conop.cleanup – Sanitize structures¶

Cleanup(entity, strip_water=True, canonicalize=True, remove_ligands=True)¶

This function returns a cleaned-up (simplified) version of the protein structure. Different parameters affect the behaviour of the function.

Parameters:

• strip_water – Whether to remove water from the structure

• canonicalize – Whether to strip off modifications of amino acids and map them back to their parent standard amino acid, e.g. selenium methionine to methionine.For more complex amino acids, where the relation between the modified and the standard parent amino acid is not known, sidechain atoms are removed. D-peptide-linking residues are completely removed as well.

• remove_ligands – Whether to remove ligands from the structure

Returns:

a cleaned version of the entity