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, bsAtomsDeleted, chainCount, chains, dssrCache, firstAtomIndex, frameDelay, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isPdbWithMultipleBonds, isTrajectory, loadScript, loadState, modelIndex, moleculeCount, ms, nAltLocs, orientation, properties, selectedTrajectory, 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	calcRasmolHydrogenBonds(ModelSet ms, BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
void	calcSelectedMonomersCount(BS bsSelected)
void	calculateAllPolymers(ModelSet ms, Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)
private java.lang.String	calculateDssx(javajs.util.Lst<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
private static void	calculatePolymers(ModelSet ms, Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)
void	calculateStraightnessAll(ModelSet ms)
java.lang.String	calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
int	calculateStruts(ModelSet ms, BS bs1, BS bs2)
void	clearBioPolymers()
private static void	clearRasmolHydrogenBonds(ModelSet ms, BioModel bm, BS bsAtoms)
void	fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
void	freeze()
void	getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
BS	getBasePairBits(ModelSet ms, java.lang.String specInfo)
javajs.util.Lst<BS>	getBioBranches(javajs.util.Lst<BS> biobranches)
BioPolymer	getBioPolymer(int polymerIndex)
int	getBioPolymerCount()
int	getBioPolymerCountInModel(ModelSet ms, int modelIndex)
void	getChimeInfo(javajs.util.SB sb, int nHetero)
void	getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
java.lang.String	getFullPDBHeader()
java.lang.String	getFullProteinStructureState(ModelSet ms, BS bsAtoms2, boolean taintedOnly, boolean needPhiPsi, int mode)
BS	getGroupsWithinAll(ModelSet ms, int nResidues, BS bs)
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)
void	getPolymerPointsAndVectors(BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
static java.lang.String	getProteinStructureState(ModelSet ms, BioModel m, BS bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
private void	getRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
BS	getSelectCodeRange(ModelSet ms, int[] info)
BS	getSequenceBits(ModelSet ms, java.lang.String specInfo, BS bs)
private void	recalculateLeadMidpointsAndWingVectors()
void	recalculatePoints(ModelSet ms, int modelIndex)
void	resetRasmolBonds(Model model, BS bs)
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, getChimeInfoM, getGroupCount, getGroupCountHetero, getModelSet, getTrueAtomCount, isModelkit, resetBoundCount, set

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

calculateDssx

private java.lang.String calculateDssx(javajs.util.Lst<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

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

setStructureList

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

Overrides:

setStructureList in class Model

getPolymerPointsAndVectors

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

Overrides:

getPolymerPointsAndVectors in class Model

getBioBranches

public javajs.util.Lst<BS> getBioBranches(javajs.util.Lst<BS> biobranches)

Overrides:

getBioBranches in class Model

Returns:

updated bioBranches

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.Lst<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo,
                              javajs.util.Lst<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

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

getSequenceBits

public BS getSequenceBits(ModelSet ms,
                          java.lang.String specInfo,
                          BS bs)

Overrides:

getSequenceBits in class Model

Returns:

sequence bits

getBasePairBits

public BS getBasePairBits(ModelSet ms,
                          java.lang.String specInfo)

Overrides:

getBasePairBits in class Model

Returns:

base pair bits

resetRasmolBonds

public void resetRasmolBonds(Model model,
                             BS bs)

Overrides:

resetRasmolBonds in class Model

calcRasmolHydrogenBonds

public void calcRasmolHydrogenBonds(ModelSet ms,
                                    BS bsA,
                                    BS bsB,
                                    javajs.util.Lst<Bond> vHBonds,
                                    boolean nucleicOnly,
                                    int nMax,
                                    boolean dsspIgnoreHydrogens,
                                    BS bsHBonds)

Overrides:

calcRasmolHydrogenBonds in class Model

getRasmolHydrogenBonds

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

clearRasmolHydrogenBonds

private static void clearRasmolHydrogenBonds(ModelSet ms,
                                             BioModel bm,
                                             BS bsAtoms)

getFullProteinStructureState

public java.lang.String getFullProteinStructureState(ModelSet ms,
                                                     BS bsAtoms2,
                                                     boolean taintedOnly,
                                                     boolean needPhiPsi,
                                                     int mode)

Overrides:

getFullProteinStructureState in class Model

Returns:

state

getProteinStructureState

public static java.lang.String getProteinStructureState(ModelSet ms,
                                                        BioModel m,
                                                        BS bsAtoms,
                                                        boolean taintedOnly,
                                                        boolean needPhiPsi,
                                                        int mode)

calculateAllPolymers

public void calculateAllPolymers(ModelSet ms,
                                 Group[] groups,
                                 int groupCount,
                                 int baseGroupIndex,
                                 BS modelsExcluded)

Overrides:

calculateAllPolymers in class Model

calculatePolymers

private static void calculatePolymers(ModelSet ms,
                                      Group[] groups,
                                      int groupCount,
                                      int baseGroupIndex,
                                      BS modelsExcluded)

getGroupsWithinAll

public BS getGroupsWithinAll(ModelSet ms,
                             int nResidues,
                             BS bs)

Overrides:

getGroupsWithinAll in class Model

Returns:

bitset

getSelectCodeRange

public BS getSelectCodeRange(ModelSet ms,
                             int[] info)

Overrides:

getSelectCodeRange in class Model

Returns:

bitset

calculateStruts

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

Overrides:

calculateStruts in class Model

Returns:

number of struts

recalculatePoints

public void recalculatePoints(ModelSet ms,
                              int modelIndex)

Overrides:

recalculatePoints in class Model

recalculateLeadMidpointsAndWingVectors

private void recalculateLeadMidpointsAndWingVectors()

calcSelectedMonomersCount

public void calcSelectedMonomersCount(BS bsSelected)

Overrides:

calcSelectedMonomersCount in class Model

getBioPolymerCountInModel

public int getBioPolymerCountInModel(ModelSet ms,
                                     int modelIndex)

Overrides:

getBioPolymerCountInModel in class Model

Returns:

count

calculateStraightnessAll

public void calculateStraightnessAll(ModelSet ms)

Overrides:

calculateStraightnessAll in class Model