{"paper":{"title":"Atomic Design Transformer: Scaffold-Conditioned 3D Molecule Generation via xTB-Reward Reinforcement Learning","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"physics.comp-ph","authors_text":"Takao Kotani","submitted_at":"2026-07-17T12:48:57Z","abstract_excerpt":"We present an SE(3)-invariant transformer for 3D-molecule generation,\n  the Atomic Design Transformer (ADT). ADT places atoms one\n  at a time, autoregressively. SE(3) invariance is achieved by\n  tokenization: each new atom's position is encoded in the local\n  coordinate frame of a previously placed atom. The backbone is a plain\n  causal transformer. The token stream fully specifies a 3D structure\n  together with its chemical-bond graph G, without any bond-order\n  assignment. To score generated molecules we introduce the xTB\n  topology-preservation rate (XTP): the fraction of molecules for\n  wh"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.15918","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2607.15918/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}