Metadata-Version: 2.1
Name: lpath-md
Version: 0.9.5
Summary: A user-friendly, Python tool for clustering pathways from molecular dynamics simulations.
Author-email: Anthony Bogetti <atb43@pitt.edu>, Jeremy Leung <jml230@pitt.edu>, Lillian Chong <lchong@pitt.edu>
Maintainer-email: Jeremy Leung <jml230@pitt.edu>
License: MIT
Project-URL: Source, https://github.com/jeremyleung521/lpath/
Project-URL: Documentation, https://lpath.readthedocs.io/
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scikit-learn
Requires-Dist: scipy
Requires-Dist: numpy
Requires-Dist: pylcs
Requires-Dist: ray
Requires-Dist: tqdm
Requires-Dist: networkx
Requires-Dist: matplotlib
Requires-Dist: timedinput
Requires-Dist: importlib-resources ; python_version < "3.10"
Provides-Extra: dev
Requires-Dist: lpath[test,tui,westpa] ; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest >=6.1.2 ; extra == 'test'
Requires-Dist: pytest-runner ; extra == 'test'
Provides-Extra: tui
Requires-Dist: argparse-tui ; extra == 'tui'
Provides-Extra: westpa
Requires-Dist: westpa >=2022.03 ; extra == 'westpa'

![lpath_logo.png](https://raw.githubusercontent.com/chonglab-pitt/LPATH/main/logo/lpath_logo.png)

Linguistics Pathway Analysis of Trajectories using Hierarchical clustering
==============================
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[![pre-print](https://img.shields.io/badge/pre--print-darkred)](https://www.biorxiv.org/content/10.1101/2023.08.17.553774v1)

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

#### Acknowledgements
 
Project based on the 
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.
