def test_remove_atom_mapping():
mol = Molecule(smiles="C[C:5]CCO")
assert mol.has_atom_mapping()
mol.remove_atom_mapping()
assert not mol.has_atom_mapping()
def reactants_to_fingerprint(args, config):
"""
Convert a SMILES string of reactants to a fingerprint
:param args: the SMILES in the first element
:type args: tuple
:param config: the settings
:type config: Config
:return: the fingerprint
:rtype: numpy.ndarray
"""
reactants_smiles = args[0]
fingerprints = []
for smiles in reactants_smiles.split("."):
try:
mol = Molecule(smiles=smiles, sanitize=True)
except MoleculeException:
pass
else:
if mol.has_atom_mapping():
fingerprints.append(
mol.fingerprint(
config["fingerprint_radius"], config["fingerprint_len"]
)
)
return sum(fingerprints)
def create_reactants_molecules(reactants_str: str) -> List[Molecule]:
"""
Create Molecule objects from a SMILE string of reactants.
Only molecules with atom mapping is kept.
:param reactants_str: the SMILES string of the reactants
:return: the Molecule objects
"""
mols = []
for smiles in reactants_str.split("."):
try:
mol = Molecule(smiles=smiles, sanitize=True)
except MoleculeException:
pass
else:
if mol.has_atom_mapping():
mols.append(mol)
return mols
def test_has_atom_mapping():
mol1 = Molecule(smiles="CCCCO")
mol2 = Molecule(smiles="C[C:5]CCO")
assert not mol1.has_atom_mapping()
assert mol2.has_atom_mapping()