Class BioModel

java.lang.Object
org.jmol.modelset.Model
org.jmol.modelsetbio.BioModel

public final class BioModel extends Model
  • Field Details

  • Constructor Details

    • BioModel

      public 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)