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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

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)
OneLetterCodeToAminoAcid(olc)

Get amino acid from residue or one-letter-code. For non-standard amino acids or one-letter-codes, XXX is returned.

OneLetterCodeToResidueName(olc)
AminoAcidToResidueName(amino_acid)

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

ResidueNameToOneLetterCode(rname)

Get one-letter-code for the given residue name. Returns ‘X’ if residue name is not one of the 20 standard amino acids.

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.

Mapping functions

The following functions help to convert one residue into another by reusing as much as possible from the present atoms. They are mainly meant to map from standard amino acid to other standard amino acids or from modified amino acids to standard amino acids.

CopyResidue(src_res, dst_res, editor)

Copies the atoms of src_res to dst_res using the residue names as guide to decide which of the atoms should be copied. If src_res and dst_res have the same name, or src_res is a modified version of dst_res (i.e. have the same single letter code), CopyConserved will be called, otherwise CopyNonConserved will be called.

Parameters:
  • src_res (ResidueHandle) – The source residue
  • dst_res (ResidueHandle) – The destination residue
Returns:

true if the residue could be copied, false if not.

CopyConserved(src_res, dst_res, editor)

Copies the atoms of src_res to dst_res assuming that the parent amino acid of src_res (or src_res itself) are identical to dst_res.

If src_res and dst_res are identical, all heavy atoms are copied to dst_res. If src_res is a modified version of dst_res and the modification is a pure addition (e.g. the phosphate group of phosphoserine), the modification is stripped off and all other heavy atoms are copied to dst_res. If the modification is not a pure addition, only the backbone heavy atoms are copied to dst_res.

Additionally, the selenium atom of MSE is converted to sulphur.

Parameters:
  • src_res (ResidueHandle) – The source residue
  • dst_res (ResidueHandle) – The destination residue
Returns:

a tuple of bools stating whether the residue could be copied and whether the Cbeta atom was inserted into the dst_res.

CopyNonConserved(src_res, dst_res, editor)

Copies the heavy backbone atoms and Cbeta (except for GLY) of src_res to dst_res.

Parameters:
  • src_res (ResidueHandle) – The source residue
  • dst_res (ResidueHandle) – The destination residue
Returns:

a tuple of bools stating whether the residue could be copied and whether the Cbeta atom was inserted into the dst_res.

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