Package org.jmol.modelsetbio
Class BioModel
java.lang.Object
org.jmol.modelset.Model
org.jmol.modelsetbio.BioModel
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Field Summary
FieldsModifier and TypeFieldDescription(package private) int
(package private) String
(package private) boolean
private Viewer
Fields inherited from class org.jmol.modelset.Model
act, altLocCount, auxiliaryInfo, biosymmetry, bsAsymmetricUnit, bsAtoms, bsAtomsDeleted, chainCount, chains, dssrCache, firstAtomIndex, frameDelay, groupCount, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isOrderly, isPdbWithMultipleBonds, loadScript, loadState, mat4, modelIndex, moleculeCount, ms, orientation, pdbID, properties, selectedTrajectory, simpleCage, structureTainted, trajectoryBaseIndex
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(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
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
(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) 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) Get a unitID.(package private) void
void
resetRasmolBonds
(javajs.util.BS bs, int dsspVersion) from Trajectory.setAtomPositions base models only; not trajectoriesMethods inherited from class org.jmol.modelset.Model
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getGroupCount, getTrueAtomCount, isContainedIn, resetBoundCount, resetDSSR, set, setSimpleCage
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Field Details
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vwr
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bioPolymerCount
int bioPolymerCount -
bioPolymers
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isMutated
boolean isMutated -
defaultStructure
String defaultStructure
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Constructor Details
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BioModel
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Method Details
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addBioPolymer
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addSecondaryStructure
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addStructureByBS
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calculateDssx
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calculateStructures
String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) -
clearBioPolymers
void clearBioPolymers() -
fixIndices
public void fixIndices(int modelIndex, int nAtomsDeleted, javajs.util.BS bsDeleted) - Overrides:
fixIndices
in classModel
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freeze
public boolean freeze() -
getBioBranches
public javajs.util.Lst<javajs.util.BS> getBioBranches(javajs.util.Lst<javajs.util.BS> biobranches) -
getBioPolymerCount
public int getBioPolymerCount() -
getCachedAnnotationMap
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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) -
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) -
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) -
getUnitID
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() -
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
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