Thank you so much! It helps me a lot
On Tue, Jun 9, 2020 at 6:24 PM Greg Landrum <greg.land...@gmail.com> 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 something like this;
>
> rxn =
> AllChem.ReactionFromSmarts("([C:1]=[C:2].[*:3][*+:4])>>[*:2]-[*:1][*+0:4][*:3]")
> m1 = Chem.MolFromSmiles('C=CC([CH2+])CCC=C(C)C')
> ps = rxn.RunReactants((m1,))
> for p in ps: print(Chem.MolToSmiles(p[0]))
>
> Note that I also explicitly neutralized the carbocation in the products.
> Otherwise the +1 from the reactants would be carried over.
>
> -greg
>
>
> On Tue, Jun 9, 2020 at 4:42 PM Shani Levi <levishan...@gmail.com> wrote:
>
>> 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 = Chem.MolFromSmiles('C=CC([CH2+])CCC=C(C)C')
>> ps = rxn.RunReactants((m1,))
>>
>> *and it gave me four molecules: *
>>
>> [CH2+]C [CH2+]C [CH2+]CCC
>> [CH2+]C(C)C
>>
>> the problem here that it does not describe the ring-closure molecules and
>> it somehow cuts the rest of the molecule, if someone has any suggestions of
>> how to change the SMARTS descriptions that it will define the right
>> reaction.
>>
>> Thank you very much,
>> Shani
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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