On Thu, Aug 8, 2013 at 12:38 AM, Pascal Muller
<pascal.jm.mul...@gmail.com>wrote:
> Hi all,
>
>
> With file.smi being
> C1=CC=CC=C1 single-double
> c1ccccc1 aro
> c1ccccc1N
>
> obgrep C1=CC=CC=C1 file.smi
> gives no output. But in my opinion, all 3 molecules should be matched.
>
No, the query string is a SMARTS, not a SMILES, so none of the molecules
should match. Kekule configurations are not converted to aromatic for a
SMARTS string. SMARTS are not molecules, they are pattern-matching
expressions, and the electronic configuration can't be determined. If you
want to search for an aromatic ring, you have to write the atoms and bonds
in their aromatic form.
Just to illustrate ... imagine you had a "molecule" that was
"C1=CC=CC=[C+]1=O" or something else weird. It's not aromatic, but the
original SMARTS *should* match it.
Craig
> I'm pretty sure this problem was already discussed, but I found only this
> post
>
> http://forums.openbabel.org/Fw-Re-substructure-search-problem-td4655860.html
> These problems may be related?
>
> And the output of
> obgrep c1ccccc1 file.smi
> is:
> c1ccccc1 single-double
> c1ccccc1 aro
> c1ccccc1N aro
>
> It's fine, apart the 3rd compound name (there should be no compound name).
> In my tests, a no-name compound has the name of the preceding molecule
> (this preceding molecule being matched or not).
>
> Regards,
> Pascal
>
>
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