Atom 20 appears to be an NH. Shouldn’t it be a pyridine N? On Wed, Mar 6, 2019 at 5:04 AM 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> 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 > -- -P. Sent from a cell phone. Pls forgive brvty and m1$tea@ks.
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