public abstract class JmolViewer extends Object
Modifier and Type | Field and Description |
---|---|
javajs.api.GenericPlatform |
apiPlatform |
String |
menuStructure |
Constructor and Description |
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JmolViewer() |
Modifier and Type | Method and Description |
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abstract void |
addSelectionListener(JmolSelectionListener listener) |
static JmolViewer |
allocateViewer(Object container,
JmolAdapter jmolAdapter)
a simpler option
|
static JmolViewer |
allocateViewer(Object display,
JmolAdapter modelAdapter,
String fullName,
URL documentBase,
URL codeBase,
String commandOptions,
JmolStatusListener statusListener)
legacy only
|
protected static JmolViewer |
allocateViewer(Object display,
JmolAdapter modelAdapter,
String fullName,
URL documentBase,
URL codeBase,
String commandOptions,
JmolStatusListener statusListener,
javajs.api.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 |
checkHalt(String strCommand,
boolean isInterrupt) |
abstract void |
clearMeasurements() |
abstract void |
clearSelection() |
abstract String |
clipImageOrPasteText(String text) |
abstract void |
deleteMeasurement(int i) |
void |
dispose() |
abstract String |
evalFile(String strFilename) |
abstract String |
evalString(String strScript) |
abstract String |
evalStringQuiet(String script) |
abstract Object |
evaluateExpression(Object expression) |
abstract String |
extractMolData(String what) |
abstract int |
findNearestAtomIndex(int x,
int y) |
abstract String |
generateOutputForExport(Map<String,Object> params)
for POV-Ray
|
abstract int |
getBackgroundArgb() |
abstract boolean |
getBoolean(int tok) |
abstract boolean |
getBooleanProperty(String propertyName) |
abstract javajs.util.P3 |
getBoundBoxCenter() |
abstract javajs.util.V3 |
getBoundBoxCornerVector() |
abstract String |
getClipboardText() |
abstract String |
getData(String atomExpression,
String type) |
abstract BS |
getElementsPresentBitSet(int modelIndex) |
abstract String |
getErrorMessage() |
abstract String |
getErrorMessageUn() |
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 |
getJmolVersion() |
abstract short |
getMadBond() |
abstract int |
getMeasurementCount() |
abstract int[] |
getMeasurementCountPlusIndices(int i) |
abstract String |
getMeasurementStringValue(int i) |
abstract JmolAdapter |
getModelAdapter() |
abstract int |
getModelIndexFromId(String id) |
abstract String |
getModelName(int modelIndex) |
abstract int |
getModelNumber(int modelIndex) |
abstract String |
getModelNumberDotted(int modelIndex) |
abstract Properties |
getModelProperties(int modelIndex) |
abstract Map<String,Object> |
getModelSetAuxiliaryInfo() |
abstract String |
getModelSetFileName() |
abstract String |
getModelSetPathName() |
abstract Properties |
getModelSetProperties() |
abstract int |
getMotionEventNumber() |
abstract String |
getOpenSmiles(BS atoms) |
abstract Object |
getParameter(String name) |
abstract Object |
getProperty(String returnType,
String infoType,
Object paramInfo) |
abstract int |
getScreenHeight() |
abstract Object |
getScreenImageBuffer(Object g,
boolean isImageWrite) |
abstract int |
getScreenWidth() |
abstract String |
getSetHistory(int howFarBack) |
abstract BS |
getSmartsMatch(String smarts,
BS bsSelected) |
abstract String |
getSmiles(BS atoms) |
abstract String |
getStateInfo() |
abstract BS |
getVisibleFramesBitSet() |
abstract void |
haltScriptExecution() |
abstract void |
homePosition() |
abstract boolean |
isScriptExecuting() |
abstract String |
loadInline(List<Object> arrayData,
boolean isAppend)
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
|
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 |
loadInlineAppend(String strModel,
boolean isAppend) |
abstract void |
notifyStatusReady(boolean isReady) |
abstract void |
notifyViewerRepaintDone() |
abstract String |
openDOM(Object DOMNode) |
abstract String |
openFile(String fileName) |
void |
openFileAsync(String fileName) |
abstract void |
openFileAsyncSpecial(String fileName,
int flags) |
abstract String |
openFiles(String[] fileNames) |
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 |
pushHoldRepaint() |
abstract void |
rebond() |
abstract void |
refresh(int isOrientationChange,
String strWhy) |
abstract void |
releaseScreenImage() |
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 |
rotateFront() |
abstract String |
runScript(String script)
run a script immediately and return output buffer string
Jmol 13.1.15
|
abstract String |
script(String script) |
abstract Object |
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 |
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) |
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.java
|
abstract 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 |
setJmolDefaults() |
abstract void |
setJmolStatusListener(JmolStatusListener jmolStatusListener) |
abstract void |
setMarBond(short marBond) |
abstract void |
setMenu(String menuFile,
boolean isFile) |
abstract void |
setMinBondDistance(float minBondDistance) |
abstract void |
setPercentVdwAtom(int percentVdwAtom) |
abstract void |
setPerspectiveDepth(boolean perspectiveDepth) |
abstract void |
setRasmolDefaults() |
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 |
showUrl(String urlString) |
abstract void |
syncScript(String script,
String applet,
int port) |
abstract void |
writeTextFile(String string,
String data) |
public String menuStructure
public javajs.api.GenericPlatform apiPlatform
public abstract float getFloat(int tok)
public abstract int getInt(int tok)
public abstract boolean getBoolean(int tok)
protected static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, javajs.api.GenericPlatform implementedPlatform)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- implementedPlatform
- public static JmolViewer allocateViewer(Object container, JmolAdapter jmolAdapter)
container
- jmolAdapter
- public static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- public void setConsole(JmolAppConsoleInterface console)
console
- the console to usepublic abstract void setInMotion(boolean isInMotion)
public abstract BS getSmartsMatch(String smarts, BS bsSelected) throws Exception
Exception
public static String getJmolVersion()
public abstract String generateOutputForExport(Map<String,Object> params)
params
- public abstract void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)
public abstract boolean checkHalt(String strCommand, boolean isInterrupt)
public abstract void haltScriptExecution()
public abstract void pushHoldRepaint()
public abstract void popHoldRepaint(String why)
public abstract void setScreenDimension(int width, int height)
public abstract int getScreenWidth()
public abstract int getScreenHeight()
public abstract void releaseScreenImage()
public abstract String outputToFile(Map<String,Object> params)
params
- include type, fileName, text, bytes, quality, width, heightpublic abstract byte[] getImageAsBytes(String type, int width, int height, int quality, String[] errMsg)
type
- width
- height
- quality
- errMsg
- TODOpublic abstract int getMotionEventNumber()
public String openReader(String fullPathName, Object reader)
fullPathName
- full path name or nullreader
- a Reader, byte[], or BufferedInputStreampublic abstract String openReader(String fullPathName, String fileName, Object reader)
fullPathName
- or nullfileName
- (no path) or nullreader
- Reader, byte[], or BufferedInputStreampublic abstract void showUrl(String urlString)
public abstract javajs.util.P3 getBoundBoxCenter()
public abstract javajs.util.V3 getBoundBoxCornerVector()
public abstract int getMeasurementCount()
public abstract String getMeasurementStringValue(int i)
public abstract int[] getMeasurementCountPlusIndices(int i)
public abstract BS getElementsPresentBitSet(int modelIndex)
public abstract int findNearestAtomIndex(int x, int y)
public abstract String loadInline(String[] arrayModels, boolean isAppend)
arrayModels
- and array of models, each of which is a StringisAppend
- public abstract String loadInline(List<Object> arrayData, boolean isAppend)
arrayData
- a Vector of models, where each model is either a String
or a String[] or a VectorisAppend
- TRUE to append models (no ZAP)public abstract boolean isScriptExecuting()
public abstract String getModelSetFileName()
public abstract String getModelSetPathName()
public abstract Properties getModelSetProperties()
public abstract Properties getModelProperties(int modelIndex)
public abstract int getModelNumber(int modelIndex)
public abstract String getModelName(int modelIndex)
public abstract String getModelNumberDotted(int modelIndex)
public abstract BS getVisibleFramesBitSet()
public abstract void addSelectionListener(JmolSelectionListener listener)
public abstract void removeSelectionListener(JmolSelectionListener listener)
public abstract void homePosition()
public abstract int getBackgroundArgb()
public abstract short getMadBond()
public abstract void rebond()
public abstract void refresh(int isOrientationChange, String strWhy)
public abstract void notifyViewerRepaintDone()
public abstract boolean getBooleanProperty(String propertyName)
public abstract String getSetHistory(int howFarBack)
public abstract String getStateInfo()
public abstract void setColorBackground(String colorName)
public abstract void setJmolDefaults()
public abstract void setRasmolDefaults()
public abstract void setBooleanProperty(String propertyName, boolean value)
public abstract void setIntProperty(String propertyName, int value)
public abstract void setFloatProperty(String propertyName, float value)
public abstract void setShowHydrogens(boolean showHydrogens)
public abstract void setShowMeasurements(boolean showMeasurements)
public abstract void setPerspectiveDepth(boolean perspectiveDepth)
public abstract void setAutoBond(boolean autoBond)
public abstract void setMarBond(short marBond)
public abstract void setBondTolerance(float bondTolerance)
public abstract void setMinBondDistance(float minBondDistance)
public abstract void setAxesOrientationRasmol(boolean axesMessedUp)
public abstract void setPercentVdwAtom(int percentVdwAtom)
public abstract void setAnimationFps(int framesPerSecond)
public abstract void setFrankOn(boolean frankOn)
public abstract void setDebugScript(boolean debugScript)
public abstract void deleteMeasurement(int i)
public abstract void clearMeasurements()
public abstract void setVectorScale(float vectorScaleValue)
public abstract void setVibrationScale(float vibrationScaleValue)
public abstract void setVibrationPeriod(float vibrationPeriod)
public abstract void selectAll()
public abstract void clearSelection()
public abstract void setSelectionSet(BS newSelection)
public abstract void setCenterSelected()
public abstract void rotateFront()
public abstract JmolAdapter getModelAdapter()
public abstract void openFileAsyncSpecial(String fileName, int flags)
public void openFileAsync(String fileName)
public abstract String getErrorMessage()
public abstract String getErrorMessageUn()
@Deprecated public void renderScreenImage(Object g, Object currentSize, Object rectClip)
g
- currentSize
- rectClip
- // unusedpublic abstract void renderScreenImage(Object g, int width, int height)
public abstract Object getProperty(String returnType, String infoType, Object paramInfo)
returnType
- "JSON", "string", "readable", and anything else returns the Java object.infoType
- paramInfo
- public abstract int[] resizeInnerPanel(int width, int height)
public abstract String runScript(String script)
script
- public abstract String getClipboardText()
public abstract void notifyStatusReady(boolean isReady)
public abstract int getModelIndexFromId(String id)
id
- some_id,
filename#id, or
~fileNo.modelNo
added ".basemodel" indicates to get the first model in a
series from a JDX-MOL file.public abstract void setMenu(String menuFile, boolean isFile)
public void dispose()