Package org.jmol.viewer
Class PropertyManager
- java.lang.Object
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- org.jmol.viewer.PropertyManager
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- All Implemented Interfaces:
JmolPropertyManager
public class PropertyManager extends java.lang.Object implements 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
Fields Modifier and Type Field Description private static java.lang.String
atomExpression
private java.util.Map<java.lang.String,java.lang.Integer>
map
private static int
PROP_ANIMATION_INFO
private static int
PROP_APPLET_INFO
private static int
PROP_ATOM_INFO
private static int
PROP_AUXILIARY_INFO
private static int
PROP_BOND_INFO
private static int
PROP_BOUNDBOX_INFO
private static int
PROP_CENTER_INFO
private static int
PROP_CHAIN_INFO
private static int
PROP_CIF_INFO
private static int
PROP_CONSOLE_TEXT
private static int
PROP_COUNT
private static int
PROP_DATA_INFO
private static int
PROP_DOM_INFO
private static int
PROP_ERROR_MESSAGE
private static int
PROP_EVALUATE
private static int
PROP_EXTRACT_MODEL
private static int
PROP_FILE_INFO
private static int
PROP_FILECONTENTS
private static int
PROP_FILECONTENTS_PATH
private static int
PROP_FILEHEADER
private static int
PROP_FILENAME
private static int
PROP_IMAGE
private static int
PROP_ISOSURFACE_DATA
private static int
PROP_ISOSURFACE_INFO
private static int
PROP_JMOL_STATUS
private static int
PROP_JMOL_VIEWER
private static int
PROP_JSPECVIEW
private static int
PROP_LIGAND_INFO
private static int
PROP_MEASUREMENT_INFO
private static int
PROP_MENU
private static int
PROP_MESSAGE_QUEUE
private static int
PROP_MINIMIZATION_INFO
private static int
PROP_MODEL_INFO
private static int
PROP_MODELKIT_INFO
private static int
PROP_MOLECULE_INFO
private static int
PROP_MOUSE_INFO
private static int
PROP_NMR_INFO
private static int
PROP_ORIENTATION_INFO
private static int
PROP_POINTGROUP_INFO
private static int
PROP_POLYMER_INFO
private static int
PROP_SCRIPT_QUEUE_INFO
private static int
PROP_SERVICE
private static int
PROP_SHAPE_INFO
private static int
PROP_STATE_INFO
private static int
PROP_TRANSFORM_INFO
private static int
PROP_UNITCELL_INFO
private static int
PROP_VAL_INFO
private static int
PROP_VAR_INFO
private static java.lang.String[]
propertyTypes
private static java.lang.String[]
readableTypes
(package private) Viewer
vwr
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Constructor Summary
Constructors Constructor Description PropertyManager()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description private boolean
checkKey(java.lang.String k, java.lang.String key, java.lang.String lckey)
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)
boolean
checkPropertyParameter(java.lang.String name)
private SV[]
compileSelect(SV[] args)
java.lang.Object
extractProperty(java.lang.Object prop, java.lang.Object args, int ptr, javajs.util.Lst<java.lang.Object> v2, boolean isCompiled)
java.lang.String
fixJMEFormalCharges(javajs.util.BS bsAtoms, java.lang.String jme)
Fix a JME string returned from NCI CIR to have the proper formal charges.private java.lang.String
fixSelectQuotes(java.lang.String propertyName)
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>
getAllAtomInfo(javajs.util.BS bs)
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>
getAllBondInfo(java.lang.Object bsOrArray)
java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>>
getAllChainInfo(javajs.util.BS bs)
private java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>>
getAllPolymerInfo(javajs.util.BS bs)
private java.util.Map<java.lang.String,java.lang.Object>
getAnimationInfo()
private SV
getAnnotationInfo(java.lang.Object atomExpression, int type)
private java.util.Map<java.lang.String,java.lang.Object>
getAppletInfo()
private SV[]
getArguments(java.lang.String propertyName)
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.private java.util.Map<java.lang.String,java.lang.Object>
getAtomInfoLong(int i, javajs.util.P3 ptTemp, SymmetryInterface ucell)
private static void
getAtomResidueInfo(javajs.util.SB info, Atom atom)
private java.lang.String
getBasePairInfo(javajs.util.BS bs)
private java.util.Map<java.lang.String,java.lang.Object>
getBondInfo(int i, javajs.util.P3 ptTemp)
private java.util.Map<java.lang.String,java.lang.Object>
getBoundBoxInfo()
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, javajs.util.BS bs)
java.lang.String
getChimeInfo(int tok, javajs.util.BS bs)
private java.lang.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)
java.lang.String
getDefaultPropertyParam(int propID)
(package private) static java.lang.Object
getFileInfo(java.lang.Object objHeader, java.lang.String type)
private java.lang.Object
getImage(java.lang.String params, boolean asBytes)
private javajs.util.Lst<java.lang.String>
getKeys(java.lang.String select)
java.util.Map<java.lang.String,java.lang.Object>
getLigandInfo(java.lang.Object atomExpression)
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)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>
getMeasurementInfo()
private java.lang.String
getModel(java.lang.String type, javajs.util.BS bs, java.lang.Object[] data, javajs.util.OC out)
EXPERIMENTAL create a QCJSON file -- very preliminaryjava.lang.String
getModelCml(javajs.util.BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories)
java.lang.String
getModelExtract(javajs.util.BS bs, boolean doTransform, boolean isModelKit, java.lang.String type, boolean allTrajectories)
V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON, PWMAT, XSF MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)java.lang.String
getModelFileInfo(javajs.util.BS frames)
java.util.Map<java.lang.String,java.lang.Object>
getModelInfo(java.lang.Object atomExpression)
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>
getMoleculeInfo(java.lang.Object atomExpression)
private java.lang.Object
getMouseInfo()
private static java.lang.String
getParamType(int propID)
java.lang.String
getPdbAtomData(javajs.util.BS bs, javajs.util.OC out, boolean isPQR, boolean doTransform, boolean allTrajectories)
PDB or PQR onlyjava.lang.String
getPdbData(int modelIndex, java.lang.String type, javajs.util.BS bsSelected, java.lang.Object[] parameters, javajs.util.OC out, boolean addStructure)
java.lang.Object
getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
private java.lang.Object
getPropertyAsObject(java.lang.String infoType, java.lang.Object paramInfo, java.lang.String returnType)
private static java.lang.String
getPropertyName(int propID)
int
getPropertyNumber(java.lang.String infoType)
private java.util.Map<java.lang.String,java.lang.Object>
getShapeInfo()
private java.lang.Object
getUnitCellInfo()
private java.lang.Object
getVariables(java.lang.String name)
private static boolean
isReadableAsString(java.lang.String infoType)
void
setViewer(Viewer vwr)
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Field Detail
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vwr
Viewer vwr
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map
private java.util.Map<java.lang.String,java.lang.Integer> map
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atomExpression
private static final java.lang.String atomExpression
- See Also:
- Constant Field Values
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propertyTypes
private static final java.lang.String[] propertyTypes
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PROP_APPLET_INFO
private static final int PROP_APPLET_INFO
- See Also:
- Constant Field Values
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PROP_FILENAME
private static final int PROP_FILENAME
- See Also:
- Constant Field Values
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PROP_FILEHEADER
private static final int PROP_FILEHEADER
- See Also:
- Constant Field Values
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PROP_FILECONTENTS_PATH
private static final int PROP_FILECONTENTS_PATH
- See Also:
- Constant Field Values
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PROP_FILECONTENTS
private static final int PROP_FILECONTENTS
- See Also:
- Constant Field Values
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PROP_ANIMATION_INFO
private static final int PROP_ANIMATION_INFO
- See Also:
- Constant Field Values
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PROP_MODEL_INFO
private static final int PROP_MODEL_INFO
- See Also:
- Constant Field Values
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PROP_LIGAND_INFO
private static final int PROP_LIGAND_INFO
- See Also:
- Constant Field Values
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PROP_SHAPE_INFO
private static final int PROP_SHAPE_INFO
- See Also:
- Constant Field Values
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PROP_MEASUREMENT_INFO
private static final int PROP_MEASUREMENT_INFO
- See Also:
- Constant Field Values
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PROP_CENTER_INFO
private static final int PROP_CENTER_INFO
- See Also:
- Constant Field Values
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PROP_ORIENTATION_INFO
private static final int PROP_ORIENTATION_INFO
- See Also:
- Constant Field Values
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PROP_TRANSFORM_INFO
private static final int PROP_TRANSFORM_INFO
- See Also:
- Constant Field Values
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PROP_ATOM_INFO
private static final int PROP_ATOM_INFO
- See Also:
- Constant Field Values
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PROP_BOND_INFO
private static final int PROP_BOND_INFO
- See Also:
- Constant Field Values
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PROP_CHAIN_INFO
private static final int PROP_CHAIN_INFO
- See Also:
- Constant Field Values
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PROP_POLYMER_INFO
private static final int PROP_POLYMER_INFO
- See Also:
- Constant Field Values
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PROP_MOLECULE_INFO
private static final int PROP_MOLECULE_INFO
- See Also:
- Constant Field Values
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PROP_STATE_INFO
private static final int PROP_STATE_INFO
- See Also:
- Constant Field Values
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PROP_EXTRACT_MODEL
private static final int PROP_EXTRACT_MODEL
- See Also:
- Constant Field Values
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PROP_JMOL_STATUS
private static final int PROP_JMOL_STATUS
- See Also:
- Constant Field Values
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PROP_JMOL_VIEWER
private static final int PROP_JMOL_VIEWER
- See Also:
- Constant Field Values
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PROP_MESSAGE_QUEUE
private static final int PROP_MESSAGE_QUEUE
- See Also:
- Constant Field Values
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PROP_AUXILIARY_INFO
private static final int PROP_AUXILIARY_INFO
- See Also:
- Constant Field Values
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PROP_BOUNDBOX_INFO
private static final int PROP_BOUNDBOX_INFO
- See Also:
- Constant Field Values
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PROP_DATA_INFO
private static final int PROP_DATA_INFO
- See Also:
- Constant Field Values
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PROP_IMAGE
private static final int PROP_IMAGE
- See Also:
- Constant Field Values
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PROP_EVALUATE
private static final int PROP_EVALUATE
- See Also:
- Constant Field Values
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PROP_MENU
private static final int PROP_MENU
- See Also:
- Constant Field Values
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PROP_MINIMIZATION_INFO
private static final int PROP_MINIMIZATION_INFO
- See Also:
- Constant Field Values
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PROP_POINTGROUP_INFO
private static final int PROP_POINTGROUP_INFO
- See Also:
- Constant Field Values
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PROP_FILE_INFO
private static final int PROP_FILE_INFO
- See Also:
- Constant Field Values
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PROP_ERROR_MESSAGE
private static final int PROP_ERROR_MESSAGE
- See Also:
- Constant Field Values
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PROP_MOUSE_INFO
private static final int PROP_MOUSE_INFO
- See Also:
- Constant Field Values
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PROP_ISOSURFACE_INFO
private static final int PROP_ISOSURFACE_INFO
- See Also:
- Constant Field Values
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PROP_ISOSURFACE_DATA
private static final int PROP_ISOSURFACE_DATA
- See Also:
- Constant Field Values
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PROP_CONSOLE_TEXT
private static final int PROP_CONSOLE_TEXT
- See Also:
- Constant Field Values
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PROP_JSPECVIEW
private static final int PROP_JSPECVIEW
- See Also:
- Constant Field Values
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PROP_SCRIPT_QUEUE_INFO
private static final int PROP_SCRIPT_QUEUE_INFO
- See Also:
- Constant Field Values
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PROP_NMR_INFO
private static final int PROP_NMR_INFO
- See Also:
- Constant Field Values
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PROP_VAR_INFO
private static final int PROP_VAR_INFO
- See Also:
- Constant Field Values
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PROP_DOM_INFO
private static final int PROP_DOM_INFO
- See Also:
- Constant Field Values
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PROP_VAL_INFO
private static final int PROP_VAL_INFO
- See Also:
- Constant Field Values
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PROP_SERVICE
private static final int PROP_SERVICE
- See Also:
- Constant Field Values
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PROP_CIF_INFO
private static final int PROP_CIF_INFO
- See Also:
- Constant Field Values
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PROP_MODELKIT_INFO
private static final int PROP_MODELKIT_INFO
- See Also:
- Constant Field Values
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PROP_UNITCELL_INFO
private static final int PROP_UNITCELL_INFO
- See Also:
- Constant Field Values
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PROP_COUNT
private static final int PROP_COUNT
- See Also:
- Constant Field Values
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readableTypes
private static final java.lang.String[] readableTypes
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Method Detail
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setViewer
public void setViewer(Viewer vwr)
- Specified by:
setViewer
in interfaceJmolPropertyManager
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getPropertyNumber
public int getPropertyNumber(java.lang.String infoType)
- Specified by:
getPropertyNumber
in interfaceJmolPropertyManager
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getDefaultPropertyParam
public java.lang.String getDefaultPropertyParam(int propID)
- Specified by:
getDefaultPropertyParam
in interfaceJmolPropertyManager
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checkPropertyParameter
public boolean checkPropertyParameter(java.lang.String name)
- Specified by:
checkPropertyParameter
in interfaceJmolPropertyManager
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getProperty
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
- Specified by:
getProperty
in interfaceJmolPropertyManager
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getArguments
private SV[] getArguments(java.lang.String propertyName)
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fixSelectQuotes
private java.lang.String fixSelectQuotes(java.lang.String propertyName)
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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 interfaceJmolPropertyManager
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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)
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getKeys
private javajs.util.Lst<java.lang.String> getKeys(java.lang.String select)
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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)
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checkKey
private boolean checkKey(java.lang.String k, java.lang.String key, java.lang.String lckey)
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getPropertyName
private static java.lang.String getPropertyName(int propID)
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getParamType
private static java.lang.String getParamType(int propID)
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isReadableAsString
private static boolean isReadableAsString(java.lang.String infoType)
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getPropertyAsObject
private java.lang.Object getPropertyAsObject(java.lang.String infoType, java.lang.Object paramInfo, java.lang.String returnType)
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getUnitCellInfo
private java.lang.Object getUnitCellInfo()
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getImage
private java.lang.Object getImage(java.lang.String params, boolean asBytes)
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getVariables
private java.lang.Object getVariables(java.lang.String name)
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getFileInfo
static java.lang.Object getFileInfo(java.lang.Object objHeader, java.lang.String type)
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getMoleculeInfo
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getMoleculeInfo(java.lang.Object atomExpression)
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getModelInfo
public java.util.Map<java.lang.String,java.lang.Object> getModelInfo(java.lang.Object atomExpression)
- Specified by:
getModelInfo
in interfaceJmolPropertyManager
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getLigandInfo
public java.util.Map<java.lang.String,java.lang.Object> getLigandInfo(java.lang.Object atomExpression)
- Specified by:
getLigandInfo
in interfaceJmolPropertyManager
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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 interfaceJmolPropertyManager
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getModelExtract
public java.lang.String getModelExtract(javajs.util.BS bs, boolean doTransform, boolean isModelKit, java.lang.String type, boolean allTrajectories)
V3000, SDF, MOL, JSON, CD, 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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getModel
private java.lang.String getModel(java.lang.String type, javajs.util.BS bs, java.lang.Object[] data, javajs.util.OC out)
EXPERIMENTAL create a QCJSON file -- very preliminary- Parameters:
type
-bs
-data
- to pass to readerout
-- Returns:
- file data
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getCovalentBondsForAtoms
private static javajs.util.BS getCovalentBondsForAtoms(Bond[] bonds, int bondCount, javajs.util.BS bsAtoms)
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getChimeInfo
public java.lang.String getChimeInfo(int tok, javajs.util.BS bs)
- Specified by:
getChimeInfo
in interfaceJmolPropertyManager
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getChimeInfoA
private java.lang.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|sequence- Parameters:
atoms
-tok
-bs
-- Returns:
- string \n-separated listing
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getModelFileInfo
public java.lang.String getModelFileInfo(javajs.util.BS frames)
- Specified by:
getModelFileInfo
in interfaceJmolPropertyManager
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getAllAtomInfo
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getAllAtomInfo(javajs.util.BS bs)
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getAtomInfoLong
private java.util.Map<java.lang.String,java.lang.Object> getAtomInfoLong(int i, javajs.util.P3 ptTemp, SymmetryInterface ucell)
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getAllBondInfo
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getAllBondInfo(java.lang.Object bsOrArray)
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getBondInfo
private java.util.Map<java.lang.String,java.lang.Object> getBondInfo(int i, javajs.util.P3 ptTemp)
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getAllChainInfo
public java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> getAllChainInfo(javajs.util.BS bs)
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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, javajs.util.BS bs)
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getAllPolymerInfo
private java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> getAllPolymerInfo(javajs.util.BS bs)
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getBasePairInfo
private java.lang.String getBasePairInfo(javajs.util.BS bs)
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getAtomResidueInfo
private static void getAtomResidueInfo(javajs.util.SB info, Atom atom)
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getAppletInfo
private java.util.Map<java.lang.String,java.lang.Object> getAppletInfo()
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getAnimationInfo
private java.util.Map<java.lang.String,java.lang.Object> getAnimationInfo()
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getBoundBoxInfo
private java.util.Map<java.lang.String,java.lang.Object> getBoundBoxInfo()
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getShapeInfo
private java.util.Map<java.lang.String,java.lang.Object> getShapeInfo()
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getAnnotationInfo
private SV getAnnotationInfo(java.lang.Object atomExpression, int type)
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getMeasurementInfo
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getMeasurementInfo()
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getMouseInfo
private java.lang.Object getMouseInfo()
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getPdbAtomData
public java.lang.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 java.lang.String getPdbData(int modelIndex, java.lang.String type, javajs.util.BS bsSelected, java.lang.Object[] parameters, javajs.util.OC out, boolean addStructure)
- Specified by:
getPdbData
in interfaceJmolPropertyManager
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getModelCml
public java.lang.String getModelCml(javajs.util.BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories)
- Specified by:
getModelCml
in interfaceJmolPropertyManager
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fixJMEFormalCharges
public java.lang.String fixJMEFormalCharges(javajs.util.BS bsAtoms, java.lang.String jme)
Fix a JME string returned from NCI CIR to have the proper formal charges.- Specified by:
fixJMEFormalCharges
in interfaceJmolPropertyManager
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