def main(unused_argv):
db = smu_sqlite.SMUSQLite('20220128_standard_v2.sqlite')
bond_lengths = bond_length_distribution.AllAtomPairLengthDistributions()
bond_lengths.add_from_sparse_dataframe_file(
'20220128_bond_lengths.csv',
bond_length_distribution.STANDARD_UNBONDED_RIGHT_TAIL_MASS,
bond_length_distribution.STANDARD_SIG_DIGITS)
fake_smiles_id_dict = collections.defaultdict(lambda: -1)
print('molecule_id, count_all, count_smu, count_covalent, count_allen')
for molecule in db:
if abs(hash(str(molecule.molecule_id))) % 1000 != 1:
continue
topology_from_geom.standard_topology_sensing(molecule, bond_lengths,
fake_smiles_id_dict)
count_all = len(molecule.bond_topologies)
count_smu = sum(bt.source & dataset_pb2.BondTopology.SOURCE_ITC != 0
for bt in molecule.bond_topologies)
count_covalent = sum(bt.source & dataset_pb2.BondTopology.SOURCE_MLCR != 0
for bt in molecule.bond_topologies)
count_allen = sum(bt.source & dataset_pb2.BondTopology.SOURCE_CSD != 0
for bt in molecule.bond_topologies)
print(
f'{molecule.molecule_id}, {count_all}, {count_smu}, {count_covalent}, {count_allen}'
)
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
logging.get_absl_handler().use_absl_log_file()
logging.info('Opening %s', FLAGS.output_sqlite)
db = smu_sqlite.SMUSQLite(FLAGS.output_sqlite, 'c')
if FLAGS.bond_topology_csv:
logging.info('Starting smiles to btid inserts')
smiles_id_dict = smu_utils_lib.smiles_id_dict_from_csv(
open(FLAGS.bond_topology_csv))
db.bulk_insert_smiles(smiles_id_dict.items())
logging.info('Finished smiles to btid inserts')
else:
logging.info('Skipping smiles inserts')
logging.info('Starting main inserts')
dataset = tf.data.TFRecordDataset(gfile.glob(FLAGS.input_tfrecord))
db.bulk_insert((raw.numpy() for raw in dataset), batch_size=10000)
logging.info('Starting vacuuming')
db.vacuum()
logging.info('Vacuuming finished')
def test_find_by_expanded_stoichiometry_list(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(
self.encode_molecules(
[self.make_fake_molecule(mid) for mid in [2001, 2002, 4004]]))
got_mids = [
molecule.molecule_id for molecule in
db.find_by_expanded_stoichiometry_list(['(ch2)2(ch3)2'])
]
self.assertCountEqual(got_mids, [4004])
got_mids = [
molecule.molecule_id
for molecule in db.find_by_expanded_stoichiometry_list(['(ch3)2'])
]
self.assertCountEqual(got_mids, [2001, 2002])
got_mids = [
molecule.molecule_id for molecule in
db.find_by_expanded_stoichiometry_list(['(ch2)2(ch3)2', '(ch3)2'])
]
self.assertCountEqual(got_mids, [2001, 2002, 4004])
self.assertEmpty(list(db.find_by_expanded_stoichiometry_list(['(nh)'
])))
def create_db(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(
self.encode_conformers([
self.make_fake_conformer(cid)
for cid in range(2001, 10001, 2000)
]))
return db
def test_repeat_smiles_insert(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(
self.encode_conformers(
[self.make_fake_conformer(cid) for cid in [2001, 2002, 2003]]))
got_cids = [
conformer.conformer_id for conformer in db.find_by_smiles('CC')
]
self.assertCountEqual(got_cids, [2001, 2002, 2003])
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
logging.info('Opening %s', FLAGS.output_sqlite)
db = smu_sqlite.SMUSQLite(FLAGS.output_sqlite, 'c')
dataset = tf.data.TFRecordDataset(gfile.glob(FLAGS.input_tfrecord))
db.bulk_insert((raw.numpy() for raw in dataset), batch_size=10000)
def test_repeat_smiles_insert(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(
self.encode_molecules(
[self.make_fake_molecule(mid) for mid in [2001, 2002, 2003]]))
got_mids = [
molecule.molecule_id for molecule in db.find_by_smiles_list(
['CC'], smu_utils_lib.WhichTopologies.ALL)
]
self.assertCountEqual(got_mids, [2001, 2002, 2003])
def test_no_expanded_stoichiometry_on_ineligible(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
conf = self.make_fake_conformer(2001)
# This makes the conformer ineligible
conf.properties.errors.status = 600
db.bulk_insert(self.encode_conformers([conf]))
got_cids = [
conformer.conformer_id
for conformer in db.find_by_expanded_stoichiometry('')
]
self.assertCountEqual(got_cids, [2001])
def test_read(self):
create_db = self.create_db()
del create_db
db = smu_sqlite.SMUSQLite(self.db_filename, 'r')
with self.assertRaises(smu_sqlite.ReadOnlyError):
db.bulk_insert([self.make_fake_conformer(9999)])
with self.assertRaises(KeyError):
db.find_by_conformer_id(9999)
self.assertEqual(db.find_by_conformer_id(4001).conformer_id, 4001)
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
logging.get_absl_handler().use_absl_log_file()
logging.info('Opening %s', FLAGS.input_sqlite)
db = smu_sqlite.SMUSQLite(FLAGS.input_sqlite, 'r')
if FLAGS.output_format == OutputFormat.pbtxt:
outputter = PBTextOutputter(FLAGS.output_path)
elif FLAGS.output_format == OutputFormat.sdf_init:
outputter = SDFOutputter(
FLAGS.output_path, init_geometry=True, opt_geometry=False)
elif FLAGS.output_format == OutputFormat.sdf_opt:
outputter = SDFOutputter(
FLAGS.output_path, init_geometry=False, opt_geometry=True)
elif FLAGS.output_format == OutputFormat.sdf_init_opt:
outputter = SDFOutputter(
FLAGS.output_path, init_geometry=True, opt_geometry=True)
elif FLAGS.output_format == OutputFormat.atomic_input:
outputter = AtomicInputOutputter(FLAGS.output_path)
elif FLAGS.output_format == OutputFormat.tfdata:
outputter = TfDataOutputter(FLAGS.output_path)
else:
raise ValueError(f'Bad output format {FLAGS.output_format}')
if FLAGS.redetect_geometry:
outputter = ReDetectTopologiesOutputter(outputter)
with contextlib.closing(outputter):
for cid in (int(x) for x in FLAGS.cids):
conformer = db.find_by_conformer_id(cid)
outputter.output(conformer)
for btid in (int(x) for x in FLAGS.btids):
conformers = db.find_by_bond_topology_id(btid)
if not conformers:
raise KeyError(f'Bond topology {btid} not found')
for c in conformers:
outputter.output(c)
for smiles in FLAGS.smiles:
conformers = db.find_by_smiles(smiles)
if not conformers:
raise KeyError(f'SMILES {smiles} not found')
for c in conformers:
outputter.output(c)
for smiles in FLAGS.topology_query_smiles:
for c in topology_query(db, smiles):
outputter.output(c)
if FLAGS.random_fraction:
for conformer in db:
if conformer.fate == dataset_pb2.Conformer.FATE_SUCCESS and random.random(
) < FLAGS.random_fraction:
outputter.output(conformer)
def test_read(self):
create_db = self.create_db()
del create_db
db = smu_sqlite.SMUSQLite(self.db_filename, 'r')
with self.assertRaises(smu_sqlite.ReadOnlyError):
db.bulk_insert(
self.encode_molecules([self.make_fake_molecule(9999)]))
with self.assertRaises(KeyError):
db.find_by_molecule_id(9999)
self.assertEqual(db.find_by_molecule_id(4001).molecule_id, 4001)
def test_write(self):
create_db = self.create_db()
del create_db
db = smu_sqlite.SMUSQLite(self.db_filename, 'w')
# The create_db makes conformer ids ending in 001. We'll add conformer ids
# ending in 005 as the extra written ones to make it clear that they are
# different.
db.bulk_insert(
[self.make_fake_conformer(cid) for cid in range(50005, 60005, 2000)])
# Check an id that was already there
self.assertEqual(db.find_by_conformer_id(4001).conformer_id, 4001)
# Check an id that we added
self.assertEqual(db.find_by_conformer_id(52005).conformer_id, 52005)
def test_find_by_bond_topology_id_source_filtering(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
# We'll make 2 molecules
# 2001 with bt id 10 (ITC, STARTING) and bt id 11 (MLCR)
# 4001 with bt id 10 (ITC), bt id 11 (ITC, STARTING), bt id 12 (CSD)
# 6001 with bt id 12 (MLCR)
molecules = []
molecules.append(dataset_pb2.Molecule(molecule_id=2001))
self.add_bond_topology_to_molecule(
molecules[-1], 10, dataset_pb2.BondTopology.SOURCE_STARTING
| dataset_pb2.BondTopology.SOURCE_ITC)
self.add_bond_topology_to_molecule(
molecules[-1], 11, dataset_pb2.BondTopology.SOURCE_MLCR)
molecules.append(dataset_pb2.Molecule(molecule_id=4001))
self.add_bond_topology_to_molecule(molecules[-1], 10,
dataset_pb2.BondTopology.SOURCE_ITC)
self.add_bond_topology_to_molecule(
molecules[-1], 11, dataset_pb2.BondTopology.SOURCE_STARTING
| dataset_pb2.BondTopology.SOURCE_ITC)
self.add_bond_topology_to_molecule(molecules[-1], 12,
dataset_pb2.BondTopology.SOURCE_CSD)
molecules.append(dataset_pb2.Molecule(molecule_id=6001))
self.add_bond_topology_to_molecule(
molecules[-1], 12, dataset_pb2.BondTopology.SOURCE_MLCR)
db.bulk_insert(self.encode_molecules(molecules))
def ids_for(bt_id, which):
return [
c.molecule_id
for c in db.find_by_bond_topology_id_list([bt_id], which)
]
self.assertEqual(ids_for(10, smu_utils_lib.WhichTopologies.ALL),
[2001, 4001])
self.assertEqual(ids_for(11, smu_utils_lib.WhichTopologies.ALL),
[2001, 4001])
self.assertEqual(ids_for(12, smu_utils_lib.WhichTopologies.ALL),
[4001, 6001])
self.assertEqual(ids_for(10, smu_utils_lib.WhichTopologies.STARTING),
[2001])
self.assertEqual(ids_for(11, smu_utils_lib.WhichTopologies.MLCR),
[2001])
self.assertEqual(ids_for(12, smu_utils_lib.WhichTopologies.CSD),
[4001])
self.assertEmpty(ids_for(12, smu_utils_lib.WhichTopologies.ITC))
self.assertEmpty(ids_for(11, smu_utils_lib.WhichTopologies.CSD))
def create_db_with_multiple_bond_topology(self):
# We'll set up 3 CIDS with one or more btids associated with them.
# cid: 1000 -> btid 1
# cid: 2000 -> btid 2, 1
# cid: 3000 -> btid 3, 1, 2
conf1 = self.make_fake_conformer(1000)
conf2 = self.make_fake_conformer(2000)
self.add_bond_topology_to_conformer(conf2, 1)
conf3 = self.make_fake_conformer(3000)
self.add_bond_topology_to_conformer(conf3, 1)
self.add_bond_topology_to_conformer(conf3, 2)
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(self.encode_conformers([conf1, conf2, conf3]))
return db
def test_find_by_expanded_stoichiometry(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(
self.encode_conformers(
[self.make_fake_conformer(cid) for cid in [2001, 2002, 4004]]))
got_cids = [
conformer.conformer_id
for conformer in db.find_by_expanded_stoichiometry('(ch2)2(ch3)2')
]
self.assertCountEqual(got_cids, [4004])
got_cids = [
conformer.conformer_id
for conformer in db.find_by_expanded_stoichiometry('(ch3)2')
]
self.assertCountEqual(got_cids, [2001, 2002])
self.assertEmpty(list(db.find_by_expanded_stoichiometry('(nh)')))
def create_db_with_multiple_bond_topology(self):
# We'll set up 3 CIDS with one or more btids associated with them.
# mid: 1000 -> btid 1
# mid: 2000 -> btid 2, 1
# mid: 3000 -> btid 3, 1, 2
mol1 = self.make_fake_molecule(1000)
mol2 = self.make_fake_molecule(2000)
self.add_bond_topology_to_molecule(mol2, 1,
dataset_pb2.BondTopology.SOURCE_ITC)
mol3 = self.make_fake_molecule(3000)
self.add_bond_topology_to_molecule(mol3, 1,
dataset_pb2.BondTopology.SOURCE_ITC)
self.add_bond_topology_to_molecule(mol3, 2,
dataset_pb2.BondTopology.SOURCE_ITC)
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(self.encode_molecules([mol1, mol2, mol3]))
return db
def test_find_by_stoichiometry(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
db.bulk_insert(
self.encode_conformers(
[self.make_fake_conformer(cid) for cid in [2001, 2002, 4004]]))
got_cids = [
conformer.conformer_id
for conformer in db.find_by_stoichiometry('c2h6')
]
self.assertCountEqual(got_cids, [2001, 2002])
got_cids = [
conformer.conformer_id
for conformer in db.find_by_stoichiometry('c4h10')
]
self.assertCountEqual(got_cids, [4004])
self.assertEmpty(list(db.find_by_stoichiometry('c3')))
with self.assertRaises(smu_utils_lib.StoichiometryError):
db.find_by_stoichiometry('P3Li')
def test_simple(self):
db_filename = os.path.join(tempfile.mkdtemp(),
'query_sqlite_test.sqlite')
db = smu_sqlite.SMUSQLite(db_filename, 'w')
parser = smu_parser_lib.SmuParser(
os.path.join(TESTDATA_PATH, 'pipeline_input_stage2.dat'))
db.bulk_insert(x.SerializeToString()
for (x, _) in parser.process_stage2())
with flagsaver.flagsaver(
bond_lengths_csv=os.path.join(TESTDATA_PATH,
'minmax_bond_distances.csv'),
bond_topology_csv=os.path.join(TESTDATA_PATH,
'pipeline_bond_topology.csv')):
got = list(query_sqlite.topology_query(db, 'COC(=CF)OC'))
# These are just the two conformers that came in with this smiles, so no
# interesting detection happened, but it verifies that the code ran without
# error.
self.assertEqual([c.conformer_id for c in got], [618451001, 618451123])
self.assertLen(got[0].bond_topologies, 1)
self.assertEqual(got[0].bond_topologies[0].bond_topology_id, 618451)
self.assertLen(got[1].bond_topologies, 1)
self.assertEqual(got[1].bond_topologies[0].bond_topology_id, 618451)
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
logging.info('Opening %s', FLAGS.input_sqlite)
db = smu_sqlite.SMUSQLite(FLAGS.input_sqlite, 'r')
if FLAGS.output_format == OutputFormat.pbtxt:
outputter = PBTextOutputter(FLAGS.output_path)
elif FLAGS.output_format == OutputFormat.sdf_init:
outputter = SDFOutputter(
FLAGS.output_path, init_geometry=True, opt_geometry=False)
elif FLAGS.output_format == OutputFormat.sdf_opt:
outputter = SDFOutputter(
FLAGS.output_path, init_geometry=False, opt_geometry=True)
elif FLAGS.output_format == OutputFormat.sdf_init_opt:
outputter = SDFOutputter(
FLAGS.output_path, init_geometry=True, opt_geometry=True)
else:
raise ValueError(f'Bad output format {FLAGS.output_format}')
with contextlib.closing(outputter):
for cid in (int(x) for x in FLAGS.cids):
conformer = db.find_by_conformer_id(cid)
outputter.write(conformer)
for btid in (int(x) for x in FLAGS.btids):
conformers = db.find_by_bond_topology_id(btid)
if not conformers:
raise KeyError(f'Bond topology {btid} not found')
for c in conformers:
outputter.write(c)
for smiles in FLAGS.smiles:
conformers = db.find_by_smiles(smiles)
if not conformers:
raise KeyError(f'SMILES {smiles} not found')
for c in conformers:
outputter.write(c)
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
logging.get_absl_handler().use_absl_log_file()
logging.info('Opening %s', FLAGS.input_sqlite)
db = smu_sqlite.SMUSQLite(FLAGS.input_sqlite, 'r')
if FLAGS.output_format == OutputFormat.PBTXT:
outputter = PBTextOutputter(FLAGS.output_path)
elif FLAGS.output_format == OutputFormat.SDF_INIT:
outputter = SDFOutputter(FLAGS.output_path,
init_geometry=True,
opt_geometry=False,
which_topologies=FLAGS.which_topologies)
elif FLAGS.output_format == OutputFormat.SDF_OPT:
outputter = SDFOutputter(FLAGS.output_path,
init_geometry=False,
opt_geometry=True,
which_topologies=FLAGS.which_topologies)
elif FLAGS.output_format == OutputFormat.SDF_INIT_OPT:
outputter = SDFOutputter(FLAGS.output_path,
init_geometry=True,
opt_geometry=True,
which_topologies=FLAGS.which_topologies)
elif FLAGS.output_format == OutputFormat.ATOMIC2_INPUT:
outputter = Atomic2InputOutputter(FLAGS.output_path,
FLAGS.which_topologies)
elif FLAGS.output_format == OutputFormat.DAT:
outputter = DatOutputter(FLAGS.output_path)
else:
raise ValueError(f'Bad output format {FLAGS.output_format}')
if FLAGS.redetect_topology:
outputter = ReDetectTopologiesOutputter(outputter, db)
with contextlib.closing(outputter):
for mid in (int(x) for x in FLAGS.mids):
molecule = db.find_by_molecule_id(mid)
outputter.output(molecule)
for c in db.find_by_bond_topology_id_list(
[int(x) for x in FLAGS.btids], FLAGS.which_topologies):
outputter.output(c)
for c in db.find_by_smiles_list(FLAGS.smiles, FLAGS.which_topologies):
outputter.output(c)
for stoich in FLAGS.stoichiometries:
molecules = db.find_by_stoichiometry(stoich)
for c in molecules:
outputter.output(c)
for smiles in FLAGS.topology_query_smiles:
geometry_data = GeometryData.get_singleton()
for c in db.find_by_topology(
smiles, bond_lengths=geometry_data.bond_lengths):
outputter.output(c)
smarts_query(db, FLAGS.smarts, FLAGS.which_topologies, outputter)
if FLAGS.random_fraction:
for molecule in db:
if random.random() < FLAGS.random_fraction:
outputter.output(molecule)
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Shows how to check for missing fields."""
from smu import smu_sqlite
#-----------------------------------------------------------------------------
# Note that we are loading the *complete* database
#-----------------------------------------------------------------------------
db = smu_sqlite.SMUSQLite('20220128_complete_v2.sqlite')
#-----------------------------------------------------------------------------
# We'll grab a couple of molecules with different amount of information
# stored.
#-----------------------------------------------------------------------------
PARTIAL_MOLECULE_ID = 35004068
MINIMAL_MOLECULE_ID = 35553043
partial_molecule = db.find_by_molecule_id(PARTIAL_MOLECULE_ID)
minimal_molecule = db.find_by_molecule_id(MINIMAL_MOLECULE_ID)
print('When you process the *complete* database, you have to be careful to',
'check what data is available')
print('We will examine molecules', PARTIAL_MOLECULE_ID, 'and',
MINIMAL_MOLECULE_ID)
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""How to check for missing fields."""
from smu import smu_sqlite
# Note that we are loading the *complete* database
db = smu_sqlite.SMUSQLite('20220104_complete.sqlite', 'r')
# We'll grab a couple of conformers with different amount of information
# stored.
PARTIAL_CONFORMER_ID = 35004068
MINIMAL_CONFORMER_ID = 35553043
partial_conformer = db.find_by_conformer_id(PARTIAL_CONFORMER_ID)
minimal_conformer = db.find_by_conformer_id(MINIMAL_CONFORMER_ID)
print('When you process the *complete* database, you have to be careful to',
'check what data is available')
print('We will examine conformers', PARTIAL_CONFORMER_ID, 'and',
MINIMAL_CONFORMER_ID)
print(
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""generates a Pandas DataFrame of some field values."""
import pandas as pd
from smu import smu_sqlite
db = smu_sqlite.SMUSQLite('20220104_standard.sqlite', 'r')
count = 0
data_dict = {
'conformer_id': [],
'energy': [],
'h**o': [],
'lumo': [],
'first important frequency': [],
}
# This iteration will go through all conformers in the database.
for conformer in db:
data_dict['conformer_id'].append(conformer.conformer_id)
data_dict['energy'].append(
conformer.properties.single_point_energy_atomic_b5.value)
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Basic access to different kinds of fields."""
from smu import smu_sqlite
db = smu_sqlite.SMUSQLite('20220128_standard_v2.sqlite')
#-----------------------------------------------------------------------------
# This is an arbitrary choice of the molecule to use.
#-----------------------------------------------------------------------------
molecule = db.find_by_molecule_id(57001)
print('We will examine molecule with id', molecule.molecule_id)
print('The computed properties are generally in the .properties field')
print('Scalar values are access by name (note the .value suffix),',
'like this single point energy: ',
molecule.properties.single_point_energy_atomic_b5.value)
print('Fields with repeated values',
def test_find_by_topology(self):
db = smu_sqlite.SMUSQLite(self.db_filename, 'c')
# We'll make a pretty fake molecule. N2O2H2 with
# the O at 0,0
# the Ns at 1.1,0 and 0,1.1
# The Hs right night to the Ns
# We'll given it the ring topology to start and the symetric ring broken
# topologies should be found.
molecule = dataset_pb2.Molecule(molecule_id=9999)
molecule.properties.errors.fate = dataset_pb2.Properties.FATE_SUCCESS
bt = molecule.bond_topologies.add(smiles='N1NO1', bond_topology_id=100)
geom = molecule.optimized_geometry.atom_positions
bt.atoms.append(dataset_pb2.BondTopology.ATOM_O)
geom.append(dataset_pb2.Geometry.AtomPos(x=0, y=0, z=0))
bt.atoms.append(dataset_pb2.BondTopology.ATOM_N)
geom.append(dataset_pb2.Geometry.AtomPos(x=0, y=1.1, z=0))
bt.bonds.append(
dataset_pb2.BondTopology.Bond(
atom_a=0,
atom_b=1,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE))
bt.atoms.append(dataset_pb2.BondTopology.ATOM_N)
geom.append(dataset_pb2.Geometry.AtomPos(x=1.1, y=0, z=0))
bt.bonds.append(
dataset_pb2.BondTopology.Bond(
atom_a=0,
atom_b=2,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE))
bt.bonds.append(
dataset_pb2.BondTopology.Bond(
atom_a=1,
atom_b=2,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE))
bt.atoms.append(dataset_pb2.BondTopology.ATOM_H)
geom.append(dataset_pb2.Geometry.AtomPos(x=0, y=1.2, z=0))
bt.bonds.append(
dataset_pb2.BondTopology.Bond(
atom_a=1,
atom_b=3,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE))
bt.atoms.append(dataset_pb2.BondTopology.ATOM_H)
geom.append(dataset_pb2.Geometry.AtomPos(x=1.2, y=0, z=0))
bt.bonds.append(
dataset_pb2.BondTopology.Bond(
atom_a=2,
atom_b=4,
bond_type=dataset_pb2.BondTopology.BOND_SINGLE))
for pos in geom:
pos.x /= smu_utils_lib.BOHR_TO_ANGSTROMS
pos.y /= smu_utils_lib.BOHR_TO_ANGSTROMS
pos.z /= smu_utils_lib.BOHR_TO_ANGSTROMS
db.bulk_insert([molecule.SerializeToString()])
db.bulk_insert_smiles([['N1NO1', 100], ['N=[NH+][O-]', 101]])
bond_lengths = bond_length_distribution.make_fake_empiricals()
# We'll query by the topology that was in the DB then the one that wasn't
for query_smiles in ['N1NO1', 'N=[NH+][O-]']:
got = list(
db.find_by_topology(query_smiles, bond_lengths=bond_lengths))
self.assertLen(got, 1)
self.assertCountEqual(
[100, 101, 101],
[bt.bond_topology_id for bt in got[0].bond_topologies])