WepyAnalysis

WepyAnalysis is a modular toolkit for analyzing data generated from Weighted Ensemble (WE) simulations using the Wepy framework.

The codebase is organized into five main components:

• featurization/: Tools for extracting structural features from WE data
• dataset/: Code for generating datasets from WE data
• msm/: Building Markov State Models and performing kinetic analysis
• example/: Example scripts for running simulations with Wepy and building MSMs

This repository is under active development and intended for researchers working with WE data, especially those using the Wepy framework.

Installation

We recommend installing WepyAnalysis with a Python package manager such as conda or mamba. One dependency that cannot be currently installed with pip is csnanalysis. It can be found on github here, along with installation instructions. Once csnanalysis is installed to your python environment, wepy-analysis can be installed with pip as follows:

pip install git+https://github.com/ADicksonLab/wepy-analysis

Zenodo repository

Example dataset files can be found at this link.