org.jmol.api

Class JmolViewer

public abstract class JmolViewer extends JmolSimpleViewer

This is the high-level API for the JmolViewer for simple access.

We will implement a low-level API at some point

Method Summary
abstract voidaddSelectionListener(JmolSelectionListener listener)
static JmolViewerallocateViewer(Component awtComponent, JmolAdapter jmolAdapter)
This is the main access point for creating an application or applet viewer.
abstract booleancheckHalt(String strCommand)
static booleancheckOption(JmolViewer viewer, String option)
abstract voidclearMeasurements()
abstract voidclearSelection()
abstract StringcreateImage(String file, String type, Object text_or_bytes, int quality, int width, int height)
abstract voiddeleteMeasurement(int i)
abstract StringevalStringQuiet(String script)
abstract StringgenerateOutput(String type, String fileName, int width, int height)
abstract StringgetAltLocListInModel(int modelIndex)
abstract intgetAnimationFps()
abstract intgetAtomArgb(int atomIndex)
abstract intgetAtomCount()
abstract intgetAtomCountInModel(int modelIndex)
abstract StringgetAtomInfo(int atomIndex)
abstract intgetAtomModelIndex(int atomIndex)
abstract StringgetAtomName(int atomIndex)
abstract intgetAtomNumber(int atomIndex)
abstract Point3fgetAtomPoint3f(int atomIndex)
abstract floatgetAtomRadius(int atomIndex)
abstract booleangetAutoBond()
abstract ComponentgetAwtComponent()
abstract booleangetAxesOrientationRasmol()
abstract intgetBackgroundArgb()
abstract intgetBondArgb1(int bondIndex)
abstract intgetBondArgb2(int bondIndex)
abstract intgetBondCount()
abstract intgetBondCountInModel(int modelIndex)
abstract intgetBondModelIndex(int bondIndex)
abstract shortgetBondOrder(int bondIndex)
abstract Point3fgetBondPoint3f1(int bondIndex)
abstract Point3fgetBondPoint3f2(int bondIndex)
abstract floatgetBondRadius(int bondIndex)
abstract floatgetBondTolerance()
abstract booleangetBooleanProperty(String propertyName)
abstract booleangetBooleanProperty(String key, boolean doICare)
abstract intgetChainCount()
abstract intgetChainCountInModel(int modelIindex)
abstract StringgetData(String atomExpression, String type)
abstract intgetDisplayModelIndex()
abstract BitSetgetElementsPresentBitSet(int modelIndex)
abstract StringgetFileAsString(String filename)
abstract intgetGroupCount()
abstract intgetGroupCountInModel(int modelIndex)
abstract HashtablegetHeteroList(int modelIndex)
abstract StringgetJavaVendor()
abstract StringgetJavaVersion()
static StringgetJmolVersion()
abstract shortgetMadBond()
abstract intgetMeasurementCount()
abstract int[]getMeasurementCountPlusIndices(int i)
abstract StringgetMeasurementStringValue(int i)
abstract floatgetMinBondDistance()
abstract HashtablegetModelAuxiliaryInfo(int modelIndex)
abstract ObjectgetModelAuxiliaryInfo(int modelIndex, String keyName)
abstract intgetModelCount()
abstract StringgetModelName(int modelIndex)
abstract intgetModelNumber(int modelIndex)
abstract StringgetModelNumberDotted(int modelIndex)
abstract PropertiesgetModelProperties(int modelIndex)
abstract StringgetModelProperty(int modelIndex, String propertyName)
abstract HashtablegetModelSetAuxiliaryInfo()
abstract StringgetModelSetFileName()
abstract StringgetModelSetName()
abstract StringgetModelSetPathName()
abstract PropertiesgetModelSetProperties()
abstract intgetMotionEventNumber()
abstract StringgetOperatingSystemName()
abstract ObjectgetParameter(String name)
abstract intgetPercentVdwAtom()
abstract booleangetPerspectiveDepth()
abstract intgetPolymerCount()
abstract intgetPolymerCountInModel(int modelIndex)
abstract Point3f[]getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
abstract ObjectgetProperty(String returnType, String infoType, String paramInfo)
abstract floatgetRotationRadius()
abstract intgetScreenHeight()
abstract ImagegetScreenImage()
abstract intgetScreenWidth()
abstract intgetSelectionCount()
abstract StringgetSetHistory(int howFarBack)
abstract booleangetShowAxes()
abstract booleangetShowBbcage()
abstract booleangetShowHydrogens()
abstract booleangetShowMeasurements()
abstract StringgetStateInfo()
abstract Matrix4fgetUnscaledTransformMatrix()
abstract intgetZoomPercent()
abstract floatgetZoomPercentFloat()
abstract voidhaltScriptExecution()
abstract booleanhandleOldJvm10Event(Event e)
abstract booleanhaveFrame()
abstract booleanhavePartialCharges()
abstract voidhomePosition()
abstract booleanisApplet()
abstract booleanisJvm12orGreater()
abstract booleanisScriptExecuting()
abstract voidloadInline(String strModel)
abstract voidloadInline(String strModel, boolean isMerge)
abstract voidloadInline(String strModel, char newLine)
abstract voidloadInline(String[] arrayModels)
abstract voidloadInline(String[] arrayModels, boolean isMerge)
abstract booleanmodelHasVibrationVectors(int modelIndex)
abstract voidopenClientFile(String fullPathName, String fileName, Object clientFile)
abstract voidopenReader(String fullPathName, String name, Reader reader)
abstract voidpopHoldRepaint()
abstract voidpushHoldRepaint()
abstract voidrebond()
abstract voidrefresh(int isOrientationChange, String strWhy)
abstract voidreleaseScreenImage()
abstract voidremoveSelectionListener(JmolSelectionListener listener)
abstract voidrepaintView()
abstract voidrotateFront()
abstract voidrotateX(int degrees)
abstract voidrotateX(float radians)
abstract voidrotateY(int degrees)
abstract voidrotateY(float radians)
abstract voidrotateZ(float radians)
abstract Stringscript(String script)
abstract StringscriptCheck(String script)
abstract StringscriptWait(String script)
abstract ObjectscriptWaitStatus(String script, String statusList)
abstract voidselectAll()
abstract voidsetAnimationFps(int framesPerSecond)
abstract voidsetAppletContext(String htmlName, URL documentBase, URL codeBase, String commandOptions)
abstract voidsetAutoBond(boolean autoBond)
abstract voidsetAxesOrientationRasmol(boolean axesMessedUp)
abstract voidsetBondTolerance(float bondTolerance)
abstract voidsetBooleanProperty(String propertyName, boolean value)
abstract voidsetCenterSelected()
abstract voidsetColorBackground(String colorName)
abstract voidsetDebugScript(boolean debugScript)
abstract voidsetFloatProperty(String propertyName, float value)
abstract voidsetFrankOn(boolean frankOn)
abstract voidsetIntProperty(String propertyName, int value)
abstract voidsetJmolDefaults()
abstract voidsetJmolStatusListener(JmolStatusListener jmolStatusListener)
abstract voidsetMarBond(short marBond)
abstract voidsetMinBondDistance(float minBondDistance)
abstract voidsetModeMouse(int modeMouse)
abstract voidsetPercentVdwAtom(int percentVdwAtom)
abstract voidsetPerspectiveDepth(boolean perspectiveDepth)
abstract voidsetRasmolDefaults()
abstract voidsetScreenDimension(Dimension dim)
abstract voidsetSelectionHalos(boolean haloEnabled)
abstract voidsetSelectionSet(BitSet newSelection)
abstract voidsetShowAxes(boolean showAxes)
abstract voidsetShowBbcage(boolean showBbcage)
abstract voidsetShowHydrogens(boolean showHydrogens)
abstract voidsetShowMeasurements(boolean showMeasurements)
abstract voidsetStringProperty(String propertyName, String value)
abstract voidsetVectorScale(float vectorScaleValue)
abstract voidsetVibrationPeriod(float vibrationPeriod)
abstract voidsetVibrationScale(float vibrationScaleValue)
abstract booleanshowModelSetDownload()
abstract voidshowUrl(String urlString)
abstract voidsyncScript(String script, String applet)
abstract voidwriteTextFile(String string, String data)

Method Detail

addSelectionListener

public abstract void addSelectionListener(JmolSelectionListener listener)

allocateViewer

public static JmolViewer allocateViewer(Component awtComponent, JmolAdapter jmolAdapter)
This is the main access point for creating an application or applet viewer. After allocation it is MANDATORY that one of the next commands is either viewer.evalString("ZAP"); or at least: viewer.setAppletContext("",null,null,"") One or the other of these is necessary to establish the first modelset, which might be required by one or more later evaluated commands or file loadings.

Parameters: awtComponent jmolAdapter

Returns: a JmolViewer object

checkHalt

public abstract boolean checkHalt(String strCommand)

checkOption

public static boolean checkOption(JmolViewer viewer, String option)

clearMeasurements

public abstract void clearMeasurements()

clearSelection

public abstract void clearSelection()

createImage

public abstract String createImage(String file, String type, Object text_or_bytes, int quality, int width, int height)

deleteMeasurement

public abstract void deleteMeasurement(int i)

evalStringQuiet

public abstract String evalStringQuiet(String script)

generateOutput

public abstract String generateOutput(String type, String fileName, int width, int height)

getAltLocListInModel

public abstract String getAltLocListInModel(int modelIndex)

getAnimationFps

public abstract int getAnimationFps()

getAtomArgb

public abstract int getAtomArgb(int atomIndex)

getAtomCount

public abstract int getAtomCount()

getAtomCountInModel

public abstract int getAtomCountInModel(int modelIndex)

getAtomInfo

public abstract String getAtomInfo(int atomIndex)

getAtomModelIndex

public abstract int getAtomModelIndex(int atomIndex)

getAtomName

public abstract String getAtomName(int atomIndex)

getAtomNumber

public abstract int getAtomNumber(int atomIndex)

getAtomPoint3f

public abstract Point3f getAtomPoint3f(int atomIndex)

getAtomRadius

public abstract float getAtomRadius(int atomIndex)

getAutoBond

public abstract boolean getAutoBond()

getAwtComponent

public abstract Component getAwtComponent()

getAxesOrientationRasmol

public abstract boolean getAxesOrientationRasmol()

getBackgroundArgb

public abstract int getBackgroundArgb()

getBondArgb1

public abstract int getBondArgb1(int bondIndex)

getBondArgb2

public abstract int getBondArgb2(int bondIndex)

getBondCount

public abstract int getBondCount()

getBondCountInModel

public abstract int getBondCountInModel(int modelIndex)

getBondModelIndex

public abstract int getBondModelIndex(int bondIndex)

getBondOrder

public abstract short getBondOrder(int bondIndex)

getBondPoint3f1

public abstract Point3f getBondPoint3f1(int bondIndex)

getBondPoint3f2

public abstract Point3f getBondPoint3f2(int bondIndex)

getBondRadius

public abstract float getBondRadius(int bondIndex)

getBondTolerance

public abstract float getBondTolerance()

getBooleanProperty

public abstract boolean getBooleanProperty(String propertyName)

getBooleanProperty

public abstract boolean getBooleanProperty(String key, boolean doICare)

getChainCount

public abstract int getChainCount()

getChainCountInModel

public abstract int getChainCountInModel(int modelIindex)

getData

public abstract String getData(String atomExpression, String type)

getDisplayModelIndex

public abstract int getDisplayModelIndex()

getElementsPresentBitSet

public abstract BitSet getElementsPresentBitSet(int modelIndex)

getFileAsString

public abstract String getFileAsString(String filename)

getGroupCount

public abstract int getGroupCount()

getGroupCountInModel

public abstract int getGroupCountInModel(int modelIndex)

getHeteroList

public abstract Hashtable getHeteroList(int modelIndex)

getJavaVendor

public abstract String getJavaVendor()

getJavaVersion

public abstract String getJavaVersion()

getJmolVersion

public static String getJmolVersion()

getMadBond

public abstract short getMadBond()

getMeasurementCount

public abstract int getMeasurementCount()

getMeasurementCountPlusIndices

public abstract int[] getMeasurementCountPlusIndices(int i)

getMeasurementStringValue

public abstract String getMeasurementStringValue(int i)

getMinBondDistance

public abstract float getMinBondDistance()

getModelAuxiliaryInfo

public abstract Hashtable getModelAuxiliaryInfo(int modelIndex)

getModelAuxiliaryInfo

public abstract Object getModelAuxiliaryInfo(int modelIndex, String keyName)

getModelCount

public abstract int getModelCount()

getModelName

public abstract String getModelName(int modelIndex)

getModelNumber

public abstract int getModelNumber(int modelIndex)

getModelNumberDotted

public abstract String getModelNumberDotted(int modelIndex)

getModelProperties

public abstract Properties getModelProperties(int modelIndex)

getModelProperty

public abstract String getModelProperty(int modelIndex, String propertyName)

getModelSetAuxiliaryInfo

public abstract Hashtable getModelSetAuxiliaryInfo()

getModelSetFileName

public abstract String getModelSetFileName()

getModelSetName

public abstract String getModelSetName()

getModelSetPathName

public abstract String getModelSetPathName()

getModelSetProperties

public abstract Properties getModelSetProperties()

getMotionEventNumber

public abstract int getMotionEventNumber()

getOperatingSystemName

public abstract String getOperatingSystemName()

getParameter

public abstract Object getParameter(String name)

getPercentVdwAtom

public abstract int getPercentVdwAtom()

getPerspectiveDepth

public abstract boolean getPerspectiveDepth()

getPolymerCount

public abstract int getPolymerCount()

getPolymerCountInModel

public abstract int getPolymerCountInModel(int modelIndex)

getPolymerLeadMidPoints

public abstract Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)

getProperty

public abstract Object getProperty(String returnType, String infoType, String paramInfo)

getRotationRadius

public abstract float getRotationRadius()

getScreenHeight

public abstract int getScreenHeight()

getScreenImage

public abstract Image getScreenImage()

getScreenWidth

public abstract int getScreenWidth()

getSelectionCount

public abstract int getSelectionCount()

getSetHistory

public abstract String getSetHistory(int howFarBack)

getShowAxes

public abstract boolean getShowAxes()

getShowBbcage

public abstract boolean getShowBbcage()

getShowHydrogens

public abstract boolean getShowHydrogens()

getShowMeasurements

public abstract boolean getShowMeasurements()

getStateInfo

public abstract String getStateInfo()

getUnscaledTransformMatrix

public abstract Matrix4f getUnscaledTransformMatrix()

getZoomPercent

public abstract int getZoomPercent()

getZoomPercentFloat

public abstract float getZoomPercentFloat()

haltScriptExecution

public abstract void haltScriptExecution()

handleOldJvm10Event

public abstract boolean handleOldJvm10Event(Event e)

haveFrame

public abstract boolean haveFrame()

havePartialCharges

public abstract boolean havePartialCharges()

homePosition

public abstract void homePosition()

isApplet

public abstract boolean isApplet()

isJvm12orGreater

public abstract boolean isJvm12orGreater()

isScriptExecuting

public abstract boolean isScriptExecuting()

loadInline

public abstract void loadInline(String strModel)

loadInline

public abstract void loadInline(String strModel, boolean isMerge)

loadInline

public abstract void loadInline(String strModel, char newLine)

loadInline

public abstract void loadInline(String[] arrayModels)

loadInline

public abstract void loadInline(String[] arrayModels, boolean isMerge)

modelHasVibrationVectors

public abstract boolean modelHasVibrationVectors(int modelIndex)

openClientFile

public abstract void openClientFile(String fullPathName, String fileName, Object clientFile)

openReader

public abstract void openReader(String fullPathName, String name, Reader reader)

popHoldRepaint

public abstract void popHoldRepaint()

pushHoldRepaint

public abstract void pushHoldRepaint()

rebond

public abstract void rebond()

refresh

public abstract void refresh(int isOrientationChange, String strWhy)

releaseScreenImage

public abstract void releaseScreenImage()

removeSelectionListener

public abstract void removeSelectionListener(JmolSelectionListener listener)

repaintView

public abstract void repaintView()

rotateFront

public abstract void rotateFront()

rotateX

public abstract void rotateX(int degrees)

rotateX

public abstract void rotateX(float radians)

rotateY

public abstract void rotateY(int degrees)

rotateY

public abstract void rotateY(float radians)

rotateZ

public abstract void rotateZ(float radians)

script

public abstract String script(String script)

scriptCheck

public abstract String scriptCheck(String script)

scriptWait

public abstract String scriptWait(String script)

scriptWaitStatus

public abstract Object scriptWaitStatus(String script, String statusList)

selectAll

public abstract void selectAll()

setAnimationFps

public abstract void setAnimationFps(int framesPerSecond)

setAppletContext

public abstract void setAppletContext(String htmlName, URL documentBase, URL codeBase, String commandOptions)

setAutoBond

public abstract void setAutoBond(boolean autoBond)

setAxesOrientationRasmol

public abstract void setAxesOrientationRasmol(boolean axesMessedUp)

setBondTolerance

public abstract void setBondTolerance(float bondTolerance)

setBooleanProperty

public abstract void setBooleanProperty(String propertyName, boolean value)

setCenterSelected

public abstract void setCenterSelected()

setColorBackground

public abstract void setColorBackground(String colorName)

setDebugScript

public abstract void setDebugScript(boolean debugScript)

setFloatProperty

public abstract void setFloatProperty(String propertyName, float value)

setFrankOn

public abstract void setFrankOn(boolean frankOn)

setIntProperty

public abstract void setIntProperty(String propertyName, int value)

setJmolDefaults

public abstract void setJmolDefaults()

setJmolStatusListener

public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)

setMarBond

public abstract void setMarBond(short marBond)

setMinBondDistance

public abstract void setMinBondDistance(float minBondDistance)

setModeMouse

public abstract void setModeMouse(int modeMouse)

setPercentVdwAtom

public abstract void setPercentVdwAtom(int percentVdwAtom)

setPerspectiveDepth

public abstract void setPerspectiveDepth(boolean perspectiveDepth)

setRasmolDefaults

public abstract void setRasmolDefaults()

setScreenDimension

public abstract void setScreenDimension(Dimension dim)

setSelectionHalos

public abstract void setSelectionHalos(boolean haloEnabled)

setSelectionSet

public abstract void setSelectionSet(BitSet newSelection)

setShowAxes

public abstract void setShowAxes(boolean showAxes)

setShowBbcage

public abstract void setShowBbcage(boolean showBbcage)

setShowHydrogens

public abstract void setShowHydrogens(boolean showHydrogens)

setShowMeasurements

public abstract void setShowMeasurements(boolean showMeasurements)

setStringProperty

public abstract void setStringProperty(String propertyName, String value)

setVectorScale

public abstract void setVectorScale(float vectorScaleValue)

setVibrationPeriod

public abstract void setVibrationPeriod(float vibrationPeriod)

setVibrationScale

public abstract void setVibrationScale(float vibrationScaleValue)

showModelSetDownload

public abstract boolean showModelSetDownload()

showUrl

public abstract void showUrl(String urlString)

syncScript

public abstract void syncScript(String script, String applet)

writeTextFile

public abstract void writeTextFile(String string, String data)