Linguistics Pathway Analysis of Trajectories using Hierarchical clustering

A user-friendly, Python tool for clustering pathways from molecular dynamics and weighted ensemble simulations.

Copyright

This software is distributed with the MIT License.

Copyright © 2023, Anthony Bogetti, Jeremy Leung, Lillian Chong

Quickstart Guide

Users may install this program via PyPI (recommended) or from GitHub Source. By default, LPATH is installed with the bare minimum to run analysis on classic MD simulations. Users who intend to analyze WESTPA simulations should install WESTPA in the same environment.

1. Install from PyPI: python -m pip install lpath-md
2. Install from GitHub Source:
   1. Clone the git repository: git clone https://github.com:chonglab-pitt/lpath
   2. Move into the folder: cd lpath
   3. Install the program in editable mode: python -m pip install -e .
3. There are a variety of optional dependencies you may install. These work with either installation options listed above.
   1. Install with WESTPA: python -m pip install lpath-md[westpa]
   2. Install with terminal user interface (TUI): python -m pip install lpath-md[tui]
   3. Developers can install with [dev] (all dependencies) or [test] (minimal dependencies to run tests): python -m pip install lpath-md[dev]
   4. Options may be combined: python -m pip install lpath-md[westpa,tui]

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.