On 16/11/2020 21:28, Navid Shervani-Tabar wrote:
Dear RDKit users,
I'm trying to plot a single molecule using RDKit. I use the following code
from rdkit.Chemimport Draw
from rdkitimport 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!
To my eye, it is an unconventionally-rendered [1] triple bond where the
right-hand most line is almost entirely clipped.
Paul.
[1] or is that how ring triple bonds are displayed? I would not have
thought that the outside line should be short (maybe not even the inside
line (although that does seem more elegant))
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