public final class BioModel extends Model
Modifier and Type | Field and Description |
---|---|
private int |
bioPolymerCount |
private BioPolymer[] |
bioPolymers |
private static java.lang.String[] |
pdbRecords |
atomCount, auxiliaryInfo, bsAtoms, chainCount, chains, firstAtomIndex, frameDelay, hasRasmolHBonds, hydrogenCount, isBioModel, isPdbWithMultipleBonds, modelIndex, modelSet, nAltLocs, structureTainted, trajectoryBaseIndex, unitCell
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) |
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) |
getBondCount, getChainCount, getChains, getGroupCount, getModelNumberDotted, getModelSet, getModelTitle, getTrueAtomCount, isModelkit, isStructureTainted, resetBoundCount
private int bioPolymerCount
private BioPolymer[] bioPolymers
private static final java.lang.String[] pdbRecords
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)
public void addSecondaryStructure(EnumStructure type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
addSecondaryStructure
in class Model
public java.lang.String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
calculateStructures
in class Model
public void setConformation(java.util.BitSet bsConformation)
setConformation
in class Model
public boolean getPdbConformation(java.util.BitSet bsConformation, int conformationIndex)
getPdbConformation
in class Model
public int getBioPolymerCount()
getBioPolymerCount
in class Model
public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
calcSelectedMonomersCount
in class Model
public BioPolymer getBioPolymer(int polymerIndex)
public void getDefaultLargePDBRendering(java.lang.StringBuffer sb, int maxAtoms)
getDefaultLargePDBRendering
in class Model
public void fixIndices(int modelIndex, int nAtomsDeleted, java.util.BitSet bsDeleted)
fixIndices
in class Model
public int calculateStruts(ModelSet modelSet, java.util.BitSet bs1, java.util.BitSet bs2)
calculateStruts
in class Model
public void setStructureList(java.util.Map<EnumStructure,float[]> structureList)
setStructureList
in class Model
public void calculateStraightness(Viewer viewer, char ctype, char qtype, int mStep)
calculateStraightness
in class Model
public void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.List<javax.vecmath.Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
getPolymerPointsAndVectors
in class Model
public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int iPolymer)
getPolymerLeadMidPoints
in class Model
public void recalculateLeadMidpointsAndWingVectors()
recalculateLeadMidpointsAndWingVectors
in class Model
public java.util.List<java.util.BitSet> getBioBranches(java.util.List<java.util.BitSet> biobranches)
getBioBranches
in class Model
public void getGroupsWithin(int nResidues, java.util.BitSet bs, java.util.BitSet bsResult)
getGroupsWithin
in class Model
public void getSequenceBits(java.lang.String specInfo, java.util.BitSet bs, java.util.BitSet bsResult)
getSequenceBits
in class Model
public void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID, java.util.BitSet bs, boolean caseSensitive)
selectSeqcodeRange
in class Model
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)
getRasmolHydrogenBonds
in class Model
public void clearRasmolHydrogenBonds(java.util.BitSet bsAtoms)
clearRasmolHydrogenBonds
in class Model
public void calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, java.util.BitSet modelsExcluded)
calculatePolymers
in class Model
private void addBioPolymer(BioPolymer polymer)
public void clearBioPolymers()
clearBioPolymers
in class Model
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)
getAllPolymerInfo
in class Model
public void getChimeInfo(java.lang.StringBuffer sb, int nHetero)
getChimeInfo
in class Model
public java.lang.String getProteinStructureState(java.util.BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
getProteinStructureState
in class Model
public java.lang.String getFullPDBHeader()
getFullPDBHeader
in class Model
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)
getPdbData
in class Model