Weighted Ensemble Python (wepy)
[[./info/logo/wepy.svg]]
[[https://adicksonlab.github.io/wepy/index.html][Sphinx Documentation]]
[[https://github.com/ADicksonLab/wepy/blob/master/info/README.org][Plaintext Org-Mode Docs]]
Modular implementation and framework for running weighted ensemble (WE) simulations in pure python, where the aim is to have simple things simple and complicated things possible. The latter being the priority.
The goal of the architecture is that it should be highly modular to allow extension, but provide a "killer app" for most uses that just works, no questions asked.
Comes equipped with support for [[https://github.com/pandegroup/openmm][OpenMM]] molecular dynamics, parallelization using multiprocessing, the [[http://pubs.acs.org/doi/abs/10.1021/jp411479c][WExplore]] and [[https://pubmed.ncbi.nlm.nih.gov/31255090/][REVO]] (Resampling Ensembles by Variance Optimization) resampling algorithms, and an HDF5 file format and library for storing and querying your WE datasets that can be used from the command line.
The deeper architecture of ~wepy~ is intended to be loosely coupled, so that unforeseen use cases can be accomodated, but tightly integrated for the most common of use cases, i.e. molecular dynamics.
This allows freedom for fast development of new methods.
Full [[https://github.com/ADicksonLab/wepy/blob/master/info/introduction.org][introduction]].
** Installation
Also see: [[info/installation.org][Installation Instructions]]
We recommend running this version of wepy
in a conda environment using python=3.10
or greater:
conda create -n wepy python=3.10 conda activate wepy
Next, install wepy
with pip:
pip install wepy
which will also install most dependencies.
Alternatively, the latest version of wepy
can be installed from the git repo source:
git clone https://github.com/ADicksonLab/wepy.git cd wepy pip install .
The OpenMM package can then be installed using conda:
conda install -c conda-forge openmm
Check its installed by running the command line interface:
wepy --help
** Citations
Current [[https://zenodo.org/badge/latestdoi/101077926][Zenodo DOI]].
Cite software as:
Samuel D. Lotz, Nazanin Donyapour, Alex Dickson, Tom Dixon, Nicole Roussey, & Rob Hall. (2020, August 4). ADicksonLab/wepy: 1.0.0 Major version release (Version v1.0.0). Zenodo. http://doi.org/10.5281/zenodo.3973431
Accompanying journal article: