[chimera-dev] Program code

[Eric Pettersen]

On Apr 26, 2005, at 8:47 AM, Jesse Parker wrote:
> I am currently looking for ways of visualizing proteins as they are 
> being folded by a matlab program we are developing here at the 
> University of Connecticut. I am unsure whether an extension would be 
> adequate to read and write to matlab, or modifications to the chimera 
> source would be necesarry. Would it be possible to get a copy of the 
> source code for Chimera and possibly some examples of extensions?

Hi Jesse,
	An extension should be adequate to do what you want.  Chimera was 
designed from the beginning to be as extensible as possible and the 
bulk of Chimera's functionality is provided as extensions.
	The best place to get started in finding out what extensions can do is 
to look at the programming examples, which you can find as link off of 
this page:  
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html .  The 
FAQ off of that page can also be useful.  We also try to answer any 
questions going to this list.
	All the Python source code is actually provided with your Chimera 
download.  Beneath your Chimera installation directory (which can be 
tricky to reach on a Mac -- use Terminal) there is a directory named 
"share" which contains all the Python source code.  Many complex 
extensions are written entirely in Python (e.g. FindHBond, MultAlign 
Viewer).  Some extensions do make use of compiled code, typically for 
speed, but even there the Chimera C++ isn't modified; instead a Python 
compiled shared library is created (one of the programmer's examples 
deals with this) and is loaded on demand by the Python part of the 
extension.
	We don't distribute the C++ part of Chimera basically because it would 
be a miracle if anyone else could get things set up so they could 
compile it.  We do provide the header files for download so that people 
can more easily determine the methods that various classes offer (the 
link is also off the page above).  We are in the process of making the 
source files available to some developers, so that they can determine 
exactly how certain functions operate.  If you needed that kind of 
access also, we could probably add you to the access list when it's 
ready.
	In the (hopefully unlikely) case that you actually need a modification 
to the Chimera C++ source, it would probably be easiest for you to 
request the change from us, and for us to make the change and compile a 
new version and send it to you.
	If you do wind up writing your extension for Chimera, we would really 
appreciate it if you could drop us a line saying that you did.  Things 
like that look really good on our grant-renewal application! :-)

	
                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu