Hi Markus,
This does look like a bug. Thanks for reporting it.
I'll be away for the weekend starting tomorrow, but I'll look at it next week.
Regards,
-greg
On Wed, Mar 19, 2008 at 9:31 PM, markus <m.koss...@tu-bs.de> wrote:
> Hi there, it's me again... :-)
> As you asked me to post things looking strange to me......here we go:
>
> When I read in a Tripeptid-Sequence (Lys-Leu-Gln) with isomeric Smiles
> and do any Reaction,
> suddenly Some alpha-Carbons flip their Chirality. Please have a look at
> the code:
>
>
> >>> from Chem import AllChem as Chem
> >>>
>
> InputMol=Chem.MolFromSmiles('nccc...@h](N)C(=O)N[C@@H](CC(C)C)C(n...@h](C(N)=O)CCC(N)=O)=O')
> >>> repl=Chem.ReactionFromSmarts('[C:1]=[O:2]>>[C:1]=[S:2]')
> >>> out=repl.RunReactants((InputMol,))
> >>> print Chem.MolToSmiles(out[0][0], isomericSmiles=True)
> NCCCC[C@@H](N)C(=S)n...@h](CC(C)C)C(=O)N[C@@H](C(N)=O)CCC(N)=O
>
> This happens for any reaction i tried so far. I also did the Sanitize()
> thing
> when reading in the Educt and before writing the Product, but there's
> no change.
> Doing Chem.AssignAtomChiralcodes() before the reaction does not preserve
> the
> Chirality
>
> Cheers Markus
>
>
>
>
>
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