Surge: a fast open-source chemical graph generator

Chemical structure generators are used in cheminformatics to produce or enumerate virtual molecules based on a set of boundary conditions. The result can then be tested for properties of interest, such as adherence to measured data or for their suitability as drugs. The starting point can be a potentially fuzzy set of fragments or a molecular formula. In the latter case, the generator produces the set of constitutional isomers of the given input formula. Here we present the novel constitutional isomer generator surge based on the canonical generation path method. Surge uses the nauty package to compute automorphism groups of graphs. We outline the working principles of surge and present benchmarking results which show that surge is currently the fastest structure generator. Surge is available under a liberal open-source license.

Automated summary

Chemical structure generators are crucial in cheminformatics for generating or enumerating virtual molecules based on a set of conditions, which can then be tested for properties and suitability. The novel constitutional isomer generator Surge, based on the canonical generation path method and utilizing the nauty package, is the fastest structure generator according to benchmark testing.