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arXiv · 2609.34690

Symmetry-Aware Flow Matching for End-to-end Molecular Crystal Generation

Wendi Cai·Fanyang Mo
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Abstract

Molecular crystal packing shapes properties from drug bioavailability to charge transport, yet generating realistic structures requires coordinating molecular flexibility, intermolecular interactions and symmetry. Here we introduce SALA, a flow-matching model built on state--context separation: it evolves only asymmetric-unit (ASU) atomic coordinates and symmetry-compatible lattice parameters while predicting their updates from the full periodic environment. Conditioned on molecular graphs and a space group, SALA generates molecular conformation, lattice geometry and packing end to end while preserving the specified symmetry. Across 799 held-out crystals spanning four chemical classes and all seven crystal systems, SALA achieves a 72.0\% hit rate from 50 candidates per target, compared with 8.1\% for an atomistic full-cell generative baseline. Mean best-candidate packing root-mean-square deviation decreases from 4.48 to 1.70~Å, with the advantage widening as system size and symmetry multiplicity increase. SALA thus enables end-to-end generation of complex, symmetry-constrained molecular crystals, with potential applications in CSP, structure-based pharmaceutical polymorph design and organic molecular materials discovery.

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Wendi Cai, Fanyang Mo. 2026-09-28. Symmetry-Aware Flow Matching for End-to-end Molecular Crystal Generation. https://arxiv.org/abs/2609.34690

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