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
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
