Brendan D. McKay, Mehmet Aziz Yirik and Christoph Steinbeck
Surge is a chemical structure generator based on the canonical generation path method.
Surge uses the Nauty package to compute automorphism groups of graphs and generates all non-isomorphic constitutional isomers of a given molecular formula.
Surge is available under a liberal open source license and its pre-print is also available.
A complete user manual is included in the package.
If you use
surge, please cite:
McKay, B.D., Yirik, M.A. & Steinbeck, C. Surge: a fast open-source chemical graph generator. J Cheminform 14, 24 (2022). https://doi.org/10.1186/s13321-022-00604-9
Surge is a command line tool. Running
surge -u C10H16O will generate the 452458 isomers of C10H16O in 0.1s on some vanilla flavor year-2021 PC. Running
surge -S C10H16O outputs those structures in SMILES format. You can either use
surge -S C10H16O > myresults.smi to redirect the output into a result file, or use the
-oswitch to provide a filename. Further formats supported are SD Files (SDF) and a concise Surge-specific format.
For large sets of structures, the -z option for compressing the output in gzip format will come in handy.
surge -help will show all options. For complete instructions, please see the user manual.
Surge was developed by
Brendan McKay, School of Computing, Australian National University, Canberra, ACT, Australia