Re: [Rdkit-discuss] Rendering of aromatics

[Jean-Marc N. <jm....@un...>]

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 bears an hydrogen atom (like in a pyridinium ion).
I doubt (but this is only my opinion) that Out[56] represents an entity 
with a chemical reality.

The anthracene part in Out[58] could be drawn with aromatic bonds (or a 
circle in the middle
of the two hexagons), but I think that the third ring must be left with 
an explicit double bond.

All the best,

Jean-Marc

Le 11/10/2016 à 00:31, Peter S. Shenkin a écrit :
> Hi,
>
> Please see the attached image for (1) and (2).
>
> 1. If I render a molecule via 'SVG(svg)', I get the dotted aromatic 
> representation.
>
> 2. If I render it just by displaying 'MolFromSmiles(smi)', I get the 
> kekulized representation.
>
> So I guessed that (for some reason) when SVG is used, RDKit 
> automatically uses the dotted representation.
>
> 3. However, if I display MolsToGridImage(mol, useSVG=True), I get the 
> kekulized form. (This method does not return an SVG, and therefore I 
> cannot display it using 'SVG(result)' ).
>
> So I have several questions:
>
> a. Is there a way to force MolsToGridImage to return the dotted 
> aromatic representation? Or to postprocess the result to achieve this?
>
> b. What is the underlying paradigm which dictates which representation 
> will be shown, and how can it be controlled?
>
> c. What I would really like is the "circle" representation (i.e., 
> benzene as a hexagon with a circle inside). Can this be achieved, and 
> if so, how?
>
> Thank you,
> -P.
>
>
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-- 
Jean-Marc Nuzillard
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