Package org.jmol.modelsetbio

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

  • Method Details

    • getProteinStructure

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

    • getControlPoint

      protected P3 getControlPoint(int i, V3 v)
      Overrides:
      getControlPoint in class BioPolymer
      Parameters:
      i -
      v -
      Returns:
      the leadPoint unless a protein sheet residue (see AlphaPolymer)

    • addStructure

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

    • addStructureProtected

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

    • clearStructures

      public void clearStructures()
      Overrides:
      clearStructures in class BioPolymer

    • calculateStructures

      public void calculateStructures(boolean alphaOnly)
      Uses Levitt invalid input: '&' 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

    • setStructureBS

      public int setStructureBS(int count, int dsspType, STR type, 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