Serialized Form
Package org.jmol.adapter.smarter |
atomSetIndex
int atomSetIndex
atomIndex
int atomIndex
bsSymmetry
BitSet bsSymmetry
atomSite
int atomSite
elementSymbol
String elementSymbol
elementNumber
short elementNumber
atomName
String atomName
formalCharge
int formalCharge
partialCharge
float partialCharge
vectorX
float vectorX
vectorY
float vectorY
vectorZ
float vectorZ
bfactor
float bfactor
occupancy
int occupancy
radius
float radius
isHetero
boolean isHetero
atomSerial
int atomSerial
chainID
char chainID
alternateLocationID
char alternateLocationID
group3
String group3
sequenceNumber
int sequenceNumber
insertionCode
char insertionCode
anisoBorU
float[] anisoBorU
ellipsoid
Object[] ellipsoid
ignoreSymmetry
boolean ignoreSymmetry
input
JTextArea input
output
JTextPane output
outputDocument
Document outputDocument
jf
JFrame jf
attributesCommand
SimpleAttributeSet attributesCommand
menubar
JMenuBar menubar
clearOutButton
JButton clearOutButton
clearInButton
JButton clearInButton
loadButton
JButton loadButton
map
Hashtable<K,V> map
labels
Hashtable<K,V> labels
Package org.jmol.appletwrapper |
wrappedAppletClassName
String wrappedAppletClassName
preloadImageName
String preloadImageName
preloadTextMessage
String preloadTextMessage
preloadThreadCount
int preloadThreadCount
preloadClassNames
String[] preloadClassNames
preloadClassIndex
int preloadClassIndex
previousClassName
String previousClassName
needToCompleteInitialization
boolean needToCompleteInitialization
preloadImageReadyForDisplay
boolean preloadImageReadyForDisplay
preloadImagePainted
boolean preloadImagePainted
preloadImage
Image preloadImage
mediaTracker
MediaTracker mediaTracker
bgcolor
Color bgcolor
textColor
Color textColor
wrappedApplet
WrappedApplet wrappedApplet
startTime
long startTime
clockX
int clockX
clockBaseline
int clockBaseline
clockWidth
int clockWidth
fontSize
int fontSize
font
Font font
fontMetrics
FontMetrics fontMetrics
fontAscent
int fontAscent
fontHeight
int fontHeight
isSigned
boolean isSigned
viewer
JmolViewer viewer
display
Component display
scriptEditor
ScriptEditor scriptEditor
editButton
JButton editButton
runButton
JButton runButton
historyButton
JButton historyButton
stateButton
JButton stateButton
nTab
int nTab
incompleteCmd
String incompleteCmd
editor
ScriptEditor.EditorTextPane editor
openButton
JButton openButton
closeButton
JButton closeButton
loadButton
JButton loadButton
topButton
JButton topButton
checkButton
JButton checkButton
runButton
JButton runButton
pauseButton
JButton pauseButton
haltButton
JButton haltButton
clearButton
JButton clearButton
stateButton
JButton stateButton
consoleButton
JButton consoleButton
stepButton
JButton stepButton
resumeButton
JButton resumeButton
viewer
JmolViewer viewer
jmolConsole
JmolConsole jmolConsole
title
String title
parsedData
String parsedData
parsedContext
ScriptContext parsedContext
attHighlight
SimpleAttributeSet attHighlight
attEcho
SimpleAttributeSet attEcho
attError
SimpleAttributeSet attError
buttonPanel
JPanel buttonPanel
filename
String filename
Package org.jmol.export.dialog |
extensions
String[] extensions
choice
String choice
extension
String extension
qSliderJPEG
JSlider qSliderJPEG
qSliderPNG
JSlider qSliderPNG
cb
JComboBox cb
qPanelJPEG
JPanel qPanelJPEG
qPanelPNG
JPanel qPanelPNG
openPreview
FilePreview openPreview
initialFile
File initialFile
dialogLocation
Point dialogLocation
dialogSize
Dimension dialogSize
dialog
JDialog dialog
active
JCheckBox active
append
JCheckBox append
chooser
JFileChooser chooser
display
FilePreview.FPPanel display
Package org.jmol.jvxl.readers |
Class org.jmol.jvxl.readers.Dns6BinaryReader extends Object implements Serializable |
Package org.jmol.modelkit |
viewer
JmolViewer viewer
modelkitMenu
ModelKitPopup modelkitMenu
Class org.jmol.modelkit.modelKitPopupResourceBundle extends Object implements Serializable |
Package org.jmol.modelset |
group
Group group
atomSymmetry
BitSet atomSymmetry
atomSite
int atomSite
userDefinedVanDerWaalRadius
float userDefinedVanDerWaalRadius
atomicAndIsotopeNumber
short atomicAndIsotopeNumber
formalChargeAndFlags
byte formalChargeAndFlags
valence
byte valence
alternateLocationID
char alternateLocationID
atomID
byte atomID
madAtom
short madAtom
colixAtom
short colixAtom
paletteID
byte paletteID
bonds
Bond[] bonds
nBondsDisplayed
int nBondsDisplayed
nBackbonesDisplayed
int nBackbonesDisplayed
clickabilityFlags
int clickabilityFlags
shapeVisibilityFlags
int shapeVisibilityFlags
associatedAtoms
int[] associatedAtoms
index
int index
atomName
String atomName
residueName
String residueName
residueChar
String residueChar
isBioAtom
boolean isBioAtom
bioType
char bioType
isLeadAtom
boolean isLeadAtom
notBondedIndex
int notBondedIndex
notCrossLinked
boolean notCrossLinked
not
boolean not
selected
boolean selected
hasSymbol
boolean hasSymbol
isFirst
boolean isFirst
jmolIndex
int jmolIndex
elementNumber
short elementNumber
atomicMass
short atomicMass
charge
int charge
missingHydrogenCount
int missingHydrogenCount
implicitHydrogenCount
int implicitHydrogenCount
matchingAtom
int matchingAtom
chiralClass
int chiralClass
chiralOrder
int chiralOrder
isAromatic
boolean isAromatic
parent
SmilesAtom parent
bonds
SmilesBond[] bonds
bondCount
int bondCount
iNested
int iNested
atomsOr
SmilesAtom[] atomsOr
nAtomsOr
int nAtomsOr
primitives
SmilesAtom[] primitives
nPrimitives
int nPrimitives
component
int component
atomSite
int atomSite
degree
int degree
nonhydrogenDegree
int nonhydrogenDegree
valence
int valence
connectivity
int connectivity
ringMembership
int ringMembership
ringSize
int ringSize
ringConnectivity
int ringConnectivity
covalentHydrogenCount
int covalentHydrogenCount
outStream
BufferedOutputStream outStream
JpegObj
JpegInfo JpegObj
Huf
Huffman Huf
dct
DCT dct
Quality
int Quality
index
int index
screenX
int screenX
screenY
int screenY
screenZ
int screenZ
screenDiameter
short screenDiameter
modelIndex
short modelIndex
Package org.openscience.jmol.app |
Package org.openscience.jmol.app.jmolpanel |
html
JEditorPane html
console
AppConsole.ConsoleTextPane console
varButton
JButton varButton
haltButton
JButton haltButton
closeButton
JButton closeButton
clearButton
JButton clearButton
questButton
JButton questButton
helpButton
JButton helpButton
undoButton
JButton undoButton
redoButton
JButton redoButton
checkButton
JButton checkButton
stepButton
JButton stepButton
topButton
JButton topButton
buttonPanel
JPanel buttonPanel
isError
boolean isError
execThread
AppConsole.ExecuteCommandThread execThread
undoStack
String[] undoStack
undoPointer
int undoPointer
undoSaved
boolean undoSaved
animThread
Thread animThread
propertiesTextArea
JTextArea propertiesTextArea
tree
JTree tree
treeModel
DefaultTreeModel treeModel
viewer
JmolViewer viewer
repeatCheckBox
JCheckBox repeatCheckBox
selectSlider
JSlider selectSlider
infoLabel
JLabel infoLabel
fpsSlider
JSlider fpsSlider
amplitudeSlider
JSlider amplitudeSlider
periodSlider
JSlider periodSlider
scaleSlider
JSlider scaleSlider
radiusSlider
JSlider radiusSlider
saveChooser
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
status
StatusBar status
guimap
GuiMap guimap
viewer
JmolViewer viewer
displaySpeed
String displaySpeed
startupDimension
Dimension startupDimension
haveDisplay
boolean haveDisplay
border
Point border
haveBorder
boolean haveBorder
measurementTable
MeasurementTable measurementTable
frame
JFrame frame
showPaintTime
boolean showPaintTime
dimSize
Dimension dimSize
rectClip
Rectangle rectClip
buttonRotate
AbstractButton buttonRotate
buttonModelkit
AbstractButton buttonModelkit
toolbarButtonGroup
ButtonGroup toolbarButtonGroup
homeAction
DisplayPanel.HomeAction homeAction
defineCenterAction
DisplayPanel.DefineCenterAction defineCenterAction
frontAction
Action frontAction
topAction
Action topAction
bottomAction
Action bottomAction
rightAction
Action rightAction
leftAction
Action leftAction
hydrogensAction
Action hydrogensAction
measurementsAction
Action measurementsAction
perspectiveAction
Action perspectiveAction
axesAction
Action axesAction
boundboxAction
Action boundboxAction
deleteAction
Action deleteAction
zoomAction
Action zoomAction
xlateAction
Action xlateAction
menuListener
MenuListener menuListener
timeBegin
long timeBegin
lastMotionEventNumber
int lastMotionEventNumber
useFileExtensionCheckBox
JCheckBox useFileExtensionCheckBox
fileTypeLabel
JLabel fileTypeLabel
fileTypeComboBox
JComboBox fileTypeComboBox
useFileExtension
boolean useFileExtension
choices
String[] choices
defaultTypeIndex
int defaultTypeIndex
fileType
String fileType
viewer
JmolViewer viewer
container
JPanel container
checkField
JTextField checkField
optsField
JTextField optsField
fileField
JTextField fileField
selectField
JTextField selectField
memBox
JComboBox memBox
methBox
JComboBox methBox
basisBox
JComboBox basisBox
dfBox
JComboBox dfBox
procSpinner
JSpinner procSpinner
chargeSpinner
JSpinner chargeSpinner
multSpinner
JSpinner multSpinner
fileButton
JButton fileButton
saveButton
JButton saveButton
cancelButton
JButton cancelButton
fileChooser
JFileChooser fileChooser
editArea
JTextArea editArea
inputTabs
JTabbedPane inputTabs
check
String check
mem
String mem
proc
String proc
file
String file
meth
String meth
route
String route
charge
String charge
mult
String mult
select
String select
html
JEditorPane html
viewer
JmolViewer viewer
- The data model.
modelAdapter
JmolAdapter modelAdapter
jmolApp
JmolApp jmolApp
display
DisplayPanel display
status
StatusBar status
gaussianDialog
GaussianDialog gaussianDialog
preferencesDialog
PreferencesDialog preferencesDialog
recentFiles
RecentFilesDialog recentFiles
atomSetChooser
AtomSetChooser atomSetChooser
executeScriptAction
JmolPanel.ExecuteScriptAction executeScriptAction
frame
JFrame frame
sizeFrame
JFrame sizeFrame
guimap
GuiMap guimap
startupWidth
int startupWidth
startupHeight
int startupHeight
pcs
PropertyChangeSupport pcs
splash
SplashInterface splash
- Button group for toggle buttons in the toolbar.
consoleframe
JFrame consoleframe
appletContext
String appletContext
commands
Hashtable<K,V> commands
menuItems
Hashtable<K,V> menuItems
menubar
JMenuBar menubar
toolbar
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
pasteClipboardAction
JmolPanel.PasteClipboardAction pasteClipboardAction
viewMeasurementTableAction
JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction
qualityJPG
int qualityJPG
qualityPNG
int qualityPNG
imageType
String imageType
defaultActions
Action[] defaultActions
- Actions defined by the Jmol class
webExport
WebExport webExport
viewer
JmolViewer viewer
measurementTable
JTable measurementTable
measurementTableModel
MeasurementTable.MeasurementTableModel measurementTableModel
selectedMeasurementRow
int selectedMeasurementRow
deleteButton
JButton deleteButton
deleteAllButton
JButton deleteAllButton
stringClass
Class<T> stringClass
povrayPathButton
JButton povrayPathButton
goButton
JButton goButton
saveField
JTextField saveField
savePathLabel
JTextField savePathLabel
outputWidth
int outputWidth
outputHeight
int outputHeight
povrayPathLabel
JTextField povrayPathLabel
runPovCheck
JCheckBox runPovCheck
allFramesCheck
JCheckBox allFramesCheck
antiAliasCheck
JCheckBox antiAliasCheck
displayWhileRenderingCheck
JCheckBox displayWhileRenderingCheck
imageSizeWidth
JLabel imageSizeWidth
imageSizeTextWidth
JFormattedTextField imageSizeTextWidth
imageSizeHeight
JLabel imageSizeHeight
imageSizeTextHeight
JFormattedTextField imageSizeTextHeight
imageSizeRatioBox
JCheckBox imageSizeRatioBox
imageSizeRatioCombo
JComboBox imageSizeRatioCombo
outputFormatCheck
JCheckBox outputFormatCheck
outputFormatCombo
JComboBox outputFormatCombo
outputAlphaCheck
JCheckBox outputAlphaCheck
mosaicPreviewCheck
JCheckBox mosaicPreviewCheck
mosaicPreviewStart
JLabel mosaicPreviewStart
mosaicPreviewComboStart
JComboBox mosaicPreviewComboStart
mosaicPreviewEnd
JLabel mosaicPreviewEnd
mosaicPreviewComboEnd
JComboBox mosaicPreviewComboEnd
outputExtension
String outputExtension
outputFileType
String outputFileType
autoBond
boolean autoBond
showHydrogens
boolean showHydrogens
showMeasurements
boolean showMeasurements
perspectiveDepth
boolean perspectiveDepth
showAxes
boolean showAxes
showBoundingBox
boolean showBoundingBox
axesOrientationRasmol
boolean axesOrientationRasmol
openFilePreview
boolean openFilePreview
clearConsoleButton
boolean clearConsoleButton
minBondDistance
float minBondDistance
bondTolerance
float bondTolerance
marBond
short marBond
percentVdwAtom
int percentVdwAtom
bButton
JButton bButton
pButton
JButton pButton
tButton
JButton tButton
eButton
JButton eButton
vButton
JButton vButton
abYes
JRadioButton abYes
abNo
JRadioButton abNo
vdwPercentSlider
JSlider vdwPercentSlider
bdSlider
JSlider bdSlider
bwSlider
JSlider bwSlider
btSlider
JSlider btSlider
cH
JCheckBox cH
cM
JCheckBox cM
cbPerspectiveDepth
JCheckBox cbPerspectiveDepth
cbShowAxes
JCheckBox cbShowAxes
cbShowBoundingBox
JCheckBox cbShowBoundingBox
cbAxesOrientationRasmol
JCheckBox cbAxesOrientationRasmol
cbOpenFilePreview
JCheckBox cbOpenFilePreview
cbClearConsoleButton
JCheckBox cbClearConsoleButton
originalSystemProperties
Properties originalSystemProperties
jmolDefaultProperties
Properties jmolDefaultProperties
currentProperties
Properties currentProperties
prefsAction
PreferencesDialog.PrefsAction prefsAction
commands
Hashtable<K,V> commands
jmol
JmolPanel jmol
viewer
JmolViewer viewer
guimap
GuiMap guimap
checkBoxListener
ItemListener checkBoxListener
applyButton
JButton applyButton
jmolDefaultsButton
JButton jmolDefaultsButton
rasmolDefaultsButton
JButton rasmolDefaultsButton
cancelButton
JButton cancelButton
okButton
JButton okButton
splashImage
Image splashImage
imgWidth
int imgWidth
imgHeight
int imgHeight
status
String status
textY
int textY
statusTop
int statusTop
html
JEditorPane html
Package org.openscience.jmol.app.webexport |
serialVersionUID: 1L
OrbopenButton
JButton OrbopenButton
OrbdeleteButton
JButton OrbdeleteButton
CooropenButton
JButton CooropenButton
saveButton
JButton saveButton
Coorfile
JTextField Coorfile
appletPath
JTextField appletPath
fc
JFileChooser fc
OrbList
JList OrbList
RenderMode
JComboBox RenderMode
FormatBox
JComboBox FormatBox
serialVersionUID: 1L
StateButton
JButton StateButton
FileButton
JButton FileButton
PathButton
JButton PathButton
movetoTime
JButton movetoTime
StringtoScriptButton
JButton StringtoScriptButton
appletPath
JTextField appletPath
arrayListHandler
ArrayListTransferHandler arrayListHandler
fc
JFileChooser fc
viewer
Viewer viewer