int atomSetIndex
int atomIndex
java.util.BitSet bsSymmetry
int atomSite
java.lang.String elementSymbol
short elementNumber
java.lang.String atomName
int formalCharge
float partialCharge
float vectorX
float vectorY
float vectorZ
float bfactor
int occupancy
float radius
boolean isHetero
int atomSerial
char chainID
char alternateLocationID
java.lang.String group3
int sequenceNumber
char insertionCode
float[] anisoBorU
java.lang.Object[] ellipsoid
boolean ignoreSymmetry
WrappedApplet wrappedApplet
java.lang.String wrappedAppletClassName
java.lang.String preloadImageName
java.lang.String preloadTextMessage
java.lang.String previousClassName
int preloadThreadCount
java.lang.String[] preloadClassNames
int preloadClassIndex
boolean isSigned
boolean needToCompleteInitialization
boolean preloadImageReadyForDisplay
boolean preloadImagePainted
java.awt.Color bgcolor
java.awt.Color textColor
java.awt.Image preloadImage
java.awt.MediaTracker mediaTracker
long startTime
int clockX
int clockBaseline
int clockWidth
int fontSize
java.awt.Font font
java.awt.FontMetrics fontMetrics
int fontAscent
int fontHeight
ScriptEditor.EditorTextPane editor
javax.swing.JButton openButton
javax.swing.JButton closeButton
javax.swing.JButton loadButton
javax.swing.JButton topButton
javax.swing.JButton checkButton
javax.swing.JButton runButton
javax.swing.JButton pauseButton
javax.swing.JButton haltButton
javax.swing.JButton clearButton
javax.swing.JButton stateButton
javax.swing.JButton consoleButton
javax.swing.JButton stepButton
javax.swing.JButton resumeButton
JmolViewer viewer
JmolConsole jmolConsole
java.lang.String title
java.lang.String parsedData
ScriptContext parsedContext
javax.swing.text.SimpleAttributeSet attHighlight
javax.swing.text.SimpleAttributeSet attEcho
javax.swing.text.SimpleAttributeSet attError
javax.swing.JPanel buttonPanel
java.lang.String filename
java.lang.String[] extensions
java.lang.String choice
java.lang.String extension
javax.swing.JSlider qSliderJPEG
javax.swing.JSlider qSliderPNG
javax.swing.JComboBox<E> cb
javax.swing.JPanel qPanelJPEG
javax.swing.JPanel qPanelPNG
FilePreview openPreview
java.io.File initialFile
java.lang.String[] imageChoices
java.lang.String[] imageExtensions
java.lang.String outputFileName
java.lang.String dialogType
java.lang.String inputFileName
Viewer viewer
int qualityJ
int qualityP
java.lang.String imageType
javax.swing.JCheckBox active
javax.swing.JCheckBox append
javax.swing.JFileChooser chooser
FilePreview.FPPanel display
JmolViewer viewer
ModelKitPopup modelkitMenu
Group group
java.util.BitSet atomSymmetry
int atomSite
float userDefinedVanDerWaalRadius
short atomicAndIsotopeNumber
byte formalChargeAndFlags
byte valence
char alternateLocationID
byte atomID
short madAtom
short colixAtom
byte paletteID
Bond[] bonds
int nBondsDisplayed
int nBackbonesDisplayed
int clickabilityFlags
int shapeVisibilityFlags
int index
java.lang.String atomName
java.lang.String residueName
java.lang.String residueChar
boolean isBioAtom
char bioType
boolean isLeadAtom
int notBondedIndex
boolean notCrossLinked
boolean aromaticAmbiguous
boolean not
boolean selected
boolean hasSymbol
boolean isFirst
int jmolIndex
short elementNumber
short atomicMass
int charge
int missingHydrogenCount
int implicitHydrogenCount
int matchingAtom
int chiralClass
int chiralOrder
boolean isAromatic
SmilesAtom parent
SmilesBond[] bonds
int bondCount
int iNested
SmilesAtom[] atomsOr
int nAtomsOr
SmilesAtom[] primitives
int nPrimitives
int component
int atomSite
int degree
int nonhydrogenDegree
int valence
int connectivity
int ringMembership
int ringSize
int ringConnectivity
int covalentHydrogenCount
javax.swing.JTextField chimePath
javax.swing.JButton goButton
javax.swing.JButton browseButton
javax.swing.JTextArea logArea
javax.swing.JScrollPane logScrollPane
javax.swing.JFileChooser chooser
java.io.File oldDir
java.util.List<E> pages
int nDir
int nFiles
java.awt.Checkbox checkSubs
java.awt.Checkbox checkFilenames
java.awt.Checkbox checkSigned
boolean doSubdirectories
boolean doFixFilenames
boolean doUseSigned
java.io.File myDir
java.lang.String rootDir
java.lang.Thread animThread
javax.swing.JTextArea propertiesTextArea
javax.swing.JTree tree
javax.swing.tree.DefaultTreeModel treeModel
JmolViewer viewer
javax.swing.JCheckBox repeatCheckBox
javax.swing.JSlider selectSlider
javax.swing.JLabel infoLabel
javax.swing.JSlider fpsSlider
javax.swing.JSlider amplitudeSlider
javax.swing.JSlider periodSlider
javax.swing.JSlider scaleSlider
javax.swing.JSlider radiusSlider
javax.swing.JFileChooser saveChooser
int[] indexes
int currentIndex
StatusBar status
GuiMap guimap
JmolViewer viewer
java.lang.String displaySpeed
java.awt.Dimension startupDimension
boolean haveDisplay
java.awt.Point border
boolean haveBorder
MeasurementTable measurementTable
JmolPanel jmolPanel
javax.swing.JFrame frame
boolean showPaintTime
java.awt.Dimension dimSize
java.awt.Rectangle rectClip
javax.swing.AbstractButton buttonRotate
javax.swing.AbstractButton buttonModelkit
javax.swing.ButtonGroup toolbarButtonGroup
DisplayPanel.HomeAction homeAction
DisplayPanel.DefineCenterAction defineCenterAction
javax.swing.Action frontAction
javax.swing.Action topAction
javax.swing.Action bottomAction
javax.swing.Action rightAction
javax.swing.Action leftAction
javax.swing.Action hydrogensAction
javax.swing.Action measurementsAction
javax.swing.Action perspectiveAction
javax.swing.Action axesAction
javax.swing.Action boundboxAction
javax.swing.Action deleteAction
javax.swing.Action zoomAction
javax.swing.Action xlateAction
javax.swing.event.MenuListener menuListener
long timeBegin
int lastMotionEventNumber
JmolViewer viewer
javax.swing.JPanel container
javax.swing.JTextField checkField
javax.swing.JTextField optsField
javax.swing.JTextField fileField
javax.swing.JTextField selectField
javax.swing.JComboBox<E> memBox
javax.swing.JComboBox<E> methBox
javax.swing.JComboBox<E> basisBox
javax.swing.JComboBox<E> dfBox
javax.swing.JSpinner procSpinner
javax.swing.JSpinner chargeSpinner
javax.swing.JSpinner multSpinner
javax.swing.JButton fileButton
javax.swing.JButton saveButton
javax.swing.JButton cancelButton
javax.swing.JFileChooser fileChooser
javax.swing.JTextArea editArea
javax.swing.JTabbedPane inputTabs
java.lang.String check
java.lang.String mem
java.lang.String proc
java.lang.String file
java.lang.String meth
java.lang.String route
java.lang.String charge
java.lang.String mult
java.lang.String select
JmolViewer viewer
JmolAdapter modelAdapter
JmolApp jmolApp
StatusBar status
int startupWidth
int startupHeight
JsonNioService serverService
java.lang.String appletContext
java.beans.PropertyChangeSupport pcs
DisplayPanel display
GaussianDialog gaussianDialog
RecentFilesDialog recentFiles
AtomSetChooser atomSetChooser
javax.swing.JFrame frame
SplashInterface splash
javax.swing.JFrame consoleframe
JsonNioService service
GuiMap guimap
int qualityJPG
int qualityPNG
java.lang.String imageType
JmolPanel.ExecuteScriptAction executeScriptAction
PreferencesDialog preferencesDialog
StatusListener myStatusListener
SurfaceTool surfaceTool
java.util.Map<K,V> commands
java.util.Map<K,V> menuItems
javax.swing.JMenuBar menubar
javax.swing.JToolBar toolbar
JmolPanel.ExportAction exportAction
JmolPanel.PovrayAction povrayAction
JmolPanel.ToWebAction toWebAction
JmolPanel.WriteAction writeAction
JmolPanel.PrintAction printAction
JmolPanel.CopyImageAction copyImageAction
JmolPanel.CopyScriptAction copyScriptAction
JmolPanel.SurfaceToolAction surfaceToolAction
JmolPanel.PasteClipboardAction pasteClipboardAction
JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction
javax.swing.Action[] defaultActions
WebExport webExport
JmolViewer viewer
javax.swing.JTable measurementTable
MeasurementTable.MeasurementTableModel measurementTableModel
int selectedMeasurementRow
javax.swing.JButton deleteButton
javax.swing.JButton deleteAllButton
java.lang.Class<T> stringClass
javax.swing.JButton povrayPathButton
javax.swing.JButton goButton
javax.swing.JTextField saveField
javax.swing.JTextField savePathLabel
int outputWidth
int outputHeight
javax.swing.JTextField povrayPathLabel
javax.swing.JCheckBox runPovCheck
javax.swing.JCheckBox allFramesCheck
javax.swing.JCheckBox antiAliasCheck
javax.swing.JCheckBox displayWhileRenderingCheck
javax.swing.JLabel imageSizeWidth
javax.swing.JFormattedTextField imageSizeTextWidth
javax.swing.JLabel imageSizeHeight
javax.swing.JFormattedTextField imageSizeTextHeight
javax.swing.JCheckBox imageSizeRatioBox
javax.swing.JComboBox<E> imageSizeRatioCombo
javax.swing.JCheckBox outputFormatCheck
javax.swing.JComboBox<E> outputFormatCombo
javax.swing.JCheckBox outputAlphaCheck
javax.swing.JCheckBox mosaicPreviewCheck
javax.swing.JLabel mosaicPreviewStart
javax.swing.JComboBox<E> mosaicPreviewComboStart
javax.swing.JLabel mosaicPreviewEnd
javax.swing.JComboBox<E> mosaicPreviewComboEnd
java.lang.String outputExtension
java.lang.String outputFileType
boolean autoBond
boolean showHydrogens
boolean showMeasurements
boolean perspectiveDepth
boolean showAxes
boolean showBoundingBox
boolean axesOrientationRasmol
boolean openFilePreview
boolean clearHistory
float minBondDistance
float bondTolerance
short marBond
int percentVdwAtom
javax.swing.JButton bButton
javax.swing.JButton pButton
javax.swing.JButton tButton
javax.swing.JButton eButton
javax.swing.JButton vButton
javax.swing.JRadioButton abYes
javax.swing.JRadioButton abNo
javax.swing.JSlider vdwPercentSlider
javax.swing.JSlider bdSlider
javax.swing.JSlider bwSlider
javax.swing.JSlider btSlider
javax.swing.JCheckBox cH
javax.swing.JCheckBox cM
javax.swing.JCheckBox cbPerspectiveDepth
javax.swing.JCheckBox cbShowAxes
javax.swing.JCheckBox cbShowBoundingBox
javax.swing.JCheckBox cbAxesOrientationRasmol
javax.swing.JCheckBox cbOpenFilePreview
javax.swing.JCheckBox cbClearHistory
java.util.Properties originalSystemProperties
java.util.Properties jmolDefaultProperties
java.util.Properties currentProperties
PreferencesDialog.PrefsAction prefsAction
java.util.Map<K,V> commands
JmolPanel jmol
JmolViewer viewer
GuiMap guimap
java.awt.event.ItemListener checkBoxListener
javax.swing.JButton applyButton
javax.swing.JButton jmolDefaultsButton
javax.swing.JButton rasmolDefaultsButton
javax.swing.JButton cancelButton
javax.swing.JButton okButton
javax.swing.JButton OrbopenButton
javax.swing.JButton OrbdeleteButton
javax.swing.JButton CooropenButton
javax.swing.JButton saveButton
javax.swing.JTextField Coorfile
javax.swing.JTextField appletPath
javax.swing.JFileChooser fc
javax.swing.JList<E> OrbList
javax.swing.JComboBox<E> RenderMode
javax.swing.JComboBox<E> FormatBox
javax.swing.JButton StateButton
javax.swing.JButton FileButton
javax.swing.JButton PathButton
javax.swing.JButton movetoTime
javax.swing.JButton StringtoScriptButton
javax.swing.JTextField appletPath
ArrayListTransferHandler arrayListHandler
javax.swing.JFileChooser fc
Viewer viewer