Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based protein structure generation, we extend these fragmentation ideas to 3D, treating general molecules as sets of rigid-body motifs. Utilising this representation, we employ SE(3)-equivariant generative modelling for de novo 3D molecule generation from rigid motifs. In our evaluations, we observe comparable or superior results to state-of-the-art across benchmarks, surpassing it in atom stability on GEOM-Drugs, while yielding a 2x to 10x reduction in generation steps and offering 3.5x compression in molecular representations compared to the standard atom-based methods.

翻译：三维分子结构生成通常在原子层面进行，而分子图生成技术常将片段作为结构单元。基于基于框架的蛋白质结构生成的最新进展，我们将这些片段化思想扩展到三维空间，将一般分子视为刚性基元的集合。利用这种表示方法，我们采用SE(3)等变生成模型，实现从刚性基元出发的从头三维分子生成。在评估中，我们在多个基准测试中观察到与最先进方法相当或更优的结果，在GEOM-Drugs数据集上原子稳定性方面超越现有方法，同时与标准的基于原子的方法相比，生成步骤减少2至10倍，分子表示压缩3.5倍。