Package org.jmol.modelsetbio
Class BioModelSet
java.lang.Object
org.jmol.modelsetbio.BioModelSet
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate boolean
Repetitively AND unit components to get the final set of atomsvoid
calcAllRasmolHydrogenBonds
(javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, javajs.util.BS bsHBonds, int dsspVersion) only for base models, not trajectoriesvoid
void
calculateAllPolymers
(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded) calculateAllStructuresExcept
(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) calculateAllStuctures
(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version) void
int
calculateStruts
(javajs.util.BS bs1, javajs.util.BS bs2) private javajs.util.BS
Ensure that if two models have the same name or number, we appropriately OR their bitsets.private javajs.util.BS
getAllBasePairBits
(String specInfo) getAllDefaultStructures
(javajs.util.BS bsAtoms, javajs.util.BS bsModified) getAllHeteroList
(int modelIndex) void
void
getAllPolymerPointsAndVectors
(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) javajs.util.BS
getAllSequenceBits
(String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult) private javajs.util.BS
getAllUnitIds
(String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult) boolean
getAminoAcidValenceAndCharge
(String s, String atomName, int[] aaRet) private javajs.util.BS
getAnnotationBits
(String name, int tok, String specInfo) javajs.util.BS
getAtomBitsBS
(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs) javajs.util.BS
getAtomBitsStr
(int tokType, String specInfo, javajs.util.BS bs) (package private) BioExt
int
getBioPolymerCountInModel
(int modelIndex) getFullProteinStructureState
(javajs.util.BS bsAtoms, int mode) javajs.util.BS
getGroupsWithinAll
(int nResidues, javajs.util.BS bs) javajs.util.BS
getIdentifierOrNull
(String identifier) private int
getStructureLines
(javajs.util.BS bsAtoms, javajs.util.SB cmd, javajs.util.Lst<ProteinStructure> lstStr, STR type, boolean scriptMode, int mode) private javajs.util.BS
modelsOf
(javajs.util.BS bsAtoms, javajs.util.BS bsAtomsRet) general purpose; return models associated with specific atomsboolean
void
recalculateAllPolymers
(javajs.util.BS bsModelsExcluded, Group[] groups) void
recalculatePoints
(int modelIndex) void
setAllConformation
(javajs.util.BS bsAtoms) private void
setAllDefaultStructure
(javajs.util.BS bsModels) void
setAllProteinType
(javajs.util.BS bs, STR type) called from state STRUCTURE commandvoid
setAllStructureList
(Map<STR, float[]> structureList)
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Field Details
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DEFAULT_DSSP_VERSION
private static final int DEFAULT_DSSP_VERSION- See Also:
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vwr
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ms
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ext
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unitIdSets
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Constructor Details
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BioModelSet
public BioModelSet()
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Method Details
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getBioExt
BioExt getBioExt() -
set
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calcAllRasmolHydrogenBonds
public void calcAllRasmolHydrogenBonds(javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, javajs.util.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
public void calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded) -
calculateAllStructuresExcept
public String calculateAllStructuresExcept(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version) -
calculateAllStuctures
public String calculateAllStuctures(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version) -
calculateStraightnessAll
public void calculateStraightnessAll() -
calculateStruts
public int calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2) -
getAllDefaultStructures
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getAllHeteroList
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getAllPolymerInfo
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getAllPolymerPointsAndVectors
public void getAllPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing) -
getAllSequenceBits
public javajs.util.BS getAllSequenceBits(String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult) -
getAtomBitsBS
public javajs.util.BS getAtomBitsBS(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs) -
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
public javajs.util.BS getGroupsWithinAll(int nResidues, javajs.util.BS bs) -
getIdentifierOrNull
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mutate
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recalculateAllPolymers
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recalculatePoints
public void recalculatePoints(int modelIndex) -
setAllConformation
public void setAllConformation(javajs.util.BS bsAtoms) -
setAllProteinType
called from state STRUCTURE command- Parameters:
bs
-type
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setAllStructureList
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getAllBasePairBits
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getAllUnitIds
private javajs.util.BS getAllUnitIds(String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult) -
checkMap
Ensure that if two models have the same name or number, we appropriately OR their bitsets.- Parameters:
map
-key
-bsAtoms
-- Returns:
- current BS
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addUnit
Repetitively AND unit components to get the final set of atoms- Parameters:
tok
-key
-bsTemp
-map
-- Returns:
- true if there are still atoms to consider
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getAnnotationBits
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getStructureLines
private int getStructureLines(javajs.util.BS bsAtoms, javajs.util.SB cmd, javajs.util.Lst<ProteinStructure> lstStr, STR type, boolean scriptMode, int mode) -
modelsOf
private javajs.util.BS modelsOf(javajs.util.BS bsAtoms, javajs.util.BS bsAtomsRet) general purpose; return models associated with specific atoms- Parameters:
bsAtoms
-bsAtomsRet
- all atoms associated with these models.- Returns:
- bitset of base models
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setAllDefaultStructure
private void setAllDefaultStructure(javajs.util.BS bsModels) -
getAminoAcidValenceAndCharge
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