Class AminoAcids

java.lang.Object
org.openscience.cdk.templates.AminoAcids

public class AminoAcids extends Object
Tool that provides templates for the (natural) amino acids.
Author:
Martin Eklund <martin.eklund@farmbio.uu.se>
Source code:
main
Belongs to CDK module:
pdb
Keywords:
templates, amino acids, stuctures
Created on:
2005-02-08
  • Field Details

  • Constructor Details

    • AminoAcids

      public AminoAcids()
  • Method Details

    • aaBondInfo

      public static int[][] aaBondInfo()
      Creates matrix with info about the bonds in the amino acids. 0 = bond id, 1 = atom1 in bond, 2 = atom2 in bond, 3 = bond order.
      Returns:
      info
    • createAAs

      public static AminoAcid[] createAAs()
      Creates amino acid AminoAcid objects.
      Returns:
      aminoAcids, a HashMap containing the amino acids as AminoAcids.
    • getHashMapBySingleCharCode

      public static Map<String,IAminoAcid> getHashMapBySingleCharCode()
      Returns a HashMap where the key is one of G, A, V, L, I, S, T, C, M, D, N, E, Q, R, K, H, F, Y, W and P.
    • getHashMapByThreeLetterCode

      public static Map<String,IAminoAcid> getHashMapByThreeLetterCode()
      Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER, THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO.
    • convertThreeLetterCodeToOneLetterCode

      public static String convertThreeLetterCodeToOneLetterCode(String threeLetterCode)
      Returns the one letter code of an amino acid given a three letter code. For example, it will return "V" when "Val" was passed.
    • convertOneLetterCodeToThreeLetterCode

      public static String convertOneLetterCodeToThreeLetterCode(String oneLetterCode)
      Returns the three letter code of an amino acid given a one letter code. For example, it will return "Val" when "V" was passed.