org.jmol.modelsetbio

Class BioModel

java.lang.Object

org.jmol.modelset.Model

org.jmol.modelsetbio.BioModel

All Implemented Interfaces:

JmolBioModel, JmolBioModelSet

public final class BioModel
extends Model
implements JmolBioModelSet, JmolBioModel

Field Summary

Fields

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

Fields inherited from class org.jmol.modelset.Model

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 Summary

Constructors

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)

Method Summary

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)

Methods inherited from class org.jmol.modelset.Model

fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getGroupCount, getTrueAtomCount, resetBoundCount, set

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

bioPolymerCount

int bioPolymerCount

bioPolymers

public BioPolymer[] bioPolymers

isMutated

boolean isMutated

defaultStructure

private java.lang.String defaultStructure

vwr

private Viewer vwr

unitIdSets

private java.util.Map<java.lang.String,BS>[] unitIdSets

bx

private BioExt bx

pdbRecords

private static final java.lang.String[] pdbRecords

Constructor Detail

BioModel

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)

Method Detail

getAllHeteroList

public java.util.Map<java.lang.String,java.lang.String> getAllHeteroList(int modelIndex)

Specified by:

getAllHeteroList in interface JmolBioModelSet

setAllProteinType

public void setAllProteinType(BS bs,
                              STR type)

Specified by:

setAllProteinType in interface JmolBioModelSet

modelsOf

private BS modelsOf(BS bsAtoms,
                    BS bsAtomsRet)

general purpose; return models associated with specific atoms

Parameters:

bsAtoms -

bsAtomsRet - all atoms associated with these models.

Returns:

bitset of base models

getAllDefaultStructures

public java.lang.String getAllDefaultStructures(BS bsAtoms,
                                                BS bsModified)

Specified by:

getAllDefaultStructures in interface JmolBioModelSet

calculateAllStuctures

public java.lang.String calculateAllStuctures(BS bsAtoms,
                                              boolean asDSSP,
                                              boolean doReport,
                                              boolean dsspIgnoreHydrogen,
                                              boolean setStructure)

Specified by:

calculateAllStuctures in interface JmolBioModelSet

calculateAllStructuresExcept

public java.lang.String calculateAllStructuresExcept(BS alreadyDefined,
                                                     boolean asDSSP,
                                                     boolean doReport,
                                                     boolean dsspIgnoreHydrogen,
                                                     boolean setStructure,
                                                     boolean includeAlpha)

Specified by:

calculateAllStructuresExcept in interface JmolBioModelSet

setAllDefaultStructure

public void setAllDefaultStructure(BS bsModels)

setAllStructureList

public void setAllStructureList(java.util.Map<STR,float[]> structureList)

Specified by:

setAllStructureList in interface JmolBioModelSet

setAllConformation

public void setAllConformation(BS bsAtoms)

Specified by:

setAllConformation in interface JmolBioModelSet

getAllPolymerPointsAndVectors

public void getAllPolymerPointsAndVectors(BS bs,
                                          javajs.util.Lst<javajs.util.P3[]> vList,
                                          boolean isTraceAlpha,
                                          float sheetSmoothing)

Specified by:

getAllPolymerPointsAndVectors in interface JmolBioModelSet

calcSelectedMonomersCount

public void calcSelectedMonomersCount()

Specified by:

calcSelectedMonomersCount in interface JmolBioModelSet

getBioPolymerCountInModel

public int getBioPolymerCountInModel(int modelIndex)

Specified by:

getBioPolymerCountInModel in interface JmolBioModelSet

Parameters:

modelIndex -

Returns:

number of polymers

calculateAllPolymers

public void calculateAllPolymers(Group[] groups,
                                 int groupCount,
                                 int baseGroupIndex,
                                 BS modelsExcluded)

Specified by:

calculateAllPolymers in interface JmolBioModelSet

recalculateAllPolymers

public void recalculateAllPolymers(BS bsModelsExcluded,
                                   Group[] groups)

Specified by:

recalculateAllPolymers in interface JmolBioModelSet

getGroupsWithinAll

public BS getGroupsWithinAll(int nResidues,
                             BS bs)

Specified by:

getGroupsWithinAll in interface JmolBioModelSet

calculateStruts

public int calculateStruts(BS bs1,
                           BS bs2)

Specified by:

calculateStruts in interface JmolBioModelSet

recalculatePoints

public void recalculatePoints(int modelIndex)

Specified by:

recalculatePoints in interface JmolBioModelSet

getFullProteinStructureState

public java.lang.String getFullProteinStructureState(BS bsAtoms,
                                                     int mode)

Specified by:

getFullProteinStructureState in interface JmolBioModelSet

getStructureLines

private int getStructureLines(BS bsAtoms,
                              javajs.util.SB cmd,
                              javajs.util.Lst<ProteinStructure> lstStr,
                              STR type,
                              boolean scriptMode,
                              int mode)

getAllSequenceBits

public BS getAllSequenceBits(java.lang.String specInfo,
                             BS bsAtoms,
                             BS bsResult)

Specified by:

getAllSequenceBits in interface JmolBioModelSet

getAllUnitIds

private BS getAllUnitIds(java.lang.String specInfo,
                         BS bsSelected,
                         BS bsResult)

checkMap

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.

Parameters:

map -

key -

bsAtoms -

Returns:

current BS

addUnit

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

Parameters:

tok -

key -

bsTemp -

map -

Returns:

true if there are still atoms to consider

getAllBasePairBits

private BS getAllBasePairBits(java.lang.String specInfo)

calcAllRasmolHydrogenBonds

public 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

Specified by:

calcAllRasmolHydrogenBonds in interface JmolBioModelSet

Parameters:

bsA -

bsB -

vHBonds - will be null for autobonding

nucleicOnly -

nMax -

dsspIgnoreHydrogens -

bsHBonds -

getRasmolHydrogenBonds

private void getRasmolHydrogenBonds(BS bsA,
                                    BS bsB,
                                    javajs.util.Lst<Bond> vHBonds,
                                    boolean nucleicOnly,
                                    int nMax,
                                    boolean dsspIgnoreHydrogens,
                                    BS bsHBonds)

calculateStraightnessAll

public void calculateStraightnessAll()

Specified by:

calculateStraightnessAll in interface JmolBioModelSet

mutate

public boolean mutate(BS bs,
                      java.lang.String group,
                      java.lang.String[] sequence)

Specified by:

mutate in interface JmolBioModelSet

clearBioPolymers

private void clearBioPolymers()

getBioPolymerCount

public int getBioPolymerCount()

Specified by:

getBioPolymerCount in interface JmolBioModel

fixIndices

public void fixIndices(int modelIndex,
                       int nAtomsDeleted,
                       BS bsDeleted)

Overrides:

fixIndices in class Model

recalculateLeadMidpointsAndWingVectors

private void recalculateLeadMidpointsAndWingVectors()

freeze

public boolean freeze()

Overrides:

freeze in class Model

addSecondaryStructure

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)

calculateStructures

private java.lang.String calculateStructures(boolean asDSSP,
                                             boolean doReport,
                                             boolean dsspIgnoreHydrogen,
                                             boolean setStructure,
                                             boolean includeAlpha)

calculateDssx

private java.lang.String calculateDssx(javajs.util.Lst<Bond> vHBonds,
                                       boolean doReport,
                                       boolean dsspIgnoreHydrogen,
                                       boolean setStructure)

getConformation

public boolean getConformation(int conformationIndex0,
                               boolean doSet,
                               BS bsAtoms,
                               BS bsRet)

Parameters:

conformationIndex0 -

doSet -

bsAtoms -

bsRet -

Returns:

true;

addBioPolymer

private void addBioPolymer(BioPolymer polymer)

getBioBranches

public javajs.util.Lst<BS> getBioBranches(javajs.util.Lst<BS> biobranches)

Specified by:

getBioBranches in interface JmolBioModel

getAllPolymerInfo

public void getAllPolymerInfo(BS bs,
                              java.util.Map<java.lang.String,javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>> info)

Specified by:

getAllPolymerInfo in interface JmolBioModelSet

getBioExt

private BioExt getBioExt()

getFullPDBHeader

public java.lang.String getFullPDBHeader()

Specified by:

getFullPDBHeader in interface JmolBioModel

getPdbData

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)

Specified by:

getPdbData in interface JmolBioModel

resetRasmolBonds

public void resetRasmolBonds(BS bs)

from ModelSet.setAtomPositions base models only; not trajectories

Specified by:

resetRasmolBonds in interface JmolBioModel

getDefaultLargePDBRendering

public void getDefaultLargePDBRendering(javajs.util.SB sb,
                                        int maxAtoms)

Specified by:

getDefaultLargePDBRendering in interface JmolBioModel

getAtomBitsStr

public BS getAtomBitsStr(int tokType,
                         java.lang.String specInfo,
                         BS bs)

Specified by:

getAtomBitsStr in interface JmolBioModelSet

getAtomBitsBS

public BS getAtomBitsBS(int tokType,
                        BS bsInfo,
                        BS bs)

Specified by:

getAtomBitsBS in interface JmolBioModelSet

getAnnotationBits

private BS getAnnotationBits(java.lang.String name,
                             int tok,
                             java.lang.String specInfo)

getCachedAnnotationMap

java.lang.Object getCachedAnnotationMap(java.lang.String key,
                                        java.lang.Object ann)

getIdentifierOrNull

public BS getIdentifierOrNull(java.lang.String identifier)

Specified by:

getIdentifierOrNull in interface JmolBioModelSet

getUnitID

public java.lang.String getUnitID(Atom atom,
                                  int flags)

Get a unitID. Note that we MUST go through the | after InsCode, because if we do not do that we cannot match residues only using string matching.

Parameters:

atom -

flags -

Returns:

a unitID