The python free energy analysis toolkit
Project description
The python free energy analysis toolkit.
Please note that this code is still under heavy development!
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.
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