e640424817
* reorg for clarity * moving try/except into function for clarity * reorg data parsing for clarity * remove unused function * add try/except to pass through info about failed edges * updating tests for new expected failed simulation checking behavior * pass through for raw and ddg * pass through failures for dgs * remove unused import * adding a missing check * docstrings * cleaning up logic * cleaning up logic * docstrings and formatting * fixing conditionals bug * more docstrings * make 'name' a tuple for consistency * make functions private * updating output statement for clarity (hopefully) * remove unused dg raw expected output * adding comment description * updating tests * cleaning up test to not use tmp dir * only use non-None legs for deciding whether to do rbfe/rhfe * fix typo * pass empty list instead of None through to ddg * add cmet data * add assert success tests - still need output validation * light reordering for clarity * adding pytest regressions * don't include stderr in file regression * making output more legible * switch from runtime error to exit(1) * add missing complex legs test * adding regressoin tsvs to manifest * reordering functions for clarity * updating tests * adding test for disconnected network * updating warning message, not throwing error for now * updating tests for missing runs * add disconnected network check * switch from NaN to Error * removing unused regression files * fixing typo * adding test coverage * fix typo * adding news entry
openfe - A Python package for executing alchemical free energy calculations.
The openfe package is the flagship project of Open Free Energy,
a pre competitive consortium aiming to provide robust, permissively licensed open source tools for molecular simulation in the drug discovery field.
Using openfe you can easily plan and execute alchemical free energy calculations.
See our website for more information on the project, try for yourself from the comfort of your browser, and we have documentation on using the package.
License
This library is made available under the MIT open source license.
Install
Latest release
The latest release of openfe can be installed via mamba, docker, or a single file installer. See our installation instructions for more details.
Dependencies can be installed via conda through:
Development version
The development version of openfe can be installed directly from the main branch of this repository.
First install the package dependencies using mamba:
mamba env create -f environment.yml
The openfe library can then be installed via:
python -m pip install --no-deps .
Authors
The OpenFE development team.
Acknowledgements
OpenFE is an Open Molecular Software Foundation hosted project.