Package org.jmol.modelsetbio
Class BioModel
- java.lang.Object
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- org.jmol.modelset.Model
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- org.jmol.modelsetbio.BioModel
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public final class BioModel extends Model
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Field Summary
Fields Modifier and Type Field Description (package private) int
bioPolymerCount
BioPolymer[]
bioPolymers
(package private) String
defaultStructure
(package private) boolean
isMutated
private Viewer
vwr
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Fields inherited from class org.jmol.modelset.Model
act, altLocCount, auxiliaryInfo, biosymmetry, bsAtoms, bsAtomsDeleted, chainCount, chains, dssrCache, firstAtomIndex, frameDelay, groupCount, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isPdbWithMultipleBonds, loadScript, loadState, mat4, modelIndex, moleculeCount, ms, orientation, pdbID, properties, selectedTrajectory, simpleCage, structureTainted, trajectoryBaseIndex
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) int
addBioPolymer(BioPolymer polymer)
(package private) void
addSecondaryStructure(STR type, String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, javajs.util.BS bsAssigned)
(package private) void
addStructureByBS(int count, int dsspType, STR type, javajs.util.BS bs)
private String
calculateDssx(javajs.util.Lst<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
(package private) String
calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
(package private) void
clearBioPolymers()
void
fixIndices(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted)
boolean
freeze()
void
getAtomicDSSRData(float[] dssrData, String dataType)
javajs.util.Lst<javajs.util.BS>
getBioBranches(javajs.util.Lst<javajs.util.BS> biobranches)
int
getBioPolymerCount()
(package private) Object
getCachedAnnotationMap(String key, Object ann)
boolean
getConformation(int conformationIndex0, boolean doSet, javajs.util.BS bsAtoms, javajs.util.BS bsRet)
void
getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
String
getFullPDBHeader()
void
getPdbData(String type, char ctype, boolean isDraw, javajs.util.BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten)
(package private) void
getRasmolHydrogenBonds(javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, javajs.util.BS bsHBonds, int version)
String
getUnitID(Atom atom, int flags)
Get a unitID.(package private) void
recalculateLeadMidpointsAndWingVectors()
void
resetRasmolBonds(javajs.util.BS bs, int dsspVersion)
from Trajectory.setAtomPositions base models only; not trajectories-
Methods inherited from class org.jmol.modelset.Model
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getGroupCount, getTrueAtomCount, isContainedIn, resetBoundCount, resetDSSR, set
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Field Detail
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vwr
private Viewer vwr
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bioPolymerCount
int bioPolymerCount
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bioPolymers
public BioPolymer[] bioPolymers
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isMutated
boolean isMutated
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defaultStructure
String defaultStructure
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Method Detail
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addBioPolymer
int addBioPolymer(BioPolymer polymer)
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addSecondaryStructure
void addSecondaryStructure(STR type, String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, javajs.util.BS bsAssigned)
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addStructureByBS
void addStructureByBS(int count, int dsspType, STR type, javajs.util.BS bs)
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calculateDssx
private String calculateDssx(javajs.util.Lst<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
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calculateStructures
String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
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clearBioPolymers
void clearBioPolymers()
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fixIndices
public void fixIndices(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted)
- Overrides:
fixIndices
in classModel
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getBioBranches
public javajs.util.Lst<javajs.util.BS> getBioBranches(javajs.util.Lst<javajs.util.BS> biobranches)
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getBioPolymerCount
public int getBioPolymerCount()
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getConformation
public boolean getConformation(int conformationIndex0, boolean doSet, javajs.util.BS bsAtoms, javajs.util.BS bsRet)
- Parameters:
conformationIndex0
-doSet
-bsAtoms
-bsRet
-- Returns:
- true;
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getDefaultLargePDBRendering
public void getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
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getFullPDBHeader
public String getFullPDBHeader()
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getPdbData
public void getPdbData(String type, char ctype, boolean isDraw, javajs.util.BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten)
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getRasmolHydrogenBonds
void getRasmolHydrogenBonds(javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, javajs.util.BS bsHBonds, int version)
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getUnitID
public String getUnitID(Atom atom, int flags)
Get a unitID. Note that we MUST go through the | after InsCode, because if we do not do that we cannot match residues only using string matching.- Parameters:
atom
-flags
-- Returns:
- a unitID
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recalculateLeadMidpointsAndWingVectors
void recalculateLeadMidpointsAndWingVectors()
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resetRasmolBonds
public void resetRasmolBonds(javajs.util.BS bs, int dsspVersion)
from Trajectory.setAtomPositions base models only; not trajectories- Parameters:
bs
-dsspVersion
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getAtomicDSSRData
public void getAtomicDSSRData(float[] dssrData, String dataType)
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