March 2011 - 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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Re: [chimera-dev] [Chimera-users] Energy Minimisation Citation
by Konrad Hinsen 28 Mar '11

28 Mar '11

On 28 Mar, 2011, at 5:26 , Nancy wrote: > I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option). I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc... Please let me know how I should go about this? The minimization code used by Chimera comes from MMTK, whose reference is this paper: http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2 The force field is some dialect of Amber, though I don't know which one exactly is used by Chimera. I hope someone else can provide that information. Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net ---------------------------------------------------------------------

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minimizer
by Elisabeth Ortega 17 Mar '11

17 Mar '11

Dear Chimera Dev. Team, I have a question about the Minimizer. I want to use it in the Python/IDLE to calculate the initial energy of a system during the execution of one of my scripts, but I don't found any way to call the function Minimizer and obtain the numeric result without show the addCharge window if I have a metallic system. What can I do to call this function correctly? Thank You Elisabeth Ortega Universitat Autònoma de Barcelona

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Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? the exception message as follow: ------------------------------------------------- Executing test.py... Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open models = func(filename, *args, **kw) File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 10, in <module> for arg_k, arg_v in opts: NameError: name 'opts' is not defined Error while processing test.py: NameError: name 'opts' is not defined File "test.py", line 10, in <module> for arg_k, arg_v in opts: See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing -t: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing test: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. ---------------------------------------------------------- At 2011-03-15 09:02:09，"Greg Couch" <gregc(a)cgl.ucsf.edu> wrote: (This is really achimera-dev(a)cgl.ucsf.edu mailing list question.) My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up. So in the beginning of your Python script, add: import chimeraInit chimeraInit.init(nogui=True, silent=True) before using chimera's modules. But, in general, you would be better off running those python scripts with chimera. For example: % chimera --nogui --silent script.py That would set up the the appropriate environment for chimera, execute the python script, and exit. And you would be protected against any future changes in how chimera is initialized. If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera). If you want to install other Python packages into chimera's Python that have a setup.py file, use: % chimera --nogui --silent setup.py install It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details). Right now, chimera is using Python 2.7. HTH, Greg

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Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep
by wascm 15 Mar '11

15 Mar '11

Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric

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Chimera-dev March 2011