Metadata-Version: 1.1
Name: pyfeat
Version: 0.2.2
Summary: The python free energy analysis toolkit
Home-page: http://github.com/cmb-fu/pyfeat
Author: The pyfeat team
Author-email: pyfeat@lists.fu-berlin.de
License: Simplified BSD License
Description: ******
        pyfeat
        ******
        
        The python free energy analysis toolkit.
        
        **Please note that this code is still under heavy development!**
        
        
        Authors
        =======
        
        - Antonia Mey\ :superscript:`*` <antonia.mey@fu-berlin.de>
        - Christoph Wehmeyer\ :superscript:`*` <christoph.wehmeyer@fu-berlin.de>
        - Fabian Paul
        - Hao Wu
        - Frank Noé
        
        
        ``*``) equal contribution
        
        
        Manifest
        ========
        
        - ``README.rst`` (this file)
        - ``LICENCE.rst``
        - ``CHANGELOG.rst``
        - ``setup.py``
        - ``pyfeat/`` (package)
        - ``ext/`` (C/Cython implementation)
        - ``iPythonNotebooks/`` (examples)
        
        
        Getting started
        ===============
        
        For a **development installation** from source, run ::
        
           python setup.py develop --user --verbose
        
        
        and make sure, that your ``PATH`` and ``PYTHONPATH`` environment variables are set and include the ``bin`` and ``site-packages`` directories which you can find in the verbose output.
        
        For a **regular installation**, run ::
        
           python setup.py install [--user] [--verbose]
        
        
        Example: MBAR (via shell script)
        ================================
        
        Go to your bash and run ::
        
           cd PATH_TO_REPOSITORY/iPythonNotebooks
           python generators/gen_st_adwp.py
           run_mbar.py --verbose data/ST_ADW/replica.dat --kT_file data/ST_ADW/kT.dat
        
        
        Example: WHAM (via shell script)
        ================================
        
        Go to your bash and run ::
        
           cd PATH_TO_REPOSITORY/iPythonNotebooks
           python generators/gen_st_adwp.py
           run_wham.py --verbose data/ST_ADW/replica.dat --kT_file data/ST_ADW/kT.dat --wham_file data/ST_ADW/st_wham.dat
        
        
        References
        ==========
        
        - **Shirts MR and Chodera JD**. Statistically optimal analysis of samples from multiple equilibrium states. *J. Chem. Phys.* 129:124105 (2008).
        - **Kumar, S. et al**. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. *J. Comp. Chem.* 13(8), 1011–1021 (1992).
        
        
        Copyright notice
        ================
        
        Copyright (c) 2014, Computational Molecular Biology Group, FU Berlin, 14195 Berlin, Germany.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions
        are met:
        
        1. Redistributions of source code must retain the above copyright notice,
        this list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright
        notice, this list of conditions and the following disclaimer in the
        documentation and/or other materials provided with the distribution.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
        "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
        LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
        A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
        HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
        SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
        TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
        PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
        LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
        NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
        SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Keywords: MBAR,WHAM,free energy
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
