Serialized Form


Package org.jmol.adapter.smarter

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

Serialized Fields

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

Package org.jmol.applet

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

Serialized Fields

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

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

Serialized Fields

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

Package org.jmol.console

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

Serialized Fields

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

Class org.jmol.console.ScriptEditor extends JDialog implements Serializable

Serialized Fields

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

Class org.jmol.export.dialog.Dialog extends JPanel implements Serializable

Serialized Fields

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

Class org.jmol.export.dialog.FileChooser extends JFileChooser implements Serializable

Serialized Fields

dialogLocation

Point dialogLocation

dialogSize

Dimension dialogSize

dialog

JDialog dialog

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

Serialized Fields

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

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

Serialized Fields

viewer

JmolViewer viewer

modelkitMenu

ModelKitPopup modelkitMenu

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


Package org.jmol.modelset

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

Serialized Fields

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

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

Serialized Fields

associatedAtoms

int[] associatedAtoms

Package org.jmol.smiles

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

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

Serialized Fields

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

Package org.jmol.util

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

Serialized Fields

outStream

BufferedOutputStream outStream

JpegObj

JpegInfo JpegObj

Huf

Huffman Huf

dct

DCT dct

Quality

int Quality

Class org.jmol.util.Point3fi extends 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 JDialog implements Serializable

Serialized Fields

html

JEditorPane html

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

Serialized Fields

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

Class org.openscience.jmol.app.jmolpanel.AtomSetChooser extends JFrame implements Serializable

Serialized Fields

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

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

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

Serialized Fields

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

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

Serialized Fields

useFileExtensionCheckBox

JCheckBox useFileExtensionCheckBox

fileTypeLabel

JLabel fileTypeLabel

fileTypeComboBox

JComboBox fileTypeComboBox

useFileExtension

boolean useFileExtension

choices

String[] choices

defaultTypeIndex

int defaultTypeIndex

fileType

String fileType

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

Serialized Fields

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

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

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

Class org.openscience.jmol.app.jmolpanel.MeasurementTable extends JDialog implements Serializable

Serialized Fields

viewer

JmolViewer viewer

measurementTable

JTable measurementTable

measurementTableModel

MeasurementTable.MeasurementTableModel measurementTableModel

selectedMeasurementRow

int selectedMeasurementRow

deleteButton

JButton deleteButton

deleteAllButton

JButton deleteAllButton

stringClass

Class<T> stringClass

Class org.openscience.jmol.app.jmolpanel.PovrayDialog extends JDialog implements Serializable

Serialized Fields

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

Class org.openscience.jmol.app.jmolpanel.PreferencesDialog extends 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

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

Class org.openscience.jmol.app.jmolpanel.Splash extends Window implements Serializable

Serialized Fields

splashImage

Image splashImage

imgWidth

int imgWidth

imgHeight

int imgHeight

status

String status

textY

int textY

statusTop

int statusTop

Class org.openscience.jmol.app.jmolpanel.WhatsNewDialog extends JDialog implements Serializable

Serialized Fields

html

JEditorPane html

Package org.openscience.jmol.app.webexport

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

serialVersionUID: 1L

Serialized Fields

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

Class org.openscience.jmol.app.webexport.Test extends JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

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

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

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