Linguistics Pathway Analysis of Trajectories using Hierarchical clustering

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

Copyright

Copyright (c) 2023, Anthony Bogetti, Jeremy Leung, Lillian Chong

TODO

• EXTRACT step only does WE right now, need to extend to plain MD (i.e. a states.npy)
• Usage.rst page
• example ipynbs are bare bones, need sample files
• unit testing
• extract defaults to last frame of iteration. Implement stride and actually give pcoord/auxdata to correct frame.
• command line interface/argparser
• Sphinx/Read the Docs autodoc
• Run each tool directly
• Rename Repo

Acknowledgements

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