Dear Wim,
thank you very much for your prompt response. This was quite helpful!
the '$' string was the problem as you pointed out. My mapping was also
wrong, so I was not hitting substituents on the benzyl scaffold.
Best regards
Alfredo
On 23/11/22 12:15, Wim Dehaen wrote:
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
--
*Dr. Alfredo Quevedo,*
Faculty of Chemical Sciences,
National University of Córdoba,
Argentina.
TE: +54 351 5353850 int 55437
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
