public class BioModelSet
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private BioExt |
ext |
private ModelSet |
ms |
private java.util.Map<java.lang.String,javajs.util.BS>[] |
unitIdSets |
private Viewer |
vwr |
Constructor and Description |
---|
BioModelSet() |
Modifier and Type | Method and 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 atoms
|
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
|
void |
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 atoms
|
boolean |
mutate(javajs.util.BS bs,
java.lang.String group,
java.lang.String[] sequence) |
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) |
void |
setAllStructureList(java.util.Map<STR,float[]> structureList) |
private Viewer vwr
private ModelSet ms
private BioExt ext
private java.util.Map<java.lang.String,javajs.util.BS>[] unitIdSets
BioExt getBioExt()
public BioModelSet set(Viewer vwr, ModelSet ms)
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)
bsA
- bsB
- vHBonds
- will be null for autobondingnucleicOnly
- nMax
- dsspIgnoreHydrogens
- bsHBonds
- dsspVersion
- 1 or 2public void calcSelectedMonomersCount()
public void calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, javajs.util.BS modelsExcluded)
public java.lang.String calculateAllStructuresExcept(javajs.util.BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
public java.lang.String calculateAllStuctures(javajs.util.BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
public void calculateStraightnessAll()
public int calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2)
public java.lang.String getAllDefaultStructures(javajs.util.BS bsAtoms, javajs.util.BS bsModified)
public java.util.Map<java.lang.String,java.lang.String> getAllHeteroList(int modelIndex)
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)
public void getAllPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
public javajs.util.BS getAllSequenceBits(java.lang.String specInfo, javajs.util.BS bsAtoms, javajs.util.BS bsResult)
public javajs.util.BS getAtomBitsBS(int tokType, javajs.util.BS bsInfo, javajs.util.BS bs)
public javajs.util.BS getAtomBitsStr(int tokType, java.lang.String specInfo, javajs.util.BS bs)
public int getBioPolymerCountInModel(int modelIndex)
modelIndex
- public java.lang.String getFullProteinStructureState(javajs.util.BS bsAtoms, int mode)
public javajs.util.BS getGroupsWithinAll(int nResidues, javajs.util.BS bs)
public javajs.util.BS getIdentifierOrNull(java.lang.String identifier)
public boolean mutate(javajs.util.BS bs, java.lang.String group, java.lang.String[] sequence)
public void recalculateAllPolymers(javajs.util.BS bsModelsExcluded, Group[] groups)
public void recalculatePoints(int modelIndex)
public void setAllConformation(javajs.util.BS bsAtoms)
public void setAllProteinType(javajs.util.BS bs, STR type)
public void setAllStructureList(java.util.Map<STR,float[]> structureList)
private javajs.util.BS getAllBasePairBits(java.lang.String specInfo)
private javajs.util.BS getAllUnitIds(java.lang.String specInfo, javajs.util.BS bsSelected, javajs.util.BS bsResult)
private javajs.util.BS checkMap(java.util.Map<java.lang.String,javajs.util.BS> map, java.lang.String key, javajs.util.BS bsAtoms)
map
- key
- bsAtoms
- private boolean addUnit(int tok, java.lang.String key, javajs.util.BS bsTemp, java.util.Map<java.lang.String,javajs.util.BS> map)
tok
- key
- bsTemp
- map
- private javajs.util.BS getAnnotationBits(java.lang.String name, int tok, java.lang.String specInfo)
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)
bsAtoms
- bsAtomsRet
- all atoms associated with these models.private void setAllDefaultStructure(javajs.util.BS bsModels)
public boolean getAminoAcidValenceAndCharge(java.lang.String s, java.lang.String atomName, int[] aaRet)