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

28 April 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


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.


constitutional isomer generation
algorithmic group theory
algorithmic graph theory
chemical graph generation
open-source software


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