Apologies for the double message. I just realized the SMARTS has bad mappings and therefore would fail when there are any substituents on the benzene ring. Here's a working SMARTS: reaction_smarts = "[c:0]1[c:1][c:2][c:3]([NX3H2:4])[c:5]([NX3H2:6])[c:7]1>>[c:0]1[c:1][c:2][c:3][c:5]2[*:4]-[n]=[*:6][c:7]12"
On Wed, Nov 23, 2022 at 4:02 PM Wim Dehaen <wimdeh...@gmail.com> wrote: > 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 >> >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
