Hi, The easiest thing would probably be to start with an empty ChemicalReaction object and then add the reactant and product with AddReactantTemplate and AddProductTemplate. Unfortunately it looks like there is a bug in the reaction drawing code and aromaticity perception is re-done even if it doesn't need to be, so you will end up with the aromatic reactants and products no matter what at the moment. This is something we will try to get fixed.
Best, -greg On Fri, Feb 28, 2020 at 10:19 AM Jose Manuel Gally < jose.manuel.ga...@gmail.com> wrote: > Dear RDKitters, > > I would like to represent what Murcko Scaffolds are extracted from what > molecules. > > I had the idea to look into the rdChemReactions module because it shows > a nice arrow between reactants and products. > > In my case, I have only 1 reactant and 1 product to display. I played a > bit around: > > https://gist.github.com/jose-manuel/8ef38eadbefbfc30e23f166c9e751aba > > I would like to display the kekulized molecules instead of the aromatic > form. However, I could not figure out a way to do this using the > rdChemReactions module. > > Am I missing something obvious? Does someone have another idea how to > achieve this? > > Cheers, > Jose Manuel > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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