Thanks all for informative and helpful responses, the behaviour I was
struggling to understand now makes perfect sense.
Toby Wright
--
InhibOx Ltd
On 4 March 2014 04:06, Greg Landrum <greg.land...@gmail.com> wrote:
> Bob hit the nail on the head.
>
> The first case, "N1N=CC=C1", is aromatic because the RDKit sees that the
> first nitrogen has two bonds to it, assigns a hydrogen, and then sees a
> conjugated pi system with 6 electrons that is flagged as aromatic.
> Something similar would happen with the aromatic form [nH]1nccc1: first the
> ring system is kekulized to yield N1N=CC=C1, then the sanitization proceeds
> from there. The same thing would happen with the equivalent n1[nH]ccc1.
>
> The second case, N1=NC=CC1, has a C (the last one) that only has single
> bonds to it. This is assigned sp3 hybridization, so there's no conjugated
> ring system for aromaticity to be perceived in.
>
> The final case, n1nccc1, is an instance of the "pyrrole" problem: aromatic
> N's that need an implicit H on them, should have that implicit H present in
> the aromatic SMILES.
>
> -greg
>
>
>
>
> On Mon, Mar 3, 2014 at 5:59 PM, Bob Funchess <bfunch...@kelaroo.com>wrote:
>
>> Hi Toby,
>>
>>
>>
>> I'd say it's more of a limitation inherent in Kekule representations than
>> an actual bug in RDKit. Trying to get too "clever" in figuring out what
>> the user meant usually causes more harm than good.
>>
>>
>>
>> I'm not sure what version of RDKit you're using, but the aromatic
>> specification with an explicit hydrogen on one of the nitrogen atoms works
>> for me:
>>
>>
>>
>> >>> Chem.MolFromSmiles('n1[nH]ccc1').Debug();
>>
>> Atoms:
>>
>> 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
>>
>> 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0
>>
>> 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
>>
>> 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
>>
>> 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0
>>
>> Bonds:
>>
>> 0 0->1 order: 12 conj?: 1 aromatic?: 1
>>
>> 1 1->2 order: 12 conj?: 1 aromatic?: 1
>>
>> 2 2->3 order: 12 conj?: 1 aromatic?: 1
>>
>> 3 3->4 order: 12 conj?: 1 aromatic?: 1
>>
>> 4 4->0 order: 12 conj?: 1 aromatic?: 1
>>
>>
>>
>> The double bonds in the Kekule representations here can be between atom
>> pairs 1,2 and 3,4 or between atom pairs 2,3 and 4,0. Putting one between
>> pair 0,1 leaves atom 4 with two single bonds to it (and therefore, to
>> satisfy valence requirements, two implicit hydrogens); I'm not horribly
>> surprised that RDKit perceives that as aliphatic. You can see that's
>> what's happening in your second example where the hybridization of atom 4
>> is 4 (sp3) instead of 3 (sp2).
>>
>>
>>
>> Regards,
>>
>> Bob
>>
>>
>>
>> --
>>
>> Bob Funchess, Ph.D.
>> Kelaroo, Inc
>>
>> Senior Scientist
>> www.kelaroo.com
>>
>> bfunch...@kelaroo.com (858)
>> 259-7561 x3
>>
>
>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries. Built-in WAN optimization and
> the
> freedom to use Git, Perforce or both. Make the move to Perforce.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries. Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
