I'm trying to generate CGR and in order to do so I want to use the Marvin Sketch auto mapper function on a bunch of reactions, stored as reaction smarts. But in order to use the auto mapper function from Marvin sketch I have to pass the reactions as rxn files or as a RDF file.
Pipeline Pilot (www.3dsbiovia.com) can do this. Probably, knime, a non-commercial alternative to Pipeline Pilot, is able to do this too.
You can use lillymol.
https://github.com/EliLillyCo/LillyMol/wiki
There are some others too.
1. RDkit: https://www.rdkit.org/
A short tutorial with the title of "Chemical Reactions" can be accessed from here;
https://www.rdkit.org/docs/GettingStartedInPython.html
2. Reactor
https://chemaxon.com/products/reactor
A comprehensive guide onChemAxon Reactor tool.
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