Field Detail

• vwr

  private Viewer vwr

• bioPolymerCount

  int bioPolymerCount

• bioPolymers

  public BioPolymer[] bioPolymers

• isMutated

  boolean isMutated

• defaultStructure

  java.lang.String defaultStructure

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

• addBioPolymer

  int addBioPolymer​(BioPolymer polymer)

• addSecondaryStructure

  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)

• addStructureByBS

  void addStructureByBS​(int count,
                        int dsspType,
                        STR type,
                        BS bs)

• calculateDssx

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

• calculateStructures

  java.lang.String calculateStructures​(boolean asDSSP,
                                       boolean doReport,
                                       boolean dsspIgnoreHydrogen,
                                       boolean setStructure,
                                       boolean includeAlpha,
                                       int version)

• clearBioPolymers

  void clearBioPolymers()

• fixIndices

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

  Overrides:

  fixIndices in class Model

• freeze

  public boolean freeze()

  Overrides:

  freeze in class Model

• getBioBranches

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

• getBioPolymerCount

  public int getBioPolymerCount()

• getCachedAnnotationMap

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

• getConformation

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

  Parameters:

  conformationIndex0 -

  doSet -

  bsAtoms -

  bsRet -

  Returns:

  true;

• getDefaultLargePDBRendering

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

• getFullPDBHeader

  public java.lang.String getFullPDBHeader()

• 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)

• getRasmolHydrogenBonds

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

• 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

• recalculateLeadMidpointsAndWingVectors

  void recalculateLeadMidpointsAndWingVectors()

• resetRasmolBonds

  public void resetRasmolBonds​(BS bs,
                               int dsspVersion)

  from Trajectory.setAtomPositions base models only; not trajectories

  Parameters:

  bs -

  dsspVersion -