Some NPs cannot be sanitised
COCONUT DB is the largest open collection of natural products, developed by Sorokina et al.
In this notebook I will show the first steps of working with COCONUT DB using RDKit.
I encountered some issues, so maybe this post might be helpful for others in the future.
(Overall, this was also a lesson when working with Suppliers to use a ‘context manager’ in the future, as discussed here.)
To start, I downloaded the Canonical SMILES .smi file from the COCONUT website (Jan 2022 version).
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