Package org.jmol.api
Class JmolViewer
java.lang.Object
org.jmol.api.JmolViewer
- Direct Known Subclasses:
Viewer
JmolViewer is the main API for the Viewer class.
(Mosty) we try to not change this (much), whereas the varius
"public" methods of Viewer, ModelSet, and other classes are public
only for internal cross-package access, not for external use.
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionabstract void
addSelectionListener
(JmolSelectionListener listener) static JmolViewer
allocateViewer
(Object container, JmolAdapter jmolAdapter) a simpler optionstatic JmolViewer
allocateViewer
(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener) legacy onlyprotected static JmolViewer
allocateViewer
(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, GenericPlatform implementedPlatform) This is the older main access point for creating an application or applet vwr.abstract void
calcAtomsMinMax
(BS bs, BoxInfo boxInfo) abstract boolean
abstract void
abstract void
abstract String
clipImageOrPasteText
(String text) abstract void
deleteMeasurement
(int i) void
dispose()
abstract String
abstract String
evalFileArgs
(String scriptFilename, String scriptArguments) abstract String
evalString
(String strScript) abstract String
evalStringQuiet
(String script) abstract Object
evaluateExpression
(Object expression) abstract SV
evaluateExpressionAsVariable
(Object expression) abstract String
extractMolData
(String what) abstract int
findNearestAtomIndex
(int x, int y) abstract String
generateOutputForExport
(Map<String, Object> params) for POV-Rayabstract int
abstract boolean
getBoolean
(int tok) abstract boolean
getBooleanProperty
(String propertyName) abstract P3
abstract V3
abstract String
abstract String
abstract BS
getElementsPresentBitSet
(int modelIndex) abstract String
abstract String
abstract float
getFloat
(int tok) abstract byte[]
getImageAsBytes
(String type, int width, int height, int quality, String[] errMsg) abstract int
getInt
(int tok) static String
static String
abstract short
abstract int
abstract int[]
abstract String
getMeasurementStringValue
(int i) abstract JmolAdapter
abstract int
abstract String
getModelName
(int modelIndex) abstract int
getModelNumber
(int modelIndex) abstract String
getModelNumberDotted
(int modelIndex) abstract Properties
getModelProperties
(int modelIndex) abstract String
abstract String
abstract Properties
abstract int
abstract String
getOpenSmiles
(BS atoms) abstract Object
getParameter
(String name) abstract Object
getProperty
(String returnType, String infoType, Object paramInfo) abstract int
abstract Object
getScreenImageBuffer
(Object g, boolean isImageWrite) abstract int
abstract String
getSetHistory
(int howFarBack) abstract BS
getSmartsMatch
(String smarts, BS bsSelected) abstract String
abstract String
abstract BS
abstract void
abstract void
abstract boolean
abstract String
loadInline
(String strModel) abstract String
loadInline
(String[] arrayModels) abstract String
loadInline
(String[] arrayModels, boolean isAppend) abstract String
loadInline
(String strModel, char newLine) abstract String
loadInline
(List<Object> arrayData, boolean isAppend) NOTE: THIS METHOD DOES NOT PRESERVE THE STATEabstract String
loadInlineAppend
(String strModel, boolean isAppend) abstract void
notifyStatusReady
(boolean isReady) abstract void
abstract String
abstract String
void
openFileAsync
(String fileName) abstract void
openFileAsyncSpecial
(String fileName, int flags) abstract void
openFileAsyncSpecialType
(String fileName, int flags, String fileType) abstract String
openReader
(String fullPathName, Object reader) Opens the file and creates the model set, given the reader.abstract String
openReader
(String fullPathName, String fileName, Object reader) Opens the file and creates the model set, given the reader.abstract String
openStringInline
(String strModel) abstract String
outputToFile
(Map<String, Object> params) abstract void
popHoldRepaint
(String why) abstract void
abstract void
rebond()
abstract void
abstract void
abstract void
removeSelectionListener
(JmolSelectionListener listener) abstract void
renderScreenImage
(Object g, int width, int height) void
renderScreenImage
(Object g, Object currentSize, Object rectClip) Deprecated.abstract int[]
resizeInnerPanel
(int width, int height) abstract void
abstract String
starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older versionrunScriptCautiously
(String script) Formerly runScript(script).abstract String
abstract Object
scriptCheck
(String script) abstract String
scriptWait
(String script) abstract Object
scriptWaitStatus
(String script, String statusList) abstract void
abstract void
setAnimationFps
(int framesPerSecond) abstract void
setAutoBond
(boolean autoBond) abstract void
setAxesOrientationRasmol
(boolean axesMessedUp) abstract void
setBondTolerance
(float bondTolerance) abstract void
setBooleanProperty
(String propertyName, boolean value) abstract void
abstract void
setColorBackground
(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(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.javaabstract void
setDebugScript
(boolean debugScript) abstract void
setFloatProperty
(String propertyName, float value) abstract void
setFrankOn
(boolean frankOn) abstract void
setInMotion
(boolean isInMotion) abstract void
setIntProperty
(String propertyName, int value) abstract void
setJmolCallbackListener
(JmolCallbackListener jmolCallbackListener) abstract void
abstract void
setJmolStatusListener
(JmolStatusListener jmolStatusListener) abstract void
setMarBond
(short marBond) abstract void
abstract void
setMinBondDistance
(float minBondDistance) abstract void
setPercentVdwAtom
(int percentVdwAtom) abstract void
setPerspectiveDepth
(boolean perspectiveDepth) abstract void
abstract void
setScreenDimension
(int width, int height) abstract void
setSelectionSet
(BS newSelection) 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 void
abstract void
syncScript
(String script, String applet, int port) abstract String
writeTextFile
(String string, String data)
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Field Details
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apiPlatform
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Constructor Details
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JmolViewer
public JmolViewer()
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Method Details
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getFloat
public abstract float getFloat(int tok) -
getInt
public abstract int getInt(int tok) -
getBoolean
public abstract boolean getBoolean(int tok) -
allocateViewer
protected static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, GenericPlatform implementedPlatform) This is the older main access point for creating an application or applet vwr. You can also use That is necessary when compiled into JavaScript using Java2Script In Jmol 11.6 it was manditory that one of the next commands is either vwr.evalString("ZAP"); or at least: vwr.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. Starting with Jmol 12.3.13, we allow for preconstructed ApiPlatform- Parameters:
display
-modelAdapter
-fullName
-documentBase
-codeBase
-commandOptions
-statusListener
-implementedPlatform
-- Returns:
- a JmolViewer object
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allocateViewer
a simpler option- Parameters:
container
-jmolAdapter
-- Returns:
- JmolViewer object
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allocateViewer
public static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener) legacy only- Parameters:
display
-modelAdapter
-fullName
-documentBase
-codeBase
-commandOptions
-statusListener
-- Returns:
- JmolViewer object
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setConsole
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java- Parameters:
console
- the console to use
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setInMotion
public abstract void setInMotion(boolean isInMotion) -
getSmartsMatch
- Throws:
Exception
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getJmolVersion
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getJmolVersionNoDate
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generateOutputForExport
for POV-Ray- Parameters:
params
-- Returns:
- INI file
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setJmolCallbackListener
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setJmolStatusListener
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checkHalt
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haltScriptExecution
public abstract void haltScriptExecution() -
pushHoldRepaint
public abstract void pushHoldRepaint() -
popHoldRepaint
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getData
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getSmiles
- Throws:
Exception
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getOpenSmiles
- Throws:
Exception
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setScreenDimension
public abstract void setScreenDimension(int width, int height) -
getScreenWidth
public abstract int getScreenWidth() -
getScreenHeight
public abstract int getScreenHeight() -
getScreenImageBuffer
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releaseScreenImage
public abstract void releaseScreenImage() -
writeTextFile
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outputToFile
- Parameters:
params
- include type, fileName, text, bytes, quality, width, height- Returns:
- null (canceled) or a message starting with OK or an error message
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getImageAsBytes
public abstract byte[] getImageAsBytes(String type, int width, int height, int quality, String[] errMsg) - Parameters:
type
-width
-height
-quality
-errMsg
- TODO- Returns:
- base64-encoded or binary version of the image
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getMotionEventNumber
public abstract int getMotionEventNumber() -
openReader
Opens the file and creates the model set, given the reader. not used in Jmol- Parameters:
fullPathName
- full path name or nullreader
- a Reader, byte[], or BufferedInputStream- Returns:
- null or error message
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openReader
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 not used in Jmol- Parameters:
fullPathName
- or nullfileName
- (no path) or nullreader
- Reader, byte[], or BufferedInputStream- Returns:
- null or error message
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showUrl
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calcAtomsMinMax
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getBoundBoxCenter
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getBoundBoxCornerVector
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getMeasurementCount
public abstract int getMeasurementCount() -
getMeasurementStringValue
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getMeasurementCountPlusIndices
public abstract int[] getMeasurementCountPlusIndices(int i) -
getElementsPresentBitSet
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findNearestAtomIndex
public abstract int findNearestAtomIndex(int x, int y) -
script
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scriptCheck
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scriptWait
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scriptWaitStatus
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loadInline
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loadInlineAppend
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loadInline
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loadInline
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loadInline
- Parameters:
arrayModels
- and array of models, each of which is a StringisAppend
-- Returns:
- null or error message
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loadInline
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 VectorisAppend
- TRUE to append models (no ZAP)- Returns:
- null or error message
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evalStringQuiet
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isScriptExecuting
public abstract boolean isScriptExecuting() -
getModelSetFileName
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getModelSetPathName
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getModelSetProperties
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getModelSetAuxiliaryInfo
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getModelProperties
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getModelNumber
public abstract int getModelNumber(int modelIndex) -
getModelName
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getModelNumberDotted
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getVisibleFramesBitSet
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addSelectionListener
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removeSelectionListener
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homePosition
public abstract void homePosition() -
getBackgroundArgb
public abstract int getBackgroundArgb() -
getMadBond
public abstract short getMadBond() -
rebond
public abstract void rebond() -
refresh
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notifyViewerRepaintDone
public abstract void notifyViewerRepaintDone() -
getBooleanProperty
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getParameter
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getSetHistory
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getStateInfo
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syncScript
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setColorBackground
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setJmolDefaults
public abstract void setJmolDefaults() -
setRasmolDefaults
public abstract void setRasmolDefaults() -
setBooleanProperty
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setIntProperty
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setFloatProperty
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setStringProperty
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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
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setCenterSelected
public abstract void setCenterSelected() -
rotateFront
public abstract void rotateFront() -
getModelAdapter
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openFileAsyncSpecial
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openFileAsyncSpecialType
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openFileAsync
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getErrorMessage
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getErrorMessageUn
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renderScreenImage
Deprecated.old -- not used in 12.2- Parameters:
g
-currentSize
-rectClip
- // unused
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renderScreenImage
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evalFile
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evalFileArgs
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evalString
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openStringInline
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openDOM
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openFile
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openFiles
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getProperty
- Parameters:
returnType
- "JSON", "string", "readable", and anything else returns the Java object.infoType
-paramInfo
-- Returns:
- property data -- see org.jmol.viewer.PropertyManager.java
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evaluateExpression
- Parameters:
expression
-- Returns:
- a String representation of the evaluated expression
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evaluateExpressionAsVariable
- Parameters:
expression
-- Returns:
- a String representation of the evaluated expression as a script variable (org.jmol.script.SV)
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resizeInnerPanel
public abstract int[] resizeInnerPanel(int width, int height) -
runScript
starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older version- Parameters:
script
-- Returns:
- string from ScriptEvaluator#outputBuffer
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runScriptCautiously
Formerly runScript(script). run a script immediately and return output buffer string Jmol 13.1.15- Parameters:
script
-- Returns:
- string from ScriptEvaluator#outputBuffer
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extractMolData
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getClipboardText
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clipImageOrPasteText
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notifyStatusReady
public abstract void notifyStatusReady(boolean isReady) -
getModelIndexFromId
- Parameters:
id
- some_id, filename#id, or ~fileNo.modelNo added ".basemodel" indicates to get the first model in a series from a JDX-MOL file.- Returns:
- model index if found; -2 if file found but model not found -2 if no file indicated and no model found -1 if no such file
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setMenu
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dispose
public void dispose()
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