public class PropertyManager extends Object implements JmolPropertyManager
Modifier and Type | Field and Description |
---|---|
private static String |
atomExpression |
private Map<String,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 String[] |
propertyTypes |
private static 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,
boolean noAromatic,
javajs.util.Quat q) |
private boolean |
checkKey(String k,
String key,
String lckey) |
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 Object |
compileSelect(SV[] args) |
Object |
extractProperty(Object prop,
Object args,
int ptr,
javajs.util.Lst<Object> v2,
boolean isCompiled) |
private int |
fixPDBFormat(javajs.util.Lst<String> lines,
Map<String,Integer> map,
javajs.util.OC out,
int[] firstAtomIndexNew,
int modelPt)
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 String |
fixSelectQuotes(String propertyName) |
javajs.util.Lst<Map<String,Object>> |
getAllAtomInfo(BS bs) |
javajs.util.Lst<Map<String,Object>> |
getAllBondInfo(Object bsOrArray) |
Map<String,javajs.util.Lst<Map<String,Object>>> |
getAllChainInfo(BS bs) |
private Map<String,javajs.util.Lst<Map<String,Object>>> |
getAllPolymerInfo(BS bs) |
private Map<String,Object> |
getAnimationInfo() |
private SV |
getAnnotationInfo(Object atomExpression,
int type) |
private Map<String,Object> |
getAppletInfo() |
private SV[] |
getArguments(String propertyName) |
String |
getAtomData(String atomExpression,
String type,
boolean allTrajectories)
use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.
|
private Map<String,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 String |
getBasePairInfo(BS bs) |
private Map<String,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,
boolean noAromatic) |
private Map<String,Object> |
getBoundBoxInfo() |
private javajs.util.Lst<Map<String,javajs.util.Lst<Map<String,Object>>>> |
getChainInfo(int modelIndex,
BS bs) |
String |
getChimeInfo(int tok,
BS bs) |
private String |
getChimeInfoA(Atom[] atoms,
int tok,
BS bs) |
private static BS |
getCovalentBondsForAtoms(Bond[] bonds,
int bondCount,
BS bsAtoms) |
String |
getDefaultPropertyParam(int propID) |
(package private) static Object |
getFileInfo(Object objHeader,
String type) |
private Object |
getImage(String params,
boolean asBytes) |
private javajs.util.Lst<String> |
getKeys(String select) |
Map<String,Object> |
getLigandInfo(Object atomExpression) |
private static void |
getMapSubset(Map<String,?> h,
String key,
Map<String,Object> h2,
javajs.util.Lst<Object> v2) |
private javajs.util.Lst<Map<String,Object>> |
getMeasurementInfo() |
private String |
getModelCif(BS bs)
just a very primitive CIF file reader
|
String |
getModelCml(BS bs,
int atomsMax,
boolean addBonds,
boolean doTransform,
boolean allTrajectories) |
String |
getModelExtract(BS bs,
boolean doTransform,
boolean isModelKit,
String type,
boolean allTrajectories)
V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR,
MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)
|
String |
getModelFileInfo(BS frames) |
Map<String,Object> |
getModelInfo(Object atomExpression) |
javajs.util.Lst<Map<String,Object>> |
getMoleculeInfo(Object atomExpression) |
private Object |
getMouseInfo() |
private static String |
getParamType(int propID) |
String |
getPdbAtomData(BS bs,
javajs.util.OC out,
boolean isPQR,
boolean doTransform,
boolean allTrajectories)
PDB or PQR only
|
String |
getPdbData(int modelIndex,
String type,
BS bsSelected,
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
|
Object |
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 Map<String,Object> |
getShapeInfo() |
private Object |
getVariables(String name) |
private static boolean |
isReadableAsString(String infoType) |
private String |
pdbKey(int np) |
void |
setViewer(Viewer vwr) |
Viewer vwr
private static final String atomExpression
private static final 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 String[] readableTypes
public void setViewer(Viewer vwr)
setViewer
in interface JmolPropertyManager
public int getPropertyNumber(String infoType)
getPropertyNumber
in interface JmolPropertyManager
public String getDefaultPropertyParam(int propID)
getDefaultPropertyParam
in interface JmolPropertyManager
public boolean checkPropertyParameter(String name)
checkPropertyParameter
in interface JmolPropertyManager
public Object getProperty(String returnType, String infoType, Object paramInfo)
getProperty
in interface JmolPropertyManager
public Object extractProperty(Object prop, Object args, int ptr, javajs.util.Lst<Object> v2, boolean isCompiled)
extractProperty
in interface JmolPropertyManager
private static void getMapSubset(Map<String,?> h, String key, Map<String,Object> h2, javajs.util.Lst<Object> v2)
private String checkMap(Map<String,?> h, String key, boolean isWild, javajs.util.Lst<Object> v2, Object args, int ptr, boolean isCaseSensitive)
private static String getPropertyName(int propID)
private static String getParamType(int propID)
private static boolean isReadableAsString(String infoType)
private Object getPropertyAsObject(String infoType, Object paramInfo, String returnType)
public Map<String,Object> getModelInfo(Object atomExpression)
getModelInfo
in interface JmolPropertyManager
public Map<String,Object> getLigandInfo(Object atomExpression)
getLigandInfo
in interface JmolPropertyManager
public String getAtomData(String atomExpression, String type, boolean allTrajectories)
getAtomData
in interface JmolPropertyManager
public String getModelExtract(BS bs, boolean doTransform, boolean isModelKit, String type, boolean allTrajectories)
getModelExtract
in interface JmolPropertyManager
private String getModelCif(BS bs)
bs
- private boolean addMolFile(int iModel, javajs.util.SB mol, BS bsAtoms, BS bsBonds, boolean asV3000, boolean asJSON, boolean noAromatic, 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, boolean noAromatic)
public String getChimeInfo(int tok, BS bs)
getChimeInfo
in interface JmolPropertyManager
public String getModelFileInfo(BS frames)
getModelFileInfo
in interface JmolPropertyManager
private javajs.util.Lst<Map<String,javajs.util.Lst<Map<String,Object>>>> getChainInfo(int modelIndex, BS bs)
private static void getAtomResidueInfo(javajs.util.SB info, Atom atom)
private Object getMouseInfo()
public String getPdbAtomData(BS bs, javajs.util.OC out, boolean isPQR, boolean doTransform, boolean allTrajectories)
getPdbAtomData
in interface JmolPropertyManager
bs
- selected atomsout
- StringXBuilder or BufferedWriterprivate String pdbKey(int np)
private int fixPDBFormat(javajs.util.Lst<String> lines, Map<String,Integer> map, javajs.util.OC out, int[] firstAtomIndexNew, int modelPt)
lines
- map
- out
- modelPt
- firstAtomIndexNew
- public String getPdbData(int modelIndex, String type, BS bsSelected, Object[] parameters, javajs.util.OC out, boolean addStructure)
getPdbData
in interface JmolPropertyManager
public String getModelCml(BS bs, int atomsMax, boolean addBonds, boolean doTransform, boolean allTrajectories)
getModelCml
in interface JmolPropertyManager