public class PropertyManager extends java.lang.Object implements JmolPropertyManager
Modifier and Type | Field and 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_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_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_VAL_INFO |
private static int |
PROP_VAR_INFO |
private static java.lang.String[] |
propertyTypes |
private static java.lang.String[] |
readableTypes |
(package private) Viewer |
vwr |
Constructor and Description |
---|
PropertyManager() |
Modifier and Type | Method and Description |
---|---|
private boolean |
addMolFile(int iModel,
javajs.util.SB mol,
BS bsAtoms,
BS bsBonds,
boolean asV3000,
boolean asJSON,
javajs.util.Quat q) |
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 java.lang.Object |
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) |
private void |
fixPDBFormat(javajs.util.Lst<java.lang.String> lines,
java.util.Map<java.lang.Integer,java.lang.Integer> map,
javajs.util.OC out)
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.
|
private java.lang.String |
fixSelectQuotes(java.lang.String propertyName) |
javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
getAllAtomInfo(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(BS bs) |
private java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> |
getAllPolymerInfo(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) |
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) |
private static void |
getAtomResidueInfo(javajs.util.SB info,
Atom atom) |
private java.lang.String |
getBasePairInfo(BS bs) |
private java.util.Map<java.lang.String,java.lang.Object> |
getBondInfo(int i,
javajs.util.P3 ptTemp) |
private void |
getBondRecordMOL(javajs.util.SB mol,
int n,
Bond b,
int[] atomMap,
boolean asV3000,
boolean asJSON) |
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,
BS bs) |
java.lang.String |
getChimeInfo(int tok,
BS bs) |
private java.lang.String |
getChimeInfoA(Atom[] atoms,
int tok,
BS bs) |
private static BS |
getCovalentBondsForAtoms(Bond[] bonds,
int bondCount,
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() |
java.lang.String |
getModelCml(BS bs,
int atomsMax,
boolean addBonds,
boolean doTransform,
boolean allTrajectories) |
java.lang.String |
getModelExtract(BS bs,
boolean doTransform,
boolean isModelKit,
java.lang.String type,
boolean allTrajectories)
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
|
java.lang.String |
getModelFileInfo(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(BS bs,
javajs.util.OC out,
boolean isPQR,
boolean doTransform,
boolean allTrajectories)
PDB or PQR only
|
java.lang.String |
getPdbData(int modelIndex,
java.lang.String type,
BS bsSelected,
java.lang.Object[] parameters,
javajs.util.OC out,
boolean addStructure) |
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
|
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 |
getVariables(java.lang.String name) |
private static boolean |
isReadableAsString(java.lang.String infoType) |
private java.lang.String |
pdbKey(int np) |
void |
setViewer(Viewer vwr) |
Viewer vwr
private java.util.Map<java.lang.String,java.lang.Integer> map
private static final java.lang.String atomExpression
private static final java.lang.String[] propertyTypes
private static final int PROP_APPLET_INFO
private static final int PROP_FILENAME
private static final int PROP_FILEHEADER
private static final int PROP_FILECONTENTS_PATH
private static final int PROP_FILECONTENTS
private static final int PROP_ANIMATION_INFO
private static final int PROP_MODEL_INFO
private static final int PROP_LIGAND_INFO
private static final int PROP_SHAPE_INFO
private static final int PROP_MEASUREMENT_INFO
private static final int PROP_CENTER_INFO
private static final int PROP_ORIENTATION_INFO
private static final int PROP_TRANSFORM_INFO
private static final int PROP_ATOM_INFO
private static final int PROP_BOND_INFO
private static final int PROP_CHAIN_INFO
private static final int PROP_POLYMER_INFO
private static final int PROP_MOLECULE_INFO
private static final int PROP_STATE_INFO
private static final int PROP_EXTRACT_MODEL
private static final int PROP_JMOL_STATUS
private static final int PROP_JMOL_VIEWER
private static final int PROP_MESSAGE_QUEUE
private static final int PROP_AUXILIARY_INFO
private static final int PROP_BOUNDBOX_INFO
private static final int PROP_DATA_INFO
private static final int PROP_IMAGE
private static final int PROP_EVALUATE
private static final int PROP_MENU
private static final int PROP_MINIMIZATION_INFO
private static final int PROP_POINTGROUP_INFO
private static final int PROP_FILE_INFO
private static final int PROP_ERROR_MESSAGE
private static final int PROP_MOUSE_INFO
private static final int PROP_ISOSURFACE_INFO
private static final int PROP_ISOSURFACE_DATA
private static final int PROP_CONSOLE_TEXT
private static final int PROP_JSPECVIEW
private static final int PROP_SCRIPT_QUEUE_INFO
private static final int PROP_NMR_INFO
private static final int PROP_VAR_INFO
private static final int PROP_DOM_INFO
private static final int PROP_VAL_INFO
private static final int PROP_SERVICE
private static final int PROP_COUNT
private static final java.lang.String[] readableTypes
public void setViewer(Viewer vwr)
setViewer
in interface JmolPropertyManager
public int getPropertyNumber(java.lang.String infoType)
getPropertyNumber
in interface JmolPropertyManager
public java.lang.String getDefaultPropertyParam(int propID)
getDefaultPropertyParam
in interface JmolPropertyManager
public boolean checkPropertyParameter(java.lang.String name)
checkPropertyParameter
in interface JmolPropertyManager
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
getProperty
in interface JmolPropertyManager
private SV[] getArguments(java.lang.String propertyName)
private java.lang.String fixSelectQuotes(java.lang.String propertyName)
public java.lang.Object extractProperty(java.lang.Object prop, java.lang.Object args, int ptr, javajs.util.Lst<java.lang.Object> v2, boolean isCompiled)
extractProperty
in interface JmolPropertyManager
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 java.lang.Object compileSelect(SV[] args)
private javajs.util.Lst<java.lang.String> getKeys(java.lang.String select)
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)
private boolean checkKey(java.lang.String k, java.lang.String key, java.lang.String lckey)
private static java.lang.String getPropertyName(int propID)
private static java.lang.String getParamType(int propID)
private static boolean isReadableAsString(java.lang.String infoType)
private java.lang.Object getPropertyAsObject(java.lang.String infoType, java.lang.Object paramInfo, java.lang.String returnType)
private java.lang.Object getImage(java.lang.String params, boolean asBytes)
private java.lang.Object getVariables(java.lang.String name)
static java.lang.Object getFileInfo(java.lang.Object objHeader, java.lang.String type)
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getMoleculeInfo(java.lang.Object atomExpression)
public java.util.Map<java.lang.String,java.lang.Object> getModelInfo(java.lang.Object atomExpression)
getModelInfo
in interface JmolPropertyManager
public java.util.Map<java.lang.String,java.lang.Object> getLigandInfo(java.lang.Object atomExpression)
getLigandInfo
in interface JmolPropertyManager
public java.lang.String getAtomData(java.lang.String atomExpression, java.lang.String type, boolean allTrajectories)
getAtomData
in interface JmolPropertyManager
public java.lang.String getModelExtract(BS bs, boolean doTransform, boolean isModelKit, java.lang.String type, boolean allTrajectories)
getModelExtract
in interface JmolPropertyManager
private boolean addMolFile(int iModel, javajs.util.SB mol, BS bsAtoms, BS bsBonds, boolean asV3000, boolean asJSON, javajs.util.Quat q)
private static BS getCovalentBondsForAtoms(Bond[] bonds, int bondCount, BS bsAtoms)
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)
private void getPointTransf(int i, ModelSet ms, Atom a, javajs.util.Quat q, javajs.util.P3 pTemp)
i
- ms
- a
- q
- pTemp
- private void getBondRecordMOL(javajs.util.SB mol, int n, Bond b, int[] atomMap, boolean asV3000, boolean asJSON)
public java.lang.String getChimeInfo(int tok, BS bs)
getChimeInfo
in interface JmolPropertyManager
public java.lang.String getModelFileInfo(BS frames)
getModelFileInfo
in interface JmolPropertyManager
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getAllAtomInfo(BS bs)
private java.util.Map<java.lang.String,java.lang.Object> getAtomInfoLong(int i, javajs.util.P3 ptTemp)
public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getAllBondInfo(java.lang.Object bsOrArray)
private java.util.Map<java.lang.String,java.lang.Object> getBondInfo(int i, javajs.util.P3 ptTemp)
public java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> getAllChainInfo(BS bs)
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)
private java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> getAllPolymerInfo(BS bs)
private java.lang.String getBasePairInfo(BS bs)
private static void getAtomResidueInfo(javajs.util.SB info, Atom atom)
private java.util.Map<java.lang.String,java.lang.Object> getAppletInfo()
private java.util.Map<java.lang.String,java.lang.Object> getAnimationInfo()
private java.util.Map<java.lang.String,java.lang.Object> getBoundBoxInfo()
private java.util.Map<java.lang.String,java.lang.Object> getShapeInfo()
private SV getAnnotationInfo(java.lang.Object atomExpression, int type)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> getMeasurementInfo()
private java.lang.Object getMouseInfo()
public java.lang.String getPdbAtomData(BS bs, javajs.util.OC out, boolean isPQR, boolean doTransform, boolean allTrajectories)
getPdbAtomData
in interface JmolPropertyManager
bs
- selected atomsout
- StringXBuilder or BufferedWriterprivate java.lang.String pdbKey(int np)
private void fixPDBFormat(javajs.util.Lst<java.lang.String> lines, java.util.Map<java.lang.Integer,java.lang.Integer> map, javajs.util.OC out)
lines
- map
- out
- public java.lang.String getPdbData(int modelIndex, java.lang.String type, BS bsSelected, java.lang.Object[] parameters, javajs.util.OC out, boolean addStructure)
getPdbData
in interface JmolPropertyManager
public java.lang.String getModelCml(BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories)
getModelCml
in interface JmolPropertyManager