luna.mol.validator module

class MolValidator(charge_model=<luna.mol.charge_model.OpenEyeModel object>, fix_nitro=True, fix_amidine_and_guanidine=True, fix_valence=True, fix_charges=True)[source]

Bases: object

Validate and fix molecules with the errors most commonly found when parsing PDB files with Open Babel.

Parameters

  • charge_model (ChargeModel) – A charge model object. By default, the implementation of OpenEye charge model is used.

  • fix_nitro (bool) – If True, fix nitro groups whose nitrogens are perceived as having a valence of 5 and that are double-bonded to the oxygens. SMILES representation of the error: ‘[$([NX3v5]([!#8])(=O)=O)]’.

  • fix_amidine_and_guanidine (bool) – If True, fix amidine and guanidine-like groups. When the molecule is ionized, it may happen that the charge is incorrectly assigned to the central carbon, which ends up with a +1 charge and the nitrogen double-bonded to it ends up with a +0 charge.

  • fix_valence (bool) – If True, fix the valence of atoms. Currently, we only detect and fix errors of quaternary ammonium nitrogens. These charged atoms are sometimes perceived as having a valence equal to 5 and no charge, i.e., Open Babel considers those nitrogens as hypervalent.

  • fix_charges (bool) – If True, fix charges on basis of the charge model charge_model.

validate_mol(mol_obj)[source]

Validate molecule mol_obj.

It will first try to fix the provided molecule according to the initialization flags. If any errors are detected and if it fails to fix them, then this function may return False, i.e., the molecule is invalid.

Parameters

mol_obj (MolWrapper, rdkit.Chem.rdchem.Mol, or openbabel.pybel.Molecule) – The molecule.

Returns

is_valid – If the molecule is valid or not.

Return type

bool

class RDKitValidator(sanitize_opts=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL)[source]

Bases: object

Check if RDKit molecular objects are valid or not.

Parameters

sanitize_opts (rdkit.Chem.rdchem.SanitizeFlags) – Sanitization operations to be carried out.

is_valid(rdk_mol)[source]

Try to sanitize the molecule rdk_mol. If it succeeds, returns True. Otherwise, returns False.

Parameters

rdk_mol (rdkit.Chem.rdchem.Mol)

Returns

is_valid – If the molecule is valid or not.

Return type

bool