Re: [Rdkit-discuss] Rendering of aromatics

2016-10-11 Thread Jean-Marc Nuzillard
Thanks ! Jean-Marc Le 11/10/2016 à 10:57, Greg Landrum a écrit : Here's the explanation of the RDKit's aromaticity model: https://github.com/rdkit/rdkit/blob/master/Docs/Book/RDKit_Book.rst#aromaticity -greg On Tue, Oct 11, 2016 at 9:28 AM, Jean-Marc Nuzillard mailto:jm.nuzill...@univ-reims

Re: [Rdkit-discuss] Rendering of aromatics

2016-10-11 Thread Peter S. Shenkin
Thanks, Greg. Indeed, passing "kekulize=False" to MolsToGridImage works. -P. On Tue, Oct 11, 2016 at 1:56 AM, Greg Landrum wrote: > HI Peter, > > On Tue, Oct 11, 2016 at 12:31 AM, Peter S. Shenkin > wrote: > >> >> Please see the attached image for (1) and (2). >> >> 1. If I render a molecule v

Re: [Rdkit-discuss] Rendering of aromatics

2016-10-11 Thread Greg Landrum
Here's the explanation of the RDKit's aromaticity model: https://github.com/rdkit/rdkit/blob/master/Docs/Book/RDKit_Book.rst#aromaticity -greg On Tue, Oct 11, 2016 at 9:28 AM, Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > Hi, > > maybe I am a bit off topic but I would not have said

Re: [Rdkit-discuss] Rendering of aromatics

2016-10-11 Thread Jean-Marc Nuzillard
Hi, maybe I am a bit off topic but I would not have said that the nitrogen containing ring is aromatic. Of course, if all bonds are forced to be aromatic when they are not necessarily, you may end up with inconsistencies. A nitrogen in an aromatic ring should bear a positive charge when it bea

Re: [Rdkit-discuss] Rendering of aromatics

2016-10-10 Thread Greg Landrum
HI Peter, On Tue, Oct 11, 2016 at 12:31 AM, Peter S. Shenkin wrote: > > Please see the attached image for (1) and (2). > > 1. If I render a molecule via 'SVG(svg)', I get the dotted aromatic > representation. > A bit of clarification here, to help with the later answer. The key piece is where t