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Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation

Christopher J Woods^1,2,3, Lester O Hedges^1,3, Adrian J Mulholland²

¹Advanced Computing Research Centre, University of Bristol, Bristol, United Kingdom.

The Journal of Chemical Physics

|May 30, 2024

Summary

This summary is machine-generated.

Sire is a versatile Python/C++ library that acts as an interoperability engine for molecular simulation programs. It simplifies data exchange and algorithm prototyping, enhancing research workflows.

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Published on: April 12, 2019

Area of Science:

Computational chemistry
Bioinformatics
Software engineering

Background:

Molecular simulation software often lacks interoperability.
Prototyping new algorithms requires integrating diverse computational tools.
Efficient data exchange between simulation programs is crucial for complex research.

Purpose of the Study:

To introduce Sire, a Python/C++ library designed as an interoperability engine.
To facilitate the integration of various molecular simulation programs and libraries.
To enable researchers to prototype new algorithms and streamline computational workflows.

Main Methods:

Sire provides file parsers and information converters for seamless data exchange.
It integrates with tools like Gemmi, RDKit, BioSimSpace, OpenMM, and NGLView.
Includes engines for molecular information search, trajectory manipulation, and energy evaluation.

Main Results:

Enables researchers to load, search, edit, and combine molecular information from multiple sources.
Facilitates GPU-accelerated molecular dynamics and complex workflow execution.
Sire's engine is utilized by BioSimSpace for interconversion with GROMACS, NAMD, Amber, and AmberTools.

Conclusions:

Sire significantly enhances flexibility and efficiency in molecular simulation research.
It serves as a foundational tool for developing novel algorithms and complex computational pipelines.
Sire is open-source, accessible via conda and a Jupyter notebook server, and supported by OpenBioSim.