I did something similar a while ago, and described the process at the
following link:
http://baoilleach.blogspot.com/2010/04/plug-cclib-into-avogadro.html
I dd need to use Open Babel directly though, as I couldn't access the
Open Babel bindings in Avogadro (this was 1.0.0 on Windows).
- Noel
On 3 July 2011 10:22, Rochus Schmid <rochus.sch...@rub.de> wrote:
>
> dear avogadro users and developers,
>
> i am trying to use the python bindings in Avogadro 1.0.3 to read and display
> molecules bypassing openbabel. as a first step i tried to build an extension
> that reads a tinker xyz file. it reads and generates all atoms fine, but
> when I try to add bonds, even in the first call
> bond = mol.addBond()
> (with mol = glwidget.molecule) Avogadro dies with a segfault.
> Is there anything seriously wrong in doing that? my interpretation is that a
> segfault should not happen from the scripting interface.
> any hints/comments highly appreciated.
>
> as rationale:
> in a longer term research project (python wrapped dl_poly) we consider using
> Avogadro as a graphical frontend due to its python extensions. in order to
> test this possibility i want to use it to visualize MD trajectories stored
> via h5py in the hdf5 format. reading ascii tinker files is just to
> understand the way Avogadro handles molecule data.
>
> --
> PD Dr. Rochus Schmid
> Lehrstuhl für Anorganische Chemie II
> Organometallics and Materials Chemistry
> Ruhr-Universität Bochum
> D-44780 Bochum
>
> Tel.: ++49(234) 32 24166
> Fax: ++49(234) 32 14174
> Email: rochus.sch...@rub.de
> http://www.rochusschmid.de
>
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All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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