October 2013 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Chimera/Python sparse matrices
by Greg Couch 06 Dec '13

06 Dec '13

On 8/13/2010 12:06 PM, Forbes J. Burkowski wrote: > What are the steps that need to be taken if the Python used in Chimera is > to have the ability to import functions from SciPy or PySparse? > > Thanks for any advice that you can provide. > > Cheers, > Forbes Burkowski If you want to use prebuilt SciPy binaries with chimera, you need one that is compatible with the version of chimera that chimera is using. Chimera 1.4.x uses Python 2.5, and the daily builds use Python 2.7. You would add those packages to chimera by either (1) given the '--pypath dir' command line option, (2) setting your CHIMERAPTH environment variable (instead of PYTHONPATH, PYTHONPATH is ignored so chimera won't be accidentally broken by other installed Pythons), or (3) add the installation directory to sys.path in Python. If you're not using a daily build on Linux, then you should edit CHIMERA/share/chimeraInit.py and comment out or remove the part that sets the RTLD_GLOBAL flag -- it appears to be no longer needed and its presence breaks SciPy. If you're going to compile from source, which you'll need to do if you're using a daily build, I'd recommend trying PySparse first, since it is a smaller package. Python packages that incorporate C (or C++ or Fortran) code are more difficult than prebuilt binaries because (a) you need a compiler, and (b) if the code calls the Python C API, you need a compatible compiler, ideally the same one as what the rest of Chimera was build with. PySparse needs BLAS and LAPACK libraries and optionally wants UMFPACK and/or SuperLU. On on Redhat and Fedora Linux, you can get the first three libraries by installing the blas-devel, lapack-devel, and suitesparse-devel packages. Chances are you'll be able to install PySparse into chimera's python by running "CHIMERA/bin/pythonXXX setup.py install" in the pysparse source tree (where CHIMERA is the path to where chimera was installed). On Linux, you might have to set the LD_LIBRARY_PATH environment variable to CHIMERA/lib. On Mac OS X, the path to the chimera binary is CHIMERA/Contents/Resources/bin/pythonXXX and the environment variable is DYLD_LIBRARY_PATH. Or you could install PySparse into another Python and use the --pypath/CHIMERAPATH/sys.path approach as given above. Hope this helps, Greg

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Interfacing with Chimera
by Bernard Lieberman 21 Oct '13

21 Oct '13

Hello, I'm presently writing an application that I'd like to interface with Chimera. Essentially my program will be capable of loading a specific python session with the appropriate model and then select, stylize, etc. specific residues. I'm able to generate the commands required but I'm wondering if it's best to find a way to hook the Chimera command line or if I should be going the route of editing my source py file? I'm essentially looking for the best method to have my VB6 application interface with Chimera and was looking for some suggestions if others have done this in the past. Any tips or suggestions are greatly appreciated. Thanks! *Bernard Lazarus Lieberman*

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declaring an integer to be used for the model and select command
by Moses Adenaike 08 Oct '13

08 Oct '13

Hello there! I am trying to write a python script for chimera to rotate one molecule then translate another molecule to the right. I can get the code to work when I say use select 0 and model 1. But I want to define functions Rotate and Translate and be able to parse an integer value for the model numbers: Example def Rotate (0) where 0 would be the value of a variable called model inetger then later the function would have the code runCommand("move x -1 model #modelinteger") but when I try to compile chimera says model integer is not defined. I define it outside the function as modelinteger=0 but still the same error message shows. Basically how do I get chimera to understand that my variable modelinteger is indeed an integer?

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Chimera-dev October 2013