Theoretical and Computational Chemistry

Surge - A Fast Open-Source Chemical Graph Generator

Authors

  • Brendan D. McKay School of Computing, Australian National University ,
  • Mehmet Aziz Yirik Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University ,
  • Christoph Steinbeck Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University

Abstract

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.

Content

Thumbnail image of Surge- A Fast Open-Source Chemical Graph Generator.pdf

Supplementary weblinks

Surge Website
The website at which surge is hosted. Documentation, software releases and source code are available there.