def test_with_smiles(self, smiles, expected): mol = Chem.MolFromSmiles(smiles, sanitize=False) bt = smu_utils_lib.rdkit_molecule_to_bond_topology(mol) self.assertEqual(utilities.is_single_fragment(bt), expected) Chem.SanitizeMol(mol, Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS) mol_h = Chem.AddHs(mol) bt_h = smu_utils_lib.rdkit_molecule_to_bond_topology(mol_h) self.assertEqual(utilities.is_single_fragment(bt_h), expected)
def test_single_fragment_3_atoms_0_bonds(self):
bt = text_format.Parse(
""" atoms: ATOM_C
atoms: ATOM_C
atoms: ATOM_C
""", dataset_pb2.BondTopology())
self.assertFalse(utilities.is_single_fragment(bt))
def test_single_fragment_two_connected_atoms(self):
bt = text_format.Parse(
""" atoms: ATOM_C
atoms: ATOM_C
bonds {
atom_a: 0
atom_b: 1
bond_type: BOND_SINGLE
}
""", dataset_pb2.BondTopology())
self.assertTrue(utilities.is_single_fragment(bt))
def test_single_fragment_4_atoms_3_bonds_no_ring(self):
bt = text_format.Parse(
""" atoms: ATOM_C
atoms: ATOM_C
atoms: ATOM_C
atoms: ATOM_C
bonds {
atom_a: 0
atom_b: 1
bond_type: BOND_SINGLE
}
bonds {
atom_a: 1
atom_b: 2
bond_type: BOND_SINGLE
}
bonds {
atom_a: 2
atom_b: 3
bond_type: BOND_SINGLE
}
""", dataset_pb2.BondTopology())
self.assertTrue(utilities.is_single_fragment(bt))