Hi,
After I applied SMARTS into my query substructures, mostly it turned out
> pretty well but I still found something didn't work out.
> For instance,
> *the query substructure: c1cccc2c1cCc2 *
> [image: Inline image 1]
> Since I don't know where the double bonds would be in my target molecules.
> So I replaced all "c" and "C" with [#6] and connected them by "~" (any
> bonds)
> *The SMILES turned into "[#6]1~[#6]~[#6]~[#6]~[#6]2~[#6]1~[#6]~[#6]~[#6]2"*
>
Your smarts is slightly wrong.
It should be
[#6]~1~[#6]~[#6]~2~[#6]~[#6]~[#6]~[#6]~[#6]~2~[#6]~1
Try MarvinSketch http://www.chemaxon.com/marvin/sketch/index.php (sketch
and then file --> save as smarts) or SmartsViewer
http://smartsview.zbh.uni-hamburg.de/ to check your smarts.
Regards,
Pascal
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