Hi Sabrina,
On Tue, May 14, 2013 at 5:58 PM, Syeda Sabrina <[email protected]> wrote:
> Hi Greg,
>
> I think the new version of rdkit now preserves the chirality of input
> molecule, if there is no chirality in the reaction. I was wondering does it
> work on tetrehedral chirality only? Or it works on the cis/trans chirality
> as well? For example for the following case I did not find it working as
> desired.
>
> >>rxn =
> AllChem.ReactionFromSmarts('[CX4:4][CH1:3]=[CH1:2][CX4:5].[Br:1]>>[C:5][C:2]=[C:3][C:4][Br:1]')
>
> >>rxn.Initialize()
>
> >>r = [Chem.MolFromSmiles('CCC\C=C\C(C)C'), Chem.MolFromSmiles('Br')]
>
> >>ps = rxn.RunReactants(tuple(r))
>
> >> for p in ps:
> ...: for m in p:
> ...: print Chem.MolToSmiles(m, isomericSmiles= True)
> ...:
> [out] CCC(Br)C=CC(C)C
> [out] CCCC=CC(C)(C)Br
>
> Any thoughts?
>
Just a short one: "it's a bug".
Joking aside: When I made the recent stereochemistry fixes for reactions, I
focused on atomic stereochemistry, not double bond stereochemistry. I just
filed a bug report for it: https://github.com/rdkit/rdkit/issues/31 and
will try to get it fixed for the next release. As always with
stereochemistry problems: these can be subtle and take a long time, so no
guarantees.
Thanks for reporting this!
-greg
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