Class Viewer

Method Details

• finalize

  protected void finalize() throws Throwable

  Overrides:

  finalize in class Object

  Throws:

  Throwable

• setInsertedCommand

  public void setInsertedCommand(String strScript)

• getJmolVersion

  public static String getJmolVersion()

• allocateViewer

  protected static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, GenericPlatform implementedPlatform)

  old way...

  Parameters:

  display -

  modelAdapter -

  fullName -

  documentBase -

  codeBase -

  commandOptions -

  statusListener -

  implementedPlatform -

  Returns:

  JmolViewer object

• haveAccess

  public boolean haveAccess(Viewer.ACCESS a)

• getModelAdapter

  public JmolAdapter getModelAdapter()

  Specified by:

  getModelAdapter in class JmolViewer

• getSmartsMatch

  public BS getSmartsMatch(String smarts, BS bsSelected) throws Exception

  Specified by:

  getSmartsMatch in class JmolViewer

  Throws:

  Exception

• isSubstructure

  public boolean isSubstructure(String smarts, String smiles)

• hasStructure

  public boolean hasStructure(String pattern, String smiles, boolean isSmarts)

• getSmartsMatchForNodes

  public BS getSmartsMatchForNodes(String smarts, Node[] atoms) throws Exception

  Throws:

  Exception

• getSmartsMap

  public int[][] getSmartsMap(String smilesOrSmarts, BS bsSelected, int flags) throws Exception

  Parameters:

  smilesOrSmarts -

  bsSelected -

  flags - can be bitwise OR of JC.SMILES_* options, in particular, JC.SMILES_TYPE_SMARTS, JC.SMILES_TYPE_SMILES, and JC.SMILES_MAP_UNIQUE

  Returns:

  map

  Throws:

  Exception

• setOptions

  public void setOptions(Map<String,Object> info)

• setStereo

  public void setStereo(boolean isStereoSlave, Object gRight)

• getMenu

  public String getMenu(String type)

• resizeInnerPanel

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

  Specified by:

  resizeInnerPanel in class JmolViewer

• setScreenDimension

  public void setScreenDimension(int width, int height)

  Specified by:

  setScreenDimension in class JmolViewer

• getScreenWidth

  public int getScreenWidth()

  Specified by:

  getScreenWidth in class JmolViewer

• getScreenHeight

  public int getScreenHeight()

  Specified by:

  getScreenHeight in class JmolViewer

• getScreenDim

  public int getScreenDim()

• setWidthHeightVar

  public void setWidthHeightVar()

• getBoundBoxCenterX

  public int getBoundBoxCenterX()

• getBoundBoxCenterY

  public int getBoundBoxCenterY()

• getScreenImage

  public Object getScreenImage()

• getScreenImageBuffer

  public Object getScreenImageBuffer(Object g, boolean isImageWrite)

  Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo

  Specified by:

  getScreenImageBuffer in class JmolViewer

• evalStringWaitStatusQueued

  public Object evalStringWaitStatusQueued(String returnType, String strScript, String statusList, boolean isQuiet, boolean isQueued)

• getModelkit

  public ModelKit getModelkit(boolean andShow)

• setMenu

  public void setMenu(String fileOrText, boolean isFile)

  Specified by:

  setMenu in class JmolViewer

• getJDXBaseModelIndex

  public int getJDXBaseModelIndex(int modelIndex)

  get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file. This might then allow pointing off a peak in JSpecView to switch to the model that is involved in HNMR or CNMR

  Parameters:

  modelIndex -

  Returns:

  modelIndex

• getJspecViewProperties

  public Object getJspecViewProperties(Object myParam)

• scriptEcho

  public void scriptEcho(String strEcho)

• notifyError

  public void notifyError(String errType, String errMsg, String errMsgUntranslated)

• jsEval

  public String jsEval(String strEval)

• jsEvalSV

  public SV jsEvalSV(String strEval)

• getZapName

  public String getZapName()

• setStatusMeasuring

  public void setStatusMeasuring(String status, int intInfo, String strMeasure, float value)

• notifyMinimizationStatus

  public void notifyMinimizationStatus()

• setStatusAtomPicked

  public void setStatusAtomPicked(int atomIndex, String info, Map<String,Object> map, boolean andSelect)

• getProperty

  public Object getProperty(String returnType, String infoType, Object paramInfo)

  Specified by:

  getProperty in class JmolViewer

  Parameters:

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

  infoType -

  paramInfo -

  Returns:

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

• showSystemInfo

  public void showSystemInfo()

• notifyMouseClicked

  public int notifyMouseClicked(int x, int y, int action, int mode)

• getJzt

  public GenericZipTools getJzt()

• readFileAsMap

  public void readFileAsMap(BufferedInputStream bis, Map<String,Object> map, String name)

• getZipDirectoryAsString

  public String getZipDirectoryAsString(String fileName)

• getImageAsBytes

  public byte[] getImageAsBytes(String type, int width, int height, int quality, String[] errMsg)

  Specified by:

  getImageAsBytes in class JmolViewer

  Parameters:

  type -

  width -

  height -

  quality -

  errMsg - TODO

  Returns:

  byte[] image, or null and an error message

• releaseScreenImage

  public void releaseScreenImage()

  Specified by:

  releaseScreenImage in class JmolViewer

• setDisplay

  public void setDisplay(Object canvas)

• newMeasurementData

  public MeasurementData newMeasurementData(String id, Lst<Object> points)

• getExportDriverList

  public String getExportDriverList()

• dispose

  public void dispose()

  end of life for this viewer

  Overrides:

  dispose in class JmolViewer

• reset

  public void reset(boolean includingSpin)

• homePosition

  public void homePosition()

  Specified by:

  homePosition in class JmolViewer

• initialize

  public void initialize(boolean clearUserVariables, boolean isPyMOL)

• getGLmolView

  public Object getGLmolView()

  This method is only called by JmolGLmol applet._refresh();

  Returns:

  enough data to update a WebGL view

• setRotationRadius

  public void setRotationRadius(float angstroms, boolean doAll)

• setCenterBitSet

  public void setCenterBitSet(BS bsCenter, boolean doScale)

• setNewRotationCenter

  public void setNewRotationCenter(P3 center)

• move

  public void move(JmolScriptEvaluator eval, V3 dRot, float dZoom, V3 dTrans, float dSlab, float floatSecondsTotal, int fps)

• moveTo

  public void moveTo(JmolScriptEvaluator eval, float floatSecondsTotal, P3 center, V3 rotAxis, float degrees, M3 rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY)

• moveUpdate

  public void moveUpdate(float floatSecondsTotal)

• navigatePt

  public void navigatePt(P3 center)

• navigateAxis

  public void navigateAxis(V3 rotAxis, float degrees)

• navTranslatePercent

  public void navTranslatePercent(float x, float y)

• spinXYBy

  public void spinXYBy(int xDelta, int yDelta, float speed)

• rotateZBy

  public void rotateZBy(int zDelta, int x, int y)

• translateXYBy

  public void translateXYBy(int xDelta, int yDelta)

• rotateFront

  public void rotateFront()

  Specified by:

  rotateFront in class JmolViewer

• translate

  public void translate(char xyz, float x, char type, BS bsAtoms)

• finalizeTransformParameters

  public void finalizeTransformParameters()

• getScalePixelsPerAngstrom

  public float getScalePixelsPerAngstrom(boolean asAntialiased)

• setSpin

  public void setSpin(String key, int value)

• getSpinState

  public String getSpinState()

• getOrientation

  public Object getOrientation(int type, String name, BS bs, P3[] points)

  Parameters:

  type -

  name -

  bs -

  points -

  Returns:

  String or Quat or P3[]

• getCurrentColorRange

  public float[] getCurrentColorRange()

• setElementArgb

  public void setElementArgb(int elementNumber, int argb)

• setVectorScale

  public void setVectorScale(float scale)

  Specified by:

  setVectorScale in class JmolViewer

• setVibrationScale

  public void setVibrationScale(float scale)

  Specified by:

  setVibrationScale in class JmolViewer

• setVibrationPeriod

  public void setVibrationPeriod(float period)

  Specified by:

  setVibrationPeriod in class JmolViewer

• setObjectVisibility

  public void setObjectVisibility(String name, boolean b)

• setObjectArgb

  public void setObjectArgb(String name, int argb)

• setBackgroundImage

  public void setBackgroundImage(String fileName, Object image)

• getObjectColix

  public short getObjectColix(int objId)

• setColorBackground

  public void setColorBackground(String colorName)

  Specified by:

  setColorBackground in class JmolViewer

• getBackgroundArgb

  public int getBackgroundArgb()

  Specified by:

  getBackgroundArgb in class JmolViewer

• setObjectMad10

  public void setObjectMad10(int iShape, String name, int mad10)

  input here is a JC.SHAPE_xxxx identifier

  Parameters:

  iShape -

  name -

  mad10 -

• getObjectMad10

  public int getObjectMad10(int objId)

  Parameters:

  objId -

  Returns:

  mad10

• setPropertyColorScheme

  public void setPropertyColorScheme(String scheme, boolean isTranslucent, boolean isOverloaded)

• getLightingState

  public String getLightingState()

• getColorPointForPropertyValue

  public P3 getColorPointForPropertyValue(float val)

• select

  public void select(BS bs, boolean isGroup, int addRemove, boolean isQuiet)

  Parameters:

  bs -

  isGroup -

  addRemove - T.add, T.remove, or ignored

  isQuiet -

• setSelectionSet

  public void setSelectionSet(BS set)

  Specified by:

  setSelectionSet in class JmolViewer

• selectBonds

  public void selectBonds(BS bs)

• displayAtoms

  public void displayAtoms(BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)

• getDefinedAtomSet

  public BS getDefinedAtomSet(String name)

• selectAll

  public void selectAll()

  Specified by:

  selectAll in class JmolViewer

• clearSelection

  public void clearSelection()

  Specified by:

  clearSelection in class JmolViewer

• bsA

  public BS bsA()

• addSelectionListener

  public void addSelectionListener(JmolSelectionListener listener)

  Specified by:

  addSelectionListener in class JmolViewer

• removeSelectionListener

  public void removeSelectionListener(JmolSelectionListener listener)

  Specified by:

  removeSelectionListener in class JmolViewer

• processTwoPointGesture

  public void processTwoPointGesture(float[][][] touches)

• processMouseEvent

  public boolean processMouseEvent(int id, int x, int y, int modifiers, long time)

• processKeyEvent

  public void processKeyEvent(Object event)

• getRubberBandSelection

  public Rectangle getRubberBandSelection()

• isBound

  public boolean isBound(int mouseAction, int jmolAction)

• getCursorX

  public int getCursorX()

• getCursorY

  public int getCursorY()

• getDefaultDirectory

  public String getDefaultDirectory()

• getLocalUrl

  public String getLocalUrl(String fileName)

• getFileAsString

  public String getFileAsString(String fileName)

• getBufferedInputStream

  public BufferedInputStream getBufferedInputStream(String fullPathName)

  Specified by:

  getBufferedInputStream in interface AtomDataServer

• setLoadParameters

  public Map<String,Object> setLoadParameters(Map<String,Object> htParams, boolean isAppend)

• openFileAsyncSpecial

  public void openFileAsyncSpecial(String fileName, int flags)

  opens a file as a model, a script, or a surface via the creation of a script that is queued. Called from (JSmolCore.js)Jmol.$appEvent(,,"drop").reader.onloadend()

  Specified by:

  openFileAsyncSpecial in class JmolViewer

  Parameters:

  fileName -

  flags - 1=pdbCartoons, 2=no scripting, 4=append, 8=no autoplay, 16=file dropped, 32=script only (dropped into console) 64=check dims for resize

• openFileAsyncSpecialType

  public void openFileAsyncSpecialType(String fileName, int flags, String fileType)

  Specified by:

  openFileAsyncSpecialType in class JmolViewer

• openFile

  public String openFile(String fileName)

  for JmolSimpleViewer -- external applications only (and no-script JavaScript)

  Specified by:

  openFile in class JmolViewer

  Parameters:

  fileName -

  Returns:

  null or error

• openFiles

  public String openFiles(String[] fileNames)

  for JmolSimpleViewer -- external applications only

  Specified by:

  openFiles in class JmolViewer

  Parameters:

  fileNames -

  Returns:

  null or error

• openReader

  public String openReader(String fullPathName, String fileName, Object reader)

  Opens the file, given an already-created reader.

  Specified by:

  openReader in class JmolViewer

  Parameters:

  fullPathName -

  fileName - name without path or can just be null

  reader - could be Reader, BufferedInputStream, or byte[]

  Returns:

  null or error message

• openDOM

  public String openDOM(Object DOMNode)

  applet DOM method -- does not preserve state

  Specified by:

  openDOM in class JmolViewer

  Parameters:

  DOMNode -

  Returns:

  null or error

• loadModelFromFile

  public String loadModelFromFile(String fullPathName, String fileName, String[] fileNames, Object reader, boolean isAppend, Map<String,Object> htParams, SB loadScript, SB sOptions, int tokType, String filecat)

  Used by the ScriptEvaluator LOAD command to open one or more files. Now necessary for EVERY load of a file, as loadScript must be passed to the ModelLoader.

  Parameters:

  fullPathName - may be null; used only when reader != null

  fileName - must not be null

  fileNames - when present, reader is ignored

  reader - may be a Reader, BufferedReader, byte[], or BufferedInputStream

  isAppend -

  htParams -

  loadScript -

  sOptions -

  tokType -

  filecat - + or null, -, or space

  Returns:

  null or error

• setLigandModel

  public void setLigandModel(String key, String data)

• getLigandModel

  public Object getLigandModel(String id, String prefix, String suffix, String terminator)

  obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state

  Parameters:

  id - unique key; if null, clear "bad" entries from the set.

  prefix -

  suffix - or fileName

  terminator - Only save to this if not null

  Returns:

  a ligand model or a string if just file data or null

• openStringInline

  public String openStringInline(String strModel)

  only used by file dropper.

  Specified by:

  openStringInline in class JmolViewer

• loadInline

  public String loadInline(String strModel)

  from Applet and external applications only

  Specified by:

  loadInline in class JmolViewer

• loadInline

  public String loadInline(String strModel, char newLine)

  external apps only

  Specified by:

  loadInline in class JmolViewer

• loadInlineAppend

  public String loadInlineAppend(String strModel, boolean isAppend)

  used by applet and console

  Specified by:

  loadInlineAppend in class JmolViewer

• loadInline

  public String loadInline(String[] arrayModels)

  external apps only

  Specified by:

  loadInline in class JmolViewer

• loadInline

  public String loadInline(String[] arrayModels, boolean isAppend)

  external apps and applet only

  Specified by:

  loadInline in class JmolViewer

  Parameters:

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

  isAppend -

  Returns:

  null or error message

• loadInline

  public String loadInline(List<Object> arrayData, boolean isAppend)

  External applications only; does not preserve state -- intentionally!

  Specified by:

  loadInline in class JmolViewer

  Parameters:

  arrayData -

  isAppend -

  Returns:

  null or error string

• fixInlineString

  public static String fixInlineString(String strModel, char newLine)

• openStringInlineParamsAppend

  public String openStringInlineParamsAppend(String strModel, Map<String,Object> htParams, boolean isAppend)

  Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.

  Parameters:

  strModel -

  htParams -

  isAppend -

  Returns:

  null or error string

• getInlineChar

  public char getInlineChar()

• getCurrentFileAsString

  public String getCurrentFileAsString(String state)

  /////// File-related methods ////////////

• getFullPathNameOrError

  public String[] getFullPathNameOrError(String filename)

  Parameters:

  filename -

  Returns:

  String[2] where [0] is fullpathname and [1] is error message or null

• getFileAsString3

  public String getFileAsString3(String name, boolean checkProtected, String state)

• getFileAsString4

  public String getFileAsString4(String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected, String state)

• getAsciiFileOrNull

  public String getAsciiFileOrNull(String name)

• autoCalculate

  public void autoCalculate(int tokProperty, String dataType)

• calculateStraightness

  public void calculateStraightness()

• calculateSurface

  public P3[] calculateSurface(BS bsSelected, float envelopeRadius)

• getStructureList

  public Map<STR,float[]> getStructureList()

• setStructureList

  public void setStructureList(float[] list, STR type)

• calculateStructures

  public String calculateStructures(BS bsAtoms, boolean asDSSP, boolean setStructure, int version)

  Parameters:

  bsAtoms -

  asDSSP -

  setStructure - to actually change structures

  version -

  Returns:

  structure string from DSSP

• getAnnotationParser

  public JmolAnnotationParser getAnnotationParser(boolean isDSSR)

• getSelectedAtomIterator

  public AtomIndexIterator getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)

  Specified by:

  getSelectedAtomIterator in interface AtomDataServer

• setIteratorForAtom

  public void setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)

  Specified by:

  setIteratorForAtom in interface AtomDataServer

• setIteratorForPoint

  public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, T3 pt, float distance)

  Specified by:

  setIteratorForPoint in interface AtomDataServer

• fillAtomData

  public void fillAtomData(AtomData atomData, int mode)

  Specified by:

  fillAtomData in interface AtomDataServer

• addStateScript

  public StateScript addStateScript(String script, boolean addFrameNumber, boolean postDefinitions)

• getMinimizer

  public Minimizer getMinimizer(boolean createNew)

• getSmilesMatcher

  public SmilesMatcherInterface getSmilesMatcher()

• clearModelDependentObjects

  public void clearModelDependentObjects()

• zap

  public void zap(boolean notify, boolean resetUndo, boolean zapModelKit)

• startHoverWatcher

  public void startHoverWatcher(boolean tf)

• getModelSetPathName

  public String getModelSetPathName()

  Specified by:

  getModelSetPathName in class JmolViewer

• getModelSetFileName

  public String getModelSetFileName()

  Specified by:

  getModelSetFileName in class JmolViewer

• getUnitCellInfoText

  public String getUnitCellInfoText()

• getUnitCellInfo

  public float getUnitCellInfo(int infoType)

• getUnitCellInfoStr

  public float getUnitCellInfoStr(String type)

• getV0abc

  public T3[] getV0abc(int iModel, Object def)

  Convert string abc;offset or M3d or M4d to origin and three vectors -- a, b, c. The string can be preceded by ! for "reverse of". For example, "!a-b,-5a-5b,-c;7/8,0,1/8" offset is optional.

  Parameters:

  iModel -

  def - a string or an M3 or M4

  Returns:

  vectors [origin a b c]

• getCurrentUnitCell

  public SymmetryInterface getCurrentUnitCell()

• getPolymerPointsAndVectors

  public void getPolymerPointsAndVectors(BS bs, Lst<P3[]> vList)

• getHybridizationAndAxes

  public String getHybridizationAndAxes(int atomIndex, V3 z, V3 x, String lcaoType)

• getAllAtoms

  public BS getAllAtoms()

• getFrameAtoms

  public BS getFrameAtoms()

• getVisibleFrameAtomsNoSplitData

  public BS getVisibleFrameAtomsNoSplitData()

• getVisibleFramesBitSet

  public BS getVisibleFramesBitSet()

  Specified by:

  getVisibleFramesBitSet in class JmolViewer

• getVisibleFramesBitSetNoJmolData

  public BS getVisibleFramesBitSetNoJmolData()

• getModelUndeletedAtomsBitSet

  public BS getModelUndeletedAtomsBitSet(int modelIndex)

  Parameters:

  modelIndex -

  Returns:

  modifiable copy of this bitset

• getModelUndeletedAtomsBitSetBs

  public BS getModelUndeletedAtomsBitSetBs(BS bsModels)

• getBoundBoxCenter

  public P3 getBoundBoxCenter()

  Specified by:

  getBoundBoxCenter in class JmolViewer

• calcBoundBoxDimensions

  public void calcBoundBoxDimensions(BS bs, float scale)

• getBoundBoxCornerVector

  public V3 getBoundBoxCornerVector()

  Specified by:

  getBoundBoxCornerVector in class JmolViewer

• getModelSetProperties

  public Properties getModelSetProperties()

  Specified by:

  getModelSetProperties in class JmolViewer

• getModelProperties

  public Properties getModelProperties(int modelIndex)

  Specified by:

  getModelProperties in class JmolViewer

• getModelForAtomIndex

  public Model getModelForAtomIndex(int iatom)

• getModelIndexForAtom

  public int getModelIndexForAtom(int iatom)

• getModelSetAuxiliaryInfo

  public Map<String,Object> getModelSetAuxiliaryInfo()

  Specified by:

  getModelSetAuxiliaryInfo in class JmolViewer

• getModelNumber

  public int getModelNumber(int modelIndex)

  Specified by:

  getModelNumber in class JmolViewer

• getModelFileNumber

  public int getModelFileNumber(int modelIndex)

• getModelNumberDotted

  public String getModelNumberDotted(int modelIndex)

  Specified by:

  getModelNumberDotted in class JmolViewer

• getModelName

  public String getModelName(int modelIndex)

  Specified by:

  getModelName in class JmolViewer

• modelHasVibrationVectors

  public boolean modelHasVibrationVectors(int modelIndex)

• getBondsForSelectedAtoms

  public BS getBondsForSelectedAtoms(BS bsAtoms)

• frankClicked

  public boolean frankClicked(int x, int y)

• frankClickedModelKit

  public boolean frankClickedModelKit(int x, int y)

• findNearestAtomIndex

  public int findNearestAtomIndex(int x, int y)

  Specified by:

  findNearestAtomIndex in class JmolViewer

• findNearestAtomIndexMovable

  public int findNearestAtomIndexMovable(int x, int y, boolean mustBeMovable)

• toCartesian

  public void toCartesian(T3 pt, boolean ignoreOffset)

  absolute or relative to origin of UNITCELL {x y z}

  Parameters:

  pt -

  ignoreOffset -

• toCartesianUC

  public void toCartesianUC(SymmetryInterface unitCell, T3 pt, boolean ignoreOffset)

• toFractional

  public void toFractional(T3 pt, boolean ignoreOffset)

  Parameters:

  pt -

  ignoreOffset - set true for relative to {0 0 0}; otherwise relative to origin of UNITCELL {x y z}

• toFractionalUC

  public void toFractionalUC(SymmetryInterface unitCell, T3 pt, boolean ignoreOffset)

• toUnitCell

  public void toUnitCell(P3 pt, P3 offset)

  Returns the relative to origin without regard to offset created using the UNITCELL command. This method has limited use. Used in point3f % 1, where {0 0 0} % 1 gives {a b c}

  Parameters:

  pt - a Cartesian point

  offset - a lattice offset, or null to apply the current offset

• setCurrentCage

  public void setCurrentCage(String isosurfaceId)

• addUnitCellOffset

  public void addUnitCellOffset(P3 pt)

• setAtomData

  public void setAtomData(int type, String name, String coordinateData, boolean isDefault)

• setCenterSelected

  public void setCenterSelected()

  Specified by:

  setCenterSelected in class JmolViewer

• setBondTolerance

  public void setBondTolerance(float bondTolerance)

  Specified by:

  setBondTolerance in class JmolViewer

• setMinBondDistance

  public void setMinBondDistance(float minBondDistance)

  Specified by:

  setMinBondDistance in class JmolViewer

• getAtomsNearPt

  public BS getAtomsNearPt(float distance, P3 coord, BS bs)

• getBranchBitSet

  public BS getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)

  given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.

  Parameters:

  atomIndex -

  atomIndexNot -

  allowCyclic -

  Returns:

  bitset for this branch

• getElementsPresentBitSet

  public BS getElementsPresentBitSet(int modelIndex)

  Specified by:

  getElementsPresentBitSet in class JmolViewer

• getCifData

  public Map<String,Object> getCifData(int modelIndex)

• readCifData

  public Map<String,Object> readCifData(String fileName, String type)

• readCifData

  public Map<String,Object> readCifData(String fileName, Object rdrOrStringData, String type)

  Specified by:

  readCifData in interface AtomDataServer

• getStateCreator

  public JmolStateCreator getStateCreator()

• getWrappedStateScript

  public String getWrappedStateScript()

• getStateInfo

  public String getStateInfo()

  Specified by:

  getStateInfo in class JmolViewer

• getStateInfo3

  public String getStateInfo3(String type, int width, int height)

• getStructureState

  public String getStructureState()

• getCoordinateState

  public String getCoordinateState(BS bsSelected)

• setCurrentColorRange

  public void setCurrentColorRange(String label)

• setData

  public void setData(String key, Object[] data, int dataType, int matchField, int matchFieldColumnCount, int dataField, int dataFieldColumnCount)

  A general-purpose data storage method. Note that matchFieldCount and dataFieldCount should both be positive or both be negative.

  Parameters:

  key - a simple key name for the data, starting with "property_" if user-defined

  data - data[0] -- label data[1] -- string or float[] or float[][] or float[][][] data[2] -- selection bitset or int[] atomMap when field > 0 data[3] -- arrayDepth 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indidate that it is set by data type data[4] -- Boolean.TRUE == saveInState

  dataType - see JmolDataManager interface

  matchField - if positive, data must match atomNo in this column if 0, no match column

  matchFieldColumnCount - if positive, this number of characters in match column if 0, reference is to tokens, not characters

  dataField - if positive, column containing the data if 0, values are a simple list; clear the data if Integer.MAX_VALUE, values are a simple list; don't clear the data if Integer.MIN_VALUE, have one SINGLE data value for all selected atoms

  dataFieldColumnCount - if positive, this number of characters in data column if 0, reference is to tokens, not characters

• getDataObj

  public Object getDataObj(String key, BS bsSelected, int dataType)

  Retrieve a data object

  Parameters:

  key -

  bsSelected - selected atoms; for DATA_AF only

  dataType - see JmolDataManager interface

  Returns:

  data object data[0] -- label (same as key) data[1] -- string or float[] or float[][] or float[][][] data[2] -- selection bitset or int[] atomMap when field > 0 data[3] -- arrayDepth 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indicate that it is set by data type data[4] -- Boolean.TRUE == saveInState

• autoHbond

  public int autoHbond(BS bsFrom, BS bsTo, boolean onlyIfHaveCalculated)

• getDefaultMeasurementLabel

  public String getDefaultMeasurementLabel(int nPoints)

• getMeasurementCount

  public int getMeasurementCount()

  Specified by:

  getMeasurementCount in class JmolViewer

• getMeasurementStringValue

  public String getMeasurementStringValue(int i)

  Specified by:

  getMeasurementStringValue in class JmolViewer

• getMeasurementInfoAsString

  public String getMeasurementInfoAsString()

• getMeasurementCountPlusIndices

  public int[] getMeasurementCountPlusIndices(int i)

  Specified by:

  getMeasurementCountPlusIndices in class JmolViewer

• getPendingMeasurement

  public MeasurementPending getPendingMeasurement()

• clearAllMeasurements

  public void clearAllMeasurements()

• clearMeasurements

  public void clearMeasurements()

  Specified by:

  clearMeasurements in class JmolViewer

• setAnimation

  public void setAnimation(int tok)

• setAnimationFps

  public void setAnimationFps(int fps)

  Specified by:

  setAnimationFps in class JmolViewer

• setAnimationOn

  public void setAnimationOn(boolean animationOn)

• setAnimationRange

  public void setAnimationRange(int modelIndex1, int modelIndex2)

• defineAtomSets

  public void defineAtomSets(Map<String,Object> info)

• setAnimDisplay

  public void setAnimDisplay(BS bs)

• setCurrentModelIndex

  public void setCurrentModelIndex(int modelIndex)

• getTrajectoryState

  public String getTrajectoryState()

• setFrameOffsets

  public void setFrameOffsets(BS bsAtoms, boolean isFull)

• setCurrentModelIndexClear

  public void setCurrentModelIndexClear(int modelIndex, boolean clearBackground)

• haveFileSet

  public boolean haveFileSet()

• setBackgroundModelIndex

  public void setBackgroundModelIndex(int modelIndex)

• getInMotion

  public boolean getInMotion(boolean includeAnim)

• getMotionEventNumber

  public int getMotionEventNumber()

  Specified by:

  getMotionEventNumber in class JmolViewer

• setInMotion

  public void setInMotion(boolean inMotion)

  Specified by:

  setInMotion in class JmolViewer

• getRefreshing

  public boolean getRefreshing()

• pushHoldRepaint

  public void pushHoldRepaint()

  Specified by:

  pushHoldRepaint in class JmolViewer

• pushHoldRepaintWhy

  public void pushHoldRepaintWhy(String why)

  Parameters:

  why -

• popHoldRepaint

  public void popHoldRepaint(String why)

  Specified by:

  popHoldRepaint in class JmolViewer

• refresh

  public void refresh(int mode, String strWhy)

  initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering. The repaint/update sequence will only be invoked if (a) no repaint is already pending and (b) there is no hold flag set in repaintManager. Sequence is as follows: 1) RepaintManager.refresh() checks flags and then calls Viewer.repaint() 2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless) 3) The system responds with an invocation of Jmol.update(Graphics g), which we are routing through Jmol.paint(Graphics g). 4) Jmol.update invokes Viewer.setScreenDimensions(size), which makes the necessary changes in parameters for any new window size. 5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip) 6) Viewer.renderScreenImage checks object visibility, invokes render1 to do the actual creation of the image pixel map and send it to the screen, and then invokes repaintView() 7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and then use notify() to release any threads holding on wait().

  Specified by:

  refresh in class JmolViewer

  Parameters:

  mode - REFRESH_REPAINT: ONLY do a repaint -- no syncing REFRESH_SYNC: mouse motion requiring synchronization -- not going through Eval so we bypass Eval and mainline on the other vwr! Also called from j2sApplet.js REFRESH_REPAINT_SYNC_MASK: same as REFRESH_REPAINT, but not WebGL REFRESH_NO_MOTION_ONLY: refresh only if not in motion REFRESH_SEND_WEBGL_NEW_ORIENTATION: send WebGL a "new orientation" command at the end of a script using html5applet._refresh()

  strWhy - debugging or for passing mouse command when using REFRESH_SYNC

• requestRepaintAndWait

  public void requestRepaintAndWait(String why)

• clearShapeRenderers

  public void clearShapeRenderers()

• isRepaintPending

  public boolean isRepaintPending()

• notifyViewerRepaintDone

  public void notifyViewerRepaintDone()

  Specified by:

  notifyViewerRepaintDone in class JmolViewer

• areAxesTainted

  public boolean areAxesTainted()

• generateOutputForExport

  public String generateOutputForExport(Map<String,Object> params)

  Description copied from class: JmolViewer

  for POV-Ray

  Specified by:

  generateOutputForExport in class JmolViewer

  Parameters:

  params -

  Returns:

  INI file

• renderScreenImage

  public void renderScreenImage(Object g, int width, int height)

  JmolViewer interface uses this, but that is all

  Specified by:

  renderScreenImage in class JmolViewer

• renderScreenImageStereo

  public void renderScreenImageStereo(Object gLeft, boolean checkStereoSlave, int width, int height)

• isCapturing

  public boolean isCapturing()

• doCapture

  public void doCapture()

• updateJS

  public void updateJS()

  for JavaScript only

• evalFile

  public String evalFile(String strFilename)

  Specified by:

  evalFile in class JmolViewer

• evalFileArgs

  public String evalFileArgs(String strFilename, String args)

  Specified by:

  evalFileArgs in class JmolViewer

• getInsertedCommand

  public String getInsertedCommand()

• script

  public String script(String strScript)

  Specified by:

  script in class JmolViewer

• evalString

  public String evalString(String strScript)

  Specified by:

  evalString in class JmolViewer

• evalStringQuiet

  public String evalStringQuiet(String strScript)

  Specified by:

  evalStringQuiet in class JmolViewer

• evalStringQuietSync

  public String evalStringQuietSync(String strScript, boolean isQuiet, boolean allowSyncScript)

• clearScriptQueue

  public void clearScriptQueue()

• checkHalt

  public boolean checkHalt(String str, boolean isInsert)

  Specified by:

  checkHalt in class JmolViewer

• scriptWait

  public String scriptWait(String strScript)

  Specified by:

  scriptWait in class JmolViewer

• scriptWaitStatus

  public Object scriptWaitStatus(String strScript, String statusList)

  Specified by:

  scriptWaitStatus in class JmolViewer

• exitJmol

  public void exitJmol()

• scriptCheck

  public Object scriptCheck(String strScript)

  Specified by:

  scriptCheck in class JmolViewer

• isScriptExecuting

  public boolean isScriptExecuting()

  Specified by:

  isScriptExecuting in class JmolViewer

• haltScriptExecution

  public void haltScriptExecution()

  Specified by:

  haltScriptExecution in class JmolViewer

• pauseScriptExecution

  public void pauseScriptExecution()

• hasDatabasePrefix

  public static boolean hasDatabasePrefix(String fileName)

• isDatabaseCode

  public static boolean isDatabaseCode(char ch)

• setLoadFormat

  public Object setLoadFormat(boolean isSurface, String name, char type, boolean withPrefix)

  Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first. Starting with Jmol 13.1.13, we allow a generalized search using =xxx= where xxx is a known or user-specified database designation.

  Parameters:

  isSurface - TODO

  name -

  type - a character to distinguish the type of file, '?' means we are just doing an isosurface check

  withPrefix -

  Returns:

  String or String[]

• getStandardLabelFormat

  public String getStandardLabelFormat(int type)

• getAdditionalHydrogens

  public P3[] getAdditionalHydrogens(BS bsAtoms, Lst<Atom> vConnections, int flags)

• setMarBond

  public void setMarBond(short marBond)

  Specified by:

  setMarBond in class JmolViewer

• setHoverLabel

  public void setHoverLabel(String strLabel)

• showHover

  public boolean showHover()

• isModelkitPickingRotateBond

  public boolean isModelkitPickingRotateBond()

• hoverOnPt

  public void hoverOnPt(int x, int y, String text, String id, T3 pt)

  Hover over an arbitrary point.

  Parameters:

  x -

  y -

  text -

  id - optional id to set _objecthovered to

  pt - optional pt to set "hovered" to

• setDebugScript

  public void setDebugScript(boolean debugScript)

  Specified by:

  setDebugScript in class JmolViewer

• setCursor

  public void setCursor(int cursor)

• setPickingMode

  public void setPickingMode(String strMode, int pickingMode)

• getPickingMode

  public int getPickingMode()

• getDrawHover

  public boolean getDrawHover()

• getAtomInfo

  public String getAtomInfo(int atomOrPointIndex)

• setJmolCallbackListener

  public void setJmolCallbackListener(JmolCallbackListener listener)

  Specified by:

  setJmolCallbackListener in class JmolViewer

• setJmolStatusListener

  public void setJmolStatusListener(JmolStatusListener listener)

  Specified by:

  setJmolStatusListener in class JmolViewer

• getStatusChanged

  public Lst<Lst<Lst<Object>>> getStatusChanged(String statusNameList)

• menuEnabled

  public boolean menuEnabled()

• setStatusDragDropped

  public boolean setStatusDragDropped(int mode, int x, int y, String fileName, String[] retType)

  Allows a handler to set Jmol variable doDrop=false to cancel and also set the file type directly (Java) via the Jmol variable dropFileType (Java or JavaScript) if desired.

  Parameters:

  mode -

  x -

  y -

  fileName -

  retType -

  Returns:

  true if we should still handle this.

• setStatusResized

  public void setStatusResized(int width, int height)

  resizeCallback is called whenever the applet gets a resize notification from the browser jmolSetCallback("resizeCallback", "myResizeCallback") function myResizeCallback(width, height) {}

  Parameters:

  width -

  height -

• scriptStatus

  public void scriptStatus(String strStatus)

  scriptCallback is the primary way to monitor script status. In addition, it serves to for passing information to the user over the status line of the browser as well as to the console. Note that console messages are also sent by echoCallback. If messageCallback is enabled but not scriptCallback, these messages go to the messageCallback function instead. jmolSetCallback("scriptCallback", "myScriptCallback") function myScriptCallback(app, status, message, intStatus, errorMessageUntranslated) {} intStatus == -2 script start -- message is the script itself intStatus == 0 general messages during script execution; translated error message may be present intStatus >= 1 script termination message; translated and untranslated message may be present value is time for execution in milliseconds Eval.defineAtomSet -- compilation bug indicates problem in JmolConstants array Eval.instructionDispatchLoop -- debugScript messages Eval.logDebugScript -- debugScript messages Eval.pause -- script execution paused message Eval.runEval -- "Script completed" message Eval.script -- Chime "script " message Eval.scriptStatusOrBuffer -- various messages for Eval.checkContinue (error message) Eval.connect Eval.delete Eval.hbond Eval.load (logMessages message) Eval.message Eval.runEval (error message) Eval.write (error reading file) Eval.zap (error message) FileManager.createAtomSetCollectionFromFile "requesting..." for Chime-like compatibility actionManager.atomPicked "pick one more atom in order to spin..." for example Viewer.evalStringWaitStatus -- see above -2, 0 only if error, >=1 at termination Viewer.reportSelection "xxx atoms selected"

  Parameters:

  strStatus -

• scriptStatusMsg

  public void scriptStatusMsg(String strStatus, String statusMessage)

• setScriptStatus

  public void setScriptStatus(String strStatus, String statusMessage, int msWalltime, String strErrorMessageUntranslated)

• showUrl

  public void showUrl(String urlString)

  syncCallback traps script synchronization messages and allows for cancellation (by returning "") or modification jmolSetCallback("syncCallback", "mySyncCallback") function mySyncCallback(app, script, appletName) { ...[modify script here]... return newScript } StatusManager.syncSend Viewer.setSyncTarget Viewer.syncScript

  Specified by:

  showUrl in class JmolViewer

• setMeshCreator

  public void setMeshCreator(Object meshCreator)

  an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.

  Parameters:

  meshCreator -

• showConsole

  public void showConsole(boolean showConsole)

• getConsole

  public JmolAppConsoleInterface getConsole()

• getParameter

  public Object getParameter(String key)

  Specified by:

  getParameter in class JmolViewer

• getP

  public Object getP(String key)

• getPOrNull

  public Object getPOrNull(String key)

• unsetProperty

  public void unsetProperty(String key)

• notifyStatusReady

  public void notifyStatusReady(boolean isReady)

  Specified by:

  notifyStatusReady in class JmolViewer

• getBooleanProperty

  public boolean getBooleanProperty(String key)

  Specified by:

  getBooleanProperty in class JmolViewer

• getInt

  public int getInt(int tok)

  Specified by:

  getInt in class JmolViewer

• getDelayMaximumMs

  public int getDelayMaximumMs()

• getHermiteLevel

  public int getHermiteLevel()

• getHoverDelay

  public int getHoverDelay()

• getBoolean

  public boolean getBoolean(int tok)

  Specified by:

  getBoolean in class JmolViewer

• allowEmbeddedScripts

  public boolean allowEmbeddedScripts()

• useMinimizationThread

  public boolean useMinimizationThread()

• getFloat

  public float getFloat(int tok)

  Specified by:

  getFloat in class JmolViewer

• setStringProperty

  public void setStringProperty(String key, String value)

  Specified by:

  setStringProperty in class JmolViewer

• setFloatProperty

  public void setFloatProperty(String key, float value)

  Specified by:

  setFloatProperty in class JmolViewer

• setIntProperty

  public void setIntProperty(String key, int value)

  Specified by:

  setIntProperty in class JmolViewer

• setIntPropertyTok

  public void setIntPropertyTok(String key, int tok, int value)

• setBooleanProperty

  public void setBooleanProperty(String key, boolean value)

  Specified by:

  setBooleanProperty in class JmolViewer

• setBooleanPropertyTok

  public void setBooleanPropertyTok(String key, int tok, boolean value)

• setSmilesString

  public void setSmilesString(String s)

• removeUserVariable

  public void removeUserVariable(String key)

• showParameter

  public void showParameter(String key, boolean ifNotSet, int nMax)

• showString

  public void showString(String str, boolean isPrint)

• getAllSettings

  public String getAllSettings(String prefix)

• getBindingInfo

  public String getBindingInfo(String qualifiers)

• getIsosurfacePropertySmoothing

  public int getIsosurfacePropertySmoothing(boolean asPower)

• setNavigationDepthPercent

  public void setNavigationDepthPercent(float percent)

• getShowNavigationPoint

  public boolean getShowNavigationPoint()

• setPerspectiveDepth

  public void setPerspectiveDepth(boolean perspectiveDepth)

  Specified by:

  setPerspectiveDepth in class JmolViewer

• setAxesOrientationRasmol

  public void setAxesOrientationRasmol(boolean TF)

  Specified by:

  setAxesOrientationRasmol in class JmolViewer

• getSelectionHalosEnabled

  public boolean getSelectionHalosEnabled()

• setSelectionHalosEnabled

  public void setSelectionHalosEnabled(boolean TF)

• getShowSelectedOnce

  public boolean getShowSelectedOnce()

• getStrandCount

  public int getStrandCount(int type)

• setNavigationMode

  public void setNavigationMode(boolean TF)

• setAutoBond

  public void setAutoBond(boolean TF)

  Specified by:

  setAutoBond in class JmolViewer

• makeConnections

  public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy)

• rebond

  public void rebond()

  Specified by:

  rebond in class JmolViewer

• rebondState

  public void rebondState(boolean isStateScript)

• setPercentVdwAtom

  public void setPercentVdwAtom(int value)

  Specified by:

  setPercentVdwAtom in class JmolViewer

• getMadBond

  public short getMadBond()

  Specified by:

  getMadBond in class JmolViewer

• setShowHydrogens

  public void setShowHydrogens(boolean TF)

  Specified by:

  setShowHydrogens in class JmolViewer

• setShowBbcage

  public void setShowBbcage(boolean value)

• getShowBbcage

  public boolean getShowBbcage()

• setShowUnitCell

  public void setShowUnitCell(boolean value)

• getShowUnitCell

  public boolean getShowUnitCell()

• setShowAxes

  public void setShowAxes(boolean value)

• getShowAxes

  public boolean getShowAxes()

• setFrankOn

  public void setFrankOn(boolean TF)

  Specified by:

  setFrankOn in class JmolViewer

• getShowFrank

  public boolean getShowFrank()

• setShowMeasurements

  public void setShowMeasurements(boolean TF)

  Specified by:

  setShowMeasurements in class JmolViewer

• setUnits

  public void setUnits(String units, boolean isDistance)

• setRasmolDefaults

  public void setRasmolDefaults()

  Specified by:

  setRasmolDefaults in class JmolViewer

• setJmolDefaults

  public void setJmolDefaults()

  Specified by:

  setJmolDefaults in class JmolViewer

• allocTempPoints

  public P3[] allocTempPoints(int size)

• freeTempPoints

  public void freeTempPoints(P3[] tempPoints)

• allocTempScreens

  public P3i[] allocTempScreens(int size)

• freeTempScreens

  public void freeTempScreens(P3i[] tempScreens)

• allocTempEnum

  public STR[] allocTempEnum(int size)

• freeTempEnum

  public void freeTempEnum(STR[] temp)

• getFont3D

  public Font getFont3D(String fontFace, String fontStyle, float fontSize)

• getAtomGroupQuaternions

  public Quat[] getAtomGroupQuaternions(BS bsAtoms, int nMax)

• setStereoMode

  public void setStereoMode(int[] twoColors, STER stereoMode, float degrees)

• getChimeInfo

  public String getChimeInfo(int tok)

• getModelFileInfo

  public String getModelFileInfo()

• getModelFileInfoAll

  public String getModelFileInfoAll()

• showEditor

  public void showEditor(String[] file_text)

• setTainted

  public void setTainted(boolean TF)

• checkObjectHovered

  public boolean checkObjectHovered(int x, int y)

• rotateAxisAngleAtCenter

  public boolean rotateAxisAngleAtCenter(JmolScriptEvaluator eval, P3 rotCenter, V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected)

• rotateAboutPointsInternal

  public boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, Lst<P3> finalPoints, float[] dihedralList, M3 vectorMatrix, M4 m4, boolean useModelKit, P3[][] centerAndPoints)

• startSpinningAxis

  public void startSpinningAxis(T3 pt1, T3 pt2, boolean isClockwise)

• getModelDipole

  public V3 getModelDipole()

• calculateMolecularDipole

  public V3 calculateMolecularDipole(BS bsAtoms) throws Exception

  Parameters:

  bsAtoms -

  Returns:

  dipole vector

  Throws:

  Exception

• setDefaultLattice

  public void setDefaultLattice(P3 p)

• getDefaultLattice

  public P3 getDefaultLattice()

• getModelExtract

  public String getModelExtract(Object atomExpression, boolean doTransform, boolean isModelKit, String type)

  V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR

  Parameters:

  atomExpression -

  doTransform -

  isModelKit -

  type -

  Returns:

  full file data

• getData

  public String getData(String atomExpression, String type)

  Specified by:

  getData in class JmolViewer

• getModelFileData

  public String getModelFileData(String atomExpression, String type, boolean allTrajectories)

  Parameters:

  atomExpression - -- will be wrapped in { } and evaluated

  type - -- lower case means "atom data only; UPPERCASE returns full file data

  allTrajectories -

  Returns:

  full or atom-only data formatted as specified

• getModelCml

  public String getModelCml(BS bs, int nAtomsMax, boolean addBonds, boolean doTransform)

• getPdbAtomData

  public String getPdbAtomData(BS bs, OC out, boolean asPQR, boolean doTransform)

• isJmolDataFrame

  public boolean isJmolDataFrame()

• getJmolDataSourceFrame

  public int getJmolDataSourceFrame()

• getJmolDataFrameTypeInt

  public int getJmolDataFrameTypeInt()

• setFrameTitle

  public void setFrameTitle(int modelIndex, String title)

• setFrameTitleObj

  public void setFrameTitleObj(Object title)

• getFrameTitle

  public String getFrameTitle()

• setAtomProperty

  public void setAtomProperty(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)

• checkCoordinatesChanged

  public void checkCoordinatesChanged(BS bsAtoms)

• setAtomCoords

  public void setAtomCoords(BS bs, int tokType, Object xyzValues)

• setAtomCoordsRelative

  public void setAtomCoordsRelative(T3 offset, BS bs)

• invertAtomCoord

  public void invertAtomCoord(P3 pt, P4 plane, BS bs, int ringAtomIndex, boolean isClick)

• invertSelected

  public void invertSelected(P3 pt, P4 plane, int iAtom, BS bsAtoms)

• moveAtoms

  public void moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation, P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly, boolean useModelKit)

• warnAtom

  public void warnAtom(int iatom)

• highlightBond

  public void highlightBond(int index, int closestAtomIndex, int x, int y)

  from Sticks

  Parameters:

  index -

  closestAtomIndex - ignored

  x -

  y -

• highlight

  public void highlight(BS bs)

• refreshMeasures

  public void refreshMeasures(boolean andStopMinimization)

• functionXY

  public float[][] functionXY(String functionName, int nX, int nY)

  fills an array with data -- if nX invalid input: '<' 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call. Otherwise it reads the values using individual function calls, which each return Double. If the functionName begins with "file:" then data are read from a file specified after the colon. The sign of nX is not relevant in that case. The file may contain mixed numeric and non-numeric values; the non-numeric values will be skipped by Parser.parseFloatArray

  Parameters:

  functionName -

  nX -

  nY -

  Returns:

  nX by nY array of floating values

• functionXYZ

  public float[][][] functionXYZ(String functionName, int nX, int nY, int nZ)

• extractMolData

  public String extractMolData(String what)

  Specified by:

  extractMolData in class JmolViewer

• getNMRPredict

  public String getNMRPredict(String type)

  Parameters:

  type - C13 or H1

  Returns:

  null

• getHelp

  public void getHelp(String what)

• getChemicalInfo

  public String getChemicalInfo(String smiles, String info, BS bsAtoms)

• addCommand

  public void addCommand(String command)

  Adds one or more commands to the command history

  Parameters:

  command - the command to add

• pushState

  public void pushState()

• popState

  public void popState()

• removeCommand

  public String removeCommand()

  Removes one command from the command history

  Returns:

  command removed

• getSetHistory

  public String getSetHistory(int howFarBack)

  Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n invalid input: '<'= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;

  Specified by:

  getSetHistory in class JmolViewer

  Parameters:

  howFarBack - number of lines (-1 for next line)

  Returns:

  one or more lines of command history

• historyFind

  public String historyFind(String cmd, int dir)

• setHistory

  public void setHistory(String fileName)

• getOutputChannel

  public OC getOutputChannel(String localName, String[] fullPath)

• writeTextFile

  public String writeTextFile(String fileName, String data)

  Specified by:

  writeTextFile in class JmolViewer

• writeFile

  public String writeFile(String fileName, Object data, String type)

• clipImageOrPasteText

  public String clipImageOrPasteText(String text)

  Specified by:

  clipImageOrPasteText in class JmolViewer

  Parameters:

  text - null here clips image; String pastes text

  Returns:

  "OK image to clipboard: [width] * [height] or "OK text to clipboard: [length]

• getClipboardText

  public String getClipboardText()

  Specified by:

  getClipboardText in class JmolViewer

• processWriteOrCapture

  public String processWriteOrCapture(Map<String,Object> params)

  from eval write command only includes option to write set of files

  Parameters:

  params -

  Returns:

  message starting with "OK" or an error message

• createZip

  public Object createZip(String fileName, String type, Map<String,Object> params)

• outputToFile

  public String outputToFile(Map<String,Object> params)

  Specified by:

  outputToFile in class JmolViewer

  Parameters:

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

  Returns:

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

• syncScript

  public void syncScript(String script, String applet, int port)

  Specified by:

  syncScript in class JmolViewer

• getModelIndexFromId

  public int getModelIndexFromId(String id)

  Specified by:

  getModelIndexFromId in class JmolViewer

  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

• setSyncDriver

  public void setSyncDriver(int mode)

• setProteinType

  public void setProteinType(STR type, BS bs)

• getVanderwaalsMar

  public int getVanderwaalsMar(int i)

• getVanderwaalsMarType

  public int getVanderwaalsMarType(int atomicAndIsotopeNumber, VDW type)

• getDefaultVdwNameOrData

  public String getDefaultVdwNameOrData(int mode, VDW type, BS bs)

• deleteAtoms

  public int deleteAtoms(BS bsAtoms, boolean fullModels)

• deleteModels

  public int deleteModels(int modelIndex, BS bsAtoms)

  called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1

  Parameters:

  modelIndex -

  bsAtoms -

  Returns:

  number of atoms deleted

• deleteBonds

  public void deleteBonds(BS bsDeleted)

• deleteModelAtoms

  public void deleteModelAtoms(int modelIndex, int firstAtomIndex, int nAtoms, BS bsModelAtoms)

• getQuaternionFrame

  public char getQuaternionFrame()

• loadImageData

  public boolean loadImageData(Object image, String nameOrError, String echoName, Object sco)

  NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage

  Parameters:

  image - could be a byte array

  nameOrError -

  echoName - if this is an echo rather than the background

  sco - delivered in JavaScript from Platform.java

  Returns:

  false

• cd

  public String cd(String dir)

• setErrorMessage

  public String setErrorMessage(String errMsg, String errMsgUntranslated)

• getErrorMessage

  public String getErrorMessage()

  Specified by:

  getErrorMessage in class JmolViewer

• getErrorMessageUn

  public String getErrorMessageUn()

  Specified by:

  getErrorMessageUn in class JmolViewer

• setShapeErrorState

  public void setShapeErrorState(int shapeID, String state)

• getShapeErrorState

  public String getShapeErrorState()

• handleError

  public void handleError(Throwable er, boolean doClear)

• getFunctions

  public Map<String, JmolScriptFunction> getFunctions(boolean isStatic)

• removeFunction

  public void removeFunction(String name)

• getFunction

  public JmolScriptFunction getFunction(String name)

• isFunction

  public boolean isFunction(String name)

• clearFunctions

  public void clearFunctions()

• addFunction

  public void addFunction(JmolScriptFunction function)

• getFunctionCalls

  public String getFunctionCalls(String selectedFunction)

• checkPrivateKey

  public boolean checkPrivateKey(double privateKey)

  Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet. When the image creator is used it requires both a vwr object and that vwr's private key. But the private key is private, so it is not possible to create a useable image creator without working through a vwr's own methods. Bob Hanson, 9/20/2009

  Parameters:

  privateKey -

  Returns:

  true if privateKey matches

• bindAction

  public void bindAction(String desc, String name)

• unBindAction

  public void unBindAction(String desc, String name)

• calculateStruts

  public int calculateStruts(BS bs1, BS bs2)

• getPreserveState

  public boolean getPreserveState()

  This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.

  Returns:

  TRUE or FALSE

• hasFocus

  public boolean hasFocus()

• setFocus

  public void setFocus()

• getMinimizationInfo

  public String getMinimizationInfo()

• minimize

  public void minimize(JmolScriptEvaluator eval, int steps, float crit, BS bsSelected, BS bsFixed, BS bsInFrame, float rangeFixed, int flags) throws Exception

  From the MINIMIZE command and other sources.

  Parameters:

  eval -

  steps - Integer.MAX_VALUE --> use defaults

  crit - -1 --> use defaults

  bsSelected -

  bsFixed -

  bsInFrame -

  rangeFixed -

  flags -

  Throws:

  Exception

• setMotionFixedAtoms

  public void setMotionFixedAtoms(BS bs)

• setMotionFixed

  public void setMotionFixed(BS bs)

• getMotionFixedAtoms

  public BS getMotionFixedAtoms(SymmetryInterface sym, BS bsFixed)

  For the current SINGLE model only.

  Parameters:

  sym - operationalSymmetry

  bsFixed - optional starting BitSet to be added to

  Returns:

  bsFixed

• getCenterAndPoints

  public P3[][] getCenterAndPoints(Lst<Object[]> atomSets, boolean addCenter)

• writeFileData

  public String writeFileData(String fileName, String type, int modelIndex, Object[] parameters)

• getPdbData

  public String getPdbData(int modelIndex, String type, BS bsAtoms, Object[] parameters, OC oc, boolean getStructure)

• getGroupsWithin

  public BS getGroupsWithin(int nResidues, BS bs)

• setShapeSize

  public void setShapeSize(int shapeID, int madOrMad10, BS bsSelected)

  Parameters:

  shapeID -

  madOrMad10 - for axes, unitcell, and boundbox 10*mad; otherwise milliangstrom diameter

  bsSelected -

• setShapeProperty

  public void setShapeProperty(int shapeID, String propertyName, Object value)

• getShapeProperty

  public Object getShapeProperty(int shapeType, String propertyName)

• setModelVisibility

  public void setModelVisibility()

• resetShapes

  public void resetShapes(boolean andCreateNew)

• setParallel

  public boolean setParallel(boolean TF)

• isParallel

  public boolean isParallel()

• undoMoveAction

  public int undoMoveAction(int action, int n)

  Parameters:

  action - Token.undo or Token.redo

  n - number of steps to go back/forward; 0 for all; -1 for clear; -2 for clear BOTH

  Returns:

  stack list count for action = T.count, or 0

• undoMoveActionClear

  public void undoMoveActionClear(int taintedAtom, int type, boolean clearRedo)

• moveAtomWithHydrogens

  public int moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, P3 ptNew, BS bsAtoms)

• isModelPDB

  public boolean isModelPDB(int i)

• deleteMeasurement

  public void deleteMeasurement(int i)

  Specified by:

  deleteMeasurement in class JmolViewer

• getSmiles

  public String getSmiles(BS bs) throws Exception

  NOT getting aromatic smiles

  Specified by:

  getSmiles in class JmolViewer

  Throws:

  Exception

• getOpenSmiles

  public String getOpenSmiles(BS bs) throws Exception

  Specified by:

  getOpenSmiles in class JmolViewer

  Throws:

  Exception

• getBioSmiles

  public String getBioSmiles(BS bs) throws Exception

  Throws:

  Exception

• getSmilesOpt

  public String getSmilesOpt(BS bsSelected, int index1, int index2, int flags, String options) throws Exception

  returns the SMILES string for a sequence or atom set does not include attached protons on groups

  Parameters:

  bsSelected - selected atom set or null for current or specified range

  index1 - when bsSeleced == null, first atomIndex or -1 for current

  index2 - when bsSeleced == null, end atomIndex or -1 for current

  flags - see JC.SMILES_xxxx

  options - e.g. /strict,open/

  Returns:

  SMILES string

  Throws:

  Exception

• alert

  public void alert(String msg)

• prompt

  public String prompt(String label, String data, String[] list, boolean asButtons)

• dialogAsk

  public String dialogAsk(String type, String fileName, Map<String,Object> params)

  Ask for new file name when saving or opening a file in Java and saving a file in JavaScript. JavaScript use of FileReader goes through loadFileAsync

  Parameters:

  type -

  fileName -

  params -

  Returns:

  new file name

• initializeExporter

  public JmolRendererInterface initializeExporter(Map<String,Object> params)

• getMouseEnabled

  public boolean getMouseEnabled()

• calcAtomsMinMax

  public void calcAtomsMinMax(BS bs, BoxInfo boxInfo)

  Specified by:

  calcAtomsMinMax in class JmolViewer

• getObjectMap

  public void getObjectMap(Map<String,?> map, char c)

  used in autocompletion in console using TAB

  Parameters:

  map -

  c -

• setPicked

  public void setPicked(int atomIndex, boolean andReset)

• runScript

  public String runScript(String script)

  Run a script immediately using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )

  Specified by:

  runScript in class JmolViewer

  Parameters:

  script -

  Returns:

  string from ScriptEvaluator#outputBuffer

• runScriptCautiously

  public String runScriptCautiously(String script)

  formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script. If it is invoked by a separate thread, it can wreak havoc on any queued thread, since they are not thread safe.

  Overrides:

  runScriptCautiously in class JmolViewer

  Parameters:

  script -

  Returns:

  output of the script.

• setFrameDelayMs

  public void setFrameDelayMs(long millis)

• getBaseModelBitSet

  public BS getBaseModelBitSet()

• clearTimeouts

  public void clearTimeouts()

• setTimeout

  public void setTimeout(String name, int mSec, String script)

• triggerTimeout

  public void triggerTimeout(String name)

• clearTimeout

  public void clearTimeout(String name)

• showTimeout

  public String showTimeout(String name)

• getOrCalcPartialCharges

  public float[] getOrCalcPartialCharges(BS bsSelected, BS bsIgnore) throws JmolAsyncException

  Throws:

  JmolAsyncException

• calculatePartialCharges

  public void calculatePartialCharges(BS bsSelected) throws JmolAsyncException

  Throws:

  JmolAsyncException

• setCurrentModelID

  public void setCurrentModelID(String id)

• cacheClear

  public void cacheClear()

• cachePut

  public void cachePut(String key, Object data)

  JSInterface -- allows saving files in memory for later retrieval

  Parameters:

  key -

  data -

• cacheFileByName

  public int cacheFileByName(String fileName, boolean isAdd)

• clearThreads

  public void clearThreads()

• getEvalContextAndHoldQueue

  public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator eval)

• getDefaultPropertyParam

  public String getDefaultPropertyParam(int propertyID)

• getPropertyNumber

  public int getPropertyNumber(String name)

• checkPropertyParameter

  public boolean checkPropertyParameter(String name)

• extractProperty

  public Object extractProperty(Object property, Object args, int pt)

• addHydrogens

  public BS addHydrogens(BS bsAtoms, int flags)

  / requiring ScriptEvaluator:

• addHydrogensInline

  public BS addHydrogensInline(BS bsAtoms, Lst<Atom> vConnections, P3[] pts, Map<String,Object> htParams) throws Exception

  Throws:

  Exception

• evalFunctionFloat

  public float evalFunctionFloat(Object func, Object params, float[] values)

  Specified by:

  evalFunctionFloat in interface AtomDataServer

• evalParallel

  public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)

• evaluateExpression

  public Object evaluateExpression(Object stringOrTokens)

  synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable

  Specified by:

  evaluateExpression in class JmolViewer

  Parameters:

  stringOrTokens -

  Returns:

  a String representation of the evaluated expression

• evaluateExpressionAsVariable

  public SV evaluateExpressionAsVariable(Object stringOrTokens)

  Specified by:

  evaluateExpressionAsVariable in class JmolViewer

  Parameters:

  stringOrTokens -

  Returns:

  a String representation of the evaluated expression as a script variable (org.jmol.script.SV)

• getAtomBitSet

  public BS getAtomBitSet(Object atomExpression)

• getScriptContext

  public ScriptContext getScriptContext(String why)

• getAtomDefs

  public String getAtomDefs(Map<String,Object> names)

• setCGO

  public void setCGO(Map<String,Object> map)

• setModelSet

  public void setModelSet(ModelSet modelSet)

• setObjectProp

  public String setObjectProp(String id, int tokCommand)

• setDihedrals

  public void setDihedrals(float[] dihedralList, BS[] bsBranches, float rate)

• getChainID

  public int getChainID(String id, boolean isAssign)

  Create a unique integer for any chain string. Note that if there are any chains that are more than a single character, chainCaseSensitive is automatically set TRUE

  Parameters:

  id - invalid input: '<' 256 is just the character of a single-character upper-case chain id, upper or lower case query; >= 256 invalid input: '<' 300 is lower case found in structure

  isAssign - from a file reader, not a select query

  Returns:

  i

• getChainIDStr

  public String getChainIDStr(int id)

• getScriptQueueInfo

  public Boolean getScriptQueueInfo()

• getNMRCalculation

  public JmolNMRInterface getNMRCalculation()

• getDistanceUnits

  public String getDistanceUnits(String s)

• calculateFormalCharges

  public int calculateFormalCharges(BS bs)

• setModulation

  public void setModulation(BS bs, boolean isOn, P3 t1, boolean isQ)

• checkInMotion

  public void checkInMotion(int state)

• checkMotionRendering

  public boolean checkMotionRendering(int tok)

  check motion for rendering during mouse movement, spin, vibration, and animation

  Parameters:

  tok -

  Returns:

  TRUE if allowed

• openExportChannel

  public OC openExportChannel(double privateKey, String fileName, boolean asWriter) throws IOException

  Throws:

  IOException

• log

  public void log(String data)

  Specified by:

  log in interface AtomDataServer

• getLogFileName

  public String getLogFileName()

• getCommands

  public String getCommands(Map<String,BS> htDefine, Map<String,BS> htMore, String select)

• allowCapture

  public boolean allowCapture()

• compileExpr

  public T[] compileExpr(String expr)

• checkSelect

  public boolean checkSelect(Map<String,SV> h, T[] value)

• getAnnotationInfo

  public String getAnnotationInfo(SV d, String match, int type)

• getAtomValidation

  public Lst<Float> getAtomValidation(String type, Atom atom)

• getJBR

  public BioResolver getJBR()

• checkMenuUpdate

  public void checkMenuUpdate()

• getChimeMessenger

  public JmolChimeMessenger getChimeMessenger()

• getModelSetAuxiliaryInfoForAtoms

  public Map<String,Object> getModelSetAuxiliaryInfoForAtoms(Object atomExpression)

• parseJSON

  public Object parseJSON(String str)

• parseJSONMap

  public Map<String,Object> parseJSONMap(String jsonMap)

• parseJSONArray

  public Lst<Object> parseJSONArray(String jsonArray)

• getSymTemp

  public SymmetryInterface getSymTemp()

  Retrieve a new Symmetry object.

  Returns:

  org.jmol.symmetry.Symmetry object

• getSymStatic

  public SymmetryInterface getSymStatic()

  Retrieve the static Symmetry object, which should be used only statically

  Returns:

  org.jmol.symmetry.Symmetry object

• setWindowDimensions

  public void setWindowDimensions(float[] dims)

• getTriangulator

  public Triangulator getTriangulator()

• getCurrentModelAuxInfo

  public Map<String,Object> getCurrentModelAuxInfo()

• startNBO

  public void startNBO(String options)

• startPlugin

  public void startPlugin(String plugin)

  startup -U nbo option

  Parameters:

  plugin -

• connectNBO

  public void connectNBO(String type)

• getNBOAtomLabel

  public String getNBOAtomLabel(Atom atom)

• calculateChirality

  public String calculateChirality(BS bsAtoms)

• getSubstructureSetArray

  public BS[] getSubstructureSetArray(Object pattern, BS bsSelected, int flags) throws Exception

  Throws:

  Exception

• getSubstructureSetArrayForNodes

  public BS[] getSubstructureSetArrayForNodes(Object pattern, Node[] nodes, int flags) throws Exception

  Throws:

  Exception

• getSmilesAtoms

  public Node[] getSmilesAtoms(String smiles) throws Exception

  Throws:

  Exception

• calculateChiralityForSmiles

  public String[] calculateChiralityForSmiles(String smiles)

• getPdbID

  public String getPdbID()

• getModelInfo

  public Object getModelInfo(String key)

  get a value from the current model's Model.auxiliaryInfo

  Parameters:

  key -

  Returns:

  value, or null if there is no SINGLE current model

• notifyScriptEditor

  public void notifyScriptEditor(int msWalltime, Object[] data)

• sendConsoleMessage

  public void sendConsoleMessage(String msg)

• getModelkitPropertySafely

  public Object getModelkitPropertySafely(String name)

  Get a ModelKit property, but only if the modelkit exists already.

  Parameters:

  name - if null returns Boolean.TRUE if modelkit is instantiated

  Returns:

  value

• setModelkitPropertySafely

  public Object setModelkitPropertySafely(String key, Object value)

  Set a ModelKit property, but only if the modelkit exists already.

  Parameters:

  key -

  value -

  Returns:

  varies, quite possibly null

• isModelKitOption

  public boolean isModelKitOption(char type, String value)

  Check for an option type 'M' 'S' 'U' 'B'.

  Parameters:

  type -

  value -

  Returns:

  true or false, but true only if the modelkit already exists

• getSymmetryInfo

  public Object getSymmetryInfo(int iatom, String xyz, int iOp, P3 translation, P3 pt1, P3 pt2, int type, String desc, float scaleFactor, int nth, int options, int[] opList)

  A general method for retrieving symmetry information with full capability of the symop() scripting function.

  Parameters:

  iatom - atom index specifying the model set and used for pt1 if that is null and also for matching element type.

  xyz - the desired Jones-Faithful representation of the symmetry operation or null

  iOp - the desired symmetry operation [1-n] or 0

  translation - [i j k] translational addition to symop

  pt1 - the starting point, or null if to use iatom or otherwise unnecessary

  pt2 - the target point, if this is a point-to-point determination, or the offset if not and options is nonzero

  type - a token type such as T.list or T.array

  desc - if type == T.nada (0), a name evaluating to a type, or one of the special names: "info", "description", "matrix", "axispoint", or "time" (as in time-reversal); otherwise, if type == T.draw, the root id given to a returned DRAW command set

  scaleFactor - if nonzero and type == T.draw, a scaling factor to be applied to the rotational vector

  nth - in the case of a point-to-point determination, the nth matching operator, or 0 for "all"

  options - if nonzero, a option, currently just T.offset, indicating that pt1 is an {i j k} offset from cell 555

  opList -

  Returns:

  string, Object[], or Lstinvalid input: '<'Object[]>

• getMacro

  public String getMacro(String key)

  retrieve macros.json from the directory

  Parameters:

  key -

  Returns:

  the macro path

• getConsoleFontScale

  public int getConsoleFontScale()

• setConsoleFontScale

  public void setConsoleFontScale(int scale)

• confirm

  public int confirm(String msg, String msgNo)

• evalStringGUI

  public void evalStringGUI(String script)

  Run a script asynchronously, adding the GUI flag to indicate that we should fire the SELECT callback at the end if there is one.

  Parameters:

  script -

• selectStatus

  public void selectStatus(BS bs, boolean isGroup, int addRemove, boolean isQuiet, boolean reportStatus)

  "SELECT" starting with comma triggers the SELECT callback from a SELECT command. GUI scripts also trigger this if a select command has been given and the last select command given did not start with comma.

  Parameters:

  bs -

  isGroup -

  addRemove -

  isQuiet -

  reportStatus -

• setStatusSelect

  public void setStatusSelect(BS bs)

  Make the SelectCallback call and reset the hasSelected value to false. This method is called by SELECT , ... or by a GUI script command completion or an atom selection using the mouse.

  Parameters:

  bs -

• wasmInchiHack

  public String wasmInchiHack(String cmd)

  WASM inchi must be initialized asynchronously

  Parameters:

  cmd -

  Returns:

  cmd

• getInchi

  public String getInchi(BS atoms, Object molData, String options)

  Get an InChI or InChIKey for a set of atoms or MOL data.

  Parameters:

  atoms -

  molData - null, or MOL data, or a database $ or : call, or SMILES, or "InChI=...." to retrieve the key or (Java Only) internal InChI structure as a string

  options -

  Returns:

  InChI or InChIKey

• findSpaceGroup

  public Object findSpaceGroup(SymmetryInterface sym, BS bsAtoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags)

  Parameters:

  sym -

  bsAtoms -

  xyzList - if present, a semicolon-separated list of operators

  unitCellParams -

  origin -

  oabc -

  flags - special flags

  Returns:

  either an array of space group identifiers or, if asString, "", or null

• restrictToModel

  public BS restrictToModel(BS bs, int mi)

  Restrict this bitset to the current model or its initial atom's model.

  Parameters:

  bs - or null for selected (or if none selected, then the current model)

  mi - >=0 for a specific model, -1 to restrict to current model if a single model or the first model of multiply displayed models

  Returns:

  restricted atom set

• getThisModelAtoms

  public BS getThisModelAtoms()

• getSymmetryEquivPoints

  public Lst<Point3fi> getSymmetryEquivPoints(Point3fi pt, String flags)

• getSymmetryEquivPointList

  public Lst<Point3fi> getSymmetryEquivPointList(Lst<Point3fi> pts, String flags)

• getOperativeSymmetry

  public SymmetryInterface getOperativeSymmetry()

  Only return symmetry that has operators.

  Returns:

  SymmetryInterface or null

• formatText

  public String formatText(String text0)

• getScaleText

  public String getScaleText(String units, boolean isAntialiased, float min, float[] ret)

  Depending upon the measure text, we need to indicate |-------| 1 A or 0.1 A for example.

  Parameters:

  units -

  isAntialiased -

  min -

  ret - return bar length in pixels

  Returns:

  text

• setStatusAtomMoved

  public void setStatusAtomMoved(boolean andCheckMinimize, BS bs)

• getFormulaForAtoms

  public String getFormulaForAtoms(BS bs, String type, boolean isEmpirical)

  Get formula -- MF or CELLFORMULA, possibly empirical

  Parameters:

  bs -

  type -

  isEmpirical -

  Returns:

  formula as H xx C xx X xx...

• evalCallback

  public void evalCallback(String cmd, Object[] params, boolean doWait)

• checkConsoleScript

  public boolean checkConsoleScript(String strScript)

• haveAccessInternal

  public final boolean haveAccessInternal(String path)

  Check for allowed access only to the designated path starting with this path. Restricts access to internal PNGJ files and disallows WRITE and JAVASCRIPT commands from within PNGJ files. Java only.

  Parameters:

  path -

  Returns:

  if path is not null, return true if access is allowed to this path; when path is null, return true if this access is internal only

• setAccessInternal

  public void setAccessInternal(String path)

  Set access to the specified path only; used for restricting file read/write access to only those files within the zip block of a PNGJ file Java only.

  Parameters:

  path -

• getItaNumberFor

  public int getItaNumberFor(String name)

• is2D

  public boolean is2D()

• getUnitCellCenter

  public P3 getUnitCellCenter()

• setUnitCellAtomIndex

  public void setUnitCellAtomIndex(int iAtom)

• getUnitCellAtomIndex

  public int getUnitCellAtomIndex()

• writeBinaryFile

  public String writeBinaryFile(String fname, byte[] bytes)

• rotateModelSpinVectors

  public void rotateModelSpinVectors(int modelIndex, M3 rot)

• rotateSpins

  public void rotateSpins(int deltaX, int deltaY)