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MAYGEN V1.1.pdf (1.28 MB)

MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle

revised on 30.04.2021, 15:36 and posted on 03.05.2021, 09:34 by Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.

Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.


Email Address of Submitting Author


University Friedrich-Schiller



ORCID For Submitting Author


Declaration of Conflict of Interest

All authors declare no conflict of interest.

Version Notes

Version 1.1