Functions and classes for standard amino acids
This document describes functions and classes to work with the 20 standard amino acids. The functions convert between different representations, e.g. one-letter-code, three-letter-code or the AminoAcid enum
The AminoAcid enum
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class
AminoAcid
The amino acid enum enumerates all 20 standard amino acid and the special
value XXX, to signify an unknown amino acid. The amino acid enum supports the
following values:
ALA, ARG, ASN, ASP, GLN, GLU, LYS, SER, CYS, MET
TRP, TYR, THR, VAL, ILE, LEU, GLY, PRO, HIS, PHE
XXX
Converter functions
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ResidueToAminoAcid (residue)
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ResidueNameToAminoAcid (rname)
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OneLetterCodeToAminoAcid (olc)
Returns: | Amino acid from residue, residue name (three-letter-code)
or one-letter-code. Returns XXX if residue, residue name or
one-letter-code is not one of the 20 standard amino acids. |
Return type: | AminoAcid |
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OneLetterCodeToResidueName (olc)
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AminoAcidToResidueName (amino_acid)
Returns: | Residue name from one-letter-code or amino_acid. For invalid
one-letter-codes or XXX, ‘UNK’ is returned.
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Return type: | str
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Parameters: |
- olc (
str ) – One-letter-code
- amino_acid (
AminoAcid ) – Amino acid type
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ResidueNameToOneLetterCode (rname)
Returns: | One-letter-code for the given residue name. Returns ‘X’ if residue
name is not one of the 20 standard amino acids. |
Return type: | str |
Parameters: | rname (str ) – Residue name |
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class
AminoAcidSet
A set of amino acids, with constant-time access
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static
CreatePolarSet ()
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static
CreateAromaticSet ()
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static
CreateApolarSet ()
Returns a set containing all polar, aromatic or apolar amino acids,
respectively.
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Add (amino_acid)
Add amino acid to the set.
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Remove (amino_acid)
Remove amino acid from the set
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Empty ()
Whether the set is empty, i.e. doesn’t contain any amino acids.
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