org.jmol.modelset

Class Model

public final class Model extends Object

Field Summary
intatomCount
HashtableauxiliaryInfo
intbioPolymerCount
Polymer[]bioPolymers
intbiosymmetryCount
intbondCount
BitSetbsAtoms
intchainCount
Chain[]chains
HashtabledataFrames
intdataSourceFrame
floatdefaultRotationRadius
intfileIndex
intfirstAtomIndex
intfirstMolecule
intgroupCount
booleanhasCalculatedHBonds
booleanisPDB
booleanisTrajectory
StringjmolData
StringjmolFrameType
intmodelIndex
ModelSetmodelSet
intmoleculeCount
intnAltLocs
intnInsertions
StateManager.Orientationorientation
Propertiesproperties
intselectedTrajectory
booleanstructureTainted
inttrajectoryBaseIndex
Constructor Summary
Model(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Hashtable auxiliaryInfo)
Method Summary
voidaddHydrogenBond(Atom atom1, Atom atom2, short order, BitSet bsA, BitSet bsB)
voidaddSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
voidcalcHydrogenBonds(BitSet bsA, BitSet bsB)
voidcalcSelectedGroupsCount(BitSet bsSelected)
voidcalcSelectedMonomersCount(BitSet bsSelected)
voidcalculateStructures()
voidfixIndices(int modelIndex, int nAtomsDeleted, BitSet bsDeleted)
PolymergetBioPolymer(int polymerIndex)
intgetBioPolymerCount()
ChaingetChain(char chainID)
ChaingetChain(int i)
intgetChainCount(boolean countWater)
Chain[]getChains()
intgetGroupCount(boolean isHetero)
intgetGroupCount()
intgetModelIndex()
ModelSetgetModelSet()
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
booleanisAtomHidden(int index)
booleanisStructureTainted()
voidselectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, BitSet bs, boolean caseSensitive)
voidsetConformation(BitSet bsConformation)
voidsetNAltLocs(int nAltLocs)
voidsetNInsertions(int nInsertions)

Field Detail

atomCount

int atomCount

auxiliaryInfo

Hashtable auxiliaryInfo

bioPolymerCount

int bioPolymerCount

bioPolymers

Polymer[] bioPolymers

biosymmetryCount

int biosymmetryCount

bondCount

int bondCount

bsAtoms

BitSet bsAtoms

chainCount

int chainCount

chains

Chain[] chains

dataFrames

Hashtable dataFrames

dataSourceFrame

int dataSourceFrame

defaultRotationRadius

float defaultRotationRadius

fileIndex

int fileIndex

firstAtomIndex

int firstAtomIndex

firstMolecule

int firstMolecule

groupCount

int groupCount

hasCalculatedHBonds

boolean hasCalculatedHBonds

isPDB

boolean isPDB

isTrajectory

boolean isTrajectory

jmolData

String jmolData

jmolFrameType

String jmolFrameType

modelIndex

int modelIndex

modelSet

ModelSet modelSet

moleculeCount

int moleculeCount

nAltLocs

int nAltLocs

nInsertions

int nInsertions

orientation

StateManager.Orientation orientation

properties

Properties properties

selectedTrajectory

int selectedTrajectory

structureTainted

boolean structureTainted

trajectoryBaseIndex

int trajectoryBaseIndex

Constructor Detail

Model

Model(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, String jmolData, Properties properties, Hashtable auxiliaryInfo)

Method Detail

addHydrogenBond

public void addHydrogenBond(Atom atom1, Atom atom2, short order, BitSet bsA, BitSet bsB)

addSecondaryStructure

void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)

calcHydrogenBonds

void calcHydrogenBonds(BitSet bsA, BitSet bsB)

calcSelectedGroupsCount

void calcSelectedGroupsCount(BitSet bsSelected)

calcSelectedMonomersCount

void calcSelectedMonomersCount(BitSet bsSelected)

calculateStructures

void calculateStructures()

fixIndices

void fixIndices(int modelIndex, int nAtomsDeleted, BitSet bsDeleted)

getBioPolymer

public Polymer getBioPolymer(int polymerIndex)

getBioPolymerCount

public int getBioPolymerCount()

getChain

Chain getChain(char chainID)

getChain

Chain getChain(int i)

getChainCount

public int getChainCount(boolean countWater)

getChains

public Chain[] getChains()

getGroupCount

public int getGroupCount(boolean isHetero)

getGroupCount

int getGroupCount()

getModelIndex

public int getModelIndex()

getModelSet

public ModelSet getModelSet()
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.

Returns: associated ModelSet

isAtomHidden

public boolean isAtomHidden(int index)

isStructureTainted

public boolean isStructureTainted()

selectSeqcodeRange

void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, BitSet bs, boolean caseSensitive)

setConformation

void setConformation(BitSet bsConformation)

setNAltLocs

void setNAltLocs(int nAltLocs)

setNInsertions

void setNInsertions(int nInsertions)