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 void | addSelectionListener(JmolSelectionListener listener) |
static JmolViewer | allocateViewer(Component awtComponent, JmolAdapter jmolAdapter)
This is the main access point for creating an application
or applet viewer. |
abstract boolean | checkHalt(String strCommand) |
static boolean | checkOption(JmolViewer viewer, String option) |
abstract void | clearMeasurements() |
abstract void | clearSelection() |
abstract String | createImage(String file, String type, Object text_or_bytes, int quality, int width, int height) |
abstract void | deleteMeasurement(int i) |
abstract String | evalStringQuiet(String script) |
abstract String | generateOutput(String type, String fileName, int width, int height) |
abstract String | getAltLocListInModel(int modelIndex) |
abstract int | getAnimationFps() |
abstract int | getAtomArgb(int atomIndex) |
abstract int | getAtomCount() |
abstract int | getAtomCountInModel(int modelIndex) |
abstract String | getAtomInfo(int atomIndex) |
abstract int | getAtomModelIndex(int atomIndex) |
abstract String | getAtomName(int atomIndex) |
abstract int | getAtomNumber(int atomIndex) |
abstract Point3f | getAtomPoint3f(int atomIndex) |
abstract float | getAtomRadius(int atomIndex) |
abstract boolean | getAutoBond() |
abstract 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) |
abstract Point3f | getBondPoint3f1(int bondIndex) |
abstract Point3f | getBondPoint3f2(int bondIndex) |
abstract float | getBondRadius(int bondIndex) |
abstract float | getBondTolerance() |
abstract boolean | getBooleanProperty(String propertyName) |
abstract boolean | getBooleanProperty(String key, boolean doICare) |
abstract int | getChainCount() |
abstract int | getChainCountInModel(int modelIindex) |
abstract String | getData(String atomExpression, String type) |
abstract int | getDisplayModelIndex() |
abstract BitSet | getElementsPresentBitSet(int modelIndex) |
abstract String | getFileAsString(String filename) |
abstract int | getGroupCount() |
abstract int | getGroupCountInModel(int modelIndex) |
abstract Hashtable | getHeteroList(int modelIndex) |
abstract String | getJavaVendor() |
abstract String | getJavaVersion() |
static String | getJmolVersion() |
abstract short | getMadBond() |
abstract int | getMeasurementCount() |
abstract int[] | getMeasurementCountPlusIndices(int i) |
abstract String | getMeasurementStringValue(int i) |
abstract float | getMinBondDistance() |
abstract Hashtable | getModelAuxiliaryInfo(int modelIndex) |
abstract Object | getModelAuxiliaryInfo(int modelIndex, String keyName) |
abstract int | getModelCount() |
abstract String | getModelName(int modelIndex) |
abstract int | getModelNumber(int modelIndex) |
abstract String | getModelNumberDotted(int modelIndex) |
abstract Properties | getModelProperties(int modelIndex) |
abstract String | getModelProperty(int modelIndex, String propertyName) |
abstract Hashtable | getModelSetAuxiliaryInfo() |
abstract String | getModelSetFileName() |
abstract String | getModelSetName() |
abstract String | getModelSetPathName() |
abstract Properties | getModelSetProperties() |
abstract int | getMotionEventNumber() |
abstract String | getOperatingSystemName() |
abstract Object | getParameter(String name) |
abstract int | getPercentVdwAtom() |
abstract boolean | getPerspectiveDepth() |
abstract int | getPolymerCount() |
abstract int | getPolymerCountInModel(int modelIndex) |
abstract Point3f[] | getPolymerLeadMidPoints(int modelIndex, int polymerIndex) |
abstract Object | getProperty(String returnType, String infoType, String paramInfo) |
abstract float | getRotationRadius() |
abstract int | getScreenHeight() |
abstract Image | getScreenImage() |
abstract int | getScreenWidth() |
abstract int | getSelectionCount() |
abstract String | getSetHistory(int howFarBack) |
abstract boolean | getShowAxes() |
abstract boolean | getShowBbcage() |
abstract boolean | getShowHydrogens() |
abstract boolean | getShowMeasurements() |
abstract String | getStateInfo() |
abstract Matrix4f | getUnscaledTransformMatrix() |
abstract int | getZoomPercent() |
abstract float | getZoomPercentFloat() |
abstract void | haltScriptExecution() |
abstract boolean | handleOldJvm10Event(Event e) |
abstract boolean | haveFrame() |
abstract boolean | havePartialCharges() |
abstract void | homePosition() |
abstract boolean | isApplet() |
abstract boolean | isJvm12orGreater() |
abstract boolean | isScriptExecuting() |
abstract void | loadInline(String strModel) |
abstract void | loadInline(String strModel, boolean isMerge) |
abstract void | loadInline(String strModel, char newLine) |
abstract void | loadInline(String[] arrayModels) |
abstract void | loadInline(String[] arrayModels, boolean isMerge) |
abstract boolean | modelHasVibrationVectors(int modelIndex) |
abstract void | openClientFile(String fullPathName, String fileName, Object clientFile) |
abstract void | openReader(String fullPathName, String name, Reader reader) |
abstract void | popHoldRepaint() |
abstract void | pushHoldRepaint() |
abstract void | rebond() |
abstract void | refresh(int isOrientationChange, String strWhy) |
abstract void | releaseScreenImage() |
abstract void | removeSelectionListener(JmolSelectionListener listener) |
abstract void | repaintView() |
abstract void | rotateFront() |
abstract void | rotateX(int degrees) |
abstract void | rotateX(float radians) |
abstract void | rotateY(int degrees) |
abstract void | rotateY(float radians) |
abstract void | rotateZ(float radians) |
abstract String | script(String script) |
abstract String | scriptCheck(String script) |
abstract String | scriptWait(String script) |
abstract Object | scriptWaitStatus(String script, String statusList) |
abstract void | selectAll() |
abstract void | setAnimationFps(int framesPerSecond) |
abstract void | setAppletContext(String htmlName, URL documentBase, URL codeBase, String commandOptions) |
abstract void | setAutoBond(boolean autoBond) |
abstract void | setAxesOrientationRasmol(boolean axesMessedUp) |
abstract void | setBondTolerance(float bondTolerance) |
abstract void | setBooleanProperty(String propertyName, boolean value) |
abstract void | setCenterSelected() |
abstract void | setColorBackground(String colorName) |
abstract void | setDebugScript(boolean debugScript) |
abstract void | setFloatProperty(String propertyName, float value) |
abstract void | setFrankOn(boolean frankOn) |
abstract void | setIntProperty(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(Dimension dim) |
abstract void | setSelectionHalos(boolean haloEnabled) |
abstract void | setSelectionSet(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(String propertyName, String value) |
abstract void | setVectorScale(float vectorScaleValue) |
abstract void | setVibrationPeriod(float vibrationPeriod) |
abstract void | setVibrationScale(float vibrationScaleValue) |
abstract boolean | showModelSetDownload() |
abstract void | showUrl(String urlString) |
abstract void | syncScript(String script, String applet) |
abstract void | writeTextFile(String string, String data) |
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
public abstract boolean checkHalt(String strCommand)
public static boolean checkOption(
JmolViewer viewer, String option)
public abstract void clearMeasurements()
public abstract void clearSelection()
public abstract String createImage(String file, String type, Object text_or_bytes, int quality, int width, int height)
public abstract void deleteMeasurement(int i)
public abstract String evalStringQuiet(String script)
public abstract String generateOutput(String type, String fileName, int width, int height)
public abstract String getAltLocListInModel(int modelIndex)
public abstract int getAnimationFps()
public abstract int getAtomArgb(int atomIndex)
public abstract int getAtomCount()
public abstract int getAtomCountInModel(int modelIndex)
public abstract String getAtomInfo(int atomIndex)
public abstract int getAtomModelIndex(int atomIndex)
public abstract String getAtomName(int atomIndex)
public abstract int getAtomNumber(int atomIndex)
public abstract Point3f getAtomPoint3f(int atomIndex)
public abstract float getAtomRadius(int atomIndex)
public abstract boolean getAutoBond()
public abstract Component getAwtComponent()
public abstract boolean getAxesOrientationRasmol()
public abstract int getBackgroundArgb()
public abstract int getBondArgb1(int bondIndex)
public abstract int getBondArgb2(int bondIndex)
public abstract int getBondCount()
public abstract int getBondCountInModel(int modelIndex)
public abstract int getBondModelIndex(int bondIndex)
public abstract short getBondOrder(int bondIndex)
public abstract Point3f getBondPoint3f1(int bondIndex)
public abstract Point3f getBondPoint3f2(int bondIndex)
public abstract float getBondRadius(int bondIndex)
public abstract float getBondTolerance()
public abstract boolean getBooleanProperty(String propertyName)
public abstract boolean getBooleanProperty(String key, boolean doICare)
public abstract int getChainCount()
public abstract int getChainCountInModel(int modelIindex)
public abstract String getData(String atomExpression, String type)
public abstract int getDisplayModelIndex()
public abstract BitSet getElementsPresentBitSet(int modelIndex)
public abstract String getFileAsString(String filename)
public abstract int getGroupCount()
public abstract int getGroupCountInModel(int modelIndex)
public abstract Hashtable getHeteroList(int modelIndex)
public abstract String getJavaVendor()
public abstract String getJavaVersion()
public static String getJmolVersion()
public abstract short getMadBond()
public abstract int getMeasurementCount()
public abstract int[] getMeasurementCountPlusIndices(int i)
public abstract String getMeasurementStringValue(int i)
public abstract float getMinBondDistance()
public abstract Hashtable getModelAuxiliaryInfo(int modelIndex)
public abstract Object getModelAuxiliaryInfo(int modelIndex, String keyName)
public abstract int getModelCount()
public abstract String getModelName(int modelIndex)
public abstract int getModelNumber(int modelIndex)
public abstract String getModelNumberDotted(int modelIndex)
public abstract Properties getModelProperties(int modelIndex)
public abstract String getModelProperty(int modelIndex, String propertyName)
public abstract Hashtable getModelSetAuxiliaryInfo()
public abstract String getModelSetFileName()
public abstract String getModelSetName()
public abstract String getModelSetPathName()
public abstract Properties getModelSetProperties()
public abstract int getMotionEventNumber()
public abstract String getOperatingSystemName()
public abstract Object getParameter(String name)
public abstract int getPercentVdwAtom()
public abstract boolean getPerspectiveDepth()
public abstract int getPolymerCount()
public abstract int getPolymerCountInModel(int modelIndex)
public abstract Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
public abstract Object getProperty(String returnType, String infoType, String paramInfo)
public abstract float getRotationRadius()
public abstract int getScreenHeight()
public abstract Image getScreenImage()
public abstract int getScreenWidth()
public abstract int getSelectionCount()
public abstract String getSetHistory(int howFarBack)
public abstract boolean getShowAxes()
public abstract boolean getShowBbcage()
public abstract boolean getShowHydrogens()
public abstract boolean getShowMeasurements()
public abstract String getStateInfo()
public abstract Matrix4f getUnscaledTransformMatrix()
public abstract int getZoomPercent()
public abstract float getZoomPercentFloat()
public abstract void haltScriptExecution()
public abstract boolean handleOldJvm10Event(Event e)
public abstract boolean haveFrame()
public abstract boolean havePartialCharges()
public abstract void homePosition()
public abstract boolean isApplet()
public abstract boolean isJvm12orGreater()
public abstract boolean isScriptExecuting()
public abstract void loadInline(String strModel)
public abstract void loadInline(String strModel, boolean isMerge)
public abstract void loadInline(String strModel, char newLine)
public abstract void loadInline(String[] arrayModels)
public abstract void loadInline(String[] arrayModels, boolean isMerge)
public abstract boolean modelHasVibrationVectors(int modelIndex)
public abstract void openClientFile(String fullPathName, String fileName, Object clientFile)
public abstract void openReader(String fullPathName, String name, Reader reader)
public abstract void popHoldRepaint()
public abstract void pushHoldRepaint()
public abstract void rebond()
public abstract void refresh(int isOrientationChange, String strWhy)
public abstract void releaseScreenImage()
public abstract void repaintView()
public abstract void rotateFront()
public abstract void rotateX(int degrees)
public abstract void rotateX(float radians)
public abstract void rotateY(int degrees)
public abstract void rotateY(float radians)
public abstract void rotateZ(float radians)
public abstract String script(String script)
public abstract String scriptCheck(String script)
public abstract String scriptWait(String script)
public abstract Object scriptWaitStatus(String script, String statusList)
public abstract void selectAll()
public abstract void setAnimationFps(int framesPerSecond)
public abstract void setAppletContext(String htmlName, URL documentBase, URL codeBase, String commandOptions)
public abstract void setAutoBond(boolean autoBond)
public abstract void setAxesOrientationRasmol(boolean axesMessedUp)
public abstract void setBondTolerance(float bondTolerance)
public abstract void setBooleanProperty(String propertyName, boolean value)
public abstract void setCenterSelected()
public abstract void setColorBackground(String colorName)
public abstract void setDebugScript(boolean debugScript)
public abstract void setFloatProperty(String propertyName, float value)
public abstract void setFrankOn(boolean frankOn)
public abstract void setIntProperty(String propertyName, int value)
public abstract void setJmolDefaults()
public abstract void setMarBond(short marBond)
public abstract void setMinBondDistance(float minBondDistance)
public abstract void setModeMouse(int modeMouse)
public abstract void setPercentVdwAtom(int percentVdwAtom)
public abstract void setPerspectiveDepth(boolean perspectiveDepth)
public abstract void setRasmolDefaults()
public abstract void setScreenDimension(Dimension dim)
public abstract void setSelectionHalos(boolean haloEnabled)
public abstract void setSelectionSet(BitSet newSelection)
public abstract void setShowAxes(boolean showAxes)
public abstract void setShowBbcage(boolean showBbcage)
public abstract void setShowHydrogens(boolean showHydrogens)
public abstract void setShowMeasurements(boolean showMeasurements)
public abstract void setStringProperty(String propertyName, String value)
public abstract void setVectorScale(float vectorScaleValue)
public abstract void setVibrationPeriod(float vibrationPeriod)
public abstract void setVibrationScale(float vibrationScaleValue)
public abstract boolean showModelSetDownload()
public abstract void showUrl(String urlString)
public abstract void syncScript(String script, String applet)
public abstract void writeTextFile(String string, String data)