public final class BioModel extends Model implements JmolBioModelSet, JmolBioModel
Modifier and Type | Field and Description |
---|---|
(package private) int |
bioPolymerCount |
BioPolymer[] |
bioPolymers |
private BioExt |
bx |
private java.lang.String |
defaultStructure |
(package private) boolean |
isMutated |
private static java.lang.String[] |
pdbRecords |
private java.util.Map<java.lang.String,BS>[] |
unitIdSets |
private Viewer |
vwr |
act, altLocCount, auxiliaryInfo, biosymmetry, bsAtoms, bsAtomsDeleted, chainCount, chains, dssrCache, firstAtomIndex, frameDelay, groupCount, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isPdbWithMultipleBonds, loadScript, loadState, modelIndex, moleculeCount, ms, orientation, pdbID, properties, selectedTrajectory, simpleCage, structureTainted, trajectoryBaseIndex
Constructor and Description |
---|
BioModel(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
java.lang.String jmolData,
java.util.Properties properties,
java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo) |
Modifier and Type | Method and Description |
---|---|
private void |
addBioPolymer(BioPolymer polymer) |
void |
addSecondaryStructure(STR type,
java.lang.String structureID,
int serialID,
int strandCount,
int startChainID,
int startSeqcode,
int endChainID,
int endSeqcode,
int istart,
int iend,
BS bsAssigned) |
private boolean |
addUnit(int tok,
java.lang.String key,
BS bsTemp,
java.util.Map<java.lang.String,BS> map)
Repetitively AND unit components to get the final set of atoms
|
void |
calcAllRasmolHydrogenBonds(BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
BS bsHBonds)
only for base models, not trajectories
|
void |
calcSelectedMonomersCount() |
void |
calculateAllPolymers(Group[] groups,
int groupCount,
int baseGroupIndex,
BS modelsExcluded) |
java.lang.String |
calculateAllStructuresExcept(BS alreadyDefined,
boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha) |
java.lang.String |
calculateAllStuctures(BS bsAtoms,
boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
private java.lang.String |
calculateDssx(javajs.util.Lst<Bond> vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
void |
calculateStraightnessAll() |
private java.lang.String |
calculateStructures(boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha) |
int |
calculateStruts(BS bs1,
BS bs2) |
private BS |
checkMap(java.util.Map<java.lang.String,BS> map,
java.lang.String key,
BS bsAtoms)
Ensure that if two models have the same name or number, we
appropriately OR their bitsets.
|
private void |
clearBioPolymers() |
void |
fixIndices(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
boolean |
freeze() |
private BS |
getAllBasePairBits(java.lang.String specInfo) |
java.lang.String |
getAllDefaultStructures(BS bsAtoms,
BS bsModified) |
java.util.Map<java.lang.String,java.lang.String> |
getAllHeteroList(int modelIndex) |
void |
getAllPolymerInfo(BS bs,
java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info) |
void |
getAllPolymerPointsAndVectors(BS bs,
javajs.util.Lst<javajs.util.P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
BS |
getAllSequenceBits(java.lang.String specInfo,
BS bsAtoms,
BS bsResult) |
private BS |
getAllUnitIds(java.lang.String specInfo,
BS bsSelected,
BS bsResult) |
private BS |
getAnnotationBits(java.lang.String name,
int tok,
java.lang.String specInfo) |
BS |
getAtomBitsBS(int tokType,
BS bsInfo,
BS bs) |
BS |
getAtomBitsStr(int tokType,
java.lang.String specInfo,
BS bs) |
javajs.util.Lst<BS> |
getBioBranches(javajs.util.Lst<BS> biobranches) |
private BioExt |
getBioExt() |
int |
getBioPolymerCount() |
int |
getBioPolymerCountInModel(int modelIndex) |
(package private) java.lang.Object |
getCachedAnnotationMap(java.lang.String key,
java.lang.Object ann) |
boolean |
getConformation(int conformationIndex0,
boolean doSet,
BS bsAtoms,
BS bsRet) |
void |
getDefaultLargePDBRendering(javajs.util.SB sb,
int maxAtoms) |
java.lang.String |
getFullPDBHeader() |
java.lang.String |
getFullProteinStructureState(BS bsAtoms,
int mode) |
BS |
getGroupsWithinAll(int nResidues,
BS bs) |
BS |
getIdentifierOrNull(java.lang.String identifier) |
void |
getPdbData(java.lang.String type,
char ctype,
boolean isDraw,
BS bsSelected,
javajs.util.OC out,
LabelToken[] tokens,
javajs.util.SB pdbCONECT,
BS bsWritten) |
private void |
getRasmolHydrogenBonds(BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
BS bsHBonds) |
private int |
getStructureLines(BS bsAtoms,
javajs.util.SB cmd,
javajs.util.Lst<ProteinStructure> lstStr,
STR type,
boolean scriptMode,
int mode) |
java.lang.String |
getUnitID(Atom atom,
int flags)
Get a unitID.
|
private BS |
modelsOf(BS bsAtoms,
BS bsAtomsRet)
general purpose; return models associated with specific atoms
|
boolean |
mutate(BS bs,
java.lang.String group,
java.lang.String[] sequence) |
void |
recalculateAllPolymers(BS bsModelsExcluded,
Group[] groups) |
private void |
recalculateLeadMidpointsAndWingVectors() |
void |
recalculatePoints(int modelIndex) |
void |
resetRasmolBonds(BS bs)
from ModelSet.setAtomPositions
base models only; not trajectories
|
void |
setAllConformation(BS bsAtoms) |
void |
setAllDefaultStructure(BS bsModels) |
void |
setAllProteinType(BS bs,
STR type) |
void |
setAllStructureList(java.util.Map<STR,float[]> structureList) |
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getGroupCount, getTrueAtomCount, resetBoundCount, set
int bioPolymerCount
public BioPolymer[] bioPolymers
boolean isMutated
private java.lang.String defaultStructure
private Viewer vwr
private java.util.Map<java.lang.String,BS>[] unitIdSets
private BioExt bx
private static final java.lang.String[] pdbRecords
BioModel(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, java.lang.String jmolData, java.util.Properties properties, java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo)
public java.util.Map<java.lang.String,java.lang.String> getAllHeteroList(int modelIndex)
getAllHeteroList
in interface JmolBioModelSet
public void setAllProteinType(BS bs, STR type)
setAllProteinType
in interface JmolBioModelSet
private BS modelsOf(BS bsAtoms, BS bsAtomsRet)
bsAtoms
- bsAtomsRet
- all atoms associated with these models.public java.lang.String getAllDefaultStructures(BS bsAtoms, BS bsModified)
getAllDefaultStructures
in interface JmolBioModelSet
public java.lang.String calculateAllStuctures(BS bsAtoms, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
calculateAllStuctures
in interface JmolBioModelSet
public java.lang.String calculateAllStructuresExcept(BS alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
calculateAllStructuresExcept
in interface JmolBioModelSet
public void setAllDefaultStructure(BS bsModels)
public void setAllStructureList(java.util.Map<STR,float[]> structureList)
setAllStructureList
in interface JmolBioModelSet
public void setAllConformation(BS bsAtoms)
setAllConformation
in interface JmolBioModelSet
public void getAllPolymerPointsAndVectors(BS bs, javajs.util.Lst<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
getAllPolymerPointsAndVectors
in interface JmolBioModelSet
public void calcSelectedMonomersCount()
calcSelectedMonomersCount
in interface JmolBioModelSet
public int getBioPolymerCountInModel(int modelIndex)
getBioPolymerCountInModel
in interface JmolBioModelSet
modelIndex
- public void calculateAllPolymers(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded)
calculateAllPolymers
in interface JmolBioModelSet
public void recalculateAllPolymers(BS bsModelsExcluded, Group[] groups)
recalculateAllPolymers
in interface JmolBioModelSet
public BS getGroupsWithinAll(int nResidues, BS bs)
getGroupsWithinAll
in interface JmolBioModelSet
public int calculateStruts(BS bs1, BS bs2)
calculateStruts
in interface JmolBioModelSet
public void recalculatePoints(int modelIndex)
recalculatePoints
in interface JmolBioModelSet
public java.lang.String getFullProteinStructureState(BS bsAtoms, int mode)
getFullProteinStructureState
in interface JmolBioModelSet
private int getStructureLines(BS bsAtoms, javajs.util.SB cmd, javajs.util.Lst<ProteinStructure> lstStr, STR type, boolean scriptMode, int mode)
public BS getAllSequenceBits(java.lang.String specInfo, BS bsAtoms, BS bsResult)
getAllSequenceBits
in interface JmolBioModelSet
private BS checkMap(java.util.Map<java.lang.String,BS> map, java.lang.String key, BS bsAtoms)
map
- key
- bsAtoms
- private boolean addUnit(int tok, java.lang.String key, BS bsTemp, java.util.Map<java.lang.String,BS> map)
tok
- key
- bsTemp
- map
- private BS getAllBasePairBits(java.lang.String specInfo)
public void calcAllRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
calcAllRasmolHydrogenBonds
in interface JmolBioModelSet
bsA
- bsB
- vHBonds
- will be null for autobondingnucleicOnly
- nMax
- dsspIgnoreHydrogens
- bsHBonds
- private void getRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds)
public void calculateStraightnessAll()
calculateStraightnessAll
in interface JmolBioModelSet
public boolean mutate(BS bs, java.lang.String group, java.lang.String[] sequence)
mutate
in interface JmolBioModelSet
private void clearBioPolymers()
public int getBioPolymerCount()
getBioPolymerCount
in interface JmolBioModel
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
fixIndices
in class Model
private void recalculateLeadMidpointsAndWingVectors()
public void addSecondaryStructure(STR type, java.lang.String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, BS bsAssigned)
private java.lang.String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
private java.lang.String calculateDssx(javajs.util.Lst<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
public boolean getConformation(int conformationIndex0, boolean doSet, BS bsAtoms, BS bsRet)
conformationIndex0
- doSet
- bsAtoms
- bsRet
- private void addBioPolymer(BioPolymer polymer)
public javajs.util.Lst<BS> getBioBranches(javajs.util.Lst<BS> biobranches)
getBioBranches
in interface JmolBioModel
public void getAllPolymerInfo(BS bs, java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info)
getAllPolymerInfo
in interface JmolBioModelSet
private BioExt getBioExt()
public java.lang.String getFullPDBHeader()
getFullPDBHeader
in interface JmolBioModel
public void getPdbData(java.lang.String type, char ctype, boolean isDraw, BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, BS bsWritten)
getPdbData
in interface JmolBioModel
public void resetRasmolBonds(BS bs)
resetRasmolBonds
in interface JmolBioModel
public void getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
getDefaultLargePDBRendering
in interface JmolBioModel
public BS getAtomBitsStr(int tokType, java.lang.String specInfo, BS bs)
getAtomBitsStr
in interface JmolBioModelSet
public BS getAtomBitsBS(int tokType, BS bsInfo, BS bs)
getAtomBitsBS
in interface JmolBioModelSet
private BS getAnnotationBits(java.lang.String name, int tok, java.lang.String specInfo)
java.lang.Object getCachedAnnotationMap(java.lang.String key, java.lang.Object ann)
public BS getIdentifierOrNull(java.lang.String identifier)
getIdentifierOrNull
in interface JmolBioModelSet
public java.lang.String getUnitID(Atom atom, int flags)
atom
- flags
-