def test_matched_and_h_stripping(self):
bond_topology = str_to_bond_topology('''
atoms: ATOM_O
atoms: ATOM_H
atoms: ATOM_H
bonds {
atom_b: 1
bond_type: BOND_SINGLE
}
bonds {
atom_b: 2
bond_type: BOND_SINGLE
}
smiles: "O"
''')
result, with_h, without_h = smu_utils_lib.bond_topology_smiles_comparison(
bond_topology)
self.assertEqual(smu_utils_lib.SmilesCompareResult.MATCH, result)
self.assertEqual('[H]O[H]', with_h)
self.assertEqual('O', without_h)
# Also directly test compute_smiles_for_bond_topology
self.assertEqual(
'[H]O[H]',
smu_utils_lib.compute_smiles_for_bond_topology(
bond_topology, include_hs=True))
self.assertEqual(
'O',
smu_utils_lib.compute_smiles_for_bond_topology(
bond_topology, include_hs=False))
def test_mismatch(self):
bond_topology = str_to_bond_topology('''
atoms: ATOM_O
atoms: ATOM_O
bonds {
atom_b: 1
bond_type: BOND_DOUBLE
}
smiles: "BlahBlahBlah"
''')
result, with_h, without_h = smu_utils_lib.bond_topology_smiles_comparison(
bond_topology)
self.assertEqual(smu_utils_lib.SmilesCompareResult.MISMATCH, result)
self.assertEqual('O=O', with_h)
self.assertEqual('O=O', without_h)
def _compare_smiles(self, conformer):
if len(conformer.bond_topologies) != 1:
raise ValueError(
'compare_smiles expects 1 bond topology; for CID {} got {}'.
format(conformer.conformer_id, len(conformer.bond_topologies)))
result, smiles_with_h, smiles_without_h = (
smu_utils_lib.bond_topology_smiles_comparison(
conformer.bond_topologies[0]))
if result != smu_utils_lib.SmilesCompareResult.MATCH:
yield beam.pvalue.TaggedOutput(
UpdateConformerFn.OUTPUT_TAG_SMILES_MISMATCH,
(conformer.conformer_id, result,
conformer.bond_topologies[0].smiles, smiles_with_h,
smiles_without_h))
conformer.bond_topologies[0].smiles = smiles_without_h
def _compare_smiles(self, molecule):
if len(molecule.bond_topologies) != 1:
raise ValueError(
'compare_smiles expects 1 bond topology; for CID {} got {}'.format(
molecule.molecule_id, len(molecule.bond_topologies)))
result, smiles_with_h, smiles_without_h = (
smu_utils_lib.bond_topology_smiles_comparison(
molecule.bond_topologies[0]))
if result != smu_utils_lib.SmilesCompareResult.MATCH:
yield beam.pvalue.TaggedOutput(
UpdateMoleculeFn.OUTPUT_TAG_SMILES_MISMATCH,
(molecule.molecule_id, result, molecule.bond_topologies[0].smiles,
smiles_with_h, smiles_without_h))
molecule.properties.smiles_openbabel = (
molecule.bond_topologies[0].smiles)
molecule.bond_topologies[0].smiles = smiles_without_h
def test_missing(self):
bond_topology = str_to_bond_topology('''
atoms: ATOM_O
atoms: ATOM_O
bonds {
atom_b: 1
bond_type: BOND_DOUBLE
}
''')
result, with_h, without_h = smu_utils_lib.bond_topology_smiles_comparison(
bond_topology)
self.assertEqual(smu_utils_lib.SmilesCompareResult.MISSING, result)
self.assertEqual('O=O', with_h)
self.assertEqual('O=O', without_h)
# Also directly test compute_smiles_for_bond_topology
self.assertEqual(
'O=O',
smu_utils_lib.compute_smiles_for_bond_topology(
bond_topology, include_hs=True))
