Field Detail

• pt0

  public int pt0

• dsspTypes

  private static final java.lang.String[] dsspTypes

Constructor Detail

• AlphaPolymer

  AlphaPolymer​(Monomer[] monomers,
               int pt0)

Method Detail

• 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,
                           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)

• 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,
                            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