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 ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
