[chimera-dev] C/C++ libraries in Chimera

[Elaine Meng]

Hi Viktor,
Actually, I'm the one person on the Chimera team that doesn't do  
programming!  I'll share your  mail with the chimera-dev at cgl.ucsf.edu  
list (for programmer/developer issues) - I believe it has a handful  
of subscribers in addition to the Chimera team members, and this set  
of people may have some valuable insights.
Best,
Elaine

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Dec 6, 2006, at 9:28 AM, Viktor Hornak wrote:

> Dear Elaine,
>
> sorry to write directly to you and not to chimera list but I have a  
> question which is rather off-topic. It concerns developing C  
> extensions in Python, and I don't even mean specifically for  
> chimera (at this time), but in general. I know that you guys (I am  
> not sure who specifically on chimera team does this sort of a "hard  
> core" programming work) develop a lot of extensions (.so libraries)  
> that can be called from Python and thus you must have a lot of  
> experience doing it. I attempted a couple times to write C  
> extensions in Python as described in Python extension guide but  
> always got burned by reference counting, programs crashing at  
> allocating memory or releasing pointers, etc. In other words, there  
> must be a better/easier way to write extensions. All I need is to  
> transfer integer/float variables and arrays to or from Python to my  
> C subroutine, e.g. I just need to wrap my existing C subroutines  
> and pass arrays back and forth between C and Python (I guess Python  
> lists versus C arrays). I was hoping someone on your team could  
> point me to the right direction. I saw people use SWIG (that looked  
> rather complex though and an overkill for what I need), or Pyrex,  
> etc but I wasn't sure which solution was worth picking up in terms  
> of time I have to spend to learn it and future support (so that the  
> project doesn't disappear in a year).
> I would really appreciate if you could provide any hints or point  
> me to some resources.
>
> Many thanks for your help and sorry for such an unrelated question!!!
>
> Cheers,
> -Viktor
>
> -- 
> ===================================================================
> Viktor Hornak
> Center for Structural Biology   Phone: (631)632-1439
> SUNY at Stony Brook             Fax:   (631)632-1555
> Stony Brook, NY 11794-5115      E-mail: viktor.hornak at sunysb.edu
> ===================================================================