RDKit One component reaction with rxn reaction


I am using the RDKit One component Reaction to generate a library of compounds obtained by virtual amide coupling. Reactions provided in rxn format were generated with ChemDraw. Note that this is the only available option.

However, in all the cases, I get the error “A product molecule could not be sanitized successfully”. In fact, the attached group appears bound to the rest of the molecule by a straight long line.

I have tried to map the reaction atoms and /or indexing all of them, but it works neither.

Could you please help me?

Hello @marpin ,
Welcome to the community. Honestly I don’t think I can help as this is more into cheminformatics.

But you may be can see some example workflows related to RDKit.

Also, you can post the same question in

So that relevant people can help you.

Welcome to the forum @marpin.

Can you upload your workflow and data files here or on the KNIME Hub so that we can have a look?