[chimera-dev] Extensions with C code

[Greg Couch]

Since you are at UCSF and in the same department as us, why don't you come 
by N453 Genentech Hall and talk to us.  We can probably figure out how 
best to help you easier in person than in email.  That said ...

For accessing chimera's molecular data from python, see the examples in 
the Chimera Programmer's Guide, 
<http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html>.
Specifically the use of chimera.openModels.list() in the Molecular Editing 
example.  Please give us feedback on the examples so we can improve them.

For generating a python wrapper for C code, the first question is why? 
Generally, you should prototype your code in python first and only after 
profiling convert part of it to C (or C++).  The exception is when you 
wish to use an existing library.  swig is the best supported wrapping tool 
out there.  It has extensive documentation and examples at 
<http://www.swig.org>.  For C code, there is also Pyrex, 
<http://nz.cosc.canterbury.ac.nz/~greg/python/Pyrex/>.  If you want a 
wrapper for C++ code, then we prefer our own wrappy tool (currently only 
available on our systems), but you should look at boost::python, 
<http://www.boost.org>.

 	Hope this helps,

 	Greg Couch
 	UCSF Computer Graphics Lab
 	gregc at cgl.ucsf.edu

On Mon, 1 Nov 2004, Thomas Goddard wrote:

> Date: Mon, 1 Nov 2004 09:34:33 -0800 (PST)
> From: Thomas Goddard <goddard at cgl.ucsf.edu>
> To: chimera-dev at cgl.ucsf.edu
> Subject: [chimera-dev] Extensions with C code
> 
>
> Jerome Nilmeier has some questions about writing C code extensions to Chimera.
>
> ------- Start of forwarded message -------
>
> Date: Sun, 31 Oct 2004 18:42:34 -0800 (PST)
> From: Jerome Nilmeier <jnilmeier at yahoo.com>
> Subject: rudimentary chimera questions
> To: goddard at cgl.ucsf.edu
>
> Hello Tom:
>
> I'm not sure exactly who to ask about this... I am a UCSF grad student, 
> and I'd like to use chimera for my reserach.  I am thinking of trying to 
> interface some c code with chimera, and had just a couple of basic 
> questions:
>
> 1) how do you access the information about loaded molecules from the 
> idle prompt?  I went through the example, but it doesn't say how to work 
> with molecules that have been loaded using the menu.
>
> 2) I was trying to use swig to generate a python wrapper...so far 
> without success.  Do you have a recommended (hopefully straightforward) 
> method for interfacing python with c code?
>
> Any help you could offer would be most appreciated.
>
> Thank you, Jerome
>
> ------- End of forwarded message -------
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