Hi,

In SMARTS, 'a' matches an aromatic atom. So you would match your molecule
with the pattern 'aaa', or if you wanted to restrict yourself to carbons,
'ccc'.

This would match whether you created the molecule from a Kekulized or an
aromatic SMILES. Remember that it's the molecular recognition code, not the
form of the input SMILES, that determines whether a molecule is aromatic.

-P.

On Fri, Sep 8, 2017 at 6:19 PM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Hello,
>
>     Suppose I read in the SMILES of an aromatic molecule e.g., for
> benzene
>
>     c1ccccc1
>
>     I then want to convert the molecule to a Kekule representation and
> then perform various SMARTS pattern recognition e.g.
>
>     [C]=[C]-[C]
>
>     I have tried various Kekule commands in RDkit, but I can not figure
> out how to (or if it is possible) to recognize a SMARTS pattern for
> a portion of a molecule which is aromatic, but is currently being
> stored as a Kekule structure.
>
>     Also, is it possible to generate and store more than one Kekule
> form in RDkit?
>
>     Thank you.
>
>     Regards,
>     Jim Metz
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to