[](https://badge.fury.io/py/py-packman) [](https://github.com/Pranavkhade/PACKMAN/actions/workflows/python-package.yml) [](https://py-packman.readthedocs.io/en/latest/?badge=latest) [](https://pepy.tech/project/py-packman)
PACKMAN: PACKing and Motion ANalysis
------------------------------------
<img src="https://github.com/Pranavkhade/PACKMAN/blob/master/docs/_static/gallary/logo.gif" width="250">
This package focuses on studying molecular structures and their dynamics using a simple yet informative property known as Protein Packing. Over the last few years, we have worked on several techniques to capture and quantify the protein packing, resulting in a few publications. This package has all the code to repeat and further develop these techniques.
DOCUMENTATION
-------------
* [IMPORTANT : Documentation, Tutorials & More](https://py-packman.readthedocs.io)
INSTALLATION
------------
1. Installing with pip (Recommended)
```
pip install py-packman
```
2. Installing from source
```
git clone https://github.com/Pranavkhade/PACKMAN
cd PACKMAN
python setup.py install
```
HOW TO USE
----------
PACKMAN, along with its components, can be accessed via Graphical User Interface (GUI), Command-line Interface (CLI), and Application programming interface (API).
For the GUI, please run the following command.
```
python -m packman gui
```
OR
```
python3 -m packman gui
```
For the CLI and API, please read the tutorials & documentation.
REPORTING ISSUES
----------------
[Click here](https://github.com/Pranavkhade/PACKMAN/issues/new) to report issues with any aspect of the package. Please search for the resolved issues first.
WEB SERVERS
-----------
* [Hinge Prediction Web Server](https://packman.bb.iastate.edu/)
* [hd-ANM Web Server](https://hdanm.bb.iastate.edu/)
* [Packing Entropy Web Server](https://packing-entropy.bb.iastate.edu/)
* [DCI web server](https://dci.bb.iastate.edu/)
RELATED RESEARCH ARTICLES
-------------------------
* [PACKMAN-molecule](https://doi.org/10.1093/bioadv/vbac007)
* [Hinge Prediction](https://doi.org/10.1016/j.jmb.2019.11.018)
* [Compliance](https://doi.org/10.1002/prot.25968)
* [hd-ANM](https://doi.org/10.1016/j.bpj.2021.10.017)
* [Packing Entropy](https://doi.org/10.1021/acsomega.2c00999)
* [DCI](https://doi.org/10.1093/bioinformatics/btac159)
ACKNOWLEDGEMENTS
----------------
The development of the PACKMAN package webservers are supported by [NSF](https://www.nsf.gov/) grant DBI 1661391. The authors also thank [ResearchIT@Iowa State University](https://researchit.las.iastate.edu/about-research-it-iowa-state-university) for helping with many aspects of computing.
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