Sorry, I mistakenly replied to just Colin before, rather than the whole list.
I think the answer is that the outer ring is aromatic, but the two inner rings, the 5-ring and the 6-ring, aren’t. This would mean that the bond between 11 and 16 isn’t aromatic. It is certainly true that the bond between 2 aromatic atoms can be non-aromatic. The bond between the two benzene rings in bi-phenyl would be the classic example. Cheers, Dave On Wed, Mar 6, 2019 at 10:25 AM Colin Bournez <colin.bour...@univ-orleans.fr> wrote: > 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> > 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>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 >>> >>> >>> -- >>> *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 >>> <+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> >>> <https://twitter.com/ICOA_UMR7311> >>> >>> <https://www.linkedin.com/company/institut-de-chimie-organique-et-analytique---icoa-umr7311/> >>> _______________________________________________ Rdkit-discuss mailing >>> list Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> -- >> *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 >> <+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> >> <https://twitter.com/ICOA_UMR7311> >> >> <https://www.linkedin.com/company/institut-de-chimie-organique-et-analytique---icoa-umr7311/> >> _______________________________________________ Rdkit-discuss mailing >> list Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- > *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 > <+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> > <https://twitter.com/ICOA_UMR7311> > > <https://www.linkedin.com/company/institut-de-chimie-organique-et-analytique---icoa-umr7311/> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk
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