Package org.jmol.modelsetbio

Class ProteinStructure

java.lang.Object
org.jmol.modelsetbio.ProteinStructure
All Implemented Interfaces:
Structure
Direct Known Subclasses:
Annotation, Helix, Sheet, Turn
public abstract class ProteinStructure extends Object implements Structure

  • Field Details

    • ids

      private static int ids

    • type

      STR type

    • subtype

      STR subtype

    • structureID

      String structureID

    • strucNo

      int strucNo

    • serialID

      int serialID

    • strandCount

      int strandCount

    • id

      int id

    • nRes

      public int nRes

    • apolymer

      public AlphaPolymer apolymer

    • monomerIndexFirst

      protected int monomerIndexFirst

    • monomerIndexLast

      int monomerIndexLast

    • axisA

      protected javajs.util.P3 axisA

    • axisB

      protected javajs.util.P3 axisB

    • axisUnitVector

      protected javajs.util.V3 axisUnitVector

    • vectorProjection

      protected javajs.util.V3 vectorProjection

    • globalStrucNo

      private static int globalStrucNo

    • segments

      private javajs.util.P3[] segments

    • resMap

      private Map<Monomer,Integer> resMap

  • Constructor Details

    • ProteinStructure

      protected ProteinStructure()

  • Method Details

    • setupPS

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

    • addMonomer

      void addMonomer(int index)
      Note that this method does not check to see that there are no overlapping protein structures.
      Parameters:
      index -

    • removeMonomer

      void removeMonomer(int index)
      should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
      Parameters:
      index -

    • calcAxis

      public void calcAxis()

    • isWithin

      public boolean isWithin(int monomerIndex)

    • getIndex

      public int getIndex(Monomer monomer)

    • getSegments

      public javajs.util.P3[] getSegments()
      Returns:
      points for rocket segment rendering

    • getStructureMidPoint

      javajs.util.P3 getStructureMidPoint(int index)

    • calcSegments

      private void calcSegments()

    • getAxisStartPoint

      public javajs.util.P3 getAxisStartPoint()

    • getAxisEndPoint

      public javajs.util.P3 getAxisEndPoint()

    • resetAxes

      void resetAxes()

    • setAtomBits

      public void setAtomBits(javajs.util.BS bs)
      Specified by:
      setAtomBits in interface Structure

    • setAtomBitsAndClear

      public void setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut)
      Specified by:
      setAtomBitsAndClear in interface Structure

    • findMonomer

      public Monomer findMonomer(javajs.util.BS bsAtoms, boolean isFirst)

    • toString

      public String toString()
      Overrides:
      toString in class Object