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

03 May 2021, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

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 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.

Keywords

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

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.