Package org.jmol.modelsetbio
Class BioModelSet
java.lang.Object
org.jmol.modelsetbio.BioModelSet
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
calcAllRasmolHydrogenBonds
(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int dsspVersion) only for base models, not trajectoriesvoid
void
calculateAllPolymers
(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded) calculateAllStructuresExcept
(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) calculateAllStuctures
(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version) void
int
calculateStruts
(BS bs1, BS bs2) getAllDefaultStructures
(BS bsAtoms, BS bsModified) getAllHeteroList
(int modelIndex) void
void
getAllPolymerPointsAndVectors
(BS bs, Lst<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) getAllSequenceBits
(String specInfo, BS bsAtoms, BS bsResult) boolean
getAminoAcidValenceAndCharge
(String s, String atomName, int[] aaRet) getAtomBitsBS
(int tokType, BS bsInfo, BS bs) getAtomBitsStr
(int tokType, String specInfo, BS bs) int
getBioPolymerCountInModel
(int modelIndex) getFullProteinStructureState
(BS bsAtoms, int mode) getGroupsWithinAll
(int nResidues, BS bs) getIdentifierOrNull
(String identifier) boolean
void
recalculateAllPolymers
(BS bsModelsExcluded, Group[] groups) void
recalculatePoints
(int modelIndex) void
setAllConformation
(BS bsAtoms) void
setAllProteinType
(BS bs, STR type) called from state STRUCTURE commandvoid
setAllStructureList
(Map<STR, float[]> structureList)
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Constructor Details
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BioModelSet
public BioModelSet()
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Method Details
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set
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calcAllRasmolHydrogenBonds
public void calcAllRasmolHydrogenBonds(BS bsA, BS bsB, Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int dsspVersion) only for base models, not trajectories- Parameters:
bsA
-bsB
-vHBonds
- will be null for autobondingnucleicOnly
-nMax
-dsspIgnoreHydrogens
-bsHBonds
-dsspVersion
- 1 or 2
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calcSelectedMonomersCount
public void calcSelectedMonomersCount() -
calculateAllPolymers
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calculateAllStructuresExcept
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calculateAllStuctures
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calculateStraightnessAll
public void calculateStraightnessAll() -
calculateStruts
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getAllDefaultStructures
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getAllHeteroList
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getAllPolymerInfo
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getAllPolymerPointsAndVectors
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getAllSequenceBits
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getAtomBitsBS
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getAtomBitsStr
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getBioPolymerCountInModel
public int getBioPolymerCountInModel(int modelIndex) - Parameters:
modelIndex
-- Returns:
- number of polymers
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getFullProteinStructureState
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getGroupsWithinAll
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getIdentifierOrNull
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mutate
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recalculateAllPolymers
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recalculatePoints
public void recalculatePoints(int modelIndex) -
setAllConformation
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setAllProteinType
called from state STRUCTURE command- Parameters:
bs
-type
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setAllStructureList
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getAminoAcidValenceAndCharge
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