Class AlphaPolymer

    • Field Detail

      • pt0

        public int pt0
      • dsspTypes

        private static final java.lang.String[] dsspTypes
    • Constructor Detail

      • AlphaPolymer

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

      • 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,
                                 java.lang.String structureID,
                                 int serialID,
                                 int strandCount,
                                 int startChainID,
                                 int startSeqcode,
                                 int endChainID,
                                 int endSeqcode,
                                 int istart,
                                 int iend,
                                 BS bsAssigned)
      • addStructureProtected

        public boolean addStructureProtected​(STR type,
                                             java.lang.String structureID,
                                             int serialID,
                                             int strandCount,
                                             int indexStart,
                                             int indexEnd)
      • 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()
      • checkBetaSheetAlphaHelixOverlap

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