polymerist.rdutils.sanitization

For automating RDKit molecule sanitization and chemical property cleanup

Attributes

P

Functions

sanitize_mol(→ None)	Apply chemical sanitization operations, including bond aromaticity
sanitizable_mol_outputs(...)	Decorator which injects molecule sanitization capability into a function which returns RDKit Mols
explicit_mol_from_SMILES(→ rdkit.Chem.Mol)	Convenience method for creating a chemically-explicit AND chemically-validated RDKit Mol from a SMILES string

Module Contents

polymerist.rdutils.sanitization.P

polymerist.rdutils.sanitization.sanitize_mol(mol: rdkit.Chem.Mol, sanitize_ops: None | int | rdkit.Chem.rdmolops.SanitizeFlags = SANITIZE_NONE, aromaticity_model: rdkit.Chem.rdmolops.AromaticityModel | None = None) → None

Apply chemical sanitization operations, including bond aromaticity By default, performs NO sanitization; all sanitization operations must be explicitly specified!

polymerist.rdutils.sanitization.sanitizable_mol_outputs(mol_func: Callable[P, rdkit.Chem.Mol | Iterable[rdkit.Chem.Mol]]) → Callable[Concatenate[None | int | rdkit.Chem.rdmolops.SanitizeFlags, rdkit.Chem.rdmolops.AromaticityModel | None, P], rdkit.Chem.Mol | tuple[rdkit.Chem.Mol, Ellipsis]]

Decorator which injects molecule sanitization capability into a function which returns RDKit Mols By default, performs NO sanitization; all sanitization operations must be explicitly specified!

Acts on functions which are assumed to return a single mol object, or an iterable containing Mols Decorated function will return a single mol in the former case, or a tuple of mols in the latter

polymerist.rdutils.sanitization.explicit_mol_from_SMILES(smiles: polymerist.smileslib.cleanup.Smiles, assign_map_nums: bool = False, sanitize_ops: None | int | rdkit.Chem.rdmolops.SanitizeFlags = SANITIZE_ALL, aromaticity_model: rdkit.Chem.rdmolops.AromaticityModel | None = AROMATICITY_MDL) → rdkit.Chem.Mol

Convenience method for creating a chemically-explicit AND chemically-validated RDKit Mol from a SMILES string