
doAction(Object) - Method in class org.jmol.console.GenericConsole
doAction(MeasurementData, String, int) - Method in class org.jmol.shape.Measures
doAddHydrogens - Variable in class org.jmol.jvxl.readers.AtomDataReader
doAddHydrogens - Variable in class org.jmol.modelset.ModelLoader
doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCache - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
doCache - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
doCalcArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
doCalculateTroughs - Variable in class org.jmol.jvxl.readers.IsoSolventReader
doCap - Variable in class org.jmol.util.MeshSlicer
doCap0 - Variable in class org.jmol.renderbio.BioMeshRenderer
doCap1 - Variable in class org.jmol.renderbio.BioMeshRenderer
doCentralize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
doCheckAtom(int) - Method in class org.jmol.smiles.SmilesSearch
doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doClear - Variable in class org.jmol.util.MeshSlicer
doClose(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
doColor - Variable in class org.jmol.rendercgo.CGORenderer
doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
Document - Interface in org.jmol.awtjs.swing
documentBase - Variable in class org.jmol.util.GenericApplet
doDebug - Variable in class org.jmol.quantum.QuantumCalculation
doDelay(int) - Method in class org.jmol.script.ScriptEval
doDisplace - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
doDrop(PropertyChangeEvent) - Method in class org.jmol.awt.FileDropper
doEndMove - Variable in class org.jmol.thread.MoveToThread
doEval(String) - Method in class org.jmol.applet.Jmol
doEval(String) - Method in class org.jmol.appletjs.Jmol
  return RAW JAVASCRIPT OBJECT, NOT A STRING
doEval(String) - Method in class org.jmol.util.GenericApplet
doFinalize() - Method in class org.jmol.symmetry.SymmetryOperation
doFinalTransform() - Method in class org.jmol.thread.MoveToThread
doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
doFormatText - Variable in class org.jmol.modelset.Text
doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
doFunctionXY(String, int, int) - Method in class org.jmol.applet.Jmol
doFunctionXY(String, int, int) - Method in class org.jmol.appletjs.Jmol
doFunctionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
doFunctionXYZ(String, int, int, int) - Method in class org.jmol.applet.Jmol
doFunctionXYZ(String, int, int, int) - Method in class org.jmol.appletjs.Jmol
doFunctionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
doGetModel(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
doGhost - Variable in class org.jmol.util.MeshSlicer
doHaveJDX() - Method in class org.jmol.viewer.Viewer
doHighlight(int, int, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor.EditorDocument
doIterate - Variable in class org.jmol.jvxl.data.VolumeData
doJustify - Variable in class org.jmol.render.MeasuresRenderer
dollarsign - Static variable in class org.jmol.script.T
doLogLevel(boolean) - Static method in class org.jmol.util.Logger
  Indicates if the level is logged.
domains - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
domains - Static variable in class org.jmol.script.T
doMenuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
doMenuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
doMenuClickCallbackMK(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
doMinimize - Variable in class org.jmol.modelset.ModelLoader
domObj - Variable in class org.jmol.adapter.readers.xml.XmlReader
DOMReader - Class in org.jmol.io
DOMReader() - Constructor for class org.jmol.io.DOMReader
DOMResolve(Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
  a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
doNavStep(int) - Method in class org.jmol.navigate.Navigator
done - Variable in class org.jmol.adapter.readers.cif.MMCifReader
done - Variable in class org.jmol.dssx.DSSP
done - Variable in class org.jmol.symmetry.UnitCellIterator
doneHere - Variable in class org.jmol.multitouch.ActionManagerMT
doneHere - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
doNew() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
doNormalize - Variable in class org.jmol.adapter.smarter.XtalSymmetry
doNormalize - Variable in class org.jmol.symmetry.SpaceGroup
doNormalize - Variable in class org.jmol.symmetry.SymmetryOperation
  "normalization" is the process of adjusting symmetry operator definitions such that the center of geometry of a molecule is within the 555 unit cell for each operation.
dontsave - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
doOpen() - Method in class org.jmol.console.ScriptEditor
doOverWrite(JFileChooser, File) - Static method in class org.jmol.dialog.Dialog
doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doPackUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
doPoly(Object, int[], int[], int, boolean) - Method in class org.jmol.awtjs2d.JsG2D
doPopPush - Variable in class org.jmol.script.ScriptDelayThread
doPreSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
doPreSymmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
doPreSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
doPreviewAction(boolean) - Method in class org.jmol.dialog.FilePreview
doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doReadMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doRender - Variable in class org.jmol.render.MeshRenderer
doReport - Variable in class org.jmol.dssx.DSSP
doReport() - Method in class org.jmol.script.ScriptEval
doReportProperty(String) - Static method in class org.jmol.viewer.GlobalSettings
doResize - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
doResume() - Method in class org.jmol.console.ScriptEditor
doSaveSurfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
doSelection() - Method in class org.jmol.script.ScriptMathProcessor
doSelections - Variable in class org.jmol.script.ScriptMathProcessor
doSendCallback(String, Object[], String) - Method in class org.jmol.applet.Jmol
doSendCallback(String, Object[], String) - Method in class org.jmol.appletjs.Jmol
doSendCallback(String, Object[], String) - Method in class org.jmol.util.GenericApplet
doSendJsTextareaStatus(String) - Method in class org.jmol.applet.Jmol
doSendJsTextareaStatus(String) - Method in class org.jmol.appletjs.Jmol
doSendJsTextareaStatus(String) - Method in class org.jmol.util.GenericApplet
doSendJsTextStatus(String) - Method in class org.jmol.applet.Jmol
doSendJsTextStatus(String) - Method in class org.jmol.appletjs.Jmol
doSendJsTextStatus(String) - Method in class org.jmol.util.GenericApplet
doSetBonds - Variable in class org.jmol.adapter.readers.cif.MMCifReader
doSetOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
doShowDocument(URL) - Method in class org.jmol.applet.Jmol
doShowDocument(URL) - Method in class org.jmol.appletjs.Jmol
doShowDocument(URL) - Method in class org.jmol.util.GenericApplet
doShowShellType - Variable in class org.jmol.quantum.MOCalculation
doShowStatus(String) - Method in class org.jmol.applet.Jmol
doShowStatus(String) - Method in class org.jmol.appletjs.Jmol
doShowStatus(String) - Method in class org.jmol.util.GenericApplet
doSmoothProperty - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
doSort - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
doStep() - Method in class org.jmol.console.ScriptEditor
doStepTransform() - Method in class org.jmol.thread.MoveToThread
doStroke(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
doStroke(Object, boolean) - Method in class org.jmol.awt.AwtG2D
doStroke(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
doSymmetry - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
doSync() - Method in class org.jmol.viewer.StatusManager
dot - Static variable in class org.jmol.script.T
dot_as_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_density - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_hydrogens - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dot_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dotColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
dotCount - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
dotdensity - Static variable in class org.jmol.script.T
dotDensity - Variable in class org.jmol.viewer.GlobalSettings
doTrack - Variable in class org.jmol.symmetry.CIPChirality
  are we tracking pathways for _M.CIPInfo?
doTransform() - Method in class org.jmol.thread.SpinThread
doTransform4D - Variable in class org.jmol.viewer.TransformManager
doTranslate - Variable in class org.jmol.i18n.GT
doTranslate - Variable in class org.jmol.util.GenericApplet
dots - Variable in class org.jmol.jvxl.readers.IsoSolventReader
dots - Static variable in class org.jmol.script.T
Dots - Class in org.jmol.shapespecial
Dots() - Constructor for class org.jmol.shapespecial.Dots
dots() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Provide an indent for clarity in debugging messages
dotScale - Variable in class org.jmol.renderspecial.DotsRenderer
dotScale - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
dotscale - Static variable in class org.jmol.script.T
dotScale - Variable in class org.jmol.viewer.GlobalSettings
dotsConvexMaps - Variable in class org.jmol.geodesic.EnvelopeCalculation
dotsConvexMax - Variable in class org.jmol.geodesic.EnvelopeCalculation
dotsOrDashes - Variable in class org.jmol.render.FontLineShapeRenderer
DotsRenderer - Class in org.jmol.renderspecial
DotsRenderer() - Constructor for class org.jmol.renderspecial.DotsRenderer
dotsselectedonly - Static variable in class org.jmol.script.T
dotsSelectedOnly - Variable in class org.jmol.viewer.GlobalSettings
dotsurface - Static variable in class org.jmol.script.T
dotSurface - Variable in class org.jmol.viewer.GlobalSettings
dotted - Static variable in class org.jmol.script.T
DOTWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
DOUBLE - Static variable in class org.jmol.viewer.binding.Binding
doubleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
doUpdatePreview(File) - Method in class org.jmol.dialog.FilePreview
  Update preview
doUseIterator - Variable in class org.jmol.jvxl.readers.AtomDataReader
DOWN - Static variable in class org.jmol.viewer.binding.Binding
DownLoadWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
downsample - Static variable in class org.jmol.script.T
downsample2d(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
downsample2dZ(int[], int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
downsampleFactor - Variable in class org.jmol.jvxl.readers.Parameters
downsampleFactor - Variable in class org.jmol.jvxl.readers.VolumeFileReader
downsampleFullSceneAntialiasing(boolean) - Method in class org.jmol.g3d.Graphics3D
downsampleRemainders - Variable in class org.jmol.jvxl.readers.VolumeFileReader
dPlane - Variable in class org.jmol.util.MeshSlicer
DRAG - Static variable in class org.jmol.viewer.binding.Binding
DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
dragAction - Variable in class org.jmol.viewer.ActionManager
dragAtomIndex - Variable in class org.jmol.viewer.ActionManager
dragBinding - Variable in class org.jmol.viewer.ActionManager
DragBinding - Class in org.jmol.viewer.binding
DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
dragEnter(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
dragExit(DropTargetEvent) - Method in class org.jmol.awt.FileDropper
DRAGGED - Static variable in class org.jmol.awtjs.Event
dragged(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
dragged - Variable in class org.jmol.viewer.ActionManager
dragGesture - Variable in class org.jmol.viewer.ActionManager
dragMinimizeAtom(int) - Method in class org.jmol.viewer.Viewer
dragOver(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
dragselected - Static variable in class org.jmol.script.T
dragSelected(int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
  change actual coordinates of selected atoms from set dragSeleted TRUE or set PICKING DRAGSELECTED Basically, set dragSelected adds new functionality to Jmol with alt-drag and alt-shift drag, and set picking dragSelected replaces the standard mouse drag with a move action and also adds rotate and z-shift options.
dragSelected - Variable in class org.jmol.viewer.GlobalSettings
dragSelectedMode - Variable in class org.jmol.viewer.ActionManager
drange - Variable in class org.jmol.jvxl.readers.MapFileReader
draw - Static variable in class org.jmol.script.T
draw() - Method in class org.jmol.scriptext.IsoExt
Draw - Class in org.jmol.shapespecial
Draw() - Constructor for class org.jmol.shapespecial.Draw
Draw.EnumDrawType - Enum in org.jmol.shapespecial
draw000 - Variable in class org.jmol.render.FontLineShapeRenderer
draw_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
draw_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
drawAtom(Atom, float) - Method in interface org.jmol.api.JmolRendererInterface
drawAtom(Atom, float) - Method in class org.jmol.export.___Exporter
drawAtom(Atom, float) - Method in class org.jmol.export.__CartesianExporter
drawAtom(Atom, float) - Method in class org.jmol.export.__RayTracerExporter
drawAtom(Atom, float) - Method in class org.jmol.export.Export3D
drawAtom(Atom, float) - Method in class org.jmol.g3d.Graphics3D
drawBanana(Atom, Atom, V3, int) - Method in class org.jmol.render.SticksRenderer
drawBond(P3, P3, short, short, byte, short, int) - Method in interface org.jmol.api.JmolRendererInterface
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.export.Export3D
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
drawBond(int) - Method in class org.jmol.render.SticksRenderer
drawCap - Variable in class org.jmol.renderspecial.VectorsRenderer
drawCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.___Exporter
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__CartesianExporter
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
  draws a simple circle (draw circle)
drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.___Exporter
drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.__CartesianExporter
  bond order -1 -- single bond, Cartesian bond order -2 -- multiple bond, Cartesian
drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.__RayTracerExporter
drawDashed(int, int, int, int, int, int, int[]) - Method in class org.jmol.render.FontLineShapeRenderer
drawDashedLineBits(int, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.export.Export3D
drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawData - Variable in class org.jmol.modelkit.ModelKitPopup
drawEdge(int, int, boolean, T3, T3, P3i, P3i) - Method in class org.jmol.render.MeshRenderer
drawEdges(P3[], P3[], int) - Method in class org.jmol.renderbio.NucleicRenderer
drawEdges - Variable in class org.jmol.renderspecial.PolyhedraRenderer
drawEdges(short, P3, P3, P3, int) - Method in class org.jmol.renderspecial.PolyhedraRenderer
drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
drawEllipse(P3, P3, P3, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.___Exporter
drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.__CartesianExporter
drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.export.Export3D
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  draws a ring and filled circle (halos, draw CIRCLE, draw handles)
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.___Exporter
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
  draws a screened circle ...
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawfontsize - Static variable in class org.jmol.script.T
drawFontSize - Variable in class org.jmol.viewer.GlobalSettings
drawFrameLine(String, P3, V3, float, P3, SB, String, String) - Static method in class org.jmol.symmetry.SymmetryDesc
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawHermite4(int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in interface org.jmol.api.JmolRendererInterface
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.export.Export3D
drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.g3d.Graphics3D
drawHLine(int, int, int, int) - Method in class org.jmol.export.Export3D
drawHLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawhover - Static variable in class org.jmol.script.T
drawHover - Variable in class org.jmol.viewer.GlobalSettings
drawImage(Object, Object, int, int, int, int, boolean) - Method in interface org.jmol.api.GenericPlatform
drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawImage(Object, Object, int, int, int, int) - Static method in class org.jmol.awt.Display
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awt.Platform
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs.Platform
drawImage(Object, Object, int, int, int, int, boolean) - Static method in class org.jmol.awtjs2d.Display
  Draw the completed image from rendering.
drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Platform
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
drawImage(Object, Object, int, int, boolean) - Method in class org.jmol.viewer.Viewer
drawImageDTI(Object, Object, int, int, int, int) - Static method in class org.jmol.awt.Display
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
drawImageToBuffer(Object, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
drawIndex - Variable in class org.jmol.symmetry.PointGroup
drawInfo(String, int, String) - Method in class org.jmol.render.UccageRenderer
drawInfo - Variable in class org.jmol.symmetry.PointGroup
drawing - Static variable in class org.jmol.script.T
drawLcaoCartoon(V3, V3, V3, int) - Method in class org.jmol.shapesurface.Isosurface
drawLine(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawLine(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawLine(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.MeasuresRenderer
drawLine(int, int, int, int, int, int) - Method in class org.jmol.render.StarsRenderer
drawLine(SB, String, float, P3, P3, String) - Static method in class org.jmol.symmetry.SymmetryDesc
drawLine2(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
drawLineAB(P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawLineAB(P3, P3) - Method in class org.jmol.export.Export3D
drawLineAB(P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawLineBits(short, short, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
drawLineBits(short, short, P3, P3) - Method in class org.jmol.export.Export3D
drawLineBits(P3, P3, short, short) - Method in class org.jmol.export.Export3D
drawLineBits(short, short, P3, P3) - Method in class org.jmol.g3d.Graphics3D
drawLineData(Lst<P3[]>) - Method in class org.jmol.renderspecial.DrawRenderer
drawLineXYZ(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
DrawMesh - Class in org.jmol.shapespecial
DrawMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
drawMeshSphere(P3i) - Method in class org.jmol.render.MeshRenderer
drawMode - Variable in class org.jmol.viewer.ActionManager
drawpicking - Static variable in class org.jmol.script.T
drawPicking - Variable in class org.jmol.viewer.GlobalSettings
drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.___Exporter
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawPoint(int, boolean) - Method in class org.jmol.render.MeshRenderer
drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
drawPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
drawQuadrilateralBits(JmolRendererInterface, short, P3, P3, P3, P3) - Method in class org.jmol.util.GData
drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.modelsetbio.BioExt
drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.util.Escape
drawRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  draws a rectangle
drawRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
drawRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
  draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
  draws a rectangle
DrawRenderer - Class in org.jmol.renderspecial
DrawRenderer() - Constructor for class org.jmol.renderspecial.DrawRenderer
drawScript - Variable in class org.jmol.modelkit.ModelKitPopup
drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.BioShapeRenderer
drawShaft - Variable in class org.jmol.renderspecial.VectorsRenderer
drawSlicePlane(SB, int, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
drawString(Object, String, int, int) - Method in interface org.jmol.api.GenericGraphics
drawString(String, Font, int, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
  draws the specified string in the current font.
drawString(Object, String, int, int) - Method in class org.jmol.awt.AwtG2D
drawString(Object, String, int, int) - Method in class org.jmol.awtjs2d.JsG2D
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.export.Export3D
  draws the specified string in the current font.
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
  draws the specified string in the current font.
drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.render.FontLineShapeRenderer
drawStringNoSlab(String, Font, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
  draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.export.Export3D
  draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
  draws the specified string in the current font.
drawStringRotated(Object, String, int, int, double) - Method in interface org.jmol.api.GenericGraphics
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awt.AwtG2D
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awtjs2d.JsG2D
drawSubzonePolygons(BZone) - Method in class org.jmol.util.BZone
drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
drawSurface(MeshSurface, short) - Method in class org.jmol.export.___Exporter
drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.___Exporter
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
drawTextPixel(int, int, int, int) - Method in class org.jmol.export._MayaExporter
drawTicks(int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
drawTicks2(float, int, int, String[]) - Method in class org.jmol.render.FontLineShapeRenderer
drawTriangle(P3i, short, P3i, short, P3i, short, int, int) - Method in class org.jmol.render.MeshRenderer
drawTriangle(int, MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex, String) - Method in class org.jmol.util.MeshCapper
  for debugging
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.export.Export3D
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.g3d.Graphics3D
drawTriangleBits(P3, short, P3, short, P3, short, int, int) - Method in class org.jmol.render.MeshRenderer
drawTriangleBits(JmolRendererInterface, P3, short, P3, short, P3, short, int) - Method in class org.jmol.util.GData
drawTriangles - Variable in class org.jmol.shape.Mesh
drawType - Variable in class org.jmol.renderspecial.DrawRenderer
drawType - Variable in class org.jmol.shapespecial.DrawMesh
drawType - Variable in class org.jmol.symmetry.PointGroup
drawTypes - Variable in class org.jmol.shapespecial.DrawMesh
drawVector(SB, String, String, String, T3, T3, String) - Static method in class org.jmol.symmetry.SymmetryDesc
drawVertexCount - Variable in class org.jmol.shapespecial.DrawMesh
drawVertexCounts - Variable in class org.jmol.shapespecial.DrawMesh
drawVLine(int, int, int, int) - Method in class org.jmol.export.Export3D
drawVLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawZoneCenters(BZone) - Method in class org.jmol.util.BZone
DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
drivingSync - Variable in class org.jmol.viewer.StatusManager
drop(DropTargetDropEvent) - Method in class org.jmol.awt.FileDropper
dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
dropListener - Variable in class org.jmol.awt.FileDropper
dropper - Variable in class org.jmol.applet.Jmol
dRot - Variable in class org.jmol.thread.MoveToThread
DS - Static variable in class org.jmol.quantum.QS
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
dSlab - Variable in class org.jmol.thread.MoveToThread
dslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
Dsn6BinaryReader - Class in org.jmol.jvxl.readers
Dsn6BinaryReader() - Constructor for class org.jmol.jvxl.readers.Dsn6BinaryReader
dSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
DSSP - Class in org.jmol.dssx
DSSP() - Constructor for class org.jmol.dssx.DSSP
dssp - Static variable in class org.jmol.script.T
dsspcalchydrogen - Static variable in class org.jmol.script.T
dsspCalcHydrogen - Variable in class org.jmol.viewer.GlobalSettings
dsspIgnoreHydrogens - Variable in class org.jmol.dssx.DSSP
dsspTypes - Static variable in class org.jmol.modelsetbio.AlphaPolymer
dssr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
dssr - Static variable in class org.jmol.script.T
DSSR0 - Class in org.jmol.dssx
  The original non-JSON parser for output from 3DNA web service.
DSSR0() - Constructor for class org.jmol.dssx.DSSR0
DSSR1 - Class in org.jmol.dssx
  A parser for output from 3DNA web service.
DSSR1() - Constructor for class org.jmol.dssx.DSSR1
DSSR_PATHS - Static variable in class org.jmol.dssx.DSSR1
  The paths to the unit id data within the structure.
dssrBox - Variable in class org.jmol.modelsetbio.NucleicMonomer
dssrBoxHeight - Variable in class org.jmol.modelsetbio.NucleicMonomer
dssrCache - Variable in class org.jmol.modelset.Model
dssrData - Variable in class org.jmol.modelset.AtomCollection
dssrFrame - Variable in class org.jmol.modelsetbio.NucleicMonomer
dssrNT - Variable in class org.jmol.modelset.Group
dssrParser - Variable in class org.jmol.viewer.Viewer
dTrans - Variable in class org.jmol.thread.MoveToThread
dtype - Variable in class org.jmol.adapter.smarter.XtalSymmetry
DUMMY_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
dump_binary - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dumpAll() - Static method in class org.jmol.symmetry.SpaceGroup
dumpAllSeitz() - Static method in class org.jmol.symmetry.SpaceGroup
dumpCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
dumpDipoles(String) - Method in class org.jmol.shapespecial.Dipoles
dumpInfo(int) - Method in class org.jmol.quantum.MOCalculation
dumpInfo() - Method in class org.jmol.symmetry.HallInfo
dumpInfo(String) - Method in class org.jmol.symmetry.HallRotationTerm
dumpInfo() - Method in class org.jmol.symmetry.SpaceGroup
dumpInfo() - Method in class org.jmol.symmetry.SymmetryOperation
dumpInfo(boolean) - Method in class org.jmol.symmetry.UnitCell
dumpInfoObj() - Method in class org.jmol.symmetry.SpaceGroup
dumping - Variable in class org.jmol.util.MeshCapper
  for debugging
dumpLine(P3, T3, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
dumpLine2(P3, P3, String, float, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
dumpMatrix(String, int, int[][]) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
dumpPoint(P3, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
dumpRegion() - Method in class org.jmol.util.MeshCapper.CapVertex
  for debugging
dumpRingKeys(SB, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
dumpSeitz(M4, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
dumpStacks(String) - Method in class org.jmol.script.ScriptMathProcessor
dumpStructure(String[][]) - Method in class org.jmol.popup.PopupResource
dumpSummary(AminoPolymer, char[]) - Method in class org.jmol.dssx.DSSP
dumpTags(AminoPolymer, String, BS, int) - Method in class org.jmol.dssx.DSSP
dumpWords() - Method in class org.jmol.popup.PopupResource
duplicateAtomProperties(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
dVal - Variable in class org.jmol.minimize.forcefield.FFParam
dval(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
dx - Variable in class org.jmol.bspt.CubeIterator
dx - Variable in class org.jmol.render.SticksRenderer
dx - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping min/max x and y
dx - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
dx - Variable in class org.jmol.shape.Frank
dxB - Variable in class org.jmol.g3d.CylinderRenderer
dxBf - Variable in class org.jmol.g3d.CylinderRenderer
dxStep - Variable in class org.jmol.render.SticksRenderer
DXY - Variable in class org.jmol.quantum.MOCalculation
dxyz - Variable in class org.jmol.g3d.SphereRenderer
DXZ - Variable in class org.jmol.quantum.MOCalculation
dy - Variable in class org.jmol.bspt.CubeIterator
dy - Variable in class org.jmol.render.SticksRenderer
dy - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping min/max x and y
dy - Variable in class org.jmol.shape.Frank
dyB - Variable in class org.jmol.g3d.CylinderRenderer
dyBf - Variable in class org.jmol.g3d.CylinderRenderer
dynamic_measures - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dynamic_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dynamic_width_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dynamic_width_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dynamic_width_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
dynamicmeasurements - Static variable in class org.jmol.script.T
dyStep - Variable in class org.jmol.render.SticksRenderer
DYZ - Variable in class org.jmol.quantum.MOCalculation
dz - Variable in class org.jmol.bspt.CubeIterator
dzB - Variable in class org.jmol.g3d.CylinderRenderer
dzBf - Variable in class org.jmol.g3d.CylinderRenderer
dZoom - Variable in class org.jmol.thread.MoveToThread

## E

e - Variable in class org.jmol.scriptext.MathExt
e - Variable in class org.jmol.scriptext.ScriptExt
e - Variable in class org.jmol.scriptext.SmilesExt
e(Object) - Static method in class org.jmol.util.Escape
e0 - Variable in class org.jmol.minimize.forcefield.ForceField
E_ANG_PER_DEBYE - Static variable in class org.jmol.shapespecial.Dipoles
e_charge - Static variable in class org.jmol.quantum.NMRCalculation
E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
eAD(double[]) - Static method in class org.jmol.util.Escape
eAF(float[]) - Static method in class org.jmol.util.Escape
eAI(int[]) - Static method in class org.jmol.util.Escape
EANGLE - Static variable in class org.jmol.minimize.forcefield.ForceField
eAP(T3[]) - Static method in class org.jmol.util.Escape
eAS(String[], boolean) - Static method in class org.jmol.util.Escape
EAST - Static variable in class org.jmol.awtjs.swing.BorderLayout
EAST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
EBOND - Static variable in class org.jmol.minimize.forcefield.ForceField
eBond(BS) - Static method in class org.jmol.util.Escape
eBS(BS) - Static method in class org.jmol.util.Escape
eButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
ec - Variable in class org.jmol.shapespecial.Dots
eccentricity - Static variable in class org.jmol.script.T
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.Parameters
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.Parameters
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
eccentricityRatio - Variable in class org.jmol.jvxl.readers.Parameters
eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
eccentricityScale - Variable in class org.jmol.jvxl.readers.Parameters
eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
echo - Static variable in class org.jmol.script.T
Echo - Class in org.jmol.shape
Echo() - Constructor for class org.jmol.shape.Echo
ECHO_BOTTOM - Static variable in class org.jmol.viewer.JC
ECHO_MIDDLE - Static variable in class org.jmol.viewer.JC
ECHO_TOP - Static variable in class org.jmol.viewer.JC
ECHO_XY - Static variable in class org.jmol.viewer.JC
ECHO_XYZ - Static variable in class org.jmol.viewer.JC
echoMessage(String) - Method in class org.jmol.viewer.Viewer
echoNames - Static variable in class org.jmol.viewer.JC
EchoRenderer - Class in org.jmol.render
EchoRenderer() - Constructor for class org.jmol.render.EchoRenderer
echoShapeActive - Variable in class org.jmol.modelset.ModelSet
ecosASB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
eCounts - Variable in class org.jmol.symmetry.PointGroup
ed - Static variable in class org.jmol.script.T
Edge(IsoSolventReader, int, int, float) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Edge
Edge - Class in org.jmol.util
Edge() - Constructor for class org.jmol.util.Edge
Edge.EnumBondOrder - Enum in org.jmol.util
EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
edgeData - Variable in class org.jmol.adapter.readers.xtal.CgdReader
edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
edges - Static variable in class org.jmol.script.T
edges - Variable in class org.jmol.smiles.SmilesRing
edges - Static variable in class org.jmol.util.BoxInfo
EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
EDGES_NONE - Static variable in class org.jmol.shapespecial.Polyhedra
EDGES_ONLY - Static variable in class org.jmol.shapespecial.Polyhedra
edgesOnly - Variable in class org.jmol.renderspecial.PolyhedraRenderer
edgesonly - Static variable in class org.jmol.script.T
edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVector - Variable in class org.jmol.jvxl.data.VolumeData
edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexes - Static variable in class org.jmol.util.TriangleData
edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
edit_light - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
editButton - Variable in class org.jmol.console.GenericConsole
editor - Variable in class org.jmol.console.ScriptEditor
editor_auto_dihedral - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
editor_auto_origin - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
editor_bond_cycle_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
editor_label_fragments - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
editorDoc - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
EditorDocument() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument
editorScrollPane - Variable in class org.openscience.jmol.app.webexport.WebPanel
EditorTextPane - Variable in class org.jmol.console.ScriptEditor.EditorDocument
EditorTextPane() - Constructor for class org.jmol.console.ScriptEditor.EditorTextPane
editPane - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
eds - Static variable in class org.jmol.script.T
edsdiff - Static variable in class org.jmol.script.T
EELECTROSTATIC - Static variable in class org.jmol.minimize.forcefield.ForceField
EfvetReader - Class in org.jmol.jvxl.readers
EfvetReader() - Constructor for class org.jmol.jvxl.readers.EfvetReader
EIG_VAL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
EIG_VEC - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
EIG_VEC_COMPRESSED - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
eigen - Variable in class org.jmol.quantum.NciCalculation
eigenSignMask - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
eigenSignMask - Variable in class org.jmol.util.Tensor
EigenSort - Class in org.jmol.util
  sort from smallest to largest absolute
EigenSort() - Constructor for class org.jmol.util.EigenSort
eigenValues - Variable in class org.jmol.quantum.NciCalculation
eigenValues - Variable in class org.jmol.util.Tensor
eigenVectors - Variable in class org.jmol.util.Tensor
eightPiSquared100 - Static variable in class org.jmol.shapebio.BioShape
ELECRADIUS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
electroNegativities - Static variable in class org.jmol.util.Elements
electronEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
eleLeft - Variable in class org.jmol.bspt.Node
ELEM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
Element - Class in org.jmol.bspt
  the internal tree is made up of elements ...
Element() - Constructor for class org.jmol.bspt.Element
element - Static variable in class org.jmol.script.T
elementCharMasks - Static variable in class org.jmol.adapter.smarter.Atom
elementContext - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
elementCount - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
elementCounts - Variable in class org.jmol.util.JmolMolecule
elementDefined - Variable in class org.jmol.smiles.SmilesAtom
elementLabel - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
elementNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
elementNames - Static variable in class org.jmol.util.Elements
elementNumber - Variable in class org.jmol.adapter.smarter.Atom
elementNumber - Variable in class org.jmol.smiles.SmilesAtom
elementNumberFromName(String) - Static method in class org.jmol.util.Elements
elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
elementNumberMax - Static variable in class org.jmol.util.Elements
  one larger than the last elementNumber, same as elementSymbols.length
elementNumberMax - Variable in class org.jmol.util.JmolMolecule
elementPt - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
elements - Variable in class org.jmol.symmetry.PointGroup
Elements - Class in org.jmol.util
Elements() - Constructor for class org.jmol.util.Elements
elementsPresent - Variable in class org.jmol.modelset.ModelSet
elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
elementSymbols - Static variable in class org.jmol.util.Elements
  The default elementSymbols.
elemisono - Static variable in class org.jmol.script.T
elemNo - Variable in class org.jmol.minimize.forcefield.AtomType
elemno - Static variable in class org.jmol.script.T
elemNo - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  Rule 1a nominal element number; may be fractional for Kekule issues
elemnoMax - Variable in class org.jmol.minimize.Minimizer
elemNos - Variable in class org.jmol.shapespecial.Polyhedron
eleRight - Variable in class org.jmol.bspt.Node
eleRoot - Variable in class org.jmol.bspt.Bspt
ellipseNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
ellipsoid - Static variable in class org.jmol.script.T
ellipsoid() - Method in class org.jmol.scriptext.CmdExt
ELLIPSOID - Static variable in class org.jmol.shapecgo.CGOMesh
Ellipsoid - Class in org.jmol.shapespecial
Ellipsoid() - Constructor for class org.jmol.shapespecial.Ellipsoid
ellipsoid_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ellipsoid_probability - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ellipsoid_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ellipsoid_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ellipsoid_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ellipsoidarcs - Static variable in class org.jmol.script.T
ellipsoidArcs - Variable in class org.jmol.viewer.GlobalSettings
ellipsoidarrows - Static variable in class org.jmol.script.T
ellipsoidArrows - Variable in class org.jmol.viewer.GlobalSettings
ellipsoidaxes - Static variable in class org.jmol.script.T
ellipsoidAxes - Variable in class org.jmol.viewer.GlobalSettings
ellipsoidaxisdiameter - Static variable in class org.jmol.script.T
ellipsoidAxisDiameter - Variable in class org.jmol.viewer.GlobalSettings
ellipsoidball - Static variable in class org.jmol.script.T
ellipsoidBall - Variable in class org.jmol.viewer.GlobalSettings
ellipsoiddotcount - Static variable in class org.jmol.script.T
ellipsoidDotCount - Variable in class org.jmol.viewer.GlobalSettings
ellipsoiddots - Static variable in class org.jmol.script.T
ellipsoidDots - Variable in class org.jmol.viewer.GlobalSettings
ellipsoidfill - Static variable in class org.jmol.script.T
ellipsoidFill - Variable in class org.jmol.viewer.GlobalSettings
ellipsoidNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
ellipsoids - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
Ellipsoids - Class in org.jmol.shapespecial
Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
ellipsoidSet - Variable in class org.jmol.shapespecial.Ellipsoids
ellipsoidShades - Variable in class org.jmol.util.Shader
EllipsoidsRenderer - Class in org.jmol.renderspecial
EllipsoidsRenderer() - Constructor for class org.jmol.renderspecial.EllipsoidsRenderer
elsecmd - Static variable in class org.jmol.script.T
elseif - Static variable in class org.jmol.script.T
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JC
embeddedCrystal - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
embedScript(String) - Static method in class org.jmol.viewer.JC
empty - Variable in class org.jmol.viewer.SelectionManager
EMPTY_DICT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
EMPTY_LIST - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
EMPTY_SET - Static variable in class org.jmol.geodesic.EnvelopeCalculation
EMPTY_TUPLE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
emptyListPt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
emptySet - Static variable in class org.jmol.util.BSUtil
ENABLE - Static variable in class org.jmol.shapecgo.CGOMesh
enableButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
enableButtons(JList<?>) - Method in class org.openscience.jmol.app.webexport.WebPanel
enabled - Variable in class org.jmol.awtjs.swing.Component
enabled - Variable in class org.jmol.util.ModulationSet
  indicates state of modulated or unmodulated
enableShell(int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...
ENC_CALC_MAX_DIST - Static variable in class org.jmol.viewer.JC
encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
encodeColor(short) - Static method in class org.jmol.shape.Shape
encodeImage(int, int, Object) - Method in class org.jmol.viewer.OutputManager
  general image encoder, allows for BufferedImage, int[], or HTML5 2D canvas
encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
END - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
end - Static variable in class org.jmol.script.T
END - Static variable in class org.jmol.shapecgo.CGOMesh
END_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
END_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
END_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
endAssignment() - Method in class org.jmol.script.ScriptMathProcessor
endcap - Variable in class org.jmol.render.FontLineShapeRenderer
endCapHidden - Variable in class org.jmol.g3d.CylinderRenderer
endcaps - Variable in class org.jmol.g3d.CylinderRenderer
endcaps - Variable in class org.jmol.render.SticksRenderer
ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
ENDCAPS_FLAT_TO_SPHERICAL - Static variable in class org.jmol.util.GData
ENDCAPS_HIDDEN - Static variable in class org.jmol.util.GData
ENDCAPS_NONE - Static variable in class org.jmol.util.GData
ENDCAPS_OPEN_TO_SPHERICAL - Static variable in class org.jmol.util.GData
ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
endcapShadeIndex - Variable in class org.jmol.g3d.CylinderRenderer
endChainID - Variable in class org.jmol.adapter.smarter.Structure
endChainStr - Variable in class org.jmol.adapter.smarter.Structure
endCheck - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
endCheck - Static variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
endCoord - Variable in class org.jmol.shapespecial.Dipoles
endDegrees - Variable in class org.jmol.thread.SpinThread
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
endFlag - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
endifcmd - Static variable in class org.jmol.script.T
endIndexPending - Variable in class org.jmol.renderbio.RocketRenderer
endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
endMinimization() - Method in class org.jmol.minimize.Minimizer
endOfData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
endOfLine - Variable in class org.jmol.script.ScriptCompiler
endPositions - Variable in class org.jmol.thread.SpinThread
endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
endRendering() - Method in class org.jmol.g3d.Graphics3D
endRendering() - Method in class org.jmol.util.GData
endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
energy - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
energy - Variable in class org.jmol.minimize.forcefield.Calculation
ENERGY - Static variable in class org.jmol.minimize.forcefield.ForceField
energy - Variable in class org.jmol.modelset.HBond
energy - Static variable in class org.jmol.script.T
energy - Variable in class org.jmol.viewer.Connection
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyES(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyES(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyKey - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
  Type of energy calculated, e.g., E(RB+HF-PW91).
energyKey - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
  The type of energy last calculated.
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyStretchBend(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyStretchBend(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyString - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
  Calculated energy with units (if possible).
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
energyUnits - Variable in class org.jmol.adapter.readers.xtal.GulpReader
energyunits - Static variable in class org.jmol.script.T
energyUnits - Variable in class org.jmol.viewer.GlobalSettings
energyValue - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
  The last calculated energy value.
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
energyWithUnits - Variable in class org.jmol.adapter.readers.simple.MopacArchiveReader
ensureCapacity(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
ensureFourier(int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Make sure that F_n record is present.
ensureMeshSource() - Method in class org.jmol.shapesurface.Isosurface
enterListener - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
EnterListener - Interface in org.openscience.jmol.app.jmolpanel.console
enterMeasurementMode(int) - Method in class org.jmol.viewer.ActionManager
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
enterPressed() - Method in interface org.openscience.jmol.app.jmolpanel.console.EnterListener
enthalpy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
entities - Variable in class org.jmol.adapter.readers.cif.MMTFReader
entries - Variable in class org.jmol.util.Int2IntHash
entry(long, int, int, boolean) - Method in class org.jmol.awtjs2d.Mouse
entryCount - Variable in class org.jmol.util.Int2IntHash
EnumBondOrder(int, String, String) - Constructor for enum org.jmol.util.Edge.EnumBondOrder
EnumDrawType(int, String) - Constructor for enum org.jmol.shapespecial.Draw.EnumDrawType
EnumType() - Constructor for enum org.jmol.atomdata.RadiusData.EnumType
ENV_CALC_MAX_LEVEL - Static variable in class org.jmol.viewer.JC
EnvelopeCalculation - Class in org.jmol.geodesic
EnvelopeCalculation() - Constructor for class org.jmol.geodesic.EnvelopeCalculation
envelopeRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
envelopeRadius - Variable in class org.jmol.jvxl.readers.Parameters
EOL - Static variable in class org.jmol.script.ScriptCompiler
eol(char) - Method in class org.jmol.script.ScriptCompiler
  look for end-of-line character \r, \n, or ; that is not within a command such as for (var i=0;i < 10; i++)
EOOP - Static variable in class org.jmol.minimize.forcefield.ForceField
eP(T3) - Static method in class org.jmol.util.Escape
  must be its own, because of the possibility of being null
eP4(P4) - Static method in class org.jmol.util.Escape
equalCount - Variable in class org.jmol.script.ScriptMathProcessor
equals(Object) - Method in class org.jmol.modelset.Atom
equals(Object) - Method in class org.jmol.script.T
equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
  The number of equivalent atom sets.
equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
  The number of equivalent atom sets.
equivalentTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
errCount - Variable in class org.openscience.jmol.app.webexport.WebPanel
error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
ERROR - Static variable in class org.jmol.script.ScriptCompiler
ERROR(int) - Method in class org.jmol.script.ScriptCompiler
ERROR(int, String) - Method in class org.jmol.script.ScriptCompiler
error - Variable in class org.jmol.script.ScriptError
error(int) - Method in class org.jmol.script.ScriptError
error - Variable in class org.jmol.script.ScriptParallelProcessor
error(int) - Method in class org.jmol.script.ScriptTokenParser
error - Static variable in class org.jmol.script.T
error(int) - Method in class org.jmol.scriptext.ScriptExt
error(String) - Method in class org.jmol.util.DefaultLogger
error(String) - Static method in class org.jmol.util.Logger
  Writes a log at ERROR level.
error(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at ERROR level.
ERROR_axisExpected - Static variable in class org.jmol.script.ScriptError
ERROR_backgroundModelError - Static variable in class org.jmol.script.ScriptError
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptError
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_badContext - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_badMillerIndices - Static variable in class org.jmol.script.ScriptError
ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptError
ERROR_booleanExpected - Static variable in class org.jmol.script.ScriptError
ERROR_booleanOrNumberExpected - Static variable in class org.jmol.script.ScriptError
ERROR_booleanOrWhateverExpected - Static variable in class org.jmol.script.ScriptError
ERROR_cannotSet - Static variable in class org.jmol.script.ScriptError
ERROR_colorExpected - Static variable in class org.jmol.script.ScriptError
ERROR_colorOrPaletteRequired - Static variable in class org.jmol.script.ScriptError
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptError
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_coordinateExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_coordinateOrNameOrExpressionRequired - Static variable in class org.jmol.script.ScriptError
ERROR_drawObjectNotDefined - Static variable in class org.jmol.script.ScriptError
ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_endOfExpressionExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptError
ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptError
ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptError
ERROR_filenameExpected - Static variable in class org.jmol.script.ScriptError
ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptError
ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
ERROR_identifierOrResidueSpecificationExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptError
ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptError
ERROR_integerExpected - Static variable in class org.jmol.script.ScriptError
ERROR_integerOutOfRange - Static variable in class org.jmol.script.ScriptError
ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptError
ERROR_invalidArgument - Static variable in class org.jmol.scriptext.CmdExt
ERROR_invalidAtomSpecification - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_invalidChainSpecification - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_invalidModelSpecification - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptError
ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptError
ERROR_missingEnd - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptError
ERROR_moIndex - Static variable in class org.jmol.script.ScriptError
ERROR_moModelError - Static variable in class org.jmol.script.ScriptError
ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptError
ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptError
ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptError
ERROR_multipleModelsNotOK - Static variable in class org.jmol.script.ScriptError
ERROR_noData - Static variable in class org.jmol.script.ScriptError
ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptError
ERROR_noUnitCell - Static variable in class org.jmol.script.ScriptError
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptError
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_numberMustBe - Static variable in class org.jmol.script.ScriptError
ERROR_numberOrVariableNameExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_numberOutOfRange - Static variable in class org.jmol.script.ScriptError
ERROR_objectNameExpected - Static variable in class org.jmol.script.ScriptError
ERROR_planeExpected - Static variable in class org.jmol.script.ScriptError
ERROR_propertyNameExpected - Static variable in class org.jmol.script.ScriptError
ERROR_residueSpecificationExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_spaceGroupNotFound - Static variable in class org.jmol.script.ScriptError
ERROR_stringExpected - Static variable in class org.jmol.script.ScriptError
ERROR_stringOrIdentifierExpected - Static variable in class org.jmol.script.ScriptError
ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_tooManyPoints - Static variable in class org.jmol.script.ScriptError
ERROR_tooManyScriptLevels - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedAtomProperty - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedBondProperty - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedCommand - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedExpression - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedExpressionToken - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_unrecognizedObject - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_unrecognizedParameterWarning - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedShowParameter - Static variable in class org.jmol.script.ScriptError
ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptTokenParser
ERROR_what - Static variable in class org.jmol.script.ScriptError
ERROR_writeWhat - Static variable in class org.jmol.script.ScriptError
errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
errorEx(String, Throwable) - Static method in class org.jmol.util.Logger
  Writes a log at ERROR level with detail on exception.
errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at ERROR level with detail on exception.
errorIntStr2(int, String, String) - Method in class org.jmol.script.ScriptTokenParser
errorLine - Variable in class org.jmol.script.ScriptTokenParser
errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
errorMessage - Variable in class org.jmol.script.ScriptContext
errorMessage - Variable in class org.jmol.script.ScriptError
errorMessage - Variable in class org.jmol.script.ScriptTokenParser
errorMessage - Variable in class org.jmol.viewer.Viewer
errorMessageUntranslated - Variable in class org.jmol.script.ScriptContext
errorMessageUntranslated - Variable in class org.jmol.script.ScriptError
errorMessageUntranslated - Variable in class org.jmol.script.ScriptTokenParser
errorMessageUntranslated - Variable in class org.jmol.viewer.Viewer
errorMore(int, String, String, String) - Method in class org.jmol.script.ScriptError
errorMsg - Variable in class org.jmol.image.AviCreator
errorOrWarn(int, String, String, String, boolean) - Method in class org.jmol.script.ScriptError
errorStr(int, String) - Method in class org.jmol.script.ScriptError
errorStr(int, String) - Method in class org.jmol.script.ScriptTokenParser
errorStr2(int, String, String) - Method in class org.jmol.script.ScriptError
errorStr2(String, String) - Method in class org.jmol.script.ScriptTokenParser
errorString(int, String, String, String, boolean) - Static method in class org.jmol.script.ScriptError
errorString(int, String, String, boolean) - Static method in class org.jmol.script.ScriptTokenParser
errorType - Variable in class org.jmol.script.ScriptContext
errorType - Variable in class org.jmol.script.ScriptError
errorType - Variable in class org.jmol.script.ScriptTokenParser
esCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
escape() - Method in class org.jmol.script.SV
Escape - Class in org.jmol.util
Escape() - Constructor for class org.jmol.util.Escape
escapeColor(int) - Static method in class org.jmol.util.Escape
escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
escapeHelical(String, int, P3, P3, T3[]) - Static method in class org.jmol.util.Escape
  Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxis
escapeHTML(String) - Static method in class org.jmol.i18n.GT
escapeMap(Map<String, Object>) - Static method in class org.jmol.util.Escape
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
escapeMultiplier(T3) - Static method in class org.jmol.util.SimpleUnitCell
  Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
escapeNice(String) - Static method in class org.jmol.util.Escape
espCharges - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
espressoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
EspressoReader - Class in org.jmol.adapter.readers.xtal
EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
ESTRBND - Static variable in class org.jmol.minimize.forcefield.ForceField
eta - Static variable in class org.jmol.script.T
ETORSION - Static variable in class org.jmol.minimize.forcefield.ForceField
eV(Lst<SV>) - Static method in class org.jmol.util.Escape
eval(String) - Method in interface org.jmol.api.JmolStatusListener
eval - Variable in exception org.jmol.script.ScriptException
eval - Variable in class org.jmol.script.ScriptManager
eval - Variable in class org.jmol.script.ScriptMathProcessor
eval(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
eval - Static variable in class org.jmol.script.T
eval - Variable in class org.jmol.thread.JmolThread
eval - Variable in class org.jmol.util.BZone
eval(String) - Method in class org.jmol.util.GenericApplet
eval - Variable in class org.jmol.viewer.Viewer
eval(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
evalError(String, String) - Method in class org.jmol.script.ScriptError
evalFile(String) - Method in interface org.jmol.api.JmolScriptManager
evalFile(String) - Method in class org.jmol.api.JmolViewer
evalFile(String) - Method in class org.jmol.script.ScriptManager
evalFile(String) - Method in class org.jmol.viewer.Viewer
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.api.JmolScriptEvaluator
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEval
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.api.JmolScriptEvaluator
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptEval
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.scriptext.CmdExt
  used for TRY command
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
evalString(String) - Method in class org.jmol.api.JmolViewer
evalString(String) - Method in class org.jmol.viewer.Viewer
evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
evalStringQuietSync(String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
evalTemp - Variable in class org.jmol.script.ScriptManager
evaluate(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
evaluate(ScriptMathProcessor, T, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateArray(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
evaluateBin(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateCache(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateColor(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateCompare(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateCompiledScript(boolean, boolean, boolean, boolean, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
evaluateCompiledScript(boolean, boolean, boolean, boolean, SB, boolean) - Method in class org.jmol.script.ScriptEval
evaluateConnected(ScriptMathProcessor, SV[], int, int) - Method in class org.jmol.scriptext.MathExt
evaluateContact(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateData(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateDotDist(ScriptMathProcessor, SV[], int, int) - Method in class org.jmol.scriptext.MathExt
  x = y.distance({atoms}) the average distance from elements of y to the CENTER of {atoms} x = {atomset1}.distance.min({atomset2}, asAtomSet) If asAtomSet is true, returns the closest atom in atomset1 to any atom of atomset2; if false or omitted, returns an array listing the distance of each atom in atomset1 to the closest atom in atomset2.
evaluateExpression(Object, boolean, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
evaluateExpression(Object) - Method in class org.jmol.api.JmolViewer
evaluateExpression(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
  a general-use method to evaluate a "SET" type expression.
evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
  synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
evaluateFind(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateFormat(ScriptMathProcessor, int, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
evaluateFunction(int) - Method in class org.jmol.script.ScriptMathProcessor
evaluateGetProperty(ScriptMathProcessor, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
  _ by itself, not as a function, is shorthand for getProperty("auxiliaryInfo") $ print _.keys boundbox group3Counts group3Lists modelLoadNote models properties someModelsHaveFractionalCoordinates someModelsHaveSymmetry someModelsHaveUnitcells symmetryRange _m by itself, not as a function, is shorthand for getProperty("auxiliaryInfo.models")[_currentFrame] $ print format("json",_m.unitCellParams) [ 0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376, 2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN ] {atomset}._ by itself delivers a subset array of auxiliaryInfo.models for all models in {atomset} $ print {*}._..1..aflowInfo (first model's aflowInfo) _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length array of information $ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]") {atomset}._(key) selects for model Auxiliary info related to models of the specified atoms {atomset}.getProperty(key) defaults to atomInfo, but also allows key to start with "bondInfo" Examples: print _("aflowInfo[select sg where volume_cell > 70]") print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
evaluateHelix(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateIn(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateList(ScriptMathProcessor, int, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateLoad(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
evaluateMath(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateMeasure(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateModulation(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluatePlane(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
  plane() or intersection()
evaluatePoint(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluatePointGroup(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluatePrompt(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateQuaternion(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateRandom(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateReplace(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateRowCol(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateScript(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
evaluateSort(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
  sort() or sort(n) or count() or count("xxxx")
evaluateSpacegroup(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateString(ScriptMathProcessor, int, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateSubstructure(ScriptMathProcessor, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
evaluateSymop(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
evaluateTensor(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateUnitCell(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
evaluateUserFunction(ScriptMathProcessor, String, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
evaluateValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
evaluateWithin(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evaluateWrite(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
evalWait(String, String, String) - Method in class org.jmol.viewer.Viewer
EVDW - Static variable in class org.jmol.minimize.forcefield.ForceField
Event - Class in org.jmol.awtjs
Event() - Constructor for class org.jmol.awtjs.Event
EventManager - Interface in org.jmol.api
eventNames - Static variable in class org.jmol.multitouch.ActionManagerMT
EX - Variable in class org.jmol.quantum.MOCalculation
excl_display_lists_shaders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
excludeAtoms(BS, boolean) - Method in class org.jmol.viewer.SelectionManager
excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
excludedTriangleCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
excludedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
excludeMaximumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
excludeMinimumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
excludePartialCubes - Variable in class org.jmol.jvxl.calc.MarchingCubes
excludeSelectionSet(BS) - Method in class org.jmol.viewer.SelectionManager
execThread - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
execute(String) - Method in class org.jmol.console.AppletConsole
execute(String) - Method in class org.jmol.console.GenericConsole
execute(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
executeCommand(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
executeCommandAsThread(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
executeCommands(boolean, boolean) - Method in class org.jmol.script.ScriptEval
ExecuteCommandThread(String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
executing - Variable in class org.jmol.script.ScriptEval
executionPaused - Variable in class org.jmol.script.ScriptContext
executionPaused - Variable in class org.jmol.script.ScriptEval
executionStepping - Variable in class org.jmol.script.ScriptContext
executionStepping - Variable in class org.jmol.script.ScriptEval
executionStopped - Variable in class org.jmol.script.ScriptEval
executor - Variable in class org.jmol.viewer.Viewer
exit - Static variable in class org.jmol.script.T
exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
exitFirstMatch - Variable in class org.jmol.smiles.SmilesSearch
exitjmol - Static variable in class org.jmol.script.T
exitJmol() - Method in class org.jmol.viewer.Viewer
exitJSpecView(boolean, Object) - Method in interface org.jmol.api.JSVInterface
exitJSpecView(boolean, Object) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
exitMeasurementMode(String) - Method in class org.jmol.viewer.ActionManager
expandFloatArray(float[], int) - Method in class org.jmol.script.ScriptEval
  Accepts a float array and expands [1 -3] to [1 2 3], for example.
expandMinMax(P3, SymmetryInterface, P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
expdta() - Method in class org.jmol.adapter.readers.pdb.PdbReader
explicitContours - Variable in class org.jmol.shapesurface.Isosurface
explicitFaces - Variable in class org.jmol.shapespecial.Polyhedra
explicitH - Variable in class org.jmol.smiles.SmilesGenerator
explicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
explicitID - Variable in class org.jmol.shape.MeshCollection
export3D - Variable in class org.jmol.export.___Exporter
Export3D - Class in org.jmol.export
Export3D() - Constructor for class org.jmol.export.Export3D
EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JC
EXPORT_NOT - Static variable in class org.jmol.util.GData
EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ExportChoiceListener() - Constructor for class org.jmol.dialog.Dialog.ExportChoiceListener
exportDone(JComponent, Transferable, int) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
exporter - Variable in class org.jmol.export.Export3D
exportName - Variable in class org.jmol.export.Export3D
exportPass - Variable in class org.jmol.render.MeshRenderer
exportScale - Variable in class org.jmol.export.___Exporter
exportscale - Static variable in class org.jmol.script.T
exportScale - Variable in class org.jmol.viewer.GlobalSettings
exportSurface(short) - Method in class org.jmol.render.MeshRenderer
exportType - Variable in class org.jmol.export.___Exporter
exportType - Variable in class org.jmol.render.ShapeRenderer
expressionBegin - Static variable in class org.jmol.script.T
expressionEnd - Static variable in class org.jmol.script.T
ext - Variable in class org.jmol.modelsetbio.BioModelSet
extendGrid - Variable in class org.jmol.jvxl.readers.Parameters
extendLadder(int, int) - Method in class org.jmol.dssx.Bridge
extendRuns(STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
extension - Variable in class org.jmol.dialog.Dialog
extensions - Variable in class org.jmol.dialog.Dialog
extents - Variable in class org.jmol.jvxl.readers.JaguarReader
externalContainer - Variable in class org.jmol.console.JmolConsole
extractFlags(String, int[]) - Static method in class org.jmol.smiles.SmilesParser
extractLatticeInfo(String) - Method in class org.jmol.symmetry.HallInfo
extractMolData(String) - Method in class org.jmol.api.JmolViewer
extractMolData(String) - Method in class org.jmol.viewer.Viewer
extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in interface org.jmol.api.JmolPropertyManager
extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in class org.jmol.viewer.PropertyManager
extractProperty(Object, Object, int) - Method in class org.jmol.viewer.Viewer
extractRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo
extractTag(String, String, String, boolean) - Static method in class org.jmol.jvxl.readers.XmlReader
extractTagOnly(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
extractVectorInfo(String) - Method in class org.jmol.symmetry.HallInfo
EY - Variable in class org.jmol.quantum.MOCalculation
EZ - Variable in class org.jmol.quantum.MOCalculation

## F

f14 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
f16 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
Face(int, int, int, P3) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Face
FACE_COUNT_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
facecenteroffset - Static variable in class org.jmol.script.T
faceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra
faceCenters - Variable in class org.jmol.util.BZone
faceIndices - Variable in class org.jmol.util.BZone
faceIndices(P3[], P3[]) - Method in class org.jmol.util.BZone
faceMap - Variable in class org.jmol.renderspecial.DotsRenderer
facePoints - Static variable in class org.jmol.util.BoxInfo
facePt1 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
facePt2 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
facePt3 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
faces - Variable in class org.jmol.shapespecial.Polyhedron
faces - Variable in class org.jmol.util.BZone
faceTriangles - Variable in class org.jmol.shapespecial.Polyhedron
faceVertexesArrays - Static variable in class org.jmol.util.Geodesic
faceVertexesIcosahedron - Static variable in class org.jmol.util.Geodesic
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
fact1 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
factoredLengths - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
factors - Variable in class org.jmol.jvxl.readers.IsoIntersectGridReader
factorType - Variable in class org.jmol.atomdata.RadiusData
FALSE - Static variable in class org.jmol.viewer.SelectionManager
falsifyMesh() - Method in class org.jmol.shapebio.BioShape
falsifyNearbyMesh(int) - Method in class org.jmol.shapebio.BioShape
FAMILY_ASSEM_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
FAMILY_CHEMCOMP_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_COMPBOND - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_COMPBOND_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_NCS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_NCS_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_OPER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_OPER_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_SEQUENCEDIF_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_SGOP - Static variable in class org.jmol.adapter.readers.cif.CifReader
FAMILY_SHEET - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_SHEET_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_STRUCSITE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_STRUCSITE_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_STRUCTCONF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_STRUCTCONF_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_STRUCTCONN - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
FAMILY_STRUCTCONN_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
fast_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fatal(String) - Method in class org.jmol.util.DefaultLogger
fatal(String) - Static method in class org.jmol.util.Logger
  Writes a log at FATAL level.
fatal(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at FATAL level.
fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger
  Writes a log at FATAL level with detail on exception.
fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at ERROR level with detail on exception.
FC - Static variable in class org.jmol.quantum.QS
fc(float) - Static method in class org.jmol.symmetry.SymmetryOperation
fc - Variable in class org.openscience.jmol.app.webexport.Test
fc - Variable in class org.openscience.jmol.app.webexport.WebPanel
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
fcadj - Variable in class org.jmol.minimize.forcefield.AtomType
fclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
fcoord(T3) - Method in interface org.jmol.api.SymmetryInterface
fcoord(T3) - Method in class org.jmol.symmetry.Symmetry
fcoord(T3) - Static method in class org.jmol.symmetry.SymmetryOperation
FD_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
fd_oldFileName - Variable in class org.jmol.awt.FileDropper
fd_propSupport - Variable in class org.jmol.awt.FileDropper
FDP_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
fetch_host - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fetch_path - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ff - Variable in class org.jmol.minimize.forcefield.Calculations
ff - Variable in class org.jmol.minimize.Minimizer
FF - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
ffAtomType - Variable in class org.jmol.minimize.MinAtom
fFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
FFParam - Class in org.jmol.minimize.forcefield
FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
ffParams - Variable in class org.jmol.minimize.forcefield.Calculations
ffParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
ffParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
ffType - Variable in class org.jmol.minimize.MinAtom
ffTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
fid - Variable in class org.jmol.modelset.Text
fid - Variable in class org.jmol.render.LabelsRenderer
fid - Variable in class org.jmol.util.Font
fidPrevious - Variable in class org.jmol.render.LabelsRenderer
fids - Variable in class org.jmol.shape.Labels
field - Variable in class org.jmol.adapter.readers.cif.CifReader
field - Variable in class org.jmol.adapter.readers.cif.MSCifParser
field_of_view - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fieldCount - Variable in class org.jmol.adapter.readers.quantum.CsfReader
fieldProperty(int) - Method in class org.jmol.adapter.readers.cif.CifReader
fieldProperty(CifReader, int) - Method in class org.jmol.adapter.readers.cif.MSCifParser
fieldTypes - Variable in class org.jmol.adapter.readers.quantum.CsfReader
FIL - Enum in org.jmol.c
FIL(int) - Constructor for enum org.jmol.c.FIL
file - Static variable in class org.jmol.script.T
file - Variable in class org.openscience.jmol.app.HistoryFile
  The location of the history file.
file - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
fileAtomCount - Variable in class org.jmol.adapter.readers.cif.MMTFReader
fileAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
fileButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
FileButton - Variable in class org.openscience.jmol.app.webexport.Test
filecachedirectory - Static variable in class org.jmol.script.T
filecaching - Static variable in class org.jmol.script.T
FileChecker(String) - Constructor for class org.jmol.console.JmolConsole.FileChecker
FileChooser - Class in org.jmol.dialog
  JFileChooser with possibility to fix size and location
FileChooser() - Constructor for class org.jmol.dialog.FileChooser
fileChooser - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
fileCoordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fileData - Variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
fileDotModel - Variable in class org.jmol.jvxl.readers.AtomDataReader
FileDropper - Class in org.jmol.awt
  A simple Dropping class to allow files to be dragged onto a target.
FileDropper(JmolStatusListener, Viewer, JmolDropEditor) - Constructor for class org.jmol.awt.FileDropper
fileField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
fileHasUnitCell - Variable in class org.jmol.popup.JmolPopup
fileHeader - Variable in class org.jmol.modelset.ModelLoader
fileIndex - Variable in class org.jmol.jvxl.readers.Parameters
fileIndex - Variable in class org.jmol.modelset.Model
fileList - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
FileLoadThread - Class in org.jmol.script
FileLoadThread(JmolScriptEvaluator, Viewer, String, String, String) - Constructor for class org.jmol.script.FileLoadThread
  JavaScript only
fileLoadThread - Variable in class org.jmol.script.ScriptEval
FileManager - Class in org.jmol.viewer
FileManager(Viewer) - Constructor for class org.jmol.viewer.FileManager
fileModelNumber - Variable in class org.jmol.adapter.readers.more.AFLOWReader
FileMolOnly - Variable in class org.jmol.popup.JmolPopup
fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fileName - Variable in class org.jmol.atomdata.AtomData
filename - Variable in class org.jmol.console.ScriptEditor
fileName - Variable in class org.jmol.export.___Exporter
fileName - Variable in class org.jmol.jvxl.readers.AtomDataReader
fileName - Variable in class org.jmol.jvxl.readers.MsmsReader
fileName - Variable in class org.jmol.jvxl.readers.Parameters
fileName - Variable in class org.jmol.script.FileLoadThread
filename - Variable in class org.jmol.script.ScriptCompiler
fileName - Variable in class org.jmol.util.JmolAudio
fileName - Variable in class org.jmol.viewer.FileManager
fileName - Variable in exception org.jmol.viewer.JmolAsyncException
fileName - Variable in class org.jmol.viewer.ModelManager
fileNameIn - Variable in class org.jmol.io.FileReader
fileOcc - Variable in class org.jmol.util.ModulationSet
fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fileOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filePath - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
FilePreview - Class in org.jmol.dialog
  File previsualisation before opening
FilePreview(Viewer, JFileChooser, boolean, Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview
  Constructor
FilePreview.FPPanel - Class in org.jmol.dialog
filePt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
FileReader - Class in org.jmol.io
FileReader(Viewer, String, String, String, String, Object, Map<String, Object>, boolean) - Constructor for class org.jmol.io.FileReader
FileReader - Class in org.openscience.jvxl
FileReader() - Constructor for class org.openscience.jvxl.FileReader
files - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filesData - Variable in class org.jmol.jvxl.readers.Parameters
fileSgName - Variable in class org.jmol.adapter.readers.pdb.PdbReader
FilesReader - Class in org.jmol.io
  open a set of models residing in different files
FilesReader() - Constructor for class org.jmol.io.FilesReader
fileStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
fileTypeIn - Variable in class org.jmol.io.FileReader
fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
FileTyper - Class in org.openscience.jmol.app.jmolpanel
FileTyper() - Constructor for class org.openscience.jmol.app.jmolpanel.FileTyper
fileTypesIn - Variable in class org.jmol.io.FilesReader
FileUnitOnly - Variable in class org.jmol.popup.JmolPopup
fileWriter(File, JList<JmolInstance>) - Method in class org.openscience.jmol.app.webexport.WebPanel
fill - Variable in class org.jmol.awtjs.swing.GridBagConstraints
fill - Static variable in class org.jmol.script.T
fill3x3(String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  fills a double[3][3]
fillADa(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
fillArc - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
fillAtomData(AtomData, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
fillBackground(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
fillBackground(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
fillBackground(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
fillCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
fillCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
fillCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.___Exporter
fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.__RayTracerExporter
fillConeScreen(P3, P3, boolean) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.export.Export3D
fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export.__RayTracerExporter
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._TachyonExporter
fillCsfArray(String, String[], int, Object, boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
fillCylinder(byte, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.export.Export3D
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
fillCylinderBits(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.export.Export3D
fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.___Exporter
fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.__CartesianExporter
fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.__RayTracerExporter
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.Export3D
fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.g3d.Graphics3D
fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.___Exporter
fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.__CartesianExporter
fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.__RayTracerExporter
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
fillDataBlockFixed(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format.
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in interface org.jmol.api.JmolRendererInterface
fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3[]) - Method in class org.jmol.export.___Exporter
fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3[]) - Method in class org.jmol.export.__CartesianExporter
fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3[]) - Method in class org.jmol.export.__RayTracerExporter
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.export.Export3D
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.Graphics3D
fillFloat(float[], int, int) - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  fills a float array with string data from a file
fillFloatArrayFromBytes(byte[], float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int, String[][]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  Extracts a block of frequency data from a file.
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
fillIntArrayFromBytes(byte[], int[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
fillOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
fillPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fillRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
fillRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
fillRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
fillSlater(int[], int, int, int) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
fillSphere(short, int, P3) - Method in class org.jmol.export.___Exporter
fillSphere(short, int, P3) - Method in class org.jmol.export.__CartesianExporter
fillSphere(short, int, P3) - Method in class org.jmol.export.__RayTracerExporter
fillSphereBits(int, P3) - Method in interface org.jmol.api.JmolRendererInterface
  fills a solid sphere
fillSphereBits(int, P3) - Method in class org.jmol.export.Export3D
  fills a solid sphere
fillSphereBits(int, P3) - Method in class org.jmol.g3d.Graphics3D
  fills a solid sphere
fillSphereI(int, P3i) - Method in interface org.jmol.api.JmolRendererInterface
  fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.export.Export3D
  fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.g3d.Graphics3D
  fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.export.Export3D
  fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
  fills a solid sphere
fillTextRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
  fills background rectangle for label
fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
  fills background rectangle for label
fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
  fills background rectangle for label
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.___Exporter
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__CartesianExporter
fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__RayTracerExporter
fillTriangle(P3i, P3i, P3i, boolean) - Method in class org.jmol.g3d.TriangleRenderer
fillTriangle() - Method in class org.jmol.rendercgo.CGORenderer
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.export.Export3D
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.export.Export3D
fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3f(P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.export.Export3D
fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangleP3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangles - Variable in class org.jmol.shape.Mesh
fillTriangleTwoSided(short, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.export.Export3D
fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filter - Static variable in class org.jmol.script.T
filter1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filter2 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAltLoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAtomName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAtomNameTerminator - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAtomType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterAtomTypeStr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterChain - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterCIFAtom(Atom, String) - Method in class org.jmol.adapter.readers.cif.CifReader
filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
filterElement - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterEveryNth - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterGroup3 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterIsNot - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  check line for filter options
filterMOs - Variable in class org.jmol.adapter.writers.QCJSONWriter
filterN - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterPDBAtom(Atom, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterShow(String, String) - Method in class org.jmol.scriptext.CmdExt
filterSymop - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
filterSymop - Variable in class org.jmol.adapter.smarter.XtalSymmetry
filterTokens - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
finalize() - Method in class org.jmol.viewer.Viewer
finalizeAromatic(Node[], BS, Lst<BS>, Lst<SmilesRing>, int[], boolean, boolean) - Static method in class org.jmol.smiles.SmilesAromatic
  Iteratively trims a set of aromatic atoms that may be initially assigned to be aromatic but because their double bonds extend to non-aromatic atoms must be removed.
finalizeAtoms(BS, boolean) - Method in class org.jmol.viewer.ShapeManager
finalized - Variable in class org.jmol.adapter.readers.cif.MSRdr
finalizeEdges() - Method in class org.jmol.adapter.readers.xtal.CgdReader
  Now that we have all the edge data we can add edges to atoms
finalizeGroupBuild() - Method in class org.jmol.modelset.ModelLoader
finalizeHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
finalizeLoad(boolean, boolean, boolean, boolean, int, int, int) - Method in class org.jmol.script.ScriptEval
finalizeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
finalizeMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeModel() - Method in class org.jmol.adapter.readers.more.AFLOWReader
finalizeModels(int) - Method in class org.jmol.modelset.ModelLoader
  Model numbers are considerably more complicated in Jmol 11.
finalizeModelSet() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
finalizeModelSet() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeModulation() - Method in class org.jmol.adapter.readers.cif.MSRdr
  Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.
finalizeModulation() - Method in interface org.jmol.adapter.smarter.MSInterface
finalizeNet() - Method in class org.jmol.adapter.readers.xtal.CgdReader
  Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
finalizeObject(PyMOLScene, ModelSet, String, boolean) - Method in class org.jmol.adapter.readers.pymol.JmolObject
finalizeObject(int, int, float, int, boolean, Object, int, BS) - Method in class org.jmol.scriptext.ScriptExt
finalizeObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Finally, we turn each JmolObject into its Jmol equivalent.
finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
finalizeOutput() - Method in class org.jmol.export.___Exporter
finalizeOutput() - Method in class org.jmol.export._IdtfExporter
finalizeOutput() - Method in class org.jmol.export._ObjExporter
finalizeOutput() - Method in class org.jmol.export._PovrayExporter
finalizeOutput() - Method in class org.jmol.export._StlExporter
finalizeOutput() - Method in class org.jmol.export.Export3D
finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
finalizeOutput2() - Method in class org.jmol.export.___Exporter
finalizeOutput2() - Method in class org.jmol.export.__RayTracerExporter
finalizePdbCharges() - Method in class org.jmol.modelsetbio.BioResolver
finalizePdbMultipleBonds() - Method in class org.jmol.modelsetbio.BioResolver
finalizeReaderASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeReaderMR() - Method in class org.jmol.adapter.readers.molxyz.MolReader
finalizeReaderPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
finalizeRna3d(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
finalizeSceneData() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Make sure atom uniqueID (vectorX) and cartoonType (vectorY) are made permanent
finalizeShapes() - Method in class org.jmol.modelset.ModelLoader
finalizeStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.CifReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.P2nReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.InputReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  Set final auxiliary info and symmetry, including "fileHeader", "magresUnits", and "interactionTensors"; note that print getProperty("auxiliaryInfo.models[1].magresUnits") should return a catalog of tensor types.
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
finalizeSubclassReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  optional reader-specific method run first.
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finalizeSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
finalizeTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
finalizeTrajectoryAs(Lst<P3[]>, Lst<V3[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
finalizeUniqueBonds() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
finalizeUnitCell(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
  Ensure that ModelLoader sets up the supercell unit cell.
finalizeValidations(Viewer, Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
  Create property_xxxx for each validation category.
finalizeVisibility() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Create group JmolObjects, and set hierarchical visibilities
finalizeZone(BZone) - Method in class org.jmol.util.BZone
  Finalize a Brillouin zone.
finalOperations - Variable in class org.jmol.symmetry.SpaceGroup
find(String, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
find(Lst<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
find - Static variable in class org.jmol.script.T
find(Measurement) - Method in class org.jmol.shape.Measures
find(String, String, int) - Method in class org.jmol.smiles.SmilesMatcher
  Searches for all matches of a pattern within a SMILES string.
find(String, int) - Method in class org.jmol.util.CommandHistory
findAdditionalAxes(int) - Method in class org.jmol.symmetry.PointGroup
findAnnotationAtoms(Viewer, String, Lst<SV>, String, BS) - Method in class org.jmol.dssx.AnnotationParser
  find annotations; allows for wild cards InterPro.* where .....
findApplets(String, String, String, Lst<String>) - Static method in class org.jmol.util.GenericApplet
findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
findAtom(int, int, int, int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
findAtom(P3) - Method in class org.jmol.adapter.readers.xtal.CgdReader
findAtomDipole(Atom, Atom, boolean) - Method in class org.jmol.shapespecial.Dipoles
findAtomForRange(int, int, int, int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
findAtomsInRectangle(Rectangle) - Method in class org.jmol.modelset.ModelSet
findAtomsLike(String) - Method in class org.jmol.modelset.Atom
findAtomsLike(String) - Method in class org.jmol.smiles.SmilesAtom
findAtomsLike(String) - Method in interface org.jmol.util.Node
findBestFit(int, int[]) - Static method in class org.jmol.util.TempArray
findBondDipole(Bond) - Method in class org.jmol.shapespecial.Dipoles
findCAxes() - Method in class org.jmol.symmetry.PointGroup
findCumulativeCenter(CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataSmiles
findDipole(String) - Method in class org.jmol.shapespecial.Dipoles
findDipoleFor(String, String) - Method in class org.jmol.shapespecial.Dipoles
findEdge(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
findElementsPresent() - Method in class org.jmol.modelset.ModelLoader
findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Have the vwr show a particular frame with frequencies if it can be found.
findHelixes(int, int[][][]) - Method in class org.jmol.dssx.DSSP
  (p.
findHelixes2(int, int, int, int[][][], STR, int, BS, boolean) - Method in class org.jmol.dssx.DSSP
findImplicitHydrogen(Node) - Method in class org.jmol.smiles.SmilesSearch
findInversionCenter() - Method in class org.jmol.symmetry.PointGroup
findLeftLeaf() - Method in class org.jmol.bspt.CubeIterator
  does the work
findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
findModelById(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
findMonomer(BS, boolean) - Method in class org.jmol.modelsetbio.ProteinStructure
findNearest2(int, int, Atom[], BS, int) - Method in class org.jmol.modelset.AtomCollection
findNearestAtom(int, int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
findNearestAtomIndex(int, int, BS, int) - Method in class org.jmol.modelset.ModelSet
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.AminoMonomer
findNearestAtomIndex(int, int, Atom[], short[], int, BS) - Method in class org.jmol.modelsetbio.BioPolymer
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.Monomer
  Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shape.Shape
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShape
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShapeCollection
findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
findNearestAtomIndexMovable(int, int, boolean) - Method in class org.jmol.viewer.Viewer
findNearestLabel(int, int) - Method in class org.jmol.shape.Labels
findNearestShapeAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.viewer.ShapeManager
findNearestThreePoints(float, float, float[][], int[]) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
findNearestVertex(Lst<MeshCapper.CapVertex>, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  Find the nearest vertex to v0 in the list v1s.
findNotAttached(int, int[][], int[], int) - Method in class org.jmol.modelset.AtomCollection
findPickedBond(int, int, BS, P3, int[]) - Method in class org.jmol.shape.Sticks
findPickedObject(int, int, boolean, BS) - Method in class org.jmol.shapespecial.Draw
findPickedObject(int, int, boolean, BS) - Method in class org.jmol.shapespecial.Ellipsoids
findPlanes() - Method in class org.jmol.symmetry.PointGroup
findPoly(String, int, boolean) - Method in class org.jmol.shapespecial.Polyhedra
findPolyBS(BS) - Method in class org.jmol.shapespecial.Polyhedra
findPriv(String, SmilesSearch, int, int) - Method in class org.jmol.smiles.SmilesMatcher
findRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
findSet(int) - Method in class org.jmol.jvxl.data.MeshData
findShorter(int, int[]) - Static method in class org.jmol.util.TempArray
findSpaceGroup(int, String) - Static method in class org.jmol.symmetry.SpaceGroup
findString - Variable in class org.jmol.jvxl.readers.KinemageReader
findValue(int, int, boolean, BS) - Method in class org.jmol.shapesurface.Isosurface
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollection
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
finish(Object) - Method in class org.jmol.api.JmolAdapter
FINISH - Static variable in class org.jmol.thread.JmolThread
first - Variable in class org.jmol.modelset.TickInfo
first - Static variable in class org.jmol.script.T
firstAtom - Variable in class org.jmol.adapter.readers.cif.CifReader
firstAtom - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
firstAtom - Variable in class org.jmol.adapter.smarter.XtalSymmetry
firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
firstAtomIndex - Variable in class org.jmol.modelset.Group
firstAtomIndex - Variable in class org.jmol.modelset.Model
firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
firstAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
firstChar - Variable in class org.jmol.adapter.readers.cif.CifReader
firstFrameDelay - Variable in class org.jmol.viewer.AnimationManager
firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
firstFrameIndex - Variable in class org.jmol.viewer.AnimationManager
firstIsotope - Static variable in class org.jmol.util.Elements
  first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstLastStep - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
firstLine - Variable in class org.jmol.adapter.readers.simple.InputReader
firstLine - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
firstModelIndex - Variable in class org.jmol.atomdata.AtomData
firstMoleculeIndex - Variable in class org.jmol.modelset.Model
firstNearbyAtom - Variable in class org.jmol.jvxl.readers.AtomDataReader
firstPosition - Variable in class org.jmol.adapter.readers.xtal.JanaReader
firstProper - Static variable in class org.jmol.symmetry.PointGroup
firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
fit_iterations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fit_kabsch - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fit_tolerance - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fix(String) - Static method in class org.jmol.i18n.Resource
fix(float) - Method in class org.jmol.symmetry.UnitCell
fixACDAtomList(String, Map<String, String>, int) - Method in class org.jmol.jsv.JDXMOLParser
fixAnnotations(int, String, int) - Method in class org.jmol.modelsetbio.BioResolver
fixAtom(Atom) - Method in class org.jmol.modelset.Trajectory
fixAtomForBonding(P3, int) - Method in class org.jmol.adapter.readers.cif.CifReader
fixAtomName(String) - Static method in class org.jmol.adapter.readers.xtal.CrystalReader
  MN33 becomes Mn33
fixAtoms(int, SV, BS, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
fixAtoms(int, SV, BS, int, int) - Method in class org.jmol.dssx.AnnotationParser
  Adjusts _atoms bitset to account for added hydrogen atoms.
fixBaseIndices() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
fixChirality(SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
fixCoefficients(double[]) - Method in class org.jmol.adapter.writers.QCJSONWriter
  Jmol allows for a set of arrays that map coefficient indicies with nonstandard order to Gaussian/Molden order.
fixD(float, boolean) - Method in class org.jmol.modelset.BondCollection
fixDataString(String) - Static method in class org.jmol.util.Parser
fixDOSName(String) - Static method in class org.jmol.viewer.FileManager
  Switch \ for / only for DOS names such as C:\temp\t.xyz, not names like http://cactus.nci.nih.gov/chemical/structure/CC/C=C\CC
fixDouble(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
fixDSSRJSONMap(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
  kissingLoops and coaxStacks use index arrays instead of duplication;
fixed - Static variable in class org.jmol.script.T
fixedCount - Variable in class org.jmol.jvxl.readers.PmeshReader
fixedLattice - Variable in class org.jmol.jvxl.data.JvxlData
fixedOrigin - Variable in class org.jmol.shape.Axes
fixedOriginUC - Variable in class org.jmol.shape.Axes
fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
fixedRotationCenter - Variable in class org.jmol.export.___Exporter
fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
fixedtemp - Static variable in class org.jmol.script.T
fixedTranslation - Variable in class org.jmol.viewer.TransformManager
fixEndsAndSortVertices(MeshCapper.CapVertex[]) - Method in class org.jmol.util.MeshCapper
  Generate yxNext links based on scanning Y large to small and if Y1==Y2, then X small to large
fixExplicitFaceWinding(int[], int, P3[], V3[]) - Method in class org.jmol.shapespecial.Polyhedra
  Check to see that the winding of the explicit face is correct.
fixFlowAddLine(ScriptFlowContext) - Method in class org.jmol.script.ScriptCompiler
fixFormalCharges(BS) - Method in class org.jmol.modelset.AtomCollection
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.PopInJmol
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.WebPanel
fixIndices(Map<String, Object>, String, String) - Method in class org.jmol.dssx.DSSR1
  create a key/value pair root+"s" for all indices of root+"_indices"
fixIndices(int, BS) - Method in class org.jmol.modelset.Chain
fixIndices(int, BS) - Method in class org.jmol.modelset.Group
fixIndices(int, int, BS) - Method in class org.jmol.modelset.Model
fixIndices(int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
fixIndicesM(int, int, BS) - Method in class org.jmol.modelset.Model
fixInlineString(String, char) - Static method in class org.jmol.viewer.Viewer
fixIntegration() - Static method in class org.jmol.adapter.writers.QCJSONWriter
  When an MO is calculated in Jmol, Jmol will check the integration so that it can be checked to be close to 1.0000.
fixJavaFloat - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
fixJMEFormalCharges(BS, String) - Method in interface org.jmol.api.JmolPropertyManager
fixJMEFormalCharges(BS, String) - Method in class org.jmol.viewer.PropertyManager
  Fix a JME string returned from NCI CIR to have the proper formal charges.
fixLabel(Atom, String) - Method in class org.jmol.render.HoverRenderer
fixLattice() - Method in class org.jmol.shapesurface.IsosurfaceMesh
fixLegendre() - Method in class org.jmol.adapter.readers.cif.MSRdr
fixLineFolding(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  allow white space between \ and \n
fixLocal(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
fixMagneticXYZ(M4, String, boolean) - Method in class org.jmol.symmetry.SymmetryOperation
fixMinus(String) - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
fixModelSpec(T) - Method in class org.jmol.script.ScriptTokenParser
fixMovieCommands(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Could possibly implement something here that interprets PyMOL script commands.
fixMovieViews(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Could implement something here that creates a Jmol view.
fixName(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
fixName(String) - Static method in class org.jmol.util.ColorEncoder
fixOrbitalType() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
fixOrder(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
fixOrder(int[], int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
fixPath(String) - Static method in class org.jmol.viewer.FileManager
fixPDBFormat(Lst<String>, Map<String, Integer>, OC, int[], int) - Method in class org.jmol.viewer.PropertyManager
  must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.
fixPeriodic(P3, P3) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
fixPoint(float, float) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
fixPropertyValue(BS, Object, boolean) - Method in class org.jmol.modelsetbio.BioResolver
fixProtocol(String) - Static method in class org.jmol.viewer.JC
  Check for databases that have changed from http:// to https:// over time.
fixRadius(float) - Static method in class org.jmol.adapter.readers.pdb.PdbReader
fixReps(BS[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
fixScreenZ(int) - Method in class org.jmol.export.___Exporter
fixScriptPath(String, String) - Method in class org.jmol.script.ScriptEval
fixSelectQuotes(String) - Method in class org.jmol.viewer.PropertyManager
fixSerialName(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
fixSettings(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Recent PyMOL files may not have all settings.
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
fixStereo(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
  Check number of connections and permute them to match a canonical version
fixTag(String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Returns a modified identifier for a tag, so that the element can be determined from it in the `Atom`.
fixTitleLine(int, Map<String, Object>) - Method in class org.jmol.jvxl.readers.IsoMOReader
fixToken(int) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
fixTrajectory(Atom) - Method in class org.jmol.modelset.AtomCollection
fixTypeOrder(int[], int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
fixTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
fixUnits(String) - Static method in class org.jmol.modelset.Measurement
fixValue(String, boolean) - Method in class org.jmol.modelset.Measurement
fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
FLAG_exfoliate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_ignore - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_inorganic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_MASK - Static variable in class org.jmol.modelset.Atom
FLAG_no_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_NOSURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_organic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_polymer - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAG_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FLAGS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
flags - Variable in class org.jmol.smiles.SmilesGenerator
flags - Variable in class org.jmol.smiles.SmilesParser
flags - Variable in class org.jmol.smiles.SmilesSearch
flat - Static variable in class org.jmol.script.T
FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
flipLighting(int) - Method in class org.jmol.shape.Mesh
fList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
flistValue(T, int) - Static method in class org.jmol.script.SV
float_labels - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
floatArraySet(int, int, int) - Method in class org.jmol.scriptext.IsoExt
floatArraySetXYZ(int, int, int, int) - Method in class org.jmol.scriptext.IsoExt
floatAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
floatparam - Static variable in class org.jmol.script.T
floatParameter(int) - Method in class org.jmol.script.ScriptParam
floatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
floatParameterRange(int, float, float) - Method in class org.jmol.script.ScriptParam
floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptParam
  process a general string or set of parameters as an array of floats, allowing for relatively free form input
floatproperty - Static variable in class org.jmol.script.T
floatRange - Variable in class org.jmol.shapebio.BioShape
floats - Variable in class org.jmol.adapter.readers.xtal.JanaReader
floatsAt(Lst<Object>, int, float[], int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
floatSecondsTotal - Variable in class org.jmol.navigate.Navigator
floatSecondsTotal - Variable in class org.jmol.thread.MoveToThread
floatSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
floatValue() - Method in class org.jmol.script.ScriptTokenParser
flowCommand - Static variable in class org.jmol.script.T
flowContext - Variable in class org.jmol.script.ScriptCompiler
FlowLayout - Class in org.jmol.awtjs.swing
FlowLayout() - Constructor for class org.jmol.awtjs.swing.FlowLayout
flowStart(T) - Method in class org.jmol.script.ScriptCompiler
flush(Object) - Static method in class org.jmol.awt.Image
flushCaches() - Method in class org.jmol.util.Shader
flushImage(Object) - Method in interface org.jmol.api.GenericPlatform
flushImage(Object) - Method in class org.jmol.awt.Platform
flushImage(Object) - Method in class org.jmol.awtjs2d.Platform
flushQueue(String) - Method in class org.jmol.script.ScriptManager
fm - Variable in class org.jmol.adapter.readers.spartan.SpartanUtil
fm - Variable in class org.jmol.io.DOMReader
fm - Variable in class org.jmol.io.FilesReader
fm - Variable in class org.jmol.viewer.Viewer
fmt(int) - Method in class org.jmol.applet.Jmol
fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
FO_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
foccupancy - Variable in class org.jmol.adapter.smarter.Atom
fog - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fog_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
FoldingXyzReader - Class in org.jmol.adapter.readers.simple
  This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
font - Variable in class org.jmol.applet.AppletWrapper
font - Variable in class org.jmol.g3d.TextString
font - Variable in class org.jmol.modelset.Text
font - Static variable in class org.jmol.script.T
FONT - Static variable in class org.jmol.shapecgo.CGOMesh
Font - Class in org.jmol.util
  Provides font support using a byte fid (Font ID) as an index into font table.
Font(FontManager, byte, int, int, float, float, Object) - Constructor for class org.jmol.util.Font
font - Variable in class org.jmol.util.Font
font3d - Variable in class org.jmol.render.FontLineShapeRenderer
font3d - Variable in class org.jmol.shape.FontLineShape
font3d - Variable in class org.jmol.shape.Frank
font3d - Variable in class org.jmol.shape.Measures
font3ds - Static variable in class org.jmol.util.Font
FONT_ALLOCATION_UNIT - Static variable in class org.jmol.util.Font
FONT_AXES - Static variable in class org.jmol.shapecgo.CGOMesh
FONT_FACE_MONO - Static variable in class org.jmol.util.Font
FONT_FACE_SANS - Static variable in class org.jmol.util.Font
FONT_FACE_SERIF - Static variable in class org.jmol.util.Font
FONT_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
FONT_STYLE_BOLD - Static variable in class org.jmol.util.Font
FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.util.Font
FONT_STYLE_ITALIC - Static variable in class org.jmol.util.Font
FONT_STYLE_PLAIN - Static variable in class org.jmol.util.Font
FONT_VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
fontAscent - Variable in class org.jmol.applet.AppletWrapper
fontButton - Variable in class org.jmol.console.ScriptEditor
fontButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
fontcaching - Static variable in class org.jmol.script.T
fontCaching - Variable in class org.jmol.viewer.GlobalSettings
fontChild - Variable in class org.jmol.export._VrmlExporter
fontFace - Static variable in class org.jmol.applet.AppletWrapper
fontFace - Variable in class org.jmol.export._VrmlExporter
FONTFACE - Static variable in class org.jmol.shape.Echo
FONTFACE - Static variable in class org.jmol.shape.Hover
fontFace - Variable in class org.jmol.util.Font
fontFaces - Static variable in class org.jmol.util.Font
fontHeight - Variable in class org.jmol.applet.AppletWrapper
fontkeyCount - Static variable in class org.jmol.util.Font
fontkeys - Static variable in class org.jmol.util.Font
FontLineShape - Class in org.jmol.shape
FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
FontLineShapeRenderer - Class in org.jmol.render
FontLineShapeRenderer() - Constructor for class org.jmol.render.FontLineShapeRenderer
FontManager - Interface in org.jmol.api
  A generic interface for font queries.
fontMetrics - Variable in class org.jmol.applet.AppletWrapper
fontMetrics - Variable in class org.jmol.util.Font
fontScale - Variable in class org.jmol.modelset.Text
fontScale - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
fontscaling - Static variable in class org.jmol.script.T
fontScaling - Variable in class org.jmol.viewer.GlobalSettings
fontSize - Variable in class org.jmol.applet.AppletWrapper
fontSize - Variable in class org.jmol.console.ScriptEditor
fontSize - Variable in class org.jmol.export._VrmlExporter
fontsize - Static variable in class org.jmol.script.T
FONTSIZE - Static variable in class org.jmol.shape.Echo
FONTSIZE - Static variable in class org.jmol.shape.Hover
fontSize - Variable in class org.jmol.util.Font
fontSize - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
fontSizeDivisor - Static variable in class org.jmol.applet.AppletWrapper
fontSizeNominal - Variable in class org.jmol.util.Font
fontStringWidth(Font, String) - Method in interface org.jmol.api.FontManager
fontStringWidth(Font, String) - Method in class org.jmol.awt.Platform
fontStringWidth(Font, String) - Method in class org.jmol.awtjs2d.Platform
fontStyle - Variable in class org.jmol.export._VrmlExporter
FONTSTYLE - Static variable in class org.jmol.shape.Hover
fontStyle - Variable in class org.jmol.util.Font
fontStyles - Static variable in class org.jmol.util.Font
FOOP - Static variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
FOOPD - Static variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
FOP_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
force - Variable in class org.jmol.minimize.MinAtom
forceAsyncLoad(String) - Method in interface org.jmol.api.GenericPlatform
forceAsyncLoad(String) - Method in class org.jmol.awt.Platform
forceAsyncLoad(String) - Method in class org.jmol.awtjs2d.Platform
forceautobond - Static variable in class org.jmol.script.T
forceAutoBond - Variable in class org.jmol.viewer.GlobalSettings
forceEndIf - Variable in class org.jmol.script.ScriptFlowContext
ForceField - Class in org.jmol.minimize.forcefield
ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
forcefield - Static variable in class org.jmol.script.T
forceField - Variable in class org.jmol.viewer.GlobalSettings
ForceFieldMMFF - Class in org.jmol.minimize.forcefield
  MMFF94 implementation 5/14/2012 - fully validated for atom types and charges - reasonably well validated for energies (see below) - TODO: add UFF for preliminary/backup calculation
ForceFieldMMFF(Minimizer) - Constructor for class org.jmol.minimize.forcefield.ForceFieldMMFF
ForceFieldReader - Class in org.jmol.adapter.readers.more
ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
ForceFieldUFF - Class in org.jmol.minimize.forcefield
ForceFieldUFF(Minimizer) - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
forceFlowContext - Variable in class org.jmol.script.ScriptCompiler
forceFlowEnd(T) - Method in class org.jmol.script.ScriptCompiler
forceNoAddHydrogens - Variable in class org.jmol.script.ScriptEval
forcePacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
forceShowTriangles - Variable in class org.jmol.render.MeshRenderer
forceSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
forcmd - Static variable in class org.jmol.script.T
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
  ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
FORMALCHARGE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
formalCharge - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
formalCharge - Variable in class org.jmol.adapter.smarter.Atom
formalCharge - Variable in class org.jmol.minimize.forcefield.AtomType
formalcharge - Static variable in class org.jmol.script.T
formalChargeAndFlags - Variable in class org.jmol.modelset.Atom
format(float, String, T3) - Method in class org.jmol.modelset.LabelToken
format(SV[], int) - Static method in class org.jmol.script.SV
  Accepts arguments from the format() function First argument is a format string.
format - Static variable in class org.jmol.script.T
formatAngle(float) - Method in class org.jmol.modelset.Measurement
formatDistance(String) - Method in class org.jmol.modelset.Measurement
formatLabel(Viewer, Atom, String, P3) - Method in class org.jmol.modelset.LabelToken
formatLabelAtomArray(Viewer, Atom, LabelToken[], char, int[], P3) - Static method in class org.jmol.modelset.LabelToken
  returns a formatted string based on the precompiled label tokens
formatLabelBond(Viewer, Bond, LabelToken[], Map<String, Object>, int[], P3) - Static method in class org.jmol.modelset.LabelToken
formatLabelMeasure(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
formatMeasurementAs(String, String, boolean) - Method in class org.jmol.modelset.Measurement
formatNumber(float) - Method in class org.jmol.adapter.writers.QCJSONWriter
formats - Variable in class org.jmol.shape.Labels
formatString(float, String, String) - Method in class org.jmol.modelset.Measurement
formatText(JmolViewer, String) - Static method in class org.jmol.util.Txt
formul() - Method in class org.jmol.adapter.readers.pdb.PdbReader
formula - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
forPoint3 - Variable in class org.jmol.script.ScriptCompiler
forThermalEllipsoid - Variable in class org.jmol.util.Tensor
fortyEighthsOf(float) - Static method in class org.jmol.symmetry.SymmetryOperation
fortyeigths - Static variable in class org.jmol.symmetry.SymmetryOperation
forVars - Variable in class org.jmol.script.ContextToken
forVars - Variable in class org.jmol.script.ScriptContext
foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
foundDistance2() - Method in class org.jmol.bspt.CubeIterator
  After calling nextElement(), allows one to find out the value of the distance squared.
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
foundDistance2() - Method in class org.jmol.symmetry.UnitCellIterator
foundDuringLastSync - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
fourdots - Static variable in class org.jmol.render.FontLineShapeRenderer
FPAR - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
FPPanel(Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview.FPPanel
fps - Static variable in class org.jmol.script.T
fps - Variable in class org.jmol.thread.MoveToThread
FPS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Maximum value for the fps slider.
fpsSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
fracB - Variable in class org.jmol.adapter.readers.more.AFLOWReader
fracs - Variable in class org.jmol.util.MeshSlicer
FRACT_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
FRACT_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
FRACT_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
fractionalizeCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fractionalOffset - Variable in class org.jmol.symmetry.UnitCell
fractionalOrigin - Variable in class org.jmol.util.SimpleUnitCell
fractionalPoint - Variable in class org.jmol.script.ScriptParam
fractionalrelative - Static variable in class org.jmol.script.T
fractionalRelative - Variable in class org.jmol.viewer.GlobalSettings
fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
fractionPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
fracx - Static variable in class org.jmol.script.T
fracxyz - Static variable in class org.jmol.script.T
fracy - Static variable in class org.jmol.script.T
fracz - Static variable in class org.jmol.script.T
frame - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
frame - Static variable in class org.jmol.script.T
frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
FRAME_FIRST - Static variable in class org.jmol.viewer.AnimationManager
FRAME_LAST - Static variable in class org.jmol.viewer.AnimationManager
frameControl(int) - Method in class org.jmol.script.ScriptEval
frameDelay - Variable in class org.jmol.modelset.Model
frameObj - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
frameOffset - Variable in class org.jmol.viewer.TransformManager
frameOffsets - Variable in class org.jmol.viewer.TransformManager
framePointer1 - Variable in class org.jmol.thread.AnimationThread
framePointer2 - Variable in class org.jmol.thread.AnimationThread
frames - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
FramesOnly - Variable in class org.jmol.popup.JmolPopup
frameStep - Variable in class org.jmol.viewer.AnimationManager
frameTimeMillis - Variable in class org.jmol.navigate.Navigator
frameTimeMillis - Variable in class org.jmol.thread.MoveToThread
frameTitles - Variable in class org.jmol.modelset.ModelSet
frank - Static variable in class org.jmol.script.T
Frank - Class in org.jmol.shape
Frank() - Constructor for class org.jmol.shape.Frank
frankAscent - Variable in class org.jmol.shape.Frank
frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
frankDescent - Variable in class org.jmol.shape.Frank
frankList - Variable in class org.jmol.popup.JmolPopup
frankMargin - Static variable in class org.jmol.shape.Frank
frankOn - Variable in class org.jmol.viewer.Viewer
frankPopup - Variable in class org.jmol.popup.JmolGenericPopup
FrankRenderer - Class in org.jmol.render
FrankRenderer() - Constructor for class org.jmol.render.FrankRenderer
frankString - Variable in class org.jmol.shape.Frank
frankWidth - Variable in class org.jmol.shape.Frank
freeBonds - Variable in class org.jmol.modelset.BondCollection
freeEnum - Variable in class org.jmol.util.TempArray
freeEnumSize - Static variable in class org.jmol.util.TempArray
freePoints - Variable in class org.jmol.util.TempArray
freePointsSize - Static variable in class org.jmol.util.TempArray
freeScreens - Variable in class org.jmol.util.TempArray
freeScreensSize - Static variable in class org.jmol.util.TempArray
freeTempArrays() - Method in class org.jmol.renderbio.BioShapeRenderer
freeTempEnum(STR[]) - Method in class org.jmol.util.TempArray
freeTempEnum(STR[]) - Method in class org.jmol.viewer.Viewer
freeTempPoints(P3[]) - Method in class org.jmol.util.TempArray
freeTempPoints(P3[]) - Method in class org.jmol.viewer.Viewer
freeTempScreens(P3i[]) - Method in class org.jmol.util.TempArray
freeTempScreens(P3i[]) - Method in class org.jmol.viewer.Viewer
freeze(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
freeze() - Method in class org.jmol.modelset.Model
freeze() - Method in class org.jmol.modelset.ModelLoader
freeze() - Method in class org.jmol.modelsetbio.BioModel
freezeM() - Method in class org.jmol.modelset.Model
freezeModels() - Method in class org.jmol.modelset.ModelSet
freqAtom0 - Variable in class org.jmol.adapter.readers.simple.AmpacReader
fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
FRIENDLY - Static variable in class org.jmol.util.ColorEncoder
from - Static variable in class org.jmol.script.T
fromOABC(T3[], boolean) - Static method in class org.jmol.symmetry.UnitCell
  A special constructor for spacially defined unit cells.
fromParams(float[], boolean) - Static method in class org.jmol.symmetry.UnitCell
front - Static variable in class org.jmol.script.T
frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
frontedges - Static variable in class org.jmol.script.T
frontlit - Static variable in class org.jmol.script.T
frontOnly - Variable in class org.jmol.render.MeshRenderer
frontOnly - Variable in class org.jmol.renderspecial.PolyhedraRenderer
frontonly - Static variable in class org.jmol.script.T
frontOnly - Variable in class org.jmol.shape.Mesh
frontonly - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
FS - Static variable in class org.jmol.quantum.QS
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
fScrPt - Variable in class org.jmol.viewer.TransformManager
fset0 - Variable in class org.jmol.render.UccageRenderer
fslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
fSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
fStep - Variable in class org.jmol.thread.MoveToThread
FSTRETCH - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
FU_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
full - Static variable in class org.jmol.script.T
full_screen - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
fullCommand - Variable in class org.jmol.script.ScriptEval
fullCommand - Variable in class org.jmol.shapesurface.LcaoCartoon
fullCubePolygon - Static variable in class org.jmol.util.Triangulator
fullName - Variable in class org.jmol.awtjs2d.JSFile
fullName - Variable in class org.jmol.util.GenericApplet
fullName - Variable in class org.jmol.viewer.Viewer
fullPathName - Variable in class org.jmol.viewer.FileManager
fullPathNameIn - Variable in class org.jmol.io.FileReader
fullPathNamesIn - Variable in class org.jmol.io.FilesReader
fullplane - Static variable in class org.jmol.script.T
fullSymmetry - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
fullylit - Static variable in class org.jmol.script.T
func - Variable in class org.jmol.jvxl.readers.IsoFxyReader
func - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
func - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
func - Variable in class org.jmol.jvxl.readers.Parameters
function - Variable in class org.jmol.script.ScriptFlowContext
function - Static variable in class org.jmol.script.T
functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
functionName - Variable in class org.jmol.script.ScriptContext
functionName - Variable in class org.jmol.script.ScriptEval
functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
  for isosurface FUNCTIONXY
functionxy - Static variable in class org.jmol.script.T
functionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
functionXY(String, int, int) - Method in class org.jmol.viewer.StatusManager
functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
  fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
functionXY(String, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
  this is just a test method for isosurface FUNCTIONXY
functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
  for isosurface FUNCTIONXYZ
functionxyz - Static variable in class org.jmol.script.T
functionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.StatusManager
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
FUP_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
fux - Static variable in class org.jmol.script.T
fuxyz - Static variable in class org.jmol.script.T
fuy - Static variable in class org.jmol.script.T
fuz - Static variable in class org.jmol.script.T
fval(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
fValue(T) - Static method in class org.jmol.script.SV
FWV_DISP_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_DISP_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_DISP_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_DISP_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_DISP_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_DISP_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_DISP_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_OCC_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_OCC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_OCC_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_OCC_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_OCC_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_OCC_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_Q_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_SPIN_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_U_TENS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_X - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_Y - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
FWV_Z - Static variable in class org.jmol.adapter.readers.cif.MSCifParser

## G

g - Variable in class org.jmol.g3d.Pixelator
g - Variable in class org.jmol.util.Rgb16
g - Variable in class org.jmol.viewer.Viewer
g1 - Variable in class org.jmol.modelsetbio.BasePair
g2 - Variable in class org.jmol.modelsetbio.BasePair
g3d - Variable in class org.jmol.g3d.CircleRenderer
g3d - Variable in class org.jmol.g3d.CylinderRenderer
g3d - Variable in class org.jmol.g3d.HermiteRenderer
g3d - Variable in class org.jmol.g3d.LineRenderer
g3d - Variable in class org.jmol.g3d.SphereRenderer
g3d - Variable in class org.jmol.g3d.TriangleRenderer
g3d - Variable in class org.jmol.modelset.AtomCollection
g3d - Variable in class org.jmol.render.ShapeRenderer
  could be vwr.gdata or an exporter
g3d - Variable in class org.jmol.renderbio.NucleicRenderer
g3d - Variable in class org.jmol.renderbio.RocketRenderer
g3d - Variable in class org.jmol.viewer.ColorManager
G3DRenderer - Interface in org.jmol.g3d
GamessReader - Class in org.jmol.adapter.readers.quantum
GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
gamessUKContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
GamessUKReader - Class in org.jmol.adapter.readers.quantum
GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
gamessUSContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
GamessUSReader - Class in org.jmol.adapter.readers.quantum
GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gamma - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
gamma - Variable in class org.jmol.adapter.readers.xtal.CastepReader
gamma - Variable in class org.jmol.adapter.readers.xtal.GulpReader
gamma - Variable in class org.jmol.jvxl.readers.MapFileReader
gamma - Variable in class org.jmol.util.SimpleUnitCell
gammaE - Variable in class org.jmol.adapter.readers.cif.MSRdr
gammaE - Variable in class org.jmol.util.ModulationSet
gammaIinv - Variable in class org.jmol.util.ModulationSet
gaussian_b_adjust - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gaussian_b_floor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gaussian_resolution - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
gaussianContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
gaussianCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
gaussianCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
GaussianDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
gaussianFchkContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
GaussianFchkReader - Class in org.jmol.adapter.readers.quantum
  Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
GaussianFchkReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianFchkReader
gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
GaussianReader - Class in org.jmol.adapter.readers.quantum
  Reader for Gaussian 94/98/03/09 output files.
GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
gaussians - Variable in class org.jmol.quantum.MOCalculation
GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
  Reader for Gaussian Wfn files -- not implemented yet
GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
GC - Static variable in class org.jmol.quantum.QS
GC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
gdata - Variable in class org.jmol.export.___Exporter
gdata - Variable in class org.jmol.export.Export3D
gdata - Variable in class org.jmol.g3d.HermiteRenderer
GData - Class in org.jmol.util
GData() - Constructor for class org.jmol.util.GData
  It is possible to instantiate this class with no Graphics3D.
gdata - Variable in class org.jmol.viewer.Viewer
generalResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
generateAllOperators(HallInfo) - Method in class org.jmol.symmetry.SpaceGroup
generateBaseEllipsePrecisely(boolean) - Method in class org.jmol.g3d.CylinderRenderer
generateColors(Object[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Set PyMOL "atom-wise" colors -- the colors that are defined initially as element colors but possibly set with the PyMOL 'color' command and are used when representation colors (cartoon, dots, etc.) are not defined (-1).
generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
generateCrystalClass(P3) - Method in interface org.jmol.api.SymmetryInterface
generateCrystalClass(int, P3) - Method in class org.jmol.modelset.AtomCollection
generateCrystalClass(P3) - Method in class org.jmol.symmetry.Symmetry
generateCube() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
generateCube() - Method in class org.jmol.jvxl.readers.IsoMepReader
generateCube() - Method in class org.jmol.jvxl.readers.IsoMOReader
generateCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
generateCube() - Method in class org.jmol.jvxl.readers.VolumeDataReader
generateOperatorsFromXyzInfo(String) - Method in class org.jmol.symmetry.SpaceGroup
generateOutputForExport(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
  for POV-Ray
generateOutputForExport(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
generateRaster(int, int, int, int[], int[], int, Rgb16[]) - Method in class org.jmol.g3d.TriangleRenderer
generateResidueSpecCode(T) - Method in class org.jmol.script.ScriptTokenParser
generateRingData() - Method in class org.jmol.smiles.SmilesGenerator
  get aromaticity, ringSets, and aromaticRings fields so that we can assign / and \ and also provide inter-aromatic single bond
generateScene(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Generate the saved scene using file settings preserved here and scene-specific information including frame, view, colors, visibilities, .
generateScene(Map<String, Object>) - Method in interface org.jmol.api.JmolSceneGenerator
generateShapes(Object[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Create all Jmol shape objects.
generateSolventCavity() - Method in class org.jmol.jvxl.readers.IsoSolventReader
generateSolventCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
generateSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
generateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
generateVisibilities(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Hide everything, then just make visible the sets of atoms specified in the visibility (i.e.
GenericApplet - Class in org.jmol.util
  A collection of all methods necessary for initialization of and communication with the applet, whether it be JavaScript or Java.
GenericApplet() - Constructor for class org.jmol.util.GenericApplet
GenericConsole - Class in org.jmol.console
GenericConsole() - Constructor for class org.jmol.console.GenericConsole
GenericConsoleTextArea - Interface in org.jmol.api.js
GenericFileInterface - Interface in org.jmol.api
GenericGraphics - Interface in org.jmol.api
GenericImageDialog - Interface in org.jmol.api
GenericMenuInterface - Interface in org.jmol.api
GenericMouseInterface - Interface in org.jmol.api
GenericPlatform - Interface in org.jmol.api
GenericPopup - Class in org.jmol.popup
  The overall parent of all popup classes in Jmol and JSmol.
GenericPopup() - Constructor for class org.jmol.popup.GenericPopup
GenericTextArea - Interface in org.jmol.console
GenericTextPane() - Constructor for class org.jmol.console.AppletConsole.GenericTextPane
GenNBOReader - Class in org.jmol.adapter.readers.quantum
  NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure
GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
Geodesic - Class in org.jmol.util
  J2SRequireImport is needed because we use ArrayUtil in a static method
Geodesic() - Constructor for class org.jmol.util.Geodesic
geodesicCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
geodesicMap - Variable in class org.jmol.geodesic.EnvelopeCalculation
GEOM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
GEOM_BOND_ATOM_SITE_LABEL_1 - Static variable in class org.jmol.adapter.readers.cif.CifReader
GEOM_BOND_ATOM_SITE_LABEL_2 - Static variable in class org.jmol.adapter.readers.cif.CifReader
GEOM_BOND_DISTANCE - Static variable in class org.jmol.adapter.readers.cif.CifReader
geomBondFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
geometry_export_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
geomOpt - Variable in class org.jmol.adapter.readers.xtal.DmolReader
geosurface - Static variable in class org.jmol.script.T
GeoSurface - Class in org.jmol.shapespecial
GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
GeoSurfaceRenderer - Class in org.jmol.renderspecial
GeoSurfaceRenderer() - Constructor for class org.jmol.renderspecial.GeoSurfaceRenderer
Gesture - Class in org.jmol.viewer
Gesture(int, Viewer) - Constructor for class org.jmol.viewer.Gesture
gestureServer - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
gestureswipefactor - Static variable in class org.jmol.script.T
gestureSwipeFactor - Variable in class org.jmol.viewer.ActionManager
get(int) - Method in class org.jmol.util.Int2IntHash
get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
get(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
get1(int) - Static method in class org.jmol.awtjs.swing.Color
get2SidedNormix(V3, BS) - Static method in class org.jmol.util.Normix
get3(int, int, int) - Method in class org.jmol.awt.AwtColor
get3(int, int, int) - Static method in class org.jmol.awtjs.swing.Color
get3dContour(IsosurfaceMesh, Lst<Object>, float, short) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
get3DStraightness(String, Quat, Quat) - Static method in class org.jmol.modelsetbio.BioExt
get4(int, int, int, int) - Method in class org.jmol.awt.AwtColor
get4(int, int, int, int) - Static method in class org.jmol.awtjs.swing.Color
getACDPeakWidth(String) - Method in class org.jmol.jsv.JDXMOLParser
getACFValue(float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Fetch the action that was created for the given command.
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
getActionCommand() - Method in interface org.jmol.api.SC
getActionCommand() - Method in class org.jmol.awt.AwtSwingComponent
getActionCommand() - Method in class org.jmol.awtjs.swing.JComponent
getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
getActionName(int) - Static method in class org.jmol.viewer.ActionManager
getActions() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
getActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getActions() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
getActiveMenu() - Method in class org.jmol.modelkit.ModelKitPopup
  for FrankRender -- the thin box on the top left
getAdditionalHydrogens(BS, boolean, boolean, Lst<Atom>) - Method in class org.jmol.viewer.Viewer
getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
getAlignment(int) - Static method in class org.jmol.viewer.JC
getAllAtomInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getAllAtoms() - Method in class org.jmol.viewer.Viewer
getAllAtomTensors(String) - Method in class org.jmol.modelset.AtomCollection
getAllAxes(V3) - Method in class org.jmol.symmetry.PointGroup
getAllBasePairBits(String) - Method in class org.jmol.modelsetbio.BioModelSet
getAllBondInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getAllChainInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getAllChimeInfo(SB) - Method in class org.jmol.viewer.ChimeMessenger
getAllChimeInfo(SB) - Method in interface org.jmol.viewer.JmolChimeMessenger
getAllDefaultStructures(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAlleneAtoms(SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
getAllHeteroList(int) - Method in class org.jmol.modelsetbio.BioModelSet
getAllInfo() - Method in class org.jmol.shape.Measures
getAllInfoAsString() - Method in class org.jmol.shape.Measures
getAllMolecularDipoles(BS) - Method in class org.jmol.shapespecial.Dipoles
getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
getAllowJSThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
getAllowJSThreads() - Method in class org.jmol.script.ScriptEval
getAllPoints(int) - Method in class org.jmol.scriptext.ScriptExt
getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>) - Method in class org.jmol.modelsetbio.BioExt
getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>) - Method in class org.jmol.modelsetbio.BioModelSet
getAllPolymerInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getAllPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioModelSet
getAllProperties(SV, String) - Method in class org.jmol.script.ScriptMathProcessor
getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
getAllRenderers() - Method in class org.jmol.render.RepaintManager
getAllSequenceBits(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAllSettings(String) - Method in class org.jmol.viewer.JmolStateCreator
getAllSettings(String) - Method in class org.jmol.viewer.StateCreator
getAllSettings(String) - Method in class org.jmol.viewer.Viewer
getAllStructures(String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
getAllUnitIds(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAllVariables() - Method in class org.jmol.viewer.GlobalSettings
getAlphasAndExponents() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
getAltLoc() - Method in class org.jmol.adapter.smarter.AtomIterator
getAltLoc() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelSet
getAmbientPercent() - Method in class org.jmol.util.GData
getAmino() - Method in class org.jmol.util.ColorEncoder
getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioExt
  returns an array if we have special hybridization or charge
getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioModelSet
getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
getAndRegisterPlugin(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getAndSetNewVariable(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
getAnglefromZ() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
getAngles() - Method in class org.jmol.minimize.Minimizer
getAngleUnits() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getAngleUnitsList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getAnimationInfo() - Method in class org.jmol.viewer.PropertyManager
getAnimRunTimeSeconds() - Method in class org.jmol.viewer.AnimationManager
getAnimState(AnimationManager, SB) - Method in class org.jmol.viewer.StateCreator
getAnnotationBits(String, int, String) - Method in class org.jmol.modelsetbio.BioModelSet
getAnnotationInfo(Viewer, SV, String, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
getAnnotationInfo(Viewer, SV, String, int, int) - Method in class org.jmol.dssx.AnnotationParser
  Get a string report of annotation data
getAnnotationInfo(Object, int) - Method in class org.jmol.viewer.PropertyManager
getAnnotationInfo(SV, String, int) - Method in class org.jmol.viewer.Viewer
getAnnotationKVPairs(SV, String, String, SB, String, boolean, boolean, int) - Method in class org.jmol.dssx.AnnotationParser
  Construct a nice listing for this annotation, including validation
getAnnotationParser(boolean) - Method in class org.jmol.viewer.Viewer
getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.PopInJmol
getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.WebPanel
getAppletDocumentBase() - Method in class org.jmol.viewer.FileManager
getAppletInfo() - Method in interface org.jmol.api.JmolAppletInterface
getAppletInfo() - Method in class org.jmol.applet.AppletWrapper
getAppletInfo() - Method in class org.jmol.util.GenericApplet
getAppletInfo() - Method in class org.jmol.viewer.PropertyManager
getAppletPath(boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
getArgb(short) - Static method in class org.jmol.util.C
getArgb(float) - Method in class org.jmol.util.ColorEncoder
getArgb() - Method in class org.jmol.util.Rgb16
getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
getArgbGreyscale(short) - Static method in class org.jmol.util.C
getArgbHbondType(int) - Static method in class org.jmol.util.Edge
getArgbMinMax(float, float, float) - Method in class org.jmol.util.ColorEncoder
getArgbParam(int) - Method in class org.jmol.script.ScriptParam
getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptParam
getArgbParamOrNone(int, boolean) - Method in class org.jmol.script.ScriptParam
getArgbs(int) - Method in class org.jmol.modelsetbio.BioResolver
getArgbs(int) - Method in class org.jmol.viewer.ColorManager
getArguments(String) - Method in class org.jmol.viewer.PropertyManager
getAromatic - Variable in class org.jmol.smiles.SmilesGenerator
getAromaticDottedBondMask() - Method in class org.jmol.render.SticksRenderer
getArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
  turn "[1,2,3]" into [1.0,2.0,3.0] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
getArrowScale() - Method in class org.jmol.renderspecial.DrawRenderer
getAscent(Object) - Static method in class org.jmol.awt.AwtFont
getAscent(Object) - Static method in class org.jmol.awtjs2d.JSFont
getAscent() - Method in class org.jmol.util.Font
getAsciiFileOrNull(String) - Method in class org.jmol.viewer.Viewer
getAssocArray(int) - Method in class org.jmol.script.ScriptExpr
getAtom() - Method in class org.jmol.adapter.readers.simple.InputReader
getAtom(int) - Method in class org.jmol.modelset.AtomCollection
getAtom(int) - Method in class org.jmol.modelset.Measurement
getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
getAtom(Symmetry, int, int, T3) - Method in class org.jmol.symmetry.SymmetryDesc
getAtom() - Method in class org.jmol.symmetry.UnitCellIterator
getAtom1() - Method in class org.jmol.smiles.SmilesBond
getAtomAndStateCount(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Look through all named objects for molecules, counting atoms and also states; see if trajectories are compatible (experimental).
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in interface org.jmol.api.JmolAnnotationParser
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.AnnotationParser
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.DSSR1
getAtomBits(int, Object) - Method in class org.jmol.script.ScriptExpr
getAtomBitsBS(int, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAtomBitSet(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
getAtomBitSet(Object) - Method in class org.jmol.script.ScriptEval
  A general method to evaluate a string representing an atom set.
getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in interface org.jmol.api.JmolScriptManager
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.script.ScriptManager
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.viewer.Viewer
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelSet
getAtomBitsMDa(int, Object, BS) - Method in class org.jmol.modelset.AtomCollection
  general unqualified lookup of atom set type
getAtomBitsMDb(int, Object) - Method in class org.jmol.modelset.BondCollection
getAtomBitsStr(int, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getAtomBondChirality(SimpleNode, Lst<int[]>, BS) - Method in class org.jmol.symmetry.CIPChirality
  Get E/Z characteristics for specific atoms.
getAtomChiralityLimited(SimpleNode, CIPChirality.CIPAtom, SimpleNode) - Method in class org.jmol.symmetry.CIPChirality
  Determine R/S or one half of E/Z determination
getAtomCIPChiralityCode(Atom) - Method in class org.jmol.modelset.ModelSet
  Determine the Cahn-Ingold-Prelog R/S chirality of an atom
getAtomCollectionReader(String, String, Object, Map<String, Object>, int) - Static method in class org.jmol.adapter.smarter.Resolver
  the main method for reading files.
getAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
  Get the estimated number of atoms contained in the file.
getAtomCount() - Method in class org.jmol.modelset.ModelLoader
getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getAtomData(String, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getAtomData(String, String, boolean) - Method in class org.jmol.viewer.PropertyManager
  use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.
getAtomDefs(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
getAtomFromName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
getAtomGeneral(Atom, int, int) - Method in class org.jmol.adapter.readers.simple.InputReader
getAtomGroupQuaternions(BS, int, char) - Method in class org.jmol.modelset.ModelSet
getAtomGroupQuaternions(BS, int) - Method in class org.jmol.viewer.Viewer
getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.Node
getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
getAtomicDSSRData(ModelSet, int, float[], String) - Method in interface org.jmol.api.JmolAnnotationParser
getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.AnnotationParser
getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.DSSR1
getAtomicDSSRData(int) - Method in class org.jmol.modelset.ModelSet
getAtomicDSSRData(float[], String) - Method in class org.jmol.modelsetbio.BioModel
getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
  Returns the atomic mass of the atom.
getAtomicMass(int) - Static method in class org.jmol.util.Elements
getAtomicNumber(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
getAtomicPotentials(BS, BS, String) - Method in class org.jmol.scriptext.IsoExt
getAtomicPropertyState(int, BS) - Method in class org.jmol.viewer.JmolStateCreator
getAtomicPropertyState(int, BS) - Method in class org.jmol.viewer.StateCreator
getAtomicPropertyState(SB, byte, BS, String, float[]) - Method in class org.jmol.viewer.Viewer
getAtomicPropertyStateBuffer(SB, int, BS, String, float[]) - Method in class org.jmol.viewer.JmolStateCreator
getAtomicPropertyStateBuffer(SB, int, BS, String, float[]) - Method in class org.jmol.viewer.StateCreator
getAtomIdentityInfo(int, Map<String, Object>, P3) - Method in class org.jmol.modelset.AtomCollection
getAtomIndex(String) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
getAtomIndex(int) - Method in class org.jmol.adapter.readers.simple.InputReader
getAtomIndex(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
getAtomIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomIndex(String, int) - Method in class org.jmol.modelset.Group
getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
getAtomIndex(String, int) - Method in class org.jmol.modelsetbio.Monomer
getAtomIndex1() - Method in class org.jmol.modelset.Bond
getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
getAtomIndex1() - Method in class org.jmol.util.Edge
getAtomIndex2() - Method in class org.jmol.modelset.Bond
getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
getAtomIndex2() - Method in class org.jmol.util.Edge
getAtomIndexFromPrimitiveIndex(int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Get the atom index from a primitive index.
getAtomIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
getAtomIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
getAtomIndices(BS) - Method in class org.jmol.modelset.AtomCollection
getAtomInfo(int, String, P3) - Method in class org.jmol.modelset.AtomCollection
getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
getAtomInfoLong(int, P3) - Method in class org.jmol.viewer.PropertyManager
getAtomInfoXYZ(int, boolean) - Method in class org.jmol.viewer.Viewer
getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
  Get an AtomIterator for retrieval of all atoms in the file.
getAtomLabel(int, int, int, int, float, int, boolean, String) - Static method in class org.jmol.smiles.SmilesAtom
  called from SmilesGenerator
getAtomList(String) - Method in class org.jmol.minimize.forcefield.Calculations
getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
getAtomMinMax(BS, BS[]) - Method in class org.jmol.jvxl.readers.AtomDataReader
getAtomName(String, String) - Static method in class org.jmol.adapter.readers.xtal.MagresReader
  combine name and index
getAtomName() - Method in class org.jmol.adapter.smarter.AtomIterator
getAtomName() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAtomName() - Method in class org.jmol.modelset.Atom
getAtomName() - Method in class org.jmol.smiles.SmilesAtom
getAtomName() - Method in interface org.jmol.util.Node
getAtomName() - Method in interface org.jmol.util.SimpleNode
getAtomNames() - Method in class org.jmol.adapter.readers.more.MdTopReader
getAtomNumber() - Method in class org.jmol.modelset.Atom
getAtomNumber() - Method in class org.jmol.smiles.SmilesAtom
  Returns the Jmol atom number
getAtomNumber() - Method in interface org.jmol.util.Node
getAtomParity(Atom) - Method in class org.jmol.util.MolWriter
getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
getAtomPointVector(BS) - Method in class org.jmol.modelset.AtomCollection
getAtomPropertiesLike(String) - Static method in class org.jmol.script.T
getAtomPropertyAsString(Atom, int) - Method in class org.jmol.util.MolWriter
getAtomR0(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
getAtomRecordMOL(int, ModelSet, SB, int, Atom, Quat, P3, boolean, boolean, SB, int, boolean) - Method in class org.jmol.util.MolWriter
getAtomResidueInfo(SB, Atom) - Static method in class org.jmol.viewer.PropertyManager
getAtoms(String) - Method in interface org.jmol.api.SmilesMatcherInterface
getAtoms(BS, boolean, boolean, boolean, boolean, boolean, boolean, float, M4) - Method in class org.jmol.jvxl.readers.AtomDataReader
getAtoms(int, Object) - Method in class org.jmol.modelset.ModelSet
  general lookup for integer type -- from Eval
getAtoms(String) - Method in class org.jmol.smiles.SmilesMatcher
getAtomsConnected(float, float, int, BS) - Method in class org.jmol.modelset.BondCollection
getAtomSetAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetAtomIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the auxiliary information for a particular atomSet.
getAtomSetAuxiliaryInfoValue(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetBondCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetCenter(BS) - Method in class org.jmol.modelset.ModelSet
getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  Create the AtomSetCollection and return it
getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollection() - Method in interface org.jmol.api.JmolDomReaderInterface
getAtomSetCollection() - Method in interface org.jmol.api.JmolFilesReaderInterface
getAtomSetCollection() - Method in class org.jmol.io.FileReader
getAtomSetCollection() - Method in class org.jmol.io.FilesReader
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
  Get the auxiliary information for this atomSetCollection.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  Direct DOM HTML4 page reading; Egon was interested in this at one point.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionFromReaderType(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
  all in one -- for TestSmarterJmolAdapter
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
  Get the name of the atom set collection, if known.
getAtomSetCollectionOrBufferedReaderFromZip(Viewer, InputStream, String, String[], Map<String, Object>, int, boolean) - Method in class org.jmol.io.JmolUtil
  A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
  Read an atomSetCollection object from a bufferedReader and close the reader.
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
  Associate an atomSetCollection object with an array of BufferedReader.
getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
  Get number of atomSets in the file.
getAtomSetIndex() - Method in class org.jmol.adapter.smarter.AtomIterator
getAtomSetIndex() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAtomSetIndex() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
getAtomSetName(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the name of an atomSet.
getAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
  Get the number identifying each atomSet.
getAtomsFromAtomNumberInFrame(int) - Method in class org.jmol.modelset.AtomCollection
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.JmolStateCreator
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.StateCreator
getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
getAtomsInFrame(BS) - Method in class org.jmol.modelset.AtomCollection
getAtomSite() - Method in class org.jmol.adapter.smarter.AtomIterator
getAtomSite() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getAtomSite() - Method in class org.jmol.modelset.Atom
getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
getAtomSite() - Method in interface org.jmol.util.Node
getAtomSiteBS(BS) - Method in class org.jmol.quantum.NMRCalculation
  Interaction tensors are not repeated for every possible combination.
getAtomsNearPlane(float, P4) - Method in class org.jmol.modelset.AtomCollection
getAtomsNearPt(float, P3) - Method in class org.jmol.viewer.Viewer
getAtomsNearPts(float, T3[], BS) - Method in class org.jmol.scriptext.MathExt
getAtomsNearSurface(float, String) - Method in class org.jmol.scriptext.MathExt
getAtomsWithin(float, T3, BS, int) - Method in class org.jmol.modelset.ModelSet
getAtomsWithin(Polyhedron, float) - Method in class org.jmol.shapespecial.Polyhedra
getAtomsWithinRadius(float, BS, boolean, RadiusData) - Method in class org.jmol.modelset.ModelSet
  Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
getAtomSymmetry(Atom, SymmetryInterface) - Method in class org.jmol.adapter.readers.cif.MSRdr
  When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.
getAtomSymmetry(Atom, SymmetryInterface) - Method in interface org.jmol.adapter.smarter.MSInterface
getAtomTensor(int, String) - Method in class org.jmol.modelset.AtomCollection
getAtomTensorList(int) - Method in class org.jmol.modelset.AtomCollection
getAtomType() - Method in class org.jmol.modelset.Atom
getAtomType() - Method in class org.jmol.smiles.SmilesAtom
getAtomType() - Method in interface org.jmol.util.Node
getAtomTypeDescriptions() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getAtomTypeDescs(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getAtomTypes() - Method in class org.jmol.adapter.readers.more.MdTopReader
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
getAtomUniqueID1() - Method in class org.jmol.adapter.smarter.BondIterator
getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapterBondIterator
getAtomUniqueID2() - Method in class org.jmol.adapter.smarter.BondIterator
getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapterBondIterator
getAtomValidation(Viewer, String, Atom) - Method in interface org.jmol.api.JmolAnnotationParser
getAtomValidation(Viewer, String, Atom) - Method in class org.jmol.dssx.AnnotationParser
  Get all validation values corresponding to a specific validation type.
getAtomValidation(String, Atom) - Method in class org.jmol.viewer.Viewer
getAtropIndex(SmilesBond, boolean) - Method in class org.jmol.smiles.SmilesSearch
getAtropismCode(int) - Static method in class org.jmol.util.Edge
getAtropismNode(int, Node, boolean) - Static method in class org.jmol.util.Edge
getAtropismOrder(int, int) - Static method in class org.jmol.util.Edge
getAtropismOrder12(int) - Static method in class org.jmol.util.Edge
getAtropisomerKeys(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  called by SmilesParser to get nn in ^nn- base on match to actual structure
getAttached(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
getAttachedAtomForPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
  Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
getAttr(String, String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
getAttribute(String, String) - Method in interface org.jmol.api.JmolJDXMOLParser
getAttribute(String, String) - Method in class org.jmol.jsv.JDXMOLParser
getAuxEneEndWinner(CIPChirality.CIPAtom, CIPChirality.CIPAtom, int[]) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Get the atom that is the highest priority of two atoms on the end of a double bond after sorting from Rule 1a through a given rule (Rule 3 or Rule 5)
getAuxEneWinnerChirality(CIPChirality.CIPAtom, CIPChirality.CIPAtom, boolean, int[]) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Determine the winner on one end of an alkene or cumulene and return also the rule by which that was determined.
getAuxiliaryData(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
getAuxiliaryFileData() - Method in class org.jmol.export._IdtfExporter
getAuxiliaryFileData() - Method in class org.jmol.export._PovrayExporter
getAuxiliaryInfo(BS) - Method in class org.jmol.modelset.ModelSet
  Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.
getAuxiliaryInfoForAtoms(Object) - Method in class org.jmol.viewer.Viewer
getAverageAtomPoint() - Method in class org.jmol.modelset.ModelSet
getAxesState(Axes) - Method in class org.jmol.viewer.StateCreator
getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
getAxisPoint(int, boolean) - Method in class org.jmol.shape.Axes
  get actual point or 1/2 vector from origin to this point
getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
getAzacyclic() - Method in class org.jmol.symmetry.CIPData
  Identify bridgehead nitrogens, as these may need to be given chirality designations.
getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
getBaseModelBitSet() - Method in class org.jmol.viewer.Viewer
getBaseModelIndex(int) - Method in interface org.jmol.api.JmolJSpecView
getBaseModelIndex(int) - Method in class org.jmol.jsv.JSpecView
getBasePairInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getBasePairs(Viewer, int) - Method in interface org.jmol.api.JmolAnnotationParser
getBasePairs(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
getBasePairs(Viewer, int) - Method in class org.jmol.dssx.DSSR1
getBasePairs() - Method in class org.jmol.modelsetbio.NucleicMonomer
getBaseRing6Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getBaseSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
  Get the symmetry that was in place prior to any supercell business
getBBoxVertices() - Method in class org.jmol.modelset.ModelSet
getBetter4bList() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Create Mata-style linear atom.listRS and return the better of R-ref or S-ref.
getBfactor() - Method in class org.jmol.adapter.smarter.AtomIterator
getBfactor() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getBfactor100() - Method in class org.jmol.modelset.Atom
getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
getBFactors() - Method in class org.jmol.modelset.AtomCollection
getBgContrast(int) - Static method in class org.jmol.util.C
getBinaryType(InputStream) - Static method in class org.jmol.adapter.smarter.Resolver
getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
getBindingInfo(String[], String[], String) - Method in class org.jmol.viewer.binding.Binding
getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
getBindings() - Method in class org.jmol.viewer.binding.Binding
getBioBranches(Lst<BS>) - Method in class org.jmol.modelsetbio.BioModel
getBioExt() - Method in class org.jmol.modelsetbio.BioModelSet
getBioModel(int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelsetbio.BioResolver
getBioPolymerCount() - Method in class org.jmol.modelsetbio.BioModel
getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getBioPolymerCountInModel(int) - Method in class org.jmol.modelsetbio.BioModelSet
getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
getBioPolymerLength() - Method in class org.jmol.modelset.Group
getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
getBioShapeState(String, boolean, Map<String, BS>, Map<String, BS>) - Method in class org.jmol.shapebio.BioShape
getBioSmiles(BS, String, int) - Method in class org.jmol.smiles.SmilesGenerator
getBioSmiles(BS) - Method in class org.jmol.viewer.Viewer
getBioSmilesType() - Method in class org.jmol.modelset.Atom
getBioSmilesType() - Method in class org.jmol.smiles.SmilesAtom
getBioSmilesType() - Method in interface org.jmol.util.Node
getBioStructureTypeName(boolean) - Method in enum org.jmol.c.STR
getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
getBioStructureTypeName() - Method in interface org.jmol.util.Node
getBitSet(SV, boolean) - Static method in class org.jmol.script.SV
getBitSetForMF(Atom[], BS, String) - Static method in class org.jmol.util.JmolMolecule
getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in class org.jmol.scriptext.CmdExt
getBitsetProperty(BS, Lst<SV>, int, P3, P4, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptExpr
getBitsetPropertyFloat(BS, int, String, float, float) - Method in class org.jmol.scriptext.CmdExt
getBitsetPropertySelector(int, int) - Method in class org.jmol.script.ScriptExpr
getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
getBlock(String, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
getBond(Atom) - Method in class org.jmol.modelset.Atom
getBond(int) - Method in class org.jmol.smiles.SmilesAtom
  Returns the bond at index `number`.
getBondChiralityLimited(SimpleEdge, SimpleNode) - Method in class org.jmol.symmetry.CIPChirality
  Determine the axial or E/Z chirality for this bond, with the given starting atom a
getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
getBondCount() - Method in class org.jmol.modelset.Atom
getBondCount() - Method in class org.jmol.modelset.Model
getBondCount() - Method in class org.jmol.smiles.SmilesAtom
getBondCount() - Method in interface org.jmol.util.SimpleNode
  Get the total number of bonds, including hydrogen bonds.
getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
  for general use
getBondCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getBondDipoles() - Method in class org.jmol.shapespecial.Dipoles
getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
getBondedAtomIndex(int) - Method in interface org.jmol.util.Node
getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
getBondIndex(int) - Method in class org.jmol.minimize.MinAtom
getBondInfo(JmolAdapter, String, Object) - Method in class org.jmol.modelsetbio.BioResolver
getBondInfo(int, P3) - Method in class org.jmol.viewer.PropertyManager
getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
getBondingRadii() - Method in class org.jmol.modelset.AtomCollection
getBondingRadius(int, int) - Static method in class org.jmol.api.JmolAdapter
getBondingRadius() - Method in class org.jmol.modelset.Atom
getBondingRadius(int, int) - Static method in class org.jmol.util.Elements
  This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.
getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
  Get a BondIterator for retrieval of all bonds in the file.
getBondIterator(BS) - Method in class org.jmol.modelset.BondCollection
getBondIteratorForType(int, BS) - Method in class org.jmol.modelset.BondCollection
getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
getBondList(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create the bond set.
getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getBondList(Object) - Method in class org.jmol.api.JmolAdapter
getBondNotTo(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
getBondOrder(String) - Method in class org.jmol.adapter.readers.cif.CifReader
getBondOrder(Edge, int, int, boolean) - Method in class org.jmol.smiles.SmilesGenerator
getBondOrder(SimpleEdge) - Method in class org.jmol.symmetry.CIPData
getBondOrder(SimpleEdge) - Method in class org.jmol.symmetry.CIPDataSmiles
getBondOrderFromFloat(float) - Static method in class org.jmol.util.Edge
getBondOrderFromString(String) - Static method in class org.jmol.script.ScriptParam
getBondOrderFromString(String) - Static method in class org.jmol.util.Edge
getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.Edge
getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.Edge
  used for formatting labels and in the connect PARTIAL command
getBondOrderString(int) - Static method in class org.jmol.smiles.SmilesBond
getBondPickingMode() - Method in class org.jmol.viewer.ActionManager
getBondRecordMOL(SB, int, Bond, int[], boolean, boolean, boolean) - Method in class org.jmol.util.MolWriter
getBonds() - Method in class org.jmol.minimize.Minimizer
getBondsForSelectedAtoms(BS, boolean) - Method in class org.jmol.modelset.BondCollection
getBondsForSelectedAtoms(BS) - Method in class org.jmol.viewer.Viewer
getBondsPickable() - Method in class org.jmol.viewer.Viewer
getBondState(Sticks) - Method in class org.jmol.viewer.StateCreator
getBondStereochemistry(Edge, SimpleNode) - Method in class org.jmol.smiles.SmilesGenerator
  Retrieves the saved character based on the index of the bond.
getBondTo(int) - Method in class org.jmol.minimize.MinAtom
getBondTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesAtom
  if atom is null, return bond TO this atom (bond.atom2 == this) otherwise, return bond connecting this atom with that atom
getBondType(Bond, AtomType, AtomType, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getBondType() - Method in class org.jmol.smiles.SmilesBond
getBondTypeFromCode(char) - Static method in class org.jmol.smiles.SmilesBond
getBoolean(int) - Method in class org.jmol.api.JmolViewer
getBoolean(boolean) - Static method in class org.jmol.script.SV
getBoolean(int) - Method in class org.jmol.viewer.Viewer
getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
getBooleanValue(String, boolean) - Method in class org.jmol.util.GenericApplet
getBoundBox(SV) - Method in class org.jmol.script.ScriptMathProcessor
getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelSet
getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelSet
getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelSet
getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
getBoundBoxInfo() - Method in class org.jmol.viewer.PropertyManager
getBoundBoxOrientation(int, BS) - Method in class org.jmol.modelset.ModelSet
getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
  Return basic info on boundbox in the form of an array.
getBoundBoxVertices() - Method in class org.jmol.util.BoxInfo
getBoundingBox() - Method in class org.jmol.shape.Mesh
getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getBox(int) - Method in class org.jmol.shape.Labels
getBoxFacesFromOABC(P3[]) - Method in class org.jmol.util.MeshSlicer
getBoxInfo() - Method in class org.jmol.modelset.ModelSet
getBoxInfo(BS, float) - Method in class org.jmol.modelset.ModelSet
getBoxVec() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getBranch2dZ(int, int, BS, BS, V3, V3, V3) - Method in class org.jmol.modelset.ModelLoader
getBranchBitSet(Node[], int, BS, Lst<BS>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
  given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
getBranchBitSet(int, int, boolean) - Method in class org.jmol.viewer.Viewer
  given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.
getBreakableContext(int) - Method in class org.jmol.script.ScriptFlowContext
getBrickValue(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
getBridge(int[][][][], int, int, int, int, Lst<Bridge>, Atom, Atom, AminoPolymer, AminoPolymer, Map<String, Boolean>, boolean) - Method in class org.jmol.dssx.DSSP
getBridges(int[][][][]) - Method in class org.jmol.dssx.DSSP
  (p.
getBS(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getBSAll() - Method in class org.jmol.adapter.smarter.StructureIterator
getBSAll() - Method in class org.jmol.api.JmolAdapterStructureIterator
getBSAromaticRings() - Method in class org.jmol.smiles.SmilesSearch
getBsAtoms(Lst<Object>, int[], BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getBsBranches(float[]) - Method in class org.jmol.modelset.ModelSet
getBsOK() - Method in class org.jmol.quantum.NciCalculation
  grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular
getBsReps(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
getBSSideChain() - Method in class org.jmol.modelset.Group
getBSSideChain() - Method in class org.jmol.modelsetbio.AminoMonomer
getBsSurfaceClone() - Method in interface org.jmol.api.JmolEnvCalc
getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
getBufferedFileInputStream(String) - Method in interface org.jmol.api.GenericPlatform
getBufferedFileInputStream(String) - Static method in class org.jmol.awt.AwtFile
getBufferedFileInputStream(String) - Method in class org.jmol.awt.Platform
getBufferedFileInputStream(String) - Method in class org.jmol.awtjs2d.Platform
getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
getBufferedInputStream(String) - Method in class org.jmol.viewer.FileManager
getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
getBufferedInputStreamOrErrorMessageFromName(String, String, boolean, boolean, byte[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
getBufferedReader(String) - Method in class org.jmol.minimize.forcefield.ForceField
getBufferedReaderForResource(Viewer, Object, String, String) - Static method in class org.jmol.viewer.FileManager
getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.io.FilesReader
  called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
getBufferedReaderOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
getBundle(String) - Method in class org.jmol.modelkit.ModelKitPopup
getBundle(String) - Method in class org.jmol.popup.JmolGenericPopup
getBundle(String) - Method in class org.jmol.popup.JmolPopup
getButtonGroup() - Method in class org.jmol.awt.AwtPopupHelper
getButtonGroup() - Method in class org.jmol.awtjs2d.JSPopupHelper
getButtonGroup() - Method in interface org.jmol.popup.PopupHelper
getButtonMods(int) - Static method in class org.jmol.viewer.binding.Binding
getByteCount() - Method in class org.jmol.export.___Exporter
getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
getC2() - Method in class org.jmol.modelsetbio.NucleicMonomer
getC4P() - Method in class org.jmol.modelsetbio.NucleicMonomer
getC5() - Method in class org.jmol.modelsetbio.NucleicMonomer
getC6() - Method in class org.jmol.modelsetbio.NucleicMonomer
getC8() - Method in class org.jmol.modelsetbio.NucleicMonomer
getCachedAnnotationMap(String, Object) - Method in class org.jmol.modelsetbio.BioModel
getCachedPngjBytes(FileManager, String) - Method in class org.jmol.io.JmolUtil
getCachedPngjBytes(String) - Method in class org.jmol.viewer.FileManager
getCallback(String) - Static method in enum org.jmol.c.CBK
getCameraDepth() - Method in class org.jmol.viewer.TransformManager
getCameraFactors() - Method in class org.jmol.viewer.TransformManager
  This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
getCanonicalCopy(float, boolean) - Method in interface org.jmol.api.SymmetryInterface
getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.Symmetry
getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.UnitCell
getCanonicalCopy(P3[], float) - Static method in class org.jmol.util.BoxInfo
getCanonicalName(String) - Method in class org.jmol.viewer.FileManager
getCanonicalSeitz(int) - Static method in class org.jmol.symmetry.SpaceGroup
getCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
getCapOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
getCapSlabObject(int, boolean) - Method in class org.jmol.scriptext.IsoExt
getCapSlabObject(String, boolean) - Method in class org.jmol.shapesurface.Isosurface
  legacy -- for some scripts with early isosurface slabbing
getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getCaretPosition() - Method in interface org.jmol.api.js.GenericConsoleTextArea
getCaretPosition() - Method in interface org.jmol.console.GenericTextArea
getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
getCartesianOffset() - Method in class org.jmol.symmetry.UnitCell
getCartoonType(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getCartoonType(int) - Method in interface org.jmol.api.PymolAtomReader
getCel() - Method in class org.jmol.util.GData
getCellRange() - Method in interface org.jmol.api.SymmetryInterface
getCellRange() - Method in class org.jmol.symmetry.Symmetry
getCellStyle(int, int, GridBagConstraints) - Method in interface org.jmol.awtjs.swing.TableCellRenderer
getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
  Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
getCellWeight(P3) - Static method in class org.jmol.util.SimpleUnitCell
  calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125 (vertex)
getCellWeights(BS) - Method in class org.jmol.modelset.ModelSet
getCelPower() - Method in class org.jmol.util.GData
getCenter() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.modelset.ModelSet
getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.viewer.Viewer
getCentering() - Method in class org.jmol.symmetry.SymmetryOperation
  assumption here is that these are in order of sets, as in ITA
getCenters() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getCenterText() - Method in class org.jmol.viewer.TransformManager
getCEState(ColorEncoder, SB) - Method in class org.jmol.viewer.StateCreator
getChain(int) - Method in class org.jmol.modelset.Model
getChainAt(int) - Method in class org.jmol.modelset.Model
getChainBits(int) - Method in class org.jmol.modelset.AtomCollection
getChainCount(boolean) - Method in class org.jmol.modelset.Model
getChainCountInModelWater(int, boolean) - Method in class org.jmol.modelset.ModelSet
getChainID() - Method in class org.jmol.adapter.smarter.AtomIterator
getChainID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getChainID() - Method in class org.jmol.modelset.Atom
getChainID() - Method in class org.jmol.smiles.SmilesAtom
getChainID() - Method in interface org.jmol.util.Node
getChainID(String, boolean) - Method in class org.jmol.viewer.Viewer
  Create a unique integer for any chain string.
getChainIDStr() - Method in class org.jmol.modelset.Atom
getChainIDStr() - Method in class org.jmol.smiles.SmilesAtom
getChainIDStr() - Method in interface org.jmol.util.Node
getChainIDStr(int) - Method in class org.jmol.viewer.Viewer
getChainInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
getChangeableColix(int, int) - Method in class org.jmol.util.GData
getChangeableColixIndex(short) - Static method in class org.jmol.util.C
getChangeableReader(Viewer, String, String) - Static method in class org.jmol.io.FileReader
getChar(String, int) - Static method in class org.jmol.smiles.SmilesParser
getCharge() - Method in class org.jmol.smiles.SmilesAtom
  Returns the charge of the atom.
getCharges() - Method in class org.jmol.adapter.readers.more.MdTopReader
getCheckBox(String) - Method in class org.jmol.awt.AwtPopupHelper
getCheckBox(AwtPopupHelper, String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
getCheckBox(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getCheckBox(String) - Method in interface org.jmol.popup.PopupHelper
getChemicalInfo(String, String, BS) - Method in class org.jmol.viewer.Viewer
getChemicalShift(Atom) - Method in interface org.jmol.api.JmolNMRInterface
  If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
getChemicalShift(Atom) - Method in class org.jmol.quantum.NMRCalculation
getChimeInfo(int, BS) - Method in interface org.jmol.api.JmolPropertyManager
getChimeInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
getChimeInfoA(Atom[], int, BS) - Method in class org.jmol.viewer.PropertyManager
getChimeMessenger() - Method in class org.jmol.viewer.Viewer
getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
getChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
getChiralityClass(String) - Static method in class org.jmol.smiles.SmilesStereo
getChiralityForAtoms(CIPData) - Method in class org.jmol.symmetry.CIPChirality
  A general determination of chirality that involves ultimately all of Rules 1-6.
getCifData(String, Object) - Method in class org.jmol.jvxl.readers.BCifDensityReader
getCifData(String, Object) - Method in class org.jmol.jvxl.readers.CifDensityReader
getCifData(int) - Method in class org.jmol.viewer.Viewer
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.Cif2Reader
getCifDataParser() - Method in class org.jmol.adapter.readers.cif.CifReader
getCifFloat(String) - Method in class org.jmol.jvxl.readers.BCifDensityReader
getCifFloat(String) - Method in class org.jmol.jvxl.readers.CifDensityReader
getCifMap(String) - Method in class org.jmol.jvxl.readers.BCifDensityReader
getCifMap(String) - Method in class org.jmol.jvxl.readers.CifDensityReader
getCifString(String) - Method in class org.jmol.jvxl.readers.BCifDensityReader
getCIPChirality(boolean) - Method in class org.jmol.modelset.Atom
  Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
getCIPChirality(boolean) - Method in class org.jmol.modelset.Bond
  Not implemented.
getCIPChirality(boolean) - Method in class org.jmol.smiles.SmilesAtom
getCIPChirality(Viewer) - Method in class org.jmol.symmetry.Symmetry
getCIPChirality(boolean) - Method in class org.jmol.util.Edge
getCIPChirality(boolean) - Method in interface org.jmol.util.Node
getCIPChiralityCode() - Method in class org.jmol.modelset.Atom
getCIPChiralityCode() - Method in class org.jmol.smiles.SmilesAtom
getCIPChiralityCode() - Method in interface org.jmol.util.Node
getCIPChiralityCode(char) - Static method in class org.jmol.viewer.JC
getCIPChiralityName(int) - Static method in class org.jmol.viewer.JC
getCIPChiralityRule() - Method in class org.jmol.modelset.Atom
getCIPRuleName(int) - Static method in class org.jmol.viewer.JC
getCircleData() - Static method in class org.jmol.export.MeshData
  Calculates the data (faces, vertices, normals) for a circle.
getCircleResource() - Method in class org.jmol.export._IdtfExporter
getClassifiedName(String, boolean) - Method in class org.jmol.viewer.FileManager
  [0] and [2] may return same as [1] in the case of a local unsigned applet.
getClickableSet(boolean) - Method in class org.jmol.modelset.AtomCollection
getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
getClip() - Method in class org.jmol.util.JmolAudio
getClipboardText() - Method in class org.jmol.api.JmolViewer
getClipboardText() - Static method in class org.jmol.awt.AwtClipboard
  Get the String residing on the clipboard.
getClipboardText() - Method in class org.jmol.viewer.OutputManager
getClipboardText() - Method in class org.jmol.viewer.OutputManagerAwt
getClipboardText() - Method in class org.jmol.viewer.OutputManagerJS
getClipboardText() - Method in class org.jmol.viewer.Viewer
getClone() - Method in class org.jmol.adapter.smarter.Atom
getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
getCmdExt() - Method in class org.jmol.script.ScriptExpr
getCmlBondOrder(int) - Static method in class org.jmol.util.Edge
getCode() - Method in enum org.jmol.c.FIL
getCodeFromName(String) - Static method in enum org.jmol.util.Edge.EnumBondOrder
getColix(int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getColix() - Method in class org.jmol.adapter.smarter.BondIterator
getColix() - Method in class org.jmol.api.JmolAdapterBondIterator
getColix(boolean) - Method in class org.jmol.rendercgo.CGORenderer
getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
getColix(int) - Static method in class org.jmol.util.C
getColix2(int, Atom, boolean) - Method in class org.jmol.shape.Labels
getColixA(short, byte, Atom) - Method in class org.jmol.shape.Shape
getColixArray(String) - Static method in class org.jmol.util.C
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
getColixB(short, int, Bond) - Method in class org.jmol.shape.Shape
getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
getColixI(short, byte, int) - Method in class org.jmol.shape.Shape
getColixInherited(short, short) - Static method in class org.jmol.util.C
getColixO(Object) - Static method in class org.jmol.util.C
getColixS(String) - Static method in class org.jmol.util.C
getColixTranslucencyFractional(short) - Static method in class org.jmol.util.C
getColixTranslucencyLabel(short) - Static method in class org.jmol.util.C
getColixTranslucencyLevel(short) - Static method in class org.jmol.util.C
getColixTranslucent(int) - Static method in class org.jmol.util.C
getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.C
getColor() - Method in enum org.jmol.c.STR
getColor(short) - Method in class org.jmol.export.JSExporter
getColor(String) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
getColor(String) - Method in class org.jmol.jvxl.readers.KinemageReader
getColor1(int) - Method in interface org.jmol.api.GenericGraphics
getColor1(int) - Method in class org.jmol.awt.AwtG2D
getColor1(int) - Method in class org.jmol.awtjs2d.JsG2D
getColor3(int, int, int) - Method in interface org.jmol.api.GenericGraphics
getColor3(int, int, int) - Method in class org.jmol.awt.AwtG2D
getColor3(int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
getColor4(int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
getColor4(int, int, int, int) - Method in class org.jmol.awt.AwtG2D
getColor4(int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
getColorArgbOrGray(short) - Method in class org.jmol.util.GData
getColorCommand(String, byte, short, boolean) - Static method in class org.jmol.shape.Shape
getColorCommandUnk(String, short, boolean) - Static method in class org.jmol.shape.Shape
getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
getColorFromName(String) - Method in class org.jmol.applet.AppletWrapper
getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
getColorKey() - Method in class org.jmol.util.ColorEncoder
getColorList(int, short[], int, BS, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
  input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
getColorPhaseIndex(String) - Static method in class org.jmol.jvxl.readers.SurfaceReader
getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
getColorPt(Object, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
getColorRange(int) - Method in class org.jmol.script.ScriptEval
getColors(short[]) - Method in class org.jmol.export.JSExporter
getColorScheme() - Method in class org.jmol.util.ColorEncoder
getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
getColorState(ColorManager, SB) - Method in class org.jmol.viewer.StateCreator
getColorTrans(ScriptEval, int, boolean, int[]) - Method in class org.jmol.scriptext.ScriptExt
  Checks color, translucent, opaque parameters.
getColorTriad(int) - Method in class org.jmol.script.ScriptParam
getColumn(int) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
getColumn(int) - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
getColumn(int) - Method in class org.jmol.awtjs.swing.JTable
getColumnClass(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
getColumnCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
getColumnModel() - Method in class org.jmol.awtjs.swing.JTable
getColumnName(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
getCommand(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
  used for recall of commands in the application console
getCommand(Mesh) - Method in class org.jmol.shapecgo.CGO
getCommand(Mesh) - Method in class org.jmol.shapespecial.Draw
getCommand() - Method in class org.jmol.util.CommandHistory
  Calculates the command to return.
getCommand(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
getCommand2(Mesh, int) - Method in class org.jmol.shapecgo.CGO
getCommand2(Mesh, int) - Method in class org.jmol.shapespecial.Draw
getCommandDown() - Method in class org.jmol.util.CommandHistory
  Retrieves the following command from the top of the list, updates list position.
getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Generates a commandline from the options set for povray path etc and sets in the textField.
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.JmolStateCreator
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.StateCreator
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.Viewer
getCommands2(Map<String, BS>, SB, String, String) - Method in class org.jmol.viewer.StateCreator
getCommandSet(String) - Static method in class org.jmol.script.T
  retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
getCommandUp() - Method in class org.jmol.util.CommandHistory
  Retrieves the following command from the bottom of the list, updates list position.
getComparison(T, int, int, String, float[]) - Method in class org.jmol.script.ScriptExpr
getComponent(int) - Method in interface org.jmol.api.SC
getComponent(int) - Method in class org.jmol.awt.AwtSwingComponent
getComponent(int) - Method in class org.jmol.awtjs.swing.Container
getComponentCount() - Method in interface org.jmol.api.SC
getComponentCount() - Method in class org.jmol.awt.AwtSwingComponent
getComponentCount() - Method in class org.jmol.awtjs.swing.Container
getComponents() - Method in interface org.jmol.api.SC
getComponents() - Method in class org.jmol.awt.AwtSwingComponent
getComponents() - Method in class org.jmol.awtjs.swing.Container
getComposition - Variable in class org.jmol.adapter.readers.more.AFLOWReader
getConeData() - Static method in class org.jmol.export.MeshData
  Calculates the data (faces, vertices, normals) for a cone.
getConeMesh(P3, M3, short) - Static method in class org.jmol.export.___Exporter
getConeResource() - Method in class org.jmol.export._IdtfExporter
getConformation(int, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
getConformation(int, boolean, BS, BS) - Method in class org.jmol.modelsetbio.BioModel
getConnectionPoints() - Method in class org.jmol.renderspecial.DrawRenderer
getConsole() - Method in class org.jmol.viewer.Viewer
getConstraintList() - Method in class org.jmol.minimize.forcefield.Calculations
getContentPane() - Method in class org.jmol.awtjs.swing.JDialog
getContext(boolean) - Method in class org.jmol.scriptext.CmdExt
getContext(String) - Method in class org.jmol.viewer.StateManager
getContextTrace(Viewer, ScriptContext, SB, boolean) - Static method in class org.jmol.script.ScriptEval
getContextVariableAsVariable(String, boolean) - Method in class org.jmol.script.ScriptParam
getContourList(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getContourPoint(T3[], int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
getContourPoint(T3[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
  create a set of contour data.
getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
  NWCHEM only
getContrastingBlackOrWhite(Color) - Method in class org.jmol.applet.AppletWrapper
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.AlphaPolymer
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.BioPolymer
getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
getControlPoints2(float) - Method in class org.jmol.modelsetbio.BioPolymer
getConventionalUnitCell(String, M3) - Method in interface org.jmol.api.SymmetryInterface
getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.Symmetry
  return a conventional lattice from a primitive
getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.UnitCell
  return a conventional lattice from a primitive
getCoord(int) - Method in class org.jmol.adapter.readers.xtal.CgdReader
getCoordinateMap(T3[], int[], BS) - Method in class org.jmol.export.__CartesianExporter
getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
getCoordinateState(BS) - Method in class org.jmol.viewer.Viewer
getCorrelationMaps(String, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getCorrelationMaps(String, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
getCovalentBondCount() - Method in class org.jmol.modelset.Atom
getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
  Returns the number of bonds of this atom.
getCovalentBondCount() - Method in interface org.jmol.util.Node
getCovalentBondCount() - Method in interface org.jmol.util.SimpleNode
  Get the total number of covalent bonds, thus not including hydrogen bonds.
getCovalentBondCountPlusMissingH() - Method in class org.jmol.modelset.Atom
getCovalentBondCountPlusMissingH() - Method in class org.jmol.smiles.SmilesAtom
getCovalentBondCountPlusMissingH() - Method in interface org.jmol.util.Node
  includes actual + missing
getCovalentBondOrder(int) - Static method in class org.jmol.util.Edge
getCovalentBondsForAtoms(Bond[], int, BS) - Static method in class org.jmol.viewer.PropertyManager
getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getCovalentHydrogenCount() - Method in interface org.jmol.util.Node
getCovalentlyConnectedBitSet(Node[], Node, BS, boolean, boolean, Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
getCovalentOrder() - Method in class org.jmol.modelset.Bond
getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
getCovalentOrder() - Method in class org.jmol.util.Edge
getCovalentOrder() - Method in interface org.jmol.util.SimpleEdge
getCovalentRadius(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getCovalentRadius(int) - Static method in class org.jmol.util.Elements
  Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR
getCParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getCPAtomInfo(String, Lst<Object>) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Process a CP data line
getCrossLinkGroup(int, Lst<Integer>, Group, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Atom
  Used by SMILES to get vector of cross-links
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Group
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.smiles.SmilesAtom
getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in interface org.jmol.util.Node
getCSSstyle(int, int) - Method in class org.jmol.awtjs.swing.Component
getCStr(byte[], int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
getCurrentBondCount() - Method in class org.jmol.modelset.Atom
getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
getCurrentColorSchemeName() - Method in class org.jmol.util.ColorEncoder
getCurrentFileAsString(String) - Method in class org.jmol.viewer.Viewer
getCurrentModelAuxInfo() - Method in class org.jmol.viewer.Viewer
getCurrentSolventProbeRadius() - Method in class org.jmol.viewer.Viewer
getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
getCurrentX() - Method in class org.jmol.viewer.ActionManager
getCurrentY() - Method in class org.jmol.viewer.ActionManager
getCursorX() - Method in class org.jmol.viewer.Viewer
getCursorY() - Method in class org.jmol.viewer.Viewer
getCylinderData(boolean) - Static method in class org.jmol.export.MeshData
  Calculates the data (faces, vertices, normals) for a cylinder.
getCylinderResource(boolean) - Method in class org.jmol.export._IdtfExporter
getData() - Method in class org.jmol.adapter.readers.cif.CifReader
getData() - Method in class org.jmol.adapter.readers.more.AFLOWReader
getData(String, String, String, int) - Method in class org.jmol.adapter.readers.quantum.NBOParser
getData(InputStream, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  called by SmarterJmolAdapter via JmolUtil to open a Spartan directory and get all the needed data as a string.
getData(String, BS, int) - Method in interface org.jmol.api.JmolDataManager
getData(String, String) - Method in class org.jmol.api.JmolViewer
getData(String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getData(String) - Method in class org.jmol.modelkit.ModelKitPopup
getData(int, int, BioPolymer, char, char, int, BS, BS, boolean, boolean, boolean, boolean, boolean, boolean, float, boolean, boolean, LabelToken[], OC, SB, BS, P3) - Method in class org.jmol.modelsetbio.BioExt
getData() - Method in class org.jmol.quantum.NMRCalculation
  Creates the data set necessary for doing NMR calculations.
getData(String) - Method in class org.jmol.script.ScriptCompiler
getData(Object[]) - Static method in class org.jmol.shapecgo.CGOMesh
getData(String, BS, int) - Method in class org.jmol.viewer.DataManager
getData(String, String) - Method in class org.jmol.viewer.Viewer
getDataBlock() - Method in class org.jmol.adapter.readers.more.MdTopReader
getDataKey(int) - Method in class org.jmol.dssx.AnnotationParser
getDataManager() - Method in class org.jmol.viewer.Viewer
getDataMinMax() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getDataObj(String, BS, int) - Method in class org.jmol.viewer.Viewer
  Retrieve a data object
getDataRange(IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
getDataRange() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getDataSeparator() - Method in class org.jmol.viewer.Viewer
getDataState(JmolStateCreator, SB) - Method in interface org.jmol.api.JmolDataManager
getDataState(JmolStateCreator, SB) - Method in class org.jmol.viewer.DataManager
getDataState(SB) - Method in class org.jmol.viewer.StateCreator
getDateFormat(String) - Method in interface org.jmol.api.GenericPlatform
getDateFormat(String) - Method in class org.jmol.awt.Platform
getDateFormat(String) - Method in class org.jmol.awtjs2d.Platform
getDE(MinAtom, int, int, double) - Method in class org.jmol.minimize.forcefield.ForceField
getDE(float[], int, int, int, int, boolean) - Method in class org.jmol.util.MeshSlicer
getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.Calculations
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.Calculations
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
getDebugHeader2(int) - Method in class org.jmol.minimize.forcefield.Calculations
getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
getDebugLineC(int, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
getDef(String) - Method in class org.jmol.export._VrmlExporter
getDef(String) - Method in class org.jmol.export.UseTable
  This Hashtable contains references to _n where n is a number.
getDefaultBoundBox() - Method in class org.jmol.modelset.ModelSet
  The default bounding box is created when the LOAD ....
getDefaultColix() - Method in class org.jmol.shapesurface.Isosurface
getDefaultCount(int, boolean) - Static method in class org.jmol.smiles.SmilesAtom
getDefaultDirectory(String) - Method in class org.jmol.viewer.FileManager
getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
getDefaultLabelState(Labels) - Method in class org.jmol.viewer.StateCreator
getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelsetbio.BioModel
getDefaultLattice() - Method in class org.jmol.viewer.Viewer
getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
  When creating a new bond, determine bond diameter from order
getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
getDefaultPropertyParam(int) - Method in interface org.jmol.api.JmolPropertyManager
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.PropertyManager
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.Viewer
getDefaultSetting(int, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
  All settings that Jmol uses should go here
getDefaultSettingPt(int, int, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
getDefaultSettingS(int, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
getDefaultStructure(BS, BS) - Method in class org.jmol.modelset.ModelSet
getDefaultUnitCell() - Method in class org.jmol.adapter.readers.cif.MSRdr
getDefaultVdwNameOrData(VDW, BS) - Method in interface org.jmol.api.JmolDataManager
getDefaultVdwNameOrData(VDW, BS) - Method in class org.jmol.viewer.DataManager
getDefaultVdwNameOrData(int, VDW, BS) - Method in class org.jmol.viewer.Viewer
getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelSet
getDefinedAtomSet(String) - Method in class org.jmol.viewer.Viewer
getDefinedState(SB, boolean) - Method in class org.jmol.viewer.StateCreator
getDefRet(String, String[]) - Method in class org.jmol.export.UseTable
  Used by JSExporter for WebGL
getDegrees(float, boolean) - Method in class org.jmol.multitouch.ActionManagerMT
getDegrees(float, boolean) - Method in class org.jmol.viewer.ActionManager
  Transform a screen pixel change to an angular change such that a full sweep of the dimension (up to 500 pixels) corresponds to 180 degrees of rotation.
getDelayMaximumMs() - Method in class org.jmol.viewer.Viewer
getDerivedSpaceGroup() - Method in class org.jmol.symmetry.SpaceGroup
getDesc(ModelSet) - Method in class org.jmol.symmetry.Symmetry
getDescent(Object) - Static method in class org.jmol.awt.AwtFont
getDescent(Object) - Static method in class org.jmol.awtjs2d.JSFont
getDescent() - Method in class org.jmol.util.Font
getDescription() - Method in class org.jmol.dialog.Dialog.TypeFilter
getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getDFMap(String, String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
  finds the position in the Jmol-required list of function types.
getDialog() - Method in class org.jmol.dialog.FileChooser
getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getDiameter(int, int) - Method in class org.jmol.render.FontLineShapeRenderer
getDiameter() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
getDictRefValue() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
getDiffusePercent() - Method in class org.jmol.util.GData
getDigits(String, int, int[]) - Static method in class org.jmol.smiles.SmilesParser
getDihedralMap(int[]) - Method in class org.jmol.modelset.ModelSet
getDimensionValue(T3, int) - Static method in class org.jmol.bspt.Node
getDimensionValue(int) - Method in class org.jmol.modelset.Atom
getDipolarConstantHz(Atom, Atom) - Method in interface org.jmol.api.JmolNMRInterface
getDipolarConstantHz(Atom, Atom) - Method in class org.jmol.quantum.NMRCalculation
getDipolarCouplingHz(Atom, Atom, V3) - Method in interface org.jmol.api.JmolNMRInterface
getDipolarCouplingHz(Atom, Atom, V3) - Method in class org.jmol.quantum.NMRCalculation
getDipoleIndex(int, int) - Method in class org.jmol.shapespecial.Dipoles
getDipoleIndexFor(String, String) - Method in class org.jmol.shapespecial.Dipoles
getDirect() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
getDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
getDocument() - Method in class org.jmol.awtjs.swing.JTextPane
getDOMAttributesA(Object[]) - Method in class org.jmol.adapter.readers.xml.XmlReader
getDoTranslate() - Static method in class org.jmol.i18n.GT
getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
getDouble(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
getDragDropFileTypeName(String) - Method in class org.jmol.script.ScriptManager
getDragSelected() - Method in class org.jmol.viewer.Viewer
getDrawHover() - Method in class org.jmol.viewer.Viewer
getDSSRForModel(Viewer, int) - Method in class org.jmol.dssx.DSSR1
getDSSRFrame(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
getDSSRFrame(Viewer) - Method in class org.jmol.modelsetbio.NucleicMonomer
getDualHydrogenBondArray() - Method in class org.jmol.dssx.DSSP
  (p.
getDX(int, int) - Method in class org.jmol.viewer.Gesture
getDY(int, int) - Method in class org.jmol.viewer.Gesture
getEchoName(int) - Static method in class org.jmol.viewer.JC
getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
getEdgePoints(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader
getEdges() - Method in class org.jmol.modelset.Atom
getEdges() - Method in class org.jmol.smiles.SmilesAtom
getEdges() - Method in interface org.jmol.util.Node
getEdges() - Method in interface org.jmol.util.SimpleNode
  Get the bond array, including hydrogen bonds.
getEigenSort() - Static method in class org.jmol.util.Tensor
getElectronCount(int[]) - Method in class org.jmol.smiles.SmilesRingSet
getElement(String) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
getElement(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
  allow for any number of characters, for which the first one or two are an element symbol.
getElementCounts() - Method in class org.jmol.symmetry.PointGroup
getElementName(int) - Method in class org.jmol.modelset.AtomCollection
getElementNumber() - Method in class org.jmol.adapter.smarter.AtomIterator
getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
getElementNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getElementNumber() - Method in class org.jmol.modelset.Atom
getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
  Returns the atomic number of the element or 0
getElementNumber(int) - Static method in class org.jmol.util.Elements
getElementNumber() - Method in interface org.jmol.util.Node
getElementNumber() - Method in interface org.jmol.util.SimpleNode
getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelSet
getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
getElementSymbol() - Method in class org.jmol.modelset.Atom
getElementSymbol(int) - Static method in class org.jmol.util.Elements
getElementSymbolIso(boolean) - Method in class org.jmol.modelset.Atom
getElemNos() - Method in class org.jmol.shapespecial.Polyhedron
getEllipsoidForAtomTensor(Tensor, Atom) - Static method in class org.jmol.shapespecial.Ellipsoid
getEllipsoidShade(float, float, float, int, M4) - Method in class org.jmol.util.Shader
getEmbeddedFileState(String, boolean, String) - Method in class org.jmol.viewer.FileManager
getEmbeddedScript(String) - Static method in class org.jmol.viewer.FileManager
getEmptyEllipsoid(String, int) - Static method in class org.jmol.shapespecial.Ellipsoid
getEncodedOrder() - Method in class org.jmol.adapter.smarter.BondIterator
getEncodedOrder() - Method in class org.jmol.api.JmolAdapterBondIterator
getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within element
getEncoding(String) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
getEndChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
getEndChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getEndInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
getEndInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
getEneChirality(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, boolean, boolean) - Method in class org.jmol.symmetry.CIPChirality
  Determine the stereochemistry of a bond
getEneKekule() - Method in class org.jmol.symmetry.CIPData
  Look for conjugated loops of any size that have atoms not already in aromatic rings
getEnergies(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
  Get the energy of a given type or types.
getEnergy() - Method in class org.jmol.minimize.forcefield.Calculation
getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
getEnergy() - Method in class org.jmol.modelset.Bond
getEnergy() - Method in class org.jmol.modelset.HBond
getEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
getEnergyOnly() - Method in class org.jmol.minimize.Minimizer
getEneTop() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Check ene for first nonduplicate.
getEntryIcon(String[]) - Method in class org.jmol.popup.GenericPopup
getEquationForQuadricWithCenter(float, float, float, M3, V3, M3, double[], M4) - Static method in class org.jmol.shapespecial.Ellipsoid
getEquivalentType(int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
  equivalent types for OOP and torsions
getErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptError
getErrorLineMessage2() - Method in class org.jmol.script.ScriptEval
getErrorMessage() - Method in interface org.jmol.api.JmolScriptEvaluator
getErrorMessage() - Method in class org.jmol.api.JmolViewer
getErrorMessage() - Method in class org.jmol.script.ScriptError
getErrorMessage() - Method in class org.jmol.viewer.Viewer
getErrorMessageUn() - Method in class org.jmol.api.JmolViewer
getErrorMessageUn() - Method in class org.jmol.viewer.Viewer
getErrorMessageUntranslated() - Method in interface org.jmol.api.JmolScriptEvaluator
getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptError
getErrorMessageUntranslated() - Method in exception org.jmol.script.ScriptException
getEvalContextAndHoldQueue(JmolScriptEvaluator) - Method in class org.jmol.viewer.Viewer
getEventName(int) - Static method in class org.jmol.multitouch.ActionManagerMT
getExecutor() - Method in interface org.jmol.api.JmolParallelProcessor
getExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
getExitRate() - Method in class org.jmol.viewer.ActionManager
getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
getExportDate() - Method in class org.jmol.export.___Exporter
getExportDriverList() - Method in class org.jmol.viewer.Viewer
getExportName() - Method in interface org.jmol.api.JmolRendererInterface
getExportName() - Method in class org.jmol.export.Export3D
getExportName() - Method in class org.jmol.g3d.Graphics3D
getExportType() - Method in interface org.jmol.api.JmolRendererInterface
getExportType() - Method in class org.jmol.export.Export3D
getExportType() - Method in class org.jmol.g3d.Graphics3D
getExt(String) - Method in class org.jmol.script.ScriptExpr
getFace(Mesh) - Method in class org.jmol.shapesurface.Pmesh
  return a cycle of points generating this face used after slabbing
getFaces() - Method in class org.jmol.jvxl.readers.IsoSolventReader
getFaces(int[][], int, Map<Integer, Object[]>) - Method in class org.jmol.shapespecial.Polyhedra
  Face: a CCW loop of edges all (within tolerance) in the same plane.
getFaces() - Method in class org.jmol.util.MeshSurface
getFaceTriangles(int, Map<Integer, Object[]>, int) - Method in class org.jmol.shapespecial.Polyhedra
getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
getFactoredValue(int) - Method in class org.jmol.util.Tensor
  Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor
getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
getField(byte) - Method in class org.jmol.adapter.readers.cif.CifReader
getField(String) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
getFile(int) - Method in class org.jmol.console.JmolConsole.FileChecker
getFile() - Method in class org.openscience.jmol.app.HistoryFile
getFile() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
getFile31() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
getFile46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
  read the labels from xxxx.46
getFileAsBytes(String, OC) - Method in class org.jmol.viewer.FileManager
getFileAsMap(String, String) - Method in class org.jmol.viewer.FileManager
getFileAsString(String) - Method in class org.jmol.viewer.Viewer
getFileAsString3(String, boolean, String) - Method in class org.jmol.viewer.Viewer
getFileAsString4(String, int, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
getFileData(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
getFileData(int) - Method in class org.jmol.modelset.ModelSet
getFileData() - Method in class org.jmol.viewer.Viewer
getFileDataAsString(String[], int, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
getFileHeader(int) - Method in class org.jmol.modelset.ModelSet
getFileHeader() - Method in class org.jmol.viewer.Viewer
getFileInfo() - Method in class org.jmol.viewer.FileManager
getFileInfo(Object, String) - Static method in class org.jmol.viewer.PropertyManager
getFileList(String, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  get a complete critical file list for a spartan file Mac directory based on file extension ".spardir.zip" or ".spardir"
getFileName() - Method in class org.jmol.viewer.FileManager
getFileName() - Method in exception org.jmol.viewer.JmolAsyncException
getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
getFileReader(String) - Method in class org.jmol.shapesurface.Isosurface
getFileReferences(String, Lst<String>) - Static method in class org.jmol.viewer.FileManager
getFiles() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
getFileState(SB) - Method in class org.jmol.viewer.StateCreator
getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
  From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  Just get the resolved file type; if a file, does NOT close the reader
getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
  Get the type of this file or molecular model, if known.
getFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
getFirstAtomIndexFromAtomNumber(int, BS) - Method in class org.jmol.modelset.AtomCollection
getFlag(int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  safely get a one-character 0 or 1 as a boolean
getFlags(String) - Static method in class org.jmol.smiles.SmilesParser
getFlexFitList(BS, BS, String, boolean) - Method in class org.jmol.scriptext.SmilesExt
getFloat() - Method in class org.jmol.adapter.readers.more.MdCrdReader
getFloat(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
getFloat(int) - Method in class org.jmol.api.JmolViewer
getFloat() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
getFloat() - Method in class org.jmol.jvxl.readers.PmeshReader
getFloat(Lst<Object>, int) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
getFloat(int) - Method in class org.jmol.shapecgo.CGOMesh
getFloat(int) - Method in class org.jmol.viewer.Viewer
getFloatEncodedInt(String) - Static method in class org.jmol.script.ScriptParam
  Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.
getFloatProperty(String) - Method in class org.jmol.modelset.Atom
getFloatProperty(String) - Method in class org.jmol.smiles.SmilesAtom
getFloatProperty(String) - Method in interface org.jmol.util.Node
getFont(float) - Method in class org.jmol.shape.Frank
getFont3D(byte) - Static method in class org.jmol.util.Font
getFont3D(float) - Method in class org.jmol.util.GData
getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
getFont3DCurrent() - Method in class org.jmol.util.GData
getFont3DFS(String, float) - Method in class org.jmol.util.GData
getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
getFont3DScaled(Font, float) - Method in class org.jmol.util.GData
getFontAscent(Object) - Method in interface org.jmol.api.FontManager
getFontAscent(Object) - Method in class org.jmol.awt.Platform
getFontAscent(Object) - Method in class org.jmol.awtjs2d.Platform
getFontCommand(String, Font) - Static method in class org.jmol.shape.Shape
getFontDescent(Object) - Method in interface org.jmol.api.FontManager
getFontDescent(Object) - Method in class org.jmol.awt.Platform
getFontDescent(Object) - Method in class org.jmol.awtjs2d.Platform
getFontFaceID(String) - Static method in class org.jmol.util.Font
getFontFid(float) - Method in class org.jmol.util.GData
getFontFidFS(String, float) - Method in class org.jmol.util.GData
getFontLineShapeState(FontLineShape) - Method in class org.jmol.viewer.StateCreator
getFontMetrics(Font, Object) - Method in interface org.jmol.api.FontManager
getFontMetrics(Font, Object) - Static method in class org.jmol.awt.AwtFont
getFontMetrics(Font, Object) - Method in class org.jmol.awt.Platform
getFontMetrics(Font, Object) - Static method in class org.jmol.awtjs2d.JSFont
getFontMetrics(Font, Object) - Method in class org.jmol.awtjs2d.Platform
getFontMetrics() - Method in class org.jmol.modelset.Text
getFontMetrics() - Method in class org.jmol.util.Font
getFontState(String, Font) - Method in class org.jmol.viewer.StateCreator
getFontStyleID(String) - Static method in class org.jmol.util.Font
getForceField(String) - Method in class org.jmol.minimize.Minimizer
getFormalCharge() - Method in class org.jmol.adapter.smarter.AtomIterator
getFormalCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getFormalCharge() - Method in class org.jmol.modelset.Atom
getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
getFormalCharge() - Method in interface org.jmol.util.Node
getFormalCharge() - Method in interface org.jmol.util.SimpleNode
getFormatType(String) - Static method in class org.jmol.script.SV
getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  get all integers after letters negative entries are spaces (1Xn)
getFractional(Atom, P3) - Method in class org.jmol.modelset.Trajectory
getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
getFractionalCoord(V3) - Method in class org.jmol.adapter.readers.xtal.CastepReader
getFractionalCoord(boolean, char, boolean, P3) - Method in class org.jmol.modelset.Atom
getFractionalCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
getFractionalOffset() - Method in class org.jmol.symmetry.UnitCell
getFractionalOrigin() - Method in interface org.jmol.api.SymmetryInterface
getFractionalOrigin() - Method in class org.jmol.symmetry.Symmetry
getFractionalOrigin() - Method in class org.jmol.util.SimpleUnitCell
getFractionalUnitCoord(boolean, char, P3) - Method in class org.jmol.modelset.Atom
getFractionalUnitCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
getFractionalUnitDistance(T3, T3, T3) - Method in class org.jmol.modelset.Atom
getFrame() - Method in interface org.jmol.awt.JmolFrame
getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
getFrame() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
getFrame() - Static method in class org.openscience.jmol.app.webexport.WebExport
getFrameAtoms() - Method in class org.jmol.viewer.Viewer
getFrameCount() - Method in class org.jmol.viewer.AnimationManager
getFrameDelayMs(int) - Method in class org.jmol.modelset.ModelSet
getFrameOffsets(BS, boolean) - Method in class org.jmol.modelset.ModelSet
getFrameScenes(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  remove all scenes that do not define a frame.
getFrameStep(int) - Method in class org.jmol.viewer.AnimationManager
getFrameTitle(int) - Method in class org.jmol.modelset.ModelSet
getFrameTitle() - Method in class org.jmol.viewer.Viewer
getFullMap() - Method in class org.jmol.script.ScriptContext
getFullName() - Method in class org.jmol.appletjs.Jmol
getFullPath() - Method in interface org.jmol.api.GenericFileInterface
getFullPath() - Method in class org.jmol.awt.AwtFile
getFullPath() - Method in class org.jmol.awtjs2d.JSFile
getFullPathName() - Method in class org.jmol.script.ScriptEval
getFullPathName(boolean) - Method in class org.jmol.viewer.FileManager
getFullPathNameOrError(String, boolean, String[]) - Method in class org.jmol.viewer.FileManager
  just check for a file as being readable.
getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
getFullPDBHeader(Map<String, Object>) - Method in class org.jmol.modelsetbio.BioExt
getFullPDBHeader() - Method in class org.jmol.modelsetbio.BioModel
getFullProteinStructureState(BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.GenericPlatform
getFullScreenDimensions(Object, int[]) - Static method in class org.jmol.awt.Display
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
getFullScreenDimensions(Object, int[]) - Static method in class org.jmol.awtjs2d.Display
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awtjs2d.Platform
getFunction(String) - Method in class org.jmol.viewer.Viewer
getFunctionCalls(String) - Method in class org.jmol.viewer.JmolStateCreator
getFunctionCalls(String) - Method in class org.jmol.viewer.StateCreator
getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
getFunctions(boolean) - Method in class org.jmol.viewer.Viewer
getFunctionZfromXY() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
getGhostOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getGLmolView() - Method in class org.jmol.appletjs.Jmol
  This method is only called by JmolGLmol applet._refresh();
getGLmolView() - Method in class org.jmol.viewer.Viewer
  This method is only called by JmolGLmol applet._refresh();
getGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
getGraphics(Object) - Static method in class org.jmol.awt.Image
getGraphics(Object) - Method in class org.jmol.awt.Platform
getGraphics(Object) - Method in class org.jmol.awtjs.Platform
getGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
getGraphicsForMetrics() - Method in class org.jmol.g3d.Platform3D
getGraphicsForTextOrImage(int, int) - Method in class org.jmol.g3d.Platform3D
getGroup(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getGroup1(char) - Method in class org.jmol.modelset.Atom
getGroup1() - Method in class org.jmol.modelset.Group
getGroup1() - Method in class org.jmol.modelsetbio.Monomer
getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
getGroup1(char) - Method in interface org.jmol.util.Node
getGroup1b() - Method in class org.jmol.modelsetbio.Monomer
getGroup1b() - Method in class org.jmol.modelsetbio.NucleicMonomer
getGroup3() - Method in class org.jmol.adapter.smarter.AtomIterator
getGroup3() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getGroup3(boolean) - Method in class org.jmol.modelset.Atom
getGroup3() - Method in class org.jmol.modelset.Group
getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
getGroup3(boolean) - Method in interface org.jmol.util.Node
getGroupBits(BS) - Method in class org.jmol.modelset.Atom
getGroupBits(BS) - Method in class org.jmol.smiles.SmilesAtom
getGroupBits(BS) - Method in interface org.jmol.util.Node
getGroupCount() - Method in class org.jmol.modelset.Model
getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getGroupID(String) - Method in class org.jmol.modelsetbio.BioResolver
getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
getGroupIdFor(String) - Static method in class org.jmol.modelsetbio.BioResolver
getGroupInfo(int, P3) - Method in class org.jmol.modelset.Group
getGroupParameter(int) - Method in class org.jmol.modelset.Group
  Monomers only
getGroupParameter(int) - Method in class org.jmol.modelsetbio.Monomer
getGroups() - Method in class org.jmol.modelset.ModelSet
  In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
getGroupsWithin(int, BS) - Method in class org.jmol.modelset.ModelSet
getGroupsWithin(int, BS) - Method in class org.jmol.viewer.Viewer
getGroupsWithinAll(int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
getHallLatticeEquivalent(int) - Static method in class org.jmol.symmetry.HallTranslation
getHallTerms() - Static method in class org.jmol.symmetry.HallRotation
getHallTerms() - Static method in class org.jmol.symmetry.HallTranslation
getHallTranslation(char, int) - Static method in class org.jmol.symmetry.HallTranslation
getHandedness(SimpleNode, SimpleNode, SimpleNode, SimpleNode, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
  determine the winding of the circuit a--b--c relative to point pt
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in interface org.jmol.api.JmolAnnotationParser
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.AnnotationParser
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.DSSR1
getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
getHeader() - Method in class org.jmol.jvxl.readers.EfvetReader
getHeight(Object) - Static method in class org.jmol.awt.Image
getHeight() - Method in class org.jmol.awtjs.swing.Component
getHeight(Object) - Static method in class org.jmol.awtjs2d.Image
getHeight() - Method in class org.jmol.util.Font
getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getHelixData(BS, int) - Method in class org.jmol.scriptext.MathExt
getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
getHelp(String) - Method in class org.jmol.viewer.Viewer
getHermiteLevel() - Method in class org.jmol.viewer.Viewer
getHermiteList(int, T3, T3, T3, T3, T3, T3[], int, int, boolean) - Static method in class org.jmol.util.GData
  Used by Navigator, BioShapeRenderer, and DrawRenderer
getHeteroList(int) - Method in class org.jmol.modelset.ModelSet
getHexCode(short) - Static method in class org.jmol.util.C
getHexCodes(short[]) - Static method in class org.jmol.util.C
getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
getHexitValue(char) - Static method in class org.jmol.util.Escape
getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
getHideNotSelected() - Method in class org.jmol.viewer.SelectionManager
getHigh - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
getHighestOrder() - Method in class org.jmol.symmetry.PointGroup
getHistoryWindowPosition(String) - Method in interface org.jmol.api.JmolAppAPI
getHistoryWindowPosition(String) - Method in class org.openscience.jmol.app.JmolApp
getHistoryWindowSize(String) - Method in interface org.jmol.api.JmolAppAPI
getHistoryWindowSize(String) - Method in class org.openscience.jmol.app.JmolApp
getHklPlane(P3) - Method in class org.jmol.script.ScriptParam
getHorizAlignmentName(int) - Static method in class org.jmol.viewer.JC
getHoverDelay() - Method in class org.jmol.viewer.Viewer
getHoverLabel(int) - Method in class org.jmol.modelkit.ModelKitPopup
  Called by Viewer.hoverOn to set the special label if desired.
getHtmlDisabled() - Method in class org.jmol.awtjs.swing.AbstractButton
getHtmlDisabled() - Method in class org.jmol.awtjs.swing.JMenuItem
getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getHybridizationAndAxes(int, int, V3, V3, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
getHybridizationAndAxes(int, V3, V3, String) - Method in class org.jmol.viewer.Viewer
getHybridizationAndAxesD(int, V3, V3, String) - Method in class org.jmol.modelset.AtomCollection
  dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)
getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
  Get the hydrogen atom count -- for ligand files
getHydrophobicity() - Method in class org.jmol.modelset.Atom
getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
getHydrophobicity(int) - Static method in class org.jmol.util.Elements
getIcon() - Method in interface org.jmol.api.SC
getIcon() - Method in class org.jmol.awt.AwtSwingComponent
getIcon() - Method in class org.jmol.awtjs.swing.AbstractButton
getIcon(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getId() - Method in enum org.jmol.c.STR
getID(String, int) - Method in class org.jmol.shapesurface.LcaoCartoon
getId(int) - Method in class org.jmol.shapesurface.MolecularOrbital
getIdentifierOrNull(String) - Method in class org.jmol.modelset.AtomCollection
  overhauled by RMH Nov 1, 2006.
getIdentifierOrNull(String) - Method in class org.jmol.modelsetbio.BioModelSet
getIdentity() - Method in class org.jmol.minimize.MinAtom
getIdentity(boolean) - Method in class org.jmol.modelset.Atom
getIdentity() - Method in class org.jmol.modelset.Bond
getIdentityXYZ(boolean, P3) - Method in class org.jmol.modelset.Atom
getIDStr() - Method in class org.jmol.modelset.Chain
getImage(Viewer, Object, String, boolean) - Method in class org.jmol.io.JmolUtil
getImage(String, boolean) - Method in class org.jmol.viewer.PropertyManager
getImage(boolean, boolean) - Method in class org.jmol.viewer.Viewer
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.api.JmolViewer
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.OutputManager
  Called when a simple image is required -- from x=getProperty("image") or for a simple preview PNG image for inclusion in a ZIP file from write xxx.zip or xxx.jmol, or for a PNGJ or PNG image that is being posted because of a URL that contains "?POST?_PNG_" or ?POST?_PNGJ_" or ?POST?_PNGJBIN_".
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
getImageDialog(String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.GenericPlatform
getImageDialog(PlatformViewer, String, Map<String, GenericImageDialog>) - Static method in class org.jmol.awt.Image
getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awt.Platform
getImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Static method in class org.jmol.awtjs2d.Image
getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awtjs2d.Platform
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in class org.jmol.dialog.Dialog
getImageHeight(Object) - Method in interface org.jmol.api.GenericPlatform
getImageHeight(Object) - Method in class org.jmol.awt.Platform
getImageHeight(Object) - Method in class org.jmol.awtjs2d.Platform
getImageIcon(String) - Method in class org.jmol.awt.AwtJmolPopup
getImageIcon(String) - Method in class org.jmol.awt.AwtModelKitPopup
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSJmolPopup
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
getImageIcon(String) - Method in class org.jmol.popup.GenericPopup
getImageWidth(Object) - Method in interface org.jmol.api.GenericPlatform
getImageWidth(Object) - Method in class org.jmol.awt.Platform
getImageWidth(Object) - Method in class org.jmol.awtjs2d.Platform
getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getImplicitHydrogenCount() - Method in interface org.jmol.util.Node
  can be > 0 for PDB model with no H atoms or for SMILES string CCC
getIndex() - Method in class org.jmol.modelset.Atom
getIndex(int, int, int, int) - Method in class org.jmol.modelsetbio.BioPolymer
getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
getIndex() - Method in class org.jmol.smiles.SmilesAtom
  Returns the atom index of the atom.
getIndex() - Method in interface org.jmol.util.Node
getIndex() - Method in interface org.jmol.util.SimpleNode
getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
getIndexFromName(String) - Method in class org.jmol.shape.Shape
getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
getIndexFromName(String) - Method in class org.jmol.shapespecial.Polyhedra
getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
getInfo(String) - Method in interface org.jmol.api.JmolNMRInterface
getInfo() - Method in class org.jmol.modelset.Atom
getInfo(int, String) - Method in class org.jmol.modelset.ModelSet
getInfo(String) - Method in class org.jmol.quantum.NMRCalculation
getInfo(int) - Method in class org.jmol.shape.Measures
getInfo(boolean) - Method in class org.jmol.shape.Mesh
getInfo(Viewer, String) - Method in class org.jmol.shapespecial.Polyhedron
getInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.PointGroup
getInfo(SpaceGroup, String, SymmetryInterface, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
getInfo(SymmetryInterface) - Method in class org.jmol.symmetry.SpaceGroup
getInfo(Object[], int) - Static method in class org.jmol.symmetry.SymmetryDesc
  Return information about a symmetry operator by type: array, angle, axis, center, draw, full, info, label, matrix4f, point, time, plane, translation, unitcell, xyz, all, or a negative number (-length, -1]: { "xyz", "xyzOriginal", "label", "draw", "fractionalTranslation", "cartesianTranslation", "inversionCenter", "axisPoint", "axisVector", "rotationAngle", "matrix", "unitTranslation", "centeringVector", "timeReversal", "plane", "_type", "id" } where "all" is the info array itself,
getInfo() - Method in class org.jmol.symmetry.SymmetryOperation
getInfo() - Method in class org.jmol.symmetry.UnitCell
getInfo() - Method in class org.jmol.util.Font
getInfo() - Method in class org.jmol.util.Modulation
getInfo(Map<String, Object>) - Method in class org.jmol.util.ModulationSet
getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
getInfo(String) - Method in class org.jmol.util.Tensor
  returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
getInfo(Map<String, Object>) - Method in class org.jmol.util.Vibration
getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
getInfoAsString(int) - Method in class org.jmol.shape.AtomShape
getInfoAsString(int) - Method in class org.jmol.shape.Measures
getInfoB(int, String) - Method in class org.jmol.modelset.ModelSet
getInfoHeight() - Method in class org.openscience.jmol.app.webexport.WebPanel
getInfoI(int, String) - Method in class org.jmol.modelset.ModelSet
getInfoIndex(String) - Static method in class org.jmol.util.Tensor
getInfoM(String) - Method in class org.jmol.modelset.ModelSet
getInfoWidth() - Method in class org.openscience.jmol.app.webexport.WebPanel
getInfoXYZ(Atom) - Method in class org.jmol.viewer.ChimeMessenger
  called when an atom is picked
getInfoXYZ(Atom) - Method in interface org.jmol.viewer.JmolChimeMessenger
getINI() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Save INI file
getInitiatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getInitiatorAtom() - Method in class org.jmol.modelsetbio.Monomer
getInitiatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
getInlineChar() - Method in class org.jmol.viewer.Viewer
getInlineData(int) - Method in class org.jmol.modelset.ModelSet
getInlineData(SB, String, boolean, String) - Method in class org.jmol.viewer.JmolStateCreator
getInlineData(SB, String, boolean, String) - Method in class org.jmol.viewer.StateCreator
getInMotion(boolean) - Method in class org.jmol.viewer.Viewer
getInputPoint(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  for debugging
getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
getInputStreamOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
getInsCode() - Method in class org.jmol.modelset.Group
getInsertedCommand() - Method in class org.jmol.viewer.Viewer
getInsertionCode() - Method in class org.jmol.adapter.smarter.AtomIterator
getInsertionCode() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getInsertionCode() - Method in class org.jmol.modelset.Atom
getInsertionCode() - Method in class org.jmol.modelset.Group
getInsertionCode() - Method in class org.jmol.smiles.SmilesAtom
getInsertionCode() - Method in interface org.jmol.util.Node
getInsertionCodeChar(int) - Static method in class org.jmol.modelset.Group
getInsertionCodeFor(int) - Static method in class org.jmol.modelset.Group
getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getInsertionListInModel(int) - Method in class org.jmol.modelset.ModelSet
getInstance() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getInstance(JmolViewer, String, int, int, int) - Static method in class org.openscience.jmol.app.webexport.JmolInstance
getInstanceList() - Method in class org.openscience.jmol.app.webexport.WebPanel
getInstanceName(int) - Method in class org.openscience.jmol.app.webexport.WebPanel
getInstanceWithParams(String, Class<?>[], Object...) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getInt(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  safe int parsing of line.substring(col1, col2);
getInt(int) - Method in class org.jmol.api.JmolViewer
getInt() - Method in class org.jmol.jvxl.readers.EfvetReader
getInt() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
getInt() - Method in class org.jmol.jvxl.readers.PmeshReader
getInt(int) - Method in class org.jmol.shapecgo.CGOMesh
getInt(Map<String, Object>, String, int) - Static method in class org.jmol.viewer.OutputManager
getInt(int) - Method in class org.jmol.viewer.Viewer
getInt(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
getIntArray2(int) - Method in class org.jmol.scriptext.ScriptExt
getIntData() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
getIntegration() - Method in class org.jmol.quantum.QuantumCalculation
getInteractionTensorList(String, BS) - Method in class org.jmol.quantum.NMRCalculation
  Returns a list of tensors that are of the specified type and have both atomIndex1 and atomIndex2 in bsA.
getInterface(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getInterface(String, Viewer, String) - Static method in class org.jmol.api.Interface
getInterface(String) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
getIntersection(float, P4, P3[], Lst<P3[]>, float[], BS, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSlicer
getIntTableNumber() - Method in interface org.jmol.api.SymmetryInterface
getIntTableNumber() - Method in class org.jmol.symmetry.Symmetry
getInverseNormix(short) - Static method in class org.jmol.util.Normix
getISCtype(Atom, String) - Method in class org.jmol.quantum.NMRCalculation
getIsHetero() - Method in class org.jmol.adapter.smarter.AtomIterator
getIsHetero() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getIsoExt() - Method in class org.jmol.script.ScriptExpr
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in interface org.jmol.api.JmolNMRInterface
  If t is null, then a1, a2, and type are used to find the appropriate tensor.
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
getIsosurfaceJvxl(int, String) - Method in class org.jmol.scriptext.CmdExt
getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
getIsotopeData(Atom, int) - Method in class org.jmol.quantum.NMRCalculation
  Get magnetogyricRatio (gamma/10^7 rad s^-1 T^-1) and quadrupoleMoment (Q/10^-2 fm^2) for a given isotope or for the default isotope of an element.
getIsotopeNumber() - Method in class org.jmol.modelset.Atom
getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
getIsotopeNumber(int) - Static method in class org.jmol.util.Elements
getIsotopeNumber() - Method in interface org.jmol.util.Node
getIsotopeNumber() - Method in interface org.jmol.util.SimpleNode
getItem(int) - Method in class org.jmol.awtjs.swing.JMenu
getItem(int) - Static method in class org.jmol.quantum.QS
getItemCount() - Method in class org.jmol.awtjs.swing.JMenu
getItemType(SC) - Method in class org.jmol.awt.AwtPopupHelper
getItemType(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
getItemType(SC) - Method in interface org.jmol.popup.PopupHelper
getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelSet
  only some models can be iterated through.
getIterator(Viewer, Atom, Atom[], BS, float) - Method in interface org.jmol.api.SymmetryInterface
getIterator(Viewer, Atom, Atom[], BS, float) - Method in class org.jmol.symmetry.Symmetry
getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
  Each Widget must implement this function and make sure to use the appletID number to specify the target applet i.e.
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
  A COPY OF THIS .JS FILE MUST BE STORED IN THE html PART OF WEBEXPORT
getJBR() - Method in class org.jmol.viewer.Viewer
getJCouplingHz(Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
getJDXBaseModelIndex(int) - Method in class org.jmol.viewer.Viewer
  get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
getJmol(JFrame, int, int, Map<String, Object>) - Static method in class org.openscience.jmol.app.Jmol
getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJmolAtom(int) - Method in class org.jmol.smiles.SmilesStereo
getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelSet
getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelSet
getJmolFrameType(int) - Method in class org.jmol.modelset.ModelSet
getJmolName(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getJmolObject(int, BS, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getJmolOrRasmolArgb(int, int) - Method in class org.jmol.viewer.ColorManager
getJmolParameter(String) - Method in class org.jmol.applet.Jmol
getJmolParameter(String) - Method in class org.jmol.appletjs.Jmol
getJmolParameter(String) - Method in class org.jmol.util.GenericApplet
getJmolPerspective() - Method in class org.jmol.export.___Exporter
getJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJmolValueAsString(Viewer, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getJmolVersion() - Static method in class org.jmol.api.JmolViewer
getJmolVersion() - Static method in class org.jmol.viewer.Viewer
getJones() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
getJSJSONParser() - Method in class org.jmol.viewer.Viewer
getJSliderLabelTable(JSlider) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
getJsObjectInfo(Object[], String, Object[]) - Method in interface org.jmol.api.GenericPlatform
getJsObjectInfo(Object[]) - Method in class org.jmol.applet.Jmol
  probably never used -- only by Java applet reading directly from the DOM in an XHTML document.
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awt.Platform
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awtjs2d.Platform
getJSONArray(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
getJsonNioServer() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getJspecViewProperties(String) - Method in class org.jmol.viewer.StatusManager
getJspecViewProperties(Object) - Method in class org.jmol.viewer.Viewer
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolStatusListener
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolSyncInterface
getJSpecViewProperty(String) - Method in class org.jmol.applet.JmolApplet
getJSpecViewProperty(String) - Method in class org.jmol.util.GenericApplet
  JSpecView shares the JmolSyncInterface; used to get JSpecView
getJSpecViewProperty(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
getJSV() - Method in class org.jmol.viewer.Viewer
getJzt() - Method in class org.jmol.viewer.Viewer
getJzu() - Method in class org.jmol.viewer.FileManager
getKekuleElementNumber() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Calculate the average element numbers of associated double-bond atoms weighted by their most significant Kekule resonance contributor(s).
getKey() - Method in interface org.jmol.api.JmolAbstractButton
getKey() - Method in class org.jmol.console.JmolButton
getKey() - Method in class org.jmol.console.JmolLabel
getKey() - Method in class org.jmol.console.JmolToggleButton
getKey() - Method in class org.jmol.console.KeyJCheckBox
getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
getKey() - Method in class org.jmol.console.KeyJMenu
getKey() - Method in class org.jmol.console.KeyJMenuItem
getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
getKey(Object, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getKey(int, int, int, int, int) - Static method in class org.jmol.minimize.MinObject
getKey(Edge) - Static method in class org.jmol.smiles.SmilesRing
getKey(int, int) - Method in class org.jmol.util.MeshSlicer
getKeyList(boolean, Lst<String>, String) - Method in class org.jmol.script.SV
getKeyMap() - Static method in class org.jmol.shapecgo.CGOMesh
getKeys(boolean) - Method in class org.jmol.script.SV
getKeys(String) - Method in class org.jmol.viewer.PropertyManager
getLabel(String) - Static method in class org.jmol.console.GenericConsole
getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
getLabel(int) - Method in class org.jmol.shape.Labels
getLabel() - Method in class org.jmol.symmetry.PointGroup.Operation
getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
getLabel1() - Method in class org.jmol.console.AppletConsole
getLabel1() - Method in class org.jmol.console.GenericConsole
getLabeler() - Method in class org.jmol.modelset.AtomCollection
getLabelKey(String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
getLabelString() - Method in class org.jmol.modelset.Measurement
getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.GenericConsole
getLanguage() - Static method in class org.jmol.i18n.GT
getLanguage() - Static method in class org.jmol.i18n.Resource
getLanguageList(GT) - Static method in class org.jmol.i18n.GT
getLanguageList() - Static method in class org.jmol.i18n.Language
  This is the place to put the list of supported languages.
getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getLastConventional - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
getLastCumuleneAtom(SimpleEdge, SimpleNode, int[], SimpleNode[]) - Method in class org.jmol.symmetry.CIPChirality
getLastError() - Static method in exception org.jmol.smiles.InvalidSmilesException
getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
getLastException() - Method in class org.jmol.smiles.SmilesMatcher
getLastIndex() - Method in class org.jmol.modelset.Measurement
getLastPoint(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  Find the lowest ascender or descender above scan line bounding the region for this point.
getLastVibrationVector(int, int) - Method in class org.jmol.modelset.ModelSet
getLatticeCode(int) - Static method in class org.jmol.symmetry.HallTranslation
getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
getLatticeDesignation() - Method in class org.jmol.symmetry.HallInfo
getLatticeDesignation(int) - Static method in class org.jmol.symmetry.HallTranslation
getLatticeDesignation() - Method in class org.jmol.symmetry.SpaceGroup
getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
getLatticeDesignation2(char, boolean) - Static method in class org.jmol.symmetry.HallTranslation
getLatticeExtension(char, boolean) - Static method in class org.jmol.symmetry.HallTranslation
getLatticeIndex(char) - Static method in class org.jmol.symmetry.HallTranslation
getLatticeOp() - Method in interface org.jmol.api.SymmetryInterface
getLatticeOp() - Method in class org.jmol.symmetry.Symmetry
getLatticePoints(int) - Method in class org.jmol.util.BZone
  Get the needed lattice points for n Brillouin zones.
getLatticeType() - Method in interface org.jmol.api.SymmetryInterface
getLatticeType() - Method in class org.jmol.symmetry.Symmetry
getLeadAtom() - Method in class org.jmol.modelset.Group
getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
getLeadAtomOr(Atom) - Method in class org.jmol.modelset.Group
getLeadColix(int) - Method in class org.jmol.renderbio.BioShapeRenderer
getLeadColixBack(int) - Method in class org.jmol.renderbio.BioShapeRenderer
getLeadMidPoint(int, P3) - Method in class org.jmol.modelsetbio.BioPolymer
getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
getLeadPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
getLeadPoints() - Method in class org.jmol.modelsetbio.BioPolymer
getLeftPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
getLength(int) - Method in class org.jmol.shapespecial.Ellipsoid
getLength() - Method in class org.openscience.jvxl.MonitorInputStream
getLevel(int) - Static method in class org.jmol.util.Logger
  Returns the text corresponding to a level.
getLexStr(byte[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getLigandBondInfo(JmolAdapter, Object, String) - Method in class org.jmol.modelsetbio.BioResolver
  reads PDB ligand CIF info and creates a bondInfo object.
getLigandInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
getLigandInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getLigandModel(String, String, String, String) - Method in class org.jmol.viewer.Viewer
  obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state
getLightingInfo() - Method in class org.jmol.export._TachyonExporter
getLightingState(boolean) - Method in class org.jmol.viewer.JmolStateCreator
getLightingState(boolean) - Method in class org.jmol.viewer.StateCreator
getLightingState() - Method in class org.jmol.viewer.Viewer
getLightSource() - Method in class org.jmol.util.GData
getLikeUnlike(BS, BS[], int) - Method in class org.jmol.symmetry.CIPDataTracker.CIPTracker
getLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
getLine() - Method in class org.jmol.jvxl.readers.XmlReader
getLine() - Method in class org.jmol.jvxl.readers.XplorReader
getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEval
getLinesUntil(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
getList(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
getList(Lst<Object>, int) - Static method in class org.jmol.jvxl.readers.PyMOLMeshReader
getList() - Method in class org.jmol.script.SV
getList(String) - Method in class org.jmol.symmetry.CIPData
  Retrieve an array of bit sets that match a given SMARTS
getList(String) - Method in class org.jmol.symmetry.CIPDataSmiles
getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
getLoadFilesList(int, SB, SB, Map<String, Object>, Lst<String>) - Method in class org.jmol.script.ScriptEval
getLoadModelIndex(int, SB, Map<String, Object>) - Method in class org.jmol.script.ScriptEval
getLoadState(Map<String, Object>) - Method in class org.jmol.viewer.GlobalSettings
  these settings are determined when the file is loaded and are kept even though they might later change.
getLoadSymmetryParams(int, SB, Map<String, Object>) - Method in class org.jmol.scriptext.CmdExt
getLocalDirectory(Viewer, boolean) - Static method in class org.jmol.viewer.FileManager
getLocalPathForWritingFile(Viewer, String) - Static method in class org.jmol.viewer.FileManager
getLocalUrl(String) - Method in interface org.jmol.api.GenericPlatform
getLocalUrl(GenericFileInterface) - Static method in class org.jmol.awt.AwtFile
getLocalUrl(String) - Method in class org.jmol.awt.Platform
getLocalUrl(String) - Method in class org.jmol.awtjs2d.Platform
getLocalUrl(String) - Method in class org.jmol.viewer.Viewer
getLogData() - Method in class org.jmol.minimize.forcefield.Calculations
getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
getLogFileName() - Method in class org.jmol.viewer.Viewer
getLogLevel() - Static method in class org.jmol.util.Logger
getLogPath(String) - Method in class org.jmol.viewer.OutputManager
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerAwt
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerJS
getLong(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
getMacro(String) - Static method in class org.jmol.viewer.JC
getMacro(String) - Method in class org.jmol.viewer.Viewer
  retrieve macros.json from the directory
getMacroList() - Static method in class org.jmol.viewer.JC
getMad(int, short) - Method in class org.jmol.shapebio.BioShape
getMadBond() - Method in class org.jmol.api.JmolViewer
getMadBond() - Method in class org.jmol.viewer.Viewer
getMadParameter() - Method in class org.jmol.script.ScriptParam
getMagneticOp() - Method in class org.jmol.symmetry.SymmetryOperation
  Magnetic spin is a pseudo (or "axial") vector.
getMagneticShielding(Atom) - Method in interface org.jmol.api.JmolNMRInterface
getMagneticShielding(Atom) - Method in class org.jmol.quantum.NMRCalculation
getMainItem(Map<String, SV>) - Method in class org.jmol.dssx.AnnotationParser
getManifestScriptPath(String) - Static method in class org.jmol.viewer.FileManager
  check a JmolManifest for a reference to a script file (.spt)
getMap(boolean) - Method in class org.jmol.adapter.readers.pymol.PickleReader
getMap() - Method in class org.jmol.script.SV
getMapForJME(String, Atom[], BS) - Method in interface org.jmol.api.SmilesMatcherInterface
getMapForJME(String, Atom[], BS) - Method in class org.jmol.smiles.SmilesMatcher
getMapKeys(int, boolean) - Method in class org.jmol.script.SV
getMapList(Map<String, Object>, String) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
getMappedTopoAtoms(SmilesAtom, SmilesAtom, Node[]) - Method in class org.jmol.smiles.SmilesStereo
getMaps - Variable in class org.jmol.smiles.SmilesSearch
getMapSafely(Map<String, Object>, String) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
  Safely get a Map from a Map using a key.
getMapSubset(Map<String, ?>, String, Map<String, Object>, Lst<Object>) - Static method in class org.jmol.viewer.PropertyManager
getMark() - Method in class org.jmol.adapter.readers.pymol.PickleReader
getMass() - Method in class org.jmol.modelset.Atom
getMass() - Method in class org.jmol.smiles.SmilesAtom
getMass() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  get the atomic mass only if needed by Rule 2, testing for three special conditions in the case of isotopes: If a duplicate, or an isotope that is 100% nat abundant is specified, or isotopic mass is not specified, just use the average mass.
getMass() - Method in interface org.jmol.util.Node
getMass() - Method in interface org.jmol.util.SimpleNode
getMasses() - Method in class org.jmol.adapter.readers.more.MdTopReader
getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
  Returns the matching atom or null.
getMatchingAtomIndex() - Method in class org.jmol.smiles.SmilesAtom
  Returns the number of a matching atom in a molecule.
getMatchingBond() - Method in class org.jmol.smiles.SmilesBond
getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
getMathExt() - Method in class org.jmol.script.ScriptExpr
getMatrices(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
getMatrix4f(M3, T3) - Static method in class org.jmol.script.ScriptMathProcessor
getMatrixFromString(String, float[], boolean, int) - Method in interface org.jmol.api.SymmetryInterface
getMatrixFromString(String, float[], boolean, int) - Method in class org.jmol.symmetry.Symmetry
getMatrixFromString(SymmetryOperation, String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
  Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format
getMatrixFromXYZ(String) - Static method in class org.jmol.symmetry.SymmetryOperation
getMaxDim() - Method in class org.jmol.util.BoxInfo
getMaxMathParams(int) - Static method in class org.jmol.script.T
getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
getMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
getMeasurementCount() - Method in class org.jmol.api.JmolViewer
getMeasurementCount() - Method in class org.jmol.viewer.Viewer
getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
getMeasurementInfo() - Method in class org.jmol.viewer.PropertyManager
getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
getMeasurements(boolean, boolean) - Method in class org.jmol.modelset.MeasurementData
  if this is the client, then this method can be called to get the result vector, either as a string or as an array.
getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
  Used by MouseManager and Picking Manager to build the script
getMeasurementState(Measures) - Method in class org.jmol.viewer.StateCreator
getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
getMemo(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
getMenu(String) - Method in class org.jmol.awt.AwtPopupHelper
getMenu(String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
getMenu(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getMenu(String) - Method in interface org.jmol.popup.PopupHelper
getMenu(String) - Method in class org.jmol.viewer.Viewer
getMenuAsText(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
getMenuAsText(String) - Method in class org.jmol.popup.MainPopupResourceBundle
getMenuAsText(String) - Method in class org.jmol.popup.PopupResource
getMenuHTML() - Method in class org.jmol.awtjs.swing.AbstractButton
getMenuIcon() - Method in interface org.openscience.jmol.app.JmolPlugin
getMenuItem(String) - Method in class org.jmol.awt.AwtPopupHelper
getMenuItem(AwtPopupHelper, String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
getMenuItem(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getMenuItem(String) - Method in interface org.jmol.popup.PopupHelper
getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Fetch the menu item that was created for the given command.
getMenuName() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
getMenuName() - Method in class org.jmol.popup.MainPopupResourceBundle
getMenuName() - Method in class org.jmol.popup.PopupResource
getMenuPopup(String, char) - Method in interface org.jmol.api.GenericPlatform
getMenuPopup(String, char) - Method in class org.jmol.awt.Platform
getMenuPopup(String, char) - Method in class org.jmol.awtjs2d.Platform
getMenuText(String) - Method in class org.jmol.popup.JmolPopup
getMenuText() - Method in interface org.openscience.jmol.app.JmolPlugin
getMesh(String) - Method in class org.jmol.shape.MeshCollection
getMeshCommand(SB, int) - Method in class org.jmol.shapesurface.Isosurface
getMeshData(String, int[][], T3[], T3[]) - Method in class org.jmol.export._IdtfExporter
getMeshHeader(String, int, int, int, int, SB) - Method in class org.jmol.export._IdtfExporter
getMeshList(String, boolean) - Method in class org.jmol.shape.MeshCollection
  Get matching list of meshes, order reversed
getMeshSlicer() - Method in class org.jmol.util.MeshSurface
getMessage() - Method in exception org.jmol.script.ScriptException
getMessage(Measurement, boolean) - Static method in class org.jmol.shape.Measures
getMessage() - Method in exception org.jmol.smiles.InvalidSmilesException
getMiddle() - Method in class org.openscience.jmol.app.surfacetool.Slice
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shape.Mesh
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getMinDistances(MeasurementData) - Method in interface org.jmol.api.JmolNMRInterface
getMinDistances(MeasurementData) - Method in class org.jmol.quantum.NMRCalculation
getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
getMiniPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
getMinMax(Object, int) - Method in class org.jmol.scriptext.MathExt
getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
getMinMaxPoint(Object, int) - Method in class org.jmol.scriptext.MathExt
  calculates the statistical value for x, y, and z independently
getMinMaxQuaternion(Lst<SV>, int) - Method in class org.jmol.scriptext.MathExt
getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
getMissingHydrogenCount(Atom, boolean) - Method in class org.jmol.modelset.AtomCollection
getMissingHydrogenCount() - Method in class org.jmol.smiles.SmilesSearch
getMKState() - Method in class org.jmol.modelkit.ModelKitPopup
getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in interface org.jmol.api.SmilesMatcherInterface
getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in class org.jmol.smiles.SmilesMatcher
  called by ForceFieldMMFF.setAtomTypes only
getMMTFAtoms(boolean) - Method in class org.jmol.adapter.readers.cif.MMTFReader
  set up all atoms, including bonding, within a group
getMMTFBioAssembly() - Method in class org.jmol.adapter.readers.cif.MMTFReader
getMnemonic(String) - Static method in class org.jmol.console.GenericConsole
getMod(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.
getMod(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getModAtom(int) - Method in class org.jmol.render.MeasuresRenderer
getModCalc() - Method in class org.jmol.util.ModulationSet
getModel() - Method in class org.jmol.modelset.Group
  BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelAdapter() - Method in class org.jmol.api.JmolViewer
getModelAdapter() - Method in class org.jmol.viewer.Viewer
getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelSet
  Note that this method returns all atoms, included deleted ones.
getModelAtomBitSetIncludingDeletedBs(BS) - Method in class org.jmol.modelset.ModelSet
  note -- this method returns ALL atoms, including deleted.
getModelAtomIndices() - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
  prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom index
getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelSet
getModelAuxiliaryInfoForAtom(int) - Method in class org.jmol.symmetry.CIPDataTracker
getModelBS(BS, boolean) - Method in class org.jmol.modelset.ModelSet
getModelBS(int, BS) - Method in class org.jmol.modelset.Trajectory
  set bits for all trajectories associated with this model
getModelCellRange(int) - Method in class org.jmol.modelset.ModelSet
getModelCenter() - Method in class org.jmol.export.__CartesianExporter
getModelCif(BS) - Method in class org.jmol.viewer.PropertyManager
  just a very primitive CIF file reader
getModelCml(BS, int, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getModelCml(BS, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
getModelCml(BS, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
getModelData(boolean) - Method in class org.jmol.jsv.JDXMOLParser
getModelDataBaseName(BS) - Method in class org.jmol.modelset.ModelSet
getModelDipole(int) - Method in class org.jmol.modelset.ModelSet
getModelDipole() - Method in class org.jmol.viewer.Viewer
getModelExtract(BS, boolean, boolean, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getModelExtract(BS, boolean, boolean, String, boolean) - Method in class org.jmol.viewer.PropertyManager
  V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)
getModelExtract(Object, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
  V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
getModelFileData(String, String, boolean) - Method in class org.jmol.viewer.Viewer
getModelFileInfo(BS) - Method in interface org.jmol.api.JmolPropertyManager
getModelFileInfo(BS) - Method in class org.jmol.viewer.PropertyManager
getModelFileInfo() - Method in class org.jmol.viewer.Viewer
getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
getModelFileName(int) - Method in class org.jmol.modelset.ModelSet
getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
getModelFileType(int) - Method in class org.jmol.modelset.ModelSet
getModelForAtomIndex(int) - Method in class org.jmol.viewer.Viewer
getModelForMode(int, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
getModelIndex(ModelSet) - Method in class org.jmol.adapter.readers.pymol.JmolObject
getModelIndex() - Method in class org.jmol.modelset.Atom
  SMILES only
getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
getModelIndex() - Method in interface org.jmol.util.Node
getModelIndexFromId(String) - Method in interface org.jmol.api.JmolAppletInterface
getModelIndexFromId(String) - Method in class org.jmol.api.JmolViewer
getModelIndexFromId(String) - Method in class org.jmol.applet.JmolApplet
getModelIndexFromId(String) - Method in class org.jmol.modelset.ModelSet
getModelIndexFromId(String) - Method in class org.jmol.util.GenericApplet
getModelIndexFromId(String) - Method in class org.jmol.viewer.Viewer
getModelIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
getModelIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
getModelInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
getModelInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getModelInfo(String) - Method in class org.jmol.viewer.Viewer
  get a value from the current model's Model.auxiliaryInfo
getModelInfoAsString() - Method in class org.jmol.modelset.ModelSet
getModelkit(boolean) - Method in class org.jmol.viewer.Viewer
getModelkitProperty(Object) - Method in class org.jmol.viewer.Viewer
getModelKitStateBitset(BS, BS) - Method in class org.jmol.modelset.ModelSet
getModelName(int) - Method in class org.jmol.api.JmolViewer
getModelName(int) - Method in class org.jmol.modelset.ModelSet
getModelName(int) - Method in class org.jmol.viewer.Viewer
getModelNumber() - Method in class org.jmol.adapter.readers.pdb.PdbReader
getModelNumber(int) - Method in class org.jmol.api.JmolViewer
getModelNumber() - Method in class org.jmol.modelset.Atom
getModelNumber(int) - Method in class org.jmol.modelset.ModelSet
getModelNumber(int) - Method in class org.jmol.viewer.Viewer
getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelSet
getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
getModelOrientation(int) - Method in class org.jmol.modelset.ModelSet
getModelProperties(int) - Method in class org.jmol.api.JmolViewer
getModelProperties(int) - Method in class org.jmol.viewer.Viewer
getModelProperty(int, String) - Method in class org.jmol.modelset.ModelSet
getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
getModelSetFileName() - Method in class org.jmol.api.JmolViewer
getModelSetFileName() - Method in class org.jmol.viewer.Viewer
getModelSetPathName() - Method in class org.jmol.api.JmolViewer
getModelSetPathName() - Method in class org.jmol.viewer.Viewer
getModelSetProperties() - Method in class org.jmol.api.JmolViewer
getModelSetProperties() - Method in class org.jmol.viewer.Viewer
getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
getModelSpecial(int) - Method in class org.jmol.viewer.AnimationManager
getModelsSelected() - Method in class org.jmol.modelset.Trajectory
getModelState(SB, boolean, boolean) - Method in class org.jmol.viewer.JmolStateCreator
getModelState(SB, boolean, boolean) - Method in class org.jmol.viewer.StateCreator
getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelSet
getModelTitle(int) - Method in class org.jmol.modelset.ModelSet
getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
getModelUndeletedAtomsBitSetBs(BS) - Method in class org.jmol.viewer.Viewer
getModMatrices() - Method in class org.jmol.adapter.readers.cif.Subsystem
getModPoint(boolean) - Method in interface org.jmol.api.JmolModulationSet
getModPoint(boolean) - Method in class org.jmol.util.ModulationSet
getModType(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
getModType(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getModulation(char, T3) - Method in interface org.jmol.api.JmolModulationSet
getModulation() - Method in class org.jmol.modelset.Atom
getModulation(int) - Method in class org.jmol.modelset.AtomCollection
getModulation(char, T3) - Method in class org.jmol.util.ModulationSet
getModulationList(BS, char, P3) - Method in class org.jmol.modelset.ModelSet
getModulationMap() - Method in class org.jmol.adapter.readers.cif.MSRdr
getModulationMap() - Method in interface org.jmol.adapter.smarter.MSInterface
getModulationReader() - Method in class org.jmol.adapter.readers.cif.CifReader
getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
getMoInfo(int) - Method in class org.jmol.shapesurface.MolecularOrbital
getMoJvxl(int, boolean) - Method in class org.jmol.scriptext.CmdExt
getMolecular(BS) - Method in class org.jmol.shapespecial.Dipoles
getMolecularFormula(String, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
getMolecularFormula(String, boolean) - Method in class org.jmol.smiles.SmilesMatcher
getMolecularFormula(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
getMolecularFormulaAtoms(Node[], BS, float[], boolean) - Static method in class org.jmol.util.JmolMolecule
getMoleculeBitSet(BS) - Method in class org.jmol.modelset.ModelSet
  return cumulative sum of all atoms in molecules containing these atoms
getMoleculeBitSetForAtom(int) - Method in class org.jmol.modelset.ModelSet
getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelSet
getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelSet
getMoleculeInfo(Object) - Method in class org.jmol.viewer.PropertyManager
getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
getMoleculeNumber(boolean) - Method in class org.jmol.smiles.SmilesAtom
getMoleculeNumber(boolean) - Method in interface org.jmol.util.Node
getMolecules() - Method in class org.jmol.modelset.ModelSet
getMolecules(Node[], BS[], Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
  Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
getMolName() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
getMonomerIndex() - Method in class org.jmol.modelset.Group
getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
getMonomerSequenceAtoms(BS, BS) - Method in class org.jmol.modelsetbio.Monomer
getMoreInfo() - Method in interface org.jmol.api.SymmetryInterface
getMoreInfo() - Method in class org.jmol.symmetry.Symmetry
getMOString(float[]) - Static method in class org.jmol.quantum.QS
getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
getMotionFixedAtoms() - Method in class org.jmol.viewer.Viewer
getMoTokens(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
getMouseAction(int, int, int) - Static method in class org.jmol.viewer.binding.Binding
getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
getMouseActionStr(String) - Static method in class org.jmol.viewer.binding.Binding
  create an action code from a string such as "CTRL-LEFT-double click"
getMouseEnabled() - Method in class org.jmol.viewer.Viewer
getMouseInfo() - Method in class org.jmol.viewer.PropertyManager
getMouseManager(double, Object) - Method in interface org.jmol.api.GenericPlatform
getMouseManager(double, Object) - Method in class org.jmol.awt.Platform
getMouseManager(double, Object) - Method in class org.jmol.awtjs2d.Platform
getMoveToText(boolean) - Method in class org.jmol.modelset.Orientation
getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
getMP() - Method in class org.jmol.viewer.ActionManager
getMpsShapeCount() - Method in class org.jmol.shapebio.BioShapeCollection
getMSInfoB(String) - Method in class org.jmol.modelset.ModelSet
getMultipleBondSettings(boolean) - Method in class org.jmol.render.SticksRenderer
getMutationBackbone(AminoMonomer, Atom[]) - Static method in class org.jmol.modelsetbio.BioExt
getMyExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
getMyInfo(P3) - Method in class org.jmol.modelsetbio.Monomer
getMyValue() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
getN1() - Method in class org.jmol.modelsetbio.NucleicMonomer
getN2() - Method in class org.jmol.modelsetbio.NucleicMonomer
getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
getN4() - Method in class org.jmol.modelsetbio.NucleicMonomer
getN6() - Method in class org.jmol.modelsetbio.NucleicMonomer
getName(String) - Method in class org.jmol.adapter.readers.xtal.CgdReader
getName() - Method in interface org.jmol.api.GenericFileInterface
getName() - Method in interface org.jmol.api.JmolAbstractButton
getName() - Method in interface org.jmol.api.JmolScriptFunction
getName() - Method in interface org.jmol.api.SC
getName() - Method in class org.jmol.awt.AwtSwingComponent
getName() - Method in class org.jmol.awtjs.swing.Component
getName() - Method in class org.jmol.awtjs2d.JSFile
getName() - Method in enum org.jmol.c.STER
getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
getName() - Method in class org.jmol.script.ScriptFunction
getName() - Method in class org.jmol.symmetry.PointGroup
getName() - Method in class org.jmol.symmetry.SpaceGroup
getName() - Method in interface org.openscience.jmol.app.JmolPlugin
getNameFromCode(int) - Static method in enum org.jmol.util.Edge.EnumBondOrder
getNameList() - Static method in enum org.jmol.c.CBK
getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
getNav() - Method in class org.jmol.viewer.TransformManager
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
getNavigationSlabOffsetPercent() - Method in class org.jmol.navigate.Navigator
getNavigationState() - Method in interface org.jmol.api.JmolNavigatorInterface
getNavigationState() - Method in class org.jmol.navigate.Navigator
getNavigationState() - Method in class org.jmol.viewer.TransformManager
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
getNavPtHeight() - Method in class org.jmol.viewer.TransformManager
getNBOAtomLabel(Atom) - Method in class org.jmol.adapter.readers.quantum.NBOParser
  get the
getNBOAtomLabel(Atom) - Method in class org.jmol.viewer.Viewer
getNBOCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
getNboCharges() - Method in class org.jmol.adapter.readers.quantum.MOReader
getNBOOccupanciesStatic(Lst<Map<String, Object>>, int, int, String, int, int[]) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
getNBOParser() - Method in class org.jmol.viewer.Viewer
getNBOs - Variable in class org.jmol.adapter.readers.quantum.MOReader
getNBOTypeFromName(String) - Static method in class org.jmol.viewer.JC
getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
getNCIPlanes - Variable in class org.jmol.jvxl.readers.VolumeFileReader
getNegCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getNeighbors(AtomIndexIterator) - Method in class org.jmol.geodesic.EnvelopeCalculation
getNeighborVertexArrays() - Static method in class org.jmol.util.Normix
getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
getNested(int) - Method in class org.jmol.smiles.SmilesSearch
getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
getNewDfCoefMap() - Static method in class org.jmol.quantum.QS
getNewFixedRotationCenter() - Method in class org.jmol.viewer.TransformManager
getNewLatticePoints(BZone) - Method in class org.jmol.util.BZone
  Loop through all points, looking for non-excluded points using St.
getNewSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getNextPreloadClassName() - Method in class org.jmol.applet.AppletWrapper
getNextStatement() - Method in interface org.jmol.api.JmolScriptEvaluator
getNextStatement() - Method in class org.jmol.script.ScriptEval
  when paused, indicates what statement will be next
getNextValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.VolumeFileReader
getNHPoint(P3, V3, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
getNitrogenAtom() - Method in class org.jmol.modelset.Group
getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getNitrogenHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
getNMRCalculation() - Method in class org.jmol.viewer.Viewer
getNMRPredict(String) - Method in class org.jmol.viewer.Viewer
getNoCase(Map<String, Object>, String) - Static method in class org.jmol.viewer.StateManager
getNode(int) - Method in class org.jmol.viewer.Gesture
getNominalMass() - Method in class org.jmol.modelset.Atom
getNormalizedDE() - Method in class org.jmol.minimize.forcefield.ForceField
getNormalMap(T3[], int, BS, Lst<String>) - Method in class org.jmol.export.__CartesianExporter
getNormals(T3[], P4) - Method in class org.jmol.shape.Mesh
getNormalsTemp() - Method in class org.jmol.shape.Mesh
getNormix() - Method in class org.jmol.rendercgo.CGORenderer
getNormix(double, double, double, int, BS) - Static method in class org.jmol.util.Normix
getNormixCount() - Static method in class org.jmol.util.Normix
getNormixes() - Method in class org.jmol.shapespecial.Polyhedron
getNormixV(V3, BS) - Static method in class org.jmol.util.Normix
getNotInCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
getNoValue() - Method in class org.jmol.quantum.NciCalculation
getNoValue() - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
getNPQ(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
getNPQd(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
  for D orbitals, MOPAC adds 1 to n for noble gases but subtracts 1 from n for transition metals
getNPQp(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
  for P orbitals, MOPAC adds 1 to n for helium only
getNPQs(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
  for S orbitals, MOPAC adds 1 to n for noble gases other than helium
getNucleic() - Method in class org.jmol.util.ColorEncoder
getNucleicPhosphorusAtom(int) - Method in class org.jmol.modelsetbio.NucleicPolymer
getNull(boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
getNumberFromCode(int) - Static method in enum org.jmol.util.Edge.EnumBondOrder
getNumericalToken() - Method in class org.jmol.script.ScriptTokenParser
getO2() - Method in class org.jmol.modelsetbio.NucleicMonomer
getO4() - Method in class org.jmol.modelsetbio.NucleicMonomer
getO6() - Method in class org.jmol.modelsetbio.NucleicMonomer
getObjectBoundingBox(String) - Method in class org.jmol.script.ScriptEval
getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEval
getObjectColix(int) - Method in class org.jmol.viewer.Viewer
getObjectID(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
getObjectMad10(int) - Method in class org.jmol.viewer.Viewer
getObjectMap(Map<String, ?>, boolean) - Method in class org.jmol.viewer.ShapeManager
getObjectMap(Map<String, ?>, char) - Method in class org.jmol.viewer.Viewer
  used in autocompletion in console using TAB
getObjectNameFromId(int) - Static method in class org.jmol.viewer.StateManager
getObjects(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
getObjectSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getObjectSettings() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getObjectType(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getOccupancy() - Method in class org.jmol.adapter.smarter.AtomIterator
getOccupancy() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getOccupancy() - Method in class org.jmol.util.ModulationSet
getOccupancy100() - Method in class org.jmol.modelset.Atom
getOccupancy100(boolean) - Method in class org.jmol.util.ModulationSet
getOccupancy100(boolean) - Method in class org.jmol.util.Vibration
getOffset(int, int, boolean) - Static method in class org.jmol.viewer.JC
  Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered".
getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.Node
getOffsetVertices(P4) - Method in class org.jmol.shape.Mesh
geTokens() - Method in interface org.jmol.api.JmolScriptFunction
geTokens() - Method in class org.jmol.script.ScriptFunction
getOpacity255() - Method in class org.jmol.awt.AwtColor
getOpacity255() - Method in class org.jmol.awtjs.swing.Color
getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in class org.jmol.dialog.Dialog
getOpenSmiles(BS) - Method in class org.jmol.api.JmolViewer
getOpenSmiles(BS) - Method in class org.jmol.viewer.Viewer
getOperation(int) - Method in class org.jmol.symmetry.SpaceGroup
getOperationCount() - Method in class org.jmol.symmetry.SpaceGroup
getOperationRsVs(int) - Method in interface org.jmol.api.SymmetryInterface
getOperationRsVs(int) - Method in class org.jmol.symmetry.Symmetry
getOpMatrix(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
getOption(String, Viewer, String) - Static method in class org.jmol.api.Interface
  Note! Do not use this method with "viewer." or "util." because when the JavaScript is built, "org.jmol.util" and "org.jmol.viewer" are condensed to "JU" and "JV" (javajs.util is also JU)
getOptions() - Method in class org.openscience.jmol.app.JmolApp
getOrAddBond(Atom, Atom, int, short, BS, float, boolean) - Method in class org.jmol.modelset.BondCollection
getOrAllocateChain(Model, int) - Method in class org.jmol.modelset.ModelLoader
getOrbitals(float[], float[], int, int) - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
getOrCalcPartialCharges(BS, BS) - Method in class org.jmol.viewer.Viewer
getOrientation() - Method in class org.jmol.viewer.StateManager
getOrientationFor(String) - Method in class org.jmol.viewer.StateManager
getOrientationInfo() - Method in class org.jmol.viewer.TransformManager
getOrientationText(int, boolean) - Method in class org.jmol.viewer.TransformManager
getOrientationText(int, String, BS) - Method in class org.jmol.viewer.Viewer
getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
getOriginVaVbVc() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
getOrSaveImage(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
  Creates an image of params.type form -- PNG, PNGJ, PNGT, JPG, JPG64, PDF, PPM, GIF, GIFT.
getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
getOtherNode(SimpleNode) - Method in class org.jmol.modelset.Bond
getOtherNode(SimpleNode) - Method in class org.jmol.smiles.SmilesBond
getOtherNode(SimpleNode) - Method in interface org.jmol.util.SimpleEdge
getOutOfPlaneParameter(int[]) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getOutputChannel(String, String[]) - Method in class org.jmol.viewer.OutputManager
getOutputChannel(String, String[]) - Method in class org.jmol.viewer.Viewer
getOutputFileNameFromDialog(String, int, Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
getOutputFromExport(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
getOutputManager() - Method in class org.jmol.viewer.Viewer
getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
getOverallSpan() - Method in class org.jmol.adapter.smarter.XtalSymmetry
getP() - Method in class org.jmol.modelsetbio.NucleicMonomer
getP(String) - Method in class org.jmol.viewer.Viewer
getPageAuthorName() - Static method in class org.openscience.jmol.app.webexport.WebExport
getPairs(BS, BS, RadiusData, int, boolean) - Method in class org.jmol.shapesurface.Contact
getPalette(String) - Static method in enum org.jmol.c.PAL
getPaletteAC() - Method in class org.jmol.util.ColorEncoder
getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
getPaletteBW() - Method in class org.jmol.util.ColorEncoder
getPaletteColorCount(int) - Method in class org.jmol.util.ColorEncoder
getPaletteID(String) - Static method in enum org.jmol.c.PAL
getPaletteName(byte) - Static method in enum org.jmol.c.PAL
getPaletteWB() - Method in class org.jmol.util.ColorEncoder
getPane() - Method in class org.jmol.console.JmolConsole
getPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
getPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
getParam(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
getParameter(String) - Method in class org.jmol.api.JmolViewer
getParameter(Object) - Method in class org.jmol.minimize.forcefield.Calculations
getParameter(float[], int, double, String) - Static method in class org.jmol.quantum.NciCalculation
getParameter(String, int, boolean) - Method in class org.jmol.script.ScriptParam
getParameter(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
  strictly a getter
getParameter(String) - Method in class org.jmol.viewer.Viewer
getParameterEscaped(String, int) - Method in class org.jmol.viewer.GlobalSettings
getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.Calculations
getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
getParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getParameterState(GlobalSettings, SB) - Method in class org.jmol.viewer.StateCreator
  note that these are not user variables, only global jmol parameters
getParamType(int) - Static method in class org.jmol.script.T
getParamType(int) - Static method in class org.jmol.viewer.PropertyManager
getParent() - Method in interface org.jmol.api.SC
getParent() - Method in class org.jmol.awt.AwtSwingComponent
getParent() - Method in class org.jmol.awtjs.swing.Component
getParentAsFile() - Method in interface org.jmol.api.GenericFileInterface
getParentAsFile() - Method in class org.jmol.awt.AwtFile
getParentAsFile() - Method in class org.jmol.awtjs2d.JSFile
getParentItem(String, M4) - Method in class org.jmol.export._IdtfExporter
getPartialBondDotted(int) - Static method in class org.jmol.util.Edge
getPartialBondOrder(int) - Static method in class org.jmol.util.Edge
getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.script.ScriptParam
  reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5 + (m % 0x1F)
getPartialBondOrderFromString(String) - Static method in class org.jmol.script.ScriptParam
getPartialCharge() - Method in class org.jmol.adapter.smarter.AtomIterator
getPartialCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getPartialCharge() - Method in class org.jmol.modelset.Atom
getPartialCharges() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
getPartialCharges(BS) - Method in class org.jmol.script.ScriptEval
getPartnerAtom(NucleicMonomer) - Method in class org.jmol.modelsetbio.BasePair
getPathForAllFiles() - Method in class org.jmol.viewer.FileManager
getPathHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Just recovers the path settings from last session.
getPatternIndex() - Method in class org.jmol.smiles.SmilesAtom
getPatternMatcher() - Method in class org.jmol.scriptext.MathExt
getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
  PDB or PQR only
getPdbAtomData(BS, OC, boolean, boolean) - Method in class org.jmol.viewer.Viewer
getPdbBondInfo(String, boolean) - Method in class org.jmol.modelsetbio.BioResolver
getPdbCharge(String, String) - Method in class org.jmol.modelset.ModelLoader
  Adjust known N and O atom formal charges.
getPdbData(int, String, BS, Object[], OC, boolean) - Method in interface org.jmol.api.JmolPropertyManager
getPdbData(BioPolymer, char, char, int, int, BS, BS, boolean, boolean, boolean, LabelToken[], OC, SB, BS, P3) - Method in class org.jmol.modelsetbio.BioExt
getPdbData(String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioModel
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.PropertyManager
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.Viewer
getPdbDataM(BioModel, Viewer, String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioExt
getPDBGroupLength(String) - Method in class org.jmol.adapter.readers.more.Mol2Reader
getPDBHeader(int) - Method in class org.jmol.modelset.ModelSet
getPdbID() - Method in class org.jmol.viewer.Viewer
getPeakAtomRecord(int) - Method in class org.jmol.jsv.JSpecView
getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
getPercentageRead() - Method in class org.openscience.jvxl.MonitorInputStream
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.CastepDensityReader
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
  calculate the perspective factor based on z
getPhase(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
getPhongExponent() - Method in class org.jmol.util.GData
getPickedPoint(T3, int) - Method in class org.jmol.shape.MeshCollection
getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
getPickingMode() - Method in class org.jmol.viewer.Viewer
getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
getPickingState() - Method in class org.jmol.viewer.ActionManager
getPickingStyle() - Method in class org.jmol.viewer.ActionManager
getPickingStyleIndex(String) - Static method in class org.jmol.viewer.ActionManager
getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
getPlane(int, boolean) - Method in class org.jmol.jvxl.calc.MarchingCubes
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoMOReader
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getPlane(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
getPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
getPlane(V3) - Method in class org.jmol.symmetry.PointGroup
getPlane(String) - Static method in class org.openscience.jvxl.Jvxl
getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptEval
getPlaneIntersection(int, P4, SymmetryInterface, float, int) - Method in class org.jmol.scriptext.IsoExt
getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
  Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneNormals(P3, P3, P3, P3, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
getPlaneSR(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getPlaneValue(int) - Method in class org.jmol.quantum.NciCalculation
  We always have four raw planes in hand; we just need to know which three to use in any particular case.
getPlaneVFR(float[], boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
getPlotMinMax(float[], boolean, int) - Method in class org.jmol.scriptext.CmdExt
getPlotText3D(int, int, Graphics3D, String, Font, boolean) - Static method in class org.jmol.g3d.TextRenderer
getPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getPmeshData(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
getPngjOrDroppedBytes(String, String) - Method in class org.jmol.viewer.FileManager
getPoint() - Method in class org.jmol.adapter.readers.more.MdCrdReader
getPoint(Map<String, Object>, String, P3) - Method in class org.jmol.dssx.DSSR1
getPoint(int, P3) - Method in class org.jmol.jvxl.data.VolumeData
getPoint(String, int, int[], boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
getPoint(String[], int) - Method in class org.jmol.jvxl.readers.Ras3DReader
getPoint(int, P3, P3i) - Method in class org.jmol.rendercgo.CGORenderer
getPoint(int, T3) - Method in class org.jmol.shapecgo.CGOMesh
getPoint(Map<String, Object>) - Method in class org.jmol.viewer.ActionManager
getPoint3f(int, boolean, boolean) - Method in class org.jmol.script.ScriptParam
getPoint3f(int, boolean) - Method in class org.jmol.scriptext.ScriptExt
getPoint4f(int) - Method in class org.jmol.script.ScriptParam
getPointArray(int, int, boolean) - Method in class org.jmol.script.ScriptParam
  may return null values in some cases
getPointCount() - Method in class org.jmol.viewer.Gesture
getPointCount2(int, int) - Method in class org.jmol.viewer.Gesture
getPointer(int) - Static method in class org.jmol.viewer.JC
getPointerName(int) - Static method in class org.jmol.viewer.JC
getPointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
getPointers(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
getPointGroup(PointGroup, T3, T3[], BS, boolean, float, float, boolean) - Static method in class org.jmol.symmetry.PointGroup
getPointGroupAsString(BS, String, int, float, P3[], P3, String) - Method in class org.jmol.modelset.ModelSet
getPointGroupInfo(int, String, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
getPointGroupInfo(BS) - Method in class org.jmol.modelset.ModelSet
getPointGroupInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
getPointIndex(int) - Method in class org.jmol.symmetry.PointGroup
getPointOrBitsetOperation(T, SV) - Method in class org.jmol.script.ScriptMathProcessor
getPointOrCenterVector(T) - Method in class org.jmol.script.ScriptParam
getPointOrPlane(int, boolean, boolean, boolean, boolean, int, int, boolean) - Method in class org.jmol.script.ScriptParam
getPoints() - Method in interface org.jmol.api.JmolEnvCalc
getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
getPoints(byte[], P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getPoints() - Method in class org.jmol.render.MeasuresRenderer
getPointsAndElements(T3[]) - Method in class org.jmol.symmetry.PointGroup
getPointTransf(int, ModelSet, Atom, Quat, P3) - Static method in class org.jmol.viewer.PropertyManager
  pick up the appropriate value for this atom
getPointVector(T, int) - Method in class org.jmol.script.ScriptParam
getPolygonColorData(int, short[], int[][], BS) - Static method in class org.jmol.shapesurface.Isosurface
getPolyhedralOrders() - Method in class org.jmol.smiles.SmilesStereo
  experimental Jmol polySMILES
getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelset.ModelSet
getPolymerPointsAndVectors(int, BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
getPolymerPointsAndVectors(BS, Lst<P3[]>) - Method in class org.jmol.viewer.Viewer
getPolymerSequenceAtoms(int, int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
getPopInHeight() - Static method in class org.openscience.jmol.app.webexport.WebExport
getPopInWidth() - Static method in class org.openscience.jmol.app.webexport.WebExport
getPopup(String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
getPopupMenu() - Method in interface org.jmol.api.SC
getPopupMenu() - Method in class org.jmol.awt.AwtSwingComponent
getPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
getPopupMenu() - Method in class org.jmol.awtjs.swing.JMenu
getPopupMenu() - Method in class org.jmol.viewer.Viewer
getPOrNull(String) - Method in class org.jmol.viewer.Viewer
getPort() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
getPort() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
getPosCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getPosition() - Method in interface org.jmol.api.AtomIndexIterator
getPosition() - Method in class org.jmol.modelset.AtomIteratorWithinModel
getPosition() - Method in class org.jmol.symmetry.UnitCellIterator
getPosition() - Method in class org.openscience.jvxl.MonitorInputStream
getPositionMin() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getPrecedence(int) - Static method in class org.jmol.script.T
getPreference(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
getPrefixToken() - Method in class org.jmol.script.ScriptCompiler
getPreserveState() - Method in class org.jmol.viewer.Viewer
  This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
getPrivateKey() - Method in class org.jmol.export.Export3D
getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
getPropC(String, int) - Method in class org.jmol.shapesurface.Contact
getPropDataMC(String, Object[]) - Method in class org.jmol.shape.MeshCollection
getProperties() - Method in class org.openscience.jmol.app.HistoryFile
getProperty(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
getProperty(String, String, Object) - Method in interface org.jmol.api.JmolPropertyManager
getProperty(String, String, Object) - Method in class org.jmol.api.JmolViewer
getProperty(String, String) - Method in class org.jmol.applet.JmolApplet
getProperty(String) - Method in class org.jmol.applet.JmolApplet
getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
  only called from org.openscience.jvxl.Jvxl.main
getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
getProperty(Object) - Method in class org.jmol.modelkit.ModelKitPopup
  Get a property of the modelkit.
getproperty - Static variable in class org.jmol.script.T
getProperty(String, int) - Method in class org.jmol.shape.Axes
getProperty(String, int) - Method in class org.jmol.shape.Labels
getProperty(String, int) - Method in class org.jmol.shape.Measures
getProperty(String, int) - Method in class org.jmol.shape.Shape
getProperty(String, int) - Method in class org.jmol.shape.Sticks
getProperty(String, int) - Method in class org.jmol.shapecgo.CGO
getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
getProperty(String, int) - Method in class org.jmol.shapespecial.Polyhedra
getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
getProperty(String, int) - Method in class org.jmol.shapesurface.Contact
getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
getProperty(String, int) - Method in class org.jmol.shapesurface.Pmesh
getProperty(String, String) - Method in class org.jmol.util.BZone
getProperty(String) - Method in class org.jmol.util.GenericApplet
getProperty(String, String) - Method in class org.jmol.util.GenericApplet
getProperty(String, boolean) - Static method in class org.jmol.util.Logger
getProperty(String, String, Object) - Method in class org.jmol.viewer.PropertyManager
getProperty(Object) - Method in class org.jmol.viewer.ShapeManager
getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
getProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
  Get the value of a property
getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsJSON(String) - Method in class org.jmol.applet.JmolApplet
getPropertyAsJSON(String, String) - Method in class org.jmol.applet.JmolApplet
getPropertyAsJSON(String) - Method in class org.jmol.util.GenericApplet
getPropertyAsJSON(String, String) - Method in class org.jmol.util.GenericApplet
getPropertyAsObject(String, Object, String) - Method in class org.jmol.viewer.PropertyManager
getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
getPropertyAsString(String) - Method in class org.jmol.applet.JmolApplet
getPropertyAsString(String, String) - Method in class org.jmol.applet.JmolApplet
getPropertyAsString(String) - Method in class org.jmol.util.GenericApplet
getPropertyAsString(String, String) - Method in class org.jmol.util.GenericApplet
getPropertyColorRange() - Method in class org.jmol.viewer.ColorManager
getPropertyCount(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Echo
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Shape
getPropertyData(String, Object[]) - Method in class org.jmol.shapecgo.CGO
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Draw
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
getPropertyData(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
getPropertyManager() - Method in class org.jmol.viewer.Viewer
getPropertyName(int) - Static method in class org.jmol.viewer.PropertyManager
getPropertyNumber(String) - Method in interface org.jmol.api.JmolPropertyManager
getPropertyNumber(String) - Method in class org.jmol.viewer.PropertyManager
getPropertyNumber(String) - Method in class org.jmol.viewer.Viewer
getPropI(String, int) - Method in class org.jmol.shapesurface.Isosurface
getPropMC(String, int) - Method in class org.jmol.shape.MeshCollection
getPropShape(String, Object[]) - Method in class org.jmol.shape.Shape
getProteinStructure(int) - Method in class org.jmol.modelsetbio.AlphaPolymer
getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
getProteinStructureState(BS, int) - Method in class org.jmol.modelset.ModelSet
getProteinStructureSubType() - Method in class org.jmol.modelset.Group
getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
getProteinStructureTag() - Method in class org.jmol.modelset.Group
getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
getProteinStructureType(String) - Static method in enum org.jmol.c.STR
  In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
getProteinStructureType() - Method in class org.jmol.modelset.Group
getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getPymolScreenOffset(P3, P3i, int, P3, float) - Method in class org.jmol.modelset.Text
  PyMOL will use 1 here for pymolOffset[0] for relative, 0 or absolute.
getPymolView(Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  adds depth_cue, fog, and fog_start
getPymolXYOffset(float, int, float) - Method in class org.jmol.modelset.Text
getQCJSON(BS) - Method in class org.jmol.viewer.PropertyManager
  EXPERIMENTAL create a QCJSON file -- very preliminary
getQCoefs(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
getQCoefs(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getQInfo(Quat) - Static method in class org.jmol.modelsetbio.BioExt
getQuadrupolarConstant(Tensor) - Method in interface org.jmol.api.JmolNMRInterface
  Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
getQuadrupolarConstant(Tensor) - Method in class org.jmol.quantum.NMRCalculation
getQuadrupoleTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
getQuality(String) - Method in class org.jmol.dialog.Dialog
getQuantumShell(String) - Static method in class org.jmol.quantum.QS
getQuantumShellTag(int) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getQuantumShellTag(int) - Static method in class org.jmol.quantum.QS
getQuantumShellTagID(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getQuantumShellTagID(String) - Static method in class org.jmol.quantum.QS
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.quantum.QS
getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
getQuaternion(char) - Method in class org.jmol.modelset.Group
getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternionAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternionArray(Object, int) - Method in class org.jmol.script.ScriptEval
getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AminoMonomer
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.Monomer
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternionFrameCenterAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
getQuaternionP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternionParameter(int, BS, boolean) - Method in class org.jmol.script.ScriptParam
getQuaternionRotation(String) - Method in interface org.jmol.api.SymmetryInterface
getQuaternionRotation(String) - Method in class org.jmol.symmetry.Symmetry
getQuaternionRotation(String) - Method in class org.jmol.symmetry.UnitCell
  Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.
getQuaternionStraightness(String, Quat, Quat) - Static method in class org.jmol.modelsetbio.BioExt
getQuotedString(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
getQuotedStringOrObject(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  final get for quoted object
getR0(MinBond) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getRadio(String) - Method in class org.jmol.awt.AwtPopupHelper
getRadio(AwtPopupHelper, String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
getRadio(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
getRadio(String) - Method in interface org.jmol.popup.PopupHelper
getRadius() - Method in class org.jmol.adapter.smarter.AtomIterator
getRadius() - Method in class org.jmol.adapter.smarter.BondIterator
getRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getRadius() - Method in class org.jmol.api.JmolAdapterBondIterator
getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
getRadius() - Method in class org.jmol.modelset.Atom
getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
getRange(BS, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
getRangeGroups(int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
getRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModel
getRasMolRadius() - Method in class org.jmol.modelset.Atom
getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
getReader(String, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
  Get a reader based on its name.
getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
getReaderData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
getReaderFromType(String) - Static method in class org.jmol.adapter.smarter.Resolver
getReadingTimeMillis() - Method in class org.openscience.jvxl.MonitorInputStream
getRealCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
getReciprocal(T3[], T3[], float) - Static method in class org.jmol.util.SimpleUnitCell
getRecord(String) - Method in interface org.jmol.api.JmolJDXMOLParser
getRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
getRefreshing() - Method in class org.jmol.viewer.Viewer
getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
getRegistryInfo() - Method in class org.jmol.util.GenericApplet
getRegistryInfo() - Method in class org.jmol.viewer.StatusManager
getRegistryInfo() - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
getRenderer(String) - Method in class org.jmol.g3d.Graphics3D
getRenderer(int) - Method in class org.jmol.render.RepaintManager
getRendering() - Method in class org.jmol.shape.Mesh
getResidueLabels() - Method in class org.jmol.adapter.readers.more.MdTopReader
getResiduePointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
getResno() - Method in class org.jmol.modelset.Atom
getResno() - Method in class org.jmol.modelset.Group
getResno() - Method in class org.jmol.smiles.SmilesAtom
getResno() - Method in interface org.jmol.util.Node
getResolution() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getResolution() - Method in class org.jmol.util.MeshSurface
getResource(Viewer, String, String) - Static method in class org.jmol.i18n.Resource
getResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getResourceFromPO(String) - Static method in class org.jmol.i18n.Resource
  applet only -- Simple reading of .po file; necessary for JavaScript; works in Java as well and avoids all those signed applets.
getResourceString(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
getResult() - Method in class org.jmol.script.ScriptMathProcessor
getRGB(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
getRGB() - Method in class org.jmol.awtjs.swing.Color
getRiboseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
getRingCache(int, int, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
getRingData(Lst<BS>[], boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
getRingNumber(String, int, char, int[]) - Static method in class org.jmol.smiles.SmilesParser
getRingPointer(int) - Method in class org.jmol.smiles.SmilesGenerator
getRna3dMap(String) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
getRnd(float) - Method in class org.jmol.jvxl.readers.IsoMOReader
getRootExt(String, String[], int) - Static method in class org.jmol.viewer.OutputManager
getRootTrackerResult(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
  CIPDataTracker only
getRootTrackerResult(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataTracker
getRotateBondIndex() - Method in class org.jmol.modelkit.ModelKitPopup
getRotateXyzText() - Method in class org.jmol.viewer.TransformManager
getRotateZyzText(boolean) - Method in class org.jmol.viewer.TransformManager
getRotation(M3) - Method in class org.jmol.viewer.TransformManager
getRotationMatrix(P3, P3, float) - Method in class org.jmol.export.___Exporter
getRotationMatrix(P3, P3, float, P3, P3) - Method in class org.jmol.export.___Exporter
getRotationQ() - Method in class org.jmol.viewer.TransformManager
getRotationText() - Method in class org.jmol.viewer.TransformManager
getRowCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
getRowFor(int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getRubberBand() - Method in class org.jmol.viewer.ActionManager
getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
getRule6Descriptor(boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  The original Rule 6 implementation; allows cubane, tetrahedrane, and bicyclo[2.2.2]octane to be ns.
getRuleBondLength(MinAtom, MinAtom, int, boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getRuleName(int) - Method in class org.jmol.symmetry.CIPChirality
getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
getSavedOrientationText(String) - Method in class org.jmol.viewer.StateManager
getSavedState(String) - Method in class org.jmol.viewer.StateManager
getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
getSaveFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
getSaveFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
getScale() - Method in interface org.jmol.api.JmolModulationSet
getScale() - Method in class org.jmol.util.ModulationSet
getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
getScaling(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
getSceneScript(String[], Map<String, String>, Lst<Integer>) - Method in class org.jmol.viewer.OutputManagerAwt
getSchemeIndex(String) - Static method in class org.jmol.util.ColorEncoder
getScreenDim() - Method in class org.jmol.viewer.Viewer
getScreenDimensions(Dimension) - Method in interface org.jmol.awtjs.swing.SwingController
  Return the width and height of the window in d.
getScreenHeight() - Method in class org.jmol.api.JmolViewer
getScreenHeight() - Method in class org.jmol.viewer.Viewer
getScreenImage(boolean) - Method in class org.jmol.g3d.Graphics3D
getScreenImage(boolean) - Method in class org.jmol.util.GData
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.api.JmolViewer
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.viewer.Viewer
  Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
getScreenNormal(T3, T3, float) - Method in class org.jmol.export.__RayTracerExporter
getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager
getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager4D
getScreenWidth() - Method in class org.jmol.api.JmolViewer
getScreenWidth() - Method in class org.jmol.viewer.Viewer
getScript() - Method in interface org.jmol.api.JmolScriptEvaluator
getScript() - Method in class org.jmol.script.ScriptEval
getScriptBitSets(String, BS[]) - Method in class org.jmol.shapesurface.Isosurface
getScriptButtonPercent() - Static method in class org.openscience.jmol.app.webexport.WebExport
getScriptContext(String) - Method in interface org.jmol.api.JmolScriptEvaluator
getScriptContext(String) - Method in class org.jmol.script.ScriptEval
getScriptContext(String) - Method in class org.jmol.viewer.Viewer
getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
getScriptEditor() - Method in class org.jmol.console.GenericConsole
getScriptEditor() - Method in class org.jmol.console.JmolConsole
getScriptEditor() - Method in class org.jmol.consolejs.AppletConsole
getScriptForCallback(SC, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
  Secondary processing of menu item click
getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.GenericPopup
getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.JmolPopup
getScriptID(ScriptContext) - Method in class org.jmol.scriptext.CmdExt
getScriptItem(boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
getScriptItem(boolean, boolean) - Method in class org.jmol.script.ScriptManager
getScriptManager() - Method in class org.jmol.viewer.Viewer
getScriptParams() - Method in class org.jmol.jvxl.readers.Parameters
getScriptQueue() - Method in interface org.jmol.api.JmolScriptManager
getScriptQueue() - Method in class org.jmol.script.ScriptManager
getScriptQueueInfo() - Method in class org.jmol.viewer.Viewer
getSearch(String, int, BS) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
getSection(String, String, boolean) - Method in class org.jmol.adapter.readers.simple.JSONReader
getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
getSelectCodeRange(int[]) - Method in class org.jmol.modelset.ModelSet
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
getSelectedAtomIterator(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
getSelectedAtoms() - Method in class org.jmol.viewer.SelectionManager
getSelectedAtomsNoSubset() - Method in class org.jmol.viewer.SelectionManager
getSelectedIndex() - Method in class org.jmol.awtjs.swing.JComboBox
getSelectedItem() - Method in class org.jmol.awtjs.swing.JComboBox
getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.BioPolymer
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
getSelectionAtoms(Lst<Object>, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Add selected atoms to a growing bit set.
getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
getSelectionHalosEnabled() - Method in class org.jmol.viewer.Viewer
getSelectionModel() - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
getSelectionModel() - Method in class org.jmol.awtjs.swing.JTable
getSelections() - Method in class org.jmol.smiles.SmilesSearch
  htNested may contain $(select xxxx) primitives.
getSelectionState(SelectionManager, SB) - Method in class org.jmol.viewer.StateCreator
getSeqCode(T) - Static method in class org.jmol.script.ScriptExpr
getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
getSeqcodeFor(int, char) - Static method in class org.jmol.modelset.Group
getSeqcodeString() - Method in class org.jmol.modelset.Group
getSeqcodeStringFor(int) - Static method in class org.jmol.modelset.Group
getSeqID() - Method in class org.jmol.adapter.smarter.AtomIterator
getSeqID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSeqID() - Method in class org.jmol.modelset.Atom
getSeqNo(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
getSeqNumberFor(int) - Static method in class org.jmol.modelset.Group
getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
getSequence() - Method in class org.jmol.viewer.ActionManager
getSequenceBits(String, BS, BS) - Method in class org.jmol.modelset.ModelSet
getSequenceCode(boolean) - Method in class org.jmol.script.ScriptTokenParser
getSequenceNumber(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getSequenceNumber() - Method in class org.jmol.adapter.smarter.AtomIterator
getSequenceNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSequenceNumber(int) - Method in interface org.jmol.api.PymolAtomReader
getSerial(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
getSerial() - Method in class org.jmol.adapter.smarter.AtomIterator
getSerial() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSerialID() - Method in class org.jmol.adapter.smarter.StructureIterator
getSerialID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getServiceCommand(String) - Static method in class org.jmol.viewer.JC
getSetAxesTypeMad10(int) - Method in class org.jmol.script.ScriptEval
getSetByEdge(Edge, Hashtable<String, SmilesRingSet>) - Static method in class org.jmol.smiles.SmilesRing
getSetHistory(int) - Method in class org.jmol.api.JmolViewer
getSetHistory(int) - Method in class org.jmol.util.CommandHistory
  Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n <= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
getSetHistory(int) - Method in class org.jmol.viewer.Viewer
  Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
getSettableTokFromString(String) - Static method in class org.jmol.script.T
getSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getSettingFloat(int) - Method in class org.jmol.script.ScriptEval
getSettingInt(int) - Method in class org.jmol.script.ScriptEval
getSettings(String) - Method in class org.jmol.shapesurface.MolecularOrbital
getSettingStr(int, boolean) - Method in class org.jmol.script.ScriptEval
  Accept an unquoted string if there is just one parameter regardless of its type.
getShadeB(float, float, float) - Method in class org.jmol.util.Shader
getShadeF(float, float, float) - Method in class org.jmol.util.Shader
getShadeFp8(float, float, float) - Method in class org.jmol.util.Shader
getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
getShadeIndex(float, float, float) - Method in class org.jmol.util.Shader
getShadeIndexP3(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
getShadeN(float, float, float, float) - Method in class org.jmol.util.Shader
getShades(short) - Method in class org.jmol.util.GData
getShades(short) - Method in class org.jmol.util.Shader
getShades2(int, boolean) - Method in class org.jmol.util.Shader
getShadesG(short) - Method in class org.jmol.util.Shader
getShape(int) - Method in class org.jmol.viewer.ShapeManager
getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JC
getShapeDetail() - Method in class org.jmol.shape.Echo
getShapeDetail() - Method in class org.jmol.shape.Shape
getShapeDetail() - Method in class org.jmol.shapecgo.CGO
getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
getShapeDetail() - Method in class org.jmol.shapespecial.Draw
getShapeDetail() - Method in class org.jmol.shapespecial.Polyhedra
getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
getShapeErrorState() - Method in class org.jmol.viewer.Viewer
getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
  Returns the shape type index for a shape object given the object name.
getShapeInfo() - Method in class org.jmol.viewer.PropertyManager
getShapely() - Method in class org.jmol.util.ColorEncoder
getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEval
getShapeProperty(int, String) - Method in class org.jmol.scriptext.ScriptExt
getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
getShapePropertyAsInt(int, String) - Method in class org.jmol.viewer.Viewer
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.script.ScriptEval
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
getShapePropertyIndex(int, String, int) - Method in class org.jmol.viewer.ShapeManager
getShapeState() - Method in class org.jmol.shape.AtomShape
getShapeState() - Method in class org.jmol.shape.FontLineShape
getShapeState() - Method in class org.jmol.shape.Frank
getShapeState() - Method in class org.jmol.shape.Shape
getShapeState() - Method in class org.jmol.shape.Sticks
getShapeState() - Method in class org.jmol.shape.TextShape
getShapeState() - Method in class org.jmol.shapebio.BioShape
getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
getShapeState() - Method in class org.jmol.shapecgo.CGO
getShapeState() - Method in class org.jmol.shapespecial.Dipole
getShapeState() - Method in class org.jmol.shapespecial.Dipoles
getShapeState() - Method in class org.jmol.shapespecial.Dots
getShapeState() - Method in class org.jmol.shapespecial.Draw
getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
getShapeState() - Method in class org.jmol.shapesurface.Isosurface
getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
getShapeState(Shape) - Method in class org.jmol.viewer.StateCreator
getShapeStatePriv(SB, boolean, int) - Method in class org.jmol.viewer.StateCreator
getShapeType(int) - Method in class org.jmol.script.ScriptEval
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JC
getSheetStructures() - Method in class org.jmol.dssx.DSSP
  "sheet =: a set of one or more ladders connected by shared residues" (p.
getShellOrder(int) - Static method in class org.jmol.quantum.MOCalculation
getShowAxes() - Method in class org.jmol.viewer.Viewer
getShowBbcage() - Method in class org.jmol.viewer.Viewer
getShowFrank() - Method in class org.jmol.viewer.Viewer
getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
getShowSelectedOnce() - Method in class org.jmol.viewer.Viewer
getShowUnitCell() - Method in class org.jmol.viewer.Viewer
getSigma() - Method in class org.jmol.adapter.readers.cif.MSRdr
getSignature() - Method in interface org.jmol.api.JmolScriptFunction
getSignature() - Method in class org.jmol.script.ScriptFunction
getSiteMultiplicity(P3) - Method in interface org.jmol.api.SymmetryInterface
getSiteMultiplicity(P3, UnitCell) - Method in class org.jmol.symmetry.SpaceGroup
getSiteMultiplicity(P3) - Method in class org.jmol.symmetry.Symmetry
getSize(int) - Method in class org.jmol.shape.AtomShape
getSize(int) - Method in class org.jmol.shape.Shape
  overridden in Dots, CGOMesh, and AtomShape
getSize(int, boolean) - Static method in class org.jmol.shapecgo.CGOMesh
getSize(int) - Method in class org.jmol.shapespecial.Dots
getSizeG(Group) - Method in class org.jmol.shape.Shape
getSizeG(Group) - Method in class org.jmol.shapebio.BioShapeCollection
getSlabColor() - Method in class org.jmol.util.MeshSurface
getSlabDepthPlane(boolean) - Method in class org.jmol.viewer.TransformManager
getSlabObjectType(int, Object, boolean, Object) - Static method in class org.jmol.util.TempArray
getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
getSlabType() - Method in class org.jmol.util.MeshSurface
getSlabWithinRange(float, float) - Static method in class org.jmol.util.TempArray
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
  scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstDSpherical(int, double, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
  spherical scaling factors specifically for x2-y2 and z2 orbitals see http://openmopac.net/Manual/real_spherical_harmonics.html dz2 sqrt((1/2p)(5/8))(2cos2(q) -sin2(q)) sqrt(5/16p)(3z2-r2)/r2 dxz sqrt((1/2p)(15/4))(cos(q)sin(q))cos(f) sqrt(15/4p)(xz)/r2 dyz sqrt((1/2p)(15/4))(cos(q)sin(q))sin(f) sqrt(15/4p)(yz)/r2 dx2-y2 sqrt((1/2p)(15/16))sin2(q)cos2(f) sqrt(15/16p)(x2-y2)/r2 dxy sqrt((1/2p)(15/16))sin2(q)sin2(f) sqrt(15/4p)(xy)/r2 The fact() method returns sqrt(15/4p) for both z2 and x2-y2.
getSlice() - Method in class org.openscience.jmol.app.surfacetool.Slice
getSliceAngleXY() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getSliceMiddle() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getSlicePosition() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getSliceThickness() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getSmartsMap(String, BS) - Method in class org.jmol.viewer.Viewer
getSmartsMatch(String, BS) - Method in class org.jmol.api.JmolViewer
getSmartsMatch(String, BS) - Method in class org.jmol.viewer.Viewer
getSmartsMatchForNodes(String, Node[]) - Method in class org.jmol.viewer.Viewer
getSmiles(BS) - Method in class org.jmol.api.JmolViewer
getSmiles(Node[], int, BS, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getSmiles(SmilesMatcher, Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesGenerator
getSmiles(Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesMatcher
  internal to Jmol -- called by org.jmol.Viewer.getSmiles
getSmiles(BS) - Method in class org.jmol.viewer.Viewer
getSmilesAt(SB, SimpleNode, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
getSmilesAtoms(String) - Method in class org.jmol.viewer.Viewer
getSmilesChiralityArray() - Method in class org.jmol.symmetry.CIPDataSmiles
getSmilesComponent(Node, BS, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
  creates a valid SMILES string from a model.
getSmilesCorrelation(BS, BS, String, Lst<P3>, Lst<P3>, M4, Lst<BS>, boolean, int[][], P3, boolean, int) - Method in class org.jmol.scriptext.SmilesExt
  The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
getSmilesExt() - Method in class org.jmol.script.ScriptExpr
getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
getSmilesMatches(String, String, BS, BS, int, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
getSmilesOpt(BS, int, int, int, String) - Method in class org.jmol.viewer.Viewer
  returns the SMILES string for a sequence or atom set does not include attached protons on groups
getSolventPoints(IsoSolventReader.Edge, int, int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
getSource(EventObject) - Method in class org.jmol.awt.AwtPopupHelper
  returns the SwingComponent wrapper for this item
getSourceActions(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupInfo(Symmetry, int, String, int, P3, P3, String, float, int, boolean, boolean, int, SymmetryInterface) - Method in class org.jmol.symmetry.SymmetryDesc
getSpaceGroupInfoObj(String, SymmetryInterface, boolean) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupInfoObj(String, SymmetryInterface, boolean) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupOperationCode(int) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupOperationCode(int) - Method in class org.jmol.symmetry.Symmetry
getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
getSpaceGroups() - Static method in class org.jmol.symmetry.SpaceGroup
getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
getSparseMatrix(CifReader, String, int, int) - Method in class org.jmol.adapter.readers.cif.MSCifParser
getSpartanDirs(String) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  read the output file from the Spartan directory and decide from that what files need to be read and in what order - usually M0001 or a set of Profiles.
getSpartanFileList(String, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  returns the list of files to read for every Spartan spardir.
getSpartanSubfiles(String[]) - Method in class org.jmol.io.JmolUtil
  Called to see if we have a zipped up Mac directory.
getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
getSpecialAtomName(int) - Static method in class org.jmol.modelsetbio.BioResolver
getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
getSpecialLabel(String, String) - Method in class org.jmol.popup.JmolPopup
  menus or menu items with SPECIAL in their name are sent here for on-the-fly labeling
getSpecName(String) - Method in class org.jmol.modelset.AtomCollection
getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
getSpecular() - Method in class org.jmol.util.GData
getSpecularExponent() - Method in class org.jmol.util.GData
getSpecularPercent() - Method in class org.jmol.util.GData
getSpecularPower() - Method in class org.jmol.util.GData
getSpeedPixelsPerMillisecond(int, int) - Method in class org.jmol.viewer.Gesture
getSPF(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.VolumeFileReader
getSphereData(int) - Static method in class org.jmol.util.MeshSurface
  Calculates the data (faces, vertices, normals) for a sphere.
getSphereResource() - Method in class org.jmol.export._IdtfExporter
getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
getSpinAxis(String, int) - Method in class org.jmol.shapespecial.Draw
getSpinCenter(String, int, int) - Method in class org.jmol.shapespecial.Draw
getSpinDensities(int) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
getSpinOp(int) - Method in interface org.jmol.api.SymmetryInterface
getSpinOp(int) - Method in class org.jmol.symmetry.Symmetry
getSpinState(boolean) - Method in class org.jmol.viewer.JmolStateCreator
getSpinState(boolean) - Method in class org.jmol.viewer.StateCreator
getSpinState() - Method in class org.jmol.viewer.Viewer
getSSMapAtom(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
getStandardPdbHydrogenCount(String) - Static method in class org.jmol.modelsetbio.BioResolver
getStartChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
getStartChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStartInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
getStartInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
getState() - Method in interface org.jmol.api.JmolGestureServerInterface
getState() - Method in interface org.jmol.api.JmolModulationSet
getState(SB) - Method in interface org.jmol.api.JmolNMRInterface
getState(SB) - Method in interface org.jmol.api.SymmetryInterface
getState() - Method in class org.jmol.modelset.Trajectory
getState(SB) - Method in class org.jmol.quantum.NMRCalculation
getState(String) - Method in class org.jmol.shape.Mesh
getState(Viewer) - Method in class org.jmol.shapespecial.Polyhedron
getState(SB) - Method in class org.jmol.symmetry.Symmetry
getState() - Method in class org.jmol.symmetry.UnitCell
getState() - Method in class org.jmol.util.ModulationSet
getStateAtoms(SB) - Method in class org.jmol.shapespecial.Ellipsoids
getStateCreator() - Method in class org.jmol.viewer.Viewer
getStateID(SB) - Method in class org.jmol.shapespecial.Ellipsoids
getStateInfo() - Method in class org.jmol.api.JmolViewer
getStateInfo() - Method in class org.jmol.viewer.Viewer
getStateInfo3(String, int, int) - Method in class org.jmol.viewer.Viewer
getStateScript(String, int, int) - Method in class org.jmol.viewer.JmolStateCreator
getStateScript(String, int, int) - Method in class org.jmol.viewer.StateCreator
getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.GenericPlatform
getStaticGraphics(Object, boolean) - Static method in class org.jmol.awt.Image
getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs.Platform
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs2d.Platform
getStatusChanged(String) - Method in class org.jmol.viewer.StatusManager
getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
getStereo() - Method in class org.jmol.smiles.SmilesAtom
getStereoEdge(SimpleNode, SimpleNode) - Method in class org.jmol.symmetry.CIPDataSmiles
getStereoFlag(SimpleNode, SimpleNode[], int, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
getStereoMode(String) - Static method in enum org.jmol.c.STER
getStereoRotationMatrix(boolean) - Method in class org.jmol.viewer.TransformManager
getStr(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  safe string parsing of line.substring(col1, col2);
getStraightness(float) - Static method in class org.jmol.modelsetbio.BioExt
getStrandCount() - Method in class org.jmol.adapter.smarter.StructureIterator
getStrandCount() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStrandCount(int) - Method in class org.jmol.viewer.Viewer
getString(String) - Method in class org.jmol.i18n.GT
getString(String) - Method in class org.jmol.i18n.Resource
getString() - Method in class org.jmol.modelset.Measurement
getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getString(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
getStringDetail() - Method in class org.jmol.modelset.Measurement
getStringInfo(String, String, String, String, String, Map<String, Object[]>, String, Lst<Object[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
getStringObjectAsVariable(Object) - Method in class org.jmol.script.ScriptExpr
getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getStringUsing(Viewer, String, String) - Method in class org.jmol.modelset.Measurement
getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
getStrucNo() - Method in class org.jmol.modelset.Group
getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
getStructure() - Method in class org.jmol.adapter.readers.cif.MMTFReader
  Get and translate the DSSP string from digit format input data
getStructure() - Method in class org.jmol.modelset.Group
getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
getStructure(String) - Method in class org.jmol.popup.PopupResource
getStructuredModels() - Method in class org.jmol.adapter.smarter.StructureIterator
getStructuredModels() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStructureID() - Method in class org.jmol.adapter.smarter.StructureIterator
getStructureID() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStructureId() - Method in class org.jmol.modelset.Group
getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
getStructureId() - Method in class org.jmol.modelsetbio.Monomer
getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
  Get a StructureIterator.
getStructureLines(BS, SB, Lst<ProteinStructure>, STR, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
getStructureList() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
getStructureList() - Method in class org.jmol.modelset.ModelSet
getStructureList() - Method in class org.jmol.viewer.GlobalSettings
getStructureList() - Method in class org.jmol.viewer.Viewer
getStructureMap(Lst<Object>, String, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
  Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
getStructureMidPoint(int) - Method in class org.jmol.modelsetbio.ProteinStructure
getStructures(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
getStructures(String, String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
  Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
getStructures46(String[], String, Lst<Object>, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
  Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
getStructureState() - Method in class org.jmol.viewer.Viewer
getStructuresTOPO(String, String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
getStructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
getStructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
getStuctureAsText(String, String[][], String[][]) - Method in class org.jmol.popup.PopupResource
getStyle(boolean) - Method in class org.jmol.awtjs.swing.GridBagConstraints
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Component
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Container
getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.JSplitPane
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Component
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Container
getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.JSplitPane
getSublist(Lst<SV>, Lst<SV>) - Method in class org.jmol.scriptext.MathExt
  [ {...},{...}...
getSubPattern(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
getSubsearch(SmilesSearch, String, int) - Method in class org.jmol.smiles.SmilesParser
getSubstructureSet(String, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getSubstructureSet(String, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  Returns a bitset matching the pattern within a set of Jmol atoms.
getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
  Returns a vector of bitsets indicating which atoms match the pattern.
getSubstructureSetArray(String, BS, int) - Method in class org.jmol.viewer.Viewer
getSubstructureSetArrayForNodes(String, Node[], int) - Method in class org.jmol.viewer.Viewer
getSubstructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
getSubstructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
getSubsystem(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
getSubSystemUnitCell() - Method in interface org.jmol.api.JmolModulationSet
getSubSystemUnitCell() - Method in class org.jmol.util.ModulationSet
getSubzonePmeshes(BZone) - Method in class org.jmol.util.BZone
  Loop through all planes, creating a pmesh for each face.
getSubzones(BZone, BZone) - Method in class org.jmol.util.BZone
getSupported(String) - Method in class org.jmol.i18n.GT
getSupported(Language[], String) - Static method in class org.jmol.i18n.Language
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
  The list of files returned by this function should contain the full path to each file.
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
getSurfaceData() - Method in class org.jmol.jvxl.readers.EfvetReader
getSurfaceData() - Method in class org.jmol.jvxl.readers.NffReader
getSurfaceData() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
getSurfaceData() - Method in class org.jmol.jvxl.readers.PmeshReader
getSurfaceData() - Method in class org.jmol.jvxl.readers.PolygonFileReader
getSurfaceData() - Method in class org.jmol.jvxl.readers.Ras3DReader
getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
getSurfaceDistance100(int) - Method in class org.jmol.modelset.AtomCollection
getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.IsoMOReader
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
  TEST: alternative EXACT position of fraction for spherical MarchingCubes FOR: ttest.xyz: 2 isosurface molecular test showing discontinuities C -2.70 0 0 C 2.75 0 0 RESULT: LINEAR (points slightly within R): $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.06620391572324] isosurfaceVolume = [41.639681683494324] NONLINEAR: $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.11873783245028] isosurfaceVolume = [41.727027252180655] revision 3/16/2014: isosurfaceArea = [75.13146821881998] isosurfaceVolume = [41.74598178064965] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F.
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.VolumeFileReader
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
  getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
getSurfaceSetForLevel(int) - Method in class org.jmol.jvxl.data.MeshData
getSurfaceSets() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
getSwingComponent(Object) - Method in class org.jmol.awt.AwtPopupHelper
getSwingComponent(Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
getSwingComponent(Object) - Method in interface org.jmol.popup.PopupHelper
getSym - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
getSymbol(String) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
getSymbolic() - Method in class org.jmol.adapter.readers.simple.InputReader
getSymbolic(String) - Method in class org.jmol.adapter.readers.simple.InputReader
getSymEditState() - Method in class org.jmol.modelkit.ModelKitPopup
getSymMatrices(int) - Method in class org.jmol.modelset.ModelSet
getSymmetry(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
getSymmetry() - Method in class org.jmol.adapter.readers.cif.Subsystem
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomIterator
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
getSymmetry(Viewer, String) - Static method in class org.jmol.api.Interface
getSymmetry() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getSymmetry(Viewer, boolean) - Method in class org.jmol.shapespecial.Polyhedron
getSymmetryFromCode(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
getSymmetryFromCode(String) - Method in interface org.jmol.adapter.smarter.MSInterface
getSymmetryInfo(Symmetry, int, int, Symmetry, String, int, P3, P3, String, int, float, int, int) - Method in class org.jmol.symmetry.SymmetryDesc
  multipurpose function handling a variety of tasks, including: processing of "lattice", "list", "atom", "point", and some "draw" output types finding the operator in the given space group creating a temporary space group for an xyz operator
getSymmetryInfo(int, String, int, P3, P3, int, String, float, int, int) - Method in class org.jmol.viewer.Viewer
  A general method for retrieving symmetry information with full capability of the symop() scripting function.
getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelSet
getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, String, int, float, int, int) - Method in interface org.jmol.api.SymmetryInterface
getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, String, int, float, int, int) - Method in class org.jmol.symmetry.Symmetry
getSymmetryInfoStr() - Method in interface org.jmol.api.SymmetryInterface
getSymmetryInfoStr() - Method in class org.jmol.symmetry.Symmetry
getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
getSymmetryOperatorList(boolean) - Method in class org.jmol.modelset.Atom
getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
  Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
getSymOp() - Method in class org.jmol.modelset.Atom
getSymopInfo(int, String, int, P3, P3, String, int, float, int, int) - Method in class org.jmol.symmetry.SymmetryDesc
getSymopInfoForPoints(Symmetry, int, int, P3, P3, String, String, float, int, boolean, int) - Method in class org.jmol.symmetry.SymmetryDesc
  get information about a symmetry operation relating two specific points or atoms
getSymTemp() - Method in class org.jmol.viewer.Viewer
  Retrieve a Symmetry object, possibly re-using an old one.
getSymViewState() - Method in class org.jmol.modelkit.ModelKitPopup
getSyncMode() - Method in class org.jmol.viewer.StatusManager
getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
getTaintedAtoms(int) - Method in class org.jmol.modelset.AtomCollection
getTargetValence() - Method in class org.jmol.modelset.Atom
getTensor(Atom, String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
getTensor(Viewer, float[]) - Method in interface org.jmol.api.SymmetryInterface
getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.Symmetry
getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.UnitCell
getTensorInfo(String, String, BS) - Method in interface org.jmol.api.JmolNMRInterface
getTensorInfo(String, String, BS) - Method in class org.jmol.quantum.NMRCalculation
getTensorList(Lst<Object>) - Static method in class org.jmol.modelset.AtomCollection
getTensors() - Method in class org.jmol.adapter.smarter.AtomIterator
getTensors() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getTensors() - Method in class org.jmol.modelset.Atom
getTerminatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
getTerminatorAtom() - Method in class org.jmol.modelsetbio.Monomer
getTerminatorAtom() - Method in class org.jmol.modelsetbio.NucleicMonomer
getTerminatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
getText() - Method in interface org.jmol.api.JmolScriptEditorInterface
getText() - Method in interface org.jmol.api.js.GenericConsoleTextArea
getText() - Method in interface org.jmol.api.SC
getText() - Method in class org.jmol.awt.AwtSwingComponent
getText() - Method in class org.jmol.awtjs.swing.Component
getText() - Method in class org.jmol.console.GenericConsole
getText() - Method in interface org.jmol.console.GenericTextArea
getText() - Method in class org.jmol.console.ScriptEditor
getText() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
getText() - Static method in class org.openscience.jmol.app.webexport.LogPanel
getTextPixels(String, Font, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
getTextPixels(String, Font, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
getTextPixels(String, Font, Object, int, int, int) - Static method in class org.jmol.awtjs2d.Image
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
getTextPosition() - Method in class org.jmol.util.GData
getTextState(Text) - Method in class org.jmol.viewer.StateCreator
getTextureName(short) - Method in class org.jmol.export._ObjExporter
  Returns the name to be used for the texture associated with the given colix.
getTextWrapper - Static variable in class org.jmol.i18n.GT
getTextWrapper() - Static method in class org.jmol.i18n.GT
getThermalRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoid
getThicknessMax() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getThisContext() - Method in interface org.jmol.api.JmolScriptEvaluator
getThisContext() - Method in class org.jmol.script.ScriptEval
getThread() - Method in class org.jmol.minimize.Minimizer
getTimeDifference(int) - Method in class org.jmol.viewer.Gesture
getTimeFrom(String) - Static method in class org.jmol.util.Logger
getTimerMsg(String, int) - Static method in class org.jmol.util.Logger
getTlsGroups - Variable in class org.jmol.adapter.readers.pdb.PdbReader
getTok() - Method in interface org.jmol.api.JmolScriptFunction
getTok() - Method in class org.jmol.script.ScriptFunction
getToken(int) - Method in class org.jmol.script.ScriptContext
getToken(int) - Method in class org.jmol.script.ScriptParam
getToken() - Method in class org.jmol.script.ScriptTokenParser
  gets the next token and sets global theToken and theValue
getToken(int) - Method in class org.jmol.scriptext.ScriptExt
getTokenCount() - Method in class org.jmol.script.ScriptContext
getTokenFromName(String) - Static method in class org.jmol.script.T
getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getTokens() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
getTokensLike(String) - Static method in class org.jmol.script.T
getTokensType(Map<String, Object>, int) - Static method in class org.jmol.script.T
getTokFromName(String) - Static method in class org.jmol.script.T
getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
getTopoMapPt(int[], int, SmilesAtom, SmilesAtom, SmilesBond[], int) - Static method in class org.jmol.smiles.SmilesStereo
getTopPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
getTorsionAngleRadians(double[], double[], double[], double[], V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
getTorsionKey(int, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getTorsions() - Method in class org.jmol.minimize.Minimizer
getTorsions(Atom[], int[][], float[][], int) - Static method in class org.jmol.scriptext.SmilesExt
getTotalHydrogenCount() - Method in class org.jmol.modelset.Atom
getTotalHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
getTotalHydrogenCount() - Method in interface org.jmol.util.Node
getTotalValence() - Method in class org.jmol.modelset.Atom
getTotalValence() - Method in class org.jmol.smiles.SmilesAtom
getTotalValence() - Method in interface org.jmol.util.Node
getTrackerKey(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Static method in class org.jmol.symmetry.CIPDataTracker
getTrackerLine(CIPChirality.CIPAtom, BS, BS, int) - Method in class org.jmol.symmetry.CIPDataTracker.CIPTracker
getTrajectoryState() - Method in class org.jmol.viewer.Viewer
getTrajectoryStep(P3[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
getTrajectoryStep(P3[], boolean) - Method in class org.jmol.adapter.readers.more.MdCrdReader
getTransferData(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
getTransferData(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
getTransferDataFlavors() - Method in class org.jmol.awt.AwtClipboard
getTransferDataFlavors() - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
getTransformedVertexVectors() - Method in class org.jmol.util.GData
getTransformManager(Viewer, int, int, boolean) - Static method in class org.jmol.viewer.TransformManager
getTranslation(int) - Method in class org.jmol.modelset.ModelSet
getTranslationScript() - Method in class org.jmol.viewer.TransformManager
getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
getTranslucentFlag(float) - Static method in class org.jmol.util.C
getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEval
getTriad(T3) - Method in class org.jmol.export.___Exporter
getTriad(T3) - Method in class org.jmol.export._PovrayExporter
getTriad(int[]) - Method in class org.jmol.export._PovrayExporter
getTriadC(T3) - Method in class org.jmol.export.___Exporter
getTriangleData(T3, T3, T3) - Static method in class org.jmol.export.MeshData
  Calculates the data (faces, vertices, normals) for a triangle.
getTriangleResource(String, T3, T3, T3) - Method in class org.jmol.export._IdtfExporter
getTriangles() - Method in class org.jmol.jvxl.readers.EfvetReader
getTriangulator() - Method in class org.jmol.viewer.Viewer
getTrigonality(SimpleNode, V3) - Method in class org.jmol.symmetry.CIPData
  Determine the trigonality of an atom in order to determine whether it might have a lone pair.
getTrimmedLineImpl() - Method in class org.jmol.g3d.LineRenderer
  Cohen-Sutherland line clipping used to check visibility.
getTrueAtomCount() - Method in class org.jmol.modelset.Model
  not actually accessed -- just pointing out what it is
getType() - Method in interface org.jmol.api.JmolDialogInterface
getType(Atom) - Static method in enum org.jmol.c.HB
getType() - Method in class org.jmol.dialog.Dialog
getType() - Method in class org.jmol.modelsetbio.BioPolymer
getType(int) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
getType(String) - Static method in class org.jmol.symmetry.SymmetryDesc
getType(String) - Static method in class org.jmol.util.Tensor
getType(Object[]) - Method in class org.jmol.viewer.DataManager
getUndeletedGroupAtomBits(BS) - Method in class org.jmol.viewer.Viewer
getUnescapedStringLiteral(boolean) - Method in class org.jmol.script.ScriptCompiler
  lookingAtString returned true, and we need to unescape any t, r, n, ", ', x, u, or backslash after a backslash
getUniqueFloatDef(int, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getUniqueID(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getUniqueID() - Method in class org.jmol.adapter.smarter.AtomIterator
getUniqueID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getUniqueID(int) - Method in interface org.jmol.api.PymolAtomReader
getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
getUniquePoint(int, int, P3) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getUniqueTensorSet(BS) - Method in interface org.jmol.api.JmolNMRInterface
  An attempt to find unique atoms using tensors.
getUniqueTensorSet(BS) - Method in class org.jmol.quantum.NMRCalculation
getUnitCell(T3[], boolean, String) - Method in interface org.jmol.api.SymmetryInterface
getUnitCell() - Method in class org.jmol.modelset.Atom
getUnitCell(int) - Method in class org.jmol.modelset.ModelSet
getUnitCell() - Method in class org.jmol.shape.Mesh
getUnitCell() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getUnitCell(T3[], boolean, String) - Method in class org.jmol.symmetry.Symmetry
getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
getUnitCellForAtom(int) - Method in class org.jmol.modelset.ModelSet
getUnitCellInfo() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfo() - Method in class org.jmol.symmetry.Symmetry
getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
getUnitCellInfoMap() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfoMap() - Method in class org.jmol.symmetry.Symmetry
getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
getUnitCellInfoType(int) - Method in interface org.jmol.api.SymmetryInterface
getUnitCellInfoType(int) - Method in class org.jmol.symmetry.Symmetry
getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
getUnitCellMultiplier() - Method in class org.jmol.symmetry.UnitCell
getUnitCellParams() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellParams() - Method in class org.jmol.modelset.ModelSet
  deprecated due to multimodel issues, but required by an interface -- do NOT remove.
getUnitCellParams() - Method in class org.jmol.symmetry.Symmetry
getUnitCellParams() - Method in class org.jmol.util.SimpleUnitCell
getUnitCellPointsWithin(float, BS, P3, boolean) - Method in class org.jmol.modelset.ModelSet
getUnitCellState() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellState() - Method in class org.jmol.modelkit.ModelKitPopup
getUnitCellState() - Method in class org.jmol.symmetry.Symmetry
getUnitCellVectors() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellVectors() - Method in class org.jmol.symmetry.Symmetry
getUnitCellVectors() - Method in class org.jmol.symmetry.UnitCell
getUnitCellVerticesNoOffset() - Method in interface org.jmol.api.SymmetryInterface
getUnitCellVerticesNoOffset() - Method in class org.jmol.symmetry.Symmetry
getUnitID(int) - Method in class org.jmol.modelset.Atom
getUnitID(Atom, int) - Method in class org.jmol.modelsetbio.BioModel
  Get a unitID.
getUnitIDFlags(String) - Static method in class org.jmol.viewer.JC
  Get a unitID type
getUnits() - Method in class org.jmol.minimize.forcefield.Calculations
getUnits() - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
getUnits() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
getUnitsymmetryInfo() - Method in class org.jmol.symmetry.Symmetry
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
  From JmolGenericPopup.appRunSpecialCheckBox when name starts with "mk" or has "??" in it.
getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
getUnzippedReaderOrStreamFromName(String, Object, boolean, boolean, boolean, boolean, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
getUParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getURLContents(URL, byte[], String, boolean) - Method in interface org.jmol.api.GenericPlatform
getURLContents(URL, byte[], String) - Static method in class org.jmol.awt.AwtFile
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awt.Platform
getURLContents(URL, byte[], String) - Static method in class org.jmol.awtjs2d.JSFile
  Note that the JS equivalent passes back a javajs.util.SB
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awtjs2d.Platform
getURLContentsStatic(URL, byte[], String, boolean) - Static method in class org.jmol.awtjs2d.Platform
  In case this needs to be performed directly, without interface
getUseMolecular() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserFunctionResult(String, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
getUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
getUtil(String, Viewer, String) - Static method in class org.jmol.api.Interface
getV0abc(Object) - Method in interface org.jmol.api.SymmetryInterface
getV0abc(Object) - Method in class org.jmol.symmetry.Symmetry
getV0abc(Object) - Method in class org.jmol.symmetry.UnitCell
getV0abc(Object) - Method in class org.jmol.viewer.Viewer
  convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c.
getV3() - Method in interface org.jmol.api.JmolModulationSet
getV3() - Method in class org.jmol.util.ModulationSet
getVal(MoveToThread.Slider) - Method in class org.jmol.thread.MoveToThread
getVal(float) - Method in class org.jmol.thread.MoveToThread.Slider
getValence() - Method in class org.jmol.modelset.Atom
  return the total bond order for this atom
getValence() - Method in class org.jmol.modelset.Bond
getValence() - Method in class org.jmol.smiles.SmilesAtom
getValence() - Method in class org.jmol.smiles.SmilesBond
getValence() - Method in interface org.jmol.util.Node
getValence() - Method in interface org.jmol.util.SimpleNode
getValue(int) - Method in class org.jmol.adapter.readers.simple.InputReader
getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
  for readers only
getValue(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
getValue(double, boolean) - Method in class org.jmol.quantum.NciCalculation
getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
getValue(String, String) - Method in class org.jmol.util.GenericApplet
getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
getValue2(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
getValueAB(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
getValueAB(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
getValueArray(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
getValueAt(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
getValueAtPoint(P3) - Method in class org.jmol.quantum.MepCalculation
getValueAtPoint2(T3, BS) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
getValueAtPoint2(T3, BS) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
getValueLowerCase(String, String) - Method in class org.jmol.util.GenericApplet
getValues() - Method in class org.jmol.jvxl.readers.IsoMOReader
getVanderwaalsMar(int, VDW) - Static method in class org.jmol.util.Elements
getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
getVanderwaalsMarType(int, VDW) - Method in class org.jmol.viewer.Viewer
getVanderwaalsRadiusFloat(Viewer, VDW) - Method in class org.jmol.modelset.Atom
getVariable(String) - Method in class org.jmol.script.ScriptContext
  Context variables go up the stack until a function is found.
getVariable(Object) - Static method in class org.jmol.script.SV
getVariableAB(byte[]) - Static method in class org.jmol.script.SV
getVariableAD(double[]) - Static method in class org.jmol.script.SV
getVariableADD(double[][]) - Static method in class org.jmol.script.SV
getVariableAF(float[]) - Static method in class org.jmol.script.SV
getVariableAFF(float[][]) - Static method in class org.jmol.script.SV
getVariableAI(int[]) - Static method in class org.jmol.script.SV
getVariableAII(int[][]) - Static method in class org.jmol.script.SV
getVariableAO(Object[]) - Static method in class org.jmol.script.SV
getVariableAP(T3[]) - Static method in class org.jmol.script.SV
getVariableAS(String[]) - Static method in class org.jmol.script.SV
getVariableASS(String[][]) - Static method in class org.jmol.script.SV
getVariableAV(SV[]) - Static method in class org.jmol.script.SV
getVariableList(Lst<?>) - Static method in class org.jmol.script.SV
getVariableList() - Method in class org.jmol.viewer.GlobalSettings
getVariableList(Map<String, SV>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
getVariableMap(Map<String, ?>) - Static method in class org.jmol.script.SV
getVariables(String) - Method in class org.jmol.viewer.PropertyManager
getVarParameter(String, boolean) - Method in class org.jmol.script.ScriptParam
getVArray(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
getVArrayB(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
getVDW(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
getVDW(int) - Method in interface org.jmol.api.PymolAtomReader
getVdwClashRadius(ContactPair, double, double, double, double) - Static method in class org.jmol.shapesurface.Contact
  well, heh, heh...
getVdwLabel() - Method in enum org.jmol.c.VDW
getVdwType(String) - Static method in enum org.jmol.c.VDW
getVdwType(VDW) - Method in class org.jmol.modelset.Atom
getVdwType2(String) - Static method in enum org.jmol.c.VDW
getVectorsAndOrigin() - Method in class org.jmol.jvxl.readers.MapFileReader
getVersion() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
getVersion() - Method in interface org.openscience.jmol.app.JmolPlugin
getVertex() - Method in class org.jmol.jvxl.readers.NffReader
getVertex(short, short) - Static method in class org.jmol.util.Geodesic
getVertexCount(int) - Static method in class org.jmol.util.Geodesic
getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
getVertexList(DrawMesh, int, int) - Static method in class org.jmol.shapespecial.Draw
getVertexValues(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
getVertexVector(int) - Static method in class org.jmol.util.Geodesic
getVertexVectors() - Static method in class org.jmol.util.Geodesic
getVertexVectors() - Static method in class org.jmol.util.Normix
getVertices() - Method in class org.jmol.jvxl.readers.EfvetReader
getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
getVertices() - Method in class org.jmol.symmetry.UnitCell
getVertices() - Method in class org.jmol.util.MeshSurface
getVerticesFromOABC(P3[]) - Static method in class org.jmol.util.BoxInfo
getVib() - Method in class org.jmol.adapter.smarter.AtomIterator
  Note that atom.vib also serves to deliver specific data items.
getVib() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getVib(char) - Method in class org.jmol.modelset.Atom
getVibCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
  also handles modulation info
getVibration(boolean) - Method in interface org.jmol.api.JmolModulationSet
getVibration(int, boolean) - Method in class org.jmol.modelset.AtomCollection
getVibration(boolean) - Method in class org.jmol.util.ModulationSet
getVibrationPoint(Vibration, T3, float) - Method in class org.jmol.viewer.TransformManager
  return
getVibrationVector() - Method in class org.jmol.modelset.Atom
getViewerData() - Method in class org.jmol.popup.JmolPopup
getViewpoint() - Method in class org.jmol.export._VrmlExporter
getViewScript(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
getViewState() - Method in class org.jmol.modelkit.ModelKitPopup
getViewState(TransformManager, SB) - Method in class org.jmol.viewer.StateCreator
getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
getVisibleSet(boolean) - Method in class org.jmol.modelset.AtomCollection
getVisibleVBS() - Method in class org.jmol.shape.Mesh
getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
getVisibleVertexBitSet() - Method in class org.jmol.shapesurface.IsosurfaceMesh
getVolume(Viewer, VDW) - Method in class org.jmol.modelset.Atom
getVolume() - Method in class org.jmol.shapespecial.Polyhedron
  allows for n-gon, not just triangle; if last component index is negative, then that's a mesh code
getVolume() - Method in class org.jmol.util.ContactPair
getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
getVoxel(int, int, int, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
getVoxelDataAt(int) - Method in class org.jmol.jvxl.data.VolumeData
getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
getVParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getWebSite() - Method in interface org.openscience.jmol.app.JmolPlugin
getWidth(Object) - Static method in class org.jmol.awt.Image
getWidth() - Method in class org.jmol.awtjs.swing.Component
getWidth(Object) - Static method in class org.jmol.awtjs2d.Image
getWindow(Container) - Static method in class org.jmol.awt.Platform
getWindowBorder(String) - Method in class org.openscience.jmol.app.HistoryFile
getWindowPosition(String) - Method in class org.openscience.jmol.app.HistoryFile
getWindowSize(String) - Method in class org.openscience.jmol.app.HistoryFile
getWindowState(SB, int, int) - Method in class org.jmol.viewer.StateCreator
getWindowVisibility(String) - Method in class org.openscience.jmol.app.HistoryFile
getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
getWingPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
getWithinDistanceVector(Lst<Object[]>, float, P3, BS, boolean) - Method in class org.jmol.scriptext.IsoExt
getWord(String) - Method in class org.jmol.popup.PopupResource
getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
getWordContents() - Method in class org.jmol.popup.PopupResource
getWorkingRadius(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
getWorkingRadius(Atom, AtomData) - Method in class org.jmol.modelset.AtomCollection
getWrappedState(String, String[], Object, OC) - Method in class org.jmol.viewer.OutputManager
getWrappedStateScript() - Method in class org.jmol.viewer.Viewer
getX() - Method in class org.jmol.script.ScriptMathProcessor
getXlink(String, String, boolean) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
getXmlAttrib(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
getXmlData(String, String, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
getXmlPoint(String, String) - Method in class org.jmol.jvxl.readers.XmlReader
getXmlType(String) - Static method in class org.jmol.adapter.smarter.Resolver
getXOffset(int) - Static method in class org.jmol.viewer.JC
  X offset in pixels.
getXPlatformLook(JFileChooser) - Static method in class org.jmol.dialog.Dialog
getXSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
getXTok() - Method in class org.jmol.script.ScriptMathProcessor
getXYZ() - Method in class org.jmol.adapter.smarter.AtomIterator
getXYZ() - Method in interface org.jmol.api.JmolAdapterAtomIterator
getXYZ(P3, float) - Method in class org.jmol.jvxl.readers.BCifDensityReader
getXYZ() - Method in class org.jmol.modelset.Atom
getXYZ() - Method in class org.jmol.smiles.SmilesAtom
getXYZ(boolean) - Method in class org.jmol.symmetry.HallRotationTerm
getXyz(int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
getXyz(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
getXYZ() - Method in interface org.jmol.util.Node
getXYZ() - Method in interface org.jmol.util.SimpleNode
getXYZFromMatrix(M4, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getXYZFromRsVs(Matrix, Matrix, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
getYOffset(int) - Static method in class org.jmol.viewer.JC
  Y offset in pixels; negative of this is the actual screen offset
getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
getZapName() - Method in class org.jmol.viewer.Viewer
getZCurrent(float, float, int) - Method in class org.jmol.g3d.PrecisionRenderer
getZipDirectory(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
getZipDirectoryAsString(String) - Method in class org.jmol.script.ScriptManager
getZoom(int, int, BS, float) - Method in class org.jmol.script.ScriptEval
getZoomSetting() - Method in class org.jmol.viewer.TransformManager
getZParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
getZshadeState(SB, TransformManager, boolean) - Method in class org.jmol.viewer.StateCreator
ghemicalMMLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
GhemicalMMReader - Class in org.jmol.adapter.readers.simple
  Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
ghostCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
ghostPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
gibbsEnergy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
gibbsEnergy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
gibbsEntropy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
gl_ambient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
GL_LINE_LOOP - Static variable in class org.jmol.shapecgo.CGOMesh
GL_LINE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
GL_LINES - Static variable in class org.jmol.shapecgo.CGOMesh
GL_POINTS - Static variable in class org.jmol.shapecgo.CGOMesh
GL_TRIANGLE_FAN - Static variable in class org.jmol.shapecgo.CGOMesh
GL_TRIANGLE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
GL_TRIANGLES - Static variable in class org.jmol.shapecgo.CGOMesh
GLOBAL - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
GLOBAL_CONECT - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
GLOBAL_DOMAINS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
GLOBAL_FRACTCOORD - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
GLOBAL_ISPDB - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
GLOBAL_SYMMETRY - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
GLOBAL_UNITCELLS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
GLOBAL_VALIDATIONS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
globalBooleans - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
globalDoApplySymmetry - Variable in class org.jmol.adapter.readers.xtal.AimsReader
globalSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
GlobalSettings - Class in org.jmol.viewer
GlobalSettings(Viewer, GlobalSettings, boolean) - Constructor for class org.jmol.viewer.GlobalSettings
globalSlabValue - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
globalStrucNo - Static variable in class org.jmol.modelsetbio.ProteinStructure
goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
GOLD - Static variable in class org.jmol.util.C
goPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Save or else launch povray- ie do our thang!
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
gotocmd - Static variable in class org.jmol.script.T
gotoCommand(int, boolean, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor
gotoData(int, int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
gotoData(int, int) - Method in class org.jmol.jvxl.readers.XsfReader
gotoParsedLine() - Method in class org.jmol.console.ScriptEditor
gotoPosition(int, int) - Method in class org.jmol.console.ScriptEditor
gotoTop() - Method in class org.jmol.console.ScriptEditor
grabPixels(Object, int, int, int[], int, int) - Method in interface org.jmol.api.GenericPlatform
grabPixels(Object, int, int, int[], int, int) - Static method in class org.jmol.awt.Image
grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awt.Platform
grabPixels(Object, int, int) - Static method in class org.jmol.awtjs2d.Image
grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awtjs2d.Platform
grad - Variable in class org.jmol.quantum.NciCalculation
GRADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
gradient_max_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradient_min_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradient_min_slope - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradient_normal_min_dot - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradient_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradient_step_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradient_symmetry - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
gradients - Variable in class org.jmol.minimize.forcefield.Calculations
Graphics3D - Class in org.jmol.g3d
  Provides high-level graphics primitives for 3D visualization for the software renderers.
Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
graphicsForMetrics - Variable in class org.jmol.util.GData
graphicsForTextOrImage - Variable in class org.jmol.g3d.Platform3D
GRAY - Static variable in class org.jmol.util.C
GRAY - Static variable in class org.jmol.util.ColorEncoder
GREEN - Static variable in class org.jmol.util.C
greyscalerendering - Static variable in class org.jmol.script.T
greyscaleRendering - Variable in class org.jmol.viewer.GlobalSettings
Grid - Class in org.jmol.awtjs.swing
Grid(int, int) - Constructor for class org.jmol.awtjs.swing.Grid
grid - Variable in class org.jmol.awtjs.swing.Grid
grid - Variable in class org.jmol.awtjs.swing.JPanel
grid_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
grid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
grid_slot - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
GridBagConstraints - Class in org.jmol.awtjs.swing
GridBagConstraints(int, int, int, int, double, double, int, int, Insets, int, int) - Constructor for class org.jmol.awtjs.swing.GridBagConstraints
GridBagLayout - Class in org.jmol.awtjs.swing
GridBagLayout() - Constructor for class org.jmol.awtjs.swing.GridBagLayout
gridheight - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gridpoints - Static variable in class org.jmol.script.T
gridwidth - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gridx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gridy - Variable in class org.jmol.awtjs.swing.GridBagConstraints
gRight - Variable in class org.jmol.util.GenericApplet
gRight - Variable in class org.jmol.viewer.Viewer
  A graphics from a "slave" stereo display that has been synchronized with this this applet.
GromacsReader - Class in org.jmol.adapter.readers.more
GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PdbReader
group(String) - Method in class org.jmol.adapter.readers.xtal.CgdReader
group - Variable in class org.jmol.modelset.Atom
Group - Class in org.jmol.modelset
  The essential container for every atom.
Group() - Constructor for class org.jmol.modelset.Group
group - Static variable in class org.jmol.script.T
group1 - Variable in class org.jmol.modelset.Group
group1 - Static variable in class org.jmol.script.T
group3 - Variable in class org.jmol.adapter.smarter.Atom
group3Count - Static variable in class org.jmol.modelsetbio.BioResolver
group3Counts - Variable in class org.jmol.modelset.ModelLoader
group3Counts - Variable in class org.jmol.popup.JmolPopup
group3List - Variable in class org.jmol.popup.JmolPopup
group3Lists - Variable in class org.jmol.modelset.ModelLoader
group3NameCount - Static variable in class org.jmol.modelsetbio.BioResolver
group3Names - Static variable in class org.jmol.modelset.Group
group3Of - Variable in class org.jmol.modelset.ModelLoader
group3s - Variable in class org.jmol.adapter.readers.more.MdTopReader
group_arrow_prefix - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
group_auto_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
group_full_member_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
GROUP_PDB - Static variable in class org.jmol.adapter.readers.cif.CifReader
groupByModel - Variable in class org.jmol.smiles.SmilesSearch
groupCount - Variable in class org.jmol.adapter.readers.cif.MMTFReader
groupCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
groupCount - Variable in class org.jmol.modelset.Chain
groupCount - Variable in class org.jmol.modelset.Model
groupCount - Variable in class org.jmol.modelset.ModelLoader
groupDSSP - Variable in class org.jmol.adapter.readers.cif.MMTFReader
groupID - Variable in class org.jmol.modelset.Group
groupID - Variable in class org.jmol.multitouch.ActionManagerMT
groupid - Static variable in class org.jmol.script.T
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JC
GROUPID_ARGININE - Static variable in class org.jmol.viewer.JC
GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JC
GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JC
GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JC
GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JC
GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JC
GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JC
GROUPID_ION_MAX - Static variable in class org.jmol.viewer.JC
GROUPID_ION_MIN - Static variable in class org.jmol.viewer.JC
GROUPID_LYSINE - Static variable in class org.jmol.viewer.JC
GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JC
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JC
GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JC
GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JC
GROUPID_WATER - Static variable in class org.jmol.viewer.JC
groupIndex - Variable in class org.jmol.modelset.Group
groupindex - Static variable in class org.jmol.script.T
groupMap - Variable in class org.jmol.adapter.readers.cif.MMTFReader
groupModels - Variable in class org.jmol.adapter.readers.cif.MMTFReader
groups - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
groups - Variable in class org.jmol.modelset.Chain
  Groups form the essence of what a Chain is.
groups - Variable in class org.jmol.modelset.ModelLoader
growAtomArrays(int) - Method in class org.jmol.modelset.ModelSet
GS - Static variable in class org.jmol.quantum.QS
GS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
GT - Class in org.jmol.i18n
  The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
GT() - Constructor for class org.jmol.i18n.GT
GT(Viewer, String) - Constructor for class org.jmol.i18n.GT
gti(String, int) - Method in class org.jmol.popup.JmolPopup
gto(String, Object) - Method in class org.jmol.popup.JmolPopup
GTO_EXP - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
gui - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
GuiMap - Class in org.openscience.jmol.app.jmolpanel
GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
guimap - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
gulpContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
GulpReader - Class in org.jmol.adapter.readers.xtal
  Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
gxTemp - Variable in class org.jmol.quantum.NciCalculation
gxxTemp - Variable in class org.jmol.quantum.NciCalculation
gxyTemp - Variable in class org.jmol.quantum.NciCalculation
gxzTemp - Variable in class org.jmol.quantum.NciCalculation
gyTemp - Variable in class org.jmol.quantum.NciCalculation
gyyTemp - Variable in class org.jmol.quantum.NciCalculation
gyzTemp - Variable in class org.jmol.quantum.NciCalculation
gzTemp - Variable in class org.jmol.quantum.NciCalculation
gzzTemp - Variable in class org.jmol.quantum.NciCalculation

## H

h1Count - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a count of how many 1H atoms we have found on this atom; used to halt further processing of this atom
H3T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
H5T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
h_bar_planck - Static variable in class org.jmol.quantum.NMRCalculation
h_bond_cone - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_cutoff_center - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_cutoff_edge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_exclusion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_from_proton - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_max_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_power_a - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_bond_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
h_planck - Static variable in class org.jmol.quantum.NMRCalculation
half_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
halfRoot5 - Static variable in class org.jmol.util.Geodesic
hAlignNames - Static variable in class org.jmol.viewer.JC
HallInfo - Class in org.jmol.symmetry
HallInfo(String) - Constructor for class org.jmol.symmetry.HallInfo
hallInfo - Variable in class org.jmol.symmetry.SpaceGroup
HallRotation - Class in org.jmol.symmetry
HallRotation(String, String) - Constructor for class org.jmol.symmetry.HallRotation
HallRotationTerm - Class in org.jmol.symmetry
HallRotationTerm(HallInfo, String, int, char) - Constructor for class org.jmol.symmetry.HallRotationTerm
hallRotationTerms - Static variable in class org.jmol.symmetry.HallRotation
hallSymbol - Variable in class org.jmol.symmetry.HallInfo
hallSymbol - Variable in class org.jmol.symmetry.SpaceGroup
HallTranslation - Class in org.jmol.symmetry
HallTranslation(char, P3i) - Constructor for class org.jmol.symmetry.HallTranslation
hallTranslationTerms - Static variable in class org.jmol.symmetry.HallTranslation
halo - Static variable in class org.jmol.script.T
Halos - Class in org.jmol.shape
Halos() - Constructor for class org.jmol.shape.Halos
HalosRenderer - Class in org.jmol.render
HalosRenderer() - Constructor for class org.jmol.render.HalosRenderer
halt - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
haltButton - Variable in class org.jmol.console.ScriptEditor
haltButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
haltExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
haltExecution() - Method in class org.jmol.script.ScriptEval
haltScriptExecution() - Method in class org.jmol.api.JmolViewer
haltScriptExecution() - Method in class org.jmol.viewer.Viewer
handleAssignNew(MouseState, MouseState, MeasurementPending, int) - Method in class org.jmol.modelkit.ModelKitPopup
  C
handleDragAtom(MouseState, MouseState, int[]) - Method in class org.jmol.modelkit.ModelKitPopup
  Called from ActionManager for a drag-drop
handleError() - Method in class org.jmol.script.ScriptCompiler
handleError(Error, boolean) - Method in class org.jmol.viewer.Viewer
handleEvent(Event) - Method in interface org.jmol.api.JmolAppletInterface
handleEvent(Event) - Method in class org.jmol.applet.AppletWrapper
handleEvent(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
handleEvent(Event) - Method in class org.jmol.util.GenericApplet
handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManager
  general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
handleTlsMissingModels() - Method in class org.jmol.adapter.readers.pdb.PdbReader
  for now, we just ignore TLS details if user has selected a specific model
has(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
HAS_MAXGRID - Static variable in class org.jmol.jvxl.readers.Parameters
hasBfactorRange - Variable in class org.jmol.modelset.AtomCollection
hasBfactorRange - Variable in class org.jmol.shapebio.BioShape
hasChirality - Variable in class org.jmol.modelset.Model
hasColorData - Variable in class org.jmol.jvxl.readers.SurfaceReader
hasColorRange - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
hasContent() - Method in class org.jmol.g3d.Graphics3D
hasContent() - Method in class org.jmol.g3d.Platform3D
hasDatabasePrefix(String) - Static method in class org.jmol.viewer.Viewer
hasFocus(Object) - Method in interface org.jmol.api.GenericPlatform
hasFocus(Object) - Static method in class org.jmol.awt.Display
hasFocus(Object) - Method in class org.jmol.awt.Platform
hasFocus(Object) - Static method in class org.jmol.awtjs2d.Display
hasFocus(Object) - Method in class org.jmol.awtjs2d.Platform
hasFocus() - Method in class org.jmol.viewer.Viewer
hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
hash - Static variable in class org.jmol.script.T
hash_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hashCode() - Method in class org.jmol.modelset.Atom
hashCode() - Method in class org.jmol.script.T
hasLocalArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
hasMeasure(int[]) - Method in class org.jmol.modelset.Trajectory
hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
  normal iterator predicate
hasNext() - Method in class org.jmol.adapter.smarter.AtomIterator
hasNext() - Method in class org.jmol.adapter.smarter.BondIterator
hasNext() - Method in class org.jmol.adapter.smarter.StructureIterator
hasNext() - Method in interface org.jmol.api.AtomIndexIterator
hasNext() - Method in interface org.jmol.api.JmolAdapterAtomIterator
hasNext() - Method in class org.jmol.api.JmolAdapterBondIterator
hasNext() - Method in class org.jmol.api.JmolAdapterStructureIterator
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
hasNext() - Method in interface org.jmol.modelset.BondIterator
hasNext() - Method in class org.jmol.modelset.BondIteratorSelected
hasNext() - Method in class org.jmol.symmetry.UnitCellIterator
hasNext2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
hasOAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
hasOffset() - Method in class org.jmol.symmetry.UnitCell
hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
hasRasmolHBonds - Variable in class org.jmol.modelset.Model
hasRnaO2Prime - Variable in class org.jmol.modelsetbio.NucleicMonomer
hasSerialArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
HASSETTING - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hasStructure - Variable in class org.jmol.modelsetbio.BioPolymer
hasSubpattern - Variable in class org.jmol.smiles.SmilesAtom
hasSymbol - Variable in class org.jmol.smiles.SmilesAtom
hasSymmetry - Variable in class org.jmol.popup.JmolPopup
hasUnitCell - Variable in class org.jmol.modelkit.ModelKitPopup
hasValues() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
hasVibration() - Method in class org.jmol.modelset.Atom
hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
hAtomRadius - Variable in class org.jmol.atomdata.AtomData
hAtoms - Variable in class org.jmol.atomdata.AtomData
have(byte[], byte) - Static method in class org.jmol.modelsetbio.Monomer
haveAccess(Viewer.ACCESS) - Method in class org.jmol.viewer.Viewer
haveAnisou - Variable in class org.jmol.adapter.smarter.AtomSetCollection
haveAromatic - Variable in class org.jmol.adapter.readers.cif.CifReader
haveAt - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
haveAtomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
haveAtomMods - Variable in class org.jmol.adapter.readers.cif.MSRdr
haveAtoms - Variable in class org.jmol.shapespecial.Dipole
haveAtomSerials - Variable in class org.jmol.adapter.readers.molxyz.MolReader
haveAxis(int, V3) - Method in class org.jmol.symmetry.PointGroup
haveBeta - Variable in class org.jmol.adapter.readers.quantum.NBOParser
haveBFactors - Variable in class org.jmol.popup.JmolPopup
haveBinaryArrays - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
haveBioModels - Variable in class org.jmol.modelset.ModelSet
haveBitSetVertices - Variable in class org.jmol.shapespecial.Polyhedra
haveBondStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
haveBorder - Variable in class org.openscience.jmol.app.JmolApp
haveBorder - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
haveBSClickable - Variable in class org.jmol.modelset.AtomCollection
haveBsDisplay - Variable in class org.jmol.render.MeshRenderer
haveBsDisplay - Variable in class org.jmol.shapesurface.PMeshWriter
haveBSVisible - Variable in class org.jmol.modelset.AtomCollection
haveCellWaveVector - Variable in class org.jmol.adapter.readers.cif.CifReader
haveCharges - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
haveCharges - Variable in class org.jmol.adapter.readers.xtal.CastepReader
haveCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
haveCharges - Variable in class org.jmol.popup.JmolPopup
haveChirality - Variable in class org.jmol.modelset.AtomCollection
haveCircle - Variable in class org.jmol.export._IdtfExporter
haveCoeffMap - Variable in class org.jmol.adapter.readers.quantum.MOReader
haveComments - Variable in class org.jmol.script.ScriptCompiler
haveCommon(BS, BS) - Static method in class org.jmol.util.BSUtil
haveComponents - Variable in class org.jmol.smiles.SmilesSearch
haveCone - Variable in class org.jmol.export._IdtfExporter
haveConsole - Variable in class org.openscience.jmol.app.JmolApp
haveConstraints - Variable in class org.jmol.minimize.forcefield.Calculations
haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
haveControlPointScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
haveCylinder - Variable in class org.jmol.export._IdtfExporter
haveCylinderIn - Variable in class org.jmol.export._IdtfExporter
haveDisplay - Variable in class org.jmol.viewer.Viewer
haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
haveDocumentAccess - Variable in class org.jmol.util.GenericApplet
haveDoubleBonds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
haveENDIF - Variable in class org.jmol.script.ScriptCompiler
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
haveFileSet() - Method in class org.jmol.viewer.Viewer
haveHAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
haveHeader - Variable in class org.jmol.adapter.readers.simple.MopacReader
haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
haveHighPrecision - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
haveHoverCallback() - Method in class org.jmol.viewer.StatusManager
haveHsAlready - Variable in class org.jmol.modelsetbio.BioResolver
haveInversionCenter - Variable in class org.jmol.symmetry.PointGroup
haveJDX - Variable in class org.jmol.viewer.Viewer
haveLine - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
haveM40Data - Variable in class org.jmol.adapter.readers.xtal.JanaReader
haveMacro - Variable in class org.jmol.script.ScriptTokenParser
haveMacros - Variable in class org.jmol.export._PovrayExporter
haveMappedSerials - Variable in class org.jmol.adapter.readers.pdb.PdbReader
haveMeasurements - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
haveMOData(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
haveModelKit() - Method in class org.jmol.modelset.ModelSet
haveModified - Variable in class org.jmol.modelset.MeasurementPending
haveMolecule - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
haveNotified - Variable in class org.jmol.thread.SpinThread
haveNotifiedError - Variable in class org.jmol.util.GenericApplet
haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
haveNucleicLadder - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
haveOccupancy - Variable in class org.jmol.adapter.readers.cif.MSRdr
haveOneProperty - Variable in class org.jmol.jvxl.readers.AtomDataReader
haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
havePhonons - Variable in class org.jmol.adapter.readers.xtal.CastepReader
havePlanarContours - Variable in class org.jmol.shape.Mesh
havePlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
havePoints - Variable in class org.jmol.quantum.MOCalculation
havePoints - Variable in class org.jmol.quantum.NciCalculation
havePRE - Variable in class org.jmol.adapter.readers.more.AFLOWReader
havePrimitiveMapping - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
havePseudoAuxiliary - Variable in class org.jmol.symmetry.CIPChirality
  do we have r or s and so will need to recalculate Mata like/unlike lists in Rule 5?
haveQuads - Variable in class org.jmol.util.MeshSurface
haveReadColorData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
haveReference - Variable in class org.jmol.thread.JmolThread
haveScenes - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
haveScenes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
haveSelected - Variable in class org.jmol.smiles.SmilesSearch
haveSelection - Variable in class org.jmol.viewer.ActionManager
haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
haveSetAnisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
haveSetStructureList - Variable in class org.jmol.viewer.GlobalSettings
haveSpaceBeforeSquare - Variable in class org.jmol.script.ScriptMathProcessor
haveSphere - Variable in class org.jmol.export._IdtfExporter
haveStraightness - Variable in class org.jmol.modelset.AtomCollection
haveString - Variable in class org.jmol.script.ScriptTokenParser
haveStructure - Variable in class org.jmol.adapter.readers.cif.MMTFReader
haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
haveTarget - Variable in class org.jmol.modelset.MeasurementPending
haveTopo - Variable in class org.jmol.smiles.SmilesSearch
haveTranslations - Static variable in class org.jmol.dialog.Dialog
haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
haveTranslucentObjects() - Method in class org.jmol.export.Export3D
haveTranslucentObjects - Variable in class org.jmol.g3d.Graphics3D
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
haveUnitCell - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
haveUnitCells - Variable in class org.jmol.modelset.ModelSet
haveVibration - Variable in class org.jmol.symmetry.PointGroup
haveXMLUtil - Static variable in class org.jmol.jvxl.data.JvxlCoder
haveXyPoints - Variable in class org.jmol.shape.Mesh
HB - Enum in org.jmol.c
  Enum for hydrogen bonding donor/acceptor type
HB() - Constructor for enum org.jmol.c.HB
HBACCEPT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
HBAMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
HBDMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
HBDONOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
HBond - Class in org.jmol.modelset
HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
hbond - Static variable in class org.jmol.script.T
hbondHCMaxReal - Static variable in class org.jmol.modelset.ModelSet
hbondMaxReal - Static variable in class org.jmol.modelset.ModelSet
hbondMinRasmol - Static variable in class org.jmol.modelset.ModelSet
hbondsangleminimum - Static variable in class org.jmol.script.T
hbondsAngleMinimum - Variable in class org.jmol.viewer.GlobalSettings
hbondsBackbone - Variable in class org.jmol.render.SticksRenderer
hbondsbackbone - Static variable in class org.jmol.script.T
hbondsBackbone - Variable in class org.jmol.viewer.GlobalSettings
hbondsdistancemaximum - Static variable in class org.jmol.script.T
hbondsDistanceMaximum - Variable in class org.jmol.viewer.GlobalSettings
hbondsrasmol - Static variable in class org.jmol.script.T
hbondsRasmol - Variable in class org.jmol.viewer.GlobalSettings
hbondsSolid - Variable in class org.jmol.render.SticksRenderer
hbondssolid - Static variable in class org.jmol.script.T
hbondsSolid - Variable in class org.jmol.viewer.GlobalSettings
HC - Static variable in class org.jmol.quantum.QS
HC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
hCount - Variable in class org.jmol.minimize.MinAtom
hDashes - Static variable in class org.jmol.render.FontLineShapeRenderer
header() - Method in class org.jmol.adapter.readers.pdb.PdbReader
header - Variable in class org.jmol.adapter.readers.xtal.MagresReader
header - Variable in class org.jmol.export._StlExporter
header - Variable in class org.openscience.jmol.app.HistoryFile
  The information written to the header of the history file.
HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
headerContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
headerHeight - Static variable in class org.jmol.awtjs.swing.JDialog
headless - Variable in class org.jmol.viewer.Viewer
  determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN , ANIMATION ON turns SPIN into just ROTATE
headlessImageParams - Variable in class org.jmol.viewer.Viewer
headOffsetVector - Variable in class org.jmol.renderspecial.VectorsRenderer
headScale - Variable in class org.jmol.renderspecial.VectorsRenderer
headWidthPixels - Variable in class org.jmol.renderspecial.DipolesRenderer
headWidthPixels - Variable in class org.jmol.renderspecial.VectorsRenderer
heavy_neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
heavyAtomIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
height - Variable in class org.jmol.awtjs.swing.Component
height - Variable in class org.jmol.awtjs.swing.Dimension
height - Variable in class org.jmol.export.Export3D
height - Variable in class org.jmol.g3d.SphereRenderer
height - Variable in class org.jmol.g3d.TextRenderer
height - Variable in class org.jmol.util.GData
height - Variable in class org.jmol.util.Rectangle
height - Variable in class org.jmol.viewer.TransformManager
height - Variable in class org.openscience.jmol.app.webexport.JmolInstance
heightOffscreen - Variable in class org.jmol.g3d.Platform3D
heightUnitVector - Variable in class org.jmol.modelsetbio.Sheet
Helix - Class in org.jmol.modelsetbio
Helix(AlphaPolymer, int, int, STR) - Constructor for class org.jmol.modelsetbio.Helix
helix - Static variable in class org.jmol.script.T
helix310 - Static variable in class org.jmol.script.T
HELIX_CLASS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
helixalpha - Static variable in class org.jmol.script.T
helixpi - Static variable in class org.jmol.script.T
helixRockets - Variable in class org.jmol.renderbio.RocketsRenderer
helixstep - Static variable in class org.jmol.script.T
helixStep - Variable in class org.jmol.viewer.GlobalSettings
help - Static variable in class org.jmol.script.T
helpButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
helpButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
HelpDialog - Class in org.openscience.jmol.app.jmolpanel
HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
HelpDialog(JFrame, String, boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
  If url is null, then the default help url is taken.
HelpDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
  temporary class that loads synchronously (although later than the request so that a cursor change can be done).
helper - Variable in class org.jmol.popup.GenericPopup
helppath - Static variable in class org.jmol.script.T
helpPath - Variable in class org.jmol.viewer.GlobalSettings
hemisphereOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
hermite3d - Variable in class org.jmol.export.Export3D
hermite3d - Variable in class org.jmol.g3d.Graphics3D
hermiteLevel - Variable in class org.jmol.renderbio.BioShapeRenderer
hermitelevel - Static variable in class org.jmol.script.T
hermiteLevel - Variable in class org.jmol.viewer.GlobalSettings
HermiteRenderer - Class in org.jmol.g3d
  Implementation of hermite curves for drawing smoothed curves that pass through specified points.
HermiteRenderer() - Constructor for class org.jmol.g3d.HermiteRenderer
hess - Variable in class org.jmol.quantum.NciCalculation
het() - Method in class org.jmol.adapter.readers.pdb.PdbReader
HETATM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hetero - Static variable in class org.jmol.script.T
HETMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hetnam() - Method in class org.jmol.adapter.readers.pdb.PdbReader
hi - Variable in class org.jmol.util.ColorEncoder
hidden - Variable in class org.jmol.modelset.Text
hidden - Static variable in class org.jmol.script.T
hiddenlinesdashed - Static variable in class org.jmol.script.T
hiddenLinesDashed - Variable in class org.jmol.viewer.GlobalSettings
hide - Static variable in class org.jmol.script.T
hide(ModelSet, BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
hide_long_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hide_underscore_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
hidenameinpopup - Static variable in class org.jmol.script.T
hideNameInPopup - Variable in class org.jmol.viewer.GlobalSettings
hidenavigationpoint - Static variable in class org.jmol.script.T
hideNavigationPoint - Variable in class org.jmol.viewer.GlobalSettings
hidenotselected - Static variable in class org.jmol.script.T
hideNotSelected - Variable in class org.jmol.viewer.SelectionManager
HIGH - Static variable in class org.jmol.util.ColorEncoder
highLEnabled - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
highLEnabled - Variable in class org.jmol.quantum.MOCalculation
highlight - Static variable in class org.jmol.script.T
highlight(BS) - Method in class org.jmol.viewer.Viewer
highlightBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
  from Sticks
highresolution - Static variable in class org.jmol.script.T
highResolutionFlag - Variable in class org.jmol.viewer.GlobalSettings
history - Static variable in class org.jmol.script.T
historyButton - Variable in class org.jmol.console.GenericConsole
historyDisabled - Variable in class org.jmol.script.ScriptEval
HistoryFile - Class in org.openscience.jmol.app
  The history file contains data from previous uses of Jmol.
HistoryFile(File, String) - Constructor for class org.openscience.jmol.app.HistoryFile
  Creates a history file.
historyFile - Variable in class org.openscience.jmol.app.JmolApp
historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
historyFile - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
historyFile - Static variable in class org.openscience.jmol.app.webexport.WebExport
historyFind(String, int) - Method in class org.jmol.viewer.Viewer
historylevel - Static variable in class org.jmol.script.T
histWinName - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
hkl - Static variable in class org.jmol.script.T
hklParameter(int) - Method in class org.jmol.script.ScriptParam
hmSymbol - Variable in class org.jmol.symmetry.SpaceGroup
hmSymbolAbbr - Variable in class org.jmol.symmetry.SpaceGroup
hmSymbolAbbrShort - Variable in class org.jmol.symmetry.SpaceGroup
hmSymbolAlternative - Variable in class org.jmol.symmetry.SpaceGroup
hmSymbolExt - Variable in class org.jmol.symmetry.SpaceGroup
hmSymbolFull - Variable in class org.jmol.symmetry.SpaceGroup
hNames - Variable in class org.jmol.modelsetbio.BioResolver
hnmrPeaks - Variable in class org.jmol.popup.JmolPopup
holdRepaint - Variable in class org.jmol.render.RepaintManager
homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
HomeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
homePosition() - Method in class org.jmol.api.JmolViewer
homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
homePosition() - Method in class org.jmol.viewer.Viewer
homo - Static variable in class org.jmol.script.T
HORIZONTAL_SPLIT - Static variable in class org.jmol.awtjs.swing.JSplitPane
HOTPINK - Static variable in class org.jmol.util.C
hover - Static variable in class org.jmol.script.T
Hover - Class in org.jmol.shape
Hover() - Constructor for class org.jmol.shape.Hover
hoverable - Static variable in class org.jmol.viewer.ShapeManager
hoverActive - Variable in class org.jmol.viewer.ActionManager
hoverAtomIndex - Variable in class org.jmol.viewer.Viewer
hoverdelay - Static variable in class org.jmol.script.T
hoverDelay - Variable in class org.jmol.thread.HoverWatcherThread
hoverDelayMs - Variable in class org.jmol.viewer.GlobalSettings
hoverEnabled - Variable in class org.jmol.thread.JmolThread
hoverEnabled - Variable in class org.jmol.viewer.Viewer
hoverKey(int, int) - Method in class org.jmol.shapesurface.Isosurface
hoverlabel - Static variable in class org.jmol.script.T
hoverLabel - Variable in class org.jmol.viewer.Viewer
hoverOff() - Method in class org.jmol.viewer.Viewer
hoverOn(int, boolean) - Method in class org.jmol.viewer.Viewer
hoverOnPt(int, int, String, String, T3) - Method in class org.jmol.viewer.Viewer
  Hover over an arbitrary point.
HoverRenderer - Class in org.jmol.render
HoverRenderer() - Constructor for class org.jmol.render.HoverRenderer
hoverText - Variable in class org.jmol.shape.Hover
hoverText - Variable in class org.jmol.viewer.Viewer
HoverWatcherThread - Class in org.jmol.thread
HoverWatcherThread(ActionManager, MouseState, MouseState, Viewer) - Constructor for class org.jmol.thread.HoverWatcherThread
hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
HS - Static variable in class org.jmol.quantum.QS
HS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
ht3 - Variable in class org.jmol.util.GData
htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
htAtomMap - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htAtomMap - Variable in class org.jmol.modelset.ModelLoader
htAtomMods - Variable in class org.jmol.adapter.readers.cif.MSRdr
htAudit - Variable in class org.jmol.adapter.readers.cif.CifReader
htBasisMap - Variable in class org.jmol.adapter.writers.QCJSONWriter
htBiomts - Variable in class org.jmol.adapter.readers.cif.MMCifReader
htBondMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
htBondMap - Variable in class org.jmol.modelsetbio.BioResolver
htBonds - Variable in class org.jmol.adapter.readers.quantum.CsfReader
htBooleanParameterFlags - Variable in class org.jmol.viewer.GlobalSettings
htBridges - Variable in class org.jmol.dssx.DSSP
htByOpCount - Static variable in class org.jmol.symmetry.SpaceGroup
htCarveSets - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htCellTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
htCheckbox - Variable in class org.jmol.popup.GenericPopup
htCriticalPoints - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
htDefinedAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htDefs - Variable in class org.jmol.export._IdtfExporter
htEdges - Variable in class org.jmol.adapter.readers.xtal.CgdReader
htEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
htElementMap - Static variable in class org.jmol.util.Elements
htElementsInCurrentGroup - Variable in class org.jmol.adapter.readers.pdb.PdbReader
htExponents - Variable in class org.jmol.adapter.readers.quantum.DgridReader
htFileCache - Variable in class org.jmol.script.ScriptContext
htFont3d - Static variable in class org.jmol.g3d.TextRenderer
htFont3dAntialias - Static variable in class org.jmol.g3d.TextRenderer
htFormul - Variable in class org.jmol.adapter.readers.pdb.PdbReader
htFuncMap - Variable in class org.jmol.adapter.readers.quantum.DgridReader
htGroup - Static variable in class org.jmol.modelsetbio.BioResolver
htGroup1 - Variable in class org.jmol.adapter.readers.cif.CifReader
htGroup1 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
htGroup1 - Variable in class org.jmol.modelset.ModelLoader
htGroup1 - Static variable in class org.jmol.modelsetbio.NucleicPolymer
htGroupBonds - Variable in class org.jmol.modelsetbio.BioResolver
htHetero - Variable in class org.jmol.adapter.readers.cif.MMCifReader
htHetero - Variable in class org.jmol.adapter.readers.pdb.PdbReader
htHiddenObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htLadders - Variable in class org.jmol.dssx.DSSP
htLanguages - Static variable in class org.jmol.i18n.GT
htMeasures - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htMeasures - Variable in class org.jmol.smiles.SmilesParser
htMenus - Variable in class org.jmol.popup.GenericPopup
htMin - Variable in class org.jmol.modelset.MeasurementData
htMin - Variable in class org.jmol.shape.Measures
html - Variable in class org.jmol.awtjs.swing.JDialog
html - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog
html5Applet - Variable in class org.jmol.export.JSExporter
html5Applet - Variable in class org.jmol.viewer.Viewer
htmlAppletTemplate - Variable in class org.openscience.jmol.app.webexport.WebPanel
HTMLElement - Interface in org.jmol.awtjs.swing
htmlLabel() - Method in class org.jmol.awtjs.swing.JMenuItem
htmlMenuOpener(String) - Method in class org.jmol.awtjs.swing.AbstractButton
htmlName - Variable in class org.jmol.awtjs.swing.AbstractButton
htmlName - Variable in class org.jmol.util.GenericApplet
htmlName - Variable in class org.jmol.viewer.Viewer
htmlPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
HTMLWindowEvent - Interface in org.jmol.awtjs.swing
  The window.Event in HTML5 See SwingController.
htModelAtomMap - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
htModels - Variable in class org.jmol.shapesurface.MolecularOrbital
htModulation - Variable in class org.jmol.adapter.readers.cif.MSRdr
htMolIds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
htMOs - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
htNested - Variable in class org.jmol.smiles.SmilesSearch
htNodes - Variable in class org.jmol.export._IdtfExporter
htNonbooleanParameterValues - Variable in class org.jmol.viewer.GlobalSettings
htObjectAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htObjectGroups - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htObjects - Variable in class org.jmol.export.JSExporter
htObjects - Variable in class org.jmol.shape.MeshCollection
htObjectSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htOxStates - Variable in class org.jmol.adapter.readers.cif.CifReader
htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
htParams - Variable in class org.jmol.appletjs.Jmol
htParams - Variable in class org.jmol.io.DOMReader
htParams - Variable in class org.jmol.io.FileReader
htParams - Variable in class org.jmol.io.FilesReader
htPathPoints - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  Rule 1b hash table that maintains distance of the associated nonduplicated atom node
htPdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
htPeaks - Variable in class org.jmol.modelset.ModelSet
htPropertyFlagsRemoved - Variable in class org.jmol.viewer.GlobalSettings
htPts - Variable in class org.jmol.jvxl.calc.MarchingSquares
htRegistry - Static variable in class org.jmol.util.GenericApplet
htRings - Variable in class org.jmol.smiles.SmilesGenerator
htRingsSequence - Variable in class org.jmol.smiles.SmilesGenerator
htSites - Variable in class org.jmol.adapter.readers.cif.MMCifReader
htSites - Variable in class org.jmol.adapter.readers.pdb.PdbReader
htSlaterIDs - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
htSources - Variable in class org.jmol.awt.AwtPopupHelper
htSpacefill - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htSpecialAtoms - Static variable in class org.jmol.modelsetbio.BioResolver
htSpecies - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
htSpheresRendered - Variable in class org.jmol.export._VrmlExporter
htSpheresRendered - Variable in class org.jmol.export.JSExporter
htStateSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
htSubsystems - Variable in class org.jmol.adapter.readers.cif.MSRdr
htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
htTiming - Static variable in class org.jmol.util.Logger
htTracker - Variable in class org.jmol.symmetry.CIPDataTracker
  a table to track decision making when only one atom is selected for calculation
htUij - Variable in class org.jmol.util.ModulationSet
  current value of anisotropic parameter modulation
htUserFunctions - Variable in class org.jmol.script.ScriptTokenParser
htUserVariables - Variable in class org.jmol.viewer.GlobalSettings
htVertex - Static variable in class org.jmol.util.Geodesic
htVertices - Variable in class org.jmol.jvxl.readers.Ras3DReader
hType - Variable in class org.jmol.minimize.forcefield.AtomType
HUGE - Static variable in class org.jmol.util.GData
hydrogen - Static variable in class org.jmol.script.T
hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
hydrogenAtomPsi(P3) - Method in class org.jmol.jvxl.readers.IsoShapeReader
hydrogenCount - Variable in class org.jmol.modelset.Model
hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
hydrophobicities - Variable in class org.jmol.modelset.AtomCollection
hydrophobicities - Static variable in class org.jmol.util.Elements
hydrophobicity - Static variable in class org.jmol.script.T
hyperChemLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
HyperChemReader - Class in org.jmol.adapter.readers.simple
  Support for .hin, HyperChem's native file format.
HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog

## I

i(String, int) - Static method in class org.jmol.i18n.GT
i(int) - Static method in class org.jmol.script.T
i - Variable in class org.jmol.util.Point3fi
  index in full collection
i0 - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
i0 - Variable in class org.jmol.shapesurface.PMeshWriter
ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
ia - Variable in class org.jmol.minimize.forcefield.Calculation
ia - Variable in class org.jmol.minimize.forcefield.Calculations
iA - Variable in class org.jmol.util.MeshSurface
iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
iAtom - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
iAtom - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
iatom - Variable in class org.jmol.adapter.smarter.AtomIterator
iatom0 - Variable in class org.jmol.adapter.readers.molxyz.MolReader
iatom0 - Variable in class org.jmol.modelkit.ModelKitPopup
iAtomSurface - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
iAtomSurface - Variable in class org.jmol.jvxl.readers.IsoSolventReader
ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
ib - Variable in class org.jmol.minimize.forcefield.Calculation
ib - Variable in class org.jmol.minimize.forcefield.Calculations
iB - Variable in class org.jmol.util.MeshSurface
ibond - Variable in class org.jmol.adapter.smarter.BondIterator
iBond - Variable in class org.jmol.modelset.BondIteratorSelected
iBrace - Variable in class org.jmol.script.ScriptCompiler
ic - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
ic - Variable in class org.jmol.minimize.forcefield.Calculation
ic - Variable in class org.jmol.minimize.forcefield.Calculations
IC - Static variable in class org.jmol.quantum.QS
iC - Variable in class org.jmol.util.MeshSurface
IC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
iChain - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
iChain - Variable in class org.jmol.modelset.ModelLoader
ichBrace - Variable in class org.jmol.script.ScriptCompiler
ichCommand - Variable in class org.jmol.script.ScriptFlowContext
ichComment - Variable in class org.jmol.script.ScriptTokenParser
ichCurrentCommand - Variable in class org.jmol.script.ScriptTokenParser
ichEnd - Variable in class org.jmol.script.ScriptTokenParser
ichToken - Variable in class org.jmol.script.ScriptTokenParser
iCommand - Variable in class org.jmol.script.ScriptTokenParser
iCommandError - Variable in class org.jmol.script.ScriptContext
iCommandError - Variable in class org.jmol.script.ScriptError
icon - Variable in class org.jmol.awtjs.swing.AbstractButton
iCutout - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
id - Variable in class org.jmol.adapter.readers.pymol.JmolObject
id - Variable in class org.jmol.adapter.readers.pymol.PickleReader
ID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ID - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
id - Variable in class org.jmol.awtjs.swing.ButtonGroup
id - Variable in class org.jmol.awtjs.swing.Component
id - Variable in enum org.jmol.c.PAL
id - Variable in enum org.jmol.c.STR
id - Variable in class org.jmol.export._MayaExporter
id - Variable in class org.jmol.minimize.forcefield.Calculation
id - Variable in class org.jmol.minimize.forcefield.Calculations
id - Variable in class org.jmol.modelset.TickInfo
id - Variable in class org.jmol.script.ScriptContext
id - Static variable in class org.jmol.script.T
id - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
id - Variable in class org.jmol.shapespecial.Ellipsoid
id - Variable in class org.jmol.shapespecial.Polyhedron
id - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  unique ID for this CIPAtom for debugging only
id - Variable in class org.jmol.util.BZone
id - Variable in class org.jmol.util.JmolAudio
id - Variable in class org.jmol.util.MeshCapper.CapVertex
  for debugging
iD - Variable in class org.jmol.util.MeshSlicer
id - Variable in class org.jmol.util.ModulationSet
  an identifier for this modulation
id - Variable in class org.jmol.util.Tensor
id - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
iData - Variable in class org.jmol.minimize.forcefield.Calculation
idCount - Static variable in class org.jmol.util.JmolAudio
ident - Variable in class org.jmol.script.ScriptCompiler
ident - Variable in class org.jmol.script.ScriptFlowContext
identifier - Static variable in class org.jmol.script.T
identify - Static variable in class org.jmol.script.T
identLC - Variable in class org.jmol.script.ScriptCompiler
idFontFace - Variable in class org.jmol.util.Font
idFontStyle - Variable in class org.jmol.util.Font
idle_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
idSpherical - Static variable in class org.jmol.quantum.QS
iE - Variable in class org.jmol.util.MeshSlicer
ifcmd - Static variable in class org.jmol.script.T
iFirstAtom - Variable in class org.jmol.modelset.MeasurementData
ifPt - Variable in class org.jmol.script.ScriptMathProcessor
ifStack - Variable in class org.jmol.script.ScriptMathProcessor
ignore - Static variable in class org.jmol.script.T
IGNORE - Static variable in class org.jmol.symmetry.CIPChirality
ignore_case - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ignore_pdb_segi - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ignoreApplicationBundle - Static variable in class org.jmol.i18n.GT
ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
ignoreAtomClass - Variable in class org.jmol.smiles.SmilesSearch
ignoreError - Variable in class org.jmol.script.ScriptError
ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesParser
ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
ignoreStructure - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ignoreSymmetry - Variable in class org.jmol.adapter.smarter.Atom
iGroup - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
ihalf - Variable in class org.jmol.util.ColorEncoder
iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
iHaveCenterBitSet - Variable in class org.jmol.shapespecial.Polyhedra
iHaveCoefMaps - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cif.CifReader
iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHaveModelIndex - Variable in class org.jmol.shapesurface.Isosurface
iHaveModelStatement - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
iHaveNewDir - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
iHaveQuotedString - Variable in class org.jmol.script.ScriptCompiler
iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHaveTwoEnds - Variable in class org.jmol.shapespecial.Dipoles
iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
iHideBackground - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
iHypervalent - Variable in class org.jmol.smiles.SmilesGenerator
ijkToPoint3f(int, P3, int, int) - Static method in class org.jmol.util.SimpleUnitCell
  Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499
iList - Variable in class org.jmol.navigate.Navigator
image - Variable in class org.jmol.awt.AwtClipboard
  The image to transfer into the clipboard.
Image - Class in org.jmol.awt
  methods required by Jmol that access java.awt.Image private to org.jmol.awt
Image() - Constructor for class org.jmol.awt.Image
Image - Class in org.jmol.awtjs2d
  methods required by Jmol that access java.awt.Image private to org.jmol.awt
Image() - Constructor for class org.jmol.awtjs2d.Image
image - Variable in class org.jmol.console.ImageDialog
image - Variable in class org.jmol.modelset.Text
image - Static variable in class org.jmol.script.T
image() - Method in class org.jmol.scriptext.CmdExt
image_copy_always - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
image_dots_per_inch - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
IMAGE_OR_SCENE - Static variable in class org.jmol.viewer.JC
IMAGE_TYPES - Static variable in class org.jmol.viewer.JC
ImageCanvas() - Constructor for class org.jmol.console.ImageDialog.ImageCanvas
imageChoices - Variable in class org.jmol.dialog.Dialog
imageChoices - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
imageChooser - Static variable in class org.jmol.dialog.Dialog
ImageDialog - Class in org.jmol.console
ImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Constructor for class org.jmol.console.ImageDialog
ImageDialog.ImageCanvas - Class in org.jmol.console
imageExtensions - Variable in class org.jmol.dialog.Dialog
imageExtensions - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
imageFontScaling - Variable in class org.jmol.render.FontLineShapeRenderer
imageFontScaling - Variable in class org.jmol.render.MeshRenderer
imageFontScaling - Variable in class org.jmol.viewer.Viewer
imageMap - Variable in class org.jmol.console.ImageDialog
imageMap - Variable in class org.jmol.viewer.StatusManager
imageScale - Variable in class org.jmol.modelset.Text
imageSizeChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Called when the ImageSize check box is modified
imageSizeHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
imageSizeRatioBox - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
imageSizeRatioCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
imageSizeTextHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
imageSizeTextWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
imageSizeWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
imagestate - Static variable in class org.jmol.script.T
imageState - Variable in class org.jmol.viewer.GlobalSettings
imageType - Variable in class org.jmol.dialog.Dialog
imageType - Variable in class org.jmol.viewer.StatusManager
imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
imap - Variable in class org.jmol.shapesurface.PMeshWriter
imesh - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
imesh - Variable in class org.jmol.shapesurface.PMeshWriter
imgHeight - Variable in class org.openscience.jmol.app.jmolpanel.Splash
imgWidth - Variable in class org.openscience.jmol.app.jmolpanel.Splash
iMo0 - Variable in class org.jmol.adapter.readers.quantum.MOReader
iModel - Variable in class org.jmol.modelset.ModelLoader
iModelMO - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
iMolecule - Variable in class org.jmol.quantum.QMAtom
implicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
implicitString - Variable in class org.jmol.script.ScriptCompiler
implicitStringCommand - Static variable in class org.jmol.script.T
importData(JComponent, Transferable) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
in - Static variable in class org.jmol.script.T
IN_JMOL - Static variable in class org.openscience.jmol.app.webexport.WebExport
inchi - Static variable in class org.jmol.script.T
inchikey - Static variable in class org.jmol.script.T
includeAllRelatedFrames(BS) - Method in class org.jmol.modelset.ModelSet
includes(int, int) - Static method in class org.jmol.viewer.binding.Binding
includeValueNaN - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
incompleteCmd - Variable in class org.jmol.console.GenericConsole
increment(int) - Method in class org.jmol.script.SV
increment - Static variable in class org.jmol.script.T
incrementLineCount(String) - Method in class org.jmol.script.ScriptCompiler
incrementModel(int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
inDefinedStateBlock - Variable in class org.jmol.modelset.StateScript
INDENT - Static variable in class org.jmol.shapecgo.CGOMesh
indent - Variable in class org.jmol.util.JSONWriter
index - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
index - Variable in class org.jmol.adapter.smarter.Atom
index - Variable in class org.jmol.bspt.Bspt
index - Variable in class org.jmol.minimize.MinAtom
index - Variable in class org.jmol.minimize.MinBond
index - Variable in class org.jmol.modelset.Measurement
index - Variable in class org.jmol.quantum.QMAtom
index - Variable in class org.jmol.quantum.SlaterData
index - Variable in class org.jmol.script.SV
index - Variable in class org.jmol.shape.Mesh
index - Variable in class org.jmol.smiles.SmilesAtom
index - Variable in class org.jmol.smiles.SmilesMeasure
index - Variable in class org.jmol.symmetry.PointGroup.Operation
index - Variable in class org.jmol.symmetry.SpaceGroup
index - Variable in class org.jmol.symmetry.SymmetryOperation
index - Variable in class org.jmol.thread.SpinThread
index - Variable in class org.jmol.util.BZone
index - Variable in class org.jmol.util.Edge
index - Variable in class org.jmol.viewer.MotionPoint
indexes - Variable in class org.jmol.minimize.MMConstraint
indexes - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
indexI - Variable in class org.jmol.geodesic.EnvelopeCalculation
indexInModel - Variable in class org.jmol.util.JmolMolecule
indexLower(float, int) - Method in class org.jmol.jvxl.data.VolumeData
  periodic grids should have val[0] == val[xMax] voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4....
indexUpper(float, int, int) - Method in class org.jmol.jvxl.data.VolumeData
indicatedModelIndex - Variable in class org.jmol.shapecgo.CGO
indicatedModelIndex - Variable in class org.jmol.shapespecial.Draw
indices - Variable in class org.jmol.smiles.SmilesMeasure
iNested - Variable in class org.jmol.smiles.SmilesAtom
iNext - Variable in class org.jmol.modelset.AtomIteratorWithinModel
iNext - Variable in class org.jmol.renderbio.BioShapeRenderer
iNext2 - Variable in class org.jmol.renderbio.BioShapeRenderer
iNext3 - Variable in class org.jmol.renderbio.BioShapeRenderer
info - Variable in class org.jmol.adapter.readers.pymol.JmolObject
info - Variable in class org.jmol.atomdata.RadiusData
info - Variable in class org.jmol.awtjs.swing.JComboBox
info - Variable in class org.jmol.modelsetbio.BasePair
info - Static variable in class org.jmol.script.T
info - Variable in class org.jmol.shapespecial.Ellipsoid
info - Variable in class org.jmol.shapespecial.Polyhedra
info - Variable in class org.jmol.shapespecial.Polyhedron
info - Variable in class org.jmol.shapesurface.IsosurfaceMesh
info - Variable in class org.jmol.symmetry.PointGroup
info - Variable in class org.jmol.symmetry.SpaceGroup
info - Variable in class org.jmol.symmetry.SymmetryOperation
info(String) - Method in class org.jmol.util.DefaultLogger
info(String) - Static method in class org.jmol.util.Logger
  og* Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at INFO level.
info - Variable in class org.openscience.jmol.app.JmolApp
INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
infofontsize - Static variable in class org.jmol.script.T
infoFontSize - Variable in class org.jmol.viewer.GlobalSettings
infoLabel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
infoList - Static variable in class org.jmol.util.Tensor
infoStr - Variable in class org.jmol.symmetry.SymmetryInfo
inGreyscaleMode - Variable in class org.jmol.util.GData
INHERIT - Static variable in class org.jmol.util.ColorEncoder
INHERIT_ALL - Static variable in class org.jmol.util.C
INHERIT_COLOR - Static variable in class org.jmol.util.C
inInput - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
INIT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
init() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
init(String, Object, String, SC) - Method in interface org.jmol.api.SC
init() - Method in class org.jmol.applet.AppletWrapper
init(String, Object, String, SC) - Method in class org.jmol.awt.AwtSwingComponent
init(String, Object, String, SC) - Method in class org.jmol.awtjs.swing.AbstractButton
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoFxyReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMepReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMlpReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMOReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoShapeReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoSolventReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceReader
  implemented in SurfaceFileReader and
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.VolumeDataReader
init(String, Viewer, Lst<Object>) - Method in class org.jmol.modelset.MeasurementData
init(Object) - Method in class org.jmol.scriptext.MathExt
init(Object) - Method in class org.jmol.scriptext.ScriptExt
init(Object) - Method in class org.jmol.scriptext.SmilesExt
init(int, String, String, short, short, boolean) - Method in class org.jmol.shapespecial.Dipole
init() - Method in class org.jmol.symmetry.CIPData
  initializer -- called also by CIPDataSmiles
init(boolean) - Method in class org.jmol.symmetry.SpaceGroup
INIT - Static variable in class org.jmol.thread.JmolThread
init(Object) - Method in class org.jmol.util.GenericApplet
init(float[]) - Method in class org.jmol.util.SimpleUnitCell
init(URL, String) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.ApbsReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.BCifDensityReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.CastepDensityReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.CubeReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.EfvetReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JaguarReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.KinemageReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MapFileReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MsmsReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.NffReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.ObjReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PltFormattedReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Pmesh4Reader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PmeshReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Ras3DReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.UhbdReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VaspChgcarReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VolumeFileReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.XplorReader
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.XsfReader
init2JXR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
init2MFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MapFileReader
init2PFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PolygonFileReader
init2PR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PmeshReader
init2PR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Ras3DReader
init2SFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
init2VFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VolumeFileReader
initADR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.AtomDataReader
initApplication() - Method in class org.jmol.util.GenericApplet
initBS() - Method in class org.jmol.renderbio.BioMeshRenderer
initCGO() - Method in class org.jmol.shapecgo.CGO
initCML() - Method in class org.jmol.adapter.readers.xml.XmlReader
initDraw() - Method in class org.jmol.shapespecial.Draw
initEllipsoids(Object) - Method in class org.jmol.shapespecial.Ellipsoids
initialFile - Variable in class org.jmol.dialog.Dialog
initialize(AtomSetCollectionReader, int) - Method in class org.jmol.adapter.readers.cif.MSRdr
initialize(BasisFunctionReader, String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
initialize() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initialize(AtomSetCollectionReader, int) - Method in interface org.jmol.adapter.smarter.MSInterface
initialize(int, P3[], BS) - Method in class org.jmol.bspt.Bspf
initialize(T3, float, boolean) - Method in class org.jmol.bspt.CubeIterator
  initialize to return all points within the sphere defined by center and radius
initialize(Viewer, GenericPlatform) - Method in class org.jmol.g3d.Graphics3D
initialize() - Method in class org.jmol.jvxl.readers.Parameters
initialize(Viewer, PopupResource, String) - Method in class org.jmol.modelkit.ModelKitPopup
initialize(Bspf, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.AtomIteratorWithinModel
  ############## ITERATOR SHOULD BE RELEASED #################
initialize(Viewer, PopupResource, String) - Method in class org.jmol.popup.JmolGenericPopup
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.MOCalculation
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
initialize(ShapeRenderer, BioShape, int) - Method in class org.jmol.renderbio.BioMeshRenderer
initialize - Static variable in class org.jmol.script.T
initialize(int, T3[], P4) - Method in class org.jmol.shape.Mesh
initialize() - Method in class org.jmol.shapebio.BioShapeCollection
initialize() - Method in class org.jmol.shapespecial.Dots
initialize(Viewer, GenericPlatform) - Method in class org.jmol.util.GData
initialize(Node[], int, int, BS, int, int) - Static method in class org.jmol.util.JmolMolecule
initialize(boolean, boolean) - Method in class org.jmol.viewer.Viewer
initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
initialize0(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
initializeAnnotation(SV, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
initializeAnnotation(SV, int, int) - Method in class org.jmol.dssx.AnnotationParser
  We create a main list of mappings, where each mapping has _atoms and _path
initializeAtomBondModelCounts(int) - Method in class org.jmol.modelset.ModelLoader
initializeBonding() - Method in class org.jmol.modelset.ModelLoader
initializeBspf() - Method in class org.jmol.modelset.ModelSet
initializeBspt(int) - Method in class org.jmol.modelset.ModelSet
initializeCartesianToFractional() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeEigen() - Method in class org.jmol.quantum.NciCalculation
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.Export3D
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
initializeExporter(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
initializeForModel() - Method in class org.jmol.modelkit.ModelKitPopup
initializeHydrogenAddition() - Method in class org.jmol.modelsetbio.BioResolver
initializeInfo(String, Map<String, Object>) - Method in class org.jmol.modelset.ModelLoader
initializeIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
initializeIsosurface() - Method in class org.jmol.shapesurface.Isosurface
initializeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
initializeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
initializeModel(boolean) - Method in class org.jmol.viewer.Viewer
initializeMSCIF() - Method in class org.jmol.adapter.readers.cif.CifReader
initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
initializeOnePointQC() - Method in class org.jmol.quantum.QuantumCalculation
initializeOrientation(M3) - Method in interface org.jmol.api.SymmetryInterface
initializeOrientation(M3) - Method in class org.jmol.symmetry.Symmetry
initializeOutput(Viewer, double, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._ObjExporter
initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._TachyonExporter
initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.export.Export3D
initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
initializePointers(int) - Method in class org.jmol.viewer.AnimationManager
initializePolymer(BioShape) - Method in class org.jmol.renderbio.BioShapeRenderer
initializeProperties() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
initializeReader() - Method in class org.jmol.adapter.readers.cif.CifReader
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
initializeReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
initializeReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
initializeReader() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
initializeReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
initializeReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.JSONReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
initializeReader() - Method in class org.jmol.adapter.readers.spartan.OdysseyReader
initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  not sure how to work with symmetry here...
initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
initializeReader() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeShape(Viewer, ModelSet, int) - Method in class org.jmol.shape.Shape
initializeSurfaceData() - Method in class org.jmol.jvxl.readers.VolumeFileReader
initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeSymmetryOptions() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeTrajectoryFile() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
initializeUnitCellAndSymmetry() - Method in class org.jmol.modelset.ModelLoader
initializeVolumetricData() - Method in class org.jmol.jvxl.readers.SurfaceReader
initIFR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoFxyReader
initIMR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMepReader
initIsosurface(int) - Method in class org.jmol.scriptext.IsoExt
initModelSet() - Method in class org.jmol.shape.AtomShape
initModelSet() - Method in class org.jmol.shape.Measures
initModelSet() - Method in class org.jmol.shape.Shape
initModelSet() - Method in class org.jmol.shape.TextShape
initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
initModelSet() - Method in class org.jmol.shapespecial.Vectors
initModForStructure(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
initOptions() - Method in class org.jmol.applet.Jmol
initOptions() - Method in class org.jmol.appletjs.Jmol
initOptions() - Method in class org.jmol.util.GenericApplet
initOrientation(M3) - Method in class org.jmol.symmetry.UnitCell
initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.__RayTracerExporter
initPlanes() - Method in class org.jmol.jvxl.readers.SurfaceReader
initRenderer() - Method in class org.jmol.render.AxesRenderer
initRenderer() - Method in class org.jmol.render.BbcageRenderer
initRenderer() - Method in class org.jmol.render.MeasuresRenderer
initRenderer() - Method in class org.jmol.render.ShapeRenderer
initRenderer() - Method in class org.jmol.render.UccageRenderer
initRenderer() - Method in class org.jmol.renderspecial.DotsRenderer
initShape() - Method in class org.jmol.shape.AtomShape
initShape() - Method in class org.jmol.shape.Axes
initShape() - Method in class org.jmol.shape.Bbcage
initShape() - Method in class org.jmol.shape.Echo
initShape() - Method in class org.jmol.shape.FontLineShape
initShape() - Method in class org.jmol.shape.Frank
initShape() - Method in class org.jmol.shape.Hover
initShape() - Method in class org.jmol.shape.Labels
initShape() - Method in class org.jmol.shape.Measures
initShape() - Method in class org.jmol.shape.MeshCollection
initShape() - Method in class org.jmol.shape.Shape
initShape() - Method in class org.jmol.shape.Sticks
initShape() - Method in class org.jmol.shape.Uccage
initShape() - Method in class org.jmol.shapebio.Backbone
initShape() - Method in class org.jmol.shapebio.BioShapeCollection
initShape() - Method in class org.jmol.shapebio.Cartoon
initShape() - Method in class org.jmol.shapebio.MeshRibbon
initShape() - Method in class org.jmol.shapebio.Rockets
initShape() - Method in class org.jmol.shapebio.Trace
initShape() - Method in class org.jmol.shapespecial.Dipoles
initShape() - Method in class org.jmol.shapespecial.Dots
initShape() - Method in class org.jmol.shapespecial.Draw
initShape() - Method in class org.jmol.shapespecial.Ellipsoids
initShape() - Method in class org.jmol.shapespecial.GeoSurface
initShape() - Method in class org.jmol.shapesurface.Contact
initShape() - Method in class org.jmol.shapesurface.Isosurface
initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
initShape() - Method in class org.jmol.shapesurface.NBO
initShape() - Method in class org.jmol.shapesurface.Plot3D
initShape() - Method in class org.jmol.shapesurface.Pmesh
initSlice() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
initSR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceReader
initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
initState() - Method in class org.jmol.shape.Halos
initState() - Method in class org.jmol.shapesurface.Isosurface
initSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
initSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
initSwing(String, PopupResource, Object, boolean, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
initUnitcellVertices() - Method in class org.jmol.symmetry.UnitCell
initVariables() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
initVars() - Method in class org.jmol.export.__RayTracerExporter
initVDR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.VolumeDataReader
inline - Static variable in class org.jmol.script.T
inlineNewlineChar - Variable in class org.jmol.viewer.GlobalSettings
inMotion - Variable in class org.jmol.viewer.Viewer
inMovie - Variable in class org.jmol.adapter.readers.pymol.PickleReader
inNames - Variable in class org.jmol.adapter.readers.pymol.PickleReader
inPath - Variable in class org.jmol.awtjs2d.JsG2D
input - Variable in class org.jmol.console.GenericConsole
inputCode - Variable in class org.jmol.symmetry.HallRotationTerm
inputContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
inputFileName - Variable in class org.jmol.dialog.Dialog
inputFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
inputOnly - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
inputOnly - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
inputOnly - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
inputOnly - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
InputReader - Class in org.jmol.adapter.readers.simple
InputReader() - Constructor for class org.jmol.adapter.readers.simple.InputReader
InputScannerThread - Class in org.openscience.jmol.app
InputScannerThread(JmolViewer, boolean) - Constructor for class org.openscience.jmol.app.InputScannerThread
inRange(int, int, int) - Method in class org.jmol.viewer.MouseState
INS_CODE - Static variable in class org.jmol.adapter.readers.cif.CifReader
INSCODE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
inscode - Static variable in class org.jmol.script.T
insCode - Variable in class org.jmol.smiles.SmilesAtom
insert(SC, int) - Method in interface org.jmol.api.SC
insert(SC, int) - Method in class org.jmol.awt.AwtSwingComponent
insert(SC, int) - Method in class org.jmol.awtjs.swing.AbstractButton
insertComponent(Component, int) - Method in class org.jmol.awtjs.swing.Container
insertedCommand - Variable in class org.jmol.viewer.Viewer
insertion - Static variable in class org.jmol.script.T
INSERTION_CODE_MASK - Static variable in class org.jmol.modelset.Group
insertionCode - Variable in class org.jmol.adapter.smarter.Atom
insertionCount - Variable in class org.jmol.modelset.Model
insertString(int, String, Object) - Method in interface org.jmol.awtjs.swing.Document
insertString(int, String, Object) - Method in class org.jmol.awtjs.swing.JTextPane
insertString(int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
insets - Variable in class org.jmol.awtjs.swing.GridBagConstraints
Insets - Class in org.jmol.awtjs.swing
Insets(int, int, int, int) - Constructor for class org.jmol.awtjs.swing.Insets
insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
insideOut - Variable in class org.jmol.jvxl.data.JvxlData
insideOut - Variable in class org.jmol.jvxl.readers.Parameters
insideout - Static variable in class org.jmol.script.T
insideOut - Variable in class org.jmol.shape.Mesh
inSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
instance - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
InstanceCellRenderer() - Constructor for class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
instanceList - Variable in class org.openscience.jmol.app.webexport.WebPanel
INT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
Int2IntHash - Class in org.jmol.util
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
Int2IntHashEntry - Class in org.jmol.util
Int2IntHashEntry(int, int, Int2IntHashEntry) - Constructor for class org.jmol.util.Int2IntHashEntry
intAnimThread - Variable in class org.jmol.viewer.AnimationManager
intAsFloat - Variable in class org.jmol.modelset.LabelToken
intAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
integer - Static variable in class org.jmol.script.T
integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptError
integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
integration - Variable in class org.jmol.jvxl.data.JvxlData
integration - Variable in class org.jmol.quantum.QuantumCalculation
integrationKeyMap - Static variable in class org.jmol.adapter.writers.QCJSONWriter
intenseFraction - Variable in class org.jmol.util.Shader
INTERACTION_FACTOR - Static variable in class org.jmol.util.Tensor
interactionTensors - Variable in class org.jmol.adapter.readers.xtal.MagresReader
intercept(MarchingSquares.Triangle, int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
interestingAminoAtomIDs - Static variable in class org.jmol.modelsetbio.AminoMonomer
interestingNucleicAtomIDs - Static variable in class org.jmol.modelsetbio.NucleicMonomer
Interface - Class in org.jmol.api
Interface() - Constructor for class org.jmol.api.Interface
interior - Static variable in class org.jmol.script.T
intermolecular - Static variable in class org.jmol.script.T
internal - Static variable in class org.jmol.script.T
internal_feedback - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
internal_gui - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
internal_gui_control_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
internal_gui_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
internal_gui_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
internal_prompt - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
internalRotationAngle - Variable in class org.jmol.viewer.TransformManager
internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
internalRotationCenter - Variable in class org.jmol.viewer.TransformManager
internalSlab - Variable in class org.jmol.viewer.TransformManager
internalTranslation - Variable in class org.jmol.viewer.TransformManager
interpolate(int, int, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
interpolateFraction(T3, T3, float, float, float, int) - Method in class org.jmol.util.MeshSlicer
interpolatePoint(T3, T3, float, float, float, float, int) - Method in class org.jmol.util.MeshSlicer
interpolatePrecisely(int, int, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
interpolateSphere(T3, T3, float, float, double, float, float, int) - Method in class org.jmol.util.MeshSlicer
interpolateX(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
  Get interpolated x for the scan line intersection with an edge.
interrupt() - Method in interface org.jmol.api.JmolNavigatorInterface
interrupt() - Method in class org.jmol.thread.AnimationThread
interrupt() - Method in class org.jmol.thread.JmolThread
interrupt() - Method in class org.jmol.thread.MoveToThread
interruptQueueThreads() - Method in class org.jmol.script.ScriptManager
intersectID - Variable in class org.jmol.shapespecial.Draw
intersection - Variable in class org.jmol.jvxl.readers.Parameters
intersection - Static variable in class org.jmol.script.T
intersectPlane(P4, T3[], int) - Method in class org.jmol.util.Triangulator
  a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.
intlTableNo - Variable in class org.jmol.symmetry.SymmetryInfo
intlTableNumber - Variable in class org.jmol.symmetry.SpaceGroup
intlTableNumberExt - Variable in class org.jmol.symmetry.SpaceGroup
intlTableNumberFull - Variable in class org.jmol.symmetry.SpaceGroup
intparam - Static variable in class org.jmol.script.T
intParameter(int) - Method in class org.jmol.script.ScriptParam
intParameter(int) - Method in class org.jmol.scriptext.ScriptExt
intParameterRange(int, int, int) - Method in class org.jmol.script.ScriptParam
intPeek() - Method in class org.jmol.script.ScriptTokenParser
intproperty - Static variable in class org.jmol.script.T
intramolecular - Variable in class org.jmol.modelset.MeasurementData
intramolecular - Static variable in class org.jmol.script.T
intramolecular - Variable in class org.jmol.shape.Measures
intTableNo - Variable in class org.jmol.adapter.readers.cif.CifReader
intThread - Variable in class org.jmol.thread.AnimationThread
intValue - Variable in class org.jmol.script.T
INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
invalidatedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
invalidateMesh - Variable in class org.jmol.renderbio.BioShapeRenderer
invalidatePolygons() - Method in class org.jmol.util.MeshSurface
invalidateSheets - Variable in class org.jmol.renderbio.BioShapeRenderer
invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
invalidateVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
invalidLead - Variable in class org.jmol.modelsetbio.BioPolymer
InvalidSmilesException - Exception in org.jmol.smiles
  Exception thrown for invalid SMILES String
InvalidSmilesException(String) - Constructor for exception org.jmol.smiles.InvalidSmilesException
  Constructs a `InvalidSmilesException` with a detail message.
invArg() - Method in class org.jmol.script.ScriptError
invArg() - Method in class org.jmol.scriptext.ScriptExt
inverseMatrix - Variable in class org.jmol.jvxl.data.VolumeData
inverseNormixes - Static variable in class org.jmol.util.Normix
invertAtomCoordPlane(P4, BS) - Method in class org.jmol.viewer.Viewer
invertAtomCoordPt(P3, BS) - Method in class org.jmol.viewer.Viewer
invertInPlace(BS, int) - Static method in class org.jmol.util.BSUtil
  inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertNormixes() - Method in class org.jmol.shape.Mesh
invertRingAt(int, boolean) - Method in class org.jmol.viewer.Viewer
invertSelected(P3, P4, int, BS) - Method in class org.jmol.modelset.ModelSet
  Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.
invertSelected - Static variable in class org.jmol.script.T
invertSelected() - Method in class org.jmol.scriptext.CmdExt
invertSelected(P3, P4, int, BS) - Method in class org.jmol.viewer.Viewer
invertSelection() - Method in class org.jmol.viewer.SelectionManager
invertStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
invMatrix - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
invPO() - Method in class org.jmol.scriptext.ScriptExt
iObj - Variable in class org.jmol.export._IdtfExporter
iObj - Variable in class org.jmol.export.UseTable
iop - Variable in class org.jmol.util.ModulationSet
  the symmetry operation used to generate this atom
iopLast - Variable in class org.jmol.adapter.readers.cif.MSRdr
ipadx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
ipady - Variable in class org.jmol.awtjs.swing.GridBagConstraints
iPlaneNCI - Variable in class org.jmol.jvxl.readers.VolumeFileReader
iPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
iProcess - Static variable in class org.jmol.script.ScriptEval
ipt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
ipt - Variable in class org.jmol.symmetry.UnitCellIterator
ipt - Variable in class org.jmol.util.MeshCapper.CapVertex
  external reference
is(int) - Method in class org.jmol.modelset.Bond
IS - Static variable in class org.jmol.quantum.QS
is(MouseState) - Method in class org.jmol.viewer.MouseState
is2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
is2D - Variable in class org.jmol.modelset.ModelLoader
is2D - Variable in class org.jmol.rendercgo.CGORenderer
is2DPercent - Variable in class org.jmol.rendercgo.CGORenderer
is47File - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
is4D - Variable in class org.jmol.viewer.TransformManager4D
IS_HETERO_FLAG - Static variable in class org.jmol.modelset.Atom
IS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
IS_POINTMAPPABLE - Static variable in class org.jmol.jvxl.readers.Parameters
IS_SILENT - Static variable in class org.jmol.jvxl.readers.Parameters
IS_SLABBABLE - Static variable in class org.jmol.jvxl.readers.Parameters
IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
isAbsolute - Variable in class org.jmol.render.LabelsRenderer
isActive - Variable in class org.jmol.shape.AtomShape
isActive - Variable in class org.jmol.shapebio.BioShapeCollection
isActive() - Method in class org.jmol.shapespecial.Ellipsoids
isActiveLevel(int) - Static method in class org.jmol.util.Logger
  Tells if a logging level is active.
isAdded(int) - Method in class org.jmol.modelset.Group
isAdjacentSp2(Atom) - Method in class org.jmol.modelset.AtomCollection
isAFLOW - Variable in class org.jmol.adapter.readers.cif.CifReader
isAligned(T3, T3, T3) - Method in class org.jmol.smiles.PolyhedronStereoSorter
  check alignment, within 10 degrees is considered aligned.
isAlkene - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  is one atom of a double bond
isAlkeneAtom2 - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a flag used in Rule 3 to indicate the second carbon of a double bond
isAll - Variable in class org.jmol.modelset.MeasurementData
isAll - Variable in class org.jmol.renderspecial.PolyhedraRenderer
isAll - Variable in class org.jmol.shape.TextShape
isAllQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
isAlphaMonomer() - Method in class org.jmol.modelsetbio.AlphaMonomer
isAltKeyReleased - Variable in class org.jmol.viewer.ActionManager
isAltLoc(char, String) - Method in class org.jmol.modelset.AtomCollection
isAmide - Variable in class org.jmol.minimize.MinBond
isAminoMonomer() - Method in class org.jmol.modelsetbio.AminoMonomer
isAND - Variable in class org.jmol.smiles.SmilesAtom
isAngstroms - Variable in class org.jmol.adapter.readers.simple.CubeReader
isAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
isAngstroms - Variable in class org.jmol.jvxl.readers.VolumeFileReader
isAnisotropic - Variable in class org.jmol.jvxl.readers.Parameters
isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
isAntialiased() - Method in interface org.jmol.api.JmolGraphicsInterface
isAntialiased() - Method in class org.jmol.export.Export3D
  is full scene / oversampling antialiasing in effect
isAntialiased - Variable in class org.jmol.render.HalosRenderer
isAntialiased - Variable in class org.jmol.render.SticksRenderer
isAntialiased() - Method in class org.jmol.util.GData
  is full scene / oversampling antialiasing in effect
isAntiparallel - Variable in class org.jmol.dssx.Bridge
isAppend - Variable in class org.jmol.io.FileReader
isAppend - Variable in class org.jmol.io.FilesReader
isAppendSelected() - Method in class org.jmol.dialog.FilePreview
isApplet - Variable in class org.jmol.popup.GenericPopup
isApplet - Variable in class org.jmol.viewer.Viewer
isApprox(V3d, V3d, double) - Static method in class org.jmol.minimize.Util
isArc - Variable in class org.jmol.shapespecial.Draw
isAromatic - Variable in class org.jmol.minimize.MinBond
isAromatic() - Method in class org.jmol.modelset.Bond
isaromatic - Static variable in class org.jmol.script.T
isAromatic - Variable in class org.jmol.smiles.SmilesAtom
isAromaticBond(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
isArray(Object) - Static method in class org.jmol.script.SV
  Must be updated if getVariable is updated!
isArrayItem - Variable in class org.jmol.script.ScriptMathProcessor
isArrayParameter(int) - Method in class org.jmol.script.ScriptParam
isArrow - Variable in class org.jmol.shapespecial.Draw
isAssignment - Variable in class org.jmol.script.ScriptMathProcessor
isASV(Object) - Static method in class org.jmol.script.SV
isAtEnd() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
isAtomExpression(int) - Method in class org.jmol.script.ScriptEval
isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
isAtomInLastModel(int) - Method in class org.jmol.modelset.ModelSet
isAtomNameMatch(Atom, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
isAtomPDB(int) - Method in class org.jmol.modelset.ModelSet
isAtoms - Variable in class org.jmol.symmetry.PointGroup
isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
isAtropism(int) - Static method in class org.jmol.util.Edge
isAuto - Variable in class org.jmol.shapespecial.Polyhedra
isAux - Variable in class org.jmol.symmetry.CIPChirality
  are we in the midst of auxiliary center creation?
isAV(Object) - Static method in class org.jmol.util.Escape
isBarb - Variable in class org.jmol.shapespecial.Draw
isBarb - Variable in class org.jmol.shapespecial.DrawMesh
isBbcageDefault - Variable in class org.jmol.modelset.ModelSet
isBCSfile - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
isBiColor - Variable in enum org.jmol.c.STER
isBiColor() - Method in enum org.jmol.c.STER
isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
isBicolorMap - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
isBilbao - Variable in class org.jmol.symmetry.SpaceGroup
isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isBinary - Variable in class org.jmol.jvxl.readers.PmeshReader
isBinary - Variable in class org.jmol.shapesurface.PMeshWriter
isBio() - Method in interface org.jmol.api.SymmetryInterface
isBio - Variable in class org.jmol.symmetry.SpaceGroup
isBio - Variable in class org.jmol.symmetry.Symmetry
isBio() - Method in class org.jmol.symmetry.Symmetry
isBio - Variable in class org.jmol.symmetry.SymmetryOperation
isBioAtom - Variable in class org.jmol.smiles.SmilesAtom
isBioAtomWild - Variable in class org.jmol.smiles.SmilesAtom
isBioModel - Variable in class org.jmol.modelset.Model
isbiomol - Variable in class org.jmol.adapter.readers.pdb.PdbReader
isBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
isBioResidue - Variable in class org.jmol.smiles.SmilesAtom
isBioSequence - Variable in class org.jmol.smiles.SmilesParser
isBioShape - Variable in class org.jmol.shape.Shape
isBold - Variable in class org.jmol.util.Font
isBond - Variable in class org.jmol.shapespecial.Dipoles
isBondable(float, float, float, float, float) - Method in class org.jmol.modelset.ModelSet
isBondDipole(int) - Method in class org.jmol.shapespecial.Dipoles
isBonded(Atom) - Method in class org.jmol.modelset.Atom
isBondedCorrectly(int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
isBondedCorrectlyRange(int, int, int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
isBondSet - Variable in class org.jmol.script.ScriptParam
isBondType() - Method in class org.jmol.shapespecial.Dipole
isBondType(char, boolean, boolean) - Static method in class org.jmol.smiles.SmilesBond
isBondType1(AtomType, AtomType) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
isBound(int, int) - Method in class org.jmol.viewer.Viewer
isBreakableContext(int) - Static method in class org.jmol.script.ScriptCompiler
isBXSF - Variable in class org.jmol.jvxl.readers.XsfReader
isCA2(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isCarbohydrate() - Method in class org.jmol.modelset.Group
isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
isCarbohydrate - Variable in class org.jmol.renderbio.BioShapeRenderer
isCartesian - Variable in class org.jmol.export.Export3D
isCartesian - Variable in class org.jmol.render.SticksRenderer
isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
isCartoonsSelected() - Method in class org.jmol.dialog.FilePreview
isCavity - Variable in class org.jmol.jvxl.readers.IsoSolventReader
isCavity - Variable in class org.jmol.jvxl.readers.Parameters
isCell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
isCellEditable(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
isCenteringOp - Variable in class org.jmol.symmetry.SymmetryOperation
isCenterParameter(int) - Method in class org.jmol.script.ScriptParam
isCentrosymmetric - Variable in class org.jmol.symmetry.HallInfo
isChain - Variable in class org.jmol.smiles.SmilesBond
isCheckOnly - Variable in class org.jmol.script.ScriptCompiler
isChiralPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a check for downstream chirality
isCircle - Variable in class org.jmol.shapespecial.Draw
isCis(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
  Check cis vs.
isCis(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataSmiles
  Check cis vs.
isClickable() - Method in class org.jmol.modelset.Atom
isClipped(int, int, int) - Method in class org.jmol.export.Export3D
isClipped(int, int) - Method in class org.jmol.export.Export3D
isClipped(int, int) - Method in class org.jmol.util.GData
isClipped3(int, int, int) - Method in class org.jmol.util.GData
isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
isClippedXY(int, int, int) - Method in class org.jmol.util.GData
isClippedZ(int) - Method in class org.jmol.util.GData
isClosedFace - Variable in class org.jmol.jvxl.readers.PmeshReader
isCmdf - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
isCmdLine_C_Option - Variable in class org.jmol.script.ScriptEval
isCmdLine_c_or_C_Option - Variable in class org.jmol.script.ScriptEval
isColixColorInherited(short) - Static method in class org.jmol.util.C
isColixLastAvailable(short) - Static method in class org.jmol.util.C
isColixTranslucent(short) - Static method in class org.jmol.util.C
isCollapsed - Variable in class org.jmol.shapespecial.Polyhedra
isColorExplicit - Variable in class org.jmol.shapesurface.Isosurface
isColorIndex - Variable in class org.jmol.util.ColorEncoder
isColorParam(int) - Method in class org.jmol.script.ScriptParam
isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
isColorReversed - Variable in class org.jmol.jvxl.readers.Parameters
isColorSolid - Variable in class org.jmol.util.MeshSurface
isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptTokenParser
isCommandDisplayable(int) - Method in class org.jmol.script.ScriptEval
  provides support for the script editor
isCommensurate - Variable in class org.jmol.adapter.readers.cif.MSRdr
isCommensurate - Variable in class org.jmol.util.ModulationSet
  commensurate modulations cannot be "undone" and they cannot be turned off
isComment - Variable in class org.jmol.script.ScriptCompiler
isComplete - Variable in class org.jmol.script.ScriptContext
isCompoundDocument - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
isConcatenated - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isConnect() - Method in class org.jmol.modelset.StateScript
isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AlphaMonomer
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AminoMonomer
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.Monomer
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.NucleicMonomer
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isConnectedPrevious() - Method in class org.jmol.modelset.Group
isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
isConnection - Variable in class org.jmol.smiles.SmilesBond
isConnectStateBug - Variable in class org.jmol.adapter.readers.pdb.PdbReader
isContainedIn(BS) - Method in class org.jmol.modelset.Model
isContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
isContoured - Variable in class org.jmol.jvxl.data.JvxlData
isContoured - Variable in class org.jmol.jvxl.readers.Parameters
isCore - Variable in class org.jmol.quantum.SlaterData
isCourseGrained - Variable in class org.jmol.adapter.readers.cif.CifReader
isCourseGrained - Variable in class org.jmol.adapter.readers.pdb.PdbReader
isCovalent() - Method in class org.jmol.modelset.Bond
isCovalent() - Method in class org.jmol.smiles.SmilesBond
isCovalent() - Method in class org.jmol.util.Edge
isCovalent() - Method in interface org.jmol.util.SimpleEdge
isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
iscroll - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
isCrossed - Variable in class org.jmol.shapespecial.Draw
isCrossLinked(Node) - Method in class org.jmol.modelset.Atom
isCrossLinked(Group) - Method in class org.jmol.modelset.Group
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
isCrossLinked(Node) - Method in class org.jmol.smiles.SmilesAtom
isCrossLinked(Node) - Method in interface org.jmol.util.Node
iScrPt - Variable in class org.jmol.viewer.TransformManager
isCursorOnTopOf(int, int, int, Atom) - Method in class org.jmol.modelset.Atom
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.AtomCollection
  used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
isCurve - Variable in class org.jmol.shapespecial.Draw
isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
isCyclic() - Method in class org.jmol.modelsetbio.BioPolymer
isCyclic - Variable in class org.jmol.renderbio.BioShapeRenderer
isCylinder - Variable in class org.jmol.shapespecial.Draw
isDatabaseCode(char) - Static method in class org.jmol.viewer.Viewer
isDataFlavorSupported(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
isDataFlavorSupported(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
isDataFrame - Variable in class org.jmol.renderbio.BackboneRenderer
isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
isDebug - Variable in class org.jmol.export._StlExporter
isDecimal(SV) - Method in class org.jmol.script.ScriptMathProcessor
isDefaultColorRasmol - Variable in class org.jmol.viewer.ColorManager
isDefined() - Method in class org.jmol.smiles.SmilesAtom
isDeleted() - Method in class org.jmol.modelset.Atom
isDeleted() - Method in class org.jmol.smiles.SmilesAtom
isDeleted() - Method in interface org.jmol.util.Node
isDiaxial(SimpleNode, SimpleNode, SimpleNode, SimpleNode, VTemp, float) - Static method in class org.jmol.smiles.SmilesStereo
isDiff - Variable in class org.jmol.jvxl.readers.BCifDensityReader
isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
isDirectory() - Method in interface org.jmol.api.GenericFileInterface
isDirectory() - Method in class org.jmol.awtjs2d.JSFile
isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
isDna() - Method in class org.jmol.modelset.Group
  group ID-based definition
isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isDnaByID() - Method in class org.jmol.modelset.Group
  group ID-based definition
isDone - Variable in class org.jmol.thread.SpinThread
isDotDot - Variable in class org.jmol.script.ScriptCompiler
isDraggedIsShiftDown() - Method in class org.jmol.viewer.ActionManager
isDrawOrLabelAction(int) - Method in class org.jmol.viewer.ActionManager
isDrawPolygon - Variable in class org.jmol.util.MeshSurface
isDrawType(String, int, float) - Method in class org.jmol.symmetry.PointGroup
isDSSP1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isDSSP2 - Variable in class org.jmol.dssx.DSSP
isDssrSet - Variable in class org.jmol.modelsetbio.NucleicPolymer
isDuplicate - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a flag to indicate atom that is a duplicate, either due to ring closure or multiple bonding -- element number and mass, but no substituents; slightly lower in priority than standard atoms.
isE_fr_energy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
isE_wo_entrp - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
isEccentric - Variable in class org.jmol.jvxl.readers.Parameters
isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
isEcho - Variable in class org.jmol.modelset.Text
isEdge(int, int) - Method in class org.jmol.util.MeshCapper
isElectronDensityCalc - Variable in class org.jmol.jvxl.readers.IsoMOReader
isElement(int, int) - Static method in class org.jmol.util.Elements
isEmbedded - Variable in class org.jmol.script.ScriptEval
isEmbeddedExpression - Variable in class org.jmol.script.ScriptTokenParser
isEmpty() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
isEnabled() - Method in interface org.jmol.api.JmolModulationSet
isEnabled() - Method in interface org.jmol.api.SC
isEnabled() - Method in class org.jmol.awt.AwtSwingComponent
isEnabled() - Method in class org.jmol.awtjs.swing.Component
isEnabled() - Method in class org.jmol.util.ModulationSet
isEndOfCommand - Variable in class org.jmol.script.ScriptCompiler
isEqual(PointGroup) - Method in class org.jmol.symmetry.PointGroup
isEquiv(Tensor) - Method in class org.jmol.util.Tensor
isError - Variable in exception org.jmol.script.ScriptException
isError() - Method in class org.jmol.script.ScriptTokenParser
isError - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
iSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
isEvenEne - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  alkene or even cumulene, so chirality will be EZ, not MP
isExecuting() - Method in interface org.jmol.api.JmolScriptEvaluator
isExecuting() - Method in class org.jmol.script.ScriptEval
isExport - Variable in class org.jmol.render.ShapeRenderer
isExpressionNext() - Method in class org.jmol.script.ScriptTokenParser
isFinalized - Variable in class org.jmol.adapter.readers.cif.Subsystem
isFinalized - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isFinalized - Variable in class org.jmol.symmetry.SymmetryOperation
isFinite(double) - Static method in class org.jmol.minimize.Util
isFirst - Variable in class org.jmol.smiles.SmilesAtom
  true if this atom is the first SMILES atom or first after a .
isFirst - Variable in class org.jmol.thread.AnimationThread
isFirstJob - Variable in class org.jmol.adapter.readers.quantum.QchemReader
isFirstRow(SimpleNode) - Static method in class org.jmol.symmetry.CIPChirality
  Check if an atom is 1st row.
isFixed - Variable in class org.jmol.shape.MeshCollection
isFixed - Variable in class org.jmol.shapespecial.DrawMesh
isFloat(String) - Static method in class org.jmol.adapter.smarter.Resolver
isFloatInfo(String) - Static method in class org.jmol.util.Tensor
isFloatParameter(int) - Method in class org.jmol.script.ScriptParam
isFloatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
isFlowIfContextOK(ScriptFlowContext) - Method in class org.jmol.script.ScriptCompiler
  check for proper sequence: if...[any number of elseif]...[zero or one else]...[endif]
isFractional - Variable in class org.jmol.adapter.readers.xtal.AimsReader
isFractional - Variable in class org.jmol.modelset.Trajectory
isFromPreviousTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
  Check to see if this is the bond to the previous atom
isFront(P3, P3, P3) - Static method in class org.jmol.g3d.HermiteRenderer
isFull - Variable in class org.jmol.shapespecial.Polyhedra
isFullSceneAntialiasingEnabled - Variable in class org.jmol.g3d.Graphics3D
isFullyLit() - Method in class org.jmol.jvxl.readers.Parameters
isFullyLit - Variable in class org.jmol.shapespecial.Polyhedron
isFuncReturn - Variable in class org.jmol.script.ScriptEval
isFunction - Variable in class org.jmol.script.ScriptContext
isFunction(String) - Method in class org.jmol.viewer.Viewer
isGesture - Variable in class org.jmol.thread.SpinThread
isGhostPass - Variable in class org.jmol.render.MeshRenderer
isGreaterOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
isH - Variable in class org.jmol.awtjs.swing.JSplitPane
isHbonded(int, int, int, int, int[][][][]) - Method in class org.jmol.dssx.DSSP
isHeader - Variable in class org.jmol.adapter.readers.simple.InputReader
isHeadless() - Method in interface org.jmol.api.GenericPlatform
isHeadless() - Method in class org.jmol.awt.Platform
isHeadless() - Method in class org.jmol.awtjs2d.Platform
isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
isHelix(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
isHelix() - Method in class org.jmol.modelsetbio.Monomer
isHetero - Variable in class org.jmol.adapter.smarter.Atom
isHetero() - Method in class org.jmol.modelset.Atom
isHetero(String) - Method in class org.jmol.modelsetbio.BioResolver
  MMCif, Gromacs, MdTop, Mol2 readers only
isHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
isHidden - Variable in class org.jmol.modelset.Measurement
isHighPrecision - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
isHighRes - Variable in class org.jmol.renderbio.BioShapeRenderer
isHover - Variable in class org.jmol.shape.TextShape
iShowNormals - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
iShowSolid - Variable in class org.jmol.renderspecial.DotsRenderer
isHydrogen() - Method in class org.jmol.modelset.Bond
isHydrogen() - Method in class org.jmol.smiles.SmilesBond
isHydrogen() - Method in class org.jmol.util.Edge
isIDcmd(int) - Static method in class org.jmol.script.T
  commands that allow implicit ID as first parameter
isImproper - Variable in class org.jmol.symmetry.HallRotationTerm
isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
isInDisplayRange(int, int) - Method in class org.jmol.util.GData
isInitializedIndex(int) - Method in class org.jmol.bspt.Bspf
isInLatticeCell(int, P3, P3, boolean) - Method in class org.jmol.modelset.ModelSet
isInPosition(V3, float) - Method in class org.jmol.viewer.TransformManager
isInputFirst - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
isInRange(Atom, Atom, float, float, boolean, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
isInSelectionSubset(int) - Method in class org.jmol.viewer.SelectionManager
isInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
isInsideOut() - Method in class org.jmol.jvxl.readers.Parameters
isInt(float) - Static method in class org.jmol.adapter.readers.xtal.CastepReader
isInt(String) - Static method in class org.jmol.adapter.smarter.Resolver
isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
isInvalid - Variable in class org.jmol.g3d.TextRenderer
isInvertible(MinAtom) - Static method in class org.jmol.minimize.forcefield.CalculationsMMFF
isInvertible(int) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
isIsotropic - Variable in class org.jmol.util.Tensor
isItalic - Variable in class org.jmol.util.Font
isJmolDataFrame - Variable in class org.jmol.modelset.Model
isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
isJmolDataFrameForAtom(Atom) - Method in class org.jmol.modelset.ModelSet
isJmolDataFrameForModel(int) - Method in class org.jmol.modelset.ModelSet
isJmolVariable(String) - Method in class org.jmol.viewer.GlobalSettings
isJmolZformat - Variable in class org.jmol.adapter.readers.simple.InputReader
isJNLP - Variable in class org.jmol.util.GenericApplet
isJNLP - Variable in class org.jmol.viewer.Viewer
isJPEG - Variable in class org.jmol.dialog.Dialog.QualityListener
isJS - Variable in class org.jmol.popup.GenericPopup
isJS - Variable in class org.jmol.script.ScriptEval
isJS - Variable in class org.jmol.thread.JmolThread
isJS - Variable in class org.jmol.util.GenericApplet
isJS - Static variable in class org.jmol.viewer.Viewer
isJSNoAWT - Static variable in class org.jmol.viewer.Viewer
isJSThread - Variable in class org.jmol.script.ScriptContext
isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
isKekuleAmbiguous - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  is an atom that is involved in more than one Kekule form
iskiosk - Static variable in class org.jmol.script.T
isKiosk - Variable in class org.jmol.viewer.Viewer
isKiosk() - Method in class org.jmol.viewer.Viewer
isKiosk - Variable in class org.openscience.jmol.app.JmolApp
isKnownPDBGroup(String, int) - Method in class org.jmol.modelsetbio.BioResolver
isLabelPropertyTok(int) - Static method in class org.jmol.modelset.LabelToken
isLastFrame - Variable in class org.jmol.popup.JmolPopup
isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  after reading a model, Q: Is this the last model?
isLeadAtom() - Method in class org.jmol.modelset.Atom
isLeadAtom(int) - Method in class org.jmol.modelset.Group
isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
isLeadAtom - Variable in class org.jmol.smiles.SmilesAtom
isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
isLeadAtom() - Method in interface org.jmol.util.Node
isLegacyModelType - Variable in class org.jmol.adapter.readers.pdb.PdbReader
isLegendre - Variable in class org.jmol.adapter.readers.xtal.JanaReader
isLigand - Variable in class org.jmol.adapter.readers.cif.CifReader
isLigandBondBug - Variable in class org.jmol.adapter.readers.cif.MMCifReader
isLike(SV, SV) - Static method in class org.jmol.script.SV
  a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
isLine - Variable in class org.jmol.shapespecial.Draw
isLinear(int) - Method in class org.jmol.minimize.forcefield.Calculations
isLinear(int) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
isLinear(MinAtom) - Static method in class org.jmol.minimize.MinAtom
isLinear(T3[]) - Method in class org.jmol.symmetry.PointGroup
isLineContinuation(int, boolean) - Method in class org.jmol.script.ScriptCompiler
isLoadOption(int) - Method in class org.jmol.script.ScriptEval
isLonePair - Variable in class org.jmol.shapesurface.LcaoCartoon
isLongMode - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
isLoop - Variable in class org.jmol.adapter.readers.cif.CifReader
isM3D - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
isMac - Static variable in class org.jmol.dialog.Dialog
isMagCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
isMapped - Variable in class org.jmol.jvxl.readers.Parameters
isMapped - Variable in class org.jmol.rendercgo.CGORenderer
isMatch(String) - Method in class org.jmol.shapespecial.Polyhedra
isMathExpressionCommand - Variable in class org.jmol.script.ScriptTokenParser
isMeasure - Variable in class org.jmol.modelset.Text
isMenuItem(Object) - Method in class org.jmol.console.GenericConsole
isMenuItem(Object) - Method in class org.jmol.console.JmolConsole
isMenuItem(Object) - Method in class org.jmol.consolejs.AppletConsole
isMerged - Variable in class org.jmol.util.MeshSurface
isMesh - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
isMesh - Variable in class org.jmol.shapebio.Strands
isMin(Map<String, Integer>) - Method in class org.jmol.modelset.Measurement
isMixed(Matrix) - Method in class org.jmol.adapter.readers.cif.Subsystem
isMMCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
isModelConnected - Variable in class org.jmol.jvxl.data.JvxlData
isModelConnected - Variable in class org.jmol.jvxl.readers.Parameters
isModelConnected - Variable in class org.jmol.shape.Mesh
isModelKit - Variable in class org.jmol.modelset.Model
isModelPDB(int) - Method in class org.jmol.viewer.Viewer
isModulated(int) - Method in class org.jmol.modelset.AtomCollection
isModulated - Variable in class org.jmol.util.Tensor
isMolecular - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isMolecular - Variable in class org.jmol.shapesurface.LcaoCartoon
isMonomerSelected(int) - Method in class org.jmol.modelsetbio.BioPolymer
isMopac - Variable in class org.jmol.adapter.readers.simple.InputReader
isMouseDown - Variable in class org.jmol.awt.Mouse
isMouseDown - Variable in class org.jmol.awtjs2d.Mouse
isMove - Variable in class org.jmol.thread.MoveToThread
isMovie - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
isMovie - Variable in class org.jmol.viewer.AnimationManager
isMTClient() - Method in class org.jmol.viewer.ActionManager
isMTServer() - Method in class org.jmol.viewer.ActionManager
isMultiCell - Variable in class org.jmol.symmetry.SymmetryInfo
isMultiConfiguration - Variable in class org.jmol.popup.JmolPopup
isMultiFrame - Variable in class org.jmol.popup.JmolPopup
isMultiModel - Variable in class org.jmol.adapter.readers.pdb.PdbReader
isMultiTouch - Variable in class org.jmol.viewer.ActionManager
isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
isMutate - Variable in class org.jmol.modelset.ModelLoader
isMutated - Variable in class org.jmol.modelsetbio.BioModel
isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
isNav - Variable in class org.jmol.thread.SpinThread
isNavigating() - Method in class org.jmol.viewer.TransformManager
isNavigationMode - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
isNavTo - Variable in class org.jmol.navigate.Navigator
isNci - Variable in class org.jmol.jvxl.readers.IsoMOReader
isNear(double, double) - Static method in class org.jmol.minimize.Util
isNear3(double, double, double) - Static method in class org.jmol.minimize.Util
isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
isNearZero(double) - Static method in class org.jmol.minimize.Util
isNearZero2(double, double) - Static method in class org.jmol.minimize.Util
isNegligible(double, double) - Static method in class org.jmol.minimize.Util
isNegligible3(double, double, double) - Static method in class org.jmol.minimize.Util
isNewChain - Variable in class org.jmol.modelset.ModelLoader
isNewFormat - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
isNewSet - Variable in class org.jmol.script.ScriptTokenParser
isNext(String) - Method in class org.jmol.jvxl.readers.XmlReader
isNonzero() - Method in class org.jmol.util.ModulationSet
isNonzero() - Method in class org.jmol.util.Vibration
isNormalized - Variable in class org.jmol.smiles.SmilesSearch
isNot - Variable in class org.jmol.smiles.SmilesBond
isNot - Variable in class org.jmol.smiles.SmilesMeasure
isNot - Variable in class org.jmol.smiles.SmilesStereo
isNotCentroid(P3, int, int[], boolean) - Method in class org.jmol.symmetry.Symmetry
isNotInRange(float) - Method in class org.jmol.viewer.AnimationManager
isNucleic() - Method in class org.jmol.modelset.Group
  group ID-based definition
isNucleic() - Method in class org.jmol.modelsetbio.BioPolymer
isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isNucleic - Variable in class org.jmol.renderbio.BioShapeRenderer
isNucleic() - Method in class org.jmol.smiles.SmilesAtom
isNucleicMonomer() - Method in class org.jmol.modelset.Group
isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
isNull(String) - Method in class org.jmol.adapter.readers.cif.CifReader
isNumericAndNonZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
isOccupied() - Method in class org.jmol.modelset.Atom
isoExt - Variable in class org.jmol.script.ScriptExpr
IsoExt - Class in org.jmol.scriptext
IsoExt() - Constructor for class org.jmol.scriptext.IsoExt
isOffsetAbsolute(int) - Static method in class org.jmol.viewer.JC
IsoFxyReader - Class in org.jmol.jvxl.readers
IsoFxyReader() - Constructor for class org.jmol.jvxl.readers.IsoFxyReader
IsoFxyzReader - Class in org.jmol.jvxl.readers
IsoFxyzReader() - Constructor for class org.jmol.jvxl.readers.IsoFxyzReader
IsoIntersectAtomReader - Class in org.jmol.jvxl.readers
IsoIntersectAtomReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectAtomReader
IsoIntersectGridReader - Class in org.jmol.jvxl.readers
  A class to read a linear combination of cube file data.
IsoIntersectGridReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectGridReader
IsoIntersectReader - Class in org.jmol.jvxl.readers
IsoIntersectReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectReader
isOK - Variable in class org.jmol.smiles.SmilesRing
IsoMepReader - Class in org.jmol.jvxl.readers
IsoMepReader() - Constructor for class org.jmol.jvxl.readers.IsoMepReader
isomesh_auto_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
isomeshes - Variable in class org.jmol.shapesurface.Isosurface
IsoMlpReader - Class in org.jmol.jvxl.readers
IsoMlpReader() - Constructor for class org.jmol.jvxl.readers.IsoMlpReader
IsoMOReader - Class in org.jmol.jvxl.readers
IsoMOReader() - Constructor for class org.jmol.jvxl.readers.IsoMOReader
isOn - Variable in class org.jmol.shapespecial.Ellipsoid
isOn - Variable in class org.jmol.util.CommandHistory
isOpenShell - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
isOpenShell() - Method in class org.jmol.adapter.readers.quantum.NBOParser
isOpFunc(T) - Static method in class org.jmol.script.ScriptMathProcessor
IsoPlaneReader - Class in org.jmol.jvxl.readers
IsoPlaneReader() - Constructor for class org.jmol.jvxl.readers.IsoPlaneReader
isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
isOrderH(int) - Static method in class org.jmol.util.Edge
isOrthographic - Variable in class org.jmol.g3d.PrecisionRenderer
IsoShapeReader - Class in org.jmol.jvxl.readers
IsoShapeReader() - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
IsoSolventReader - Class in org.jmol.jvxl.readers
IsoSolventReader() - Constructor for class org.jmol.jvxl.readers.IsoSolventReader
IsoSolventReader.Edge - Class in org.jmol.jvxl.readers
IsoSolventReader.Face - Class in org.jmol.jvxl.readers
isosurface - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
isosurface - Static variable in class org.jmol.script.T
isosurface(int) - Method in class org.jmol.scriptext.IsoExt
Isosurface - Class in org.jmol.shapesurface
Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
isosurfacekey - Static variable in class org.jmol.script.T
isosurfaceKey - Variable in class org.jmol.viewer.GlobalSettings
IsosurfaceMesh - Class in org.jmol.shapesurface
IsosurfaceMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapesurface.IsosurfaceMesh
isosurfacepropertysmoothing - Static variable in class org.jmol.script.T
isosurfacePropertySmoothing - Variable in class org.jmol.viewer.GlobalSettings
isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.T
isosurfacePropertySmoothingPower - Variable in class org.jmol.viewer.GlobalSettings
IsosurfaceRenderer - Class in org.jmol.rendersurface
IsosurfaceRenderer() - Constructor for class org.jmol.rendersurface.IsosurfaceRenderer
isotopeData - Variable in class org.jmol.quantum.NMRCalculation
  isotopeData keyed by nnnSym, for example: 1H, 19F, etc.; and also by element name itself: H, F, etc., for default
isotopeMass - Static variable in class org.jmol.util.Elements
isotropy() - Method in class org.jmol.util.Tensor
  isotropy = average of eigenvalues
isOutput - Variable in class org.jmol.adapter.readers.xtal.CastepReader
isOutputFile - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
isPaletteVariable(byte) - Static method in enum org.jmol.c.PAL
isParallel(V3, V3) - Method in class org.jmol.symmetry.PointGroup
isParallel - Variable in class org.jmol.viewer.Viewer
isParallel() - Method in class org.jmol.viewer.Viewer
isPartial() - Method in class org.jmol.modelset.Bond
isPass2 - Variable in class org.jmol.render.SticksRenderer
isPass2 - Variable in class org.jmol.util.GData
isPathGuide - Variable in class org.jmol.navigate.Navigator
isPaused() - Method in interface org.jmol.api.JmolScriptEvaluator
isPaused() - Method in class org.jmol.script.ScriptEval
isPaused - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
isPauseDelay - Variable in class org.jmol.script.ScriptDelayThread
isPDB - Variable in class org.jmol.adapter.readers.more.Mol2Reader
isPDB - Variable in class org.jmol.popup.JmolPopup
isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
isPeriodic - Variable in class org.jmol.jvxl.readers.SurfaceReader
isPerpendicular - Variable in class org.jmol.shapespecial.Draw
isPerpendicular(V3, V3) - Method in class org.jmol.symmetry.PointGroup
isPhaseColored - Variable in class org.jmol.shapesurface.Isosurface
isPhonon - Variable in class org.jmol.adapter.readers.xtal.CastepReader
isPhosphorusOnly - Variable in class org.jmol.renderbio.BioShapeRenderer
isPickable(IsosurfaceMesh, BS) - Method in class org.jmol.shapesurface.Isosurface
isPickAtomAssignCharge - Variable in class org.jmol.modelkit.ModelKitPopup
isPickAtomAssignCharge() - Method in class org.jmol.modelkit.ModelKitPopup
isPickingMode() - Method in class org.jmol.shape.Labels
isPlanar(P3, P3, P3, P3) - Method in class org.jmol.shapespecial.Polyhedra
isPlanarMapping - Variable in class org.jmol.jvxl.readers.IsoFxyReader
isPlane - Variable in class org.jmol.shapespecial.Draw
isPocket - Variable in class org.jmol.jvxl.readers.IsoSolventReader
isPoint3f(int) - Method in class org.jmol.script.ScriptParam
isPolygonDisplayable(int) - Method in class org.jmol.render.MeshRenderer
isPolygonDisplayable(int) - Method in class org.jmol.renderspecial.DrawRenderer
isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
isPolyhedral - Variable in class org.jmol.smiles.SmilesGenerator
isPolymer - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
isPolymer - Variable in class org.jmol.adapter.readers.xtal.GulpReader
isPolymer() - Method in interface org.jmol.api.SymmetryInterface
isPolymer - Variable in class org.jmol.render.CageRenderer
isPolymer() - Method in class org.jmol.symmetry.Symmetry
isPolymer() - Method in class org.jmol.util.SimpleUnitCell
isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
isPositiveTorsion(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
  Checks the torsion angle and returns true if it is positive
isPositiveTorsion(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataSmiles
  Checks the torsion angle and returns true if it is positive
isPossibleHBond(HB, HB) - Static method in enum org.jmol.c.HB
isPreliminary - Variable in class org.jmol.minimize.forcefield.Calculations
isPreviewOnly - Variable in class org.jmol.viewer.Viewer
isPrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
isPrimitive - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isPrintOnly - Variable in class org.jmol.viewer.Viewer
isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
isPromolecular - Variable in class org.jmol.quantum.NciCalculation
isProperties - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
isProtein() - Method in enum org.jmol.c.STR
isProtein() - Method in class org.jmol.modelset.Group
  group ID-based definition
isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
isPS - Variable in class org.jmol.rendercgo.CGORenderer
isPurine() - Method in class org.jmol.modelset.Atom
isPurine() - Method in class org.jmol.modelset.Group
  group ID-based definition
isPurine - Variable in class org.jmol.modelsetbio.NucleicMonomer
isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isPurine() - Method in class org.jmol.smiles.SmilesAtom
isPurine() - Method in interface org.jmol.util.Node
isPurineByID() - Method in class org.jmol.modelset.Group
  group ID-based definition
isPyMOLsession - Variable in class org.jmol.modelset.ModelLoader
isPyrimidine() - Method in class org.jmol.modelset.Atom
isPyrimidine() - Method in class org.jmol.modelset.Group
  group ID-based definition
isPyrimidine - Variable in class org.jmol.modelsetbio.NucleicMonomer
isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
isPyrimidine() - Method in interface org.jmol.util.Node
isPyrimidineByID() - Method in class org.jmol.modelset.Group
isQ - Variable in class org.jmol.util.ModulationSet
isQuantumBasisSupported(char) - Static method in class org.jmol.quantum.QS
isQueueProcessing() - Method in interface org.jmol.api.JmolScriptManager
isQueueProcessing() - Method in class org.jmol.script.ScriptManager
isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
isQuote(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Includes all possible operator tokens
isRadical - Variable in class org.jmol.shapesurface.LcaoCartoon
isRadio - Variable in class org.jmol.awtjs.swing.JRadioButtonMenuItem
isRawType(int) - Static method in class org.jmol.script.SV
isReadableAsString(String) - Static method in class org.jmol.viewer.PropertyManager
isReducedDensity - Variable in class org.jmol.quantum.NciCalculation
isRenderScalable() - Method in class org.jmol.shapespecial.DrawMesh
isRepaintPending() - Method in interface org.jmol.api.JmolRepaintManager
isRepaintPending() - Method in class org.jmol.render.RepaintManager
isRepaintPending() - Method in class org.jmol.viewer.Viewer
isReset - Variable in class org.jmol.thread.JmolThread
isReversed - Variable in class org.jmol.shapespecial.Draw
isReversed - Variable in class org.jmol.util.ColorEncoder
isrhombohedral - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
isRingBond(Lst<BS>, BS, int, int) - Static method in class org.jmol.smiles.SmilesSearch
isRingCheck - Variable in class org.jmol.smiles.SmilesSearch
isRLE - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
isRna() - Method in class org.jmol.modelset.Group
  group ID-based definition
isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
isRnaByID() - Method in class org.jmol.modelset.Group
  group ID-based definition
isRockets - Variable in class org.jmol.renderbio.RocketRenderer
isRockets - Variable in class org.jmol.renderbio.RocketsRenderer
isRotateBond - Variable in class org.jmol.modelkit.ModelKitPopup
isRotated45 - Variable in class org.jmol.shapespecial.Draw
isRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
isRubberBandSelect(int) - Method in class org.jmol.viewer.ActionManager
isRule5Pseudo - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  odd/even toggle for comparisons of Rule5 results that would make for R/S, not r/s, if this flag is false.
isSameAromaticRing(int, int) - Method in class org.jmol.smiles.SmilesGenerator
isSameAs(UnitCell) - Method in class org.jmol.symmetry.UnitCell
isSameAtoms(Dipole, String) - Method in class org.jmol.shapespecial.Dipoles
isScalar(SV) - Static method in class org.jmol.script.SV
isScaled - Variable in class org.jmol.shape.Labels
isScaledAlready - Variable in class org.jmol.jvxl.readers.VolumeFileReader
isScaleSet - Variable in class org.jmol.shapespecial.DrawMesh
isScaleSet - Variable in class org.jmol.util.BoxInfo
isScriptExecuting() - Method in class org.jmol.api.JmolViewer
isScriptExecuting() - Method in class org.jmol.viewer.Viewer
isScriptQueued() - Method in interface org.jmol.api.JmolScriptManager
isScriptQueued - Variable in class org.jmol.script.ScriptManager
isScriptQueued() - Method in class org.jmol.script.ScriptManager
isScriptQueued() - Method in class org.jmol.viewer.Viewer
isScriptType(String) - Static method in class org.jmol.viewer.FileManager
isSelectAction(int) - Method in class org.jmol.viewer.ActionManager
isSelected() - Method in interface org.jmol.api.JmolAbstractButton
isSelected() - Method in interface org.jmol.api.SC
isSelected() - Method in class org.jmol.awt.AwtSwingComponent
isSelected() - Method in class org.jmol.awtjs.swing.AbstractButton
isSelected() - Method in class org.jmol.console.JmolLabel
isSelected(BS) - Method in class org.jmol.modelset.Group
isSelected(BS, int) - Method in class org.jmol.util.Tensor
isSelected(int) - Method in class org.jmol.viewer.SelectionManager
isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
isSet - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
isSet - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a flag to prevent finalization of an atom node more than once
isSetBrace - Variable in class org.jmol.script.ScriptTokenParser
isSetOrDefine - Variable in class org.jmol.script.ScriptTokenParser
isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
isSheet(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
isSheet() - Method in class org.jmol.modelsetbio.Monomer
isShell - Variable in class org.jmol.render.MeshRenderer
isShell - Variable in class org.jmol.shape.Mesh
isShell - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
isShifted - Variable in class org.jmol.awtjs2d.JsG2D
isShowCommand - Variable in class org.jmol.script.ScriptCompiler
isShowScriptOutput - Variable in class org.jmol.script.ScriptCompiler
isSigned - Variable in class org.jmol.applet.AppletWrapper
isSigned() - Method in class org.jmol.applet.AppletWrapper
isSigned - Variable in class org.jmol.applet.WrappedAppletLoader
isSigned - Variable in class org.jmol.popup.GenericPopup
isSigned - Variable in class org.jmol.util.GenericApplet
isSignedApplet - Variable in class org.jmol.viewer.Viewer
isSignedAppletLocal - Variable in class org.jmol.viewer.Viewer
isSilent - Variable in class org.jmol.jvxl.readers.Parameters
isSilent - Variable in class org.jmol.minimize.Minimizer
isSilent - Variable in class org.jmol.script.ScriptCompiler
isSilent - Variable in class org.jmol.smiles.SmilesSearch
isSilent - Variable in class org.jmol.viewer.Viewer
isSilent - Variable in class org.openscience.jmol.app.InputScannerThread
isSilent - Variable in class org.openscience.jmol.app.JmolApp
isSimple() - Method in interface org.jmol.api.SymmetryInterface
isSimple() - Method in class org.jmol.symmetry.Symmetry
isSingleThreaded() - Method in interface org.jmol.api.GenericPlatform
isSingleThreaded() - Method in class org.jmol.awt.Platform
isSingleThreaded() - Method in class org.jmol.awtjs2d.Platform
isSingleThreaded - Variable in class org.jmol.viewer.Viewer
isSlab - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
isSlab - Variable in class org.jmol.adapter.readers.xtal.GulpReader
isSlab() - Method in interface org.jmol.api.SymmetryInterface
isSlab - Variable in class org.jmol.render.CageRenderer
isSlab() - Method in class org.jmol.symmetry.Symmetry
isSlab() - Method in class org.jmol.util.SimpleUnitCell
isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
isSlabEnabled - Variable in class org.jmol.export.__RayTracerExporter
isSmarts - Variable in class org.jmol.smiles.SmilesParser
isSmarts - Variable in class org.jmol.smiles.SmilesSearch
isSmiles() - Method in class org.jmol.symmetry.CIPData
  Subclass identifier
isSmiles() - Method in class org.jmol.symmetry.CIPDataSmiles
isSmilesCanonical(String) - Static method in class org.jmol.viewer.JC
isSMOL - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
isSp2Ring(int, Node[], BS, BS, float, boolean, boolean) - Static method in class org.jmol.smiles.SmilesAromatic
  3D-SEARCH aromaticity test.
isSP3 - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a flag set false in evaluation of Rule 5 to indicate that there was more than one R/S decision made, so this center cannot be r/s; initially just indicates that the atom has 4 covalent bonds or is trigonal pyriamidal
isSpaceOrColon(int) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  used by readTable
isSpaceOrTab(char) - Static method in class org.jmol.script.ScriptCompiler
isSpartanArchive(String) - Method in class org.jmol.adapter.readers.spartan.SpartanReader
isSpartanZip(String[]) - Method in class org.jmol.io.JmolUtil
  check for a Spartan directory.
isSpecialAssignment - Variable in class org.jmol.script.ScriptMathProcessor
isSpherical - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
isSpinFixed - Variable in class org.jmol.viewer.TransformManager
isSpinInternal - Variable in class org.jmol.viewer.TransformManager
isSpinSelected - Variable in class org.jmol.viewer.TransformManager
isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
isSquared - Variable in class org.jmol.jvxl.data.VolumeData
isSquared - Variable in class org.jmol.jvxl.readers.Parameters
isSquaredLinear - Variable in class org.jmol.jvxl.readers.Parameters
isSquaredLinear - Variable in class org.jmol.quantum.MOCalculation
isSSG - Variable in class org.jmol.symmetry.SpaceGroup
isStarted() - Method in interface org.openscience.jmol.app.JmolPlugin
isStateScript - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
isStateScript() - Method in interface org.jmol.api.JmolScriptEvaluator
isStateScript - Variable in class org.jmol.script.ScriptContext
isStateScript - Variable in class org.jmol.script.ScriptEval
isStateScript() - Method in class org.jmol.script.ScriptEval
isStateScript - Variable in class org.jmol.script.ScriptTokenParser
isStaticFunction(String) - Static method in class org.jmol.viewer.Viewer
isStep - Variable in class org.jmol.navigate.Navigator
isStepping() - Method in interface org.jmol.api.JmolScriptEvaluator
isStepping() - Method in class org.jmol.script.ScriptEval
isStereo() - Method in class org.jmol.modelset.Bond
isStereoSlave - Variable in class org.jmol.util.GenericApplet
isStereoSlave - Variable in class org.jmol.viewer.Viewer
  A flag to indicate that THIS is the right-side panel of a pair of synced applets running a left-right stereo display (that would be piped into a dual-image polarized projector system such as GeoWall).
isStopped() - Method in interface org.jmol.api.JmolScriptEvaluator
isStopped() - Method in class org.jmol.script.ScriptEval
isStringArray(String) - Static method in class org.jmol.util.Escape
isSubsystem - Variable in class org.jmol.util.ModulationSet
  subsystems can deliver their own unique unit cell; they are commensurate
isSupercell() - Method in interface org.jmol.api.SymmetryInterface
isSupercell() - Method in class org.jmol.symmetry.Symmetry
isSupercell() - Method in class org.jmol.util.SimpleUnitCell
isSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
isSurface - Variable in class org.jmol.shapespecial.Dots
isSurfacePoint - Variable in class org.jmol.jvxl.readers.IsoSolventReader
isSurfaceType(String) - Static method in class org.jmol.viewer.FileManager
isSwingJS - Static variable in class org.jmol.viewer.Viewer
isSynced - Variable in class org.jmol.viewer.StatusManager
isSyntaxAndFileCheck - Variable in class org.jmol.viewer.Viewer
isSyntaxCheck - Variable in class org.jmol.viewer.Viewer
isTainted() - Method in class org.jmol.modelset.Measurement
isTainted - Variable in class org.jmol.popup.GenericPopup
isTainted(BS[], int, int) - Static method in class org.jmol.viewer.StateCreator
isTainted - Variable in class org.jmol.viewer.Viewer
isTarget - Variable in class org.jmol.smiles.SmilesParser
iStep - Variable in class org.jmol.navigate.Navigator
iStep - Variable in class org.jmol.thread.MoveToThread
isTerminal - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  a flag to indicate an atom that has no substituents; a branch end point; typically H or a halogen (F, Cl, Br, I); also set TRUE if there is a problem setting an atom; does not include duplicates
isTerminator(int) - Method in class org.jmol.script.ScriptTokenParser
  we allow : and % to have null values
isTopoAtom - Variable in class org.jmol.smiles.SmilesAtom
isTopology - Variable in class org.jmol.smiles.SmilesSearch
isTraceAlpha - Variable in class org.jmol.renderbio.BioShapeRenderer
isTracker() - Method in class org.jmol.symmetry.CIPData
  Subclass identifier
isTracker() - Method in class org.jmol.symmetry.CIPDataTracker
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollection
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
isTrajectory - Variable in class org.jmol.modelset.Measurement
isTrajectory - Variable in class org.jmol.modelset.Model
isTrajectory - Variable in class org.jmol.modelset.ModelLoader
isTrajectory(int) - Method in class org.jmol.modelset.ModelSet
  could be the base model or one of the subframes
isTrajectoryMeasurement(int[]) - Method in class org.jmol.modelset.ModelSet
isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelSet
isTranslucent - Variable in class org.jmol.render.MeshRenderer
isTranslucent - Variable in class org.jmol.util.ColorEncoder
isTranslucentInherit - Variable in class org.jmol.render.MeshRenderer
istructure - Variable in class org.jmol.adapter.smarter.StructureIterator
isTrue(Object) - Static method in class org.jmol.modelkit.ModelKitPopup
isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
isTryCatch - Variable in class org.jmol.script.ScriptContext
isTS - Variable in class org.jmol.adapter.readers.xtal.CastepReader
isTurn(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
isTwoSided - Variable in class org.jmol.shape.Mesh
isType(String) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
isTypeSet - Variable in class org.jmol.adapter.readers.quantum.GamessReader
isUnitCell - Variable in class org.jmol.popup.JmolPopup
isUnmodulated - Variable in class org.jmol.util.Tensor
isUpdating - Variable in class org.jmol.applet.Jmol
isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
isUserFunction(String) - Method in class org.jmol.script.ScriptTokenParser
isUserToken - Variable in class org.jmol.script.ScriptCompiler
isUserValue - Variable in class org.jmol.shapespecial.Dipole
isUserValue - Variable in class org.jmol.shapespecial.Dipoles
isValid - Variable in class org.jmol.bspt.Bspf
isValid - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
isValid - Variable in class org.jmol.jvxl.data.JvxlData
isValid() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
isValid - Variable in class org.jmol.modelset.Measurement
isValid() - Method in class org.jmol.modelset.Measurement
isValid() - Method in class org.jmol.modelset.StateScript
isValid - Variable in class org.jmol.shape.Mesh
isValid - Variable in class org.jmol.shapespecial.Dipole
isValid - Variable in class org.jmol.shapespecial.Draw
isValid - Variable in class org.jmol.shapespecial.Ellipsoid
isValid - Variable in class org.jmol.shapespecial.Polyhedron
isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.readers.xtal.ShelxReader
isValidSym1(char) - Static method in class org.jmol.adapter.smarter.Atom
isValidSym2(char, char) - Static method in class org.jmol.adapter.smarter.Atom
isValidSymChar1(char) - Static method in class org.jmol.adapter.smarter.Atom
isValidSymNoCase(char, char) - Static method in class org.jmol.adapter.smarter.Atom
isVariable(String) - Method in class org.jmol.script.ScriptFunction
isVariableType(Object) - Static method in class org.jmol.script.SV
  Must be updated if getVariable is updated!
isVdw - Variable in class org.jmol.modelset.AtomIteratorWithinModel
isVector - Variable in class org.jmol.shapespecial.Draw
isVector - Variable in class org.jmol.shapespecial.DrawMesh
isVersion3 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
isVersion5 - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
isVertices - Variable in class org.jmol.shapespecial.Draw
isVibration(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
isVibration - Variable in class org.jmol.popup.JmolPopup
isVibrationOn() - Method in class org.jmol.viewer.TransformManager
isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
isVisible() - Method in class org.jmol.awtjs.swing.Component
isVisible(int) - Method in class org.jmol.modelset.Atom
isVisible - Variable in class org.jmol.modelset.Measurement
isVisible - Variable in class org.jmol.shape.Bbcage
isVisibleForMe(Atom) - Method in class org.jmol.render.ShapeRenderer
isVisibleNormix(short) - Method in class org.jmol.render.MeshRenderer
isVwrRotateBond() - Method in class org.jmol.modelkit.ModelKitPopup
isWebGL() - Method in interface org.jmol.api.JmolRendererInterface
isWebGL - Variable in class org.jmol.export.___Exporter
isWebGL() - Method in class org.jmol.export.Export3D
isWebGL() - Method in class org.jmol.g3d.Graphics3D
isWebGL - Variable in class org.jmol.popup.GenericPopup
isWebGL - Static variable in class org.jmol.viewer.Viewer
isWignerSeitz - Variable in class org.jmol.util.BZone
isWindowCentered() - Method in class org.jmol.viewer.TransformManager
isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
isWithin(P3) - Method in class org.jmol.util.BoxInfo
isWithinCell(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
isWithinFourBonds(Atom, Atom) - Method in class org.jmol.shapesurface.Contact
isWithinNot - Variable in class org.jmol.shapesurface.Isosurface
isWithinRadius(T3) - Method in class org.jmol.bspt.CubeIterator
  checks one Point3f for box-based distance
isWithinStructure(STR) - Method in class org.jmol.modelset.Group
isWithinStructure(STR) - Method in class org.jmol.modelsetbio.AlphaMonomer
isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
isXtalState() - Method in class org.jmol.modelkit.ModelKitPopup
isXYZ - Variable in class org.jmol.modelset.ModelSet
isZapped - Variable in class org.jmol.popup.JmolPopup
isZeroBased - Variable in class org.jmol.modelset.AtomIteratorWithinModel
isZoomArea(int) - Method in class org.jmol.viewer.ActionManager
itemListener - Variable in class org.jmol.awtjs.swing.AbstractButton
itemMax - Static variable in class org.jmol.popup.JmolPopup
itemStateChanged(ItemEvent) - Method in class org.jmol.awt.AwtPopupHelper
itemStateChanged(ItemEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
itemStateChanged(ItemEvent) - Method in class org.jmol.dialog.Dialog.ExportChoiceListener
itemStateChanged(ItemEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
iter - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
iter - Variable in class org.jmol.jvxl.readers.IsoSolventReader
iter - Variable in class org.jmol.symmetry.PointGroup
iterateOverAllNewAtoms(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
iterateOverAllNewBonds(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
iterateOverAllNewModels(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelsetbio.BioResolver
  Pull in all spans of helix, etc.
iToken - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
iToken - Variable in class org.jmol.jvxl.readers.PmeshReader
iToken - Variable in class org.jmol.script.ScriptContext
iToken - Variable in class org.jmol.script.ScriptParam
itokenInfix - Variable in class org.jmol.script.ScriptTokenParser
iType - Variable in class org.jmol.util.Tensor
iVal - Variable in class org.jmol.minimize.forcefield.FFParam
ival(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
iValue(T) - Static method in class org.jmol.script.SV

## J

J_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
jaguarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
JaguarReader - Class in org.jmol.adapter.readers.quantum
  Jaguar reader tested for the two samples files in CVS.
JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
JaguarReader - Class in org.jmol.jvxl.readers
JaguarReader() - Constructor for class org.jmol.jvxl.readers.JaguarReader
JANA_FWV_Q1_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
JANA_FWV_Q2_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
JANA_FWV_Q3_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
JANA_OCC_ABS_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
JANA_OCC_ABS_O_0 - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
JanaReader - Class in org.jmol.adapter.readers.xtal
  A reader for Jana M50+M40 file pairs.
JanaReader() - Constructor for class org.jmol.adapter.readers.xtal.JanaReader
janaStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
javaname - Variable in class org.openscience.jmol.app.webexport.JmolInstance
javascript - Static variable in class org.jmol.script.T
jbr - Variable in class org.jmol.modelset.ModelLoader
jbr - Variable in class org.jmol.viewer.Viewer
JButton - Class in org.jmol.awtjs.swing
JButton() - Constructor for class org.jmol.awtjs.swing.JButton
jc - Variable in class org.jmol.awt.AwtSwingComponent
JC - Class in org.jmol.viewer
JC() - Constructor for class org.jmol.viewer.JC
JcampdxReader - Class in org.jmol.adapter.readers.more
  A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...
JcampdxReader() - Constructor for class org.jmol.adapter.readers.more.JcampdxReader
jcampdxStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
jcd - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
JCheckBox - Class in org.jmol.awtjs.swing
JCheckBox() - Constructor for class org.jmol.awtjs.swing.JCheckBox
JCheckBoxMenuItem - Class in org.jmol.awtjs.swing
JCheckBoxMenuItem() - Constructor for class org.jmol.awtjs.swing.JCheckBoxMenuItem
jcm - Variable in class org.jmol.viewer.Viewer
JComboBox<T> - Class in org.jmol.awtjs.swing
JComboBox(String[]) - Constructor for class org.jmol.awtjs.swing.JComboBox
JComponent - Class in org.jmol.awtjs.swing
JComponent(String) - Constructor for class org.jmol.awtjs.swing.JComponent
JComponentImp - Class in org.jmol.awtjs.swing
  implementation of a JComponent
JComponentImp(String) - Constructor for class org.jmol.awtjs.swing.JComponentImp
JContentPane - Class in org.jmol.awtjs.swing
JContentPane() - Constructor for class org.jmol.awtjs.swing.JContentPane
JDialog - Class in org.jmol.awtjs.swing
  There is really no need here for awt.Dialog.
JDialog() - Constructor for class org.jmol.awtjs.swing.JDialog
JDXMOLParser - Class in org.jmol.jsv
  Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
JDXMOLParser() - Constructor for class org.jmol.jsv.JDXMOLParser
JEditorPane - Class in org.jmol.awtjs.swing
  A simple implementation of a Swing JTextPane.
JEditorPane() - Constructor for class org.jmol.awtjs.swing.JEditorPane
JLabel - Class in org.jmol.awtjs.swing
JLabel(String) - Constructor for class org.jmol.awtjs.swing.JLabel
jm - Variable in class org.jmol.awt.AwtSwingComponent
JMenu - Class in org.jmol.awtjs.swing
JMenu() - Constructor for class org.jmol.awtjs.swing.JMenu
JMenuItem - Class in org.jmol.awtjs.swing
JMenuItem(String) - Constructor for class org.jmol.awtjs.swing.JMenuItem
JMenuItem(String, int) - Constructor for class org.jmol.awtjs.swing.JMenuItem
JmeReader - Class in org.jmol.adapter.readers.simple
JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
jmi - Variable in class org.jmol.awt.AwtSwingComponent
Jmol - Class in org.jmol.applet
Jmol() - Constructor for class org.jmol.applet.Jmol
Jmol - Class in org.jmol.appletjs
  Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
Jmol(Map<String, Object>) - Constructor for class org.jmol.appletjs.Jmol
  cannot ignore super because it involves preparing fields
Jmol() - Static method in class org.jmol.awtjs2d.Platform
jmol - Static variable in class org.jmol.script.T
JMOL - Static variable in class org.jmol.util.ColorEncoder
Jmol - Class in org.openscience.jmol.app
Jmol(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.Jmol
jmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
jmol - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
JMOL_DIAMETER - Static variable in class org.jmol.shapecgo.CGOMesh
JMOL_PS - Static variable in class org.jmol.shapecgo.CGOMesh
JMOL_SCREEN - Static variable in class org.jmol.shapecgo.CGOMesh
JMOL_UVMAP - Static variable in class org.jmol.shapecgo.CGOMesh
JmolAbstractButton - Interface in org.jmol.api
JmolAdapter - Class in org.jmol.api
  The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapter() - Constructor for class org.jmol.api.JmolAdapter
JmolAdapterAtomIterator - Interface in org.jmol.api
JmolAdapterBondIterator - Class in org.jmol.api
JmolAdapterBondIterator() - Constructor for class org.jmol.api.JmolAdapterBondIterator
JmolAdapterStructureIterator - Class in org.jmol.api
JmolAdapterStructureIterator() - Constructor for class org.jmol.api.JmolAdapterStructureIterator
JmolAnnotationParser - Interface in org.jmol.api
JmolApp - Class in org.openscience.jmol.app
JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
  standard Jmol application entry point
jmolApp - Variable in class org.openscience.jmol.app.JmolData
jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
JmolApp.OptSort - Class in org.openscience.jmol.app
JmolAppAPI - Interface in org.jmol.api
JmolAppConsoleInterface - Interface in org.jmol.api
JmolApplet - Class in org.jmol.applet
JmolApplet() - Constructor for class org.jmol.applet.JmolApplet
JmolAppletInterface - Interface in org.jmol.api
  This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAsyncException - Exception in org.jmol.viewer
JmolAsyncException(String) - Constructor for exception org.jmol.viewer.JmolAsyncException
jmolAtoms - Variable in class org.jmol.smiles.SmilesStereo
JmolAudio - Class in org.jmol.util
JmolAudio() - Constructor for class org.jmol.util.JmolAudio
JmolAudioPlayer - Interface in org.jmol.api
jmolBinding - Variable in class org.jmol.viewer.ActionManager
JmolBinding - Class in org.jmol.viewer.binding
JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
JmolButton - Class in org.jmol.console
JmolButton(String) - Constructor for class org.jmol.console.JmolButton
JmolButton(ImageIcon) - Constructor for class org.jmol.console.JmolButton
JmolCallbackListener - Interface in org.jmol.api
JmolChimeMessenger - Interface in org.jmol.viewer
JmolConsole - Class in org.jmol.console
JmolConsole() - Constructor for class org.jmol.console.JmolConsole
jmolConsole - Variable in class org.jmol.console.ScriptEditor
JmolConsole.FileChecker - Class in org.jmol.console
jmolData - Variable in class org.jmol.modelset.Model
jmolData - Variable in class org.jmol.modelset.ModelLoader
JmolData - Class in org.openscience.jmol.app
JmolData(JmolApp) - Constructor for class org.openscience.jmol.app.JmolData
JmolDataManager - Interface in org.jmol.api
JmolDataReader - Class in org.jmol.adapter.readers.pdb
  JmolData file reader, for a modified PDB format
JmolDataReader() - Constructor for class org.jmol.adapter.readers.pdb.JmolDataReader
jmoldataStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
jmolDefaultProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
jmolDefaults - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
jmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
JmolDialogInterface - Interface in org.jmol.api
JmolDomReaderInterface - Interface in org.jmol.api
JmolDropEditor - Interface in org.jmol.api
JmolEnvCalc - Interface in org.jmol.api
JmolFilesReaderInterface - Interface in org.jmol.api
JmolFrame - Interface in org.jmol.awt
jmolFrameType - Variable in class org.jmol.modelset.Model
JmolGenericPopup - Class in org.jmol.popup
  An abstract popup class that is instantiated for a given platform and context as one of:
JmolGenericPopup() - Constructor for class org.jmol.popup.JmolGenericPopup
JmolGestureServerInterface - Interface in org.jmol.api
JmolGraphicsInterface - Interface in org.jmol.api
jmolIndex - Variable in class org.jmol.smiles.SmilesAtom
jmolinjspecview - Static variable in class org.jmol.script.T
jmolInJSpecView - Variable in class org.jmol.viewer.GlobalSettings
JmolInstance - Class in org.openscience.jmol.app.webexport
JmolInstance(JmolViewer, String, int, int, int) - Constructor for class org.openscience.jmol.app.webexport.JmolInstance
jmolJarPath() - Method in class org.openscience.jmol.app.webexport.WebPanel
  Returns a string version of the path to Jmol.jar (including the trailing Jmol.jar) decoded using the system default text encoding (usually UTF-8).
jmolJarURL() - Method in class org.openscience.jmol.app.webexport.WebPanel
JmolJDXMOLParser - Interface in org.jmol.api
JmolJDXMOLReader - Interface in org.jmol.api
JmolJniClientAdapter - Class in org.jmol.multitouch.jni
JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
JmolJSpecView - Interface in org.jmol.api
JmolLabel - Class in org.jmol.console
JmolLabel(String, int) - Constructor for class org.jmol.console.JmolLabel
JmolMeasurementClient - Interface in org.jmol.api
JmolModulationSet - Interface in org.jmol.api
JmolMolecule - Class in org.jmol.util
  an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
JmolMovieCreatorInterface - Interface in org.jmol.api
JmolMultiTouchAdapter - Interface in org.jmol.multitouch
JmolMultiTouchClient - Interface in org.jmol.multitouch
JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
jmolName - Variable in class org.jmol.adapter.readers.pymol.JmolObject
JmolNavigatorInterface - Interface in org.jmol.api
JmolNMRInterface - Interface in org.jmol.api
JmolObject - Class in org.jmol.adapter.readers.pymol
  a class to store rendering information prior to finishing file loading, specifically designed for reading PyMOL PSE files.
JmolObject(int, String, BS, Object) - Constructor for class org.jmol.adapter.readers.pymol.JmolObject
jmolObject - Static variable in class org.jmol.viewer.Viewer
jmolObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
JmolPanel - Class in org.openscience.jmol.app.jmolpanel
JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.AnimButton - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
  To shutdown when run as an application.
JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
  An Action to copy the current image into the clipboard.
JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.CreditsAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
JmolParallelProcessor - Interface in org.jmol.api
JmolPatternMatcher - Interface in org.jmol.api
JmolPdfCreatorInterface - Interface in org.jmol.api
JmolPlugin - Interface in org.openscience.jmol.app
JmolPopup - Class in org.jmol.popup
  An abstract popup class that is instantiated for a given platform and context as one of:
JmolPopup() - Constructor for class org.jmol.popup.JmolPopup
jmolpopup - Variable in class org.jmol.viewer.Viewer
jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
JmolPropertyManager - Interface in org.jmol.api
JmolRendererInterface - Interface in org.jmol.api
JmolRepaintManager - Interface in org.jmol.api
JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
  Provides access to resources (for example, strings and images).
JmolResourceHandler() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
JmolSceneGenerator - Interface in org.jmol.api
jmolScriptCallback(CBK) - Method in class org.jmol.viewer.StatusManager
jmolScriptCallbacks - Variable in class org.jmol.viewer.StatusManager
JmolScriptEditorInterface - Interface in org.jmol.api
JmolScriptEvaluator - Interface in org.jmol.api
JmolScriptFunction - Interface in org.jmol.api
JmolScriptManager - Interface in org.jmol.api
JmolSelectionListener - Interface in org.jmol.api
  listen to atom selections in a Jmol Viewer
JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
JmolStateCreator - Class in org.jmol.viewer
JmolStateCreator() - Constructor for class org.jmol.viewer.JmolStateCreator
JmolStatusListener - Interface in org.jmol.api
JmolSyncInterface - Interface in org.jmol.api
jmolTest() - Method in class org.jmol.viewer.Viewer
JmolThread - Class in org.jmol.thread
JmolThread() - Constructor for class org.jmol.thread.JmolThread
JmolToggleButton - Class in org.jmol.console
JmolToggleButton(ImageIcon) - Constructor for class org.jmol.console.JmolToggleButton
JmolToJSmolInterface - Interface in org.jmol.api.js
  methods in JSmol JavaScript accessed in Jmol
JmolTouchSimulatorInterface - Interface in org.jmol.api
JmolUtil - Class in org.jmol.io
JmolUtil() - Constructor for class org.jmol.io.JmolUtil
JmolViewer - Class in org.jmol.api
  JmolViewer is the main API for the Viewer class.
JmolViewer() - Constructor for class org.jmol.api.JmolViewer
JmolZipUtilities - Interface in org.jmol.api
job - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
jobCount - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
join - Static variable in class org.jmol.script.T
join(Lst<P3[]>) - Method in class org.jmol.util.BZone
joinList - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
JPanel - Class in org.jmol.awtjs.swing
JPanel(LayoutManager) - Constructor for class org.jmol.awtjs.swing.JPanel
JPEG_CONTINUE_STRING - Static variable in class org.jmol.viewer.FileManager
JPEG_EXTENSIONS - Static variable in class org.jmol.viewer.JC
jpiDispose() - Method in interface org.jmol.api.GenericMenuInterface
jpiDispose() - Method in class org.jmol.popup.JmolGenericPopup
jpiDispose() - Method in class org.jmol.popup.JmolPopup
jpiGetMenuAsObject() - Method in interface org.jmol.api.GenericMenuInterface
jpiGetMenuAsObject() - Method in class org.jmol.popup.JmolGenericPopup
jpiGetMenuAsString(String) - Method in interface org.jmol.api.GenericMenuInterface
jpiGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
jpiInitialize(PlatformViewer, String) - Method in interface org.jmol.api.GenericMenuInterface
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.popup.JmolGenericPopup
jpiShow(int, int) - Method in interface org.jmol.api.GenericMenuInterface
jpiShow(int, int) - Method in class org.jmol.popup.JmolGenericPopup
jpiUpdateComputedMenus() - Method in interface org.jmol.api.GenericMenuInterface
jpiUpdateComputedMenus() - Method in class org.jmol.modelkit.ModelKitPopup
jpiUpdateComputedMenus() - Method in class org.jmol.popup.JmolPopup
JPopupMenu - Class in org.jmol.awtjs.swing
JPopupMenu(String) - Constructor for class org.jmol.awtjs.swing.JPopupMenu
JRadioButtonMenuItem - Class in org.jmol.awtjs.swing
JRadioButtonMenuItem() - Constructor for class org.jmol.awtjs.swing.JRadioButtonMenuItem
jsc - Variable in class org.jmol.viewer.Viewer
JSConsole - Interface in org.jmol.api.js
jsConsole - Variable in class org.jmol.consolejs.AppletConsole
JSConsole - Interface in org.jmol.consolejs
JScrollPane - Class in org.jmol.awtjs.swing
JScrollPane(JComponent) - Constructor for class org.jmol.awtjs.swing.JScrollPane
jsCylinder(Object, String, boolean, P3, P3, Object[]) - Method in class org.jmol.export.JSExporter
jsDocumentBase - Static variable in class org.jmol.viewer.Viewer
jsEndExport(Object) - Method in class org.jmol.export.JSExporter
jsEval(String) - Method in class org.jmol.viewer.StatusManager
jsEval(String) - Method in class org.jmol.viewer.Viewer
jsEvalSV(String) - Method in class org.jmol.viewer.Viewer
JSExporter - Class in org.jmol.export
  A class to output WebGL graphics.
JSExporter() - Constructor for class org.jmol.export.JSExporter
jsExporter3D - Variable in class org.jmol.viewer.Viewer
JSFile - Class in org.jmol.awtjs2d
  A class that mimics java.io.File
JSFile(String) - Constructor for class org.jmol.awtjs2d.JSFile
JSFont - Class in org.jmol.awtjs2d
  methods required by Jmol that access java.awt.Font private to org.jmol.awtjs2d
JSFont() - Constructor for class org.jmol.awtjs2d.JSFont
JsG2D - Class in org.jmol.awtjs2d
  generic 2D drawing methods -- JavaScript version
JsG2D() - Constructor for class org.jmol.awtjs2d.JsG2D
jsInitExport(Object) - Method in class org.jmol.export.JSExporter
JSJmolPopup - Class in org.jmol.awtjs2d
JSJmolPopup() - Constructor for class org.jmol.awtjs2d.JSJmolPopup
  The main popup window for the applet -- as JavaScript
jsl - Variable in class org.jmol.viewer.StatusManager
JSModelKitPopup - Class in org.jmol.awtjs2d
JSModelKitPopup() - Constructor for class org.jmol.awtjs2d.JSModelKitPopup
JSmolAppletObject - Interface in org.jmol.api.js
jsObjectCall(Object[], String, Object[]) - Method in class org.jmol.adapter.readers.xml.XmlReader
jsObjectGetMember(Object[], String) - Method in class org.jmol.adapter.readers.xml.XmlReader
jsoDocument - Variable in class org.jmol.applet.Jmol
json - Static variable in class org.jmol.script.T
JsonNioClient - Interface in org.openscience.jmol.app.jsonkiosk
  a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
JsonNioServer - Interface in org.openscience.jmol.app.jsonkiosk
JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
JsonNioService - Class in org.openscience.jmol.app.jsonkiosk
JsonNioService() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService
JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jsonkiosk
JsonNioService.JsonNioThread - Class in org.openscience.jmol.app.jsonkiosk
JsonNioService.JSONObject - Class in org.openscience.jmol.app.jsonkiosk
JsonNioThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioThread
JSONObject() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
JSONObject(String) - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
JSONObject(Map<String, Object>) - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
jsonParser - Variable in class org.jmol.viewer.Viewer
JSONReader - Class in org.jmol.adapter.readers.simple
JSONReader() - Constructor for class org.jmol.adapter.readers.simple.JSONReader
jsonStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
JSONWriter - Class in org.jmol.util
JSONWriter() - Constructor for class org.jmol.util.JSONWriter
jsParams - Variable in class org.jmol.viewer.Viewer
JSpecView - Class in org.jmol.jsv
JSpecView() - Constructor for class org.jmol.jsv.JSpecView
jSpecViewForceNew - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
jSpecViewFrame - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
JSplitPane - Class in org.jmol.awtjs.swing
JSplitPane(int) - Constructor for class org.jmol.awtjs.swing.JSplitPane
JSPopupHelper - Class in org.jmol.awtjs2d
  For menus, popup-related awt/swing class references are in this file.
JSPopupHelper(GenericPopup) - Constructor for class org.jmol.awtjs2d.JSPopupHelper
jsSphere(Object, String, boolean, T3, Object[]) - Method in class org.jmol.export.JSExporter
jsSurface(Object, T3[], T3[], int[][], int, int, int, BS, int, int, int[], int[]) - Method in class org.jmol.export.JSExporter
jsTriangle(Object, int, T3, T3, T3) - Method in class org.jmol.export.JSExporter
jsv - Variable in class org.jmol.viewer.Viewer
JSV_CLOSE - Static variable in class org.jmol.viewer.JC
JSV_NOT - Static variable in class org.jmol.viewer.JC
JSV_SELECT - Static variable in class org.jmol.viewer.JC
JSV_SEND_C13SIMULATE - Static variable in class org.jmol.viewer.JC
JSV_SEND_H1SIMULATE - Static variable in class org.jmol.viewer.JC
JSV_SEND_JDXMOL - Static variable in class org.jmol.viewer.JC
JSV_SETPEAKS - Static variable in class org.jmol.viewer.JC
JSV_STRUCTURE - Static variable in class org.jmol.viewer.JC
JSVInterface - Interface in org.jmol.api
  and interface for JSpecView for the Jmol application
JTable - Class in org.jmol.awtjs.swing
JTable(AbstractTableModel) - Constructor for class org.jmol.awtjs.swing.JTable
JTextField - Class in org.jmol.awtjs.swing
JTextField(String) - Constructor for class org.jmol.awtjs.swing.JTextField
JTextPane - Class in org.jmol.awtjs.swing
  A simple implementation of a Swing JTextPane.
JTextPane() - Constructor for class org.jmol.awtjs.swing.JTextPane
junk - Variable in class org.jmol.thread.JmolThread
justifymeasurements - Static variable in class org.jmol.script.T
justifyMeasurements - Variable in class org.jmol.viewer.GlobalSettings
justOneModel - Variable in class org.jmol.modelset.MeasurementData
Jvxl - Class in org.openscience.jvxl
Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
jvxlAppendCharacter2(float, float, float, int, int, SB, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlAppendCommandState(SB, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlAppendEncodedNumber(SB, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
JvxlCoder - Class in org.jmol.jvxl.data
JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlColorEncodingRead - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlCreateHeader(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
  Creates a two-line header for the XJVXL file.
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
JvxlData - Class in org.jmol.jvxl.data
JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlData - Variable in class org.jmol.shapesurface.Isosurface
jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlDecodeBitSetRange(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlDecodeTriangleData(String, String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  decode triangle data found within element as created with jvxlEncodeTriangleData (see above)
jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  decode vertex data found within element as created by jvxlEncodeVertexData (see above)
jvxlDecompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlEncodeBitSet(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEncodeBitSet0(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEncodeBitSetBuffer(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlEncodeContourData(Lst<Object>[], SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
  contour data are appended to a string buffer in the form of a triangle bitset data triangle bitset data triangle bitset data ...
jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlFractionAsCharacterRange(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], Lst<P3>, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetInfoData(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlGetNextFraction(int, int, float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
jvxlReadDefinitionLine(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
JvxlReader - Class in org.jmol.jvxl.readers
JvxlReader() - Constructor for class org.jmol.jvxl.readers.JvxlReader
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
  "edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlSetCompressionRatio(SB, JvxlData, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
jvxlSkipDataBlock(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
jvxlUpdateInfo() - Method in class org.jmol.jvxl.readers.SurfaceReader
jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
JvxlWrite - Class in org.openscience.jvxl.simplewriter
JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
JvxlXmlReader - Class in org.jmol.jvxl.readers
JvxlXmlReader() - Constructor for class org.jmol.jvxl.readers.JvxlXmlReader
jzt - Variable in class org.jmol.viewer.Viewer
jzu - Variable in class org.jmol.viewer.FileManager

## K

ka - Variable in class org.jmol.minimize.MinAngle
kb - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
kb - Variable in class org.jmol.minimize.forcefield.UFFDistanceCalc
KCAL22 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
KCAL332 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
KCAL44 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
KCAL6 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
KCAL644 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
KCAL_TO_KJ - Static variable in class org.jmol.minimize.forcefield.Calculations
keep_alive - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
keepCharsList - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
keepRunning - Variable in class org.jmol.applet.TickerThread
keepRunning - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
key - Variable in class org.jmol.adapter.readers.cif.CifReader
key - Variable in class org.jmol.console.KeyJCheckBox
key - Variable in class org.jmol.console.KeyJCheckBoxMenuItem
key - Variable in class org.jmol.console.KeyJMenu
key - Variable in class org.jmol.console.KeyJMenuItem
key - Variable in class org.jmol.console.KeyJRadioButtonMenuItem
key - Variable in class org.jmol.minimize.forcefield.Calculation
key - Variable in class org.jmol.minimize.MinObject
key - Variable in class org.jmol.modelset.LabelToken
key - Variable in class org.jmol.script.FileLoadThread
key - Variable in class org.jmol.util.Int2IntHashEntry
key0 - Variable in class org.jmol.adapter.readers.cif.CifReader
key2col - Variable in class org.jmol.adapter.readers.cif.CifReader
KEY_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
KEY_DRAW - Static variable in class org.jmol.symmetry.SymmetryDesc
KEY_LIST - Static variable in class org.jmol.shapecgo.CGOMesh
KEY_OOP - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
KEY_PBCI - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
KEY_POINT - Static variable in class org.jmol.symmetry.SymmetryDesc
KEY_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
KEY_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
keyBuffer - Variable in class org.jmol.awt.Mouse
keyBuffer - Variable in class org.jmol.awtjs2d.Mouse
KeyJCheckBox - Class in org.jmol.console
KeyJCheckBox(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
KeyJCheckBoxMenuItem - Class in org.jmol.console
KeyJCheckBoxMenuItem(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
KeyJMenu - Class in org.jmol.console
KeyJMenu(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenu
KeyJMenuItem - Class in org.jmol.console
KeyJMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenuItem
KeyJRadioButtonMenuItem - Class in org.jmol.console
KeyJRadioButtonMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
keyMap - Variable in class org.jmol.adapter.readers.more.AFLOWReader
keyMap - Static variable in class org.jmol.shapecgo.CGOMesh
keyPressed(int, int) - Method in interface org.jmol.api.EventManager
keyPressed(KeyEvent) - Method in class org.jmol.awt.Mouse
keyPressed(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
  called by MouseManager.keyPressed
keyProcessing - Variable in class org.jmol.viewer.ActionManager
keyReleased(int) - Method in interface org.jmol.api.EventManager
keyReleased(KeyEvent) - Method in class org.jmol.awt.Mouse
keyReleased(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
keyReleased(int) - Method in class org.jmol.viewer.ActionManager
keys - Static variable in class org.jmol.script.T
keys - Static variable in class org.jmol.symmetry.SymmetryDesc
keyTyped(int, int) - Method in interface org.jmol.api.EventManager
keyTyped(KeyEvent) - Method in class org.jmol.awt.Mouse
keyTyped(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
keyTyped(int, int) - Method in class org.jmol.viewer.ActionManager
keyword - Variable in class org.jmol.export.UseTable
keyword - Static variable in class org.jmol.script.T
keyXy - Variable in class org.jmol.shapesurface.Isosurface
kind - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
KinemageReader - Class in org.jmol.jvxl.readers
KinemageReader() - Constructor for class org.jmol.jvxl.readers.KinemageReader
kinEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
KioskFrame - Class in org.openscience.jmol.app.jsonkiosk
  A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in http://molecularPlayground.org
KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jsonkiosk.KioskFrame
KNOWN_TYPES - Static variable in class org.jmol.util.Tensor
knownGroupID(String) - Static method in class org.jmol.modelsetbio.BioResolver
kvec - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader

## L

LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
LABEL - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
label - Static variable in class org.jmol.script.T
label - Variable in class org.jmol.shapespecial.Ellipsoid
label1 - Variable in class org.jmol.console.GenericConsole
label_anchor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
label_angle_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
LABEL_CENTERED - Static variable in class org.jmol.viewer.JC
label_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
LABEL_DEFAULT_OFFSET - Static variable in class org.jmol.viewer.JC
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JC
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JC
label_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
label_dihedral_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
label_distance_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
LABEL_EXPLICIT - Static variable in class org.jmol.viewer.JC
LABEL_FLAGS - Static variable in class org.jmol.viewer.JC
LABEL_FLAGX_OFFSET_SHIFT - Static variable in class org.jmol.viewer.JC
LABEL_FLAGY_OFFSET_SHIFT - Static variable in class org.jmol.viewer.JC
label_font_id - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
LABEL_OFFSET_MASK - Static variable in class org.jmol.viewer.JC
LABEL_OFFSET_MAX - Static variable in class org.jmol.viewer.JC
label_outline_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
LABEL_POINTER_BACKGROUND - Static variable in class org.jmol.viewer.JC
LABEL_POINTER_FLAGS - Static variable in class org.jmol.viewer.JC
LABEL_POINTER_NONE - Static variable in class org.jmol.viewer.JC
LABEL_POINTER_ON - Static variable in class org.jmol.viewer.JC
label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
label_shadow_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
label_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
LABEL_ZPOS_FLAGS - Static variable in class org.jmol.viewer.JC
LABEL_ZPOS_FRONT - Static variable in class org.jmol.viewer.JC
LABEL_ZPOS_GROUP - Static variable in class org.jmol.viewer.JC
labelAsymList - Variable in class org.jmol.adapter.readers.cif.MMTFReader
labelBoxes - Variable in class org.jmol.shape.Labels
labelColix - Variable in class org.jmol.modelset.Measurement
labelColix - Variable in class org.jmol.render.LabelsRenderer
labelColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
labeler - Variable in class org.jmol.modelset.AtomCollection
labelFontId - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
labelFormat - Variable in class org.jmol.shape.Hover
labelMode - Variable in class org.jmol.viewer.ActionManager
labelPosition - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
labelPosition0 - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
labels - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
labels - Static variable in class org.jmol.console.GenericConsole
labels - Variable in class org.jmol.dssx.DSSP
labels - Variable in class org.jmol.jvxl.readers.MrcBinaryReader
labels - Variable in class org.jmol.shape.Axes
Labels - Class in org.jmol.shape
Labels() - Constructor for class org.jmol.shape.Labels
labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
labelSize - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
LabelsRenderer - Class in org.jmol.render
LabelsRenderer() - Constructor for class org.jmol.render.LabelsRenderer
labelsXn - Static variable in class org.jmol.symmetry.SymmetryOperation
labelsXnSub - Static variable in class org.jmol.symmetry.SymmetryOperation
labelsXYZ - Static variable in class org.jmol.symmetry.SymmetryOperation
LabelToken - Class in org.jmol.modelset
LabelToken() - Constructor for class org.jmol.modelset.LabelToken
labelTokenIds - Static variable in class org.jmol.modelset.LabelToken
labelTokenParams - Static variable in class org.jmol.modelset.LabelToken
ladder - Variable in class org.jmol.dssx.Bridge
language - Variable in class org.jmol.i18n.GT
Language - Class in org.jmol.i18n
Language(String, String, String, boolean) - Constructor for class org.jmol.i18n.Language
language - Variable in class org.jmol.i18n.Language
language - Static variable in class org.jmol.script.T
language - Variable in class org.jmol.util.GenericApplet
language - Static variable in class org.openscience.jmol.app.jmolpanel.GuiMap
languageList - Static variable in class org.jmol.i18n.GT
languagetranslation - Static variable in class org.jmol.script.T
last - Variable in class org.jmol.awtjs.swing.JPanel
last - Static variable in class org.jmol.script.T
LAST - Static variable in class org.jmol.util.MeshCapper
LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.C
lastAltLoc - Variable in class org.jmol.adapter.readers.cif.CifReader
lastAltLoc - Variable in class org.jmol.adapter.readers.pdb.PdbReader
lastAssignedString - Variable in class org.jmol.script.ScriptMathProcessor
lastAtom - Variable in class org.jmol.jvxl.readers.KinemageReader
lastAtomIndex - Variable in class org.jmol.modelset.Group
lastBasisID - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
lastCenter - Variable in class org.jmol.modelkit.ModelKitPopup
lastChainAtom - Variable in class org.jmol.smiles.SmilesSearch
lastColix - Variable in class org.jmol.util.MeshSurface
lastColor - Variable in class org.jmol.util.MeshSurface
lastConnections - Variable in class org.jmol.viewer.StateManager
lastContext - Variable in class org.jmol.viewer.StateManager
lastCoordinates - Variable in class org.jmol.viewer.StateManager
lastData - Variable in class org.jmol.viewer.Viewer
lastDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
lastDisorderAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
lastElement - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
lastElement() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
lastError - Static variable in exception org.jmol.smiles.InvalidSmilesException
lastFlowCommand - Variable in class org.jmol.script.ScriptTokenParser
lastFrameDelay - Variable in class org.jmol.viewer.AnimationManager
lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
lastFrameIndex - Variable in class org.jmol.viewer.AnimationManager
lastFramePainted - Variable in class org.jmol.viewer.AnimationManager
lastFullPathName - Variable in class org.jmol.viewer.FileManager
lastGaussianPtr - Variable in class org.jmol.quantum.MOCalculation
lastGroup - Variable in class org.jmol.adapter.readers.cif.MMTFReader
lastGroup - Variable in class org.jmol.adapter.readers.pdb.PdbReader
lastIndex - Variable in class org.jmol.modelset.MeasurementPending
lastIndex - Variable in class org.jmol.symmetry.CIPDataTracker
lastInfo - Variable in class org.jmol.symmetry.CIPDataTracker
lastInfo - Static variable in class org.jmol.symmetry.SpaceGroup
lastInsertion - Variable in class org.jmol.adapter.readers.pdb.PdbReader
lastLogTime - Variable in class org.jmol.multitouch.ActionManagerMT
lastMark - Variable in class org.jmol.adapter.readers.pymol.PickleReader
lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
lastModel - Variable in class org.jmol.jsv.JDXMOLParser
lastModelIndex - Variable in class org.jmol.atomdata.AtomData
lastModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
lastModelPainted - Variable in class org.jmol.viewer.AnimationManager
lastModelSet - Variable in class org.jmol.modelkit.ModelKitPopup
lastMotionEventNumber - Variable in class org.jmol.applet.Jmol
lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
lastName - Variable in class org.jmol.adapter.readers.xtal.CgdReader
lastNameAsGiven - Variable in class org.jmol.viewer.FileManager
lastOffset - Variable in class org.jmol.modelkit.ModelKitPopup
lastOpened - Static variable in class org.jmol.console.ScriptEditor
lastOrientation - Variable in class org.jmol.viewer.StateManager
lastPicked - Variable in class org.jmol.shape.Labels
lastPressTime - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
lastQPt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
lastRawColor - Variable in class org.jmol.g3d.Graphics3D
lastRepaintTime - Variable in class org.jmol.thread.JmolThread
lastScene - Variable in class org.jmol.viewer.StateManager
lastSelected - Variable in class org.jmol.viewer.StateManager
lastSequenceNumber - Variable in class org.jmol.adapter.readers.more.Mol2Reader
lastSetH - Variable in class org.jmol.modelsetbio.BioResolver
lastShape - Variable in class org.jmol.viewer.StateManager
lastSimulate - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
lastSourceSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
lastSpaceGroupName - Variable in class org.jmol.adapter.readers.cif.CifReader
lastState - Variable in class org.jmol.viewer.StateManager
lastTargetSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
lastToken - Variable in class org.jmol.script.ScriptTokenParser
latestMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
LATT - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
lattice - Static variable in class org.jmol.script.T
lattice - Variable in class org.jmol.shape.Mesh
LATTICE_VECTOR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
latticeCells - Variable in class org.jmol.adapter.smarter.XtalSymmetry
latticeCode - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
latticeCode - Variable in class org.jmol.symmetry.HallInfo
latticeConstant - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
latticeExtension - Variable in class org.jmol.symmetry.HallInfo
latticeOffset - Variable in class org.jmol.render.MeshRenderer
latticeOnly - Variable in class org.jmol.adapter.smarter.XtalSymmetry
latticeOp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
latticeOp - Variable in class org.jmol.symmetry.SpaceGroup
latticeParameter - Variable in class org.jmol.symmetry.SpaceGroup
latticePts - Variable in class org.jmol.util.BZone
latticeScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
latticeTranslationData - Static variable in class org.jmol.symmetry.HallTranslation
latticeType - Variable in class org.jmol.adapter.readers.cif.CifReader
latticeType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
latticeType - Variable in class org.jmol.symmetry.SpaceGroup
latticeType - Variable in class org.jmol.symmetry.SymmetryInfo
latticeUnits - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
latticeVectorPtr - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
lattvecs - Variable in class org.jmol.adapter.readers.cif.CifReader
lattvecs - Variable in class org.jmol.adapter.readers.xtal.JanaReader
LayoutManager - Class in org.jmol.awtjs.swing
LayoutManager() - Constructor for class org.jmol.awtjs.swing.LayoutManager
layoutWindow(String) - Method in class org.jmol.console.AppletConsole
layoutWindow(String) - Method in class org.jmol.console.GenericConsole
layoutWindow(Container) - Method in class org.jmol.console.ScriptEditor
layoutWindow(String) - Method in class org.jmol.consolejs.AppletConsole
layoutWindow(Container) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
lcaocartoon - Static variable in class org.jmol.script.T
lcaoCartoon() - Method in class org.jmol.scriptext.IsoExt
LcaoCartoon - Class in org.jmol.shapesurface
LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
LcaoCartoonRenderer - Class in org.jmol.rendersurface
LcaoCartoonRenderer() - Constructor for class org.jmol.rendersurface.LcaoCartoonRenderer
lcaoColorNeg - Variable in class org.jmol.shapesurface.LcaoCartoon
lcaoColorPos - Variable in class org.jmol.shapesurface.LcaoCartoon
lcaoDir - Variable in class org.jmol.shapesurface.Isosurface
lcaoID - Variable in class org.jmol.shapesurface.LcaoCartoon
lcaoScale - Variable in class org.jmol.shapesurface.LcaoCartoon
lcaoTranslucent - Variable in class org.jmol.shapesurface.LcaoCartoon
lcaoTranslucentLevel - Variable in class org.jmol.shapesurface.LcaoCartoon
lcaoType - Variable in class org.jmol.jvxl.readers.Parameters
leadatom - Static variable in class org.jmol.script.T
leadAtomIndex - Variable in class org.jmol.modelset.Group
leadAtomIndices - Variable in class org.jmol.modelsetbio.BioPolymer
leadAtomIndices - Variable in class org.jmol.renderbio.BioShapeRenderer
leadAtomIndices - Variable in class org.jmol.shapebio.BioShape
LEADER_CHAR_MAX - Static variable in class org.jmol.adapter.smarter.Resolver
leadMidpoints - Variable in class org.jmol.modelsetbio.BioPolymer
leadPoints - Variable in class org.jmol.modelsetbio.BioPolymer
leaf - Variable in class org.jmol.bspt.CubeIterator
Leaf - Class in org.jmol.bspt
  A leaf of Point3f objects in the bsp tree
Leaf(Bspt, Leaf, int) - Constructor for class org.jmol.bspt.Leaf
leafCountMax - Static variable in class org.jmol.bspt.Bspt
leafIndex - Variable in class org.jmol.bspt.CubeIterator
left - Variable in class org.jmol.awtjs.swing.Insets
left - Variable in class org.jmol.awtjs.swing.JSplitPane
LEFT - Static variable in class org.jmol.awtjs.swing.SwingConstants
left - Static variable in class org.jmol.script.T
left - Variable in class org.jmol.util.Modulation
LEFT - Static variable in class org.jmol.viewer.binding.Binding
LEFT_CLICKED - Variable in class org.jmol.viewer.ActionManager
LEFT_DRAGGED - Variable in class org.jmol.viewer.ActionManager
leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
leftbrace - Static variable in class org.jmol.script.T
leftdivide - Static variable in class org.jmol.script.T
leftOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
leftparen - Static variable in class org.jmol.script.T
leftPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
leftsquare - Static variable in class org.jmol.script.T
LEG_DISP_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_DISP_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_DISP_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_DISP_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_OCC_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_OCC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_OCC_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_U_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_U_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_U_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
LEG_U_TENS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
legacy_mouse_zoom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
legacy_vdw_radii - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
legacyautobonding - Static variable in class org.jmol.script.T
legacyAutoBonding - Variable in class org.jmol.viewer.GlobalSettings
legacyhaddition - Static variable in class org.jmol.script.T
legacyHAddition - Variable in class org.jmol.viewer.GlobalSettings
legacyjavafloat - Static variable in class org.jmol.script.T
legacyJavaFloat - Variable in class org.jmol.viewer.GlobalSettings
legendre - Static variable in class org.jmol.util.Modulation
legendres - Variable in class org.jmol.adapter.readers.cif.MSRdr
LEN - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
length() - Method in interface org.jmol.api.GenericFileInterface
length() - Method in class org.jmol.awtjs2d.JSFile
length - Static variable in class org.jmol.script.T
length - Variable in class org.jmol.shapespecial.Draw
length - Variable in class org.openscience.jvxl.MonitorInputStream
lengths - Variable in class org.jmol.shapespecial.Ellipsoid
lengthsFreeEnum - Variable in class org.jmol.util.TempArray
lengthsFreePoints - Variable in class org.jmol.util.TempArray
lengthsFreeScreens - Variable in class org.jmol.util.TempArray
lengthUnitFactors - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
lengthUnitIds - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
lenLine - Variable in class org.jmol.adapter.readers.more.MdCrdReader
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
LEVEL_INFO - Static variable in class org.jmol.util.Logger
LEVEL_MAX - Static variable in class org.jmol.util.Logger
LEVEL_WARN - Static variable in class org.jmol.util.Logger
ligandModels - Variable in class org.jmol.viewer.Viewer
ligandModelSet - Variable in class org.jmol.viewer.Viewer
light - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light3 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light4 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light5 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light6 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light7 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light8 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light9 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
light_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
lighting - Variable in class org.jmol.export._TachyonExporter
lighting - Static variable in class org.jmol.script.T
lighting - Variable in class org.jmol.shape.Mesh
lighting - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
lightSource - Variable in class org.jmol.export.___Exporter
lightSource - Variable in class org.jmol.util.Shader
LIME - Static variable in class org.jmol.util.C
line - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
line - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
line - Variable in class org.jmol.jsv.JDXMOLParser
line - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
line - Variable in class org.jmol.jvxl.readers.XmlReader
line - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
line - Static variable in class org.jmol.script.T
line0 - Variable in class org.jmol.script.ScriptFlowContext
line3d - Variable in class org.jmol.g3d.CylinderRenderer
line3d - Variable in class org.jmol.g3d.Graphics3D
line_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
line_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
line_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
line_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
line_stick_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
line_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
line_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
linearCombination - Variable in class org.jmol.jvxl.readers.IsoMOReader
linearCombination - Variable in class org.jmol.quantum.MOCalculation
linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
linearRotTrans - Variable in class org.jmol.symmetry.SymmetryOperation
linearSearch() - Method in class org.jmol.minimize.forcefield.ForceField
linearTolerance - Variable in class org.jmol.symmetry.PointGroup
lineBits - Variable in class org.jmol.g3d.LineRenderer
lineBuffer - Variable in class org.jmol.adapter.readers.simple.InputReader
lineCache - Variable in class org.jmol.g3d.LineRenderer
lineCurrent - Variable in class org.jmol.script.ScriptTokenParser
linedata - Static variable in class org.jmol.script.T
lineData - Variable in class org.jmol.shape.Mesh
lineData - Variable in class org.jmol.shapespecial.Draw
lineEnd - Variable in class org.jmol.script.ScriptContext
lineEnd - Variable in class org.jmol.script.ScriptEval
lineHeight - Variable in class org.jmol.modelset.Text
lineheight - Variable in class org.jmol.render.UccageRenderer
lineIndices - Variable in class org.jmol.script.ScriptCompiler
lineIndices - Variable in class org.jmol.script.ScriptContext
lineIndices - Variable in class org.jmol.script.ScriptEval
lineIndices - Variable in class org.jmol.script.ScriptFunction
lineLength - Variable in class org.jmol.adapter.readers.pdb.PdbReader
lineNumbers - Variable in class org.jmol.script.ScriptCompiler
lineNumbers - Variable in class org.jmol.script.ScriptContext
lineNumbers - Variable in class org.jmol.script.ScriptEval
lineNumbers - Variable in class org.jmol.script.ScriptFunction
lineOptions - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
linePt - Variable in class org.jmol.jvxl.readers.XplorReader
LineRenderer - Class in org.jmol.g3d
LineRenderer(Graphics3D) - Constructor for class org.jmol.g3d.LineRenderer
lines - Variable in class org.jmol.modelset.Text
lines - Static variable in class org.jmol.script.T
lineStart - Variable in class org.jmol.script.ScriptFlowContext
lineStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
lineTo(Object, int, int) - Method in interface org.jmol.api.GenericGraphics
lineTo(Object, int, int) - Method in class org.jmol.awt.AwtG2D
lineTo(Object, int, int) - Method in class org.jmol.awtjs2d.JsG2D
lineTypeX - Variable in class org.jmol.g3d.LineRenderer
LINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
lineWidthMad - Variable in class org.jmol.export.___Exporter
link - Static variable in class org.jmol.script.T
link(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
  Link this vertex with v or remove it from the chain.
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
  Opens a web page in an external browser
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
  Follows the reference in an link.
linkedMesh - Variable in class org.jmol.shape.Mesh
linkedMesh - Variable in class org.jmol.shape.MeshCollection
list - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
list - Variable in class org.jmol.awtjs.swing.Container
list - Variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
list - Static variable in class org.jmol.script.T
listAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
listBS(BS) - Method in class org.jmol.script.ScriptExpr
listCommands - Variable in class org.jmol.script.ScriptEval
listCommands - Variable in class org.jmol.viewer.Viewer
listCompositions() - Method in class org.jmol.adapter.readers.more.AFLOWReader
listeners - Variable in class org.jmol.viewer.SelectionManager
listf - Static variable in class org.jmol.script.T
listIsosurface(int) - Method in class org.jmol.scriptext.IsoExt
listKey - Variable in class org.jmol.adapter.readers.more.AFLOWReader
listKeyCase - Variable in class org.jmol.adapter.readers.more.AFLOWReader
listLabel - Variable in class org.openscience.jmol.app.webexport.WebPanel
listParameter(int, int, int) - Method in class org.jmol.script.ScriptParam
listParameter4(int, int, int, boolean) - Method in class org.jmol.script.ScriptParam
listPt - Variable in class org.jmol.symmetry.UnitCellIterator
listRS - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  bitsets for tracking R and S for Rule 4b
listSavedStates() - Method in class org.jmol.viewer.StateManager
ListSelectionModel - Interface in org.jmol.awtjs.swing
listToMap(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
  return a map of lists of the type: [ [name1,...], [name2,...], ...]
listToSettings(Lst<Object>, Map<Integer, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
lltoken - Variable in class org.jmol.script.ScriptCompiler
lnLength - Variable in class org.jmol.script.ScriptCompiler
lo - Variable in class org.jmol.util.ColorEncoder
load - Static variable in class org.jmol.script.T
load() - Method in class org.openscience.jmol.app.HistoryFile
  Loads properties from the history file.
LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JC
loadAtomDataAndReturnError(Object, int) - Method in class org.jmol.viewer.Viewer
  or just apply the data to the current model set
loadatomdatatolerance - Static variable in class org.jmol.script.T
loadAtomDataTolerance - Variable in class org.jmol.viewer.GlobalSettings
loadButton - Variable in class org.jmol.console.GenericConsole
loadButton - Variable in class org.jmol.console.ScriptEditor
loadContent(String) - Method in interface org.jmol.api.JmolDropEditor
loadContent(String) - Method in class org.jmol.console.ScriptEditor
loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
loadCoordinates(String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
loadDOMNode(Object) - Method in interface org.jmol.api.JmolAppletInterface
loadDOMNode(Object) - Method in class org.jmol.applet.JmolApplet
loadDOMNode(Object) - Method in class org.jmol.util.GenericApplet
loadDssr(int, String) - Method in class org.jmol.script.ScriptEval
loader - Variable in class org.jmol.jsv.JDXMOLParser
loadFile(String) - Method in interface org.jmol.api.JmolDropEditor
loadFile(String, int, int) - Method in class org.jmol.awt.FileDropper
loadFile(String) - Method in class org.jmol.console.ScriptEditor
loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
loadFileAsync(String, String, int, boolean) - Method in class org.jmol.script.ScriptEval
  Allows asynchronous file loading from the LOAD or SCRIPT command.
loadFileResourceAsync(String) - Method in interface org.jmol.api.JmolScriptEvaluator
loadFileResourceAsync(String) - Method in class org.jmol.script.ScriptEval
  load a static file asynchronously
loadFiles(List<File>) - Method in class org.jmol.awt.FileDropper
loadformat - Static variable in class org.jmol.script.T
loadFormat - Variable in class org.jmol.viewer.GlobalSettings
loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
loadImage(GenericPlatform, String, String, byte[], Object) - Method in interface org.jmol.api.js.JmolToJSmolInterface
loadImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
  Load an image
loadImageData(Object, String, String, ScriptContext) - Method in class org.jmol.viewer.Viewer
  NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage
loading - Variable in class org.jmol.util.GenericApplet
loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
  Deprecated.
loadInline(String) - Method in class org.jmol.api.JmolViewer
loadInline(String, char) - Method in class org.jmol.api.JmolViewer
loadInline(String[]) - Method in class org.jmol.api.JmolViewer
loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
loadInline(List<Object>, boolean) - Method in class org.jmol.api.JmolViewer
  NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
loadInline(String) - Method in class org.jmol.applet.JmolApplet
  Deprecated.
loadInline(String, String) - Method in class org.jmol.applet.JmolApplet
  Deprecated.
loadInline(String[]) - Method in class org.jmol.applet.JmolApplet
  Deprecated.
loadInline(String[], String) - Method in class org.jmol.applet.JmolApplet
  Deprecated.
loadInline(String) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String, String) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String[]) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String[], String) - Method in class org.jmol.util.GenericApplet
  Deprecated.
loadInline(String) - Method in class org.jmol.viewer.Viewer
  from Applet and external applications only
loadInline(String, char) - Method in class org.jmol.viewer.Viewer
  external apps only
loadInline(String[]) - Method in class org.jmol.viewer.Viewer
  external apps only
loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
  external apps and applet only
loadInline(List<Object>, boolean) - Method in class org.jmol.viewer.Viewer
  External applications only; does not preserve state -- intentionally!
loadInlineAppend(String, boolean) - Method in class org.jmol.api.JmolViewer
loadInlineAppend(String, boolean) - Method in class org.jmol.viewer.Viewer
  used by applet and console
loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
loadInlineArray(String[], String, boolean) - Method in class org.jmol.applet.JmolApplet
loadInlineArray(String[], String, boolean) - Method in class org.jmol.util.GenericApplet
loadInlineScript(String, char, boolean, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
  used by loadInline and openFileFull
loadInlineScriptRepaint(String, char, boolean) - Method in class org.jmol.viewer.Viewer
loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
loadInlineString(String, String, boolean) - Method in class org.jmol.applet.JmolApplet
loadInlineString(String, String, boolean) - Method in class org.jmol.util.GenericApplet
loadligandformat - Static variable in class org.jmol.script.T
loadModelFromFile(String, String, String[], Object, boolean, Map<String, Object>, SB, SB, int, String) - Method in class org.jmol.viewer.Viewer
  Used by the ScriptEvaluator LOAD command to open one or more files.
loadModelFromFileRepaint(String, String, String[], Object) - Method in class org.jmol.viewer.Viewer
  for JmolSimpleViewer -- external applications only (and no-script JavaScript)
loadNote - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
loadPNGJVar(String, Object, Map<String, Object>) - Method in class org.jmol.script.ScriptEval
loadScript - Variable in class org.jmol.modelset.Model
loadShape(int) - Method in class org.jmol.viewer.ShapeManager
loadState - Variable in class org.jmol.modelset.Model
loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
lobe - Static variable in class org.jmol.script.T
loc - Variable in class org.jmol.awtjs.swing.JDialog
localAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
localAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
localArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
localArrayListType - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
localEnvOnly - Variable in class org.jmol.symmetry.PointGroup
localFunctions - Variable in class org.jmol.viewer.Viewer
localize(boolean, Properties) - Method in class org.jmol.popup.PopupResource
localSpaceGroupName - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
lock - Variable in class org.jmol.script.ScriptParallelProcessor
log(String) - Method in class org.jmol.adapter.readers.pymol.PickleReader
log(String) - Method in interface org.jmol.atomdata.AtomDataServer
log(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
log(String) - Method in class org.jmol.minimize.forcefield.ForceField
log - Static variable in class org.jmol.script.T
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
  Method to output a log.
log(String) - Method in class org.jmol.viewer.Viewer
log(String) - Static method in class org.openscience.jmol.app.webexport.LogPanel
log_box_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
log_conformations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
logArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
logcommands - Static variable in class org.jmol.script.T
logCommands - Variable in class org.jmol.viewer.GlobalSettings
logCompression - Variable in class org.jmol.jvxl.readers.Parameters
logCube - Variable in class org.jmol.jvxl.readers.Parameters
logData - Variable in class org.jmol.minimize.forcefield.Calculations
logDebugScript(T[], int) - Method in class org.jmol.script.ScriptEval
logEvent(String, P3) - Method in class org.jmol.multitouch.ActionManagerMT
logfile - Static variable in class org.jmol.script.T
logFileName - Variable in class org.jmol.viewer.Viewer
logFilePath - Variable in class org.jmol.viewer.Viewer
Logger - Class in org.jmol.util
  Logger mechanism.
Logger() - Constructor for class org.jmol.util.Logger
LoggerInterface - Interface in org.jmol.util
  Interface used for the logging mechanism.
loggestures - Static variable in class org.jmol.script.T
logGestures - Variable in class org.jmol.viewer.GlobalSettings
logging - Variable in class org.jmol.adapter.readers.pymol.PickleReader
logging - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
logging - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
logging - Variable in class org.jmol.minimize.forcefield.Calculations
loggingEnabled - Variable in class org.jmol.minimize.forcefield.Calculations
loglevel - Static variable in class org.jmol.script.T
logLevel() - Static method in class org.jmol.util.Logger
  Indicates if the level is logged.
logLoadInfo(String) - Method in class org.jmol.script.ScriptEval
logMessages - Variable in class org.jmol.jvxl.readers.Parameters
logMessages - Variable in class org.jmol.script.ScriptTokenParser
LogPanel - Class in org.openscience.jmol.app.webexport
LogPanel() - Constructor for class org.openscience.jmol.app.webexport.LogPanel
logToFile(String) - Method in class org.jmol.viewer.OutputManager
lonepair - Static variable in class org.jmol.script.T
LONG - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
LONG_BINGET - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
LONG_BINPUT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
lookForSyncID() - Method in class org.jmol.script.ScriptCompiler
  Check for a set of characters that does not start with double quote or at-sign and terminates with #, }, or an end of line.
lookingAtBitset() - Method in class org.jmol.script.ScriptCompiler
lookingAtComment() - Method in class org.jmol.script.ScriptCompiler
lookingAtDecimal() - Method in class org.jmol.script.ScriptCompiler
lookingAtEndOfLine() - Method in class org.jmol.script.ScriptCompiler
  Look for end of script or a new line.
lookingAtExponential() - Method in class org.jmol.script.ScriptCompiler
lookingAtImpliedString(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
  An "implied string" is a parameter that is not quoted but because of its position in a command is implied to be a string.
lookingAtInteger() - Method in class org.jmol.script.ScriptCompiler
lookingAtLeadingWhitespace() - Method in class org.jmol.script.ScriptCompiler
lookingAtLoadFormat(boolean) - Method in class org.jmol.script.ScriptCompiler
lookingAtLookupToken(int) - Method in class org.jmol.script.ScriptCompiler
lookingAtMathContinuation(int) - Method in class org.jmol.script.ScriptCompiler
lookingAtMatrix() - Method in class org.jmol.script.ScriptCompiler
lookingAtObjectID() - Method in class org.jmol.script.ScriptCompiler
  Look for a valid $...
lookingAtSeqcode() - Method in class org.jmol.script.ScriptCompiler
lookingAtSetBraceSyntax() - Method in class org.jmol.script.ScriptCompiler
  look for '{' at the start of a command, allowing for syntaxes {xxx}.yyy = ...
lookingAtString(boolean) - Method in class org.jmol.script.ScriptCompiler
  look for a quoted string, possibly allowing single quotes.
lookingAtTerminator() - Method in class org.jmol.script.ScriptCompiler
  Look for valid terminating semicolon -- one not within for(), for example.
lookup(String) - Static method in class org.jmol.symmetry.HallRotation
lookupCode - Variable in class org.jmol.symmetry.HallRotationTerm
lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEval
lookupInterpolatedVoxelValue(T3, boolean) - Method in class org.jmol.jvxl.data.VolumeData
lookupSpecialAtomID(String) - Method in class org.jmol.modelsetbio.BioResolver
lookupValue(String, boolean) - Method in class org.jmol.script.ScriptEval
loop - Static variable in class org.jmol.script.T
LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
LOW - Static variable in class org.jmol.util.ColorEncoder
lowdenCharges - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
lp - Static variable in class org.jmol.script.T
lstCoords - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
lstDipoles - Variable in class org.jmol.shapespecial.Dipole
lstGaussians - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
lstMatrix - Variable in class org.jmol.export._StlExporter
lstNCS - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
lstRegions - Variable in class org.jmol.util.MeshCapper
  dynamic region processing.
lstSmallRings - Variable in class org.jmol.symmetry.CIPData
  all 3- to 7-membered rings; used to exclude E/Z and N-SP3 descriptors
lstStates - Variable in class org.jmol.util.CommandHistory
lstTriangles - Variable in class org.jmol.util.MeshCapper
ltoken - Variable in class org.jmol.script.ScriptCompiler
ltokenPostfix - Variable in class org.jmol.script.ScriptTokenParser
lumo - Static variable in class org.jmol.script.T
lumoEnergy - Variable in class org.jmol.adapter.readers.quantum.JaguarReader

## M

m - Variable in class org.jmol.export._IdtfExporter
m - Variable in class org.jmol.render.MeasuresRenderer
m - Variable in class org.jmol.util.MeshSlicer
m2_rotate - Variable in class org.jmol.viewer.TransformManager4D
m3 - Variable in class org.jmol.util.MeshCapper
m3_toScreen - Variable in class org.jmol.viewer.TransformManager4D
m3dStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
m3inv - Variable in class org.jmol.util.MeshCapper
m4 - Variable in class org.jmol.export._StlExporter
m4 - Variable in class org.jmol.thread.SpinThread
m4 - Variable in class org.jmol.viewer.TransformManager4D
m4a - Variable in class org.jmol.export._StlExporter
MAC_COMMAND - Static variable in class org.jmol.awtjs.Event
MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
macro - Static variable in class org.jmol.script.T
macro() - Method in class org.jmol.scriptext.CmdExt
macrodirectory - Static variable in class org.jmol.script.T
macroDirectory - Variable in class org.jmol.viewer.GlobalSettings
macros - Static variable in class org.jmol.viewer.JC
macros - Variable in class org.jmol.viewer.Viewer
mad - Variable in class org.jmol.modelset.Bond
mad - Variable in class org.jmol.modelset.Measurement
mad - Variable in class org.jmol.modelset.MeasurementData
mad - Variable in class org.jmol.render.ShapeRenderer
mad - Variable in class org.jmol.renderbio.RocketRenderer
mad - Variable in class org.jmol.shape.AtomShape
mad - Variable in class org.jmol.shapespecial.Dipole
mad - Variable in class org.jmol.shapespecial.Dipoles
mad - Variable in class org.jmol.viewer.Connection
mad0 - Variable in class org.jmol.render.MeasuresRenderer
MAD_GLOBAL - Static variable in class org.jmol.modelset.Atom
madAtom - Variable in class org.jmol.modelset.Atom
madBeg - Variable in class org.jmol.renderbio.BioShapeRenderer
madDnaRna - Variable in class org.jmol.shapebio.BioShapeCollection
madEnd - Variable in class org.jmol.renderbio.BioShapeRenderer
madHelixSheet - Variable in class org.jmol.shapebio.BioShapeCollection
madMid - Variable in class org.jmol.renderbio.BioShapeRenderer
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JC
madOn - Variable in class org.jmol.shapebio.BioShapeCollection
mads - Variable in class org.jmol.geodesic.EnvelopeCalculation
mads - Variable in class org.jmol.renderbio.BioShapeRenderer
mads - Variable in class org.jmol.shape.AtomShape
madTurnRandom - Variable in class org.jmol.shapebio.BioShapeCollection
mag2d - Variable in class org.jmol.render.SticksRenderer
magCenterings - Variable in class org.jmol.adapter.readers.cif.CifReader
magCifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MAGENTA - Static variable in class org.jmol.util.C
MAGNETIC_SUSCEPTIBILITY_FACTOR - Static variable in class org.jmol.util.Tensor
magneticshielding - Static variable in class org.jmol.script.T
MAGNETOGYRIC_RATIO - Static variable in class org.jmol.quantum.NMRCalculation
magOp - Variable in class org.jmol.symmetry.SymmetryOperation
magresFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MagresReader - Class in org.jmol.adapter.readers.xtal
MagresReader() - Constructor for class org.jmol.adapter.readers.xtal.MagresReader
magresUnits - Variable in class org.jmol.adapter.readers.xtal.MagresReader
MAIN - Static variable in class org.jmol.thread.JmolThread
main(String[]) - Static method in class org.openscience.jmol.app.Jmol
main(String[]) - Static method in class org.openscience.jmol.app.JmolData
main(String[]) - Static method in class org.openscience.jvxl.Jvxl
main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
MainPopupResourceBundle - Class in org.jmol.popup
MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
majorVersion - Static variable in class org.jmol.viewer.JC
makeBonds(String[][], boolean) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
makeColorScheme(String, int[], boolean) - Method in class org.jmol.util.ColorEncoder
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
makeConnections2(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
makeNewAtomSet() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
makePlane(float, float, float, P4) - Static method in class org.openscience.jmol.app.surfacetool.Slice
makePoints - Variable in class org.jmol.shapespecial.Draw
manager - Variable in class org.jmol.awt.Mouse
manager - Variable in class org.jmol.awtjs2d.Mouse
manager - Variable in class org.jmol.util.Font
manifest - Static variable in class org.jmol.script.T
mantissa(float) - Method in class org.jmol.jvxl.data.VolumeData
map - Variable in class org.jmol.adapter.readers.cif.MMTFReader
map(Object, String, String, Map<String, Object>) - Static method in class org.jmol.console.GenericConsole
map - Variable in class org.jmol.console.ScriptEditor
map - Variable in class org.jmol.quantum.MOCalculation
map - Variable in class org.jmol.viewer.PropertyManager
map - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
map0 - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping Cartesian origin, X, and Y
map_auto_expand_sym - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mapAddKey(String) - Method in class org.jmol.util.JSONWriter
mapAddKeyValue(String, Object, String) - Method in class org.jmol.util.JSONWriter
mapAddKeyValueRaw(String, Object, String) - Method in class org.jmol.util.JSONWriter
  Add a key:value pair where value is already quoted
mapAddMapAllExcept(String, Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
mapAtomResIDs(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
  Map all atom and residue unit ids to atom indexes
mapc - Variable in class org.jmol.jvxl.readers.MapFileReader
mapClose() - Method in class org.jmol.util.JSONWriter
MapFileReader - Class in org.jmol.jvxl.readers
MapFileReader() - Constructor for class org.jmol.jvxl.readers.MapFileReader
mapGet(String) - Method in class org.jmol.script.SV
mapIndex - Variable in class org.jmol.smiles.SmilesAtom
mapLattice - Variable in class org.jmol.jvxl.data.JvxlData
mapLattice - Variable in class org.jmol.jvxl.readers.Parameters
mapObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
mapOpen() - Method in class org.jmol.util.JSONWriter
mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
mappedDataMax - Variable in class org.jmol.jvxl.readers.Parameters
mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
mappedDataMin - Variable in class org.jmol.jvxl.readers.Parameters
mappingPlane - Variable in class org.jmol.jvxl.calc.MarchingCubes
mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
mappingPlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
mapproperty - Static variable in class org.jmol.script.T
mapProperty() - Method in class org.jmol.scriptext.CmdExt
mapPut(String, SV) - Method in class org.jmol.script.SV
mapr - Variable in class org.jmol.jvxl.readers.MapFileReader
mapRtoA - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
maps - Variable in class org.jmol.jvxl.readers.MapFileReader
mapSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
mapT - Variable in class org.jmol.geodesic.EnvelopeCalculation
mapUnique - Variable in class org.jmol.smiles.SmilesSearch
mapValue(String) - Method in class org.jmol.script.SV
mapWidth - Variable in class org.jmol.g3d.TextRenderer
mar - Variable in class org.jmol.render.StarsRenderer
marBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
MarchingCubes - Class in org.jmol.jvxl.calc
MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
MarchingCubes(VertexDataServer, VolumeData, Parameters, BS) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
MarchingSquares - Class in org.jmol.jvxl.calc
MarchingSquares(VertexDataServer, VolumeData, P4, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
MarchingSquares.ContourVertex - Class in org.jmol.jvxl.calc
MarchingSquares.Triangle - Class in org.jmol.jvxl.calc
margin - Variable in class org.jmol.jvxl.readers.AtomDataReader
margin - Variable in class org.jmol.util.BoxInfo
MARK - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
mark(int) - Method in class org.openscience.jvxl.MonitorInputStream
markCount - Variable in class org.jmol.adapter.readers.pymol.PickleReader
markFaceVoxels(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
markLines(String, char) - Static method in class org.jmol.util.Parser
markPlaneVoxels(P3, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
markPosition - Variable in class org.openscience.jvxl.MonitorInputStream
marks - Variable in class org.jmol.adapter.readers.pymol.PickleReader
markSphereVoxels(float, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
markToroidVoxels() - Method in class org.jmol.jvxl.readers.IsoSolventReader
MAROON - Static variable in class org.jmol.util.C
MASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MASMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mass - Static variable in class org.jmol.script.T
mass - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  Rule 2 isotope mass number if identified or average atomic mass if not C (12.011) > 12C, O (15.999) < 16O, and F (18.998) < 19F Source:
mat - Variable in class org.jmol.g3d.SphereRenderer
mat - Variable in class org.jmol.renderbio.BioMeshRenderer
mat - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
mat4 - Variable in class org.jmol.modelset.Model
  mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
mat4 - Variable in class org.jmol.modelset.ModelSet
mat4 - Variable in class org.jmol.util.MeshSurface
mat4t - Variable in class org.jmol.modelset.ModelSet
match(String) - Method in class org.jmol.symmetry.CIPData
  Return a bit set corresponding to a SMARTS
match(String) - Method in class org.jmol.symmetry.CIPDataSmiles
matchingBond - Variable in class org.jmol.smiles.SmilesBond
matchingComponent - Variable in class org.jmol.smiles.SmilesAtom
matchingIndex - Variable in class org.jmol.smiles.SmilesAtom
matchingNode - Variable in class org.jmol.smiles.SmilesAtom
matchPriv(String, Node[], int, BS, BS, boolean, int, int) - Method in class org.jmol.smiles.SmilesMatcher
matEllipsoidToScreen - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
mathExpressionCommand - Static variable in class org.jmol.script.T
mathExt - Variable in class org.jmol.script.ScriptExpr
MathExt - Class in org.jmol.scriptext
MathExt() - Constructor for class org.jmol.scriptext.MathExt
mathfunc - Static variable in class org.jmol.script.T
mathop - Static variable in class org.jmol.script.T
mathproperty - Static variable in class org.jmol.script.T
matInv - Variable in class org.jmol.modelset.ModelSet
matR - Variable in class org.jmol.adapter.readers.xtal.JanaReader
matrix3f - Static variable in class org.jmol.script.T
matrix4f - Static variable in class org.jmol.script.T
matrix_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
matrixCtoFNoOffset - Variable in class org.jmol.util.SimpleUnitCell
matrixEnd - Variable in class org.jmol.thread.MoveToThread
matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
matrixFtoCNoOffset - Variable in class org.jmol.util.SimpleUnitCell
matrixRotate - Variable in class org.jmol.viewer.TransformManager
matrixStart - Variable in class org.jmol.thread.MoveToThread
matrixStartInv - Variable in class org.jmol.thread.MoveToThread
matrixStep - Variable in class org.jmol.thread.MoveToThread
matrixStereo - Variable in class org.jmol.viewer.TransformManager
matrixT - Variable in class org.jmol.render.MeasuresRenderer
matrixTemp - Variable in class org.jmol.viewer.TransformManager
matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
matrixTemp4 - Variable in class org.jmol.viewer.TransformManager
matrixTest - Variable in class org.jmol.viewer.TransformManager
matrixToScript(Object) - Static method in class org.jmol.util.Escape
matrixTransform - Variable in class org.jmol.viewer.TransformManager
matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
matRot - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
matScreenToCartesian - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
matScreenToEllipsoid - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
matSupercell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
matTemp - Variable in class org.jmol.modelset.ModelSet
matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
max - Static variable in class org.jmol.script.T
MAX_ACTION_UNDO - Static variable in class org.jmol.viewer.StateCreator
MAX_ADJACENT_PHOSPHORUS_DISTANCE - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
MAX_BOND_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shape.Sticks
MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
MAX_DISTANCE_TO_PLANE - Static variable in class org.jmol.shapespecial.Polyhedra
MAX_DOUBLE_CLICK_MILLIS - Static variable in class org.jmol.viewer.ActionManager
MAX_FILES - Static variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
MAX_LABEL - Static variable in class org.jmol.modelkit.ModelKitPopup
MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
MAX_LOOP - Static variable in class org.jmol.util.JmolAudio
MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Draw
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Ellipsoids
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapesurface.Isosurface
MAX_OTHER - Static variable in class org.jmol.shapespecial.Polyhedra
MAX_PATH - Static variable in class org.jmol.symmetry.CIPChirality
  maximum path to display for debugging only using SET DEBUG in Jmol
max_squarable_double - Static variable in class org.jmol.minimize.Util
max_threads - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MAX_TREE_DEPTH - Static variable in class org.jmol.bspt.Bspt
max_triangles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MAX_TYPE_SUPPORTED - Static variable in class org.jmol.quantum.QS
max_ups - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MAX_VERTICES - Static variable in class org.jmol.shapespecial.Polyhedra
maxAxis - Static variable in class org.jmol.symmetry.PointGroup
maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
maxBondWarned - Variable in class org.jmol.modelset.ModelSet
maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
maxContraction - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
maxData - Variable in class org.jmol.shapesurface.Contact
maxDistance - Variable in class org.jmol.jvxl.readers.AtomDataReader
maxDistance2 - Variable in class org.jmol.symmetry.UnitCellIterator
maxElement - Variable in class org.jmol.symmetry.PointGroup
maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
maxGrid - Variable in class org.jmol.jvxl.readers.VolumeDataReader
maxHbondAlphaDistance - Static variable in class org.jmol.modelsetbio.AminoPolymer
maxHbondAlphaDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
MAXID - Static variable in class org.jmol.quantum.QS
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JC
MAXIMUM_CLICK_TIME - Static variable in class org.jmol.multitouch.sparshui.SinglePointGesture
MAXIMUM_QUEUE_LENGTH - Static variable in class org.jmol.viewer.StatusManager
MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
MAXIMUM_ZOOM_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
maximumSize - Variable in class org.jmol.viewer.Viewer
maxL - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
maxLeft - Variable in class org.jmol.bspt.Node
maxLength - Variable in class org.jmol.adapter.readers.pdb.PdbReader
maxLevel - Static variable in class org.jmol.util.Geodesic
maxOddSizeSphere - Static variable in class org.jmol.g3d.SphereRenderer
maxr - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
maxRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
maxRight - Variable in class org.jmol.bspt.Node
maxRS - Variable in class org.jmol.jvxl.readers.AtomDataReader
  maximun (atom radius + solvent radius)
maxSerial - Variable in class org.jmol.adapter.readers.cif.CifReader
maxSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
maxSerial - Variable in class org.jmol.modelsetbio.BioResolver
maxSet - Variable in class org.jmol.jvxl.readers.Parameters
maxset - Static variable in class org.jmol.script.T
maxSize - Variable in class org.jmol.util.CommandHistory
maxSphereCache - Static variable in class org.jmol.util.Shader
maxSphereDiameter - Static variable in class org.jmol.g3d.SphereRenderer
maxSphereDiameter2 - Static variable in class org.jmol.g3d.SphereRenderer
MAXUNDO - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
maxVanderwaalsRadius - Variable in class org.jmol.modelset.AtomCollection
maxVectorLength - Variable in class org.jmol.jvxl.data.VolumeData
maxXYZ - Variable in class org.jmol.adapter.smarter.XtalSymmetry
maxXYZ - Variable in class org.jmol.symmetry.UnitCellIterator
maxXYZ0 - Variable in class org.jmol.adapter.readers.cif.MSRdr
maxXYZ0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
maybeGetBaseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
mayScript - Variable in class org.jmol.util.GenericApplet
mc - Variable in class org.jmol.modelset.ModelSet
  model count
MdCrdReader - Class in org.jmol.adapter.readers.more
  Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
mDeriv - Variable in class org.jmol.g3d.SphereRenderer
mDeriv - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
mdlLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
mDsimulation - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
mdTopLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MdTopReader - Class in org.jmol.adapter.readers.more
  A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
MEAS_DIGITS - Static variable in class org.jmol.adapter.readers.pymol.PyMOLScene
measure - Static variable in class org.jmol.script.T
measure() - Method in class org.jmol.scriptext.CmdExt
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
measureallmodels - Static variable in class org.jmol.script.T
measureAllModels - Variable in class org.jmol.shape.Measures
measureAllModels - Variable in class org.jmol.viewer.GlobalSettings
measureDistanceUnits - Variable in class org.jmol.viewer.GlobalSettings
Measurement - Class in org.jmol.modelset
Measurement() - Constructor for class org.jmol.modelset.Measurement
measurementCount - Variable in class org.jmol.shape.Measures
MeasurementData - Class in org.jmol.modelset
MeasurementData() - Constructor for class org.jmol.modelset.MeasurementData
measurementHeaders - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
measurementlabels - Static variable in class org.jmol.script.T
measurementLabels - Variable in class org.jmol.viewer.GlobalSettings
MeasurementListWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
measurementnumbers - Static variable in class org.jmol.script.T
MeasurementPending - Class in org.jmol.modelset
MeasurementPending() - Constructor for class org.jmol.modelset.MeasurementPending
measurementQueued - Variable in class org.jmol.viewer.ActionManager
measurements - Variable in class org.jmol.modelset.MeasurementData
measurements - Static variable in class org.jmol.script.T
measurements - Variable in class org.jmol.shape.Measures
measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
measurementStrings - Variable in class org.jmol.modelset.MeasurementData
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
MeasurementTable(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
  Constructor
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
MeasurementTable.MeasurementListWindowListener - Class in org.openscience.jmol.app.jmolpanel
MeasurementTable.MeasurementTableModel - Class in org.openscience.jmol.app.jmolpanel
measurementTableModel - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
MeasurementTableModel() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
measurementunits - Static variable in class org.jmol.script.T
Measures - Class in org.jmol.shape
Measures() - Constructor for class org.jmol.shape.Measures
measures - Variable in class org.jmol.smiles.SmilesSearch
measuresEnabled - Variable in class org.jmol.viewer.ActionManager
MeasuresRenderer - Class in org.jmol.render
MeasuresRenderer() - Constructor for class org.jmol.render.MeasuresRenderer
mediaTracker - Variable in class org.jmol.applet.AppletWrapper
mem - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
memBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
memo - Variable in class org.jmol.adapter.readers.pymol.PickleReader
MEMORY_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
menu - Static variable in class org.jmol.script.T
MENU_NAME - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
MENU_NAME - Static variable in class org.jmol.popup.MainPopupResourceBundle
menuAddButtonGroup(SC) - Method in class org.jmol.awt.AwtPopupHelper
menuAddButtonGroup(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuAddButtonGroup(SC) - Method in interface org.jmol.popup.PopupHelper
menuAddItem(SC, SC) - Method in class org.jmol.popup.GenericPopup
menuAddSeparator(SC) - Method in class org.jmol.popup.GenericPopup
menuAddSubMenu(SC, SC) - Method in class org.jmol.popup.GenericPopup
menubar - Variable in class org.jmol.console.ImageDialog
menuCheckBoxCallback(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
menuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
menuClearListeners(SC) - Method in class org.jmol.awt.AwtPopupHelper
menuClearListeners(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuClearListeners(SC) - Method in interface org.jmol.popup.PopupHelper
menuClickCallback(SC, String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
menuClickCallback(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
menuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
menuContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
menuContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
menuCreateCheckboxItem(SC, String, String, String, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
menuCreateItem(SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
menuCreatePopup(String, Object) - Method in class org.jmol.awt.AwtPopupHelper
menuCreatePopup(String, Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuCreatePopup(String, Object) - Method in interface org.jmol.popup.PopupHelper
menuEnable(SC, boolean) - Method in class org.jmol.popup.GenericPopup
menuEnabled() - Method in class org.jmol.viewer.Viewer
menuFile - Variable in class org.openscience.jmol.app.JmolApp
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
menuFocusCallback(String, String, boolean) - Method in class org.jmol.popup.GenericPopup
menuGetAsText(SB, int, SC, String) - Method in class org.jmol.popup.GenericPopup
menuGetId(SC) - Method in class org.jmol.popup.GenericPopup
menuGetListPosition(SC) - Method in class org.jmol.popup.GenericPopup
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awt.AwtPopupHelper
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awtjs2d.JSPopupHelper
menuInsertSubMenu(SC, SC, int) - Method in interface org.jmol.popup.PopupHelper
MENUITEM_HEIGHT - Static variable in class org.jmol.popup.JmolPopup
menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
menuMap - Variable in class org.jmol.console.GenericConsole
menuName - Variable in class org.jmol.popup.GenericPopup
menuNewSubMenu(String, String) - Method in class org.jmol.popup.GenericPopup
menuRemoveAll(SC, int) - Method in class org.jmol.popup.GenericPopup
menuSetAutoscrolls(SC) - Method in class org.jmol.popup.GenericPopup
menuSetLabel(SC, String) - Method in class org.jmol.popup.GenericPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtJmolPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtModelKitPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSJmolPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSModelKitPopup
menuShowPopup(SC, int, int) - Method in class org.jmol.popup.GenericPopup
menuStructure - Variable in class org.jmol.api.JmolViewer
menuText - Variable in class org.jmol.popup.JmolGenericPopup
mep - Static variable in class org.jmol.script.T
mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
mep_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
mep_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
mep_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
mepCalc - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
MepCalculation - Class in org.jmol.quantum
MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
mepList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
mepType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
merge(MeshCollection) - Method in class org.jmol.shape.MeshCollection
  called by ParallelProcessor at completion
merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
merge(MeshCollection) - Method in class org.jmol.shapesurface.LcaoCartoon
merge(MeshCollection) - Method in class org.jmol.shapesurface.MolecularOrbital
mergeAssociatedNormalCount - Variable in class org.jmol.shapesurface.IsosurfaceMesh
mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
mergeBufferPixel(int, int, int) - Static method in class org.jmol.g3d.Graphics3D
mergeGroups - Variable in class org.jmol.modelset.ModelLoader
mergeGroups() - Method in class org.jmol.modelset.ModelLoader
mergeMesh(MeshData) - Method in class org.jmol.shapesurface.Contact
mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelSet
  initial transfer of model data from old to new model set.
mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
mergePolygons(MeshSurface, int, int, int[][]) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
mergeResults(Lst<ShapeManager>) - Method in class org.jmol.script.ScriptParallelProcessor
mergeSets(int, int) - Method in class org.jmol.jvxl.data.MeshData
mergeShapes(ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
mergeTrajAndVib(ModelSet, ModelSet) - Method in class org.jmol.modelset.ModelLoader
mergeTrajectories(AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
merging - Variable in class org.jmol.modelset.ModelLoader
mesh - Variable in class org.jmol.render.MeshRenderer
mesh - Static variable in class org.jmol.script.T
Mesh - Class in org.jmol.shape
Mesh() - Constructor for class org.jmol.shape.Mesh
  always use Mesh().mesh1(thisID, colix, index)
mesh1(Viewer, String, short, int) - Method in class org.jmol.shape.Mesh
mesh_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_carve_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_carve_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_carve_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_clear_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_clear_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_clear_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_grid_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_negative_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_negative_visible - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_skip - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_type - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mesh_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MeshCapper - Class in org.jmol.util
  A class to properly cap a convoluted, closed slice of an isosurface inspired by: Computational Geometry: Algorithms and Applications Mark de Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
MeshCapper() - Constructor for class org.jmol.util.MeshCapper
MeshCapper.CapVertex - Class in org.jmol.util
  A class to provide linked vertices for MeshCapper
MeshCapper.MeshCapperSorter - Class in org.jmol.util
MeshCapperSorter() - Constructor for class org.jmol.util.MeshCapper.MeshCapperSorter
meshColix - Variable in class org.jmol.shape.Mesh
meshColix - Variable in class org.jmol.shapesurface.Isosurface
MeshCollection - Class in org.jmol.shape
MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
meshColor - Variable in class org.jmol.jvxl.data.JvxlData
meshColor - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
meshCount - Variable in class org.jmol.shape.MeshCollection
MeshData - Class in org.jmol.export
  Class to generate mesh data (faces, vertices, and normals) for several kinds of generic meshes.
MeshData() - Constructor for class org.jmol.export.MeshData
MeshData - Class in org.jmol.jvxl.data
MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
MeshData.SortSet - Class in org.jmol.jvxl.data
MeshData.SSet - Class in org.jmol.jvxl.data
MeshDataServer - Interface in org.jmol.jvxl.api
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
meshes - Variable in class org.jmol.renderbio.BioMeshRenderer
meshes - Variable in class org.jmol.shape.MeshCollection
meshes - Variable in class org.jmol.shapebio.BioShape
meshOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
meshReady - Variable in class org.jmol.renderbio.BioMeshRenderer
meshReady - Variable in class org.jmol.shapebio.BioShape
MeshRenderer - Class in org.jmol.render
  an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
MeshRenderer() - Constructor for class org.jmol.render.MeshRenderer
meshRenderer - Variable in class org.jmol.renderbio.BioShapeRenderer
meshRibbon - Static variable in class org.jmol.script.T
MeshRibbon - Class in org.jmol.shapebio
MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
MeshRibbonRenderer - Class in org.jmol.renderbio
MeshRibbonRenderer() - Constructor for class org.jmol.renderbio.MeshRibbonRenderer
meshScale - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
meshscale - Static variable in class org.jmol.script.T
meshScale - Variable in class org.jmol.viewer.GlobalSettings
meshSlabValue - Variable in class org.jmol.render.MeshRenderer
MeshSlicer - Class in org.jmol.util
MeshSlicer() - Constructor for class org.jmol.util.MeshSlicer
meshSurface - Variable in class org.jmol.renderbio.RocketRenderer
meshSurface - Variable in class org.jmol.renderspecial.PolyhedraRenderer
MeshSurface - Class in org.jmol.util
MeshSurface() - Constructor for class org.jmol.util.MeshSurface
meshTranslucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
meshType - Variable in class org.jmol.util.MeshSurface
meshWidth - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
message - Variable in exception org.jmol.script.ScriptException
message - Static variable in class org.jmol.script.T
messageQueue - Variable in class org.jmol.viewer.StatusManager
messagestylechime - Static variable in class org.jmol.script.T
messageStyleChime - Variable in class org.jmol.viewer.GlobalSettings
META_MASK - Static variable in class org.jmol.awtjs.Event
meth - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
methBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
METHOD_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mf - Variable in class org.jmol.util.JmolMolecule
mi - Variable in class org.jmol.util.Point3fi
  model index -- may be to a trajectory
middle - Static variable in class org.jmol.script.T
MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
middle - Variable in class org.openscience.jmol.app.surfacetool.Slice
mident - Variable in class org.jmol.adapter.readers.cif.MMCifReader
millis - Variable in class org.jmol.script.ScriptDelayThread
min - Static variable in class org.jmol.script.T
MIN_ALIGNED - Static variable in class org.jmol.smiles.PolyhedronStereoSorter
MIN_AXIS_LEN - Static variable in class org.jmol.shape.Axes
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
MIN_DELAY_MS - Static variable in class org.jmol.viewer.MouseState
MIN_MESH_RENDER_SIZE - Static variable in class org.jmol.renderbio.BioMeshRenderer
min_mesh_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MIN_RESNO - Static variable in class org.jmol.adapter.readers.pymol.PyMOLReader
min_squarable_double - Static variable in class org.jmol.minimize.Util
MinAngle - Class in org.jmol.minimize
MinAngle(int[]) - Constructor for class org.jmol.minimize.MinAngle
minAngles - Variable in class org.jmol.minimize.forcefield.Calculations
minAngles - Variable in class org.jmol.minimize.forcefield.ForceField
minAngles - Variable in class org.jmol.minimize.Minimizer
minArray - Variable in class org.jmol.modelset.MeasurementData
MinAtom - Class in org.jmol.minimize
MinAtom(int, Atom, double[], int) - Constructor for class org.jmol.minimize.MinAtom
minAtomCount - Variable in class org.jmol.minimize.forcefield.ForceField
minAtoms - Variable in class org.jmol.minimize.forcefield.Calculations
minAtoms - Variable in class org.jmol.minimize.forcefield.ForceField
minAtoms - Variable in class org.jmol.minimize.Minimizer
MinBond - Class in org.jmol.minimize
MinBond(int, int, int, int, int, int, Integer) - Constructor for class org.jmol.minimize.MinBond
minBondCount - Variable in class org.jmol.minimize.forcefield.ForceField
minbonddistance - Static variable in class org.jmol.script.T
minBondDistance - Variable in class org.jmol.viewer.GlobalSettings
minBondDistance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
minBonds - Variable in class org.jmol.minimize.forcefield.Calculations
minBonds - Variable in class org.jmol.minimize.forcefield.ForceField
minBonds - Variable in class org.jmol.minimize.Minimizer
minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
minData - Variable in class org.jmol.shapesurface.Contact
minGrid - Variable in class org.jmol.jvxl.data.VolumeData
minHeight - Variable in class org.jmol.awtjs.swing.Component
miniLogArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
MINIMIZATION_ATOM_MAX - Static variable in class org.jmol.viewer.JC
minimizationcriterion - Static variable in class org.jmol.script.T
minimizationCriterion - Variable in class org.jmol.viewer.GlobalSettings
minimizationOn - Variable in class org.jmol.minimize.Minimizer
minimizationOn() - Method in class org.jmol.minimize.Minimizer
minimizationrefresh - Static variable in class org.jmol.script.T
minimizationRefresh - Variable in class org.jmol.viewer.GlobalSettings
minimizationsilent - Static variable in class org.jmol.script.T
minimizationSilent - Variable in class org.jmol.viewer.GlobalSettings
minimizationsteps - Static variable in class org.jmol.script.T
minimizationSteps - Variable in class org.jmol.viewer.GlobalSettings
MinimizationThread - Class in org.jmol.minimize
MinimizationThread() - Constructor for class org.jmol.minimize.MinimizationThread
minimizationThread - Variable in class org.jmol.minimize.Minimizer
minimize(int, double, BS, BS, boolean, boolean, String) - Method in class org.jmol.minimize.Minimizer
minimize - Static variable in class org.jmol.script.T
minimize() - Method in class org.jmol.scriptext.CmdExt
minimize(boolean) - Method in class org.jmol.viewer.ActionManager
minimize(JmolScriptEvaluator, int, float, BS, BS, float, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JC
minimizer - Variable in class org.jmol.minimize.forcefield.ForceField
minimizer - Variable in class org.jmol.minimize.MinimizationThread
Minimizer - Class in org.jmol.minimize
Minimizer() - Constructor for class org.jmol.minimize.Minimizer
minimizer - Variable in class org.jmol.viewer.Viewer
minimizeWithoutThread() - Method in class org.jmol.minimize.Minimizer
MINIMUM_ELAPSED_SECONDS - Static variable in class org.jmol.applet.AppletWrapper
minimumHbondDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
minL - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
minLeft - Variable in class org.jmol.bspt.Node
minList - Variable in class org.jmol.minimize.MMConstraint
minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
minmax - Variable in class org.jmol.smiles.SmilesMeasure
minmaxmask - Static variable in class org.jmol.script.T
MinObject - Class in org.jmol.minimize
MinObject() - Constructor for class org.jmol.minimize.MinObject
minpixelselradius - Static variable in class org.jmol.script.T
minPixelSelRadius - Variable in class org.jmol.viewer.GlobalSettings
MinPosition - Class in org.jmol.minimize
  not implemented -- would be a force toward a given position in space
MinPosition(int[], double[]) - Constructor for class org.jmol.minimize.MinPosition
minPositions - Variable in class org.jmol.minimize.forcefield.Calculations
minPositions - Variable in class org.jmol.minimize.forcefield.ForceField
minPositions - Variable in class org.jmol.minimize.Minimizer
minPtsPerAng - Variable in class org.jmol.jvxl.readers.AtomDataReader
minRight - Variable in class org.jmol.bspt.Node
minScreenDimension - Variable in class org.jmol.export.__RayTracerExporter
minSet - Variable in class org.jmol.jvxl.readers.Parameters
minset - Static variable in class org.jmol.script.T
minSyncRepeatMs - Variable in class org.jmol.viewer.StatusManager
minToPlaneDistance - Variable in class org.jmol.jvxl.data.VolumeData
MinTorsion - Class in org.jmol.minimize
MinTorsion(int[]) - Constructor for class org.jmol.minimize.MinTorsion
minTorsions - Variable in class org.jmol.minimize.forcefield.Calculations
minTorsions - Variable in class org.jmol.minimize.forcefield.ForceField
minTorsions - Variable in class org.jmol.minimize.Minimizer
minus - Static variable in class org.jmol.script.T
minusMinus - Static variable in class org.jmol.script.T
minWidth - Variable in class org.jmol.awtjs.swing.Component
minXYZ - Variable in class org.jmol.adapter.smarter.XtalSymmetry
minXYZ - Variable in class org.jmol.symmetry.UnitCellIterator
minXYZ0 - Variable in class org.jmol.adapter.readers.cif.MSRdr
minXYZ0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
minZ - Variable in class org.jmol.render.LabelsRenderer
misc - Static variable in class org.jmol.script.T
missingHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
mkBondPressed - Variable in class org.jmol.viewer.ActionManager
  set to true in checkPressedAction if the screen coordinates of the press are relatively close to the coordinates of the hover that highlighted the bond, indicating that we can alias a left-click to a shift-left-click
mkdata - Variable in class org.jmol.modelkit.ModelKitPopup
ml - Variable in class org.jmol.modelsetbio.BioResolver
mlp - Static variable in class org.jmol.script.T
MlpCalculation - Class in org.jmol.quantum
MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
mltb - Variable in class org.jmol.minimize.forcefield.AtomType
mm - Variable in class org.jmol.viewer.Viewer
mmcifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MMCifReader - Class in org.jmol.adapter.readers.cif
  mmCIF files are recognized prior to class creation.
MMCifReader() - Constructor for class org.jmol.adapter.readers.cif.MMCifReader
MMCifValidationParser - Class in org.jmol.adapter.readers.cif
MMCifValidationParser() - Constructor for class org.jmol.adapter.readers.cif.MMCifValidationParser
MMConstraint - Class in org.jmol.minimize
MMConstraint(int[], double) - Constructor for class org.jmol.minimize.MMConstraint
mmff - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
MMFFAngleCalc - Class in org.jmol.minimize.forcefield
MMFFAngleCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFAngleCalc
MMFFDistanceCalc - Class in org.jmol.minimize.forcefield
MMFFDistanceCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFDistanceCalc
MMFFESCalc - Class in org.jmol.minimize.forcefield
MMFFESCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFESCalc
MMFFOOPCalc - Class in org.jmol.minimize.forcefield
MMFFOOPCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFOOPCalc
MMFFSBCalc - Class in org.jmol.minimize.forcefield
MMFFSBCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFSBCalc
MMFFTorsionCalc - Class in org.jmol.minimize.forcefield
MMFFTorsionCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFTorsionCalc
MMFFVDWCalc - Class in org.jmol.minimize.forcefield
MMFFVDWCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFVDWCalc
MMSTEREO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MMTFReader - Class in org.jmol.adapter.readers.cif
  JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md full specification Version: v0.2+dev (as of 2016.08.08) is implemented,including: reading atoms, bonds, and DSSP 1.0 secondary structure load =1f88.mmtf filter "DSSP1" [Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0 calculations, while the standard for Jmol itself is DSSP 2.0.
MMTFReader() - Constructor for class org.jmol.adapter.readers.cif.MMTFReader
mmType - Variable in class org.jmol.minimize.forcefield.AtomType
mo - Variable in class org.jmol.jvxl.readers.IsoMOReader
mo - Static variable in class org.jmol.script.T
mo(boolean, int) - Method in class org.jmol.scriptext.IsoExt
MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
MO_OCC - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
moBases - Variable in class org.jmol.adapter.writers.QCJSONWriter
MOCalculation - Class in org.jmol.quantum
MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
moCoeff - Variable in class org.jmol.quantum.MOCalculation
moCoefficients - Variable in class org.jmol.quantum.MOCalculation
moColorNeg - Variable in class org.jmol.shapesurface.MolecularOrbital
moColorPos - Variable in class org.jmol.shapesurface.MolecularOrbital
moCombo(Lst<Object[]>) - Method in class org.jmol.scriptext.IsoExt
moCount - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
moCount - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
moCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
moCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
moCutoff - Variable in class org.jmol.shapesurface.MolecularOrbital
moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
moData - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
moData - Variable in class org.jmol.jvxl.readers.Parameters
modAverage - Variable in class org.jmol.adapter.readers.cif.MSRdr
modAxes - Variable in class org.jmol.adapter.readers.cif.MSRdr
modAxes - Variable in class org.jmol.adapter.readers.xtal.JanaReader
modCalc - Variable in class org.jmol.util.ModulationSet
  modCalc is used for calculations independent of what the current setting is
modCell - Variable in class org.jmol.adapter.readers.cif.MSRdr
modCoord - Variable in class org.jmol.adapter.readers.cif.MSRdr
modCount - Variable in class org.jmol.adapter.readers.cif.MSRdr
modDebug - Variable in class org.jmol.adapter.readers.cif.MSRdr
modDim - Variable in class org.jmol.adapter.readers.cif.MSRdr
modDim - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
modDim - Variable in class org.jmol.symmetry.SpaceGroup
modDim - Variable in class org.jmol.symmetry.SymmetryOperation
modDim - Variable in class org.jmol.util.Vibration
  modDim will be > 0 for modulation
mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
mode - Variable in class org.jmol.jvxl.readers.MapFileReader
mode - Static variable in class org.jmol.script.T
mode - Variable in class org.jmol.viewer.TransformManager
MODE_3D - Static variable in class org.jmol.viewer.TransformManager4D
MODE_4D_WX - Static variable in class org.jmol.viewer.TransformManager4D
MODE_4D_WY - Static variable in class org.jmol.viewer.TransformManager4D
MODE_4D_WZ - Static variable in class org.jmol.viewer.TransformManager4D
MODE_ARRAY - Static variable in class org.jmol.smiles.SmilesMatcher
MODE_ATROP - Static variable in class org.jmol.smiles.SmilesMatcher
MODE_BITSET - Static variable in class org.jmol.shapespecial.Polyhedra
MODE_BITSET - Static variable in class org.jmol.smiles.SmilesMatcher
MODE_BONDING - Static variable in class org.jmol.shapespecial.Polyhedra
MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
MODE_ELLIPTICAL - Static variable in class org.jmol.renderbio.BioMeshRenderer
MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_MODEL - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
MODE_FLAT - Static variable in class org.jmol.renderbio.BioMeshRenderer
MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
MODE_HEX - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
MODE_HYBRID36 - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
MODE_INFO - Static variable in class org.jmol.shapespecial.Polyhedra
MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
MODE_MAP - Static variable in class org.jmol.smiles.SmilesMatcher
MODE_MASK - Static variable in class org.jmol.viewer.binding.Binding
MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
MODE_NONELLIPTICAL - Static variable in class org.jmol.renderbio.BioMeshRenderer
MODE_OPTIONS - Static variable in class org.jmol.modelkit.ModelKitPopup
MODE_PDB - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
MODE_PERSPECTIVE_PYMOL - Static variable in class org.jmol.viewer.TransformManager
MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
MODE_POINTS - Static variable in class org.jmol.shapespecial.Polyhedra
MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
MODE_RADIUS - Static variable in class org.jmol.shapespecial.Polyhedra
MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
MODE_TUBE - Static variable in class org.jmol.renderbio.BioMeshRenderer
MODE_UNITCELL - Static variable in class org.jmol.shapespecial.Polyhedra
moDebug - Variable in class org.jmol.shapesurface.MolecularOrbital
model(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
model - Variable in class org.jmol.modelset.Chain
Model - Class in org.jmol.modelset
Model() - Constructor for class org.jmol.modelset.Model
model - Variable in class org.jmol.modelset.ModelLoader
model - Variable in class org.jmol.modelsetbio.BioPolymer
model - Static variable in class org.jmol.script.T
MODEL_CURRENT - Static variable in class org.jmol.viewer.AnimationManager
MODEL_NO - Static variable in class org.jmol.adapter.readers.cif.CifReader
modelAdapter - Variable in class org.jmol.viewer.Viewer
modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
modelbased - Static variable in class org.jmol.script.T
modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
modelCount - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
modelCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
modelCount - Variable in class org.jmol.popup.JmolPopup
modelFilename - Variable in class org.openscience.jmol.app.JmolApp
modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelSet
modelFileNumbers - Variable in class org.jmol.modelset.ModelSet
modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
modelIdList - Variable in class org.jmol.jsv.JDXMOLParser
modelIndex - Variable in class org.jmol.adapter.readers.cif.MMCifReader
modelIndex - Variable in class org.jmol.adapter.readers.pymol.JmolObject
modelIndex - Variable in class org.jmol.atomdata.AtomData
modelIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
modelIndex - Variable in class org.jmol.modelset.Model
modelIndex - Variable in class org.jmol.modelset.StateScript
modelIndex - Variable in class org.jmol.modelset.Text
modelIndex - Variable in class org.jmol.popup.JmolPopup
modelindex - Static variable in class org.jmol.script.T
modelIndex - Variable in class org.jmol.shape.Mesh
modelIndex - Variable in class org.jmol.shape.MeshCollection
modelIndex - Variable in class org.jmol.shapebio.BioShape
modelIndex - Variable in class org.jmol.shapespecial.Dipole
modelIndex - Variable in class org.jmol.shapespecial.Ellipsoid
modelIndex - Variable in class org.jmol.shapespecial.Polyhedra
modelIndex - Variable in class org.jmol.shapespecial.Polyhedron
modelIndex - Variable in class org.jmol.util.JmolMolecule
modelIndex - Variable in class org.jmol.util.Tensor
modelIndexForFrame(int) - Method in class org.jmol.viewer.AnimationManager
modelInfo - Variable in class org.jmol.popup.JmolPopup
modelInfo - Variable in class org.jmol.shapespecial.Draw
modelInvRotation - Variable in class org.jmol.jvxl.readers.Parameters
modelIsRawPDB() - Method in class org.jmol.modelset.Atom
modelIsRawPDB() - Method in class org.jmol.smiles.SmilesAtom
modelIsRawPDB() - Method in interface org.jmol.util.Node
modelkit() - Method in class org.jmol.scriptext.CmdExt
  Configure the ModelKitPopup for Crystallographic symmetry viewing and structure editing new 14.29.45 see modelkit.ModelKitPopup.java
modelkit - Variable in class org.jmol.viewer.Viewer
MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JC
MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JC
modelkitmode - Static variable in class org.jmol.script.T
modelKitMode - Variable in class org.jmol.viewer.GlobalSettings
ModelKitPopup - Class in org.jmol.modelkit
  An abstract popup class that is instantiated for a given platform and context as one of:
ModelKitPopup() - Constructor for class org.jmol.modelkit.ModelKitPopup
ModelKitPopupResourceBundle - Class in org.jmol.modelkit
ModelKitPopupResourceBundle(String, Properties) - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
ModelLoader - Class in org.jmol.modelset
ModelLoader(Viewer, String, SB, Object, ModelSet, BS) - Constructor for class org.jmol.modelset.ModelLoader
ModelManager - Class in org.jmol.viewer
ModelManager(Viewer) - Constructor for class org.jmol.viewer.ModelManager
modelMap - Variable in class org.jmol.adapter.readers.cif.CifReader
modelMolecule - Variable in class org.jmol.adapter.readers.xtal.JanaReader
modelName - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
modelName - Variable in class org.jmol.atomdata.AtomData
modelNames - Variable in class org.jmol.modelset.ModelSet
modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
modelNumberParameter(int) - Method in class org.jmol.script.ScriptParam
modelNumbers - Variable in class org.jmol.modelset.ModelSet
modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelSet
modelRadius - Variable in class org.jmol.viewer.TransformManager
modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
models - Variable in class org.jmol.export._IdtfExporter
ModelSet - Class in org.jmol.modelset
ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
modelSet - Variable in class org.jmol.symmetry.SymmetryDesc
modelSet - Variable in class org.jmol.viewer.ModelManager
modelSet0 - Variable in class org.jmol.modelset.ModelLoader
modelSetFileName - Variable in class org.jmol.popup.JmolPopup
modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
modelSetInfo - Variable in class org.jmol.popup.JmolPopup
modelSetName - Variable in class org.jmol.modelset.ModelSet
modelSetName - Variable in class org.jmol.popup.JmolPopup
modelSetPathName - Variable in class org.jmol.viewer.ModelManager
modelSetProperties - Variable in class org.jmol.modelset.ModelSet
modelSetRoot - Variable in class org.jmol.popup.JmolPopup
modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
modelsOf(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
  general purpose; return models associated with specific atoms
modelStartEnd - Variable in class org.jmol.adapter.smarter.Structure
modelStrings - Variable in class org.jmol.adapter.readers.cif.MMCifReader
modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
modelZeroBased - Variable in class org.jmol.geodesic.EnvelopeCalculation
modeMultipleBond - Variable in class org.jmol.render.SticksRenderer
modeMultipleBond - Variable in class org.jmol.viewer.GlobalSettings
modificationMode - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
modifiedKeys - Variable in class org.jmol.util.JSONWriter
  allows writing of one or more keys different from the original
modifiers - Variable in class org.jmol.export._IdtfExporter
modifiers - Variable in class org.jmol.viewer.MouseState
modifiersDown - Variable in class org.jmol.awt.Mouse
modifiersDown - Variable in class org.jmol.awtjs2d.Mouse
modifiersWhenPressed10 - Variable in class org.jmol.awt.Mouse
modifiersWhenPressed10 - Variable in class org.jmol.awtjs2d.Mouse
modify - Static variable in class org.jmol.script.T
modifyorcreate - Static variable in class org.jmol.script.T
modifySend(int, int, int, String) - Method in class org.jmol.viewer.StatusManager
modLast - Variable in class org.jmol.adapter.readers.cif.MSRdr
modMatrices - Variable in class org.jmol.adapter.readers.cif.MSRdr
modMatrices - Variable in class org.jmol.adapter.readers.cif.Subsystem
modo - Static variable in class org.jmol.script.T
moDots - Variable in class org.jmol.shapesurface.MolecularOrbital
modPack - Variable in class org.jmol.adapter.readers.cif.MSRdr
modr - Variable in class org.jmol.adapter.readers.cif.CifReader
mods - Variable in class org.jmol.util.ModulationSet
  the list of all modulations associated with this atom
modScale - Variable in class org.jmol.util.Vibration
modSelected - Variable in class org.jmol.adapter.readers.cif.MSRdr
modt1 - Static variable in class org.jmol.script.T
modt2 - Static variable in class org.jmol.script.T
modt3 - Static variable in class org.jmol.script.T
modTUV - Variable in class org.jmol.adapter.readers.cif.MSRdr
modType - Variable in class org.jmol.adapter.readers.cif.MSRdr
modulateAtom(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
  The displacement will be set as the atom vibration vector; the string buffer will be appended with the t value for a given unit cell.
modulated - Variable in class org.jmol.adapter.readers.cif.CifReader
modulateoccupancy - Static variable in class org.jmol.script.T
modulateOccupancy - Variable in class org.jmol.viewer.GlobalSettings
modulating - Variable in class org.jmol.render.MeasuresRenderer
modulation - Static variable in class org.jmol.script.T
modulation() - Method in class org.jmol.scriptext.CmdExt
  Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
Modulation - Class in org.jmol.util
  A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
Modulation(char, char, double[], String, double[]) - Constructor for class org.jmol.util.Modulation
  Each atomic modulation involves a fractional coordinate wave vector q, a Fourier power n, a modulation axis (x, y, or, z), and specified parameters that depend upon the type of function.
modulationFields - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
modulationOn - Variable in class org.jmol.modelset.ModelLoader
modulationscale - Static variable in class org.jmol.script.T
modulationScale - Variable in class org.jmol.viewer.GlobalSettings
ModulationSet - Class in org.jmol.util
  A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
ModulationSet() - Constructor for class org.jmol.util.ModulationSet
modulationTUV - Variable in class org.jmol.modelset.ModelLoader
MODULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
moduleNestingLevel - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
modVib - Variable in class org.jmol.adapter.readers.cif.MSRdr
modx - Static variable in class org.jmol.script.T
modxyz - Static variable in class org.jmol.script.T
mody - Static variable in class org.jmol.script.T
modz - Static variable in class org.jmol.script.T
moe_separate_chains - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MOEnergySorter() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
moFactor - Variable in class org.jmol.quantum.MOCalculation
moFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
moFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
moFill - Variable in class org.jmol.shapesurface.MolecularOrbital
moFrontOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
moIsPositiveOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
Mol2Reader - Class in org.jmol.adapter.readers.more
  A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
mol2Records - Static variable in class org.jmol.adapter.smarter.Resolver
Mol3DReader - Class in org.jmol.adapter.readers.molxyz
  3D only
Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
molAtoms - Variable in class org.jmol.adapter.readers.xtal.JanaReader
moldenFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MoldenReader - Class in org.jmol.adapter.readers.quantum
  A molecular structure and orbital reader for MolDen files.
MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
molecular - Static variable in class org.jmol.script.T
MolecularOrbital - Class in org.jmol.shapesurface
MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
MolecularOrbitalRenderer - Class in org.jmol.rendersurface
MolecularOrbitalRenderer() - Constructor for class org.jmol.rendersurface.MolecularOrbitalRenderer
molecularType - Variable in class org.jmol.adapter.readers.cif.CifReader
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
molecule - Static variable in class org.jmol.script.T
MOLECULE_ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_ATOM_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_BOND_STEREO - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
MOLECULE_FORMULA - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
moleculeCount - Variable in class org.jmol.modelset.BondCollection
moleculeCount - Variable in class org.jmol.modelset.Model
moleculeID - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
moleculeIndex - Variable in class org.jmol.util.JmolMolecule
moleculeNames - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
moleculeNesting - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
molecules - Variable in class org.jmol.modelset.BondCollection
Molecules - Class in org.openscience.jmol.app.webexport
Molecules() - Constructor for class org.openscience.jmol.app.webexport.Molecules
moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
molHasTLS - Variable in class org.jmol.adapter.readers.xtal.JanaReader
moLinearCombination - Variable in class org.jmol.shapesurface.Isosurface
moLinearCombination - Variable in class org.jmol.shapesurface.MolecularOrbital
molName - Variable in class org.jmol.adapter.readers.xtal.JanaReader
MolReader - Class in org.jmol.adapter.readers.molxyz
  A reader for MDLI mol and sdf files.
MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
molTtypes - Variable in class org.jmol.adapter.readers.xtal.JanaReader
MolWriter - Class in org.jmol.util
MolWriter() - Constructor for class org.jmol.util.MolWriter
MOMENT_LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
MOMENT_PRELIM_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
MOMENT_PRELIM_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
MOMENT_PRELIM_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
MOMENT_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
MOMENT_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
MOMENT_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
moMesh - Variable in class org.jmol.shapesurface.MolecularOrbital
moModelSet - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
moMonteCarloCount - Variable in class org.jmol.shapesurface.MolecularOrbital
monitorenergy - Static variable in class org.jmol.script.T
monitorEnergy - Variable in class org.jmol.viewer.GlobalSettings
MonitorInputStream - Class in org.openscience.jvxl
MonitorInputStream(InputStream, int) - Constructor for class org.openscience.jvxl.MonitorInputStream
Monomer - Class in org.jmol.modelsetbio
  A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
Monomer() - Constructor for class org.jmol.modelsetbio.Monomer
monomer - Static variable in class org.jmol.script.T
monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
monomerCount - Variable in class org.jmol.renderbio.BioShapeRenderer
monomerCount - Variable in class org.jmol.shape.AtomShape
monomerIndex - Variable in class org.jmol.modelsetbio.Monomer
monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
monomerIndexLast - Variable in class org.jmol.modelsetbio.ProteinStructure
monomers - Variable in class org.jmol.modelsetbio.BioPolymer
monomers - Variable in class org.jmol.renderbio.BioShapeRenderer
monomers - Variable in class org.jmol.shapebio.BioShape
monteCarloCount - Variable in class org.jmol.jvxl.readers.IsoShapeReader
moNumber - Variable in class org.jmol.shapesurface.Isosurface
moNumber - Variable in class org.jmol.shapesurface.MolecularOrbital
moOffset(int) - Method in class org.jmol.scriptext.IsoExt
mopacArchiveContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MopacArchiveReader - Class in org.jmol.adapter.readers.simple
  Mopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cell
MopacArchiveReader() - Constructor for class org.jmol.adapter.readers.simple.MopacArchiveReader
mopacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
  Reads Mopac 2007 GRAPHF output files
MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
MopacReader - Class in org.jmol.adapter.readers.simple
  Reads Mopac 93, 6, 7, 2002, or 2009 output files
MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
MopacSlaterReader - Class in org.jmol.adapter.readers.quantum
MopacSlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacSlaterReader
mopacVersion - Variable in class org.jmol.adapter.readers.simple.MopacReader
moPlane - Variable in class org.jmol.shapesurface.MolecularOrbital
moRandomSeed - Variable in class org.jmol.shapesurface.MolecularOrbital
MOReader - Class in org.jmol.adapter.readers.quantum
  General methods for reading molecular orbital data, including embedded output from the NBO program.
MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
moReader - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
moreColors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
moreInfo - Variable in class org.jmol.symmetry.UnitCell
moResolution - Variable in class org.jmol.shapesurface.MolecularOrbital
moreTokens() - Method in class org.jmol.script.ScriptTokenParser
moreUnitCellInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
morph(int, int, float) - Method in class org.jmol.modelset.Trajectory
morph - Static variable in class org.jmol.script.T
morph(float) - Method in class org.jmol.viewer.AnimationManager
morphCount - Variable in class org.jmol.viewer.AnimationManager
morphTrajectories(int, int, float) - Method in class org.jmol.modelset.ModelSet
mos - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
mos - Variable in class org.jmol.jvxl.readers.IsoMOReader
mosaicPreviewChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Called when the MosaicPreview check box is modified
mosaicPreviewCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
mosaicPreviewComboEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
mosaicPreviewComboStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
mosaicPreviewEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
mosaicPreviewStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
moScale - Variable in class org.jmol.shapesurface.MolecularOrbital
moShell - Variable in class org.jmol.shapesurface.MolecularOrbital
moSlab - Variable in class org.jmol.shapesurface.MolecularOrbital
moSlabValue - Variable in class org.jmol.shapesurface.MolecularOrbital
moSquareData - Variable in class org.jmol.shapesurface.MolecularOrbital
moSquareLinear - Variable in class org.jmol.shapesurface.MolecularOrbital
moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
motion_bias - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
motion_hand - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
motion_linear - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
motion_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
motion_simple - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
motionDisabled - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
motionEventNumber - Variable in class org.jmol.viewer.Viewer
MotionPoint - Class in org.jmol.viewer
MotionPoint() - Constructor for class org.jmol.viewer.MotionPoint
moTitleFormat - Variable in class org.jmol.shapesurface.MolecularOrbital
moTranslucency - Variable in class org.jmol.shapesurface.MolecularOrbital
moTranslucentLevel - Variable in class org.jmol.shapesurface.MolecularOrbital
moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
Mouse - Class in org.jmol.awt
  formerly org.jmol.viewer.MouseManager14 methods required by Jmol that access java.awt.event private to org.jmol.awt
Mouse(double, PlatformViewer, Object) - Constructor for class org.jmol.awt.Mouse
  Mouse is the listener for all events.
Mouse - Class in org.jmol.awtjs2d
  JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
Mouse(double, Viewer, Object) - Constructor for class org.jmol.awtjs2d.Mouse
mouse - Static variable in class org.jmol.script.T
mouse - Variable in class org.jmol.viewer.Viewer
  either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse
MOUSE_DOWN - Static variable in class org.jmol.awtjs.Event
MOUSE_DRAG - Static variable in class org.jmol.awtjs.Event
MOUSE_ENTER - Static variable in class org.jmol.awtjs.Event
MOUSE_EXIT - Static variable in class org.jmol.awtjs.Event
mouse_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MOUSE_LEFT - Static variable in class org.jmol.awtjs.Event
mouse_limit - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MOUSE_MIDDLE - Static variable in class org.jmol.awtjs.Event
MOUSE_MOVE - Static variable in class org.jmol.awtjs.Event
MOUSE_NONE - Static variable in class org.jmol.viewer.JC
mouse_restart_movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MOUSE_RIGHT - Static variable in class org.jmol.awtjs.Event
mouse_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mouse_selection_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
MOUSE_UP - Static variable in class org.jmol.awtjs.Event
MOUSE_WHEEL - Static variable in class org.jmol.awtjs.Event
mouse_wheel_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mouse_z_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
mouseAction(int, long, int, int, int, int) - Method in interface org.jmol.api.EventManager
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
mouseClicked(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseClicked(MouseEvent) - Method in class org.jmol.awt.Mouse
mouseClicked(long, int, int, int, int) - Method in class org.jmol.awt.Mouse
mouseClicked(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseDown - Variable in class org.jmol.multitouch.ActionManagerMT
mousedragfactor - Static variable in class org.jmol.script.T
mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
mouseDragged(MouseEvent) - Method in class org.jmol.awt.Mouse
mouseDragged(long, int, int) - Method in class org.jmol.awt.Mouse
mouseDragged(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseEntered(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseEntered(MouseEvent) - Method in class org.jmol.awt.Mouse
mouseEntered(long, int, int) - Method in class org.jmol.awt.Mouse
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseEnterExit(long, int, int, boolean) - Method in interface org.jmol.api.EventManager
mouseEnterExit(long, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
mouseExited(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseExited(MouseEvent) - Method in class org.jmol.awt.Mouse
mouseExited(long, int, int) - Method in class org.jmol.awt.Mouse
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseListener - Variable in class org.jmol.awtjs.swing.Component
mouseMode - Variable in class org.jmol.viewer.TransformManager4D
mouseMoved(MouseEvent) - Method in class org.jmol.awt.Mouse
mouseMoved(long, int, int, int) - Method in class org.jmol.awt.Mouse
mouseMoved(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
mousePressed(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mousePressed(MouseEvent) - Method in class org.jmol.awt.Mouse
mousePressed(long, int, int, int, boolean) - Method in class org.jmol.awt.Mouse
mousePressed(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
mouseReleased(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
mouseReleased(MouseEvent) - Method in class org.jmol.awt.Mouse
mouseReleased(long, int, int, int) - Method in class org.jmol.awt.Mouse
mouseReleased(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
mouseScript(String) - Method in class org.jmol.viewer.JmolStateCreator
mouseScript(String) - Method in class org.jmol.viewer.StateCreator
MouseState - Class in org.jmol.viewer
MouseState(String) - Constructor for class org.jmol.viewer.MouseState
mouseWheel(long, int, int) - Method in class org.jmol.awt.Mouse
mousewheelfactor - Static variable in class org.jmol.script.T
mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awt.Mouse
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awtjs2d.Mouse
movableBitSet - Variable in class org.jmol.viewer.Viewer
movableX - Variable in class org.jmol.modelset.Text
movableXPercent - Variable in class org.jmol.modelset.Text
movableY - Variable in class org.jmol.modelset.Text
movableYPercent - Variable in class org.jmol.modelset.Text
movableZ - Variable in class org.jmol.modelset.Text
movableZPercent - Variable in class org.jmol.modelset.Text
MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
move - Static variable in class org.jmol.script.T
move(M4, BS) - Method in class org.jmol.shapespecial.Polyhedron
move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.TransformManager
move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.Viewer
move2D(int, int, int) - Method in class org.jmol.shape.Labels
move2D(DrawMesh, int[], int, int, int, boolean) - Method in class org.jmol.shapespecial.Draw
moveAtoms(M4, M3, M3, V3, BS, P3, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
moveAtoms(M4, M3, M3, V3, P3, boolean, BS, boolean) - Method in class org.jmol.viewer.Viewer
moveAtomWithHydrogens(int, int, int, int, BS) - Method in class org.jmol.viewer.Viewer
MOVED - Static variable in class org.jmol.awtjs.Event
moved(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
moved - Variable in class org.jmol.thread.HoverWatcherThread
moved - Variable in class org.jmol.viewer.ActionManager
movepict(String) - Method in class org.openscience.jmol.app.webexport.JmolInstance
moveRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
moveSelected(int, int, int, int, int, BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
moveto - Static variable in class org.jmol.script.T
moveTo(JmolScriptEvaluator, float, P3, T3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
moveTo(JmolScriptEvaluator, float, P3, V3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.Viewer
MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
moveToPyMOL(JmolScriptEvaluator, float, float[]) - Method in class org.jmol.viewer.TransformManager
moveToText - Variable in class org.jmol.modelset.Orientation
MoveToThread - Class in org.jmol.thread
MoveToThread() - Constructor for class org.jmol.thread.MoveToThread
movetoThread - Variable in class org.jmol.viewer.TransformManager
MoveToThread.Slider - Class in org.jmol.thread
movetoTime - Variable in class org.openscience.jmol.app.webexport.Test
moveUpdate(float) - Method in class org.jmol.viewer.Viewer
movie - Static variable in class org.jmol.script.T
movie_animate_by_frame - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_auto_interpolate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_auto_store - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_fps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_loop - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_panel - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_panel_row_height - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movie_rock - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
movingSelected - Variable in class org.jmol.viewer.Viewer
mp - Variable in class org.jmol.viewer.ActionManager
mPending - Variable in class org.jmol.shape.Measures
mpr - Variable in class org.jmol.adapter.readers.more.JcampdxReader
mpts - Variable in class org.jmol.render.MeasuresRenderer
  modulation points, which must be refreshed based on phase of the vibration; keyed on atom index.
mr - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
mrc - Static variable in class org.jmol.script.T
MrcBinaryReader - Class in org.jmol.jvxl.readers
MrcBinaryReader() - Constructor for class org.jmol.jvxl.readers.MrcBinaryReader
ms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ms - Variable in class org.jmol.modelset.Measurement
ms - Variable in class org.jmol.modelset.MeasurementData
ms - Variable in class org.jmol.modelset.Model
  BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
ms - Variable in class org.jmol.modelset.ModelLoader
ms - Variable in class org.jmol.modelset.Trajectory
ms - Variable in class org.jmol.modelsetbio.BioExt
ms - Variable in class org.jmol.modelsetbio.BioModelSet
ms - Variable in class org.jmol.modelsetbio.BioResolver
ms - Variable in class org.jmol.render.ShapeRenderer
ms - Variable in class org.jmol.shape.Shape
ms - Variable in class org.jmol.viewer.ShapeManager
ms - Variable in class org.jmol.viewer.Viewer
MSCifParser - Class in org.jmol.adapter.readers.cif
MSCifParser() - Constructor for class org.jmol.adapter.readers.cif.MSCifParser
msg - Variable in class org.jmol.jvxl.data.JvxlData
msInfo - Variable in class org.jmol.modelset.ModelSet
MSInterface - Interface in org.jmol.adapter.smarter
  Modulated Structure Reader Interface
msms - Static variable in class org.jmol.script.T
MsmsReader - Class in org.jmol.jvxl.readers
MsmsReader() - Constructor for class org.jmol.jvxl.readers.MsmsReader
MSRdr - Class in org.jmol.adapter.readers.cif
  generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
MSRdr() - Constructor for class org.jmol.adapter.readers.cif.MSRdr
msRdr - Variable in class org.jmol.adapter.readers.cif.Subsystem
mTemp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
mTemp - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
mtlout - Variable in class org.jmol.export._ObjExporter
  BufferedWriter for the .mtl file.
mu - Variable in class org.jmol.modelsetbio.Monomer
mul - Static variable in class org.jmol.script.T
mul3 - Static variable in class org.jmol.script.T
mult - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JC
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JC
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JC
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JC
multiModel - Variable in class org.jmol.geodesic.EnvelopeCalculation
multiplebondbananas - Static variable in class org.jmol.script.T
multipleBondBananas - Variable in class org.jmol.viewer.GlobalSettings
multipleBondDuplicate - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  potentially useful information that this duplicate is from an double- or triple-bond, not a ring closure
multipleBondRadiusFactor - Variable in class org.jmol.render.SticksRenderer
multiplebondradiusfactor - Static variable in class org.jmol.script.T
multipleBondRadiusFactor - Variable in class org.jmol.viewer.GlobalSettings
multipleBondSpacing - Variable in class org.jmol.render.SticksRenderer
multiplebondspacing - Static variable in class org.jmol.script.T
multipleBondSpacing - Variable in class org.jmol.viewer.GlobalSettings
multiplex - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
multiplier - Variable in class org.jmol.navigate.Navigator
multiprocessor - Static variable in class org.jmol.script.T
multiProcessor - Variable in class org.jmol.viewer.GlobalSettings
multiTouch - Variable in class org.jmol.viewer.Viewer
multSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
mustBeConnected - Variable in class org.jmol.shape.Measures
mustFinalizeModelSet - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
mustNotBeConnected - Variable in class org.jmol.shape.Measures
mustRender - Variable in class org.jmol.viewer.Viewer
mustResumeEval - Variable in class org.jmol.script.ScriptContext
mustResumeEval - Variable in class org.jmol.script.ScriptEval
mutate(Viewer, BS, String, String[]) - Method in class org.jmol.modelsetbio.BioExt
mutate(BS, String, String[]) - Method in class org.jmol.modelsetbio.BioModelSet
mutate - Static variable in class org.jmol.script.T
mutate() - Method in class org.jmol.scriptext.CmdExt
mutateAtom(Viewer, int, String) - Static method in class org.jmol.modelsetbio.BioExt
mxyz - Variable in class org.jmol.util.ModulationSet
  the modulated magnetic spin
myAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
myAtoms - Variable in class org.jmol.util.ContactPair
myBsA - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
myBsA - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
myBsB - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
myBsB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
myClip - Variable in class org.jmol.util.JmolAudio
myColorPt - Variable in class org.jmol.shapesurface.LcaoCartoon
myColorPt - Variable in class org.jmol.shapesurface.MolecularOrbital
myFps - Variable in class org.jmol.thread.SpinThread
myIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
myKey - Variable in class org.jmol.script.SV.Sort
myLabels - Variable in class org.jmol.symmetry.SymmetryOperation
myMask - Variable in class org.jmol.shape.Sticks
myName - Variable in class org.jmol.script.SV
myName - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
myPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  String path, for debugging
mySlabValue - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
myType - Variable in class org.jmol.shape.Shape
mytypes - Static variable in class org.jmol.modelsetbio.BioResolver
MyUndoableEditListener() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
myVisibilityFlag - Variable in class org.jmol.render.ShapeRenderer
myX - Variable in class org.jmol.quantum.QMAtom
myX2 - Variable in class org.jmol.quantum.QMAtom
myY - Variable in class org.jmol.quantum.QMAtom
myY2 - Variable in class org.jmol.quantum.QMAtom
myZ - Variable in class org.jmol.quantum.QMAtom
myZ2 - Variable in class org.jmol.quantum.QMAtom

## N

n - Static variable in class org.jmol.adapter.smarter.Resolver
n - Variable in class org.jmol.jvxl.data.MeshData.SSet
N - Static variable in class org.jmol.modelsetbio.AminoMonomer
n(int, int) - Static method in class org.jmol.script.T
n - Variable in class org.jmol.smiles.SmilesRing
n0 - Variable in class org.jmol.jvxl.readers.MapFileReader
n1 - Variable in class org.jmol.jvxl.readers.MapFileReader
N1 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
n2 - Variable in class org.jmol.jvxl.readers.MapFileReader
N2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
N3 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
N4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
N6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
N7 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
N9 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
na - Variable in class org.jmol.jvxl.readers.MapFileReader
na - Variable in class org.jmol.util.SimpleUnitCell
nada - Static variable in class org.jmol.script.T
NAME - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
name - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
name - Variable in class org.jmol.adapter.readers.xml.XmlReader.NVPair
name - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
name - Variable in class org.jmol.awtjs.swing.Component
name - Variable in class org.jmol.awtjs2d.JSFile
name - Variable in enum org.jmol.c.PAL
name - Variable in enum org.jmol.c.STER
name - Variable in class org.jmol.export._MayaExporter
name - Variable in class org.jmol.minimize.forcefield.ForceField
name - Variable in class org.jmol.script.ScriptFunction
name - Static variable in class org.jmol.script.T
name - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
name - Variable in class org.jmol.symmetry.PointGroup
name - Variable in class org.jmol.symmetry.SpaceGroup
name - Variable in class org.jmol.symmetry.UnitCell
name - Variable in class org.jmol.thread.JmolThread
name - Variable in enum org.jmol.util.Edge.EnumBondOrder
name - Variable in class org.jmol.viewer.binding.Binding
name - Variable in class org.jmol.viewer.MouseState
name - Variable in class org.openscience.jmol.app.webexport.JmolInstance
name - Variable in class org.openscience.jmol.app.webexport.Widgets.Widget
name0 - Variable in class org.jmol.script.ContextToken
NAME_HALL - Static variable in class org.jmol.symmetry.SpaceGroup
NAME_HM - Static variable in class org.jmol.symmetry.SpaceGroup
NAME_UNK - Static variable in class org.jmol.symmetry.SpaceGroup
nameAsGiven - Variable in class org.jmol.viewer.FileManager
nameAsGivenIn - Variable in class org.jmol.io.FileReader
namedSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
nameList - Static variable in enum org.jmol.c.CBK
nameOf(int) - Static method in class org.jmol.script.T
  note: nameOf is a very inefficient mechanism for getting the name of a token.
nameRequired - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
names - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
names - Variable in class org.jmol.script.ScriptFunction
namesAsGivenIn - Variable in class org.jmol.io.FilesReader
naNoH - Static variable in class org.jmol.modelsetbio.BioExt
nAOs - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
natCharges - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
nativeLanguage - Variable in class org.jmol.i18n.Language
nAtom - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
nAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
nAtoms - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
nAtoms - Variable in class org.jmol.adapter.readers.more.MdTopReader
nAtoms - Variable in class org.jmol.adapter.readers.more.Mol2Reader
nAtoms - Variable in class org.jmol.adapter.readers.quantum.CsfReader
nAtoms - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
nAtoms - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
nAtoms - Variable in class org.jmol.minimize.MMConstraint
nAtoms - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  number of substituent atoms (non-null atoms[] entries)
nAtoms - Variable in class org.jmol.symmetry.PointGroup
nAtoms - Variable in class org.jmol.symmetry.UnitCellIterator
nAtoms0 - Variable in class org.jmol.adapter.readers.cif.CifReader
naturalIsotopes - Static variable in class org.jmol.util.Elements
nav - Variable in class org.jmol.viewer.TransformManager
NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager
NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager
navCenter - Variable in class org.jmol.modelset.Orientation
navCenter - Variable in class org.jmol.thread.MoveToThread
navDepth - Variable in class org.jmol.modelset.Orientation
navDepth - Variable in class org.jmol.thread.MoveToThread
navfps - Static variable in class org.jmol.script.T
navFps - Variable in class org.jmol.viewer.TransformManager
navigate(float, P3[][], P3[], float[], int, int) - Method in class org.jmol.navigate.Navigator
navigate - Static variable in class org.jmol.script.T
navigate() - Method in class org.jmol.scriptext.CmdExt
navigate(int, int) - Method in class org.jmol.viewer.Viewer
navigateAxis(V3, float) - Method in interface org.jmol.api.JmolNavigatorInterface
navigateAxis(V3, float) - Method in class org.jmol.navigate.Navigator
navigateAxis(V3, float) - Method in class org.jmol.viewer.TransformManager
  scripted entry point for navigation
navigateAxis(V3, float) - Method in class org.jmol.viewer.Viewer
navigateKey(int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
navigateKey(int, int) - Method in class org.jmol.navigate.Navigator
navigateKey(int, int) - Method in class org.jmol.viewer.TransformManager
  entry point for keyboard-based navigation
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in interface org.jmol.api.JmolNavigatorInterface
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.navigate.Navigator
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.viewer.TransformManager
navigatePt(P3) - Method in class org.jmol.viewer.Viewer
navigatesurface - Static variable in class org.jmol.script.T
navigateTo(float, V3, float, P3, float, float, float) - Method in class org.jmol.navigate.Navigator
navigating - Variable in class org.jmol.viewer.TransformManager
navigationCenter - Variable in class org.jmol.viewer.TransformManager
navigationdepth - Static variable in class org.jmol.script.T
navigationDepthPercent - Variable in class org.jmol.viewer.TransformManager
navigationList - Variable in class org.jmol.navigate.Navigator
navigationMode - Variable in class org.jmol.modelset.Orientation
navigationmode - Static variable in class org.jmol.script.T
navigationMode - Variable in class org.jmol.viewer.GlobalSettings
navigationOffset - Variable in class org.jmol.viewer.TransformManager
navigationperiodic - Static variable in class org.jmol.script.T
navigationPeriodic - Variable in class org.jmol.viewer.GlobalSettings
navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
navigationslab - Static variable in class org.jmol.script.T
navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager
navigationspeed - Static variable in class org.jmol.script.T
navigationSpeed - Variable in class org.jmol.viewer.GlobalSettings
Navigator - Class in org.jmol.navigate
  Navigator is a user input mechanism that utilizes the keypad to drive through the model.
Navigator() - Constructor for class org.jmol.navigate.Navigator
navInterrupt() - Method in class org.jmol.viewer.TransformManager
navMinMax - Variable in class org.jmol.viewer.ShapeManager
navMode - Variable in class org.jmol.viewer.TransformManager
navOn - Variable in class org.jmol.viewer.TransformManager
navTranslatePercent(float, float) - Method in class org.jmol.viewer.Viewer
navTranslatePercentOrTo(float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.navigate.Navigator
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.viewer.TransformManager
  seconds < 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"
navx - Static variable in class org.jmol.script.T
navX - Variable in class org.jmol.viewer.TransformManager
navy - Static variable in class org.jmol.script.T
NAVY - Static variable in class org.jmol.util.C
navY - Variable in class org.jmol.viewer.TransformManager
navz - Static variable in class org.jmol.script.T
navZ - Variable in class org.jmol.viewer.TransformManager
nAxes - Variable in class org.jmol.symmetry.PointGroup
nb - Variable in class org.jmol.jvxl.readers.MapFileReader
nb - Variable in class org.jmol.util.SimpleUnitCell
nb_spheres_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nb_spheres_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nb_spheres_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
nBalls - Variable in class org.jmol.export._MayaExporter
nBasis - Variable in class org.jmol.adapter.readers.quantum.QchemReader
nBasisFunctions - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
nBF - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
nBits - Variable in class org.jmol.g3d.LineRenderer
nBlock - Variable in class org.jmol.jvxl.readers.XplorReader
nbo - Static variable in class org.jmol.script.T
NBO - Class in org.jmol.shapesurface
NBO() - Constructor for class org.jmol.shapesurface.NBO
NBO_CONFIG - Static variable in class org.jmol.viewer.JC
NBO_MODEL - Static variable in class org.jmol.viewer.JC
NBO_RUN - Static variable in class org.jmol.viewer.JC
NBO_SEARCH - Static variable in class org.jmol.viewer.JC
NBO_TYPES - Static variable in class org.jmol.viewer.JC
NBO_VIEW - Static variable in class org.jmol.viewer.JC
nbocharges - Static variable in class org.jmol.script.T
nboCharges - Variable in class org.jmol.viewer.GlobalSettings
nBonds - Variable in class org.jmol.minimize.MinAtom
nBondsDisplayed - Variable in class org.jmol.modelset.Atom
nBondsOr - Variable in class org.jmol.smiles.SmilesBond
nboOptions - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
nboParser - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
NBOParser - Class in org.jmol.adapter.readers.quantum
NBOParser() - Constructor for class org.jmol.adapter.readers.quantum.NBOParser
nboParser - Variable in class org.jmol.viewer.Viewer
NBORenderer - Class in org.jmol.rendersurface
NBORenderer() - Constructor for class org.jmol.rendersurface.NBORenderer
nboType - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
nboType - Variable in class org.jmol.shapesurface.MolecularOrbital
nBrickX - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
nBrickY - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
nBytes - Variable in class org.jmol.jvxl.data.JvxlData
nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
nc - Variable in class org.jmol.jvxl.readers.MapFileReader
nc - Variable in class org.jmol.util.SimpleUnitCell
nCharNewLine(int) - Method in class org.jmol.script.ScriptCompiler
  Check for line ending at this point in script.
nci - Static variable in class org.jmol.script.T
NciCalculation - Class in org.jmol.quantum
NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
nCoef - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
nCoefficients - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
ncols - Variable in class org.jmol.awtjs.swing.Grid
nContourMax - Static variable in class org.jmol.jvxl.calc.MarchingSquares
nContourMax - Static variable in class org.jmol.jvxl.readers.Parameters
nContours - Variable in class org.jmol.jvxl.data.JvxlData
nContours - Variable in class org.jmol.jvxl.readers.Parameters
nContourSegments - Variable in class org.jmol.jvxl.calc.MarchingSquares
ncsoperFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
nCyl - Variable in class org.jmol.export._MayaExporter
nData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
nDegrees - Variable in class org.jmol.thread.SpinThread
NDIM - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
ndim() - Method in class org.jmol.adapter.readers.xtal.JanaReader
nDots - Variable in class org.jmol.jvxl.readers.KinemageReader
ndots - Static variable in class org.jmol.render.FontLineShapeRenderer
nDouble - Variable in class org.jmol.smiles.SmilesSearch
ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
nearbyAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
nEdges - Variable in class org.jmol.jvxl.data.JvxlData
needAromatic - Variable in class org.jmol.smiles.SmilesSearch
needRightParen - Variable in class org.jmol.script.ScriptCompiler
needRingData - Variable in class org.jmol.smiles.SmilesSearch
needRingMemberships - Variable in class org.jmol.smiles.SmilesSearch
needSelections() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
needToCompleteInitialization - Variable in class org.jmol.applet.AppletWrapper
needToFill - Variable in class org.jmol.g3d.HermiteRenderer
needTranslucent - Variable in class org.jmol.render.MeshRenderer
needTranslucent - Variable in class org.jmol.renderbio.BioShapeRenderer
negativeAtomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
negCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
neighborCenters - Variable in class org.jmol.geodesic.EnvelopeCalculation
neighborCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
neighborIndices - Variable in class org.jmol.geodesic.EnvelopeCalculation
neighborPlusProbeRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
neighborRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
neighborVertexesArrays - Static variable in class org.jmol.util.Geodesic
neighborVertexesArrays - Static variable in class org.jmol.util.Normix
neighborVertexesIcosahedron - Static variable in class org.jmol.util.Geodesic
nElements - Variable in class org.jmol.awtjs.swing.JPanel
nElements - Variable in class org.jmol.util.JmolMolecule
nError - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
nestedBond - Variable in class org.jmol.smiles.SmilesSearch
newA(float[]) - Static method in class org.jmol.util.SimpleUnitCell
newAction(int, String, String) - Static method in class org.jmol.viewer.ActionManager
newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
newAndSetBit(int) - Static method in class org.jmol.util.BSUtil
newAntialiasing - Variable in class org.jmol.util.GData
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.DmolReader
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
newAtomSet(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Create a new atoms set, clearing the atom map
newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
newAtomSetClear(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Create a new atom set, optionally clearing the atom map.
newBinaryDocument() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
newBinding(Viewer, String) - Static method in class org.jmol.viewer.binding.Binding
newBitSet2(int, int) - Static method in class org.jmol.util.BSUtil
newBS(BS, int[]) - Static method in class org.jmol.modelset.BondSet
newBufferedImage(Object, int, int) - Method in interface org.jmol.api.GenericPlatform
newBufferedImage(Object, int, int) - Static method in class org.jmol.awt.Image
newBufferedImage(int, int) - Static method in class org.jmol.awt.Image
newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs.Platform
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs2d.Platform
newBZ(int) - Method in class org.jmol.util.BZone
  initialize a new Brillouin zone
newChain - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
newCmd(int, Object) - Static method in class org.jmol.script.ContextToken
newContext(boolean) - Static method in class org.jmol.script.ContextToken
newContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
newDataReader(Viewer, Object) - Static method in class org.jmol.viewer.FileManager
newEcho(Viewer, Font, String, short, int, int, float) - Static method in class org.jmol.modelset.Text
newF(float) - Static method in class org.jmol.script.SV
newFile(String) - Method in interface org.jmol.api.GenericPlatform
newFile(String) - Method in class org.jmol.awt.Platform
newFile(String) - Static method in class org.jmol.awtjs2d.JSFile
newFile(String) - Method in class org.jmol.awtjs2d.Platform
newFileName - Variable in class org.jmol.shapesurface.Isosurface
newFilesReader(String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.FontManager
newFont(String, boolean, boolean, float) - Static method in class org.jmol.awt.AwtFont
newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
newFont(String, boolean, boolean, float, String) - Static method in class org.jmol.awtjs2d.JSFont
newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs2d.Platform
newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface org.jmol.api.GenericGraphics
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awt.AwtG2D
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awtjs2d.JsG2D
newI(int) - Static method in class org.jmol.script.SV
newI(int) - Static method in class org.jmol.util.Rgb16
newID(String) - Static method in class org.jmol.awtjs.swing.Component
newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJMenu(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
newJMenu(String) - Method in class org.jmol.console.JmolConsole
newJMenu(String) - Method in class org.jmol.consolejs.AppletConsole
newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJMenuItem(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
newJMenuItem(String) - Method in class org.jmol.console.JmolConsole
newJMenuItem(String) - Method in class org.jmol.consolejs.AppletConsole
newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
newJSVar(Object) - Static method in class org.jmol.script.SV
  Conversion to Jmol variables of JavaScript variables using y = javascript("x")
newLabel(Viewer, Font, String, short, short, int, float) - Static method in class org.jmol.modelset.Text
newLattice(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
newLatticePts - Variable in class org.jmol.util.BZone
newMeasure(Viewer, Font, short) - Static method in class org.jmol.modelset.Text
newMeasurementData(String, Lst<Object>) - Method in class org.jmol.viewer.Viewer
newMenuItem(SC, SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
newMesh(boolean, T3[], int, int[][], T3[], int) - Static method in class org.jmol.util.MeshSurface
newModel(int) - Method in class org.jmol.adapter.readers.cif.CifReader
newNavigationCenter() - Method in class org.jmol.navigate.Navigator
  We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
newOffScreenImage(int, int) - Method in interface org.jmol.api.GenericPlatform
newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
newOffScreenImage(int, int) - Method in class org.jmol.awtjs.Platform
newOffScreenImage(int, int) - Method in class org.jmol.awtjs2d.Platform
newPlanePts - Variable in class org.jmol.util.BZone
newPlanes - Variable in class org.jmol.util.BZone
newPoint(int, P3, P3, int, int, int) - Method in class org.jmol.symmetry.SpaceGroup
newPoint(M4, P3, P3, int, int, int) - Static method in class org.jmol.symmetry.SymmetryOperation
newPoint(int, int, int, P3) - Method in class org.jmol.util.BZone
newReader(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
newReaderBr(String, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
newRegion(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  Add a new region to the list of regions.
newS(String) - Static method in class org.jmol.script.SV
newScale - Variable in class org.jmol.shapecgo.CGO
newScale - Variable in class org.jmol.shapespecial.Draw
newScriptEvaluator() - Method in class org.jmol.script.ScriptManager
newSearch(String, boolean, boolean) - Static method in class org.jmol.smiles.SmilesParser
newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
newSg() - Method in class org.jmol.shapesurface.Isosurface
newSlider(float, float) - Method in class org.jmol.thread.MoveToThread
newSpaceGroupPoint(int, P3, P3, int, int, int, M4) - Method in interface org.jmol.api.SymmetryInterface
newSpaceGroupPoint(int, P3, P3, int, int, int, M4) - Method in class org.jmol.symmetry.Symmetry
newStereo(SmilesSearch) - Static method in class org.jmol.smiles.SmilesStereo
newSubZone(BZone, String, int) - Method in class org.jmol.util.BZone
newSurface(int, ContactPair, BS, BS, RadiusData, float[], Object, boolean, VolumeData, float) - Method in class org.jmol.shapesurface.Contact
newSV(int, int, Object) - Static method in class org.jmol.script.SV
newT(T) - Static method in class org.jmol.script.SV
newTensorType(V3[], float[], String, String) - Method in class org.jmol.util.Tensor
  common processing of eigenvectors.
newTextLabel(String, float[], int, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
newTrajectory(ModelSet, Lst<P3[]>) - Method in class org.jmol.modelset.ModelLoader
newV(int, Object) - Static method in class org.jmol.script.SV
newVertex(P3, V3, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
newVertexBitSet() - Static method in class org.jmol.util.Normix
newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
newWindowHeight - Variable in class org.jmol.util.GData
newWindowWidth - Variable in class org.jmol.util.GData
next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
next() - Method in interface org.jmol.api.AtomIndexIterator
next - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
next() - Method in interface org.jmol.modelset.BondIterator
next() - Method in class org.jmol.modelset.BondIteratorSelected
next - Static variable in class org.jmol.script.T
next() - Method in class org.jmol.symmetry.UnitCellIterator
next - Variable in class org.jmol.util.Int2IntHashEntry
next - Variable in class org.jmol.util.MeshCapper.CapVertex
NEXT - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
nextAtomSet() - Method in class org.jmol.adapter.readers.cif.CifReader
nextCell() - Method in class org.jmol.symmetry.UnitCellIterator
nextChiralBranch - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  points to next branching point that has two or more chiral branches
nextCommand - Variable in class org.jmol.util.CommandHistory
  Position of the next command.
nextElement() - Method in class org.jmol.bspt.CubeIterator
  normal iterator method
nextFileName(String, int) - Method in class org.jmol.console.GenericConsole
nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
nextFileName(String, int) - Method in class org.jmol.consolejs.AppletConsole
nextIndex() - Method in interface org.jmol.modelset.BondIterator
nextIndex() - Method in class org.jmol.modelset.BondIteratorSelected
nextList(Object[], P3) - Method in class org.jmol.navigate.Navigator
nextMeasure(int, int, Measurement, int) - Method in class org.jmol.modelset.MeasurementData
  iterator for measurements
nextPatternAtom(int, int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch
nextRandom8Bit() - Method in class org.jmol.util.Shader
  Implements RANDU algorithm for random noise in lighting/shading.
nextSP2 - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  first =X= atom in a string of =X=X=X=...
nextTargetAtom(SmilesAtom, Node, int, int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch
  Check for a specific match of a model set atom with a pattern position
nextToken() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
nextToken() - Method in class org.jmol.jvxl.readers.PmeshReader
nextVoxel() - Method in class org.jmol.jvxl.readers.BCifDensityReader
nextVoxel() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
nextVoxel() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
nextVoxel() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
nextVoxel() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
nextVoxel() - Method in class org.jmol.jvxl.readers.UhbdReader
nextVoxel() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
nextVoxel() - Method in class org.jmol.jvxl.readers.VolumeFileReader
nextVoxel() - Method in class org.jmol.jvxl.readers.XplorReader
nFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
nFast - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
NffReader - Class in org.jmol.jvxl.readers
NffReader() - Constructor for class org.jmol.jvxl.readers.NffReader
nFilePoints - Variable in class org.jmol.jvxl.readers.CastepDensityReader
nFiltered - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
nFound - Variable in class org.jmol.symmetry.UnitCellIterator
nFrankList - Variable in class org.jmol.popup.JmolGenericPopup
nFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
nGaussians - Variable in class org.jmol.adapter.readers.quantum.CsfReader
nGaussians - Variable in class org.jmol.quantum.MOCalculation
nHallOperators - Variable in class org.jmol.symmetry.SpaceGroup
nhChecked - Variable in class org.jmol.modelsetbio.AminoMonomer
nHits - Variable in class org.jmol.navigate.Navigator
nihresolverformat - Static variable in class org.jmol.script.T
nihResolverFormat - Variable in class org.jmol.viewer.GlobalSettings
nImage - Variable in class org.jmol.export.___Exporter
nIn - Variable in class org.jmol.util.Shader
nInvalid - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
nioClosed(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
nioClosed(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
nioRunContent(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
nioRunContent(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
nLatticeTypes - Static variable in class org.jmol.symmetry.HallTranslation
nLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.AimsReader
nLCAO - Variable in class org.jmol.shapesurface.Isosurface
nList - Variable in class org.jmol.shapecgo.CGOMesh
nMatrixElements - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
nModels - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
nModels - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
nMolecular - Variable in class org.jmol.adapter.readers.cif.CifReader
nMolecules - Variable in class org.jmol.quantum.NciCalculation
nmr - Static variable in class org.jmol.script.T
NMR_DC - Static variable in class org.jmol.modelset.Measurement
NMR_JC - Static variable in class org.jmol.modelset.Measurement
NMR_NOT - Static variable in class org.jmol.modelset.Measurement
NMRCalculation - Class in org.jmol.quantum
NMRCalculation() - Constructor for class org.jmol.quantum.NMRCalculation
nmrCalculation - Variable in class org.jmol.viewer.Viewer
nmrpredictformat - Static variable in class org.jmol.script.T
nmrPredictFormat - Variable in class org.jmol.viewer.GlobalSettings
nmrType(String) - Static method in class org.jmol.modelset.Measurement
nmrurlformat - Static variable in class org.jmol.script.T
nmrUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
nMtlBytes - Variable in class org.jmol.export._ObjExporter
  Bytes written to the .mtl file.
nNested - Variable in class org.jmol.smiles.SmilesSearch
nNOs - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
NO_ANISOTROPY - Static variable in class org.jmol.jvxl.readers.Parameters
NO_CHIRALITY - Static variable in class org.jmol.symmetry.CIPChirality
no_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
NO_VALUE - Static variable in class org.jmol.quantum.NciCalculation
noArgs - Static variable in class org.jmol.script.T
noAromatic - Variable in class org.jmol.smiles.SmilesSearch
noAtoms - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
noAutoBond - Variable in class org.jmol.modelset.ModelLoader
nobackshell - Static variable in class org.jmol.script.T
NOBASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
noBioComment - Variable in class org.jmol.smiles.SmilesGenerator
noBondSym - Variable in class org.jmol.adapter.readers.xtal.CgdReader
noColor - Variable in class org.jmol.export.__CartesianExporter
noColor - Variable in class org.jmol.shapesurface.PMeshWriter
nocontourlines - Static variable in class org.jmol.script.T
noCopy(int, int) - Method in class org.jmol.script.ScriptExpr
noCross - Variable in class org.jmol.renderspecial.DipolesRenderer
nocross - Static variable in class org.jmol.script.T
noCross - Variable in class org.jmol.shapespecial.Dipole
Node - Class in org.jmol.bspt
  Nodes of the bspt.
Node(Bspt, int, Leaf) - Constructor for class org.jmol.bspt.Node
Node - Interface in org.jmol.util
nodebug - Static variable in class org.jmol.script.T
nodelay - Static variable in class org.jmol.script.T
noDelay - Variable in class org.jmol.viewer.GlobalSettings
  ensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1
nodes - Variable in class org.jmol.symmetry.CIPDataSmiles
nodes - Variable in class org.jmol.util.JmolMolecule
nodes - Variable in class org.jmol.viewer.Gesture
nodots - Static variable in class org.jmol.script.T
noedges - Static variable in class org.jmol.script.T
noFaceSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
nofill - Static variable in class org.jmol.script.T
noFrankEcho - Variable in class org.jmol.viewer.Viewer
noGraphicsAllowed - Variable in class org.jmol.viewer.Viewer
nohead - Static variable in class org.jmol.script.T
noHead - Variable in class org.jmol.shapespecial.Draw
noHead - Variable in class org.jmol.shapespecial.DrawMesh
NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
noload - Static variable in class org.jmol.script.T
nomesh - Static variable in class org.jmol.script.T
nonbonded_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nonbonded_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nonbonded_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nonbonded_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
nonbondedSize - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
nonbondedTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
NONE - Static variable in class org.jmol.adapter.readers.cif.CifReader
NONE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
NONE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
NONE - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
none - Static variable in class org.jmol.script.T
noneSelected - Variable in class org.jmol.viewer.SelectionManager
nonhydrogenDegree - Variable in class org.jmol.smiles.SmilesAtom
noplane - Static variable in class org.jmol.script.T
nOps - Variable in class org.jmol.adapter.readers.cif.MSRdr
nOps - Variable in class org.jmol.symmetry.PointGroup
nOps - Variable in class org.jmol.util.ModulationSet
  the number of operators in this space group -- needed for occupancy calculation
nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
nOrbitals0 - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
norm - Variable in class org.jmol.renderbio.BioMeshRenderer
norm - Variable in class org.jmol.util.MeshSlicer
NORM_NBO - Static variable in class org.jmol.quantum.MOCalculation
NORM_NONE - Static variable in class org.jmol.quantum.MOCalculation
NORM_NWCHEM - Static variable in class org.jmol.quantum.MOCalculation
NORM_STANDARD - Static variable in class org.jmol.quantum.MOCalculation
normal - Static variable in class org.jmol.script.T
NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
NORMAL_MODE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
normal_workaround - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
normalCount - Variable in class org.jmol.util.MeshSurface
normalize48ths(float, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
normalize_ccp4_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
normalize_grd_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
normalize_o_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
normalizeAromaticity(SmilesAtom[], BS, int) - Static method in class org.jmol.smiles.SmilesSearch
  create a temporary object to generate the aromaticity in a SMILES pattern for which there is no explicit aromaticity (Kekule) Not applicable to SMARTS
normalizeClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
  re-order bonds to match standard @ and @@ types
normalizeTwelfths(float, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
normalizeUV - Variable in class org.jmol.export._ObjExporter
  Whether to normalize UV texture coordinates.
normalOrAxis - Variable in class org.jmol.symmetry.PointGroup.Operation
normals - Variable in class org.jmol.shapespecial.Polyhedron
normals - Variable in class org.jmol.util.MeshSurface
normalsInverted - Variable in class org.jmol.shape.Mesh
normalsT - Variable in class org.jmol.shapespecial.Polyhedra
normalsTemp - Variable in class org.jmol.util.MeshSurface
normAnglePanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
normDispl - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
normix - Variable in class org.jmol.rendercgo.CGORenderer
Normix - Class in org.jmol.util
  Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix() - Constructor for class org.jmol.util.Normix
normix0 - Variable in class org.jmol.rendercgo.CGORenderer
normix1 - Variable in class org.jmol.rendercgo.CGORenderer
normix2 - Variable in class org.jmol.rendercgo.CGORenderer
NORMIX_GEODESIC_LEVEL - Static variable in class org.jmol.util.Normix
NORMIX_NULL - Static variable in class org.jmol.util.Normix
normixCount - Static variable in class org.jmol.util.GData
normixCount - Variable in class org.jmol.util.MeshSurface
normixCount - Static variable in class org.jmol.util.Normix
normixes - Variable in class org.jmol.render.MeshRenderer
normixes - Variable in class org.jmol.shape.Mesh
normixes - Variable in class org.jmol.shapespecial.Polyhedron
norml - Variable in class org.jmol.renderbio.BioMeshRenderer
normType - Variable in class org.jmol.quantum.MOCalculation
NORTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
noStereo - Variable in class org.jmol.smiles.SmilesGenerator
noSymmetryCount - Variable in class org.jmol.adapter.smarter.XtalSymmetry
not - Variable in class org.jmol.smiles.SmilesAtom
notBondedIndex - Variable in class org.jmol.smiles.SmilesAtom
notCrossLinked - Variable in class org.jmol.smiles.SmilesAtom
note - Variable in class org.jmol.modelset.MeasurementData
NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JC
notfrontonly - Static variable in class org.jmol.script.T
notHelixOrSheet(int) - Method in class org.jmol.modelsetbio.Sheet
notify(int, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
notify(int, Object[]) - Method in class org.jmol.console.ScriptEditor
notifyAtomPicked(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
notifyAtomPositionsChanged(int, BS, M4) - Method in class org.jmol.viewer.ShapeManager
notifyAudioEnded(Object) - Method in interface org.jmol.api.JmolAppletInterface
notifyAudioEnded(Object) - Method in class org.jmol.applet.JmolApplet
notifyAudioEnded(Object) - Method in class org.jmol.util.GenericApplet
notifyAudioStatus(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
  called from JmolAudio
notifyCallback(CBK, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
notifyCallback(CBK, Object[]) - Method in class org.jmol.console.GenericConsole
notifyCallback(CBK, Object[]) - Method in class org.jmol.util.GenericApplet
notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
notifyCallback(CBK, Object[]) - Method in interface org.openscience.jmol.app.JmolPlugin
notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
notifyEnabled(CBK) - Method in interface org.jmol.api.JmolCallbackListener
notifyEnabled(CBK) - Method in class org.jmol.console.GenericConsole
notifyEnabled(CBK) - Method in class org.jmol.util.GenericApplet
notifyEnabled(CBK) - Method in class org.jmol.viewer.StatusManager
notifyEnabled(CBK) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
notifyEndOfRendering() - Method in interface org.jmol.api.GenericPlatform
notifyEndOfRendering() - Method in class org.jmol.awt.Platform
notifyEndOfRendering() - Method in class org.jmol.awtjs2d.Platform
notifyEndOfRendering() - Method in class org.jmol.g3d.Platform3D
notifyError(String, String, String) - Method in class org.jmol.viewer.StatusManager
notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
notifyFileLoaded(String, String, String, String, Boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
notifyFileOpen(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
notifyFileOpen(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
  " (*)" appended to a file name indicates that this file was loaded asynchronously
notifyMinimizationStatus(String, Integer, Float, Float, String) - Method in class org.jmol.viewer.StatusManager
notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
notifyResumeStatus() - Method in interface org.jmol.api.JmolScriptEvaluator
notifyResumeStatus() - Method in class org.jmol.script.ScriptEval
notifyScriptEditor(int, Object[]) - Method in class org.jmol.viewer.Viewer
notifyScriptStart() - Method in interface org.jmol.api.JmolScriptEditorInterface
notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
notifyScriptTermination() - Method in interface org.jmol.api.JmolScriptEditorInterface
notifyScriptTermination() - Method in class org.jmol.console.ScriptEditor
notifyStatusReady(boolean) - Method in class org.jmol.api.JmolViewer
notifyStatusReady(boolean) - Method in class org.jmol.viewer.Viewer
notifyStructureModified(int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
notifySync(String, String) - Method in class org.jmol.util.GenericApplet
notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
notImplemented(String) - Static method in class org.jmol.modelkit.ModelKitPopup
notInCentroid(ModelSet, BS, int[]) - Method in interface org.jmol.api.SymmetryInterface
notInCentroid(ModelSet, BS, int[]) - Method in class org.jmol.symmetry.Symmetry
NotPDB - Variable in class org.jmol.popup.JmolPopup
notriangles - Static variable in class org.jmol.script.T
nOut - Variable in class org.jmol.util.Shader
noValuesAtAll - Variable in class org.jmol.quantum.NciCalculation
now - Static variable in class org.jmol.script.T
noZapped - Variable in class org.jmol.popup.JmolPopup
NP - Static variable in class org.jmol.modelsetbio.NucleicMonomer
nPairs - Variable in class org.jmol.smiles.SmilesGenerator
nPairsMax - Variable in class org.jmol.smiles.SmilesGenerator
nParameters - Variable in class org.jmol.script.ScriptFunction
nPeaks - Variable in class org.jmol.adapter.readers.more.JcampdxReader
nPerLine - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
nPoints - Variable in class org.jmol.jvxl.data.VolumeData
nPoints - Variable in class org.jmol.shapespecial.Draw
nPoints - Variable in class org.jmol.shapespecial.Polyhedra
nPoints - Variable in class org.jmol.smiles.SmilesMeasure
nPoints - Variable in class org.jmol.util.MeshCapper
nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
nPolygons - Variable in class org.jmol.jvxl.readers.NffReader
nPolygons - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
nPolygons - Variable in class org.jmol.jvxl.readers.PmeshReader
nPolygons - Variable in class org.jmol.jvxl.readers.Ras3DReader
npqd - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
nPrimitives - Variable in class org.jmol.smiles.SmilesBond
nPriorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  the number of distinct priorities determined for this atom for the current rule; 0-4 for the root atom; 0-3 for all others
nProcessors - Static variable in class org.jmol.viewer.Viewer
nRead - Variable in class org.jmol.jvxl.readers.XplorReader
nRegions - Variable in class org.jmol.util.MeshCapper
  informational only
nRes - Variable in class org.jmol.adapter.readers.pdb.PdbReader
nRes - Variable in class org.jmol.modelsetbio.ProteinStructure
nRootDuplicates - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  number of root-duplicate atoms (root atom only
nRotations - Variable in class org.jmol.symmetry.HallInfo
nrows - Variable in class org.jmol.awtjs.swing.Grid
nSemiSkip - Variable in class org.jmol.script.ScriptCompiler
nSets - Variable in class org.jmol.util.MeshSurface
nSFO - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
nSkip - Variable in class org.jmol.jvxl.readers.CastepDensityReader
nSkipX - Variable in class org.jmol.jvxl.readers.VolumeFileReader
nSkipY - Variable in class org.jmol.jvxl.readers.VolumeFileReader
nSkipZ - Variable in class org.jmol.jvxl.readers.VolumeFileReader
nSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
nSPDF - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
nStructures - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
nSubAtoms - Variable in class org.jmol.smiles.SmilesAtom
nSurfaceAtoms - Variable in class org.jmol.modelset.AtomCollection
nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
nSurfaces - Variable in class org.jmol.jvxl.readers.VolumeFileReader
nTab - Variable in class org.jmol.console.GenericConsole
nTest - Variable in class org.jmol.jvxl.readers.IsoSolventReader
nText - Variable in class org.jmol.export.___Exporter
nTokens - Variable in class org.jmol.script.ScriptTokenParser
nTri - Variable in class org.jmol.export._StlExporter
nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
nTriangles - Variable in class org.jmol.jvxl.readers.PolygonFileReader
nTriangles - Variable in class org.jmol.util.MeshCapper
  informational only
nTries - Variable in class org.jmol.jvxl.readers.IsoShapeReader
nType - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
nuclearCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
nucleic - Static variable in class org.jmol.adapter.readers.pymol.PyMOLReader
nucleic - Static variable in class org.jmol.script.T
NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
NucleicMonomer - Class in org.jmol.modelsetbio
NucleicMonomer() - Constructor for class org.jmol.modelsetbio.NucleicMonomer
NucleicPolymer - Class in org.jmol.modelsetbio
NucleicPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.NucleicPolymer
nucleicRenderer - Variable in class org.jmol.renderbio.CartoonRenderer
NucleicRenderer - Class in org.jmol.renderbio
  extends CartoonRenderer for nucleics
NucleicRenderer() - Constructor for class org.jmol.renderbio.NucleicRenderer
nucleus - Variable in class org.jmol.adapter.readers.more.JcampdxReader
nullGroup - Variable in class org.jmol.modelset.ModelLoader
nullModelSetName - Variable in class org.jmol.popup.JmolPopup
nullObj - Variable in class org.jmol.adapter.readers.xml.XmlReader
nullReturn(int) - Static method in class org.jmol.symmetry.SymmetryDesc
nullShadeIndex - Static variable in class org.jmol.g3d.Graphics3D
nullToken - Static variable in class org.jmol.shape.Labels
number - Variable in enum org.jmol.util.Edge.EnumBondOrder
numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptError
numCached - Variable in class org.jmol.modelset.BondCollection
numSet - Variable in class org.jmol.modelset.MeasurementPending
numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
nUnique - Static variable in class org.jmol.symmetry.PointGroup
nUNK - Variable in class org.jmol.adapter.readers.pdb.PdbReader
nUnnamed - Variable in class org.jmol.shape.MeshCollection
nValue(T) - Static method in class org.jmol.script.SV
nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
nVertices - Variable in class org.jmol.jvxl.readers.PolygonFileReader
nVertices - Variable in class org.jmol.shapespecial.Polyhedra
nVertices - Variable in class org.jmol.shapespecial.Polyhedron
nVib - Variable in class org.jmol.adapter.smarter.XtalSymmetry
nVibrations - Variable in class org.jmol.adapter.readers.quantum.CsfReader
nvidia_bugs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
NVPair() - Constructor for class org.jmol.adapter.readers.xml.XmlReader.NVPair
nwchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
NWChemReader - Class in org.jmol.adapter.readers.quantum
  A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
nWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
nX - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
nX - Variable in class org.jmol.quantum.QuantumCalculation
nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
nY - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
nY - Variable in class org.jmol.quantum.QuantumCalculation
nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
nZ - Variable in class org.jmol.quantum.QuantumCalculation

## O

o(String, Object) - Static method in class org.jmol.i18n.GT
O - Static variable in class org.jmol.modelsetbio.AminoMonomer
o(int, Object) - Static method in class org.jmol.script.T
O1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O2Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O3P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O5P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
O6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
oabc - Variable in class org.jmol.jvxl.data.VolumeData
oabc - Variable in class org.jmol.util.MeshSurface
OBJ - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
obj - Static variable in class org.jmol.script.T
OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
objCls1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
objCls2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
objColors - Variable in class org.jmol.viewer.GlobalSettings
object - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
object - Static variable in class org.jmol.script.T
OBJECT_ALIGNMENT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_CALCULATOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_CALLBACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_CGO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_GADGET - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_GROUP - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_MAPDATA - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_MAPDATA - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
OBJECT_MAPMESH - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_MAPMESH - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
OBJECT_MEASURE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_MOLECULE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_SELECTION - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_SLICE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OBJECT_SURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
objectHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objectInfo - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objectJmolName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objectName - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
objectName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objectNameID - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
objectNameID - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objectNameList - Static variable in class org.jmol.viewer.StateManager
objectNameParameter(int) - Method in class org.jmol.script.ScriptParam
objectOf(DefaultListModel<?>, Object) - Static method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
objects - Variable in class org.jmol.shape.TextShape
objectSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objectsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
objectType - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
objFileRootName - Variable in class org.jmol.export._ObjExporter
  Path of the OBJ file without the extension.
objID1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
objID2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
objMad10 - Variable in class org.jmol.viewer.GlobalSettings
ObjReader - Class in org.jmol.jvxl.readers
ObjReader() - Constructor for class org.jmol.jvxl.readers.ObjReader
objStateOn - Variable in class org.jmol.viewer.GlobalSettings
oc - Variable in class org.jmol.export._StlExporter
oc - Variable in class org.jmol.shapesurface.PMeshWriter
oc - Variable in class org.jmol.util.JSONWriter
OCC_CRENEL_C - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
OCC_CRENEL_W - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
OCC_SPECIAL_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
occAbsolute - Variable in class org.jmol.util.ModulationSet
  for Crenels (simple occupational modulation or Legendre displacement modulation, the value determined here is absolute (0 or 1), not an adjustment; set in calculate() by one of the modulations
occluded - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
occludedObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
occParams - Variable in class org.jmol.util.ModulationSet
occSiteMultiplicity - Variable in class org.jmol.util.ModulationSet
occupancies - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
occupancies - Variable in class org.jmol.modelset.AtomCollection
OCCUPANCY - Static variable in class org.jmol.adapter.readers.cif.CifReader
OCCUPANCY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
occupancy - Static variable in class org.jmol.script.T
occValue - Variable in class org.jmol.util.ModulationSet
  final occupancy value -- absolute; in range [0,1]
OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
octants - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OdysseyReader - Class in org.jmol.adapter.readers.spartan
OdysseyReader() - Constructor for class org.jmol.adapter.readers.spartan.OdysseyReader
off - Static variable in class org.jmol.script.T
officialRelease - Static variable in class org.jmol.viewer.JC
offscreen_rendering_for_antialiasing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
offscreen_rendering_multiplier - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
offscreenImage - Variable in class org.jmol.g3d.Platform3D
offset(int, int) - Method in class org.jmol.adapter.readers.pymol.JmolObject
  offset is carried out in ModelLoader when the "script" is processed to move the bits to skip the base atom index.
offset - Variable in class org.jmol.jvxl.calc.MarchingCubes
offset - Variable in class org.jmol.modelkit.Constraint
offset - Variable in class org.jmol.render.LabelsRenderer
offset - Variable in class org.jmol.render.UccageRenderer
offset - Variable in class org.jmol.renderspecial.DipolesRenderer
offset - Static variable in class org.jmol.script.T
offset - Variable in class org.jmol.shapespecial.Draw
offset(V3) - Method in class org.jmol.shapespecial.DrawMesh
offset - Variable in class org.jmol.shapespecial.Polyhedron
offset(BS, int, int) - Static method in class org.jmol.util.BSUtil
  offset the bitset in place by the specified number of bits starting at a given position
offset - Variable in class org.jmol.util.BZone
offset - Variable in class org.jmol.util.MeshSurface
offsetAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
offsetCenter(P3) - Method in class org.jmol.jvxl.data.VolumeData
offsetObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
offsetPbufBeginLine - Variable in class org.jmol.g3d.SphereRenderer
offsetPercent - Variable in class org.jmol.shapespecial.Dipole
offsetPolyhedra(P3) - Method in class org.jmol.shapespecial.Polyhedra
offsetPt - Variable in class org.jmol.shapespecial.Dipole
offsets - Variable in class org.jmol.modelsetbio.Monomer
offsets - Variable in class org.jmol.shape.Labels
offsetSide - Variable in class org.jmol.renderspecial.DipolesRenderer
offsetside - Static variable in class org.jmol.script.T
offsetSide - Variable in class org.jmol.shapespecial.Dipole
offsetT - Variable in class org.jmol.render.UccageRenderer
offsetX - Variable in class org.jmol.modelset.Text
offsetY - Variable in class org.jmol.modelset.Text
OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
OK - Static variable in class org.jmol.script.ScriptCompiler
ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
OK2 - Static variable in class org.jmol.script.ScriptCompiler
okButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
okButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
oldFileName - Variable in class org.jmol.shapesurface.Isosurface
oldNPriorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  the number of distinct priorities determined for this atom for the current rule; 0-4 for the root atom; 0-3 for all others
oldPriorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  priorities associated with each subsituent from high (0) to low (3); due to equivaliencies at a given rule level, these numbers may duplicate and have gaps - for example, [0 2 0 3]
oldType - Variable in class org.jmol.util.ContactPair
OLIVE - Static variable in class org.jmol.util.C
omega - Variable in class org.jmol.modelsetbio.Monomer
omega - Static variable in class org.jmol.script.T
on - Static variable in class org.jmol.script.T
once - Static variable in class org.jmol.script.T
ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
oneFace - Variable in class org.jmol.export._VrmlExporter
oneFifth - Static variable in class org.jmol.util.Geodesic
onePerLine - Variable in class org.jmol.jvxl.readers.PmeshReader
oneTenth - Static variable in class org.jmol.util.Geodesic
only - Static variable in class org.jmol.script.T
onlySelectedDots - Variable in class org.jmol.geodesic.EnvelopeCalculation
oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
oops(Exception) - Method in class org.jmol.minimize.MinimizationThread
oops(Exception) - Method in class org.jmol.navigate.Navigator
oops(Exception) - Method in class org.jmol.thread.JmolThread
opacity - Variable in class org.jmol.awt.AwtColor
opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
opAnd - Static variable in class org.jmol.script.T
opAND - Static variable in class org.jmol.script.T
opaque - Static variable in class org.jmol.script.T
opaque_background - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OPAQUE_MASK - Static variable in class org.jmol.util.C
opCount - Variable in class org.jmol.adapter.readers.cif.MMTFReader
openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
openBufferedReader(String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
openButton - Variable in class org.jmol.console.ScriptEditor
openChooser - Static variable in class org.jmol.dialog.Dialog
openDOM(Object) - Method in class org.jmol.api.JmolViewer
openDOM(Object) - Method in class org.jmol.viewer.Viewer
  applet DOM method -- does not preserve state
openExportChannel(double, String, boolean) - Method in class org.jmol.viewer.Viewer
openFile(String) - Method in class org.jmol.api.JmolViewer
openFile(String) - Method in class org.jmol.appletjs.Jmol
  possibly called from JSmolApplet.js upon start up
openFile(String) - Method in class org.jmol.viewer.Viewer
  for JmolSimpleViewer -- external applications only (and no-script JavaScript)
openFile() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
openFileAsync(String, int) - Method in interface org.jmol.api.JmolScriptManager
openFileAsync(String) - Method in class org.jmol.api.JmolViewer
openFileAsync(String, int) - Method in class org.jmol.script.ScriptManager
  From file dropping.
openFileAsyncSpecial(String, int) - Method in class org.jmol.api.JmolViewer
openFileAsyncSpecial(String, int) - Method in class org.jmol.appletjs.Jmol
openFileAsyncSpecial(String, int) - Method in class org.jmol.viewer.Viewer
  opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file.
openFileFull(String, boolean, Map<String, Object>, SB) - Method in class org.jmol.viewer.Viewer
  does NOT repaint
openFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
openFiles(String[]) - Method in class org.jmol.api.JmolViewer
openFiles(String[]) - Method in class org.jmol.viewer.Viewer
  for JmolSimpleViewer -- external applications only
openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManager
openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManagerAwt
openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManagerJS
openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
openPreview - Variable in class org.jmol.dialog.Dialog
openReader(String, Object) - Method in class org.jmol.api.JmolViewer
  Opens the file and creates the model set, given the reader.
openReader(String, String, Object) - Method in class org.jmol.api.JmolViewer
  Opens the file and creates the model set, given the reader.
openReader(String, String, Object) - Method in class org.jmol.viewer.Viewer
  Opens the file, given an already-created reader.
openSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
openSMILES - Variable in class org.jmol.smiles.SmilesGenerator
openStringInline(String) - Method in class org.jmol.api.JmolViewer
openStringInline(String) - Method in class org.jmol.viewer.Viewer
  only used by file dropper.
openStringInlineParamsAppend(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
  Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
openStringsInlineParamsAppend(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
  opens multiple files inline; does NOT repaint
openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
opEQ - Static variable in class org.jmol.script.T
OPER_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
OPER_XYZ - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
operate() - Method in class org.jmol.script.ScriptMathProcessor
Operation() - Constructor for class org.jmol.symmetry.PointGroup.Operation
Operation(V3, int) - Constructor for class org.jmol.symmetry.PointGroup.Operation
Operation(V3) - Constructor for class org.jmol.symmetry.PointGroup.Operation
OPERATION_IMPROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
OPERATION_INVERSION_CENTER - Static variable in class org.jmol.symmetry.PointGroup
OPERATION_PLANE - Static variable in class org.jmol.symmetry.PointGroup
OPERATION_PROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
operationCount - Variable in class org.jmol.symmetry.SpaceGroup
operations - Variable in class org.jmol.symmetry.SpaceGroup
operFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
opGE - Static variable in class org.jmol.script.T
opGT - Static variable in class org.jmol.script.T
opId - Variable in class org.jmol.symmetry.SymmetryOperation
opIf - Static variable in class org.jmol.script.T
opLE - Static variable in class org.jmol.script.T
opLIKE - Static variable in class org.jmol.script.T
opLT - Static variable in class org.jmol.script.T
opNE - Static variable in class org.jmol.script.T
opNot - Static variable in class org.jmol.script.T
opOr - Static variable in class org.jmol.script.T
oPt - Variable in class org.jmol.script.ScriptMathProcessor
OPT_ARCS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_ARROWS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_AXES - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_BALL - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_COUNT - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_DOTS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_FILL - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
OPT_WIREFRAME - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
optimize2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
optimize2d - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
options - Static variable in class org.jmol.script.T
options - Variable in class org.jmol.shapespecial.Ellipsoid
opToggle - Static variable in class org.jmol.script.T
opTokenFor(int) - Method in class org.jmol.scriptext.MathExt
optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
optParameterAsString(int) - Method in class org.jmol.script.ScriptParam
OPTS - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
optsField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
OptSort() - Constructor for class org.openscience.jmol.app.JmolApp.OptSort
opXor - Static variable in class org.jmol.script.T
ORANGE - Static variable in class org.jmol.util.C
orbEnergy - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
orbital - Static variable in class org.jmol.script.T
orbitalData - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
orbitalInfo - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
orbitalMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
orbitals - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
Orbitals - Class in org.openscience.jmol.app.webexport
Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
OrbitalSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
orbOcc - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
order - Variable in class org.jmol.adapter.smarter.Bond
order - Variable in class org.jmol.minimize.MinBond
order - Variable in class org.jmol.symmetry.HallRotationTerm
order - Variable in class org.jmol.symmetry.PointGroup.Operation
order - Variable in class org.jmol.util.Edge
order - Variable in class org.jmol.util.Modulation
order - Variable in class org.jmol.viewer.Connection
ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_HEX - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_QUAD - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_QUINT - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
ORDER_PYMOL_MULT - Static variable in class org.jmol.api.JmolAdapter
ORDER_PYMOL_SINGLE - Static variable in class org.jmol.api.JmolAdapter
ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
org.jmol.adapter.readers.cif - package org.jmol.adapter.readers.cif
org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
org.jmol.adapter.readers.pdb - package org.jmol.adapter.readers.pdb
org.jmol.adapter.readers.pymol - package org.jmol.adapter.readers.pymol
org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
org.jmol.adapter.readers.spartan - package org.jmol.adapter.readers.spartan
org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
org.jmol.adapter.smarter - package org.jmol.adapter.smarter
org.jmol.adapter.writers - package org.jmol.adapter.writers
org.jmol.api - package org.jmol.api
org.jmol.api.js - package org.jmol.api.js
org.jmol.applet - package org.jmol.applet
org.jmol.appletjs - package org.jmol.appletjs
org.jmol.atomdata - package org.jmol.atomdata
org.jmol.awt - package org.jmol.awt
org.jmol.awtjs - package org.jmol.awtjs
org.jmol.awtjs.swing - package org.jmol.awtjs.swing
org.jmol.awtjs2d - package org.jmol.awtjs2d
org.jmol.bspt - package org.jmol.bspt
  Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
org.jmol.c - package org.jmol.c
org.jmol.console - package org.jmol.console
org.jmol.consolejs - package org.jmol.consolejs
org.jmol.dialog - package org.jmol.dialog
org.jmol.dssx - package org.jmol.dssx
org.jmol.export - package org.jmol.export
org.jmol.g3d - package org.jmol.g3d
  Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
org.jmol.geodesic - package org.jmol.geodesic
org.jmol.i18n - package org.jmol.i18n
org.jmol.image - package org.jmol.image
org.jmol.io - package org.jmol.io
org.jmol.jsv - package org.jmol.jsv
org.jmol.jvxl.api - package org.jmol.jvxl.api
org.jmol.jvxl.calc - package org.jmol.jvxl.calc
org.jmol.jvxl.data - package org.jmol.jvxl.data
org.jmol.jvxl.readers - package org.jmol.jvxl.readers
org.jmol.minimize - package org.jmol.minimize
org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
org.jmol.modelkit - package org.jmol.modelkit
org.jmol.modelset - package org.jmol.modelset
org.jmol.modelsetbio - package org.jmol.modelsetbio
org.jmol.multitouch - package org.jmol.multitouch
org.jmol.multitouch.jni - package org.jmol.multitouch.jni
org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
org.jmol.navigate - package org.jmol.navigate
org.jmol.popup - package org.jmol.popup
org.jmol.quantum - package org.jmol.quantum
org.jmol.quantum.mo - package org.jmol.quantum.mo
org.jmol.render - package org.jmol.render
org.jmol.renderbio - package org.jmol.renderbio
org.jmol.rendercgo - package org.jmol.rendercgo
org.jmol.renderspecial - package org.jmol.renderspecial
org.jmol.rendersurface - package org.jmol.rendersurface
org.jmol.script - package org.jmol.script
org.jmol.scriptext - package org.jmol.scriptext
org.jmol.shape - package org.jmol.shape
org.jmol.shapebio - package org.jmol.shapebio
org.jmol.shapecgo - package org.jmol.shapecgo
org.jmol.shapespecial - package org.jmol.shapespecial
org.jmol.shapesurface - package org.jmol.shapesurface
org.jmol.smiles - package org.jmol.smiles
  Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
org.jmol.symmetry - package org.jmol.symmetry
org.jmol.thread - package org.jmol.thread
org.jmol.translation - package org.jmol.translation
org.jmol.util - package org.jmol.util
org.jmol.viewer - package org.jmol.viewer
org.jmol.viewer.binding - package org.jmol.viewer.binding
org.openscience.jmol.app - package org.openscience.jmol.app
org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
org.openscience.jmol.app.jmolpanel.console - package org.openscience.jmol.app.jmolpanel.console
org.openscience.jmol.app.jsonkiosk - package org.openscience.jmol.app.jsonkiosk
org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
org.openscience.jvxl - package org.openscience.jvxl
org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
orientation - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
orientation - Variable in class org.jmol.modelset.Model
Orientation - Class in org.jmol.modelset
Orientation(Viewer, boolean, float[]) - Constructor for class org.jmol.modelset.Orientation
orientation - Static variable in class org.jmol.script.T
orientationInput - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
origin - Variable in class org.jmol.jvxl.data.VolumeData
origin - Variable in class org.jmol.jvxl.readers.MapFileReader
origin - Variable in class org.jmol.jvxl.readers.Parameters
origin - Static variable in class org.jmol.script.T
origin - Variable in class org.jmol.shapespecial.Dipole
originalSystemProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
originBohr - Variable in class org.jmol.quantum.QuantumCalculation
originPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
originPoint - Variable in class org.jmol.shape.Axes
originScreen - Variable in class org.jmol.render.AxesRenderer
orthoscopic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
OS_PI_COUNTS - Static variable in class org.jmol.smiles.SmilesAromatic
  Index to inner array is covalent bond count (b) + valence (v) + charge (c, carbon only) - 4.
oStack - Variable in class org.jmol.script.ScriptMathProcessor
OT - Static variable in class org.jmol.modelsetbio.AminoMonomer
otherAtoms - Variable in class org.jmol.shapespecial.Polyhedra
out - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
out - Variable in class org.jmol.export.___Exporter
out - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
out - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
out - Static variable in class org.jmol.script.T
output(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
output - Variable in class org.jmol.console.GenericConsole
output(String) - Method in class org.jmol.console.ScriptEditor
output(String) - Method in class org.jmol.export.___Exporter
output(T3) - Method in class org.jmol.export.___Exporter
output(T3) - Method in class org.jmol.export._IdtfExporter
output(T3, SB, boolean) - Method in class org.jmol.export._IdtfExporter
output(T3) - Method in class org.jmol.export._MayaExporter
output(T3) - Method in class org.jmol.export._ObjExporter
output(T3) - Method in class org.jmol.export._PovrayExporter
output(String) - Method in class org.jmol.export._StlExporter
output(T3) - Method in class org.jmol.export._TachyonExporter
output(T3) - Method in class org.jmol.export._VrmlExporter
output(T3) - Method in class org.jmol.export.JSExporter
output(String) - Method in class org.jmol.util.GenericApplet
output80CharWrap(SB, String, int) - Method in class org.jmol.util.MolWriter
outputAlphaCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
outputAttr(String, float, float, float) - Method in class org.jmol.export._StlExporter
outputAttr(String, float, float, float) - Method in class org.jmol.export._VrmlExporter
outputAttr(String, float, float, float) - Method in class org.jmol.export._X3dExporter
outputAttrPt(String, T3) - Method in class org.jmol.export._StlExporter
outputAttrPt(String, T3) - Method in class org.jmol.export._VrmlExporter
outputAttrPt(String, T3) - Method in class org.jmol.export._X3dExporter
outputBeforePrompt(String, SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
outputBuffer - Variable in class org.jmol.script.ScriptContext
outputBuffer - Variable in class org.jmol.script.ScriptEval
outputBuffer - Variable in class org.jmol.util.GenericApplet
outputChildClose() - Method in class org.jmol.export._StlExporter
outputChildClose() - Method in class org.jmol.export._VrmlExporter
outputChildClose() - Method in class org.jmol.export._X3dExporter
outputChildShapeClose() - Method in class org.jmol.export._VrmlExporter
outputChildShapeClose() - Method in class org.jmol.export._X3dExporter
outputChildShapeStart() - Method in class org.jmol.export._VrmlExporter
outputChildShapeStart() - Method in class org.jmol.export._X3dExporter
outputChildStart() - Method in class org.jmol.export._StlExporter
outputChildStart() - Method in class org.jmol.export._VrmlExporter
outputChildStart() - Method in class org.jmol.export._X3dExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
outputCircle(P3, P3, short, float) - Method in class org.jmol.export._IdtfExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._StlExporter
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._X3dExporter
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
outputCircle1(P3, P3, short, float) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputCircle.
outputCloseTag() - Method in class org.jmol.export._VrmlExporter
outputCloseTag() - Method in class org.jmol.export._X3dExporter
outputColorIndices(int[][], int, BS, int, Map<Short, Integer>, short[], short[]) - Method in class org.jmol.export._VrmlExporter
outputColors(Lst<Short>) - Method in class org.jmol.export._VrmlExporter
outputComment(String) - Method in class org.jmol.export.___Exporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export.__CartesianExporter
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._IdtfExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._MayaExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export._VrmlExporter
outputCone(P3, P3, float, short) - Method in class org.jmol.export.JSExporter
outputCone1(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputCone.
outputConeGeometry(boolean) - Method in class org.jmol.export._VrmlExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._IdtfExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._MayaExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._ObjExporter
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._VrmlExporter
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.JSExporter
outputCylinder1(P3, P3, P3, short, byte, float, P3, P3) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputCylinder.
outputCylinderChildScaled(short, byte) - Method in class org.jmol.export._VrmlExporter
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._PovrayExporter
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._TachyonExporter
outputCylinderGeometry(int) - Method in class org.jmol.export._VrmlExporter
outputDefChildFaceSet(String) - Method in class org.jmol.export._VrmlExporter
outputDefChildFaceSet(String) - Method in class org.jmol.export._X3dExporter
outputDocument - Variable in class org.jmol.console.AppletConsole.GenericTextPane
outputEcho(String) - Method in class org.jmol.console.ScriptEditor.EditorDocument
outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
outputEdge(int, int, int) - Method in class org.jmol.shapesurface.PMeshWriter
outputEllipse(P3, P3, P3, P3, short) - Method in class org.jmol.export._IdtfExporter
outputEllipse1(P3, P3, P3, P3, short) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputEllipse.
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.__CartesianExporter
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export.__RayTracerExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._IdtfExporter
outputEllipsoid(T3, M4, short) - Method in class org.jmol.export._IdtfExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._MayaExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._ObjExporter
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._PovrayExporter
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._TachyonExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._VrmlExporter
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.JSExporter
outputEllipsoid1(T3, float, float, float, A4, short) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputEllipsoid.
outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
outputExtension - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
outputFace(int[], int[], int) - Method in class org.jmol.export.JSExporter
outputFace1(int[], int[], int[]) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputFace used for no texture coordinates.
outputFace2(int[], int, int[], int[]) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputFace used with texture coordinates.
outputFaceSetClose() - Method in class org.jmol.export._VrmlExporter
outputFaceSetClose() - Method in class org.jmol.export._X3dExporter
outputFaceSetStart() - Method in class org.jmol.export._VrmlExporter
outputFaceSetStart() - Method in class org.jmol.export._X3dExporter
outputFileName - Variable in class org.jmol.dialog.Dialog
outputFileType - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputFooter() - Method in class org.jmol.export.___Exporter
outputFooter() - Method in class org.jmol.export._IdtfExporter
outputFooter() - Method in class org.jmol.export._TachyonExporter
outputFooter() - Method in class org.jmol.export._VrmlExporter
outputFooter() - Method in class org.jmol.export._X3dExporter
outputFooter() - Method in class org.jmol.export.JSExporter
outputFormatChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Called when the OutputFormat check box is modified
outputFormatCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputFormatCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._StlExporter
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._X3dExporter
outputHeader() - Method in class org.jmol.export.___Exporter
outputHeader() - Method in class org.jmol.export._IdtfExporter
outputHeader() - Method in class org.jmol.export._MayaExporter
outputHeader() - Method in class org.jmol.export._ObjExporter
outputHeader() - Method in class org.jmol.export._PovrayExporter
outputHeader() - Method in class org.jmol.export._StlExporter
outputHeader() - Method in class org.jmol.export._TachyonExporter
outputHeader() - Method in class org.jmol.export._VrmlExporter
outputHeader() - Method in class org.jmol.export._X3dExporter
outputHeader() - Method in class org.jmol.export.JSExporter
outputHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputIndices(int[][], int[], int, BS, int) - Method in class org.jmol.export.__CartesianExporter
outputInitialTransform() - Method in class org.jmol.export._VrmlExporter
outputInt(int) - Method in class org.jmol.shapesurface.PMeshWriter
outputJmolPerspective() - Method in class org.jmol.export.___Exporter
outputLines(SB, String, int) - Method in class org.jmol.util.MolWriter
outputList(T3[], int, M4, String, BS) - Method in class org.jmol.export._ObjExporter
  create the v or vn list
OutputManager - Class in org.jmol.viewer
OutputManager() - Constructor for class org.jmol.viewer.OutputManager
outputManager - Variable in class org.jmol.viewer.Viewer
OutputManagerAwt - Class in org.jmol.viewer
OutputManagerAwt() - Constructor for class org.jmol.viewer.OutputManagerAwt
OutputManagerJS - Class in org.jmol.viewer
OutputManagerJS() - Constructor for class org.jmol.viewer.OutputManagerJS
outputMsg(String) - Method in class org.jmol.console.GenericConsole
outputMtl(String) - Method in class org.jmol.export._ObjExporter
  Write to the .mtl file and keep track of the bytes written.
outputNodes() - Method in class org.jmol.export._IdtfExporter
outputNormals(Lst<String>) - Method in class org.jmol.export._VrmlExporter
outputPoint(int, int) - Method in class org.jmol.shapesurface.PMeshWriter
outputPoints(BS) - Method in class org.jmol.shapesurface.PMeshWriter
outputQuaternionFrame(P3, P3, P3, P3, float, float, float) - Method in class org.jmol.export._VrmlExporter
outputRing(int, int, int, V3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
outputRotation(A4) - Method in class org.jmol.export._StlExporter
outputRotation(A4) - Method in class org.jmol.export._VrmlExporter
outputRotation(A4) - Method in class org.jmol.export._X3dExporter
outputShapeClose() - Method in class org.jmol.export._VrmlExporter
outputShapeClose() - Method in class org.jmol.export._X3dExporter
outputShapeStart() - Method in class org.jmol.export._VrmlExporter
outputShapeStart() - Method in class org.jmol.export._X3dExporter
outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export.__CartesianExporter
outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export._VrmlExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
outputSphere(float, float, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
outputSphereChildScaled(P3, float, P3[], short) - Method in class org.jmol.export._VrmlExporter
outputSphereGeometry() - Method in class org.jmol.export._VrmlExporter
outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.___Exporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._IdtfExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._MayaExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._PovrayExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._TachyonExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.JSExporter
outputTextPixel(P3, int) - Method in class org.jmol.export.__CartesianExporter
outputTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._IdtfExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._MayaExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._ObjExporter
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._VrmlExporter
outputTextPixel(P3, int) - Method in class org.jmol.export._X3dExporter
outputTextPixel(P3, int) - Method in class org.jmol.export.JSExporter
outputTexture(short, boolean) - Method in class org.jmol.export._TachyonExporter
outputTexture(int, boolean) - Method in class org.jmol.export._TachyonExporter
outputTexture2(String, String, boolean) - Method in class org.jmol.export._TachyonExporter
outputTextureCode() - Method in class org.jmol.export._TachyonExporter
outputToFile(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._VrmlExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__CartesianExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__RayTracerExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._IdtfExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._MayaExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._PovrayExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._TachyonExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._X3dExporter
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.JSExporter
outputTriangle(int, int, int, int, int) - Method in class org.jmol.shapesurface.PMeshWriter
outputTriangle(int, int, int) - Method in class org.jmol.util.MeshCapper
  Export triangle to MeshSlicer
outputTriangle1(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
  Local implementation of outputCylinder.
outputTriangleGeometry(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
outputTriangles(boolean, BS, BS) - Method in class org.jmol.shapesurface.PMeshWriter
outputUseChildClose(String) - Method in class org.jmol.export._VrmlExporter
outputUseChildClose(String) - Method in class org.jmol.export._X3dExporter
outputVertex(T3, T3) - Method in class org.jmol.export.___Exporter
outputVertex(T3, T3) - Method in class org.jmol.export.__RayTracerExporter
outputVertices(T3[], int, T3) - Method in class org.jmol.export.___Exporter
outputWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
outputXYZ(T3) - Method in class org.jmol.shapesurface.PMeshWriter
outSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
oValue(Object) - Static method in class org.jmol.script.SV
overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
overlay_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL

## P

p - Variable in class org.jmol.jvxl.readers.IsoSolventReader
P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
P - Static variable in class org.jmol.quantum.QS
p - Variable in class org.jmol.render.MeasuresRenderer
p - Variable in class org.jmol.symmetry.UnitCellIterator
p0 - Variable in class org.jmol.g3d.Pixelator
p0 - Variable in class org.jmol.quantum.NciCalculation
p1 - Variable in class org.jmol.quantum.NciCalculation
p1 - Variable in class org.jmol.render.SticksRenderer
p2 - Variable in class org.jmol.quantum.NciCalculation
p2 - Variable in class org.jmol.render.SticksRenderer
P2nReader - Class in org.jmol.adapter.readers.pdb
  P2N file reader.
P2nReader() - Constructor for class org.jmol.adapter.readers.pdb.P2nReader
p2nStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
p3 - Variable in class org.jmol.jvxl.readers.MapFileReader
p3Screens - Variable in class org.jmol.render.CageRenderer
p3Screens - Variable in class org.jmol.render.MeshRenderer
p4 - Variable in class org.jmol.viewer.TransformManager4D
P_CHECK - Static variable in class org.jmol.util.MeshSurface
P_CONTOUR - Static variable in class org.jmol.util.MeshSurface
P_EXPLICIT_COLOR - Static variable in class org.jmol.util.MeshSurface
P_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
P_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
pack() - Method in class org.jmol.awtjs.swing.JDialog
packageReadable(String, String, String) - Static method in class org.jmol.util.Escape
packageReadableSb(String, String, SB) - Static method in class org.jmol.util.Escape
packed - Static variable in class org.jmol.script.T
packingError - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
packingError - Variable in class org.jmol.adapter.smarter.XtalSymmetry
pageAuthorName - Static variable in class org.openscience.jmol.app.webexport.WebExport
pageAuthorName - Variable in class org.openscience.jmol.app.webexport.WebPanel
PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
pageUpBuffer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
paint(Graphics) - Method in class org.jmol.applet.AppletWrapper
paint(Graphics) - Method in class org.jmol.applet.Jmol
paint(Graphics) - Method in interface org.jmol.applet.WrappedApplet
paint(Graphics) - Method in class org.jmol.dialog.FilePreview.FPPanel
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
paintComponent(Graphics) - Method in class org.jmol.console.ImageDialog.ImageCanvas
pairSearch(Lst<Object[]>, Calculation, Lst<Object[]>, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
PAL - Enum in org.jmol.c
  Enum for animation mode.
PAL(String, int) - Constructor for enum org.jmol.c.PAL
PALETTE_ALTLOC - Static variable in enum org.jmol.c.PAL
PALETTE_AMINO - Static variable in enum org.jmol.c.PAL
PALETTE_CHAIN - Static variable in enum org.jmol.c.PAL
PALETTE_CPK - Static variable in enum org.jmol.c.PAL
PALETTE_ENERGY - Static variable in enum org.jmol.c.PAL
PALETTE_FIXEDTEMP - Static variable in enum org.jmol.c.PAL
PALETTE_FORMAL_CHARGE - Static variable in enum org.jmol.c.PAL
PALETTE_GROUP - Static variable in enum org.jmol.c.PAL
PALETTE_INSERTION - Static variable in enum org.jmol.c.PAL
PALETTE_JMOL - Static variable in enum org.jmol.c.PAL
PALETTE_MOLECULE - Static variable in enum org.jmol.c.PAL
PALETTE_MONOMER - Static variable in enum org.jmol.c.PAL
PALETTE_NONE - Static variable in enum org.jmol.c.PAL
PALETTE_NUCLEIC - Static variable in enum org.jmol.c.PAL
PALETTE_PARTIAL_CHARGE - Static variable in enum org.jmol.c.PAL
PALETTE_POLYMER - Static variable in enum org.jmol.c.PAL
PALETTE_PROPERTY - Static variable in enum org.jmol.c.PAL
PALETTE_RASMOL - Static variable in enum org.jmol.c.PAL
PALETTE_SHAPELY - Static variable in enum org.jmol.c.PAL
PALETTE_STRAIGHTNESS - Static variable in enum org.jmol.c.PAL
PALETTE_STRUCTURE - Static variable in enum org.jmol.c.PAL
PALETTE_SURFACE - Static variable in enum org.jmol.c.PAL
PALETTE_TEMP - Static variable in enum org.jmol.c.PAL
PALETTE_TYPE - Static variable in enum org.jmol.c.PAL
PALETTE_VARIABLE - Static variable in enum org.jmol.c.PAL
PALETTE_VOLATILE - Static variable in enum org.jmol.c.PAL
paletteBW - Variable in class org.jmol.util.ColorEncoder
paletteFriendly - Variable in class org.jmol.util.ColorEncoder
paletteID - Variable in class org.jmol.modelset.Atom
paletteIDs - Variable in class org.jmol.shape.AtomShape
paletteWB - Variable in class org.jmol.util.ColorEncoder
palindrome - Static variable in class org.jmol.script.T
panel() - Method in class org.openscience.jmol.app.webexport.Test
panelIndex - Variable in class org.openscience.jmol.app.webexport.WebPanel
panelName - Variable in class org.openscience.jmol.app.webexport.WebPanel
PAR_D - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_HARD - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_R - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_RADIUS - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_THETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_U - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_V - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_X - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_XI - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_Z - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
PAR_ZETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
parA - Variable in class org.jmol.minimize.forcefield.Calculations
parallel - Static variable in class org.jmol.script.T
parallelProcessor - Variable in class org.jmol.script.ScriptContext
parallelProcessor - Variable in class org.jmol.script.ScriptEval
parallelProcessor - Variable in class org.jmol.script.ScriptProcessRunnable
paramAsStr(int) - Method in class org.jmol.script.ScriptParam
paramAsStr(int) - Method in class org.jmol.scriptext.ScriptExt
parameterExpression(int, int, String, boolean, boolean, int, boolean, Map<String, SV>, String, boolean) - Method in class org.jmol.script.ScriptExpr
  This is the primary driver of the RPN (reverse Polish notation) expression processor.
parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptExpr
parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptExpr
parameterExpressionSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptExpr
parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptExpr
parameterExpressionToken(int) - Method in class org.jmol.script.ScriptExpr
parameterIndex(String) - Static method in class org.jmol.adapter.readers.xtal.GulpReader
Parameters - Class in org.jmol.jvxl.readers
Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
parameters - Variable in class org.jmol.jvxl.readers.Parameters
parameters - Static variable in class org.jmol.script.T
params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
params - Variable in class org.jmol.jvxl.readers.SurfaceReader
params - Variable in class org.jmol.util.JmolAudio
params - Variable in class org.jmol.util.Modulation
paramTypes - Static variable in class org.jmol.script.T
parB - Variable in class org.jmol.minimize.forcefield.Calculations
parBorU - Variable in class org.jmol.util.Tensor
parC - Variable in class org.jmol.minimize.forcefield.Calculations
parenCount - Variable in class org.jmol.script.ScriptCompiler
parenCount - Variable in class org.jmol.script.ScriptMathProcessor
parent - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
parent - Variable in class org.jmol.awt.AwtSwingComponent
parent - Variable in class org.jmol.awtjs.swing.Component
parent - Variable in class org.jmol.script.ScriptFlowContext
parent - Variable in class org.jmol.smiles.SmilesAtom
parent - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  direct ancestor of this atom
parentContext - Variable in class org.jmol.script.ScriptContext
parse(String) - Method in class org.jmol.smiles.SmilesParser
  Parses a SMILES String
parseAtom(SmilesSearch, SmilesAtom, String, SmilesAtom, SmilesBond, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
  Parses an atom definition
parseAtomTokens(Atom, String) - Method in class org.jmol.adapter.readers.simple.InputReader
parseBond(SmilesSearch, SmilesBond, String, SmilesBond, SmilesAtom, boolean, boolean, int, int[]) - Method in class org.jmol.smiles.SmilesParser
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
parseCommandParameter(short, boolean) - Method in class org.jmol.script.ScriptCompiler
parseConnection(SmilesSearch, int, SmilesAtom, SmilesBond) - Method in class org.jmol.smiles.SmilesParser
  Parses a ring definition
parseDataArray(String, boolean) - Method in class org.jmol.scriptext.CmdExt
parsedContext - Variable in class org.jmol.console.ScriptEditor
parsedData - Variable in class org.jmol.console.ScriptEditor
parseEPSData(String, Lst<Object>) - Static method in class org.jmol.shapecgo.CGOMesh
parseFloat(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseFloat() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseFloatArrayBsData(String[], BS, float[]) - Static method in class org.jmol.util.Parser
parseFloatArrayFromMatchAndField(String, BS, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
  the major lifter here.
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseFloatRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseFloatStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseInt(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseInt() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseIntAt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseIntNext(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseIntRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseIntStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseIntStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
parseJSON(String) - Method in class org.jmol.viewer.Viewer
parseJSONArray(String) - Method in class org.jmol.viewer.Viewer
parseJSONMap(String) - Method in class org.jmol.viewer.Viewer
parseKnownToken() - Method in class org.jmol.script.ScriptCompiler
parseLattRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
parseLineParameters(String[], byte[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
  sets up arrays and variables for tokenizer.getData()
parseLoopParametersFor(String, String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
parseM40Floats() - Method in class org.jmol.adapter.readers.xtal.JanaReader
parseMeasure(SmilesSearch, String, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
parseNested(SmilesSearch, String, String) - Method in class org.jmol.smiles.SmilesParser
parser - Variable in class org.jmol.adapter.readers.cif.CifReader
Parser - Class in org.jmol.util
Parser() - Constructor for class org.jmol.util.Parser
parseScript(String) - Method in class org.jmol.console.ScriptEditor
parseSfacCoefficients(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
parseSfacElementSymbols(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
parseSfacRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
parseSmiles(SmilesSearch, String, SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesParser
  Parses a part of a SMILES String
parseStringInfestedFloatArray(String, BS, float[]) - Static method in class org.jmol.util.Parser
  parses a "dirty" string for floats.
parseSymmRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseTokenRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseTokenStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
parseVariableLength(String) - Method in class org.jmol.smiles.SmilesParser
parseVariables(String) - Method in class org.jmol.smiles.SmilesParser
  variables can be defined, as in select within(SMARTS,'$R1="[CH3, NH2]";$R2="[$([$R1]),OH]"; {a}[$R2]') select within(SMARTS,'$R1="[CH3,NH2]";$R2="[OH]"; {a}[$([$R1]),$([$R2])]') "select aromatic atoms bearing CH3, NH2, or OH"
parseXML(XmlReader, Object, BufferedReader) - Method in class org.jmol.adapter.readers.xml.XmlHandler
parseXML() - Method in class org.jmol.adapter.readers.xml.XmlReader
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JC
PARTIALCHARGE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
partialCharge - Variable in class org.jmol.adapter.smarter.Atom
partialCharge - Variable in class org.jmol.minimize.MinAtom
partialcharge - Static variable in class org.jmol.script.T
partialCharges - Variable in class org.jmol.adapter.readers.simple.AmpacReader
partialCharges - Variable in class org.jmol.minimize.Minimizer
partialCharges - Variable in class org.jmol.modelset.AtomCollection
partialdots - Static variable in class org.jmol.script.T
partialDots - Variable in class org.jmol.viewer.GlobalSettings
PARTICLE_CHAIN - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
PARTICLE_NONE - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
PARTICLE_SYMOP - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
particleradius - Static variable in class org.jmol.script.T
particleRadius - Variable in class org.jmol.viewer.GlobalSettings
pass2Flag01 - Variable in class org.jmol.g3d.Graphics3D
pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
path - Variable in class org.jmol.awt.AwtG2D
path() - Method in class org.jmol.script.ScriptFlowContext
path - Static variable in class org.jmol.script.T
PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
  AtomSetCollectionReader.readData() will close any BufferedReader
PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
PathButton - Variable in class org.openscience.jmol.app.webexport.Test
pathforallfiles - Static variable in class org.jmol.script.T
pathForAllFiles - Variable in class org.jmol.viewer.FileManager
pattern - Variable in class org.jmol.smiles.SmilesAtom
pattern - Variable in class org.jmol.smiles.SmilesSearch
patternAromatic - Variable in class org.jmol.smiles.SmilesSearch
  Set in set() to indicate to SmilesMatcher that the string already has aromatic atoms indicated and so no aromaticity model should be applied.
patternAtoms - Variable in class org.jmol.smiles.SmilesSearch
patternBioSequence - Variable in class org.jmol.smiles.SmilesSearch
patternIndex - Variable in class org.jmol.smiles.SmilesAtom
PatternMatcher - Class in org.jmol.util
PatternMatcher() - Constructor for class org.jmol.util.PatternMatcher
pause - Static variable in class org.jmol.script.T
PAUSE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
PAUSE_DELAY - Static variable in class org.jmol.script.ScriptDelayThread
pauseAnimation() - Method in class org.jmol.viewer.AnimationManager
pauseButton - Variable in class org.jmol.console.ScriptEditor
pauseExecution(boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
pauseExecution(boolean) - Method in class org.jmol.script.ScriptEval
pauseScript(boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
pb - Variable in class org.jmol.g3d.Pixelator
pBotLeft - Variable in class org.jmol.g3d.HermiteRenderer
pBotRight - Variable in class org.jmol.g3d.HermiteRenderer
pbuf - Variable in class org.jmol.g3d.Graphics3D
pBuffer - Variable in class org.jmol.g3d.Platform3D
pBufferT - Variable in class org.jmol.g3d.Platform3D
pbufT - Variable in class org.jmol.g3d.Graphics3D
pButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
pc - Variable in class org.jmol.script.ScriptContext
pc - Variable in class org.jmol.script.ScriptEval
pc - Variable in class org.jmol.util.MeshSurface
  polygon count
pc0 - Variable in class org.jmol.script.ScriptContext
pcEnd - Variable in class org.jmol.script.ScriptContext
pcEnd - Variable in class org.jmol.script.ScriptEval
PCHRG - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
pcl - Variable in class org.jmol.awt.FileDropper
pcResume - Variable in class org.jmol.script.ScriptEval
pcs - Variable in class org.jmol.util.MeshSurface
  polygon color index "colix" array
pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
pdb - Static variable in class org.jmol.script.T
PDB_ANNOTATIONS - Static variable in class org.jmol.viewer.JC
pdb_conect_all - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_discrete_chains - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_echo_tags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_formal_charges - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_hetatm_guess_valences - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_hetatm_sort - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_honor_model_number - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_ignore_conect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_insertions_go_first - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_insure_orthogonal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_literal_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_no_end_record - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_reformat_names_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_retain_ids - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_standard_order - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_truncate_residue_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_unbond_cations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdb_use_ter_records - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pdbaddhydrogens - Static variable in class org.jmol.script.T
pdbAddHydrogens - Variable in class org.jmol.viewer.GlobalSettings
pdbAtomForH - Static variable in class org.jmol.dssx.AnnotationParser
pdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
  pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid.
pdbCartoonChecked - Static variable in class org.jmol.dialog.FilePreview
pdbgetheader - Static variable in class org.jmol.script.T
pdbGetHeader - Variable in class org.jmol.viewer.GlobalSettings
pdbHeader - Variable in class org.jmol.adapter.readers.pdb.PdbReader
pdbheader - Static variable in class org.jmol.script.T
pdbHydrogenCount - Static variable in class org.jmol.modelsetbio.BioResolver
pdbID - Variable in class org.jmol.adapter.readers.cif.CifReader
pdbID - Variable in class org.jmol.adapter.readers.cif.MMTFReader
pdbID - Variable in class org.jmol.adapter.readers.pdb.PdbReader
pdbID - Variable in class org.jmol.modelset.Model
pdbKey(int) - Method in class org.jmol.viewer.PropertyManager
pdbLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
pdbLoadFormat - Variable in class org.jmol.viewer.GlobalSettings
pdbLoadLigandFormat - Variable in class org.jmol.viewer.GlobalSettings
PDBOnly - Variable in class org.jmol.popup.JmolPopup
PdbReader - Class in org.jmol.adapter.readers.pdb
  PDB file reader.
PdbReader() - Constructor for class org.jmol.adapter.readers.pdb.PdbReader
pdbRecords - Static variable in class org.jmol.modelsetbio.BioExt
pdbsequential - Static variable in class org.jmol.script.T
pdbSequential - Variable in class org.jmol.viewer.GlobalSettings
peakData - Variable in class org.jmol.adapter.readers.more.JcampdxReader
peakFilePath - Variable in class org.jmol.jsv.JDXMOLParser
peakIndex - Variable in class org.jmol.jsv.JDXMOLParser
peek() - Method in class org.jmol.adapter.readers.pymol.PickleReader
per - Static variable in class org.jmol.script.T
percent - Static variable in class org.jmol.script.T
percent - Variable in class org.jmol.shapespecial.Ellipsoid
percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
percentvdwatom - Static variable in class org.jmol.script.T
percentVdwAtom - Variable in class org.jmol.viewer.GlobalSettings
percentVdwAtom - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
period - Static variable in class org.jmol.script.T
PERIOD_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Maximum value for the vibration period in seconds.
PERIOD_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Precision of the vibration period slider in seconds.
PERIOD_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Initial value for the vibration period in seconds.
PeriodicVolumeFileReader - Class in org.jmol.jvxl.readers
PeriodicVolumeFileReader() - Constructor for class org.jmol.jvxl.readers.PeriodicVolumeFileReader
periodSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
PERM_OCT - Static variable in class org.jmol.smiles.SmilesStereo
PERM_SS - Static variable in class org.jmol.smiles.SmilesStereo
PERM_TB - Static variable in class org.jmol.smiles.SmilesStereo
perpendicular - Static variable in class org.jmol.script.T
perper - Static variable in class org.jmol.script.T
perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
perspectivedepth - Static variable in class org.jmol.script.T
perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
perspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
perspectiveFactor - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
perspectivemodel - Static variable in class org.jmol.script.T
perspectiveModel - Variable in class org.jmol.viewer.TransformManager
perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
pfaatBinding - Variable in class org.jmol.viewer.ActionManager
PfaatBinding - Class in org.jmol.viewer.binding
PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
pfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
pFF - Variable in class org.jmol.minimize.Minimizer
phase - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
phase - Static variable in class org.jmol.script.T
phi - Variable in class org.jmol.modelsetbio.Monomer
phi - Static variable in class org.jmol.script.T
phong - Variable in class org.jmol.export._TachyonExporter
phongexponent - Static variable in class org.jmol.script.T
phongExponent - Variable in class org.jmol.util.Shader
PhosphorusMonomer - Class in org.jmol.modelsetbio
PhosphorusMonomer() - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
phosphorusOffsets - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
PhosphorusPolymer - Class in org.jmol.modelsetbio
PhosphorusPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.PhosphorusPolymer
PI_OVER_2 - Static variable in class org.jmol.minimize.forcefield.Calculations
PICK_COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
pickable - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pickAtomAssignType - Variable in class org.jmol.modelkit.ModelKitPopup
pickBondAssignType - Variable in class org.jmol.modelkit.ModelKitPopup
pickedAtom - Variable in class org.jmol.shape.Labels
pickedMesh - Variable in class org.jmol.shape.MeshCollection
pickedModel - Variable in class org.jmol.shape.MeshCollection
pickedOffset - Variable in class org.jmol.shape.Labels
pickedPt - Variable in class org.jmol.shape.MeshCollection
pickedVertex - Variable in class org.jmol.shape.MeshCollection
pickedX - Variable in class org.jmol.shape.Labels
pickedY - Variable in class org.jmol.shape.Labels
picking - Static variable in class org.jmol.script.T
PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_LIGAND - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
PICKING_MK_RESET - Static variable in class org.jmol.viewer.ActionManager
PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
pickingModeNames - Static variable in class org.jmol.viewer.ActionManager
pickingspinrate - Static variable in class org.jmol.script.T
pickingSpinRate - Variable in class org.jmol.viewer.GlobalSettings
pickingstyle - Static variable in class org.jmol.script.T
pickingStyle - Variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
  picking styles
PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
pickingStyleMeasure - Variable in class org.jmol.viewer.ActionManager
pickingStyleNames - Static variable in class org.jmol.viewer.ActionManager
pickingStyleSelect - Variable in class org.jmol.viewer.ActionManager
picklabel - Static variable in class org.jmol.script.T
pickLabel(int) - Method in class org.jmol.viewer.ActionManager
pickLabel - Variable in class org.jmol.viewer.GlobalSettings
PickleReader - Class in org.jmol.adapter.readers.pymol
  generic Python Pickle file reader only utilizing records needed for PyMOL.
PickleReader(GenericBinaryDocument, Viewer) - Constructor for class org.jmol.adapter.readers.pymol.PickleReader
pictFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
pictIsScratchFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
pid - Variable in class org.jmol.shapespecial.Ellipsoid
pidOf(Object) - Static method in enum org.jmol.c.PAL
pilp - Variable in class org.jmol.minimize.forcefield.AtomType
PINK - Static variable in class org.jmol.util.C
pipedIS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
pipedOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
pis - Variable in class org.jmol.util.MeshSurface
  polygon indexes
piUnitsX - Variable in class org.jmol.jsv.JDXMOLParser
piUnitsY - Variable in class org.jmol.jsv.JDXMOLParser
pivot - Static variable in class org.jmol.script.T
pixel - Variable in class org.jmol.g3d.Graphics3D
pixel0 - Variable in class org.jmol.g3d.Graphics3D
Pixelator - Class in org.jmol.g3d
Pixelator(Graphics3D) - Constructor for class org.jmol.g3d.Pixelator
PixelatorScreened - Class in org.jmol.g3d
  A class to create a "screened" translucent effect by discarding pixels in a checkerboard fashion.
PixelatorScreened(Graphics3D, Pixelator) - Constructor for class org.jmol.g3d.PixelatorScreened
PixelatorShaded - Class in org.jmol.g3d
  A class to do Z Shading of pixels.
PixelatorShaded(Graphics3D) - Constructor for class org.jmol.g3d.PixelatorShaded
PixelatorT - Class in org.jmol.g3d
  Handle pixels in Pass 2 - Translucency
PixelatorT(Graphics3D) - Constructor for class org.jmol.g3d.PixelatorT
pixelScale - Variable in class org.jmol.thread.MoveToThread
pixelScreened - Variable in class org.jmol.g3d.Graphics3D
pixelShaded - Variable in class org.jmol.g3d.Graphics3D
pixelT0 - Variable in class org.jmol.g3d.Graphics3D
planarparam - Static variable in class org.jmol.script.T
planarParam - Variable in class org.jmol.shapespecial.Polyhedra
plane - Variable in class org.jmol.jvxl.readers.IsoSolventReader
plane - Variable in class org.jmol.modelsetbio.BioResolver
plane - Static variable in class org.jmol.script.T
plane - Variable in class org.jmol.shapespecial.Draw
plane(P3, P3, float) - Method in class org.jmol.util.BZone
plane1 - Variable in class org.jmol.adapter.readers.simple.InputReader
plane2 - Variable in class org.jmol.adapter.readers.simple.InputReader
plane_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
plane_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
planeCenter - Variable in class org.jmol.jvxl.readers.IsoShapeReader
planeCount - Variable in class org.jmol.jvxl.readers.UhbdReader
planeParameter(int) - Method in class org.jmol.script.ScriptParam
planeRadius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
planes - Variable in class org.jmol.shapespecial.Polyhedron
planes - Variable in class org.jmol.util.BZone
planeShade - Variable in class org.jmol.g3d.SphereRenderer
planeShades - Variable in class org.jmol.g3d.SphereRenderer
planesT - Variable in class org.jmol.shapespecial.Polyhedra
planesUnused - Variable in class org.jmol.util.BZone
planeU - Variable in class org.jmol.jvxl.readers.IsoShapeReader
planeV - Variable in class org.jmol.jvxl.readers.IsoShapeReader
planeValue(T) - Method in class org.jmol.script.ScriptMathProcessor
plateColixes - Variable in class org.jmol.export._VrmlExporter
plateIndices - Variable in class org.jmol.export._VrmlExporter
plateVertices - Variable in class org.jmol.export._VrmlExporter
Platform - Class in org.jmol.awt
Platform() - Constructor for class org.jmol.awt.Platform
Platform - Class in org.jmol.awtjs
  WebGL interface
Platform() - Constructor for class org.jmol.awtjs.Platform
Platform - Class in org.jmol.awtjs2d
  JavaScript 2D canvas version requires Ajax-based URL stream processing.
Platform() - Constructor for class org.jmol.awtjs2d.Platform
platform - Variable in class org.jmol.g3d.Graphics3D
Platform3D - Class in org.jmol.g3d
  Specifies the API to an underlying int[] buffer of ARGB values that can be converted into an Image object and a short[] for z-buffer depth.
Platform3D(GenericPlatform) - Constructor for class org.jmol.g3d.Platform3D
platformspeed - Static variable in class org.jmol.script.T
platformSpeed - Variable in class org.jmol.viewer.GlobalSettings
PlatformViewer - Interface in org.jmol.api
play - Static variable in class org.jmol.script.T
PLAY - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
playAudio(JSmolAppletObject, Map<String, Object>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
playAudio(Viewer, Map<String, Object>) - Method in class org.jmol.util.JmolAudio
  WAV only for application
playAudio(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
playrev - Static variable in class org.jmol.script.T
pLeft - Variable in class org.jmol.g3d.HermiteRenderer
plot(int, int, int, int, int, String, Font, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.TextRenderer
plot - Static variable in class org.jmol.script.T
plot(T[]) - Method in class org.jmol.scriptext.CmdExt
plot3d - Static variable in class org.jmol.script.T
Plot3D - Class in org.jmol.shapesurface
Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
Plot3DRenderer - Class in org.jmol.rendersurface
Plot3DRenderer() - Constructor for class org.jmol.rendersurface.Plot3DRenderer
plotByCharacter(int, int, int, int, int, String, Font, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.TextRenderer
plotCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
plotCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
plotFilledCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
plotFilledCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.___Exporter
plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.__CartesianExporter
plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.JSExporter
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.util.GData
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in interface org.jmol.api.JmolRendererInterface
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.export.Export3D
plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.g3d.Graphics3D
plotLineBits(int, int, P3i, P3i, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
plotLineClippedOld(int, int, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.LineRenderer
  low-resolution linear z-buffer (old style)
plotLineDeltaABitsFloat(int[], int[], int, P3, P3, int, boolean) - Method in class org.jmol.g3d.LineRenderer
plotLineDeltaABitsInt(int[], int[], int, P3i, P3i, int, boolean) - Method in class org.jmol.g3d.LineRenderer
plotLineDeltaAOld(int[], int[], int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
  low-precision old-style linear z, even in perspective mode
plotLineDeltaOld(int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
  low-resolution linear z
plotLineOld(int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.LineRenderer
plotPixelClipped(int, int, int) - Method in class org.jmol.export.Export3D
plotPixelClippedArgb(int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
plotPixelClippedP3i(P3i) - Method in interface org.jmol.api.JmolRendererInterface
plotPixelClippedP3i(P3i) - Method in class org.jmol.export.Export3D
plotPixelClippedP3i(P3i) - Method in class org.jmol.g3d.Graphics3D
plotPixelsClipped(int, int, int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.CircleRenderer
plotPixelsClippedRaster(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
plotPixelsClippedRasterBits(int, int, int, int, int, Rgb16, Rgb16, float, float) - Method in class org.jmol.g3d.Graphics3D
plotPixelsUnclippedCount(int, int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
plotPixelsUnclippedRaster(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
plotPixelsUnclippedRasterBits(int, int, int, Rgb16, Rgb16, float, float) - Method in class org.jmol.g3d.Graphics3D
plotPixelUnclipped(int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
plotPoints(int, int[], int, int) - Method in class org.jmol.g3d.Graphics3D
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.___Exporter
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.__CartesianExporter
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._StlExporter
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._VrmlExporter
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._X3dExporter
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.JSExporter
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.util.GData
PltFormattedReader - Class in org.jmol.jvxl.readers
PltFormattedReader() - Constructor for class org.jmol.jvxl.readers.PltFormattedReader
pluginFile - Variable in class org.openscience.jmol.app.JmolApp
pluginFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
pluginMenu - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
plugins - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
plus - Static variable in class org.jmol.script.T
plusMinus(String, float, String) - Static method in class org.jmol.symmetry.SymmetryOperation
plusPlus - Static variable in class org.jmol.script.T
pm - Variable in class org.jmol.scriptext.MathExt
pm - Variable in class org.jmol.viewer.Viewer
pmesh - Static variable in class org.jmol.script.T
Pmesh - Class in org.jmol.shapesurface
Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
Pmesh4Reader - Class in org.jmol.jvxl.readers
Pmesh4Reader() - Constructor for class org.jmol.jvxl.readers.Pmesh4Reader
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
pmeshError - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
pmeshError - Variable in class org.jmol.jvxl.readers.PmeshReader
pmeshError - Variable in class org.jmol.jvxl.readers.Ras3DReader
pmeshes - Variable in class org.jmol.util.BZone
PmeshReader - Class in org.jmol.jvxl.readers
  PMESH format created for Jmol.
PmeshReader() - Constructor for class org.jmol.jvxl.readers.PmeshReader
PmeshRenderer - Class in org.jmol.rendersurface
PmeshRenderer() - Constructor for class org.jmol.rendersurface.PmeshRenderer
PMeshWriter - Class in org.jmol.shapesurface
  A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
PMeshWriter() - Constructor for class org.jmol.shapesurface.PMeshWriter
png_file_gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
png_screen_gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pngjCache - Variable in class org.jmol.viewer.FileManager
PO - Class in org.jmol.translation
  Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.
PO() - Constructor for class org.jmol.translation.PO
pocket - Variable in class org.jmol.jvxl.readers.Parameters
pocket - Static variable in class org.jmol.script.T
point - Variable in class org.jmol.jvxl.readers.Parameters
point - Variable in class org.jmol.jvxl.readers.VolumeDataReader
point - Static variable in class org.jmol.script.T
point3f - Static variable in class org.jmol.script.T
Point3fi - Class in org.jmol.util
  the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
Point3fi() - Constructor for class org.jmol.util.Point3fi
point4f - Static variable in class org.jmol.script.T
pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
pointA - Variable in class org.jmol.jvxl.calc.MarchingSquares
pointArrowHead - Variable in class org.jmol.renderspecial.VectorsRenderer
pointAt(Lst<Object>, int, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
pointB - Variable in class org.jmol.jvxl.calc.MarchingSquares
pointer - Variable in class org.jmol.modelset.Text
pointer - Variable in class org.jmol.render.LabelsRenderer
pointerPt - Variable in class org.jmol.modelset.Text
pointers - Variable in class org.jmol.script.ScriptContext
pointFromTriad(String) - Static method in class org.jmol.modelkit.ModelKitPopup
pointGroup - Variable in class org.jmol.modelset.AtomCollection
pointgroup - Static variable in class org.jmol.script.T
pointGroup - Variable in class org.jmol.shapespecial.Polyhedron
  includes vertices as atoms, with atomic numbers
PointGroup - Class in org.jmol.symmetry
PointGroup() - Constructor for class org.jmol.symmetry.PointGroup
pointGroup - Variable in class org.jmol.symmetry.Symmetry
PointGroup.Operation - Class in org.jmol.symmetry
pointgroupdistancetolerance - Static variable in class org.jmol.script.T
pointGroupDistanceTolerance - Variable in class org.jmol.viewer.GlobalSettings
pointGroupFamily - Variable in class org.jmol.shapespecial.Polyhedron
  includes vertices as generic points
pointgrouplineartolerance - Static variable in class org.jmol.script.T
pointGroupLinearTolerance - Variable in class org.jmol.viewer.GlobalSettings
pointGuides - Variable in class org.jmol.navigate.Navigator
PointIterator - Class in org.jmol.bspt
PointIterator() - Constructor for class org.jmol.bspt.PointIterator
pointPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d, boolean) - Static method in class org.jmol.minimize.Util
  calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
points - Variable in class org.jmol.jvxl.readers.IsoMOReader
points - Variable in class org.jmol.jvxl.readers.Parameters
points - Variable in class org.jmol.modelkit.Constraint
points - Variable in class org.jmol.modelset.MeasurementData
points - Variable in class org.jmol.navigate.Navigator
points - Variable in class org.jmol.quantum.QuantumCalculation
points - Variable in class org.jmol.renderspecial.DipolesRenderer
points - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
points - Variable in class org.jmol.smiles.SmilesMeasure
points - Variable in class org.jmol.symmetry.PointGroup
POINTS_ALL - Static variable in class org.jmol.jvxl.readers.KinemageReader
POINTS_HETS - Static variable in class org.jmol.jvxl.readers.KinemageReader
POINTS_MCMC - Static variable in class org.jmol.jvxl.readers.KinemageReader
POINTS_MCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
POINTS_SCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
pointScale - Variable in class org.jmol.shapespecial.Polyhedra
pointScale - Variable in class org.jmol.shapespecial.Polyhedron
pointSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
pointSize - Variable in class org.jmol.jvxl.data.JvxlData
pointSize - Variable in class org.jmol.jvxl.readers.Parameters
pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
pointsperangstrom - Static variable in class org.jmol.script.T
pointsPolyhedra(BS, float) - Method in class org.jmol.shapespecial.Polyhedra
pointT - Variable in class org.jmol.geodesic.EnvelopeCalculation
pointT - Variable in class org.jmol.render.FontLineShapeRenderer
pointT - Variable in class org.jmol.renderbio.BioShapeRenderer
pointT2 - Variable in class org.jmol.render.FontLineShapeRenderer
pointT2 - Variable in class org.jmol.viewer.TransformManager
pointT3 - Variable in class org.jmol.render.FontLineShapeRenderer
pointType - Variable in class org.jmol.jvxl.readers.KinemageReader
pointVectorEnd - Variable in class org.jmol.renderspecial.VectorsRenderer
pointVectorStart - Variable in class org.jmol.renderspecial.VectorsRenderer
polar_neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
polygon - Static variable in class org.jmol.script.T
polygon - Variable in class org.jmol.shapespecial.Draw
polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
polygonCount0 - Variable in class org.jmol.util.MeshSurface
PolygonFileReader - Class in org.jmol.jvxl.readers
PolygonFileReader() - Constructor for class org.jmol.jvxl.readers.PolygonFileReader
polygonIndexes - Variable in class org.jmol.shapesurface.PMeshWriter
polyhedra - Static variable in class org.jmol.script.T
polyhedra() - Method in class org.jmol.scriptext.CmdExt
Polyhedra - Class in org.jmol.shapespecial
Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
POLYHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
polyhedralOrders - Variable in class org.jmol.smiles.SmilesStereo
PolyhedraRenderer - Class in org.jmol.renderspecial
PolyhedraRenderer() - Constructor for class org.jmol.renderspecial.PolyhedraRenderer
Polyhedron - Class in org.jmol.shapespecial
Polyhedron() - Constructor for class org.jmol.shapespecial.Polyhedron
polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
PolyhedronStereoSorter - Class in org.jmol.smiles
PolyhedronStereoSorter() - Constructor for class org.jmol.smiles.PolyhedronStereoSorter
polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in interface org.jmol.api.SmilesMatcherInterface
polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in class org.jmol.smiles.SmilesMatcher
  Generate a topological SMILES string from a set of faces
polyid - Variable in class org.jmol.util.BZone
polymer - Static variable in class org.jmol.script.T
polymerlength - Static variable in class org.jmol.script.T
polySmiles - Variable in class org.jmol.shapespecial.Polyhedron
polySmilesCenter - Variable in class org.jmol.smiles.SmilesGenerator
pop() - Method in class org.jmol.adapter.readers.pymol.PickleReader
pop - Static variable in class org.jmol.script.T
popContext(boolean, boolean) - Method in class org.jmol.script.ScriptEval
popHoldRepaint(boolean, String) - Method in interface org.jmol.api.JmolRepaintManager
popHoldRepaint(String) - Method in class org.jmol.api.JmolViewer
popHoldRepaint(boolean, String) - Method in class org.jmol.render.RepaintManager
popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
popInHeight - Static variable in class org.openscience.jmol.app.webexport.WebExport
PopInJmol - Class in org.openscience.jmol.app.webexport
PopInJmol(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.PopInJmol
popInWidth - Static variable in class org.openscience.jmol.app.webexport.WebExport
popMatrix() - Method in class org.jmol.export._StlExporter
popMatrix() - Method in class org.jmol.export._VrmlExporter
popMatrix() - Method in class org.jmol.export._X3dExporter
popState() - Method in class org.jmol.util.CommandHistory
popState() - Method in class org.jmol.viewer.Viewer
popup - Variable in class org.jmol.awt.AwtPopupHelper
popup - Variable in class org.jmol.awtjs2d.JSPopupHelper
  used here and by SwingController to refer to the Java class being handled by this helper.
PopupHelper - Interface in org.jmol.popup
popupMenu - Variable in class org.jmol.awtjs.swing.AbstractButton
popupMenu - Variable in class org.jmol.popup.GenericPopup
popupMenu(int, int, char) - Method in class org.jmol.viewer.Viewer
PopupResource - Class in org.jmol.popup
PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
port - Variable in class org.openscience.jmol.app.JmolApp
  The data model.
port - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
posCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
position - Variable in class org.openscience.jmol.app.surfacetool.Slice
position - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
position - Variable in class org.openscience.jvxl.MonitorInputStream
positionAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
positionBeforePrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
positionMin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
positionSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
positionThicknessPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
postByteArray(String, byte[]) - Method in class org.jmol.viewer.FileManager
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoMOReader
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoSolventReader
postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
potentials - Variable in class org.jmol.quantum.MepCalculation
povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
  A dialog for controling the creation of a povray input file from a Chemframe and a display.
PovrayDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Creates a dialog for getting info related to output frames in povray format.
PovrayDialog.PovrayWindowListener - Class in org.openscience.jmol.app.jmolpanel
  Listener for responding to dialog window events.
povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
PovrayWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
power4 - Static variable in class org.jmol.geodesic.EnvelopeCalculation
pqr_workarounds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
PqrReader - Class in org.jmol.adapter.readers.pdb
  PQR file reader.
PqrReader() - Constructor for class org.jmol.adapter.readers.pdb.PqrReader
pqrStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
precalculateVoxelData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
precision - Variable in class org.jmol.modelset.LabelToken
PrecisionRenderer - Class in org.jmol.g3d
  Note added 4/2015 BH: Well, it turns out that the calculation of the intermediate pixel z value in all methods involving rasterization of lines is incorrect and has been incorrect since Jmol's inception.
PrecisionRenderer() - Constructor for class org.jmol.g3d.PrecisionRenderer
predefinedGroup1Names - Static variable in class org.jmol.modelsetbio.BioResolver
predefinedGroup3Names - Static variable in class org.jmol.modelsetbio.BioResolver
predefinedset - Static variable in class org.jmol.script.T
predefinedStatic - Static variable in class org.jmol.viewer.JC
predefinedVariable - Static variable in class org.jmol.viewer.JC
preDefining - Variable in class org.jmol.script.ScriptCompiler
predragBinding - Variable in class org.jmol.viewer.ActionManager
preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
PreferencesDialog(JmolPanel, JFrame, GuiMap, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
PreferencesDialog.PrefsAction - Class in org.openscience.jmol.app.jmolpanel
preFilterAtomList(SimpleNode[], BS, BS) - Method in class org.jmol.symmetry.CIPChirality
  Remove unnecessary atoms from the list and let us know if we have alkenes to consider.
prefsAction - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
PrefsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
preloadClasses - Static variable in class org.jmol.applet.JmolApplet
preloadClassIndex - Variable in class org.jmol.applet.AppletWrapper
preloadClassNames - Variable in class org.jmol.applet.AppletWrapper
preloadImage - Variable in class org.jmol.applet.AppletWrapper
preloadImageName - Variable in class org.jmol.applet.AppletWrapper
preloadImagePainted - Variable in class org.jmol.applet.AppletWrapper
preloadImageReadyForDisplay - Variable in class org.jmol.applet.AppletWrapper
preloadTextMessage - Variable in class org.jmol.applet.AppletWrapper
preloadThreadCount - Variable in class org.jmol.applet.AppletWrapper
prepareBinaryOutput(SV) - Method in class org.jmol.scriptext.CmdExt
preprocessString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  initial processing; returns a string bounded by \1
presentation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
presentation_auto_quit - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
presentation_auto_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
presentation_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
preserve_chempy_ids - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
preserveState - Variable in class org.jmol.modelset.AtomCollection
preservestate - Static variable in class org.jmol.script.T
preserveState - Variable in class org.jmol.viewer.GlobalSettings
pressAction - Variable in class org.jmol.viewer.ActionManager
PRESSED - Static variable in class org.jmol.awtjs.Event
pressed(long, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Mouse
pressed - Variable in class org.jmol.viewer.ActionManager
pressedCount - Variable in class org.jmol.viewer.ActionManager
prev - Static variable in class org.jmol.script.T
prev - Variable in class org.jmol.util.MeshCapper.CapVertex
  edge double links
prevAtom - Variable in class org.jmol.smiles.SmilesGenerator
prevCovalentVersion - Static variable in class org.jmol.script.ScriptManager
prevFrame - Variable in class org.jmol.viewer.Viewer
PREVIOUS - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
previousClassName - Variable in class org.jmol.applet.AppletWrapper
previousMeshID - Variable in class org.jmol.shape.MeshCollection
previousMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
previousScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
previousSpaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
previousUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
previousX - Variable in class org.jmol.viewer.TransformManager
previousY - Variable in class org.jmol.viewer.TransformManager
prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
prevMorphModel - Variable in class org.jmol.viewer.Viewer
prevSp2Atoms - Variable in class org.jmol.smiles.SmilesGenerator
prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
pRight - Variable in class org.jmol.g3d.HermiteRenderer
primitiveCode - Variable in class org.jmol.symmetry.HallRotationTerm
primitiveData - Variable in class org.jmol.adapter.readers.xtal.GulpReader
primitiveDensity - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
primitiveHallSymbol - Variable in class org.jmol.symmetry.HallInfo
primitives - Variable in class org.jmol.smiles.SmilesBond
primitiveToCrystal - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
primitiveToIndex - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
primitiveType - Variable in class org.jmol.smiles.SmilesAtom
primitiveVolume - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
principalAxis - Variable in class org.jmol.symmetry.PointGroup
principalPlane - Variable in class org.jmol.symmetry.PointGroup
principalQuantumNumber - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
print - Static variable in class org.jmol.script.T
print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
  added print command, so that it can be used by RasmolScriptHandler
printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
priorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  priorities associated with each subsituent from high (0) to low (3); due to equivaliencies at a given rule level, these numbers may duplicate and have gaps - for example, [0 2 0 3]
PRIORITY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
priority - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  current priority 0-3; used for Rule 4b and 5 priority sorting
privateKey - Variable in class org.jmol.export.___Exporter
privateKey - Variable in class org.jmol.export.Export3D
privateKey - Variable in class org.jmol.viewer.OutputManager
privateKey - Variable in class org.jmol.viewer.Viewer
probe - Static variable in class org.jmol.script.T
proc - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
process(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  The main processor.
process() - Method in class org.jmol.quantum.MepCalculation
process() - Method in class org.jmol.quantum.MOCalculation
process() - Method in class org.jmol.quantum.NciCalculation
process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
  Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
process() - Method in class org.jmol.quantum.QuantumCalculation
process(int, int, float) - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
process - Variable in class org.jmol.script.ScriptProcessRunnable
process - Static variable in class org.jmol.script.T
process(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  Handle the point; mark as processed.
processAssemblyGenBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processAtom(Atom, String, char, String, int, int, char, boolean, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
processAtom() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
processAtomClick(int) - Method in class org.jmol.modelkit.ModelKitPopup
  An atom has been clicked -- handle it.
processAtomicCharges() - Method in class org.jmol.adapter.readers.simple.MopacReader
  Reads the section in MOPAC files with atomic charges.
processAtomObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
processAtoms() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
processAtoms(int, int, int, int) - Method in class org.jmol.quantum.NciCalculation
  At each grid point we need to calculate the sum of the atom-based promolecular data.
processAtomSiteLoopBlock(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
  reads atom data in any order
processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
  reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
processBasisObject(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.MMTFReader
processBinaryDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
processBinaryDocument() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
processBinaryDocument() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processBondObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
processBonds(Lst<Object[]>, Map<Object, Integer>, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
processBonds() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
processCellParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
  unit cell parameters -- two options, so we use MOD 6
processCGO(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create a CGO JmolObject, just passing on key information.
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
  incorporates double-click gesture
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processChangeSync(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processCharges() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  a general name definition field.
processChemicalInfo(String) - Method in class org.jmol.adapter.readers.cif.CifReader
  reads some of the more interesting info into specific atomSetAuxiliaryInfo elements
processCitationListBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
processCmdfAtoms() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
processCommand(int) - Method in class org.jmol.script.ScriptEval
processCompBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processComponentKeyEvent(KeyEvent) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
processConnectorObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
processCoord() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
processCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacReader
  Reads the section in MOPAC files with cartesian coordinates.
processCoordLines() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Now create atoms from the coordinate lines.
processCtab(boolean) - Method in class org.jmol.adapter.readers.molxyz.MolReader
processDataParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
  initialize a new atom set
processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processDefinitions() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create a JmolObject that will define atom sets based on PyMOL objects
processDeletedModelAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
processDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
processDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
processEndMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
processEntry() - Method in class org.jmol.adapter.readers.cif.MSCifParser
processes - Variable in class org.jmol.script.ScriptParallelProcessor
processEvent(int, int, int, int, long) - Method in interface org.jmol.api.GenericMouseInterface
processEvent(int, int, int, int, long) - Method in class org.jmol.awt.Mouse
processEvent(int, int, int, int, long) - Method in class org.jmol.awtjs2d.Mouse
processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
  Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
processGadget(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Only process _e_pot objects -- which we need for color settings
processGeomBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
  reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms.
processHeader() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
processInfo() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
processJob(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
processJSON(JsonNioService.JSONObject, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
processKey(int, int, boolean) - Method in class org.jmol.console.GenericConsole
processKeyEvent(KeyEvent) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
processKeyEvent(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
  Custom key event processing for command 0 implementation.
processLocalTransform() - Method in class org.jmol.adapter.readers.quantum.CsfReader
processLock - Variable in class org.jmol.script.ScriptProcessRunnable
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
  processes loop_ blocks of interest or skips the data
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
  creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.
processMap(Lst<Object>, boolean, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create mapObjects and volumeData; create an ISOSURFACE JmolObject.
processMeasure(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create a MEASURE JmolObject.
processMeshes() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create mesh or mep JmolObjects.
processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
processMKPropertyItem(String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
processModeClick(String) - Method in class org.jmol.modelkit.ModelKitPopup
processModelData(String, String, String, String, String, float, float, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
processModelData(String, String, String, String, String, float, float, boolean) - Method in interface org.jmol.api.JmolJDXMOLReader
processMol() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
processMolCryst(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Pick up the crystal data.
processMolecularOrbitalObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
processMolecule() - Method in class org.jmol.adapter.readers.more.Mol2Reader
processMolecule(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create everything necessary to generate a molecule in Jmol.
processMolSdHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
processMonotonic(MeshCapper.CapVertex, boolean) - Method in class org.jmol.util.MeshCapper
  Process a standard monotonic region, cleaving off as many triangles as possible.
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.appletjs.Jmol
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
processMovie(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create a JmolObject that will represent the movie.
processMultiFrameOutput(String, BS, int, Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.multitouch.ActionManagerMT
processMultitouchEvent(int, int, int, int, P3, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.viewer.ActionManager
  Specific to ActionManagerMT -- for processing SparshUI gestures
processName - Variable in class org.jmol.script.ScriptProcess
processNextCriticalPoint() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
processNextMeasure(Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
processNextMeasure(Measurement) - Method in class org.jmol.modelset.MeasurementData
  if this is the client, then this method is called by MeasurementData when a measurement is ready
processNextMeasure(Measurement) - Method in class org.jmol.shape.Measures
processObject(Lst<Object>, boolean, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  The main object processor.
processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
processPeakData() - Method in class org.jmol.adapter.readers.more.JcampdxReader
  integrate the records into the associated models, and delete unreferenced n.m models
processPeakSelectAtom(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
processPeakSelectModel(int, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
processPoints() - Method in class org.jmol.quantum.MOCalculation
processPoints() - Method in class org.jmol.quantum.QuantumCalculation
processPosition(String, Atom, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  We process the Pos#n record here.
processPt(T3) - Method in class org.jmol.quantum.QuantumCalculation
processQuotedString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Handle all forms of quotation, including '...', "...", '''...''', """...""", and ;...\n...\n;
processScript(Object[]) - Method in class org.jmol.viewer.StatusManager
processSelClick(String) - Method in class org.jmol.modelkit.ModelKitPopup
processSelection(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  process the selection sets (sele), (...)
processSelectionsAndScenes(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  A PyMOL scene consists of one or more of: view frame visibilities, by object colors, by color reps, by type currently just extracts viewpoint
processSelOpClick(String) - Method in class org.jmol.modelkit.ModelKitPopup
processSemiString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Sets a multiline semicolon-eclipsed string to be parsed from the beginning, allowing for CIF 2.0-type prefixed text lines and removing line folding.
processSequence() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  get canonical 1-letter DNA/RNA sequence code from 3-letter code.
processService(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
  service is expected to return a value in the "ret" key
processShapeCommand(int) - Method in class org.jmol.script.ScriptEval
processShell(int) - Method in class org.jmol.quantum.MOCalculation
processSlater(int) - Method in class org.jmol.quantum.MOCalculation
processSplit(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
  Process what M3O refer to as a "split" vertex, which we handle differently here, cloning the "helper" point and the "split" point, creating a new region if necessary, and then swapping pointers.
processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
processStartMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
processState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  identifies ranges for HELIX and TURN
processStructConnLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processStructOperListBlock(boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  identifies sheet ranges
processStructSiteBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  identifies structure sites
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.CifReader
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
processSubsystemLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
processSupportedRecord(int) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
processSymClick(String) - Method in class org.jmol.modelkit.ModelKitPopup
processSymmetryOperationsLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
  retrieves symmetry operations
processSymmetrySpaceGroupName() - Method in class org.jmol.adapter.readers.cif.CifReader
  done by AtomSetCollectionReader
processSymop(String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
processSync(String, int) - Method in interface org.jmol.api.JmolJSpecView
processSync(String, int) - Method in class org.jmol.jsv.JSpecView
processTokenList(short, boolean) - Method in class org.jmol.script.ScriptCompiler
processTotalEnergy() - Method in class org.jmol.adapter.readers.simple.MopacReader
processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
processTry(Map<String, SV>) - Method in class org.jmol.script.ScriptEval
processTwoPointGesture(float[][][]) - Method in interface org.jmol.api.GenericMouseInterface
processTwoPointGesture(float[][][]) - Method in class org.jmol.appletjs.Jmol
processTwoPointGesture(float[][][]) - Method in class org.jmol.awt.Mouse
processTwoPointGesture(float[][][]) - Method in class org.jmol.awtjs2d.Mouse
  called by JSmol as processTwoPointGesture(canvas.touches);
processTwoPointGesture(float[][][]) - Method in class org.jmol.viewer.Viewer
processType() - Method in class org.jmol.util.Tensor
  Sets typeFactor, altType, isIsotropic, forThermalEllipsoid; type "iso" changed to "" here.
processUCClick(String) - Method in class org.jmol.modelkit.ModelKitPopup
processUnitCellTransform() - Method in class org.jmol.adapter.readers.cif.CifReader
processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cif.CifReader
  the PDB transformation matrix cartesian --> fractional
processUpdate(String) - Method in class org.jmol.util.JmolAudio
processVibrationObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
  from eval write command only includes option to write set of files
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
  the current state
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
processXtalClick(String, String) - Method in class org.jmol.modelkit.ModelKitPopup
procSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
programInfo - Variable in class org.jmol.atomdata.AtomData
prompt(String, String, String[], boolean) - Method in interface org.jmol.api.GenericPlatform
prompt(String, String, String[], boolean) - Static method in class org.jmol.awt.Display
prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
prompt(String, String, String[], boolean) - Static method in class org.jmol.awtjs2d.Display
prompt(String, String, String[], boolean) - Method in class org.jmol.awtjs2d.Platform
prompt - Static variable in class org.jmol.script.T
prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
promptUser(String, String) - Method in class org.jmol.modelkit.ModelKitPopup
prop - Static variable in class org.openscience.jmol.app.webexport.WebExport
PROP_ANIMATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_APPLET_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_ATOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_AUXILIARY_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_BOND_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_BOUNDBOX_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_CENTER_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_CHAIN_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_CIF_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_CONSOLE_TEXT - Static variable in class org.jmol.viewer.PropertyManager
PROP_COUNT - Static variable in class org.jmol.viewer.PropertyManager
PROP_DATA_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_DOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_ERROR_MESSAGE - Static variable in class org.jmol.viewer.PropertyManager
PROP_EVALUATE - Static variable in class org.jmol.viewer.PropertyManager
PROP_EXTRACT_MODEL - Static variable in class org.jmol.viewer.PropertyManager
PROP_FILE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_FILECONTENTS - Static variable in class org.jmol.viewer.PropertyManager
PROP_FILECONTENTS_PATH - Static variable in class org.jmol.viewer.PropertyManager
PROP_FILEHEADER - Static variable in class org.jmol.viewer.PropertyManager
PROP_FILENAME - Static variable in class org.jmol.viewer.PropertyManager
PROP_IMAGE - Static variable in class org.jmol.viewer.PropertyManager
PROP_ISOSURFACE_DATA - Static variable in class org.jmol.viewer.PropertyManager
PROP_ISOSURFACE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_JMOL_STATUS - Static variable in class org.jmol.viewer.PropertyManager
PROP_JMOL_VIEWER - Static variable in class org.jmol.viewer.PropertyManager
PROP_JSPECVIEW - Static variable in class org.jmol.viewer.PropertyManager
PROP_LIGAND_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_MEASUREMENT_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_MENU - Static variable in class org.jmol.viewer.PropertyManager
PROP_MESSAGE_QUEUE - Static variable in class org.jmol.viewer.PropertyManager
PROP_MINIMIZATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_MODEL_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_MODELKIT_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_MOLECULE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_MOUSE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_NMR_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_ORIENTATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_POINTGROUP_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_POLYMER_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_SCRIPT_QUEUE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_SERVICE - Static variable in class org.jmol.viewer.PropertyManager
PROP_SHAPE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_STATE_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_TRANSFORM_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_VAL_INFO - Static variable in class org.jmol.viewer.PropertyManager
PROP_VAR_INFO - Static variable in class org.jmol.viewer.PropertyManager
properties - Variable in class org.jmol.modelset.Model
properties - Variable in class org.openscience.jmol.app.HistoryFile
  The data stored in the history file.
propertiesFileName - Static variable in class org.openscience.jmol.app.jmolpanel.StatusListener
propertiesTextArea - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
property - Static variable in class org.jmol.script.T
PROPERTY_MODES - Static variable in class org.jmol.shapespecial.Ellipsoids
propertyatomnumbercolumncount - Static variable in class org.jmol.script.T
propertyatomnumberfield - Static variable in class org.jmol.script.T
propertyChange(PropertyChangeEvent) - Method in class org.jmol.dialog.FilePreview
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
propertycolorscheme - Static variable in class org.jmol.script.T
propertyColorScheme - Variable in class org.jmol.viewer.GlobalSettings
propertydatacolumncount - Static variable in class org.jmol.script.T
propertydatafield - Static variable in class org.jmol.script.T
propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
PROPERTYFLAGS - Static variable in class org.jmol.script.T
propertyItemCounts - Variable in class org.jmol.adapter.readers.quantum.CsfReader
PropertyManager - Class in org.jmol.viewer
  The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
propertySmoothing - Variable in class org.jmol.jvxl.readers.Parameters
propertySmoothingPower - Variable in class org.jmol.jvxl.readers.Parameters
propertyTypes - Static variable in class org.jmol.viewer.PropertyManager
props - Variable in class org.jmol.adapter.readers.pdb.JmolDataReader
props - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
propselector - Static variable in class org.jmol.script.T
protein - Static variable in class org.jmol.script.T
proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
ProteinStructure - Class in org.jmol.modelsetbio
ProteinStructure() - Constructor for class org.jmol.modelsetbio.ProteinStructure
proteinstructurePending - Variable in class org.jmol.renderbio.RocketRenderer
proteinStructureTainted - Variable in class org.jmol.modelset.ModelSet
PROTEKTED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
PROTONS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pS - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
PS_CLOSEPATH - Static variable in class org.jmol.shapecgo.CGOMesh
PS_LINETO - Static variable in class org.jmol.shapecgo.CGOMesh
PS_MOVETO - Static variable in class org.jmol.shapecgo.CGOMesh
PS_NEWPATH - Static variable in class org.jmol.shapecgo.CGOMesh
PS_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
PS_SETLINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
PS_SHOWPAGE - Static variable in class org.jmol.shapecgo.CGOMesh
PS_STROKE - Static variable in class org.jmol.shapecgo.CGOMesh
psi - Variable in class org.jmol.modelsetbio.Monomer
psi - Static variable in class org.jmol.script.T
psi_l - Variable in class org.jmol.jvxl.readers.IsoShapeReader
psi_l - Variable in class org.jmol.jvxl.readers.Parameters
psi_m - Variable in class org.jmol.jvxl.readers.IsoShapeReader
psi_m - Variable in class org.jmol.jvxl.readers.Parameters
psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
psi_n - Variable in class org.jmol.jvxl.readers.IsoShapeReader
psi_n - Variable in class org.jmol.jvxl.readers.Parameters
psi_normalization - Variable in class org.jmol.jvxl.readers.IsoShapeReader
psi_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
psi_Znuc - Variable in class org.jmol.jvxl.readers.IsoShapeReader
psi_Znuc - Variable in class org.jmol.jvxl.readers.Parameters
psiContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
PsiReader - Class in org.jmol.adapter.readers.quantum
  Reader for Psi3 output files.
PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
pt - Variable in enum org.jmol.c.VDW
pt - Variable in class org.jmol.jvxl.readers.BCifDensityReader
pt - Variable in class org.jmol.jvxl.readers.DelPhiBinaryReader
pt - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
pt - Variable in class org.jmol.jvxl.readers.NffReader
pt - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
pt - Variable in class org.jmol.jvxl.readers.UhbdReader
pt - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
pt - Variable in class org.jmol.modelset.LabelToken
pt - Variable in class org.jmol.render.CageRenderer
pt - Variable in class org.jmol.renderbio.BioMeshRenderer
pt - Variable in class org.jmol.script.ScriptQueueThread
pt - Variable in class org.jmol.util.ContactPair
pt - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
pt0 - Variable in class org.jmol.adapter.readers.simple.InputReader
pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
pt0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
pt0 - Variable in class org.jmol.modelsetbio.AlphaPolymer
pt0 - Variable in class org.jmol.render.FontLineShapeRenderer
pt0 - Variable in class org.jmol.renderspecial.DrawRenderer
pt0 - Variable in class org.jmol.script.ScriptFlowContext
pt0 - Variable in class org.jmol.script.ScriptFunction
pt0 - Static variable in class org.jmol.script.SV
pt0 - Variable in class org.jmol.shape.Axes
Pt000 - Static variable in class org.jmol.modelkit.ModelKitPopup
pt000 - Variable in class org.jmol.render.AxesRenderer
pt0f - Variable in class org.jmol.renderspecial.DrawRenderer
pt0i - Variable in class org.jmol.render.FontLineShapeRenderer
pt0i - Variable in class org.jmol.renderspecial.DrawRenderer
pt1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
pt1 - Variable in class org.jmol.render.FontLineShapeRenderer
pt1 - Variable in class org.jmol.renderbio.BioMeshRenderer
pt1 - Variable in class org.jmol.renderspecial.DrawRenderer
pt1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
pt1 - Variable in class org.jmol.script.ScriptParam
pt1 - Variable in class org.jmol.shapesurface.Contact
pt1f - Variable in class org.jmol.render.MeshRenderer
pt1i - Variable in class org.jmol.render.MeshRenderer
pt2 - Variable in class org.jmol.renderspecial.DrawRenderer
pt2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
pt2 - Variable in class org.jmol.script.ScriptParam
pt2 - Variable in class org.jmol.shapesurface.Contact
pt2f - Variable in class org.jmol.render.MeshRenderer
pt2i - Variable in class org.jmol.render.FontLineShapeRenderer
pt2i - Variable in class org.jmol.render.MeshRenderer
pt3 - Variable in class org.jmol.rendercgo.CGORenderer
pt3 - Variable in class org.jmol.script.ScriptParam
pt3i - Variable in class org.jmol.render.MeshRenderer
pt4Value(SV) - Static method in class org.jmol.script.SV
PT_BITSET - Static variable in class org.jmol.shapespecial.Draw
PT_CHARGE - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
PT_CONNECT - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
PT_COORD - Static variable in class org.jmol.shapespecial.Draw
PT_ELEMENT - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
PT_IDENTIFIER - Static variable in class org.jmol.shapespecial.Draw
PT_MODEL_BASED_POINTS - Static variable in class org.jmol.shapespecial.Draw
PT_MODEL_INDEX - Static variable in class org.jmol.shapespecial.Draw
ptA - Variable in class org.jmol.export.Export3D
ptA0 - Variable in class org.jmol.g3d.CylinderRenderer
ptA0i - Variable in class org.jmol.g3d.CylinderRenderer
ptAtom - Variable in class org.jmol.smiles.SmilesGenerator
ptB - Variable in class org.jmol.export.Export3D
ptB0 - Variable in class org.jmol.g3d.CylinderRenderer
ptB0i - Variable in class org.jmol.g3d.CylinderRenderer
ptC - Variable in class org.jmol.export.Export3D
ptC - Variable in class org.jmol.renderbio.RocketRenderer
ptCenter - Variable in class org.jmol.shape.Mesh
ptCenters - Variable in class org.jmol.shapespecial.DrawMesh
ptColor - Variable in class org.jmol.rendercgo.CGORenderer
ptCommand - Variable in class org.jmol.script.ScriptFlowContext
ptD - Variable in class org.jmol.export.Export3D
ptDefault - Variable in class org.jmol.script.ScriptFlowContext
ptDefaultLattice - Variable in class org.jmol.viewer.GlobalSettings
pTemp - Variable in class org.jmol.render.LabelsRenderer
pTemp3 - Variable in class org.jmol.renderspecial.VectorsRenderer
ptFloat - Variable in class org.jmol.adapter.readers.more.MdCrdReader
ptid - Variable in class org.jmol.script.ScriptMathProcessor
ptIDLogger - Variable in class org.jmol.symmetry.CIPChirality
  incremental pointer providing a unique ID to every CIPAtom for debugging
ptInner - Static variable in class org.jmol.util.BZone
ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ptLine - Variable in class org.jmol.script.ScriptFlowContext
ptList - Variable in class org.jmol.shapespecial.Draw
ptMax - Variable in class org.jmol.export._IdtfExporter
ptMin - Variable in class org.jmol.export._IdtfExporter
ptMoveToCenter - Variable in class org.jmol.thread.MoveToThread
ptNewSetModifier - Variable in class org.jmol.script.ScriptTokenParser
ptNext - Variable in class org.jmol.renderbio.BioMeshRenderer
ptNext - Variable in class org.jmol.viewer.Gesture
ptNormal - Variable in class org.jmol.rendercgo.CGORenderer
pto - Variable in class org.jmol.script.ScriptMathProcessor
ptOffset - Variable in class org.jmol.adapter.readers.cif.CifReader
ptOffset - Variable in class org.jmol.adapter.smarter.XtalSymmetry
ptOffset - Variable in class org.jmol.viewer.TransformManager
pTopLeft - Variable in class org.jmol.g3d.HermiteRenderer
pTopRight - Variable in class org.jmol.g3d.HermiteRenderer
ptOriginShift - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
ptPrev - Variable in class org.jmol.renderbio.BioMeshRenderer
ptPsi - Variable in class org.jmol.jvxl.readers.IsoShapeReader
ptRef - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
pts - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
pts - Variable in class org.jmol.modelset.Measurement
pts - Variable in class org.jmol.util.BZone
pts - Variable in class org.jmol.util.MeshSlicer
ptS1 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
ptS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
ptSemi - Variable in class org.jmol.script.ScriptCompiler
ptSp2Atom0 - Variable in class org.jmol.smiles.SmilesGenerator
ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.VolumeDataReader
ptsUnused - Variable in class org.jmol.util.BZone
ptSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
ptTemp - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
ptTemp - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
ptTemp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
ptTemp - Variable in class org.jmol.export._ObjExporter
ptTemp - Variable in class org.jmol.g3d.SphereRenderer
ptTemp - Variable in class org.jmol.jvxl.calc.MarchingSquares
ptTemp - Variable in class org.jmol.jvxl.data.VolumeData
ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
ptTemp - Variable in class org.jmol.modelset.ModelSet
ptTemp - Variable in class org.jmol.modelsetbio.AminoMonomer
ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
ptTemp - Variable in class org.jmol.render.HoverRenderer
ptTemp - Variable in class org.jmol.renderbio.NucleicRenderer
ptTemp - Variable in class org.jmol.renderspecial.VectorsRenderer
ptTemp - Variable in class org.jmol.script.ScriptExpr
ptTemp - Variable in class org.jmol.shape.Axes
ptTemp - Variable in class org.jmol.shape.Labels
ptTemp - Variable in class org.jmol.util.ModulationSet
ptTemp - Variable in class org.jmol.util.MolWriter
ptTemp - Variable in class org.jmol.viewer.Viewer
ptTemp1 - Variable in class org.jmol.modelset.ModelSet
ptTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
ptTemp2 - Variable in class org.jmol.modelset.ModelSet
ptTemp2 - Variable in class org.jmol.renderspecial.VectorsRenderer
ptTemp4 - Variable in class org.jmol.renderspecial.VectorsRenderer
ptTest1 - Variable in class org.jmol.viewer.TransformManager
ptTest2 - Variable in class org.jmol.viewer.TransformManager
ptTest3 - Variable in class org.jmol.viewer.TransformManager
ptTip - Variable in class org.jmol.renderbio.RocketRenderer
ptTrans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
ptV - Variable in class org.jmol.jvxl.readers.AtomDataReader
ptValue(SV, BS) - Method in class org.jmol.script.ScriptMathProcessor
ptValue(SV) - Static method in class org.jmol.script.SV
ptVibTemp - Variable in class org.jmol.viewer.TransformManager
ptx - Variable in class org.jmol.script.ScriptMathProcessor
ptXY - Variable in class org.jmol.shape.Sticks
ptXY - Variable in class org.jmol.shapespecial.Draw
ptXY - Variable in class org.jmol.shapespecial.Ellipsoids
ptXY - Variable in class org.jmol.shapesurface.Isosurface
ptXyzTemp - Variable in class org.jmol.jvxl.data.VolumeData
ptY0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
ptZ0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
pubChemFormat - Variable in class org.jmol.viewer.GlobalSettings
purging - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
purine - Static variable in class org.jmol.script.T
PURINE_MASK - Static variable in class org.jmol.viewer.JC
PURPLE - Static variable in class org.jmol.util.C
push(Object) - Method in class org.jmol.adapter.readers.pymol.PickleReader
push - Static variable in class org.jmol.script.T
pushContext(T) - Method in class org.jmol.script.ScriptCompiler
pushContext(ContextToken, String) - Method in class org.jmol.script.ScriptEval
pushContext2(ContextToken, String) - Method in class org.jmol.script.ScriptEval
pushContextDown(String) - Method in interface org.jmol.api.JmolScriptEvaluator
pushContextDown(String) - Method in class org.jmol.script.ScriptEval
pushCount - Variable in class org.jmol.script.ScriptCompiler
pushHoldRepaint(String) - Method in interface org.jmol.api.JmolRepaintManager
pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
pushHoldRepaint(String) - Method in class org.jmol.render.RepaintManager
pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
pushHoldRepaintWhy(String) - Method in class org.jmol.viewer.Viewer
pushMatrix() - Method in class org.jmol.export._StlExporter
pushMatrix() - Method in class org.jmol.export._VrmlExporter
pushMatrix() - Method in class org.jmol.export._X3dExporter
pushPop(SV, SV) - Method in class org.jmol.script.SV
  Script variables are pushed after cloning, because the name comes with them when we do otherwise they are not mutable anyway.
pushState(String) - Method in class org.jmol.util.CommandHistory
pushState() - Method in class org.jmol.viewer.Viewer
put(int, int) - Method in class org.jmol.util.Int2IntHash
putBox(int, float[]) - Method in class org.jmol.shape.Labels
putCoord(V3d, double[]) - Static method in class org.jmol.minimize.Util
putIf(char) - Method in class org.jmol.script.ScriptMathProcessor
putLabel(int, Text) - Method in class org.jmol.shape.Labels
putMark(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
putMemo(int, boolean) - Method in class org.jmol.adapter.readers.pymol.PickleReader
putOp(T) - Method in class org.jmol.script.ScriptMathProcessor
PUTTY_AbsoluteLinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_AbsoluteNonlinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_ImpliedRMS - Static variable in class org.jmol.shapebio.Trace
PUTTY_NormalizedLinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_NormalizedNonlinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_RelativeLinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_RelativeNonlinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_ScaledLinear - Static variable in class org.jmol.shapebio.Trace
PUTTY_ScaledNonlinear - Static variable in class org.jmol.shapebio.Trace
putX(SV) - Method in class org.jmol.script.ScriptMathProcessor
Pwr2 - Static variable in class org.jmol.util.TriangleData
PyMOL - Class in org.jmol.adapter.readers.pymol
  PyMOL settings and constants.
PyMOL() - Constructor for class org.jmol.adapter.readers.pymol.PyMOL
pymol - Static variable in class org.jmol.script.T
pymol_space_max_blue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pymol_space_max_green - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pymol_space_max_red - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
pymol_space_min_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
PymolAtomReader - Interface in org.jmol.api
pymolFrame - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
PyMOLGroup - Class in org.jmol.adapter.readers.pymol
PyMOLGroup(String) - Constructor for class org.jmol.adapter.readers.pymol.PyMOLGroup
PyMOLMeshReader - Class in org.jmol.jvxl.readers
  PyMOL surface/mesh reader.
PyMOLMeshReader() - Constructor for class org.jmol.jvxl.readers.PyMOLMeshReader
pymolOffset - Variable in class org.jmol.modelset.Text
PyMOLReader - Class in org.jmol.adapter.readers.pymol
  PyMOL PSE (binary Python session) file reader.
PyMOLReader() - Constructor for class org.jmol.adapter.readers.pymol.PyMOLReader
pymolScene - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
PyMOLScene - Class in org.jmol.adapter.readers.pymol
  A class to allow manipulation of scenes dissociated from file loading.
PyMOLScene(PymolAtomReader, Viewer, Lst<Object>, Map<Integer, Lst<Object>>, int, boolean, int, int, boolean, String) - Constructor for class org.jmol.adapter.readers.pymol.PyMOLScene
pymolStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
pymolType - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
pymolVersion - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
pymolVersion - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
pymolView - Variable in class org.jmol.modelset.Orientation
pyrimidine - Static variable in class org.jmol.script.T
PYRIMIDINE_MASK - Static variable in class org.jmol.viewer.JC

## Q

q - Variable in class org.jmol.jvxl.readers.IsoMOReader
Q_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
qchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
QchemReader - Class in org.jmol.adapter.readers.quantum
  A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
qcJsonContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
QCJSONReader - Class in org.jmol.adapter.readers.quantum
  A molecular structure and orbital reader for MolDen files.
QCJSONReader() - Constructor for class org.jmol.adapter.readers.quantum.QCJSONReader
QCJSONWriter - Class in org.jmol.adapter.writers
  A very experimental class for writing QCJSON files.
QCJSONWriter() - Constructor for class org.jmol.adapter.writers.QCJSONWriter
QCJSONWriter.SparseArray - Class in org.jmol.adapter.writers
qCoefs - Variable in class org.jmol.util.Modulation
qColor - Static variable in class org.jmol.modelsetbio.BioExt
QConst - Static variable in class org.jmol.modelset.HBond
QI - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
qi() - Method in class org.jmol.adapter.readers.xtal.JanaReader
qicount - Variable in class org.jmol.adapter.readers.xtal.JanaReader
qlist100 - Variable in class org.jmol.adapter.readers.cif.MSRdr
qm_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
qm_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
qm_moLinearCombination - Variable in class org.jmol.jvxl.readers.Parameters
qm_moNumber - Variable in class org.jmol.jvxl.readers.Parameters
qm_nAtoms - Variable in class org.jmol.jvxl.readers.Parameters
qm_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
QM_TYPE_GAUSSIAN - Static variable in class org.jmol.jvxl.readers.Parameters
QM_TYPE_NCI_PRO - Static variable in class org.jmol.jvxl.readers.Parameters
QM_TYPE_NCI_SCF - Static variable in class org.jmol.jvxl.readers.Parameters
QM_TYPE_SLATER - Static variable in class org.jmol.jvxl.readers.Parameters
QM_TYPE_UNKNOWN - Static variable in class org.jmol.jvxl.readers.Parameters
QM_TYPE_VOLUME_DATA - Static variable in class org.jmol.jvxl.readers.Parameters
QMAtom - Class in org.jmol.quantum
QMAtom(int, T3, Atom, float[], float[], float[], float[], float[], float[], float) - Constructor for class org.jmol.quantum.QMAtom
qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
qMods - Static variable in class org.jmol.script.ScriptMathProcessor
qmOrbitalCount - Variable in class org.jmol.jvxl.readers.Parameters
qmOrbitalType - Variable in class org.jmol.jvxl.readers.Parameters
qPanelJPEG - Variable in class org.jmol.dialog.Dialog
qPanelPNG - Variable in class org.jmol.dialog.Dialog
qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
qpt2 - Variable in class org.jmol.adapter.readers.xtal.CastepReader
qs - Variable in class org.jmol.adapter.readers.cif.MSRdr
QS - Class in org.jmol.quantum
  Constants and static methods for quantum shells.
QS() - Constructor for class org.jmol.quantum.QS
qSetupDone - Variable in class org.jmol.jvxl.readers.IsoMOReader
qSliderJPEG - Variable in class org.jmol.dialog.Dialog
qSliderPNG - Variable in class org.jmol.dialog.Dialog
qtOffset - Variable in class org.jmol.util.ModulationSet
QUADRIC - Static variable in class org.jmol.shapecgo.CGOMesh
quadruple(int, short[]) - Static method in class org.jmol.util.Geodesic
QUADRUPOLE_MOMENT - Static variable in class org.jmol.quantum.NMRCalculation
qualityJ - Variable in class org.jmol.dialog.Dialog
qualityJPG - Static variable in class org.jmol.dialog.Dialog
qualityJPG - Variable in class org.jmol.viewer.StatusManager
qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
QualityListener(boolean, JSlider) - Constructor for class org.jmol.dialog.Dialog.QualityListener
qualityP - Variable in class org.jmol.dialog.Dialog
qualityPNG - Static variable in class org.jmol.dialog.Dialog
qualityPNG - Variable in class org.jmol.viewer.StatusManager
qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
  gets the value at the color boundary for this color range fraction
quantize4(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
QuantumCalculation - Class in org.jmol.quantum
QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
QuantumPlaneCalculation - Class in org.jmol.quantum
  Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
QuantumPlaneCalculation() - Constructor for class org.jmol.quantum.QuantumPlaneCalculation
quaternion - Static variable in class org.jmol.script.T
quaternionframe - Static variable in class org.jmol.script.T
quaternionFrame - Variable in class org.jmol.viewer.GlobalSettings
queueAtom(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
queueOnHold - Variable in class org.jmol.viewer.Viewer
queueThreadFinished(int) - Method in interface org.jmol.api.JmolScriptManager
queueThreadFinished(int) - Method in class org.jmol.script.ScriptManager
queueThreads - Variable in class org.jmol.script.ScriptManager
quiet - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
quit - Static variable in class org.jmol.script.T

## R

r - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
r - Variable in class org.jmol.quantum.SlaterData
r - Variable in class org.jmol.util.Rgb16
r0 - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
r0 - Variable in class org.jmol.minimize.forcefield.UFFDistanceCalc
r0 - Variable in class org.jmol.util.ModulationSet
  the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself
R3 - Static variable in class org.jmol.minimize.forcefield.ForceField
R4 - Static variable in class org.jmol.minimize.forcefield.ForceField
R5 - Static variable in class org.jmol.minimize.forcefield.ForceField
rab - Variable in class org.jmol.minimize.forcefield.Calculation
rad - Static variable in class org.jmol.script.T
RAD_COV_BODR_2014_02_22 - Static variable in class org.jmol.util.Elements
RAD_COV_IONIC_OB1_100_1 - Static variable in class org.jmol.util.Elements
RAD_PER_DEG - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
RAD_TO_DEG - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
RAD_TO_DEG - Static variable in class org.jmol.minimize.forcefield.Calculations
RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
radialPart(double) - Method in class org.jmol.jvxl.readers.IsoShapeReader
RADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
radiansPerDegree - Static variable in class org.jmol.smiles.SmilesMeasure
radiansPerDegree - Static variable in class org.jmol.viewer.JC
radiansXStep - Variable in class org.jmol.thread.MoveToThread
radiansYStep - Variable in class org.jmol.thread.MoveToThread
radiansZStep - Variable in class org.jmol.thread.MoveToThread
radical - Static variable in class org.jmol.script.T
radii - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
radii - Variable in class org.jmol.util.ContactPair
radiiIP2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
radius - Variable in class org.jmol.adapter.smarter.Atom
radius - Variable in class org.jmol.adapter.smarter.Bond
radius - Variable in class org.jmol.bspt.CubeIterator
radius - Variable in class org.jmol.g3d.CylinderRenderer
radius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
radius - Static variable in class org.jmol.script.T
radius - Variable in class org.jmol.shapespecial.Polyhedra
radius - Variable in class org.jmol.symmetry.PointGroup
radius2 - Variable in class org.jmol.g3d.CylinderRenderer
RADIUS_GLOBAL - Static variable in class org.jmol.modelset.Atom
RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
RADIUS_MAX - Static variable in class org.jmol.shape.Shape
RADIUS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Maximum value for vector radius.
RADIUS_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Initial value of vector radius.
radiusData - Variable in class org.jmol.atomdata.AtomData
RadiusData - Class in org.jmol.atomdata
RadiusData(float[], float, RadiusData.EnumType, VDW) - Constructor for class org.jmol.atomdata.RadiusData
radiusData - Variable in class org.jmol.modelset.AtomIteratorWithinModel
radiusData - Variable in class org.jmol.modelset.MeasurementData
radiusData - Variable in class org.jmol.shape.Measures
RadiusData.EnumType - Enum in org.jmol.atomdata
radiusHermites - Variable in class org.jmol.renderbio.BioMeshRenderer
radiusI - Variable in class org.jmol.geodesic.EnvelopeCalculation
radiusMin - Variable in class org.jmol.shapespecial.Polyhedra
radiusP - Variable in class org.jmol.geodesic.EnvelopeCalculation
radiusPt - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
radiusSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
radiusValue - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
raise_exceptions - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ramachandran - Static variable in class org.jmol.script.T
ramp_blend_nearby_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
rand - Variable in class org.jmol.scriptext.MathExt
random - Variable in class org.jmol.jvxl.readers.IsoMOReader
random - Variable in class org.jmol.jvxl.readers.IsoShapeReader
random - Static variable in class org.jmol.script.T
randomizeUnitVector(V3d) - Static method in class org.jmol.minimize.Util
randomPoint() - Static method in class org.jmol.shapespecial.Draw
randomPoint - Static variable in class org.jmol.shapespecial.Polyhedra
randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
range - Static variable in class org.jmol.script.T
range - Variable in class org.jmol.shapebio.BioShape
range(double) - Method in class org.jmol.util.Modulation
  Check that left < x4 < right, but allow for folding
rangeAll - Variable in class org.jmol.jvxl.readers.Parameters
rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
rangeSelected - Variable in class org.jmol.jvxl.readers.Parameters
rangeselected - Static variable in class org.jmol.script.T
rangeSelected - Variable in class org.jmol.viewer.GlobalSettings
RANK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
rank4bAndRead(BS) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  A thread-based sphere-ordered implementation that takes into account that lists cross the boundaries of branches.
rank_assisted_sorts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
Raromatic - Static variable in class org.jmol.minimize.forcefield.ForceField
rAS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
rAS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
Ras3DReader - Class in org.jmol.jvxl.readers
Ras3DReader() - Constructor for class org.jmol.jvxl.readers.Ras3DReader
rasmol - Static variable in class org.jmol.script.T
RASMOL - Static variable in class org.jmol.util.ColorEncoder
rasmolBinding - Variable in class org.jmol.viewer.ActionManager
RasmolBinding - Class in org.jmol.viewer.binding
RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
rasmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
rasmolHeteroSetting - Variable in class org.jmol.viewer.GlobalSettings
rasmolHydrogenSetting - Variable in class org.jmol.viewer.GlobalSettings
rasmolOverrides - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
rasmolScale - Static variable in class org.jmol.util.ColorEncoder
rasterCount - Variable in class org.jmol.g3d.CylinderRenderer
RAW_RGB - Static variable in class org.jmol.util.C
RAW_RGB_INT - Static variable in class org.jmol.util.C
rawAtomTypes - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
rawBondCount - Variable in class org.jmol.minimize.Minimizer
rawBondTypes - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
rawIndex - Variable in class org.jmol.minimize.MinBond
rawMMFF94Charges - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
ray_blend_blue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_blend_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_blend_green - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_blend_red - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_clip_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_color_ramps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_default_renderer - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_direct_shade - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_hint_camera - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_hint_shadow - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_improve_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_interior_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_interior_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_interior_reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_interior_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_interior_texture - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_label_specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_legacy_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_max_passes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_opaque_background - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_orthoscopic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_oversample_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_pixel_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_scatter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_shadow_decay_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_shadow_decay_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_shadow_fudge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_spec_local - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_texture - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_texture_settings - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_depth_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_disco_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_fog - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_fog_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_gain - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_persist_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_slope_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_trace_trans_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_transparency_contrast - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_transparency_oblique - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_transparency_oblique_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_transparency_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_transparency_spec_cut - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_transparency_specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_triangle_fudge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ray_volume - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
rBS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
rBS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
rd() - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
rd - Variable in class org.jmol.adapter.readers.pymol.JmolObject
rd() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
rd() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
rd() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
rd() - Method in interface org.jmol.api.JmolJDXMOLReader
rd() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
rd - Variable in class org.jmol.shape.AtomShape
rd - Variable in class org.jmol.viewer.Viewer
rdLast - Variable in class org.jmol.shapespecial.Dots
rdLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
rdline() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
rdSiesta() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
rdVDW - Static variable in class org.jmol.shapesurface.Contact
read() - Method in class org.openscience.jvxl.MonitorInputStream
read(byte[]) - Method in class org.openscience.jvxl.MonitorInputStream
read(byte[], int, int) - Method in class org.openscience.jvxl.MonitorInputStream
read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
readableTypes - Static variable in class org.jmol.viewer.PropertyManager
readACDAssignments(int, boolean) - Method in interface org.jmol.api.JmolJDXMOLParser
readACDAssignments(int, boolean) - Method in class org.jmol.jsv.JDXMOLParser
readACDMolFile() - Method in interface org.jmol.api.JmolJDXMOLParser
readACDMolFile() - Method in class org.jmol.jsv.JDXMOLParser
  MOL file embedded in JDX file
readAllData() - Method in class org.jmol.adapter.readers.cif.CifReader
readAllData() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readAllData - Variable in class org.jmol.jvxl.readers.Parameters
readAndSetVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readAparam() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
readArchive(String, boolean, int, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readArchive() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
readArchiveHeader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
readAtom(String[], boolean) - Method in class org.jmol.adapter.readers.xtal.AimsReader
readAtom() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  Allowing for BOHR units here; probably unnecessary.
readAtomCountAndOrigin() - Method in class org.jmol.adapter.readers.simple.CubeReader
readAtomCountAndSetNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readAtomData(float) - Method in class org.jmol.adapter.readers.xtal.CastepReader
readAtomicCoordinatesFormat() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
readAtomicOrbitalOrder() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readAtomicPos(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
readAtomNames() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readAtomRecord(Atom, P3, P3, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Read the atom or pos# record, including occupancy, various flags, and, especially, modulations.
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
readAtoms() - Method in class org.jmol.adapter.readers.more.GromacsReader
readAtoms(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
readAtoms(String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Reads the output coordinates section into a new AtomSet.
readAtoms(boolean) - Method in class org.jmol.adapter.readers.quantum.PsiReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.QchemReader
readAtoms() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readAtoms() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
readAtoms() - Method in class org.jmol.adapter.readers.simple.CubeReader
readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
  Lots of possibilities here: atom count is real; atom count is one less than true atom count sixth column is atom type; sixth column is first bond
readAtoms(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
readAtoms(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readAtoms() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
readAtoms() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readAtoms() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readAtoms() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
readAtoms() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
readAtoms() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
readAtomsAndBonds(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
readAtomsAndBonds(String[]) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
readAtomsCartGeomThenCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
readAtomSet(String, boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readAtomsInAngstromCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readAtomSpecies() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readAtomValues() - Method in class org.jmol.adapter.readers.molxyz.MolReader
  Read all V nnn lines as string data; user can adapt as needed.
readAtSign() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.PsiReader
readBasis() - Method in class org.jmol.adapter.readers.quantum.QchemReader
readBasis(String) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
readBasis() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readBasisNormalized() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
readBilbaoDataFile() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
readBilbaoFormat(String, float) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
readBinaryHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
readBlock(String) - Method in class org.jmol.adapter.readers.simple.InputReader
readBlock(String) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
readBonds(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
readBonds(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
readBonds() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readBonds() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readBonds() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
readBonds(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
readBonds(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
readBonds(int) - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readBornChargeTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readBrickLayer() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
readCalculationInfo(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
readCalculationType() - Method in class org.jmol.adapter.readers.quantum.QchemReader
readCellParam() - Method in class org.jmol.adapter.readers.xtal.DmolReader
readCellParam(boolean) - Method in class org.jmol.adapter.readers.xtal.EspressoReader
readCellParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
readCellParams() - Method in class org.jmol.adapter.readers.xtal.MagresReader
readCFI() - Method in class org.jmol.adapter.readers.simple.InputReader
readCharges() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
readCifData() - Method in class org.jmol.adapter.readers.cif.CifReader
readCifData(String, Object, String) - Method in interface org.jmol.atomdata.AtomDataServer
readCifData(String, String) - Method in class org.jmol.viewer.Viewer
readCifData(String, Object, String) - Method in class org.jmol.viewer.Viewer
readCifFloats(String, float[]) - Method in class org.jmol.jvxl.readers.BCifDensityReader
readCifFloats(String, float[]) - Method in class org.jmol.jvxl.readers.CifDensityReader
readCifP3(String, P3) - Method in class org.jmol.jvxl.readers.BCifDensityReader
readCifP3(String, P3) - Method in class org.jmol.jvxl.readers.CifDensityReader
readColor() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
readConFile() - Method in class org.jmol.adapter.readers.simple.InputReader
readConstraints() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readCoord() - Method in class org.jmol.adapter.readers.xtal.DmolReader
readCoordinates() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
readCoordinates() - Method in class org.jmol.adapter.readers.more.MdCrdReader
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
  Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.DgridReader
  Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.simple.AmpacReader
  Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
readCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
readCoordinates() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
readCoordLines() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Read coordinates, either input or crystallographic, just saving their lines in a vector for now.
readCrystalInfo() - Method in class org.jmol.adapter.readers.more.Mol2Reader
readData(String, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.
readData() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
readData31(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
readData46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
  read labels and not proper number of NOs, nNOs, for this nboType
readData47() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
readDataObject(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
readDimensionality() - Method in class org.jmol.adapter.readers.xtal.GulpReader
readDipole() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readDisplacements(float) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
readDots() - Method in class org.jmol.jvxl.readers.KinemageReader
readDoubleArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readElementLabelsOnly() - Method in class org.jmol.adapter.readers.more.AFLOWReader
  scan the AFLOWReader PRE structure for elements in coord section
readElementNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readEmbeddedScript() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
readEnergy() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readEnergy() - Method in class org.jmol.adapter.readers.quantum.QchemReader
readEnergy() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readEnergy(int, String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
readEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
readEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
readEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
readEnergy() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
reader - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
reader - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollection
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
READER_NOT_FOUND - Static variable in class org.jmol.viewer.JC
readerClosed - Variable in class org.jmol.jvxl.readers.VolumeFileReader
readerData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
readerList - Variable in class org.jmol.adapter.smarter.AtomSetCollection
readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
readerOrDocument - Variable in class org.jmol.io.FileReader
readers - Variable in class org.jmol.jvxl.readers.IsoIntersectGridReader
readerSets - Static variable in class org.jmol.adapter.smarter.Resolver
readESym(boolean) - Method in class org.jmol.adapter.readers.quantum.QchemReader
readEventCount - Variable in class org.openscience.jvxl.MonitorInputStream
readExtents(int) - Method in class org.jmol.jvxl.readers.JaguarReader
  read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
readFileData() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readFinalCell() - Method in class org.jmol.adapter.readers.xtal.GulpReader
readFloatArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
readFloatArray() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
readFreq() - Method in class org.jmol.adapter.readers.xtal.DmolReader
readFreqFragments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Select only specific atoms for frequency generation.
readFreqsAndModes() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readFreqsAndModes(ArrayList<Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
  Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
readFrequencies(String, boolean) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Reads the AtomSet and projected frequencies in the frequency section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.PsiReader
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.QchemReader
  Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.simple.AmpacReader
  Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.simple.MopacReader
  Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
readFrequencies() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readFrequency() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readGaussianBasis(ArrayList<Object>, ArrayList<Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readGeometryOptimization() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readGradient() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Read minimization measures
readGradients() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Reads the energy gradients section into a new AtomSet.
readHeader(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
readHeader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readHeader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readIdeal - Variable in class org.jmol.adapter.readers.cif.CifReader
readInitialCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readInputAtoms() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readInputDeck() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readInputHeader() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readInputRecords() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readIntiallattice() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readIsotopes() - Method in class org.jmol.adapter.readers.molxyz.MolReader
  Read all M ISO lines.
readJaguarMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
readKeywords() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
readLatticeAbc() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readLatticeCart() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readLatticeParams(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Read the lattice parameters.
readLatticeVector(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
readLengthUnit(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
readLine() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readLine() - Method in class org.jmol.jsv.JDXMOLParser
readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
readList() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Read a CIF 2.0 list structure, converting it to either a JSON string or to a Java data structure
readM40Data(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  read the M40 file, possibly as the extension of M50+M40
readM40FloatLines(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
readM40Floats() - Method in class org.jmol.adapter.readers.xtal.JanaReader
readM40WaveVectors() - Method in class org.jmol.adapter.readers.xtal.JanaReader
readMdyn() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readModels() - Method in interface org.jmol.api.JmolJDXMOLParser
readModels() - Method in class org.jmol.jsv.JDXMOLParser
readMolData(Map<String, Object>, Lst<String>) - Method in class org.jmol.adapter.readers.molxyz.MolReader
  Read the SDF data with name in lower case
readMolecularFormula() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
  try various ways to read the optional atom labels.
readMolecularObitals() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readMolecularOrbital() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readMolecularOrbitals(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
readMolecularOrbitals(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
  Read basis and orbital information.
readMOs() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
readMOs() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
readMOs(boolean, QchemReader.MOInfo[]) - Method in class org.jmol.adapter.readers.quantum.QchemReader
readMultipole(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
readMyTransform() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
readNBO37Occupancies(int) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
  Read occupancies from .37 file.
readNBOCoefficients(Map<String, Object>, String, Viewer) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
  Called by setNBOType in IsoExt when use issues NBO TYPE xxx
readNextLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
readNoatom() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readNostep() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
readNotypes() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
readOutput() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
readOutputAtomIndex() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readOutputAtoms() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readOutputBornChargeTensors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readOutputCharges() - Method in class org.jmol.adapter.readers.xtal.CastepReader
  read Mulliken or Hirshfield charges
readOutputUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readParameters() - Method in class org.jmol.jvxl.readers.ApbsReader
readParameters() - Method in class org.jmol.jvxl.readers.BCifDensityReader
readParameters() - Method in class org.jmol.jvxl.readers.CastepDensityReader
readParameters() - Method in class org.jmol.jvxl.readers.CubeReader
readParameters() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
  this reader has the critical scaling information at the end, so we just load the data straight into an array.
readParameters() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
readParameters() - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
readParameters() - Method in class org.jmol.jvxl.readers.JaguarReader
  nothing much here
readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readParameters() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
readParameters() - Method in class org.jmol.jvxl.readers.PltFormattedReader
readParameters() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
readParameters() - Method in class org.jmol.jvxl.readers.UhbdReader
readParameters() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
readParameters() - Method in class org.jmol.jvxl.readers.VolumeFileReader
readParameters() - Method in class org.jmol.jvxl.readers.XplorReader
readParameters() - Method in class org.jmol.jvxl.readers.XsfReader
readParams(BufferedReader, int, Map<Object, Object>) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.QchemReader
readPartialCharges() - Method in class org.jmol.adapter.readers.simple.AmpacReader
readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.GulpReader
readPeaks(boolean, int) - Method in interface org.jmol.api.JmolJDXMOLParser
readPeaks(boolean, int) - Method in class org.jmol.jsv.JDXMOLParser
readPhononFractionalCoord() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readPhononFrequencies() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readPhononTrajectories() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readPhononUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readPolygons() - Method in class org.jmol.jvxl.readers.KinemageReader
readPolygons() - Method in class org.jmol.jvxl.readers.MsmsReader
readPolygons() - Method in class org.jmol.jvxl.readers.ObjReader
readPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
readPolygonsPM() - Method in class org.jmol.jvxl.readers.PmeshReader
readPOSITION() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readPositionsAbs() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readPositionsFrac() - Method in class org.jmol.adapter.readers.xtal.CastepReader
readPRE - Variable in class org.jmol.adapter.readers.more.AFLOWReader
readPrePost() - Method in class org.jmol.adapter.readers.more.AFLOWReader
readPrimitiveLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Read transform matrix primitive to conventional.
readProperties() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readProperties() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
readProperty() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readPsiMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.PsiReader
readQchemMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.QchemReader
readRaman(Lst<String>) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readResInfo(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
readSCFDone() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Interprets the SCF Done: section.
readSCFDone() - Method in class org.jmol.adapter.readers.quantum.PsiReader
  Interprets the SCF Done: section.
readSecondOrderData() - Method in class org.jmol.adapter.readers.quantum.MOReader
readShift() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
  Read the origin shift
readSingleAtom() - Method in class org.jmol.adapter.readers.cif.CifReader
  No need for anything other than the atom name and symbol; coordinates will be (0 0 0), and no other information is needed.
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.DgridReader
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
readSlaterBasis(ArrayList<Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.GulpReader
readSpecies() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
readSteps() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
readString() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
readStringAsBytes() - Method in class org.jmol.adapter.readers.pymol.PickleReader
readStructure(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
readSurfaceDataJXR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSurfaceDataVDR(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
readSurfaceDataXML() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
readSymmetry() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Read the symmetry information and set the property.
readSymmetry() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  not doing anything with this -- P1 assumed
readSymmetry() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
readSymmetryOperators() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readTable() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Read a CIF 2.0 table into either a JSON string or a java data structure
readTensor() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  Read a tensor line.
readTitleLines() - Method in class org.jmol.adapter.readers.simple.CubeReader
readTlsData() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
readTotal() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
  Interpret a line starting with a line with "Total" in it.
readTotalAtomicCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
readTransform() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
readTypesequence() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
readUniqueAtoms() - Method in class org.jmol.adapter.readers.quantum.PsiReader
readUnitCell() - Method in class org.jmol.adapter.readers.more.GromacsReader
readUnitCell() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
readUnitCell() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
readUnnormalizedBasis() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
readUserData(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
readValue(String) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readVectors() - Method in class org.jmol.jvxl.readers.KinemageReader
readVertices() - Method in class org.jmol.jvxl.readers.KinemageReader
readVertices() - Method in class org.jmol.jvxl.readers.MsmsReader
readVertices() - Method in class org.jmol.jvxl.readers.ObjReader
readVertices() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
readVertices() - Method in class org.jmol.jvxl.readers.PmeshReader
readVertices() - Method in class org.jmol.jvxl.readers.Ras3DReader
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.NffReader
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.Ras3DReader
readVerticesPM() - Method in class org.jmol.jvxl.readers.PmeshReader
readVFI() - Method in class org.jmol.adapter.readers.simple.InputReader
readVibFreqs() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
readVirtual() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
readVolumetricHeader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
readVoxelDataIndividually(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
reallocRgb16s(Rgb16[], int) - Method in class org.jmol.g3d.TriangleRenderer
rebond() - Method in class org.jmol.api.JmolViewer
rebond() - Method in class org.jmol.viewer.Viewer
rebond() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
rebondState(boolean) - Method in class org.jmol.viewer.Viewer
recachePngjBytes(String, byte[]) - Method in class org.jmol.viewer.FileManager
recalc() - Method in class org.jmol.modelset.Text
recalcAltVertices - Variable in class org.jmol.shape.Mesh
reCalculate(BS, M3) - Method in class org.jmol.geodesic.EnvelopeCalculation
  problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
recalculateAllPolymers(BS, Group[]) - Method in class org.jmol.modelsetbio.BioModelSet
recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelSet
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioModel
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
recalculatePoints(int) - Method in class org.jmol.modelsetbio.BioModelSet
recalculatePolymers(BS) - Method in class org.jmol.modelset.ModelSet
recalculatePositionDependentQuantities(BS, M4) - Method in class org.jmol.modelset.ModelSet
recallCommand(boolean) - Method in class org.jmol.console.GenericConsole
recallCommand(boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
  Recall command history.
recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
RecentFilesDialog - Class in org.openscience.jmol.app.jmolpanel
  Manages a list of recently opened files.
RecentFilesDialog(Frame) - Constructor for class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
  Creates a hidden recent files dialog
recordData(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
records - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
recordStatus(String) - Method in class org.jmol.viewer.StatusManager
recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
Rectangle - Class in org.jmol.util
Rectangle() - Constructor for class org.jmol.util.Rectangle
rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
rectRubber - Variable in class org.jmol.viewer.ActionManager
RED - Static variable in class org.jmol.util.C
redo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
redoButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
redomove - Static variable in class org.jmol.script.T
REDUCE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
reducedAnisotropy() - Method in class org.jmol.util.Tensor
  reduced anisotropy = largest difference from isotropy (may be negative)
reduceFilename(String) - Static method in class org.jmol.viewer.ModelManager
referance - Variable in class org.jmol.smiles.SmilesAtom
reference - Variable in class org.jmol.modelset.TickInfo
reference - Static variable in class org.jmol.script.T
referenceCenter - Variable in class org.jmol.export.___Exporter
referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
reflect_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
reformatDistanceIfSelected() - Method in class org.jmol.modelset.Measurement
reformatDistances() - Method in class org.jmol.shape.Measures
refresh(int, String) - Method in class org.jmol.api.JmolViewer
refresh(Point3fi[]) - Method in class org.jmol.modelset.Measurement
refresh(boolean) - Method in class org.jmol.script.ScriptEval
  Refresh the display NOW
refresh - Static variable in class org.jmol.script.T
refresh(int, String) - Method in class org.jmol.viewer.Viewer
  initiate a repaint/update sequence if it has not already been requested.
REFRESH_REPAINT - Static variable in class org.jmol.viewer.Viewer
REFRESH_REPAINT_NO_MOTION_ONLY - Static variable in class org.jmol.viewer.Viewer
REFRESH_SEND_WEBGL_NEW_ORIENTATION - Static variable in class org.jmol.viewer.Viewer
REFRESH_SYNC - Static variable in class org.jmol.viewer.Viewer
REFRESH_SYNC_MASK - Static variable in class org.jmol.viewer.Viewer
refreshButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
refreshing - Static variable in class org.jmol.script.T
refreshing - Variable in class org.jmol.viewer.Viewer
refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
region - Variable in class org.jmol.util.MeshCapper.CapVertex
  dynamic region pointers
register(String, JmolSyncInterface) - Method in interface org.jmol.api.JmolSyncInterface
register(String, JmolSyncInterface) - Method in class org.jmol.applet.JmolApplet
register(Component, String) - Method in interface org.jmol.awtjs.swing.SwingController
  Set c's id to a unique identifier and add it to an associative array that will associate that id with c.
register(String, JmolSyncInterface) - Method in class org.jmol.util.GenericApplet
register(String, JmolSyncInterface) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
registerApplet(String, String) - Method in class org.jmol.applet.JmolApplet
registerAudio(String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
reinitializeLightingAndColor(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
reinitShape() - Method in class org.jmol.shape.Axes
reinstateMenu(JMenuItem, MenuElement[]) - Method in class org.jmol.awt.AwtPopupHelper
  Cause the menu to persist in its open state.
rejectAtomName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
release() - Method in interface org.jmol.api.AtomIndexIterator
release() - Method in class org.jmol.bspt.CubeIterator
  nulls internal references
release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
release() - Method in class org.jmol.symmetry.UnitCellIterator
releaseBuffers() - Method in class org.jmol.g3d.Graphics3D
releaseBuffers() - Method in class org.jmol.g3d.Platform3D
RELEASED - Static variable in class org.jmol.awtjs.Event
released(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
releaseModelSet() - Method in class org.jmol.modelset.ModelSet
releaseModelSetAC() - Method in class org.jmol.modelset.AtomCollection
releaseModelSetBC() - Method in class org.jmol.modelset.BondCollection
releaseScreenImage() - Method in class org.jmol.api.JmolViewer
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
releaseScreenImage() - Method in class org.jmol.util.GData
releaseScreenImage() - Method in class org.jmol.viewer.Viewer
releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
remapColors(Viewer, ColorEncoder, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
  remaps colors based on a new color scheme or translucency level
remark285() - Method in class org.jmol.adapter.readers.pdb.PdbReader
remark290() - Method in class org.jmol.adapter.readers.pdb.PdbReader
remark350() - Method in class org.jmol.adapter.readers.pdb.PdbReader
remarkTls() - Method in class org.jmol.adapter.readers.pdb.PdbReader
rememberCheckbox(String, SC) - Method in class org.jmol.popup.GenericPopup
remoteAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
remoteAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
remove(int) - Method in interface org.jmol.api.SC
remove(int) - Method in class org.jmol.awt.AwtSwingComponent
remove(int) - Method in class org.jmol.awtjs.swing.Container
remove - Static variable in class org.jmol.script.T
remove(int, int) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
removeAll() - Method in interface org.jmol.api.SC
removeAll() - Method in class org.jmol.awt.AwtSwingComponent
removeAll() - Method in class org.jmol.awtjs.swing.Container
removeAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells
removeBinding(Iterator<String>, String) - Method in class org.jmol.viewer.binding.Binding
removeBridgingRings(Lst<BS>, Lst<SmilesRing>) - Static method in class org.jmol.smiles.SmilesAromatic
  check for any two rings with more than two common atoms and remove them from the pool
removeCommand() - Method in class org.jmol.util.CommandHistory
removeCommand(int) - Method in class org.jmol.util.CommandHistory
removeCommand() - Method in class org.jmol.viewer.Viewer
  Removes one command from the command history
removeCurrentAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
removeFunction(String) - Method in class org.jmol.viewer.Viewer
removeLastUnselectedAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
removeMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
  should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
removeParam(String) - Method in class org.jmol.viewer.GlobalSettings
removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
removeUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
render(GData, ModelSet, boolean, int[]) - Method in interface org.jmol.api.JmolRepaintManager
render(int[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.SphereRenderer
render() - Method in class org.jmol.render.AxesRenderer
render() - Method in class org.jmol.render.BallsRenderer
render() - Method in class org.jmol.render.BbcageRenderer
render() - Method in class org.jmol.render.EchoRenderer
render() - Method in class org.jmol.render.FrankRenderer
render() - Method in class org.jmol.render.HalosRenderer
render() - Method in class org.jmol.render.HoverRenderer
render() - Method in class org.jmol.render.LabelsRenderer
render() - Method in class org.jmol.render.MeasuresRenderer
render(GData, ModelSet, boolean, int[]) - Method in class org.jmol.render.RepaintManager
render() - Method in class org.jmol.render.ShapeRenderer
render() - Method in class org.jmol.render.StarsRenderer
render() - Method in class org.jmol.render.SticksRenderer
render(Text, JmolRendererInterface, float, float, boolean, float[], float[]) - Static method in class org.jmol.render.TextRenderer
render() - Method in class org.jmol.render.UccageRenderer
render() - Method in class org.jmol.renderbio.BioMeshRenderer
render() - Method in class org.jmol.renderbio.BioShapeRenderer
render() - Method in class org.jmol.rendercgo.CGORenderer
render() - Method in class org.jmol.renderspecial.DipolesRenderer
render() - Method in class org.jmol.renderspecial.DotsRenderer
render() - Method in class org.jmol.renderspecial.DrawRenderer
render() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
render() - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
render() - Method in class org.jmol.renderspecial.PolyhedraRenderer
render() - Method in class org.jmol.renderspecial.VectorsRenderer
render() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
render() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
render() - Method in class org.jmol.rendersurface.PmeshRenderer
render() - Method in class org.jmol.viewer.Viewer
render1(Atom) - Method in class org.jmol.render.HalosRenderer
render1(Atom, short) - Method in class org.jmol.render.StarsRenderer
render1(int) - Method in class org.jmol.render.UccageRenderer
render1(Dots) - Method in class org.jmol.renderspecial.DotsRenderer
render1(Polyhedron) - Method in class org.jmol.renderspecial.PolyhedraRenderer
render2(boolean) - Method in class org.jmol.render.MeshRenderer
  Overridden in DrawRenderer and IsosurfaceRenderer
render2(Mesh) - Method in class org.jmol.rendercgo.CGORenderer
render2(boolean) - Method in class org.jmol.renderspecial.DrawRenderer
render2(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
render2b(boolean) - Method in class org.jmol.render.MeshRenderer
render2Strand(boolean, float, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
render_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
renderAllStrings(Object) - Method in interface org.jmol.api.JmolGraphicsInterface
renderAllStrings(Object) - Method in class org.jmol.export.Export3D
renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
renderAllStrings(Object) - Method in class org.jmol.util.GData
renderAngle(String, Point3fi, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
renderArc - Variable in class org.jmol.modelset.Measurement
renderArc(int, int) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderArcs() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderArrowHead(T3, T3, float, boolean, boolean, boolean) - Method in class org.jmol.renderspecial.DrawRenderer
renderArrowHeads - Variable in class org.jmol.renderbio.RocketRenderer
renderArrowHeads - Variable in class org.jmol.renderbio.RocketsRenderer
renderArrows() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderAxes() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderAxis - Variable in class org.jmol.modelset.Measurement
renderBackground(JmolRendererInterface) - Method in interface org.jmol.api.JmolRendererInterface
renderBackground(JmolRendererInterface) - Method in class org.jmol.export.Export3D
renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
renderBackground(JmolRendererInterface) - Method in class org.jmol.util.GData
renderBall() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderBioMesh(Mesh) - Method in class org.jmol.renderbio.BioMeshRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.BackboneRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.BioShapeRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.CartoonRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RibbonsRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RocketsRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.StrandsRenderer
renderBioShape(BioShape) - Method in class org.jmol.renderbio.TraceRenderer
renderBits(short, short, int, byte, int, P3i, P3i) - Method in class org.jmol.g3d.CylinderRenderer
renderBitsFloat(short, short, int, byte, int, P3, P3) - Method in class org.jmol.g3d.CylinderRenderer
renderBlock(NucleicMonomer) - Method in class org.jmol.renderbio.NucleicRenderer
renderBond() - Method in class org.jmol.render.SticksRenderer
renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.CageRenderer
renderConeOld(short, byte, int, float, float, float, float, float, float, boolean, boolean) - Method in class org.jmol.g3d.CylinderRenderer
renderContourLines() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.DotsRenderer
  generic renderer -- dots and geosurface
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
renderCrossHairs(int[], int, int, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.export.Export3D
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.g3d.Graphics3D
renderCyl(P3, P3, P3, P3) - Method in class org.jmol.renderbio.NucleicRenderer
renderDipoleVector(Dipole, BS) - Method in class org.jmol.renderspecial.DipolesRenderer
renderDistance(String, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
renderDots(int) - Method in class org.jmol.renderspecial.DotsRenderer
  also called by GeoSurface when in motion
renderDots() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderEdge(P3[], P3[], int, int) - Method in class org.jmol.renderbio.NucleicRenderer
renderEllipsoids(Map<?, Ellipsoid>, boolean) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderer - Variable in class org.jmol.awtjs.swing.Grid
renderers - Variable in class org.jmol.render.RepaintManager
renderExport(GData, ModelSet, Map<String, Object>) - Method in interface org.jmol.api.JmolRepaintManager
renderExport(GData, ModelSet, Map<String, Object>) - Method in class org.jmol.render.RepaintManager
renderFlatEndcap(boolean, boolean, int[][]) - Method in class org.jmol.g3d.CylinderRenderer
renderFrameTitle(String) - Method in class org.jmol.render.EchoRenderer
renderHandles() - Method in class org.jmol.renderspecial.DrawRenderer
renderHeight - Variable in class org.jmol.awtjs.swing.Component
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.BioShapeRenderer
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.BioShapeRenderer
renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.BioShapeRenderer
renderHermiteRibbon(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, int) - Method in class org.jmol.g3d.HermiteRenderer
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.BioShapeRenderer
renderHermiteRope(boolean, int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
renderInfo() - Method in class org.jmol.render.UccageRenderer
renderInfo() - Method in class org.jmol.renderspecial.DrawRenderer
renderInfo() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderInfo() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
rendering - Variable in class org.jmol.jvxl.data.JvxlData
renderIso() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderLabel(String, float, float, float, float, float) - Method in class org.jmol.render.AxesRenderer
renderLabelOrMeasure(Text, String) - Method in class org.jmol.render.LabelsRenderer
renderLeontisWesthofEdges(NucleicMonomer) - Method in class org.jmol.renderbio.NucleicRenderer
renderLine(P3, P3, int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
renderLonePair(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderLow - Variable in class org.jmol.g3d.Graphics3D
renderLow - Variable in class org.jmol.render.MeshRenderer
renderMeasurement(boolean) - Method in class org.jmol.render.MeasuresRenderer
renderMesh2(Mesh) - Method in class org.jmol.render.MeshRenderer
  overridden in BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
renderMeshes() - Method in class org.jmol.renderbio.BioMeshRenderer
renderMeshRibbon() - Method in class org.jmol.renderbio.MeshRibbonRenderer
renderMeshSlab() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderNormals() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderNucleic(BioShapeRenderer) - Method in class org.jmol.renderbio.NucleicRenderer
renderNucleicBaseStep(int, T3, T3) - Method in class org.jmol.renderbio.NucleicRenderer
renderOld(short, short, int, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.CylinderRenderer
renderOne(Ellipsoid) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
renderParallelPair(boolean, int, P3, P3, P3, P3, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
renderPart(int[][]) - Method in class org.jmol.renderbio.RocketRenderer
renderPass2(short) - Static method in class org.jmol.util.C
renderPending() - Method in class org.jmol.renderbio.RocketRenderer
renderPendingMeasurement() - Method in class org.jmol.render.MeasuresRenderer
renderPendingRocketSegment(int, P3, P3, P3, boolean) - Method in class org.jmol.renderbio.RocketRenderer
renderPendingSheetPlank(P3, P3, P3, boolean) - Method in class org.jmol.renderbio.RocketRenderer
renderPoints() - Method in class org.jmol.render.MeshRenderer
renderPoints() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderProtein() - Method in class org.jmol.renderbio.CartoonRenderer
renderQuadrant(int, int, int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
renderQuadrantClipped(int, int, int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
renderQuadrantUnclipped(int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
renderRibose() - Method in class org.jmol.renderbio.NucleicRenderer
renderRing5() - Method in class org.jmol.renderbio.NucleicRenderer
renderRing6() - Method in class org.jmol.renderbio.NucleicRenderer
renderRockets() - Method in class org.jmol.renderbio.RocketRenderer
renderRockets() - Method in class org.jmol.renderbio.RocketsRenderer
renderScreenImage(Object, Object) - Method in interface org.jmol.api.GenericPlatform
  Deprecated.
renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
  Deprecated.
renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolViewer
renderScreenImage(PlatformViewer, Object, Object) - Static method in class org.jmol.awt.Display
  Deprecated.
renderScreenImage(Object, Object) - Method in class org.jmol.awt.Platform
  legacy apps will use this
renderScreenImage(PlatformViewer, Object, Object) - Static method in class org.jmol.awtjs2d.Display
  legacy apps will use this
renderScreenImage(Object, Object) - Method in class org.jmol.awtjs2d.Platform
  legacy apps will use this
renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
  JmolViewer interface uses this, but that is all
renderScreenImageStereo(Object, boolean, int, int) - Method in class org.jmol.viewer.Viewer
renderShape(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
renderShapes() - Method in class org.jmol.renderbio.BioShapeRenderer
renderSimpleLabel(JmolRendererInterface, Font, String, short, short, float[], int, int, int, int, float, int, boolean, short, boolean) - Static method in class org.jmol.render.TextRenderer
renderSpecialSegment(AlphaMonomer, short, short) - Method in class org.jmol.renderbio.RocketRenderer
renderSphereClipped(int[], int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
renderSphereUnclipped(int[], int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
renderSphericalEndcaps() - Method in class org.jmol.g3d.CylinderRenderer
renderSteps(NucleicMonomer, int) - Method in class org.jmol.renderbio.NucleicRenderer
renderStrand(P3[]) - Method in class org.jmol.renderbio.StrandsRenderer
renderStrands() - Method in class org.jmol.renderbio.StrandsRenderer
renderStrandShape() - Method in class org.jmol.renderbio.StrandsRenderer
renderSurface(BS) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
renderTorsion(String, Point3fi, Point3fi, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
renderTrace() - Method in class org.jmol.renderbio.TraceRenderer
renderTriangle(P3[], P3[], int, int, int, boolean) - Method in class org.jmol.renderbio.NucleicRenderer
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.render.MeshRenderer
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
renderVector(V3, P3, P3, float, boolean) - Method in class org.jmol.renderspecial.DipolesRenderer
renderVector(Atom, Vibration) - Method in class org.jmol.renderspecial.VectorsRenderer
renderWidth - Variable in class org.jmol.awtjs.swing.Component
renderXyArrow(int) - Method in class org.jmol.renderspecial.DrawRenderer
renderXyPoint() - Method in class org.jmol.renderspecial.DrawRenderer
REP_ANGLES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_CALLBACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_CARTOON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_CELL - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_CGO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_DASHES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_DIHEDRALS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_DOTS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_ELLIPSOID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_EXTENT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_JMOL_MAX - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_JMOL_PUTTY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_JMOL_TRACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_LABELS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_LINES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_LIST - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_MAX - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_MESH - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_NBSPHERES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_NONBONDED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_RIBBON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_SLICE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_SPHERES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_STICKS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_SURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
REP_VOLUME - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
repaint(Object) - Method in interface org.jmol.api.GenericPlatform
repaint(Object) - Static method in class org.jmol.awt.Display
repaint(Object) - Method in class org.jmol.awt.Platform
repaint() - Method in class org.jmol.awtjs.swing.Component
repaint() - Method in class org.jmol.awtjs.swing.JDialog
repaint(Object) - Method in class org.jmol.awtjs2d.Platform
REPAINT_IGNORE - Static variable in class org.jmol.viewer.JC
repaintClock() - Method in class org.jmol.applet.AppletWrapper
repaintDone() - Method in interface org.jmol.api.JmolRepaintManager
repaintDone() - Method in class org.jmol.render.RepaintManager
repaintDone() - Method in class org.jmol.viewer.AnimationManager
repaintIfReady(String) - Method in interface org.jmol.api.JmolRepaintManager
repaintIfReady(String) - Method in class org.jmol.render.RepaintManager
RepaintManager - Class in org.jmol.render
RepaintManager() - Constructor for class org.jmol.render.RepaintManager
repaintNow(String) - Method in class org.jmol.render.RepaintManager
repaintPending - Variable in class org.jmol.render.RepaintManager
repaintwaitms - Static variable in class org.jmol.script.T
repaintWaitMs - Variable in class org.jmol.viewer.GlobalSettings
repeatCheckBox - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
repeatCount - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
replace - Static variable in class org.jmol.script.T
replace(int, int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
replaceCommand(T) - Method in class org.jmol.script.ScriptCompiler
replaceCommand(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
  Replaces current command on script.
replaceGroup(Group, Group) - Method in class org.jmol.shape.Shape
replaceGroup(Group, Group) - Method in class org.jmol.shapebio.BioShapeCollection
replaceGroup(Group, Group) - Method in class org.jmol.viewer.ShapeManager
replaceMutatedMonomer(Viewer, AminoMonomer, AminoMonomer) - Static method in class org.jmol.modelsetbio.BioExt
replaceParentSubstituent(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Swap a substituent and the parent in preparation for reverse traversal of this path back to the root atom.
replaceQuotedStrings(String, ArrayList<String>, ArrayList<String>) - Static method in class org.openscience.jmol.app.webexport.WebPanel
replaceXn(String, int) - Static method in class org.jmol.symmetry.SymmetryOperation
report(String, boolean) - Method in class org.jmol.minimize.Minimizer
report(String, boolean) - Method in class org.jmol.script.ScriptEval
report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
reportAll - Variable in class org.jmol.shape.Sticks
reportEnergy() - Method in class org.jmol.minimize.Minimizer
reportSelection(int) - Method in class org.jmol.viewer.ChimeMessenger
  report atom selection in Chime format
reportSelection(int) - Method in interface org.jmol.viewer.JmolChimeMessenger
reportSelection(String) - Method in class org.jmol.viewer.Viewer
repositionWindow(String, Component, int, int, boolean) - Method in class org.openscience.jmol.app.HistoryFile
  Uses the informations in the history to reposition the window.
repositionWindow(String, Component) - Method in class org.openscience.jmol.app.HistoryFile
  Uses the informations in the history to reposition the window.
reps - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
requestFocusInWindow(Object) - Method in interface org.jmol.api.GenericPlatform
requestFocusInWindow(Object) - Static method in class org.jmol.awt.Display
requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
requestFocusInWindow(Object) - Static method in class org.jmol.awtjs2d.Display
requestFocusInWindow(Object) - Method in class org.jmol.awtjs2d.Platform
requestRepaintAndWait(String) - Method in interface org.jmol.api.JmolRepaintManager
requestRepaintAndWait(String) - Method in class org.jmol.render.RepaintManager
requestRepaintAndWait(String) - Method in class org.jmol.viewer.Viewer
requiresBSFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
requiresSorting - Variable in class org.jmol.adapter.readers.cif.MMCifReader
requireTranslucent - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
reset() - Method in class org.jmol.adapter.smarter.XtalSymmetry
reset() - Method in class org.jmol.bspt.Bspt
reset - Static variable in class org.jmol.script.T
reset() - Method in class org.jmol.symmetry.UnitCell
reset() - Method in class org.jmol.thread.JmolThread
reset() - Method in class org.jmol.util.BoxInfo
reset(int) - Method in class org.jmol.util.CommandHistory
  Resets instance.
reset() - Method in class org.jmol.viewer.ActionManager
reset(boolean) - Method in class org.jmol.viewer.Viewer
reset() - Method in class org.openscience.jvxl.MonitorInputStream
RESET_NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
resetAromatic() - Method in class org.jmol.modelset.BondCollection
resetAxes() - Method in class org.jmol.modelsetbio.ProteinStructure
resetAxisCoordinates() - Method in class org.jmol.render.SticksRenderer
resetBioshapes(BS) - Method in class org.jmol.viewer.ShapeManager
resetBondFields(String) - Method in class org.jmol.modelkit.ModelKitPopup
resetBoundCount() - Method in class org.jmol.modelset.Model
resetChirality() - Method in class org.jmol.modelset.ModelSet
resetDefaults(String[]) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
resetDSSR(boolean) - Method in class org.jmol.modelset.Model
  Something has changed; clear the DSSR cache and possibly remove DSSR entirely.
resetError() - Method in class org.jmol.script.ScriptEval
resetFitToScreen(boolean) - Method in class org.jmol.viewer.TransformManager
resetFlag - Static variable in class org.openscience.jmol.app.webexport.LogPanel
resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
  reset some parameters at the "MAP" keyword or initially
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
resetIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
resetKey - Variable in class org.jmol.adapter.readers.pdb.PdbReader
resetLighting() - Method in class org.jmol.viewer.StateManager
  Reset lighting to Jmol defaults
resetMeasurement() - Method in class org.jmol.viewer.ActionManager
resetMessage - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
resetMolecules() - Method in class org.jmol.modelset.ModelSet
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
  something has arisen that requires resetting of the navigation point.
resetNeeded - Variable in class org.jmol.multitouch.ActionManagerMT
resetObjects() - Method in class org.jmol.shape.MeshCollection
resetPartialCharges() - Method in class org.jmol.modelset.AtomCollection
resetPlane(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
resetRasmolBonds(BS, int) - Method in class org.jmol.modelsetbio.BioModel
  from Trajectory.setAtomPositions base models only; not trajectories
resetRotation() - Method in class org.jmol.viewer.TransformManager
resetRotation() - Method in class org.jmol.viewer.TransformManager4D
resetShapes() - Method in class org.jmol.viewer.ShapeManager
resetShapes(boolean) - Method in class org.jmol.viewer.Viewer
resetSlab() - Method in class org.jmol.util.MeshSurface
resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
resetValue(String, GlobalSettings) - Method in class org.jmol.viewer.GlobalSettings
resetVoxelData(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
resetXYCenter(int, int) - Method in class org.jmol.viewer.TransformManager
RESI - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
residue - Static variable in class org.jmol.script.T
residueChar - Variable in class org.jmol.smiles.SmilesAtom
residueName - Variable in class org.jmol.smiles.SmilesAtom
residueNames - Variable in class org.jmol.adapter.readers.pdb.JmolDataReader
residueNumber - Variable in class org.jmol.smiles.SmilesAtom
residueSpecCodeGenerated - Variable in class org.jmol.script.ScriptTokenParser
resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
resizeDisplay(int, int) - Method in class org.jmol.appletjs.Jmol
resizeDisplay(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
resizeImage(int, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
resizeInnerPanel(int, int) - Method in class org.jmol.api.JmolViewer
resizeInnerPanel(String) - Method in class org.jmol.applet.Jmol
resizeInnerPanel(String) - Method in class org.jmol.appletjs.Jmol
resizeInnerPanel(String) - Method in class org.jmol.util.GenericApplet
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.StatusManager
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.Viewer
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
resizeInnerPanelString(String) - Method in class org.jmol.viewer.StatusManager
  called by file droppers
resMap - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
resMap - Variable in class org.jmol.modelsetbio.ProteinStructure
RESN - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
resno - Static variable in class org.jmol.script.T
resolution - Variable in class org.jmol.jvxl.readers.Parameters
resolution - Static variable in class org.jmol.script.T
resolveDataBase(String, String, String) - Static method in class org.jmol.viewer.JC
resolveDatabaseFormat(String) - Method in class org.jmol.viewer.Viewer
resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
Resolver - Class in org.jmol.adapter.smarter
Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
Resource - Class in org.jmol.i18n
Resource(Object, String) - Constructor for class org.jmol.i18n.Resource
resource - Variable in class org.jmol.i18n.Resource
resource - Static variable in class org.jmol.quantum.NMRCalculation
  NOTE! Do not change this txt file! Instead, edit trunk/Jmol/_documents/nmr_data.xls and then clip its contents to org/jmol/quantum/nmr_data.txt.
resourceCount - Variable in class org.jmol.i18n.GT
resourceMap - Variable in class org.jmol.i18n.Resource
resourceName - Variable in class org.jmol.quantum.MepCalculation
resources - Variable in class org.jmol.export._IdtfExporter
resources - Variable in class org.jmol.i18n.GT
RESTART - Static variable in class org.jmol.script.ScriptCompiler
restorativeForceAndAngleRadians(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restorativeForceAndDistance(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restorativeForceAndOutOfPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restorativeForceAndTorsionAngleRadians(V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
restore(float, boolean) - Method in class org.jmol.modelset.Orientation
restore - Static variable in class org.jmol.script.T
restore() - Method in class org.jmol.viewer.Connections
restore(Viewer, float) - Method in class org.jmol.viewer.Scene
restoreBonds(String) - Method in class org.jmol.viewer.StateManager
restoreCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
restoreCoordinates() - Method in class org.jmol.minimize.Minimizer
restoreFunction(JmolScriptFunction, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
  note that functions requiring motion cannot be run in JavaScript
restoreModelOrientation(int) - Method in class org.jmol.viewer.Viewer
restoreModelRotation(int) - Method in class org.jmol.viewer.Viewer
restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
restoreScene(String, float) - Method in class org.jmol.viewer.StateManager
restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
restoreSelection(String) - Method in class org.jmol.viewer.StateManager
restoreTokens() - Method in class org.jmol.script.ScriptContext
restrict - Static variable in class org.jmol.script.T
restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEval
restrictSelected(boolean, boolean) - Method in class org.jmol.viewer.ShapeManager
RESU - Static variable in class org.jmol.util.ColorEncoder
resume - Static variable in class org.jmol.script.T
resumeAnimation() - Method in class org.jmol.viewer.AnimationManager
resumeButton - Variable in class org.jmol.console.ScriptEditor
resumeEval(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
resumeEval(Object) - Method in class org.jmol.script.ScriptEval
  From dispatchCommands and JmolThread resumeEval.
resumeEval() - Method in class org.jmol.thread.JmolThread
resumePausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
resumePausedExecution() - Method in class org.jmol.script.ScriptEval
resumeViewer(String) - Method in class org.jmol.script.ScriptEval
RESV - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ret - Variable in class org.jmol.export.JSExporter
ret - Variable in class org.jmol.util.BZone
retain_order - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
retrieveCount - Variable in class org.jmol.adapter.readers.pymol.PickleReader
returncmd - Static variable in class org.jmol.script.T
returnToken() - Method in class org.jmol.script.ScriptTokenParser
returnValue - Variable in class org.jmol.script.ScriptFunction
reverse - Static variable in class org.jmol.script.T
reverseAnimation() - Method in class org.jmol.viewer.AnimationManager
reverseArray(int[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
reverseAtomSets() - Method in class org.jmol.adapter.smarter.AtomSetCollection
reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
  Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE.
reversecolor - Static variable in class org.jmol.script.T
reversed - Variable in class org.jmol.modelsetbio.BioPolymer
reversed - Variable in class org.jmol.renderbio.BioShapeRenderer
reverseList(Lst<?>) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
reverseModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
reverseObject(Object[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
reverseSets(AtomSetObject[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
rewind - Static variable in class org.jmol.script.T
REWIND - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
rewindAnimation() - Method in class org.jmol.viewer.AnimationManager
rfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
Rgb16 - Class in org.jmol.util
Rgb16() - Constructor for class org.jmol.util.Rgb16
rgb16sE - Variable in class org.jmol.g3d.TriangleRenderer
rgb16sGouraud - Variable in class org.jmol.g3d.TriangleRenderer
rgb16sW - Variable in class org.jmol.g3d.TriangleRenderer
rgb16t1 - Variable in class org.jmol.g3d.TriangleRenderer
rgb16t2 - Variable in class org.jmol.g3d.TriangleRenderer
rgbColorModel - Static variable in class org.jmol.awt.Image
rgbFractionalFromArgb(int) - Method in class org.jmol.export.___Exporter
rgbFractionalFromColix(short) - Method in class org.jmol.export.___Exporter
rho - Variable in class org.jmol.adapter.readers.xtal.JanaReader
rhoMin - Variable in class org.jmol.quantum.NciCalculation
rhoMolecules - Variable in class org.jmol.quantum.NciCalculation
rhoParam - Variable in class org.jmol.quantum.NciCalculation
rhoPlot - Variable in class org.jmol.quantum.NciCalculation
rI - Variable in class org.jmol.util.ModulationSet
ribbon - Static variable in class org.jmol.script.T
ribbon_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_nucleic_acid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_sampling - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_side_chain_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_throw - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_trace_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbon_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ribbonaspectratio - Static variable in class org.jmol.script.T
ribbonAspectRatio - Variable in class org.jmol.viewer.GlobalSettings
ribbonBorder - Variable in class org.jmol.renderbio.BioShapeRenderer
ribbonborder - Static variable in class org.jmol.script.T
ribbonBorder - Variable in class org.jmol.viewer.GlobalSettings
ribbonBottomScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
ribbonColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
Ribbons - Class in org.jmol.shapebio
Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
RibbonsRenderer - Class in org.jmol.renderbio
RibbonsRenderer() - Constructor for class org.jmol.renderbio.RibbonsRenderer
ribbonTopScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
ribbonTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
riboseOffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
right - Variable in class org.jmol.awtjs.swing.Insets
right - Variable in class org.jmol.awtjs.swing.JSplitPane
RIGHT - Static variable in class org.jmol.awtjs.swing.SwingConstants
right - Static variable in class org.jmol.script.T
right - Variable in class org.jmol.util.Modulation
RIGHT - Static variable in class org.jmol.viewer.binding.Binding
rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
rightbrace - Static variable in class org.jmol.script.T
rightOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
rightparen - Static variable in class org.jmol.script.T
rightPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
rightsquare - Static variable in class org.jmol.script.T
ring5OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
ring6OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
ringConnections - Variable in class org.jmol.smiles.SmilesSearch
ringConnectivity - Variable in class org.jmol.smiles.SmilesAtom
ringCount - Variable in class org.jmol.smiles.SmilesSearch
ringCounts - Variable in class org.jmol.smiles.SmilesSearch
ringData - Variable in class org.jmol.smiles.SmilesSearch
ringDataMax - Variable in class org.jmol.smiles.SmilesSearch
ringMembership - Variable in class org.jmol.smiles.SmilesAtom
ringSets - Variable in class org.jmol.smiles.SmilesGenerator
ringSets - Variable in class org.jmol.smiles.SmilesSearch
ringSize - Variable in class org.jmol.smiles.SmilesAtom
RL() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
rm - Variable in class org.jmol.viewer.Viewer
rmaxx - Variable in class org.jmol.adapter.smarter.XtalSymmetry
  range minima and maxima -- also usedf for cartesians comparisons
rmaxy - Variable in class org.jmol.adapter.smarter.XtalSymmetry
  range minima and maxima -- also usedf for cartesians comparisons
rmaxz - Variable in class org.jmol.adapter.smarter.XtalSymmetry
  range minima and maxima -- also usedf for cartesians comparisons
rminx - Variable in class org.jmol.adapter.smarter.XtalSymmetry
  range minima and maxima -- also usedf for cartesians comparisons
rminy - Variable in class org.jmol.adapter.smarter.XtalSymmetry
  range minima and maxima -- also usedf for cartesians comparisons
rminz - Variable in class org.jmol.adapter.smarter.XtalSymmetry
  range minima and maxima -- also usedf for cartesians comparisons
rmsd - Static variable in class org.jmol.script.T
rna - Static variable in class org.jmol.script.T
rna3d - Static variable in class org.jmol.script.T
RNA_MASK - Static variable in class org.jmol.viewer.JC
rnl - Variable in class org.jmol.jvxl.readers.IsoShapeReader
robust_logs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
rock - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
rock - Static variable in class org.jmol.script.T
rock_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
rocket - Static variable in class org.jmol.script.T
rocketbarrels - Static variable in class org.jmol.script.T
rocketBarrels - Variable in class org.jmol.viewer.GlobalSettings
RocketRenderer - Class in org.jmol.renderbio
RocketRenderer() - Constructor for class org.jmol.renderbio.RocketRenderer
Rockets - Class in org.jmol.shapebio
Rockets() - Constructor for class org.jmol.shapebio.Rockets
RocketsRenderer - Class in org.jmol.renderbio
RocketsRenderer() - Constructor for class org.jmol.renderbio.RocketsRenderer
root - Variable in class org.jmol.symmetry.CIPChirality
  The atom for which we are determining the stereochemistry
ROOT2 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
ROOT3 - Static variable in class org.jmol.adapter.readers.quantum.JaguarReader
ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
rootDistance - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  Rule 1b measure: Distance from root of the corresponding nonduplicated atom (duplicate nodes only).
rootPickingStyle - Variable in class org.jmol.viewer.ActionManager
rootSubstituent - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  sphere-1 node in this atom's root branch
rot - Variable in class org.jmol.render.SticksRenderer
rotate - Static variable in class org.jmol.script.T
rotate3DBall(float, float, BS) - Method in class org.jmol.viewer.TransformManager
rotate45 - Static variable in class org.jmol.script.T
rotate4DBall(float, float, float) - Method in class org.jmol.viewer.TransformManager4D
ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
rotateAboutPointsInternal(JmolScriptEvaluator, T3, T3, float, float, boolean, boolean, BS, boolean, V3, Lst<P3>, float[], M4) - Method in class org.jmol.viewer.TransformManager
rotateAboutPointsInternal(JmolScriptEvaluator, P3, P3, float, float, boolean, BS, V3, Lst<P3>, float[], M4) - Method in class org.jmol.viewer.Viewer
rotateAxes(int, V3[], P3, M3) - Method in interface org.jmol.api.SymmetryInterface
rotateAxes(int, V3[], P3, M3) - Method in class org.jmol.symmetry.Symmetry
rotateAxes(V3[], UnitCell, P3, M3) - Method in class org.jmol.symmetry.SymmetryOperation
rotateAxisAngle(V3, float) - Method in class org.jmol.viewer.TransformManager
rotateAxisAngle2(A4, BS) - Method in class org.jmol.viewer.TransformManager
rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.TransformManager
rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.Viewer
rotateAxisAngleRadiansFixed(float, BS) - Method in class org.jmol.viewer.TransformManager
rotateAxisAngleRadiansInternal(float, BS, M4) - Method in class org.jmol.viewer.TransformManager
rotateFront() - Method in class org.jmol.api.JmolViewer
rotateFront() - Method in class org.jmol.viewer.Viewer
rotateHexCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
rotatePoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
rotateSelected - Static variable in class org.jmol.script.T
rotateSelected(float, float, BS) - Method in class org.jmol.viewer.Viewer
rotateTranslate(Quat, T3, boolean) - Method in class org.jmol.shape.Mesh
rotateXRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager4D
rotateXYBy(float, float) - Method in class org.jmol.viewer.Viewer
rotateYRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
rotateZBy(int, int, int) - Method in class org.jmol.viewer.TransformManager
rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
rotation - Static variable in class org.jmol.script.T
rotation - Variable in class org.jmol.symmetry.HallRotationTerm
rotationAxis - Variable in class org.jmol.shapesurface.LcaoCartoon
rotationAxis - Variable in class org.jmol.viewer.TransformManager
rotationCenterDefault - Variable in class org.jmol.viewer.TransformManager
rotationDeg - Variable in class org.jmol.modelkit.ModelKitPopup
rotationMatrix - Variable in class org.jmol.modelset.Orientation
rotationOrder - Variable in class org.jmol.symmetry.HallTranslation
rotationRadius - Variable in class org.jmol.modelset.Orientation
rotationradius - Static variable in class org.jmol.script.T
rotationRadius - Variable in class org.jmol.thread.MoveToThread
rotationRadiusDefault - Variable in class org.jmol.viewer.TransformManager
rotationRate - Variable in class org.jmol.viewer.TransformManager
rotationShift12ths - Variable in class org.jmol.symmetry.HallTranslation
rotationTerms - Variable in class org.jmol.symmetry.HallInfo
rotCode - Variable in class org.jmol.symmetry.HallRotation
rotTransCart(SymmetryOperation, SymmetryInterface, P3, V3) - Static method in class org.jmol.symmetry.SymmetryDesc
round(double) - Static method in class org.jmol.export.___Exporter
round(T3) - Static method in class org.jmol.export.___Exporter
roundInt(int) - Static method in class org.jmol.util.GData
  JavaScript won't really have an integer here after integer division.
route - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
roving_byres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_cartoon - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_detail - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_isomesh - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_isosurface - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_labels - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_map1_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_map1_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_map2_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_map2_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_map3_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_map3_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_nb_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_nonbonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_origin - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_origin_z - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_origin_z_cushion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_polar_contacts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_polar_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_ribbon - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
roving_sticks - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
row - Static variable in class org.jmol.script.T
rowSelectionAllowed - Variable in class org.jmol.awtjs.swing.JTable
rowspan - Variable in class org.jmol.awtjs.swing.Cell
ROYGB - Static variable in class org.jmol.util.ColorEncoder
rpower - Static variable in class org.jmol.quantum.NciCalculation
rPt - Variable in class org.jmol.renderbio.NucleicRenderer
rPt5 - Variable in class org.jmol.renderbio.NucleicRenderer
rr - Variable in class org.jmol.renderbio.RocketRenderer
rr - Variable in class org.jmol.renderbio.RocketsRenderer
rs - Variable in class org.jmol.jvxl.readers.AtomDataReader
  atom radius + solvent radius
rs2 - Variable in class org.jmol.jvxl.readers.AtomDataReader
  square of (atom radius + solvent radius)
rScr - Variable in class org.jmol.renderbio.NucleicRenderer
rScr5 - Variable in class org.jmol.renderbio.NucleicRenderer
rsvs - Variable in class org.jmol.symmetry.SymmetryOperation
rsvs - Variable in class org.jmol.util.ModulationSet
  the matrix representation for this atom's symmetry operation
rTheta - Variable in class org.jmol.render.SticksRenderer
rubberband - Static variable in class org.jmol.script.T
rubberbandSelectionMode - Variable in class org.jmol.viewer.ActionManager
rule - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
rule4Ref - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  Rule 4b reference chirality (R or S, 1 or 2); root only
rule4Type - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  the auxiiary chirality type: 0: ~, 1: R, 2: S; normalized to R/S even if M/P or C/T
rule6refIndex - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  reference index for Rule 6 -- root atom only
RULE_1a - Static variable in class org.jmol.symmetry.CIPChirality
RULE_1b - Static variable in class org.jmol.symmetry.CIPChirality
RULE_2 - Static variable in class org.jmol.symmetry.CIPChirality
RULE_2_nXX_EQ_XX - Static variable in class org.jmol.symmetry.CIPChirality
  These elements have 100% natural abundance; we will use their isotope mass number instead of their actual average mass, since there is no difference
RULE_2_REDUCE_ISOTOPE_MASS_NUMBER - Static variable in class org.jmol.symmetry.CIPChirality
  These elements have an isotope number that is a bit higher than the average mass, even though their actual isotope mass is a bit lower.
RULE_3 - Static variable in class org.jmol.symmetry.CIPChirality
RULE_4a - Static variable in class org.jmol.symmetry.CIPChirality
RULE_4b - Static variable in class org.jmol.symmetry.CIPChirality
RULE_4c - Static variable in class org.jmol.symmetry.CIPChirality
RULE_5 - Static variable in class org.jmol.symmetry.CIPChirality
RULE_6 - Static variable in class org.jmol.symmetry.CIPChirality
ruleNames - Static variable in class org.jmol.symmetry.CIPChirality
ruleNames - Static variable in class org.jmol.viewer.JC
run() - Method in class org.jmol.applet.ClassPreloader
run() - Method in class org.jmol.applet.TickerThread
run() - Method in class org.jmol.applet.WrappedAppletLoader
run() - Method in class org.jmol.io.DOMReader
run() - Method in class org.jmol.io.FileReader
run() - Method in class org.jmol.io.FilesReader
run() - Method in class org.jmol.script.CommandWatcherThread
run() - Method in class org.jmol.script.ScriptProcessRunnable
run() - Method in class org.jmol.thread.JmolThread
run() - Method in class org.openscience.jmol.app.InputScannerThread
run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
run() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
run() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioThread
run1(int) - Method in class org.jmol.minimize.MinimizationThread
run1(int) - Method in class org.jmol.navigate.Navigator
run1(int) - Method in class org.jmol.script.CommandWatcherThread
run1(int) - Method in class org.jmol.script.FileLoadThread
run1(int) - Method in class org.jmol.script.ScriptDelayThread
run1(int) - Method in class org.jmol.script.ScriptQueueThread
run1(int) - Method in class org.jmol.thread.AnimationThread
run1(int) - Method in class org.jmol.thread.HoverWatcherThread
run1(int) - Method in class org.jmol.thread.JmolThread
run1(int) - Method in class org.jmol.thread.MoveToThread
run1(int) - Method in class org.jmol.thread.SpinThread
  Java: run1(INIT) while(!interrupted()) { run1(MAIN) } run1(FINISH) JavaScript: run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or run1(FINISH) and return
run1(int) - Method in class org.jmol.thread.TimeoutThread
run1(int) - Method in class org.jmol.thread.VibrationThread
run1Move(int) - Method in class org.jmol.thread.MoveToThread
run1MoveTo(int) - Method in class org.jmol.thread.MoveToThread
runAllProcesses(Viewer) - Method in interface org.jmol.api.JmolParallelProcessor
runAllProcesses(Viewer) - Method in class org.jmol.script.ScriptParallelProcessor
runBufferedSafely(String, SB) - Method in class org.jmol.script.ScriptEval
runButton - Variable in class org.jmol.console.GenericConsole
runButton - Variable in class org.jmol.console.ScriptEditor
runCheckBoxScript(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
runFunctionAndRet(JmolScriptFunction, String, Lst<SV>, SV, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
runNextScript() - Method in class org.jmol.script.ScriptQueueThread
runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
runProcess(ScriptProcess, ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
runScript(String) - Method in interface org.jmol.api.JmolScriptEvaluator
runScript(String) - Method in class org.jmol.api.JmolViewer
  starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older version
runScript(String) - Method in interface org.jmol.api.JSVInterface
runScript(String) - Method in class org.jmol.script.ScriptEval
runScript(String) - Method in class org.jmol.viewer.ActionManager
runScript(String) - Method in class org.jmol.viewer.Viewer
  Run a script using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )
runScript(String, boolean, JmolViewer) - Method in class org.openscience.jmol.app.JmolApp
runScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
  no queuing here -- called by MainFrame
runScriptBuffer(String, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
runScriptBuffer(String, SB, boolean) - Method in class org.jmol.script.ScriptEval
  runs a script immediately and sends selected output to a provided SB
runScriptBuffered(String) - Method in class org.jmol.modelkit.ModelKitPopup
runScriptCautiously(String) - Method in class org.jmol.api.JmolViewer
  Formerly runScript(script).
runScriptCautiously(String) - Method in class org.jmol.viewer.Viewer
  formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script.
runScriptNow() - Method in class org.jmol.script.ScriptManager
runSleep(int, int) - Method in class org.jmol.thread.JmolThread
runStatus - Static variable in class org.openscience.jmol.app.webexport.WebExport
runUserAction(String, Object[], Viewer) - Static method in class org.jmol.script.ScriptEval
RWB - Static variable in class org.jmol.util.ColorEncoder

## S

S - Static variable in class org.jmol.quantum.QS
s0 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
s0f - Variable in class org.jmol.renderspecial.DrawRenderer
s1 - Variable in class org.jmol.render.FontLineShapeRenderer
s1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
s10 - Static variable in class org.jmol.symmetry.PointGroup
s12 - Static variable in class org.jmol.symmetry.PointGroup
s1f - Variable in class org.jmol.renderspecial.DrawRenderer
s2 - Variable in class org.jmol.render.FontLineShapeRenderer
s2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
s2f - Variable in class org.jmol.renderspecial.DrawRenderer
s3 - Static variable in class org.jmol.symmetry.PointGroup
s4 - Static variable in class org.jmol.symmetry.PointGroup
s5 - Static variable in class org.jmol.symmetry.PointGroup
s6 - Static variable in class org.jmol.symmetry.PointGroup
s8 - Static variable in class org.jmol.symmetry.PointGroup
sA - Variable in class org.jmol.g3d.Graphics3D
safeJSON(String, Object) - Static method in class org.jmol.script.SV
  Safely create a JSON key - object pair, allowing for already-named arrays
sameAs(int, int) - Method in class org.jmol.modelset.Measurement
sameAsIJ(int[], Point3fi[], int, int) - Method in class org.jmol.modelset.Measurement
sameAsPoints(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
sampleModelBitMasks - Static variable in class org.jmol.awt.Image
sasurface - Static variable in class org.jmol.script.T
SAUSAGE - Static variable in class org.jmol.shapecgo.CGOMesh
save - Static variable in class org.jmol.script.T
save() - Method in class org.openscience.jmol.app.HistoryFile
  Saves properties to the history file.
SAVE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
save() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
save() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
save_pdb_ss - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
saveAmbient - Variable in class org.jmol.g3d.Graphics3D
saveAs() - Method in class org.jmol.console.ImageDialog
saveAsButton - Variable in class org.jmol.console.ScriptEditor
saveBonds(String) - Method in class org.jmol.viewer.StateManager
saveButton - Variable in class org.jmol.console.ScriptEditor
saveButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
saveButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
saveChooser - Static variable in class org.jmol.dialog.Dialog
saveChooser - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
saveContext(String) - Method in class org.jmol.script.ScriptEval
saveContext(String, Object) - Method in class org.jmol.viewer.StateManager
saveCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
saveCoordinates() - Method in class org.jmol.minimize.Minimizer
saveCoordinates(String, BS) - Method in class org.jmol.viewer.StateManager
saved - Static variable in class org.jmol.script.T
saved - Variable in class org.jmol.viewer.StateManager
saveDiffuse - Variable in class org.jmol.g3d.Graphics3D
saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
saveHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Just saves the path settings from this session.
saveHistory() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
saveList - Static variable in class org.jmol.script.ScriptEval
saveList() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
  Saves the list to the history file.
saveModelOrientation(int, Orientation) - Method in class org.jmol.modelset.ModelSet
saveModelOrientation() - Method in class org.jmol.viewer.Viewer
saveName - Variable in class org.jmol.modelset.Orientation
saveName - Variable in class org.jmol.viewer.Connections
saveName - Variable in class org.jmol.viewer.Scene
saveOrientation(String, float[]) - Method in class org.jmol.viewer.StateManager
savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
saveProperties(Properties) - Method in interface org.jmol.api.JSVInterface
saveProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
saveproteinstructurestate - Static variable in class org.jmol.script.T
saveProteinStructureState - Variable in class org.jmol.viewer.GlobalSettings
saveRestorePriorities(boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Reset priorities after each Rule 6 test.
saveScene(String, Map<String, Object>) - Method in class org.jmol.viewer.StateManager
saveSelection(String, BS) - Method in class org.jmol.viewer.StateManager
saveState(String) - Method in class org.jmol.viewer.StateManager
saveStructure(String) - Method in class org.jmol.viewer.StateManager
saveTokens(T[][]) - Method in class org.jmol.script.ScriptContext
  save pointers indicating state of if/then
saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
saveWindowSizes() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Saves the currently active collection as a multistep XYZ file.
saveZip(boolean) - Method in class org.jmol.console.ScriptEditor
say(String) - Method in class org.openscience.jmol.app.InputScannerThread
say(String) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
sb - Variable in class org.jmol.adapter.readers.pdb.PdbReader
sB - Variable in class org.jmol.g3d.Graphics3D
sbCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
sbConect - Variable in class org.jmol.adapter.readers.pdb.PdbReader
sbIgnored - Variable in class org.jmol.adapter.readers.pdb.PdbReader
sbKey - Variable in class org.jmol.minimize.MinAngle
sbMap - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
sbmb - Variable in class org.jmol.minimize.forcefield.AtomType
sbSelected - Variable in class org.jmol.adapter.readers.pdb.PdbReader
sbTemp - Variable in class org.jmol.export._IdtfExporter
sbTlsErrors - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
sbTlsErrors - Variable in class org.jmol.adapter.readers.pdb.PdbReader
sbType - Variable in class org.jmol.minimize.MinAngle
SC - Interface in org.jmol.api
  SwingComponent interface common to javax.swing and org.jmol.awtjs.swing Can be augmented as needed, provided classes of org.jmol.awtjs.swing are also updated.
sC - Variable in class org.jmol.g3d.Graphics3D
sc - Variable in class org.jmol.thread.JmolThread
scalarDictRef - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
scalarDictValue - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
scalarTitle - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
scale(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
scale - Variable in class org.jmol.adapter.readers.simple.JSONReader
scale - Variable in class org.jmol.jvxl.readers.Parameters
scale - Variable in class org.jmol.modelset.TickInfo
scale - Static variable in class org.jmol.script.T
scale - Variable in class org.jmol.shape.Axes
scale(Mesh, float) - Method in class org.jmol.shapecgo.CGO
scale(Mesh, float) - Method in class org.jmol.shapespecial.Draw
scale - Variable in class org.jmol.shapespecial.DrawMesh
scale - Variable in class org.jmol.shapespecial.Ellipsoid
scale - Variable in class org.jmol.shapespecial.Polyhedron
scale - Variable in class org.jmol.symmetry.PointGroup
scale - Variable in class org.jmol.util.ModulationSet
  an adjustable scaling factor, as for vibrations
scale3d - Variable in class org.jmol.jvxl.data.JvxlData
scale3d - Variable in class org.jmol.jvxl.readers.Parameters
scale3d - Static variable in class org.jmol.script.T
scale3d - Variable in class org.jmol.shape.Mesh
scale3d - Variable in class org.jmol.shapesurface.Isosurface
scale3D - Variable in class org.jmol.viewer.TransformManager
scale3DAngstromsPerInch - Variable in class org.jmol.viewer.TransformManager
SCALE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Maximum value for vector scale.
SCALE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Precision of the vector scale slider
SCALE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Initial value of vector scale.
scaleangstromsperinch - Static variable in class org.jmol.script.T
scaleAxes(float[]) - Method in class org.jmol.shapespecial.Ellipsoid
scaleBox(P3[], float) - Static method in class org.jmol.util.BoxInfo
scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
scaleFac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
scaleFitToScreen(boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
scaleFractionalVibs() - Method in class org.jmol.adapter.smarter.XtalSymmetry
  magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes.
scaleIsosurface(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
scalePixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
scalePixelsPerMicron - Variable in class org.jmol.modelset.Text
scalePixelsPerMicron - Variable in class org.jmol.render.LabelsRenderer
scalePixelsPerMicron - Variable in class org.jmol.render.MeshRenderer
scalePixelsPerMicron - Variable in class org.jmol.shape.Labels
scalePolyhedra(float) - Method in class org.jmol.shapespecial.Polyhedra
scalePrimitiveData(int, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
  overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
  Perform implementation-specific scaling.
scaleSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
scaleVectorsToMax(float) - Method in class org.jmol.modelset.AtomCollection
  Scales vibrations and associated vectors such that the maximum length is the given value
scaleVibration(float) - Method in interface org.jmol.api.JmolModulationSet
scaleVibration(float) - Method in class org.jmol.util.ModulationSet
scaleX - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping min/max x and y
scaleXYZ - Variable in class org.jmol.shapespecial.Ellipsoid
scaleY - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping min/max x and y
scaling - Variable in class org.jmol.shape.Frank
scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
scanInput - Variable in class org.openscience.jmol.app.JmolApp
scanner - Variable in class org.openscience.jmol.app.InputScannerThread
scanPoint - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
  The scan point, where -1 denotes no scan information.
scene - Static variable in class org.jmol.script.T
Scene - Class in org.jmol.viewer
Scene(Map<String, Object>) - Constructor for class org.jmol.viewer.Scene
scene - Variable in class org.jmol.viewer.Scene
scene_animation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_animation_duration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_buttons - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_buttons_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_current_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_frame_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_loop - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
scene_restart_movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SCENE_TAG - Static variable in class org.jmol.viewer.OutputManager
sceneOrder - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
scenes_changed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
schemes - Variable in class org.jmol.util.ColorEncoder
scm - Variable in class org.jmol.viewer.Viewer
score - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
score - Variable in class org.jmol.util.ContactPair
scrBox - Variable in class org.jmol.renderbio.NucleicRenderer
scrCoords - Variable in class org.jmol.renderspecial.DotsRenderer
screen - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
screen - Variable in class org.jmol.render.LabelsRenderer
screenA - Variable in class org.jmol.renderbio.RocketRenderer
screenArrowBot - Variable in class org.jmol.renderbio.BioShapeRenderer
screenArrowBotPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
screenArrowHead - Variable in class org.jmol.renderspecial.VectorsRenderer
screenArrowTop - Variable in class org.jmol.renderbio.BioShapeRenderer
screenArrowTopPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
screenB - Variable in class org.jmol.renderbio.RocketRenderer
screenC - Variable in class org.jmol.renderbio.RocketRenderer
screenCorners - Variable in class org.jmol.renderbio.RocketRenderer
screenDotCount - Variable in class org.jmol.renderspecial.DotsRenderer
screenHeight - Variable in class org.jmol.export.___Exporter
screenHeight - Variable in class org.jmol.viewer.TransformManager
screenHeight - Variable in class org.jmol.viewer.Viewer
screenLevel - Variable in class org.jmol.renderspecial.DotsRenderer
screenPixelCount - Variable in class org.jmol.viewer.TransformManager
screens - Variable in class org.jmol.render.MeshRenderer
screens - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
screens3f - Variable in class org.jmol.renderspecial.DipolesRenderer
screens3f - Variable in class org.jmol.renderspecial.PolyhedraRenderer
screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
screenVectorEnd - Variable in class org.jmol.renderspecial.VectorsRenderer
screenVectorStart - Variable in class org.jmol.renderspecial.VectorsRenderer
screenWidth - Variable in class org.jmol.export.___Exporter
screenWidth - Variable in class org.jmol.viewer.TransformManager
screenWidth - Variable in class org.jmol.viewer.Viewer
screenx - Static variable in class org.jmol.script.T
screenXY - Variable in class org.jmol.modelkit.ModelKitPopup
screenxyz - Static variable in class org.jmol.script.T
screeny - Static variable in class org.jmol.script.T
screenZ - Variable in class org.jmol.rendercgo.CGORenderer
screenz - Static variable in class org.jmol.script.T
script(String) - Method in interface org.jmol.api.JmolAppletInterface
script(String) - Method in class org.jmol.api.JmolViewer
script(String) - Method in class org.jmol.applet.JmolApplet
script - Variable in class org.jmol.jvxl.readers.Parameters
script - Variable in class org.jmol.modelset.Text
script - Variable in class org.jmol.script.ScriptContext
script - Variable in class org.jmol.script.ScriptEval
script - Variable in class org.jmol.script.ScriptFunction
script - Variable in class org.jmol.script.ScriptTokenParser
script - Static variable in class org.jmol.script.T
script - Variable in class org.jmol.shapesurface.Isosurface
script - Variable in class org.jmol.thread.TimeoutThread
script(String) - Method in class org.jmol.util.GenericApplet
script(String) - Method in class org.jmol.viewer.Viewer
script(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
script - Variable in class org.openscience.jmol.app.webexport.JmolInstance
script1 - Variable in class org.jmol.modelset.StateScript
script1 - Variable in class org.openscience.jmol.app.JmolApp
script2 - Variable in class org.jmol.modelset.StateScript
script2 - Variable in class org.openscience.jmol.app.JmolApp
SCRIPT_CHECK - Static variable in class org.jmol.util.GenericApplet
SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.JC
SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JC
SCRIPT_NOWAIT - Static variable in class org.jmol.util.GenericApplet
SCRIPT_WAIT - Static variable in class org.jmol.util.GenericApplet
SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
scriptAppendix - Variable in class org.jmol.shapesurface.Isosurface
scriptButtonPercent - Static variable in class org.openscience.jmol.app.webexport.WebExport
ScriptButtons - Class in org.openscience.jmol.app.webexport
ScriptButtons(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.ScriptButtons
scriptCallback(String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
  from StatusManager
scriptCallback(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptCheck(String) - Method in class org.jmol.api.JmolViewer
scriptCheck(String) - Method in class org.jmol.applet.JmolApplet
scriptCheck(String) - Method in class org.jmol.util.GenericApplet
scriptCheck(String) - Method in class org.jmol.viewer.Viewer
scriptCheckRet(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
scriptCheckRet(String, boolean) - Method in class org.jmol.script.ScriptManager
scriptCheckRet(String, boolean) - Method in class org.jmol.viewer.Viewer
scriptCommand - Static variable in class org.jmol.script.T
scriptCommand - Variable in class org.jmol.shape.Mesh
ScriptCompiler - Class in org.jmol.script
ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
scriptCompleted(StatusManager, String, String) - Method in class org.jmol.viewer.ChimeMessenger
  called when a script exits.
scriptCompleted(StatusManager, String, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
ScriptContext - Class in org.jmol.script
ScriptContext() - Constructor for class org.jmol.script.ScriptContext
scriptDelay - Variable in class org.jmol.viewer.GlobalSettings
ScriptDelayThread - Class in org.jmol.script
ScriptDelayThread(JmolScriptEvaluator, Viewer, int) - Constructor for class org.jmol.script.ScriptDelayThread
scriptDelayThread - Variable in class org.jmol.script.ScriptEval
scriptEcho(String) - Method in class org.jmol.viewer.Viewer
scriptEditor - Variable in class org.jmol.console.JmolConsole
ScriptEditor - Class in org.jmol.console
ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
ScriptEditor(Viewer, JFrame, JmolConsole) - Constructor for class org.jmol.console.ScriptEditor
scriptEditor - Variable in class org.jmol.viewer.Viewer
ScriptEditor.EditorDocument - Class in org.jmol.console
ScriptEditor.EditorDocument.MyUndoableEditListener - Class in org.jmol.console
ScriptEditor.EditorTextPane - Class in org.jmol.console
ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
ScriptError - Class in org.jmol.script
  Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
ScriptError() - Constructor for class org.jmol.script.ScriptError
ScriptEval - Class in org.jmol.script
ScriptEval() - Constructor for class org.jmol.script.ScriptEval
ScriptException - Exception in org.jmol.script
ScriptException(ScriptError, String, String, boolean) - Constructor for exception org.jmol.script.ScriptException
ScriptExpr - Class in org.jmol.script
  The ScriptExpr class holds the main functions for processing mathematical and atom selection expressions.
ScriptExpr() - Constructor for class org.jmol.script.ScriptExpr
ScriptExt - Class in org.jmol.scriptext
ScriptExt() - Constructor for class org.jmol.scriptext.ScriptExt
scriptExtensions - Variable in class org.jmol.script.ScriptCompiler
scriptExtensions - Variable in class org.jmol.script.ScriptContext
scriptExtensions - Variable in class org.jmol.script.ScriptEval
scriptFileName - Variable in class org.jmol.script.ScriptContext
scriptFileName - Variable in class org.jmol.script.ScriptEval
scriptFilename - Variable in class org.openscience.jmol.app.JmolApp
scriptFilePrefixes - Static variable in class org.jmol.viewer.FileManager
ScriptFlowContext - Class in org.jmol.script
ScriptFlowContext(ScriptCompiler, ContextToken, int, ScriptFlowContext, int, short) - Constructor for class org.jmol.script.ScriptFlowContext
ScriptFunction - Class in org.jmol.script
ScriptFunction() - Constructor for class org.jmol.script.ScriptFunction
ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
scriptIndex - Variable in class org.jmol.script.ScriptManager
ScriptInterruption - Exception in org.jmol.script
ScriptInterruption(ScriptEval, String, int) - Constructor for exception org.jmol.script.ScriptInterruption
scriptLevel - Variable in class org.jmol.script.ScriptContext
scriptLevel - Variable in class org.jmol.script.ScriptEval
scriptManager - Variable in class org.jmol.script.CommandWatcherThread
ScriptManager - Class in org.jmol.script
ScriptManager() - Constructor for class org.jmol.script.ScriptManager
scriptManager - Variable in class org.jmol.script.ScriptQueueThread
ScriptMathProcessor - Class in org.jmol.script
  Reverse Polish Notation Engine for IF, SET, and @{...} Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f -- Bob Hanson 2/16/2007
ScriptMathProcessor(ScriptExpr, boolean, boolean, boolean, boolean, boolean, String) - Constructor for class org.jmol.script.ScriptMathProcessor
scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptNoWait(String) - Method in class org.jmol.applet.JmolApplet
scriptNoWait(String) - Method in class org.jmol.util.GenericApplet
ScriptParallelProcessor - Class in org.jmol.script
ScriptParallelProcessor() - Constructor for class org.jmol.script.ScriptParallelProcessor
  parallel operations
ScriptParam - Class in org.jmol.script
  The ScriptParam class holds methods used to parse parameters in Jmol scripts.
ScriptParam() - Constructor for class org.jmol.script.ScriptParam
ScriptProcess - Class in org.jmol.script
  the idea here is that the process { ...
ScriptProcess(String, ScriptContext) - Constructor for class org.jmol.script.ScriptProcess
scriptProcessor(String, String, int) - Method in class org.jmol.util.GenericApplet
ScriptProcessRunnable - Class in org.jmol.script
ScriptProcessRunnable(ScriptParallelProcessor, ScriptProcess, Object, ShapeManager) - Constructor for class org.jmol.script.ScriptProcessRunnable
scriptQueue - Variable in class org.jmol.script.ScriptManager
scriptqueue - Static variable in class org.jmol.script.T
scriptQueueRunning - Variable in class org.jmol.script.ScriptManager
ScriptQueueThread - Class in org.jmol.script
ScriptQueueThread(ScriptManager, Viewer, boolean, int) - Constructor for class org.jmol.script.ScriptQueueThread
scriptReportingLevel - Static variable in class org.jmol.script.ScriptEval
scriptreportinglevel - Static variable in class org.jmol.script.T
scriptStatus(String) - Method in class org.jmol.viewer.Viewer
scriptStatusMsg(String, String) - Method in class org.jmol.viewer.Viewer
ScriptTokenParser - Class in org.jmol.script
ScriptTokenParser() - Constructor for class org.jmol.script.ScriptTokenParser
scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
scriptWait(String) - Method in class org.jmol.api.JmolViewer
scriptWait(String) - Method in class org.jmol.applet.JmolApplet
scriptWait(String, String) - Method in class org.jmol.applet.JmolApplet
scriptWait(String) - Method in class org.jmol.util.GenericApplet
scriptWait(String, String) - Method in class org.jmol.util.GenericApplet
scriptWait(String) - Method in class org.jmol.viewer.Viewer
scriptWaitOutput(String) - Method in interface org.jmol.api.JmolAppletInterface
scriptWaitOutput(String) - Method in class org.jmol.applet.JmolApplet
scriptWaitOutput(String) - Method in class org.jmol.util.GenericApplet
scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
scrTemp - Variable in class org.jmol.renderspecial.DotsRenderer
scrVib - Variable in class org.jmol.renderspecial.PolyhedraRenderer
sculpt_angl_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_auto_center - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_avd_excl - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_avd_gap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_avd_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_avd_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_bond_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_field_mask - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_hb_overlap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_hb_overlap_base - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_line_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_max_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_max_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_max_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_max_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_memory - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_min_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_min_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_min_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_min_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_nb_interval - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_plan_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_pyra_inv_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_pyra_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tors_tolerance - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tors_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tri_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tri_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tri_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tri_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_tri_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_scale14 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_vis_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_vis_mid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_vis_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_vis_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpt_vdw_weight14 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sculpting_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sD - Variable in class org.jmol.util.Point3fi
  screen diameter
SDIM - Static variable in class org.jmol.util.Shader
sdof_drag_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
search - Static variable in class org.jmol.script.T
search - Variable in class org.jmol.smiles.SmilesMeasure
search() - Method in class org.jmol.smiles.SmilesSearch
  the start of the search.
search - Variable in class org.jmol.smiles.SmilesStereo
search2(boolean) - Method in class org.jmol.smiles.SmilesSearch
searchForTurns(AlphaPolymer.Code[], float[], STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
secondary_structure - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
secondAtomIndex - Variable in class org.jmol.modelkit.ModelKitPopup
secondCharOnly - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
seconds - Variable in class org.jmol.script.ScriptDelayThread
security - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seed - Variable in class org.jmol.util.Shader
SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
SEESAW - Static variable in class org.jmol.smiles.SmilesStereo
SEGI - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
segments - Variable in class org.jmol.modelsetbio.ProteinStructure
seitzMatrix - Variable in class org.jmol.symmetry.HallRotation
seitzMatrix12ths - Variable in class org.jmol.symmetry.HallRotationTerm
seitzMatrixInv - Variable in class org.jmol.symmetry.HallRotation
sel_counter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
select - Static variable in class org.jmol.script.T
select(BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
select(BS, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
select - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
selectAll() - Method in class org.jmol.api.JmolViewer
selectAll(boolean) - Method in class org.jmol.viewer.SelectionManager
selectAll() - Method in class org.jmol.viewer.Viewer
selectAllAtoms(Lst<Object>, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Collect all the atoms specified by an object state into a bit set.
selectallmodels - Static variable in class org.jmol.script.T
selectAllModels - Variable in class org.jmol.viewer.GlobalSettings
selectAtoms(String) - Method in class org.jmol.viewer.ActionManager
selectBonds(BS) - Method in class org.jmol.viewer.Viewer
selectDisplayed(BS) - Method in class org.jmol.modelset.Trajectory
  Remove trajectories that are not currently displayed from the visible frames bitset.
selected - Variable in class org.jmol.awtjs.swing.AbstractButton
selected - Static variable in class org.jmol.script.T
selected - Variable in class org.jmol.smiles.SmilesAtom
selectedAtomCount - Variable in class org.jmol.smiles.SmilesSearch
selectedAtoms - Variable in class org.jmol.shapespecial.Ellipsoids
selectedBonds - Variable in class org.jmol.shape.Sticks
selectedFileName - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
selectedfloat - Static variable in class org.jmol.script.T
selectedGroupCount - Variable in class org.jmol.modelset.Chain
  Calculated just prior to coloring by group so that the range is appropriate for each chain.
selectedIndex - Variable in class org.jmol.awtjs.swing.JComboBox
selectedIndex - Variable in class org.jmol.modelset.Group
  for coloring by group
selectedMeasurementRow - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
selectedModel - Variable in class org.jmol.adapter.readers.more.JcampdxReader
selectedMolecules - Variable in class org.jmol.modelset.ModelSet
selectedMonomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
selectedOctant - Variable in class org.jmol.g3d.SphereRenderer
selectedOctant - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
selectedPoints - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
selectedPolyOnly - Variable in class org.jmol.render.MeshRenderer
selectedPolyOnly - Variable in class org.jmol.shapesurface.PMeshWriter
selectedTrajectory - Variable in class org.jmol.modelset.Model
selectField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
selecthetero - Static variable in class org.jmol.script.T
selecthydrogen - Static variable in class org.jmol.script.T
selection - Static variable in class org.jmol.script.T
selection_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
selection_round_points - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
selection_visible_only - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
selection_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
selection_width_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
selection_width_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
selectionChanged(BS) - Method in interface org.jmol.api.JmolSelectionListener
  Called when the selected atoms change
selectionChanged(boolean) - Method in class org.jmol.viewer.SelectionManager
selectionhalos - Static variable in class org.jmol.script.T
selectionHalosEnabled - Variable in class org.jmol.viewer.Viewer
selectionListener - Variable in class org.jmol.awtjs.swing.JTable
SelectionManager - Class in org.jmol.viewer
SelectionManager(Viewer) - Constructor for class org.jmol.viewer.SelectionManager
selectionWorking - Variable in class org.jmol.viewer.ActionManager
selectItemTok(T, int) - Static method in class org.jmol.script.SV
selectItemVar(SV) - Static method in class org.jmol.script.SV
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
selectRb(int) - Method in class org.jmol.viewer.ActionManager
selectReaderAndGo(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
selectSeqcodeRange(Group[], int, int, int, int, BS) - Static method in class org.jmol.modelset.ModelSet
selectSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
semicolon - Static variable in class org.jmol.script.T
send(int, String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
  from JmolPanel and SYNC command
send(int, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
sendConsoleEcho(String) - Method in class org.jmol.console.GenericConsole
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
sendConsoleMessage(String) - Method in class org.jmol.console.GenericConsole
sendConsoleMessage(String) - Method in class org.jmol.viewer.Viewer
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
sendJSpecView(String) - Method in class org.jmol.jsv.JSpecView
sendKeyBuffer() - Method in class org.jmol.awt.Mouse
sendKeyBuffer() - Method in class org.jmol.awtjs2d.Mouse
sendMessage(JsonNioService.JSONObject, String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
sendNioMessage(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
sendScript(String, String, boolean, boolean) - Method in class org.jmol.util.GenericApplet
sendScript(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
sep - Variable in class org.jmol.adapter.readers.xtal.GulpReader
sep - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
seq_view - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_alignment - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_discrete_by_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_fill_char - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_fill_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_format - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_label_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_label_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_label_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_label_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_location - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_unaligned_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seq_view_unaligned_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
seqAdv() - Method in class org.jmol.adapter.readers.pdb.PdbReader
seqcode - Variable in class org.jmol.modelset.Group
seqcode - Static variable in class org.jmol.script.T
seqcodes - Variable in class org.jmol.modelset.ModelLoader
seqid - Static variable in class org.jmol.script.T
seqMode - Variable in class org.jmol.adapter.readers.pdb.PdbReader
sequence - Static variable in class org.jmol.script.T
SEQUENCE_NUMBER_FLAG - Static variable in class org.jmol.modelset.Group
SEQUENCE_NUMBER_SHIFT - Static variable in class org.jmol.modelset.Group
sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
sequenceNumbers - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
serial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
SERIAL_NO - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
serialArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
serialID - Variable in class org.jmol.adapter.smarter.Structure
serialID - Variable in class org.jmol.modelsetbio.ProteinStructure
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Test
serMode - Variable in class org.jmol.adapter.readers.pdb.PdbReader
serverConnection - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
serverService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
serverSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
serverThread - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
service - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
session_cache_optimize - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
session_changed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
session_compression - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
session_file - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
session_migration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
session_version_check - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
set() - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
set(Viewer) - Method in class org.jmol.adapter.readers.quantum.NBOParser
set(FileManager) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
set(int, int, char, int, int, char, int, int) - Method in class org.jmol.adapter.smarter.Structure
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.smarter.XtalSymmetry
set(Viewer, OutputStream) - Method in class org.jmol.adapter.writers.QCJSONWriter
set(Viewer) - Method in interface org.jmol.api.JmolDataManager
set(FileManager, Viewer, Object, Map<String, Object>) - Method in interface org.jmol.api.JmolDomReaderInterface
set(AtomDataServer, int, short[]) - Method in interface org.jmol.api.JmolEnvCalc
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
set(JmolJDXMOLReader, String, Map<String, Object>) - Method in interface org.jmol.api.JmolJDXMOLParser
set(TransformManager, Viewer) - Method in interface org.jmol.api.JmolNavigatorInterface
set(String, int) - Method in interface org.jmol.api.JmolParallelProcessor
set(Viewer, ShapeManager) - Method in interface org.jmol.api.JmolRepaintManager
set(int, int) - Method in class org.jmol.awtjs.swing.Dimension
set(Bspt) - Method in class org.jmol.bspt.CubeIterator
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.CircleRenderer
set(JmolRendererInterface, GData) - Method in interface org.jmol.g3d.G3DRenderer
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.HermiteRenderer
set(int, int, int) - Method in class org.jmol.g3d.PixelatorShaded
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.TriangleRenderer
set(AtomDataServer, int, short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
set(FileManager, Viewer, Object, Map<String, Object>) - Method in class org.jmol.io.DOMReader
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.io.FilesReader
set(JmolJDXMOLReader, String, Map<String, Object>) - Method in class org.jmol.jsv.JDXMOLParser
set(Calculations) - Method in class org.jmol.minimize.forcefield.Calculation
set() - Method in class org.jmol.minimize.MinAtom
set(int, BS, int[]) - Method in class org.jmol.minimize.MMConstraint
set(int) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
set(String, int) - Method in class org.jmol.modelset.LabelToken
set(int, Map<String, Integer>, RadiusData, String, String, TickInfo, boolean, boolean, Boolean, boolean, int, short, Text) - Method in class org.jmol.modelset.MeasurementData
set(ModelSet) - Method in class org.jmol.modelset.MeasurementPending
set(ModelSet, int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelset.Model
set(Font, short, int, float) - Method in class org.jmol.modelset.Text
set(Viewer, ModelSet, Lst<P3[]>) - Method in class org.jmol.modelset.Trajectory
set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioExt
set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioModelSet
set(Monomer[]) - Method in class org.jmol.modelsetbio.BioPolymer
set(TransformManager, Viewer) - Method in class org.jmol.navigate.Navigator
set(Viewer) - Method in class org.jmol.quantum.MepCalculation
set(Viewer, ShapeManager) - Method in class org.jmol.render.RepaintManager
set(RocketsRenderer) - Method in class org.jmol.renderbio.RocketRenderer
set(String, int) - Method in class org.jmol.script.ScriptFunction
set - Static variable in class org.jmol.script.T
set(Lst<Object>) - Method in class org.jmol.shapecgo.CGOMesh
set(Dipole) - Method in class org.jmol.shapespecial.Dipole
set(String, int, P3, P3[], int, int, int[][], int, int[][], int[][], V3[], BS, boolean, float, float) - Method in class org.jmol.shapespecial.Polyhedron
set(SmilesBond) - Method in class org.jmol.smiles.SmilesBond
set - Variable in class org.jmol.smiles.SmilesRing
set() - Method in class org.jmol.smiles.SmilesSearch
set(Viewer, BS) - Method in class org.jmol.symmetry.CIPData
  Actual constructor.
set(PointGroup, T3[]) - Method in class org.jmol.symmetry.PointGroup
set(ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
set(SymmetryInterface, Atom, Atom[], BS, float) - Method in class org.jmol.symmetry.UnitCellIterator
set(int, String) - Method in class org.jmol.thread.TimeoutThread
set(MeshSlicer) - Method in class org.jmol.util.MeshCapper
set(MeshSurface) - Method in class org.jmol.util.MeshSlicer
set(float, float, float) - Method in interface org.jmol.util.Node
set(String) - Method in class org.jmol.viewer.binding.JmolBinding
set(Viewer) - Method in class org.jmol.viewer.ChimeMessenger
set(Viewer) - Method in class org.jmol.viewer.DataManager
set(Viewer) - Method in interface org.jmol.viewer.JmolChimeMessenger
set(int, int, int, long) - Method in class org.jmol.viewer.MotionPoint
set(long, int, int, int) - Method in class org.jmol.viewer.MouseState
set2(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.Monomer
set2(P3, P3) - Method in class org.jmol.shapespecial.Dipole
set2(int, boolean) - Method in class org.jmol.smiles.SmilesBond
set2a(SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
set2AtomValue(Atom, Atom, float) - Method in class org.jmol.shapespecial.Dipole
set2D(boolean) - Method in class org.jmol.adapter.readers.molxyz.MolReader
set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
set2dZ(int, int) - Method in class org.jmol.modelset.ModelLoader
set2Value(P3, P3, float) - Method in class org.jmol.shapespecial.Dipole
set3dContourVector(Lst<Object>, int[][], T3[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
  Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
set4(int, int, int, int) - Method in class org.jmol.awtjs.swing.Color
set4(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
SET_OPTIONS - Static variable in class org.jmol.modelkit.ModelKitPopup
setAaTokenCompiled() - Method in class org.jmol.script.ScriptCompiler
setABC(int) - Method in class org.jmol.util.MeshSurface
setABC(V3, V3, V3) - Method in class org.jmol.util.SimpleUnitCell
setAbstractButtonLabels(Map<String, Object>, Map<String, String>) - Static method in class org.jmol.console.GenericConsole
setACDAssignments(String, String, int, Lst<String[]>, String) - Method in interface org.jmol.api.JmolJDXMOLParser
setACDAssignments(String, String, int, Lst<String[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
setAction(int, long) - Method in class org.jmol.viewer.Gesture
setActionCommand(String) - Method in interface org.jmol.api.SC
setActionCommand(String) - Method in class org.jmol.awt.AwtSwingComponent
setActionCommand(String) - Method in class org.jmol.awtjs.swing.JComponent
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
  Changes the activation state for a logging level.
setActiveMenu(String) - Method in class org.jmol.modelkit.ModelKitPopup
  Set the active menu and request a repaint.
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.P2nReader
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PdbReader
  adaptable via subclassing
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PqrReader
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
setAlignment(int) - Method in class org.jmol.modelset.Text
setAlignmentLCR(String) - Method in class org.jmol.modelset.Text
setAll(int) - Static method in class org.jmol.util.BSUtil
setAll(P3, M3, P3, float, float, float, float, float, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
setAllConformation(BS) - Method in class org.jmol.modelsetbio.BioModelSet
setAllDefaultStructure(BS) - Method in class org.jmol.modelsetbio.BioModelSet
setAllowJSThreads(boolean) - Method in class org.jmol.script.ScriptEval
setAllProteinType(BS, STR) - Method in class org.jmol.modelsetbio.BioModelSet
setAllStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.BioModelSet
setAmbientOcclusion(int) - Method in class org.jmol.util.GData
setAmbientPercent(int) - Method in class org.jmol.util.GData
  fractional distance from black for ambient color
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
setAngleType(MinAngle) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setAngleUnits(int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setAngleVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
setAnimation(int) - Method in class org.jmol.viewer.Viewer
setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
setAnimationFps(int) - Method in class org.jmol.viewer.AnimationManager
setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
setAnimationLast() - Method in class org.jmol.viewer.AnimationManager
setAnimationMode(String) - Method in class org.jmol.viewer.Viewer
setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
setAnimationPrevious() - Method in class org.jmol.viewer.AnimationManager
setAnimationRange(int, int) - Method in class org.jmol.viewer.AnimationManager
setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
setAnimationRelative(int) - Method in class org.jmol.viewer.AnimationManager
setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.AnimationManager
setAnimDisplay(BS) - Method in class org.jmol.viewer.Viewer
setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAnisotropy(P3) - Method in class org.jmol.jvxl.readers.Parameters
setAnnotationAtoms(Viewer, Map<String, SV>, int) - Method in class org.jmol.dssx.AnnotationParser
setAntialias(boolean) - Method in class org.jmol.viewer.TransformManager
setAntialias(int, boolean) - Method in class org.jmol.viewer.Viewer
setAPa(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
setAPm(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
setApplet(Applet, boolean) - Method in class org.jmol.applet.Jmol
setApplet(Applet, boolean) - Method in interface org.jmol.applet.WrappedApplet
setAppletContext(String) - Method in class org.jmol.viewer.FileManager
setAppletPath(String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
setAppletProxy(String) - Method in class org.jmol.viewer.FileManager
setApplySymmetryToBonds(boolean) - Method in class org.jmol.viewer.Viewer
setArc(T3, T3, T3, float, float, float, float) - Method in class org.jmol.renderspecial.DrawRenderer
setAromatic(int, Node[], BS, Lst<Object>, BS, int, boolean, boolean, boolean, VTemp, Lst<BS>, Lst<SmilesRing>, int[], boolean) - Static method in class org.jmol.smiles.SmilesAromatic
  Main entry point.
setArrays(Atom[], BS, Bond[], int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setAsBallRotation(M4, float, float, float, float) - Method in class org.jmol.viewer.TransformManager4D
  4D ball rotation from nominal dx, dy, dz motion.
setAtom(Atom, int, int, int, float, float, float) - Method in class org.jmol.adapter.readers.simple.InputReader
setAtom(int, int, P3, float, BS, int, short, int, boolean) - Method in class org.jmol.modelset.Atom
setAtom2(SmilesAtom, SmilesSearch) - Method in class org.jmol.smiles.SmilesBond
  from parse ring
setAtom2dZ(Atom, Atom, V3, V3, V3) - Static method in class org.jmol.modelset.ModelLoader
  set the z based on a cos relationship to the y axis.
setAtomBits(BS) - Method in class org.jmol.modelset.Chain
setAtomBits(BS) - Method in class org.jmol.modelset.Group
  note that we may pick up additional bits here that were added later
setAtomBits(BS) - Method in interface org.jmol.modelset.Structure
setAtomBits(BS) - Method in class org.jmol.modelsetbio.BioPolymer
setAtomBits(BS) - Method in class org.jmol.modelsetbio.ProteinStructure
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Chain
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Group
  Setting and clearing
setAtomBitsAndClear(BS, BS) - Method in interface org.jmol.modelset.Structure
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.ProteinStructure
setAtomClickability() - Method in class org.jmol.shape.AtomShape
setAtomClickability() - Method in class org.jmol.shape.Balls
setAtomClickability() - Method in class org.jmol.shape.Labels
setAtomClickability() - Method in class org.jmol.shape.Shape
setAtomClickability() - Method in class org.jmol.shape.Sticks
setAtomClickability() - Method in class org.jmol.shapebio.Backbone
setAtomClickability() - Method in class org.jmol.shapebio.BioShape
setAtomClickability() - Method in class org.jmol.shapebio.BioShapeCollection
setAtomClickability() - Method in class org.jmol.shapespecial.Dots
setAtomClickability() - Method in class org.jmol.shapespecial.Ellipsoids
setAtomColor(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
setAtomCoord2(BS, int, Object) - Method in class org.jmol.modelset.AtomCollection
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
setAtomCoords(BS, int, Object) - Method in class org.jmol.modelset.ModelSet
setAtomCoords(BS, int, Object) - Method in class org.jmol.viewer.Viewer
setAtomCoordScaled(Atom, String[], int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.modelset.ModelSet
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.viewer.Viewer
setAtomCoordTokens(Atom, String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
setAtomDefs() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setAtomI(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the atomic mass of the atom.
setAtomicOrbital(float[]) - Method in class org.jmol.jvxl.readers.Parameters
setAtomIndexes(int, int) - Method in class org.jmol.util.Tensor
setAtomInfo(int[], int[], int[], boolean[], float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
setAtomMap(int[], int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setAtomName(Atom, String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
setAtomName(int, String, boolean) - Method in class org.jmol.modelset.AtomCollection
setAtomName(String) - Method in class org.jmol.smiles.SmilesAtom
setAtomNames() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
setAtomNamesAndNumbers(int, int, AtomCollection) - Method in class org.jmol.modelset.ModelSet
setAtomNumber(int, int, boolean) - Method in class org.jmol.modelset.AtomCollection
setAtomPositions() - Method in class org.jmol.minimize.Minimizer
setAtomPositions(int, int, P3[], P3[], float, V3[], boolean) - Method in class org.jmol.modelset.Trajectory
  A generic way to set atom positions, possibly from trajectories but also possibly from an array.
setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptEval
setAtomProperties(String, Object, int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomProperties() - Method in class org.jmol.modelset.ModelLoader
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
setAtomResno(int, int) - Method in class org.jmol.modelset.AtomCollection
setAtomsCoordRelative(BS, float, float, float) - Method in class org.jmol.modelset.AtomCollection
setAtomSeqID(int, int) - Method in class org.jmol.modelset.AtomCollection
setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the partial atomic charges based on asc auxiliary info
setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomSetFrequency(int, String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomSetInfo() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
setAtomSetInfoMd() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies
setAtomSetModelPropertyForSet(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the a property for the an AtomSet
setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the name for the current AtomSet
setAtomSetNumber(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setAtomSetPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the partial atomic charges based on atomSet auxiliary info
setAtomSetSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setAtomsForSmiles(Viewer, String) - Method in class org.jmol.symmetry.CIPDataSmiles
setAtomsPicked(BS, String) - Method in class org.jmol.viewer.ActionManager
setAtomTensors(int, Lst<Object>) - Method in class org.jmol.modelset.AtomCollection
setAtomType(int, String) - Method in class org.jmol.modelset.AtomCollection
setAtomTypes(Atom[], BS, SmilesMatcherInterface, Lst<BS>[], boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
  The file MMFF94-smarts.txt is derived from MMFF94-smarts.xlsx.
setAtomTypes(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
setAtomVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
setAtropicity - Variable in class org.jmol.smiles.SmilesSearch
setAtropisomerOptions(BS, BS) - Method in class org.jmol.modelset.Bond
setAtropType(int) - Method in class org.jmol.smiles.SmilesBond
setAttr(String, float) - Method in class org.jmol.export._MayaExporter
setAttr(String, int) - Method in class org.jmol.export._MayaExporter
setAttr(String, T3) - Method in class org.jmol.export._MayaExporter
setAttributes() - Method in class org.jmol.console.ScriptEditor
setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
setAutoscrolls(boolean) - Method in interface org.jmol.api.SC
setAutoscrolls(boolean) - Method in class org.jmol.awt.AwtSwingComponent
setAutoscrolls(boolean) - Method in class org.jmol.awtjs.swing.JComponent
setAxes(int) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
setAxes(DrawMesh) - Static method in class org.jmol.shapespecial.Draw
setAxesMode(int) - Method in class org.jmol.viewer.Viewer
setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
setAxesScale(int, float) - Method in class org.jmol.viewer.Viewer
setB(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
setBackground(GenericColor) - Method in class org.jmol.awtjs.swing.Component
setBackgroundArgb(int) - Method in class org.jmol.util.GData
  sets background color to the specified argb value
setBackgroundColor(int) - Method in class org.jmol.g3d.Platform3D
setBackgroundImage(Object) - Method in class org.jmol.util.GData
setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.AnimationManager
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Platform3D
setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
setBanner(String, boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
setBannerLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setBannerLabel(String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
setBaseModels(BS) - Method in class org.jmol.modelset.Trajectory
  set bits for all base models only
setBbcage(float) - Method in class org.jmol.util.BoxInfo
setBBox(T3, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
setBBoxAll() - Method in class org.jmol.jvxl.readers.SurfaceReader
setBf(int) - Method in class org.jmol.modelset.AtomCollection
setBFactor(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
setBgcolix(int, short) - Method in class org.jmol.shape.Labels
setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
setBioAtom(char) - Method in class org.jmol.smiles.SmilesAtom
setBioColix(short) - Method in class org.jmol.renderbio.BioShapeRenderer
setBiomolecule(Map<String, Object>, BS) - Method in class org.jmol.adapter.readers.cif.MMCifReader
setBiomoleculeAtomCounts() - Method in class org.jmol.adapter.readers.pdb.PdbReader
setBiomolecules() - Method in class org.jmol.adapter.readers.cif.MMCifReader
setBioPolymer(BioPolymer, int) - Method in class org.jmol.modelsetbio.Monomer
setBioPolymers(BioModel, boolean) - Method in class org.jmol.dssx.DSSR1
setBitSet(BS, BS, int) - Static method in class org.jmol.viewer.SelectionManager
setBitsetProperty(BS, int, int, float, T) - Method in class org.jmol.script.ScriptExpr
setBond(Bond, String[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
setBondArray() - Method in class org.jmol.smiles.SmilesAtom
setBondAtom(SmilesBond, SmilesAtom, SmilesAtom, SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
  set the bond and look for a=a, setting AROMATIC_DOUBLE automatically if found
setBondChirality(SimpleNode, SimpleNode, SimpleNode, SimpleNode, boolean) - Method in class org.jmol.symmetry.CIPChirality
  Determine the axial or E/Z chirality for the a-b bond.
setBondDirections() - Method in class org.jmol.smiles.SmilesGenerator
  Creates global BitSets bsBondsUp and bsBondsDown.
setBondIndex(int, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
  Set the bond for rotation -- called by Sticks.checkObjectHovered via Viewer.highlightBond.
setBonding(AtomSetCollection, int) - Method in class org.jmol.adapter.readers.more.JcampdxReader
  add bonding to a set of ModelData based on a MOL file only if the this set has no bonding already
setBondingAndMolecules() - Method in class org.jmol.adapter.readers.cif.CifReader
  (1) If GEOM_BOND records are present, we (a) use them to generate bonds (b) add H atoms to bonds if necessary (c) turn off autoBonding ("hasBonds") (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined (b) use asc.bonds[] to construct a preliminary molecule and connect as we go (c) check symmetry for connections to molecule in any one of the 27 3x3 adjacent cells (d) move those atoms and their connected branch set (e) iterate as necessary to get all atoms desired (f) delete unselected atoms (g) set all coordinates as Cartesians (h) remove all unit cell information
setBondingRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
setBondParameters(Bond, int, float, float, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  used in PyMOL reader to set unique bond settings and for valence
setBonds() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  Note that setting bonds from _struct_conn is only done if we have updated CIF files, which include _chem_comp_bond.
setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
setBondTypes(Bond[], int, BS) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptParam
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
setBooleanPropertyTok(String, int, boolean) - Method in class org.jmol.viewer.Viewer
setBorder() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.modelset.ModelSet
setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.util.BoxInfo
setBoundBoxFromOABC(T3[]) - Method in class org.jmol.util.BoxInfo
setBoundingBox(P3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setBoundingBox(P3[]) - Method in class org.jmol.util.MeshSurface
setBox(float, float, P3, V3, V3, P3, float) - Method in class org.jmol.modelsetbio.Sheet
setBox(float, float, P3) - Method in class org.jmol.renderbio.RocketRenderer
setBox(P3, P3) - Method in class org.jmol.util.MeshSurface
setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.modelset.Text
setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.modelset.Text
setBraceCount - Variable in class org.jmol.script.ScriptCompiler
setBranch2dZ(Atom, BS, BS, V3, V3, V3) - Static method in class org.jmol.modelset.ModelLoader
setBs(Atom[], int, BS[], BS) - Method in class org.jmol.adapter.readers.cif.CifReader
  iteratively run through connected atoms, adding them to the set
setBsHidden(BS) - Method in class org.jmol.modelset.AtomCollection
setBsVdw() - Method in class org.jmol.shapesurface.Isosurface
setBuf() - Method in class org.jmol.g3d.Pixelator
setButton(String) - Method in class org.jmol.console.GenericConsole
setButton(String) - Method in class org.jmol.console.JmolConsole
setButton(String) - Method in class org.jmol.console.ScriptEditor
setButton(String) - Method in class org.jmol.consolejs.AppletConsole
setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setC(short) - Method in interface org.jmol.api.JmolRendererInterface
  sets current color from colix color index
setC(short) - Method in class org.jmol.export.Export3D
  sets current color from colix color index
setC(short) - Method in class org.jmol.g3d.Graphics3D
  sets current color from colix color index
setC(short) - Method in class org.jmol.util.GData
setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.ModulationSet
  get updated value for offset vector and for occupancy
setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.Vibration
setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
setCallbackFunction(String, String) - Method in class org.jmol.console.GenericConsole
setCallbackFunction(String, String) - Method in class org.jmol.util.GenericApplet
setCallbackFunction(String, String) - Method in class org.jmol.viewer.StatusManager
setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
setCamera(float, float) - Method in class org.jmol.viewer.TransformManager
setCameraDepthPercent(float, boolean) - Method in class org.jmol.viewer.TransformManager
  either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
setCapacity(int) - Method in class org.jmol.modelset.AtomCollection
setCapOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setCartesianOffset(T3) - Method in class org.jmol.symmetry.UnitCell
setCarveSets(Map<String, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setCE(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
setCel(boolean) - Method in class org.jmol.util.GData
setCel(boolean, int, int) - Method in class org.jmol.util.Shader
setCell(String) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
setCellParams() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
setCellParams() - Method in class org.jmol.util.SimpleUnitCell
setCellSelectionEnabled(boolean) - Method in class org.jmol.awtjs.swing.JTable
setCelPower(int) - Method in class org.jmol.util.GData
setCenter(T3, float) - Method in interface org.jmol.api.AtomIndexIterator
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
setCenter(int) - Method in class org.jmol.shapespecial.DrawMesh
setCenter(P3) - Method in class org.jmol.shapespecial.Ellipsoid
setCenter(T3, float) - Method in class org.jmol.symmetry.UnitCellIterator
setCenter() - Method in class org.jmol.viewer.TransformManager
setCenter2(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
setCenterAt(int, P3) - Method in class org.jmol.viewer.TransformManager
setCenterBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
setCenters() - Method in class org.jmol.shapespecial.DrawMesh
setCenterSelected() - Method in class org.jmol.api.JmolViewer
setCenterSelected() - Method in class org.jmol.viewer.Viewer
setCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
  deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell
setCGO(Lst<Object>) - Method in class org.jmol.shapecgo.CGO
setCGO(Lst<Object>) - Method in class org.jmol.viewer.Viewer
setChainID(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setChainID(int, String) - Method in class org.jmol.modelset.AtomCollection
setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the charge of the atom.
setCharges() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
setChemicalShiftReference(String, float) - Method in interface org.jmol.api.JmolNMRInterface
setChemicalShiftReference(String, float) - Method in class org.jmol.quantum.NMRCalculation
setChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
setCIPChirality(int) - Method in class org.jmol.modelset.Atom
setCIPChirality(int) - Method in class org.jmol.modelset.Bond
  Not implemented.
setCIPChirality(int) - Method in class org.jmol.smiles.SmilesAtom
setCIPChirality(int) - Method in class org.jmol.util.Edge
setCIPChirality(int) - Method in interface org.jmol.util.Node
setCIPChirality(int) - Method in interface org.jmol.util.SimpleNode
setCIPInfo(String, int, String) - Method in class org.jmol.symmetry.CIPDataTracker
setClickable(int) - Method in class org.jmol.modelset.Atom
setClipboard(Object) - Static method in class org.jmol.awt.AwtClipboard
  Transfers text or image into the clipboard.
setCoeffs(int, boolean) - Method in class org.jmol.quantum.MOCalculation
setColix(short) - Method in class org.jmol.render.MeshRenderer
setColix(short) - Method in class org.jmol.renderbio.BioShapeRenderer
setColix(short) - Method in class org.jmol.util.MeshSurface
setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
setColixBack(short, BS) - Method in class org.jmol.shapebio.BioShape
setColixBack(short) - Method in class org.jmol.util.MeshSurface
setColixBackgroundContrast(int) - Method in class org.jmol.viewer.ColorManager
setColixBS(short, byte, BS) - Method in class org.jmol.shapebio.BioShape
setColixDipole(short, int, BS) - Method in class org.jmol.shapespecial.Dipoles
setColixes(short[], BS) - Method in class org.jmol.shapebio.BioShape
setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setColor(short) - Method in class org.jmol.shape.Measures
setColor(int) - Method in class org.jmol.util.GData
setColorBackground(String) - Method in class org.jmol.api.JmolViewer
setColorBackground(String) - Method in class org.jmol.viewer.Viewer
setColorByScore(float, int) - Method in class org.jmol.shapesurface.Contact
setColorCommand() - Method in class org.jmol.shapesurface.IsosurfaceMesh
  just sets the color command for this isosurface.
setColorNoisy(int) - Method in class org.jmol.g3d.Graphics3D
setColorOptions(SB, int, int, int) - Method in class org.jmol.scriptext.IsoExt
setColorPhase(IsosurfaceMesh, short, short) - Method in class org.jmol.shapesurface.Isosurface
setColors(short[], float) - Method in class org.jmol.adapter.readers.pymol.JmolObject
setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
setColorsFromJvxlData(int) - Method in class org.jmol.shapesurface.IsosurfaceMesh
  from Isosurface.notifySurfaceGenerationCompleted() starting with Jmol 12.1.50, JVXL files contain color, translucency, color scheme information, and vertex color mappings (as from COLOR ISOSURFACE {hydrophobic} WHITE), returning these settings when the JVXL file is opened.
setCommand(T) - Method in class org.jmol.script.ScriptCompiler
setCommonDefaults() - Method in class org.jmol.viewer.StateManager
setCompiler() - Method in interface org.jmol.api.JmolScriptEvaluator
setCompiler() - Method in class org.jmol.script.ScriptEval
setConformation(BS) - Method in class org.jmol.modelset.ModelSet
setConformation(BS) - Method in class org.jmol.modelsetbio.BioPolymer
setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
  sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
setConsoleTextPane(AppConsole.ConsoleTextPane) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
setConstraints(Lst<MMConstraint>) - Method in class org.jmol.minimize.forcefield.Calculations
setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in class org.jmol.scriptext.MathExt
setContacts(Object[], boolean) - Method in class org.jmol.shapesurface.Contact
setContext(ScriptContext) - Method in class org.jmol.console.ScriptEditor
setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
setContourVector(Lst<Object>, int, BS, float, short, int, SB) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
setCoord(SimpleNode, CIPChirality.CIPAtom[]) - Method in class org.jmol.symmetry.CIPData
  set the coordinate -- SMILES only
setCoord(SimpleNode, CIPChirality.CIPAtom[]) - Method in class org.jmol.symmetry.CIPDataSmiles
setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setCoords(Calculation, int) - Method in class org.jmol.minimize.forcefield.Calculations
setCount(int) - Method in class org.jmol.modelset.Measurement
setCount(int) - Method in class org.jmol.modelset.MeasurementPending
setCountM(int) - Method in class org.jmol.modelset.Measurement
setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelSet
setCrystallographicDefaults() - Method in class org.jmol.viewer.StateManager
setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
setCurrent(MouseState, int) - Method in class org.jmol.viewer.MouseState
setCurrentAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets the number for the current AtomSet
setCurrentCage(String) - Method in class org.jmol.viewer.Viewer
setCurrentCagePts(T3[], String) - Method in class org.jmol.script.ScriptEval
setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
setCurrentModelID(String) - Method in class org.jmol.viewer.Viewer
setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
setCurrentModelIndexClear(int, boolean) - Method in class org.jmol.viewer.Viewer
setCurrentModelInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets auxiliary information for the AtomSet
setCursor(int, Object) - Method in interface org.jmol.api.GenericPlatform
setCursor(JSmolAppletObject, int) - Method in interface org.jmol.api.js.JmolToJSmolInterface
setCursor(int, Object) - Static method in class org.jmol.awt.Display
setCursor(int, Object) - Method in class org.jmol.awt.Platform
setCursor(int, Object) - Method in class org.jmol.awtjs2d.Platform
setCursor(int) - Method in class org.jmol.viewer.Viewer
setCursorWait(boolean) - Method in class org.jmol.script.ScriptError
setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.MapFileReader
setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
setData(String, Object[], int, int, int, int, int, int) - Method in interface org.jmol.api.JmolDataManager
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.Calculation
setData(Lst<Object[]>, MinAngle) - Method in class org.jmol.minimize.forcefield.MMFFAngleCalc
setData(Lst<Object[]>, MinBond) - Method in class org.jmol.minimize.forcefield.MMFFDistanceCalc
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.MMFFESCalc
setData(Lst<Object[]>, int) - Method in class org.jmol.minimize.forcefield.MMFFOOPCalc
setData(Lst<Object[]>, MinAngle) - Method in class org.jmol.minimize.forcefield.MMFFSBCalc
setData(Lst<Object[]>, MinTorsion) - Method in class org.jmol.minimize.forcefield.MMFFTorsionCalc
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.MMFFVDWCalc
setData(Lst<Object[]>, int[]) - Method in class org.jmol.minimize.forcefield.UFFAngleCalc
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFDistanceCalc
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFOOPCalc
setData(Lst<Object[]>, int[]) - Method in class org.jmol.minimize.forcefield.UFFTorsionCalc
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFVDWCalc
setData(String, String, Object, Object) - Method in class org.jmol.script.FileLoadThread
  Called by Jmol._loadFileAsyncDone(this.vwr.html5Applet).
setData(String, Object[], int, int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
  This method needs to be redone using a class instead of Object[]
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
  A general-purpose data storage method.
setDataDistanceToPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
setDebugging() - Method in interface org.jmol.api.JmolScriptEvaluator
setDebugging() - Method in class org.jmol.script.ScriptEval
setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
setDefaultColors(boolean) - Method in class org.jmol.viewer.ColorManager
setDefaultColors(boolean) - Method in class org.jmol.viewer.Viewer
setDefaultLattice(P3) - Method in class org.jmol.viewer.Viewer
setDefaultPerspective() - Method in class org.jmol.viewer.TransformManager
setDefaultRendering(int) - Method in class org.jmol.modelset.ModelLoader
setDefaults - Variable in class org.jmol.shape.Labels
setDefaultState(int) - Method in class org.jmol.modelkit.ModelKitPopup
setDefaultsType(String) - Method in class org.jmol.viewer.Viewer
setDefinedFaces(P3[], int[][]) - Method in class org.jmol.shapespecial.Polyhedra
setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
setDepth(int) - Method in class org.jmol.util.GData
  clipping from the front and the back
setDesiredQpt(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
setDFCoord(Map<String, Object>) - Method in class org.jmol.adapter.writers.QCJSONWriter
setDialog() - Method in class org.jmol.awtjs.swing.JDialog
  Set it into DOM, but don't show it yet.
setDialog(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  The HTML for this dialog has been generated.
setDialogLocation(Point) - Method in class org.jmol.dialog.FileChooser
setDialogSize(Dimension) - Method in class org.jmol.dialog.FileChooser
setDiffusePercent(int) - Method in class org.jmol.util.GData
  df in I = df * (N dot L) + sf * (R dot V)^p
setDihedrals(float[], BS[], float) - Method in class org.jmol.modelset.ModelSet
setDihedrals(float[], BS[], float) - Method in class org.jmol.viewer.Viewer
setDipole(String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
setDipole() - Method in class org.jmol.shapespecial.Dipoles
setDipoleAtoms(Atom, Atom, float, float) - Method in class org.jmol.shapespecial.Dipoles
setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setDisplay(Object) - Method in class org.jmol.appletjs.Jmol
setDisplay(BS) - Method in class org.jmol.viewer.AnimationManager
setDisplay(Object) - Method in class org.jmol.viewer.Viewer
setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
setDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
setDragAtomIndex(int) - Method in class org.jmol.viewer.ActionManager
setDrawing(int[]) - Method in class org.jmol.shapespecial.Draw
setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
setEccentricity(P4) - Method in class org.jmol.jvxl.readers.Parameters
setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
setEditorTextPane(ScriptEditor.EditorTextPane) - Method in class org.jmol.console.ScriptEditor.EditorDocument
setElement(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
setElementAndIsotope(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
  allow 13C, 15N, 2H, etc.
setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
setElementColor(String, int) - Method in class org.jmol.script.ScriptEval
setEllipsoidAF(float[]) - Method in class org.jmol.jvxl.readers.Parameters
setEllipsoidP4(P4) - Method in class org.jmol.jvxl.readers.Parameters
setEnabled(boolean) - Method in interface org.jmol.api.JmolAbstractButton
setEnabled(boolean) - Method in interface org.jmol.api.SC
setEnabled(boolean) - Method in class org.jmol.awt.AwtSwingComponent
setEnabled(boolean) - Method in class org.jmol.awtjs.swing.Component
setEnabled(JmolAbstractButton, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setEnabled(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
setEnabled() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
setEne() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Set all ene-related fields upon finding the second atom.
setEnergies(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
setEnergy() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
  Interpret the Energy= line for non SCF type energy output
setEnergy(String, String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
setEnergy(float) - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
setEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
setEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
setEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
setEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
setEnergyUnits() - Method in class org.jmol.minimize.Minimizer
setEqualPt - Variable in class org.jmol.script.ScriptCompiler
setError(Throwable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setError(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setErrorMessage(String) - Method in class org.jmol.script.ScriptError
setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
setEval(JmolScriptEvaluator) - Method in class org.jmol.thread.JmolThread
  JavaScript only -- -- scriptDelay, moveTo, spin -- save context for restoration later -- move program counter forward one command
setException(ScriptException, String, String) - Method in class org.jmol.script.ScriptEval
setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the number of explicit hydrogen atoms bonded with this atom.
setF(String, float) - Method in class org.jmol.viewer.GlobalSettings
setFancyArrowHead(int) - Method in class org.jmol.renderbio.BioMeshRenderer
setFancyConic(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
setFancyRibbon(int) - Method in class org.jmol.renderbio.BioMeshRenderer
setFile() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
setFileData(Viewer, Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
  Set fullPathName, fileName, and nameAsGiven
setFileLoadStatus(String, String, String, String, int, boolean, Boolean) - Method in class org.jmol.viewer.StatusManager
setFileLoadStatus(FIL, String, String, String, String, Boolean) - Method in class org.jmol.viewer.Viewer
setFilename(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
setFilename(String) - Method in class org.jmol.console.ScriptEditor
setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setFilterAtomTypeStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setFinalOperations(String, P3[], int, int, boolean, String) - Method in interface org.jmol.api.SymmetryInterface
setFinalOperations(P3[], int, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
setFinalOperations(String, P3[], int, int, boolean, String) - Method in class org.jmol.symmetry.Symmetry
setFixedRotationCenter(T3) - Method in class org.jmol.viewer.TransformManager
setFlags(AtomType) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setFlags(int) - Method in class org.jmol.smiles.SmilesSearch
setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
setFloatProperty(String, float) - Method in class org.jmol.script.ScriptParam
setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
setFloatPropertyTok(String, int, float) - Method in class org.jmol.viewer.Viewer
setFlowEnd(int, String) - Method in class org.jmol.script.ScriptCompiler
  generate a new end token with pointer to the start or to default as the intValue and set it as the command token
setFocus() - Method in class org.jmol.viewer.Viewer
setFont(Object, Font) - Method in interface org.jmol.api.GenericGraphics
setFont(Object, Font) - Method in class org.jmol.awt.AwtG2D
setFont(Object, Font) - Method in class org.jmol.awtjs2d.JsG2D
setFont(short, String, Font) - Method in class org.jmol.export._VrmlExporter
setFont(Font) - Method in class org.jmol.g3d.Graphics3D
setFont(Font, boolean) - Method in class org.jmol.modelset.Text
setFont(int, byte) - Method in class org.jmol.shape.Labels
setFont(Font) - Method in class org.jmol.util.GData
setFontFid(byte) - Method in class org.jmol.g3d.Graphics3D
setFontFid(byte) - Method in class org.jmol.util.GData
setFontFromFid(byte) - Method in class org.jmol.modelset.Text
setFontScale(float) - Method in class org.jmol.modelset.Text
setFontScale(int) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
setForcesUsingNumericalDerivative(MinAtom, int) - Method in class org.jmol.minimize.forcefield.ForceField
setFormalCharge(int) - Method in class org.jmol.modelset.Atom
setFormalCharges(BS, int) - Method in class org.jmol.modelset.AtomCollection
setFormats(String) - Method in class org.jmol.shape.Measures
setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
setFractional(SymmetryInterface, T3, P3, P3) - Static method in class org.jmol.symmetry.SymmetryDesc
  Set pt01 to pt00, possibly adding offset into unit cell
setFractionalCoord(int, float, boolean) - Method in class org.jmol.modelset.Atom
setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setFractionalCoordPt(P3, P3, boolean) - Method in class org.jmol.modelset.Atom
setFractionalCoordTo(P3, boolean) - Method in class org.jmol.modelset.Atom
setFrame(int) - Method in class org.jmol.viewer.AnimationManager
setFrameDelayMs(long, BS) - Method in class org.jmol.modelset.ModelSet
setFrameDelayMs(long) - Method in class org.jmol.viewer.Viewer
setFrameObject(int, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setFrameOffset(int) - Method in class org.jmol.viewer.TransformManager
setFrameOffsets(BS, boolean) - Method in class org.jmol.viewer.Viewer
setFrameRangeVisible() - Method in class org.jmol.viewer.AnimationManager
setFrameSet(int) - Method in class org.jmol.script.ScriptEval
setFrameTitle(BS, Object) - Method in class org.jmol.modelset.ModelSet
setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
setFrameTitleObj(Object) - Method in class org.jmol.viewer.Viewer
setFrameVariables() - Method in class org.jmol.viewer.Viewer
setFrankMenu(String) - Method in class org.jmol.popup.JmolPopup
setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
setFreqValue(float, String[]) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
setFromAsymmetricTensor(double[][], String, String) - Method in class org.jmol.util.Tensor
  Standard constructor for QM tensors
setFromAxes(V3[]) - Method in class org.jmol.util.Tensor
  Standard constructor for ellipsoids based on axes
setFromBits(int, BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
setFromEigenVectors(T3[], float[], String, String, Tensor) - Method in class org.jmol.util.Tensor
  Standard constructor for charge and iso.
setFromMatrix(float[], boolean) - Method in class org.jmol.symmetry.SymmetryOperation
setFromThermalEquation(double[], String) - Method in class org.jmol.util.Tensor
  standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
setFullPath(Map<String, Object>, String) - Method in class org.jmol.viewer.OutputManager
setFunction(ScriptFunction) - Method in class org.jmol.script.ScriptFlowContext
setFunction(ScriptFunction, String, int, int, short[], int[][], Lst<T[]>) - Static method in class org.jmol.script.ScriptFunction
setFunctionXY(Lst<Object>) - Method in class org.jmol.jvxl.readers.Parameters
setFunctionXYZ(Lst<Object>) - Method in class org.jmol.jvxl.readers.Parameters
setGamma(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
  rsvs is the superspace group rotation-translation matrix.
setGap(P3, int) - Method in class org.jmol.shapespecial.Polyhedra
setGeneralBindings() - Method in class org.jmol.viewer.binding.JmolBinding
setGestureSwipeFactor(float) - Method in class org.jmol.viewer.ActionManager
setGhostOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setGlobals() - Method in class org.jmol.renderbio.BioShapeRenderer
setGlobals() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
setGlobals() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
setGouraud(int, int, int) - Method in class org.jmol.g3d.TriangleRenderer
setGraphicsColor(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
  controls greyscale rendering
setGridLimitsForAtom(P3, float, P3i, P3i) - Method in class org.jmol.jvxl.readers.AtomDataReader
setGroup(Chain, String, int, int, int) - Method in class org.jmol.modelset.Group
setGroup1(ModelSet, int) - Method in interface org.jmol.api.JmolAnnotationParser
setGroup1(ModelSet, int) - Method in class org.jmol.dssx.AnnotationParser
setGroup1(ModelSet, int) - Method in class org.jmol.dssx.DSSR1
setGroup1(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
setGroupID(String) - Method in class org.jmol.modelset.Group
setGroupID(String) - Method in class org.jmol.modelsetbio.Monomer
setGroupLists(int) - Method in class org.jmol.modelsetbio.BioResolver
setGroupParameter(int, float) - Method in class org.jmol.modelsetbio.Monomer
setGroupVisibilities() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setGroupVisible(PyMOLGroup, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Iterate through groups, setting visibility flags.
setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.BioResolver
setHeader(String, String) - Method in class org.jmol.jvxl.readers.AtomDataReader
setHeader(String) - Method in class org.jmol.jvxl.readers.IsoShapeReader
setHeader() - Method in class org.jmol.jvxl.readers.NffReader
setHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
setHeader() - Method in class org.jmol.jvxl.readers.Ras3DReader
setHetero() - Method in class org.jmol.adapter.readers.cif.MMCifReader
setHideNotSelected(boolean) - Method in class org.jmol.viewer.SelectionManager
setHistory(String) - Method in class org.jmol.viewer.Viewer
setHMSymbol(String) - Method in class org.jmol.symmetry.SpaceGroup
setHorizAlignment(int, int) - Method in class org.jmol.shape.Labels
setHorizAlignment(int, int) - Static method in class org.jmol.viewer.JC
setHoverEnabled(boolean) - Method in class org.jmol.viewer.Viewer
setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
setHydrogen(int, int, String, P3) - Method in class org.jmol.modelsetbio.BioResolver
setHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
  Finalizes the hydrogen count hydrogens in a `SmilesMolecule`.
setHydrophobicity(int, float) - Method in class org.jmol.modelset.AtomCollection
setI(String, int) - Method in class org.jmol.viewer.GlobalSettings
setIcon(Object) - Method in interface org.jmol.api.SC
setIcon(Object) - Method in class org.jmol.awt.AwtSwingComponent
setIcon(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
setImage(Object) - Method in interface org.jmol.api.GenericImageDialog
setImage(Object) - Method in class org.jmol.console.ImageDialog
setImage(Object) - Method in class org.jmol.modelset.Text
setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Sets the output image dimensions.
setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
setImageInfo(int, int, String) - Method in class org.jmol.dialog.Dialog
setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the number of implicit hydrogen atoms bonded with this atom.
setIndex(int) - Method in class org.jmol.smiles.SmilesAtom
  Constructs a `SmilesAtom`.
setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Sets the indexes to the atomSetIndex values of each leaf of the node.
setIndices() - Method in class org.jmol.shape.Measures
setInfo(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
setInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelSet
setInfo(Viewer, Map<String, Object>, Atom[]) - Method in class org.jmol.shapespecial.Polyhedron
setInMotion(boolean) - Method in class org.jmol.api.JmolViewer
setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
setInsertedCommand(String) - Method in class org.jmol.viewer.Viewer
setInt(int) - Method in class org.jmol.util.Rgb16
setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
setIntProperty(String, int) - Method in class org.jmol.script.ScriptParam
setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
setIntPropertyTok(String, int, int) - Method in class org.jmol.viewer.Viewer
setInverseNormixes() - Static method in class org.jmol.util.Normix
setInvoker(Object) - Method in class org.jmol.awtjs.swing.JPopupMenu
setIsoMeshColor(IsosurfaceMesh, String) - Method in class org.jmol.shapesurface.Isosurface
setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
SETITEM - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
SETITEMS - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelSet
setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in interface org.jmol.atomdata.AtomDataServer
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.modelset.ModelSet
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.viewer.Viewer
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelSet
setJmolDefaults() - Method in class org.jmol.api.JmolViewer
setJmolDefaults() - Method in class org.jmol.viewer.StateManager
setJmolDefaults() - Method in class org.jmol.viewer.Viewer
setJmolLewisStructure(Map<String, Object>, int, int) - Method in class org.jmol.adapter.readers.quantum.NBOParser
  Starting with a structure map, do what needs to be done to change the current Jmol structure to that in terms of bonding and formal charge.
setJmolSize(Dimension) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
setJSpecView(String, boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
setJvxlColorMap(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
  set up the jvxlData fields needed for either just the header (isAll = false) or the full file (isAll = true)
setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setJvxlDataRendering() - Method in class org.jmol.shapesurface.IsosurfaceMesh
setJvxlInfo() - Method in class org.jmol.shapesurface.Isosurface
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
setLabel(String, String) - Method in class org.jmol.modelkit.ModelKitPopup
setLabel(LabelToken[][], String, int, boolean) - Method in class org.jmol.shape.Labels
setLabel(Object, BS) - Method in class org.jmol.viewer.ShapeManager
setLabel(String) - Method in class org.openscience.jmol.app.jsonkiosk.BannerFrame
setLabelColix(int, short, byte) - Method in class org.jmol.shape.Labels
setLabelPosition(P3, float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setLabels() - Method in class org.jmol.console.GenericConsole
setLastColix(int, boolean) - Method in class org.jmol.util.Shader
setLastGrey(int) - Static method in class org.jmol.util.C
setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
  set symmetry lattice type using Hall rotations
setLattice(char, boolean) - Method in class org.jmol.symmetry.SpaceGroup
setLattice(int) - Method in class org.jmol.symmetry.Symmetry
setLatticeCells() - Method in class org.jmol.adapter.smarter.XtalSymmetry
setLatticeParam(int) - Method in class org.jmol.symmetry.SpaceGroup
setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setLatticeType(String) - Method in interface org.jmol.api.SymmetryInterface
setLatticeType(String) - Method in class org.jmol.symmetry.Symmetry
setLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
setLcao(String, int) - Method in class org.jmol.jvxl.readers.Parameters
setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setLcaoOn(boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
setLcaoOn(int, boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
setLeadAtomIndex() - Method in class org.jmol.modelsetbio.Monomer
setLeftComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
setLengths() - Method in class org.jmol.shapespecial.Ellipsoid
setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
setLighting(int) - Method in class org.jmol.shape.Mesh
setLightSource(float, float, float) - Method in class org.jmol.util.Shader
setLine(String) - Method in interface org.jmol.api.JmolJDXMOLParser
setLine(String) - Method in class org.jmol.jsv.JDXMOLParser
setLine() - Method in class org.jmol.script.ScriptFlowContext
setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
setLineBits(float, float) - Method in class org.jmol.g3d.LineRenderer
setLoader(ModelLoader) - Method in class org.jmol.modelsetbio.BioResolver
setLoadFormat(String, char, boolean) - Method in class org.jmol.viewer.Viewer
  Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
setLoadNote() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
setLoadState(Map<String, Object>) - Method in class org.jmol.viewer.FileManager
setLobe(P4) - Method in class org.jmol.jvxl.readers.Parameters
setLocalPath(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
  called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
setLocation(int[]) - Method in class org.jmol.awtjs.swing.JDialog
setLogFile(String) - Method in class org.jmol.viewer.OutputManager
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
  Replaces the current logger implementation by a new one.
setLoggingEnabled(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
setLogic() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
setLogLevel(int) - Static method in class org.jmol.util.Logger
  Activates all logging levels up through a given level.
setLp(P4) - Method in class org.jmol.jvxl.readers.Parameters
setM(ModelSet, Measurement, float, short, String, int) - Method in class org.jmol.modelset.Measurement
setMad(short) - Method in class org.jmol.modelset.Bond
setMad(short, BS, float[]) - Method in class org.jmol.shapebio.BioShape
setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
setMads(int, boolean) - Method in class org.jmol.renderbio.BioShapeRenderer
  set diameters for a bioshape
setManager(Object, Viewer, Object) - Method in class org.jmol.minimize.MinimizationThread
setManager(Object, Viewer, Object) - Method in class org.jmol.script.CommandWatcherThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.AnimationThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.JmolThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.MoveToThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.SpinThread
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.VibrationThread
setManagerMove(Object[]) - Method in class org.jmol.thread.MoveToThread
  MOVE is a much simpler command.
setManagerMoveTo(Object[]) - Method in class org.jmol.thread.MoveToThread
  MOVETO is a more complex command.
setMapBitSet(Map<String, BS>, int, int, String) - Static method in class org.jmol.util.BSUtil
setMappingPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
setMapRanges(SurfaceReader, boolean) - Method in class org.jmol.jvxl.readers.Parameters
setMarBond(short) - Method in class org.jmol.api.JmolViewer
setMarBond(short) - Method in class org.jmol.viewer.Viewer
setMargin(float) - Method in class org.jmol.util.BoxInfo
SETMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
setMatchingAtom(Node, int) - Method in class org.jmol.smiles.SmilesAtom
  Sets the number of a matching atom in a molecule.
setMatrices() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
setMatrix() - Method in class org.jmol.jvxl.data.VolumeData
setMatrix(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
setMatrixFromXYZ(String, int, boolean) - Method in class org.jmol.symmetry.SymmetryOperation
setMaximumSize(int) - Method in class org.jmol.viewer.Viewer
setMaxSize(int) - Method in class org.jmol.util.CommandHistory
  Resets maximum size of command queue.
setMenu(String, boolean) - Method in class org.jmol.api.JmolViewer
setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
setMenuNBO(JMenu) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setMenuState() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setMep(float[], boolean) - Method in class org.jmol.jvxl.readers.Parameters
setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setMesh(String) - Method in class org.jmol.shape.MeshCollection
setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
  an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEval
setMeshI() - Method in class org.jmol.shapesurface.Isosurface
setMeshTokenProperty(Mesh, int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
setMinimizationOn(boolean) - Method in class org.jmol.minimize.Minimizer
setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.JScrollPane
setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
setMinMax0(P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
setMinMax0(P3, P3) - Method in interface org.jmol.adapter.smarter.MSInterface
setMinMaxLatticeParameters(int, P3i, P3i, int) - Static method in class org.jmol.util.SimpleUnitCell
setMKState(int) - Method in class org.jmol.modelkit.ModelKitPopup
setMMTFSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
setMnemonic(char) - Method in interface org.jmol.api.JmolAbstractButton
setMnemonic(char) - Method in class org.jmol.console.JmolLabel
setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
setMO(int, float[]) - Method in class org.jmol.jvxl.readers.Parameters
setMod(String, P3, P3, int, Lst<Modulation>, M3, Matrix[], SymmetryInterface, int, int, Vibration, boolean) - Method in class org.jmol.util.ModulationSet
  A collection of modulations for a specific atom.
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
setMoData(Lst<Object[]>, int, float[], int, boolean, int, String, String, boolean) - Method in class org.jmol.scriptext.IsoExt
setModDim(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
setModDim(int) - Method in class org.jmol.symmetry.SymmetryOperation
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
setModel(int) - Method in interface org.jmol.api.JmolJSpecView
setModel(int) - Method in class org.jmol.jsv.JSpecView
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceField
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
setModel(BS) - Method in class org.jmol.minimize.Minimizer
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
setModel(int) - Method in class org.jmol.modelset.Trajectory
  The user has used the MODEL command to switch to a new set of atom coordinates Or has specified a trajectory in a select, display, or hide command.
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.symmetry.UnitCellIterator
setModel(int, boolean) - Method in class org.jmol.viewer.AnimationManager
setModelCage(int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
setModelFields() - Method in class org.jmol.minimize.forcefield.ForceField
setModelIndex(short) - Method in class org.jmol.modelset.Measurement
setModelIndex(int) - Method in class org.jmol.modelset.StateScript
setModelIndex() - Method in class org.jmol.shapespecial.Dipoles
setModelInfoForSet(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
  Sets auxiliary information for an AtomSet
setModelKitMode(boolean) - Method in class org.jmol.viewer.Viewer
setModelkitMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setModelkitProperty(String, Object) - Method in class org.jmol.viewer.Viewer
setModelKitRotateBondIndex(int) - Method in class org.jmol.viewer.Viewer
setModelNameNumberProperties(int, int, String, int, Properties, Map<String, Object>, String) - Method in class org.jmol.modelset.ModelLoader
setModelParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
setModelPDB(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setModelSet(ModelSet) - Method in class org.jmol.modelset.MeasurementData
setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
setModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
setModelSet(ModelSet) - Method in class org.jmol.viewer.Viewer
setModelVisibility() - Method in class org.jmol.viewer.ShapeManager
  Sets shape visibility flags, including ATOM_VIS_INFRAME and ATOM_VIS_NOTHIDDEN.
setModelVisibility() - Method in class org.jmol.viewer.Viewer
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Bbcage
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Halos
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.MeshCollection
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Shape
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.TextShape
setModelVisibilityFlags(BS) - Method in class org.jmol.shapebio.BioShapeCollection
setModelVisibilityFlags(BS) - Method in class org.jmol.shapecgo.CGO
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Dipoles
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Draw
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Ellipsoids
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Polyhedra
setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
  only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the vwr references are all removed
setModifyKeys(Map<String, String>) - Method in class org.jmol.util.JSONWriter
setModTQ(T3, boolean, T3, boolean, float) - Method in interface org.jmol.api.JmolModulationSet
setModTQ(T3, boolean, T3, boolean, float) - Method in class org.jmol.util.ModulationSet
  Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
setModulation(boolean, SymmetryInterface) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Both the Jana reader and the CIF reader will call this to set the modulation for a given model.
setModulation(boolean, SymmetryInterface) - Method in interface org.jmol.adapter.smarter.MSInterface
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.modelset.ModelSet
  Sets the modulation for all atoms in bs.
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.viewer.Viewer
setModulationForStructure(int, boolean) - Method in class org.jmol.adapter.readers.cif.MSRdr
  Called when structure creation is complete and all modulation data has been collected.
setMolecularModulation(String, float, float) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Add the modulation after applying rigid-body phase correction
setMoment() - Method in interface org.jmol.api.JmolModulationSet
setMoment() - Method in class org.jmol.util.ModulationSet
setMorphCount(int) - Method in class org.jmol.viewer.AnimationManager
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
setMotion(int, boolean) - Method in class org.jmol.viewer.ActionManager
setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.Viewer
setMouseActions(int, int, boolean) - Method in class org.jmol.viewer.ActionManager
setMouseDragFactor(float) - Method in class org.jmol.viewer.ActionManager
setMouseMode() - Method in class org.jmol.viewer.ActionManager
setMouseWheelFactor(float) - Method in class org.jmol.viewer.ActionManager
setMovableBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
setMovableX(int) - Method in class org.jmol.modelset.Text
setMovableXPercent(int) - Method in class org.jmol.modelset.Text
setMovableY(int) - Method in class org.jmol.modelset.Text
setMovableYPercent(int) - Method in class org.jmol.modelset.Text
setMovableZPercent(int) - Method in class org.jmol.modelset.Text
setMovie(Map<String, Object>) - Method in class org.jmol.viewer.AnimationManager
  support for PyMOL movies and anim FRAMES [....] currently no support for scripted movies
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
setMustResume() - Method in class org.jmol.script.ScriptContext
setMyError(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
setName(String) - Method in interface org.jmol.api.SC
setName(String) - Method in class org.jmol.awt.AwtSwingComponent
setName(String) - Method in class org.jmol.awtjs.swing.Component
setName(String) - Method in class org.jmol.script.SV
setName(String) - Method in class org.jmol.symmetry.SpaceGroup
setNames(String, BS, int) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
setNames(String, BS, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
setNavFps(int) - Method in class org.jmol.viewer.TransformManager
setNavigatePt(P3) - Method in class org.jmol.viewer.TransformManager
  scripted entry point for navigation
setNavigationDepthPercent(float) - Method in interface org.jmol.api.JmolNavigatorInterface
setNavigationDepthPercent(float) - Method in class org.jmol.navigate.Navigator
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
  sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.Viewer
setNavigationMode(boolean) - Method in class org.jmol.viewer.TransformManager
setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
setNavigationOffsetRelative() - Method in interface org.jmol.api.JmolNavigatorInterface
setNavigationOffsetRelative() - Method in class org.jmol.navigate.Navigator
setNavigationOffsetRelative() - Method in class org.jmol.viewer.TransformManager
setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager
setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
setNavPercent(P3) - Method in class org.jmol.navigate.Navigator
setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
setNboLabels(String[], int, Lst<Map<String, Object>>, int, String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
setNBOType(Map<String, Object>, String) - Method in class org.jmol.scriptext.IsoExt
setNci(boolean) - Method in class org.jmol.jvxl.readers.Parameters
setNeighbors(int) - Method in class org.jmol.renderbio.BioShapeRenderer
setNested(int, Object) - Method in class org.jmol.smiles.SmilesSearch
setNewRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
setNewRotationCenter(P3) - Method in class org.jmol.viewer.Viewer
setNewSetCommand(boolean, String) - Method in class org.jmol.script.ScriptCompiler
setNewWindowParametersForExport() - Method in class org.jmol.util.GData
setNext(String, String, int[], int) - Static method in class org.jmol.jvxl.readers.XmlReader
  shift pointer to a new tag or field contents
setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setNode() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Set the atom to have substituents.
setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
setNoPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
setNormalization(Object) - Method in class org.jmol.quantum.MOCalculation
setNormixes(V3[]) - Method in class org.jmol.shape.Mesh
setO(String, Object) - Method in class org.jmol.viewer.GlobalSettings
setOabc(String, float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
  set cell vectors by string
setObjectArgb(String, int) - Method in class org.jmol.script.ScriptEval
setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
setObjectColor(String, String) - Method in class org.jmol.viewer.Viewer
setObjectMad10(int, String, int) - Method in class org.jmol.script.ScriptEval
setObjectMad10(int, String, int) - Method in class org.jmol.viewer.Viewer
  input here is a JC.SHAPE_xxxx identifier
setObjectProp(String, int, int) - Method in class org.jmol.script.ScriptEval
setObjectProp(String, int) - Method in class org.jmol.viewer.Viewer
setObjectProperty() - Method in class org.jmol.script.ScriptEval
setObjectPropSafe(String, int) - Method in interface org.jmol.api.JmolScriptEvaluator
setObjectPropSafe(String, int) - Method in class org.jmol.script.ScriptEval
  called by Viewer in setting up a PyMOL scene.
setObjectVisibility(String, boolean) - Method in class org.jmol.viewer.Viewer
setOccupancy(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
setOccupancy(double[], double, double) - Method in class org.jmol.util.ModulationSet
  get the occupancy, first from the reader, then from renderer
setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
setOffset(int) - Method in class org.jmol.modelset.Text
setOffset(P3) - Method in class org.jmol.shapespecial.Polyhedron
setOffset(int) - Method in class org.jmol.symmetry.Symmetry
setOffset(M4, P3[], int, int) - Static method in class org.jmol.symmetry.SymmetryOperation
setOffset(T3) - Method in class org.jmol.symmetry.UnitCell
setOffsetPositions() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
setOffsetPt(T3) - Method in interface org.jmol.api.SymmetryInterface
setOffsetPt(P3) - Method in class org.jmol.shapespecial.Dipole
setOffsetPt(T3) - Method in class org.jmol.symmetry.Symmetry
setOffsets(int, int) - Method in class org.jmol.shape.Labels
setOopVariables(Calculation, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
setOpacity255(int) - Method in class org.jmol.awt.AwtColor
setOpacity255(int) - Method in class org.jmol.awtjs.swing.Color
setOptions(String) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
setOptions(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
setOrbital(int, float[]) - Method in class org.jmol.shapesurface.MolecularOrbital
setOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
setOrder(int) - Method in class org.jmol.modelset.Bond
setOutputChannel(GenericBinaryDocument, OC) - Method in interface org.jmol.jvxl.api.MeshDataServer
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceReader
setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.shapesurface.Isosurface
setPairVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
setPanel(JPanel) - Method in class org.openscience.jmol.app.jsonkiosk.KioskFrame
setParallel() - Method in class org.jmol.viewer.ShapeManager
setParallel(boolean) - Method in class org.jmol.viewer.Viewer
setparam - Static variable in class org.jmol.script.T
setParameter(String, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
setParams(Object[], int[], BS) - Method in class org.jmol.shapebio.BioShape
setParamsFromMatrix() - Method in class org.jmol.util.SimpleUnitCell
setParent(Object) - Method in class org.jmol.awtjs.swing.Component
setPartialCharge(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
setPass2(boolean) - Method in class org.jmol.util.GData
setPathForAllFiles(String) - Method in class org.jmol.viewer.FileManager
setPdbConectBonding(int, int, BS) - Method in class org.jmol.modelset.ModelSet
setPeakData(Lst<Object[]>, int) - Method in class org.jmol.jsv.JDXMOLParser
setPendingMeasurement(MeasurementPending) - Method in class org.jmol.viewer.Viewer
setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.TransformManager
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
setPhongExponent(int) - Method in class org.jmol.util.GData
  p in I = df * (N dot L) + sf * (R dot V)^p
setPhononVector(float[], Atom, V3, V3, V3) - Method in class org.jmol.adapter.readers.xtal.CastepReader
  transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v
setPicked(int, boolean) - Method in class org.jmol.viewer.Viewer
setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
setPickingStyle(int) - Method in class org.jmol.viewer.ActionManager
setPickingStyle(String, int) - Method in class org.jmol.viewer.Viewer
setPlane(int, float[]) - Method in class org.jmol.jvxl.readers.IsoFxyReader
setPlane(P4) - Method in class org.jmol.jvxl.readers.Parameters
setPlaneParameters(P4) - Method in class org.jmol.jvxl.data.VolumeData
setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
  Raw file data planes are passed to us here from VolumeFileReader
setPlanes(float[][]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
  Planes to use for holding raw file data.
setPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
setPoint(float[], int, int, int) - Static method in class org.jmol.util.MeshSlicer
setPointer(int, int) - Method in class org.jmol.shape.Labels
setPointer(int, int) - Static method in class org.jmol.viewer.JC
setPointGroup(SymmetryInterface, T3, T3[], BS, boolean, float, float, boolean) - Method in interface org.jmol.api.SymmetryInterface
setPointGroup(SymmetryInterface, T3, T3[], BS, boolean, float, float, boolean) - Method in class org.jmol.symmetry.Symmetry
setPoints(ModelSet, int[], Point3fi[], TickInfo) - Method in class org.jmol.modelset.Measurement
setPoints(int, int) - Method in class org.jmol.shapespecial.Draw
setPointsFromBitset() - Method in class org.jmol.shapespecial.Polyhedra
setPolygon(int) - Method in class org.jmol.shapespecial.Draw
setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
setPopInDim(int, int) - Static method in class org.openscience.jmol.app.webexport.WebExport
setPos(float) - Method in class org.jmol.modelset.Text
setPosition(float, float, boolean, float[]) - Method in class org.jmol.modelset.Text
setPositions() - Method in class org.jmol.adapter.readers.simple.AmpacReader
setPreferredScrollableViewportSize(Dimension) - Method in class org.jmol.awtjs.swing.JTable
setPreferredSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
setPreferredWidth(int) - Method in interface org.jmol.awtjs.swing.TableColumn
setPreliminary(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
setPreviewOptions(boolean) - Method in class org.jmol.dialog.FilePreview
setPrimitive(int) - Method in class org.jmol.smiles.SmilesBond
setPrincipalAxis(int, int) - Method in class org.jmol.symmetry.PointGroup
setPrincipalPlane(int, int) - Method in class org.jmol.symmetry.PointGroup
setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
setProp(String, Object, BS) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setProp(Ellipsoid, int, Object) - Method in class org.jmol.shapespecial.Ellipsoids
setPropAS(String, Object, BS) - Method in class org.jmol.shape.AtomShape
setPropBSC(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
setProperties(Lst<Object>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
  Set property_xxx for atoms from list of name, data, modelIndex series.
setProperties(Properties) - Method in interface org.jmol.api.JSVInterface
setProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
setProperty(String, Object) - Method in class org.jmol.modelkit.ModelKitPopup
  Modify the state by setting a property -- primarily from CmdExt.modelkit.
setProperty(String, Object, BS) - Method in class org.jmol.shape.Axes
setProperty(String, Object, BS) - Method in class org.jmol.shape.Balls
setProperty(String, Object, BS) - Method in class org.jmol.shape.Bbcage
setProperty(String, Object, BS) - Method in class org.jmol.shape.Echo
setProperty(String, Object, BS) - Method in class org.jmol.shape.Frank
setProperty(String, Object, BS) - Method in class org.jmol.shape.Halos
setProperty(String, Object, BS) - Method in class org.jmol.shape.Hover
setProperty(String, Object, BS) - Method in class org.jmol.shape.Labels
setProperty(String, Object, BS) - Method in class org.jmol.shape.Measures
setProperty(String, Object, BS) - Method in class org.jmol.shape.Shape
setProperty(String, Object, BS) - Method in class org.jmol.shape.Stars
setProperty(String, Object, BS) - Method in class org.jmol.shape.Sticks
setProperty(String, Object, BS) - Method in class org.jmol.shape.Uccage
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Backbone
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShape
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Trace
setProperty(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dipoles
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dots
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Ellipsoids
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Polyhedra
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Vectors
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Contact
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.LcaoCartoon
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.MolecularOrbital
setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
setPropertyColorRangeData(float[], BS) - Method in class org.jmol.viewer.ColorManager
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.ColorManager
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
setPropertyFor(int, Dipole, int, float) - Method in class org.jmol.shapespecial.Dipoles
setPropertySuper(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
setPropertySuper(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
setPropertySuper(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
setPropertyTok(int, boolean, int, float) - Method in class org.jmol.shapespecial.Dipoles
setPropFLS(String, Object) - Method in class org.jmol.shape.FontLineShape
setPropI(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
setPropMC(String, Object, BS) - Method in class org.jmol.shape.MeshCollection
setProps(String, String, int) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
setProps(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
setPropS(String, Object, BS) - Method in class org.jmol.shape.Shape
setPropTS(String, Object, BS) - Method in class org.jmol.shape.TextShape
setProteinStructureType(STR, int) - Method in class org.jmol.modelset.Group
setProteinStructureType(STR, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
setProteinType(BS, STR) - Method in class org.jmol.modelset.ModelSet
setProteinType(STR, BS) - Method in class org.jmol.viewer.Viewer
setPt0(int, boolean) - Method in class org.jmol.script.ScriptFlowContext
setPtVector(P3, V3) - Method in class org.jmol.shapespecial.Dipole
setPutty(float[], BS) - Method in class org.jmol.shapebio.Trace
  PyMOL-based "putty"
setPyMOLDefaults() - Method in class org.jmol.viewer.StateManager
setPymolLabel(int, Text, String) - Method in class org.jmol.shape.Labels
setPymolLabels(Map<Integer, Text>, BS) - Method in class org.jmol.shape.Labels
setPymolOffset(int, float[]) - Method in class org.jmol.shape.Labels
  Sets offset using PyMOL standard array; only operates in cases where label is already defined
setRadical(P4) - Method in class org.jmol.jvxl.readers.Parameters
setRadii() - Method in class org.jmol.jvxl.readers.AtomDataReader
setRadius(float) - Method in class org.jmol.modelset.Atom
setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
setRanges(float, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
setRasMolDefaults() - Method in class org.jmol.viewer.StateManager
setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
setRastAB(int, int, int, int) - Method in class org.jmol.g3d.PrecisionRenderer
setRastABFloat(float, float, float, float) - Method in class org.jmol.g3d.PrecisionRenderer
setReader() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setReaderObjectInfo(String, int, String, boolean, Lst<Object>, Lst<Object>, String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setReaderObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setRef(V3) - Method in class org.jmol.smiles.PolyhedronStereoSorter
setRefreshing(boolean) - Method in class org.jmol.viewer.Viewer
setRequiredFile(String, String) - Method in interface org.jmol.jvxl.api.MeshDataServer
setRequiredFile(String, String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
setRequiredFile(String, String) - Method in class org.jmol.shapesurface.Isosurface
setRes(Atom) - Method in class org.jmol.dssx.DSSR1
setResno(int) - Method in class org.jmol.modelset.Group
setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
setRightComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
setRigidBodyPhase(String, double[]) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Adjust phases to match the difference between the atom's position and the rigid molecular fragment's reference point.
setRigidBodyRotations(String, float[][]) - Method in class org.jmol.adapter.readers.xtal.JanaReader
  Transform unphased Fourier x,y,z cos/sin coefficients in a rigid body system based on distance from center.
setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
setRingData(BS, Lst<BS>[], boolean) - Method in class org.jmol.smiles.SmilesSearch
  Sets up all aromatic and ring data.
setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
setRingsClickable() - Method in class org.jmol.modelsetbio.NucleicMonomer
setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
setRingsVisible(boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
setRotateBondIndex(int) - Method in class org.jmol.viewer.Viewer
setRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setRotation(M3) - Method in class org.jmol.viewer.TransformManager
setRotationCenterAndRadiusXYZ(T3, boolean) - Method in class org.jmol.viewer.TransformManager
setRotationMatrix(M3) - Method in class org.jmol.g3d.Graphics3D
setRotationPointXY(P3) - Method in class org.jmol.viewer.TransformManager
setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelSet
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
setRowSelectionAllowed(boolean) - Method in class org.jmol.awtjs.swing.JTable
setRowSelectionInterval(int, int) - Method in class org.jmol.awtjs.swing.JTable
setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
setRule6Full(boolean) - Method in class org.jmol.symmetry.CIPData
setSaveEnabled(String) - Method in class org.jmol.console.ScriptEditor
setScale(float) - Method in class org.jmol.modelset.Text
setScale(float) - Method in class org.jmol.shape.Axes
setScale(float, boolean) - Method in class org.jmol.shapespecial.Ellipsoid
setScaleAngstromsPerInch(float) - Method in class org.jmol.viewer.TransformManager
setScalePixelsPerMicron(float) - Method in class org.jmol.modelset.Text
setScaling() - Method in class org.jmol.shape.Labels
setSceneObject(String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Set scene object/state-specific global fields and settings based on the name and state or stored values from when the file was loaded.
setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
setScreenDimension(int, int) - Method in class org.jmol.appletjs.Jmol
setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
setScreened(boolean) - Method in class org.jmol.g3d.Graphics3D
setScreeni(P3, P3i) - Method in class org.jmol.g3d.Graphics3D
setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
setScreenParameters0(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
setScript(String) - Method in class org.jmol.modelset.Text
setScript(String) - Method in class org.jmol.script.ScriptFunction
setScriptButtonPercent(int) - Static method in class org.openscience.jmol.app.webexport.WebExport
setScriptEcho(String, boolean) - Method in class org.jmol.viewer.StatusManager
setScriptExtensions() - Method in class org.jmol.script.ScriptEval
setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
setScriptFileRefs(String, String, boolean) - Static method in class org.jmol.viewer.FileManager
  Sets all local file references in a script file to point to files within dataPath.
setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
setScriptQueue(boolean) - Method in class org.jmol.viewer.Viewer
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.StatusManager
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
setSecStrucMenu(SC, Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
setSelectAllSubset(boolean) - Method in class org.jmol.viewer.AnimationManager
setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
setSelected(boolean) - Method in interface org.jmol.api.SC
setSelected(boolean) - Method in class org.jmol.awt.AwtSwingComponent
setSelected(boolean) - Method in class org.jmol.awtjs.swing.AbstractButton
setSelected(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this check box's selection has been changed.
setSelected(BS) - Method in class org.jmol.smiles.SmilesSearch
setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
setSelectedFloats(float, BS, float[]) - Static method in class org.jmol.viewer.DataManager
setSelectedIndex(int) - Method in class org.jmol.awtjs.swing.JComboBox
setSelectedIndex(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this combo box's selected item has been changed.
setSelectedOctant() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
setSelectedTranslation(BS, char, int) - Method in class org.jmol.viewer.TransformManager
setSelectedValue(int, int, SV) - Method in class org.jmol.script.SV
setSelectionHalosEnabled(boolean) - Method in class org.jmol.viewer.Viewer
setSelectionSet(BS) - Method in class org.jmol.api.JmolViewer
setSelectionSet(BS, int) - Method in class org.jmol.viewer.SelectionManager
setSelectionSet(BS) - Method in class org.jmol.viewer.Viewer
setSelectionSubset(BS) - Method in class org.jmol.viewer.SelectionManager
setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
setShapeId(int, int, boolean) - Method in class org.jmol.scriptext.ScriptExt
setShapeNameParameter(int) - Method in class org.jmol.script.ScriptEval
setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEval
setShapeProperty(int, String, Object) - Method in class org.jmol.scriptext.ScriptExt
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.script.ScriptEval
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.viewer.ShapeManager
setShapeSize(int, RadiusData) - Method in class org.jmol.script.ScriptEval
setShapeSize(int, int, BS) - Method in class org.jmol.viewer.Viewer
setShapeSizeBs(int, int, BS) - Method in class org.jmol.script.ScriptEval
setShapeSizeBs(int, int, RadiusData, BS) - Method in class org.jmol.viewer.ShapeManager
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shape.Shape
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.Backbone
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.BioShapeCollection
setShapeTranslucency(int, String, String, float, BS) - Method in class org.jmol.script.ScriptEval
setShapeVis() - Method in class org.jmol.viewer.ShapeManager
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
setShapeVisibility(boolean) - Method in class org.jmol.modelset.Bond
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
setShowWithin(Lst<P3>, float, boolean) - Method in class org.jmol.shape.Mesh
setSigma(String, Matrix) - Method in class org.jmol.symmetry.SymmetryOperation
setSilent(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
setSingleItem(Lst<Object>) - Method in class org.jmol.shape.Measures
setSize(float) - Method in class org.jmol.adapter.readers.pymol.JmolObject
setSize(int, float) - Method in class org.jmol.script.ScriptEval
setSize(int, BS) - Method in class org.jmol.shape.AtomShape
setSize(int, BS) - Method in class org.jmol.shape.Balls
setSize(int, BS) - Method in class org.jmol.shape.Measures
setSize(int, BS) - Method in class org.jmol.shape.Shape
setSize(int, BS) - Method in class org.jmol.shape.Sticks
  sets the size of a bond, or sets the selectedBonds set
setSize(int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
setSize2(int, BS) - Method in class org.jmol.shape.AtomShape
setSizeBio(int) - Method in class org.jmol.script.ScriptEval
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.AtomShape
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Balls
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Shape
setSizeRD(RadiusData, BS) - Method in class org.jmol.shapespecial.Dots
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shape.AtomShape
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shapespecial.Vectors
setSlab(int) - Method in interface org.jmol.api.JmolGraphicsInterface
setSlab(int) - Method in class org.jmol.export.Export3D
setSlab(int) - Method in class org.jmol.util.GData
  clipping from the front and the back
setSlabAndZShade(int, int, int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.export.Export3D
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.util.GData
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
  set internal slab or depth from screen-based slab or depth
setSlabEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
setSlaters(boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
  after the vectors intinfo and floatinfo are completed, we
setSlice(float, float, float, float, P3, V3, boolean) - Method in class org.openscience.jmol.app.surfacetool.Slice
  Sets the right plane and left plane bounding a slice.
setSlice(float, float, float, float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
  Defines a slice within which isosurfaces (and in future? atoms) are displayed.
setSliceAnglefromZ(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setSliceAngleXY(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setSlicePosition(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setSliceThickness(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setSmilesString(String) - Method in class org.jmol.viewer.Viewer
setSolvent(String, float) - Method in class org.jmol.jvxl.readers.Parameters
setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
setSpaceGroupFrom(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setSpaceGroupFrom(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
setSpaceGroupFrom(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setSpaceGroupName(String) - Method in interface org.jmol.api.SymmetryInterface
setSpaceGroupName(String) - Method in class org.jmol.symmetry.Symmetry
setSpectraMenu(SC, Lst<String>) - Method in class org.jmol.popup.JmolPopup
setSpectrumPeaks(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
setSpectrumPeaks(int, String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
setSpecular(boolean) - Method in class org.jmol.util.GData
setSpecularExponent(int) - Method in class org.jmol.util.GData
  log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
setSpecularPercent(int) - Method in class org.jmol.util.GData
  sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
setSpecularPower(int) - Method in class org.jmol.util.GData
  fractional distance to white for specular dot
setSphere(float, boolean) - Method in class org.jmol.jvxl.readers.Parameters
setSphereMatrix(T3, float, float, float, A4, M4) - Method in class org.jmol.export.__CartesianExporter
setSpin(JmolScriptEvaluator, boolean, float, Lst<P3>, float[], BS, boolean) - Method in class org.jmol.viewer.TransformManager
setSpin(String, int) - Method in class org.jmol.viewer.Viewer
setSpinFps(int) - Method in class org.jmol.viewer.TransformManager
setSpinOff() - Method in class org.jmol.viewer.TransformManager
setSpinOn() - Method in class org.jmol.viewer.TransformManager
setSpinVectors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
setSpinXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
setsSuccessful - Variable in class org.jmol.jvxl.data.MeshData
setStartupBooleans() - Method in class org.jmol.viewer.Viewer
setStateCount(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setStatement(T[], int) - Method in class org.jmol.script.ScriptExpr
  provides support for @x and @{....} in statements.
setStateScriptVersion(Viewer, String) - Static method in class org.jmol.script.ScriptManager
setStatic(int, int) - Method in interface org.jmol.api.JmolScriptEvaluator
setStatic(int, int) - Method in class org.jmol.script.ScriptEval
  set a static variable, with checking for range
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
setStatusAppletReady(String, boolean) - Method in class org.jmol.viewer.StatusManager
setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.StatusManager
setStatusAtomMoved(BS) - Method in class org.jmol.viewer.StatusManager
setStatusAtomPicked(int, String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
setStatusAtomPicked(int, String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
setStatusChanged(String, int, Object, boolean) - Method in class org.jmol.viewer.StatusManager
setStatusClicked(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
setStatusDragDropped(int, int, int, String) - Method in class org.jmol.appletjs.Jmol
setStatusDragDropped(int, int, int, String) - Method in class org.jmol.viewer.StatusManager
setStatusDragDropped(int, int, int, String) - Method in class org.jmol.viewer.Viewer
setStatusFrameChanged(int, int, int, int, int, float, String) - Method in class org.jmol.viewer.StatusManager
setStatusFrameChanged(boolean, boolean) - Method in class org.jmol.viewer.Viewer
setStatusListener(JmolStatusListener) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.StatusManager
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
setStatusObjectHovered(String, String, T3) - Method in class org.jmol.viewer.StatusManager
setStatusPicked(int, T3, Map<String, Object>) - Method in class org.jmol.shape.MeshCollection
setStatusResized(int, int) - Method in class org.jmol.viewer.StatusManager
setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
setStereo(boolean, Object) - Method in class org.jmol.viewer.Viewer
setStereoDegrees(float) - Method in class org.jmol.viewer.TransformManager
setStereoFromSmiles(BS, int, SimpleNode[]) - Method in class org.jmol.symmetry.CIPChirality
setStereoGraphics(boolean) - Method in interface org.jmol.api.JmolAppletInterface
setStereoGraphics(boolean) - Method in class org.jmol.applet.Jmol
setStereoGraphics(boolean) - Method in class org.jmol.applet.JmolApplet
setStereoGraphics(boolean) - Method in class org.jmol.appletjs.Jmol
setStereoMode(STER) - Method in class org.jmol.viewer.TransformManager
setStereoMode(int[], STER, float) - Method in class org.jmol.viewer.Viewer
setStereoMode2(int[]) - Method in class org.jmol.viewer.TransformManager
setStrandCount() - Method in class org.jmol.renderbio.StrandsRenderer
setStrandCount(int, int) - Method in class org.jmol.viewer.Viewer
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
setStream(OutputStream) - Method in class org.jmol.util.JSONWriter
setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
setStringProperty(String, String) - Method in class org.jmol.script.ScriptParam
setStringProperty(String, String) - Method in class org.jmol.util.GenericApplet
setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
setStringPropertyTok(String, int, String) - Method in class org.jmol.viewer.Viewer
setStrokeBold(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
setStrokeBold(Object, boolean) - Method in class org.jmol.awt.AwtG2D
setStrokeBold(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
setStrucNo(int) - Method in class org.jmol.modelset.Group
setStrucNo(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
setStrucNo(int) - Method in class org.jmol.modelsetbio.Monomer
setStructure - Variable in class org.jmol.dssx.DSSP
setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.AlphaMonomer
setStructure(JmolAdapterStructureIterator) - Method in class org.jmol.modelsetbio.BioResolver
  note that istart and iend will be adjusted.
setStructure(String, Translator) - Method in class org.jmol.popup.PopupResource
setStructureBS(int, int, STR, BS, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
  bits in the bitset determines the type
setStructureIndexes() - Method in class org.jmol.modelset.ModelSet
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelset.ModelSet
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
setStructureList(float[], STR) - Method in class org.jmol.viewer.GlobalSettings
setStructureList(float[], STR) - Method in class org.jmol.viewer.Viewer
setStructureTypes() - Method in class org.jmol.renderbio.BioShapeRenderer
setStrut(int, int, int, Lst<Atom>, BS, BS, Lst<Atom[]>, BS, BS, BS, int) - Static method in class org.jmol.modelsetbio.BioExt
setSubsystem(String, Subsystem) - Method in class org.jmol.adapter.readers.cif.MSRdr
setSubsystemOptions() - Method in class org.jmol.adapter.readers.cif.MSRdr
setSurfaceInfo(P4, P3, int, String) - Method in class org.jmol.jvxl.data.JvxlData
setSurfaceInfoFromBitSet(BS, P4) - Method in class org.jmol.jvxl.data.JvxlData
setSurfaceInfoFromBitSetPts(BS, P4, P3) - Method in class org.jmol.jvxl.data.JvxlData
setSurfaceToolParam() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
  Sets the symbol of the atm.
setSymEdit(int) - Method in class org.jmol.modelkit.ModelKitPopup
setSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.Subsystem
setSymmetry() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
setSymmetry() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
setSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setSymmetryInfo(int, Map<String, Object>, float[]) - Method in interface org.jmol.api.SymmetryInterface
setSymmetryInfo(int, Map<String, Object>, float[]) - Method in class org.jmol.symmetry.Symmetry
  Set space group and unit cell from the auxiliary info generated by the model adapter.
setSymmetryInfo(Map<String, Object>, float[]) - Method in class org.jmol.symmetry.SymmetryInfo
setSymmetryMinMax(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setSymmetryOps() - Method in class org.jmol.adapter.smarter.XtalSymmetry
setSymmetryRange(float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setSymmOps() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
setSymViewState(int) - Method in class org.jmol.modelkit.ModelKitPopup
setSync(String) - Method in class org.jmol.viewer.StatusManager
setSync() - Method in class org.jmol.viewer.Viewer
setSyncDriver(int) - Method in class org.jmol.viewer.StatusManager
setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
setSyncStarting() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setSyncTarget(int, boolean) - Method in class org.jmol.viewer.Viewer
settable - Static variable in class org.jmol.script.T
setTag(char[], BS, char) - Method in class org.jmol.dssx.DSSP
setTainted(boolean) - Method in class org.jmol.viewer.Viewer
setTaintedAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
setTempPoints(P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
setTempVertex(T3, T3, T3) - Static method in class org.jmol.export.___Exporter
setTensor(Tensor) - Method in class org.jmol.shapespecial.Ellipsoid
setTensors() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setTensors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
setText(String) - Method in interface org.jmol.api.JmolAbstractButton
setText(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
setText(String) - Method in interface org.jmol.api.SC
setText(String) - Method in class org.jmol.awt.AwtSwingComponent
setText(String) - Method in class org.jmol.awtjs.swing.Component
setText(String) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this component's text has been changed.
setText(String) - Method in interface org.jmol.console.GenericTextArea
setText(String, Font, int, int, int, int, int) - Method in class org.jmol.g3d.TextString
setText(String) - Method in class org.jmol.modelset.Text
setText(String, String) - Method in class org.jmol.popup.GenericPopup
setTextPosition(int) - Method in class org.jmol.util.GData
setThisScheme(String, int[]) - Method in class org.jmol.util.ColorEncoder
setTimeout(Viewer, Map<String, Object>, String, int, String) - Static method in class org.jmol.thread.TimeoutThread
setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
setTimeReversal(int, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setTimeReversal(int, int) - Method in interface org.jmol.api.SymmetryInterface
setTimeReversal(int, int) - Method in class org.jmol.symmetry.Symmetry
setTimeReversal(int) - Method in class org.jmol.symmetry.SymmetryOperation
  set the time reversal, and indicate internally in xyz as appended ",m" or ",-m"
settings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
setTitle(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
setTitle(String) - Method in interface org.jmol.api.js.JSConsole
setTitle(String) - Method in class org.jmol.awtjs.swing.JDialog
setTitle() - Method in class org.jmol.console.GenericConsole
setTitle() - Method in class org.jmol.console.JmolConsole
setTitle() - Method in class org.jmol.consolejs.AppletConsole
setTitle(String) - Method in interface org.jmol.consolejs.JSConsole
setTlsGroups(int, int, SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
  Sets the atom property property_tlsGroup based on TLS group ranges and adds "TLS" key to model's auxiliaryInfo.
setTlsTensor(Atom, Map<String, Object>, SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
setToken(Viewer, String, LabelToken, int, int, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
  sets a label token based on a label string
setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
setToolTipText(String) - Method in interface org.jmol.api.JmolAbstractButton
setTop(SmilesSearch) - Method in class org.jmol.smiles.SmilesSearch
setTopoAtom(int, int, String, int, int) - Method in class org.jmol.smiles.SmilesAtom
setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, Node[]) - Method in class org.jmol.smiles.SmilesStereo
setTorsionData(T3, T3, T3, T3, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
  calculate temporary points
setTorsionType(MinTorsion) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
setTorsionVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
setTrajectoryBs(BS) - Method in class org.jmol.modelset.ModelSet
setTrajectoryName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setTranslationFractions() - Method in class org.jmol.viewer.TransformManager
setTranslations() - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
  allows for web page material to be internationalized, inserting language-specific code, as for WebExport, or by inserting boiler-plate information, as for About_xx.html
setTranslucency(String, Font, Graphics3D) - Method in class org.jmol.g3d.TextRenderer
  retrieve grey-scale pixel map from the platform, then round it off
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
setTranslucent(float, boolean) - Method in class org.jmol.modelset.Text
setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
setTranslucent(boolean, BS, float) - Method in class org.jmol.shapebio.BioShape
setTranslucent(boolean, float) - Method in class org.jmol.shapespecial.Dipole
setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setTranslucentVertices(BS) - Method in class org.jmol.util.MeshSurface
  Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygons
setTransparentCursor(Object) - Method in interface org.jmol.api.GenericPlatform
setTransparentCursor(Object) - Static method in class org.jmol.awt.Display
setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
setTransparentCursor(Object) - Method in class org.jmol.awtjs2d.Platform
setTriangleTranslucency(short, short, short) - Method in class org.jmol.g3d.Graphics3D
setType(String) - Method in class org.jmol.util.Tensor
  Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.
setType(int) - Method in class org.jmol.util.Vibration
setU(Atom, int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
setUniqueBond(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setUniqueBonds(BS, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setUniqueObjects(int, BS, int, int, int, float, int, float, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
setUniqueSettings(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
  Create uniqueSettings from the "unique_settings" map item.
setUnitCell() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setUnitCell(float[], M3, P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
setUnitCell(float[], boolean) - Method in interface org.jmol.api.SymmetryInterface
setUnitCell(Symmetry) - Method in interface org.jmol.api.SymmetryInterface
setUnitCell(int) - Method in class org.jmol.modelkit.ModelKitPopup
setUnitCell(int) - Method in class org.jmol.modelset.Trajectory
setUnitCell(float[], boolean) - Method in class org.jmol.symmetry.Symmetry
setUnitCell(Symmetry) - Method in class org.jmol.symmetry.Symmetry
setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setUnitCellOffset(SymmetryInterface, T3, int) - Method in class org.jmol.modelset.ModelSet
setUnitCellOrientation() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
setUnits(boolean) - Method in class org.jmol.adapter.readers.xtal.MagresReader
  catalog units
setUnits(String, int) - Method in class org.jmol.script.ScriptEval
setUnits(String) - Method in class org.jmol.viewer.GlobalSettings
setUnits(String, boolean) - Method in class org.jmol.viewer.Viewer
setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.cif.MMTFReader
  standard set up
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.MdCrdReader
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setup(boolean) - Method in class org.jmol.jvxl.readers.AtomDataReader
setup(boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMepReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
setup(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
setup(int, float[], P3[], BS) - Method in class org.jmol.quantum.MepCalculation
setup(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
setup(boolean) - Method in class org.jmol.shapesurface.PMeshWriter
setup(Viewer, Container, String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setup2() - Method in class org.jmol.jvxl.readers.AtomDataReader
setupAC() - Method in class org.jmol.modelset.AtomCollection
setupASCR(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
setupBC() - Method in class org.jmol.modelset.BondCollection
setupCalculation() - Method in class org.jmol.jvxl.readers.IsoMOReader
setupCalculation(Map<String, Object>, boolean, VolumeData, BS, T3[], Atom[], int, int[][], float[], float[], boolean, float[][], T3[]) - Method in class org.jmol.quantum.MOCalculation
setupCalculation(VolumeData, BS, BS, BS[], T3[], int, boolean, T3[], float[], int) - Method in class org.jmol.quantum.NciCalculation
setupCalculations() - Method in class org.jmol.minimize.forcefield.Calculations
setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
setupCoordinates(float[], float[], BS, T3[], Atom[], T3[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
setupLabels(Map<String, String>) - Method in class org.jmol.console.GenericConsole
setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
setupLabels0(Map<String, String>) - Method in class org.jmol.console.GenericConsole
setupLabels0(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
setupMinimization() - Method in class org.jmol.minimize.Minimizer
setupNav(float, P3[][], P3[], int, int) - Method in class org.jmol.navigate.Navigator
setupNavTo() - Method in class org.jmol.navigate.Navigator
setupPS(AlphaPolymer, STR, int, int) - Method in class org.jmol.modelsetbio.ProteinStructure
setupRR(BioShape, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
setupType(String) - Method in class org.jmol.jvxl.readers.IsoFxyReader
setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
setupUI(boolean) - Method in class org.jmol.dialog.Dialog
setupUIManager() - Static method in class org.jmol.dialog.Dialog
  Setup the UIManager (for i18n)
setUseMolecular(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
setUserVariable(String, SV) - Method in class org.jmol.viewer.GlobalSettings
setUserVdw(VDW) - Method in class org.jmol.viewer.Viewer
setv(SV) - Method in class org.jmol.script.SV
  Creates a NEW version of the variable.
setValence(int) - Method in class org.jmol.modelset.Atom
setValence(int) - Method in class org.jmol.smiles.SmilesAtom
setValue(float) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
setValue(float) - Method in class org.jmol.shapespecial.Dipole
setValue(String, String) - Method in class org.jmol.util.GenericApplet
setValueMinMax() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
setValues(M3, P3, P3) - Method in class org.jmol.thread.MoveToThread
setVariable(int, int, String, boolean) - Method in class org.jmol.script.ScriptExpr
setVariables() - Method in class org.jmol.render.MeshRenderer
setVariables(Map<String, SV>, Lst<SV>) - Method in class org.jmol.script.ScriptFunction
setVdwStr(String) - Method in class org.jmol.viewer.Viewer
setVectorAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
setVectorScale(float) - Method in class org.jmol.api.JmolViewer
setVectorScale(float) - Method in class org.jmol.viewer.Viewer
setVersionSettings() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
  Attempt to adjust for PyMOL versions.
setVertexAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
setVertexColixesForAtoms(Viewer, short[], int[], BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
setVertexColorMap() - Method in class org.jmol.shapesurface.IsosurfaceMesh
setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
setVertexSource() - Method in class org.jmol.jvxl.readers.AtomDataReader
setVib(boolean, float) - Method in class org.jmol.util.ModulationSet
setVibrationOn(boolean) - Method in class org.jmol.viewer.TransformManager
setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
  sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
setVibrationScale(float) - Method in class org.jmol.viewer.TransformManager
setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
setVibrationsFromProperties() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
setVibrationVector() - Method in class org.jmol.modelset.Atom
setVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
setVibrationVector2(int, int, float) - Method in class org.jmol.modelset.AtomCollection
setViewer(PlatformViewer, Object) - Method in interface org.jmol.api.GenericPlatform
setViewer(Viewer) - Method in interface org.jmol.api.JmolJSpecView
setViewer(Viewer) - Method in interface org.jmol.api.JmolNMRInterface
setViewer(Viewer) - Method in interface org.jmol.api.JmolPropertyManager
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptEvaluator
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptManager
setViewer(PlatformViewer, Object) - Method in class org.jmol.awt.Platform
setViewer(PlatformViewer, Object) - Method in class org.jmol.awtjs2d.Platform
setViewer(Viewer) - Method in class org.jmol.console.GenericConsole
setViewer(Viewer) - Method in class org.jmol.jsv.JSpecView
setViewer(Viewer) - Method in class org.jmol.modelsetbio.BioResolver
setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
setViewer(Viewer) - Method in class org.jmol.quantum.NMRCalculation
setViewer(Viewer) - Method in class org.jmol.script.ScriptEval
setViewer(Viewer) - Method in class org.jmol.script.ScriptManager
setViewer(Viewer, String) - Method in class org.jmol.thread.JmolThread
setViewer(Viewer) - Method in class org.jmol.util.BZone
setViewer(Viewer) - Method in class org.jmol.util.MolWriter
setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
setViewer(boolean) - Method in class org.jmol.viewer.AnimationManager
setViewer(Viewer) - Method in class org.jmol.viewer.JmolStateCreator
setViewer(Viewer, double) - Method in class org.jmol.viewer.OutputManager
setViewer(Viewer) - Method in class org.jmol.viewer.PropertyManager
setViewer(Viewer) - Method in class org.jmol.viewer.StateCreator
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
setViewerG3dShapeID(Viewer, int) - Method in class org.jmol.render.ShapeRenderer
setVis(Map<?, Ellipsoid>, BS, Atom[]) - Method in class org.jmol.shapespecial.Ellipsoids
setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
setVisibilityInfo() - Method in class org.jmol.shape.Measures
setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
setVisible(boolean) - Method in interface org.jmol.api.js.JSConsole
setVisible(boolean) - Method in class org.jmol.awtjs.swing.Component
setVisible(boolean) - Method in class org.jmol.awtjs.swing.JDialog
setVisible(Component) - Method in interface org.jmol.awtjs.swing.SwingController
  Convey to the HTML object that this component's text has been changed.
setVisible(boolean) - Method in class org.jmol.console.AppletConsole
setVisible(boolean) - Method in class org.jmol.console.GenericConsole
setVisible(boolean) - Method in class org.jmol.console.JmolConsole
setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
setVisible(boolean) - Method in class org.jmol.consolejs.AppletConsole
setVisible(boolean) - Method in interface org.jmol.consolejs.JSConsole
setVisible(boolean) - Method in class org.jmol.shapespecial.Polyhedra
setVisible(boolean) - Method in interface org.openscience.jmol.app.JmolPlugin
setVolumeData() - Method in class org.jmol.jvxl.readers.AtomDataReader
setVolumeData() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
setVolumeData() - Method in class org.jmol.jvxl.readers.IsoFxyReader
setVolumeData() - Method in class org.jmol.jvxl.readers.IsoShapeReader
setVolumeData() - Method in class org.jmol.jvxl.readers.VolumeDataReader
setVolumeData(int, VolumeData, ContactPair, float, int) - Method in class org.jmol.shapesurface.Contact
setVolumeDataADR() - Method in class org.jmol.jvxl.readers.AtomDataReader
setVolumeDataParams() - Method in class org.jmol.jvxl.readers.VolumeDataReader
setVolumeDataV(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
setVolumeForPlane() - Method in class org.jmol.jvxl.readers.AtomDataReader
setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
setVoxel(int, int, int, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
setVoxelDataAsArray(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
  for sparse data mapping, as for a plane
setVoxelRange(int, float, float, float, int, float) - Method in class org.jmol.jvxl.readers.VolumeDataReader
setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
setWebPageAuthor(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
setWidthHeight(boolean) - Method in class org.jmol.util.GData
setWidthHeightVar() - Method in class org.jmol.viewer.Viewer
setWindow(int, int, float) - Method in class org.jmol.modelset.Text
setWindowCentered(boolean) - Method in class org.jmol.viewer.TransformManager
setWindowDimensions(float[]) - Method in class org.jmol.viewer.Viewer
setWindowParameters(int, int) - Method in interface org.jmol.api.GenericGraphics
setWindowParameters(int, int) - Method in class org.jmol.awt.AwtG2D
setWindowParameters(int, int) - Method in class org.jmol.awtjs2d.JsG2D
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
setWinParams(int, int, boolean) - Method in class org.jmol.util.GData
setWriteNullAsString(boolean) - Method in class org.jmol.util.JSONWriter
  Set option to write a null as the string "null" or just null itself.
setXYA(float[], int) - Method in class org.jmol.modelset.Text
setXYZ(P3, boolean) - Method in class org.jmol.modelset.Text
setXYZ(QuantumCalculation, boolean) - Method in class org.jmol.quantum.QMAtom
setXYZ(T3) - Method in class org.jmol.util.ModulationSet
setXYZ(T3) - Method in class org.jmol.util.Vibration
setXYZBohr(T3[]) - Method in class org.jmol.quantum.QuantumCalculation
setXYZBohrI(float[], int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
setXYZs(int, int, int, int) - Method in class org.jmol.modelset.Text
setZIndex(int) - Method in class org.jmol.awtjs.swing.JDialog
setZMargin(int) - Method in class org.jmol.g3d.Graphics3D
setZoomEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
setZoomHeight(boolean, boolean) - Method in class org.jmol.viewer.TransformManager
setZPos(int, int, boolean) - Method in class org.jmol.shape.Labels
setZPosition(int, int) - Static method in class org.jmol.viewer.JC
setZs(int, int) - Method in class org.jmol.modelset.Text
setZShadeEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
sfacElementSymbols - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
sg - Variable in class org.jmol.shapesurface.Isosurface
SG - Static variable in class org.jmol.symmetry.SpaceGroup
SG_ALIASES - Static variable in class org.jmol.adapter.readers.xtal.CgdReader
sgIndex - Static variable in class org.jmol.symmetry.SpaceGroup
sgName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
sgName - Variable in class org.jmol.symmetry.SymmetryInfo
SHADE_INDEX_LAST - Static variable in class org.jmol.util.Shader
SHADE_INDEX_MAX - Static variable in class org.jmol.util.Shader
SHADE_INDEX_NOISY_LIMIT - Static variable in class org.jmol.util.Shader
SHADE_INDEX_NORMAL - Static variable in class org.jmol.util.Shader
SHADE_SLAB_CLIPPED - Static variable in class org.jmol.g3d.SphereRenderer
shadeIndexes - Variable in class org.jmol.g3d.Graphics3D
shadeIndexes2Sided - Variable in class org.jmol.g3d.Graphics3D
shader - Variable in class org.jmol.g3d.CylinderRenderer
shader - Variable in class org.jmol.g3d.LineRenderer
shader - Variable in class org.jmol.g3d.SphereRenderer
shader - Variable in class org.jmol.util.GData
Shader - Class in org.jmol.util
  All functions.
Shader() - Constructor for class org.jmol.util.Shader
shader_path - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
shadesA - Variable in class org.jmol.g3d.CylinderRenderer
shadesB - Variable in class org.jmol.g3d.CylinderRenderer
shadesCurrent - Variable in class org.jmol.g3d.Graphics3D
shape - Variable in class org.jmol.render.ShapeRenderer
shape - Static variable in class org.jmol.script.T
Shape - Class in org.jmol.shape
  Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
Shape() - Constructor for class org.jmol.shape.Shape
shape - Variable in class org.jmol.shapebio.BioShape
SHAPE_AXES - Static variable in class org.jmol.viewer.JC
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JC
SHAPE_BALLS - Static variable in class org.jmol.viewer.JC
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JC
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JC
SHAPE_CGO - Static variable in class org.jmol.viewer.JC
SHAPE_CONTACT - Static variable in class org.jmol.viewer.JC
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JC
SHAPE_DOTS - Static variable in class org.jmol.viewer.JC
SHAPE_DRAW - Static variable in class org.jmol.viewer.JC
SHAPE_ECHO - Static variable in class org.jmol.viewer.JC
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JC
SHAPE_FRANK - Static variable in class org.jmol.viewer.JC
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_HALOS - Static variable in class org.jmol.viewer.JC
SHAPE_HOVER - Static variable in class org.jmol.viewer.JC
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JC
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_LABELS - Static variable in class org.jmol.viewer.JC
SHAPE_LAST_ATOM_VIS_FLAG - Static variable in class org.jmol.viewer.JC
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JC
SHAPE_MAX - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JC
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JC
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JC
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JC
SHAPE_MO - Static variable in class org.jmol.viewer.JC
SHAPE_NBO - Static variable in class org.jmol.viewer.JC
SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JC
SHAPE_PMESH - Static variable in class org.jmol.viewer.JC
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JC
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JC
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JC
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JC
SHAPE_STARS - Static variable in class org.jmol.viewer.JC
SHAPE_STICKS - Static variable in class org.jmol.viewer.JC
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JC
SHAPE_STRUTS - Static variable in class org.jmol.viewer.JC
SHAPE_TRACE - Static variable in class org.jmol.viewer.JC
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JC
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JC
shapeClassBases - Static variable in class org.jmol.viewer.JC
shapeCommand - Static variable in class org.jmol.script.T
shapeID - Variable in class org.jmol.render.ShapeRenderer
shapeID - Variable in class org.jmol.shape.Shape
shapely - Static variable in class org.jmol.script.T
SHAPELY - Static variable in class org.jmol.util.ColorEncoder
shapeManager - Variable in class org.jmol.render.RepaintManager
shapeManager - Variable in class org.jmol.script.ScriptProcessRunnable
ShapeManager - Class in org.jmol.viewer
ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
ShapeRenderer - Class in org.jmol.render
ShapeRenderer() - Constructor for class org.jmol.render.ShapeRenderer
shapes - Variable in class org.jmol.viewer.ShapeManager
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JC
shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
shapeVisibilityFlags - Variable in class org.jmol.viewer.Connection
Sheet - Class in org.jmol.modelsetbio
Sheet(AlphaPolymer, int, int, STR) - Constructor for class org.jmol.modelsetbio.Sheet
sheet - Static variable in class org.jmol.script.T
SHEET_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
sheetOffsets - Variable in class org.jmol.dssx.DSSP
sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
sheetSmoothing - Variable in class org.jmol.renderbio.BioShapeRenderer
sheetsmoothing - Static variable in class org.jmol.script.T
sheetSmoothing - Variable in class org.jmol.viewer.GlobalSettings
SHELL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
shellCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
shellOrder - Static variable in class org.jmol.quantum.MOCalculation
shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
shells - Variable in class org.jmol.adapter.writers.QCJSONWriter
shells - Variable in class org.jmol.quantum.MOCalculation
shellsByUniqueAtom - Variable in class org.jmol.adapter.readers.quantum.PsiReader
shelxLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
ShelxReader - Class in org.jmol.adapter.readers.xtal
  A reader for SHELX output (RES) files.
ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
SHIFT - Static variable in class org.jmol.viewer.binding.Binding
SHIFT_MASK - Static variable in class org.jmol.awtjs.Event
shiftBits(BS, BS, boolean, int) - Static method in class org.jmol.util.BSUtil
  this one slides bits to higher positions based on a pattern.
shiftRefsPPM - Variable in class org.jmol.quantum.NMRCalculation
shininess - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
shm - Variable in class org.jmol.viewer.Viewer
SHORT_BINSTRING - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
shortSceneFilename(String) - Method in class org.jmol.io.JmolUtil
show(String[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
show(Component, int, int) - Method in class org.jmol.awtjs.swing.JPopupMenu
show(String[]) - Method in class org.jmol.console.ScriptEditor
show(int, int, boolean) - Method in class org.jmol.popup.GenericPopup
show - Static variable in class org.jmol.script.T
show() - Method in class org.jmol.scriptext.CmdExt
show - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
show_alpha_checker - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
show_frame_rate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
show_progress - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Show an atom set from the indexes array
showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
showaxes - Static variable in class org.jmol.script.T
showAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
showboundbox - Static variable in class org.jmol.script.T
showBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
showBox(JmolRendererInterface, short, int, int, int, int, int, int, float, boolean) - Static method in class org.jmol.render.TextRenderer
showConsole(boolean) - Method in class org.jmol.viewer.Viewer
showContourLines - Variable in class org.jmol.shape.Mesh
showEditor(String[]) - Method in class org.jmol.viewer.Viewer
showfrank - Static variable in class org.jmol.script.T
showFrankMenu() - Method in class org.jmol.popup.JmolGenericPopup
showFrankMenu() - Method in class org.jmol.popup.JmolPopup
showGridInfo() - Method in class org.jmol.jvxl.readers.VolumeDataReader
showHash(SB, String) - Method in class org.jmol.viewer.ChimeMessenger
  #xxxx command output
showHash(SB, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
showhiddenselectionhalos - Static variable in class org.jmol.script.T
showHiddenSelectionHalos - Variable in class org.jmol.viewer.GlobalSettings
showHide(boolean) - Method in class org.jmol.shape.Measures
showHideM(Measurement, boolean) - Method in class org.jmol.shape.Measures
showhydrogens - Static variable in class org.jmol.script.T
showHydrogens - Variable in class org.jmol.viewer.GlobalSettings
showHydrogens - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
showImage(String, Object) - Method in class org.jmol.viewer.StatusManager
  called by Viewer.loadImageData to pop up a window with an image in it
showInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
showKey - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
showkeystrokes - Static variable in class org.jmol.script.T
showKeyStrokes - Variable in class org.jmol.viewer.GlobalSettings
showmeasurements - Static variable in class org.jmol.script.T
showMeasurements - Variable in class org.jmol.viewer.GlobalSettings
showMeasurements - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
showModVecs - Variable in class org.jmol.renderspecial.VectorsRenderer
showmodvecs - Static variable in class org.jmol.script.T
showModVecs - Variable in class org.jmol.viewer.GlobalSettings
showMoleculesAndOrbitals - Static variable in class org.openscience.jmol.app.webexport.WebExport
showMultipleBonds - Variable in class org.jmol.render.SticksRenderer
showmultiplebonds - Static variable in class org.jmol.script.T
showMultipleBonds - Variable in class org.jmol.viewer.GlobalSettings
shownavigationpointalways - Static variable in class org.jmol.script.T
showNavigationPointAlways - Variable in class org.jmol.viewer.GlobalSettings
showNumbers - Variable in class org.jmol.renderspecial.PolyhedraRenderer
showNumbers - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
showPaintTime - Variable in class org.jmol.applet.Jmol
showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
showPlugin(String, String, Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
showPoints - Variable in class org.jmol.shape.Mesh
showPovrayPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Show a file selector when the savePath button is pressed.
showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  Shows the properties in the propertiesPane of the AtomSetChooser window
showRebondTimes - Variable in class org.jmol.modelset.ModelSet
showSaveDialog(Component, JFileChooser, File) - Method in class org.jmol.dialog.Dialog
showSavePathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Show a file selector when the savePath button is pressed.
showscript - Static variable in class org.jmol.script.T
showSelected - Variable in class org.jmol.viewer.Viewer
showSliceBoundaryPlanes(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
showString(String) - Method in class org.jmol.script.ScriptEval
showString(String) - Method in class org.jmol.scriptext.ScriptExt
showString(String, boolean) - Method in class org.jmol.viewer.Viewer
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptError
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptEval
showSymop(Object) - Method in class org.jmol.modelkit.ModelKitPopup
showSymopInfo - Variable in class org.jmol.modelkit.ModelKitPopup
showTimeout(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
showTimeout(String) - Method in class org.jmol.viewer.Viewer
showTimes(int, int, Graphics) - Method in class org.jmol.applet.Jmol
showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
showTiming - Variable in class org.jmol.jvxl.readers.Parameters
showtiming - Static variable in class org.jmol.script.T
showTiming - Variable in class org.jmol.viewer.GlobalSettings
showTrace - Variable in class org.jmol.util.Vibration
showTriangles - Variable in class org.jmol.render.MeshRenderer
showTriangles - Variable in class org.jmol.shape.Mesh
showunitcell - Static variable in class org.jmol.script.T
showunitcelldetails - Static variable in class org.jmol.script.T
showUnitCellDetails - Variable in class org.jmol.viewer.GlobalSettings
showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
showUrl(String) - Method in class org.jmol.api.JmolViewer
showUrl(String) - Method in class org.jmol.util.GenericApplet
showUrl(String) - Method in class org.jmol.viewer.StatusManager
showUrl(String) - Method in class org.jmol.viewer.Viewer
showUrl(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
showXtalSymmetry() - Method in class org.jmol.modelkit.ModelKitPopup
  Draw the symmetry element
showZBuffer() - Method in class org.jmol.g3d.PixelatorShaded
sidechain - Static variable in class org.jmol.script.T
siestaContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
SiestaReader - Class in org.jmol.adapter.readers.xtal
  SIESTA http://www.icmab.es/siesta/
SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
sigma - Variable in class org.jmol.adapter.readers.cif.MSRdr
sigma - Variable in class org.jmol.jvxl.readers.Parameters
sigma - Static variable in class org.jmol.script.T
sigma - Variable in class org.jmol.symmetry.SymmetryOperation
sigma - Variable in class org.jmol.util.ModulationSet
sign - Static variable in class org.jmol.script.T
sign(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Just a simple signum for integers
SignedOnly - Variable in class org.jmol.popup.GenericPopup
signFactor - Variable in class org.jmol.modelset.TickInfo
silent - Variable in class org.jmol.minimize.forcefield.Calculations
silent - Static variable in class org.jmol.script.T
SILVER - Static variable in class org.jmol.util.C
SIMPLE_LINE - Static variable in class org.jmol.shapecgo.CGOMesh
simpleCage - Variable in class org.jmol.modelset.Model
SimpleEdge - Interface in org.jmol.util
  minimal bond interface for SMILES and CIP
simpleEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, Lst<P3>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
SimpleMarchingCubesOld() - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
SimpleNode - Interface in org.jmol.util
  Just the bare minimum for CIP, and non-BioSMILES
simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
SimpleUnitCell - Class in org.jmol.util
  general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
SimpleUnitCell() - Constructor for class org.jmol.util.SimpleUnitCell
simplify_display_lists - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SIMULATION_PROTOCOL - Static variable in class org.jmol.viewer.FileManager
simulationPhase - Variable in class org.jmol.multitouch.ActionManagerMT
simulator - Variable in class org.jmol.multitouch.ActionManagerMT
sin - Static variable in class org.jmol.script.T
sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
sinBeta - Variable in class org.jmol.util.SimpleUnitCell
sinGamma - Variable in class org.jmol.util.SimpleUnitCell
SINGLE - Static variable in class org.jmol.viewer.binding.Binding
single_image - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SINGLE_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
singleAtomID - Static variable in class org.jmol.adapter.readers.cif.CifReader
SingleModelOnly - Variable in class org.jmol.popup.JmolPopup
SinglePointGesture - Class in org.jmol.multitouch.sparshui
  SINGLE_POINT_GESTURE only passes single-touch gestures.
SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
sinPhi - Variable in class org.jmol.g3d.CylinderRenderer
site() - Method in class org.jmol.adapter.readers.pdb.PdbReader
site - Static variable in class org.jmol.script.T
SITE_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
SITE_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
SITE_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
SITE_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
SITE_MULT - Static variable in class org.jmol.adapter.readers.cif.CifReader
SITE_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
siteScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
sixdots - Static variable in class org.jmol.render.FontLineShapeRenderer
size - Variable in class org.jmol.adapter.readers.pymol.JmolObject
size - Variable in class org.jmol.g3d.TextRenderer
size - Static variable in class org.jmol.script.T
sizeOf(T) - Static method in class org.jmol.script.SV
sizes - Static variable in class org.jmol.shapecgo.CGOMesh
sizes2D - Static variable in class org.jmol.shapecgo.CGOMesh
skew() - Method in class org.jmol.util.Tensor
  a measure of asymmetry.
skip(long) - Method in class org.openscience.jvxl.MonitorInputStream
skipAtomSet(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
skipComments(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
skipData(int) - Method in class org.jmol.jvxl.readers.BCifDensityReader
skipData(int) - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
skipData(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
skipData(int) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
skipData(int) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
skipData(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
skipData(int) - Method in class org.jmol.jvxl.readers.XsfReader
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
skipFloats(int) - Method in class org.jmol.adapter.readers.more.MdCrdReader
skipHeader() - Method in class org.jmol.jvxl.readers.MsmsReader
skipModel() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
skipMOs - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
skipping - Variable in class org.jmol.adapter.readers.cif.CifReader
skipping - Variable in class org.jmol.script.ScriptMathProcessor
skipPoints(int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
skipTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
skipTo(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
skipTo(String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
skipTo(String) - Method in class org.jmol.jvxl.readers.XmlReader
skipTo(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
skipToNextAtom() - Method in class org.jmol.adapter.readers.xtal.JanaReader
skipVoxels(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
slab - Variable in class org.jmol.export.Export3D
slab - Variable in class org.jmol.g3d.SphereRenderer
slab - Static variable in class org.jmol.script.T
slab - Variable in class org.jmol.thread.MoveToThread
slab - Variable in class org.jmol.util.GData
slabbing - Variable in class org.jmol.render.SticksRenderer
slabbingObject - Variable in class org.jmol.shape.Mesh
slabbingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSlicer
  "slabs" an isosurface into the first Brillouin zone moving points as necessary.
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSurface
slabByAtom - Variable in class org.jmol.render.SticksRenderer
slabbyatom - Static variable in class org.jmol.script.T
slabByAtom - Variable in class org.jmol.viewer.GlobalSettings
slabbymolecule - Static variable in class org.jmol.script.T
slabByMolecule - Variable in class org.jmol.viewer.GlobalSettings
slabByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
slabByPixels(int) - Method in class org.jmol.viewer.Viewer
slabColix - Variable in class org.jmol.util.MeshSurface
slabData - Variable in class org.jmol.shapespecial.Draw
slabDepthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
slabDepthByPixels(int) - Method in class org.jmol.viewer.Viewer
slabDepthChanged() - Method in class org.jmol.viewer.TransformManager
slabenabled - Static variable in class org.jmol.script.T
slabEnabled - Variable in class org.jmol.viewer.TransformManager
slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
slabInternal(P4, boolean) - Method in class org.jmol.viewer.TransformManager
slabIsosurface(Lst<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
slabMeshType - Variable in class org.jmol.util.MeshSurface
slabOptions - Variable in class org.jmol.util.MeshSurface
slabPercentSetting - Variable in class org.jmol.viewer.TransformManager
slabPlane - Variable in class org.jmol.viewer.TransformManager
slabPlaneOffset - Variable in class org.jmol.jvxl.readers.Parameters
slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSlicer
slabPolygonsList(Lst<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
slabrange - Static variable in class org.jmol.script.T
slabRange - Variable in class org.jmol.viewer.TransformManager
slabReset() - Method in class org.jmol.viewer.TransformManager
slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
slabValue - Variable in class org.jmol.jvxl.data.JvxlData
slabValue - Variable in class org.jmol.viewer.TransformManager
slabZ - Variable in class org.jmol.export.___Exporter
slaterArray - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
slaterCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
SlaterData - Class in org.jmol.quantum
SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
SlaterReader - Class in org.jmol.adapter.readers.quantum
SlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter - Class in org.jmol.adapter.readers.quantum
SlaterReader.SlaterSorter - Class in org.jmol.adapter.readers.quantum
slaters - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
slaters - Variable in class org.jmol.quantum.MOCalculation
SlaterSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
sleepTime - Variable in class org.jmol.thread.JmolThread
sLeft - Variable in class org.jmol.g3d.HermiteRenderer
slen - Variable in class org.jmol.script.ScriptParam
slen - Variable in class org.jmol.scriptext.ScriptExt
Slice - Class in org.openscience.jmol.app.surfacetool
Slice() - Constructor for class org.openscience.jmol.app.surfacetool.Slice
slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
slice_dynamic_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
slice_dynamic_grid_resolution - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
slice_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
slice_height_map - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
slice_height_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
slice_track_camera - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sliceObject(String, int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
slicer - Variable in class org.jmol.util.MeshCapper
  source of edges; consumer of triangles
slicer - Variable in class org.jmol.util.MeshSurface
slicer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
slicerFrame - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
sliceSelected() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
SLIDE_ZOOM_X_PERCENT - Static variable in class org.jmol.viewer.ActionManager
slider - Variable in class org.jmol.dialog.Dialog.QualityListener
Slider(float, float) - Constructor for class org.jmol.thread.MoveToThread.Slider
sliderPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
SLIM - Static variable in class org.jmol.util.Shader
slm - Variable in class org.jmol.viewer.Viewer
SLOP - Static variable in class org.jmol.util.SimpleUnitCell
SLOP1 - Static variable in class org.jmol.util.SimpleUnitCell
slope - Variable in class org.jmol.g3d.LineRenderer
slopeKey - Variable in class org.jmol.g3d.LineRenderer
slow_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sm - Variable in class org.jmol.modelset.ModelSet
sm - Variable in class org.jmol.script.ScriptEval
sm - Variable in class org.jmol.scriptext.SmilesExt
sm - Variable in class org.jmol.smiles.SmilesGenerator
sm - Variable in class org.jmol.viewer.Viewer
SMALL_RING_MAX - Static variable in class org.jmol.symmetry.CIPChirality
  maximum ring size that can have a double bond with no E/Z designation; also used for identifying aromatic rings and bridgehead nitrogens
smallmoleculemaxatoms - Static variable in class org.jmol.script.T
smallMoleculeMaxAtoms - Variable in class org.jmol.viewer.GlobalSettings
smap - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
smartaromatic - Static variable in class org.jmol.script.T
smartAromatic - Variable in class org.jmol.viewer.GlobalSettings
SmarterJmolAdapter - Class in org.jmol.adapter.smarter
SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
smarts - Variable in class org.jmol.shapespecial.Polyhedron
smartsCode - Variable in class org.jmol.minimize.forcefield.AtomType
smiles - Static variable in class org.jmol.script.T
smiles - Variable in class org.jmol.shapespecial.Polyhedron
smiles - Variable in class org.jmol.symmetry.CIPDataSmiles
smiles2dimageformat - Static variable in class org.jmol.script.T
SMILES_AROMATIC_DEFINED - Static variable in class org.jmol.viewer.JC
  AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.
SMILES_AROMATIC_DOUBLE - Static variable in class org.jmol.viewer.JC
  AROMATIC_DOUBLE allows a distinction between single and double, as for example is necessary to distinguish between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing)
SMILES_AROMATIC_MMFF94 - Static variable in class org.jmol.viewer.JC
  AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.
SMILES_AROMATIC_PLANAR - Static variable in class org.jmol.viewer.JC
  AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)
SMILES_AROMATIC_STRICT - Static variable in class org.jmol.viewer.JC
  AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds
SMILES_BONDS - Static variable in class org.jmol.smiles.SmilesBond
SMILES_FIRST_MATCH_ONLY - Static variable in class org.jmol.viewer.JC
SMILES_GEN_ATOM_COMMENT - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_COMMENT - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_COV_CROSSLINK - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_HH_CROSSLINK - Static variable in class org.jmol.viewer.JC
SMILES_GEN_BIO_NOCOMMENTS - Static variable in class org.jmol.viewer.JC
SMILES_GEN_EXPLICIT_H - Static variable in class org.jmol.viewer.JC
SMILES_GEN_POLYHEDRAL - Static variable in class org.jmol.viewer.JC
SMILES_GEN_TOPOLOGY - Static variable in class org.jmol.viewer.JC
SMILES_GROUP_BY_MODEL - Static variable in class org.jmol.viewer.JC
SMILES_IGNORE_ATOM_CLASS - Static variable in class org.jmol.viewer.JC
SMILES_IGNORE_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
SMILES_INVERT_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
SMILES_MAP_UNIQUE - Static variable in class org.jmol.viewer.JC
SMILES_NO_AROMATIC - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_OPENSMARTS - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_OPENSMILES - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_SMARTS - Static variable in class org.jmol.viewer.JC
SMILES_TYPE_SMILES - Static variable in class org.jmol.viewer.JC
SmilesAromatic - Class in org.jmol.smiles
SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
SmilesAtom - Class in org.jmol.smiles
  This class represents an atom in a `SmilesMolecule`.
SmilesAtom() - Constructor for class org.jmol.smiles.SmilesAtom
SmilesBond - Class in org.jmol.smiles
  Bond in a SmilesMolecule
SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
  SmilesBond constructor
smilesExt - Variable in class org.jmol.script.ScriptExpr
SmilesExt - Class in org.jmol.scriptext
SmilesExt() - Constructor for class org.jmol.scriptext.SmilesExt
SmilesGenerator - Class in org.jmol.smiles
  Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
SmilesMatcher - Class in org.jmol.smiles
  Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
smilesMatcher - Variable in class org.jmol.viewer.Viewer
SmilesMatcherInterface - Interface in org.jmol.api
SmilesMeasure - Class in org.jmol.smiles
SmilesMeasure(SmilesSearch, int, int, boolean, float[]) - Constructor for class org.jmol.smiles.SmilesMeasure
SmilesParser - Class in org.jmol.smiles
  Parses a SMILES string or SMARTS pattern to create a `SmilesSearch`.
SmilesParser(boolean, boolean) - Constructor for class org.jmol.smiles.SmilesParser
SmilesRing - Class in org.jmol.smiles
  Ring of (tentatively) aromatic nodes and edges
SmilesRing(int, BS, Lst<Edge>, boolean) - Constructor for class org.jmol.smiles.SmilesRing
SmilesRingSet - Class in org.jmol.smiles
  a list of fused rings
SmilesRingSet() - Constructor for class org.jmol.smiles.SmilesRingSet
SmilesSearch - Class in org.jmol.smiles
  A class to build and carry out a SMILES or SMARTS match
SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
smilesStereo - Variable in class org.jmol.smiles.SmilesGenerator
SmilesStereo - Class in org.jmol.smiles
  This class relates to stereochemical issues
SmilesStereo(int, int, int, String, String) - Constructor for class org.jmol.smiles.SmilesStereo
smilesurlformat - Static variable in class org.jmol.script.T
smilesUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
smooth_color_triangle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
smooth_half_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
smoothingPower - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
Snn - Static variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
solid - Static variable in class org.jmol.script.T
solidOnly - Variable in class org.jmol.export.___Exporter
solvent - Static variable in class org.jmol.script.T
solvent_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
solvent_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
solvent_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
solventAccessible - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
solventDistance(float, float, float, float, float, float) - Method in class org.jmol.jvxl.readers.IsoSolventReader
solventExtendedAtomRadius - Variable in class org.jmol.jvxl.readers.Parameters
solventOn - Variable in class org.jmol.viewer.GlobalSettings
solventprobe - Static variable in class org.jmol.script.T
solventproberadius - Static variable in class org.jmol.script.T
solventProbeRadius - Variable in class org.jmol.viewer.GlobalSettings
solventRadius - Variable in class org.jmol.jvxl.readers.Parameters
someModelsAreModulated - Variable in class org.jmol.modelset.ModelLoader
someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelSet
someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelSet
someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelSet
someModelsHaveUnitcells - Variable in class org.jmol.modelset.ModelLoader
sort(int) - Method in class org.jmol.bspt.Leaf
sort - Static variable in class org.jmol.g3d.Graphics3D
Sort(int, String) - Constructor for class org.jmol.script.SV.Sort
sort - Static variable in class org.jmol.script.T
sortAndNormalize() - Method in class org.jmol.util.Tensor
  The expression: |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso| simply sorts the values from largest to smallest or smallest to largest, depending upon the direction of the asymmetry, always setting the last value to be the farthest from the mean.
sortAssemblyModels() - Method in class org.jmol.adapter.readers.cif.MMCifReader
  issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...
sortBonds(SimpleNode, SimpleNode, P3) - Method in class org.jmol.smiles.SmilesGenerator
sortBondsByStereo(SimpleNode, SimpleNode, T3, SimpleEdge[], V3) - Method in class org.jmol.smiles.SmilesStereo
  Sort bond array as ccw rotation around the axis connecting the atom and the reference point (polyhedron center) as seen from outside the polyhedron looking in.
sorter - Variable in class org.jmol.smiles.SmilesStereo
sortInorganic(SimpleNode, Lst<Edge>, VTemp) - Method in class org.jmol.smiles.SmilesGenerator
  We must sort the bond vector such that a diaxial pair is first and last.
sortIso - Variable in class org.jmol.util.Tensor
sortMapArray(String) - Method in class org.jmol.script.SV
sortMOs() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
sortMOs() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
sortOop(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
  sorts coefficients by atomic number for speed later
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.SlaterReader
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrReverse(int) - Method in class org.jmol.script.SV
SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
sortSubstituents(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  Deep-Sort the substituents of an atom, setting the node's atoms[] and priorities[] arrays.
source - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
sourceIndices - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
sourcePNGJ - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
sources - Variable in class org.jmol.util.MeshSlicer
SOUTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
sp - Variable in class org.jmol.bspt.CubeIterator
SP - Static variable in class org.jmol.quantum.QS
SP_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
spacebeforesquare - Static variable in class org.jmol.script.T
spacefill - Static variable in class org.jmol.script.T
spacegroup - Static variable in class org.jmol.script.T
SpaceGroup - Class in org.jmol.symmetry
SpaceGroup(int, String, boolean) - Constructor for class org.jmol.symmetry.SpaceGroup
spaceGroup - Variable in class org.jmol.symmetry.Symmetry
spaceGroupName - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
SPACES - Static variable in class org.jmol.util.JSONWriter
span() - Method in class org.jmol.util.Tensor
  width of the signal; |e2 - e0|
spardirCache - Variable in class org.jmol.viewer.FileManager
SparseArray(String) - Constructor for class org.jmol.adapter.writers.QCJSONWriter.SparseArray
SpartanArchive - Class in org.jmol.adapter.readers.spartan
SpartanArchive(BasisFunctionReader, String, String, int) - Constructor for class org.jmol.adapter.readers.spartan.SpartanArchive
spartanArchive - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
spartanBinaryContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
spartanContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
spartanDoc - Variable in class org.jmol.viewer.FileManager
spartanFileList(String, String) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  Special loading for file directories.
spartanGetObjectAsSections(String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
  delivers file contents and directory listing for a ZIP/JAR file into sb
SpartanInputReader - Class in org.jmol.adapter.readers.spartan
SpartanInputReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanInputReader
SpartanReader - Class in org.jmol.adapter.readers.spartan
SpartanReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanReader
spartanSmolLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
SpartanSmolReader - Class in org.jmol.adapter.readers.spartan
SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanSmolReader
SpartanUtil - Class in org.jmol.adapter.readers.spartan
  A class to isolate Spartan file reading methods from the rest of Jmol.
SpartanUtil() - Constructor for class org.jmol.adapter.readers.spartan.SpartanUtil
spartanUtil() - Method in class org.jmol.viewer.FileManager
  An isolated class to retrieve Spartan file data from compound documents, zip files, and directories
spec_alternate - Static variable in class org.jmol.script.T
spec_atom - Static variable in class org.jmol.script.T
spec_chain - Static variable in class org.jmol.script.T
spec_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spec_direct - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spec_direct_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spec_model - Static variable in class org.jmol.script.T
spec_model2 - Static variable in class org.jmol.script.T
spec_name_pattern - Static variable in class org.jmol.script.T
spec_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spec_reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spec_resid - Static variable in class org.jmol.script.T
spec_seqcode - Static variable in class org.jmol.script.T
spec_seqcode_range - Static variable in class org.jmol.script.T
Special - Variable in class org.jmol.popup.JmolPopup
SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.C
specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
specialAtomNames - Static variable in class org.jmol.modelset.Group
specialAtomNames - Static variable in class org.jmol.modelsetbio.BioResolver
specialLabel - Variable in class org.jmol.shape.Hover
specialposition - Static variable in class org.jmol.script.T
specialTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
specular - Static variable in class org.jmol.script.T
specular_intensity - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
specularexponent - Static variable in class org.jmol.script.T
specularExponent - Variable in class org.jmol.util.Shader
specularFactor - Variable in class org.jmol.util.Shader
specularOn - Variable in class org.jmol.util.Shader
specularpercent - Static variable in class org.jmol.script.T
specularPercent - Variable in class org.jmol.util.Shader
specularpower - Static variable in class org.jmol.script.T
specularPower - Variable in class org.jmol.util.Shader
SPG - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
sphere - Static variable in class org.jmol.script.T
SPHERE - Static variable in class org.jmol.shapecgo.CGOMesh
sphere - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
  bond distance from the root atom to this atom
sphere - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
sphere3d - Variable in class org.jmol.g3d.Graphics3D
sphere_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_point_max_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_point_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_radiusAngstroms - Variable in class org.jmol.jvxl.readers.IsoShapeReader
sphere_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphere_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sphereColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
sphereNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
spherePoint - Variable in class org.jmol.modelkit.ModelKitPopup
SphereRenderer - Class in org.jmol.g3d
  Implements high performance rendering of shaded spheres.
SphereRenderer(Graphics3D) - Constructor for class org.jmol.g3d.SphereRenderer
sphereScale - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
sphereShadeIndexes - Variable in class org.jmol.util.Shader
sphereShapeCache - Variable in class org.jmol.util.Shader
sphereTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
sphericalDValues - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
spheroid_fill - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spheroid_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spheroid_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
spin - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
spin - Static variable in class org.jmol.script.T
SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
SPIN_SAW_AX - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
SPIN_SAW_AY - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
SPIN_SAW_AZ - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
SPIN_SAW_C - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
SPIN_SAW_W - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
SPIN_SPEC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
spine - Static variable in class org.jmol.script.T
spinfps - Static variable in class org.jmol.script.T
spinFps - Variable in class org.jmol.viewer.TransformManager
spinIsGesture - Variable in class org.jmol.viewer.TransformManager
spinOn - Variable in class org.jmol.viewer.TransformManager
spinOn - Variable in class org.openscience.jmol.app.webexport.JmolInstance
SpinOnWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
spinOp - Variable in class org.jmol.util.ModulationSet
  the spin operation for this atom: +1/0/-1
SpinThread - Class in org.jmol.thread
SpinThread() - Constructor for class org.jmol.thread.SpinThread
spinThread - Variable in class org.jmol.viewer.TransformManager
spinx - Static variable in class org.jmol.script.T
spinX - Variable in class org.jmol.viewer.TransformManager
spinXYBy(int, int, float) - Method in class org.jmol.viewer.TransformManager
spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
spiny - Static variable in class org.jmol.script.T
spinY - Variable in class org.jmol.viewer.TransformManager
spinz - Static variable in class org.jmol.script.T
spinZ - Variable in class org.jmol.viewer.TransformManager
splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
Splash - Class in org.openscience.jmol.app.jmolpanel
Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
Splash.WindowListener - Class in org.openscience.jmol.app.jmolpanel
splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
splashImage - Variable in class org.openscience.jmol.app.jmolpanel.Splash
SplashInterface - Interface in org.openscience.jmol.app
split(String, int) - Static method in class org.jmol.adapter.smarter.Resolver
split - Variable in class org.jmol.awtjs.swing.JSplitPane
split - Static variable in class org.jmol.script.T
splitCommandLine(String) - Static method in class org.jmol.console.GenericConsole
  separate a command line into three sections: prefix....;cmd ........
sppm - Variable in class org.jmol.render.LabelsRenderer
sprintf(String, SV) - Static method in class org.jmol.script.SV
sprintf(String, SV, Object[], int[], float[], double[], boolean, boolean, boolean) - Static method in class org.jmol.script.SV
sptRecords - Static variable in class org.jmol.adapter.smarter.Resolver
sqrt - Static variable in class org.jmol.script.T
sqrt3_2 - Static variable in class org.jmol.modelset.AtomCollection
SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesStereo
squareCount - Variable in class org.jmol.script.ScriptMathProcessor
squared - Static variable in class org.jmol.script.T
sr - Variable in class org.jmol.jvxl.data.VolumeData
sr - Variable in class org.jmol.jvxl.readers.AtomDataReader
  solvent radius
sRight - Variable in class org.jmol.g3d.HermiteRenderer
ss_helix_phi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_helix_phi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_helix_phi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_helix_psi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_helix_psi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_helix_psi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_strand_phi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_strand_phi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_strand_phi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_strand_psi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_strand_psi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ss_strand_psi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
ssbond - Static variable in class org.jmol.script.T
ssbondsBackbone - Variable in class org.jmol.render.SticksRenderer
ssbondsbackbone - Static variable in class org.jmol.script.T
ssbondsBackbone - Variable in class org.jmol.viewer.GlobalSettings
SSet(BS) - Constructor for class org.jmol.jvxl.data.MeshData.SSet
ssMapAtom - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
ssMapSeq - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
SSTYPE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
st - Variable in class org.jmol.script.ScriptParam
st - Variable in class org.jmol.scriptext.ScriptExt
stack - Variable in class org.jmol.adapter.readers.pymol.PickleReader
stack - Variable in class org.jmol.bspt.CubeIterator
STAND_ALONE - Static variable in class org.openscience.jmol.app.webexport.WebExport
STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
standardGroupList - Static variable in class org.jmol.modelset.Group
standardLevel - Static variable in class org.jmol.util.Geodesic
  3 levels, 0 through 3
standardVector - Variable in class org.jmol.renderspecial.VectorsRenderer
star - Static variable in class org.jmol.script.T
Stars - Class in org.jmol.shape
Stars() - Constructor for class org.jmol.shape.Stars
StarsRenderer - Class in org.jmol.render
StarsRenderer() - Constructor for class org.jmol.render.StarsRenderer
START - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
start(Viewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
start(Viewer) - Method in class org.jmol.console.AppletConsole
start(Viewer) - Method in class org.jmol.consolejs.AppletConsole
start() - Method in class org.jmol.thread.JmolThread
start - Variable in class org.jmol.thread.MoveToThread.Slider
start() - Method in class org.openscience.jmol.app.InputScannerThread
start(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
start(JFrame, Viewer, Map<String, Object>) - Method in interface org.openscience.jmol.app.JmolPlugin
startByteArrayReaderThread() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
startChainID - Variable in class org.jmol.adapter.smarter.Structure
startChainStr - Variable in class org.jmol.adapter.smarter.Structure
startCommandWatcher(boolean) - Method in interface org.jmol.api.JmolScriptManager
startCommandWatcher(boolean) - Method in class org.jmol.script.ScriptManager
startConsoleReaderThread(InputStream) - Method in class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
startCoord - Variable in class org.jmol.shapespecial.Dipoles
startDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
startedByCommandThread - Variable in class org.jmol.script.ScriptQueueThread
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlHandler
startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
startHoverWatcher(boolean) - Method in class org.jmol.appletjs.Jmol
startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
startHoverWatcher(boolean) - Method in class org.jmol.viewer.Viewer
startIndexPending - Variable in class org.jmol.renderbio.RocketRenderer
startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
startJmol(JmolApp) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
startMinimization() - Method in class org.jmol.minimize.Minimizer
startNBO(String) - Method in class org.jmol.viewer.Viewer
startNBO(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
startPaintClock() - Method in class org.jmol.applet.Jmol
startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
startPlugin(String) - Method in class org.jmol.viewer.Viewer
  startup -U nbo option
startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
startScriptQueue(boolean) - Method in class org.jmol.script.ScriptManager
startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
startServerService() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
startService(int, JsonNioClient, Viewer, String, int) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
startService(int, JsonNioClient, Viewer, String, int) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
startSparshUIService(boolean) - Method in class org.jmol.multitouch.ActionManagerMT
startSpinningAxis(T3, T3, boolean) - Method in class org.jmol.viewer.Viewer
startTime - Variable in class org.jmol.applet.AppletWrapper
startTime - Variable in class org.jmol.thread.JmolThread
startTimer(String) - Static method in class org.jmol.util.Logger
startTrace(int) - Method in class org.jmol.util.Vibration
startupDimension - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
startupHeight - Variable in class org.openscience.jmol.app.JmolApp
startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
startupWidth - Variable in class org.openscience.jmol.app.JmolApp
startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
startViewer(JmolViewer, SplashInterface, boolean) - Method in class org.openscience.jmol.app.JmolApp
starwidth - Static variable in class org.jmol.script.T
starWidth - Variable in class org.jmol.viewer.GlobalSettings
state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
state - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
state - Variable in class org.jmol.jvxl.readers.Parameters
state - Variable in class org.jmol.modelkit.ModelKitPopup
state - Static variable in class org.jmol.script.T
STATE_BITS_SYM_EDIT - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_BITS_SYM_VIEW - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_BITS_UNITCELL - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_BITS_XTAL - Static variable in class org.jmol.modelkit.ModelKitPopup
state_counter_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_FREQ - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_INPUT - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_INPUT - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
STATE_INPUT_FROM - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_MOLECULAR - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_NONE - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_OPT_FINAL - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_OPT_POINT - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_OUTPUT - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
STATE_SYM_APPLYFULL - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_SYM_APPLYLOCAL - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_SYM_NONE - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_SYM_RETAINLOCAL - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_SYM_SHOW - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
STATE_UNITCELL_EXTEND - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_UNITCELL_PACKED - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_UNKNOWN - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.JC
STATE_WAVEFUNCTION - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
STATE_XTALEDIT - Static variable in class org.jmol.modelkit.ModelKitPopup
STATE_XTALVIEW - Static variable in class org.jmol.modelkit.ModelKitPopup
stateButton - Variable in class org.jmol.console.GenericConsole
stateButton - Variable in class org.jmol.console.ScriptEditor
StateButton - Variable in class org.openscience.jmol.app.webexport.Test
stateChanged(ChangeEvent) - Method in class org.jmol.dialog.Dialog.QualityListener
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.webexport.PopInJmol
stateCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
stateCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
StateCreator - Class in org.jmol.viewer
  StateCreator handles all aspects of working with the "state" as generally defined, including -- creating the state script -- general output, including logging -- handling undo/redo -- processing SYNC directives Called by reflection only; all state generation script here, for modularization in JavaScript
StateCreator() - Constructor for class org.jmol.viewer.StateCreator
StateManager - Class in org.jmol.viewer
StateManager(Viewer) - Constructor for class org.jmol.viewer.StateManager
statement - Variable in class org.jmol.script.ScriptContext
statementAsString(Viewer, T[], int, boolean) - Static method in class org.jmol.script.ScriptEval
statementLength - Variable in class org.jmol.script.ScriptContext
StateScript - Class in org.jmol.modelset
StateScript(int, String, BS, BS, BS, String, boolean) - Constructor for class org.jmol.modelset.StateScript
stateScripts - Variable in class org.jmol.modelset.ModelSet
stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
stateSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
static_singletons - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
staticFunctions - Static variable in class org.jmol.viewer.Viewer
staticGetAtomSetCollection(AtomSetCollectionReader) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
staticGetAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
  The primary file or string reader -- returns just the reader now
stats() - Method in class org.jmol.bspt.Bspf
stats() - Method in class org.jmol.bspt.Bspt
  prints some simple stats to stdout
status - Variable in class org.jmol.thread.TimeoutThread
status - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
status - Variable in class org.openscience.jmol.app.jmolpanel.Splash
status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
StatusBar - Class in org.openscience.jmol.app.jmolpanel
StatusBar() - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
statusForm - Variable in class org.jmol.util.GenericApplet
statusList - Variable in class org.jmol.viewer.StatusManager
statusListener - Variable in class org.jmol.awt.FileDropper
statusListener - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
StatusListener - Class in org.openscience.jmol.app.jmolpanel
StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
StatusManager - Class in org.jmol.viewer
  The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
StatusManager(Viewer) - Constructor for class org.jmol.viewer.StatusManager
statusPtr - Variable in class org.jmol.viewer.StatusManager
statusreporting - Static variable in class org.jmol.script.T
statusReporting - Variable in class org.jmol.viewer.GlobalSettings
STATUSSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
statusText - Variable in class org.jmol.util.GenericApplet
statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
statusTextarea - Variable in class org.jmol.util.GenericApplet
statusTop - Variable in class org.openscience.jmol.app.jmolpanel.Splash
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET - Static variable in class org.jmol.adapter.readers.quantum.GaussianReader
  Word index of atomic number in line with atom coordinates in an orientation block.
stddev - Static variable in class org.jmol.script.T
stdinchi - Static variable in class org.jmol.script.T
stdinchikey - Static variable in class org.jmol.script.T
steepestDescentInitialize(int, double) - Method in class org.jmol.minimize.forcefield.ForceField
steepestDescentTakeNSteps(int) - Method in class org.jmol.minimize.forcefield.ForceField
step - Static variable in class org.jmol.script.T
stepAxisCoordinates() - Method in class org.jmol.render.SticksRenderer
stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
stepButton - Variable in class org.jmol.console.ScriptEditor
stepButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
stepMax - Variable in class org.jmol.minimize.forcefield.ForceField
stepMinimization() - Method in class org.jmol.minimize.Minimizer
stepNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
stepPausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
stepPausedExecution() - Method in class org.jmol.script.ScriptEval
steps - Variable in class org.jmol.jvxl.readers.Parameters
steps - Variable in class org.jmol.minimize.Minimizer
steps - Variable in class org.jmol.modelset.Trajectory
STER - Enum in org.jmol.c
STER(String, boolean) - Constructor for enum org.jmol.c.STER
stereo - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stereo - Static variable in class org.jmol.script.T
stereo() - Method in class org.jmol.scriptext.CmdExt
stereo - Variable in class org.jmol.smiles.SmilesAtom
stereo - Variable in class org.jmol.smiles.SmilesSearch
stereo_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
STEREO_BOTH_EZ - Static variable in class org.jmol.symmetry.CIPChirality
STEREO_BOTH_RS - Static variable in class org.jmol.symmetry.CIPChirality
stereo_double_pump_mono - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stereo_dynamic_strength - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
STEREO_E - Static variable in class org.jmol.symmetry.CIPChirality
STEREO_M - Static variable in class org.jmol.symmetry.CIPChirality
stereo_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
STEREO_P - Static variable in class org.jmol.symmetry.CIPChirality
STEREO_R - Static variable in class org.jmol.symmetry.CIPChirality
STEREO_S - Static variable in class org.jmol.symmetry.CIPChirality
stereo_shift - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
STEREO_Z - Static variable in class org.jmol.symmetry.CIPChirality
stereoColors - Variable in class org.jmol.viewer.TransformManager
stereodegrees - Static variable in class org.jmol.script.T
stereoDegrees - Variable in class org.jmol.viewer.TransformManager
stereoDoubleDTI - Variable in class org.jmol.viewer.TransformManager
stereoDoubleFull - Variable in class org.jmol.viewer.TransformManager
stereoFrame - Variable in class org.jmol.viewer.TransformManager
stereoMode - Variable in class org.jmol.viewer.TransformManager
stereoRadians - Variable in class org.jmol.viewer.TransformManager
stereoState - Variable in class org.jmol.viewer.GlobalSettings
stereoSync - Variable in class org.jmol.viewer.StatusManager
StereoViewWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
stick_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_ball - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_ball_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_ball_ratio - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_fixed_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_good_geometry - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_h_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_nub - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_overlap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_round_nub - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stick_valence_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
Sticks - Class in org.jmol.shape
Sticks() - Constructor for class org.jmol.shape.Sticks
SticksRenderer - Class in org.jmol.render
SticksRenderer() - Constructor for class org.jmol.render.SticksRenderer
stickTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
stm - Variable in class org.jmol.viewer.Viewer
STO_EXP - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
STOP - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
stop - Static variable in class org.jmol.script.T
STOP - Static variable in class org.jmol.shapecgo.CGOMesh
stop_on_exceptions - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
stopAudio(String) - Method in class org.jmol.viewer.StatusManager
stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
stopMinimization() - Method in class org.jmol.viewer.Viewer
stopMotion() - Method in class org.jmol.viewer.TransformManager
stopPaintClock() - Method in class org.jmol.applet.Jmol
stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
stopped - Variable in class org.jmol.thread.JmolThread
stopScriptThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
stopScriptThreads() - Method in class org.jmol.script.ScriptEval
stopThread(boolean) - Method in class org.jmol.viewer.AnimationManager
STR - Enum in org.jmol.c
STR(int, int) - Constructor for enum org.jmol.c.STR
STR_SG - Static variable in class org.jmol.symmetry.SpaceGroup
  intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag
straightness - Variable in class org.jmol.modelsetbio.Monomer
straightness - Static variable in class org.jmol.script.T
STRAND_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
strandCount - Variable in class org.jmol.adapter.smarter.Structure
strandCount - Variable in class org.jmol.modelsetbio.ProteinStructure
strandCount - Variable in class org.jmol.renderbio.StrandsRenderer
strandcount - Static variable in class org.jmol.script.T
strandcountformeshribbon - Static variable in class org.jmol.script.T
strandCountForMeshRibbon - Variable in class org.jmol.viewer.GlobalSettings
strandcountforstrands - Static variable in class org.jmol.script.T
strandCountForStrands - Variable in class org.jmol.viewer.GlobalSettings
strands - Static variable in class org.jmol.script.T
Strands - Class in org.jmol.shapebio
Strands() - Constructor for class org.jmol.shapebio.Strands
strandSeparation - Variable in class org.jmol.renderbio.StrandsRenderer
StrandsRenderer - Class in org.jmol.renderbio
StrandsRenderer() - Constructor for class org.jmol.renderbio.StrandsRenderer
strAtomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
strCommand - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
strCoord(T3, boolean) - Static method in class org.jmol.symmetry.SymmetryDesc
strFormat - Variable in class org.jmol.modelset.Measurement
strFormat - Variable in class org.jmol.modelset.MeasurementData
strFormat - Variable in class org.jmol.shape.Measures
strFractionTemp - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
strID - Variable in class org.jmol.shapesurface.MolecularOrbital
string - Static variable in class org.jmol.script.T
stringAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
stringClass - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
stringCount - Variable in class org.jmol.g3d.Graphics3D
stringParameter(int) - Method in class org.jmol.script.ScriptParam
stringParameter(int) - Method in class org.jmol.scriptext.ScriptExt
stringParameterSet(int) - Method in class org.jmol.script.ScriptParam
strings - Variable in class org.jmol.g3d.Graphics3D
strings - Variable in class org.jmol.shape.Labels
stringSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
stringsResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
StringtoScriptButton - Variable in class org.openscience.jmol.app.webexport.Test
stringWidth(Object, String) - Static method in class org.jmol.awt.AwtFont
stringWidth(Font, Object, String) - Static method in class org.jmol.awtjs2d.JSFont
stringWidth(String) - Method in class org.jmol.modelset.Text
stringWidth(String) - Method in class org.jmol.util.Font
stripPath(String) - Static method in class org.jmol.viewer.FileManager
strJavaVendor - Static variable in class org.jmol.viewer.Viewer
strJavaVersion - Static variable in class org.jmol.viewer.Viewer
strListValue(T) - Static method in class org.jmol.script.SV
strMeasurement - Variable in class org.jmol.modelset.Measurement
strMenuStructure - Variable in class org.jmol.popup.GenericPopup
strokeBasic - Variable in class org.jmol.awt.AwtG2D
strokeBold - Variable in class org.jmol.awt.AwtG2D
strop - Variable in class org.jmol.util.ModulationSet
  a string description of the atom's symmetry operator
strOSName - Static variable in class org.jmol.viewer.Viewer
strparam - Static variable in class org.jmol.script.T
strproperty - Static variable in class org.jmol.script.T
strSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
strucid - Static variable in class org.jmol.script.T
strucNo - Variable in class org.jmol.modelsetbio.ProteinStructure
strucno - Static variable in class org.jmol.script.T
STRUCT_CONN_ALT1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_ALT2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_ASYM1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_ASYM2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_ATOM1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_ATOM2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_COMP1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_COMP2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_ORDER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_SEQ1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_SEQ2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_SYMM1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_SYMM2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_CONN_TYPE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_REF_G1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
STRUCT_REF_G3 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
structConfFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
structConnFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
structConnList - Variable in class org.jmol.adapter.readers.cif.MMCifReader
structConnMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
structRefFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
structSheetRangeFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
structSiteFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
structure() - Method in class org.jmol.adapter.readers.pdb.PdbReader
Structure - Class in org.jmol.adapter.smarter
Structure(int, STR, STR, String, int, int, BS[]) - Constructor for class org.jmol.adapter.smarter.Structure
structure - Variable in class org.jmol.adapter.smarter.StructureIterator
Structure - Interface in org.jmol.modelset
structure - Variable in class org.jmol.popup.PopupResource
structure - Static variable in class org.jmol.script.T
structureContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
structureContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
structureCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
structureCount - Variable in class org.jmol.adapter.smarter.StructureIterator
structureID - Variable in class org.jmol.adapter.smarter.Structure
structureID - Variable in class org.jmol.modelsetbio.ProteinStructure
StructureIterator - Class in org.jmol.adapter.smarter
StructureIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.StructureIterator
structureList - Variable in class org.jmol.modelsetbio.AminoPolymer
structureList - Variable in class org.jmol.viewer.GlobalSettings
structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
structures - Variable in class org.jmol.adapter.smarter.StructureIterator
structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
structureTainted - Variable in class org.jmol.modelset.Model
structureType - Variable in class org.jmol.adapter.smarter.Structure
structureTypes - Variable in class org.jmol.renderbio.BioShapeRenderer
strutdefaultradius - Static variable in class org.jmol.script.T
strutDefaultRadius - Variable in class org.jmol.viewer.GlobalSettings
strutlengthmaximum - Static variable in class org.jmol.script.T
strutLengthMaximum - Variable in class org.jmol.viewer.GlobalSettings
strutPoint(int, int, int) - Static method in class org.jmol.modelsetbio.BioExt
struts - Static variable in class org.jmol.script.T
struts() - Method in class org.jmol.scriptext.CmdExt
strutsmultiple - Static variable in class org.jmol.script.T
strutsMultiple - Variable in class org.jmol.viewer.GlobalSettings
strutspacing - Static variable in class org.jmol.script.T
strutSpacing - Variable in class org.jmol.viewer.GlobalSettings
stub - Variable in class org.jmol.console.JmolConsole.FileChecker
sType - Variable in class org.jmol.minimize.MinAtom
sub(double[], double[], V3d) - Static method in class org.jmol.minimize.Util
sub - Static variable in class org.jmol.script.T
subAtoms - Variable in class org.jmol.smiles.SmilesAtom
sublistAt(Lst<Object>, int...) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
SUBMODE_NESTED - Static variable in class org.jmol.smiles.SmilesSearch
SUBMODE_OR - Static variable in class org.jmol.smiles.SmilesSearch
SUBMODE_RINGCHECK - Static variable in class org.jmol.smiles.SmilesSearch
subsearch(SmilesSearch, int) - Method in class org.jmol.smiles.SmilesSearch
subSearches - Variable in class org.jmol.smiles.SmilesSearch
subset - Static variable in class org.jmol.script.T
substructure - Static variable in class org.jmol.script.T
substructureType - Variable in class org.jmol.adapter.smarter.Structure
SUBSYS_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
Subsystem - Class in org.jmol.adapter.readers.cif
Subsystem(MSRdr, String, Matrix) - Constructor for class org.jmol.adapter.readers.cif.Subsystem
subsystem - Static variable in class org.jmol.script.T
subsystemCode - Variable in class org.jmol.symmetry.SymmetryOperation
subtype - Variable in class org.jmol.modelsetbio.ProteinStructure
subzones - Variable in class org.jmol.util.BZone
sum - Variable in class org.jmol.quantum.MOCalculation
sum - Static variable in class org.jmol.script.T
sum2 - Static variable in class org.jmol.script.T
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shape.Mesh
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
sumVertexNormals2(Mesh, T3[], V3[]) - Static method in class org.jmol.shape.Mesh
supercell - Static variable in class org.jmol.script.T
supercellSymmetry - Variable in class org.jmol.adapter.readers.cif.MSRdr
supportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
suppress_hidden - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface - Static variable in class org.jmol.script.T
SURFACE_ATOMICORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
surface_best - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_carve_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_carve_normal_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_carve_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_carve_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_cavity_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_cavity_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_cavity_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_circumscribe - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_clear_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_clear_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_clear_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_color_smoothing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_color_smoothing_threshold - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.shapespecial.Dots
SURFACE_ELLIPSOID2 - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_ELLIPSOID3 - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_FUNCTIONXY - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_FUNCTIONXYZ - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_GEODESIC - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_INTERSECT_ATOM - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_INTERSECT_FILE - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_LCAOCARTOON - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_LOBE - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_MEP - Static variable in class org.jmol.jvxl.readers.Parameters
surface_miserable - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_MLP - Static variable in class org.jmol.jvxl.readers.Parameters
surface_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_MOLECULAR - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_MOLECULARORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_NCI - Static variable in class org.jmol.jvxl.readers.Parameters
surface_negative_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_negative_visible - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_NOMAP - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_NONE - Static variable in class org.jmol.jvxl.readers.Parameters
surface_normal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_optimize_subsets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_poor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_PROPERTY - Static variable in class org.jmol.jvxl.readers.Parameters
surface_proximity - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
surface_ramp_above_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_residue_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_SASURFACE - Static variable in class org.jmol.jvxl.readers.Parameters
surface_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SURFACE_SOLVENT - Static variable in class org.jmol.jvxl.readers.Parameters
SURFACE_SPHERE - Static variable in class org.jmol.jvxl.readers.Parameters
surface_trim_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_trim_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_type - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surface_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
surfaceAtoms - Variable in class org.jmol.jvxl.readers.Parameters
surfaceAtoms - Variable in class org.jmol.util.MeshSurface
surfaceColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
surfacedistance - Static variable in class org.jmol.script.T
surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
surfaceDistanceMax - Variable in class org.jmol.modelset.AtomCollection
surfaceDone - Variable in class org.jmol.jvxl.readers.IsoShapeReader
SurfaceFileReader - Class in org.jmol.jvxl.readers
  PolygonFileReader or VolumeFileReader
SurfaceFileReader() - Constructor for class org.jmol.jvxl.readers.SurfaceFileReader
SurfaceGenerator - Class in org.jmol.jvxl.readers
SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
surfaceInfoName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
surfaceList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
SurfaceListCellRenderer() - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
surfaceMode - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
surfaceName - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
surfaceNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
surfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingSquares
surfaceReader - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
SurfaceReader - Class in org.jmol.jvxl.readers
SurfaceReader() - Constructor for class org.jmol.jvxl.readers.SurfaceReader
surfaces - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
surfaceScrollPane - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
surfaceSet - Variable in class org.jmol.util.MeshSurface
surfacesOnly - Variable in class org.jmol.export._ObjExporter
  Flag to cause only surfaces to be output.
SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
  Class that holds the surface status information that the surface tool needs.
SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
SurfaceTool - Class in org.openscience.jmol.app.surfacetool
SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
SurfaceToolGUI - Class in org.openscience.jmol.app.surfacetool
  GUI for the Jmol surfaceTool
SurfaceToolGUI(JmolViewer, HistoryFile, String, SurfaceTool) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
  Builds and opens a GUI to control slicing.
SurfaceToolGUI(LayoutManager) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
SurfaceToolGUI(boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
SurfaceToolGUI(LayoutManager, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
SurfaceToolGUI.SurfaceListCellRenderer - Class in org.openscience.jmol.app.surfacetool
surfaceType - Variable in class org.jmol.jvxl.readers.Parameters
suspend_undo - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
suspend_undo_atom_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
suspend_updates - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SV - Class in org.jmol.script
  ScriptVariable class
SV() - Constructor for class org.jmol.script.SV
SV.Sort - Class in org.jmol.script
sVal - Variable in class org.jmol.minimize.forcefield.FFParam
sValue(T) - Static method in class org.jmol.script.SV
sValueAddKeys(SB, String, Map<String, SV>, String, boolean, boolean, int, boolean) - Static method in class org.jmol.script.SV
sValueArray(SB, SV, String, String, boolean, boolean, boolean, int, boolean) - Static method in class org.jmol.script.SV
swap(int[], int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
swap_dsn6_bytes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
swapArray(SimpleNode[], int, int, int) - Method in class org.jmol.smiles.SmilesGenerator
  swap slices of an array [i0 i1) with [i1 i2)
swapXZ() - Method in class org.jmol.jvxl.readers.VolumeFileReader
sweep_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sweep_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sweep_phase - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
sweep_speed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
SwingConstants - Class in org.jmol.awtjs.swing
SwingConstants() - Constructor for class org.jmol.awtjs.swing.SwingConstants
SwingController - Interface in org.jmol.awtjs.swing
  SwingController is an interface that org.jmol.awtjs.swing classes will need.
swipeCount - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
swipeCutoff - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
swipeDelayMs - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
swipeFactor - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
swipeStartTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
switchAtoms() - Method in class org.jmol.smiles.SmilesBond
  Ensure that atom ordering is proper.
switchAtoms() - Method in class org.jmol.util.ContactPair
switchcmd - Static variable in class org.jmol.script.T
sX - Variable in class org.jmol.util.Point3fi
  screen X
sY - Variable in class org.jmol.util.Point3fi
  screen Y
sym - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
SYM - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
SYM - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
sym2 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
SYM_EQ_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_CENTERING - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_REV - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_REV_PRELIM - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_SSG_ALG - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_SSG_CENT_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_SSG_CENTERING - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_SSG_REV - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_MAGN_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_SSG_ALG - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_SSG_EQ_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
SYM_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
symbol - Static variable in class org.jmol.script.T
symbol - Variable in class org.jmol.smiles.SmilesAtom
symbolicMap - Variable in class org.jmol.adapter.readers.simple.InputReader
symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
symMatrix - Variable in class org.jmol.util.Tensor
symmetries - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
symmetry - Variable in class org.jmol.adapter.readers.cif.MSRdr
symmetry - Variable in class org.jmol.adapter.readers.cif.Subsystem
SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
  state constants
symmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
symmetry - Variable in class org.jmol.adapter.smarter.XtalSymmetry
symmetry - Static variable in class org.jmol.script.T
Symmetry - Class in org.jmol.symmetry
Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
symmetry - Variable in class org.jmol.util.ModulationSet
  the space group appropriate to this atom
SYMMETRY_OPTIONS - Static variable in class org.jmol.modelkit.ModelKitPopup
symmetryAddAtoms(int, int, int, int, int, int, P3[], MSInterface, BS, int[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry
SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
SymmetryDesc - Class in org.jmol.symmetry
  A class to handle requests for information about space groups and symmetry operations.
SymmetryDesc() - Constructor for class org.jmol.symmetry.SymmetryDesc
symmetryInfo - Variable in class org.jmol.symmetry.Symmetry
SymmetryInfo - Class in org.jmol.symmetry
SymmetryInfo() - Constructor for class org.jmol.symmetry.SymmetryInfo
SymmetryInterface - Interface in org.jmol.api
SymmetryOnly - Variable in class org.jmol.popup.JmolPopup
SymmetryOperation - Class in org.jmol.symmetry
SymmetryOperation(SymmetryOperation, P3[], int, int, boolean) - Constructor for class org.jmol.symmetry.SymmetryOperation
symmetryOperations - Variable in class org.jmol.symmetry.SymmetryInfo
symmetryOperationsFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
symmetryRange - Variable in class org.jmol.adapter.smarter.XtalSymmetry
symop - Variable in class org.jmol.modelkit.Constraint
symop - Variable in class org.jmol.modelkit.ModelKitPopup
symop - Static variable in class org.jmol.script.T
symopColixes - Variable in class org.jmol.shape.Mesh
symopNormixes - Variable in class org.jmol.shape.Mesh
symops - Variable in class org.jmol.adapter.readers.cif.CifReader
symops - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
symops - Variable in class org.jmol.shape.Mesh
sync - Static variable in class org.jmol.script.T
SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
syncDisabled - Variable in class org.jmol.viewer.StatusManager
syncDone() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
syncId - Variable in class org.jmol.util.GenericApplet
syncId - Variable in class org.jmol.viewer.Viewer
syncingMouse - Variable in class org.jmol.viewer.StatusManager
syncingScripts - Variable in class org.jmol.viewer.StatusManager
syncLists() - Method in class org.openscience.jmol.app.webexport.WebPanel
syncmouse - Static variable in class org.jmol.script.T
syncScript(String) - Method in interface org.jmol.api.JmolSyncInterface
syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
syncScript(String) - Method in class org.jmol.applet.JmolApplet
syncscript - Static variable in class org.jmol.script.T
syncScript(String) - Method in class org.jmol.util.GenericApplet
syncScript(String, String, int) - Method in class org.jmol.viewer.JmolStateCreator
syncScript(String, String, int) - Method in class org.jmol.viewer.StateCreator
syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
syncScript(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
syncSend(String, Object, int) - Method in class org.jmol.viewer.StatusManager
syncToJmol(String) - Method in interface org.jmol.api.JSVInterface
syncToJmol(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
sZ - Variable in class org.jmol.util.Point3fi
  screen Z

## T

T - Class in org.jmol.script
  Script token class.
T() - Constructor for class org.jmol.script.T
t(int) - Static method in class org.jmol.script.T
t - Variable in class org.jmol.symmetry.UnitCellIterator
T1 - Variable in class org.jmol.g3d.HermiteRenderer
T2 - Variable in class org.jmol.g3d.HermiteRenderer
T_SHAPED - Static variable in class org.jmol.smiles.SmilesStereo
TableCellRenderer - Interface in org.jmol.awtjs.swing
TableColumn - Interface in org.jmol.awtjs.swing
tableModel - Variable in class org.jmol.awtjs.swing.JTable
tabPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
tags - Static variable in class org.jmol.adapter.readers.xtal.GulpReader
tags - Static variable in class org.jmol.quantum.QS
tags2 - Static variable in class org.jmol.quantum.QS
TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_BONDINGRADIUS - Static variable in class org.jmol.modelset.AtomCollection
TAINT_CHAIN - Static variable in class org.jmol.modelset.AtomCollection
TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_RESNO - Static variable in class org.jmol.modelset.AtomCollection
TAINT_SEQID - Static variable in class org.jmol.modelset.AtomCollection
TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
taintAtom(int, int) - Method in class org.jmol.modelset.AtomCollection
taintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
tainted - Variable in class org.jmol.awtjs.swing.JPopupMenu
tainted - Variable in class org.jmol.modelset.AtomCollection
tainted - Variable in class org.jmol.modelset.Measurement
taintModelCoord(int) - Method in class org.jmol.modelset.AtomCollection
target - Variable in class org.jmol.modelset.Text
targetAtomCount - Variable in class org.jmol.smiles.SmilesSearch
targetAtoms - Variable in class org.jmol.smiles.SmilesSearch
targetTime - Variable in class org.jmol.thread.JmolThread
taskNumber - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
  The number of the task begin interpreted.
tau - Variable in class org.jmol.util.ModulationSet
TBI_AB - Static variable in class org.jmol.minimize.forcefield.ForceField
TBI_BC - Static variable in class org.jmol.minimize.forcefield.ForceField
TBI_CD - Static variable in class org.jmol.minimize.forcefield.ForceField
tButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
TEAL - Static variable in class org.jmol.util.C
temp - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
temp - Variable in class org.jmol.viewer.StateCreator
temp2 - Variable in class org.jmol.viewer.StateCreator
temp3 - Variable in class org.jmol.viewer.StateCreator
TempArray - Class in org.jmol.util
TempArray() - Constructor for class org.jmol.util.TempArray
tempArray - Variable in class org.jmol.viewer.Viewer
tempC - Variable in class org.jmol.export.___Exporter
tempDataXml - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
tempDipole - Variable in class org.jmol.shapespecial.Dipoles
temperature - Static variable in class org.jmol.script.T
TemperatureOnly - Variable in class org.jmol.popup.JmolPopup
templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
tempP1 - Variable in class org.jmol.export.___Exporter
tempP2 - Variable in class org.jmol.export.___Exporter
tempP3 - Variable in class org.jmol.export.___Exporter
tempQ1 - Variable in class org.jmol.export._VrmlExporter
tempQ2 - Variable in class org.jmol.export._VrmlExporter
tempQ3 - Variable in class org.jmol.export._VrmlExporter
tempStatement - Variable in class org.jmol.script.ScriptExpr
tempV1 - Variable in class org.jmol.export.___Exporter
tempV2 - Variable in class org.jmol.export.___Exporter
tempXY - Variable in class org.jmol.render.HoverRenderer
tensor - Static variable in class org.jmol.script.T
tensor - Variable in class org.jmol.shapespecial.Ellipsoid
Tensor - Class in org.jmol.util
Tensor() - Constructor for class org.jmol.util.Tensor
  Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods.
tensors - Variable in class org.jmol.adapter.smarter.Atom
term - Variable in class org.jmol.export.UseTable
terminatorMessage - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
Test - Class in org.openscience.jmol.app.webexport
Test(Viewer) - Constructor for class org.openscience.jmol.app.webexport.Test
test1 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
test1 - Variable in class org.jmol.quantum.NciCalculation
test2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
testAsync - Variable in class org.jmol.viewer.Viewer
testDiff(P3, P3, P3, P3) - Method in class org.jmol.shapespecial.Polyhedra
testflag1 - Static variable in class org.jmol.script.T
testFlag1 - Variable in class org.jmol.viewer.GlobalSettings
testflag2 - Static variable in class org.jmol.script.T
testFlag2 - Variable in class org.jmol.viewer.GlobalSettings
testflag3 - Static variable in class org.jmol.script.T
testFlag3 - Variable in class org.jmol.viewer.GlobalSettings
testflag4 - Static variable in class org.jmol.script.T
testFlag4 - Variable in class org.jmol.viewer.GlobalSettings
testFlags - Variable in class org.jmol.jvxl.readers.Parameters
testing - Variable in class org.jmol.quantum.MOCalculation
testLinear - Static variable in class org.jmol.jvxl.readers.IsoSolventReader
testRule6Full - Variable in class org.jmol.symmetry.CIPData
  A flag that, if set, returns rr for bicyclo[2.2.2]octane
TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
tEvenDiameter - Variable in class org.jmol.g3d.CylinderRenderer
text - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
text - Variable in class org.jmol.awt.AwtClipboard
text - Variable in class org.jmol.awtjs.swing.Component
text - Variable in class org.jmol.g3d.TextString
text - Variable in class org.jmol.modelset.LabelToken
text - Variable in class org.jmol.modelset.Measurement
text - Variable in class org.jmol.modelset.MeasurementData
Text - Class in org.jmol.modelset
Text() - Constructor for class org.jmol.modelset.Text
text - Variable in class org.jmol.modelset.Text
text - Variable in class org.jmol.shape.Hover
TEXT_ALIGN_CENTER - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_FLAGS - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_LEFT - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_NONE - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_RIGHT - Static variable in class org.jmol.viewer.JC
TEXT_ALIGN_SHIFT - Static variable in class org.jmol.viewer.JC
textAlign - Variable in class org.jmol.awtjs.swing.Cell
textAlign - Variable in class org.jmol.render.LabelsRenderer
textColor - Variable in class org.jmol.applet.AppletWrapper
TEXTCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
textHeight - Variable in class org.jmol.modelset.Text
textInfo - Variable in class org.jmol.symmetry.PointGroup
TextRenderer - Class in org.jmol.g3d
  implementation for text rendering
TextRenderer(String, Font) - Constructor for class org.jmol.g3d.TextRenderer
TextRenderer - Class in org.jmol.render
TextRenderer() - Constructor for class org.jmol.render.TextRenderer
TextShape - Class in org.jmol.shape
TextShape() - Constructor for class org.jmol.shape.TextShape
TextString - Class in org.jmol.g3d
TextString() - Constructor for class org.jmol.g3d.TextString
TEXTTYPE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
textUnformatted - Variable in class org.jmol.modelset.Text
texture_fonts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
textureCode - Variable in class org.jmol.export._TachyonExporter
textureFiles - Variable in class org.jmol.export._ObjExporter
  List of texture files created.
textures - Variable in class org.jmol.export._ObjExporter
  HashSet for textures.
textures - Variable in class org.jmol.export._TachyonExporter
textWidth - Variable in class org.jmol.modelset.Text
textY - Variable in class org.jmol.util.GData
textY - Variable in class org.openscience.jmol.app.jmolpanel.Splash
tFactorInv - Variable in class org.jmol.util.ModulationSet
tHemisphere - Variable in class org.jmol.bspt.CubeIterator
thePlane - Variable in class org.jmol.jvxl.data.VolumeData
thePlane - Variable in class org.jmol.jvxl.readers.Parameters
thePlane - Variable in class org.jmol.render.MeshRenderer
thePlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
theProperty - Variable in class org.jmol.jvxl.readers.AtomDataReader
theProperty - Variable in class org.jmol.jvxl.readers.Parameters
THERMAL_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
theta - Variable in class org.jmol.minimize.forcefield.Calculation
theta - Variable in class org.jmol.modelsetbio.Monomer
theta - Static variable in class org.jmol.script.T
theta0 - Variable in class org.jmol.minimize.MinAngle
theTok - Variable in class org.jmol.script.ScriptContext
theTok - Variable in class org.jmol.script.ScriptParam
theTok - Variable in class org.jmol.script.ScriptTokenParser
theToken - Variable in class org.jmol.script.ScriptContext
theToken - Variable in class org.jmol.script.ScriptParam
theToken - Variable in class org.jmol.script.ScriptTokenParser
theValue - Variable in class org.jmol.script.ScriptTokenParser
theWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
thickness - Variable in class org.openscience.jmol.app.surfacetool.Slice
thickness - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
thicknessMax - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
thicknessSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
thisArgb - Variable in class org.jmol.shapespecial.Dots
thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
thisAtom - Variable in class org.jmol.shapespecial.Dots
thisAtomSet - Variable in class org.jmol.jvxl.readers.AtomDataReader
thisBiomolecule - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
thisChain - Variable in class org.jmol.adapter.readers.cif.MMCifReader
thisCommand - Variable in class org.jmol.script.ScriptEval
thisContext - Variable in class org.jmol.script.ScriptParam
thisContour - Variable in class org.jmol.jvxl.calc.MarchingSquares
thisContour - Variable in class org.jmol.jvxl.data.JvxlData
thisContour - Variable in class org.jmol.jvxl.readers.Parameters
thisData - Variable in class org.jmol.jvxl.readers.BCifDensityReader
thisDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
thisFormula - Variable in class org.jmol.adapter.readers.cif.CifReader
thisFunction - Variable in class org.jmol.script.ScriptCompiler
thisID - Variable in class org.jmol.modelset.Measurement
thisID - Variable in class org.jmol.modelset.MeasurementData
thisID - Variable in class org.jmol.shape.Mesh
thisID - Variable in class org.jmol.shape.TextShape
thisID - Variable in class org.jmol.shapespecial.Dipole
thisID - Variable in class org.jmol.shapespecial.Polyhedra
thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
thisMesh - Variable in class org.jmol.shapespecial.Draw
thisMesh - Variable in class org.jmol.shapesurface.Isosurface
thismodel - Static variable in class org.jmol.script.T
thisModel - Variable in class org.jmol.shapesurface.MolecularOrbital
thisModelID - Variable in class org.jmol.jsv.JDXMOLParser
thisName - Variable in class org.jmol.adapter.readers.pymol.PickleReader
thisName - Variable in class org.jmol.util.ColorEncoder
thisPlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
thisPlaneB - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
thisPlaneB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
thisPopup - Variable in class org.jmol.popup.GenericPopup
thisRadius - Variable in class org.jmol.shapespecial.Dots
thisScale - Variable in class org.jmol.util.ColorEncoder
thisSection - Variable in class org.jmol.adapter.readers.pymol.PickleReader
thisSet - Variable in class org.jmol.jvxl.data.JvxlData
thisSet - Variable in class org.jmol.shapesurface.LcaoCartoon
thisState - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
thisStateModel - Variable in class org.jmol.modelset.ModelSet
thisStructuralFormula - Variable in class org.jmol.adapter.readers.cif.CifReader
thisSub - Variable in class org.jmol.adapter.readers.xtal.JanaReader
thisType - Variable in class org.jmol.dialog.Dialog.TypeFilter
thisType - Variable in class org.jmol.shapesurface.LcaoCartoon
thisX - Variable in class org.jmol.jvxl.readers.AtomDataReader
thisx - Variable in class org.jmol.popup.GenericPopup
thisy - Variable in class org.jmol.popup.GenericPopup
thread - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
threadIndex - Static variable in class org.jmol.thread.JmolThread
threadSafe - Variable in class org.jmol.modelset.AtomIteratorWithinModel
threeVertices - Variable in class org.jmol.export._VrmlExporter
throwcmd - Static variable in class org.jmol.script.T
tickA - Variable in class org.jmol.render.FontLineShapeRenderer
tickAs - Variable in class org.jmol.render.FontLineShapeRenderer
tickB - Variable in class org.jmol.render.FontLineShapeRenderer
tickBs - Variable in class org.jmol.render.FontLineShapeRenderer
tickEdges - Variable in class org.jmol.render.CageRenderer
TickerThread - Class in org.jmol.applet
TickerThread(Applet) - Constructor for class org.jmol.applet.TickerThread
tickInfo - Variable in class org.jmol.modelset.Measurement
tickInfo - Variable in class org.jmol.modelset.MeasurementData
TickInfo - Class in org.jmol.modelset
TickInfo(P3) - Constructor for class org.jmol.modelset.TickInfo
tickInfo - Variable in class org.jmol.render.FontLineShapeRenderer
tickInfo - Variable in class org.jmol.shape.Measures
tickInfos - Variable in class org.jmol.shape.FontLineShape
tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
tickParamAsStr(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
ticks - Variable in class org.jmol.modelset.TickInfo
ticks - Static variable in class org.jmol.script.T
TIED - Static variable in class org.jmol.symmetry.CIPChirality
time - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
time - Variable in class org.jmol.viewer.MotionPoint
time - Variable in class org.jmol.viewer.MouseState
time0 - Variable in class org.jmol.viewer.Gesture
timeBegin - Variable in class org.jmol.applet.Jmol
timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
timeBegin - Variable in class org.openscience.jvxl.MonitorInputStream
timeBeginExecution - Variable in class org.jmol.script.ScriptEval
timeCount - Variable in class org.jmol.applet.Jmol
timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
timeEndExecution - Variable in class org.jmol.script.ScriptEval
timeLast - Variable in class org.jmol.applet.Jmol
timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
timeout - Static variable in class org.jmol.script.T
timeouts - Variable in class org.jmol.viewer.Viewer
TimeoutThread - Class in org.jmol.thread
TimeoutThread(Viewer, String, int, String) - Constructor for class org.jmol.thread.TimeoutThread
timePerStep - Variable in class org.jmol.thread.MoveToThread
timeReversal - Variable in class org.jmol.symmetry.SymmetryOperation
times - Static variable in class org.jmol.script.T
TimeStamp_WebLink() - Static method in class org.openscience.jmol.app.webexport.WebExport
timestimes - Static variable in class org.jmol.script.T
timeTotal - Variable in class org.jmol.applet.Jmol
timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
TinkerReader - Class in org.jmol.adapter.readers.simple
  simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
TinkerReader() - Constructor for class org.jmol.adapter.readers.simple.TinkerReader
title - Variable in class org.jmol.adapter.readers.more.JcampdxReader
title() - Method in class org.jmol.adapter.readers.pdb.PdbReader
title - Variable in class org.jmol.adapter.readers.quantum.DgridReader
title - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
TITLE - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
title - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
title - Variable in class org.jmol.awtjs.swing.JDialog
title - Variable in class org.jmol.console.ImageDialog
title - Variable in class org.jmol.console.ScriptEditor
title - Variable in class org.jmol.jvxl.data.JvxlData
title - Variable in class org.jmol.jvxl.readers.Parameters
title - Static variable in class org.jmol.script.T
title - Variable in class org.jmol.shape.Mesh
title - Variable in class org.jmol.shape.MeshCollection
title - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
titleAtomSet - Variable in class org.jmol.adapter.readers.cif.CifReader
titleformat - Static variable in class org.jmol.script.T
titleMsg - Variable in class org.jmol.adapter.readers.more.AFLOWReader
titleRecords - Static variable in class org.jmol.adapter.readers.cif.CifReader
titles - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
titleWidthMax - Variable in class org.jmol.popup.JmolPopup
TLnn - Static variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
tlsAddError(String) - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
tlsAddError(String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
tlsDataOnlyFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
TlsDataOnlyReader - Class in org.jmol.adapter.readers.more
TlsDataOnlyReader() - Constructor for class org.jmol.adapter.readers.more.TlsDataOnlyReader
tlsGroupID - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
tlsGroupID - Variable in class org.jmol.adapter.readers.pdb.PdbReader
tlsU - Variable in class org.jmol.adapter.readers.pdb.PdbReader
tm - Variable in class org.jmol.export.___Exporter
tm - Variable in class org.jmol.navigate.Navigator
tm - Variable in class org.jmol.render.ShapeRenderer
tm - Variable in class org.jmol.renderbio.NucleicRenderer
tm - Variable in class org.jmol.renderbio.RocketRenderer
tm - Variable in class org.jmol.viewer.Viewer
tmap - Variable in class org.jmol.g3d.TextRenderer
tmp - Variable in class org.jmol.g3d.PixelatorShaded
to - Static variable in class org.jmol.script.T
toArray() - Method in class org.jmol.script.SV
toCanonical - Static variable in class org.jmol.util.BoxInfo
toCap(String, int) - Static method in class org.jmol.symmetry.SpaceGroup
toCartesian(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
toCartesian(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
toCartesian(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
toCartesian(T3, boolean) - Method in class org.jmol.viewer.Viewer
  absolute or relative to origin of UNITCELL {x y z}
toFloat(String) - Static method in class org.jmol.script.SV
toFloatArray(double[]) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
toFractional(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
toFractional(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
toFractional(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
toFractional(T3, boolean) - Method in class org.jmol.viewer.Viewer
toFractionalM(M4) - Method in interface org.jmol.api.SymmetryInterface
toFractionalM(M4) - Method in class org.jmol.symmetry.Symmetry
toFractionalM(M4) - Method in class org.jmol.util.SimpleUnitCell
toFractionalX(float) - Static method in class org.jmol.symmetry.UnitCell
toFromPrimitive(boolean, char, T3[], M3) - Method in interface org.jmol.api.SymmetryInterface
toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.Symmetry
toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.UnitCell
toFront() - Method in class org.jmol.awtjs.swing.JDialog
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
  Brings the surfaceTool to the front and updates sliders, etc...
toFrontOrGotFocus() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
toggle(Measurement) - Method in class org.jmol.shape.Measures
toggleInPlace(BS, BS) - Static method in class org.jmol.util.BSUtil
  a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
togglelabel - Static variable in class org.jmol.script.T
toggleMeasurement() - Method in class org.jmol.viewer.ActionManager
toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
toggleOn(int[]) - Method in class org.jmol.shape.Measures
toHTML(SB, String, BS) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
toHTML(String) - Method in class org.jmol.awtjs.swing.Cell
toHTML() - Method in class org.jmol.awtjs.swing.Component
toHTML(String) - Method in class org.jmol.awtjs.swing.Grid
toHTML() - Method in class org.jmol.awtjs.swing.JButton
toHTML() - Method in class org.jmol.awtjs.swing.JCheckBox
toHTML() - Method in class org.jmol.awtjs.swing.JComboBox
toHTML() - Method in class org.jmol.awtjs.swing.JComponentImp
toHTML() - Method in class org.jmol.awtjs.swing.JContentPane
toHTML() - Method in class org.jmol.awtjs.swing.JDialog
toHTML() - Method in class org.jmol.awtjs.swing.JEditorPane
toHTML() - Method in class org.jmol.awtjs.swing.JLabel
toHTML() - Method in class org.jmol.awtjs.swing.JMenu
toHTML() - Method in class org.jmol.awtjs.swing.JMenuItem
toHTML() - Method in class org.jmol.awtjs.swing.JPanel
toHTML() - Method in class org.jmol.awtjs.swing.JPopupMenu
toHTML() - Method in class org.jmol.awtjs.swing.JScrollPane
toHTML() - Method in class org.jmol.awtjs.swing.JSplitPane
toHTML() - Method in class org.jmol.awtjs.swing.JTable
toHTML() - Method in class org.jmol.awtjs.swing.JTextField
toHTML() - Method in class org.jmol.awtjs.swing.JTextPane
toInt2(boolean, Object) - Method in class org.jmol.shapespecial.Polyhedron
toIntARGB(int[]) - Static method in class org.jmol.awtjs2d.Image
toJSON() - Method in class org.jmol.script.SV
tok - Variable in class org.jmol.modelset.LabelToken
tok - Variable in class org.jmol.script.ScriptFunction
tok - Variable in class org.jmol.script.T
tok0 - Variable in class org.jmol.script.ScriptFlowContext
tokAction - Variable in class org.jmol.modelset.MeasurementData
tokAction - Variable in class org.jmol.shape.Measures
tokAt(int) - Method in class org.jmol.script.ScriptCompiler
tokAt(int) - Method in class org.jmol.script.ScriptParam
tokAt(int) - Method in class org.jmol.script.ScriptTokenParser
tokAt(int) - Method in class org.jmol.scriptext.ScriptExt
tokAtArray(int, T[]) - Static method in class org.jmol.scriptext.CmdExt
tokAttr(int, int) - Static method in class org.jmol.script.T
tokAttrOr(int, int, int) - Static method in class org.jmol.script.T
tokCommand - Variable in class org.jmol.script.ScriptTokenParser
token - Variable in class org.jmol.script.ScriptContext
token - Variable in class org.jmol.script.ScriptFlowContext
TOKEN_AROMATIC - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
TOKEN_ELEMENT_ALLYLIC - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
TOKEN_ELEMENT_CHARGED - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
TOKEN_ELEMENT_CONNECTED - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
TOKEN_ELEMENT_ONLY - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
TOKEN_ELEMENT_SP - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
tokenAll - Static variable in class org.jmol.script.T
tokenAnd - Static variable in class org.jmol.script.T
tokenAndEquals - Variable in class org.jmol.script.ScriptTokenParser
tokenAndFALSE - Static variable in class org.jmol.script.T
tokenAndSpec - Static variable in class org.jmol.script.T
tokenArrayClose - Static variable in class org.jmol.script.T
tokenArrayOpen - Static variable in class org.jmol.script.T
tokenArraySquare - Static variable in class org.jmol.script.T
tokenAt(int) - Method in class org.jmol.script.ScriptCompiler
tokenAt(int, T[]) - Method in class org.jmol.scriptext.CmdExt
tokenAttr(T, int) - Static method in class org.jmol.script.ScriptTokenParser
tokenColon - Static variable in class org.jmol.script.T
tokenComma - Static variable in class org.jmol.script.T
tokenCommand - Variable in class org.jmol.script.ScriptTokenParser
tokenConnected - Static variable in class org.jmol.script.T
tokenCoordinateBegin - Static variable in class org.jmol.script.T
tokenCoordinateEnd - Static variable in class org.jmol.script.T
tokenCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
tokenDefineString - Static variable in class org.jmol.script.T
tokenDivide - Static variable in class org.jmol.script.T
tokenEquals - Static variable in class org.jmol.script.T
tokenExpressionBegin - Static variable in class org.jmol.script.T
tokenExpressionEnd - Static variable in class org.jmol.script.T
tokenIf - Static variable in class org.jmol.script.T
tokenizeCastepCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
tokenizePlusPlus(int, boolean) - Method in class org.jmol.script.ScriptCompiler
tokenLeftBrace - Static variable in class org.jmol.script.T
tokenLeftParen - Static variable in class org.jmol.script.T
tokenMap - Static variable in class org.jmol.script.T
tokenMinus - Static variable in class org.jmol.script.T
tokenMul3 - Static variable in class org.jmol.script.T
tokenNext() - Method in class org.jmol.script.ScriptTokenParser
  increments the pointer; does NOT set theToken or theValue
tokenNextTok(int) - Method in class org.jmol.script.ScriptTokenParser
tokenOff - Static variable in class org.jmol.script.T
tokenOn - Static variable in class org.jmol.script.T
tokenOpIf - Static variable in class org.jmol.script.T
tokenOr - Static variable in class org.jmol.script.T
tokenOrTRUE - Static variable in class org.jmol.script.T
tokenPlus - Static variable in class org.jmol.script.T
tokenRightBrace - Static variable in class org.jmol.script.T
tokenRightParen - Static variable in class org.jmol.script.T
tokens - Variable in class org.jmol.adapter.readers.simple.InputReader
tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
tokens - Variable in class org.jmol.adapter.readers.xtal.CastepReader
tokens - Variable in class org.jmol.adapter.readers.xtal.CgdReader
tokens - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
tokens - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
tokens - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
tokens - Variable in class org.jmol.jvxl.readers.PmeshReader
tokenScript - Static variable in class org.jmol.script.T
tokenSet - Static variable in class org.jmol.script.T
tokenSetArray - Static variable in class org.jmol.script.T
tokenSetCmd - Static variable in class org.jmol.script.T
tokenSetProperty - Static variable in class org.jmol.script.T
tokenSetVar - Static variable in class org.jmol.script.T
tokenSpaceBeforeSquare - Static variable in class org.jmol.script.T
tokenSwitch - Static variable in class org.jmol.script.T
tokenTimes - Static variable in class org.jmol.script.T
tokenTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
tokInitialPlusPlus - Variable in class org.jmol.script.ScriptCompiler
tokLastMath - Variable in class org.jmol.script.ScriptCompiler
tokPeek() - Method in class org.jmol.script.ScriptTokenParser
tokPeekIs(int) - Method in class org.jmol.script.ScriptTokenParser
toOABC(P3[], T3) - Static method in class org.jmol.util.BoxInfo
  Delivers [center a b c] for generation of unit cells from a boundbox
toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
toolbarButtonGroup - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
top - Variable in class org.jmol.awtjs.swing.Insets
top - Static variable in class org.jmol.script.T
top - Variable in class org.jmol.smiles.SmilesSearch
toP3(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
topButton - Variable in class org.jmol.console.ScriptEditor
topButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
topologyOnly - Variable in class org.jmol.smiles.SmilesGenerator
topoType - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
topPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
toRadians - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
toRadians - Static variable in class org.jmol.util.SimpleUnitCell
toReadable(String, Object) - Static method in class org.jmol.util.Escape
  Used only for getProperty("readable",...)
torsion - Static variable in class org.jmol.script.T
torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
torsionCount - Variable in class org.jmol.minimize.forcefield.Calculations
toScript(P4) - Method in class org.jmol.util.BZone
toStdAmino3(String) - Method in class org.jmol.modelsetbio.BioResolver
toString() - Method in class org.jmol.adapter.readers.cif.Subsystem
toString() - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
toString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
toString() - Method in class org.jmol.adapter.writers.QCJSONWriter
toString() - Method in class org.jmol.atomdata.RadiusData
toString() - Method in class org.jmol.awtjs.swing.Color
toString() - Method in class org.jmol.dssx.Bridge
toString() - Method in class org.jmol.g3d.TextString
toString() - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Face
toString() - Method in class org.jmol.minimize.MinAtom
toString() - Method in class org.jmol.minimize.MinObject
toString() - Method in class org.jmol.modelset.Atom
toString() - Method in class org.jmol.modelset.Bond
toString() - Method in class org.jmol.modelset.Group
toString() - Method in class org.jmol.modelset.StateScript
toString() - Method in class org.jmol.modelsetbio.BasePair
toString() - Method in class org.jmol.quantum.SlaterData
toString() - Method in class org.jmol.script.ScriptEval
toString() - Method in exception org.jmol.script.ScriptException
toString() - Method in class org.jmol.script.ScriptFlowContext
toString() - Method in class org.jmol.script.ScriptFunction
toString() - Method in class org.jmol.script.SV
toString() - Method in class org.jmol.script.T
toString() - Method in class org.jmol.smiles.SmilesAtom
toString() - Method in class org.jmol.smiles.SmilesBond
toString() - Method in class org.jmol.smiles.SmilesMeasure
toString() - Method in class org.jmol.smiles.SmilesSearch
toString() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
toString() - Method in class org.jmol.symmetry.SpaceGroup
toString() - Method in class org.jmol.symmetry.SymmetryOperation
toString() - Method in class org.jmol.thread.TimeoutThread
toString() - Method in class org.jmol.util.ContactPair
toString() - Method in class org.jmol.util.MeshCapper.CapVertex
toString() - Method in class org.jmol.util.Rgb16
toString() - Method in class org.jmol.util.Tensor
toString() - Method in class org.jmol.viewer.Gesture
toString() - Method in class org.jmol.viewer.MotionPoint
toString() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
toString() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
toString2() - Method in class org.jmol.script.T
toSupercell(P3) - Method in interface org.jmol.api.SymmetryInterface
toSupercell(P3) - Method in class org.jmol.symmetry.Symmetry
toSupercell(P3) - Method in class org.jmol.util.SimpleUnitCell
  convenience return only after changing fpt
toTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
totalArea - Variable in class org.jmol.util.BZone
totalAtomCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
totalSteps - Variable in class org.jmol.navigate.Navigator
totalSteps - Variable in class org.jmol.thread.MoveToThread
totE - Variable in class org.jmol.adapter.readers.xtal.DmolReader
totEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
totEnergy - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
totEnergy - Variable in class org.jmol.adapter.readers.xtal.GulpReader
TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
toUnicode(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  There is no need to convert to unicode in CIF 2.0.
toUnitCell(T3, T3) - Method in interface org.jmol.api.SymmetryInterface
toUnitCell(T3, T3) - Method in class org.jmol.symmetry.Symmetry
toUnitCell(T3, T3) - Method in class org.jmol.symmetry.UnitCell
  when offset is null, use the current cell, otherwise use the original unit cell
toUnitCell(P3, P3) - Method in class org.jmol.viewer.Viewer
  relative to origin without regard to UNITCELL {x y z}
toUnits(double, String) - Method in class org.jmol.minimize.forcefield.ForceField
toUserUnits(double) - Method in class org.jmol.minimize.forcefield.ForceField
toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
tPending - Variable in class org.jmol.renderbio.RocketRenderer
tQuiet - Variable in class org.jmol.script.ScriptEval
trace - Static variable in class org.jmol.script.T
Trace - Class in org.jmol.shapebio
Trace() - Constructor for class org.jmol.shapebio.Trace
trace - Variable in class org.jmol.util.Vibration
trace_atoms_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
tracealpha - Static variable in class org.jmol.script.T
traceAlpha - Variable in class org.jmol.viewer.GlobalSettings
tracePt - Variable in class org.jmol.util.Vibration
TraceRenderer - Class in org.jmol.renderbio
TraceRenderer() - Constructor for class org.jmol.renderbio.TraceRenderer
traceX - Variable in class org.jmol.modelset.Measurement
traceY - Variable in class org.jmol.modelset.Measurement
track(CIPChirality, CIPChirality.CIPAtom, CIPChirality.CIPAtom, int, int, boolean) - Method in class org.jmol.symmetry.CIPData
  Track this decision - CIPDataTracker only
track(CIPChirality, CIPChirality.CIPAtom, CIPChirality.CIPAtom, int, int, boolean) - Method in class org.jmol.symmetry.CIPDataTracker
trackTerminal - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
trajectory - Variable in class org.jmol.modelset.AtomCollection
Trajectory - Class in org.jmol.modelset
Trajectory() - Constructor for class org.jmol.modelset.Trajectory
trajectory - Static variable in class org.jmol.script.T
trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
trajectoryNames - Variable in class org.jmol.adapter.smarter.AtomSetCollection
trajectoryPtr - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
trajectoryStep - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
trajectoryStepCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
trajectoryUnitCells - Variable in class org.jmol.adapter.smarter.XtalSymmetry
trans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
transform(V3, V3) - Method in class org.jmol.jvxl.data.VolumeData
transform(short, Atom, Vibration, JmolModulationSet) - Method in class org.jmol.renderspecial.VectorsRenderer
transform - Static variable in class org.jmol.script.T
transformedVectors - Variable in class org.jmol.render.MeshRenderer
transformedVectors - Variable in class org.jmol.util.GData
TransformFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
transformManager - Variable in class org.jmol.thread.MoveToThread
transformManager - Variable in class org.jmol.thread.SpinThread
transformManager - Variable in class org.jmol.thread.VibrationThread
TransformManager - Class in org.jmol.viewer
TransformManager() - Constructor for class org.jmol.viewer.TransformManager
TransformManager4D - Class in org.jmol.viewer
TransformManager4D() - Constructor for class org.jmol.viewer.TransformManager4D
TRANSFORMMAT - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
transformPoints(int, T3[], P3[]) - Method in class org.jmol.renderbio.NucleicRenderer
transformPt(T3) - Method in class org.jmol.viewer.TransformManager
  CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPt2D(T3) - Method in class org.jmol.viewer.TransformManager
transformPt3f(T3, P3) - Method in class org.jmol.viewer.TransformManager
transformPtNoClip(T3, T3) - Method in class org.jmol.viewer.TransformManager
transformPtScr(T3, P3i) - Method in class org.jmol.viewer.TransformManager
transformPtScrT3(T3, T3) - Method in class org.jmol.viewer.TransformManager
transformPtVib(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
transformXYZ(M4, BS) - Method in class org.jmol.atomdata.AtomData
  allow for transformed XYZ
translate(String) - Method in interface org.jmol.api.Translator
translate(String) - Method in class org.jmol.i18n.GT
  used in custom menu translation only
translate - Static variable in class org.jmol.script.T
translate(char, float, char, BS) - Method in class org.jmol.viewer.Viewer
translate(String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
translateModel(int, T3) - Method in class org.jmol.modelset.ModelSet
  move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE
translateScale(Object, double, double, double) - Method in interface org.jmol.api.GenericGraphics
translateScale(Object, double, double, double) - Method in class org.jmol.awt.AwtG2D
translateScale(Object, double, double, double) - Method in class org.jmol.awtjs2d.JsG2D
translateSelected - Static variable in class org.jmol.script.T
translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
translateXYBy(int, int) - Method in class org.jmol.viewer.TransformManager
translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
translateZBy(int) - Method in class org.jmol.viewer.TransformManager
translation - Variable in class org.jmol.modelset.Model
translation - Static variable in class org.jmol.script.T
translation - Variable in class org.jmol.symmetry.HallRotationTerm
translation - Variable in class org.jmol.symmetry.UnitCellIterator
translationCode - Variable in class org.jmol.symmetry.HallTranslation
translations - Variable in class org.jmol.modelset.ModelSet
translations - Static variable in class org.openscience.jmol.app.jmolpanel.GuiMap
translationString - Variable in class org.jmol.symmetry.HallRotationTerm
Translator - Interface in org.jmol.api
translucency - Variable in class org.jmol.adapter.readers.pymol.JmolObject
translucency - Static variable in class org.jmol.g3d.TextRenderer
translucency - Variable in class org.jmol.jvxl.data.JvxlData
translucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
translucencyLog - Variable in class org.jmol.g3d.Graphics3D
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
translucent - Static variable in class org.jmol.script.T
translucent - Variable in class org.jmol.viewer.GlobalSettings
TRANSLUCENT_MASK - Static variable in class org.jmol.util.C
TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.C
TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.C
translucentAllowed - Variable in class org.jmol.shape.Shape
translucentCoverOnly - Variable in class org.jmol.util.GData
translucentLevel - Variable in class org.jmol.shape.Shape
transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
transparency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
transparency - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
transparency_global_sort - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
transparency_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
transparency_picking_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
TRANSPARENT - Static variable in class org.jmol.util.C
transX - Variable in class org.jmol.thread.MoveToThread
transY - Variable in class org.jmol.thread.MoveToThread
tree - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
treeDepth - Variable in class org.jmol.bspt.Bspt
treeModel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
triad(float, float, float) - Method in class org.jmol.export._TachyonExporter
triad(T3) - Method in class org.jmol.export._TachyonExporter
Triangle(int, int, int, int, int) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.Triangle
triangle3d - Variable in class org.jmol.g3d.Graphics3D
triangle_max_passes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
triangleArea(int, int, int, V3, V3, V3) - Method in class org.jmol.shapespecial.Polyhedron
triangleCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
TriangleData - Class in org.jmol.util
  An adaptation of Marching Cubes that allows for indicating edges on triangles.
TriangleData() - Constructor for class org.jmol.util.TriangleData
triangleFace - Variable in class org.jmol.export._IdtfExporter
triangleNum - Variable in class org.jmol.export._ObjExporter
  Number for the next mesh of this type.
TriangleRenderer - Class in org.jmol.g3d
  renders triangles
TriangleRenderer() - Constructor for class org.jmol.g3d.TriangleRenderer
triangles - Variable in class org.jmol.jvxl.calc.MarchingSquares
triangles - Variable in class org.jmol.renderbio.NucleicRenderer
triangles - Static variable in class org.jmol.script.T
triangles - Variable in class org.jmol.shapespecial.Polyhedron
triangleTable2 - Static variable in class org.jmol.util.TriangleData
  The new triangle table developed specifically for Jmol.
triangleVolume(int, int, int, V3, V3, V3) - Method in class org.jmol.shapespecial.Polyhedron
triangulateFaces(int[][], P3[], int[][]) - Method in class org.jmol.util.MeshCapper
  generic entry for a set of faces
triangulatePolygon(P3[], int) - Method in class org.jmol.util.MeshCapper
  generic entry for a polygon
Triangulator - Class in org.jmol.util
Triangulator() - Constructor for class org.jmol.util.Triangulator
triangulator - Variable in class org.jmol.viewer.Viewer
TRICOLOR_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
trigger(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
triggered - Variable in class org.jmol.thread.TimeoutThread
triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
TRIGONAL_PYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
TRIGONALITY_MIN - Static variable in class org.jmol.symmetry.CIPData
  measure of planarity in a trigonal system, in Angstroms
trim - Static variable in class org.jmol.script.T
trim_dots - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
trimAtomSet() - Method in class org.jmol.adapter.readers.cif.MSRdr
trimLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
  All characters after hash ignored; lines are trimmed.
trimString(String) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
TRUE - Static variable in class org.jmol.viewer.SelectionManager
truncate0(SB, float) - Static method in class org.jmol.viewer.TransformManager
truncate2(SB, float) - Static method in class org.jmol.viewer.TransformManager
trycmd - Static variable in class org.jmol.script.T
tryPt - Variable in class org.jmol.script.ScriptContext
tryPt - Variable in class org.jmol.viewer.Viewer
tSort - Static variable in class org.jmol.util.Tensor
tsType - Variable in class org.jmol.adapter.readers.xtal.CastepReader
TUPLE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
tuples - Variable in class org.jmol.bspt.Leaf
Turn - Class in org.jmol.modelsetbio
Turn(AlphaPolymer, int, int) - Constructor for class org.jmol.modelsetbio.Turn
tv(int, int, Object) - Static method in class org.jmol.script.T
twelfths - Static variable in class org.jmol.symmetry.SymmetryOperation
twelfthsOf(float) - Static method in class org.jmol.symmetry.SymmetryOperation
twistedSheets - Variable in class org.jmol.modelsetbio.BioPolymer
twistedsheets - Static variable in class org.jmol.script.T
twistedSheets - Variable in class org.jmol.viewer.GlobalSettings
TWO_PI - Static variable in class org.jmol.minimize.forcefield.Calculations
TWO_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
two_sided_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
twoChar - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
twoCharLabelTokenIds - Static variable in class org.jmol.modelset.LabelToken
twoCharLabelTokenParams - Static variable in class org.jmol.modelset.LabelToken
twodots - Static variable in class org.jmol.render.FontLineShapeRenderer
twoP2 - Static variable in class org.jmol.symmetry.UnitCell
twoPass - Variable in class org.jmol.g3d.Graphics3D
TWOPI - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
TWOPI - Static variable in class org.jmol.util.Modulation
twoPI - Static variable in class org.jmol.util.Vibration
TwoPointGesture - Class in org.jmol.multitouch.sparshui
  TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
Txt - Class in org.jmol.util
Txt() - Constructor for class org.jmol.util.Txt
type - Variable in class org.jmol.adapter.readers.more.JcampdxReader
type - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
type - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
type - Variable in enum org.jmol.c.VDW
type - Variable in class org.jmol.jvxl.readers.IsoMepReader
type - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
type - Variable in class org.jmol.jvxl.readers.PmeshReader
type - Variable in class org.jmol.jvxl.readers.Ras3DReader
type - Variable in class org.jmol.minimize.MinObject
type - Variable in class org.jmol.minimize.MMConstraint
type - Variable in class org.jmol.modelkit.Constraint
type - Variable in class org.jmol.modelset.Measurement
type - Variable in class org.jmol.modelset.TickInfo
type - Variable in class org.jmol.modelsetbio.BioPolymer
type - Variable in class org.jmol.modelsetbio.ProteinStructure
type - Variable in class org.jmol.quantum.NciCalculation
type - Static variable in class org.jmol.script.T
type - Variable in class org.jmol.shapespecial.Dipole
type - Variable in class org.jmol.smiles.SmilesMeasure
type - Variable in class org.jmol.symmetry.PointGroup.Operation
type - Variable in class org.jmol.util.Modulation
type - Variable in class org.jmol.util.Tensor
type2 - Variable in enum org.jmol.c.VDW
TYPE_ADP - Static variable in class org.jmol.util.Tensor
TYPE_ALL - Static variable in class org.jmol.quantum.NciCalculation
TYPE_AMINO - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_ANGLE - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_ANGLE - Static variable in class org.jmol.minimize.MMConstraint
TYPE_ANGLE - Static variable in class org.jmol.modelkit.Constraint
TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
TYPE_ATROPISOMER - Static variable in class org.jmol.util.Edge
TYPE_ATROPISOMER_REV - Static variable in class org.jmol.util.Edge
TYPE_BIO_CROSSLINK - Static variable in class org.jmol.smiles.SmilesBond
TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
TYPE_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_BOND - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_BUTTON - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_CHARGE - Static variable in class org.jmol.util.Tensor
TYPE_CHECKBOX - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_CHRG - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_DIFF - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
TYPE_DIFF - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
TYPE_DIFF_PAIR - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
TYPE_DIFF_PAIR - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
TYPE_DIHEDRAL - Static variable in class org.jmol.minimize.MMConstraint
TYPE_DIHEDRAL - Static variable in class org.jmol.modelkit.Constraint
TYPE_DISP_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_DISP_LEGENDRE - Static variable in class org.jmol.util.Modulation
TYPE_DISP_SAWTOOTH - Static variable in class org.jmol.util.Modulation
TYPE_DISTANCE - Static variable in class org.jmol.minimize.MMConstraint
TYPE_DISTANCE - Static variable in class org.jmol.modelkit.Constraint
TYPE_EFG - Static variable in class org.jmol.util.Tensor
TYPE_FUNCTION - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
TYPE_FUNCTION - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
TYPE_INTER - Static variable in class org.jmol.quantum.NciCalculation
TYPE_INTRA - Static variable in class org.jmol.quantum.NciCalculation
TYPE_ISC - Static variable in class org.jmol.util.Tensor
TYPE_ISO - Static variable in class org.jmol.util.Tensor
TYPE_LIGAND - Static variable in class org.jmol.quantum.NciCalculation
TYPE_MAX - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
TYPE_MAX - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
TYPE_MENU - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_MS - Static variable in class org.jmol.util.Tensor
TYPE_NOBONDING - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
TYPE_NUCLEIC - Static variable in class org.jmol.modelsetbio.BioPolymer
TYPE_OCC_CRENEL - Static variable in class org.jmol.util.Modulation
TYPE_OCC_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_OOP - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_OTHER - Static variable in class org.jmol.util.Tensor
TYPE_PBCI - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_QUADRUPOLE - Static variable in class org.jmol.util.Tensor
TYPE_RADIO - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_RAMAN - Static variable in class org.jmol.util.Tensor
TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
TYPE_SB - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_SEPARATOR - Static variable in class org.jmol.awtjs.swing.JMenuItem
TYPE_SPIN - Static variable in class org.jmol.util.Vibration
TYPE_SPIN_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_SPIN_SAWTOOTH - Static variable in class org.jmol.util.Modulation
TYPE_SUM - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
TYPE_SUM - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cif.CifReader
TYPE_SYMMETRY - Static variable in class org.jmol.modelkit.Constraint
TYPE_TLS_R - Static variable in class org.jmol.util.Tensor
TYPE_TLS_U - Static variable in class org.jmol.util.Tensor
TYPE_TORSION - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_U_FOURIER - Static variable in class org.jmol.util.Modulation
TYPE_U_LEGENDRE - Static variable in class org.jmol.util.Modulation
TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
TYPE_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
TYPE_VIBRATION - Static variable in class org.jmol.util.Vibration
typeArray - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
typeData - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
typeFactor - Variable in class org.jmol.util.Tensor
TypeFilter(String) - Constructor for class org.jmol.dialog.Dialog.TypeFilter
typeName - Variable in class org.jmol.script.ScriptFunction
typeNames - Static variable in class org.jmol.symmetry.PointGroup
typeOf(int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
typeOf(SV) - Static method in class org.jmol.script.ScriptMathProcessor
types - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
types - Static variable in class org.jmol.modelsetbio.BioResolver
TYPES - Static variable in class org.jmol.smiles.SmilesMeasure
typeSelected - Variable in class org.jmol.shapespecial.Ellipsoids

## U

U_ISO_OR_EQUIV - Static variable in class org.jmol.adapter.readers.cif.CifReader
U_LIST - Static variable in class org.jmol.adapter.readers.cif.MSRdr
U_LIST - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
uABsM(String) - Static method in class org.jmol.util.Escape
Uccage - Class in org.jmol.shape
Uccage() - Constructor for class org.jmol.shape.Uccage
UccageRenderer - Class in org.jmol.render
UccageRenderer() - Constructor for class org.jmol.render.UccageRenderer
uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
UFFAngleCalc - Class in org.jmol.minimize.forcefield
UFFAngleCalc() - Constructor for class org.jmol.minimize.forcefield.UFFAngleCalc
UFFDistanceCalc - Class in org.jmol.minimize.forcefield
UFFDistanceCalc() - Constructor for class org.jmol.minimize.forcefield.UFFDistanceCalc
UFFOOPCalc - Class in org.jmol.minimize.forcefield
UFFOOPCalc() - Constructor for class org.jmol.minimize.forcefield.UFFOOPCalc
UFFTorsionCalc - Class in org.jmol.minimize.forcefield
UFFTorsionCalc() - Constructor for class org.jmol.minimize.forcefield.UFFTorsionCalc
UFFVDWCalc - Class in org.jmol.minimize.forcefield
UFFVDWCalc() - Constructor for class org.jmol.minimize.forcefield.UFFVDWCalc
uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
UhbdReader - Class in org.jmol.jvxl.readers
  UHBD reader
UhbdReader() - Constructor for class org.jmol.jvxl.readers.UhbdReader
uicrcifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
unaryMinus - Static variable in class org.jmol.script.T
unbind - Static variable in class org.jmol.script.T
unbindAction(String, String) - Method in class org.jmol.viewer.ActionManager
unbindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
unbindName(int, String) - Method in class org.jmol.viewer.binding.Binding
unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
UNBRACKETED_SET - Static variable in class org.jmol.smiles.SmilesAtom
unCentered - Variable in class org.jmol.symmetry.SymmetryOperation
undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
  called from org.jmol.modelsetbio.resolver when adding hydrogens.
UNDETERMINED - Static variable in class org.jmol.symmetry.CIPChirality
undo - Variable in class org.jmol.console.ScriptEditor.EditorDocument
undo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
undo - Static variable in class org.jmol.script.T
undoableEditHappened(UndoableEditEvent) - Method in class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
undoButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoClear() - Method in class org.jmol.viewer.Viewer
undoClear() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undomove - Static variable in class org.jmol.script.T
undoMoveAction(int, int) - Method in class org.jmol.viewer.JmolStateCreator
undoMoveAction(int, int) - Method in class org.jmol.viewer.StateCreator
undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.JmolStateCreator
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.StateCreator
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.Viewer
undoPointer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoRedo(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoSave(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoSaved - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoSetEnabled() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoStack - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
undoWorking - Variable in class org.jmol.viewer.StateCreator
unEscapeBitSet(SV, BS) - Static method in class org.jmol.script.SV
  Turn the string "({3:5})" into a bitset
unEscapeBitSetArray(Lst<SV>, boolean) - Static method in class org.jmol.script.SV
  Turn an array of strings in the form of "{n,n,n:n...} or an array of integers into a bitset.
unescapeMatrix(String) - Static method in class org.jmol.util.Escape
unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.SV
unescapeString(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
unescapeStringArray(String) - Static method in class org.jmol.util.Escape
unescapeUnicode(String) - Static method in class org.jmol.util.Escape
uniqueAtomMap - Variable in class org.jmol.adapter.readers.quantum.PsiReader
uniqueAxis - Variable in class org.jmol.symmetry.SpaceGroup
UNIQUEID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
uniqueID - Variable in class org.jmol.adapter.smarter.Bond
uniqueIDs - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
uniqueList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
uniqueList - Variable in class org.jmol.smiles.SmilesSearch
uniqueSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
uniqueSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
unitAxisVectors - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
unitAxisVectors - Static variable in class org.jmol.viewer.JC
unitBboxPoints - Static variable in class org.jmol.util.BoxInfo
unitcell - Variable in class org.jmol.render.UccageRenderer
unitcell - Static variable in class org.jmol.script.T
unitcell(int) - Method in class org.jmol.scriptext.CmdExt
unitCell - Variable in class org.jmol.shape.Mesh
unitCell - Variable in class org.jmol.symmetry.Symmetry
UnitCell - Class in org.jmol.symmetry
  a class private to the org.jmol.symmetry package to be accessed only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
UnitCell() - Constructor for class org.jmol.symmetry.UnitCell
unitCell - Variable in class org.jmol.symmetry.UnitCellIterator
UNITCELL_OPTIONS - Static variable in class org.jmol.modelkit.ModelKitPopup
unitcellcolor - Static variable in class org.jmol.script.T
unitCellData - Variable in class org.jmol.adapter.readers.xtal.DmolReader
unitCellData - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
unitCellEquals(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
unitCellEquals(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
UnitCellIterator - Class in org.jmol.symmetry
UnitCellIterator() - Constructor for class org.jmol.symmetry.UnitCellIterator
unitCellMultiplier - Variable in class org.jmol.symmetry.UnitCell
unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
unitCellOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
UnitcellOnly - Variable in class org.jmol.popup.JmolPopup
unitCellParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
unitCellParams - Variable in class org.jmol.adapter.smarter.XtalSymmetry
unitCellParams - Variable in class org.jmol.util.SimpleUnitCell
unitCellParamsS - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
unitCellParamTags - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
unitCells - Variable in class org.jmol.modelset.ModelSet
unitCellTranslations - Variable in class org.jmol.adapter.smarter.XtalSymmetry
unitCellVectors - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
unitCubePoints - Static variable in class org.jmol.util.BoxInfo
unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
UNITID_ATOM - Static variable in class org.jmol.viewer.JC
UNITID_INSCODE - Static variable in class org.jmol.viewer.JC
UNITID_MODEL - Static variable in class org.jmol.viewer.JC
UNITID_RESIDUE - Static variable in class org.jmol.viewer.JC
UNITID_TRIM - Static variable in class org.jmol.viewer.JC
unitIdSets - Variable in class org.jmol.modelsetbio.BioModelSet
unitize(T3) - Method in interface org.jmol.api.SymmetryInterface
unitize(T3) - Method in class org.jmol.symmetry.Symmetry
unitize(T3) - Method in class org.jmol.symmetry.UnitCell
  returns [0,1)
unitList - Variable in class org.jmol.symmetry.UnitCellIterator
units - Variable in class org.jmol.minimize.Minimizer
units - Variable in class org.jmol.modelset.MeasurementData
UNITS_PI - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
unitVectors - Static variable in class org.jmol.symmetry.UnitCell
unitVectorX - Variable in class org.jmol.modelsetbio.BioPolymer
unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
unitx - Static variable in class org.jmol.script.T
unitxyz - Static variable in class org.jmol.script.T
unity - Static variable in class org.jmol.script.T
unitz - Static variable in class org.jmol.script.T
UNKNOWN - Static variable in class org.jmol.viewer.SelectionManager
unlikeDuplicates(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
  This check is not technically one of those listed in the rules, but it is useful when preparing to check substituents because if one of the atoms has substituents and the other doesn't, we are done -- there is no reason to check substituents.
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.C
unquoted(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
  Handle unquoted value as Integer or Float if we can.
unreportedProperties - Static variable in class org.jmol.viewer.GlobalSettings
unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
UNSET - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
unsetProperty(String) - Method in class org.jmol.viewer.Viewer
unsetUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
unsetVariables(Map<String, SV>, Lst<SV>) - Method in class org.jmol.script.ScriptFunction
unsetVoxelData() - Method in class org.jmol.jvxl.readers.AtomDataReader
unsetVoxelData() - Method in class org.jmol.jvxl.readers.IsoSolventReader
unsetVoxelData2() - Method in class org.jmol.jvxl.readers.AtomDataReader
unsupportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
untaint(int, int) - Method in class org.jmol.modelset.AtomCollection
unTaintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
untransformedPoint - Variable in class org.jmol.viewer.TransformManager
unTransformPoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
untranslated - Variable in exception org.jmol.script.ScriptException
unused_boolean_def_true - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
unwrapCdata(String) - Static method in class org.jmol.jvxl.readers.XmlReader
uP(String) - Static method in class org.jmol.util.Escape
UP - Static variable in class org.jmol.viewer.binding.Binding
update(Graphics) - Method in class org.jmol.applet.AppletWrapper
update(Graphics) - Method in class org.jmol.applet.Jmol
update(Graphics, String) - Method in class org.jmol.applet.Jmol
update(Graphics) - Method in interface org.jmol.applet.WrappedApplet
update() - Method in class org.jmol.appletjs.Jmol
update(LineEvent) - Method in class org.jmol.util.JmolAudio
update(String) - Method in class org.jmol.viewer.ChimeMessenger
  called upon script exit and file opening
update(String) - Method in interface org.jmol.viewer.JmolChimeMessenger
UPDATE_ALL - Static variable in class org.jmol.popup.JmolPopup
UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolPopup
UPDATE_NEVER - Static variable in class org.jmol.popup.JmolPopup
UPDATE_SHOW - Static variable in class org.jmol.popup.JmolPopup
updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
updateAllXtalMenuOptions() - Method in class org.jmol.modelkit.ModelKitPopup
updateAllXtalMenus() - Method in class org.jmol.modelkit.ModelKitPopup
updateAngleSliders() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
updateAtomXYZ() - Method in class org.jmol.minimize.Minimizer
updateBSAtoms() - Method in class org.jmol.adapter.smarter.XtalSymmetry
  Update asc.bsAtoms to include all atoms, or at least all atoms that are still viable from the reader.
updateButton(SC, String, String) - Method in class org.jmol.popup.GenericPopup
updateCheckBoxesForShow() - Method in class org.jmol.popup.GenericPopup
updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
updateComponents() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateConsoleFont() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
updateCoordinates(M4, BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
  bs will be null if this is a set from the new isosurface MOVE [mat4] command
updateElementsComputedMenu(BS) - Method in class org.jmol.popup.JmolPopup
updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
updateFileMenu() - Method in class org.jmol.popup.JmolPopup
updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolPopup
updateFontSize() - Method in class org.jmol.console.JmolConsole
updateFontSize() - Method in class org.jmol.console.ScriptEditor
updateFontSize() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateGroup3List(SC, String) - Method in class org.jmol.popup.JmolPopup
updateHeteroComputedMenu(Map<String, String>) - Method in class org.jmol.popup.JmolPopup
updateInvalidatedVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
updateJS() - Method in class org.jmol.viewer.Viewer
  for JavaScript only
updateJSView(int, int) - Method in class org.jmol.viewer.Viewer
  File has been loaded or model has been changed or atom picked.
updateLabels() - Method in class org.jmol.console.GenericConsole
updateLabels() - Method in class org.jmol.console.JmolConsole
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
updateLocations(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
updateMeasurementTableData() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
updateMeshInfo(Shape[], int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
updateMode - Variable in class org.jmol.popup.JmolPopup
updateModel(int) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
updateModelIDs(String, int, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
  The first model set is allowed to be a single model and given no extension.
updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateOffsetsForAlternativeLocations(Atom[], BS) - Method in class org.jmol.modelsetbio.Monomer
updateOperatorMenu() - Method in class org.jmol.modelkit.ModelKitPopup
updateParameters() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
updatePDBComputedMenus() - Method in class org.jmol.popup.JmolPopup
updatePositionSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
updateSceneComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
  Update screen informations
updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
updateSignedAppletItems() - Method in class org.jmol.popup.GenericPopup
updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
updateSlices() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
updateSpecialMenuItem(SC) - Method in class org.jmol.popup.JmolPopup
updateSpectraMenu() - Method in class org.jmol.popup.JmolPopup
updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
updateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
updateSurfaceInfo() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
updateSurfaceList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
updateSurfMoComputedMenu(Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolPopup
updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolPopup
updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
updateThicknessSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
updateTriangles() - Method in class org.jmol.jvxl.readers.SurfaceReader
updateUI() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
updateVars() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
updateWindow(int, int) - Method in class org.jmol.viewer.Viewer
updatingForShow - Variable in class org.jmol.popup.GenericPopup
url - Static variable in class org.jmol.script.T
url - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
urlEncode(String) - Method in class org.jmol.viewer.FileManager
urlPrefixPairs - Static variable in class org.jmol.awt.AwtFile
use_display_lists - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
USE_PALETTE - Static variable in class org.jmol.util.C
use_shaders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
useAbsolute - Variable in class org.jmol.quantum.NciCalculation
useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
useAuthorChainID - Variable in class org.jmol.adapter.readers.cif.CifReader
useBananas - Variable in class org.jmol.render.SticksRenderer
useColix - Variable in class org.jmol.shape.Mesh
useColix - Variable in class org.jmol.shapecgo.CGO
useCommandThread - Variable in class org.jmol.viewer.Viewer
useCommandWatcherThread - Variable in class org.jmol.script.ScriptManager
useFileModelNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
useGUI - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
useLight - Variable in class org.jmol.util.Shader
useminimizationthread - Static variable in class org.jmol.script.T
useMinimizationThread - Variable in class org.jmol.viewer.GlobalSettings
useMinimizationThread() - Method in class org.jmol.viewer.Viewer
useMolecular - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
usenumberlocalization - Static variable in class org.jmol.script.T
useNumberLocalization - Variable in class org.jmol.viewer.GlobalSettings
useOriginStepsPoints - Variable in class org.jmol.jvxl.readers.VolumeDataReader
usePercent - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
usePhongExponent - Variable in class org.jmol.util.Shader
usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
user - Static variable in class org.jmol.script.T
USER - Static variable in class org.jmol.util.ColorEncoder
userAction(int, Object[]) - Method in class org.jmol.viewer.ActionManager
  If the user has created a function to handle this action, run it and cancel action processing if that function returns an explicit FALSE;
userActionEnabled(int) - Method in class org.jmol.viewer.ActionManager
userAtomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
usercolorscheme - Static variable in class org.jmol.script.T
userData - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
userDefinedVanDerWaalRadius - Variable in class org.jmol.modelset.Atom
userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
userScale - Variable in class org.jmol.util.ColorEncoder
userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
userVdwMars - Variable in class org.jmol.viewer.Viewer
userVdws - Variable in class org.jmol.viewer.Viewer
useScriptQueue - Variable in class org.jmol.viewer.GlobalSettings
useTable - Variable in class org.jmol.export._VrmlExporter
useTable - Variable in class org.jmol.export.JSExporter
UseTable - Class in org.jmol.export
UseTable(String) - Constructor for class org.jmol.export.UseTable
useThreads() - Method in class org.jmol.script.ScriptEval
useTimeout - Variable in class org.jmol.thread.JmolThread
useUnitCell - Variable in class org.jmol.shapespecial.Polyhedra
useZoomLarge - Variable in class org.jmol.viewer.TransformManager
utens - Variable in class org.jmol.util.Modulation
Util - Class in org.jmol.minimize
Util() - Constructor for class org.jmol.minimize.Util

## V

v - Variable in class org.jmol.console.JmolConsole.FileChecker
v - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
v - Variable in class org.jmol.smiles.SmilesSearch
v - Variable in class org.jmol.smiles.SmilesStereo
v0 - Variable in class org.jmol.util.ModulationSet
v0Cart - Variable in class org.jmol.adapter.readers.xtal.JanaReader
v1 - Variable in class org.jmol.adapter.readers.simple.InputReader
v1 - Variable in class org.jmol.minimize.forcefield.Calculations
v1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
v1 - Variable in class org.jmol.viewer.TransformManager4D
v176 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
v176b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
v177 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
v177b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
v181 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
v181b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
v2 - Variable in class org.jmol.adapter.readers.simple.InputReader
v2 - Variable in class org.jmol.minimize.forcefield.Calculations
v2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
v3 - Variable in class org.jmol.minimize.forcefield.Calculations
v3 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
V3000Rdr - Class in org.jmol.adapter.readers.molxyz
  A reader for Accelrys V3000 files.
V3000Rdr() - Constructor for class org.jmol.adapter.readers.molxyz.V3000Rdr
v3temp - Variable in class org.jmol.renderspecial.DotsRenderer
vA - Variable in class org.jmol.smiles.VTemp
vAB - Static variable in class org.jmol.g3d.HermiteRenderer
vAB - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
vAB - Variable in class org.jmol.modelsetbio.BioResolver
vAB - Variable in class org.jmol.shape.Mesh
vAB - Variable in class org.jmol.shapespecial.Draw
vAB - Variable in class org.jmol.shapespecial.Polyhedra
vAB - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
vAC - Static variable in class org.jmol.g3d.HermiteRenderer
vAC - Variable in class org.jmol.shapespecial.Polyhedra
vAC - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
val - Variable in class org.jmol.minimize.forcefield.AtomType
val - Static variable in class org.jmol.script.T
valence - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
VALENCE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
valence - Variable in class org.jmol.modelset.Atom
valence - Static variable in class org.jmol.script.T
valence - Variable in class org.jmol.smiles.SmilesAtom
valence_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
valence_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
validate() - Method in class org.jmol.awtjs.swing.JDialog
validate(boolean) - Method in class org.jmol.shapespecial.Ellipsoid
VALIDATE - Static variable in class org.jmol.util.Geodesic
validate_object_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
validateAndAllocate(Chain, String, int, int, int) - Static method in class org.jmol.modelsetbio.CarbohydrateMonomer
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
validateAndAllocateA(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.AlphaMonomer
validateAndAllocateP(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.PhosphorusMonomer
validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
validateBspfForModel(int, boolean) - Method in class org.jmol.modelset.AtomCollection
validateFace(int, int, int, IsoSolventReader.Edge, P3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
validateModel(int, boolean) - Method in class org.jmol.bspt.Bspf
validatePolyhedron(P3, int) - Method in class org.jmol.shapespecial.Polyhedra
validation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
validation - Static variable in class org.jmol.script.T
validSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
valign - Variable in class org.jmol.modelset.Text
value - Variable in class org.jmol.adapter.readers.xml.XmlReader.NVPair
value - Variable in class org.jmol.atomdata.RadiusData
value - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
value - Variable in class org.jmol.minimize.MMConstraint
value - Variable in class org.jmol.modelkit.Constraint
value - Variable in class org.jmol.modelset.Measurement
value - Variable in class org.jmol.script.T
value - Variable in class org.jmol.thread.MoveToThread.Slider
value - Variable in class org.jmol.util.Int2IntHashEntry
valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
valueCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
valueExtended - Variable in class org.jmol.atomdata.RadiusData
valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
valueMappedToBlue - Variable in class org.jmol.jvxl.readers.Parameters
valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
valueMappedToRed - Variable in class org.jmol.jvxl.readers.Parameters
valueMax - Variable in class org.jmol.jvxl.calc.MarchingSquares
valueMin - Variable in class org.jmol.jvxl.calc.MarchingSquares
valueMin - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
valueOf(String) - Static method in enum org.jmol.atomdata.RadiusData.EnumType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.CBK
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.FIL
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.HB
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.PAL
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.STER
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.STR
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.VDW
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.util.Edge.EnumBondOrder
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.viewer.Viewer.ACCESS
  Returns the enum constant of this type with the specified name.
valuePeek() - Method in class org.jmol.script.ScriptTokenParser
valueRange - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
values() - Static method in enum org.jmol.atomdata.RadiusData.EnumType
  Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.atomdata.RadiusData
values() - Static method in enum org.jmol.c.CBK
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.FIL
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.HB
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.PAL
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.STER
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.STR
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.VDW
  Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.jvxl.readers.BCifDensityReader
values - Variable in class org.jmol.jvxl.readers.IsoFxyReader
values - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
values - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
values() - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.util.Edge.EnumBondOrder
  Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.util.MeshSlicer
values() - Static method in enum org.jmol.viewer.Viewer.ACCESS
  Returns an array containing the constants of this enum type, in the order they are declared.
vanderwaals - Static variable in class org.jmol.script.T
vanderwaalsMars - Static variable in class org.jmol.util.Elements
  Default table of van der Waals Radii.
var - Variable in class org.jmol.script.ScriptFlowContext
var - Static variable in class org.jmol.script.T
varButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
variable - Static variable in class org.jmol.script.T
variables - Variable in class org.jmol.script.ScriptFunction
variables - Static variable in class org.jmol.script.T
varray - Static variable in class org.jmol.script.T
vars - Variable in class org.jmol.script.ScriptContext
VaspChgcarReader - Class in org.jmol.adapter.readers.xtal
  http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
VaspChgcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspChgcarReader
VaspChgcarReader - Class in org.jmol.jvxl.readers
VaspChgcarReader() - Constructor for class org.jmol.jvxl.readers.VaspChgcarReader
vaspOutcarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
  http://cms.mpi.univie.ac.at/vasp/
VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
VaspPoscarReader - Class in org.jmol.adapter.readers.xtal
  adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
VaspPoscarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspPoscarReader
vAtoms - Variable in class org.jmol.adapter.readers.simple.InputReader
vB - Variable in class org.jmol.smiles.VTemp
vBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
vBC - Variable in class org.jmol.shapespecial.Polyhedra
vBiomolecules - Variable in class org.jmol.adapter.readers.cif.MMCifReader
vBiomolecules - Variable in class org.jmol.adapter.readers.pdb.PdbReader
vBraces - Variable in class org.jmol.script.ScriptCompiler
vButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
vc - Variable in class org.jmol.util.MeshSurface
  vertex count
vCompnds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
vConnect - Variable in class org.jmol.adapter.readers.pdb.PdbReader
vContours - Variable in class org.jmol.jvxl.data.JvxlData
vcs - Variable in class org.jmol.util.MeshSurface
  vertex color index "colix" array
vData - Variable in class org.jmol.shapespecial.Draw
vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
vDist - Variable in class org.jmol.jvxl.readers.IsoMOReader
VDW - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
VDW - Enum in org.jmol.c
VDW(int, String, String) - Constructor for enum org.jmol.c.VDW
vdw1 - Variable in class org.jmol.modelset.AtomIteratorWithinModel
vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
vdwKey - Variable in class org.jmol.minimize.MinAtom
vdwPercentSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
VdwPROBE - Static variable in class org.jmol.util.Elements
vdws - Variable in class org.jmol.util.ContactPair
vdwType - Variable in class org.jmol.atomdata.RadiusData
vdwVolume - Variable in class org.jmol.util.ContactPair
vecs - Static variable in class org.jmol.adapter.readers.xtal.CgdReader
vector - Static variable in class org.jmol.script.T
vector - Variable in class org.jmol.shapespecial.Dipole
VECTOR - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
  String for prefix/resource identifier for the vector area.
vector12ths - Variable in class org.jmol.symmetry.HallInfo
vectorAB - Variable in class org.jmol.g3d.Graphics3D
vectorAC - Variable in class org.jmol.g3d.Graphics3D
vectorAngleRadians(V3d, V3d) - Static method in class org.jmol.minimize.Util
vectorCode - Variable in class org.jmol.symmetry.HallInfo
vectorNormal - Variable in class org.jmol.g3d.Graphics3D
vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
vectors - Variable in class org.jmol.jvxl.readers.MapFileReader
Vectors - Class in org.jmol.shapespecial
Vectors() - Constructor for class org.jmol.shapespecial.Vectors
vectorScale - Variable in class org.jmol.renderspecial.VectorsRenderer
vectorscale - Static variable in class org.jmol.script.T
vectorScale - Variable in class org.jmol.viewer.GlobalSettings
vectorsCentered - Variable in class org.jmol.renderspecial.VectorsRenderer
vectorscentered - Static variable in class org.jmol.script.T
vectorsCentered - Variable in class org.jmol.viewer.GlobalSettings
vectorShift12ths - Variable in class org.jmol.symmetry.HallTranslation
VectorsRenderer - Class in org.jmol.renderspecial
VectorsRenderer() - Constructor for class org.jmol.renderspecial.VectorsRenderer
vectorSymmetry - Variable in class org.jmol.renderspecial.VectorsRenderer
vectorsymmetry - Static variable in class org.jmol.script.T
vectorSymmetry - Variable in class org.jmol.viewer.GlobalSettings
vectorT - Variable in class org.jmol.render.FontLineShapeRenderer
vectorT - Variable in class org.jmol.viewer.TransformManager
vectorT2 - Variable in class org.jmol.render.FontLineShapeRenderer
vectorT2 - Variable in class org.jmol.viewer.TransformManager
vectorT3 - Variable in class org.jmol.render.FontLineShapeRenderer
vectorTemp - Variable in class org.jmol.viewer.TransformManager
vectorTrail - Variable in class org.jmol.renderspecial.VectorsRenderer
vectortrail - Static variable in class org.jmol.script.T
vectorTrail - Variable in class org.jmol.viewer.GlobalSettings
vEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
version - Variable in class org.jmol.jvxl.data.JvxlData
version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
version - Static variable in class org.jmol.viewer.JC
version - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
VERSION - Static variable in class org.openscience.jvxl.Jvxl
version_date - Static variable in class org.jmol.viewer.Viewer
versionInt - Static variable in class org.jmol.viewer.JC
VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
vertexBase - Variable in class org.jmol.jvxl.readers.PmeshReader
vertexColixes - Variable in class org.jmol.shapesurface.PMeshWriter
vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
vertexColorMap - Variable in class org.jmol.shape.Mesh
vertexColors - Variable in class org.jmol.jvxl.data.JvxlData
vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
vertexCount - Variable in class org.jmol.render.MeshRenderer
vertexCount - Variable in class org.jmol.shapesurface.PMeshWriter
vertexCount0 - Variable in class org.jmol.util.MeshSurface
vertexCounts - Static variable in class org.jmol.util.Geodesic
vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
vertexDataOnly - Variable in class org.jmol.jvxl.readers.SurfaceReader
VertexDataServer - Interface in org.jmol.jvxl.api
vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
vertexMap - Variable in class org.jmol.jvxl.readers.EfvetReader
vertexMap - Variable in class org.jmol.jvxl.readers.NffReader
vertexMap - Variable in class org.jmol.jvxl.readers.PmeshReader
vertexNext - Static variable in class org.jmol.util.Geodesic
vertexSets - Variable in class org.jmol.util.MeshSurface
vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
vertexSource - Variable in class org.jmol.util.MeshSurface
vertexTest - Variable in class org.jmol.geodesic.EnvelopeCalculation
vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
vertexValues - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
vertexValues - Variable in class org.jmol.shapesurface.PMeshWriter
vertexVectors - Static variable in class org.jmol.util.Geodesic
vertexVectors - Static variable in class org.jmol.util.Normix
vertices - Variable in class org.jmol.render.MeshRenderer
vertices - Static variable in class org.jmol.script.T
vertices - Variable in class org.jmol.shapespecial.Polyhedron
vertices - Variable in class org.jmol.symmetry.UnitCell
vertices - Variable in class org.jmol.util.MeshCapper
verticesT - Variable in class org.jmol.render.UccageRenderer
vF - Static variable in class org.jmol.script.SV
vf - Variable in class org.jmol.shape.Shape
  shape visibility flag
vFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader
vFunctionStack - Variable in class org.jmol.script.ScriptCompiler
vH - Variable in class org.jmol.renderbio.RocketRenderer
vHBonds - Variable in class org.jmol.dssx.DSSP
vib - Variable in class org.jmol.adapter.smarter.Atom
vib - Variable in class org.jmol.util.ModulationSet
  vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
VIB_ENERGY - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
vibFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
vibFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
vibration - Static variable in class org.jmol.script.T
Vibration - Class in org.jmol.util
  A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
Vibration() - Constructor for class org.jmol.util.Vibration
VIBRATION_VECTOR_FLAG - Static variable in class org.jmol.modelset.Atom
vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
vibrationOn - Variable in class org.jmol.renderspecial.VectorsRenderer
vibrationOn - Variable in class org.jmol.viewer.TransformManager
VibrationOnly - Variable in class org.jmol.popup.JmolPopup
vibrationperiod - Static variable in class org.jmol.script.T
vibrationPeriod - Variable in class org.jmol.viewer.GlobalSettings
vibrationPeriod - Variable in class org.jmol.viewer.TransformManager
vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
vibrations - Variable in class org.jmol.modelset.AtomCollection
vibrationscale - Static variable in class org.jmol.script.T
vibrationScale - Variable in class org.jmol.viewer.GlobalSettings
vibrationScale - Variable in class org.jmol.viewer.TransformManager
vibrationSteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
vibrationSteps - Variable in class org.jmol.modelset.ModelSet
vibrationT - Variable in class org.jmol.viewer.TransformManager
VibrationThread - Class in org.jmol.thread
VibrationThread() - Constructor for class org.jmol.thread.VibrationThread
vibrationThread - Variable in class org.jmol.viewer.TransformManager
vibs - Variable in class org.jmol.renderspecial.PolyhedraRenderer
vibScale - Variable in class org.jmol.adapter.smarter.AtomSetCollection
vibScale - Variable in class org.jmol.jsv.JDXMOLParser
vibsFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
vibTemp - Variable in class org.jmol.renderspecial.VectorsRenderer
vibx - Static variable in class org.jmol.script.T
vibxyz - Static variable in class org.jmol.script.T
viby - Static variable in class org.jmol.script.T
vibz - Static variable in class org.jmol.script.T
viewButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
viewCenterButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
viewer - Variable in class org.jmol.util.GenericApplet
Viewer - Class in org.jmol.viewer
Viewer(Map<String, Object>) - Constructor for class org.jmol.viewer.Viewer
  new way...
Viewer.ACCESS - Enum in org.jmol.viewer
viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
viewOffset - Variable in class org.jmol.modelkit.ModelKitPopup
viewpoint - Variable in class org.jmol.export.__CartesianExporter
virtual_trackball - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
VIS_BACKBONE_FLAG - Static variable in class org.jmol.viewer.JC
VIS_BALLS_FLAG - Static variable in class org.jmol.viewer.JC
VIS_BOND_FLAG - Static variable in class org.jmol.viewer.JC
VIS_CARTOON_FLAG - Static variable in class org.jmol.viewer.JC
VIS_LABEL_FLAG - Static variable in class org.jmol.viewer.JC
VISIBILITY_CLIPPED - Static variable in class org.jmol.g3d.LineRenderer
VISIBILITY_OFFSCREEN - Static variable in class org.jmol.g3d.LineRenderer
VISIBILITY_UNCLIPPED - Static variable in class org.jmol.g3d.LineRenderer
visibilityFlags - Variable in class org.jmol.shape.Mesh
visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedron
visible - Variable in class org.jmol.adapter.readers.pymol.JmolObject
visible - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
visible - Variable in class org.jmol.modelset.Text
visible - Static variable in class org.jmol.script.T
visible - Variable in class org.jmol.shape.Mesh
visible - Variable in class org.jmol.shapespecial.Dipole
visible - Variable in class org.jmol.shapespecial.Ellipsoid
visible - Variable in class org.jmol.shapespecial.Polyhedron
VISREP - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
visualrange - Static variable in class org.jmol.script.T
visualRangeAngstroms - Variable in class org.jmol.viewer.TransformManager
VK_ALT - Static variable in class org.jmol.awtjs.Event
VK_BACK_SPACE - Static variable in class org.jmol.awtjs.Event
VK_CONTROL - Static variable in class org.jmol.awtjs.Event
VK_DELETE - Static variable in class org.jmol.awtjs.Event
VK_DOWN - Static variable in class org.jmol.awtjs.Event
VK_ESCAPE - Static variable in class org.jmol.awtjs.Event
VK_LEFT - Static variable in class org.jmol.awtjs.Event
VK_META - Static variable in class org.jmol.awtjs.Event
VK_PAGE_DOWN - Static variable in class org.jmol.awtjs.Event
VK_PAGE_UP - Static variable in class org.jmol.awtjs.Event
VK_PERIOD - Static variable in class org.jmol.awtjs.Event
VK_RIGHT - Static variable in class org.jmol.awtjs.Event
VK_SHIFT - Static variable in class org.jmol.awtjs.Event
VK_SPACE - Static variable in class org.jmol.awtjs.Event
VK_UP - Static variable in class org.jmol.awtjs.Event
vl0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
vl1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
vl2 - Variable in class org.jmol.jvxl.readers.AtomDataReader
vMax - Variable in class org.jmol.jvxl.readers.KinemageReader
vMin - Variable in class org.jmol.jvxl.readers.KinemageReader
vNorm - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
vNorm - Variable in class org.jmol.modelsetbio.BioResolver
vNorm - Variable in class org.jmol.symmetry.CIPData
vNorm - Variable in class org.jmol.util.MolWriter
vNorm2 - Variable in class org.jmol.smiles.VTemp
vNorm3 - Variable in class org.jmol.smiles.VTemp
vNorm4 - Variable in class org.jmol.smiles.VTemp
vOcc - Variable in class org.jmol.util.ModulationSet
  the current value of the occupancy modulation
volume - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
volume - Variable in class org.jmol.quantum.QuantumCalculation
volume - Static variable in class org.jmol.script.T
volume - Variable in class org.jmol.shapespecial.Polyhedron
volume - Variable in class org.jmol.util.BZone
volume - Variable in class org.jmol.util.ContactPair
volume - Variable in class org.jmol.util.SimpleUnitCell
volume_bit_depth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
volume_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
volume_data_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
volume_layers - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
volumeData - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
volumeData - Variable in class org.jmol.jvxl.calc.MarchingSquares
VolumeData - Class in org.jmol.jvxl.data
VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
volumeData - Variable in class org.jmol.jvxl.readers.Parameters
volumeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
volumeData - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
VolumeDataReader - Class in org.jmol.jvxl.readers
VolumeDataReader() - Constructor for class org.jmol.jvxl.readers.VolumeDataReader
volumeDataTemp - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
VolumeFileReader - Class in org.jmol.jvxl.readers
VolumeFileReader() - Constructor for class org.jmol.jvxl.readers.VolumeFileReader
volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
volumeRender(boolean) - Method in class org.jmol.export.Export3D
volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
volumeRender - Variable in class org.jmol.render.MeshRenderer
volumeRender4(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
volumeRender4(int, int, int, int) - Method in class org.jmol.export.Export3D
volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
volumeRenderPointSize - Variable in class org.jmol.shape.Mesh
volumetricMatrix - Variable in class org.jmol.jvxl.data.VolumeData
volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
vOrientations - Variable in class org.jmol.modelset.ModelSet
voxelCount - Variable in class org.jmol.jvxl.readers.UhbdReader
voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
voxelData - Variable in class org.jmol.jvxl.calc.MarchingCubes
voxelData - Variable in class org.jmol.jvxl.data.VolumeData
voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
voxelData - Variable in class org.jmol.quantum.QuantumCalculation
VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
VoxelDataCreator(VolumeData) - Constructor for class org.openscience.jvxl.simplewriter.VoxelDataCreator
voxelDataTemp - Variable in class org.jmol.quantum.QuantumCalculation
voxelList - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
voxelMap - Variable in class org.jmol.jvxl.data.VolumeData
voxelPtToXYZ(int, int, int, T3) - Method in class org.jmol.jvxl.data.VolumeData
voxelSource - Variable in class org.jmol.jvxl.readers.AtomDataReader
voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
vPush - Variable in class org.jmol.script.ScriptCompiler
vr - Variable in class org.jmol.adapter.readers.molxyz.MolReader
vR - Variable in class org.jmol.adapter.readers.xtal.JanaReader
vRef - Static variable in class org.jmol.modelset.AtomCollection
vRef - Variable in class org.jmol.smiles.PolyhedronStereoSorter
vReturn - Variable in class org.jmol.smiles.SmilesSearch
vRings - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
vs - Variable in class org.jmol.util.MeshSurface
  vertices
vStereo - Variable in class org.jmol.modelset.ModelLoader
vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
vT - Static variable in class org.jmol.script.SV
vTemp - Variable in class org.jmol.jvxl.readers.IsoMOReader
vTemp - Variable in class org.jmol.jvxl.readers.IsoSolventReader
vTemp - Variable in class org.jmol.modelset.ModelSet
vtemp - Variable in class org.jmol.renderbio.RocketRenderer
vTemp - Variable in class org.jmol.renderspecial.DrawRenderer
vTemp - Variable in class org.jmol.shape.Mesh
vTemp - Variable in class org.jmol.smiles.PolyhedronStereoSorter
vTemp - Variable in class org.jmol.smiles.SmilesGenerator
VTemp - Class in org.jmol.smiles
VTemp() - Constructor for class org.jmol.smiles.VTemp
vTemp - Variable in class org.jmol.smiles.VTemp
vTemp - Variable in class org.jmol.symmetry.CIPData
vTemp - Variable in class org.jmol.symmetry.PointGroup
vTemp - Variable in class org.jmol.util.MolWriter
vTemp - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
vTemp1 - Variable in class org.jmol.smiles.VTemp
vTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
vTemp2 - Variable in class org.jmol.renderspecial.DrawRenderer
vTemp2 - Variable in class org.jmol.smiles.VTemp
vTlsModels - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
vTlsModels - Variable in class org.jmol.adapter.readers.pdb.PdbReader
vvs - Variable in class org.jmol.util.MeshSurface
  vertex values
vW - Variable in class org.jmol.renderbio.RocketRenderer
vwr - Variable in class org.jmol.adapter.readers.pymol.PickleReader
vwr - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
vwr - Variable in class org.jmol.adapter.readers.quantum.NBOParser
vwr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
vwr - Variable in class org.jmol.adapter.writers.QCJSONWriter
vwr - Variable in class org.jmol.awt.FileDropper
vwr - Variable in class org.jmol.awt.Mouse
vwr - Variable in class org.jmol.awt.Platform
vwr - Variable in class org.jmol.awtjs2d.Mouse
vwr - Variable in class org.jmol.awtjs2d.Platform
vwr - Variable in class org.jmol.console.GenericConsole
vwr - Variable in class org.jmol.console.ImageDialog
vwr - Variable in class org.jmol.console.ScriptEditor
vwr - Variable in class org.jmol.dialog.Dialog
vwr - Variable in class org.jmol.dialog.FilePreview.FPPanel
vwr - Variable in class org.jmol.dialog.FilePreview
vwr - Variable in class org.jmol.export.___Exporter
vwr - Variable in class org.jmol.geodesic.EnvelopeCalculation
vwr - Static variable in class org.jmol.i18n.GT
vwr - Variable in class org.jmol.io.DOMReader
vwr - Variable in class org.jmol.io.FileReader
vwr - Variable in class org.jmol.io.FilesReader
vwr - Variable in class org.jmol.jsv.JSpecView
vwr - Variable in class org.jmol.minimize.Minimizer
vwr - Variable in class org.jmol.modelset.AtomCollection
vwr - Variable in class org.jmol.modelset.AtomIteratorWithinModel
vwr - Variable in class org.jmol.modelset.Measurement
vwr - Variable in class org.jmol.modelset.MeasurementData
vwr - Variable in class org.jmol.modelset.ModelLoader
vwr - Variable in class org.jmol.modelset.Orientation
vwr - Variable in class org.jmol.modelset.Text
vwr - Variable in class org.jmol.modelset.Trajectory
vwr - Variable in class org.jmol.modelsetbio.BioExt
vwr - Variable in class org.jmol.modelsetbio.BioModel
vwr - Variable in class org.jmol.modelsetbio.BioModelSet
vwr - Variable in class org.jmol.modelsetbio.BioResolver
vwr - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
vwr - Variable in class org.jmol.popup.JmolGenericPopup
vwr - Variable in class org.jmol.quantum.MepCalculation
vwr - Variable in class org.jmol.quantum.NMRCalculation
vwr - Variable in class org.jmol.render.RepaintManager
vwr - Variable in class org.jmol.render.ShapeRenderer
vwr - Variable in class org.jmol.renderbio.NucleicRenderer
vwr - Variable in class org.jmol.renderbio.RocketRenderer
vwr - Variable in class org.jmol.script.ScriptError
vwr - Variable in class org.jmol.script.ScriptManager
vwr - Variable in class org.jmol.script.ScriptMathProcessor
vwr - Variable in class org.jmol.script.ScriptParallelProcessor
vwr - Variable in class org.jmol.script.ScriptTokenParser
vwr - Variable in class org.jmol.scriptext.MathExt
vwr - Variable in class org.jmol.scriptext.ScriptExt
vwr - Variable in class org.jmol.shape.Shape
vwr - Variable in class org.jmol.symmetry.CIPData
  Jmol's viewer class
vwr - Variable in class org.jmol.thread.JmolThread
vwr - Variable in class org.jmol.util.BZone
vwr - Variable in class org.jmol.util.ColorEncoder
vwr - Variable in class org.jmol.util.GData
vwr - Variable in class org.jmol.util.JmolAudio
vwr - Variable in class org.jmol.util.MeshSurface
vwr - Variable in class org.jmol.util.MolWriter
vwr - Variable in class org.jmol.viewer.ActionManager
vwr - Variable in class org.jmol.viewer.AnimationManager
vwr - Variable in class org.jmol.viewer.ChimeMessenger
vwr - Variable in class org.jmol.viewer.ColorManager
vwr - Variable in class org.jmol.viewer.Connections
vwr - Variable in class org.jmol.viewer.DataManager
vwr - Variable in class org.jmol.viewer.FileManager
vwr - Variable in class org.jmol.viewer.Gesture
vwr - Variable in class org.jmol.viewer.GlobalSettings
vwr - Variable in class org.jmol.viewer.ModelManager
vwr - Variable in class org.jmol.viewer.OutputManager
vwr - Variable in class org.jmol.viewer.PropertyManager
vwr - Variable in class org.jmol.viewer.SelectionManager
vwr - Variable in class org.jmol.viewer.ShapeManager
vwr - Variable in class org.jmol.viewer.StateCreator
vwr - Variable in class org.jmol.viewer.StateManager
vwr - Variable in class org.jmol.viewer.StatusManager
vwr - Variable in class org.jmol.viewer.TransformManager
vwr - Variable in class org.openscience.jmol.app.InputScannerThread
vwr - Variable in class org.openscience.jmol.app.JmolData
vwr - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
vwr - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
vwr - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
vwr - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
vwr - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
vwr - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
vwr - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
vwr - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
vwr - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
vwr - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
vwr - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
vwr - Variable in class org.openscience.jmol.app.webexport.JmolInstance
vwr - Variable in class org.openscience.jmol.app.webexport.Test
vwr - Variable in class org.openscience.jmol.app.webexport.WebPanel
vwrFrame - Variable in class org.jmol.console.JmolConsole
vwrOptions - Variable in class org.jmol.util.GenericApplet
vwrOptions - Variable in class org.jmol.viewer.Viewer
vwrOptions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
vX - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping Cartesian origin, X, and Y
vX - Variable in class org.jmol.shapesurface.Contact
vY - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping Cartesian origin, X, and Y
vY - Variable in class org.jmol.shapesurface.Contact
vZ - Variable in class org.jmol.shapesurface.Contact

## W

w - Variable in class org.jmol.adapter.readers.cif.Subsystem
w - Static variable in class org.jmol.script.T
waitForDisplay(Object, Object) - Method in interface org.jmol.api.GenericPlatform
  can be ignored (return false) if platform cannot save images
waitForDisplay(PlatformViewer, Object) - Static method in class org.jmol.awt.Image
waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
waitForDisplay(Object, Object) - Method in class org.jmol.awtjs2d.Platform
waitformoveto - Static variable in class org.jmol.script.T
waitForMoveTo - Variable in class org.jmol.viewer.GlobalSettings
waitForQueue() - Method in interface org.jmol.api.JmolScriptManager
waitForQueue() - Method in class org.jmol.script.ScriptManager
walkDOMTree() - Method in class org.jmol.adapter.readers.xml.XmlReader
warn(String) - Method in class org.jmol.util.DefaultLogger
warn(String) - Static method in class org.jmol.util.Logger
  Writes a log at WARN level.
warn(String) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at WARN level.
warned - Variable in class org.jmol.quantum.MOCalculation
warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
  Writes a log at WARN level with detail on exception.
warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
  Writes a log at WARN level with detail on exception.
warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
warning(int, String, String) - Method in class org.jmol.script.ScriptError
wasClicked(int, int) - Method in class org.jmol.shape.Frank
wasClicked(int, int) - Method in class org.jmol.shape.Shape
wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
wasImpliedScript() - Method in class org.jmol.script.ScriptCompiler
  Check for improperly parsed implied script command: only two tokens: [implied script] xxx.SORT/REVERSE/PUSH/POP more than two tokens: xxxx.spt(3,4,5)
wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
wasPerspective - Variable in class org.jmol.export.__RayTracerExporter
wasScreened - Variable in class org.jmol.g3d.Graphics3D
wasSpinOn - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
wasSyntaxCheck - Variable in class org.jmol.script.ScriptMathProcessor
wasX - Variable in class org.jmol.script.ScriptMathProcessor
WB - Static variable in class org.jmol.util.ColorEncoder
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
webExport - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
WebExport - Class in org.openscience.jmol.app.webexport
WebExport(Viewer, HistoryFile) - Constructor for class org.openscience.jmol.app.webexport.WebExport
webExport - Static variable in class org.openscience.jmol.app.webexport.WebExport
webFrame - Static variable in class org.openscience.jmol.app.webexport.WebExport
webGL - Variable in class org.jmol.export.Export3D
webmoFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
WebMOReader - Class in org.jmol.adapter.readers.quantum
  A molecular orbital reader for WebMO files.
WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
webPageTitle - Variable in class org.openscience.jmol.app.webexport.WebPanel
webPanel - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
WebPanel - Class in org.openscience.jmol.app.webexport
WebPanel(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.WebPanel
WebPanel.InstanceCellRenderer - Class in org.openscience.jmol.app.webexport
webPanels - Static variable in class org.openscience.jmol.app.webexport.WebExport
webPanels - Variable in class org.openscience.jmol.app.webexport.WebPanel
weightx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
weighty - Variable in class org.jmol.awtjs.swing.GridBagConstraints
WEST - Static variable in class org.jmol.awtjs.swing.BorderLayout
WEST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
WHEEL - Static variable in class org.jmol.viewer.binding.Binding
WHEELED - Static variable in class org.jmol.awtjs.Event
wheeled(long, int, int) - Method in class org.jmol.awtjs2d.Mouse
wheeling - Variable in class org.jmol.awt.Mouse
wheeling - Variable in class org.jmol.awtjs2d.Mouse
whichOrigin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
whichWidgets - Variable in class org.openscience.jmol.app.webexport.JmolInstance
whilecmd - Static variable in class org.jmol.script.T
WHITE - Static variable in class org.jmol.util.C
Widget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.Widget
widgetCheckboxes - Variable in class org.openscience.jmol.app.webexport.WebPanel
widgetList - Variable in class org.openscience.jmol.app.webexport.Widgets
Widgets - Class in org.openscience.jmol.app.webexport
Widgets() - Constructor for class org.openscience.jmol.app.webexport.Widgets
Widgets.AnimationWidget - Class in org.openscience.jmol.app.webexport
Widgets.BackgroundColorWidget - Class in org.openscience.jmol.app.webexport
Widgets.ConsoleWidget - Class in org.openscience.jmol.app.webexport
Widgets.DownLoadWidget - Class in org.openscience.jmol.app.webexport
Widgets.SpinOnWidget - Class in org.openscience.jmol.app.webexport
Widgets.StereoViewWidget - Class in org.openscience.jmol.app.webexport
Widgets.Widget - Class in org.openscience.jmol.app.webexport
width - Variable in class org.jmol.awtjs.swing.Component
width - Variable in class org.jmol.awtjs.swing.Dimension
width - Variable in class org.jmol.export.Export3D
width - Variable in class org.jmol.g3d.Pixelator
width - Variable in class org.jmol.g3d.SphereRenderer
width - Variable in class org.jmol.g3d.TextRenderer
width - Variable in class org.jmol.modelset.LabelToken
width - Variable in class org.jmol.render.FontLineShapeRenderer
width - Variable in class org.jmol.render.MeshRenderer
width - Variable in class org.jmol.render.StarsRenderer
width - Static variable in class org.jmol.script.T
width - Variable in class org.jmol.shape.Mesh
width - Variable in class org.jmol.shapespecial.Draw
width - Variable in class org.jmol.util.GData
width - Variable in class org.jmol.util.Rectangle
width - Variable in class org.jmol.viewer.TransformManager
width - Variable in class org.openscience.jmol.app.webexport.JmolInstance
widthOffscreen - Variable in class org.jmol.g3d.Platform3D
widths - Variable in class org.jmol.modelset.Text
WIDTHSCALE - Static variable in class org.jmol.shapecgo.CGOMesh
widthUnitVector - Variable in class org.jmol.modelsetbio.Sheet
Wien2kReader - Class in org.jmol.adapter.readers.xtal
  A reader for Wein2k DFT files.
Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
wigner - Static variable in class org.jmol.script.T
wildcard - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
wildID - Variable in class org.jmol.shapespecial.Dipoles
window - Static variable in class org.jmol.script.T
windowActivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowActivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowcentered - Static variable in class org.jmol.script.T
windowCentered - Variable in class org.jmol.viewer.TransformManager
windowCenteredFlag - Variable in class org.jmol.modelset.Orientation
windowClosed(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowClosed(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowClosing(HTMLElement) - Method in interface org.jmol.awtjs.swing.SwingController
  Called by clicking the [x] in the corner of the dialog; send a notification back to the manager via processWindowClosing(key) var id = $("div.JDialog:has(#" + element.id + ")")[0].id var dialog = Jmol.Swing.htDialogs[id]; dialog.manager.processWindowClosing(dialog.registryKey);
windowClosing(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowClosing(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
  Closes the dialog when window closing event occurs.
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowDeactivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowDeactivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowDeiconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowDeiconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowHeight - Variable in class org.jmol.awtjs2d.JsG2D
windowHeight - Variable in class org.jmol.g3d.Platform3D
windowHeight - Variable in class org.jmol.modelset.Text
windowHeight - Variable in class org.jmol.util.GData
windowIconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowIconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
WindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowName - Static variable in class org.openscience.jmol.app.webexport.WebExport
windowOpened(WindowEvent) - Method in class org.jmol.console.ImageDialog
windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
windowOpened(WindowEvent) - Method in class org.jmol.console.ScriptEditor
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowSize - Variable in class org.jmol.g3d.Platform3D
windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
windowWidth - Variable in class org.jmol.awtjs2d.JsG2D
windowWidth - Variable in class org.jmol.g3d.Platform3D
windowWidth - Variable in class org.jmol.modelset.Text
windowWidth - Variable in class org.jmol.util.GData
wing - Variable in class org.jmol.renderbio.BioMeshRenderer
wing1 - Variable in class org.jmol.renderbio.BioMeshRenderer
wingHermites - Variable in class org.jmol.renderbio.BioMeshRenderer
wingT - Variable in class org.jmol.renderbio.BioMeshRenderer
wingVectors - Variable in class org.jmol.modelsetbio.BioPolymer
wingVectors - Variable in class org.jmol.renderbio.BioShapeRenderer
wingVectors - Variable in class org.jmol.shapebio.BioShape
wireframe - Static variable in class org.jmol.script.T
wireframeOnly - Variable in class org.jmol.render.SticksRenderer
wireframeOnly - Variable in class org.jmol.renderbio.BioShapeRenderer
wireframerotation - Static variable in class org.jmol.script.T
wireframeRotation - Variable in class org.jmol.viewer.GlobalSettings
within - Static variable in class org.jmol.script.T
within(float, P3, Lst<P3>) - Method in class org.jmol.util.BZone
withinDistance2 - Variable in class org.jmol.shapesurface.Isosurface
withinDistPoints(float, P3, P3[], P3[], Object[]) - Static method in class org.jmol.bspt.PointIterator
  carry out various functions of the within() script function
withinPoints - Variable in class org.jmol.shapesurface.Isosurface
wizard_prompt_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
WMATRIX - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
words - Variable in class org.jmol.popup.PopupResource
working - Static variable in class org.jmol.g3d.TextRenderer
wPlane - Variable in class org.jmol.util.MeshSlicer
wrap_output - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManager
wrappedApplet - Variable in class org.jmol.applet.AppletWrapper
WrappedApplet - Interface in org.jmol.applet
WrappedAppletLoader - Class in org.jmol.applet
WrappedAppletLoader(Applet, boolean) - Constructor for class org.jmol.applet.WrappedAppletLoader
write - Static variable in class org.jmol.script.T
write(T[]) - Method in class org.jmol.scriptext.CmdExt
write(IsosurfaceMesh, boolean) - Method in class org.jmol.shapesurface.PMeshWriter
writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
writeArray(Object) - Method in class org.jmol.util.JSONWriter
writeAtoms(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeBonds(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeBoolean(Boolean) - Method in class org.jmol.util.JSONWriter
writeFacet(T3[], int[], int, int, int) - Method in class org.jmol.export._StlExporter
writeFile(String, String) - Static method in class org.openscience.jvxl.Jvxl
writeFile(String, String) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.OutputManager
  Generates file data and passes it on either to a FileOuputStream (Java) or via POSTing to a url using a ByteOutputStream (JavaScript)
writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
writeFileZipped(String[], byte[], int) - Static method in class org.openscience.jmol.app.webexport.WebPanel
writeFloat(float) - Method in class org.jmol.export._StlExporter
writeFrame(int, String[], Map<String, Object>, SB) - Method in class org.jmol.viewer.OutputManager
writeJob(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeJobMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeJobs() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeJSON() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeList(List<Object>) - Method in class org.jmol.util.JSONWriter
writeMacros() - Method in class org.jmol.export._PovrayExporter
writeMacros2() - Method in class org.jmol.export._PovrayExporter
writeMacrosAtom() - Method in class org.jmol.export._PovrayExporter
writeMacrosBond() - Method in class org.jmol.export._PovrayExporter
writeMacrosFinish() - Method in class org.jmol.export._PovrayExporter
writeMagic() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeMap(Map<String, Object>) - Method in class org.jmol.util.JSONWriter
writeMapKeyValueUnits(String, Object, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeMOBases() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeMOData(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeModel(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeModelMetadata(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeModels() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeMsg(String) - Method in class org.jmol.scriptext.CmdExt
writeNull() - Method in class org.jmol.util.JSONWriter
writeNullAsString - Variable in class org.jmol.util.JSONWriter
writeNumber(Number) - Method in class org.jmol.util.JSONWriter
writeObject(Object) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeObject(Object) - Method in class org.jmol.util.JSONWriter
writePmeshHeader(int) - Method in class org.jmol.shapesurface.PMeshWriter
writePoint(String, T3) - Method in class org.jmol.export._StlExporter
writePrefix_Units(String, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeSchemaMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
writeString(String) - Method in class org.jmol.util.JSONWriter
writeString(String, SB) - Method in class org.jmol.util.JSONWriter
writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
writeToOutputChannel(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
  From handleOutputToFile, write text, byte[], or image data to a file;
writeTopology(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeVibrations(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
writeZipFile(OC, Lst<Object>, String, String) - Method in class org.jmol.viewer.OutputManager
  generic method to create a zip file based on http://www.exampledepot.com/egs/java.util.zip/CreateZip.html
WV_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
WV_X - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
WV_Y - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
WV_Z - Static variable in class org.jmol.adapter.readers.cif.MSCifParser

## X

X - Variable in class org.jmol.quantum.QuantumCalculation
x - Variable in class org.jmol.quantum.SlaterData
x - Variable in class org.jmol.render.SticksRenderer
x - Static variable in class org.jmol.script.T
x - Variable in class org.jmol.shape.Frank
X - Static variable in class org.jmol.util.BoxInfo
x - Variable in class org.jmol.util.Rectangle
x - Variable in class org.jmol.viewer.MotionPoint
x - Variable in class org.jmol.viewer.MouseState
x0 - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping min/max x and y
x1t - Variable in class org.jmol.g3d.LineRenderer
X2 - Variable in class org.jmol.quantum.QuantumCalculation
x2t - Variable in class org.jmol.g3d.LineRenderer
xA - Variable in class org.jmol.g3d.CylinderRenderer
xA - Variable in class org.jmol.render.SticksRenderer
xAdj - Variable in class org.jmol.modelset.Text
xAf - Variable in class org.jmol.g3d.CylinderRenderer
xAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
xAxis1 - Variable in class org.jmol.render.SticksRenderer
xAxis2 - Variable in class org.jmol.render.SticksRenderer
xB - Variable in class org.jmol.render.SticksRenderer
xBohr - Variable in class org.jmol.quantum.QuantumCalculation
xcrysDenContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
XcrysdenReader - Class in org.jmol.adapter.readers.xtal
XcrysdenReader() - Constructor for class org.jmol.adapter.readers.xtal.XcrysdenReader
xEndcap - Variable in class org.jmol.g3d.CylinderRenderer
xGT - Static variable in class org.jmol.util.GData
xIndex - Variable in class org.jmol.jvxl.readers.MapFileReader
xLast - Variable in class org.jmol.util.GData
xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
xLight - Variable in class org.jmol.util.Shader
xLT - Static variable in class org.jmol.util.GData
xMax - Variable in class org.jmol.quantum.QuantumCalculation
xMin - Variable in class org.jmol.quantum.QuantumCalculation
XmlArgusReader - Class in org.jmol.adapter.readers.xml
  A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
XmlChem3dReader - Class in org.jmol.adapter.readers.xml
  An chem3d c3xml reader
XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
XmlCmlReader - Class in org.jmol.adapter.readers.xml
  A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
xmlContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
xmlData - Variable in class org.jmol.jvxl.data.VolumeData
XmlHandler - Class in org.jmol.adapter.readers.xml
  a SAX handler -- Java only
XmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlHandler
XmlMagResReader - Class in org.jmol.adapter.readers.xml
XmlMagResReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMagResReader
XmlMolproReader - Class in org.jmol.adapter.readers.xml
  A Molpro 2005 reader
XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
XmlMOReader - Class in org.jmol.adapter.readers.xml
  An abstract class accessing MOReader -- currently just for XmlMolproReader only.
XmlMOReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMOReader
XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
  An Odyssey xodydata reader
XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
XmlQEReader - Class in org.jmol.adapter.readers.xml
  QuantumEspresso XML reader
XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
xmlReader - Variable in class org.jmol.adapter.readers.xml.XmlHandler
XmlReader - Class in org.jmol.adapter.readers.xml
  A generic XML reader template -- by itself, does nothing.
XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
XmlReader - Class in org.jmol.jvxl.readers
XmlReader(BufferedReader) - Constructor for class org.jmol.jvxl.readers.XmlReader
XmlReader.NVPair - Class in org.jmol.adapter.readers.xml
xmlStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
XmlVaspReader - Class in org.jmol.adapter.readers.xml
  Vasp vasprun.xml reader
XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
XmlXsdReader - Class in org.jmol.adapter.readers.xml
  An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
xNav - Variable in class org.jmol.modelset.Orientation
xNav - Variable in class org.jmol.thread.MoveToThread
XplorReader - Class in org.jmol.jvxl.readers
XplorReader() - Constructor for class org.jmol.jvxl.readers.XplorReader
xpos - Variable in class org.jmol.render.UccageRenderer
xPt - Variable in class org.jmol.script.ScriptMathProcessor
xr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
XsfReader - Class in org.jmol.jvxl.readers
XsfReader() - Constructor for class org.jmol.jvxl.readers.XsfReader
xStack - Variable in class org.jmol.script.ScriptMathProcessor
xtalHoverLabel - Variable in class org.jmol.modelkit.ModelKitPopup
xtalSymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
XtalSymmetry - Class in org.jmol.adapter.smarter
  A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
XtalSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry
xTip - Variable in class org.jmol.g3d.CylinderRenderer
xTrans - Variable in class org.jmol.modelset.Orientation
xTrans - Variable in class org.jmol.navigate.Navigator
xTrans - Variable in class org.jmol.thread.MoveToThread
xTransDelta - Variable in class org.jmol.navigate.Navigator
xTranslationFraction - Variable in class org.jmol.viewer.TransformManager
xTransStart - Variable in class org.jmol.navigate.Navigator
xVdwClash - Variable in class org.jmol.util.ContactPair
xWhenPressed - Variable in class org.jmol.awt.Mouse
xWhenPressed - Variable in class org.jmol.awtjs2d.Mouse
xy - Variable in class org.jmol.render.LabelsRenderer
xy - Variable in class org.jmol.shape.Hover
XY_RANGE - Static variable in class org.jmol.viewer.ActionManager
XY_THREASHOLD - Static variable in class org.jmol.shape.Sticks
XY_ZTOP - Static variable in class org.jmol.viewer.JC
xyCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
xypParameter(int) - Method in class org.jmol.script.ScriptParam
XYZ - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
XYZ - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
xyz - Variable in class org.jmol.atomdata.AtomData
xyz - Variable in class org.jmol.modelset.Text
xyz - Static variable in class org.jmol.script.T
xyz - Variable in class org.jmol.symmetry.SymmetryOperation
XYZ - Static variable in class org.jmol.util.BoxInfo
xyzFraction12(float, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
xyzFraction48ths(float, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
xyzfRaster - Variable in class org.jmol.g3d.CylinderRenderer
xyzIsSlabbedInternal(T3) - Method in class org.jmol.viewer.TransformManager
xyzList - Variable in class org.jmol.symmetry.SpaceGroup
xyzMax - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
xyzMin - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
xyzOriginal - Variable in class org.jmol.symmetry.SymmetryOperation
xyzpParameter(int) - Method in class org.jmol.script.ScriptParam
XyzReader - Class in org.jmol.adapter.readers.molxyz
  Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
xyzStart - Variable in class org.jmol.jvxl.readers.MapFileReader
xyzToVoxelPt(float, float, float, T3i) - Method in class org.jmol.jvxl.data.VolumeData
xyztRaster - Variable in class org.jmol.g3d.CylinderRenderer

## Y

Y - Variable in class org.jmol.quantum.QuantumCalculation
y - Variable in class org.jmol.quantum.SlaterData
y - Variable in class org.jmol.render.SticksRenderer
y - Static variable in class org.jmol.script.T
y - Variable in class org.jmol.shape.Frank
Y - Static variable in class org.jmol.util.BoxInfo
y - Variable in class org.jmol.util.Rectangle
y - Variable in class org.jmol.viewer.MotionPoint
y - Variable in class org.jmol.viewer.MouseState
y0 - Variable in class org.jmol.modelset.Text
y0 - Variable in class org.jmol.rendercgo.CGORenderer
  UV mapping min/max x and y
y1t - Variable in class org.jmol.g3d.LineRenderer
Y2 - Variable in class org.jmol.quantum.QuantumCalculation
y2t - Variable in class org.jmol.g3d.LineRenderer
yA - Variable in class org.jmol.g3d.CylinderRenderer
yA - Variable in class org.jmol.render.SticksRenderer
yAdj - Variable in class org.jmol.modelset.Text
yAf - Variable in class org.jmol.g3d.CylinderRenderer
yAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
yAxis1 - Variable in class org.jmol.render.SticksRenderer
yAxis2 - Variable in class org.jmol.render.SticksRenderer
yB - Variable in class org.jmol.render.SticksRenderer
yBohr - Variable in class org.jmol.quantum.QuantumCalculation
YELLOW - Static variable in class org.jmol.util.C
yEndcap - Variable in class org.jmol.g3d.CylinderRenderer
yGT - Static variable in class org.jmol.util.GData
yIndex - Variable in class org.jmol.jvxl.readers.MapFileReader
yLast - Variable in class org.jmol.util.GData
yLight - Variable in class org.jmol.util.Shader
yLT - Static variable in class org.jmol.util.GData
yMax - Variable in class org.jmol.quantum.QuantumCalculation
yMin - Variable in class org.jmol.quantum.QuantumCalculation
yNav - Variable in class org.jmol.modelset.Orientation
yNav - Variable in class org.jmol.thread.MoveToThread
ypos - Variable in class org.jmol.render.UccageRenderer
yTip - Variable in class org.jmol.g3d.CylinderRenderer
yTrans - Variable in class org.jmol.modelset.Orientation
yTrans - Variable in class org.jmol.navigate.Navigator
yTrans - Variable in class org.jmol.thread.MoveToThread
yTransDelta - Variable in class org.jmol.navigate.Navigator
yTranslationFraction - Variable in class org.jmol.viewer.TransformManager
yTransStart - Variable in class org.jmol.navigate.Navigator
yWhenPressed - Variable in class org.jmol.awt.Mouse
yWhenPressed - Variable in class org.jmol.awtjs2d.Mouse
yxNext - Variable in class org.jmol.util.MeshCapper.CapVertex
  Y-X scan queue forward link
yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
yzCount - Variable in class org.jmol.jvxl.data.VolumeData
yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
yzCount - Variable in class org.jmol.quantum.NciCalculation
yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader
yzPlanesRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
yzPlanesRaw - Variable in class org.jmol.quantum.NciCalculation
yzPlanesRho - Variable in class org.jmol.quantum.NciCalculation

## Z

z - Variable in class org.jmol.modelset.Text
Z - Variable in class org.jmol.quantum.QuantumCalculation
z - Variable in class org.jmol.quantum.SlaterData
z - Variable in class org.jmol.render.SticksRenderer
z - Static variable in class org.jmol.script.T
Z - Static variable in class org.jmol.util.BoxInfo
z1t - Variable in class org.jmol.g3d.LineRenderer
Z2 - Variable in class org.jmol.quantum.QuantumCalculation
z2t - Variable in class org.jmol.g3d.LineRenderer
zA - Variable in class org.jmol.g3d.CylinderRenderer
zA - Variable in class org.jmol.render.SticksRenderer
zAf - Variable in class org.jmol.g3d.CylinderRenderer
zAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
zap() - Method in class org.jmol.console.GenericConsole
zap - Static variable in class org.jmol.script.T
zap() - Method in class org.jmol.viewer.ModelManager
zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
ZAP_TITLE - Static variable in class org.jmol.viewer.JC
zapMsg(String) - Method in class org.jmol.viewer.Viewer
zb - Variable in class org.jmol.g3d.Pixelator
zB - Variable in class org.jmol.render.SticksRenderer
zBohr - Variable in class org.jmol.quantum.QuantumCalculation
zBox - Variable in class org.jmol.render.LabelsRenderer
zbuf - Variable in class org.jmol.g3d.Graphics3D
zbuf - Variable in class org.jmol.g3d.SphereRenderer
zBuffer - Variable in class org.jmol.g3d.Platform3D
zBufferT - Variable in class org.jmol.g3d.Platform3D
zbufT - Variable in class org.jmol.g3d.Graphics3D
zDepth - Variable in class org.jmol.g3d.PixelatorShaded
zdepth - Static variable in class org.jmol.script.T
zDepth - Variable in class org.jmol.viewer.GlobalSettings
zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
zDepthToPercent(int) - Method in class org.jmol.viewer.TransformManager
zDepthValue - Variable in class org.jmol.viewer.TransformManager
zEndcap - Variable in class org.jmol.g3d.CylinderRenderer
zero - Variable in class org.jmol.viewer.TransformManager4D
zeroBase - Variable in class org.jmol.modelset.AtomIteratorWithinModel
zerobasedxyzrasmol - Static variable in class org.jmol.script.T
zeroBasedXyzRasmol - Variable in class org.jmol.viewer.GlobalSettings
zeroFontId - Variable in class org.jmol.shape.Labels
zeroPad - Variable in class org.jmol.modelset.LabelToken
zeta - Variable in class org.jmol.quantum.SlaterData
zeta1 - Static variable in class org.jmol.quantum.NciCalculation
zeta2 - Static variable in class org.jmol.quantum.NciCalculation
zeta3 - Static variable in class org.jmol.quantum.NciCalculation
zGT - Static variable in class org.jmol.util.GData
zIndex - Variable in class org.jmol.awtjs.swing.JDialog
zIndex - Variable in class org.jmol.jvxl.readers.MapFileReader
zipFileName - Variable in class org.jmol.console.ScriptEditor
zLight - Variable in class org.jmol.util.Shader
zLT - Static variable in class org.jmol.util.GData
zMargin - Variable in class org.jmol.g3d.Graphics3D
zMax - Variable in class org.jmol.quantum.QuantumCalculation
zMin - Variable in class org.jmol.quantum.QuantumCalculation
zmPct - Variable in class org.jmol.viewer.TransformManager
  zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled
zmPctSet - Variable in class org.jmol.viewer.TransformManager
  zoom percent setting the current setting of zoom; may not be the same as zmPct, particularly if zoom is not enabled
znuc - Variable in class org.jmol.quantum.QMAtom
znucl - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
zOffset - Variable in class org.jmol.viewer.TransformManager4D
zoneIndex - Variable in class org.jmol.util.BZone
zoom - Variable in class org.jmol.modelset.Orientation
zoom - Static variable in class org.jmol.script.T
zoom - Variable in class org.jmol.thread.MoveToThread
ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
zoomBy(int) - Method in class org.jmol.viewer.TransformManager
  standard response to user mouse vertical shift-drag
zoomBy(int) - Method in class org.jmol.viewer.Viewer
zoomByFactor(float, int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
zoomByFactor(float, int, int) - Method in class org.jmol.navigate.Navigator
zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.TransformManager
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.Viewer
zoomByPercent(float) - Method in class org.jmol.viewer.TransformManager
zoomenabled - Static variable in class org.jmol.script.T
zoomEnabled - Variable in class org.jmol.viewer.TransformManager
zoomFactor - Variable in class org.jmol.viewer.TransformManager
zoomheight - Static variable in class org.jmol.script.T
zoomHeight - Variable in class org.jmol.viewer.GlobalSettings
zoomHeight - Variable in class org.jmol.viewer.TransformManager
zoomlarge - Static variable in class org.jmol.script.T
zoomLarge - Variable in class org.jmol.viewer.GlobalSettings
zoomPercent0 - Variable in class org.jmol.thread.MoveToThread
zoomRatio - Variable in class org.jmol.viewer.TransformManager
zoomTo - Static variable in class org.jmol.script.T
zoomTo(int) - Method in class org.jmol.viewer.ActionManager
zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
zoomTrigger - Variable in class org.jmol.viewer.ActionManager
zroot - Variable in class org.jmol.g3d.SphereRenderer
zshade - Static variable in class org.jmol.script.T
zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
zShadePower - Variable in class org.jmol.g3d.PixelatorShaded
zshadepower - Static variable in class org.jmol.script.T
zShadePower - Variable in class org.jmol.viewer.GlobalSettings
zSlab - Variable in class org.jmol.g3d.PixelatorShaded
zSlab - Variable in class org.jmol.modelset.Text
zSlab - Variable in class org.jmol.render.LabelsRenderer
zslab - Static variable in class org.jmol.script.T
zSlab - Variable in class org.jmol.viewer.GlobalSettings
zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
zSlabPoint - Variable in class org.jmol.viewer.TransformManager
zSlabToPercent(int) - Method in class org.jmol.viewer.TransformManager
zSlabValue - Variable in class org.jmol.viewer.TransformManager
zTip - Variable in class org.jmol.g3d.CylinderRenderer
zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager

## _

_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
_8PI2_ - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
__ - Static variable in class org.jmol.script.T
___Exporter - Class in org.jmol.export
___Exporter() - Constructor for class org.jmol.export.___Exporter
__CartesianExporter - Class in org.jmol.export
__CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
__RayTracerExporter - Class in org.jmol.export
__RayTracerExporter() - Constructor for class org.jmol.export.__RayTracerExporter
_activeLevels - Static variable in class org.jmol.util.Logger
_atomPickedCallback(int, int) - Method in interface org.jmol.api.js.JSmolAppletObject
_birth - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
_id1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_id2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_IdtfExporter - Class in org.jmol.export
_IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
_logger - Static variable in class org.jmol.util.Logger
_logLevel - Static variable in class org.jmol.util.Logger
_MayaExporter - Class in org.jmol.export
_MayaExporter() - Constructor for class org.jmol.export._MayaExporter
_myId - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
_myType - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_nCurrent - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
_nMoves - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
_nTraces - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_ObjExporter - Class in org.jmol.export
  Class to export Wavefront OBJ files.
_ObjExporter() - Constructor for class org.jmol.export._ObjExporter
_offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_PovrayExporter - Class in org.jmol.export
_PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
_refresh() - Method in interface org.jmol.api.js.JSmolAppletObject
_rotation - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_scale - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_StlExporter - Class in org.jmol.export
  STereoLithography file format exporter for 3D printing.
_StlExporter() - Constructor for class org.jmol.export._StlExporter
_TachyonExporter - Class in org.jmol.export
_TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
_traces1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_traces2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
_visible - Variable in class org.jmol.awtjs.swing.Component
_VrmlExporter - Class in org.jmol.export
  A basic VRML generator.
_VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
_X3dExporter - Class in org.jmol.export
_X3dExporter() - Constructor for class org.jmol.export._X3dExporter

$ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _