public final class BioModel extends Model
Modifier and Type | Field and Description |
---|---|
(package private) int |
bioPolymerCount |
BioPolymer[] |
bioPolymers |
(package private) java.lang.String |
defaultStructure |
(package private) boolean |
isMutated |
private Viewer |
vwr |
act, altLocCount, auxiliaryInfo, biosymmetry, bsAtoms, bsAtomsDeleted, chainCount, chains, dssrCache, firstAtomIndex, frameDelay, groupCount, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isPdbWithMultipleBonds, loadScript, loadState, mat4, 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 |
---|---|
(package private) int |
addBioPolymer(BioPolymer polymer) |
(package private) 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) |
(package private) void |
addStructureByBS(int count,
int dsspType,
STR type,
BS bs) |
private java.lang.String |
calculateDssx(javajs.util.Lst<Bond> vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
int version) |
(package private) java.lang.String |
calculateStructures(boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha,
int version) |
(package private) void |
clearBioPolymers() |
void |
fixIndices(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
boolean |
freeze() |
javajs.util.Lst<BS> |
getBioBranches(javajs.util.Lst<BS> biobranches) |
int |
getBioPolymerCount() |
(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() |
void |
getPdbData(java.lang.String type,
char ctype,
boolean isDraw,
BS bsSelected,
javajs.util.OC out,
LabelToken[] tokens,
javajs.util.SB pdbCONECT,
BS bsWritten) |
(package private) void |
getRasmolHydrogenBonds(BS bsA,
BS bsB,
javajs.util.Lst<Bond> vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens,
BS bsHBonds,
int version) |
java.lang.String |
getUnitID(Atom atom,
int flags)
Get a unitID.
|
(package private) void |
recalculateLeadMidpointsAndWingVectors() |
void |
resetRasmolBonds(BS bs,
int dsspVersion)
from Trajectory.setAtomPositions
base models only; not trajectories
|
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getGroupCount, getTrueAtomCount, isContainedIn, resetBoundCount, set
private Viewer vwr
int bioPolymerCount
public BioPolymer[] bioPolymers
boolean isMutated
java.lang.String defaultStructure
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)
int 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 java.lang.String calculateDssx(javajs.util.Lst<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, int version)
java.lang.String calculateStructures(boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha, int version)
void clearBioPolymers()
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
fixIndices
in class Model
public int getBioPolymerCount()
java.lang.Object getCachedAnnotationMap(java.lang.String key, java.lang.Object ann)
public boolean getConformation(int conformationIndex0, boolean doSet, BS bsAtoms, BS bsRet)
conformationIndex0
- doSet
- bsAtoms
- bsRet
- public void getDefaultLargePDBRendering(javajs.util.SB sb, int maxAtoms)
public java.lang.String getFullPDBHeader()
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)
void getRasmolHydrogenBonds(BS bsA, BS bsB, javajs.util.Lst<Bond> vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens, BS bsHBonds, int version)
public java.lang.String getUnitID(Atom atom, int flags)
atom
- flags
- void recalculateLeadMidpointsAndWingVectors()
public void resetRasmolBonds(BS bs, int dsspVersion)
bs
- dsspVersion
-