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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
org.jmol.modelset.ModelCollection
public abstract class ModelCollection
Nested Class Summary | |
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static class |
ModelCollection.StateScript
|
private static class |
ModelCollection.Structure
|
Field Summary | |
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private javax.vecmath.Point3f |
averageAtomPoint
|
protected int |
baseGroupIndex
|
private java.util.BitSet |
bboxAtoms
|
private java.util.BitSet |
bboxModels
|
private BoxInfo |
boxInfo
|
protected java.util.BitSet |
bsAll
|
protected java.util.BitSet |
bsSymmetry
|
private java.util.BitSet |
bsTemp
|
private static float |
defaultHbondMax
|
protected java.util.BitSet[] |
elementsPresent
|
protected java.lang.String[] |
frameTitles
|
protected int |
groupCount
|
protected Group[] |
groups
|
protected boolean |
haveBioClasses
|
private static float |
hbondMin
|
private boolean |
isBbcageDefault
|
protected boolean |
isPDB
|
protected boolean |
isXYZ
|
protected JmolBioResolver |
jbr
|
private javax.vecmath.Matrix3f |
matInv
|
private javax.vecmath.Matrix3f |
matTemp
|
protected int |
modelCount
|
protected int[] |
modelFileNumbers
|
protected java.lang.String[] |
modelNames
|
protected int[] |
modelNumbers
|
protected java.lang.String[] |
modelNumbersForAtomLabel
|
protected Model[] |
models
|
private java.util.Hashtable |
modelSetAuxiliaryInfo
|
protected java.lang.String |
modelSetName
|
private java.util.Properties |
modelSetProperties
|
protected int |
moleculeCount
|
protected Molecule[] |
molecules
|
private static java.lang.String[] |
pdbRecords
|
(package private) boolean |
proteinStructureTainted
|
private javax.vecmath.Point3f |
ptTemp
|
private int |
selectedMoleculeCount
|
private java.util.BitSet |
selectedMolecules
|
protected boolean |
someModelsHaveAromaticBonds
|
protected boolean |
someModelsHaveFractionalCoordinates
|
protected boolean |
someModelsHaveSymmetry
|
protected java.util.Vector |
stateScripts
|
private int |
structureCount
|
private ModelCollection.Structure[] |
structures
|
protected java.util.BitSet |
structuresDefinedInFile
|
private SymmetryInterface |
symTemp
|
private int |
thisStateModel
|
protected java.util.Vector |
trajectorySteps
|
(package private) SymmetryInterface[] |
unitCells
|
private AtomIteratorWithinSet |
withinAtomSetIterator
|
private AtomIteratorWithinModel |
withinModelIterator
|
Fields inherited from class org.jmol.modelset.BondCollection |
---|
bondCount, bonds, bsAromatic, bsPseudoHBonds, defaultCovalentMad, freeBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, numCached, showRebondTimes |
Fields inherited from class org.jmol.modelset.AtomCollection |
---|
atomCount, atomNames, atoms, atomSerials, atomTypes, bfactor100s, bspf, clientAtomReferences, ellipsoids, g3d, haveStraightness, maxBondingRadius, occupancies, partialCharges, specialAtomIDs, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMTYPE, TAINT_COORD, TAINT_MAX, tainted, vibrationVectors, viewer |
Constructor Summary | |
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ModelCollection()
|
Method Summary | |
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protected void |
addBioPolymerToModel(Polymer polymer,
Model model)
|
ModelCollection.StateScript |
addStateScript(java.lang.String script1,
java.util.BitSet bsBonds,
java.util.BitSet bsAtoms1,
java.util.BitSet bsAtoms2,
java.lang.String script2,
boolean addFrameNumber,
boolean postDefinitions)
|
int |
autoBond(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsExclude,
java.util.BitSet bsBonds)
|
private int[] |
autoBond(short order,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds,
boolean matchHbond)
|
protected int |
autoHbond(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
float maxXYDistance,
float minAttachedAngle)
|
private int |
calcAtomsMinMax(java.util.BitSet bs,
BoxInfo boxInfo)
|
void |
calcBoundBoxDimensions(java.util.BitSet bs)
|
void |
calcHydrogenBonds(java.util.BitSet bsA,
java.util.BitSet bsB)
|
float |
calcRotationRadius(java.util.BitSet bs)
|
float |
calcRotationRadius(int modelIndex,
javax.vecmath.Point3f center)
|
void |
calcSelectedGroupsCount(java.util.BitSet bsSelected)
|
void |
calcSelectedMoleculesCount(java.util.BitSet bsSelected)
|
void |
calcSelectedMonomersCount(java.util.BitSet bsSelected)
|
javax.vecmath.Vector3f |
calculateMolecularDipole(int modelIndex)
|
protected void |
calculatePolymers(java.util.BitSet alreadyDefined)
|
void |
calculateStraightness()
|
protected void |
calculateStructuresAllExcept(java.util.BitSet alreadyDefined,
boolean addFileData)
allows rebuilding of PDB structures; also accessed by ModelManager from Eval |
private void |
calcUnitCellMinMax()
|
private static boolean |
checkMinAttachedAngle(Atom atom1,
Atom atom2,
float minAngle,
javax.vecmath.Vector3f v1,
javax.vecmath.Vector3f v2)
|
private static boolean |
checkMinAttachedAngle(Atom atom1,
Bond[] bonds1,
Atom atom2,
float minAngle,
javax.vecmath.Vector3f v1,
javax.vecmath.Vector3f v2)
|
void |
clearCalculatedHydrogenBonds(int baseIndex,
java.util.BitSet bsAtoms)
|
protected void |
clearDataFrameReference(int modelIndex)
|
protected void |
defineStructure(int modelIndex,
java.lang.String structureType,
java.lang.String structureID,
int serialID,
int strandCount,
char startChainID,
int startSequenceNumber,
char startInsertionCode,
char endChainID,
int endSequenceNumber,
char endInsertionCode)
|
protected void |
deleteModel(int modelIndex,
int firstAtomIndex,
int nAtoms,
java.util.BitSet bsAtoms,
java.util.BitSet bsBonds)
|
private void |
freezeModels()
|
java.util.Vector |
getAllAtomInfo(java.util.BitSet bs)
|
java.util.Vector |
getAllBondInfo(java.util.BitSet bs)
|
java.util.Hashtable |
getAllChainInfo(java.util.BitSet bs)
|
java.util.Hashtable |
getAllPolymerInfo(java.util.BitSet bs)
|
int |
getAltLocCountInModel(int modelIndex)
|
int |
getAltLocIndexInModel(int modelIndex,
char alternateLocationID)
|
java.lang.String |
getAltLocListInModel(int modelIndex)
|
java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general unqualified lookup of atom set type |
int |
getAtomCountInModel(int modelIndex)
|
void |
getAtomIdentityInfo(int i,
java.util.Hashtable info)
|
private java.util.Hashtable |
getAtomInfoLong(int i)
|
private void |
getAtomRecordMOL(java.lang.StringBuffer s,
int i)
|
java.util.BitSet |
getAtomsConnected(float min,
float max,
int intType,
java.util.BitSet bs)
|
javax.vecmath.Point3f |
getAtomSetCenter(java.util.BitSet bs)
|
java.util.BitSet |
getAtomsWithin(float distance,
java.util.BitSet bs,
boolean withinAllModels)
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms |
java.util.BitSet |
getAtomsWithin(float distance,
javax.vecmath.Point3f coord,
java.util.BitSet bsResult,
int modelIndex)
|
java.util.Hashtable |
getAuxiliaryInfo(java.util.BitSet bsModels)
|
javax.vecmath.Point3f |
getAverageAtomPoint()
|
javax.vecmath.Point3f[] |
getBboxVertices()
|
int |
getBioPolymerCount()
|
int |
getBioPolymerCountInModel(int modelIndex)
|
int |
getBondCountInModel(int modelIndex)
for general use |
private java.util.Hashtable |
getBondInfo(int i)
|
private void |
getBondRecordMOL(java.lang.StringBuffer s,
int i,
int[] atomMap)
|
javax.vecmath.Point3f |
getBoundBoxCenter(int modelIndex)
|
java.lang.String |
getBoundBoxCommand(boolean withOptions)
|
javax.vecmath.Vector3f |
getBoundBoxCornerVector()
|
java.util.Hashtable |
getBoundBoxInfo()
|
java.util.BitSet |
getBoundBoxModels()
|
BoxInfo |
getBoxInfo(java.util.BitSet bs)
|
java.util.BitSet |
getBranchBitSet(int atomIndex,
int atomIndexNot)
|
SymmetryInterface[] |
getCellInfos()
|
int |
getChainCount(boolean addWater)
|
int |
getChainCountInModel(int modelIndex,
boolean countWater)
|
private java.util.Vector |
getChainInfo(int modelIndex,
java.util.BitSet bs)
|
java.lang.String |
getChimeInfo(int tok,
java.util.BitSet bs)
|
private void |
getCovalentlyConnectedBitSet(Atom atom,
java.util.BitSet bs,
java.util.BitSet bsToTest)
|
java.util.BitSet |
getElementsPresentBitSet(int modelIndex)
|
java.lang.String |
getFileHeader(int modelIndex)
|
javax.vecmath.Point3f[] |
getFrameOffsets(java.util.BitSet bsAtoms)
|
java.lang.String |
getFrameTitle(int modelIndex)
|
private java.lang.String |
getFullPDBHeader(int modelIndex)
|
int |
getGroupCount()
|
int |
getGroupCountInModel(int modelIndex)
|
java.util.Hashtable |
getHeteroList(int modelIndex)
|
int |
getInsertionCodeIndexInModel(int modelIndex,
char insertionCode)
|
int |
getInsertionCountInModel(int modelIndex)
|
private java.lang.String |
getInsertionListInModel(int modelIndex)
|
java.util.BitSet |
getIterativeModels(boolean allowJmolData)
only some models can be iterated through. |
int |
getJmolDataFrameIndex(int modelIndex,
java.lang.String type)
|
int |
getJmolDataSourceFrame(int modelIndex)
|
java.lang.String |
getJmolFrameType(int modelIndex)
|
protected Model |
getModel(int modelIndex)
|
java.util.BitSet |
getModelAtomBitSet(int modelIndex,
boolean asCopy)
|
java.util.Hashtable |
getModelAuxiliaryInfo(int modelIndex)
|
java.lang.Object |
getModelAuxiliaryInfo(int modelIndex,
java.lang.String key)
|
protected boolean |
getModelAuxiliaryInfoBoolean(int modelIndex,
java.lang.String keyName)
|
protected int |
getModelAuxiliaryInfoInt(int modelIndex,
java.lang.String keyName)
|
java.util.BitSet |
getModelBitSet(java.util.BitSet atomList,
boolean allTrajectories)
|
int[] |
getModelCellRange(int modelIndex)
|
int |
getModelCount()
|
javax.vecmath.Vector3f |
getModelDipole(int modelIndex)
|
java.lang.String |
getModelExtract(java.util.BitSet bs)
|
java.lang.String |
getModelFileInfo(java.util.BitSet frames)
|
java.lang.String |
getModelFileName(int modelIndex)
|
int |
getModelFileNumber(int modelIndex)
|
java.lang.String |
getModelFileType(int modelIndex)
|
java.util.Hashtable |
getModelInfo(java.util.BitSet bsModels)
|
java.lang.String |
getModelInfoAsString()
|
java.lang.String |
getModelName(int modelIndex)
|
int |
getModelNumber(int modelIndex)
|
java.lang.String |
getModelNumberDotted(int modelIndex)
|
java.lang.String |
getModelNumberForAtomLabel(int modelIndex)
|
StateManager.Orientation |
getModelOrientation(int modelIndex)
|
java.util.Properties |
getModelProperties(int modelIndex)
|
java.lang.String |
getModelProperty(int modelIndex,
java.lang.String property)
|
Model[] |
getModels()
|
java.util.Hashtable |
getModelSetAuxiliaryInfo()
|
java.lang.Object |
getModelSetAuxiliaryInfo(java.lang.String keyName)
|
protected boolean |
getModelSetAuxiliaryInfoBoolean(java.lang.String keyName)
|
java.lang.String |
getModelSetName()
|
java.util.Properties |
getModelSetProperties()
|
java.lang.String |
getModelSetProperty(java.lang.String propertyName)
|
int |
getModelSymmetryCount(int modelIndex)
|
java.lang.String |
getModelTitle(int modelIndex)
|
java.lang.String |
getMoInfo(int modelIndex)
|
java.util.BitSet |
getMoleculeBitSet(java.util.BitSet bs)
|
java.util.BitSet |
getMoleculeBitSet(int atomIndex)
|
int |
getMoleculeCountInModel(int modelIndex)
|
int |
getMoleculeIndex(int atomIndex)
|
java.util.Vector |
getMoleculeInfo(java.util.BitSet bsAtoms)
|
private void |
getMolecules()
|
float[] |
getNotionalUnitcell()
deprecated due to multimodel issues, but required by an interface -- do NOT remove. |
java.lang.String |
getPdbAtomData(java.util.BitSet bs)
|
java.lang.String |
getPdbData(int modelIndex,
java.lang.String type,
java.util.BitSet bsSelected,
boolean addHeader)
|
java.lang.String |
getPDBHeader(int modelIndex)
|
javax.vecmath.Point3f[] |
getPolymerLeadMidPoints(int iModel,
int iPolymer)
|
void |
getPolymerPointsAndVectors(java.util.BitSet bs,
java.util.Vector vList)
|
java.lang.String |
getProteinStructureState(java.util.BitSet bsAtoms,
boolean taintedOnly,
boolean needPhiPsi,
boolean pdbFormat)
|
java.util.BitSet |
getSequenceBits(java.lang.String specInfo,
java.util.BitSet bs)
|
java.util.Hashtable |
getSpaceGroupInfo(java.lang.String spaceGroup)
|
java.lang.Object |
getSymmetryInfo(java.util.BitSet bsAtoms,
java.lang.String xyz,
int op,
javax.vecmath.Point3f pt,
java.lang.String id,
int type)
|
java.lang.String |
getSymmetryInfoAsString()
|
private java.lang.String |
getSymmetryInfoAsString(int modelIndex)
|
private void |
getSymTemp()
|
protected int |
getTrajectoryCount()
|
int |
getTrajectoryIndex(int modelIndex)
|
SymmetryInterface |
getUnitCell(int modelIndex)
|
java.lang.String |
getUnitCellInfoText()
|
AtomIndexIterator |
getWithinAtomSetIterator(int atomIndex,
float distance,
java.util.BitSet bsSelected,
boolean isGreaterOnly,
boolean modelZeroBased)
|
AtomIndexIterator |
getWithinModelIterator(Atom atomCenter,
float radius)
|
private AtomIndexIterator |
getWithinModelIterator(int modelIndex,
javax.vecmath.Point3f center,
float radius)
|
boolean |
hasCalculatedHBonds(java.util.BitSet bsAtoms)
|
protected void |
initializeBspf()
|
protected void |
initializeBspt(int modelIndex)
|
void |
invertSelected(javax.vecmath.Point3f pt,
javax.vecmath.Point4f plane,
java.util.BitSet bs)
|
private boolean |
isJmolDataFrame(Atom atom)
|
boolean |
isJmolDataFrame(int modelIndex)
|
boolean |
isTrajectory(int modelIndex)
|
boolean |
isTrajectory(int[] countPlusIndices)
|
protected int[] |
makeConnections(float minDistance,
float maxDistance,
short order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds)
|
protected void |
merge(ModelSet modelSet)
initial transfer of model data from old to new model set. |
static int |
modelFileNumberFromFloat(float fDotM)
|
boolean |
modelHasVibrationVectors(int modelIndex)
|
private void |
propagateSecondaryStructure()
|
void |
recalculateLeadMidpointsAndWingVectors(int modelIndex)
|
private void |
recalculatePositionDependentQuantities()
|
protected void |
releaseModelSet()
|
void |
rotateAtoms(javax.vecmath.Matrix3f mNew,
javax.vecmath.Matrix3f matrixRotate,
java.util.BitSet bsAtoms,
boolean fullMolecule,
javax.vecmath.Point3f center,
boolean isInternal)
|
void |
saveModelOrientation(int modelIndex,
StateManager.Orientation orientation)
|
void |
selectDisplayedTrajectories(java.util.BitSet bs)
|
void |
setAtomCoord(java.util.BitSet bs,
int tokType,
java.lang.Object xyzValues)
|
void |
setAtomCoordRelative(javax.vecmath.Point3f offset,
java.util.BitSet bs)
|
void |
setAtomProperty(java.util.BitSet bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list)
|
void |
setBoundBox(javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
boolean byCorner)
|
java.util.BitSet |
setConformation(int modelIndex,
java.util.BitSet bsConformation)
|
java.util.BitSet |
setConformation(int modelIndex,
int conformationIndex)
|
boolean |
setCrystallographicDefaults()
|
void |
setFrameTitle(int modelIndex,
java.lang.String title)
|
void |
setJmolDataFrame(java.lang.String type,
int modelIndex,
int modelDataIndex)
|
void |
setModelAuxiliaryInfo(int modelIndex,
java.lang.Object key,
java.lang.Object value)
|
protected void |
setModelSetAuxiliaryInfo(java.util.Hashtable modelSetAuxiliaryInfo)
|
protected void |
setModelSetProperties(java.util.Properties modelSetProperties)
|
void |
setProteinType(java.util.BitSet bs,
byte iType)
|
boolean |
setRotationRadius(int modelIndex,
float angstroms)
|
(package private) void |
setStructureIds()
|
boolean |
setUnitCellOffset(int modelIndex,
int nnn)
|
boolean |
setUnitCellOffset(int modelIndex,
javax.vecmath.Point3f pt)
|
void |
toCartesian(int modelIndex,
javax.vecmath.Point3f pt)
|
void |
toFractional(int modelIndex,
javax.vecmath.Point3f pt)
|
void |
toUnitCell(int modelIndex,
javax.vecmath.Point3f pt,
javax.vecmath.Point3f offset)
|
Methods inherited from class org.jmol.modelset.BondCollection |
---|
addHydrogenBond, assignAromaticBonds, assignAromaticBonds, bondAtoms, bondMutually, checkValencesAndBond, deleteAllBonds, deleteBonds, deleteConnections, getBondAt, getBondAtom1, getBondAtom2, getBondColix1, getBondColix2, getBondCount, getBondIterator, getBondIterator, getBondModelIndex, getBondOrder, getBondOrder, getBondRadius, getBonds, getBondsForSelectedAtoms, getDefaultMadFromOrder, getOrAddBond, hBondMutually, resetAromatic, setBond |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected java.util.BitSet bsSymmetry
protected java.lang.String modelSetName
protected Model[] models
protected int modelCount
SymmetryInterface[] unitCells
protected int[] modelNumbers
protected int[] modelFileNumbers
protected java.lang.String[] modelNumbersForAtomLabel
protected java.lang.String[] modelNames
protected java.lang.String[] frameTitles
protected java.util.BitSet[] elementsPresent
protected boolean isXYZ
protected boolean isPDB
private java.util.Properties modelSetProperties
private java.util.Hashtable modelSetAuxiliaryInfo
protected Group[] groups
protected int groupCount
protected int baseGroupIndex
private int structureCount
private ModelCollection.Structure[] structures
protected boolean haveBioClasses
protected JmolBioResolver jbr
protected java.util.BitSet structuresDefinedInFile
protected boolean someModelsHaveSymmetry
protected boolean someModelsHaveAromaticBonds
protected boolean someModelsHaveFractionalCoordinates
protected Molecule[] molecules
protected int moleculeCount
private final javax.vecmath.Matrix3f matTemp
private final javax.vecmath.Matrix3f matInv
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3f averageAtomPoint
private boolean isBbcageDefault
private java.util.BitSet bboxModels
private java.util.BitSet bboxAtoms
private final BoxInfo boxInfo
protected java.util.Vector stateScripts
private int thisStateModel
protected java.util.Vector trajectorySteps
private static final java.lang.String[] pdbRecords
private java.util.BitSet bsTemp
private java.util.BitSet selectedMolecules
private int selectedMoleculeCount
private AtomIteratorWithinModel withinModelIterator
private AtomIteratorWithinSet withinAtomSetIterator
protected java.util.BitSet bsAll
private static float defaultHbondMax
private static float hbondMin
boolean proteinStructureTainted
private SymmetryInterface symTemp
Constructor Detail |
---|
public ModelCollection()
Method Detail |
---|
protected void merge(ModelSet modelSet)
merge
in class BondCollection
modelSet
- protected void releaseModelSet()
releaseModelSet
in class BondCollection
public java.lang.String getModelSetName()
public Model[] getModels()
public int getModelCount()
public SymmetryInterface[] getCellInfos()
public SymmetryInterface getUnitCell(int modelIndex)
public java.lang.String getModelName(int modelIndex)
public java.lang.String getModelTitle(int modelIndex)
public java.lang.String getModelFileName(int modelIndex)
public void setFrameTitle(int modelIndex, java.lang.String title)
public java.lang.String getFrameTitle(int modelIndex)
public java.lang.String getModelNumberForAtomLabel(int modelIndex)
protected void calculatePolymers(java.util.BitSet alreadyDefined)
protected void addBioPolymerToModel(Polymer polymer, Model model)
public float[] getNotionalUnitcell()
public boolean setCrystallographicDefaults()
public javax.vecmath.Point3f getAverageAtomPoint()
public javax.vecmath.Point3f getBoundBoxCenter(int modelIndex)
public javax.vecmath.Vector3f getBoundBoxCornerVector()
public javax.vecmath.Point3f[] getBboxVertices()
public java.util.Hashtable getBoundBoxInfo()
public java.util.BitSet getBoundBoxModels()
public void setBoundBox(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean byCorner)
public java.lang.String getBoundBoxCommand(boolean withOptions)
public boolean setRotationRadius(int modelIndex, float angstroms)
public float calcRotationRadius(int modelIndex, javax.vecmath.Point3f center)
public void calcBoundBoxDimensions(java.util.BitSet bs)
public BoxInfo getBoxInfo(java.util.BitSet bs)
private int calcAtomsMinMax(java.util.BitSet bs, BoxInfo boxInfo)
private void calcUnitCellMinMax()
public float calcRotationRadius(java.util.BitSet bs)
public javax.vecmath.Point3f getAtomSetCenter(java.util.BitSet bs)
public void setAtomProperty(java.util.BitSet bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
setAtomProperty
in class AtomCollection
public ModelCollection.StateScript addStateScript(java.lang.String script1, java.util.BitSet bsBonds, java.util.BitSet bsAtoms1, java.util.BitSet bsAtoms2, java.lang.String script2, boolean addFrameNumber, boolean postDefinitions)
protected void defineStructure(int modelIndex, java.lang.String structureType, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSequenceNumber, char startInsertionCode, char endChainID, int endSequenceNumber, char endInsertionCode)
protected void calculateStructuresAllExcept(java.util.BitSet alreadyDefined, boolean addFileData)
alreadyDefined
- set to skip calculationaddFileData
- in the case of loading, we add the PDB datapublic void setProteinType(java.util.BitSet bs, byte iType)
private void freezeModels()
public java.util.BitSet setConformation(int modelIndex, java.util.BitSet bsConformation)
public java.util.BitSet setConformation(int modelIndex, int conformationIndex)
public java.util.Hashtable getHeteroList(int modelIndex)
protected void setModelSetProperties(java.util.Properties modelSetProperties)
protected void setModelSetAuxiliaryInfo(java.util.Hashtable modelSetAuxiliaryInfo)
public java.util.Properties getModelSetProperties()
public java.util.Hashtable getModelSetAuxiliaryInfo()
public java.lang.String getModelSetProperty(java.lang.String propertyName)
public java.lang.Object getModelSetAuxiliaryInfo(java.lang.String keyName)
protected boolean getModelSetAuxiliaryInfoBoolean(java.lang.String keyName)
protected int getTrajectoryCount()
public int getTrajectoryIndex(int modelIndex)
public boolean isTrajectory(int modelIndex)
public boolean isTrajectory(int[] countPlusIndices)
public java.util.BitSet getModelBitSet(java.util.BitSet atomList, boolean allTrajectories)
public java.util.BitSet getIterativeModels(boolean allowJmolData)
allowJmolData
-
public void selectDisplayedTrajectories(java.util.BitSet bs)
public java.lang.String getModelNumberDotted(int modelIndex)
public int getModelNumber(int modelIndex)
public int getModelFileNumber(int modelIndex)
public java.util.Properties getModelProperties(int modelIndex)
public java.lang.String getModelProperty(int modelIndex, java.lang.String property)
public java.util.Hashtable getModelAuxiliaryInfo(int modelIndex)
public void setModelAuxiliaryInfo(int modelIndex, java.lang.Object key, java.lang.Object value)
public java.lang.Object getModelAuxiliaryInfo(int modelIndex, java.lang.String key)
protected boolean getModelAuxiliaryInfoBoolean(int modelIndex, java.lang.String keyName)
protected int getModelAuxiliaryInfoInt(int modelIndex, java.lang.String keyName)
protected Model getModel(int modelIndex)
public int getInsertionCountInModel(int modelIndex)
public java.lang.String getModelFileType(int modelIndex)
public static int modelFileNumberFromFloat(float fDotM)
public int getAltLocCountInModel(int modelIndex)
private void propagateSecondaryStructure()
public int getChainCount(boolean addWater)
public int getBioPolymerCount()
public int getBioPolymerCountInModel(int modelIndex)
public void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.Vector vList)
public void recalculateLeadMidpointsAndWingVectors(int modelIndex)
public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int iModel, int iPolymer)
public int getChainCountInModel(int modelIndex, boolean countWater)
public int getGroupCount()
public int getGroupCountInModel(int modelIndex)
public void calcSelectedGroupsCount(java.util.BitSet bsSelected)
public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
public void calcHydrogenBonds(java.util.BitSet bsA, java.util.BitSet bsB)
public void calculateStraightness()
public java.lang.String getPdbAtomData(java.util.BitSet bs)
public java.lang.String getPdbData(int modelIndex, java.lang.String type, java.util.BitSet bsSelected, boolean addHeader)
public boolean isJmolDataFrame(int modelIndex)
private boolean isJmolDataFrame(Atom atom)
public void setJmolDataFrame(java.lang.String type, int modelIndex, int modelDataIndex)
public int getJmolDataFrameIndex(int modelIndex, java.lang.String type)
protected void clearDataFrameReference(int modelIndex)
public java.lang.String getJmolFrameType(int modelIndex)
public int getJmolDataSourceFrame(int modelIndex)
public void saveModelOrientation(int modelIndex, StateManager.Orientation orientation)
public StateManager.Orientation getModelOrientation(int modelIndex)
private java.lang.String getFullPDBHeader(int modelIndex)
public java.lang.String getPDBHeader(int modelIndex)
public java.lang.String getFileHeader(int modelIndex)
public java.util.Hashtable getModelInfo(java.util.BitSet bsModels)
public int getAltLocIndexInModel(int modelIndex, char alternateLocationID)
public int getInsertionCodeIndexInModel(int modelIndex, char insertionCode)
public java.lang.String getAltLocListInModel(int modelIndex)
private java.lang.String getInsertionListInModel(int modelIndex)
public int getModelSymmetryCount(int modelIndex)
public int[] getModelCellRange(int modelIndex)
public boolean modelHasVibrationVectors(int modelIndex)
public java.util.BitSet getElementsPresentBitSet(int modelIndex)
private java.lang.String getSymmetryInfoAsString(int modelIndex)
public void toCartesian(int modelIndex, javax.vecmath.Point3f pt)
public void toFractional(int modelIndex, javax.vecmath.Point3f pt)
public void toUnitCell(int modelIndex, javax.vecmath.Point3f pt, javax.vecmath.Point3f offset)
public boolean setUnitCellOffset(int modelIndex, javax.vecmath.Point3f pt)
public boolean setUnitCellOffset(int modelIndex, int nnn)
public java.util.Vector getMoleculeInfo(java.util.BitSet bsAtoms)
public int getMoleculeIndex(int atomIndex)
public void rotateAtoms(javax.vecmath.Matrix3f mNew, javax.vecmath.Matrix3f matrixRotate, java.util.BitSet bsAtoms, boolean fullMolecule, javax.vecmath.Point3f center, boolean isInternal)
public java.util.BitSet getMoleculeBitSet(java.util.BitSet bs)
public java.util.BitSet getMoleculeBitSet(int atomIndex)
public void invertSelected(javax.vecmath.Point3f pt, javax.vecmath.Point4f plane, java.util.BitSet bs)
public javax.vecmath.Vector3f getModelDipole(int modelIndex)
public javax.vecmath.Vector3f calculateMolecularDipole(int modelIndex)
public int getMoleculeCountInModel(int modelIndex)
public void calcSelectedMoleculesCount(java.util.BitSet bsSelected)
private void getMolecules()
public java.util.BitSet getBranchBitSet(int atomIndex, int atomIndexNot)
private void getCovalentlyConnectedBitSet(Atom atom, java.util.BitSet bs, java.util.BitSet bsToTest)
public boolean hasCalculatedHBonds(java.util.BitSet bsAtoms)
public void clearCalculatedHydrogenBonds(int baseIndex, java.util.BitSet bsAtoms)
protected void initializeBspf()
protected void initializeBspt(int modelIndex)
public AtomIndexIterator getWithinAtomSetIterator(int atomIndex, float distance, java.util.BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
public AtomIndexIterator getWithinModelIterator(Atom atomCenter, float radius)
private AtomIndexIterator getWithinModelIterator(int modelIndex, javax.vecmath.Point3f center, float radius)
public int getBondCountInModel(int modelIndex)
BondCollection
getBondCountInModel
in class BondCollection
modelIndex
- the model of interest or -1 for all
public void setAtomCoordRelative(javax.vecmath.Point3f offset, java.util.BitSet bs)
public void setAtomCoord(java.util.BitSet bs, int tokType, java.lang.Object xyzValues)
setAtomCoord
in class AtomCollection
private void recalculatePositionDependentQuantities()
public int getAtomCountInModel(int modelIndex)
getAtomCountInModel
in class AtomCollection
public java.util.BitSet getModelAtomBitSet(int modelIndex, boolean asCopy)
modelIndex
- asCopy
- MUST BE TRUE IF THE BITSET IS GOING TO BE MODIFIED!
public java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
getAtomBits
in class BondCollection
tokType
- specInfo
-
public java.util.BitSet getAtomsWithin(float distance, java.util.BitSet bs, boolean withinAllModels)
distance
- bs
- withinAllModels
-
public java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point3f coord, java.util.BitSet bsResult, int modelIndex)
public java.util.BitSet getSequenceBits(java.lang.String specInfo, java.util.BitSet bs)
protected int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds)
public int autoBond(java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsExclude, java.util.BitSet bsBonds)
private int[] autoBond(short order, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds, boolean matchHbond)
private static boolean checkMinAttachedAngle(Atom atom1, Atom atom2, float minAngle, javax.vecmath.Vector3f v1, javax.vecmath.Vector3f v2)
private static boolean checkMinAttachedAngle(Atom atom1, Bond[] bonds1, Atom atom2, float minAngle, javax.vecmath.Vector3f v1, javax.vecmath.Vector3f v2)
protected int autoHbond(java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, float maxXYDistance, float minAttachedAngle)
void setStructureIds()
public java.lang.String getProteinStructureState(java.util.BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi, boolean pdbFormat)
public java.lang.String getModelInfoAsString()
public java.lang.String getSymmetryInfoAsString()
public java.util.BitSet getAtomsConnected(float min, float max, int intType, java.util.BitSet bs)
public java.lang.String getModelExtract(java.util.BitSet bs)
private void getAtomRecordMOL(java.lang.StringBuffer s, int i)
private void getBondRecordMOL(java.lang.StringBuffer s, int i, int[] atomMap)
public java.lang.String getChimeInfo(int tok, java.util.BitSet bs)
getChimeInfo
in class AtomCollection
public java.lang.String getModelFileInfo(java.util.BitSet frames)
public java.util.Hashtable getAuxiliaryInfo(java.util.BitSet bsModels)
public java.util.Vector getAllAtomInfo(java.util.BitSet bs)
public void getAtomIdentityInfo(int i, java.util.Hashtable info)
private java.util.Hashtable getAtomInfoLong(int i)
public java.util.Vector getAllBondInfo(java.util.BitSet bs)
private java.util.Hashtable getBondInfo(int i)
public java.util.Hashtable getAllChainInfo(java.util.BitSet bs)
private java.util.Vector getChainInfo(int modelIndex, java.util.BitSet bs)
public java.util.Hashtable getAllPolymerInfo(java.util.BitSet bs)
public java.lang.String getUnitCellInfoText()
public java.util.Hashtable getSpaceGroupInfo(java.lang.String spaceGroup)
private void getSymTemp()
public java.lang.Object getSymmetryInfo(java.util.BitSet bsAtoms, java.lang.String xyz, int op, javax.vecmath.Point3f pt, java.lang.String id, int type)
protected void deleteModel(int modelIndex, int firstAtomIndex, int nAtoms, java.util.BitSet bsAtoms, java.util.BitSet bsBonds)
public javax.vecmath.Point3f[] getFrameOffsets(java.util.BitSet bsAtoms)
public java.lang.String getMoInfo(int modelIndex)
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