Surge: a fast open-source chemical graph generator

Abstract

AbstractChemical 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 based on the canonical generation path method. uses the package to compute automorphism groups of graphs. We outline the working principles of and present benchmarking results which show that is currently the fastest structure generator. is available under a liberal open-source license.