On Mon, 3 Mar 2014 15:41:43 +0000
Toby Wright <[email protected]> wrote:
> 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?
I would say that the behavior you described is rather due to Daylight's
specification of aromaticity-detection algorithm in SMILES which I assume
RDKit follows.
For more details see, section 3.4.2 "Aromaticity" of the document below
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
Following it, I think to make RDKit recognized your aromatic heterocycle
properly, its SMILES should read e.g. [nH]1nccc1.
Hope it helps.
--
MikoĊaj Kowalik
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