Dear Geoffrey，
It really helped me. Thank you very much!!!
But I'd like to know whether there exists a solution or
even trick to solve this problem?
I used Marvin Sketch Web plugin to provide interface for
users to draw chemical structure on the page (such as
http://www.chemaxon.com/marvin/sketch/index.php). But when I export the
structure as "SMARTS", it is NOT a "Canonical" SMARTS. (e.g.benzene outputs
as C1=CC=CC=C1). When the SMARTS is a SMILES , I can convert it. But if the
users draw structure like "[F,Cl,Br,I]C1=CC=CC=C1", it can not be converted
to smiles. But "C1=CC=CC=C1" really means beneze, what should I do?
Could you help me?
shen
2011/3/15 Geoffrey Hutchison <ge...@geoffhutchison.net>
>
> On Mar 13, 2011, at 3:57 AM, qiancheng shen wrote:
>
> > smarts = pybel.Smarts([F,Cl,Br,I]C1=CC=CC=C1)
> > matched_list = smarts.findall(sdf)
> > /**End**/
> > Can't find any matched molecule.
>
> Right. Because that SMARTS says to match a molecule with a bunch of
> non-aromatic carbons connected by three double bonds. But cyclohexatriene =
> benzene and will be perceived as aromatic. So there cannot be any matches to
> a kekulized SMARTS.
>
> Hope that helps,
> -Geoff
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