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

Attachment: NotSanitizing.ipynb
Description: Binary data

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