Package org.openscience.cdk.templates
Class AminoAcids
java.lang.Object
org.openscience.cdk.templates.AminoAcids
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
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic int[][]
Creates matrix with info about the bonds in the amino acids.static String
convertOneLetterCodeToThreeLetterCode
(String oneLetterCode) Returns the three letter code of an amino acid given a one letter code.static String
convertThreeLetterCodeToOneLetterCode
(String threeLetterCode) Returns the one letter code of an amino acid given a three letter code.static AminoAcid[]
Creates amino acid AminoAcid objects.static Map<String,
IAminoAcid> 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.static Map<String,
IAminoAcid> 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.
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Field Details
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RESIDUE_NAME
- See Also:
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RESIDUE_NAME_SHORT
- See Also:
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NO_ATOMS
- See Also:
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NO_BONDS
- See Also:
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ID
- See Also:
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Constructor Details
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AminoAcids
public AminoAcids()
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Method Details
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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
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createAAs
Creates amino acid AminoAcid objects.- Returns:
- aminoAcids, a HashMap containing the amino acids as AminoAcids.
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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
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
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
Returns the three letter code of an amino acid given a one letter code. For example, it will return "Val" when "V" was passed.
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