def test_fully_saturated(self):
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('C', '', '4')), '(ch4)')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('N', '', '3')), '(nh3)')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('O', '', '2')), '(oh2)')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
smu_utils_lib.create_bond_topology('F', '', '1')), '(fh)')
def topology_query(db, smiles):
"""Find all conformers which have a detected bond topology.
Note that this *redoes* the detection. If you want to use the default detected
versions, you can just query by SMILES string. This is only useful if you
adjust the distance thresholds for what a matching bond is.
Args:
db: smu_sqlite.SMUSQLite
smiles: smiles string for the target bond topology
Yields:
dataset_pb2.Conformer
"""
mol = Chem.MolFromSmiles(smiles, sanitize=False)
Chem.SanitizeMol(mol, Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS)
mol = Chem.AddHs(mol)
query_bt = utilities.molecule_to_bond_topology(mol)
expanded_stoich = smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
query_bt)
matching_parameters = _get_geometry_matching_parameters()
geometry_data = GeometryData.get_singleton()
cnt_matched_conformer = 0
cnt_conformer = 0
logging.info('Starting query for %s with stoich %s', smiles, expanded_stoich)
for conformer in db.find_by_expanded_stoichiometry(expanded_stoich):
if not smu_utils_lib.conformer_eligible_for_topology_detection(conformer):
continue
cnt_conformer += 1
matches = topology_from_geom.bond_topologies_from_geom(
bond_lengths=geometry_data.bond_lengths,
conformer_id=conformer.conformer_id,
fate=conformer.fate,
bond_topology=conformer.bond_topologies[0],
geometry=conformer.optimized_geometry,
matching_parameters=matching_parameters)
if smiles in [bt.smiles for bt in matches.bond_topology]:
cnt_matched_conformer += 1
del conformer.bond_topologies[:]
conformer.bond_topologies.extend(matches.bond_topology)
for bt in conformer.bond_topologies:
try:
bt.bond_topology_id = geometry_data.smiles_id_dict[bt.smiles]
except KeyError:
logging.error('Did not find bond topology id for smiles %s',
bt.smiles)
yield conformer
logging.info('Topology query for %s matched %d / %d', smiles,
cnt_matched_conformer, cnt_conformer)
def test_ethylene(self):
bt = smu_utils_lib.create_bond_topology('CC', '2', '22')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt), '(ch2)2')
def test_cyclobutane(self):
bt = smu_utils_lib.create_bond_topology('CCCC', '110011', '2222')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt), '(ch2)4')
def test_nplus_oneg(self):
bt = smu_utils_lib.create_bond_topology('NO', '1', '30')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt),
'(nh3)(o)')
def test_fluorine(self):
bt = smu_utils_lib.create_bond_topology('OFF', '110', '000')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt), '(o)(f)2')
def test_acrylic_acid(self):
bt = smu_utils_lib.create_bond_topology('CCCOO', '2000100210', '21001')
self.assertEqual(
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(bt),
'(c)(ch)(ch2)(o)(oh)')
def bulk_insert(self, encoded_conformers, batch_size=10000, limit=None):
"""Inserts conformers into the database.
Args:
encoded_conformers: iterable for encoded dataset_pb2.Conformer
batch_size: insert performance is greatly improved by putting multiple
insert into one transaction. 10k was a reasonable default from some
early exploration.
limit: maximum number of records to insert
Raises:
ReadOnlyError: if mode is 'r'
ValueError: If encoded_conformers is empty.
"""
if self._read_only:
raise ReadOnlyError()
if not encoded_conformers:
raise ValueError()
insert_conformer = (f'INSERT INTO {_CONFORMER_TABLE_NAME} '
'VALUES (?, ?, ?)')
insert_btid = f'INSERT INTO {_BTID_TABLE_NAME} VALUES (?, ?)'
insert_smiles = (f'INSERT INTO {_SMILES_TABLE_NAME} VALUES (?, ?) '
f'ON CONFLICT(smiles) DO NOTHING')
cur = self._conn.cursor()
start_time = datetime.datetime.now()
pending_conformer_args = []
pending_btid_args = []
pending_smiles_args = []
def commit_pending():
cur.executemany(insert_conformer, pending_conformer_args)
cur.executemany(insert_btid, pending_btid_args)
cur.executemany(insert_smiles, pending_smiles_args)
pending_conformer_args.clear()
pending_btid_args.clear()
pending_smiles_args.clear()
self._conn.commit()
idx = None
for idx, encoded_conformer in enumerate(encoded_conformers, 1):
conformer = dataset_pb2.Conformer.FromString(encoded_conformer)
# A small efficiency hack: the expanded stoich is only intended for use
# with topology_detection, so we only put a real value for those so that
# we dont' even have to return the entries we don't want.
if smu_utils_lib.conformer_eligible_for_topology_detection(conformer):
expanded_stoich = (
smu_utils_lib.get_canonical_stoichiometry_with_hydrogens(
conformer.bond_topologies[0]))
else:
expanded_stoich = ''
pending_conformer_args.append((conformer.conformer_id, expanded_stoich,
snappy.compress(encoded_conformer)))
for bond_topology in conformer.bond_topologies:
pending_btid_args.append(
(bond_topology.bond_topology_id, conformer.conformer_id))
pending_smiles_args.append(
(bond_topology.smiles, bond_topology.bond_topology_id))
if batch_size and idx % batch_size == 0:
commit_pending()
elapsed = datetime.datetime.now() - start_time
logging.info(
'bulk_insert: committed at index %d, %f s total, %.6f s/record',
idx, elapsed.total_seconds(),
elapsed.total_seconds() / idx)
if limit and idx >= limit:
break
# Commit a final time
commit_pending()
elapsed = datetime.datetime.now() - start_time
logging.info('bulk_insert: Total records %d, %f s, %.6f s/record', idx,
elapsed.total_seconds(),
elapsed.total_seconds() / idx)
