[Ifeffit] [OT] Ball&sticks open source Perl/Python libraries

Bruce Ravel bravel at bnl.gov
Thu Jul 31 09:41:37 CDT 2008


On Thursday 31 July 2008 10:24:09 Mauro Rovezzi wrote:
> Dear all,
>
> I'm sorry if I introduce an off-topic (OT) subject but I would like to
> ask if you have knowledge of a simple ball&stick open source library
> that could be called from Perl or Python in order to generate "on the
> fly" theoretical paths visualization (or any atomic structure).
>
> At the moment the simplest (and useful!) utility I have found is XBS
> (http://ihp02.ihp-ffo.de/~msm/) but it is not the best solution because
> it needs input files and the output quality is low.

Hi Mauro,

This is a topic I have thought about from time to time.  The only two
realistic solutions that I have come up with are to communicate
directly with OpenGL (http://graphcomp.com/opengl/) or to make system
calls to a ball and stick viewer (my current favorite is Avogadro
http://avogadro.openmolecules.net/wiki/Main_Page; pymol
http://pymol.sourceforge.net/ is quite good as well and might actually
be what you are looking for as a scriptable python solution).

The OpenGL soultion has always seemed like a very large programming
chore and the system call solution seems fragile and better suited for
a one-off application.  (Although, feff gets called by artemis via a
system call and that works well.  Of course, I am quite sure that
someone who has artemis on their computer also has feff!)

All that said, I will be very interested to see what you come up with.

B




-- 
 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/




More information about the Ifeffit mailing list