org.jmol.modelset

Class ModelCollection

public abstract class ModelCollection extends BondCollection

Nested Class Summary
protected static classModelCollection.StateScript
static classModelCollection.Structure
Field Summary
Point3faverageAtomPoint
protected intbaseGroupIndex
BitSetbboxAtoms
BitSetbboxModels
BoxInfoboxInfo
protected BitSetbsAll
protected BitSetbsSymmetry
BitSetbsTemp
protected BitSet[]elementsPresent
String[]frameTitles
protected intgroupCount
protected Group[]groups
protected booleanhaveBioClasses
booleanisBbcageDefault
protected booleanisPDB
protected booleanisXYZ
protected JmolBioResolverjbr
Matrix3fmatInv
Matrix3fmatTemp
protected intmodelCount
int[]modelFileNumbers
String[]modelNames
int[]modelNumbers
String[]modelNumbersForAtomLabel
protected Model[]models
HashtablemodelSetAuxiliaryInfo
protected StringmodelSetName
PropertiesmodelSetProperties
protected intmoleculeCount
protected Molecule[]molecules
static String[]pdbRecords
booleanproteinStructureTainted
Point3fptTemp
intselectedMoleculeCount
BitSetselectedMolecules
protected booleansomeModelsHaveAromaticBonds
protected booleansomeModelsHaveFractionalCoordinates
protected booleansomeModelsHaveSymmetry
protected VectorstateScripts
intstructureCount
ModelCollection.Structure[]structures
protected BitSetstructuresDefinedInFile
SymmetryInterfacesymTemp
intthisStateModel
protected Vectortrajectories
SymmetryInterface[]unitCells
AtomIteratorWithinSetwithinAtomSetIterator
AtomIteratorWithinModelwithinModelIterator
Method Summary
protected voidaddBioPolymerToModel(Polymer polymer, Model model)
voidaddStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
intautoBond(BitSet bsA, BitSet bsB, BitSet bsExclude, BitSet bsBonds)
int[]autoBond(short order, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, boolean matchHbond)
intcalcAtomsMinMax(BitSet bs, BoxInfo boxInfo)
voidcalcBoundBoxDimensions(BitSet bs)
voidcalcHydrogenBonds(BitSet bsA, BitSet bsB)
floatcalcRotationRadius(int modelIndex, Point3f center)
floatcalcRotationRadius(BitSet bs)
voidcalcSelectedGroupsCount(BitSet bsSelected)
voidcalcSelectedMoleculesCount(BitSet bsSelected)
voidcalcSelectedMonomersCount(BitSet bsSelected)
Vector3fcalculateMolecularDipole(int modelIndex)
protected voidcalculatePolymers(BitSet alreadyDefined)
voidcalculateStraightness()
voidcalculateStructuresAllExcept(BitSet alreadyDefined, boolean addFileData)
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
voidcalcUnitCellMinMax()
voidclearCalculatedHydrogenBonds(int baseIndex, BitSet bsAtoms)
protected voidclearDataFrameReference(int modelIndex)
protected voiddefineStructure(int modelIndex, String structureType, char startChainID, int startSequenceNumber, char startInsertionCode, char endChainID, int endSequenceNumber, char endInsertionCode)
voiddeleteAtoms(int modelIndex, int firstAtomIndex, int nAtoms, BitSet bsAtoms, BitSet bsBonds)
voidfreezeModels()
VectorgetAllAtomInfo(BitSet bs)
VectorgetAllBondInfo(BitSet bs)
HashtablegetAllChainInfo(BitSet bs)
HashtablegetAllPolymerInfo(BitSet bs)
intgetAltLocCountInModel(int modelIndex)
intgetAltLocIndexInModel(int modelIndex, char alternateLocationID)
StringgetAltLocListInModel(int modelIndex)
BitSetgetAtomBits(int tokType, Object specInfo)
general unqualified lookup of atom set type
intgetAtomCountInModel(int modelIndex)
voidgetAtomIdentityInfo(int i, Hashtable info)
HashtablegetAtomInfoLong(int i)
voidgetAtomRecordMOL(StringBuffer s, int i)
BitSetgetAtomsConnected(float min, float max, int intType, BitSet bs)
BitSetgetAtomsWithin(float distance, 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
BitSetgetAtomsWithin(float distance, Point3f coord)
Point3fgetAtomSetCenter(BitSet bs)
HashtablegetAuxiliaryInfo(BitSet bsModels)
Point3fgetAverageAtomPoint()
Point3f[]getBboxVertices()
intgetBioPolymerCount()
intgetBioPolymerCountInModel(int modelIndex)
intgetBondCountInModel(int modelIndex)
HashtablegetBondInfo(int i)
voidgetBondRecordMOL(StringBuffer s, int i, int[] atomMap)
Point3fgetBoundBoxCenter(int modelIndex)
StringgetBoundBoxCommand(boolean withOptions)
Vector3fgetBoundBoxCornerVector()
HashtablegetBoundBoxInfo()
BitSetgetBoundBoxModels()
BoxInfogetBoxInfo(BitSet bs)
BitSetgetBranchBitSet(int atomIndex, int atomIndexNot)
SymmetryInterface[]getCellInfos()
intgetChainCount(boolean addWater)
intgetChainCountInModel(int modelIndex, boolean countWater)
VectorgetChainInfo(int modelIndex, BitSet bs)
StringgetChimeInfo(int tok, BitSet bs)
voidgetCovalentlyConnectedBitSet(Atom atom, BitSet bs, BitSet bsToTest)
BitSetgetElementsPresentBitSet(int modelIndex)
StringgetFileHeader(int modelIndex)
StringgetFrameTitle(int modelIndex)
StringgetFullPDBHeader(int modelIndex)
intgetGroupCount()
intgetGroupCountInModel(int modelIndex)
HashtablegetHeteroList(int modelIndex)
intgetInsertionCodeIndexInModel(int modelIndex, char insertionCode)
intgetInsertionCountInModel(int modelIndex)
StringgetInsertionListInModel(int modelIndex)
BitSetgetIterativeModels(boolean allowJmolData)
only some models can be iterated through. models for which trajectoryBaseIndexes[i] !
intgetJmolDataFrameIndex(int modelIndex, String type)
intgetJmolDataSourceFrame(int modelIndex)
StringgetJmolFrameType(int modelIndex)
ModelgetModel(int modelIndex)
BitSetgetModelAtomBitSet(int modelIndex, boolean asCopy)
HashtablegetModelAuxiliaryInfo(int modelIndex)
ObjectgetModelAuxiliaryInfo(int modelIndex, String key)
protected booleangetModelAuxiliaryInfoBoolean(int modelIndex, String keyName)
protected intgetModelAuxiliaryInfoInt(int modelIndex, String keyName)
int[]getModelCellRange(int modelIndex)
intgetModelCount()
Vector3fgetModelDipole(int modelIndex)
StringgetModelExtract(BitSet bs)
StringgetModelFileInfo(BitSet frames)
StringgetModelFileName(int modelIndex)
intgetModelFileNumber(int modelIndex)
StringgetModelFileType(int modelIndex)
HashtablegetModelInfo(BitSet bsModels)
StringgetModelInfoAsString()
StringgetModelName(int modelIndex)
intgetModelNumber(int modelIndex)
StringgetModelNumberDotted(int modelIndex)
StringgetModelNumberForAtomLabel(int modelIndex)
StateManager.OrientationgetModelOrientation(int modelIndex)
PropertiesgetModelProperties(int modelIndex)
StringgetModelProperty(int modelIndex, String property)
Model[]getModels()
HashtablegetModelSetAuxiliaryInfo()
ObjectgetModelSetAuxiliaryInfo(String keyName)
booleangetModelSetAuxiliaryInfoBoolean(String keyName)
intgetModelSetAuxiliaryInfoInt(String keyName)
StringgetModelSetName()
PropertiesgetModelSetProperties()
StringgetModelSetProperty(String propertyName)
intgetModelSymmetryCount(int modelIndex)
protected StringgetModelSymmetryList(int modelIndex)
StringgetModelTitle(int modelIndex)
BitSetgetMoleculeBitSet(BitSet bs)
BitSetgetMoleculeBitSet(int atomIndex)
intgetMoleculeCountInModel(int modelIndex)
intgetMoleculeIndex(int atomIndex)
VectorgetMoleculeInfo(BitSet bsAtoms)
voidgetMolecules()
float[]getNotionalUnitcell()
deprecated due to multimodel issues, but required by an interface -- do NOT remove.
StringgetPdbAtomData(BitSet bs)
StringgetPdbData(int modelIndex, String type, BitSet bsSelected, boolean addHeader)
StringgetPDBHeader(int modelIndex)
Point3f[]getPolymerLeadMidPoints(int iModel, int iPolymer)
voidgetPolymerPointsAndVectors(BitSet bs, Vector vList)
StringgetProteinStructureState(BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi)
BitSetgetSequenceBits(String specInfo, BitSet bs)
StringgetSpaceGroupInfoText(String spaceGroup)
StringgetSymmetryInfoAsString(int modelIndex)
StringgetSymmetryInfoAsString()
SymmetryInterfacegetSymTemp()
protected intgetTrajectoryCount()
intgetTrajectoryIndex(int modelIndex)
SymmetryInterfacegetUnitCell(int modelIndex)
StringgetUnitCellInfoText()
Point3fgetUnitCellOffset(int modelIndex)
AtomIndexIteratorgetWithinAtomSetIterator(int atomIndex, float distance, BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
AtomIndexIteratorgetWithinModelIterator(Atom atomCenter, float radius)
AtomIndexIteratorgetWithinModelIterator(int modelIndex, Point3f center, float radius)
booleanhasCalculatedHBonds(BitSet bsAtoms)
protected voidinitializeBspf()
protected voidinitializeBspt(int modelIndex)
voidinvertSelected(Point3f pt, Point4f plane, BitSet bs)
booleanisJmolDataFrame(int modelIndex)
booleanisJmolDataFrame(Atom atom)
booleanisTrajectory(int modelIndex)
booleanisTrajectory(int[] countPlusIndices)
protected int[]makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)
voidmerge(ModelSet modelSet)
initial transfer of model data from old to new model set.
static intmodelFileNumberFromFloat(float fDotM)
booleanmodelHasVibrationVectors(int modelIndex)
voidpropagateSecondaryStructure()
voidrecalculateLeadMidpointsAndWingVectors(int modelIndex)
protected voidreleaseModelSet()
voidrotateAtoms(Matrix3f mNew, Matrix3f matrixRotate, BitSet bsAtoms, boolean fullMolecule, Point3f center, boolean isInternal)
voidsaveModelOrientation(int modelIndex, StateManager.Orientation orientation)
voidselectDisplayedTrajectories(BitSet bs)
voidsetAtomCoord(BitSet bs, int tokType, Object xyzValues)
voidsetAtomCoordRelative(Point3f offset, BitSet bs)
voidsetAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)
voidsetBoundBox(Point3f pt1, Point3f pt2, boolean byCorner)
BitSetsetConformation(int modelIndex, BitSet bsConformation)
BitSetsetConformation(int modelIndex, int conformationIndex)
booleansetCrystallographicDefaults()
voidsetFrameTitle(int modelIndex, String title)
voidsetJmolDataFrame(String type, int modelIndex, int modelDataIndex)
voidsetModelAuxiliaryInfo(int modelIndex, Object key, Object value)
voidsetModelSetAuxiliaryInfo(Hashtable modelSetAuxiliaryInfo)
voidsetModelSetProperties(Properties modelSetProperties)
voidsetProteinType(BitSet bs, byte iType)
booleansetRotationRadius(int modelIndex, float angstroms)
booleansetUnitCellOffset(int modelIndex, Point3f pt)
booleansetUnitCellOffset(int modelIndex, int nnn)
voidtoCartesian(int modelIndex, Point3f pt)
voidtoFractional(int modelIndex, Point3f pt)
voidtoUnitCell(int modelIndex, Point3f pt, Point3f offset)

Field Detail

averageAtomPoint

private final Point3f averageAtomPoint

baseGroupIndex

protected int baseGroupIndex

bboxAtoms

private BitSet bboxAtoms

bboxModels

private BitSet bboxModels

boxInfo

private final BoxInfo boxInfo

bsAll

protected BitSet bsAll

bsSymmetry

protected BitSet bsSymmetry

bsTemp

private BitSet bsTemp

elementsPresent

protected BitSet[] elementsPresent

frameTitles

String[] frameTitles

groupCount

protected int groupCount

groups

protected Group[] groups

haveBioClasses

protected boolean haveBioClasses

isBbcageDefault

private boolean isBbcageDefault

isPDB

protected boolean isPDB

isXYZ

protected boolean isXYZ

jbr

protected JmolBioResolver jbr

matInv

private final Matrix3f matInv

matTemp

private final Matrix3f matTemp

modelCount

protected int modelCount

modelFileNumbers

int[] modelFileNumbers

modelNames

String[] modelNames

modelNumbers

int[] modelNumbers

modelNumbersForAtomLabel

String[] modelNumbersForAtomLabel

models

protected Model[] models

modelSetAuxiliaryInfo

Hashtable modelSetAuxiliaryInfo

modelSetName

protected String modelSetName

modelSetProperties

Properties modelSetProperties

moleculeCount

protected int moleculeCount

molecules

protected Molecule[] molecules

pdbRecords

static final String[] pdbRecords

proteinStructureTainted

boolean proteinStructureTainted

ptTemp

private final Point3f ptTemp

selectedMoleculeCount

private int selectedMoleculeCount

selectedMolecules

private BitSet selectedMolecules

someModelsHaveAromaticBonds

protected boolean someModelsHaveAromaticBonds

someModelsHaveFractionalCoordinates

protected boolean someModelsHaveFractionalCoordinates

someModelsHaveSymmetry

protected boolean someModelsHaveSymmetry

stateScripts

protected Vector stateScripts

structureCount

private int structureCount

structures

private ModelCollection.Structure[] structures

structuresDefinedInFile

protected BitSet structuresDefinedInFile

symTemp

SymmetryInterface symTemp

thisStateModel

private int thisStateModel

trajectories

protected Vector trajectories

unitCells

SymmetryInterface[] unitCells

withinAtomSetIterator

private AtomIteratorWithinSet withinAtomSetIterator

withinModelIterator

private AtomIteratorWithinModel withinModelIterator

Method Detail

addBioPolymerToModel

protected void addBioPolymerToModel(Polymer polymer, Model model)

addStateScript

public void addStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)

autoBond

public int autoBond(BitSet bsA, BitSet bsB, BitSet bsExclude, BitSet bsBonds)

autoBond

private int[] autoBond(short order, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, boolean matchHbond)

calcAtomsMinMax

private int calcAtomsMinMax(BitSet bs, BoxInfo boxInfo)

calcBoundBoxDimensions

public void calcBoundBoxDimensions(BitSet bs)

calcHydrogenBonds

public void calcHydrogenBonds(BitSet bsA, BitSet bsB)

calcRotationRadius

public float calcRotationRadius(int modelIndex, Point3f center)

calcRotationRadius

public float calcRotationRadius(BitSet bs)

calcSelectedGroupsCount

public void calcSelectedGroupsCount(BitSet bsSelected)

calcSelectedMoleculesCount

public void calcSelectedMoleculesCount(BitSet bsSelected)

calcSelectedMonomersCount

public void calcSelectedMonomersCount(BitSet bsSelected)

calculateMolecularDipole

public Vector3f calculateMolecularDipole(int modelIndex)

calculatePolymers

protected void calculatePolymers(BitSet alreadyDefined)

calculateStraightness

public void calculateStraightness()

calculateStructuresAllExcept

void calculateStructuresAllExcept(BitSet alreadyDefined, boolean addFileData)
allows rebuilding of PDB structures; also accessed by ModelManager from Eval

Parameters: alreadyDefined set to skip calculation addFileData in the case of loading, we add the PDB data

calcUnitCellMinMax

private void calcUnitCellMinMax()

clearCalculatedHydrogenBonds

public void clearCalculatedHydrogenBonds(int baseIndex, BitSet bsAtoms)

clearDataFrameReference

protected void clearDataFrameReference(int modelIndex)

defineStructure

protected void defineStructure(int modelIndex, String structureType, char startChainID, int startSequenceNumber, char startInsertionCode, char endChainID, int endSequenceNumber, char endInsertionCode)

deleteAtoms

public void deleteAtoms(int modelIndex, int firstAtomIndex, int nAtoms, BitSet bsAtoms, BitSet bsBonds)

freezeModels

private void freezeModels()

getAllAtomInfo

public Vector getAllAtomInfo(BitSet bs)

getAllBondInfo

public Vector getAllBondInfo(BitSet bs)

getAllChainInfo

public Hashtable getAllChainInfo(BitSet bs)

getAllPolymerInfo

public Hashtable getAllPolymerInfo(BitSet bs)

getAltLocCountInModel

public int getAltLocCountInModel(int modelIndex)

getAltLocIndexInModel

public int getAltLocIndexInModel(int modelIndex, char alternateLocationID)

getAltLocListInModel

public String getAltLocListInModel(int modelIndex)

getAtomBits

public BitSet getAtomBits(int tokType, Object specInfo)
general unqualified lookup of atom set type

Parameters: tokType specInfo

Returns: BitSet; or null if we mess up the type

getAtomCountInModel

public int getAtomCountInModel(int modelIndex)

getAtomIdentityInfo

public void getAtomIdentityInfo(int i, Hashtable info)

getAtomInfoLong

private Hashtable getAtomInfoLong(int i)

getAtomRecordMOL

void getAtomRecordMOL(StringBuffer s, int i)

getAtomsConnected

public BitSet getAtomsConnected(float min, float max, int intType, BitSet bs)

getAtomsWithin

public BitSet getAtomsWithin(float distance, 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

Parameters: distance bs withinAllModels

Returns: the set of atoms

getAtomsWithin

public BitSet getAtomsWithin(float distance, Point3f coord)

getAtomSetCenter

public Point3f getAtomSetCenter(BitSet bs)

getAuxiliaryInfo

public Hashtable getAuxiliaryInfo(BitSet bsModels)

getAverageAtomPoint

public Point3f getAverageAtomPoint()

getBboxVertices

public Point3f[] getBboxVertices()

getBioPolymerCount

public int getBioPolymerCount()

getBioPolymerCountInModel

public int getBioPolymerCountInModel(int modelIndex)

getBondCountInModel

public int getBondCountInModel(int modelIndex)

getBondInfo

private Hashtable getBondInfo(int i)

getBondRecordMOL

void getBondRecordMOL(StringBuffer s, int i, int[] atomMap)

getBoundBoxCenter

public Point3f getBoundBoxCenter(int modelIndex)

getBoundBoxCommand

public String getBoundBoxCommand(boolean withOptions)

getBoundBoxCornerVector

public Vector3f getBoundBoxCornerVector()

getBoundBoxInfo

public Hashtable getBoundBoxInfo()

getBoundBoxModels

public BitSet getBoundBoxModels()

getBoxInfo

public BoxInfo getBoxInfo(BitSet bs)

getBranchBitSet

public BitSet getBranchBitSet(int atomIndex, int atomIndexNot)

getCellInfos

public SymmetryInterface[] getCellInfos()

getChainCount

public int getChainCount(boolean addWater)

getChainCountInModel

public int getChainCountInModel(int modelIndex, boolean countWater)

getChainInfo

private Vector getChainInfo(int modelIndex, BitSet bs)

getChimeInfo

public String getChimeInfo(int tok, BitSet bs)

getCovalentlyConnectedBitSet

private void getCovalentlyConnectedBitSet(Atom atom, BitSet bs, BitSet bsToTest)

getElementsPresentBitSet

public BitSet getElementsPresentBitSet(int modelIndex)

getFileHeader

public String getFileHeader(int modelIndex)

getFrameTitle

public String getFrameTitle(int modelIndex)

getFullPDBHeader

private String getFullPDBHeader(int modelIndex)

getGroupCount

public int getGroupCount()

getGroupCountInModel

public int getGroupCountInModel(int modelIndex)

getHeteroList

public Hashtable getHeteroList(int modelIndex)

getInsertionCodeIndexInModel

public int getInsertionCodeIndexInModel(int modelIndex, char insertionCode)

getInsertionCountInModel

public int getInsertionCountInModel(int modelIndex)

getInsertionListInModel

private String getInsertionListInModel(int modelIndex)

getIterativeModels

public BitSet getIterativeModels(boolean allowJmolData)
only some models can be iterated through. models for which trajectoryBaseIndexes[i] != i are trajectories only

Parameters: allowJmolData

Returns: bitset of models

getJmolDataFrameIndex

public int getJmolDataFrameIndex(int modelIndex, String type)

getJmolDataSourceFrame

public int getJmolDataSourceFrame(int modelIndex)

getJmolFrameType

public String getJmolFrameType(int modelIndex)

getModel

Model getModel(int modelIndex)

getModelAtomBitSet

public BitSet getModelAtomBitSet(int modelIndex, boolean asCopy)

Parameters: modelIndex asCopy MUST BE TRUE IF THE BITSET IS GOING TO BE MODIFIED!

Returns: either the actual bitset or a copy

getModelAuxiliaryInfo

public Hashtable getModelAuxiliaryInfo(int modelIndex)

getModelAuxiliaryInfo

public Object getModelAuxiliaryInfo(int modelIndex, String key)

getModelAuxiliaryInfoBoolean

protected boolean getModelAuxiliaryInfoBoolean(int modelIndex, String keyName)

getModelAuxiliaryInfoInt

protected int getModelAuxiliaryInfoInt(int modelIndex, String keyName)

getModelCellRange

public int[] getModelCellRange(int modelIndex)

getModelCount

public int getModelCount()

getModelDipole

public Vector3f getModelDipole(int modelIndex)

getModelExtract

public String getModelExtract(BitSet bs)

getModelFileInfo

public String getModelFileInfo(BitSet frames)

getModelFileName

public String getModelFileName(int modelIndex)

getModelFileNumber

public int getModelFileNumber(int modelIndex)

getModelFileType

public String getModelFileType(int modelIndex)

getModelInfo

public Hashtable getModelInfo(BitSet bsModels)

getModelInfoAsString

public String getModelInfoAsString()

getModelName

public String getModelName(int modelIndex)

getModelNumber

public int getModelNumber(int modelIndex)

getModelNumberDotted

public String getModelNumberDotted(int modelIndex)

getModelNumberForAtomLabel

public String getModelNumberForAtomLabel(int modelIndex)

getModelOrientation

public StateManager.Orientation getModelOrientation(int modelIndex)

getModelProperties

public Properties getModelProperties(int modelIndex)

getModelProperty

public String getModelProperty(int modelIndex, String property)

getModels

public Model[] getModels()

getModelSetAuxiliaryInfo

public Hashtable getModelSetAuxiliaryInfo()

getModelSetAuxiliaryInfo

public Object getModelSetAuxiliaryInfo(String keyName)

getModelSetAuxiliaryInfoBoolean

boolean getModelSetAuxiliaryInfoBoolean(String keyName)

getModelSetAuxiliaryInfoInt

int getModelSetAuxiliaryInfoInt(String keyName)

getModelSetName

public String getModelSetName()

getModelSetProperties

public Properties getModelSetProperties()

getModelSetProperty

public String getModelSetProperty(String propertyName)

getModelSymmetryCount

public int getModelSymmetryCount(int modelIndex)

getModelSymmetryList

protected String getModelSymmetryList(int modelIndex)

getModelTitle

public String getModelTitle(int modelIndex)

getMoleculeBitSet

public BitSet getMoleculeBitSet(BitSet bs)

getMoleculeBitSet

public BitSet getMoleculeBitSet(int atomIndex)

getMoleculeCountInModel

public int getMoleculeCountInModel(int modelIndex)

getMoleculeIndex

public int getMoleculeIndex(int atomIndex)

getMoleculeInfo

public Vector getMoleculeInfo(BitSet bsAtoms)

getMolecules

private void getMolecules()

getNotionalUnitcell

public float[] getNotionalUnitcell()
deprecated due to multimodel issues, but required by an interface -- do NOT remove.

Returns: just the first unit cell

getPdbAtomData

public String getPdbAtomData(BitSet bs)

getPdbData

public String getPdbData(int modelIndex, String type, BitSet bsSelected, boolean addHeader)

getPDBHeader

public String getPDBHeader(int modelIndex)

getPolymerLeadMidPoints

public Point3f[] getPolymerLeadMidPoints(int iModel, int iPolymer)

getPolymerPointsAndVectors

public void getPolymerPointsAndVectors(BitSet bs, Vector vList)

getProteinStructureState

public String getProteinStructureState(BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi)

getSequenceBits

public BitSet getSequenceBits(String specInfo, BitSet bs)

getSpaceGroupInfoText

public String getSpaceGroupInfoText(String spaceGroup)

getSymmetryInfoAsString

String getSymmetryInfoAsString(int modelIndex)

getSymmetryInfoAsString

public String getSymmetryInfoAsString()

getSymTemp

SymmetryInterface getSymTemp()

getTrajectoryCount

protected int getTrajectoryCount()

getTrajectoryIndex

public int getTrajectoryIndex(int modelIndex)

getUnitCell

public SymmetryInterface getUnitCell(int modelIndex)

getUnitCellInfoText

public String getUnitCellInfoText()

getUnitCellOffset

public Point3f getUnitCellOffset(int modelIndex)

getWithinAtomSetIterator

public AtomIndexIterator getWithinAtomSetIterator(int atomIndex, float distance, BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)

getWithinModelIterator

public AtomIndexIterator getWithinModelIterator(Atom atomCenter, float radius)

getWithinModelIterator

private AtomIndexIterator getWithinModelIterator(int modelIndex, Point3f center, float radius)

hasCalculatedHBonds

public boolean hasCalculatedHBonds(BitSet bsAtoms)

initializeBspf

protected void initializeBspf()

initializeBspt

protected void initializeBspt(int modelIndex)

invertSelected

public void invertSelected(Point3f pt, Point4f plane, BitSet bs)

isJmolDataFrame

public boolean isJmolDataFrame(int modelIndex)

isJmolDataFrame

private boolean isJmolDataFrame(Atom atom)

isTrajectory

public boolean isTrajectory(int modelIndex)

isTrajectory

public boolean isTrajectory(int[] countPlusIndices)

makeConnections

protected int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)

merge

void merge(ModelSet modelSet)
initial transfer of model data from old to new model set. Note that all new models are added later, AFTER the old ones. This is very important, because all of the old atom numbers must map onto the same numbers in the new model set, or the state script will not run properly, among other problems. We subclass these just for sanity sake.

Parameters: modelSet

modelFileNumberFromFloat

public static int modelFileNumberFromFloat(float fDotM)

modelHasVibrationVectors

public boolean modelHasVibrationVectors(int modelIndex)

propagateSecondaryStructure

private void propagateSecondaryStructure()

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors(int modelIndex)

releaseModelSet

protected void releaseModelSet()

rotateAtoms

public void rotateAtoms(Matrix3f mNew, Matrix3f matrixRotate, BitSet bsAtoms, boolean fullMolecule, Point3f center, boolean isInternal)

saveModelOrientation

public void saveModelOrientation(int modelIndex, StateManager.Orientation orientation)

selectDisplayedTrajectories

public void selectDisplayedTrajectories(BitSet bs)

setAtomCoord

public void setAtomCoord(BitSet bs, int tokType, Object xyzValues)

setAtomCoordRelative

public void setAtomCoordRelative(Point3f offset, BitSet bs)

setAtomProperty

public void setAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)

setBoundBox

public void setBoundBox(Point3f pt1, Point3f pt2, boolean byCorner)

setConformation

public BitSet setConformation(int modelIndex, BitSet bsConformation)

setConformation

public BitSet setConformation(int modelIndex, int conformationIndex)

setCrystallographicDefaults

public boolean setCrystallographicDefaults()

setFrameTitle

public void setFrameTitle(int modelIndex, String title)

setJmolDataFrame

public void setJmolDataFrame(String type, int modelIndex, int modelDataIndex)

setModelAuxiliaryInfo

public void setModelAuxiliaryInfo(int modelIndex, Object key, Object value)

setModelSetAuxiliaryInfo

void setModelSetAuxiliaryInfo(Hashtable modelSetAuxiliaryInfo)

setModelSetProperties

void setModelSetProperties(Properties modelSetProperties)

setProteinType

public void setProteinType(BitSet bs, byte iType)

setRotationRadius

public boolean setRotationRadius(int modelIndex, float angstroms)

setUnitCellOffset

public boolean setUnitCellOffset(int modelIndex, Point3f pt)

setUnitCellOffset

public boolean setUnitCellOffset(int modelIndex, int nnn)

toCartesian

public void toCartesian(int modelIndex, Point3f pt)

toFractional

public void toFractional(int modelIndex, Point3f pt)

toUnitCell

public void toUnitCell(int modelIndex, Point3f pt, Point3f offset)