def test_scores(self):
carbon = dataset_pb2.BondTopology.AtomType.ATOM_C
single_bond = dataset_pb2.BondTopology.BondType.BOND_SINGLE
double_bond = dataset_pb2.BondTopology.BondType.BOND_DOUBLE
# For testing, turn off the need for complete matching.
smu_molecule.default_must_match_all_bonds = False
all_distributions = bond_length_distribution.AllAtomPairLengthDistributions(
)
x, y = triangular_distribution(1.0, 1.4, 2.0)
df = pd.DataFrame({"length": x, "count": y})
bldc1c = bond_length_distribution.EmpiricalLengthDistribution(df, 0.0)
all_distributions.add(carbon, carbon, single_bond, bldc1c)
x, y = triangular_distribution(1.0, 1.5, 2.0)
df = pd.DataFrame({"length": x, "count": y})
bldc2c = bond_length_distribution.EmpiricalLengthDistribution(df, 0.0)
all_distributions.add(carbon, carbon, double_bond, bldc2c)
bond_topology = text_format.Parse(
"""
atoms: ATOM_C
atoms: ATOM_C
bonds: {
atom_a: 0
atom_b: 1
bond_type: BOND_SINGLE
}
""", dataset_pb2.BondTopology())
geometry = text_format.Parse(
"""
atom_positions {
x: 0.0
y: 0.0
z: 0.0
},
atom_positions {
x: 0.0
y: 0.0
z: 0.0
}
""", dataset_pb2.Geometry())
geometry.atom_positions[1].x = 1.4 / smu_utils_lib.BOHR_TO_ANGSTROMS
matching_parameters = smu_molecule.MatchingParameters()
matching_parameters.must_match_all_bonds = False
result = topology_from_geom.bond_topologies_from_geom(
all_distributions, bond_topology, geometry, matching_parameters)
self.assertIsNotNone(result)
self.assertEqual(len(result.bond_topology), 2)
self.assertEqual(len(result.bond_topology[0].bonds), 1)
self.assertEqual(len(result.bond_topology[1].bonds), 1)
self.assertGreater(result.bond_topology[0].score,
result.bond_topology[1].score)
self.assertEqual(result.bond_topology[0].bonds[0].bond_type,
single_bond)
self.assertEqual(result.bond_topology[1].bonds[0].bond_type,
double_bond)
def zero2():
"""Return a Geometry with two points at the origin."""
return text_format.Parse(
"""
atom_positions: {
x:0.0,
y:0.0,
z:0.0
},
atom_positions: {
x:0.0,
y:0.0,
z:0.0
}
""", dataset_pb2.Geometry())
def geom_to_angstroms(geometry):
"""Convert all the coordinates in `geometry` to Angstroms.
Args:
geometry: starting Geometry Returns New Geometry with adjusted coordinates.
Returns:
Coordinates in Angstroms.
"""
result = dataset_pb2.Geometry()
for atom in geometry.atom_positions:
new_atom = dataset_pb2.Geometry.AtomPos()
new_atom.x = smu_utils_lib.bohr_to_angstroms(atom.x)
new_atom.y = smu_utils_lib.bohr_to_angstroms(atom.y)
new_atom.z = smu_utils_lib.bohr_to_angstroms(atom.z)
result.atom_positions.append(new_atom)
return result
def test_scores(self):
carbon = dataset_pb2.BondTopology.ATOM_C
single_bond = dataset_pb2.BondTopology.BondType.BOND_SINGLE
double_bond = dataset_pb2.BondTopology.BondType.BOND_DOUBLE
# For testing, turn off the need for complete matching.
topology_molecule.default_must_match_all_bonds = False
all_distributions = bond_length_distribution.AllAtomPairLengthDistributions(
)
bldc1c = triangular_distribution(1.0, 1.4, 2.0)
all_distributions.add(carbon, carbon, single_bond, bldc1c)
bldc2c = triangular_distribution(1.0, 1.5, 2.0)
all_distributions.add(carbon, carbon, double_bond, bldc2c)
molecule = dataset_pb2.Molecule()
molecule.bond_topologies.append(
text_format.Parse(
"""
atoms: ATOM_C
atoms: ATOM_C
bonds: {
atom_a: 0
atom_b: 1
bond_type: BOND_SINGLE
}
""", dataset_pb2.BondTopology()))
molecule.optimized_geometry.MergeFrom(
text_format.Parse(
"""
atom_positions {
x: 0.0
y: 0.0
z: 0.0
},
atom_positions {
x: 0.0
y: 0.0
z: 0.0
}
""", dataset_pb2.Geometry()))
molecule.optimized_geometry.atom_positions[1].x = (
1.4 / smu_utils_lib.BOHR_TO_ANGSTROMS)
matching_parameters = topology_molecule.MatchingParameters()
matching_parameters.must_match_all_bonds = False
molecule.properties.errors.fate = dataset_pb2.Properties.FATE_SUCCESS
molecule.molecule_id = 1001
result = topology_from_geom.bond_topologies_from_geom(
molecule, all_distributions, matching_parameters)
self.assertIsNotNone(result)
self.assertLen(result.bond_topology, 2)
self.assertLen(result.bond_topology[0].bonds, 1)
self.assertLen(result.bond_topology[1].bonds, 1)
self.assertEqual(result.bond_topology[0].bonds[0].bond_type, single_bond)
self.assertEqual(result.bond_topology[1].bonds[0].bond_type, double_bond)
self.assertGreater(result.bond_topology[0].topology_score,
result.bond_topology[1].topology_score)
self.assertAlmostEqual(
np.sum(np.exp([bt.topology_score for bt in result.bond_topology])), 1.0)
self.assertAlmostEqual(result.bond_topology[0].geometry_score,
np.log(bldc1c.pdf(1.4)))
self.assertAlmostEqual(result.bond_topology[1].geometry_score,
np.log(bldc2c.pdf(1.4)))