From: Noel O'B. <bao...@gm...> - 2016-10-20 13:35:34
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Take a look at the draw method. On 20 Oct 2016 2:08 p.m., "T V" <th...@uc...> 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 > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > |