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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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Surge: a fast open-source chemical graph generator.

Brendan D McKay¹, Mehmet Aziz Yirik², Christoph Steinbeck³

¹School of Computing, Australian National University, Canberra, ACT, 2601, Australia. brendan.mckay@anu.edu.au.

Journal of Cheminformatics

|April 24, 2022

Summary

This summary is machine-generated.

This study introduces Surge, a novel constitutional isomer generator for cheminformatics. Surge is the fastest structure generator currently available, utilizing a canonical generation path method and graph automorphism computations.

Keywords:

Canonical generation path Constitutional isomers Structure generation

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Area of Science:

Cheminformatics
Computational Chemistry
Graph Theory

Background:

Chemical structure generators are vital in cheminformatics for creating virtual molecules.
These generators can start from molecular formulas to produce constitutional isomers.
Existing methods face challenges in efficiency and speed for isomer generation.

Purpose of the Study:

To introduce Surge, a novel and highly efficient constitutional isomer generator.
To present the canonical generation path method as the core principle of Surge.
To demonstrate Surge's superior performance through benchmarking.

Main Methods:

Development of the Surge algorithm based on the canonical generation path method.
Integration of the nauty package for computing graph automorphism groups.
Benchmarking Surge against existing chemical structure generators.

Main Results:

Surge successfully generates constitutional isomers from molecular formulas.
Benchmarking confirms Surge as the fastest chemical structure generator to date.
The canonical generation path method provides a robust framework for isomer enumeration.

Conclusions:

Surge represents a significant advancement in the speed and efficiency of constitutional isomer generation.
The open-source availability of Surge promotes its adoption in cheminformatics research.
This novel generator facilitates drug discovery and materials science through rapid virtual molecule creation.