On Tue, Dec 3, 2013 at 1:11 PM, Yoel <yoe...@gmail.com> wrote:
> Craig,
>
> Thanks a lot for this. I do not know the smile notation in details
> however as a chemist I’m pretty sure I understand chirality. If I
> understood your article I see that explains how chirality is
> represented in smile notations but I still don’t see how do you know
> what chirality to represent starting from a mol file lets say.
>
The reason that Dave Weininger invented SMILES' way of representing
chirality is that it's much more sensible from a
mathematical/graph-theoretical perspective than R/S and E/Z
representation. R/S and E/Z are potentially time-consuming to compute.
They are usually illustrated with trivial examples, such as Cl/C=C/Cl,
where it's obvious that it's trans. But what is CCC/C(\CCO)=C(/CCCl)\CCBr
-- E or Z? There is a formal definition, but most chemists probably
couldn't tell you at a glance whether this molecule should be called E or
Z. The same goes for R/S naming conventions. With SMILES, the algorithm
only has to look out one atom from the chiral center, or one atom out from
the double-bonded atoms, to figure out how to write the SMILES (with the
caveat that it first has to do a symmetry analysis).
Cheers,
Craig
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