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.
A complete user manual is included in the package.
Releases, source code and an issue tracker can be found at the surge
github repository.
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 -o
switch 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
Mehmet Aziz Yirik, Christoph Steinbeck, Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany