Field Detail

• maxHbondAlphaDistance

  private static final float maxHbondAlphaDistance

  See Also:

  Constant Field Values

• maxHbondAlphaDistance2

  private static final float maxHbondAlphaDistance2

  See Also:

  Constant Field Values

• minimumHbondDistance2

  private static final float minimumHbondDistance2

  See Also:

  Constant Field Values

• structureList

  private java.util.Map<STR,​float[]> structureList

Constructor Detail

• AminoPolymer

  AminoPolymer​(Monomer[] monomers,
               int pt0)

Method Detail

• resetHydrogenPoints

  protected void resetHydrogenPoints()

  Overrides:

  resetHydrogenPoints in class BioPolymer

• calcPhiPsiAngles

  protected boolean calcPhiPsiAngles()

  Overrides:

  calcPhiPsiAngles in class BioPolymer

• calcPhiPsiAngles2

  private void calcPhiPsiAngles2​(AminoMonomer residue1,
                                 AminoMonomer residue2)

• calculateRamachandranHelixAngle

  protected float calculateRamachandranHelixAngle​(int m,
                                                  char qtype)

  Overrides:

  calculateRamachandranHelixAngle in class BioPolymer

  Returns:

  calculated value

• calcRasmolHydrogenBonds

  public void calcRasmolHydrogenBonds​(BioPolymer polymer,
                                      BS bsA,
                                      BS bsB,
                                      javajs.util.Lst<Bond> vHBonds,
                                      int nMaxPerResidue,
                                      int[][][] min,
                                      boolean checkDistances,
                                      boolean dsspIgnoreHydrogens)

  Overrides:

  calcRasmolHydrogenBonds in class BioPolymer

• checkRasmolHydrogenBond

  private void checkRasmolHydrogenBond​(AminoMonomer source,
                                       BioPolymer polymer,
                                       int indexDonor,
                                       javajs.util.P3 hydrogenPoint,
                                       BS bsB,
                                       javajs.util.Lst<Bond> vHBonds,
                                       int[][] min,
                                       boolean checkDistances)

• calcHbondEnergy

  private int calcHbondEnergy​(javajs.util.P3 nitrogenPoint,
                              javajs.util.P3 hydrogenPoint,
                              AminoMonomer target,
                              boolean checkDistances)

  based on RasMol 2.7.2.1.1 model checkDistances: When we are seriously looking for H bonds, we want to also check that distCN > distCH and that the OH distance is less than 3 Angstroms. Otherwise that's just too strange a hydrogen bond. (We get hydrogen bonds from i to i+2, for example) This check is skipped for an actual DSSP calc., where we want the original definition and are not actually creating hydrogen bonds H .......... O | | | | N C

  Parameters:

  nitrogenPoint -

  hydrogenPoint -

  target -

  checkDistances -

  Returns:

  energy in cal/mol or 0 (none)

• addResidueHydrogenBond

  private void addResidueHydrogenBond​(Atom nitrogen,
                                      Atom oxygen,
                                      int indexAminoGroup,
                                      int indexCarbonylGroup,
                                      float energy,
                                      javajs.util.Lst<Bond> vHBonds)

• calculateStructures

  public void calculateStructures​(boolean alphaOnly)

  Description copied from class: AlphaPolymer
  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

  Overrides:

  calculateStructures in class AlphaPolymer

  Parameters:

  alphaOnly - caught by AminoPolymer and discarded if desired

• isTurn

  private boolean isTurn​(float psi,
                         float phi)

  Parameters:

  psi - N-C-CA-N torsion for NEXT group

  phi - C-CA-N-C torsion for THIS group

  Returns:

  whether this corresponds to a helix

• isSheet

  private boolean isSheet​(float psi,
                          float phi)

• isHelix

  private boolean isHelix​(float psi,
                          float phi)

• checkPhiPsi

  private static boolean checkPhiPsi​(float[] list,
                                     float psi,
                                     float phi)

• setStructureList

  public void setStructureList​(java.util.Map<STR,​float[]> structureList)

  Parameters:

  structureList - protein only -- helix, sheet, turn definitions