Handle duplicate AF3 residue IDs during inference

test/check_alphafold3_predictions.py

@@ -1262,6 +1262,39 @@ class TestAlphaFold3RunModes(_TestBase):
         self.assertEqual(relative_encoding[3, 4, inter_chain_bin], 0)
         self.assertEqual(np.argmax(relative_encoding[3, 4, : 2 * 4 + 2]), 0)
 
+    def test_af3_duplicate_residue_ids_survive_empty_structure_round_trip(self):
+        """AF3 must preserve duplicate residue IDs when rebuilding empty structures."""
+        from alphafold3.common import folding_input
+        from alphafold3.constants import chemical_components
+        from alphafold3.model.atom_layout import atom_layout
+
+        expected_residue_ids = list(range(1, 11)) + list(range(2, 6)) + list(range(12, 16))
+        chain = folding_input.ProteinChain(
+            id="A",
+            sequence="ACDEFGHIKLCDEFMNPQ",
+            ptms=[],
+            residue_ids=expected_residue_ids,
+            unpaired_msa="",
+            paired_msa="",
+            templates=[],
+        )
+        fold_input = folding_input.Input(
+            name="duplicate_residue_ids_test",
+            chains=[chain],
+            rng_seeds=[1],
+        )
+        ccd = chemical_components.Ccd()
+        struc = fold_input.to_structure(ccd=ccd)
+        flat_layout = atom_layout.atom_layout_from_structure(struc)
+        rebuilt = atom_layout.make_structure(
+            flat_layout,
+            atom_coords=np.zeros((flat_layout.atom_name.shape[0], 3), dtype=np.float32),
+            name="duplicate_residue_ids_test",
+            all_physical_residues=struc.present_residues,
+        )
+
+        self.assertEqual(rebuilt.present_residues.id.tolist(), expected_residue_ids)
+
     def test_af3_keeps_discontinuous_chopped_regions_in_one_gapped_chain(self):
         """AF3 must keep multi-region chopped inputs as one gapped protein chain."""
         from alphapulldown.folding_backend.alphafold3_backend import (