Dear Puck,
Sure; I'll get back to you later today.
Cheers,
p.
On 12/02/2020 10:03, Puck van Gerwen wrote:
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/
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