org.jmol.modelset
Class Model

java.lang.Object
  extended by org.jmol.modelset.Model

public final class Model
extends java.lang.Object


Field Summary
(package private)  int atomCount
           
(package private)  java.util.Hashtable auxiliaryInfo
           
(package private)  int bioPolymerCount
           
(package private)  Polymer[] bioPolymers
           
(package private)  int biosymmetryCount
           
(package private)  int bondCount
           
(package private)  java.util.BitSet bsAtoms
           
(package private)  int chainCount
           
(package private)  Chain[] chains
           
(package private)  java.util.Hashtable dataFrames
           
(package private)  int dataSourceFrame
           
(package private)  float defaultRotationRadius
           
(package private)  int fileIndex
           
(package private)  int firstAtomIndex
           
(package private)  int firstMolecule
           
(package private)  int groupCount
           
(package private)  boolean hasCalculatedHBonds
           
(package private)  boolean isPDB
           
(package private)  boolean isTrajectory
           
(package private)  java.lang.String jmolData
           
(package private)  java.lang.String jmolFrameType
           
(package private)  int modelIndex
           
(package private)  ModelSet modelSet
           
(package private)  int moleculeCount
           
(package private)  int nAltLocs
           
(package private)  int nInsertions
           
(package private)  StateManager.Orientation orientation
           
(package private)  java.util.Properties properties
           
(package private)  int selectedTrajectory
           
(package private)  boolean structureTainted
           
(package private)  int trajectoryBaseIndex
           
 
Constructor Summary
Model(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, java.lang.String jmolData, java.util.Properties properties, java.util.Hashtable auxiliaryInfo)
           
 
Method Summary
 void addHydrogenBond(Atom atom1, Atom atom2, short order, java.util.BitSet bsA, java.util.BitSet bsB)
           
(package private)  void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
           
(package private)  void calcHydrogenBonds(java.util.BitSet bsA, java.util.BitSet bsB)
           
(package private)  void calcSelectedGroupsCount(java.util.BitSet bsSelected)
           
(package private)  void calcSelectedMonomersCount(java.util.BitSet bsSelected)
           
(package private)  void calculateStructures()
           
(package private)  void fixIndices(int modelIndex, int nAtomsDeleted, java.util.BitSet bsDeleted)
           
 Polymer getBioPolymer(int polymerIndex)
           
 int getBioPolymerCount()
           
(package private)  Chain getChain(char chainID)
           
(package private)  Chain getChain(int i)
           
 int getChainCount(boolean countWater)
           
 Chain[] getChains()
           
(package private)  int getGroupCount()
           
 int getGroupCount(boolean isHetero)
           
 int getModelIndex()
           
 ModelSet getModelSet()
          BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
 boolean isAtomHidden(int index)
           
 boolean isStructureTainted()
           
(package private)  void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, java.util.BitSet bs, boolean caseSensitive)
           
(package private)  void setConformation(java.util.BitSet bsConformation)
           
(package private)  void setNAltLocs(int nAltLocs)
           
(package private)  void setNInsertions(int nInsertions)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

modelSet

ModelSet modelSet

modelIndex

int modelIndex

fileIndex

int fileIndex

isPDB

boolean isPDB

isTrajectory

boolean isTrajectory

trajectoryBaseIndex

int trajectoryBaseIndex

selectedTrajectory

int selectedTrajectory

hasCalculatedHBonds

boolean hasCalculatedHBonds

dataFrames

java.util.Hashtable dataFrames

dataSourceFrame

int dataSourceFrame

jmolData

java.lang.String jmolData

jmolFrameType

java.lang.String jmolFrameType

firstAtomIndex

int firstAtomIndex

atomCount

int atomCount

bsAtoms

java.util.BitSet bsAtoms

bondCount

int bondCount

firstMolecule

int firstMolecule

moleculeCount

int moleculeCount

nAltLocs

int nAltLocs

nInsertions

int nInsertions

groupCount

int groupCount

chainCount

int chainCount

chains

Chain[] chains

bioPolymerCount

int bioPolymerCount

bioPolymers

Polymer[] bioPolymers

biosymmetryCount

int biosymmetryCount

auxiliaryInfo

java.util.Hashtable auxiliaryInfo

properties

java.util.Properties properties

defaultRotationRadius

float defaultRotationRadius

orientation

StateManager.Orientation orientation

structureTainted

boolean structureTainted
Constructor Detail

Model

Model(ModelSet modelSet,
      int modelIndex,
      int trajectoryBaseIndex,
      java.lang.String jmolData,
      java.util.Properties properties,
      java.util.Hashtable auxiliaryInfo)
Method Detail

getModelSet

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

Returns:
associated ModelSet

setNAltLocs

void setNAltLocs(int nAltLocs)

setNInsertions

void setNInsertions(int nInsertions)

addSecondaryStructure

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

calculateStructures

void calculateStructures()

isStructureTainted

public boolean isStructureTainted()

setConformation

void setConformation(java.util.BitSet bsConformation)

getChains

public Chain[] getChains()

getChainCount

public int getChainCount(boolean countWater)

getGroupCount

public int getGroupCount(boolean isHetero)

getBioPolymerCount

public int getBioPolymerCount()

calcSelectedGroupsCount

void calcSelectedGroupsCount(java.util.BitSet bsSelected)

calcSelectedMonomersCount

void calcSelectedMonomersCount(java.util.BitSet bsSelected)

selectSeqcodeRange

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

getGroupCount

int getGroupCount()

getChain

Chain getChain(char chainID)

getChain

Chain getChain(int i)

getBioPolymer

public Polymer getBioPolymer(int polymerIndex)

calcHydrogenBonds

void calcHydrogenBonds(java.util.BitSet bsA,
                       java.util.BitSet bsB)

isAtomHidden

public boolean isAtomHidden(int index)

addHydrogenBond

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

getModelIndex

public int getModelIndex()

fixIndices

void fixIndices(int modelIndex,
                int nAtomsDeleted,
                java.util.BitSet bsDeleted)