Please disregard this email -- I hit the send button with too much haste...
-
Jean-Paul Ebejer
Early Stage Researcher
On 9 November 2011 15:47, JP <jeanpaul.ebe...@inhibox.com> wrote:
>
> Hi there RDKiters,
>
> Using the greatest/latest official RDKit release (2011_09_1), I am
> generating 50 conformers of a molecule, (+/-) endo-2-amino norbornane,
> with specified stereochemistry.
> The smiles string I use is C1CCC(S(N[C@H]2[C@H]3CC[C@@H](C2)C3)(=O)=O)C1
>
> However the stereochemistry of the bridge is not always maintained in the
> conformers generated. In particular I am attaching my output file
> (50confs.sdf) - and this can be seen in molecules 12 (good) and 13 (bad) -
> starting to count from 1 (!).
>
> I am also attaching two pictures (good.png and bad.png) of the output with
> the inverted stereochemistry of the bridge highlighted in the "bad"
> structure.
> Also, please find the minimal script (conformer_ex.py) which I used to
> generate these conformers.
>
> Any ideas what I can do to rectify this situation?
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
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