Date: 2019-10-22

# Serialized Form

- ## Package org.jmol.adapter.smarter

  - ### Class org.jmol.adapter.smarter.Atom extends javajs.util.P3 implements Serializable

    - ### Serialized Fields

      - #### atomSetIndex

            int atomSetIndex

      - #### index

            int index

      - #### bsSymmetry

            javajs.util.BS bsSymmetry

      - #### atomSite

            int atomSite

      - #### elementSymbol

            java.lang.String elementSymbol

      - #### elementNumber

            short elementNumber

      - #### atomName

            java.lang.String atomName

      - #### formalCharge

            int formalCharge

      - #### partialCharge

            float partialCharge

      - #### vib

            javajs.util.V3 vib

      - #### bfactor

            float bfactor

      - #### foccupancy

            float foccupancy

      - #### radius

            float radius

      - #### isHetero

            boolean isHetero

      - #### atomSerial

            int atomSerial

      - #### chainID

            int chainID

      - #### altLoc

            char altLoc

      - #### group3

            java.lang.String group3

      - #### sequenceNumber

            int sequenceNumber

      - #### insertionCode

            char insertionCode

      - #### anisoBorU

            float[] anisoBorU

      - #### tensors

            javajs.util.Lst<V> tensors

      - #### ignoreSymmetry

            boolean ignoreSymmetry

- ## Package org.jmol.applet

  - ### Class org.jmol.applet.AppletWrapper extends javax.swing.JApplet implements Serializable

    - ### Serialized Fields

      - #### wrappedApplet

            WrappedApplet wrappedApplet

      - #### preloadImageName

            java.lang.String preloadImageName

      - #### preloadTextMessage

            java.lang.String preloadTextMessage

      - #### previousClassName

            java.lang.String previousClassName

      - #### preloadThreadCount

            int preloadThreadCount

      - #### preloadClassNames

            java.lang.String[] preloadClassNames

      - #### preloadClassIndex

            int preloadClassIndex

      - #### isSigned

            boolean isSigned

      - #### needToCompleteInitialization

            boolean needToCompleteInitialization

      - #### preloadImageReadyForDisplay

            boolean preloadImageReadyForDisplay

      - #### preloadImagePainted

            boolean preloadImagePainted

      - #### bgcolor

            java.awt.Color bgcolor

      - #### textColor

            java.awt.Color textColor

      - #### preloadImage

            java.awt.Image preloadImage

      - #### mediaTracker

            java.awt.MediaTracker mediaTracker

      - #### startTime

            long startTime

      - #### clockX

            int clockX

      - #### clockBaseline

            int clockBaseline

      - #### clockWidth

            int clockWidth

      - #### fontSize

            int fontSize

      - #### font

            java.awt.Font font

      - #### fontMetrics

            java.awt.FontMetrics fontMetrics

      - #### fontAscent

            int fontAscent

      - #### fontHeight

            int fontHeight

  - ### Class org.jmol.applet.JmolApplet extends AppletWrapper implements Serializable

- ## Package org.jmol.awt

  - ### Class org.jmol.awt.AwtColor extends java.awt.Color implements Serializable

    - ### Serialized Fields

      - #### opacity

            int opacity

- ## Package org.jmol.console

  - ### Class org.jmol.console.ImageDialog extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### menubar

            javax.swing.JMenuBar menubar

      - #### image

            java.awt.Image image

      - #### vwr

            Viewer vwr

      - #### canvas

            javax.swing.JPanel canvas

      - #### title

            java.lang.String title

      - #### imageMap

            java.util.Map<K,V> imageMap

      - #### console

            JmolAppConsoleInterface console

  - ### Class org.jmol.console.JmolButton extends javax.swing.JButton implements Serializable

  - ### Class org.jmol.console.JmolLabel extends javax.swing.JLabel implements Serializable

  - ### Class org.jmol.console.JmolToggleButton extends javax.swing.JToggleButton implements Serializable

  - ### Class org.jmol.console.KeyJCheckBox extends javax.swing.JCheckBox implements Serializable

    - ### Serialized Fields

      - #### key

            java.lang.String key

  - ### Class org.jmol.console.KeyJCheckBoxMenuItem extends javax.swing.JCheckBoxMenuItem implements Serializable

    - ### Serialized Fields

      - #### key

            java.lang.String key

  - ### Class org.jmol.console.KeyJMenu extends javax.swing.JMenu implements Serializable

    - ### Serialized Fields

      - #### key

            java.lang.String key

  - ### Class org.jmol.console.KeyJMenuItem extends javax.swing.JMenuItem implements Serializable

    - ### Serialized Fields

      - #### key

            java.lang.String key

  - ### Class org.jmol.console.KeyJRadioButtonMenuItem extends javax.swing.JRadioButtonMenuItem implements Serializable

    - ### Serialized Fields

      - #### key

            java.lang.String key

  - ### Class org.jmol.console.ScriptEditor extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### editor

            ScriptEditor.EditorTextPane editor

      - #### openButton

            javax.swing.JButton openButton

      - #### closeButton

            javax.swing.JButton closeButton

      - #### loadButton

            javax.swing.JButton loadButton

      - #### topButton

            javax.swing.JButton topButton

      - #### fontButton

            javax.swing.JButton fontButton

      - #### checkButton

            javax.swing.JButton checkButton

      - #### runButton

            javax.swing.JButton runButton

      - #### pauseButton

            javax.swing.JButton pauseButton

      - #### saveButton

            javax.swing.JButton saveButton

      - #### saveAsButton

            javax.swing.JButton saveAsButton

      - #### haltButton

            javax.swing.JButton haltButton

      - #### clearButton

            javax.swing.JButton clearButton

      - #### stateButton

            javax.swing.JButton stateButton

      - #### consoleButton

            javax.swing.JButton consoleButton

      - #### stepButton

            javax.swing.JButton stepButton

      - #### resumeButton

            javax.swing.JButton resumeButton

      - #### vwr

            Viewer vwr

      - #### jmolConsole

            JmolConsole jmolConsole

      - #### title

            java.lang.String title

      - #### parsedData

            java.lang.String parsedData

      - #### parsedContext

            ScriptContext parsedContext

      - #### attHighlight

            javax.swing.text.SimpleAttributeSet attHighlight

      - #### attEcho

            javax.swing.text.SimpleAttributeSet attEcho

      - #### attError

            javax.swing.text.SimpleAttributeSet attError

      - #### buttonPanel

            javax.swing.JPanel buttonPanel

      - #### filename

            java.lang.String filename

      - #### map

            java.util.Map<K,V> map

      - #### fontSize

            int fontSize

      - #### zipFileName

            java.lang.String zipFileName

- ## Package org.jmol.dialog

  - ### Class org.jmol.dialog.Dialog extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### extensions

            java.lang.String[] extensions

      - #### choice

            java.lang.String choice

      - #### extension

            java.lang.String extension

      - #### qSliderJPEG

            javax.swing.JSlider qSliderJPEG

      - #### qSliderPNG

            javax.swing.JSlider qSliderPNG

      - #### cb

            javax.swing.JComboBox<E> cb

      - #### qPanelJPEG

            javax.swing.JPanel qPanelJPEG

      - #### qPanelPNG

            javax.swing.JPanel qPanelPNG

      - #### openPreview

            FilePreview openPreview

      - #### initialFile

            java.io.File initialFile

      - #### imageChoices

            java.lang.String[] imageChoices

      - #### imageExtensions

            java.lang.String[] imageExtensions

      - #### outputFileName

            java.lang.String outputFileName

      - #### dialogType

            java.lang.String dialogType

      - #### inputFileName

            java.lang.String inputFileName

      - #### vwr

            Viewer vwr

      - #### qualityJ

            int qualityJ

      - #### qualityP

            int qualityP

      - #### imageType

            java.lang.String imageType

  - ### Class org.jmol.dialog.FileChooser extends javax.swing.JFileChooser implements Serializable

    - ### Serialized Fields

      - #### dialogLocation

            java.awt.Point dialogLocation

      - #### dialogSize

            java.awt.Dimension dialogSize

      - #### dialog

            javax.swing.JDialog dialog

  - ### Class org.jmol.dialog.FilePreview extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### active

            javax.swing.JCheckBox active

      - #### append

            javax.swing.JCheckBox append

      - #### cartoons

            javax.swing.JCheckBox cartoons

      - #### chooser

            javax.swing.JFileChooser chooser

      - #### display

            FilePreview.FPPanel display

      - #### vwr

            Viewer vwr

- ## Package org.jmol.modelset

  - ### Class org.jmol.modelset.Atom extends Point3fi implements Serializable

    - ### Serialized Fields

      - #### altloc

            char altloc

      - #### atomID

            byte atomID

      - #### atomSite

            int atomSite

      - #### group

            Group group

      - #### userDefinedVanDerWaalRadius

            float userDefinedVanDerWaalRadius

      - #### valence

            byte valence

      - #### atomicAndIsotopeNumber

            short atomicAndIsotopeNumber

      - #### atomSymmetry

            javajs.util.BS atomSymmetry

      - #### formalChargeAndFlags

            int formalChargeAndFlags

      - #### madAtom

            short madAtom

      - #### colixAtom

            short colixAtom

      - #### paletteID

            byte paletteID

      - #### bonds

            Bond[] bonds

        MAY BE NULL

      - #### nBondsDisplayed

            int nBondsDisplayed

      - #### nBackbonesDisplayed

            int nBackbonesDisplayed

      - #### clickabilityFlags

            int clickabilityFlags

      - #### shapeVisibilityFlags

            int shapeVisibilityFlags

- ## Package org.jmol.script

  - ### Class org.jmol.script.ScriptException extends java.lang.Exception implements Serializable

    - ### Serialized Fields

      - #### eval

            ScriptEval eval

      - #### message

            java.lang.String message

      - #### untranslated

            java.lang.String untranslated

      - #### isError

            boolean isError

  - ### Class org.jmol.script.ScriptInterruption extends ScriptException implements Serializable

- ## Package org.jmol.smiles

  - ### Class org.jmol.smiles.InvalidSmilesException extends java.lang.Exception implements Serializable

  - ### Class org.jmol.smiles.SmilesAtom extends javajs.util.P3 implements Serializable

    - ### Serialized Fields

      - #### patternIndex

            int patternIndex

      - #### pattern

            java.lang.String pattern

      - #### primitiveType

            int primitiveType

      - #### isAND

            boolean isAND

      - #### subAtoms

            SmilesAtom[] subAtoms

      - #### nSubAtoms

            int nSubAtoms

      - #### index

            int index

      - #### referance

            java.lang.String referance

      - #### residueName

            java.lang.String residueName

      - #### residueChar

            java.lang.String residueChar

      - #### insCode

            char insCode

      - #### isBioAtom

            boolean isBioAtom

      - #### isBioResidue

            boolean isBioResidue

      - #### isBioAtomWild

            boolean isBioAtomWild

      - #### bioType

            char bioType

      - #### isLeadAtom

            boolean isLeadAtom

      - #### notBondedIndex

            int notBondedIndex

      - #### notCrossLinked

            boolean notCrossLinked

      - #### aromaticAmbiguous

            boolean aromaticAmbiguous

      - #### covalentHydrogenCount

            int covalentHydrogenCount

      - #### not

            boolean not

      - #### selected

            boolean selected

      - #### hasSymbol

            boolean hasSymbol

      - #### elementDefined

            boolean elementDefined

      - #### atomType

            java.lang.String atomType

      - #### bioAtomName

            java.lang.String bioAtomName

      - #### isFirst

            boolean isFirst

        true if this atom is the first SMILES atom or first after a . with no connector

      - #### jmolIndex

            int jmolIndex

      - #### elementNumber

            int elementNumber

      - #### atomNumber

            int atomNumber

      - #### residueNumber

            int residueNumber

      - #### explicitHydrogenCount

            int explicitHydrogenCount

      - #### implicitHydrogenCount

            int implicitHydrogenCount

      - #### parent

            SmilesAtom parent

      - #### bonds

            SmilesBond[] bonds

      - #### bondCount

            int bondCount

      - #### iNested

            int iNested

      - #### isAromatic

            boolean isAromatic

      - #### atomicMass

            int atomicMass

      - #### charge

            int charge

      - #### matchingIndex

            int matchingIndex

      - #### stereo

            SmilesStereo stereo

      - #### component

            int component

      - #### matchingComponent

            int matchingComponent

      - #### atomSite

            int atomSite

      - #### degree

            int degree

      - #### nonhydrogenDegree

            int nonhydrogenDegree

      - #### valence

            int valence

      - #### connectivity

            int connectivity

      - #### ringMembership

            int ringMembership

      - #### ringSize

            int ringSize

      - #### ringConnectivity

            int ringConnectivity

      - #### matchingNode

            Node matchingNode

      - #### hasSubpattern

            boolean hasSubpattern

      - #### mapIndex

            int mapIndex

      - #### atomClass

            float atomClass

      - #### symbol

            java.lang.String symbol

      - #### isTopoAtom

            boolean isTopoAtom

      - #### missingHydrogenCount

            int missingHydrogenCount

      - #### cipChirality

            int cipChirality

- ## Package org.jmol.util

  - ### Class org.jmol.util.ModulationSet extends Vibration implements Serializable

    - ### Serialized Fields

      - #### id

            java.lang.String id

        an identifier for this modulation

      - #### r0

            javajs.util.P3 r0

        the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself

      - #### symmetry

            SymmetryInterface symmetry

        the space group appropriate to this atom

      - #### axesLengths

            float[] axesLengths

        unit cell axes -- used in Modulation for calculating magnetic modulations

      - #### nOps

            int nOps

        the number of operators in this space group -- needed for occupancy calculation

      - #### iop

            int iop

        the symmetry operation used to generate this atom

      - #### strop

            java.lang.String strop

        a string description of the atom's symmetry operator

      - #### spinOp

            float spinOp

        the spin operation for this atom: +1/0/-1

      - #### rsvs

            javajs.util.Matrix rsvs

        the matrix representation for this atom's symmetry operation

      - #### vib

            Vibration vib

        vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.

      - #### mods

            javajs.util.Lst<V> mods

        the list of all modulations associated with this atom

      - #### isSubsystem

            boolean isSubsystem

        subsystems can deliver their own unique unit cell; they are commensurate

      - #### isCommensurate

            boolean isCommensurate

        commensurate modulations cannot be "undone" and they cannot be turned off

      - #### fileOcc

            double fileOcc

      - #### occParams

            double[] occParams

      - #### occSiteMultiplicity

            double occSiteMultiplicity

      - #### occAbsolute

            boolean occAbsolute

        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

      - #### modCalc

            ModulationSet modCalc

        modCalc is used for calculations independent of what the current setting is

      - #### mxyz

            javajs.util.V3 mxyz

        the modulated magnetic spin

      - #### htUij

            java.util.Map<K,V> htUij

        current value of anisotropic parameter modulation

      - #### vOcc

            float vOcc

        the current value of the occupancy modulation

      - #### occValue

            float occValue

        final occupancy value -- absolute; in range [0,1]

      - #### qtOffset

            javajs.util.P3 qtOffset

      - #### isQ

            boolean isQ

      - #### enabled

            boolean enabled

        indicates state of modulated or unmodulated

      - #### scale

            float scale

        an adjustable scaling factor, as for vibrations

      - #### gammaE

            javajs.util.M3 gammaE

      - #### gammaIinv

            javajs.util.Matrix gammaIinv

      - #### sigma

            javajs.util.Matrix sigma

      - #### tau

            javajs.util.Matrix tau

      - #### rI

            javajs.util.Matrix rI

      - #### tFactorInv

            javajs.util.Matrix tFactorInv

      - #### ptTemp

            javajs.util.P3 ptTemp

      - #### v0

            javajs.util.V3 v0

  - ### Class org.jmol.util.Point3fi extends javajs.util.P3 implements Serializable

    - ### Serialized Fields

      - #### mi

            short mi

        model index -- may be to a trajectory

      - #### i

            int i

        index in full collection

      - #### sX

            int sX

        screen X

      - #### sY

            int sY

        screen Y

      - #### sZ

            int sZ

        screen Z

      - #### sD

            short sD

        screen diameter

  - ### Class org.jmol.util.Vibration extends javajs.util.V3 implements Serializable

    - ### Serialized Fields

      - #### modDim

            int modDim

        modDim will be > 0 for modulation

      - #### modScale

            float modScale

      - #### showTrace

            boolean showTrace

      - #### trace

            javajs.util.P3[] trace

      - #### tracePt

            int tracePt

- ## Package org.jmol.viewer

  - ### Class org.jmol.viewer.JmolAsyncException extends java.io.IOException implements Serializable

    - ### Serialized Fields

      - #### fileName

            java.lang.String fileName

- ## Package org.openscience.jmol.app

  - ### Class org.openscience.jmol.app.Jmol extends JmolPanel implements Serializable

- ## Package org.openscience.jmol.app.jmolpanel

  - ### Class org.openscience.jmol.app.jmolpanel.AtomSetChooser extends javax.swing.JFrame implements Serializable

    - ### Serialized Fields

      - #### animThread

            java.lang.Thread animThread

      - #### propertiesTextArea

            javax.swing.JTextArea propertiesTextArea

      - #### tree

            javax.swing.JTree tree

      - #### treeModel

            javax.swing.tree.DefaultTreeModel treeModel

      - #### vwr

            Viewer vwr

      - #### repeatCheckBox

            javax.swing.JCheckBox repeatCheckBox

      - #### selectSlider

            javax.swing.JSlider selectSlider

      - #### infoLabel

            javax.swing.JLabel infoLabel

      - #### fpsSlider

            javax.swing.JSlider fpsSlider

      - #### amplitudeSlider

            javax.swing.JSlider amplitudeSlider

      - #### periodSlider

            javax.swing.JSlider periodSlider

      - #### scaleSlider

            javax.swing.JSlider scaleSlider

      - #### radiusSlider

            javax.swing.JSlider radiusSlider

      - #### saveChooser

            javax.swing.JFileChooser saveChooser

      - #### indexes

            int[] indexes

        Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.

      - #### currentIndex

            int currentIndex

      - #### radiusValue

            int radiusValue

  - ### Class org.openscience.jmol.app.jmolpanel.CreditsDialog extends HelpDialog implements Serializable

  - ### Class org.openscience.jmol.app.jmolpanel.DisplayPanel extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### status

            StatusBar status

      - #### vwr

            Viewer vwr

      - #### displaySpeed

            java.lang.String displaySpeed

      - #### startupDimension

            java.awt.Dimension startupDimension

      - #### haveDisplay

            boolean haveDisplay

      - #### border

            java.awt.Point border

      - #### haveBorder

            boolean haveBorder

      - #### measurementTable

            MeasurementTable measurementTable

      - #### jmolPanel

            JmolPanel jmolPanel

      - #### frame

            javax.swing.JFrame frame

      - #### showPaintTime

            boolean showPaintTime

      - #### dimSize

            java.awt.Dimension dimSize

      - #### rectClip

            java.awt.Rectangle rectClip

      - #### buttonRotate

            javax.swing.AbstractButton buttonRotate

      - #### buttonModelkit

            javax.swing.AbstractButton buttonModelkit

      - #### toolbarButtonGroup

            javax.swing.ButtonGroup toolbarButtonGroup

      - #### homeAction

            DisplayPanel.HomeAction homeAction

      - #### defineCenterAction

            DisplayPanel.DefineCenterAction defineCenterAction

      - #### frontAction

            javax.swing.Action frontAction

      - #### topAction

            javax.swing.Action topAction

      - #### bottomAction

            javax.swing.Action bottomAction

      - #### rightAction

            javax.swing.Action rightAction

      - #### leftAction

            javax.swing.Action leftAction

      - #### hydrogensAction

            javax.swing.Action hydrogensAction

      - #### measurementsAction

            javax.swing.Action measurementsAction

      - #### perspectiveAction

            javax.swing.Action perspectiveAction

      - #### axesAction

            javax.swing.Action axesAction

      - #### boundboxAction

            javax.swing.Action boundboxAction

      - #### deleteAction

            javax.swing.Action deleteAction

      - #### zoomAction

            javax.swing.Action zoomAction

      - #### xlateAction

            javax.swing.Action xlateAction

      - #### timeBegin

            long timeBegin

      - #### lastMotionEventNumber

            int lastMotionEventNumber

  - ### Class org.openscience.jmol.app.jmolpanel.GaussianDialog extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### vwr

            Viewer vwr

      - #### container

            javax.swing.JPanel container

      - #### checkField

            javax.swing.JTextField checkField

      - #### optsField

            javax.swing.JTextField optsField

      - #### fileField

            javax.swing.JTextField fileField

      - #### selectField

            javax.swing.JTextField selectField

      - #### memBox

            javax.swing.JComboBox<E> memBox

      - #### methBox

            javax.swing.JComboBox<E> methBox

      - #### basisBox

            javax.swing.JComboBox<E> basisBox

      - #### dfBox

            javax.swing.JComboBox<E> dfBox

      - #### procSpinner

            javax.swing.JSpinner procSpinner

      - #### chargeSpinner

            javax.swing.JSpinner chargeSpinner

      - #### multSpinner

            javax.swing.JSpinner multSpinner

      - #### fileButton

            javax.swing.JButton fileButton

      - #### saveButton

            javax.swing.JButton saveButton

      - #### closeButton

            javax.swing.JButton closeButton

      - #### refreshButton

            javax.swing.JButton refreshButton

      - #### fileChooser

            javax.swing.JFileChooser fileChooser

      - #### editArea

            javax.swing.JTextPane editArea

      - #### check

            java.lang.String check

      - #### mem

            java.lang.String mem

      - #### proc

            java.lang.String proc

      - #### file

            java.lang.String file

      - #### meth

            java.lang.String meth

      - #### route

            java.lang.String route

      - #### charge

            java.lang.String charge

      - #### mult

            java.lang.String mult

      - #### select

            java.lang.String select

      - #### editPane

            javax.swing.JScrollPane editPane

      - #### iscroll

            int iscroll

  - ### Class org.openscience.jmol.app.jmolpanel.HelpDialog extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### html

            javax.swing.JEditorPane html

  - ### Class org.openscience.jmol.app.jmolpanel.JmolPanel extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### vwr

            Viewer vwr

      - #### modelAdapter

            JmolAdapter modelAdapter

      - #### jmolApp

            JmolApp jmolApp

      - #### status

            StatusBar status

      - #### startupWidth

            int startupWidth

      - #### startupHeight

            int startupHeight

      - #### serverService

            JsonNioServer serverService

      - #### appletContext

            java.lang.String appletContext

      - #### pcs

            java.beans.PropertyChangeSupport pcs

      - #### display

            DisplayPanel display

      - #### gaussianDialog

            GaussianDialog gaussianDialog

      - #### recentFiles

            RecentFilesDialog recentFiles

      - #### atomSetChooser

            AtomSetChooser atomSetChooser

      - #### frame

            javax.swing.JFrame frame

      - #### splash

            SplashInterface splash

      - #### consoleframe

            javax.swing.JFrame consoleframe

      - #### service

            JsonNioServer service

      - #### qualityJPG

            int qualityJPG

      - #### qualityPNG

            int qualityPNG

      - #### imageType

            java.lang.String imageType

      - #### guimap

            GuiMap guimap

      - #### executeScriptAction

            JmolPanel.ExecuteScriptAction executeScriptAction

      - #### preferencesDialog

            PreferencesDialog preferencesDialog

      - #### myStatusListener

            StatusListener myStatusListener

      - #### surfaceTool

            SurfaceTool surfaceTool

      - #### commands

            java.util.Map<K,V> commands

      - #### menuItems

            java.util.Map<K,V> menuItems

      - #### toolbar

            javax.swing.JToolBar toolbar

      - #### exportAction

            JmolPanel.ExportAction exportAction

      - #### povrayAction

            JmolPanel.PovrayAction povrayAction

      - #### toWebAction

            JmolPanel.ToWebAction toWebAction

      - #### writeAction

            JmolPanel.WriteAction writeAction

      - #### printAction

            JmolPanel.PrintAction printAction

      - #### copyImageAction

            JmolPanel.CopyImageAction copyImageAction

      - #### copyScriptAction

            JmolPanel.CopyScriptAction copyScriptAction

      - #### surfaceToolAction

            JmolPanel.SurfaceToolAction surfaceToolAction

      - #### pasteClipboardAction

            JmolPanel.PasteClipboardAction pasteClipboardAction

      - #### viewMeasurementTableAction

            JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction

      - #### vwrOptions

            java.util.Map<K,V> vwrOptions

      - #### plugins

            java.util.Map<K,V> plugins

      - #### pluginMenu

            javax.swing.JMenu pluginMenu

      - #### defaultActions

            javax.swing.Action[] defaultActions

        Actions defined by the Jmol class

      - #### webExport

            WebExport webExport

  - ### Class org.openscience.jmol.app.jmolpanel.MeasurementTable extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### vwr

            Viewer vwr

      - #### measurementTable

            javax.swing.JTable measurementTable

      - #### measurementTableModel

            MeasurementTable.MeasurementTableModel measurementTableModel

      - #### selectedMeasurementRow

            int selectedMeasurementRow

      - #### deleteButton

            javax.swing.JButton deleteButton

      - #### deleteAllButton

            javax.swing.JButton deleteAllButton

      - #### stringClass

            java.lang.Class<T> stringClass

  - ### Class org.openscience.jmol.app.jmolpanel.PovrayDialog extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### povrayPathButton

            javax.swing.JButton povrayPathButton

      - #### goButton

            javax.swing.JButton goButton

      - #### saveField

            javax.swing.JTextField saveField

      - #### savePathLabel

            javax.swing.JTextField savePathLabel

      - #### outputWidth

            int outputWidth

      - #### outputHeight

            int outputHeight

      - #### povrayPathLabel

            javax.swing.JTextField povrayPathLabel

      - #### runPovCheck

            javax.swing.JCheckBox runPovCheck

      - #### allFramesCheck

            javax.swing.JCheckBox allFramesCheck

      - #### antiAliasCheck

            javax.swing.JCheckBox antiAliasCheck

      - #### displayWhileRenderingCheck

            javax.swing.JCheckBox displayWhileRenderingCheck

      - #### imageSizeWidth

            javax.swing.JLabel imageSizeWidth

      - #### imageSizeTextWidth

            javax.swing.JFormattedTextField imageSizeTextWidth

      - #### imageSizeHeight

            javax.swing.JLabel imageSizeHeight

      - #### imageSizeTextHeight

            javax.swing.JFormattedTextField imageSizeTextHeight

      - #### imageSizeRatioBox

            javax.swing.JCheckBox imageSizeRatioBox

      - #### imageSizeRatioCombo

            javax.swing.JComboBox<E> imageSizeRatioCombo

      - #### outputFormatCheck

            javax.swing.JCheckBox outputFormatCheck

      - #### outputFormatCombo

            javax.swing.JComboBox<E> outputFormatCombo

      - #### outputAlphaCheck

            javax.swing.JCheckBox outputAlphaCheck

      - #### mosaicPreviewCheck

            javax.swing.JCheckBox mosaicPreviewCheck

      - #### mosaicPreviewStart

            javax.swing.JLabel mosaicPreviewStart

      - #### mosaicPreviewComboStart

            javax.swing.JComboBox<E> mosaicPreviewComboStart

      - #### mosaicPreviewEnd

            javax.swing.JLabel mosaicPreviewEnd

      - #### mosaicPreviewComboEnd

            javax.swing.JComboBox<E> mosaicPreviewComboEnd

      - #### outputExtension

            java.lang.String outputExtension

      - #### outputFileType

            java.lang.String outputFileType

  - ### Class org.openscience.jmol.app.jmolpanel.PreferencesDialog extends javax.swing.JDialog implements Serializable

    - ### Serialized Fields

      - #### autoBond

            boolean autoBond

      - #### showHydrogens

            boolean showHydrogens

      - #### showMeasurements

            boolean showMeasurements

      - #### perspectiveDepth

            boolean perspectiveDepth

      - #### showAxes

            boolean showAxes

      - #### showBoundingBox

            boolean showBoundingBox

      - #### axesOrientationRasmol

            boolean axesOrientationRasmol

      - #### openFilePreview

            boolean openFilePreview

      - #### clearHistory

            boolean clearHistory

      - #### fontScale

            int fontScale

      - #### minBondDistance

            float minBondDistance

      - #### bondTolerance

            float bondTolerance

      - #### marBond

            short marBond

      - #### percentVdwAtom

            int percentVdwAtom

      - #### bondingVersion

            int bondingVersion

      - #### bButton

            javax.swing.JButton bButton

      - #### pButton

            javax.swing.JButton pButton

      - #### tButton

            javax.swing.JButton tButton

      - #### eButton

            javax.swing.JButton eButton

      - #### vButton

            javax.swing.JButton vButton

      - #### abYes

            javax.swing.JRadioButton abYes

      - #### abNo

            javax.swing.JRadioButton abNo

      - #### vdwPercentSlider

            javax.swing.JSlider vdwPercentSlider

      - #### bdSlider

            javax.swing.JSlider bdSlider

      - #### bwSlider

            javax.swing.JSlider bwSlider

      - #### btSlider

            javax.swing.JSlider btSlider

      - #### cH

            javax.swing.JCheckBox cH

      - #### cM

            javax.swing.JCheckBox cM

      - #### cbPerspectiveDepth

            javax.swing.JCheckBox cbPerspectiveDepth

      - #### cbShowAxes

            javax.swing.JCheckBox cbShowAxes

      - #### cbShowBoundingBox

            javax.swing.JCheckBox cbShowBoundingBox

      - #### cbAxesOrientationRasmol

            javax.swing.JCheckBox cbAxesOrientationRasmol

      - #### cbOpenFilePreview

            javax.swing.JCheckBox cbOpenFilePreview

      - #### cbClearHistory

            javax.swing.JCheckBox cbClearHistory

      - #### originalSystemProperties

            java.util.Properties originalSystemProperties

      - #### jmolDefaultProperties

            java.util.Properties jmolDefaultProperties

      - #### currentProperties

            java.util.Properties currentProperties

      - #### prefsAction

            PreferencesDialog.PrefsAction prefsAction

      - #### commands

            java.util.Map<K,V> commands

      - #### jmol

            JmolPanel jmol

      - #### vwr

            Viewer vwr

      - #### guimap

            GuiMap guimap

      - #### checkBoxListener

            java.awt.event.ItemListener checkBoxListener

      - #### applyButton

            javax.swing.JButton applyButton

      - #### jmolDefaultsButton

            javax.swing.JButton jmolDefaultsButton

      - #### rasmolDefaultsButton

            javax.swing.JButton rasmolDefaultsButton

      - #### cancelButton

            javax.swing.JButton cancelButton

      - #### okButton

            javax.swing.JButton okButton

  - ### Class org.openscience.jmol.app.jmolpanel.Splash extends java.awt.Window implements Serializable

    - ### Serialized Fields

      - #### splashImage

            java.awt.Image splashImage

      - #### imgWidth

            int imgWidth

      - #### imgHeight

            int imgHeight

      - #### status

            java.lang.String status

      - #### textY

            int textY

      - #### statusTop

            int statusTop

  - ### Class org.openscience.jmol.app.jmolpanel.WhatsNewDialog extends HelpDialog implements Serializable

- ## Package org.openscience.jmol.app.jmolpanel.console

  - ### Class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea extends javax.swing.JTextArea implements Serializable

- ## Package org.openscience.jmol.app.jsonkiosk

  - ### Class org.openscience.jmol.app.jsonkiosk.BannerFrame extends javax.swing.JFrame implements Serializable

    - ### Serialized Fields

      - #### bannerLabel

            javax.swing.JLabel bannerLabel

  - ### Class org.openscience.jmol.app.jsonkiosk.KioskFrame extends javax.swing.JFrame implements Serializable

- ## Package org.openscience.jmol.app.webexport

  - ### Class org.openscience.jmol.app.webexport.Orbitals extends javax.swing.JPanel implements Serializable

  - ### Class org.openscience.jmol.app.webexport.Test extends javax.swing.JPanel implements Serializable

    serialVersionUID:
      1L

    - ### Serialized Fields

      - #### StateButton

            javax.swing.JButton StateButton

      - #### FileButton

            javax.swing.JButton FileButton

      - #### PathButton

            javax.swing.JButton PathButton

      - #### movetoTime

            javax.swing.JButton movetoTime

      - #### StringtoScriptButton

            javax.swing.JButton StringtoScriptButton

      - #### appletPath

            javax.swing.JTextField appletPath

      - #### arrayListHandler

            ArrayListTransferHandler arrayListHandler

      - #### fc

            javax.swing.JFileChooser fc

      - #### vwr

            Viewer vwr

  - ### Class org.openscience.jmol.app.webexport.WebExport extends javax.swing.JPanel implements Serializable

  - ### Class org.openscience.jmol.app.webexport.WebMaker extends java.lang.Object implements Serializable