schrodinger.rdkit.rdkit_nonstrict module

Parse R-group SMILES strings which use [Ar] as an R-group placeholder.

BLDMGR-8895 includes an RDKit patch that enables the isoelectronic valence model. A side effect of this new model for valences is that Ar is no longer allowed to form covalent bonds (unless charged).

This is a problem because AD uses Ar as a placeholder for R-groups in SMILES strings.

This file provides a temporary fix for this issue by using a SMILES parser and a sanitization function that do not enforce strict valences, allowing covalent bonds to Ar atoms.

schrodinger.rdkit.rdkit_nonstrict.sanitize_nonstrict(mol: rdkit.Chem.rdchem.Mol) → Optional[rdkit.Chem.rdchem.Mol]

Sanitize a molecule without strict valences.

schrodinger.rdkit.rdkit_nonstrict.parse_smiles_nonstrict(smi: str) → Optional[rdkit.Chem.rdchem.Mol]

Parse a SMILES string without strict valences.