Serialized Form


Package org.jmol.adapter.smarter

Class org.jmol.adapter.smarter.Atom extends javax.vecmath.Point3f implements Serializable

Serialized Fields

atomSetIndex

int atomSetIndex

atomIndex

int atomIndex

bsSymmetry

java.util.BitSet bsSymmetry

atomSite

int atomSite

elementSymbol

java.lang.String elementSymbol

elementNumber

short elementNumber

atomName

java.lang.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

java.lang.String group3

sequenceNumber

int sequenceNumber

insertionCode

char insertionCode

anisoBorU

float[] anisoBorU

ellipsoid

java.lang.Object[] ellipsoid

ignoreSymmetry

boolean ignoreSymmetry

Package org.jmol.applet

Class org.jmol.applet.AppletConsole extends JmolConsole implements Serializable

Serialized Fields

input

javax.swing.JTextArea input

output

javax.swing.JTextPane output

outputDocument

javax.swing.text.Document outputDocument

jf

javax.swing.JFrame jf

attributesCommand

javax.swing.text.SimpleAttributeSet attributesCommand

menubar

javax.swing.JMenuBar menubar

clearOutButton

javax.swing.JButton clearOutButton

clearInButton

javax.swing.JButton clearInButton

loadButton

javax.swing.JButton loadButton

map

java.util.Hashtable<K,V> map

labels

java.util.Hashtable<K,V> labels

Package org.jmol.appletwrapper

Class org.jmol.appletwrapper.AppletWrapper extends java.applet.Applet implements Serializable

Serialized Fields

wrappedAppletClassName

java.lang.String wrappedAppletClassName

preloadImageName

java.lang.String preloadImageName

preloadTextMessage

java.lang.String preloadTextMessage

preloadThreadCount

int preloadThreadCount

preloadClassNames

java.lang.String[] preloadClassNames

preloadClassIndex

int preloadClassIndex

previousClassName

java.lang.String previousClassName

needToCompleteInitialization

boolean needToCompleteInitialization

preloadImageReadyForDisplay

boolean preloadImageReadyForDisplay

preloadImagePainted

boolean preloadImagePainted

preloadImage

java.awt.Image preloadImage

mediaTracker

java.awt.MediaTracker mediaTracker

bgcolor

java.awt.Color bgcolor

textColor

java.awt.Color textColor

wrappedApplet

WrappedApplet wrappedApplet

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

isSigned

boolean isSigned

Package org.jmol.console

Class org.jmol.console.JmolConsole extends javax.swing.JDialog implements Serializable

Serialized Fields

viewer

JmolViewer viewer

display

java.awt.Component display

scriptEditor

ScriptEditor scriptEditor

editButton

javax.swing.JButton editButton

runButton

javax.swing.JButton runButton

historyButton

javax.swing.JButton historyButton

stateButton

javax.swing.JButton stateButton

nTab

int nTab

incompleteCmd

java.lang.String incompleteCmd

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

checkButton

javax.swing.JButton checkButton

runButton

javax.swing.JButton runButton

pauseButton

javax.swing.JButton pauseButton

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

viewer

JmolViewer viewer

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

Package org.jmol.export.dialog

Class org.jmol.export.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 cb

qPanelJPEG

javax.swing.JPanel qPanelJPEG

qPanelPNG

javax.swing.JPanel qPanelPNG

openPreview

FilePreview openPreview

initialFile

java.io.File initialFile

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

Serialized Fields

active

javax.swing.JCheckBox active

append

javax.swing.JCheckBox append

chooser

javax.swing.JFileChooser chooser

display

FilePreview.FPPanel display

Package org.jmol.jvxl.readers

Class org.jmol.jvxl.readers.Dns6BinaryReader extends java.lang.Object implements Serializable


Package org.jmol.modelkit

Class org.jmol.modelkit.ModelKit extends javax.swing.JDialog implements Serializable

Serialized Fields

viewer

JmolViewer viewer

modelkitMenu

ModelKitPopup modelkitMenu

Class org.jmol.modelkit.modelKitPopupResourceBundle extends java.lang.Object implements Serializable


Package org.jmol.modelset

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

Serialized Fields

group

Group group

atomSymmetry

java.util.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

Class org.jmol.modelset.Bond.BondSet extends java.util.BitSet implements Serializable

Serialized Fields

associatedAtoms

int[] associatedAtoms

Package org.jmol.smiles

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

Class org.jmol.smiles.SmilesAtom extends javax.vecmath.Point3f implements Serializable

Serialized Fields

index

int index

atomName

java.lang.String atomName

residueName

java.lang.String residueName

residueChar

java.lang.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

Package org.jmol.util

Class org.jmol.util.JpegEncoder extends java.awt.Frame implements Serializable

Serialized Fields

outStream

java.io.BufferedOutputStream outStream

JpegObj

JpegInfo JpegObj

Huf

Huffman Huf

dct

DCT dct

Quality

int Quality

Class org.jmol.util.Point3fi extends javax.vecmath.Point3f implements Serializable

Serialized Fields

index

int index

screenX

int screenX

screenY

int screenY

screenZ

int screenZ

screenDiameter

short screenDiameter

modelIndex

short modelIndex

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.AboutDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

html

javax.swing.JEditorPane html

Class org.openscience.jmol.app.jmolpanel.AppConsole extends JmolConsole implements Serializable

Serialized Fields

console

AppConsole.ConsoleTextPane console

varButton

javax.swing.JButton varButton

haltButton

javax.swing.JButton haltButton

closeButton

javax.swing.JButton closeButton

clearButton

javax.swing.JButton clearButton

questButton

javax.swing.JButton questButton

helpButton

javax.swing.JButton helpButton

undoButton

javax.swing.JButton undoButton

redoButton

javax.swing.JButton redoButton

checkButton

javax.swing.JButton checkButton

stepButton

javax.swing.JButton stepButton

topButton

javax.swing.JButton topButton

buttonPanel

javax.swing.JPanel buttonPanel

isError

boolean isError

execThread

AppConsole.ExecuteCommandThread execThread

undoStack

java.lang.String[] undoStack

undoPointer

int undoPointer

undoSaved

boolean undoSaved

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

viewer

JmolViewer viewer

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

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

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

Serialized Fields

status

StatusBar status

guimap

GuiMap guimap

viewer

JmolViewer viewer

displaySpeed

java.lang.String displaySpeed

startupDimension

java.awt.Dimension startupDimension

haveDisplay

boolean haveDisplay

border

java.awt.Point border

haveBorder

boolean haveBorder

measurementTable

MeasurementTable measurementTable

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

menuListener

javax.swing.event.MenuListener menuListener

timeBegin

long timeBegin

lastMotionEventNumber

int lastMotionEventNumber

Class org.openscience.jmol.app.jmolpanel.FileTyper extends javax.swing.JPanel implements Serializable

Serialized Fields

useFileExtensionCheckBox

javax.swing.JCheckBox useFileExtensionCheckBox

fileTypeLabel

javax.swing.JLabel fileTypeLabel

fileTypeComboBox

javax.swing.JComboBox fileTypeComboBox

useFileExtension

boolean useFileExtension

choices

java.lang.String[] choices

defaultTypeIndex

int defaultTypeIndex

fileType

java.lang.String fileType

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

Serialized Fields

viewer

JmolViewer viewer

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 memBox

methBox

javax.swing.JComboBox methBox

basisBox

javax.swing.JComboBox basisBox

dfBox

javax.swing.JComboBox 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

cancelButton

javax.swing.JButton cancelButton

fileChooser

javax.swing.JFileChooser fileChooser

editArea

javax.swing.JTextArea editArea

inputTabs

javax.swing.JTabbedPane inputTabs

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

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

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

javax.swing.JFrame frame

sizeFrame

javax.swing.JFrame sizeFrame

guimap

GuiMap guimap

startupWidth

int startupWidth

startupHeight

int startupHeight

pcs

java.beans.PropertyChangeSupport pcs

splash

SplashInterface splash
Button group for toggle buttons in the toolbar.


consoleframe

javax.swing.JFrame consoleframe

appletContext

java.lang.String appletContext

commands

java.util.Hashtable<K,V> commands

menuItems

java.util.Hashtable<K,V> menuItems

menubar

javax.swing.JMenuBar menubar

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

pasteClipboardAction

JmolPanel.PasteClipboardAction pasteClipboardAction

viewMeasurementTableAction

JmolPanel.ViewMeasurementTableAction viewMeasurementTableAction

qualityJPG

int qualityJPG

qualityPNG

int qualityPNG

imageType

java.lang.String imageType

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

viewer

JmolViewer viewer

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 imageSizeRatioCombo

outputFormatCheck

javax.swing.JCheckBox outputFormatCheck

outputFormatCombo

javax.swing.JComboBox outputFormatCombo

outputAlphaCheck

javax.swing.JCheckBox outputAlphaCheck

mosaicPreviewCheck

javax.swing.JCheckBox mosaicPreviewCheck

mosaicPreviewStart

javax.swing.JLabel mosaicPreviewStart

mosaicPreviewComboStart

javax.swing.JComboBox mosaicPreviewComboStart

mosaicPreviewEnd

javax.swing.JLabel mosaicPreviewEnd

mosaicPreviewComboEnd

javax.swing.JComboBox 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

clearConsoleButton

boolean clearConsoleButton

minBondDistance

float minBondDistance

bondTolerance

float bondTolerance

marBond

short marBond

percentVdwAtom

int percentVdwAtom

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

cbClearConsoleButton

javax.swing.JCheckBox cbClearConsoleButton

originalSystemProperties

java.util.Properties originalSystemProperties

jmolDefaultProperties

java.util.Properties jmolDefaultProperties

currentProperties

java.util.Properties currentProperties

prefsAction

PreferencesDialog.PrefsAction prefsAction

commands

java.util.Hashtable<K,V> commands

jmol

JmolPanel jmol

viewer

JmolViewer viewer

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 javax.swing.JDialog implements Serializable

Serialized Fields

html

javax.swing.JEditorPane html

Package org.openscience.jmol.app.webexport

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

serialVersionUID: 1L

Serialized Fields

OrbopenButton

javax.swing.JButton OrbopenButton

OrbdeleteButton

javax.swing.JButton OrbdeleteButton

CooropenButton

javax.swing.JButton CooropenButton

saveButton

javax.swing.JButton saveButton

Coorfile

javax.swing.JTextField Coorfile

appletPath

javax.swing.JTextField appletPath

fc

javax.swing.JFileChooser fc

OrbList

javax.swing.JList OrbList

RenderMode

javax.swing.JComboBox RenderMode

FormatBox

javax.swing.JComboBox FormatBox

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

viewer

Viewer viewer

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

Class org.openscience.jmol.app.webexport.WebMaker extends javax.swing.JPanel implements Serializable