Dear all, I am trying to read in SMILES to generate mol objects which I then break into fragments using rwmol.RemoveBond(). Thereafter I want to sanitize the fragments by saturating with hydrogen. However, I am finding that rdkit often doesn't sanitize the fragments consistently, leaving trivalent carbon atoms. I've attached a jupyter notebook of an example. Could anyone help me consistently generate sanitized fragments?
Best regards -- *Puck van Gerwen* Doktorandin / PhD candidate Departement Chemie Klingelbergstrasse 80 CH-4056 Basel https://chemspacelab.org/
NotSanitizing.ipynb
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