Working with COCONUT DB using RDKit

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).