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
*From:* Toby Wright [mailto:toby.wri...@inhibox.com]
*Sent:* Monday, March 03, 2014 7:42 AM
*To:* RDKit Discuss
*Subject:* [Rdkit-discuss] Two nitrogens in a 5 membered ring
Hi,
If I have a five membered ring with 2 consecutive Ns and alternating single
and double bonds expressed by the smiles: N1N=CC=C1 RDKit gives me a
molecule in which every atom is aromatic. If I give it: N1=NC=CC1 it gives
me a molecule in which every atom is aliphatic. If I give it: n1nccc1 it
gives me a kekulization error. I, possibly naively, thought the forms would
be all aromatic or all aliphatic. Am I missing something or is this a bug?
>>> Chem.MolFromSmiles('N1N=CC=C1').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
>>> Chem.MolFromSmiles('N1=NC=CC1').Debug()
Atoms:
0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 0 chi: 0
1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 0 chi: 0
2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0
4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0
Bonds:
0 0->1 order: 2 conj?: 1 aromatic?: 0
1 1->2 order: 1 conj?: 1 aromatic?: 0
2 2->3 order: 2 conj?: 1 aromatic?: 0
3 3->4 order: 1 conj?: 0 aromatic?: 0
4 4->0 order: 1 conj?: 0 aromatic?: 0
>>> Chem.MolFromSmiles('n1nccc1').Debug()
[15:31:44] Can't kekulize mol
Yours,
Toby Wright
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