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

Project description

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Linguistics Pathway Analysis of Trajectories using Hierarchical clustering

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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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