Package org.openscience.cdk.templates

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 Summary

Fields

Modifier and Type	Field	Description
static final String	ID
static final String	NO_ATOMS
static final String	NO_BONDS
static final String	RESIDUE_NAME
static final String	RESIDUE_NAME_SHORT

Constructor Summary

Constructors

Constructor	Description
AminoAcids()

Method Summary

Modifier and Type	Method	Description
static int[][]	aaBondInfo()	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[]	createAAs()	Creates amino acid AminoAcid objects.
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.
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

RESIDUE_NAME

public static final String RESIDUE_NAME

See Also:

• Constant Field Values

RESIDUE_NAME_SHORT

public static final String RESIDUE_NAME_SHORT

See Also:

• Constant Field Values

NO_ATOMS

public static final String NO_ATOMS

See Also:

• Constant Field Values

NO_BONDS

public static final String NO_BONDS

See Also:

• Constant Field Values

ID

public static final String ID

See Also:

• Constant Field Values

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.