Hi, I'm trying to obtain the reaction center from a RxnMolecule. I have no problem with the molecule creation but i really don`t know how to extract the reaction center in terms of atoms and bonds and further create a SMIRKS or reaction to implement in Reactor.
Hope someone could help me.
Could you describe your workflow? Why do you need to obtain the reaction center? The reaction scheme - required by Reactor - can be created manually. Reactor product also contains a reaction library.
There's no public ChemAxon Java API that can extract the reaction center. We have the implementation, but it's not public.
the thing is that I reacently download a Biochemical reaction database (BRENDA) , and I'm realy intresting in study the reaction mechanism involved in these reaction. I would like to compare and group all the reactions in terms of reaction mechanism. I'd like to do a reclasification of biochemical reactions, based on specifics reaction mechanism. If you can provide me the implementation it would be perfect.
I suggest you to perform reaction similarity search using different reaction fingerprint metrics. Please let us know if it suits your needs.