def testGetAtomTypeFromProto(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual(
[atom.type for atom in pb.atoms],
[mgpb.MoleculeGraph.Atom.ATOM_C] * 10 + [
mgpb.MoleculeGraph.Atom.ATOM_O, mgpb.MoleculeGraph.Atom.ATOM_F,
mgpb.MoleculeGraph.Atom.ATOM_CL
])
mol = Chem.MolFromSmiles('FB(F)F')
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual(
[atom.type for atom in pb.atoms],
[mgpb.MoleculeGraph.Atom.ATOM_F] * 3 + [mgpb.MoleculeGraph.Atom.ATOM_B])
mol = Chem.MolFromSmiles('Cl[Se][Se]Cl')
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual(
[atom.type for atom in pb.atoms],
[mgpb.MoleculeGraph.Atom.ATOM_CL] * 2 + [
mgpb.MoleculeGraph.Atom.ATOM_SE] * 2)
def testCircularFingerprintUsesChirality(self):
# These molecules differ only in the chirality of their stereocenters.
mol1 = Chem.MolFromSmiles(
'CN[C@H]1CC[C@H](C2=CC=CC=C12)C3=CC(=C(C=C3)Cl)Cl')
mol2 = Chem.MolFromSmiles(
'CN[C@@H]1CC[C@@H](C2=CC=CC=C12)C3=CC(=C(C=C3)Cl)Cl')
mg1 = molecule_graph.MoleculeGraph(mol1)
mg2 = molecule_graph.MoleculeGraph(mol2)
pb1 = mg1.to_proto()
pb2 = mg2.to_proto()
self.assertNotEqual(pb1.binary_features, pb2.binary_features)
def testHasNonZeroSpatialDistance(self):
mol = Chem.MolFromSmiles('CCCC')
mol_pb = molecule_graph.MoleculeGraph(
mol, partial_charges=None, compute_conformer=True).to_proto(
calc_pair_spatial_distances=True)
self.assertTrue(mol_pb.atom_pairs[0].HasField('spatial_distance'))
self.assertGreater(mol_pb.atom_pairs[0].spatial_distance, 0)
def testGetChirality(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
[mg.get_atom_chirality(atom) for atom in mol.GetAtoms()],
[mgpb.MoleculeGraph.Atom.CHIRAL_R
] + [mgpb.MoleculeGraph.Atom.CHIRAL_NONE] * 12)
def testPermutation(self):
# Cyanic acid is handy because all 4 atoms are different.
mol = Chem.AddHs(Chem.MolFromSmiles('C(#N)O'))
mg = molecule_graph.MoleculeGraph(mol, partial_charges=None)
random_state = np.random.RandomState(seed=123)
num_times_carbon_first = 0
for _ in range(50):
mol_pb = mg.to_proto(max_pair_distance=-1,
calc_pair_spatial_distances=False,
random_permute=random_state)
self.assertEqual(len(mol_pb.atoms), 4)
self.assertEqual(len(mol_pb.atom_pairs), 6)
pos_to_atom = [mol_pb.atoms[i].element for i in range(4)]
if pos_to_atom[0] == 'C':
num_times_carbon_first += 1
# Checks that the carbon is triple bonded to nitrogen and single bonded to
# oxygen.
num_pairs_checked = 0
for pair in mol_pb.atom_pairs:
atom_types = set([pos_to_atom[pair.a_idx], pos_to_atom[pair.b_idx]])
if atom_types == set(['C', 'N']):
self.assertEqual(pair.bond_type,
mgpb.MoleculeGraph.AtomPair.BOND_TRIPLE)
num_pairs_checked += 1
if atom_types == set(['C', 'O']):
self.assertEqual(pair.bond_type,
mgpb.MoleculeGraph.AtomPair.BOND_SINGLE)
num_pairs_checked += 1
self.assertEqual(num_pairs_checked, 2)
self.assertLess(num_times_carbon_first, 50)
self.assertGreater(num_times_carbon_first, 0)
def smiles_to_features(self, smiles):
mol = Chem.MolFromSmiles(smiles)
mg = molecule_graph.MoleculeGraph(
mol, partial_charges='gasteiger', compute_conformer=True)
mol_pb = mg.to_proto(max_pair_distance=-1,
calc_pair_spatial_distances=True)
return molecule_graph.proto_to_simple_features(mol_pb)
def testGetBondTypesFromProto(self):
mol = Chem.MolFromSmiles('C(Cl)Cl') # CID6344
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual([pair.bond_type for pair in pb.atom_pairs],
[mgpb.MoleculeGraph.AtomPair.BOND_SINGLE] * 2 +
[mgpb.MoleculeGraph.AtomPair.BOND_NONE])
def testGetRingSizes(self):
mol = Chem.MolFromSmiles('C1=NC2=C(N1)C(=NC=N2)N') # CID190
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
six.iteritems(mg.get_ring_sizes()),
[(0, [5]), (1, [5]), (2, [5, 6]), (3, [5, 6]), (4, [5]), (5, [6]),
(6, [6]), (7, [6]), (8, [6])])
def testGetRingSizesFromProto(self):
mol = Chem.MolFromSmiles('C1=NC2=C(N1)C(=NC=N2)N') # CID190
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual(
[atom.ring_sizes for atom in pb.atoms],
[[5], [5], [5], [5, 6], [5, 6], [6], [6], [6], [6], []])
def testNoMismatches(self):
"""Test that using atom indices doesn't cause any mismatches.
Smallest ring sizes and bond types use atom indices.
"""
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
count = 0
for atom in pb.atoms:
# Each aromatic carbon should be in a single ring of size 6
if atom.type == mgpb.MoleculeGraph.Atom.ATOM_C and atom.aromatic:
self.assertListEqual(list(atom.ring_sizes), [6])
count += 1
self.assertEqual(count, 6) # should be six aromatic carbons
count = 0
for pair in pb.atom_pairs:
# Each bonded aromatic pair should have aromatic bond type.
a = pb.atoms[pair.a_idx]
b = pb.atoms[pair.b_idx]
if (a.type == b.type == mgpb.MoleculeGraph.Atom.ATOM_C and a.aromatic and
b.aromatic and pair.graph_distance == 1):
self.assertEqual(
pair.bond_type, mgpb.MoleculeGraph.AtomPair.BOND_AROMATIC)
count += 1
self.assertEqual(count, 6) # should be six aromatic bonds
def testGetChiralityFromProto(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual([atom.chirality for atom in pb.atoms],
[mgpb.MoleculeGraph.Atom.CHIRAL_R
] + [mgpb.MoleculeGraph.Atom.CHIRAL_NONE] * 12)
def testGetBondTypesNeighborsFromProto(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto(max_pair_distance=1)
self.assertCountEqual([pair.bond_type for pair in pb.atom_pairs],
[mgpb.MoleculeGraph.AtomPair.BOND_SINGLE] * 6 + [
mgpb.MoleculeGraph.AtomPair.BOND_DOUBLE
] + [mgpb.MoleculeGraph.AtomPair.BOND_AROMATIC] * 6)
def testGetBondTypes(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
six.itervalues(mg.get_bond_types()),
[mgpb.MoleculeGraph.AtomPair.BOND_SINGLE] * 6 + [
mgpb.MoleculeGraph.AtomPair.BOND_DOUBLE
] + [mgpb.MoleculeGraph.AtomPair.BOND_AROMATIC] * 6)
def testGetHydrogenBondingFromProto(self):
# CID91796808
mol = Chem.MolFromSmiles('CC(C)(C#CC1=CC=C(C=C1)C(=O)N2CCC(C2)OC)O')
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual(
[(atom.acceptor, atom.donor) for atom in pb.atoms],
[(True, False)] * 3 + [(True, True)] + [(False, False)] * 17)
def testGetHydrogenBonding(self):
# CID91796808
mol = Chem.MolFromSmiles('CC(C)(C#CC1=CC=C(C=C1)C(=O)N2CCC(C2)OC)O')
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
six.itervalues(mg.get_hydrogen_bonding()),
[molecule_graph.HydrogenBonding(acceptor=True, donor=False)] * 3 +
[molecule_graph.HydrogenBonding(acceptor=True, donor=True)])
def testGetGasteigerPartialCharges(self):
mol = Chem.MolFromSmiles('CC(=O)OC1=CC=CC=C1C(=O)O') # CID2244
mg = molecule_graph.MoleculeGraph(mol, partial_charges='gasteiger')
self.assertCountEqual(
np.round(list(mg.get_partial_charges().values()), 2), [
-0.48, -0.43, -0.25, -0.25, -0.06, -0.06, -0.04, -0.02, 0.03, 0.1,
0.14, 0.31, 0.34
])
def testGetHybridization(self):
# CID91796808: the amide nitrogen is sp2
mol = Chem.MolFromSmiles('CC(C)(C#CC1=CC=C(C=C1)C(=O)N2CCC(C2)OC)O')
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
[mg.get_hybridization(atom) for atom in mol.GetAtoms()],
[mgpb.MoleculeGraph.Atom.HYBRIDIZATION_SP3] * 10 +
[mgpb.MoleculeGraph.Atom.HYBRIDIZATION_SP2] * 9 +
[mgpb.MoleculeGraph.Atom.HYBRIDIZATION_SP] * 2)
def testMethaneWithHs(self):
mol = Chem.rdmolops.AddHs(Chem.MolFromSmiles('C'))
mg = molecule_graph.MoleculeGraph(mol)
mol_pb = mg.to_proto(max_pair_distance=-1,
calc_pair_spatial_distances=False)
out_features = molecule_graph.proto_to_simple_features(mol_pb)
self.assertEqual(out_features.num_atoms, 5)
self.assertEqual(out_features.num_heavy_atoms, 1)
self.assertEqual(out_features.element_type_counts, {'C': 1, 'H': 4})
def testGetHybridizationFromProto(self):
# CID91796808: the amide nitrogen is sp2
mol = Chem.MolFromSmiles('CC(C)(C#CC1=CC=C(C=C1)C(=O)N2CCC(C2)OC)O')
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual([atom.hybridization for atom in pb.atoms],
[mgpb.MoleculeGraph.Atom.HYBRIDIZATION_SP3] * 10 +
[mgpb.MoleculeGraph.Atom.HYBRIDIZATION_SP2] * 9 +
[mgpb.MoleculeGraph.Atom.HYBRIDIZATION_SP] * 2)
def testGetMMFF94PartialCharges(self):
mol = Chem.MolFromSmiles('CC(=O)OC1=CC=CC=C1C(=O)O') # CID2244
mg = molecule_graph.MoleculeGraph(mol, partial_charges='mmff94')
# Compares with PubChem partial charges for non-hydrogen atoms.
self.assertCountEqual(
np.round(list(mg.get_partial_charges().values()), 2), [
-0.65, -0.57, -0.57, -0.23, -0.15, -0.15, -0.15, -0.15, 0.06, 0.08,
0.09, 0.63, 0.66
])
def testGetPartialChargesFromProto(self):
mol = Chem.MolFromSmiles('CC(=O)OC1=CC=CC=C1C(=O)O') # CID2244
mg = molecule_graph.MoleculeGraph(mol, partial_charges='mmff94')
pb = mg.to_proto()
self.assertCountEqual(
np.round([atom.partial_charge for atom in pb.atoms], 2), [
-0.65, -0.57, -0.57, -0.23, -0.15, -0.15, -0.15, -0.15, 0.06, 0.08,
0.09, 0.63, 0.66
])
def testGetAtomType(self):
mol = Chem.MolFromSmiles('C1=CC=C(C=C1)C(=O)[C@@H](CCF)Cl') # CID88643715
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
[mg.get_atom_type(atom) for atom in mol.GetAtoms()],
[mgpb.MoleculeGraph.Atom.ATOM_C] * 10 + [
mgpb.MoleculeGraph.Atom.ATOM_O, mgpb.MoleculeGraph.Atom.ATOM_F,
mgpb.MoleculeGraph.Atom.ATOM_CL
])
mol = Chem.MolFromSmiles('FB(F)F')
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
[mg.get_atom_type(atom) for atom in mol.GetAtoms()],
[mgpb.MoleculeGraph.Atom.ATOM_F] * 3 + [mgpb.MoleculeGraph.Atom.ATOM_B])
mol = Chem.MolFromSmiles('Cl[Se][Se]Cl')
mg = molecule_graph.MoleculeGraph(mol)
self.assertCountEqual(
[mg.get_atom_type(atom) for atom in mol.GetAtoms()],
[mgpb.MoleculeGraph.Atom.ATOM_CL] * 2 + [
mgpb.MoleculeGraph.Atom.ATOM_SE] * 2)
def testGetSmilesFromProto(self):
# CID68617
mol = Chem.MolFromSmiles('CN[C@H]1CC[C@H](C2=CC=CC=C12)C3=CC(=C(C=C3)Cl)Cl')
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertEqual(pb.smiles, 'CN[C@H]1CC[C@@H](c2ccc(Cl)c(Cl)c2)c2ccccc21')
def testGetNeighborsFromProto(self):
mol = Chem.MolFromSmiles('C(Cl)Cl') # CID6344
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto(max_pair_distance=1)
self.assertCountEqual([p.graph_distance for p in pb.atom_pairs], [1, 1])
def testGetSameRingFromProto(self):
mol = Chem.MolFromSmiles('C1=CC=C2C=CC=CC2=C1') # CID931
mg = molecule_graph.MoleculeGraph(mol)
pb = mg.to_proto()
self.assertCountEqual([pair.same_ring for pair in pb.atom_pairs],
[True] * 29 + [False] * 16)
def testHasNoSpatialDistance(self):
mol = Chem.MolFromSmiles('CCCC')
mol_pb = molecule_graph.MoleculeGraph(
mol, partial_charges=None).to_proto(
calc_pair_spatial_distances=False)
self.assertFalse(mol_pb.atom_pairs[0].HasField('spatial_distance'))
def testGetCircularFingerprintFromProto(self):
mol = Chem.MolFromSmiles('CC(=O)OC1=CC=CC=C1C(=O)O') # CID2244
mg = molecule_graph.MoleculeGraph(mol, partial_charges='mmff94')
pb = mg.to_proto()
self.assertEqual(len(pb.binary_features), 1024)
self.assertGreater(sum(pb.binary_features), 0)
