Hello, I think the error is in the placement of the $ in the SMARTS query, I am not sure what is the purpose in there. if i run
reaction_smarts = '[cX3]1[cX3][cX3][cX3]([NX3H2:1])[cX3]([NX3H2:2])[cX3]1>>[cX3]1[cX3][cX3][cX3][cX3]2[nX3:1]=[nX3]-[nX3H:2][cX3]12' rxn = AllChem.ReactionFromSmarts(reaction_smarts) product = rxn.RunReactants((reactant,)) Chem.SanitizeMol(product[0][0]) print(Chem.MolToSmiles(product[0][0])) i get c1ccc2[nH]nnc2c1 an alternative, somewhat shorter way to write this formation of a benzotriazole would be: reaction_smarts = 'c1ccc([NX3H2:1])c([NX3H2:2])[cX3]1>>c1cccc2[*:1]-[n]=[*:2]c12' best wishes wim On Wed, Nov 23, 2022 at 3:36 PM Alfredo Quevedo <maquevedo....@gmail.com> wrote: > Dear users, > > I have been struggling for days trying to model a specific reaction but > cannot succeed in matching the corresponding SMARTS notation, I am > reproducing my code below, > > My molecule is: > > *reactant = 'c1ccc(N)c(N)c1'* > > I am trying to prepare a second ring by reacting the two primary amines. > The final molecule should be: > > *product = 'c1cccc2nn[nH]c12'* > > In this way, I am setting the SMARTS reaction pattern as: > > *reaction_smarts = > '[cX3]1[cX3][cX3][cX3]($[NX3H2:1])[cX3]($[NX3H2:2])[cX3]1>>[cX3]1[cX3][cX3][cX3][cX3]2$[nX3:1]=[nX3]-[nX3H:2]$[cX3]12'* > > And after running the reaction, > > *rxn = AllChem.ReactionFromSmarts(reaction_smarts)* > > *product = rxn.RunReactants((reactant,))* > > I am not getting no product at all, > > Any hint on what may be my problem would be greatly appreciated, > > Thank you very much in advance for the help, > > regards > > Alfredo > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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