Class AlphaPolymer

java.lang.Object
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
All Implemented Interfaces:
Structure
Direct Known Subclasses:
AminoPolymer

public class AlphaPolymer extends BioPolymer
  • Field Details

    • pt0

      public int pt0
      Specifically for mmTF bitset setting of structures
    • dsspTypes

      private static final String[] dsspTypes
  • Constructor Details

    • AlphaPolymer

      AlphaPolymer(Monomer[] monomers, int pt0)
  • Method Details

    • getProteinStructure

      public ProteinStructure getProteinStructure(int monomerIndex)
      Overrides:
      getProteinStructure in class BioPolymer
      Returns:
      "HELIX" "TURN" etc
    • getControlPoint

      protected javajs.util.P3 getControlPoint(int i, javajs.util.V3 v)
      Overrides:
      getControlPoint in class BioPolymer
      Returns:
      the leadPoint unless a protein sheet residue (see AlphaPolymer)
    • addStructure

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

      public boolean addStructureProtected(STR type, String structureID, int serialID, int strandCount, int indexStart, int indexEnd)
    • clearStructures

      public void clearStructures()
      Overrides:
      clearStructures in class BioPolymer
    • calculateStructures

      public void calculateStructures(boolean alphaOnly)
      Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.

      Levitt and Greer
      Automatic Identification of Secondary Structure in Globular Proteins
      J.Mol.Biol.(1977) 114, 181-293

      http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf

      Parameters:
      alphaOnly - caught by AminoPolymer and discarded if desired
    • calculateAnglesInDegrees

      private float[] calculateAnglesInDegrees()
    • calculateCodes

      private AlphaPolymer.Code[] calculateCodes(float[] angles)
    • checkBetaSheetAlphaHelixOverlap

      private void checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[] codes, float[] angles)
    • calculateRunsFourOrMore

      private STR[] calculateRunsFourOrMore(AlphaPolymer.Code[] codes)
    • extendRuns

      private void extendRuns(STR[] tags)
    • searchForTurns

      private void searchForTurns(AlphaPolymer.Code[] codes, float[] angles, STR[] tags)
    • addStructuresFromTags

      private void addStructuresFromTags(STR[] tags)
    • setStructureBS

      public int setStructureBS(int count, int dsspType, STR type, javajs.util.BS bs, boolean doOffset)
      bits in the bitset determines the type
      Parameters:
      count -
      dsspType -
      type -
      bs -
      doOffset - allows us to examine just a portion of the
      Returns:
      updated count