Package org.jmol.viewer
Class PropertyManager
java.lang.Object
org.jmol.viewer.PropertyManager
- All Implemented Interfaces:
JmolPropertyManager
The PropertyManager handles all operations relating to delivery of properties
with the getProperty() method, or its specifically cast forms
getPropertyString() or getPropertyJSON().
It is instantiated by reflection
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
checkPropertyParameter
(String name) extractProperty
(Object prop, Object args, int ptr, Lst<Object> v2, boolean isCompiled) fixJMEFormalCharges
(BS bsAtoms, String jme) Fix a JME string returned from NCI CIR to have the proper formal charges.getAllAtomInfo
(BS bs) getAllBondInfo
(Object bsOrArray) getAllChainInfo
(BS bs) getAtomData
(String atomExpression, String type, boolean allTrajectories) use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.getChimeInfo
(int tok, BS bs) getDefaultPropertyParam
(int propID) getLigandInfo
(Object atomExpression) getModelCml
(BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories) 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)getModelFileInfo
(BS frames) getModelInfo
(Object atomExpression) getMoleculeInfo
(Object atomExpression) getPdbAtomData
(BS bs, OC out, boolean isPQR, boolean doTransform, boolean allTrajectories) PDB or PQR onlygetPdbData
(int modelIndex, String type, BS bsSelected, Object[] parameters, OC out, boolean addStructure) getProperty
(String returnType, String infoType, Object paramInfo) int
getPropertyNumber
(String infoType) static String
getSDFDateLine
(String version, boolean is2d) void
-
Constructor Details
-
PropertyManager
public PropertyManager()
-
-
Method Details
-
setViewer
- Specified by:
setViewer
in interfaceJmolPropertyManager
-
getPropertyNumber
- Specified by:
getPropertyNumber
in interfaceJmolPropertyManager
-
getDefaultPropertyParam
- Specified by:
getDefaultPropertyParam
in interfaceJmolPropertyManager
-
checkPropertyParameter
- Specified by:
checkPropertyParameter
in interfaceJmolPropertyManager
-
getProperty
- Specified by:
getProperty
in interfaceJmolPropertyManager
-
extractProperty
public Object extractProperty(Object prop, Object args, int ptr, Lst<Object> v2, boolean isCompiled) - Specified by:
extractProperty
in interfaceJmolPropertyManager
-
getMoleculeInfo
-
getModelInfo
- Specified by:
getModelInfo
in interfaceJmolPropertyManager
-
getLigandInfo
- Specified by:
getLigandInfo
in interfaceJmolPropertyManager
-
getAtomData
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 interfaceJmolPropertyManager
-
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 interfaceJmolPropertyManager
-
getChimeInfo
- Specified by:
getChimeInfo
in interfaceJmolPropertyManager
-
getModelFileInfo
- Specified by:
getModelFileInfo
in interfaceJmolPropertyManager
-
getAllAtomInfo
-
getAllBondInfo
-
getAllChainInfo
-
getPdbAtomData
public String getPdbAtomData(BS bs, OC out, boolean isPQR, boolean doTransform, boolean allTrajectories) PDB or PQR only- Specified by:
getPdbAtomData
in interfaceJmolPropertyManager
- Parameters:
bs
- selected atomsout
- 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 interfaceJmolPropertyManager
-
getModelCml
public String getModelCml(BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories) - Specified by:
getModelCml
in interfaceJmolPropertyManager
-
fixJMEFormalCharges
Fix a JME string returned from NCI CIR to have the proper formal charges.- Specified by:
fixJMEFormalCharges
in interfaceJmolPropertyManager
-
getSDFDateLine
-