Segfault for addBond() in python extension

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.schmid@rub.de
http://www.rochusschmid.de

On Jul 3, 2011, at 5:22 AM, Rochus Schmid wrote:

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()

I have not used the python extensions in a while. It’s possible there needs to be some updating with different versions of Boost::Python. I take it from your message that you’re creating new atoms using Python (i.e. the tinker xyz file is read through Python, not Avogadro and Open Babel), correct?

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.

This would be great. We have some introductory support for the HISTORY trajectory files from DL_POLY, and certainly there are others who desire to retrieve data from hdf5 as well.

Best regards,
-Geoff

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.schmid@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.schmid@rub.de
http://www.rochusschmid.de


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


Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss