peppr.sanitize

peppr.sanitize(mol: Mol, max_fix_iterations: int = 1000) → None

Fix small issues with RDKit SanitizeMol and sanitize molecule.

This is an alternative to using SanitizeMol() directly, in cases it fails due to issues with the molecule which are fixed by this function.

Parameters:

molChem.rdchem.Mol

The molecule to sanitize.

max_fix_iterationsint, optional

The maximum number of iterations to fix problems.

Notes

Deals with cases:

• AtomValenceException: add charge if total valence is exceeding default (for N, O atoms only)

• KekulizeException: for ring N atoms with unspecified protonation