LigParGen-GUI

Quick Installation

Contents of this document

• Description
• Contents of this repository
  • Sources
  • Documentation
  • Assets
• Installation
  • Windows
  • Source code
• Dependencies
• Citation
• References and useful links
• Acknowledgements

Description

LigParGen-GUI is an open software project that builds upon the software LigParGen v2.1 by providing a graphical user interface for easy use on a local computer. This software aims to make running LigParGen more accessible for the scientific end-user.

Contents of this repository

Sources

The ligpargen_gui subfolder contains all source code including Python modules, Qt .ui files and cascading stylesheets.

Documentation

The "docs" folder contains the end-user documentation in the form of markdown and HTML files. The subfolder "dev-notes", contains development notes.

Assets

The "assets" folder consists of the subfolder "images" which contains the LigParGen-GUI logo. If you are using LigParGen-GUI for your own projects, you are welcome to give credit to LigParGen-GUI by using the logo in your presentations, etc.

Installation

LigParGen-GUI is tested and available for Windows 10 and 11.

Windows

For a convenient and user-friendly installation, follow the instructions in the Quick Installation document.

Important:

• WSL2 cannot be uninstalled once it is installed! Windows will integrate the WSL2 as a system component.
• Be aware that the computer needs to be restarted after installing WSL2.

Source code

This is a Python project based on a virtual environment. To modify the source code, download or clone the repository and open it in an IDE that supports virtual environments (e.g. PyCharm). Finally, run pip install -r requirements.txt to set up the virtual environment used for development.

The project supports using a setup.py file to create a package that works with the LigParGen-GUI Component Installer. To build the inno setup EXE run: run_automation.bat build-setup-exe.

Dependencies

Needs to be installed yourself if prompted

• BOSS
  • Download the BOSS software from the official William L. Jorgensen lab website: http://zarbi.chem.yale.edu/software.html Managed by LigParGen-GUI:
• Windows Subsystem for Linux 2
  • WSL2
  • License: Microsoft Software License Terms
• LigParGen
  • LigParGen v2.1
  • License: MIT License
• PyQt6
  • License: GNU General Public License (GPL)

Citation

You can cite this software or this repository as it is defined in the CITATION.cff file.

References and useful links

LigParGen

• LigParGen v2.1 GitHub repository
• LigParGen Web Server
• Dodda, L., Cabeza de Vaca, I., Tirado-Rives, J., Jorgensen, W. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Research 45, 331–336 (2017). https://doi.org/10.1038/s41592-022-01488-1

Acknowledgements

Developers:

• Martin Urban
• Hannah Kullik

End-user testers

• Mirco Daniel
• Achim Zielesny

Logo:

• Martin Urban
• Hannah Kullik

Initialization, conceptualization, and supervision:

• Mirco Daniel and Achim Zielesny

The LigParGen-GUI project team would like to thank the communities behind the open software libraries for their amazing work.