HI Peter,
On Tue, Oct 11, 2016 at 12:31 AM, Peter S. Shenkin <[email protected]>
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 the SVG itself is generated: the call to
drawer.DrawMolecule() in your render_mol() function.
> 2. If I render it just by displaying 'MolFromSmiles(smi)', I get the
> kekulized representation.
>
Here's the python code that does that generates that SVG (if you've
configured SVG generation with IPythonConsole.ipython_useSVG):
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Draw/IPythonConsole.py#L132
or the PNG (the default):
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Draw/IPythonConsole.py#L103
Notice the call to rdMolDraw2D.PrepareMolForDrawing() in each function.
This does the kekulization.
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?
>
>
Try passing the "kekulize=False" argument to MolsToGridImage(). That should
do it.
> b. What is the underlying paradigm which dictates which representation
> will be shown, and how can it be controlled?
>
By default the code kekulizes things before rendering them. You can change
this default for normal molecule rendering in the notebook by setting
IPythonConsole.kekulizeStructures to False. This doesn't currently impact
what MolsToGridImage does, though it should.
> 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?
>
Nope, not currently possible.
-greg
>
> Thank you,
> -P.
>
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