CSB Computational Structural Biology Toolbox
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Python library Python framework biology

CSB Description

CSB is a Python library and application framework, which can be used to solve problems in the field of Computational Structural Biology. If you are a bioinformatician, software engineer or a researcher working in this field, chances are you may find something useful here. Our package consists of a few major components:1. Core class library -- object-oriented, granular, with an emphasis on design and clean interfaces.2. Application framework -- console applications ("protocols"), which consume objects from the core library in order to build something executable (and hopefully useful).3. Test framework -- makes sure the library actually works.CompatibilityIn short: requires python 2.6 or higher.CSB is being developed on Linux, under python 2.7. However, compatibility is a design goal and the package works on any platform, on any modern python interpreter since version 2.6 (yes, that includes python 3 support out of the box). If you found any issues on a platform/interpreter different from our development environment, please let us know. We will kindly apologize, fix the problem and write a regression test case to make sure that the problem will be solved once and forever.InstallationIs your interpreter Compatible? If yes, proceed with the installation of a few trivial packages, on which CSB depends:1. numpy -- mandatory (numpy.scipy.org)2. scipy -- mandatory (scipy.org)3. matplotlib and wxPython -- optional, needed only if you want to use csb.io.plots4. unittest2 -- needed only if you are using python 2.65. argparse -- may be needed if you are using python 2.6If you are installing CSB on Windows, numpy, scipy and matplotlib can be installed from binary MSI/exe packages, the rest can be installed from PyPi. On Debian-like Linux distributions use your package manager: apt-get install *package*where package is one of: python-numpy, python-scipy, python-matplotlib.Finally, install CSB itself: python setup.py installCSB has been just installed at the following location: python -c "import csb, os; print(os.path.abspath(os.path.join(csb.__path__, '..')))"Let's call this path $LIB.TestingRunning the CSB test suite may be useful if you made any modifications to the source code, or if you simply want to check if your installation works.All CSB tests are executed with the csb.test.Console. A typical way to run the console is: python $LIB/csb/test/app.py "csb.test.cases.*"or just:python $LIB/csb/test/app.pyFor help try: python $LIB/csb/test/app.py -hFor more details on our test framework, including guidelines for writing unit test, please refer to the API documentation, package "csb.test".Product's homepage

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