Package org.openscience.cdk.templates
Class AminoAcids
- java.lang.Object
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- org.openscience.cdk.templates.AminoAcids
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Field Summary
Fields Modifier and Type Field Description static String
ID
static String
NO_ATOMS
static String
NO_BONDS
static String
RESIDUE_NAME
static String
RESIDUE_NAME_SHORT
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Constructor Summary
Constructors Constructor Description AminoAcids()
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Method Summary
All Methods Static Methods Concrete Methods 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.
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Field Detail
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RESIDUE_NAME
public static final String RESIDUE_NAME
- See Also:
- Constant Field Values
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RESIDUE_NAME_SHORT
public static final String RESIDUE_NAME_SHORT
- See Also:
- Constant Field Values
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NO_ATOMS
public static final String NO_ATOMS
- See Also:
- Constant Field Values
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NO_BONDS
public static final String NO_BONDS
- See Also:
- Constant Field Values
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ID
public static final String ID
- See Also:
- Constant Field Values
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Method Detail
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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
public static AminoAcid[] createAAs()
Creates amino acid AminoAcid objects.- Returns:
- aminoAcids, a HashMap containing the amino acids as AminoAcids.
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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.
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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.
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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.
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