Package org.jmol.modelsetbio

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

      public 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