fix filename bug in fold-to-scaffold forwarding

examples/small_molecule_binding/run_test_small_molecule_binding.py

@@ -43,6 +43,24 @@ def setup_mock_inputs(pipeline_name: str) -> None:
                 fh.write(f"# mock placeholder: {fname}\n")
 
 
+def check_af2_filename_derivation() -> None:
+    """Regression check for analysis_fold()'s scores.json -> unrelaxed.pdb
+    filename derivation, against real ColabFold (colabfold_batch) naming."""
+    cases = [
+        (
+            "binder_scores_rank_001_alphafold2_model_3_seed_999.json",
+            "binder_unrelaxed_rank_001_alphafold2_model_3_seed_999.pdb",
+        ),
+        (
+            "binder_scores_rank_005_alphafold2_ptm_model_1_seed_000.json",
+            "binder_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb",
+        ),
+    ]
+    for sf, expected in cases:
+        derived = sf.replace('_scores_', '_unrelaxed_').replace('.json', '.pdb')
+        assert derived == expected, f"{sf!r} -> {derived!r}, expected {expected!r}"
+
+
 async def run_mock_test() -> None:
     pipeline_name = "p1"
     setup_mock_inputs(pipeline_name)
@@ -70,4 +88,5 @@ async def run_mock_test() -> None:
 
 
 if __name__ == "__main__":
+    check_af2_filename_derivation()
     asyncio.run(run_mock_test())

examples/small_molecule_binding/small_molecule_binding.py

@@ -540,7 +540,7 @@ async def analysis_fold():
                     mean_plddt = sum(arr) / len(arr)
                     if mean_plddt > best_plddt:
                         best_plddt = mean_plddt
-                        best_model = sf.replace('_scores.json', '.pdb')
+                        best_model = sf.replace('_scores_', '_unrelaxed_').replace('.json', '.pdb')
 
             if best_model:
                 full_model_path = f"{out_dir}/{best_model}"