On Fri, Mar 14, 2014 at 3:27 PM, Toby Wright <toby.wri...@inhibox.com>wrote:
> Hi,
>
> Looking over the documentation and discussion threads I've found solid and
> sensible answers for how chiral molecules and reactions in almost every
> case, but I've hit what seems to be an issue in a situation I can't find
> discussed.
> I have atoms in my product that are untagged and do not appear in my
> reactants. This is because I'm shortcutting a number of steps in what is
> happening in the real chemistry where these extra atoms are added. And
> RDKit behaves exactly as I would hope in general when I do this, adding
> these new atoms to the product without taking them from any reactant. But
> where these new atoms have chiral information it is being lost, as shown by
> the following example:
>
> > rxn =
> AllChem.ReactionFromSmarts("[F:1][C:2]([C:3])[I:4]>>[F:1][C:2]([C:3][C@H
> ]([OH])Br)[Cl:4]")
> > m = Chem.MolFromSmiles('FC(C)I')
> > p = rxn.RunReactants((m,))[0][0]
> > Chem.SanitizeMol(p)
> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
> > Chem.MolToSmiles(p,isomericSmiles=True)
> 'OC(Br)CC(F)Cl'
>
> The output I was hoping for was O[C@@H](CC(F)Cl)Br but the chiral
> information in the unmapped atoms in the product part of the reaction
> specification appears to have been lost. Is this a bug or am I going about
> my reaction in the wrong way?
>
It looks like a bug to me. I will look into it.
-greg
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