org.jmol.api
Class JmolViewer

java.lang.Object
  extended by org.jmol.api.JmolSimpleViewer
      extended by org.jmol.api.JmolViewer
Direct Known Subclasses:
Viewer

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


Field Summary
 java.lang.String menuStructure
           
 
Fields inherited from class org.jmol.api.JmolSimpleViewer
apiPlatform
 
Constructor Summary
JmolViewer()
           
 
Method Summary
abstract  void addSelectionListener(JmolSelectionListener listener)
           
static JmolViewer allocateViewer(java.lang.Object container, JmolAdapter jmolAdapter)
          default null htmlName, URL bases, comandOptions, and statusListener.
static JmolViewer allocateViewer(java.lang.Object container, JmolAdapter jmolAdapter, java.lang.String htmlName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener)
          This is the main access point for creating an application or applet viewer.
abstract  void calcAtomsMinMax(java.util.BitSet bs, BoxInfo boxInfo)
           
abstract  boolean checkHalt(java.lang.String strCommand, boolean isInterrupt)
           
static boolean checkOption(JmolViewer viewer, java.lang.String option)
           
abstract  boolean checkPrivateKey(double privateKey)
           
abstract  void clearMeasurements()
           
abstract  void clearSelection()
           
abstract  java.lang.String clipImage(java.lang.String text)
           
abstract  java.lang.Object createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height)
           
abstract  void deleteMeasurement(int i)
           
abstract  java.lang.String evalStringQuiet(java.lang.String script)
           
abstract  int findNearestAtomIndex(int x, int y)
           
abstract  java.lang.String generateOutput(java.lang.String type, java.lang.String[] fileName, int width, int height)
           
abstract  java.lang.String getAltLocListInModel(int modelIndex)
           
abstract  int getAnimationFps()
           
abstract  int getAtomArgb(int atomIndex)
           
abstract  int getAtomCount()
           
abstract  int getAtomCountInModel(int modelIndex)
           
abstract  java.lang.String getAtomInfo(int atomIndex)
           
abstract  int getAtomModelIndex(int atomIndex)
           
abstract  java.lang.String getAtomName(int atomIndex)
           
abstract  int getAtomNumber(int atomIndex)
           
abstract  javax.vecmath.Point3f getAtomPoint3f(int atomIndex)
           
abstract  float getAtomRadius(int atomIndex)
           
abstract  boolean getAutoBond()
           
abstract  boolean getAxesOrientationRasmol()
           
abstract  int getBackgroundArgb()
           
abstract  int getBondArgb1(int bondIndex)
           
abstract  int getBondArgb2(int bondIndex)
           
abstract  int getBondCount()
           
abstract  int getBondCountInModel(int modelIndex)
           
abstract  int getBondModelIndex(int bondIndex)
           
abstract  int getBondOrder(int bondIndex)
           
abstract  javax.vecmath.Point3f getBondPoint3f1(int bondIndex)
           
abstract  javax.vecmath.Point3f getBondPoint3f2(int bondIndex)
           
abstract  float getBondRadius(int bondIndex)
           
abstract  float getBondTolerance()
           
abstract  boolean getBooleanProperty(java.lang.String propertyName)
           
 boolean getBooleanProperty(java.lang.String key, boolean doICare)
           
abstract  javax.vecmath.Point3f getBoundBoxCenter()
           
abstract  javax.vecmath.Vector3f getBoundBoxCornerVector()
           
abstract  int getChainCount()
           
abstract  int getChainCountInModel(int modelIindex)
           
abstract  java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
           
abstract  java.lang.Object getDisplay()
           
abstract  int getDisplayModelIndex()
           
abstract  java.util.BitSet getElementsPresentBitSet(int modelIndex)
           
abstract  java.lang.String getErrorMessage()
           
abstract  java.lang.String getErrorMessageUntranslated()
           
abstract  java.lang.Object getFileAsBytes(java.lang.String fullPathName, java.io.OutputStream os)
           
abstract  java.lang.String getFileAsString(java.lang.String filename)
           
abstract  boolean getFileAsString(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
           
abstract  int getGroupCount()
           
abstract  int getGroupCountInModel(int modelIndex)
           
abstract  java.util.Map<java.lang.String,java.lang.String> getHeteroList(int modelIndex)
           
abstract  java.lang.Object getImageAs(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.io.OutputStream os)
           
abstract  java.lang.String getJavaVendor()
           
abstract  java.lang.String getJavaVersion()
           
static java.lang.String getJmolVersion()
           
abstract  short getMadBond()
           
abstract  int getMeasurementCount()
           
abstract  int[] getMeasurementCountPlusIndices(int i)
           
abstract  java.lang.String getMeasurementStringValue(int i)
           
abstract  float getMinBondDistance()
           
abstract  JmolAdapter getModelAdapter()
           
abstract  java.util.Map<java.lang.String,java.lang.Object> getModelAuxiliaryInfo(int modelIndex)
           
abstract  java.lang.Object getModelAuxiliaryInfo(int modelIndex, java.lang.String keyName)
           
abstract  int getModelCount()
           
abstract  java.lang.String getModelFileName(int modelIndex)
           
abstract  java.lang.String getModelName(int modelIndex)
           
abstract  int getModelNumber(int modelIndex)
           
abstract  java.lang.String getModelNumberDotted(int modelIndex)
           
abstract  java.util.Properties getModelProperties(int modelIndex)
           
abstract  java.lang.String getModelProperty(int modelIndex, java.lang.String propertyName)
           
abstract  java.util.Map<java.lang.String,java.lang.Object> getModelSetAuxiliaryInfo()
           
abstract  java.lang.String getModelSetFileName()
           
abstract  java.lang.String getModelSetName()
           
abstract  java.lang.String getModelSetPathName()
           
abstract  java.util.Properties getModelSetProperties()
           
abstract  int getMotionEventNumber()
           
abstract  void getObjectMap(java.util.Map<java.lang.String,Token> map, boolean b)
          retrieves list of draw/isosurface objects
abstract  java.lang.String getOperatingSystemName()
           
abstract  java.lang.Object getParameter(java.lang.String name)
           
abstract  int getPercentVdwAtom()
           
abstract  boolean getPerspectiveDepth()
           
abstract  int getPolymerCount()
           
abstract  int getPolymerCountInModel(int modelIndex)
           
abstract  javax.vecmath.Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
           
abstract  float getRotationRadius()
           
abstract  int getScreenHeight()
           
abstract  java.lang.Object getScreenImage(java.lang.Object g)
           
abstract  int getScreenWidth()
           
abstract  int getSelectionCount()
           
abstract  java.lang.String getSetHistory(int howFarBack)
           
abstract  boolean getShowAxes()
           
abstract  boolean getShowBbcage()
           
abstract  boolean getShowHydrogens()
           
abstract  boolean getShowMeasurements()
           
abstract  java.util.BitSet getSmartsMatch(java.lang.String smarts, java.util.BitSet bsSelected)
           
abstract  java.lang.String getStateInfo()
           
abstract  javax.vecmath.Matrix4f getUnscaledTransformMatrix()
           
abstract  java.util.BitSet getVisibleFramesBitSet()
           
abstract  int getZoomPercent()
           
abstract  float getZoomPercentFloat()
           
abstract  void haltScriptExecution()
           
abstract  boolean handleOldJvm10Event(int id, int x, int y, int modifiers, long when)
           
abstract  boolean haveFrame()
           
abstract  boolean havePartialCharges()
           
abstract  void homePosition()
           
abstract  boolean isApplet()
           
abstract  boolean isScriptExecuting()
           
abstract  java.lang.String loadInline(java.util.List<java.lang.Object> arrayData, boolean isAppend)
          NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
abstract  java.lang.String loadInline(java.lang.String strModel)
           
abstract  java.lang.String loadInline(java.lang.String[] arrayModels)
           
abstract  java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
           
abstract  java.lang.String loadInline(java.lang.String strModel, boolean isAppend)
           
abstract  java.lang.String loadInline(java.lang.String strModel, char newLine)
           
abstract  boolean modelHasVibrationVectors(int modelIndex)
           
abstract  void notifyViewerRepaintDone()
           
abstract  void openFileAsynchronously(java.lang.String fileName)
           
abstract  java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
          Opens the file and creates the model set, given the reader.
abstract  void popHoldRepaint()
           
abstract  void processEvent(int groupID, int eventType, int touchID, int iData, javax.vecmath.Point3f pt, long time)
           
abstract  void pushHoldRepaint()
           
abstract  void rebond()
           
abstract  void refresh(int isOrientationChange, java.lang.String strWhy)
           
abstract  void releaseScreenImage()
           
abstract  void removeSelectionListener(JmolSelectionListener listener)
           
abstract  void renderScreenImage(java.lang.Object gLeft, java.lang.Object gRight, int width, int height)
          an added class for rendering stereo in two independent applets
 void renderScreenImage(java.lang.Object g, java.lang.Object currentSize, java.lang.Object rectClip)
          old -- not used in 12.2
abstract  void rotateFront()
           
abstract  void rotateX(float radians)
           
abstract  void rotateX(int degrees)
           
abstract  void rotateY(float radians)
           
abstract  void rotateY(int degrees)
           
abstract  void rotateZ(float radians)
           
abstract  java.lang.String script(java.lang.String script)
           
abstract  java.lang.Object scriptCheck(java.lang.String script)
           
abstract  java.lang.String scriptWait(java.lang.String script)
           
abstract  java.lang.Object scriptWaitStatus(java.lang.String script, java.lang.String statusList)
           
abstract  void selectAll()
           
abstract  void setAnimationFps(int framesPerSecond)
           
abstract  void setAppletContext(java.lang.String htmlName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions)
           
abstract  void setAutoBond(boolean autoBond)
           
abstract  void setAxesOrientationRasmol(boolean axesMessedUp)
           
abstract  void setBondTolerance(float bondTolerance)
           
abstract  void setBooleanProperty(java.lang.String propertyName, boolean value)
           
abstract  void setCenterSelected()
           
abstract  void setColorBackground(java.lang.String colorName)
           
 void setConsole(JmolAppConsoleInterface console)
          sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(viewer, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
abstract  void setDebugScript(boolean debugScript)
           
abstract  void setFloatProperty(java.lang.String propertyName, float value)
           
abstract  void setFrankOn(boolean frankOn)
           
abstract  void setIntProperty(java.lang.String propertyName, int value)
           
abstract  void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
           
abstract  void setJmolDefaults()
           
abstract  void setJmolStatusListener(JmolStatusListener jmolStatusListener)
           
abstract  void setMarBond(short marBond)
           
abstract  void setMinBondDistance(float minBondDistance)
           
abstract  void setModeMouse(int modeMouse)
           
abstract  void setPercentVdwAtom(int percentVdwAtom)
           
abstract  void setPerspectiveDepth(boolean perspectiveDepth)
           
abstract  void setRasmolDefaults()
           
abstract  void setScreenDimension(int width, int height)
           
abstract  void setSelectionHalos(boolean haloEnabled)
           
abstract  void setSelectionSet(java.util.BitSet newSelection)
           
abstract  void setShowAxes(boolean showAxes)
           
abstract  void setShowBbcage(boolean showBbcage)
           
abstract  void setShowHydrogens(boolean showHydrogens)
           
abstract  void setShowMeasurements(boolean showMeasurements)
           
abstract  void setStringProperty(java.lang.String propertyName, java.lang.String value)
           
abstract  void setVectorScale(float vectorScaleValue)
           
abstract  void setVibrationPeriod(float vibrationPeriod)
           
abstract  void setVibrationScale(float vibrationScaleValue)
           
abstract  boolean showModelSetDownload()
           
abstract  void showUrl(java.lang.String urlString)
           
abstract  void syncScript(java.lang.String script, java.lang.String applet, int port)
           
abstract  void writeTextFile(java.lang.String string, java.lang.String data)
           
 
Methods inherited from class org.jmol.api.JmolSimpleViewer
allocateSimpleViewer, evalFile, evalString, getProperty, openDOM, openFile, openFiles, openStringInline, renderScreenImage
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

menuStructure

public java.lang.String menuStructure
Constructor Detail

JmolViewer

public JmolViewer()
Method Detail

allocateViewer

public static JmolViewer allocateViewer(java.lang.Object container,
                                        JmolAdapter jmolAdapter,
                                        java.lang.String htmlName,
                                        java.net.URL documentBase,
                                        java.net.URL codeBase,
                                        java.lang.String commandOptions,
                                        JmolStatusListener statusListener)
This is the main access point for creating an application or applet viewer. In Jmol 11.6 it was manditory that one of the next commands is either viewer.evalString("ZAP"); or at least: viewer.setAppletContext("",null,null,"") One or the other of these was necessary to establish the first modelset, which might be required by one or more later evaluated commands or file loadings. Starting with Jmol 11.7, setAppletContext is rolled into allocateViewer so that the full initialization is done all at once.

Parameters:
container -
jmolAdapter -
htmlName -
documentBase -
codeBase -
commandOptions -
statusListener -
Returns:
a JmolViewer object

allocateViewer

public static JmolViewer allocateViewer(java.lang.Object container,
                                        JmolAdapter jmolAdapter)
default null htmlName, URL bases, comandOptions, and statusListener.

Parameters:
container -
jmolAdapter -
Returns:
a viewer

setConsole

public void setConsole(JmolAppConsoleInterface console)
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(viewer, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java

Parameters:
console - the console to use

getSmartsMatch

public abstract java.util.BitSet getSmartsMatch(java.lang.String smarts,
                                                java.util.BitSet bsSelected)

renderScreenImage

public abstract void renderScreenImage(java.lang.Object gLeft,
                                       java.lang.Object gRight,
                                       int width,
                                       int height)
an added class for rendering stereo in two independent applets

Parameters:
gLeft -
gRight -
width -
height -

getJmolVersion

public static java.lang.String getJmolVersion()

checkOption

public static boolean checkOption(JmolViewer viewer,
                                  java.lang.String option)

generateOutput

public abstract java.lang.String generateOutput(java.lang.String type,
                                                java.lang.String[] fileName,
                                                int width,
                                                int height)

setJmolCallbackListener

public abstract void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)

setJmolStatusListener

public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)

setAppletContext

public abstract void setAppletContext(java.lang.String htmlName,
                                      java.net.URL documentBase,
                                      java.net.URL codeBase,
                                      java.lang.String commandOptions)

checkHalt

public abstract boolean checkHalt(java.lang.String strCommand,
                                  boolean isInterrupt)

haltScriptExecution

public abstract void haltScriptExecution()

getOperatingSystemName

public abstract java.lang.String getOperatingSystemName()

getJavaVersion

public abstract java.lang.String getJavaVersion()

getJavaVendor

public abstract java.lang.String getJavaVendor()

haveFrame

public abstract boolean haveFrame()

pushHoldRepaint

public abstract void pushHoldRepaint()

popHoldRepaint

public abstract void popHoldRepaint()

getData

public abstract java.lang.String getData(java.lang.String atomExpression,
                                         java.lang.String type)

setScreenDimension

public abstract void setScreenDimension(int width,
                                        int height)

getScreenWidth

public abstract int getScreenWidth()

getScreenHeight

public abstract int getScreenHeight()

getScreenImage

public abstract java.lang.Object getScreenImage(java.lang.Object g)

releaseScreenImage

public abstract void releaseScreenImage()

writeTextFile

public abstract void writeTextFile(java.lang.String string,
                                   java.lang.String data)

clipImage

public abstract java.lang.String clipImage(java.lang.String text)
Parameters:
text - null here clips image; String clips text
Returns:
"OK" for image or "OK [number of bytes]"

createImage

public abstract java.lang.Object createImage(java.lang.String fileName,
                                             java.lang.String type,
                                             java.lang.Object text_or_bytes,
                                             int quality,
                                             int width,
                                             int height)
Parameters:
fileName -
type -
text_or_bytes -
quality -
width -
height -
Returns:
null (canceled) or a message starting with OK or an error message

getImageAs

public abstract java.lang.Object getImageAs(java.lang.String type,
                                            int quality,
                                            int width,
                                            int height,
                                            java.lang.String fileName,
                                            java.io.OutputStream os)
Parameters:
type - "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"
quality -
width -
height -
fileName -
os -
Returns:
base64-encoded or binary version of the image

getMotionEventNumber

public abstract int getMotionEventNumber()

openReader

public abstract java.lang.String openReader(java.lang.String fullPathName,
                                            java.lang.String fileName,
                                            java.io.Reader reader)
Opens the file and creates the model set, given the reader. name is a text name of the file ... to be displayed in the window no need to pass a BufferedReader ... ... the FileManager will wrap a buffer around it DO NOT USE IN JMOL -- THIS METHOD IS ONLY HERE BECAUSE IT IS PART OF THE LEGACY INTERFACE IF USED BY ANOTHER APPLICATION, YOU ARE RESPONSIBLE FOR CLOSING THE READER

Parameters:
fullPathName -
fileName -
reader -
Returns:
null or error message

showUrl

public abstract void showUrl(java.lang.String urlString)

calcAtomsMinMax

public abstract void calcAtomsMinMax(java.util.BitSet bs,
                                     BoxInfo boxInfo)

getBoundBoxCenter

public abstract javax.vecmath.Point3f getBoundBoxCenter()

getBoundBoxCornerVector

public abstract javax.vecmath.Vector3f getBoundBoxCornerVector()

getMeasurementCount

public abstract int getMeasurementCount()

getMeasurementStringValue

public abstract java.lang.String getMeasurementStringValue(int i)

getMeasurementCountPlusIndices

public abstract int[] getMeasurementCountPlusIndices(int i)

getDisplay

public abstract java.lang.Object getDisplay()

getElementsPresentBitSet

public abstract java.util.BitSet getElementsPresentBitSet(int modelIndex)

getAnimationFps

public abstract int getAnimationFps()

findNearestAtomIndex

public abstract int findNearestAtomIndex(int x,
                                         int y)

script

public abstract java.lang.String script(java.lang.String script)

scriptCheck

public abstract java.lang.Object scriptCheck(java.lang.String script)

scriptWait

public abstract java.lang.String scriptWait(java.lang.String script)

scriptWaitStatus

public abstract java.lang.Object scriptWaitStatus(java.lang.String script,
                                                  java.lang.String statusList)

loadInline

public abstract java.lang.String loadInline(java.lang.String strModel)

loadInline

public abstract java.lang.String loadInline(java.lang.String strModel,
                                            boolean isAppend)

loadInline

public abstract java.lang.String loadInline(java.lang.String strModel,
                                            char newLine)

loadInline

public abstract java.lang.String loadInline(java.lang.String[] arrayModels)

loadInline

public abstract java.lang.String loadInline(java.lang.String[] arrayModels,
                                            boolean isAppend)
Parameters:
arrayModels - and array of models, each of which is a String
isAppend -
Returns:
null or error message

loadInline

public abstract java.lang.String loadInline(java.util.List<java.lang.Object> arrayData,
                                            boolean isAppend)
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE

Parameters:
arrayData - a Vector of models, where each model is either a String or a String[] or a Vector
isAppend - TRUE to append models (no ZAP)
Returns:
null or error message

evalStringQuiet

public abstract java.lang.String evalStringQuiet(java.lang.String script)

isScriptExecuting

public abstract boolean isScriptExecuting()

getModelSetName

public abstract java.lang.String getModelSetName()

getModelSetFileName

public abstract java.lang.String getModelSetFileName()

getModelSetPathName

public abstract java.lang.String getModelSetPathName()

getFileAsString

public abstract java.lang.String getFileAsString(java.lang.String filename)

getFileAsString

public abstract boolean getFileAsString(java.lang.String[] data,
                                        int nBytesMax,
                                        boolean doSpecialLoad)

getModelSetProperties

public abstract java.util.Properties getModelSetProperties()

getModelSetAuxiliaryInfo

public abstract java.util.Map<java.lang.String,java.lang.Object> getModelSetAuxiliaryInfo()

getModelNumber

public abstract int getModelNumber(int modelIndex)

getModelName

public abstract java.lang.String getModelName(int modelIndex)

getModelNumberDotted

public abstract java.lang.String getModelNumberDotted(int modelIndex)

getModelProperties

public abstract java.util.Properties getModelProperties(int modelIndex)

getModelProperty

public abstract java.lang.String getModelProperty(int modelIndex,
                                                  java.lang.String propertyName)

getModelAuxiliaryInfo

public abstract java.util.Map<java.lang.String,java.lang.Object> getModelAuxiliaryInfo(int modelIndex)

getModelAuxiliaryInfo

public abstract java.lang.Object getModelAuxiliaryInfo(int modelIndex,
                                                       java.lang.String keyName)

modelHasVibrationVectors

public abstract boolean modelHasVibrationVectors(int modelIndex)

getModelCount

public abstract int getModelCount()

getDisplayModelIndex

public abstract int getDisplayModelIndex()

getVisibleFramesBitSet

public abstract java.util.BitSet getVisibleFramesBitSet()

getAtomCount

public abstract int getAtomCount()

getBondCount

public abstract int getBondCount()

getGroupCount

public abstract int getGroupCount()

getChainCount

public abstract int getChainCount()

getPolymerCount

public abstract int getPolymerCount()

getAtomCountInModel

public abstract int getAtomCountInModel(int modelIndex)

getBondCountInModel

public abstract int getBondCountInModel(int modelIndex)

getGroupCountInModel

public abstract int getGroupCountInModel(int modelIndex)

getChainCountInModel

public abstract int getChainCountInModel(int modelIindex)

getPolymerCountInModel

public abstract int getPolymerCountInModel(int modelIndex)

getSelectionCount

public abstract int getSelectionCount()

addSelectionListener

public abstract void addSelectionListener(JmolSelectionListener listener)

removeSelectionListener

public abstract void removeSelectionListener(JmolSelectionListener listener)

homePosition

public abstract void homePosition()

getHeteroList

public abstract java.util.Map<java.lang.String,java.lang.String> getHeteroList(int modelIndex)

getPerspectiveDepth

public abstract boolean getPerspectiveDepth()

getShowHydrogens

public abstract boolean getShowHydrogens()

getShowMeasurements

public abstract boolean getShowMeasurements()

getShowAxes

public abstract boolean getShowAxes()

getShowBbcage

public abstract boolean getShowBbcage()

getAtomNumber

public abstract int getAtomNumber(int atomIndex)

getAtomName

public abstract java.lang.String getAtomName(int atomIndex)

getAtomInfo

public abstract java.lang.String getAtomInfo(int atomIndex)

getRotationRadius

public abstract float getRotationRadius()

getZoomPercent

public abstract int getZoomPercent()

getZoomPercentFloat

public abstract float getZoomPercentFloat()

getUnscaledTransformMatrix

public abstract javax.vecmath.Matrix4f getUnscaledTransformMatrix()

getBackgroundArgb

public abstract int getBackgroundArgb()

getAtomRadius

public abstract float getAtomRadius(int atomIndex)

getAtomPoint3f

public abstract javax.vecmath.Point3f getAtomPoint3f(int atomIndex)

getAtomArgb

public abstract int getAtomArgb(int atomIndex)

getAtomModelIndex

public abstract int getAtomModelIndex(int atomIndex)

getBondRadius

public abstract float getBondRadius(int bondIndex)

getBondPoint3f1

public abstract javax.vecmath.Point3f getBondPoint3f1(int bondIndex)

getBondPoint3f2

public abstract javax.vecmath.Point3f getBondPoint3f2(int bondIndex)

getBondArgb1

public abstract int getBondArgb1(int bondIndex)

getBondArgb2

public abstract int getBondArgb2(int bondIndex)

getBondOrder

public abstract int getBondOrder(int bondIndex)

getBondModelIndex

public abstract int getBondModelIndex(int bondIndex)

getPolymerLeadMidPoints

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

getAxesOrientationRasmol

public abstract boolean getAxesOrientationRasmol()

getPercentVdwAtom

public abstract int getPercentVdwAtom()

getAutoBond

public abstract boolean getAutoBond()

getMadBond

public abstract short getMadBond()

getBondTolerance

public abstract float getBondTolerance()

rebond

public abstract void rebond()

getMinBondDistance

public abstract float getMinBondDistance()

refresh

public abstract void refresh(int isOrientationChange,
                             java.lang.String strWhy)

showModelSetDownload

public abstract boolean showModelSetDownload()

notifyViewerRepaintDone

public abstract void notifyViewerRepaintDone()

getBooleanProperty

public abstract boolean getBooleanProperty(java.lang.String propertyName)

getBooleanProperty

public boolean getBooleanProperty(java.lang.String key,
                                  boolean doICare)
Parameters:
key -
doICare - IGNORED
Returns:
T/F

getParameter

public abstract java.lang.Object getParameter(java.lang.String name)

getSetHistory

public abstract java.lang.String getSetHistory(int howFarBack)

havePartialCharges

public abstract boolean havePartialCharges()

isApplet

public abstract boolean isApplet()

getAltLocListInModel

public abstract java.lang.String getAltLocListInModel(int modelIndex)

getStateInfo

public abstract java.lang.String getStateInfo()

syncScript

public abstract void syncScript(java.lang.String script,
                                java.lang.String applet,
                                int port)

setColorBackground

public abstract void setColorBackground(java.lang.String colorName)

setShowAxes

public abstract void setShowAxes(boolean showAxes)

setShowBbcage

public abstract void setShowBbcage(boolean showBbcage)

setJmolDefaults

public abstract void setJmolDefaults()

setRasmolDefaults

public abstract void setRasmolDefaults()

setBooleanProperty

public abstract void setBooleanProperty(java.lang.String propertyName,
                                        boolean value)

setIntProperty

public abstract void setIntProperty(java.lang.String propertyName,
                                    int value)

setFloatProperty

public abstract void setFloatProperty(java.lang.String propertyName,
                                      float value)

setStringProperty

public abstract void setStringProperty(java.lang.String propertyName,
                                       java.lang.String value)

setModeMouse

public abstract void setModeMouse(int modeMouse)

setShowHydrogens

public abstract void setShowHydrogens(boolean showHydrogens)

setShowMeasurements

public abstract void setShowMeasurements(boolean showMeasurements)

setPerspectiveDepth

public abstract void setPerspectiveDepth(boolean perspectiveDepth)

setAutoBond

public abstract void setAutoBond(boolean autoBond)

setMarBond

public abstract void setMarBond(short marBond)

setBondTolerance

public abstract void setBondTolerance(float bondTolerance)

setMinBondDistance

public abstract void setMinBondDistance(float minBondDistance)

setAxesOrientationRasmol

public abstract void setAxesOrientationRasmol(boolean axesMessedUp)

setPercentVdwAtom

public abstract void setPercentVdwAtom(int percentVdwAtom)

setAnimationFps

public abstract void setAnimationFps(int framesPerSecond)

setFrankOn

public abstract void setFrankOn(boolean frankOn)

setDebugScript

public abstract void setDebugScript(boolean debugScript)

deleteMeasurement

public abstract void deleteMeasurement(int i)

clearMeasurements

public abstract void clearMeasurements()

setVectorScale

public abstract void setVectorScale(float vectorScaleValue)

setVibrationScale

public abstract void setVibrationScale(float vibrationScaleValue)

setVibrationPeriod

public abstract void setVibrationPeriod(float vibrationPeriod)

selectAll

public abstract void selectAll()

clearSelection

public abstract void clearSelection()

setSelectionSet

public abstract void setSelectionSet(java.util.BitSet newSelection)

setSelectionHalos

public abstract void setSelectionHalos(boolean haloEnabled)

setCenterSelected

public abstract void setCenterSelected()

rotateFront

public abstract void rotateFront()

rotateX

public abstract void rotateX(int degrees)

rotateY

public abstract void rotateY(int degrees)

rotateX

public abstract void rotateX(float radians)

rotateY

public abstract void rotateY(float radians)

rotateZ

public abstract void rotateZ(float radians)

getModelAdapter

public abstract JmolAdapter getModelAdapter()

openFileAsynchronously

public abstract void openFileAsynchronously(java.lang.String fileName)

getFileAsBytes

public abstract java.lang.Object getFileAsBytes(java.lang.String fullPathName,
                                                java.io.OutputStream os)

getErrorMessage

public abstract java.lang.String getErrorMessage()

getErrorMessageUntranslated

public abstract java.lang.String getErrorMessageUntranslated()

getModelFileName

public abstract java.lang.String getModelFileName(int modelIndex)

checkPrivateKey

public abstract boolean checkPrivateKey(double privateKey)
Parameters:
privateKey -
Returns:
T/F

getObjectMap

public abstract void getObjectMap(java.util.Map<java.lang.String,Token> map,
                                  boolean b)
retrieves list of draw/isosurface objects

Parameters:
map -
b -

processEvent

public abstract void processEvent(int groupID,
                                  int eventType,
                                  int touchID,
                                  int iData,
                                  javax.vecmath.Point3f pt,
                                  long time)

handleOldJvm10Event

public abstract boolean handleOldJvm10Event(int id,
                                            int x,
                                            int y,
                                            int modifiers,
                                            long when)

renderScreenImage

public void renderScreenImage(java.lang.Object g,
                              java.lang.Object currentSize,
                              java.lang.Object rectClip)
old -- not used in 12.2

Parameters:
g -
currentSize -
rectClip - // unused