Package org.jmol.modelsetbio
Class BioModelSet
- java.lang.Object
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- org.jmol.modelsetbio.BioModelSet
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public class BioModelSet extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description private static int
DEFAULT_DSSP_VERSION
private BioExt
ext
private ModelSet
ms
private java.util.Map<java.lang.String,javajs.util.BS>[]
unitIdSets
private Viewer
vwr
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Constructor Summary
Constructors Constructor Description BioModelSet()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private boolean
addUnit(int tok, java.lang.String key, javajs.util.BS bsTemp, java.util.Map<java.lang.String,javajs.util.BS> map)
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
calcSelectedMonomersCount()
void
calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded)
java.lang.String
calculateAllStructuresExcept(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
java.lang.String
calculateAllStuctures(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
void
calculateStraightnessAll()
int
calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2)
private javajs.util.BS
checkMap(java.util.Map<java.lang.String,javajs.util.BS> map, java.lang.String key, javajs.util.BS bsAtoms)
Ensure that if two models have the same name or number, we appropriately OR their bitsets.private javajs.util.BS
getAllBasePairBits(java.lang.String specInfo)
java.lang.String
getAllDefaultStructures(javajs.util.BS bsAtoms, javajs.util.BS bsModified)
java.util.Map<java.lang.String,java.lang.String>
getAllHeteroList(int modelIndex)
void
getAllPolymerInfo(javajs.util.BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info)
void
getAllPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
javajs.util.BS
getAllSequenceBits(java.lang.String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult)
private javajs.util.BS
getAllUnitIds(java.lang.String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult)
boolean
getAminoAcidValenceAndCharge(java.lang.String s, java.lang.String atomName, int[] aaRet)
private javajs.util.BS
getAnnotationBits(java.lang.String name, int tok, java.lang.String specInfo)
javajs.util.BS
getAtomBitsBS(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs)
javajs.util.BS
getAtomBitsStr(int tokType, java.lang.String specInfo, javajs.util.BS bs)
(package private) BioExt
getBioExt()
int
getBioPolymerCountInModel(int modelIndex)
java.lang.String
getFullProteinStructureState(javajs.util.BS bsAtoms, int mode)
javajs.util.BS
getGroupsWithinAll(int nResidues, javajs.util.BS bs)
javajs.util.BS
getIdentifierOrNull(java.lang.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
mutate(javajs.util.BS bs, java.lang.String group, java.lang.String[] sequence, java.lang.String alphaType, float[] phipsi)
void
recalculateAllPolymers(javajs.util.BS bsModelsExcluded, Group[] groups)
void
recalculatePoints(int modelIndex)
BioModelSet
set(Viewer vwr, ModelSet ms)
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(java.util.Map<STR,float[]> structureList)
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Field Detail
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DEFAULT_DSSP_VERSION
private static final int DEFAULT_DSSP_VERSION
- See Also:
- Constant Field Values
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vwr
private Viewer vwr
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ms
private ModelSet ms
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ext
private BioExt ext
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unitIdSets
private java.util.Map<java.lang.String,javajs.util.BS>[] unitIdSets
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Method Detail
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getBioExt
BioExt getBioExt()
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set
public BioModelSet set(Viewer vwr, ModelSet ms)
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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()
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calculateAllPolymers
public void calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded)
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calculateAllStructuresExcept
public java.lang.String calculateAllStructuresExcept(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
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calculateAllStuctures
public java.lang.String calculateAllStuctures(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
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calculateStraightnessAll
public void calculateStraightnessAll()
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calculateStruts
public int calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2)
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getAllDefaultStructures
public java.lang.String getAllDefaultStructures(javajs.util.BS bsAtoms, javajs.util.BS bsModified)
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getAllHeteroList
public java.util.Map<java.lang.String,java.lang.String> getAllHeteroList(int modelIndex)
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getAllPolymerInfo
public void getAllPolymerInfo(javajs.util.BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info)
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getAllPolymerPointsAndVectors
public void getAllPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
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getAllSequenceBits
public javajs.util.BS getAllSequenceBits(java.lang.String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult)
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getAtomBitsBS
public javajs.util.BS getAtomBitsBS(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs)
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getAtomBitsStr
public javajs.util.BS getAtomBitsStr(int tokType, java.lang.String specInfo, javajs.util.BS bs)
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getBioPolymerCountInModel
public int getBioPolymerCountInModel(int modelIndex)
- Parameters:
modelIndex
-- Returns:
- number of polymers
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getFullProteinStructureState
public java.lang.String getFullProteinStructureState(javajs.util.BS bsAtoms, int mode)
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getGroupsWithinAll
public javajs.util.BS getGroupsWithinAll(int nResidues, javajs.util.BS bs)
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getIdentifierOrNull
public javajs.util.BS getIdentifierOrNull(java.lang.String identifier)
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mutate
public boolean mutate(javajs.util.BS bs, java.lang.String group, java.lang.String[] sequence, java.lang.String alphaType, float[] phipsi)
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recalculateAllPolymers
public void recalculateAllPolymers(javajs.util.BS bsModelsExcluded, Group[] groups)
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recalculatePoints
public void recalculatePoints(int modelIndex)
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setAllConformation
public void setAllConformation(javajs.util.BS bsAtoms)
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setAllProteinType
public void setAllProteinType(javajs.util.BS bs, STR type)
called from state STRUCTURE command- Parameters:
bs
-type
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setAllStructureList
public void setAllStructureList(java.util.Map<STR,float[]> structureList)
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getAllBasePairBits
private javajs.util.BS getAllBasePairBits(java.lang.String specInfo)
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getAllUnitIds
private javajs.util.BS getAllUnitIds(java.lang.String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult)
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checkMap
private javajs.util.BS checkMap(java.util.Map<java.lang.String,javajs.util.BS> map, java.lang.String key, javajs.util.BS bsAtoms)
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
private boolean addUnit(int tok, java.lang.String key, javajs.util.BS bsTemp, java.util.Map<java.lang.String,javajs.util.BS> map)
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
private javajs.util.BS getAnnotationBits(java.lang.String name, int tok, java.lang.String specInfo)
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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)
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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)
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getAminoAcidValenceAndCharge
public boolean getAminoAcidValenceAndCharge(java.lang.String s, java.lang.String atomName, int[] aaRet)
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