org.jmol.modelsetbio

Class BioModel

java.lang.Object

org.jmol.modelset.Model

org.jmol.modelsetbio.BioModel

public final class BioModel
extends Model

Field Summary

Fields

Modifier and Type	Field and Description
private int	bioPolymerCount
private BioPolymer[]	bioPolymers
private static java.lang.String[]	pdbRecords

Fields inherited from class org.jmol.modelset.Model

atomCount, auxiliaryInfo, bsAtoms, chainCount, chains, firstAtomIndex, frameDelay, hasRasmolHBonds, hydrogenCount, isBioModel, isPdbWithMultipleBonds, modelIndex, modelSet, nAltLocs, structureTainted, trajectoryBaseIndex, unitCell

Constructor Summary

Constructors

Constructor and Description
BioModel(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

Methods

Modifier and Type	Method and Description
private void	addBioPolymer(BioPolymer polymer)
void	addSecondaryStructure(EnumStructure type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
void	calcSelectedMonomersCount(java.util.BitSet bsSelected)
void	calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, java.util.BitSet modelsExcluded)
void	calculateStraightness(Viewer viewer, char ctype, char qtype, int mStep)
java.lang.String	calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
int	calculateStruts(ModelSet modelSet, java.util.BitSet bs1, java.util.BitSet bs2)
void	clearBioPolymers()
void	clearRasmolHydrogenBonds(java.util.BitSet bsAtoms)
void	fixIndices(int modelIndex, int nAtomsDeleted, java.util.BitSet bsDeleted)
void	freeze()
void	getAllPolymerInfo(java.util.BitSet bs, java.util.Map<java.lang.String,java.util.List<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, java.util.List<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
java.util.List<java.util.BitSet>	getBioBranches(java.util.List<java.util.BitSet> biobranches)
BioPolymer	getBioPolymer(int polymerIndex)
int	getBioPolymerCount()
void	getChimeInfo(java.lang.StringBuffer sb, int nHetero)
void	getDefaultLargePDBRendering(java.lang.StringBuffer sb, int maxAtoms)
java.lang.String	getFullPDBHeader()
void	getGroupsWithin(int nResidues, java.util.BitSet bs, java.util.BitSet bsResult)
boolean	getPdbConformation(java.util.BitSet bsConformation, int conformationIndex)
void	getPdbData(Viewer viewer, java.lang.String type, char ctype, boolean isDraw, java.util.BitSet bsSelected, OutputStringBuffer sb, LabelToken[] tokens, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsWritten)
javax.vecmath.Point3f[]	getPolymerLeadMidPoints(int iPolymer)
void	getPolymerPointsAndVectors(java.util.BitSet bs, java.util.List<javax.vecmath.Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
java.lang.String	getProteinStructureState(java.util.BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
void	getRasmolHydrogenBonds(java.util.BitSet bsA, java.util.BitSet bsB, java.util.List<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, java.util.BitSet bsHBonds)
void	getSequenceBits(java.lang.String specInfo, java.util.BitSet bs, java.util.BitSet bsResult)
void	recalculateLeadMidpointsAndWingVectors()
void	selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, java.util.BitSet bs, boolean caseSensitive)
void	setConformation(java.util.BitSet bsConformation)
void	setStructureList(java.util.Map<EnumStructure,float[]> structureList)

Methods inherited from class org.jmol.modelset.Model

getBondCount, getChainCount, getChains, getGroupCount, getModelNumberDotted, getModelSet, getModelTitle, getTrueAtomCount, isModelkit, isStructureTainted, resetBoundCount

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

bioPolymerCount

private int bioPolymerCount

bioPolymers

private BioPolymer[] bioPolymers

pdbRecords

private static final java.lang.String[] pdbRecords

Constructor Detail

BioModel

BioModel(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

freeze

public void freeze()

Overrides:

freeze in class Model

addSecondaryStructure

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

Overrides:

addSecondaryStructure in class Model

calculateStructures

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

Overrides:

calculateStructures in class Model

Returns:

structure list

setConformation

public void setConformation(java.util.BitSet bsConformation)

Overrides:

setConformation in class Model

getPdbConformation

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

Overrides:

getPdbConformation in class Model

Returns:

true for BioModel

getBioPolymerCount

public int getBioPolymerCount()

Overrides:

getBioPolymerCount in class Model

calcSelectedMonomersCount

public void calcSelectedMonomersCount(java.util.BitSet bsSelected)

Overrides:

calcSelectedMonomersCount in class Model

getBioPolymer

public BioPolymer getBioPolymer(int polymerIndex)

getDefaultLargePDBRendering

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

Overrides:

getDefaultLargePDBRendering in class Model

fixIndices

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

Overrides:

fixIndices in class Model

calculateStruts

public int calculateStruts(ModelSet modelSet,
                  java.util.BitSet bs1,
                  java.util.BitSet bs2)

Overrides:

calculateStruts in class Model

Returns:

number of struts

setStructureList

public void setStructureList(java.util.Map<EnumStructure,float[]> structureList)

Overrides:

setStructureList in class Model

calculateStraightness

public void calculateStraightness(Viewer viewer,
                         char ctype,
                         char qtype,
                         int mStep)

Overrides:

calculateStraightness in class Model

getPolymerPointsAndVectors

public void getPolymerPointsAndVectors(java.util.BitSet bs,
                              java.util.List<javax.vecmath.Point3f[]> vList,
                              boolean isTraceAlpha,
                              float sheetSmoothing)

Overrides:

getPolymerPointsAndVectors in class Model

getPolymerLeadMidPoints

public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int iPolymer)

Overrides:

getPolymerLeadMidPoints in class Model

Returns:

list of points or null

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors()

Overrides:

recalculateLeadMidpointsAndWingVectors in class Model

getBioBranches

public java.util.List<java.util.BitSet> getBioBranches(java.util.List<java.util.BitSet> biobranches)

Overrides:

getBioBranches in class Model

Returns:

updated bioBranches

getGroupsWithin

public void getGroupsWithin(int nResidues,
                   java.util.BitSet bs,
                   java.util.BitSet bsResult)

Overrides:

getGroupsWithin in class Model

getSequenceBits

public void getSequenceBits(java.lang.String specInfo,
                   java.util.BitSet bs,
                   java.util.BitSet bsResult)

Overrides:

getSequenceBits in class Model

selectSeqcodeRange

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

Overrides:

selectSeqcodeRange in class Model

getRasmolHydrogenBonds

public void getRasmolHydrogenBonds(java.util.BitSet bsA,
                          java.util.BitSet bsB,
                          java.util.List<Bond> vHBonds,
                          boolean nucleicOnly,
                          int nMax,
                          boolean dsspIgnoreHydrogens,
                          java.util.BitSet bsHBonds)

Overrides:

getRasmolHydrogenBonds in class Model

clearRasmolHydrogenBonds

public void clearRasmolHydrogenBonds(java.util.BitSet bsAtoms)

Overrides:

clearRasmolHydrogenBonds in class Model

calculatePolymers

public void calculatePolymers(Group[] groups,
                     int groupCount,
                     int baseGroupIndex,
                     java.util.BitSet modelsExcluded)

Overrides:

calculatePolymers in class Model

addBioPolymer

private void addBioPolymer(BioPolymer polymer)

clearBioPolymers

public void clearBioPolymers()

Overrides:

clearBioPolymers in class Model

getAllPolymerInfo

public void getAllPolymerInfo(java.util.BitSet bs,
                     java.util.Map<java.lang.String,java.util.List<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo,
                     java.util.List<java.util.Map<java.lang.String,java.lang.Object>> modelVector)

Overrides:

getAllPolymerInfo in class Model

getChimeInfo

public void getChimeInfo(java.lang.StringBuffer sb,
                int nHetero)

Overrides:

getChimeInfo in class Model

getProteinStructureState

public java.lang.String getProteinStructureState(java.util.BitSet bsAtoms,
                                        boolean taintedOnly,
                                        boolean needPhiPsi,
                                        int mode)

Overrides:

getProteinStructureState in class Model

Returns:

only for BioModel

getFullPDBHeader

public java.lang.String getFullPDBHeader()

Overrides:

getFullPDBHeader in class Model

getPdbData

public void getPdbData(Viewer viewer,
              java.lang.String type,
              char ctype,
              boolean isDraw,
              java.util.BitSet bsSelected,
              OutputStringBuffer sb,
              LabelToken[] tokens,
              java.lang.StringBuffer pdbCONECT,
              java.util.BitSet bsWritten)

Overrides:

getPdbData in class Model