Re: [Rdkit-discuss] SMART reaction for closing rings

2020-06-10 Thread Shani Levi
Thank you so much! It helps me a lot On Tue, Jun 9, 2020 at 6:24 PM Greg Landrum wrote: > Hi Shani, > > If you have mapped atoms in the reactants that are not in the products, > those end up being removed > > I'm not sure exactly what reaction you're trying to do, but I think you > want

Re: [Rdkit-discuss] SMART reaction for closing rings

2020-06-09 Thread Greg Landrum
Hi Shani, If you have mapped atoms in the reactants that are not in the products, those end up being removed I'm not sure exactly what reaction you're trying to do, but I think you want something like this; rxn = AllChem.ReactionFromSmarts("([C:1]=[C:2].[*:3][*+:4])>>[*:2]-[*:1][*+0:4][*:3]")

[Rdkit-discuss] SMART reaction for closing rings

2020-06-09 Thread Shani Levi
Hello, I'm interested in using AllChem.ReactionFromSmarts to predict product for a specific reaction. For example, I want to describe the reaction between double bonds and a carbo-cations. *I tried: * rxn = AllChem.ReactionFromSmarts("([C:1]=[C:2].[*:3][*+:4])>>[*:1][*:4]") m1 =