> I had to generate a 3D molecule from SMILES to xyz. But i have noticed that,
> 'sometimes', if i give a SMILES input for a cyclic molecule, ('c1c1' for
> benzene) and convert it into xyz (3d) coordinates and take the data to
> visualize in Avogadro, it is not showing a cyclic molecule at a
Dear all,
I had to generate a 3D molecule from SMILES to xyz. But i have noticed
that, 'sometimes', if i give a SMILES input for a cyclic molecule,
('c1c1' for benzene) and convert it into xyz (3d) coordinates and take
the data to visualize in Avogadro, it is not showing a cyclic molecule at
al
> I am using Openbabel GUI on windows. I am converting SMILES to xyz format
> using 'generate 3D coordinates' option. Everything is looking fine (viewing
> in gui.svg viewer in firefox) as expected.
I'm not sure why you're generating 3D coordinates to view a 2D format (SVG).
> But when i am
I am using Openbabel GUI on windows. I am converting SMILES to xyz format
using 'generate 3D coordinates' option. Everything is looking fine (viewing
in gui.svg viewer in firefox) as expected. But when i am taking the output
xyz data to view in other molecular editors like GaussView or Avogadro, it
