Hi again,
Apologies -- I just realised that the problem was my understanding of the
chemistry rather than RDK.
James
On Fri, Jun 29, 2018 at 4:25 PM, James Skelton <
[email protected]> wrote:
> Hi,
>
> I have a quick question about how hydrogens / charges work in reactions. I've
> been trying to define a reaction, as follows:
>
> keto_glutaramate = Chem.MolFromSmiles('NC(=O)CCC(=O)C(=O)[O-]')
> rxn = AllChem.ReactionFromSmarts('[#6:1]=[#8]>>[H][#6:1]-[#7+]')
> products = rxn.RunReactants([keto_glutaramate])
>
> The ideal product I'd like to get is [N+]C(CCC(N)=O)C(=O)[O-], but I can
> only seem to get products with [NH3+], no matter how I modify the reaction
> expression. I apologise if I'm just missing something simple / trivial, but
> I can't figure it out.
>
> Thanks in advance for any insight you can offer.
>
> James
>
> - RDKit Version: 2016.03.3
> - Platform: MacOS
>
>
>
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