Re: [Rdkit-discuss] problem with overlap in drawing.

[Greg L. <gre...@gm...>]

Dear Adrian,

On Tue, Jun 19, 2012 at 9:19 AM, Adrian Jasiński
<jas...@gm...> wrote:
>
> I have some problem with drawing. When I draw molecules using RDkit
> sometimes I have some structure overlap.
> But when I draw it using for example marvin it's look fine.
>
> There is some example code:
>
> from rdkit import Chem
> from rdkit.Chem import Draw
> mol = Chem.MolFromSmiles('CC(=O)Nc1ccccc1C(=O)C1CCCC1C1CCCCC1')
> Draw.MolToFile(mol,'test.png')
>
> In attachment I added example image.

Thanks for reporting the problem. That's definitely a bug in the depiction code.

>
> I'm using Ubuntu 12.04 x64.
>
> Is there any solution?

There is not at the moment an easy one. I will take a look at your
specific molecule and see if I can fix the problem for the next
release.

Best Regards,
-greg