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

ac, auxiliaryInfo, biosymmetry, bsAtoms, chainCount, chains, firstAtomIndex, frameDelay, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isPdbWithMultipleBonds, isTrajectory, loadScript, loadState, modelIndex, moleculeCount, ms, nAltLocs, orientation, properties, simpleCage, structureTainted, trajectoryBaseIndex

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

Modifier and Type	Method and Description
private void	addBioPolymer(BioPolymer polymer)
void	addSecondaryStructure(STR type, java.lang.String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, BS bsAssigned)
void	calcSelectedMonomersCount(BS bsSelected)
private java.lang.String	calculateDssp(javajs.util.List<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
void	calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded, boolean checkConnections)
void	calculateStraightness(Viewer vwr, char ctype, char qtype, int mStep)
java.lang.String	calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
int	calculateStruts(ModelSet modelSet, BS bs1, BS bs2)
void	clearBioPolymers()
void	clearRasmolHydrogenBonds(BS bsAtoms)
void	fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
void	freeze()
void	getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,javajs.util.List<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, javajs.util.List<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
javajs.util.List<BS>	getBioBranches(javajs.util.List<BS> biobranches)
BioPolymer	getBioPolymer(int polymerIndex)
int	getBioPolymerCount()
void	getChimeInfo(javajs.util.SB sb, int nHetero)
void	getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
java.lang.String	getFullPDBHeader()
void	getGroupsWithin(int nResidues, BS bs, BS bsResult)
boolean	getPdbConformation(BS bsConformation, int conformationIndex)
void	getPdbData(Viewer vwr, java.lang.String type, char ctype, boolean isDraw, BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, BS bsWritten)
javajs.util.P3[]	getPolymerLeadMidPoints(int iPolymer)
void	getPolymerPointsAndVectors(BS bs, javajs.util.List<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
java.lang.String	getProteinStructureState(BS bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
void	getRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.List<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
void	getSequenceBits(java.lang.String specInfo, BS bs, BS bsResult)
void	recalculateLeadMidpointsAndWingVectors()
void	selectSeqcodeRange(int seqcodeA, int seqcodeB, int chainID, BS bs, boolean caseSensitive)
void	setConformation(BS bsConformation)
void	setStructureList(java.util.Map<STR,float[]> structureList)

Methods inherited from class org.jmol.modelset.Model

fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getChains, getChimeInfoM, getGroupCount, getGroupCountHetero, getModelNumberDotted, getModelSet, getModelTitle, getSelectedTrajectory, 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(STR type,
                                  java.lang.String structureID,
                                  int serialID,
                                  int strandCount,
                                  int startChainID,
                                  int startSeqcode,
                                  int endChainID,
                                  int endSeqcode,
                                  int istart,
                                  int iend,
                                  BS bsAssigned)

calculateStructures

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

Overrides:

calculateStructures in class Model

Returns:

structure list

calculateDssp

private java.lang.String calculateDssp(javajs.util.List<Bond> vHBonds,
                                       boolean doReport,
                                       boolean dsspIgnoreHydrogen,
                                       boolean setStructure)

setConformation

public void setConformation(BS bsConformation)

Overrides:

setConformation in class Model

getPdbConformation

public boolean getPdbConformation(BS 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(BS bsSelected)

Overrides:

calcSelectedMonomersCount in class Model

getBioPolymer

public BioPolymer getBioPolymer(int polymerIndex)

getDefaultLargePDBRendering

public void getDefaultLargePDBRendering(javajs.util.SB sb,
                                        int maxAtoms)

Overrides:

getDefaultLargePDBRendering in class Model

fixIndices

public void fixIndices(int modelIndex,
                       int nAtomsDeleted,
                       BS bsDeleted)

Overrides:

fixIndices in class Model

calculateStruts

public int calculateStruts(ModelSet modelSet,
                           BS bs1,
                           BS bs2)

Overrides:

calculateStruts in class Model

Returns:

number of struts

setStructureList

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

Overrides:

setStructureList in class Model

calculateStraightness

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

Overrides:

calculateStraightness in class Model

getPolymerPointsAndVectors

public void getPolymerPointsAndVectors(BS bs,
                                       javajs.util.List<javajs.util.P3[]> vList,
                                       boolean isTraceAlpha,
                                       float sheetSmoothing)

Overrides:

getPolymerPointsAndVectors in class Model

getPolymerLeadMidPoints

public javajs.util.P3[] 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 javajs.util.List<BS> getBioBranches(javajs.util.List<BS> biobranches)

Overrides:

getBioBranches in class Model

Returns:

updated bioBranches

getGroupsWithin

public void getGroupsWithin(int nResidues,
                            BS bs,
                            BS bsResult)

Overrides:

getGroupsWithin in class Model

getSequenceBits

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

Overrides:

getSequenceBits in class Model

selectSeqcodeRange

public void selectSeqcodeRange(int seqcodeA,
                               int seqcodeB,
                               int chainID,
                               BS bs,
                               boolean caseSensitive)

Overrides:

selectSeqcodeRange in class Model

getRasmolHydrogenBonds

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

Overrides:

getRasmolHydrogenBonds in class Model

clearRasmolHydrogenBonds

public void clearRasmolHydrogenBonds(BS bsAtoms)

Overrides:

clearRasmolHydrogenBonds in class Model

calculatePolymers

public void calculatePolymers(Group[] groups,
                              int groupCount,
                              int baseGroupIndex,
                              BS modelsExcluded,
                              boolean checkConnections)

Overrides:

calculatePolymers in class Model

addBioPolymer

private void addBioPolymer(BioPolymer polymer)

clearBioPolymers

public void clearBioPolymers()

Overrides:

clearBioPolymers in class Model

getAllPolymerInfo

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

Overrides:

getAllPolymerInfo in class Model

getChimeInfo

public void getChimeInfo(javajs.util.SB sb,
                         int nHetero)

Overrides:

getChimeInfo in class Model

getProteinStructureState

public java.lang.String getProteinStructureState(BS 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 vwr,
                       java.lang.String type,
                       char ctype,
                       boolean isDraw,
                       BS bsSelected,
                       javajs.util.OC out,
                       LabelToken[] tokens,
                       javajs.util.SB pdbCONECT,
                       BS bsWritten)

Overrides:

getPdbData in class Model