Draw doesn't have a means of flattening the molecule. And basically does
the same thing as write. I don't need a picture, I need the mol file, with
JUST 2d coordinates.
On Thu, Oct 20, 2016 at 6:35 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Take a look at the draw method.
>
> On 20 Oct 2016 2:08 p.m., "T V" <th...@ucdavis.edu> wrote:
>
>> Hi,
>>
>> In Pybel, it seems like every InChi or SMILES string I convert into a
>> molecule object (after "pybel.readstring") file using the method
>> ".write(format="mol")" generates mol files where the atoms are all at the
>> center. The coordinates are all 0's and it's really frustrating because I
>> know there is in fact a mol.make3d() that will add those 3d coordinates in
>> space for even the most complex molecules, so it's possible that they could
>> be given the correct coordinates. All I really need is a way to render my
>> mol files with the first two columns so that I have 2d representation as
>> you would typically expect when you save a mol file. I'm using kekule to
>> render those mol files into pngs, and just look horribly warped in 3D.
>>
>>
>> Additionally, I know openbabel is capable of generating 2d images because
>> mol.write(format="png") is possible and will generate a perfect 2d image
>> despite having all its coordinates be 0. Additionlly the obabel command
>> option of "-Opng" seems to be able to make images from inchi, smiles, or
>> mol into 2d plots regardless of the fact that I never provided the 2d
>> coordinates.
>> So why can't I just simply get the mol file with those same coordinates?
>>
>> --
>> Thanh
>>
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>>
--
Thanh
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