Serialized Form
-
Package org.jmol.adapter.smarter
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Class org.jmol.adapter.smarter.Atom extends javajs.util.P3 implements Serializable
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Serialized Fields
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altLoc
char altLoc
-
anisoBorU
float[] anisoBorU
-
atomName
String atomName
-
atomSerial
int atomSerial
-
atomSetIndex
int atomSetIndex
-
atomSite
int atomSite
-
bfactor
float bfactor
-
bsSymmetry
javajs.util.BS bsSymmetry
-
chainID
int chainID
-
elementNumber
short elementNumber
-
elementSymbol
String elementSymbol
-
foccupancy
float foccupancy
-
formalCharge
int formalCharge
-
group3
String group3
-
ignoreSymmetry
boolean ignoreSymmetry
-
index
int index
-
insertionCode
char insertionCode
-
isHetero
boolean isHetero
-
partialCharge
float partialCharge
-
radius
float radius
-
sequenceNumber
int sequenceNumber
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tensors
javajs.util.Lst<Object> tensors
-
vib
javajs.util.V3 vib
-
-
-
-
Package org.jmol.applet
-
Class org.jmol.applet.AppletWrapper extends JApplet implements Serializable
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Serialized Fields
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bgcolor
Color bgcolor
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clockBaseline
int clockBaseline
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clockWidth
int clockWidth
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clockX
int clockX
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font
Font font
-
fontAscent
int fontAscent
-
fontHeight
int fontHeight
-
fontMetrics
FontMetrics fontMetrics
-
fontSize
int fontSize
-
isSigned
boolean isSigned
-
mediaTracker
MediaTracker mediaTracker
-
needToCompleteInitialization
boolean needToCompleteInitialization
-
preloadClassIndex
int preloadClassIndex
-
preloadClassNames
String[] preloadClassNames
-
preloadImage
Image preloadImage
-
preloadImageName
String preloadImageName
-
preloadImagePainted
boolean preloadImagePainted
-
preloadImageReadyForDisplay
boolean preloadImageReadyForDisplay
-
preloadTextMessage
String preloadTextMessage
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preloadThreadCount
int preloadThreadCount
-
previousClassName
String previousClassName
-
startTime
long startTime
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textColor
Color textColor
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wrappedApplet
WrappedApplet wrappedApplet
-
-
-
Class org.jmol.applet.JmolApplet extends AppletWrapper implements Serializable
-
-
Package org.jmol.awt
-
Class org.jmol.awt.AwtColor extends Color implements Serializable
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Serialized Fields
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opacity
int opacity
-
-
-
-
Package org.jmol.console
-
Class org.jmol.console.ImageDialog extends JDialog implements Serializable
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Serialized Fields
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canvas
ImageDialog.ImageCanvas canvas
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console
JmolAppConsoleInterface console
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image
Image image
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imageMap
Map<String,GenericImageDialog> imageMap
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menubar
JMenuBar menubar
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title
String title
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vwr
Viewer vwr
-
-
-
Class org.jmol.console.JmolButton extends JButton implements Serializable
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Class org.jmol.console.JmolLabel extends JLabel implements Serializable
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Class org.jmol.console.JmolToggleButton extends JToggleButton implements Serializable
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Class org.jmol.console.KeyJCheckBox extends JCheckBox implements Serializable
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Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJCheckBoxMenuItem extends JCheckBoxMenuItem implements Serializable
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Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJMenu extends JMenu implements Serializable
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Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJMenuItem extends JMenuItem implements Serializable
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Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.KeyJRadioButtonMenuItem extends JRadioButtonMenuItem implements Serializable
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Serialized Fields
-
key
String key
-
-
-
Class org.jmol.console.ScriptEditor extends JDialog implements Serializable
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Serialized Fields
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attEcho
SimpleAttributeSet attEcho
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attError
SimpleAttributeSet attError
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attHighlight
SimpleAttributeSet attHighlight
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buttonPanel
JPanel buttonPanel
-
checkButton
JButton checkButton
-
clearButton
JButton clearButton
-
closeButton
JButton closeButton
-
consoleButton
JButton consoleButton
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editor
ScriptEditor.EditorTextPane editor
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filename
String filename
-
fontButton
JButton fontButton
-
fontSize
int fontSize
-
haltButton
JButton haltButton
-
jmolConsole
JmolConsole jmolConsole
-
loadButton
JButton loadButton
-
map
Map<String,Object> map
-
openButton
JButton openButton
-
parsedContext
ScriptContext parsedContext
-
parsedData
String parsedData
-
pauseButton
JButton pauseButton
-
resumeButton
JButton resumeButton
-
runButton
JButton runButton
-
saveAsButton
JButton saveAsButton
-
saveButton
JButton saveButton
-
stateButton
JButton stateButton
-
stepButton
JButton stepButton
-
title
String title
-
topButton
JButton topButton
-
vwr
Viewer vwr
-
zipFileName
String zipFileName
-
-
-
-
Package org.jmol.dialog
-
Class org.jmol.dialog.Dialog extends JPanel implements Serializable
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Serialized Fields
-
cb
JComboBox<String> cb
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choice
String choice
-
dialogType
String dialogType
-
extension
String extension
-
extensions
String[] extensions
-
imageChoices
String[] imageChoices
-
imageExtensions
String[] imageExtensions
-
imageType
String imageType
-
initialFile
File initialFile
-
inputFileName
String inputFileName
-
openPreview
FilePreview openPreview
-
outputFileName
String outputFileName
-
qPanelJPEG
JPanel qPanelJPEG
-
qPanelPNG
JPanel qPanelPNG
-
qSliderJPEG
JSlider qSliderJPEG
-
qSliderPNG
JSlider qSliderPNG
-
qualityJ
int qualityJ
-
qualityP
int qualityP
-
vwr
Viewer vwr
-
-
-
Class org.jmol.dialog.FileChooser extends JFileChooser implements Serializable
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Class org.jmol.dialog.FilePreview extends JPanel implements Serializable
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Serialized Fields
-
active
JCheckBox active
-
append
JCheckBox append
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cartoons
JCheckBox cartoons
-
chooser
JFileChooser chooser
-
display
FilePreview.FPPanel display
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vwr
Viewer vwr
-
-
-
-
Package org.jmol.modelset
-
Class org.jmol.modelset.Atom extends Point3fi implements Serializable
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Serialized Fields
-
altloc
char altloc
-
atomicAndIsotopeNumber
short atomicAndIsotopeNumber
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atomID
byte atomID
-
atomSite
int atomSite
-
atomSymmetry
javajs.util.BS atomSymmetry
-
bonds
Bond[] bonds
MAY BE NULL -
clickabilityFlags
int clickabilityFlags
-
colixAtom
short colixAtom
-
formalChargeAndFlags
int formalChargeAndFlags
-
group
Group group
-
madAtom
short madAtom
-
nBackbonesDisplayed
int nBackbonesDisplayed
-
nBondsDisplayed
int nBondsDisplayed
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paletteID
byte paletteID
-
shapeVisibilityFlags
int shapeVisibilityFlags
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userDefinedVanDerWaalRadius
float userDefinedVanDerWaalRadius
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valence
byte valence
-
-
-
-
Package org.jmol.script
-
Class org.jmol.script.ScriptException extends Exception implements Serializable
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Serialized Fields
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eval
ScriptEval eval
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isError
boolean isError
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message
String message
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untranslated
String untranslated
-
-
-
Class org.jmol.script.ScriptInterruption extends ScriptException implements Serializable
-
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Package org.jmol.smiles
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Class org.jmol.smiles.InvalidSmilesException extends Exception implements Serializable
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Class org.jmol.smiles.SmilesAtom extends javajs.util.P3 implements Serializable
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Serialized Fields
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aromaticAmbiguous
boolean aromaticAmbiguous
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atomClass
float atomClass
-
atomicMass
int atomicMass
-
atomNumber
int atomNumber
-
atomSite
int atomSite
-
atomType
String atomType
-
bioAtomName
String bioAtomName
-
bioType
char bioType
-
bondCount
int bondCount
-
bonds
SmilesBond[] bonds
-
charge
int charge
-
cipChirality
int cipChirality
-
component
int component
-
connectivity
int connectivity
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covalentHydrogenCount
int covalentHydrogenCount
-
degree
int degree
-
elementDefined
boolean elementDefined
-
elementNumber
int elementNumber
-
explicitHydrogenCount
int explicitHydrogenCount
-
hasSubpattern
boolean hasSubpattern
-
hasSymbol
boolean hasSymbol
-
implicitHydrogenCount
int implicitHydrogenCount
-
index
int index
-
iNested
int iNested
-
insCode
char insCode
-
isAND
boolean isAND
-
isAromatic
boolean isAromatic
-
isBioAtom
boolean isBioAtom
-
isBioAtomWild
boolean isBioAtomWild
-
isBioResidue
boolean isBioResidue
-
isFirst
boolean isFirst
true if this atom is the first SMILES atom or first after a . with no connector -
isLeadAtom
boolean isLeadAtom
-
isTopoAtom
boolean isTopoAtom
-
jmolIndex
int jmolIndex
-
mapIndex
int mapIndex
-
matchingComponent
int matchingComponent
-
matchingIndex
int matchingIndex
-
matchingNode
Node matchingNode
-
missingHydrogenCount
int missingHydrogenCount
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nonhydrogenDegree
int nonhydrogenDegree
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not
boolean not
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notBondedIndex
int notBondedIndex
-
notCrossLinked
boolean notCrossLinked
-
nSubAtoms
int nSubAtoms
-
parent
SmilesAtom parent
-
pattern
String pattern
-
patternIndex
int patternIndex
-
primitiveType
int primitiveType
-
referance
String referance
-
residueChar
String residueChar
-
residueName
String residueName
-
residueNumber
int residueNumber
-
ringConnectivity
int ringConnectivity
-
ringMembership
int ringMembership
-
ringSize
int ringSize
-
selected
boolean selected
-
stereo
SmilesStereo stereo
-
subAtoms
SmilesAtom[] subAtoms
-
symbol
String symbol
-
valence
int valence
-
-
-
-
Package org.jmol.util
-
Class org.jmol.util.ModulationSet extends Vibration implements Serializable
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Serialized Fields
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axesLengths
float[] axesLengths
unit cell axes -- used in Modulation for calculating magnetic modulations -
enabled
boolean enabled
indicates state of modulated or unmodulated -
fileOcc
double fileOcc
-
gammaE
javajs.util.M3 gammaE
-
gammaIinv
javajs.util.Matrix gammaIinv
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htUij
Map<String,Float> htUij
current value of anisotropic parameter modulation -
id
String id
an identifier for this modulation -
iop
int iop
the symmetry operation used to generate this atom -
isCommensurate
boolean isCommensurate
commensurate modulations cannot be "undone" and they cannot be turned off -
isQ
boolean isQ
-
isSubsystem
boolean isSubsystem
subsystems can deliver their own unique unit cell; they are commensurate -
modCalc
ModulationSet modCalc
modCalc is used for calculations independent of what the current setting is -
mods
javajs.util.Lst<Modulation> mods
the list of all modulations associated with this atom -
mxyz
javajs.util.V3 mxyz
the modulated magnetic spin -
nOps
int nOps
the number of operators in this space group -- needed for occupancy calculation -
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 -
occParams
double[] occParams
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occSiteMultiplicity
double occSiteMultiplicity
-
occValue
float occValue
final occupancy value -- absolute; in range [0,1] -
ptTemp
javajs.util.P3 ptTemp
-
qtOffset
javajs.util.P3 qtOffset
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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 -
rI
javajs.util.Matrix rI
-
rsvs
javajs.util.Matrix rsvs
the matrix representation for this atom's symmetry operation -
scale
float scale
an adjustable scaling factor, as for vibrations -
sigma
javajs.util.Matrix sigma
-
spinOp
float spinOp
the spin operation for this atom: +1/0/-1 -
strop
String strop
a string description of the atom's symmetry operator -
symmetry
SymmetryInterface symmetry
the space group appropriate to this atom -
tau
javajs.util.Matrix tau
-
tFactorInv
javajs.util.Matrix tFactorInv
-
v0
javajs.util.V3 v0
-
vib
Vibration vib
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration. -
vOcc
float vOcc
the current value of the occupancy modulation
-
-
-
Class org.jmol.util.Point3fi extends javajs.util.P3 implements Serializable
-
Serialized Fields
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i
int i
index in full collection -
mi
short mi
model index -- may be to a trajectory -
sD
short sD
screen diameter -
sX
int sX
screen X -
sY
int sY
screen Y -
sZ
int sZ
screen Z
-
-
-
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 IOException implements Serializable
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Serialized Fields
-
fileName
String fileName
-
-
-
-
Package org.openscience.jmol.app
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Class org.openscience.jmol.app.Jmol extends JmolPanel implements Serializable
-
-
Package org.openscience.jmol.app.janocchio
-
Class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel extends JPanel implements Serializable
-
Serialized Fields
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coupleTable
CoupleTable coupleTable
-
jLabel1
JLabel jLabel1
-
jLabel2
JLabel jLabel2
-
redField
JTextField redField
-
redLabel
JLabel redLabel
-
setAllButton
JButton setAllButton
-
yellowField
JTextField yellowField
-
yellowLabel
JLabel yellowLabel
-
-
-
Class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel extends JPanel implements Serializable
-
Serialized Fields
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chButtonGroup
ButtonGroup chButtonGroup
-
coupleTable
CoupleTable coupleTable
-
eq0RadioButton
JRadioButton eq0RadioButton
-
eq1RadioButton
JRadioButton eq1RadioButton
-
eq2RadioButton
JRadioButton eq2RadioButton
-
eq3RadioButton
JRadioButton eq3RadioButton
-
jLabel1
JLabel jLabel1
-
jLabel2
JLabel jLabel2
-
jLabel3
JLabel jLabel3
-
jLabel4
JLabel jLabel4
-
titleLabel
JLabel titleLabel
-
-
-
Class org.openscience.jmol.app.janocchio.CoupleTable extends JTabbedPane implements Serializable
-
Serialized Fields
-
calcProps
NmrMolecule calcProps
-
CHequation
String CHequation
-
colorCellRenderer
NMRTableCellRenderer colorCellRenderer
-
coupleAddAllButton
JButton coupleAddAllButton
-
coupleColourSelectionPanel
CoupleColourSelectionPanel coupleColourSelectionPanel
-
coupledeleteAllButton
JButton coupledeleteAllButton
-
coupledeleteButton
JButton coupledeleteButton
-
coupleSelection
ListSelectionModel coupleSelection
-
coupleTable
JTable coupleTable
-
coupleTableModel
CoupleTable.CoupleTableModel coupleTableModel
-
degtorad
double degtorad
-
expCouples
String[][] expCouples
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
labelArray
String[] labelArray
-
molCDKuptodate
boolean molCDKuptodate
-
natomsPerModel
int natomsPerModel
-
nmrPanel
NMR_JmolPanel nmrPanel
-
redValue
double redValue
-
selectedCoupleRow
int[] selectedCoupleRow
-
viewer
NMR_Viewer viewer
-
yellowValue
double yellowValue
-
-
-
Class org.openscience.jmol.app.janocchio.FrameCounter extends JPanel implements Serializable
-
Serialized Fields
-
field
JTextField field
-
frameCount
int frameCount
-
frameNumber
int frameNumber
-
label
JLabel label
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.FrameDeltaDisplay extends JPanel implements Serializable
-
Serialized Fields
-
coupleWeight
double coupleWeight
-
coupleWeightField
JTextField coupleWeightField
-
frameDeltaCouple
double frameDeltaCouple
-
frameDeltaNoe
double frameDeltaNoe
-
label
JLabel label
-
noeWeight
double noeWeight
-
noeWeightField
JTextField noeWeightField
-
totalfield
JTextField totalfield
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.LabelSetter extends JPanel implements Serializable
-
Serialized Fields
-
coupleTable
CoupleTable coupleTable
-
field
JTextField field
-
label
JLabel label
-
labelArray
String[] labelArray
-
minindex
int minindex
-
noeTable
NoeTable noeTable
-
selectedAtomIndex
int selectedAtomIndex
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.NamfisReader extends JPanel implements Serializable
-
Class org.openscience.jmol.app.janocchio.NamfisSaver extends JPanel implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_DisplayPanel extends DisplayPanel implements Serializable
-
Serialized Fields
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
guimap
NmrGuiMap guimap
-
populationDisplay
PopulationDisplay populationDisplay
-
status
StatusBar status
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel extends JmolPanel implements Serializable
-
Serialized Fields
-
coupleTable
CoupleTable coupleTable
-
exportChooser
JFileChooser exportChooser
-
frameCounter
FrameCounter frameCounter
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
htMessageCallbacks
Map<String,Thread> htMessageCallbacks
-
isApplet
boolean isApplet
-
labelSetter
LabelSetter labelSetter
-
mainSplitPane
JSplitPane mainSplitPane
-
nmrApplet
NmrApplet nmrApplet
-
nmrDisplay
NMR_DisplayPanel nmrDisplay
-
nmrguimap
NmrGuiMap nmrguimap
-
noeTable
NoeTable noeTable
-
openChooser
FileChooser openChooser
-
populationDisplay
PopulationDisplay populationDisplay
-
readNamfisChooser
JFileChooser readNamfisChooser
-
readNmrChooser
JFileChooser readNmrChooser
-
saveNamfisChooser
JFileChooser saveNamfisChooser
-
saveNmrChooser
JFileChooser saveNmrChooser
-
-
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction extends NMR_JmolPanel.MoleculeDependentAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction extends NMR_JmolPanel.MoleculeDependentAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.janocchio.NmrReader extends JPanel implements Serializable
-
Class org.openscience.jmol.app.janocchio.NmrSaver extends JPanel implements Serializable
-
Class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel extends JPanel implements Serializable
-
Serialized Fields
-
-
Class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel extends JPanel implements Serializable
-
Serialized Fields
-
cutoffField
JTextField cutoffField
-
cutoffLabel
JLabel cutoffLabel
-
freqField
JTextField freqField
-
freqLabel
JLabel freqLabel
-
noesyComboBox
JComboBox<String> noesyComboBox
-
noesyLabel
JLabel noesyLabel
-
noeTable
NoeTable noeTable
-
refSingleComboBox
JComboBox<String> refSingleComboBox
-
refSingleLabel
JLabel refSingleLabel
-
rhoStarField
JTextField rhoStarField
-
rhoStarLabel
JLabel rhoStarLabel
-
setAllButton
JButton setAllButton
-
tauField
JTextField tauField
-
tauLabel
JLabel tauLabel
-
titleLabel
JLabel titleLabel
-
tMixField
JTextField tMixField
-
tMixLabel
JLabel tMixLabel
-
-
-
Class org.openscience.jmol.app.janocchio.NoeTable extends JTabbedPane implements Serializable
-
Serialized Fields
-
calcProps
NmrMolecule calcProps
-
colorCellRenderer
NMRTableCellRenderer colorCellRenderer
-
cutoff
double cutoff
-
expDists
String[][] expDists
-
expNoes
String[][] expNoes
-
expOrDistButton
JComboBox<String> expOrDistButton
-
frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
-
freq
double freq
-
labelArray
String[] labelArray
-
lexpNoes
boolean lexpNoes
-
lrefSingle
boolean lrefSingle
-
molCDKuptodate
boolean molCDKuptodate
-
natomsPerModel
int natomsPerModel
-
nmrPanel
NMR_JmolPanel nmrPanel
-
noeColourSelectionPanel
NoeColourSelectionPanel noeColourSelectionPanel
-
noedeleteAllButton
JButton noedeleteAllButton
-
noedeleteButton
JButton noedeleteButton
-
noeExprefValue
double noeExprefValue
-
noeNPrefIndices
int[] noeNPrefIndices
-
noeNPrefValue
double noeNPrefValue
-
noeParameterSelectionPanel
NoeParameterSelectionPanel noeParameterSelectionPanel
-
noeSelection
ListSelectionModel noeSelection
-
noesetRefButton
JButton noesetRefButton
-
noesy
boolean noesy
-
noeTable
JTable noeTable
-
noeTableModel
NoeTable.NoeTableModel noeTableModel
-
redValue
double redValue
-
rhoStar
double rhoStar
-
selectedNoeRow
int[] selectedNoeRow
-
tau
double tau
-
tMix
double tMix
-
viewer
NMR_Viewer viewer
-
yellowValue
double yellowValue
-
-
-
Class org.openscience.jmol.app.janocchio.PopulationDisplay extends JPanel implements Serializable
-
Serialized Fields
-
field
JTextField field
-
frameNumber
int frameNumber
-
imaxp
int imaxp
-
label
JLabel label
-
maxp
double maxp
-
population
double[] population
-
populationFrames
JCheckBox populationFrames
-
storedFrameNumber
int storedFrameNumber
-
viewer
NMR_Viewer viewer
-
-
-
Class org.openscience.jmol.app.janocchio.TableSorter extends AbstractTableModel implements Serializable
-
Serialized Fields
-
columnComparators
Map columnComparators
-
modelToView
int[] modelToView
-
mouseListener
MouseListener mouseListener
-
sortingColumns
List sortingColumns
-
tableHeader
JTableHeader tableHeader
-
tableModel
TableModel tableModel
-
tableModelListener
TableModelListener tableModelListener
-
viewToModel
TableSorter.Row[] viewToModel
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-
-
-
Package org.openscience.jmol.app.jmolpanel
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Class org.openscience.jmol.app.jmolpanel.AboutDialog extends JDialog implements Serializable
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Serialized Fields
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vwr
JmolViewer vwr
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-
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Class org.openscience.jmol.app.jmolpanel.AtomSetChooser extends JFrame implements Serializable
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Serialized Fields
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amplitudeSlider
JSlider amplitudeSlider
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animThread
Thread animThread
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currentIndex
int currentIndex
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fpsSlider
JSlider fpsSlider
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indexes
int[] indexes
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf. -
infoLabel
JLabel infoLabel
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periodSlider
JSlider periodSlider
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propertiesTextArea
JTextArea propertiesTextArea
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radiusSlider
JSlider radiusSlider
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radiusValue
int radiusValue
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repeatCheckBox
JCheckBox repeatCheckBox
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saveChooser
JFileChooser saveChooser
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scaleSlider
JSlider scaleSlider
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selectSlider
JSlider selectSlider
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tree
JTree tree
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treeModel
DefaultTreeModel treeModel
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vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.CreditsDialog extends HelpDialog implements Serializable
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Class org.openscience.jmol.app.jmolpanel.DisplayPanel extends JPanel implements Serializable
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Serialized Fields
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axesAction
Action axesAction
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bottomAction
Action bottomAction
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boundboxAction
Action boundboxAction
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buttonModelkit
AbstractButton buttonModelkit
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buttonRotate
AbstractButton buttonRotate
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defineCenterAction
DisplayPanel.DefineCenterAction defineCenterAction
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deleteAction
Action deleteAction
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dimSize
Dimension dimSize
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displaySpeed
String displaySpeed
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frame
JFrame frame
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frontAction
Action frontAction
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haveDisplay
boolean haveDisplay
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homeAction
DisplayPanel.HomeAction homeAction
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hydrogensAction
Action hydrogensAction
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jmolPanel
JmolPanel jmolPanel
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lastMotionEventNumber
int lastMotionEventNumber
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leftAction
Action leftAction
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measurementsAction
Action measurementsAction
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perspectiveAction
Action perspectiveAction
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rectClip
Rectangle rectClip
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rightAction
Action rightAction
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showPaintTime
boolean showPaintTime
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startupDim
Dimension startupDim
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timeBegin
long timeBegin
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toolbarButtonGroup
ButtonGroup toolbarButtonGroup
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topAction
Action topAction
-
vwr
Viewer vwr
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xlateAction
Action xlateAction
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zoomAction
Action zoomAction
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-
-
Class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction extends AbstractAction implements Serializable
-
Serialized Fields
-
action
String action
-
-
-
Class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction extends AbstractAction implements Serializable
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Serialized Fields
-
action
String action
-
-
-
Class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction extends AbstractAction implements Serializable
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Serialized Fields
-
statusText
String statusText
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-
-
Class org.openscience.jmol.app.jmolpanel.GaussianDialog extends JDialog implements Serializable
-
Serialized Fields
-
basisBox
JComboBox<String> basisBox
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charge
String charge
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chargeSpinner
JSpinner chargeSpinner
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check
String check
-
checkField
JTextField checkField
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closeButton
JButton closeButton
-
container
JPanel container
-
dfBox
JComboBox<String> dfBox
-
editArea
JTextPane editArea
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editPane
JScrollPane editPane
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file
String file
-
fileButton
JButton fileButton
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fileChooser
JFileChooser fileChooser
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fileField
JTextField fileField
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iscroll
int iscroll
-
mem
String mem
-
memBox
JComboBox<String> memBox
-
meth
String meth
-
methBox
JComboBox<String> methBox
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mult
String mult
-
multSpinner
JSpinner multSpinner
-
optsField
JTextField optsField
-
proc
String proc
-
procSpinner
JSpinner procSpinner
-
refreshButton
JButton refreshButton
-
route
String route
-
saveButton
JButton saveButton
-
select
String select
-
selectField
JTextField selectField
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vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.HelpDialog extends JDialog implements Serializable
-
Serialized Fields
-
html
JEditorPane html
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel extends JPanel implements Serializable
-
Serialized Fields
-
appletContext
String appletContext
-
atomSetChooser
AtomSetChooser atomSetChooser
-
clientService
JsonNioServer clientService
-
commands
Map<String,Action> commands
-
consoleframe
JFrame consoleframe
-
copyImageAction
JmolPanel.CopyImageAction copyImageAction
-
copyScriptAction
JmolPanel.CopyScriptAction copyScriptAction
-
display
DisplayPanel display
-
executeScriptAction
JmolPanel.ExecuteScriptAction executeScriptAction
-
exportAction
JmolPanel.ExportAction exportAction
-
frame
JFrame frame
-
gaussianDialog
GaussianDialog gaussianDialog
-
guimap
GuiMap guimap
-
imageType
String imageType
-
isPlugin
boolean isPlugin
-
jmolApp
JmolApp jmolApp
-
measurementTable
MeasurementTable measurementTable
-
menubar
JMenuBar menubar
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menuItems
Map<String,JMenuItem> menuItems
-
modelAdapter
JmolAdapter modelAdapter
-
myStatusListener
StatusListener myStatusListener
-
pasteClipboardAction
JmolPanel.PasteClipboardAction pasteClipboardAction
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pcs
PropertyChangeSupport pcs
-
pluginMenu
JMenu pluginMenu
-
plugins
Map<String,JmolPlugin> plugins
-
povrayAction
JmolPanel.PovrayAction povrayAction
-
preferencesDialog
PreferencesDialog preferencesDialog
-
printAction
JmolPanel.PrintAction printAction
-
qualityJPG
int qualityJPG
-
qualityPNG
int qualityPNG
-
recentFiles
RecentFilesDialog recentFiles
-
serverService
JsonNioServer serverService
-
splash
SplashInterface splash
-
startupHeight
int startupHeight
-
startupWidth
int startupWidth
-
status
StatusBar status
-
surfaceTool
SurfaceTool surfaceTool
-
surfaceToolAction
JmolPanel.SurfaceToolAction surfaceToolAction
-
toolbar
JToolBar toolbar
-
touchHandler
JsonNioClient.TouchHandler touchHandler
-
toWebAction
JmolPanel.ToWebAction toWebAction
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TYPES
String TYPES
-
viewMeasurementTableAction
JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction
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vwr
Viewer vwr
-
vwrOptions
Map<String,Object> vwrOptions
-
webExport
WebExport webExport
-
windowName
String windowName
-
writeAction
JmolPanel.WriteAction writeAction
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton extends JmolButton implements Serializable
-
Serialized Fields
-
lastPressTime
long lastPressTime
-
script
String script
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction extends AbstractAction implements Serializable
-
Serialized Fields
-
script
String script
-
-
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction extends JmolPanel.NewAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction extends JmolPanel.NewAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction extends JmolPanel.NewAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction extends JmolPanel.NewAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction extends AbstractAction implements Serializable
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Class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction extends AbstractAction implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.MeasurementTable extends JDialog implements Serializable
-
Serialized Fields
-
deleteAllButton
JButton deleteAllButton
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deleteButton
JButton deleteButton
-
measurementTable
JTable measurementTable
-
measurementTableModel
MeasurementTable.MeasurementTableModel measurementTableModel
-
selectedMeasurementRow
int selectedMeasurementRow
-
stringClass
Class<? extends String> stringClass
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.PovrayDialog extends JDialog implements Serializable
-
Serialized Fields
-
allFramesCheck
JCheckBox allFramesCheck
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antiAliasCheck
JCheckBox antiAliasCheck
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displayWhileRenderingCheck
JCheckBox displayWhileRenderingCheck
-
goButton
JButton goButton
-
imageSizeHeight
JLabel imageSizeHeight
-
imageSizeRatioBox
JCheckBox imageSizeRatioBox
-
imageSizeRatioCombo
JComboBox<String> imageSizeRatioCombo
-
imageSizeTextHeight
JFormattedTextField imageSizeTextHeight
-
imageSizeTextWidth
JFormattedTextField imageSizeTextWidth
-
imageSizeWidth
JLabel imageSizeWidth
-
mosaicPreviewCheck
JCheckBox mosaicPreviewCheck
-
mosaicPreviewComboEnd
JComboBox<String> mosaicPreviewComboEnd
-
mosaicPreviewComboStart
JComboBox<String> mosaicPreviewComboStart
-
mosaicPreviewEnd
JLabel mosaicPreviewEnd
-
mosaicPreviewStart
JLabel mosaicPreviewStart
-
outputAlphaCheck
JCheckBox outputAlphaCheck
-
outputExtension
String outputExtension
-
outputFileType
String outputFileType
-
outputFormatCheck
JCheckBox outputFormatCheck
-
outputFormatCombo
JComboBox<String> outputFormatCombo
-
outputHeight
int outputHeight
-
outputWidth
int outputWidth
-
povrayPathButton
JButton povrayPathButton
-
povrayPathLabel
JTextField povrayPathLabel
-
runPovCheck
JCheckBox runPovCheck
-
saveField
JTextField saveField
-
savePathLabel
JTextField savePathLabel
-
-
-
Class org.openscience.jmol.app.jmolpanel.PreferencesDialog extends JDialog implements Serializable
-
Serialized Fields
-
abNo
JRadioButton abNo
-
abYes
JRadioButton abYes
-
actions
List<Action> actions
-
applyButton
JButton applyButton
-
autoBond
boolean autoBond
-
axesOrientationRasmol
boolean axesOrientationRasmol
-
bButton
JButton bButton
-
bdSlider
JSlider bdSlider
-
bondingVersion
int bondingVersion
-
bondTolerance
float bondTolerance
-
btSlider
JSlider btSlider
-
bwSlider
JSlider bwSlider
-
cancelButton
JButton cancelButton
-
cbAxesOrientationRasmol
JCheckBox cbAxesOrientationRasmol
-
cbClearHistory
JCheckBox cbClearHistory
-
cbOpenFilePreview
JCheckBox cbOpenFilePreview
-
cbPerspectiveDepth
JCheckBox cbPerspectiveDepth
-
cbShowAxes
JCheckBox cbShowAxes
-
cbShowBoundingBox
JCheckBox cbShowBoundingBox
-
cH
JCheckBox cH
-
checkBoxListener
ItemListener checkBoxListener
-
clearHistory
boolean clearHistory
-
cM
JCheckBox cM
-
commands
Map<String,Action> commands
-
currentProperties
Properties currentProperties
-
eButton
JButton eButton
-
fontScale
int fontScale
-
guimap
GuiMap guimap
-
jmol
JmolPanel jmol
-
jmolDefaultProperties
Properties jmolDefaultProperties
-
jmolDefaultsButton
JButton jmolDefaultsButton
-
marBond
short marBond
-
minBondDistance
float minBondDistance
-
okButton
JButton okButton
-
openFilePreview
boolean openFilePreview
-
originalSystemProperties
Properties originalSystemProperties
-
pButton
JButton pButton
-
percentVdwAtom
int percentVdwAtom
-
perspectiveDepth
boolean perspectiveDepth
-
prefsAction
PreferencesDialog.PrefsAction prefsAction
-
rasmolDefaultsButton
JButton rasmolDefaultsButton
-
showAxes
boolean showAxes
-
showBoundingBox
boolean showBoundingBox
-
showHydrogens
boolean showHydrogens
-
showMeasurements
boolean showMeasurements
-
tButton
JButton tButton
-
vButton
JButton vButton
-
vdwPercentSlider
JSlider vdwPercentSlider
-
vwr
Viewer vwr
-
-
-
Class org.openscience.jmol.app.jmolpanel.Splash extends Window implements Serializable
-
Class org.openscience.jmol.app.jmolpanel.StatusBar extends JPanel implements Serializable
-
Serialized Fields
-
status
JLabel[] status
-
-
-
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 JTextArea implements Serializable
-
-
Package org.openscience.jmol.app.jsonkiosk
-
Class org.openscience.jmol.app.jsonkiosk.BannerFrame extends JFrame implements Serializable
-
Serialized Fields
-
bannerLabel
JLabel bannerLabel
-
-
-
Class org.openscience.jmol.app.jsonkiosk.KioskFrame extends JFrame implements Serializable
-
-
Package org.openscience.jmol.app.webexport
-
Class org.openscience.jmol.app.webexport.Orbitals extends JPanel implements Serializable
-
Class org.openscience.jmol.app.webexport.Test extends JPanel implements Serializable
- serialVersionUID:
- 1L
-
Serialized Fields
-
appletPath
JTextField appletPath
-
arrayListHandler
ArrayListTransferHandler arrayListHandler
-
fc
JFileChooser fc
-
FileButton
JButton FileButton
-
movetoTime
JButton movetoTime
-
PathButton
JButton PathButton
-
StateButton
JButton StateButton
-
StringtoScriptButton
JButton StringtoScriptButton
-
vwr
Viewer vwr
-
-
Class org.openscience.jmol.app.webexport.WebExport extends JPanel implements Serializable
-