qp.structure.convert_nhie_oxo.find_and_convert_ligands_to_oxo¶
- qp.structure.convert_nhie_oxo.find_and_convert_ligands_to_oxo(atoms, iron_names, distance_cutoff=2.8)[source]¶
Convert water or NO ligands near iron to OXO residues.
Searches for water (HOH, WAT) or nitric oxide (HOA, NO) ligands within the distance cutoff of any iron atom and converts them to OXO (oxo) ligands with the Fe-O bond set to 1.65 A.
- Parameters:
atoms (list of dict) – Atom records from
read_pdb().iron_names (list of str) – Iron atom names to search for (e.g.,
['FE', 'FE2']).distance_cutoff (float, optional) – Maximum Fe-ligand distance in angstroms (default 2.8).
- Returns:
Serial numbers of iron atoms that received an OXO ligand.
- Return type:
set