My approach to this would depend on what you're trying to accomplish in the
end.
If you just want all the aromatic atoms you can just use "[a]". Unless you
do some extra work when you read in the molecules, any aromatic atom will
be in a ring. If you want to be really sure, you can do "[a;r]"
If you want all the aromatic bonds, it's "[a]:[a]"
If you want the rings themselves and you want to just use SMARTS, you have
to enumerate. Python makes getting the patterns pretty easy:
In [8]: patts = ["[a]:1"+":[a]"*i+":[a]:1" for i in range(3,22)] # 24 is
the max aromatic ring size
In [9]: patts[:3]
Out[9]:
['[a]:1:[a]:[a]:[a]:[a]:1',
'[a]:1:[a]:[a]:[a]:[a]:[a]:1',
'[a]:1:[a]:[a]:[a]:[a]:[a]:[a]:1']
The rest is just some calls to MolFromSmarts() and then
mol.GetSubstructMatches() for the molecules you want to test.
-greg
On Thu, Sep 21, 2017 at 3:56 AM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Jason,
>
> Thanks! I just thought of that for a 6-membered ring. A 5-membered
> ring would be [a]1[a][a][a][a]1.
>
> Hmmm... I was thinking of using "r" to specify a ring, but I don't
> think
> that would be necessary. Correct?
>
> Regards,
> Jim Metz
>
>
>
>
> -----Original Message-----
> From: Jason Biggs <jasondbi...@gmail.com>
> To: James T. Metz <jamestm...@aol.com>
> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> Sent: Wed, Sep 20, 2017 8:36 pm
> Subject: Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?
>
> if you don't care what type of atom it is, just that it's aromatic, you
> should use [a],
>
> so [a]1[a][a][a][a][a]1 would match any 6-membered aromatic ring
>
> Jason Biggs
>
>
> On Wed, Sep 20, 2017 at 7:57 PM, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Hello,
>
> I would like to write a SMARTS that will match all of the individual
> atoms
> in all possible heteroaromatic rings. Does anyone know of an elegant,
> compact way to do this?
>
> If one SMARTS will not work, I can concatenate SMARTS using
> a vertical pipe, "|", as I proposed in an earlier message in this forum.
>
> I am (perhaps) expecting SMARTS something like
> [c]1[c][n][c][c]1
> etc
> [c]1[c][c][c][c][c]1
> [c]1[c][n][c][c][c]1
> etc.
>
> Perhaps there is a very elegant way to specify the possible
> patterns. I can't think of a way to do it, other than exhaustive
> enumeration.
>
> Any ideas?
>
> 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
>
>
------------------------------------------------------------------------------
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
