Re: [Rdkit-discuss] Problem with Drawing a molecule

2020-11-16 Thread Paul Emsley 


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#CN2C1C2')
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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Re: [Rdkit-discuss] Problem with Drawing a molecule

2020-11-16 Thread Navid Shervani-Tabar 
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 
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#CN2C1C2')
> 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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[Rdkit-discuss] Problem with Drawing a molecule

2020-11-16 Thread Navid Shervani-Tabar 
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#CN2C1C2')
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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