def _test_get_all(
database: stk.ConstructedMoleculeDatabase,
expected_molecules: dict[str, stk.ConstructedMolecule],
) -> None:
"""
Test iteration over all entries.
Parameters:
database: A database to test.
expected_molecules: The expected molecules to get from the
databases using their smiles as the key.
"""
smiles = stk.Smiles()
for i, retrieved in enumerate(database.get_all()):
expected = expected_molecules[smiles.get_key(retrieved)]
is_equivalent_constructed_molecule(
constructed_molecule1=(expected.with_canonical_atom_ordering()),
constructed_molecule2=(retrieved.with_canonical_atom_ordering()),
)
assert i + 1 == len(expected_molecules)
def _test_database(database, molecule, key):
"""
Test a molecule or constructed molecule database.
Parameters
----------
database : :class:`.MoleculeCache`
The database to test.
molecule : :class:`.Molecule`
The molecule to put and get from the `database`.
key : :class:`object`
The key used to retrieve `molecule` from the database.
Returns
-------
None : :class:`NoneType`
"""
database.put(molecule)
retrieved = database.get(key)
is_equivalent_constructed_molecule(
molecule.with_canonical_atom_ordering(),
retrieved.with_canonical_atom_ordering(),
)
def test_get_all():
"""
Test iteration over all molecules.
"""
database_name = '_test_get_entries_constructed_molecule'
client = pymongo.MongoClient()
client.drop_database(database_name)
key_maker = stk.Inchi()
jsonizer = stk.ConstructedMoleculeJsonizer(key_makers=(key_maker, ))
database = stk.ConstructedMoleculeMongoDb(
mongo_client=client,
database=database_name,
jsonizer=jsonizer,
put_lru_cache_size=0,
get_lru_cache_size=0,
)
molecules = [
stk.ConstructedMolecule(topology_graph=stk.polymer.Linear(
building_blocks=(stk.BuildingBlock(
smiles='BrCCCBr', functional_groups=[stk.BromoFactory()]), ),
repeating_unit='A',
num_repeating_units=3,
), ),
stk.ConstructedMolecule(topology_graph=stk.polymer.Linear(
building_blocks=(
stk.BuildingBlock(smiles='BrCCBr',
functional_groups=[stk.BromoFactory()]),
stk.BuildingBlock(smiles='BrCNCBr',
functional_groups=[stk.BromoFactory()]),
),
repeating_unit='AB',
num_repeating_units=2,
), ),
]
molecules_by_key = {
key_maker.get_key(molecule): molecule
for molecule in molecules
}
for molecule in molecules:
database.put(molecule)
for i, retrieved in enumerate(database.get_all()):
key = key_maker.get_key(retrieved)
molecule = molecules_by_key[key]
is_equivalent_constructed_molecule(
molecule.with_canonical_atom_ordering(),
retrieved.with_canonical_atom_ordering(),
)
# Check number of molecules.
assert i + 1 == len(molecules)
def is_clone_constructed_molecule(
constructed_molecule1,
constructed_molecule2,
):
assert constructed_molecule1 is not constructed_molecule2
is_equivalent_constructed_molecule(
constructed_molecule1=constructed_molecule1,
constructed_molecule2=constructed_molecule2,
)