Surge: a fast open-source chemical graph generator.

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.