Metadata-Version: 2.1
Name: lpath-md
Version: 1.0.3
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/chonglab-pitt/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: test
Requires-Dist: pytest>=6.1.2; extra == "test"
Requires-Dist: pytest-runner; extra == "test"
Provides-Extra: westpa
Requires-Dist: westpa>=2022.03; extra == "westpa"
Provides-Extra: tui
Requires-Dist: argparse-tui; extra == "tui"
Provides-Extra: dev
Requires-Dist: lpath-md[test,tui,westpa]; extra == "dev"

![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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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](https://pypi.org/project/lpath-md/) (recommended) or 
from [GitHub Source](https://github.com/chonglab-pitt/lpath). 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](https://pypi.org/project/lpath-md/):
    ```python -m  pip install lpath-md```
2. Install from [GitHub Source](https://github.com/chonglab-pitt/lpath):
    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](https://github.com/molssi/cookiecutter-cms) version 1.1.
