freeenergynetworkanalysis
Software for automated processing of alchemical free energy calculations
Science Score: 44.0%
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○Scientific vocabulary similarity
Low similarity (17.5%) to scientific vocabulary
Repository
Software for automated processing of alchemical free energy calculations
Basic Info
- Host: GitHub
- Owner: michellab
- Language: Python
- Default Branch: devel
- Size: 244 KB
Statistics
- Stars: 10
- Watchers: 8
- Forks: 6
- Open Issues: 5
- Releases: 0
Metadata Files
README.md
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
summaryr1.csv is an collated output of analysefreenrg 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).
Owner
- Name: michellab
- Login: michellab
- Kind: organization
- Repositories: 84
- Profile: https://github.com/michellab
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: FreeEnergyNetworkAnalysis
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Antonia
family-names: Mey
- given-names: Paolo
family-names: Tosco
- given-names: Scheen
family-names: Jenke
- given-names: Julien
family-names: Michel
repository-code: >-
https://github.com/michellab/freenrgworkflows/tree/devel
license: CC-BY-SA-2.0
GitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Dependencies
- codecov *
- nbformat *
- networkx *
- numpy *
- pytest *
- pytest-cov *
- scipy *
- seaborn *