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

[Adrian J. <jas...@gm...>]

I have many others examples where I have found overlapping. Even rings
overlap in some of them.
It will be nice if it will be fixed for next realize.

Best Regards
Adrian

2012/6/20 Greg Landrum <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