public abstract class JmolViewer
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
javajs.api.GenericPlatform |
apiPlatform |
java.lang.String |
menuStructure |
Constructor and Description |
---|
JmolViewer() |
Modifier and Type | Method and Description |
---|---|
abstract void |
addSelectionListener(JmolSelectionListener listener) |
static JmolViewer |
allocateViewer(java.lang.Object container,
JmolAdapter jmolAdapter)
a simpler option
|
static JmolViewer |
allocateViewer(java.lang.Object display,
JmolAdapter modelAdapter,
java.lang.String fullName,
java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String commandOptions,
JmolStatusListener statusListener)
legacy only
|
protected static JmolViewer |
allocateViewer(java.lang.Object display,
JmolAdapter modelAdapter,
java.lang.String fullName,
java.net.URL documentBase,
java.net.URL codeBase,
java.lang.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(java.lang.String strCommand,
boolean isInterrupt) |
abstract void |
clearMeasurements() |
abstract void |
clearSelection() |
abstract java.lang.String |
clipImageOrPasteText(java.lang.String text) |
abstract void |
deleteMeasurement(int i) |
void |
dispose() |
abstract java.lang.String |
evalFile(java.lang.String strFilename) |
abstract java.lang.String |
evalString(java.lang.String strScript) |
abstract java.lang.String |
evalStringQuiet(java.lang.String script) |
abstract java.lang.Object |
evaluateExpression(java.lang.Object expression) |
abstract java.lang.String |
extractMolData(java.lang.String what) |
abstract int |
findNearestAtomIndex(int x,
int y) |
abstract java.lang.String |
generateOutputForExport(java.util.Map<java.lang.String,java.lang.Object> params)
for POV-Ray
|
abstract int |
getBackgroundArgb() |
abstract boolean |
getBoolean(int tok) |
abstract boolean |
getBooleanProperty(java.lang.String propertyName) |
abstract javajs.util.P3 |
getBoundBoxCenter() |
abstract javajs.util.V3 |
getBoundBoxCornerVector() |
abstract java.lang.String |
getClipboardText() |
abstract java.lang.String |
getData(java.lang.String atomExpression,
java.lang.String type) |
abstract BS |
getElementsPresentBitSet(int modelIndex) |
abstract java.lang.String |
getErrorMessage() |
abstract java.lang.String |
getErrorMessageUn() |
abstract float |
getFloat(int tok) |
abstract byte[] |
getImageAsBytes(java.lang.String type,
int width,
int height,
int quality,
java.lang.String[] errMsg) |
abstract int |
getInt(int tok) |
static java.lang.String |
getJmolVersion() |
abstract short |
getMadBond() |
abstract int |
getMeasurementCount() |
abstract int[] |
getMeasurementCountPlusIndices(int i) |
abstract java.lang.String |
getMeasurementStringValue(int i) |
abstract JmolAdapter |
getModelAdapter() |
abstract int |
getModelIndexFromId(java.lang.String id) |
abstract java.lang.String |
getModelName(int modelIndex) |
abstract int |
getModelNumber(int modelIndex) |
abstract java.lang.String |
getModelNumberDotted(int modelIndex) |
abstract java.util.Properties |
getModelProperties(int modelIndex) |
abstract java.util.Map<java.lang.String,java.lang.Object> |
getModelSetAuxiliaryInfo() |
abstract java.lang.String |
getModelSetFileName() |
abstract java.lang.String |
getModelSetPathName() |
abstract java.util.Properties |
getModelSetProperties() |
abstract int |
getMotionEventNumber() |
abstract java.lang.Object |
getParameter(java.lang.String name) |
abstract java.lang.Object |
getProperty(java.lang.String returnType,
java.lang.String infoType,
java.lang.Object paramInfo) |
abstract int |
getScreenHeight() |
abstract java.lang.Object |
getScreenImageBuffer(java.lang.Object g,
boolean isImageWrite) |
abstract int |
getScreenWidth() |
abstract java.lang.String |
getSetHistory(int howFarBack) |
abstract BS |
getSmartsMatch(java.lang.String smarts,
BS bsSelected) |
abstract java.lang.String |
getSmiles(BS atoms) |
abstract java.lang.String |
getStateInfo() |
abstract BS |
getVisibleFramesBitSet() |
abstract void |
haltScriptExecution() |
abstract void |
homePosition() |
abstract boolean |
isScriptExecuting() |
abstract java.lang.String |
loadInline(java.util.List<java.lang.Object> arrayData,
boolean isAppend)
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
|
abstract java.lang.String |
loadInline(java.lang.String strModel) |
abstract java.lang.String |
loadInline(java.lang.String[] arrayModels) |
abstract java.lang.String |
loadInline(java.lang.String[] arrayModels,
boolean isAppend) |
abstract java.lang.String |
loadInline(java.lang.String strModel,
char newLine) |
abstract java.lang.String |
loadInlineAppend(java.lang.String strModel,
boolean isAppend) |
abstract void |
notifyStatusReady(boolean isReady) |
abstract void |
notifyViewerRepaintDone() |
abstract java.lang.String |
openDOM(java.lang.Object DOMNode) |
abstract java.lang.String |
openFile(java.lang.String fileName) |
void |
openFileAsync(java.lang.String fileName) |
abstract void |
openFileAsyncSpecial(java.lang.String fileName,
int flags) |
abstract java.lang.String |
openFiles(java.lang.String[] fileNames) |
abstract java.lang.String |
openReader(java.lang.String fullPathName,
java.lang.String fileName,
java.io.Reader reader)
Opens the file and creates the model set, given the reader.
|
abstract java.lang.String |
openStringInline(java.lang.String strModel) |
abstract java.lang.String |
outputToFile(java.util.Map<java.lang.String,java.lang.Object> params) |
abstract void |
popHoldRepaint(java.lang.String why) |
abstract void |
pushHoldRepaint() |
abstract void |
rebond() |
abstract void |
refresh(int isOrientationChange,
java.lang.String strWhy) |
abstract void |
releaseScreenImage() |
abstract void |
removeSelectionListener(JmolSelectionListener listener) |
abstract void |
renderScreenImage(java.lang.Object g,
int width,
int height) |
void |
renderScreenImage(java.lang.Object g,
java.lang.Object currentSize,
java.lang.Object rectClip)
Deprecated.
|
abstract javajs.awt.Dimension |
resizeInnerPanel(int width,
int height) |
abstract void |
rotateFront() |
abstract java.lang.String |
runScript(java.lang.String script)
run a script immediately and return output buffer string
Jmol 13.1.15
|
abstract java.lang.String |
script(java.lang.String script) |
abstract java.lang.Object |
scriptCheck(java.lang.String script) |
abstract java.lang.String |
scriptWait(java.lang.String script) |
abstract java.lang.Object |
scriptWaitStatus(java.lang.String script,
java.lang.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(java.lang.String propertyName,
boolean value) |
abstract void |
setCenterSelected() |
abstract void |
setColorBackground(java.lang.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(java.lang.String propertyName,
float value) |
abstract void |
setFrankOn(boolean frankOn) |
abstract void |
setInMotion(boolean isInMotion) |
abstract void |
setIntProperty(java.lang.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(java.lang.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(java.lang.String propertyName,
java.lang.String value) |
abstract void |
setVectorScale(float vectorScaleValue) |
abstract void |
setVibrationPeriod(float vibrationPeriod) |
abstract void |
setVibrationScale(float vibrationScaleValue) |
abstract void |
showUrl(java.lang.String urlString) |
abstract void |
syncScript(java.lang.String script,
java.lang.String applet,
int port) |
abstract void |
writeTextFile(java.lang.String string,
java.lang.String data) |
public java.lang.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(java.lang.Object display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener, javajs.api.GenericPlatform implementedPlatform)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- implementedPlatform
- public static JmolViewer allocateViewer(java.lang.Object container, JmolAdapter jmolAdapter)
container
- jmolAdapter
- public static JmolViewer allocateViewer(java.lang.Object display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.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(java.lang.String smarts, BS bsSelected) throws java.lang.Exception
java.lang.Exception
public static java.lang.String getJmolVersion()
public abstract java.lang.String generateOutputForExport(java.util.Map<java.lang.String,java.lang.Object> params)
params
- public abstract void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)
public abstract boolean checkHalt(java.lang.String strCommand, boolean isInterrupt)
public abstract void haltScriptExecution()
public abstract void pushHoldRepaint()
public abstract void popHoldRepaint(java.lang.String why)
public abstract java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
public abstract java.lang.String getSmiles(BS atoms) throws java.lang.Exception
java.lang.Exception
public abstract void setScreenDimension(int width, int height)
public abstract int getScreenWidth()
public abstract int getScreenHeight()
public abstract java.lang.Object getScreenImageBuffer(java.lang.Object g, boolean isImageWrite)
public abstract void releaseScreenImage()
public abstract void writeTextFile(java.lang.String string, java.lang.String data)
public abstract java.lang.String outputToFile(java.util.Map<java.lang.String,java.lang.Object> params)
params
- include type, fileName, text, bytes, quality, width, heightpublic abstract byte[] getImageAsBytes(java.lang.String type, int width, int height, int quality, java.lang.String[] errMsg)
type
- width
- height
- quality
- errMsg
- TODOpublic abstract int getMotionEventNumber()
public abstract java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
fullPathName
- fileName
- reader
- public abstract void showUrl(java.lang.String urlString)
public abstract javajs.util.P3 getBoundBoxCenter()
public abstract javajs.util.V3 getBoundBoxCornerVector()
public abstract int getMeasurementCount()
public abstract java.lang.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 java.lang.String script(java.lang.String script)
public abstract java.lang.Object scriptCheck(java.lang.String script)
public abstract java.lang.String scriptWait(java.lang.String script)
public abstract java.lang.Object scriptWaitStatus(java.lang.String script, java.lang.String statusList)
public abstract java.lang.String loadInline(java.lang.String strModel)
public abstract java.lang.String loadInlineAppend(java.lang.String strModel, boolean isAppend)
public abstract java.lang.String loadInline(java.lang.String strModel, char newLine)
public abstract java.lang.String loadInline(java.lang.String[] arrayModels)
public abstract java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
arrayModels
- and array of models, each of which is a StringisAppend
- public abstract java.lang.String loadInline(java.util.List<java.lang.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 java.lang.String evalStringQuiet(java.lang.String script)
public abstract boolean isScriptExecuting()
public abstract java.lang.String getModelSetFileName()
public abstract java.lang.String getModelSetPathName()
public abstract java.util.Properties getModelSetProperties()
public abstract java.util.Map<java.lang.String,java.lang.Object> getModelSetAuxiliaryInfo()
public abstract java.util.Properties getModelProperties(int modelIndex)
public abstract int getModelNumber(int modelIndex)
public abstract java.lang.String getModelName(int modelIndex)
public abstract java.lang.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, java.lang.String strWhy)
public abstract void notifyViewerRepaintDone()
public abstract boolean getBooleanProperty(java.lang.String propertyName)
public abstract java.lang.Object getParameter(java.lang.String name)
public abstract java.lang.String getSetHistory(int howFarBack)
public abstract java.lang.String getStateInfo()
public abstract void syncScript(java.lang.String script, java.lang.String applet, int port)
public abstract void setColorBackground(java.lang.String colorName)
public abstract void setJmolDefaults()
public abstract void setRasmolDefaults()
public abstract void setBooleanProperty(java.lang.String propertyName, boolean value)
public abstract void setIntProperty(java.lang.String propertyName, int value)
public abstract void setFloatProperty(java.lang.String propertyName, float value)
public abstract void setStringProperty(java.lang.String propertyName, java.lang.String 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(java.lang.String fileName, int flags)
public void openFileAsync(java.lang.String fileName)
public abstract java.lang.String getErrorMessage()
public abstract java.lang.String getErrorMessageUn()
@Deprecated public void renderScreenImage(java.lang.Object g, java.lang.Object currentSize, java.lang.Object rectClip)
g
- currentSize
- rectClip
- // unusedpublic abstract void renderScreenImage(java.lang.Object g, int width, int height)
public abstract java.lang.String evalFile(java.lang.String strFilename)
public abstract java.lang.String evalString(java.lang.String strScript)
public abstract java.lang.String openStringInline(java.lang.String strModel)
public abstract java.lang.String openDOM(java.lang.Object DOMNode)
public abstract java.lang.String openFile(java.lang.String fileName)
public abstract java.lang.String openFiles(java.lang.String[] fileNames)
public abstract java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
returnType
- "JSON", "string", "readable", and anything else returns the Java object.infoType
- paramInfo
- public abstract java.lang.Object evaluateExpression(java.lang.Object expression)
public abstract javajs.awt.Dimension resizeInnerPanel(int width, int height)
public abstract java.lang.String runScript(java.lang.String script)
script
- public abstract java.lang.String extractMolData(java.lang.String what)
public abstract java.lang.String getClipboardText()
public abstract java.lang.String clipImageOrPasteText(java.lang.String text)
public abstract void notifyStatusReady(boolean isReady)
public abstract int getModelIndexFromId(java.lang.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(java.lang.String menuFile, boolean isFile)
public void dispose()