Class ProteinStructure

java.lang.Object
org.jmol.modelsetbio.ProteinStructure
All Implemented Interfaces:
Structure
Direct Known Subclasses:
Annotation, Helix, Sheet

public abstract class ProteinStructure extends Object implements Structure
  • Field Details

    • nRes

      public int nRes
    • apolymer

      public AlphaPolymer apolymer
    • monomerIndexFirst

      protected int monomerIndexFirst
    • axisA

      protected P3 axisA
    • axisB

      protected P3 axisB
    • axisUnitVector

      protected V3 axisUnitVector
    • vectorProjection

      protected V3 vectorProjection
  • Constructor Details

    • ProteinStructure

      protected ProteinStructure()
  • Method Details

    • incrementID

      protected void incrementID()
    • setupPS

      protected void setupPS(AlphaPolymer apolymer, STR type, int monomerIndex, int monomerCount)
      Parameters:
      apolymer -
      type -
      monomerIndex -
      monomerCount -
    • calcAxis

      public void calcAxis()
    • isWithin

      public boolean isWithin(int monomerIndex)
    • getIndex

      public int getIndex(Monomer monomer)
    • getSegments

      public P3[] getSegments()
      Returns:
      points for rocket segment rendering
    • getAxisStartPoint

      public P3 getAxisStartPoint()
    • getAxisEndPoint

      public P3 getAxisEndPoint()
    • setAtomBits

      public void setAtomBits(BS bs)
      Specified by:
      setAtomBits in interface Structure
    • setAtomBitsAndClear

      public void setAtomBitsAndClear(BS bs, BS bsOut)
      Specified by:
      setAtomBitsAndClear in interface Structure
    • findMonomer

      public Monomer findMonomer(BS bsAtoms, boolean isFirst)
    • toString

      public String toString()
      Overrides:
      toString in class Object