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The python free energy analysis toolkit

Project Description

The python free energy analysis toolkit.

Please note that this code is still under heavy development!

Authors

*) 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).
Release History

Release History

This version
History Node

0.2.2

History Node

0.2.1

History Node

0.2.0

Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pyfeat-0.2.2.tar.gz (317.8 kB) Copy SHA256 Checksum SHA256 Source Aug 14, 2014

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