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#!/usr/bin/python3
"""Get the set of canonical atom names for one or more residue types,
by querying CCD via RCSB. Used to populate the KNOWN_ATOM_NAMES variable
in make_mmcif.py.
"""
import collections
import ihm.format
import urllib.request
import sys
class ChemCompAtomHandler:
not_in_file = omitted = unknown = None
def __init__(self):
super().__init__()
self.atoms = collections.defaultdict(set)
def __call__(self, comp_id, atom_id):
self.atoms[comp_id].add(atom_id)
cca = ChemCompAtomHandler()
for resname in sys.argv[1:]:
with urllib.request.urlopen(
'https://files.rcsb.org/pub/pdb/refdata/chem_comp/%s/%s/%s.cif'
% (resname[-1], resname, resname)) as fh:
c = ihm.format.CifReader(fh, category_handler={'_chem_comp_atom': cca})
c.read_file()
print("KNOWN_ATOM_NAMES = {")
for comp_id in sorted(cca.atoms.keys()):
print(' %r: %r,' % (comp_id, cca.atoms[comp_id]))
print("}")
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