Hi Matt,
On Wed, Feb 12, 2014 at 4:41 PM, Matthew Swain <[email protected]> wrote:
>
> If any atoms specified in a reaction happen to form a ring, RDKit will
> break it open:
>
> >>> rxn =
> AllChem.ReactionFromSmarts('[C:1][C:2][O:3][C:4][C:5]>>[C:1][C:2][C:3][C:4][C:5]')
> >>> mol = Chem.MolFromSmiles('C1CCOC1')
> >>> prod = rxn.RunReactants((mol,))[0][0]
> >>> Chem.MolToSmiles(prod)
> 'CCCCC'
>
> Is this a bug, or "expected behaviour"?
>
>
I'm going to have to look at the code, but this looks like a bug to me. I
will investigate and try to get it cleared up in the next few days.
-greg
> It is possible to avoid this by specifying the ring manually in the
> reactants and the products:
>
> >>> rxn =
> AllChem.ReactionFromSmarts('[C:1]1[C:2][O:3][C:4][C:5]1>>[C:1]1[C:2][C:3][C:4][C:5]1')
>
> But then this won't work if there is no ring, i.e. for CCOCC.
>
> Is it possible to ensure that ring bonds are not broken if they are not
> explicitly referenced in the reactants SMARTS?
>
>
> Matt
>
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