Avogadro as visual debugger for Openbabel?

Hi all,

I am using openbabel python to create and manipulate atomic structures
and I’d love to use Avogadro as a visual debugger, i.e. to see the
changes of the obmol object while they take place.

Based on the ideas of


I already managed to visualize an obmol object by converting it to
an Avogadro Python Molecule, but maybe it can be done easier?!
As I am not familiar with the Avogadro code yet, is there maybe
a way to directly plug an openbabel molecule object into Avogadro?

Best regards,
Andreas

On Nov 18, 2010, at 8:59 AM, Andreas Kempe wrote:

Based on the ideas of
http://baoilleach.blogspot.com/2010/04/plug-cclib-into-avogadro.html
I already managed to visualize an obmol object by converting it to
an Avogadro Python Molecule, but maybe it can be done easier?!

I don’t know the Windows build. Noel was having trouble directly accessing the embedded OpenBabel python module in the Windows Avogadro build. It’s easier in Linux/Mac, for example inside Avogadro and using the same syntax as Noel:


avomol = avo.molecule
obmol = avomol.OBMol
… # operate on the OBMol

Hope that helps,
-Geoff