Class PropertyManager

Method Details

• setViewer

  public void setViewer(Viewer vwr)

  Specified by:

  setViewer in interface JmolPropertyManager

• getPropertyNumber

  public int getPropertyNumber(String infoType)

  Specified by:

  getPropertyNumber in interface JmolPropertyManager

• getDefaultPropertyParam

  public String getDefaultPropertyParam(int propID)

  Specified by:

  getDefaultPropertyParam in interface JmolPropertyManager

• checkPropertyParameter

  public boolean checkPropertyParameter(String name)

  Specified by:

  checkPropertyParameter in interface JmolPropertyManager

• getProperty

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

  / static methods used by Eval and Viewer ////

  Specified by:

  getProperty in interface JmolPropertyManager

• extractProperty

  public Object extractProperty(Object prop, Object args, int ptr, Lst<Object> v2, boolean isCompiled)

  Specified by:

  extractProperty in interface JmolPropertyManager

• getMoleculeInfo

  public Lst<Map<String,Object>> getMoleculeInfo(Object atomExpression)

  info ///

• getModelInfo

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

  Specified by:

  getModelInfo in interface JmolPropertyManager

• getLigandInfo

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

  Specified by:

  getLigandInfo in interface JmolPropertyManager

• getAtomData

  public String getAtomData(String atomExpression, 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 String getModelExtract(BS bs, boolean doTransform, boolean isModelKit, String type, boolean allTrajectories)

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

  Specified by:

  getModelExtract in interface JmolPropertyManager

• getChimeInfo

  public String getChimeInfo(int tok, BS bs)

  Specified by:

  getChimeInfo in interface JmolPropertyManager

• getModelFileInfo

  public String getModelFileInfo(BS frames)

  Specified by:

  getModelFileInfo in interface JmolPropertyManager

• getAllAtomInfo

  public Lst<Map<String,Object>> getAllAtomInfo(BS bs)

• getAllBondInfo

  public Lst<Map<String,Object>> getAllBondInfo(Object bsOrArray)

• getAllChainInfo

  public Map<String, Lst<Map<String,Object>>> getAllChainInfo(BS bs)

• getPdbAtomData

  public String getPdbAtomData(BS bs, 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

• getPdbData

  public String getPdbData(int modelIndex, String type, BS bsSelected, Object[] parameters, OC out, boolean addStructure)

  Specified by:

  getPdbData in interface JmolPropertyManager

• getModelCml

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

  Specified by:

  getModelCml in interface JmolPropertyManager

• fixJMEFormalCharges

  public String fixJMEFormalCharges(BS bsAtoms, String jme)

  Fix a JME string returned from NCI CIR to have the proper formal charges.

  Specified by:

  fixJMEFormalCharges in interface JmolPropertyManager

• getSDFDateLine

  public static String getSDFDateLine(String version, boolean is2d)