Groupy: An Open-Source Toolkit for Molecular Simulation and Property Calculation

Area of Science:

• Computational Chemistry
• cheminformatics

Background:

• Calculating molecular properties and preparing simulation input files are crucial but time-consuming tasks in computational chemistry.
• Existing tools may lack flexibility or require extensive user input.

Purpose of the Study:

• To introduce Groupy, an open-source, versatile, and flexible code for calculating molecular properties and generating input files for molecular simulation software.
• To provide a user-friendly tool that simplifies daily research for computational and experimental chemists.

Main Methods:

• The Groupy code utilizes the group contribution method for property calculations.
• It accepts Simplified Molecular Input Line Entry System (SMILES) strings as input.
• Message Passing Interface (MPI) parallelization is implemented to accelerate computations for large molecular sets.

Main Results:

• Groupy generates clear, readable output data and files in multiple formats.
• The code produces group-contribution-style molecular fingerprints suitable for machine learning applications.
• It offers detailed user guidance and exhibits strong extensibility as an external library.

Conclusions:

• Groupy offers a convenient and efficient solution for molecular property calculations and simulation file preparation.
• Its features, including parallelization and machine learning-ready outputs, enhance its utility for chemists.
• The open-source nature and extensibility of Groupy promote its adoption and further development in the scientific community.