diff --git a/src/rxn/chemutils/conversion.py b/src/rxn/chemutils/conversion.py index 154f2b5..7d4e5c0 100644 --- a/src/rxn/chemutils/conversion.py +++ b/src/rxn/chemutils/conversion.py @@ -21,7 +21,7 @@ from .exceptions import InvalidInchi, InvalidMdl, InvalidSmiles, SanitizationError -RDLogger.logger().setLevel(RDLogger.CRITICAL) +RDLogger.logger().setLevel(RDLogger.CRITICAL) # type: ignore[no-untyped-call] def smiles_to_mol( @@ -57,7 +57,7 @@ def smiles_to_mol( # function, either with no sanitization, or with radical finding. if not sanitize: if find_radicals: - sanitizations = [Chem.SANITIZE_FINDRADICALS] + sanitizations: List[SanitizeFlags | int] = [Chem.SANITIZE_FINDRADICALS] else: sanitizations = [Chem.SANITIZE_NONE] @@ -84,7 +84,7 @@ def inchi_to_mol(inchi: str, sanitize: bool = True, removeHs: bool = True) -> Mo Returns: Mol instance. """ - mol = MolFromInchi(inchi, sanitize=sanitize, removeHs=removeHs) + mol: Mol = MolFromInchi(inchi, sanitize=sanitize, removeHs=removeHs) # type: ignore[no-untyped-call] if not inchi or mol is None: raise InvalidInchi(inchi) @@ -97,7 +97,7 @@ def mol_to_smiles(mol: Mol, canonical: bool = True, isomericSmiles: bool = True) Mainly a wrapper around MolToSmiles. """ - return MolToSmiles(mol, canonical=canonical, isomericSmiles=isomericSmiles) # type: ignore + return MolToSmiles(mol, canonical=canonical, isomericSmiles=isomericSmiles) def mdl_to_mol(mdl: str, sanitize: bool = True) -> Mol: @@ -130,7 +130,7 @@ def mol_to_mdl(mol: Mol) -> str: Mainly a wrapper around MolToMolBlock. """ - return MolToMolBlock(mol) # type: ignore + return MolToMolBlock(mol) def sanitize_mol( @@ -239,7 +239,7 @@ def canonicalize_smiles(smiles: str, check_valence: bool = True) -> str: # Sanitization as a separate step, to enable exclusion of valence check try: - excluded_sanitizations = [] + excluded_sanitizations: List[SanitizeFlags | int] = [] if not check_valence: excluded_sanitizations.append(Chem.SANITIZE_PROPERTIES) sanitize_mol(mol, exclude_sanitizations=excluded_sanitizations) diff --git a/src/rxn/chemutils/miscellaneous.py b/src/rxn/chemutils/miscellaneous.py index a86f751..235c840 100644 --- a/src/rxn/chemutils/miscellaneous.py +++ b/src/rxn/chemutils/miscellaneous.py @@ -84,7 +84,7 @@ def atom_type_counter(smiles: str) -> typing.Counter[str]: """ mol: Mol = AddHs(smiles_to_mol(smiles, sanitize=False)) - atoms: List[Atom] = mol.GetAtoms() + atoms: List[Atom] = mol.GetAtoms() # type: ignore[call-arg,no-untyped-call] return Counter(atom.GetSymbol() for atom in atoms) @@ -327,7 +327,7 @@ def mol_has_atom_mapping(mol: Mol) -> bool: mol: RDKit Mol. """ atom: Atom - for atom in mol.GetAtoms(): + for atom in mol.GetAtoms(): # type: ignore[call-arg,no-untyped-call] if atom.GetAtomMapNum() != 0: return True return False