It turns out I was simply cropping the third line out when using
MolsToGridImage.
Thanks again,
Navid
On Mon, Nov 16, 2020 at 4:28 PM Navid Shervani-Tabar <nshe...@gmail.com>
wrote:
> Dear RDKit users,
>
> I'm trying to plot a single molecule using RDKit. I use the following code
>
> from rdkit.Chem import Draw
> from rdkit import Chem
>
> mol = Chem.MolFromSmiles('C1#CN2CCCCC1C2')
> Chem.rdmolops.SanitizeMol(mol)
> img = Draw.MolsToGridImage([mol], molsPerRow=1)
> img.save(res_dir + 'mol_1.png')
>
>
> and I get the attached figure. There is an alkyne bridging in the
> molecule, which as you can see in the figure, is visualized with a double
> bond instead of a triple bond. I was wondering what causes this issue and
> how to fix it. Thanks!
>
> Regards,
> Navid
>
>
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