Functions and classes for standard amino acids¶

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.