org.jmol.api
Class JmolViewer
java.lang.Object
org.jmol.api.JmolSimpleViewer
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
Method Summary |
abstract void |
addSelectionListener(JmolSelectionListener listener)
|
static JmolViewer |
allocateViewer(java.awt.Component awtComponent,
JmolAdapter jmolAdapter)
This is the main access point for creating an application
or applet viewer. |
abstract boolean |
checkHalt(java.lang.String strCommand)
|
static boolean |
checkOption(JmolViewer viewer,
java.lang.String option)
|
abstract void |
clearMeasurements()
|
abstract void |
clearSelection()
|
abstract java.lang.String |
createImage(java.lang.String file,
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 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 java.awt.Component |
getAwtComponent()
|
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 short |
getBondOrder(int bondIndex)
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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)
|
abstract boolean |
getBooleanProperty(java.lang.String key,
boolean doICare)
|
abstract int |
getChainCount()
|
abstract int |
getChainCountInModel(int modelIindex)
|
abstract java.lang.String |
getData(java.lang.String atomExpression,
java.lang.String type)
|
abstract int |
getDisplayModelIndex()
|
abstract java.util.BitSet |
getElementsPresentBitSet(int modelIndex)
|
abstract java.lang.String |
getFileAsString(java.lang.String filename)
|
abstract int |
getGroupCount()
|
abstract int |
getGroupCountInModel(int modelIndex)
|
abstract java.util.Hashtable |
getHeteroList(int modelIndex)
|
abstract java.lang.String |
getJavaVendor()
|
abstract java.lang.String |
getJavaVersion()
|
static java.lang.String |
getJmolVersion()
|
abstract short |
getMadBond()
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abstract int |
getMeasurementCount()
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abstract int[] |
getMeasurementCountPlusIndices(int i)
|
abstract java.lang.String |
getMeasurementStringValue(int i)
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abstract float |
getMinBondDistance()
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abstract java.util.Hashtable |
getModelAuxiliaryInfo(int modelIndex)
|
abstract java.lang.Object |
getModelAuxiliaryInfo(int modelIndex,
java.lang.String keyName)
|
abstract int |
getModelCount()
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abstract java.lang.String |
getModelName(int modelIndex)
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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.Hashtable |
getModelSetAuxiliaryInfo()
|
abstract java.lang.String |
getModelSetFileName()
|
abstract java.lang.String |
getModelSetName()
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abstract java.lang.String |
getModelSetPathName()
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abstract java.util.Properties |
getModelSetProperties()
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abstract int |
getMotionEventNumber()
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abstract java.lang.String |
getOperatingSystemName()
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abstract java.lang.Object |
getParameter(java.lang.String name)
|
abstract int |
getPercentVdwAtom()
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abstract boolean |
getPerspectiveDepth()
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abstract int |
getPolymerCount()
|
abstract int |
getPolymerCountInModel(int modelIndex)
|
abstract javax.vecmath.Point3f[] |
getPolymerLeadMidPoints(int modelIndex,
int polymerIndex)
|
abstract java.lang.Object |
getProperty(java.lang.String returnType,
java.lang.String infoType,
java.lang.String paramInfo)
|
abstract float |
getRotationRadius()
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abstract int |
getScreenHeight()
|
abstract java.awt.Image |
getScreenImage()
|
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.lang.String |
getStateInfo()
|
abstract javax.vecmath.Matrix4f |
getUnscaledTransformMatrix()
|
abstract int |
getZoomPercent()
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abstract float |
getZoomPercentFloat()
|
abstract void |
haltScriptExecution()
|
abstract boolean |
handleOldJvm10Event(java.awt.Event e)
|
abstract boolean |
haveFrame()
|
abstract boolean |
havePartialCharges()
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abstract void |
homePosition()
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abstract boolean |
isApplet()
|
abstract boolean |
isJvm12orGreater()
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abstract boolean |
isScriptExecuting()
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abstract void |
loadInline(java.lang.String strModel)
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abstract void |
loadInline(java.lang.String[] arrayModels)
|
abstract void |
loadInline(java.lang.String[] arrayModels,
boolean isMerge)
|
abstract void |
loadInline(java.lang.String strModel,
boolean isMerge)
|
abstract void |
loadInline(java.lang.String strModel,
char newLine)
|
abstract boolean |
modelHasVibrationVectors(int modelIndex)
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abstract void |
openClientFile(java.lang.String fullPathName,
java.lang.String fileName,
java.lang.Object clientFile)
|
abstract void |
openReader(java.lang.String fullPathName,
java.lang.String name,
java.io.Reader reader)
|
abstract void |
popHoldRepaint()
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abstract void |
pushHoldRepaint()
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abstract void |
rebond()
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abstract void |
refresh(int isOrientationChange,
java.lang.String strWhy)
|
abstract void |
releaseScreenImage()
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abstract void |
removeSelectionListener(JmolSelectionListener listener)
|
abstract void |
repaintView()
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abstract void |
rotateFront()
|
abstract void |
rotateX(float radians)
|
abstract void |
rotateX(int degrees)
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abstract void |
rotateY(float radians)
|
abstract void |
rotateY(int degrees)
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abstract void |
rotateZ(float radians)
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abstract java.lang.String |
script(java.lang.String script)
|
abstract java.lang.String |
scriptCheck(java.lang.String script)
|
abstract java.lang.String |
scriptWait(java.lang.String script)
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abstract java.lang.Object |
scriptWaitStatus(java.lang.String script,
java.lang.String statusList)
|
abstract void |
selectAll()
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abstract void |
setAnimationFps(int framesPerSecond)
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abstract void |
setAppletContext(java.lang.String htmlName,
java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String commandOptions)
|
abstract void |
setAutoBond(boolean autoBond)
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abstract void |
setAxesOrientationRasmol(boolean axesMessedUp)
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abstract void |
setBondTolerance(float bondTolerance)
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abstract void |
setBooleanProperty(java.lang.String propertyName,
boolean value)
|
abstract void |
setCenterSelected()
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abstract void |
setColorBackground(java.lang.String colorName)
|
abstract void |
setDebugScript(boolean debugScript)
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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 |
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(java.awt.Dimension dim)
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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)
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abstract boolean |
showModelSetDownload()
|
abstract void |
showUrl(java.lang.String urlString)
|
abstract void |
syncScript(java.lang.String script,
java.lang.String applet)
|
abstract void |
writeTextFile(java.lang.String string,
java.lang.String data)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
JmolViewer
public JmolViewer()
allocateViewer
public static JmolViewer allocateViewer(java.awt.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
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)
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)
haltScriptExecution
public abstract void haltScriptExecution()
isJvm12orGreater
public abstract boolean isJvm12orGreater()
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(java.awt.Dimension dim)
getScreenWidth
public abstract int getScreenWidth()
getScreenHeight
public abstract int getScreenHeight()
getScreenImage
public abstract java.awt.Image getScreenImage()
releaseScreenImage
public abstract void releaseScreenImage()
writeTextFile
public abstract void writeTextFile(java.lang.String string,
java.lang.String data)
createImage
public abstract java.lang.String createImage(java.lang.String file,
java.lang.String type,
java.lang.Object text_or_bytes,
int quality,
int width,
int height)
handleOldJvm10Event
public abstract boolean handleOldJvm10Event(java.awt.Event e)
getMotionEventNumber
public abstract int getMotionEventNumber()
openReader
public abstract void openReader(java.lang.String fullPathName,
java.lang.String name,
java.io.Reader reader)
openClientFile
public abstract void openClientFile(java.lang.String fullPathName,
java.lang.String fileName,
java.lang.Object clientFile)
showUrl
public abstract void showUrl(java.lang.String urlString)
getMeasurementCount
public abstract int getMeasurementCount()
getMeasurementStringValue
public abstract java.lang.String getMeasurementStringValue(int i)
getMeasurementCountPlusIndices
public abstract int[] getMeasurementCountPlusIndices(int i)
getAwtComponent
public abstract java.awt.Component getAwtComponent()
getElementsPresentBitSet
public abstract java.util.BitSet getElementsPresentBitSet(int modelIndex)
getAnimationFps
public abstract int getAnimationFps()
script
public abstract java.lang.String script(java.lang.String script)
scriptCheck
public abstract java.lang.String 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 void loadInline(java.lang.String strModel)
loadInline
public abstract void loadInline(java.lang.String strModel,
boolean isMerge)
loadInline
public abstract void loadInline(java.lang.String strModel,
char newLine)
loadInline
public abstract void loadInline(java.lang.String[] arrayModels)
loadInline
public abstract void loadInline(java.lang.String[] arrayModels,
boolean isMerge)
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)
getModelSetProperties
public abstract java.util.Properties getModelSetProperties()
getModelSetAuxiliaryInfo
public abstract java.util.Hashtable 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.Hashtable 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()
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.Hashtable 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 short 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()
repaintView
public abstract void repaintView()
getBooleanProperty
public abstract boolean getBooleanProperty(java.lang.String propertyName)
getBooleanProperty
public abstract boolean getBooleanProperty(java.lang.String key,
boolean doICare)
getParameter
public abstract java.lang.Object getParameter(java.lang.String name)
getProperty
public abstract java.lang.Object getProperty(java.lang.String returnType,
java.lang.String infoType,
java.lang.String paramInfo)
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)
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)