int atomSetIndex
int atomIndex
BitSet bsSymmetry
int atomSite
String elementSymbol
short elementNumber
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
String group3
int sequenceNumber
char insertionCode
float[] anisoBorU
Object[] ellipsoid
boolean ignoreSymmetry
WrappedApplet wrappedApplet
String wrappedAppletClassName
String preloadImageName
String preloadTextMessage
String previousClassName
int preloadThreadCount
String[] preloadClassNames
int preloadClassIndex
boolean isSigned
boolean needToCompleteInitialization
boolean preloadImageReadyForDisplay
boolean preloadImagePainted
Color bgcolor
Color textColor
Image preloadImage
MediaTracker mediaTracker
long startTime
int clockX
int clockBaseline
int clockWidth
int fontSize
Font font
FontMetrics fontMetrics
int fontAscent
int fontHeight
String key
String key
String key
String key
String key
ScriptEditor.EditorTextPane editor
JButton openButton
JButton closeButton
JButton loadButton
JButton topButton
JButton checkButton
JButton runButton
JButton pauseButton
JButton haltButton
JButton clearButton
JButton stateButton
JButton consoleButton
JButton stepButton
JButton resumeButton
JmolViewer viewer
JmolConsole jmolConsole
String title
String parsedData
ScriptContext parsedContext
SimpleAttributeSet attHighlight
SimpleAttributeSet attEcho
SimpleAttributeSet attError
JPanel buttonPanel
String filename
String[] extensions
String choice
String extension
JSlider qSliderJPEG
JSlider qSliderPNG
JComboBox cb
JPanel qPanelJPEG
JPanel qPanelPNG
FilePreview openPreview
File initialFile
String[] imageChoices
String[] imageExtensions
String outputFileName
String dialogType
String inputFileName
Viewer viewer
int qualityJ
int qualityP
String imageType
JCheckBox active
JCheckBox append
JFileChooser chooser
FilePreview.FPPanel display
JmolViewer viewer
ModelKitPopup modelkitMenu
Group group
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
String atomName
String residueName
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
JTextField chimePath
JButton goButton
JButton browseButton
JTextArea logArea
JScrollPane logScrollPane
JFileChooser chooser
File oldDir
List<E> pages
int nDir
int nFiles
Checkbox checkSubs
Checkbox checkFilenames
Checkbox checkSigned
boolean doSubdirectories
boolean doFixFilenames
boolean doUseSigned
File myDir
String rootDir
JEditorPane html
Thread animThread
JTextArea propertiesTextArea
JTree tree
DefaultTreeModel treeModel
JmolViewer viewer
JCheckBox repeatCheckBox
JSlider selectSlider
JLabel infoLabel
JSlider fpsSlider
JSlider amplitudeSlider
JSlider periodSlider
JSlider scaleSlider
JSlider radiusSlider
JFileChooser saveChooser
int[] indexes
int currentIndex
JLabel bannerLabel
StatusBar status
GuiMap guimap
JmolViewer viewer
String displaySpeed
Dimension startupDimension
boolean haveDisplay
Point border
boolean haveBorder
MeasurementTable measurementTable
JmolPanel jmolPanel
JFrame frame
boolean showPaintTime
Dimension dimSize
Rectangle rectClip
AbstractButton buttonRotate
AbstractButton buttonModelkit
ButtonGroup toolbarButtonGroup
DisplayPanel.HomeAction homeAction
DisplayPanel.DefineCenterAction defineCenterAction
Action frontAction
Action topAction
Action bottomAction
Action rightAction
Action leftAction
Action hydrogensAction
Action measurementsAction
Action perspectiveAction
Action axesAction
Action boundboxAction
Action deleteAction
Action zoomAction
Action xlateAction
MenuListener menuListener
long timeBegin
int lastMotionEventNumber
JmolViewer viewer
JPanel container
JTextField checkField
JTextField optsField
JTextField fileField
JTextField selectField
JComboBox memBox
JComboBox methBox
JComboBox basisBox
JComboBox dfBox
JSpinner procSpinner
JSpinner chargeSpinner
JSpinner multSpinner
JButton fileButton
JButton saveButton
JButton cancelButton
JFileChooser fileChooser
JTextArea editArea
JTabbedPane inputTabs
String check
String mem
String proc
String file
String meth
String route
String charge
String mult
String select
JEditorPane html
JmolViewer viewer
JmolAdapter modelAdapter
JmolApp jmolApp
StatusBar status
int startupWidth
int startupHeight
JsonNioService serverService
String appletContext
PropertyChangeSupport pcs
DisplayPanel display
GaussianDialog gaussianDialog
RecentFilesDialog recentFiles
AtomSetChooser atomSetChooser
JFrame frame
SplashInterface splash
JFrame consoleframe
JsonNioService service
GuiMap guimap
int qualityJPG
int qualityPNG
String imageType
JmolPanel.ExecuteScriptAction executeScriptAction
PreferencesDialog preferencesDialog
StatusListener myStatusListener
SurfaceTool surfaceTool
Map<K,V> commands
Map<K,V> menuItems
JMenuBar menubar
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
Action[] defaultActions
WebExport webExport
JmolViewer viewer
JTable measurementTable
MeasurementTable.MeasurementTableModel measurementTableModel
int selectedMeasurementRow
JButton deleteButton
JButton deleteAllButton
Class<T> stringClass
JButton povrayPathButton
JButton goButton
JTextField saveField
JTextField savePathLabel
int outputWidth
int outputHeight
JTextField povrayPathLabel
JCheckBox runPovCheck
JCheckBox allFramesCheck
JCheckBox antiAliasCheck
JCheckBox displayWhileRenderingCheck
JLabel imageSizeWidth
JFormattedTextField imageSizeTextWidth
JLabel imageSizeHeight
JFormattedTextField imageSizeTextHeight
JCheckBox imageSizeRatioBox
JComboBox imageSizeRatioCombo
JCheckBox outputFormatCheck
JComboBox outputFormatCombo
JCheckBox outputAlphaCheck
JCheckBox mosaicPreviewCheck
JLabel mosaicPreviewStart
JComboBox mosaicPreviewComboStart
JLabel mosaicPreviewEnd
JComboBox mosaicPreviewComboEnd
String outputExtension
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
JButton bButton
JButton pButton
JButton tButton
JButton eButton
JButton vButton
JRadioButton abYes
JRadioButton abNo
JSlider vdwPercentSlider
JSlider bdSlider
JSlider bwSlider
JSlider btSlider
JCheckBox cH
JCheckBox cM
JCheckBox cbPerspectiveDepth
JCheckBox cbShowAxes
JCheckBox cbShowBoundingBox
JCheckBox cbAxesOrientationRasmol
JCheckBox cbOpenFilePreview
JCheckBox cbClearHistory
Properties originalSystemProperties
Properties jmolDefaultProperties
Properties currentProperties
PreferencesDialog.PrefsAction prefsAction
Map<K,V> commands
JmolPanel jmol
JmolViewer viewer
GuiMap guimap
ItemListener checkBoxListener
JButton applyButton
JButton jmolDefaultsButton
JButton rasmolDefaultsButton
JButton cancelButton
JButton okButton
JEditorPane html
JButton OrbopenButton
JButton OrbdeleteButton
JButton CooropenButton
JButton saveButton
JTextField Coorfile
JTextField appletPath
JFileChooser fc
JList OrbList
JComboBox RenderMode
JComboBox FormatBox
JButton StateButton
JButton FileButton
JButton PathButton
JButton movetoTime
JButton StringtoScriptButton
JTextField appletPath
ArrayListTransferHandler arrayListHandler
JFileChooser fc
Viewer viewer