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MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation
Mehmet Aziz Yirik1, Maria Sorokina1, Christoph Steinbeck2
1Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743, Jena, Germany.
Abstract:
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 in single-threaded mode against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution PMG. Based on the benchmarking, MAYGEN is on average 47 times faster than PMG and on average three times slower than MOLGEN in performance.
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