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