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
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final String
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private static final String[]
private static final String[]
(package private) Viewer
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate boolean
private String
checkMap
(Map<String, ?> h, String key, boolean isWild, javajs.util.Lst<Object> v2, Object args, int ptr, boolean isCaseSensitive) boolean
checkPropertyParameter
(String name) private SV[]
compileSelect
(SV[] args) extractProperty
(Object prop, Object args, int ptr, javajs.util.Lst<Object> v2, boolean isCompiled) fixJMEFormalCharges
(javajs.util.BS bsAtoms, String jme) Fix a JME string returned from NCI CIR to have the proper formal charges.private String
fixSelectQuotes
(String propertyName) getAllAtomInfo
(javajs.util.BS bs) getAllBondInfo
(Object bsOrArray) getAllChainInfo
(javajs.util.BS bs) getAllPolymerInfo
(javajs.util.BS bs) private SV
getAnnotationInfo
(Object atomExpression, int type) private SV[]
getArguments
(String propertyName) getAtomData
(String atomExpression, String type, boolean allTrajectories) use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.getAtomInfoLong
(int i, javajs.util.P3 ptTemp, SymmetryInterface ucell) private static void
getAtomResidueInfo
(javajs.util.SB info, Atom atom) private String
getBasePairInfo
(javajs.util.BS bs) getBondInfo
(int i, javajs.util.P3 ptTemp) getChainInfo
(int modelIndex, javajs.util.BS bs) getChimeInfo
(int tok, javajs.util.BS bs) private String
getChimeInfoA
(Atom[] atoms, int tok, javajs.util.BS bs) Get information in the style of Chime for SHOW selected|atoms|groups|group1| chains|residues|sequenceprivate static javajs.util.BS
getCovalentBondsForAtoms
(Bond[] bonds, int bondCount, javajs.util.BS bsAtoms) getDefaultPropertyParam
(int propID) (package private) static Object
getFileInfo
(Object objHeader, String type) private Object
private javajs.util.Lst<String>
getLigandInfo
(Object atomExpression) private static void
private String
EXPERIMENTAL create a QCJSON file -- very preliminarygetModelCml
(javajs.util.BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories) getModelExtract
(javajs.util.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
(javajs.util.BS frames) getModelInfo
(Object atomExpression) getMoleculeInfo
(Object atomExpression) private Object
private static String
getParamType
(int propID) getPdbAtomData
(javajs.util.BS bs, javajs.util.OC out, boolean isPQR, boolean doTransform, boolean allTrajectories) PDB or PQR onlygetPdbData
(int modelIndex, String type, javajs.util.BS bsSelected, Object[] parameters, javajs.util.OC out, boolean addStructure) getProperty
(String returnType, String infoType, Object paramInfo) private Object
getPropertyAsObject
(String infoType, Object paramInfo, String returnType) private static String
getPropertyName
(int propID) int
getPropertyNumber
(String infoType) private Object
private Object
getVariables
(String name) private static boolean
isReadableAsString
(String infoType) void
private void
writeXYZ
(javajs.util.SB mol, javajs.util.BS bsAtoms, javajs.util.BS bsModels, javajs.util.Quat q, boolean asXYZVIB, boolean asXYZRN)
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Field Details
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vwr
Viewer vwr -
map
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atomExpression
- See Also:
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propertyTypes
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PROP_APPLET_INFO
private static final int PROP_APPLET_INFO- See Also:
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PROP_FILENAME
private static final int PROP_FILENAME- See Also:
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PROP_FILEHEADER
private static final int PROP_FILEHEADER- See Also:
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PROP_FILECONTENTS_PATH
private static final int PROP_FILECONTENTS_PATH- See Also:
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PROP_FILECONTENTS
private static final int PROP_FILECONTENTS- See Also:
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PROP_ANIMATION_INFO
private static final int PROP_ANIMATION_INFO- See Also:
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PROP_MODEL_INFO
private static final int PROP_MODEL_INFO- See Also:
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PROP_LIGAND_INFO
private static final int PROP_LIGAND_INFO- See Also:
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PROP_SHAPE_INFO
private static final int PROP_SHAPE_INFO- See Also:
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PROP_MEASUREMENT_INFO
private static final int PROP_MEASUREMENT_INFO- See Also:
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PROP_CENTER_INFO
private static final int PROP_CENTER_INFO- See Also:
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PROP_ORIENTATION_INFO
private static final int PROP_ORIENTATION_INFO- See Also:
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PROP_TRANSFORM_INFO
private static final int PROP_TRANSFORM_INFO- See Also:
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PROP_ATOM_INFO
private static final int PROP_ATOM_INFO- See Also:
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PROP_BOND_INFO
private static final int PROP_BOND_INFO- See Also:
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PROP_CHAIN_INFO
private static final int PROP_CHAIN_INFO- See Also:
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PROP_POLYMER_INFO
private static final int PROP_POLYMER_INFO- See Also:
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PROP_MOLECULE_INFO
private static final int PROP_MOLECULE_INFO- See Also:
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PROP_STATE_INFO
private static final int PROP_STATE_INFO- See Also:
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PROP_EXTRACT_MODEL
private static final int PROP_EXTRACT_MODEL- See Also:
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PROP_JMOL_STATUS
private static final int PROP_JMOL_STATUS- See Also:
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PROP_JMOL_VIEWER
private static final int PROP_JMOL_VIEWER- See Also:
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PROP_MESSAGE_QUEUE
private static final int PROP_MESSAGE_QUEUE- See Also:
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PROP_AUXILIARY_INFO
private static final int PROP_AUXILIARY_INFO- See Also:
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PROP_BOUNDBOX_INFO
private static final int PROP_BOUNDBOX_INFO- See Also:
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PROP_DATA_INFO
private static final int PROP_DATA_INFO- See Also:
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PROP_IMAGE
private static final int PROP_IMAGE- See Also:
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PROP_EVALUATE
private static final int PROP_EVALUATE- See Also:
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PROP_MENU
private static final int PROP_MENU- See Also:
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PROP_MINIMIZATION_INFO
private static final int PROP_MINIMIZATION_INFO- See Also:
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PROP_POINTGROUP_INFO
private static final int PROP_POINTGROUP_INFO- See Also:
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PROP_FILE_INFO
private static final int PROP_FILE_INFO- See Also:
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PROP_ERROR_MESSAGE
private static final int PROP_ERROR_MESSAGE- See Also:
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PROP_MOUSE_INFO
private static final int PROP_MOUSE_INFO- See Also:
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PROP_ISOSURFACE_INFO
private static final int PROP_ISOSURFACE_INFO- See Also:
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PROP_ISOSURFACE_DATA
private static final int PROP_ISOSURFACE_DATA- See Also:
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PROP_CONSOLE_TEXT
private static final int PROP_CONSOLE_TEXT- See Also:
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PROP_JSPECVIEW
private static final int PROP_JSPECVIEW- See Also:
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PROP_SCRIPT_QUEUE_INFO
private static final int PROP_SCRIPT_QUEUE_INFO- See Also:
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PROP_NMR_INFO
private static final int PROP_NMR_INFO- See Also:
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PROP_VAR_INFO
private static final int PROP_VAR_INFO- See Also:
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PROP_DOM_INFO
private static final int PROP_DOM_INFO- See Also:
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PROP_VAL_INFO
private static final int PROP_VAL_INFO- See Also:
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PROP_SERVICE
private static final int PROP_SERVICE- See Also:
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PROP_CIF_INFO
private static final int PROP_CIF_INFO- See Also:
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PROP_MODELKIT_INFO
private static final int PROP_MODELKIT_INFO- See Also:
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PROP_UNITCELL_INFO
private static final int PROP_UNITCELL_INFO- See Also:
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PROP_COUNT
private static final int PROP_COUNT- See Also:
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readableTypes
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Constructor Details
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PropertyManager
public PropertyManager()
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Method Details
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setViewer
- Specified by:
setViewer
in interfaceJmolPropertyManager
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getPropertyNumber
- Specified by:
getPropertyNumber
in interfaceJmolPropertyManager
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getDefaultPropertyParam
- Specified by:
getDefaultPropertyParam
in interfaceJmolPropertyManager
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checkPropertyParameter
- Specified by:
checkPropertyParameter
in interfaceJmolPropertyManager
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getProperty
- Specified by:
getProperty
in interfaceJmolPropertyManager
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getArguments
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fixSelectQuotes
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extractProperty
public Object extractProperty(Object prop, Object args, int ptr, javajs.util.Lst<Object> v2, boolean isCompiled) - Specified by:
extractProperty
in interfaceJmolPropertyManager
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getMapSubset
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compileSelect
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getKeys
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checkMap
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checkKey
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getPropertyName
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getParamType
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isReadableAsString
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getPropertyAsObject
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getUnitCellInfo
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getImage
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getVariables
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getFileInfo
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getMoleculeInfo
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getModelInfo
- Specified by:
getModelInfo
in interfaceJmolPropertyManager
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getLigandInfo
- Specified by:
getLigandInfo
in interfaceJmolPropertyManager
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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
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getModelExtract
public String getModelExtract(javajs.util.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
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writeXYZ
private void writeXYZ(javajs.util.SB mol, javajs.util.BS bsAtoms, javajs.util.BS bsModels, javajs.util.Quat q, boolean asXYZVIB, boolean asXYZRN) -
getModel
EXPERIMENTAL create a QCJSON file -- very preliminary- Parameters:
type
-bs
-data
- to pass to readerout
- currently only for PDB case, in which return is ignored- Returns:
- file data
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getCovalentBondsForAtoms
private static javajs.util.BS getCovalentBondsForAtoms(Bond[] bonds, int bondCount, javajs.util.BS bsAtoms) -
getChimeInfo
- Specified by:
getChimeInfo
in interfaceJmolPropertyManager
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getChimeInfoA
Get information in the style of Chime for SHOW selected|atoms|groups|group1| chains|residues|sequence- Parameters:
atoms
-tok
-bs
-- Returns:
- string \n-separated listing
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getModelFileInfo
- Specified by:
getModelFileInfo
in interfaceJmolPropertyManager
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getAllAtomInfo
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getAtomInfoLong
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getAllBondInfo
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getBondInfo
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getAllChainInfo
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getChainInfo
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getAllPolymerInfo
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getBasePairInfo
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getAtomResidueInfo
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getAppletInfo
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getAnimationInfo
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getBoundBoxInfo
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getShapeInfo
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getAnnotationInfo
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getMeasurementInfo
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getMouseInfo
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getPdbAtomData
public String getPdbAtomData(javajs.util.BS bs, javajs.util.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
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getPdbData
public String getPdbData(int modelIndex, String type, javajs.util.BS bsSelected, Object[] parameters, javajs.util.OC out, boolean addStructure) - Specified by:
getPdbData
in interfaceJmolPropertyManager
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getModelCml
public String getModelCml(javajs.util.BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories) - Specified by:
getModelCml
in interfaceJmolPropertyManager
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fixJMEFormalCharges
Fix a JME string returned from NCI CIR to have the proper formal charges.- Specified by:
fixJMEFormalCharges
in interfaceJmolPropertyManager
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