Field Detail

• vwr

  Viewer vwr

• map

  private java.util.Map<java.lang.String,​java.lang.Integer> map

• atomExpression

  private static final java.lang.String atomExpression

  See Also:

  Constant Field Values

• propertyTypes

  private static final java.lang.String[] propertyTypes

• PROP_APPLET_INFO

  private static final int PROP_APPLET_INFO

  See Also:

  Constant Field Values

• PROP_FILENAME

  private static final int PROP_FILENAME

  See Also:

  Constant Field Values

• PROP_FILEHEADER

  private static final int PROP_FILEHEADER

  See Also:

  Constant Field Values

• PROP_FILECONTENTS_PATH

  private static final int PROP_FILECONTENTS_PATH

  See Also:

  Constant Field Values

• PROP_FILECONTENTS

  private static final int PROP_FILECONTENTS

  See Also:

  Constant Field Values

• PROP_ANIMATION_INFO

  private static final int PROP_ANIMATION_INFO

  See Also:

  Constant Field Values

• PROP_MODEL_INFO

  private static final int PROP_MODEL_INFO

  See Also:

  Constant Field Values

• PROP_LIGAND_INFO

  private static final int PROP_LIGAND_INFO

  See Also:

  Constant Field Values

• PROP_SHAPE_INFO

  private static final int PROP_SHAPE_INFO

  See Also:

  Constant Field Values

• PROP_MEASUREMENT_INFO

  private static final int PROP_MEASUREMENT_INFO

  See Also:

  Constant Field Values

• PROP_CENTER_INFO

  private static final int PROP_CENTER_INFO

  See Also:

  Constant Field Values

• PROP_ORIENTATION_INFO

  private static final int PROP_ORIENTATION_INFO

  See Also:

  Constant Field Values

• PROP_TRANSFORM_INFO

  private static final int PROP_TRANSFORM_INFO

  See Also:

  Constant Field Values

• PROP_ATOM_INFO

  private static final int PROP_ATOM_INFO

  See Also:

  Constant Field Values

• PROP_BOND_INFO

  private static final int PROP_BOND_INFO

  See Also:

  Constant Field Values

• PROP_CHAIN_INFO

  private static final int PROP_CHAIN_INFO

  See Also:

  Constant Field Values

• PROP_POLYMER_INFO

  private static final int PROP_POLYMER_INFO

  See Also:

  Constant Field Values

• PROP_MOLECULE_INFO

  private static final int PROP_MOLECULE_INFO

  See Also:

  Constant Field Values

• PROP_STATE_INFO

  private static final int PROP_STATE_INFO

  See Also:

  Constant Field Values

• PROP_EXTRACT_MODEL

  private static final int PROP_EXTRACT_MODEL

  See Also:

  Constant Field Values

• PROP_JMOL_STATUS

  private static final int PROP_JMOL_STATUS

  See Also:

  Constant Field Values

• PROP_JMOL_VIEWER

  private static final int PROP_JMOL_VIEWER

  See Also:

  Constant Field Values

• PROP_MESSAGE_QUEUE

  private static final int PROP_MESSAGE_QUEUE

  See Also:

  Constant Field Values

• PROP_AUXILIARY_INFO

  private static final int PROP_AUXILIARY_INFO

  See Also:

  Constant Field Values

• PROP_BOUNDBOX_INFO

  private static final int PROP_BOUNDBOX_INFO

  See Also:

  Constant Field Values

• PROP_DATA_INFO

  private static final int PROP_DATA_INFO

  See Also:

  Constant Field Values

• PROP_IMAGE

  private static final int PROP_IMAGE

  See Also:

  Constant Field Values

• PROP_EVALUATE

  private static final int PROP_EVALUATE

  See Also:

  Constant Field Values

• PROP_MENU

  private static final int PROP_MENU

  See Also:

  Constant Field Values

• PROP_MINIMIZATION_INFO

  private static final int PROP_MINIMIZATION_INFO

  See Also:

  Constant Field Values

• PROP_POINTGROUP_INFO

  private static final int PROP_POINTGROUP_INFO

  See Also:

  Constant Field Values

• PROP_FILE_INFO

  private static final int PROP_FILE_INFO

  See Also:

  Constant Field Values

• PROP_ERROR_MESSAGE

  private static final int PROP_ERROR_MESSAGE

  See Also:

  Constant Field Values

• PROP_MOUSE_INFO

  private static final int PROP_MOUSE_INFO

  See Also:

  Constant Field Values

• PROP_ISOSURFACE_INFO

  private static final int PROP_ISOSURFACE_INFO

  See Also:

  Constant Field Values

• PROP_ISOSURFACE_DATA

  private static final int PROP_ISOSURFACE_DATA

  See Also:

  Constant Field Values

• PROP_CONSOLE_TEXT

  private static final int PROP_CONSOLE_TEXT

  See Also:

  Constant Field Values

• PROP_JSPECVIEW

  private static final int PROP_JSPECVIEW

  See Also:

  Constant Field Values

• PROP_SCRIPT_QUEUE_INFO

  private static final int PROP_SCRIPT_QUEUE_INFO

  See Also:

  Constant Field Values

• PROP_NMR_INFO

  private static final int PROP_NMR_INFO

  See Also:

  Constant Field Values

• PROP_VAR_INFO

  private static final int PROP_VAR_INFO

  See Also:

  Constant Field Values

• PROP_DOM_INFO

  private static final int PROP_DOM_INFO

  See Also:

  Constant Field Values

• PROP_VAL_INFO

  private static final int PROP_VAL_INFO

  See Also:

  Constant Field Values

• PROP_SERVICE

  private static final int PROP_SERVICE

  See Also:

  Constant Field Values

• PROP_COUNT

  private static final int PROP_COUNT

  See Also:

  Constant Field Values

• readableTypes

  private static final java.lang.String[] readableTypes

Constructor Detail

• PropertyManager

  public PropertyManager()

Method Detail

• setViewer

  public void setViewer​(Viewer vwr)

  Specified by:

  setViewer in interface JmolPropertyManager

• getPropertyNumber

  public int getPropertyNumber​(java.lang.String infoType)

  Specified by:

  getPropertyNumber in interface JmolPropertyManager

• getDefaultPropertyParam

  public java.lang.String getDefaultPropertyParam​(int propID)

  Specified by:

  getDefaultPropertyParam in interface JmolPropertyManager

• checkPropertyParameter

  public boolean checkPropertyParameter​(java.lang.String name)

  Specified by:

  checkPropertyParameter in interface JmolPropertyManager

• getProperty

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

  Specified by:

  getProperty in interface JmolPropertyManager

• getArguments

  private SV[] getArguments​(java.lang.String propertyName)

• fixSelectQuotes

  private java.lang.String fixSelectQuotes​(java.lang.String propertyName)

• extractProperty

  public java.lang.Object extractProperty​(java.lang.Object prop,
                                          java.lang.Object args,
                                          int ptr,
                                          javajs.util.Lst<java.lang.Object> v2,
                                          boolean isCompiled)

  Specified by:

  extractProperty in interface JmolPropertyManager

• getMapSubset

  private static void getMapSubset​(java.util.Map<java.lang.String,​?> h,
                                   java.lang.String key,
                                   java.util.Map<java.lang.String,​java.lang.Object> h2,
                                   javajs.util.Lst<java.lang.Object> v2)

• compileSelect

  private java.lang.Object compileSelect​(SV[] args)

• getKeys

  private javajs.util.Lst<java.lang.String> getKeys​(java.lang.String select)

• checkMap

  private java.lang.String checkMap​(java.util.Map<java.lang.String,​?> h,
                                    java.lang.String key,
                                    boolean isWild,
                                    javajs.util.Lst<java.lang.Object> v2,
                                    java.lang.Object args,
                                    int ptr,
                                    boolean isCaseSensitive)

• checkKey

  private boolean checkKey​(java.lang.String k,
                           java.lang.String key,
                           java.lang.String lckey)

• getPropertyName

  private static java.lang.String getPropertyName​(int propID)

• getParamType

  private static java.lang.String getParamType​(int propID)

• isReadableAsString

  private static boolean isReadableAsString​(java.lang.String infoType)

• getPropertyAsObject

  private java.lang.Object getPropertyAsObject​(java.lang.String infoType,
                                               java.lang.Object paramInfo,
                                               java.lang.String returnType)

• getImage

  private java.lang.Object getImage​(java.lang.String params,
                                    boolean asBytes)

• getVariables

  private java.lang.Object getVariables​(java.lang.String name)

• getFileInfo

  static java.lang.Object getFileInfo​(java.lang.Object objHeader,
                                      java.lang.String type)

• getMoleculeInfo

  public javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> getMoleculeInfo​(java.lang.Object atomExpression)

• getModelInfo

  public java.util.Map<java.lang.String,​java.lang.Object> getModelInfo​(java.lang.Object atomExpression)

  Specified by:

  getModelInfo in interface JmolPropertyManager

• getLigandInfo

  public java.util.Map<java.lang.String,​java.lang.Object> getLigandInfo​(java.lang.Object atomExpression)

  Specified by:

  getLigandInfo in interface JmolPropertyManager

• getAtomData

  public java.lang.String getAtomData​(java.lang.String atomExpression,
                                      java.lang.String type,
                                      boolean allTrajectories)

  use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb. use USER: or PROPERTY_xxxx for a property all other types return full data

  Specified by:

  getAtomData in interface JmolPropertyManager

• getModelExtract

  public java.lang.String getModelExtract​(BS bs,
                                          boolean doTransform,
                                          boolean isModelKit,
                                          java.lang.String type,
                                          boolean allTrajectories)

  V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR, MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)

  Specified by:

  getModelExtract in interface JmolPropertyManager

• getModelCif

  private java.lang.String getModelCif​(BS bs)

  just a very primitive CIF file reader

  Parameters:

  bs -

  Returns:

  CIf data

• addMolFile

  private boolean addMolFile​(int iModel,
                             javajs.util.SB mol,
                             BS bsAtoms,
                             BS bsBonds,
                             boolean asV3000,
                             boolean asJSON,
                             boolean noAromatic,
                             javajs.util.Quat q)

• getCovalentBondsForAtoms

  private static BS getCovalentBondsForAtoms​(Bond[] bonds,
                                             int bondCount,
                                             BS bsAtoms)

• getAtomRecordMOL

  private void getAtomRecordMOL​(int iModel,
                                ModelSet ms,
                                javajs.util.SB mol,
                                int n,
                                Atom a,
                                javajs.util.Quat q,
                                javajs.util.P3 pTemp,
                                boolean asV3000,
                                boolean asJSON)

• getPointTransf

  private void getPointTransf​(int i,
                              ModelSet ms,
                              Atom a,
                              javajs.util.Quat q,
                              javajs.util.P3 pTemp)

  pick up the appropriate value for this atom

  Parameters:

  i -

  ms -

  a -

  q -

  pTemp -

• getBondRecordMOL

  private void getBondRecordMOL​(javajs.util.SB mol,
                                int n,
                                Bond b,
                                int[] atomMap,
                                boolean asV3000,
                                boolean asJSON,
                                boolean noAromatic)

• getChimeInfo

  public java.lang.String getChimeInfo​(int tok,
                                       BS bs)

  Specified by:

  getChimeInfo in interface JmolPropertyManager

• getChimeInfoA

  private java.lang.String getChimeInfoA​(Atom[] atoms,
                                         int tok,
                                         BS bs)

• getModelFileInfo

  public java.lang.String getModelFileInfo​(BS frames)

  Specified by:

  getModelFileInfo in interface JmolPropertyManager

• getAllAtomInfo

  public javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> getAllAtomInfo​(BS bs)

• getAtomInfoLong

  private java.util.Map<java.lang.String,​java.lang.Object> getAtomInfoLong​(int i,
                                                                                 javajs.util.P3 ptTemp)

• getAllBondInfo

  public javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> getAllBondInfo​(java.lang.Object bsOrArray)

• getBondInfo

  private java.util.Map<java.lang.String,​java.lang.Object> getBondInfo​(int i,
                                                                             javajs.util.P3 ptTemp)

• getAllChainInfo

  public java.util.Map<java.lang.String,​javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>>> getAllChainInfo​(BS bs)

• getChainInfo

  private javajs.util.Lst<java.util.Map<java.lang.String,​javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>>>> getChainInfo​(int modelIndex,
                                                                                                                                                      BS bs)

• getAllPolymerInfo

  private java.util.Map<java.lang.String,​javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>>> getAllPolymerInfo​(BS bs)

• getBasePairInfo

  private java.lang.String getBasePairInfo​(BS bs)

• getAtomResidueInfo

  private static void getAtomResidueInfo​(javajs.util.SB info,
                                         Atom atom)

• getAppletInfo

  private java.util.Map<java.lang.String,​java.lang.Object> getAppletInfo()

• getAnimationInfo

  private java.util.Map<java.lang.String,​java.lang.Object> getAnimationInfo()

• getBoundBoxInfo

  private java.util.Map<java.lang.String,​java.lang.Object> getBoundBoxInfo()

• getShapeInfo

  private java.util.Map<java.lang.String,​java.lang.Object> getShapeInfo()

• getAnnotationInfo

  private SV getAnnotationInfo​(java.lang.Object atomExpression,
                               int type)

• getMeasurementInfo

  private javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> getMeasurementInfo()

• getMouseInfo

  private java.lang.Object getMouseInfo()

• getPdbAtomData

  public java.lang.String getPdbAtomData​(BS bs,
                                         javajs.util.OC out,
                                         boolean isPQR,
                                         boolean doTransform,
                                         boolean allTrajectories)

  PDB or PQR only

  Specified by:

  getPdbAtomData in interface JmolPropertyManager

  Parameters:

  bs - selected atoms

  out - StringXBuilder or BufferedWriter

  Returns:

  PDB file data string

• pdbKey

  private java.lang.String pdbKey​(int np)

• fixPDBFormat

  private int fixPDBFormat​(javajs.util.Lst<java.lang.String> lines,
                           java.util.Map<java.lang.String,​java.lang.Integer> map,
                           javajs.util.OC out,
                           int[] firstAtomIndexNew,
                           int modelPt)

  must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.

  Parameters:

  lines -

  map -

  out -

  modelPt -

  firstAtomIndexNew -

  Returns:

  new modelPt

• getPdbData

  public java.lang.String getPdbData​(int modelIndex,
                                     java.lang.String type,
                                     BS bsSelected,
                                     java.lang.Object[] parameters,
                                     javajs.util.OC out,
                                     boolean addStructure)

  Specified by:

  getPdbData in interface JmolPropertyManager

• getModelCml

  public java.lang.String getModelCml​(BS bs,
                                      int atomsMax,
                                      boolean addBonds,
                                      boolean doTransform,
                                      boolean allTrajectories)

  Specified by:

  getModelCml in interface JmolPropertyManager