molsysmt.element.group.amino_acid.get_standard_name#

molsysmt.element.group.amino_acid.get_standard_name(group_name)[source]#

Return the canonical standard amino-acid name for a non-standard residue.

Uses the comprehensive name_to_type mapping (derived from MDTraj, ~817 entries) which covers modified amino acids, D-amino acids, protonation-state variants, and other non-canonical residues found in the PDB.

Parameters:

group_name (str) – Name of the chemical group (residue).

Returns:

The standard 3-letter amino-acid code for the nearest standard residue (e.g. 'MET', 'SER', 'HIS'). Returns None when:

group_name is already a standard amino acid (e.g. 'ALA').
group_name is not in the amino-acid database at all (e.g. water, ions, ligands).
The residue has no known standard equivalent (maps to 'XAA').

Return type:

str or None

Notes

The source table is element.group.amino_acid.group_types.name_to_type.

Examples

>>> get_standard_name('MSE')   # selenomethionine
'MET'
>>> get_standard_name('SEP')   # phosphoserine
'SER'
>>> get_standard_name('ALA')   # already standard
None
>>> get_standard_name('HOH')   # water — not an amino acid
None

Added in version 1.0.0.