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Keep cross-ASU connections when expanding a biological assembly - #440
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finalize_expansion copied only Asu::Same (1_555) links. Cross-ASU covalent ligands, including 3TL in PDB 1b11, disappeared after transform_to_assembly. Fixes project-gemmi#432.
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transform_to_assemblycopiesConnectiononly for NCS expansion orAsu::Same(1_555). Cross-ASU links, including the covalent C2–C2 of ligand3TLin PDB 1b11, hit an empty else and vanish. The same-ASU path already remaps both partners through onechain_map; this uses the Cartesian product ofchain_mapsfor the remaining ASU class and keeps a pair when both atoms exist in the expanded model. Clearing the connection list, or changing onlyAsu::Same, would drop biological-assembly topology.Fixes #432.