Field Detail

• menuStructure

  public java.lang.String menuStructure

• apiPlatform

  public javajs.api.GenericPlatform apiPlatform

Constructor Detail

• JmolViewer

  public JmolViewer()

Method Detail

• 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​(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. 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

• allocateViewer

  public static JmolViewer allocateViewer​(java.lang.Object container,
                                          JmolAdapter jmolAdapter)

  a simpler option

  Parameters:

  container -

  jmolAdapter -

  Returns:

  JmolViewer object

• allocateViewer

  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)

  legacy only

  Parameters:

  display -

  modelAdapter -

  fullName -

  documentBase -

  codeBase -

  commandOptions -

  statusListener -

  Returns:

  JmolViewer object

• setConsole

  public 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

  Parameters:

  console - the console to use

• setInMotion

  public abstract void setInMotion​(boolean isInMotion)

• getSmartsMatch

  public abstract BS getSmartsMatch​(java.lang.String smarts,
                                    BS bsSelected)
                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• getJmolVersion

  public static java.lang.String getJmolVersion()

• generateOutputForExport

  public abstract java.lang.String generateOutputForExport​(java.util.Map<java.lang.String,​java.lang.Object> params)

  for POV-Ray

  Parameters:

  params -

  Returns:

  INI file

• setJmolCallbackListener

  public abstract void setJmolCallbackListener​(JmolCallbackListener jmolCallbackListener)

• setJmolStatusListener

  public abstract void setJmolStatusListener​(JmolStatusListener jmolStatusListener)

• checkHalt

  public abstract boolean checkHalt​(java.lang.String strCommand,
                                    boolean isInterrupt)

• haltScriptExecution

  public abstract void haltScriptExecution()

• pushHoldRepaint

  public abstract void pushHoldRepaint()

• popHoldRepaint

  public abstract void popHoldRepaint​(java.lang.String why)

• getData

  public abstract java.lang.String getData​(java.lang.String atomExpression,
                                           java.lang.String type)

• getSmiles

  public abstract java.lang.String getSmiles​(BS atoms)
                                      throws java.lang.Exception

  Throws:

  java.lang.Exception

• getOpenSmiles

  public abstract java.lang.String getOpenSmiles​(BS atoms)
                                          throws java.lang.Exception

  Throws:

  java.lang.Exception

• setScreenDimension

  public abstract void setScreenDimension​(int width,
                                          int height)

• getScreenWidth

  public abstract int getScreenWidth()

• getScreenHeight

  public abstract int getScreenHeight()

• getScreenImageBuffer

  public abstract java.lang.Object getScreenImageBuffer​(java.lang.Object g,
                                                        boolean isImageWrite)

• releaseScreenImage

  public abstract void releaseScreenImage()

• writeTextFile

  public abstract void writeTextFile​(java.lang.String string,
                                     java.lang.String data)

• outputToFile

  public abstract java.lang.String outputToFile​(java.util.Map<java.lang.String,​java.lang.Object> params)

  Parameters:

  params - include type, fileName, text, bytes, quality, width, height

  Returns:

  null (canceled) or a message starting with OK or an error message

• getImageAsBytes

  public abstract byte[] getImageAsBytes​(java.lang.String type,
                                         int width,
                                         int height,
                                         int quality,
                                         java.lang.String[] errMsg)

  Parameters:

  type -

  width -

  height -

  quality -

  errMsg - TODO

  Returns:

  base64-encoded or binary version of the image

• getMotionEventNumber

  public abstract int getMotionEventNumber()

• openReader

  public java.lang.String openReader​(java.lang.String fullPathName,
                                     java.lang.Object reader)

  Opens the file and creates the model set, given the reader. not used in Jmol

  Parameters:

  fullPathName - full path name or null

  reader - a Reader, byte[], or BufferedInputStream

  Returns:

  null or error message

• openReader

  public abstract java.lang.String openReader​(java.lang.String fullPathName,
                                              java.lang.String fileName,
                                              java.lang.Object reader)

  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 null

  fileName - (no path) or null

  reader - Reader, byte[], or BufferedInputStream

  Returns:

  null or error message

• showUrl

  public abstract void showUrl​(java.lang.String urlString)

• calcAtomsMinMax

  public abstract void calcAtomsMinMax​(BS bs,
                                       BoxInfo boxInfo)

• getBoundBoxCenter

  public abstract javajs.util.P3 getBoundBoxCenter()

• getBoundBoxCornerVector

  public abstract javajs.util.V3 getBoundBoxCornerVector()

• getMeasurementCount

  public abstract int getMeasurementCount()

• getMeasurementStringValue

  public abstract java.lang.String getMeasurementStringValue​(int i)

• getMeasurementCountPlusIndices

  public abstract int[] getMeasurementCountPlusIndices​(int i)

• getElementsPresentBitSet

  public abstract BS getElementsPresentBitSet​(int modelIndex)

• findNearestAtomIndex

  public abstract int findNearestAtomIndex​(int x,
                                           int y)

• script

  public abstract java.lang.String script​(java.lang.String script)

• scriptCheck

  public abstract java.lang.Object scriptCheck​(java.lang.String script)

• scriptWait

  public abstract java.lang.String scriptWait​(java.lang.String script)

• scriptWaitStatus

  public abstract java.lang.Object scriptWaitStatus​(java.lang.String script,
                                                    java.lang.String statusList)

• loadInline

  public abstract java.lang.String loadInline​(java.lang.String strModel)

• loadInlineAppend

  public abstract java.lang.String loadInlineAppend​(java.lang.String strModel,
                                                    boolean isAppend)

• loadInline

  public abstract java.lang.String loadInline​(java.lang.String strModel,
                                              char newLine)

• loadInline

  public abstract java.lang.String loadInline​(java.lang.String[] arrayModels)

• loadInline

  public abstract java.lang.String loadInline​(java.lang.String[] arrayModels,
                                              boolean isAppend)

  Parameters:

  arrayModels - and array of models, each of which is a String

  isAppend -

  Returns:

  null or error message

• loadInline

  public abstract java.lang.String loadInline​(java.util.List<java.lang.Object> arrayData,
                                              boolean isAppend)

  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 Vector

  isAppend - TRUE to append models (no ZAP)

  Returns:

  null or error message

• evalStringQuiet

  public abstract java.lang.String evalStringQuiet​(java.lang.String script)

• isScriptExecuting

  public abstract boolean isScriptExecuting()

• getModelSetFileName

  public abstract java.lang.String getModelSetFileName()

• getModelSetPathName

  public abstract java.lang.String getModelSetPathName()

• getModelSetProperties

  public abstract java.util.Properties getModelSetProperties()

• getModelSetAuxiliaryInfo

  public abstract java.util.Map<java.lang.String,​java.lang.Object> getModelSetAuxiliaryInfo()

• getModelProperties

  public abstract java.util.Properties getModelProperties​(int modelIndex)

• getModelNumber

  public abstract int getModelNumber​(int modelIndex)

• getModelName

  public abstract java.lang.String getModelName​(int modelIndex)

• getModelNumberDotted

  public abstract java.lang.String getModelNumberDotted​(int modelIndex)

• getVisibleFramesBitSet

  public abstract BS getVisibleFramesBitSet()

• addSelectionListener

  public abstract void addSelectionListener​(JmolSelectionListener listener)

• removeSelectionListener

  public abstract void removeSelectionListener​(JmolSelectionListener listener)

• homePosition

  public abstract void homePosition()

• getBackgroundArgb

  public abstract int getBackgroundArgb()

• getMadBond

  public abstract short getMadBond()

• rebond

  public abstract void rebond()

• refresh

  public abstract void refresh​(int isOrientationChange,
                               java.lang.String strWhy)

• notifyViewerRepaintDone

  public abstract void notifyViewerRepaintDone()

• getBooleanProperty

  public abstract boolean getBooleanProperty​(java.lang.String propertyName)

• getParameter

  public abstract java.lang.Object getParameter​(java.lang.String name)

• getSetHistory

  public abstract java.lang.String getSetHistory​(int howFarBack)

• getStateInfo

  public abstract java.lang.String getStateInfo()

• syncScript

  public abstract void syncScript​(java.lang.String script,
                                  java.lang.String applet,
                                  int port)

• setColorBackground

  public abstract void setColorBackground​(java.lang.String colorName)

• setJmolDefaults

  public abstract void setJmolDefaults()

• setRasmolDefaults

  public abstract void setRasmolDefaults()

• setBooleanProperty

  public abstract void setBooleanProperty​(java.lang.String propertyName,
                                          boolean value)

• setIntProperty

  public abstract void setIntProperty​(java.lang.String propertyName,
                                      int value)

• setFloatProperty

  public abstract void setFloatProperty​(java.lang.String propertyName,
                                        float value)

• setStringProperty

  public abstract void setStringProperty​(java.lang.String propertyName,
                                         java.lang.String value)

• 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

  public abstract void setSelectionSet​(BS newSelection)

• setCenterSelected

  public abstract void setCenterSelected()

• rotateFront

  public abstract void rotateFront()

• getModelAdapter

  public abstract JmolAdapter getModelAdapter()

• openFileAsyncSpecial

  public abstract void openFileAsyncSpecial​(java.lang.String fileName,
                                            int flags)

• openFileAsync

  public void openFileAsync​(java.lang.String fileName)

• getErrorMessage

  public abstract java.lang.String getErrorMessage()

• getErrorMessageUn

  public abstract java.lang.String getErrorMessageUn()

• renderScreenImage

  @Deprecated
  public void renderScreenImage​(java.lang.Object g,
                                java.lang.Object currentSize,
                                java.lang.Object rectClip)

  Deprecated.
  old -- not used in 12.2

  Parameters:

  g -

  currentSize -

  rectClip - // unused

• renderScreenImage

  public abstract void renderScreenImage​(java.lang.Object g,
                                         int width,
                                         int height)

• evalFile

  public abstract java.lang.String evalFile​(java.lang.String strFilename)

• evalString

  public abstract java.lang.String evalString​(java.lang.String strScript)

• openStringInline

  public abstract java.lang.String openStringInline​(java.lang.String strModel)

• openDOM

  public abstract java.lang.String openDOM​(java.lang.Object DOMNode)

• openFile

  public abstract java.lang.String openFile​(java.lang.String fileName)

• openFiles

  public abstract java.lang.String openFiles​(java.lang.String[] fileNames)

• getProperty

  public abstract java.lang.Object getProperty​(java.lang.String returnType,
                                               java.lang.String infoType,
                                               java.lang.Object paramInfo)

  Parameters:

  returnType - "JSON", "string", "readable", and anything else returns the Java object.

  infoType -

  paramInfo -

  Returns:

  property data -- see org.jmol.viewer.PropertyManager.java

• evaluateExpression

  public abstract java.lang.Object evaluateExpression​(java.lang.Object expression)

• resizeInnerPanel

  public abstract int[] resizeInnerPanel​(int width,
                                         int height)

• runScript

  public abstract java.lang.String runScript​(java.lang.String script)

  run a script immediately and return output buffer string Jmol 13.1.15

  Parameters:

  script -

  Returns:

  string from ScriptEvaluator#outputBuffer

• extractMolData

  public abstract java.lang.String extractMolData​(java.lang.String what)

• getClipboardText

  public abstract java.lang.String getClipboardText()

• clipImageOrPasteText

  public abstract java.lang.String clipImageOrPasteText​(java.lang.String text)

• notifyStatusReady

  public abstract void notifyStatusReady​(boolean isReady)

• getModelIndexFromId

  public abstract int getModelIndexFromId​(java.lang.String id)

  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

• setMenu

  public abstract void setMenu​(java.lang.String menuFile,
                               boolean isFile)

• dispose

  public void dispose()