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, isJmolDataFrame, isModelKit, isPdbWithMultipleBonds, isTrajectory, loadScript, loadState, modelIndex, modelSet, moleculeCount, nAltLocs, orientation, properties, simpleCage, structureTainted, trajectoryBaseIndex
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,
int startChainID,
int startSeqcode,
int endChainID,
int endSeqcode,
int istart,
int iend,
BS bsAssigned) |
void |
calcSelectedMonomersCount(BS bsSelected) |
void |
calculatePolymers(Group[] groups,
int groupCount,
int baseGroupIndex,
BS modelsExcluded,
boolean checkConnections) |
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,
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,JmolList<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo,
JmolList<java.util.Map<java.lang.String,java.lang.Object>> modelVector) |
JmolList<BS> |
getBioBranches(JmolList<BS> biobranches) |
BioPolymer |
getBioPolymer(int polymerIndex) |
int |
getBioPolymerCount() |
void |
getChimeInfo(SB sb,
int nHetero) |
void |
getDefaultLargePDBRendering(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 viewer,
java.lang.String type,
char ctype,
boolean isDraw,
BS bsSelected,
OutputStringBuilder sb,
LabelToken[] tokens,
SB pdbCONECT,
BS bsWritten) |
P3[] |
getPolymerLeadMidPoints(int iPolymer) |
void |
getPolymerPointsAndVectors(BS bs,
JmolList<P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
java.lang.String |
getProteinStructureState(BS bsAtoms,
boolean taintedOnly,
boolean needPhiPsi,
int mode) |
void |
getRasmolHydrogenBonds(BS bsA,
BS bsB,
JmolList<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<EnumStructure,float[]> structureList) |
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getChains, getChimeInfoM, getGroupCount, getGroupCountHetero, getModelNumberDotted, getModelSet, getModelTitle, getSelectedTrajectory, 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, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, BS bsAssigned)
public java.lang.String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
calculateStructures
in class Model
public void setConformation(BS bsConformation)
setConformation
in class Model
public boolean getPdbConformation(BS bsConformation, int conformationIndex)
getPdbConformation
in class Model
public int getBioPolymerCount()
getBioPolymerCount
in class Model
public void calcSelectedMonomersCount(BS bsSelected)
calcSelectedMonomersCount
in class Model
public BioPolymer getBioPolymer(int polymerIndex)
public void getDefaultLargePDBRendering(SB sb, int maxAtoms)
getDefaultLargePDBRendering
in class Model
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
fixIndices
in class Model
public int calculateStruts(ModelSet modelSet, BS bs1, BS 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(BS bs, JmolList<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
getPolymerPointsAndVectors
in class Model
public P3[] getPolymerLeadMidPoints(int iPolymer)
getPolymerLeadMidPoints
in class Model
public void recalculateLeadMidpointsAndWingVectors()
recalculateLeadMidpointsAndWingVectors
in class Model
public JmolList<BS> getBioBranches(JmolList<BS> biobranches)
getBioBranches
in class Model
public void getGroupsWithin(int nResidues, BS bs, BS bsResult)
getGroupsWithin
in class Model
public void getSequenceBits(java.lang.String specInfo, BS bs, BS bsResult)
getSequenceBits
in class Model
public void selectSeqcodeRange(int seqcodeA, int seqcodeB, int chainID, BS bs, boolean caseSensitive)
selectSeqcodeRange
in class Model
public void getRasmolHydrogenBonds(BS bsA, BS bsB, JmolList<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
getRasmolHydrogenBonds
in class Model
public void clearRasmolHydrogenBonds(BS bsAtoms)
clearRasmolHydrogenBonds
in class Model
public void calculatePolymers(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded, boolean checkConnections)
calculatePolymers
in class Model
private void addBioPolymer(BioPolymer polymer)
public void clearBioPolymers()
clearBioPolymers
in class Model
public void getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,JmolList<java.util.Map<java.lang.String,java.lang.Object>>> finalInfo, JmolList<java.util.Map<java.lang.String,java.lang.Object>> modelVector)
getAllPolymerInfo
in class Model
public void getChimeInfo(SB sb, int nHetero)
getChimeInfo
in class Model
public java.lang.String getProteinStructureState(BS 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, BS bsSelected, OutputStringBuilder sb, LabelToken[] tokens, SB pdbCONECT, BS bsWritten)
getPdbData
in class Model