def test_unknown_mods_removed(caplog, repaired_graph, known_mod_names):
"""
Tests that atoms that are part of modifications, but are not recognized, get
removed from the graph by CanonicalizeModifications
"""
caplog.set_level(logging.WARNING)
ff = copy.copy(repaired_graph.force_field)
for mod_name in known_mod_names:
assert mod_name in ff.modifications # Purely defensive
removed_mods = []
for name, mod in dict(ff.modifications).items():
if name not in known_mod_names:
del ff.modifications[name]
removed_mods.append(mod)
repaired_graph.force_field = ff
mol = repaired_graph.molecules[0]
assert not caplog.records
assert len(mol) == 46
vermouth.CanonicalizeModifications().run_system(repaired_graph)
assert caplog.records
for record in caplog.records:
assert record.levelname == 'WARNING'
assert len(mol) < 46
atomnames = dict(mol.nodes(data='atomname')).values()
for mod in removed_mods:
for node_key in mod.nodes:
node = mod.nodes[node_key]
if node['PTM_atom']:
assert node['atomname'] not in atomnames
for node_key in mol.nodes:
node = mol.nodes[node_key]
if node.get('PTM_atom'):
contained_by = [
mod for mod in ff.modifications.values()
if node.get('expected', node['atomname']) in dict(
mod.nodes(data='atomname')).values()
]
assert len(contained_by) == 1
def canonicalized_graph(repaired_graph):
vermouth.CanonicalizeModifications().run_system(repaired_graph)
return repaired_graph