Package org.jmol.modelsetbio

Class BioModel

java.lang.Object
org.jmol.modelset.Model
org.jmol.modelsetbio.BioModel
public final class BioModel extends Model

  • Field Details

    • vwr

      private Viewer vwr

    • bioPolymerCount

      int bioPolymerCount

    • bioPolymers

      public BioPolymer[] bioPolymers

    • isMutated

      boolean isMutated

    • defaultStructure

      String defaultStructure

  • Constructor Details

  • Method Details

    • addBioPolymer

      int addBioPolymer(BioPolymer polymer)

    • addSecondaryStructure

      void addSecondaryStructure(STR type, String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, javajs.util.BS bsAssigned)

    • addStructureByBS

      void addStructureByBS(int count, int dsspType, STR type, javajs.util.BS bs)

    • calculateDssx

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

    • calculateStructures

      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, javajs.util.BS bsDeleted)
      Overrides:
      fixIndices in class Model

    • freeze

      public boolean freeze()
      Overrides:
      freeze in class Model

    • getBioBranches

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

    • getBioPolymerCount

      public int getBioPolymerCount()

    • getCachedAnnotationMap

      Object getCachedAnnotationMap(String key, Object ann)

    • getConformation

      public boolean getConformation(int conformationIndex0, boolean doSet, javajs.util.BS bsAtoms, javajs.util.BS bsRet)
      Parameters:
      conformationIndex0 -
      doSet -
      bsAtoms -
      bsRet -
      Returns:
      true;

    • getDefaultLargePDBRendering

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

    • getFullPDBHeader

      public String getFullPDBHeader()

    • getPdbData

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

    • getRasmolHydrogenBonds

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

    • 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

    • recalculateLeadMidpointsAndWingVectors

      void recalculateLeadMidpointsAndWingVectors()

    • resetRasmolBonds

      public void resetRasmolBonds(javajs.util.BS bs, int dsspVersion)
      from Trajectory.setAtomPositions base models only; not trajectories
      Parameters:
      bs -
      dsspVersion -

    • getAtomicDSSRData

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