[chimera-dev] chimera import

[Greg Couch]

We haven't used eclipse with chimera, but we will work with you to get it 
to work.  When it does work, please send what you had to do back to the 
chimera-dev list.

First an aside for non-eclipse users and maybe this would work in eclipse 
too -- you can use Python's help facility to find out more about chimera 
internals: in an IDLE window, typing:

         help(chimera.Point)

will give you a lot information about the Point API.  Since Point is
implemented in C++, you only get the type information for the arguments
and the return value, but that information, coupled with the name of the
method, tell you a lot.

Back to eclipse, the chimera program sets up several environment variables 
before invoking python.  On Linux, it is a shell script and you can see 
everything it does.  On Windows, it's basically the same:

 	(1) set the CHIMERA environment variable to the actual path of the
 		chimera install tree (so without any symbolic links).
 	(2) make sure CHIMERA/bin is in the PATH environment
 	(3) defensively remove the PYTHONHOME and PYTHONPATH environment
 		variables so we don't get packages compiled for a
 		different version of python (e.g, the system one)
 	(4) copy CHIMERPATH environment variable to the PYTHONPATH one
 	(5) set Tcl environment variables:
 		TCL_LIBRARY is CHIMERA\lib\tcl8.4
 		TCLLIBPATH is {CHIMERA\lib}
 	(6) unset TK_LIBRARY and TIX_LIBRARY environment variables

Unix systems replace step 2 with one that set the environment variable for 
finding shared libaries, ie., LD_LIBRARY_PATH or DYLD_LIBRARY_PATH or ... 
to CHIMERA/lib.  On OS X, we also set the DYLD_FRAMEWORK_PATH.

 	Good luck,

 	Greg Couch
 	UCSF Computer Graphics Lab

On Mon, 2 Oct 2006, Javier Díez wrote:

> Date: Mon, 2 Oct 2006 20:38:53 +0200
> From: "[ISO-8859-1] Javier Díez" <jdiezperezj at gmail.com>
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] chimera import
> 
> Hi again,
> Thank you for your comments. From now I will never use the import
> construction I wrote above.
> But I have got another question.
> Well, I'm using Eclipse and PyDev Extensions, and I seted the Eclipse Python
> interpreter option using the Python version included in Chimera.
> I also included the "share" in the Eclipse, PyDev PYTHONPATH, but it doesn't
> works.
> I thought it could work, but it doesn't.
> I prefer Eclipse (because it is the enviroment  I'm used to work with) to
> the IDLE provided by Chimera.
> Thank you any way.
> Javi
>
> On 10/2/06, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> 
>> Tom Goddard's comments are exactly correct, I just want to add some
>> advice.  If anyone else will be working on your code, you should try to
>> avoid the "from module_name import *" construct because it makes it more
>> difficult to find the place where a class is defined.  Say for example you
>> use a Point object in your code.  A person trying to find the definition 
>> for
>> Point first has to look through the file using Point to see if it's defined
>> there, then through each module from which you've imported "*" to look for
>> it.  It is better to import just the names you are going to use, something
>> like:  "from chimera import Point, openModels, Molecule".  That statement
>> makes it clear where the definition of Point is going to be found.
>> The other thing is that the "chimera" module imports all the names from
>> _chimera, so typically you import from chimera rather than _chimera.  I 
>> know
>> that the chimera uses the "from _chimera import *" construct, which seems
>> somewhat hypocritical given the advice above, but it is being used to make
>> C++ classes/functions that "logically" belong in the chimera module
>> available.
>> 
>> --Eric
>>
>>                         Eric Pettersen
>>
>>                         UCSF Computer Graphics Lab
>>
>>                         pett at cgl.ucsf.edu
>>
>>                         http://www.cgl.ucsf.edu
>> 
>> 
>> On Oct 2, 2006, at 5:44 AM, Javier Díez wrote:
>> 
>> Hy,
>> I've just started working on a Chimera extension.
>> I've tried to import chimera after setting up the CHIMERA os variable, but
>> it gives me this erro message:
>> ***from _chimera import *
>> ImportError: No module named _chimera
>> *Some help?
>> Thank you.
>> Javi
>> *
>> *
>> _______________________________________________
>> Chimera-dev mailing list
>> Chimera-dev at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>> 
>> 
>> 
>