public final class BioModel extends Model
Modifier and Type | Field and Description |
---|---|
private int |
bioPolymerCount |
private BioPolymer[] |
bioPolymers |
private static java.lang.String[] |
pdbRecords |
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 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(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) |
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getChimeInfoM, getGroupCount, getGroupCountHetero, getModelSet, getTrueAtomCount, isModelkit, resetBoundCount, set
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(STR 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
private java.lang.String calculateDssx(javajs.util.Lst<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
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 BioPolymer getBioPolymer(int polymerIndex)
public void getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
getDefaultLargePDBRendering
in class Model
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
fixIndices
in class Model
public void setStructureList(java.util.Map<STR,float[]> structureList)
setStructureList
in class Model
public void getPolymerPointsAndVectors(BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
getPolymerPointsAndVectors
in class Model
public javajs.util.Lst<BS> getBioBranches(javajs.util.Lst<BS> biobranches)
getBioBranches
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,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)
getAllPolymerInfo
in class Model
public void getChimeInfo(javajs.util.SB sb, int nHetero)
getChimeInfo
in class Model
public java.lang.String getFullPDBHeader()
getFullPDBHeader
in class Model
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)
getPdbData
in class Model
public BS getSequenceBits(ModelSet ms, java.lang.String specInfo, BS bs)
getSequenceBits
in class Model
public BS getBasePairBits(ModelSet ms, java.lang.String specInfo)
getBasePairBits
in class Model
public void resetRasmolBonds(Model model, BS bs)
resetRasmolBonds
in class Model
public void calcRasmolHydrogenBonds(ModelSet ms, BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
calcRasmolHydrogenBonds
in class Model
private void getRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
private static void clearRasmolHydrogenBonds(ModelSet ms, BioModel bm, BS bsAtoms)
public java.lang.String getFullProteinStructureState(ModelSet ms, BS bsAtoms2, boolean taintedOnly, boolean needPhiPsi, int mode)
getFullProteinStructureState
in class Model
public static java.lang.String getProteinStructureState(ModelSet ms, BioModel m, BS bsAtoms, boolean taintedOnly, boolean needPhiPsi, int mode)
public void calculateAllPolymers(ModelSet ms, Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)
calculateAllPolymers
in class Model
private static void calculatePolymers(ModelSet ms, Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)
public BS getGroupsWithinAll(ModelSet ms, int nResidues, BS bs)
getGroupsWithinAll
in class Model
public BS getSelectCodeRange(ModelSet ms, int[] info)
getSelectCodeRange
in class Model
public int calculateStruts(ModelSet ms, BS bs1, BS bs2)
calculateStruts
in class Model
public void recalculatePoints(ModelSet ms, int modelIndex)
recalculatePoints
in class Model
private void recalculateLeadMidpointsAndWingVectors()
public void calcSelectedMonomersCount(BS bsSelected)
calcSelectedMonomersCount
in class Model
public int getBioPolymerCountInModel(ModelSet ms, int modelIndex)
getBioPolymerCountInModel
in class Model
public void calculateStraightnessAll(ModelSet ms)
calculateStraightnessAll
in class Model