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.

中文翻译：

---

MAYGEN：基于有序生成原理的开源化学结构生成器

自 20 世纪 60 年代初以来，组成异构体化学空间的生成一直是化学信息学的一个主题，并在结构阐明和其他方面得到应用。为了高效、彻底且无同构地执行这种生成，结构生成器需要确保在生成步骤期间就已经构建了规范图，而不是通过后续过滤。在这里，我们介绍 MAYGEN，一种开源、纯 Java 开发的结构异构体分子生成器。概述了 MAYGEN 架构和算法的原理，并在单线程模式下针对最先进的闭源解决方案 MOLGEN 以及最佳开源解决方案 PMG 对软件进行了基准测试。根据基准测试，MAYGEN 的性能平均比 PMG 快 47 倍，平均比 MOLGEN 慢 3 倍。