def to_smiles(
mol: Chem.rdchem.Mol,
canonical: bool = True,
isomeric: bool = True,
ordered: bool = False,
explicit_bonds: bool = False,
explicit_hs: bool = False,
randomize: bool = False,
cxsmiles: bool = False,
allow_to_fail: bool = False,
) -> Optional[str]:
"""Convert a mol to a SMILES.
Args:
mol: a molecule.
canonical: if false no attempt will be made to canonicalize the molecule.
isomeric: whether to include information about stereochemistry in the SMILES.
ordered: whether to force reordering of the atoms first.
explicit_bonds: if true, all bond orders will be explicitly indicated in the output SMILES.
explicit_hs: if true, all H counts will be explicitly indicated in the output SMILES.
randomize: whether to randomize the generated smiles. Override `canonical`.
cxsmiles: Whether to return a CXSMILES instead of a SMILES.
allow_to_fail: Raise an error if the conversion to SMILES fails. Return None otherwise.
"""
if ordered and canonical is False:
mol = dm.reorder_atoms(mol)
if randomize:
mol = dm.randomize_atoms(mol)
canonical = False
smiles = None
try:
if cxsmiles:
smiles = Chem.MolToCXSmiles( # type: ignore
mol,
isomericSmiles=isomeric,
canonical=canonical,
allBondsExplicit=explicit_bonds,
allHsExplicit=explicit_hs,
)
else:
smiles = Chem.MolToSmiles( # type: ignore
mol,
isomericSmiles=isomeric,
canonical=canonical,
allBondsExplicit=explicit_bonds,
allHsExplicit=explicit_hs,
)
except Exception as e:
if allow_to_fail:
raise e
return None
return smiles
def test_randomize_atoms():
smiles = "c1ccc(C(=O)O)c(c1)OC(=O)C"
mol = dm.to_mol(smiles)
orders = [a.GetAtomicNum() for a in mol.GetAtoms()]
randomized_mol = dm.randomize_atoms(mol)
randomized_orders = [a.GetAtomicNum() for a in randomized_mol.GetAtoms()]
assert sum(orders) == sum(randomized_orders)
def test_randomize_atoms_without_atoms():
mol1 = dm.to_mol("")
mol2 = dm.randomize_atoms(mol1)
assert dm.to_smiles(mol1) == dm.to_smiles(mol2)