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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

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

ResidueToAminoAcid(residue)
ResidueNameToAminoAcid(rname)
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
OneLetterCodeToResidueName(olc)
AminoAcidToResidueName(amino_acid)
Returns:

Residue name from one-letter-code or amino_acid. For invalid one-letter-codes or XXX, ‘UNK’ is returned.

Return type:

str

Parameters:
  • olc (str) – One-letter-code
  • amino_acid (AminoAcid) – Amino acid type
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
class AminoAcidSet

A set of amino acids, with constant-time access

static CreatePolarSet()
static CreateAromaticSet()
static CreateApolarSet()

Returns a set containing all polar, aromatic or apolar amino acids, respectively.

Add(amino_acid)

Add amino acid to the set.

Remove(amino_acid)

Remove amino acid from the set

Empty()

Whether the set is empty, i.e. doesn’t contain any amino acids.

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