Hi Dr.Hutchison,
Thanks for reply. It really enlightened me to use SMARTS syntax in my query
substructure.
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"*
And my target molecule is
: [nH]1ccc2c1c1sc3C=C([SiH2]c3c1c1=CCC=c21)c1cccc2ccccc12
[image: Inline image 3]
The result of the number of matches is 0 which is not correct obviously.
I've been struggling to figure this out for a couple of days.
If there is any advice could help me out, I would be very thankful.
Thanks in advance and best,
Ching-Yen
On Fri, Feb 13, 2015 at 5:51 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
>
> > I am doing substructure search with Pybel, but the results were somehow
> different from what I expected.
>
> You're searching with SMARTS on a quasi-aromatic fragment. The SMILES you
> used indicates explicit double bonds. That may not match if aromaticity is
> detected in the ring system. I don't have time for a quick check, but I'd
> guess that part of the fused ring is detected as aromatic and the third
> Si-ring is not.
>
> My suggestion would be something like this:
>
> [#14r5]@[#6r5]@[#6r5]@[#6r5]@[#6r5] # silicon in a 5-membered ring with 5
> carbons
>
> http://www.daylight.com/dayhtml_tutorials/languages/smarts/
>
> Hope that helps,
> -Geoff
>
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu
> web: http://hutchison.chem.pitt.edu/
>
>
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