Dear Rdkit team, My name is Velik Velikov and I am currently doing my bachelor's degree in Bioinformatics.
My goal is to create a preference matrix from a set of molecules that indicates how often one fragment reaction type is bound to another fragment reaction type. Based on the preference values in the matrix, I want to build a new molecule (retrosynthetically). To do this, I use BRICS to obtain all fragments. I also tried using rdChemReaction and runReactants. I am facing many problems in my implementation and after a week of reading many threads in the forum, I decided to ask for help. So far this topic has helped me a lot https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/CAD4fdRSJc2F8NaPo1FBe%3DFoBaezjn2Nc5S26UnObazmK%3De0EpQ%40mail.gmail.com/#msg36610194 I tried to go from there and one of the problems I ran into here is that when I get the fragments from rxn.RunReactants there is no information about which reaction side was used. And some extra issues that didn't match with my goal either. So I am back to my initial idea. For example, after I gett all the fragments from BRICSDecompose for the molecule Sorafenib ['[1*]C([1*])=O', '[1*]C([6*])=O', '[14*]c1cc([16*])ccn1', '[16*]c1ccc(Cl)c([16*])c1', '[16*]c1ccc([16*])cc1', '[3*]O[3*]', '[5*]NC', '[5*]N[5*]', '[8*]C(F)(F)F'] One can see every reaction type in every fragment. Let's say the first fragment has reaction type 1 ('[1*]) twice. I would now like to know for all the reaction types found, to which reaction type (in the other fragment) there was a bond in the input molecule. Then I would update the preference value for the two found reaction types in the matrix. And so on for all 16 reaction types. I couldn't continue because I couldn't figure out how to identify which fragment was connected to which fragment and on which reaction side. Would you please give me any tipps on how can I do that? Thanks in advance. Best regards, Velik Velikov
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
