A user-friendly, Python tool for clustering pathways from molecular dynamics simulations.
Project description
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.
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