Class AminoPolymer

All Implemented Interfaces:
Structure

public class AminoPolymer extends AlphaPolymer
  • Method Details

    • resetHydrogenPoints

      protected void resetHydrogenPoints()
      Overrides:
      resetHydrogenPoints in class BioPolymer
    • calcPhiPsiAngles

      protected boolean calcPhiPsiAngles()
      Overrides:
      calcPhiPsiAngles in class BioPolymer
    • calculateRamachandranHelixAngle

      protected float calculateRamachandranHelixAngle(int m, char qtype)
      Overrides:
      calculateRamachandranHelixAngle in class BioPolymer
      Parameters:
      m -
      qtype -
      Returns:
      calculated value
    • calcRasmolHydrogenBonds

      public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
      Overrides:
      calcRasmolHydrogenBonds in class BioPolymer
      Parameters:
      polymer -
      bsA -
      bsB -
      vHBonds -
      nMaxPerResidue -
      min -
      checkDistances -
      dsspIgnoreHydrogens -
    • calculateStructures

      public void calculateStructures(boolean alphaOnly)
      Description copied from class: AlphaPolymer
      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

      Overrides:
      calculateStructures in class AlphaPolymer
      Parameters:
      alphaOnly - caught by AminoPolymer and discarded if desired
    • setStructureList

      public void setStructureList(Map<STR,float[]> structureList)
      Parameters:
      structureList - protein only -- helix, sheet, turn definitions