Class BioModel

Method Details

• 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 Lst<BS> getBioBranches(Lst<BS> biobranches)

• getBioPolymerCount

  public int getBioPolymerCount()

• getConformation

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

  Parameters:

  conformationIndex0 -

  doSet -

  bsAtoms -

  bsRet - to be set

• getDefaultLargePDBRendering

  public void getDefaultLargePDBRendering(SB sb, int maxAtoms)

• getFullPDBHeader

  public String getFullPDBHeader()

• getPdbData

  public void getPdbData(String type, char ctype, boolean isDraw, BS bsSelected, OC out, LabelToken[] tokens, SB pdbCONECT, BS bsWritten)

• getUnitID

  public 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

• resetRasmolBonds

  public void resetRasmolBonds(BS bs, int dsspVersion)

  from Trajectory.setAtomPositions base models only; not trajectories

  Parameters:

  bs -

  dsspVersion -

• getAtomicDSSRData

  public void getAtomicDSSRData(float[] dssrData, String dataType)