Yes I know it's a tautomer, but I don't figure out how to handle it
without returning to the other form.
If I transform the SINGLE bond to AROMATIC, it can't be sanitized still
returns 0 NAR....
Colin
On 06/03/19 11:11, Michal Krompiec wrote:
It’s because the molecule with atom indices is a tautomer of the other
one (H at the other N), hence different Kekule structure and different
behaviour of the aromaticity perception code.
Best,
Michal
On Wed, 6 Mar 2019 at 10:04, Colin Bournez
<colin.bour...@univ-orleans.fr <mailto:colin.bour...@univ-orleans.fr>>
wrote:
Hi Greg,
Indeed it seems one bond is not tagged as aromatic.
Here are the aromatics bond (begin atom, end atom) :
0 1
1 19
19 16
11 14
14 12
12 7
7 20
11 0
20 16
We see that between the atom 11 and 16 it is not aromatic.
It is a single type:
16 11 SINGLE
The problem remains after sanitizing the molecule and both atoms are tagged
as aromatic.
A bond between two aromatic atoms can be single?
On 06/03/19 10:49, Greg Landrum wrote:
Hi Colin,
The aromatic ring counting code identifies rings where every
*bond* is aromatic, so I guess one or more bonds in the rings of
the first molecule are not aromatic.
Could it be that you haven't sanitized the molecule before
calculating descriptors?
-greg
On Tue, Mar 5, 2019 at 6:00 PM Colin Bournez
<colin.bour...@univ-orleans.fr
<mailto:colin.bour...@univ-orleans.fr>> wrote:
Dear all, I might have encountered a little problem
concerning the function
rdMolDescriptors.CalcNumAromaticRings(). For this molecule
shown with index:
Here is what I do :
So I have as expected my aromatic atoms but when I ask for aromatic
Rings it returns 0 instead of two.
Anyone has an idea?
For information if the molecule is in that form
It returns 2 NAR as expected.
Colin
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*Bournez Colin *
<https://www.linkedin.com/in/colin-bournez-b9a1b2b7/>
<http://www.icoa.fr/> /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
Université d'Orléans - Pôle de Chimie Rue de Chartres - BP 6759
45067 Orléans Cedex 2 - France +33 (0)2 38 49 45 77
<tel:+33%202%2038%2049%2045%2077> SBC Tool Platform
<http://sbc.icoa.fr/> - SBC Team <http://www.icoa.fr/bonnet>
<http://www.icoa.fr/fr/rss.xml>
<https://www.facebook.com/pages/Institut-de-Chimie-Organique-et-Analytique-ICOA-umr7311/222060911297163>
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*Bournez Colin * <https://www.linkedin.com/in/colin-bournez-b9a1b2b7/>
<http://www.icoa.fr/> /Chemoinformatics PhD Student /
* Institute of Organic and Analytical Chemistry (ICOA UMR7311)*
Université d'Orléans - Pôle de Chimie Rue de Chartres - BP 6759
45067 Orléans Cedex 2 - France +33 (0)2 38 49 45 77
<tel:+33%202%2038%2049%2045%2077> SBC Tool Platform
<http://sbc.icoa.fr/> - SBC Team <http://www.icoa.fr/bonnet>
<http://www.icoa.fr/fr/rss.xml>
<https://www.facebook.com/pages/Institut-de-Chimie-Organique-et-Analytique-ICOA-umr7311/222060911297163>
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