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.Map<java.lang.String,java.lang.Object> auxiliaryInfo
           
(package private)  int bioPolymerCount
           
(package private)  Polymer[] bioPolymers
           
(package private)  int biosymmetryCount
           
private  int bondCount
           
(package private)  java.util.BitSet bsAtoms
           
(package private)  java.util.BitSet bsAtomsDeleted
           
(package private)  int chainCount
           
(package private)  Chain[] chains
           
(package private)  java.util.Map<java.lang.String,java.lang.Integer> dataFrames
           
(package private)  int dataSourceFrame
           
(package private)  float defaultRotationRadius
           
(package private)  java.lang.String defaultStructure
           
(package private)  int fileIndex
           
(package private)  int firstAtomIndex
           
(package private)  int firstMoleculeIndex
           
(package private)  int groupCount
           
(package private)  boolean hasRasmolHBonds
           
 int hydrogenCount
           
(package private)  boolean isJmolDataFrame
           
(package private)  boolean isModelKit
           
 boolean isPDB
           
 boolean isPdbWithMultipleBonds
           
(package private)  boolean isTrajectory
           
(package private)  java.lang.String jmolData
           
(package private)  java.lang.String jmolFrameType
           
(package private)  java.lang.StringBuffer loadScript
           
(package private)  java.lang.String loadState
           
 int modelIndex
           
(package private)  ModelSet modelSet
           
(package private)  int moleculeCount
           
 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.Map<java.lang.String,java.lang.Object> auxiliaryInfo)
           
 
Method Summary
(package private)  void addSecondaryStructure(EnumStructure type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
           
(package private)  void calcSelectedGroupsCount(java.util.BitSet bsSelected)
           
(package private)  void calcSelectedMonomersCount(java.util.BitSet bsSelected)
           
(package private)  java.lang.String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
           
(package private)  void fixIndices(int modelIndex, int nAtomsDeleted, java.util.BitSet bsDeleted)
           
 Polymer getBioPolymer(int polymerIndex)
           
 int getBioPolymerCount()
           
(package private)  int getBondCount()
           
(package private)  Chain getChain(char chainID)
           
(package private)  Chain getChain(int i)
           
 int getChainCount(boolean countWater)
           
 Chain[] getChains()
           
(package private)  void getDefaultLargePDBRendering(java.lang.StringBuffer sb, int maxAtoms)
           
(package private)  int getGroupCount()
           
 int getGroupCount(boolean isHetero)
           
 int getModelIndex()
           
 java.lang.String getModelNumberDotted()
           
 ModelSet getModelSet()
          BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
 java.lang.String getModelTitle()
           
(package private)  boolean getPdbConformation(java.util.BitSet bsConformation, int conformationIndex)
           
 int getTrueAtomCount()
           
 boolean isAtomHidden(int index)
           
 boolean isModelkit()
           
 boolean isStructureTainted()
           
 void resetBoundCount()
           
(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

public int modelIndex

fileIndex

int fileIndex

hydrogenCount

public int hydrogenCount

isPDB

public boolean isPDB

isPdbWithMultipleBonds

public boolean isPdbWithMultipleBonds

loadState

java.lang.String loadState

loadScript

java.lang.StringBuffer loadScript

isModelKit

boolean isModelKit

isTrajectory

boolean isTrajectory

trajectoryBaseIndex

int trajectoryBaseIndex

selectedTrajectory

int selectedTrajectory

hasRasmolHBonds

boolean hasRasmolHBonds

dataFrames

java.util.Map<java.lang.String,java.lang.Integer> dataFrames

dataSourceFrame

int dataSourceFrame

jmolData

java.lang.String jmolData

jmolFrameType

java.lang.String jmolFrameType

firstAtomIndex

int firstAtomIndex

atomCount

int atomCount

bsAtoms

final java.util.BitSet bsAtoms

bsAtomsDeleted

final java.util.BitSet bsAtomsDeleted

bondCount

private int bondCount

firstMoleculeIndex

int firstMoleculeIndex

moleculeCount

int moleculeCount

nAltLocs

public 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.Map<java.lang.String,java.lang.Object> auxiliaryInfo

properties

java.util.Properties properties

defaultRotationRadius

float defaultRotationRadius

defaultStructure

java.lang.String defaultStructure

orientation

StateManager.Orientation orientation

structureTainted

boolean structureTainted

isJmolDataFrame

boolean isJmolDataFrame
Constructor Detail

Model

Model(ModelSet modelSet,
      int modelIndex,
      int trajectoryBaseIndex,
      java.lang.String jmolData,
      java.util.Properties properties,
      java.util.Map<java.lang.String,java.lang.Object> 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

isModelkit

public boolean isModelkit()

getTrueAtomCount

public int getTrueAtomCount()

resetBoundCount

public void resetBoundCount()

getBondCount

int getBondCount()

setNAltLocs

void setNAltLocs(int nAltLocs)

setNInsertions

void setNInsertions(int nInsertions)

addSecondaryStructure

void addSecondaryStructure(EnumStructure type,
                           java.lang.String structureID,
                           int serialID,
                           int strandCount,
                           char startChainID,
                           int startSeqcode,
                           char endChainID,
                           int endSeqcode)

getModelNumberDotted

public java.lang.String getModelNumberDotted()

getModelTitle

public java.lang.String getModelTitle()

calculateStructures

java.lang.String calculateStructures(boolean asDSSP,
                                     boolean doReport,
                                     boolean dsspIgnoreHydrogen,
                                     boolean setStructure,
                                     boolean includeAlpha)

isStructureTainted

public boolean isStructureTainted()

setConformation

void setConformation(java.util.BitSet bsConformation)

getPdbConformation

boolean getPdbConformation(java.util.BitSet bsConformation,
                           int conformationIndex)

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)

getDefaultLargePDBRendering

void getDefaultLargePDBRendering(java.lang.StringBuffer sb,
                                 int maxAtoms)

isAtomHidden

public boolean isAtomHidden(int index)

getModelIndex

public int getModelIndex()

fixIndices

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