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
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Method Summary |
abstract void |
addSelectionListener(JmolSelectionListener listener)
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static JmolViewer |
allocateViewer(java.awt.Component awtComponent,
JmolAdapter jmolAdapter)
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abstract void |
clearMeasurements()
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abstract void |
clearSelection()
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abstract void |
deleteMeasurement(int i)
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abstract java.lang.String |
evalStringQuiet(java.lang.String script)
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abstract int |
getAnimationFps()
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abstract java.awt.Color |
getAtomColor(int atomIndex)
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abstract int |
getAtomCount()
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abstract int |
getAtomModelIndex(int atomIndex)
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abstract java.lang.String |
getAtomName(int atomIndex)
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abstract int |
getAtomNumber(int atomIndex)
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abstract javax.vecmath.Point3f |
getAtomPoint3f(int atomIndex)
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abstract float |
getAtomRadius(int atomIndex)
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abstract boolean |
getAutoBond()
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abstract java.awt.Component |
getAwtComponent()
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abstract boolean |
getAxesOrientationRasmol()
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abstract java.awt.Color |
getBondColor1(int bondIndex)
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abstract java.awt.Color |
getBondColor2(int bondIndex)
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abstract int |
getBondCount()
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abstract int |
getBondModelIndex(int bondIndex)
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abstract short |
getBondOrder(int bondIndex)
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abstract javax.vecmath.Point3f |
getBondPoint3f1(int bondIndex)
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abstract javax.vecmath.Point3f |
getBondPoint3f2(int bondIndex)
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abstract float |
getBondRadius(int bondIndex)
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abstract float |
getBondTolerance()
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abstract boolean |
getBooleanProperty(java.lang.String propertyName)
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abstract int |
getChainCount()
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abstract java.awt.Color |
getColorBackground()
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abstract java.awt.Color |
getColorBond()
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abstract java.awt.Color |
getColorLabel()
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abstract java.awt.Color |
getColorMeasurement()
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abstract java.awt.Color |
getColorVector()
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abstract int |
getDisplayModelIndex()
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abstract java.util.BitSet |
getElementsPresentBitSet()
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abstract FrameRenderer |
getFrameRenderer()
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abstract int |
getGroupCount()
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abstract java.util.BitSet |
getGroupsPresentBitSet()
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abstract java.lang.String |
getJavaVendor()
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abstract java.lang.String |
getJavaVersion()
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abstract JPreview |
getJPreview()
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abstract int |
getLipidNumber()
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abstract short |
getMadBond()
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abstract int |
getMeasurementCount()
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abstract int[] |
getMeasurementCountPlusIndices(int i)
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abstract java.lang.String |
getMeasurementStringValue(int i)
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abstract float |
getMinBondDistance()
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abstract int |
getModelCount()
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abstract java.lang.String |
getModelName(int atomSetIndex)
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abstract int |
getModelNumber(int atomSetIndex)
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abstract java.util.Properties |
getModelProperties(int atomSetIndex)
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abstract java.lang.String |
getModelProperty(int atomSetIndex,
java.lang.String propertyName)
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abstract java.lang.String |
getModelSetFileName()
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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 int |
getPercentVdwAtom()
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abstract boolean |
getPerspectiveDepth()
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abstract int |
getPolymerCount()
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abstract int |
getPolymerCountInModel(int modelIndex)
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abstract javax.vecmath.Point3f[] |
getPolymerLeadMidPoints(int modelIndex,
int polymerIndex)
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abstract void |
getRotation(javax.vecmath.Matrix3f matrixRotation)
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abstract float |
getRotationRadius()
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abstract float |
getScalePixelsPerAngstrom()
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abstract int |
getScreenHeight()
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abstract java.awt.Image |
getScreenImage()
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abstract int |
getScreenWidth()
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abstract java.util.BitSet |
getSelectionSet()
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abstract boolean |
getShapeShow(int shapeID)
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abstract boolean |
getShowAxes()
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abstract boolean |
getShowBbcage()
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abstract boolean |
getShowHydrogens()
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abstract boolean |
getShowMeasurements()
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abstract javax.vecmath.Matrix4f |
getUnscaledTransformMatrix()
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abstract boolean |
getWireframeRotation()
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abstract float |
getXTranslationNormalized()
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abstract float |
getYTranslation()
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abstract float |
getYTranslationNormalized()
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abstract int |
getZoomPercent()
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abstract void |
haltScriptExecution()
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abstract boolean |
handleOldJvm10Event(java.awt.Event e)
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abstract boolean |
haveFrame()
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abstract void |
homePosition()
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abstract boolean |
isJvm12orGreater()
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abstract boolean |
isScriptExecuting()
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abstract boolean |
isShowTransparentLipids()
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abstract boolean |
modelHasVibrationVectors(int atomSetIndex)
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abstract void |
notifyRepainted()
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abstract void |
openClientFile(java.lang.String fullPathName,
java.lang.String fileName,
java.lang.Object clientFile)
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abstract void |
openReader(java.lang.String fullPathName,
java.lang.String name,
java.io.Reader reader)
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abstract void |
popHoldRepaint()
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abstract void |
pushHoldRepaint()
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abstract void |
rebond()
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abstract void |
refresh()
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abstract void |
releaseScreenImage()
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abstract void |
removeSelectionListener(JmolSelectionListener listener)
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abstract void |
rotateFront()
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abstract void |
rotateToX(float radians)
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abstract void |
rotateToX(int degrees)
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abstract void |
rotateToY(float radians)
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abstract void |
rotateToY(int degrees)
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abstract void |
rotateToZ(float radians)
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abstract void |
scaleFitToScreen()
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abstract void |
selectAll()
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abstract void |
setAnimationFps(int framesPerSecond)
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abstract void |
setAppletContext(java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String appletProxy)
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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)
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abstract void |
setCenterSelected()
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abstract void |
setColorBackground(java.awt.Color colorBackground)
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abstract void |
setColorBackground(java.lang.String colorName)
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abstract void |
setColorBond(java.awt.Color colorBond)
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abstract void |
setColorLabel(java.awt.Color colorBond)
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abstract void |
setColorMeasurement(java.awt.Color colorMeasurement)
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abstract void |
setColorSelection(java.awt.Color colorSelection)
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abstract void |
setColorVector(java.awt.Color colorVector)
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abstract void |
setDebugScript(boolean debugScript)
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abstract void |
setFrankOn(boolean frankOn)
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abstract void |
setJmolDefaults()
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abstract void |
setJmolStatusListener(JmolStatusListener jmolStatusListener)
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abstract void |
setJPreview(JPreview preview)
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abstract void |
setLipidNumber(int lipidNumber)
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abstract void |
setMarBond(short marBond)
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abstract void |
setMinBondDistance(float minBondDistance)
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abstract void |
setModeAtomColorProfile(java.lang.String mode)
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abstract void |
setModeMouse(int modeMouse)
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abstract void |
setPercentVdwAtom(int percentVdwAtom)
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abstract void |
setPerspectiveDepth(boolean perspectiveDepth)
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abstract void |
setRasmolDefaults()
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abstract void |
setRotation(javax.vecmath.Matrix3f matrixRotation)
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abstract void |
setScalePixelsPerAngstrom(float pixelsScale)
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abstract void |
setScreenDimension(java.awt.Dimension dim)
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abstract void |
setSelectionHaloEnabled(boolean haloEnabled)
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abstract void |
setSelectionSet(java.util.BitSet newSelection)
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abstract void |
setShapeShow(int shapeID,
boolean show)
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abstract void |
setShowAxes(boolean showAxes)
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abstract void |
setShowBbcage(boolean showBbcage)
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abstract void |
setShowHydrogens(boolean showHydrogens)
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abstract void |
setShowMeasurements(boolean showMeasurements)
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abstract void |
setShowTransparentLipids(boolean showTransparentLipids)
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abstract void |
setVectorScale(float vectorScaleValue)
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abstract void |
setVibrationPeriod(float vibrationPeriod)
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abstract void |
setVibrationScale(float vibrationScaleValue)
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abstract void |
setWireframeRotation(boolean wireframeRotation)
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abstract void |
setXTranslationNormalized(float xTranslation)
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abstract void |
setYTranslationNormalized(float yTranslation)
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abstract boolean |
showModelSetDownload()
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abstract void |
showUrl(java.lang.String urlString)
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abstract void |
translateXBy(int xDelta)
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abstract void |
translateYBy(int yDelta)
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abstract void |
zoomBy(int pixels)
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| Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
JmolViewer
public JmolViewer()
allocateViewer
public static JmolViewer allocateViewer(java.awt.Component awtComponent,
JmolAdapter jmolAdapter)
setJmolStatusListener
public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)
setAppletContext
public abstract void setAppletContext(java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String appletProxy)
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()
setJmolDefaults
public abstract void setJmolDefaults()
setRasmolDefaults
public abstract void setRasmolDefaults()
setDebugScript
public abstract void setDebugScript(boolean debugScript)
setFrankOn
public abstract void setFrankOn(boolean frankOn)
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()
notifyRepainted
public abstract void notifyRepainted()
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)
deleteMeasurement
public abstract void deleteMeasurement(int i)
clearMeasurements
public abstract void clearMeasurements()
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()
getAnimationFps
public abstract int getAnimationFps()
setAnimationFps
public abstract void setAnimationFps(int framesPerSecond)
evalStringQuiet
public abstract java.lang.String evalStringQuiet(java.lang.String script)
isScriptExecuting
public abstract boolean isScriptExecuting()
setVectorScale
public abstract void setVectorScale(float vectorScaleValue)
setVibrationScale
public abstract void setVibrationScale(float vibrationScaleValue)
setVibrationPeriod
public abstract void setVibrationPeriod(float vibrationPeriod)
getModelSetName
public abstract java.lang.String getModelSetName()
getModelSetFileName
public abstract java.lang.String getModelSetFileName()
getModelSetPathName
public abstract java.lang.String getModelSetPathName()
getModelSetProperties
public abstract java.util.Properties getModelSetProperties()
getModelNumber
public abstract int getModelNumber(int atomSetIndex)
getModelName
public abstract java.lang.String getModelName(int atomSetIndex)
getModelProperties
public abstract java.util.Properties getModelProperties(int atomSetIndex)
getModelProperty
public abstract java.lang.String getModelProperty(int atomSetIndex,
java.lang.String propertyName)
modelHasVibrationVectors
public abstract boolean modelHasVibrationVectors(int atomSetIndex)
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()
getPolymerCountInModel
public abstract int getPolymerCountInModel(int modelIndex)
setModeMouse
public abstract void setModeMouse(int modeMouse)
setSelectionHaloEnabled
public abstract void setSelectionHaloEnabled(boolean haloEnabled)
setShowHydrogens
public abstract void setShowHydrogens(boolean showHydrogens)
setShowMeasurements
public abstract void setShowMeasurements(boolean showMeasurements)
selectAll
public abstract void selectAll()
clearSelection
public abstract void clearSelection()
addSelectionListener
public abstract void addSelectionListener(JmolSelectionListener listener)
removeSelectionListener
public abstract void removeSelectionListener(JmolSelectionListener listener)
setSelectionSet
public abstract void setSelectionSet(java.util.BitSet newSelection)
getSelectionSet
public abstract java.util.BitSet getSelectionSet()
setModeAtomColorProfile
public abstract void setModeAtomColorProfile(java.lang.String mode)
homePosition
public abstract void homePosition()
rotateFront
public abstract void rotateFront()
rotateToX
public abstract void rotateToX(int degrees)
rotateToY
public abstract void rotateToY(int degrees)
rotateToX
public abstract void rotateToX(float radians)
rotateToY
public abstract void rotateToY(float radians)
rotateToZ
public abstract void rotateToZ(float radians)
setCenterSelected
public abstract void setCenterSelected()
getGroupsPresentBitSet
public abstract java.util.BitSet getGroupsPresentBitSet()
setWireframeRotation
public abstract void setWireframeRotation(boolean wireframeRotation)
setPerspectiveDepth
public abstract void setPerspectiveDepth(boolean perspectiveDepth)
getPerspectiveDepth
public abstract boolean getPerspectiveDepth()
getWireframeRotation
public abstract boolean getWireframeRotation()
getShowHydrogens
public abstract boolean getShowHydrogens()
getShowMeasurements
public abstract boolean getShowMeasurements()
setShowAxes
public abstract void setShowAxes(boolean showAxes)
getShowAxes
public abstract boolean getShowAxes()
setShowBbcage
public abstract void setShowBbcage(boolean showBbcage)
getShowBbcage
public abstract boolean getShowBbcage()
getAtomNumber
public abstract int getAtomNumber(int atomIndex)
getAtomName
public abstract java.lang.String getAtomName(int atomIndex)
getRotationRadius
public abstract float getRotationRadius()
getZoomPercent
public abstract int getZoomPercent()
getUnscaledTransformMatrix
public abstract javax.vecmath.Matrix4f getUnscaledTransformMatrix()
getColorBackground
public abstract java.awt.Color getColorBackground()
setColorBackground
public abstract void setColorBackground(java.awt.Color colorBackground)
setColorBackground
public abstract void setColorBackground(java.lang.String colorName)
getAtomRadius
public abstract float getAtomRadius(int atomIndex)
getAtomPoint3f
public abstract javax.vecmath.Point3f getAtomPoint3f(int atomIndex)
getAtomColor
public abstract java.awt.Color getAtomColor(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)
getBondColor1
public abstract java.awt.Color getBondColor1(int bondIndex)
getBondColor2
public abstract java.awt.Color getBondColor2(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()
setAxesOrientationRasmol
public abstract void setAxesOrientationRasmol(boolean axesMessedUp)
getPercentVdwAtom
public abstract int getPercentVdwAtom()
setPercentVdwAtom
public abstract void setPercentVdwAtom(int percentVdwAtom)
getAutoBond
public abstract boolean getAutoBond()
setAutoBond
public abstract void setAutoBond(boolean autoBond)
getMadBond
public abstract short getMadBond()
setMarBond
public abstract void setMarBond(short marBond)
getBondTolerance
public abstract float getBondTolerance()
setBondTolerance
public abstract void setBondTolerance(float bondTolerance)
rebond
public abstract void rebond()
getMinBondDistance
public abstract float getMinBondDistance()
setMinBondDistance
public abstract void setMinBondDistance(float minBondDistance)
setColorSelection
public abstract void setColorSelection(java.awt.Color colorSelection)
getColorLabel
public abstract java.awt.Color getColorLabel()
setColorLabel
public abstract void setColorLabel(java.awt.Color colorBond)
getColorBond
public abstract java.awt.Color getColorBond()
setColorBond
public abstract void setColorBond(java.awt.Color colorBond)
getColorVector
public abstract java.awt.Color getColorVector()
setColorVector
public abstract void setColorVector(java.awt.Color colorVector)
getColorMeasurement
public abstract java.awt.Color getColorMeasurement()
setColorMeasurement
public abstract void setColorMeasurement(java.awt.Color colorMeasurement)
refresh
public abstract void refresh()
getBooleanProperty
public abstract boolean getBooleanProperty(java.lang.String propertyName)
setBooleanProperty
public abstract void setBooleanProperty(java.lang.String propertyName,
boolean value)
showModelSetDownload
public abstract boolean showModelSetDownload()
translateXBy
public abstract void translateXBy(int xDelta)
translateYBy
public abstract void translateYBy(int yDelta)
zoomBy
public abstract void zoomBy(int pixels)
getFrameRenderer
public abstract FrameRenderer getFrameRenderer()
getScalePixelsPerAngstrom
public abstract float getScalePixelsPerAngstrom()
setScalePixelsPerAngstrom
public abstract void setScalePixelsPerAngstrom(float pixelsScale)
getRotation
public abstract void getRotation(javax.vecmath.Matrix3f matrixRotation)
setRotation
public abstract void setRotation(javax.vecmath.Matrix3f matrixRotation)
getYTranslation
public abstract float getYTranslation()
getXTranslationNormalized
public abstract float getXTranslationNormalized()
getYTranslationNormalized
public abstract float getYTranslationNormalized()
setXTranslationNormalized
public abstract void setXTranslationNormalized(float xTranslation)
setYTranslationNormalized
public abstract void setYTranslationNormalized(float yTranslation)
isShowTransparentLipids
public abstract boolean isShowTransparentLipids()
setShowTransparentLipids
public abstract void setShowTransparentLipids(boolean showTransparentLipids)
getJPreview
public abstract JPreview getJPreview()
setJPreview
public abstract void setJPreview(JPreview preview)
scaleFitToScreen
public abstract void scaleFitToScreen()
setShapeShow
public abstract void setShapeShow(int shapeID,
boolean show)
getShapeShow
public abstract boolean getShapeShow(int shapeID)
setLipidNumber
public abstract void setLipidNumber(int lipidNumber)
getLipidNumber
public abstract int getLipidNumber()