FreeEnergyNetworkAnalysis

What is FreeEnergyNetworkAnalysis?

It is a python (3.5+) module for analysing alchemical free energy simulations based on a given pertubration map. The tool works well with SOMD output.

Installation

with pip:
pip install freenrgworkflows

from github:

git clone git@github.com:michellab/freenrgworkflows.git   
cd freenrgworkflows   
python setup.py install  

Testing your installation

To test the installation from the github repository you can use the pytest frame work by typing:

pytest --verbosity 1 tests

in the root directory, i.e. freenrgworkflows

Getting started

Networkanalysis provides both a simple API and a commandline tool in order to extract relative free energies from a large number of perturbations. The main script can be found in the bin directory and run in the following way:

python run_networkanalysis.py --help

Gives information on the command line options available. An example usage can loook like this:

python run_networkanalysis.py ../tests/io/summary_r1.csv --target_compound FXR45 -o ~/Desktop/blub.dat -e ../tests/io/ic50_exp.dat --stats --generate_notebook

summary_r1.csv is an collated output of analyse_freenrg mbar from SOMD, the target compound is randomly selected. The output file can be anything really, such as blub.dat written to the computers desktop. If you want to compare experiments to simulations you will need to provide a file containing IC50s on the commandline or kDs with the API. The flag --generate_notebook will generate a default jupyter notebook running the analysis from a notebook including plots comparing the experimental and computed free energies. The generated notebook can be opened using jupyter notebook ~/Desktop/blub.ipynb

Authors

• Antonia Mey [antonia.mey@ed.ac.uk]: Maintainer
• Mark Mackey
• Paolo Tosco
• Jenke Scheen
• Julien Michel

Questions, Comments, Docs

Contact one of the authors.

License

This work is licensed under Attribution-ShareAlike 2.0 Generic (CC BY-SA 2.0).