def test_repair_graph_with_mutation_modification_error(system_mod, caplog,
resid, mutations,
modifications):
mol = system_mod.molecules[0]
# Let's mutate res1 to ALA
for node_idx in mol:
if mol.nodes[node_idx].get('resid') == resid:
if mutations:
mol.nodes[node_idx]['mutation'] = mutations
if modifications:
mol.nodes[node_idx]['modification'] = modifications
with pytest.raises(ValueError), caplog.at_level(logging.WARNING):
assert not caplog.records
mol = vermouth.RepairGraph().run_molecule(mol)
assert len(caplog.records) == 1
def test_repair_graph_with_mutation_modification(system_mod, resid, mutations,
modifications, atomnames):
mol = system_mod.molecules[0]
# Let's mutate res1 to ALA
for node_idx in mol:
if mol.nodes[node_idx].get('resid') == resid:
if mutations:
mol.nodes[node_idx]['mutation'] = mutations
if modifications:
mol.nodes[node_idx]['modification'] = modifications
mol = vermouth.RepairGraph().run_molecule(mol)
resid1_atomnames = set()
for node_idx in mol:
if mol.nodes[node_idx].get('resid') == resid:
if mutations:
assert mol.nodes[node_idx]['resname'] == mutations[0]
if modifications:
assert mol.nodes[node_idx].get('modification') == modifications
resid1_atomnames.add(mol.nodes[node_idx]['atomname'])
assert resid1_atomnames == set(atomnames.split())
def repaired_graph(request, system_mod):
vermouth.RepairGraph(include_graph=request.param).run_system(system_mod)
return system_mod