Pranavkhade/PACKMAN: Python package built around protein structure and dynamics. OpenBabel-inspired objects. · GitHub

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.

✨ What's new?

• New Streamlit based Web-GUI is launched which allows users to scan multiple alpha values in range and combine hinges along with option to download the .hng file for downstream hdANM analysis. Please read the instructions below for more details.
• Improved support for hinge prediction across multiple alpha parameters. You can now run and combine results for multiple structures using a single script: additional codes/ScanAlpha.py. This streamlines batch processing and saves time. Run python3 ScanAlpha.py -h for more information (Copy the script to PWD).

• IMPORTANT : Documentation, Tutorials & More

This option allows user to use the hinge prediction, hdANM and Entropy calculation all in one place with few clicks. If users do not wish to use any CLI/ Python code, this is the best option. Please install docker

✨If you struggle with the command line, please visit the packman-streamlit repo, select the latest from dropdown and click on "▶︎ Run in Docker Desktop" in bottom right to skip the commands below.

Otherwise, two command setup:

docker pull pranavkhade/packman-streamlit
docker run -p 8501:8501 pranavkhade/packman-streamlit:latest

If a webpage doesn't automatically open use either of the following address on your web-browser (Google Chrome/ Firefox etc.)

http://localhost:8501
OR
http://0.0.0.0:8501

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

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.

Click here to report issues with any aspect of the package. Please search for the resolved issues first.

• Hinge Prediction Web Server
• hd-ANM Web Server
• Packing Entropy Web Server
• DCI web server

• PACKMAN-molecule
• Hinge Prediction
• Compliance
• hd-ANM
• Packing Entropy
• DCI

The development of the PACKMAN package was in past from 2017 to 2022 and webservers still is supported by NSF grant DBI 1661391. The authors also thank ResearchIT@Iowa State University for helping with server deployment @Iowa State University.

Development past April 2022 are done without any financial or any other support of any kind.