An Autoregressive Flow Model for 3D Molecular Geometry Generation from Scratch

Youzhi Luo, Shuiwang Ji

Keywords: 3D molecular geometry generation, flow models, SphereNet

Abstract: We consider the problem of generating 3D molecular geometries from scratch. While multiple methods have been developed for generating molecular graphs, generating 3D molecular geometries from scratch is largely under-explored. In this work, we propose G-SphereNet, a novel autoregressive flow model for generating 3D molecular geometries. G-SphereNet employs a flexible sequential generation scheme by placing atoms in 3D space step-by-step. Instead of generating 3D coordinates directly, we propose to determine 3D positions of atoms by generating distances, angles and torsion angles, thereby ensuring both invariance and equivariance properties. In addition, we propose to use spherical message passing and attention mechanism for conditional information extraction. Experimental results show that G-SphereNet outperforms previous methods on random molecular geometry generation and targeted molecule discovery tasks. Our code is publicly available as part of the DIG package (https://github.com/divelab/DIG).

One-sentence Summary: We present a novel method for 3D molecular geometry generation from scratch.