def test_extract_bond_lengths_max_unbonded(self):
# This conformer does not obery valence rules, but it's fine for this test.
conf = dataset_pb2.Conformer(conformer_id=123000)
conf.properties.errors.status = 4
bt = conf.bond_topologies.add()
bt.atoms.extend([
dataset_pb2.BondTopology.ATOM_C, dataset_pb2.BondTopology.ATOM_N,
dataset_pb2.BondTopology.ATOM_O
])
bt.bonds.add(atom_a=0,
atom_b=1,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE)
bt.bonds.add(atom_a=0,
atom_b=2,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE)
conf.optimized_geometry.atom_positions.add(x=0, y=0, z=0)
conf.optimized_geometry.atom_positions.add(x=1, y=0, z=0)
conf.optimized_geometry.atom_positions.add(x=100, y=2, z=0)
got = list(
pipeline.extract_bond_lengths(conf,
dist_sig_digits=2,
unbonded_max=2.0))
# Note that these are *not* rounded, but truncated to this many digits.
self.assertEqual(
got,
[
# 1 bohr -> 0.529177249 angstroms
('c', 'n', dataset_pb2.BondTopology.BOND_SINGLE, '0.52'),
# It seems like this should be 52.91 but it looks like some
# numerical noise in np.linalg.norm.
('c', 'o', dataset_pb2.BondTopology.BOND_SINGLE, '52.92')
])
def test_extract_bond_lengths_has_errors(self):
conf = self._create_dummy_conformer()
conf.properties.errors.status = 8
got = list(
pipeline.extract_bond_lengths(
conf, dist_sig_digits=2, unbonded_max=2.0))
self.assertEqual([], got)
def test_extract_bond_lengths(self):
# This conformer does not obey valence rules, but it's fine for this test.
conf = dataset_pb2.Conformer(conformer_id=123000)
conf.properties.errors.status = 4
bt = conf.bond_topologies.add()
bt.atoms.extend([
dataset_pb2.BondTopology.ATOM_ONEG, dataset_pb2.BondTopology.ATOM_NPOS,
dataset_pb2.BondTopology.ATOM_C, dataset_pb2.BondTopology.ATOM_H
])
bt.bonds.add(
atom_a=0, atom_b=1, bond_type=dataset_pb2.BondTopology.BOND_SINGLE)
bt.bonds.add(
atom_a=0, atom_b=2, bond_type=dataset_pb2.BondTopology.BOND_DOUBLE)
bt.bonds.add(
atom_a=0, atom_b=3, bond_type=dataset_pb2.BondTopology.BOND_SINGLE)
conf.optimized_geometry.atom_positions.add(x=0, y=0, z=0)
conf.optimized_geometry.atom_positions.add(x=1, y=0, z=0)
conf.optimized_geometry.atom_positions.add(x=0, y=2, z=0)
conf.optimized_geometry.atom_positions.add(x=111, y=222, z=333)
got = list(
pipeline.extract_bond_lengths(
conf, dist_sig_digits=2, unbonded_max=2.0))
# Note that these are *not* rounded, but truncated to this many digits.
self.assertEqual(
got,
[
# 1 bohr -> 0.529177249 angstroms
('n', 'o', dataset_pb2.BondTopology.BOND_SINGLE, '0.52'),
# 2 bohr -> 2 * 0.529177249 angstroms
('c', 'o', dataset_pb2.BondTopology.BOND_DOUBLE, '1.05'),
# sqrt(1**2 + 2**2) bohr -> 2.23606 * 0.529177249 angstroms
('c', 'n', dataset_pb2.BondTopology.BOND_UNDEFINED, '1.18')
])
def test_extract_bond_lengths_has_errors(self):
mol = self._create_dummy_molecule()
mol.properties.errors.status = 8
got = list(
pipeline.extract_bond_lengths(mol,
dist_sig_digits=2,
unbonded_max=2.0))
self.assertEqual([], got)