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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