""" Validate pubchem_dataset records using ActionExecutor. Translates old-format operation dicts (raw atom_idx params) to the new ActionExecutor JSON protocol, then checks that executing the action on wrong_smiles reproduces correct_smiles. Usage: python validate_with_executor.py [--dataset ./data/pubchem_dataset] [--verbose] """ import os, sys, json, argparse from collections import Counter, defaultdict sys.path.insert(0, os.path.dirname(__file__)) from rdkit import Chem, RDLogger RDLogger.DisableLog("rdApp.*") from action_executor import ActionExecutor, ActionError # --------------------------------------------------------------------------- # Old-format → ActionExecutor JSON translation # --------------------------------------------------------------------------- def translate_operation(op: dict) -> dict: """ Convert a mol_corrupt.py correction dict to an ActionExecutor action dict. New format (atom_map / anchor_map / atom1_map / atom2_map) uses map_num refs. Old format (atom_idx / anchor_idx / atom_idx1 / atom_idx2) uses idx refs. Both are handled transparently. """ old_type = op["type"] params = op.get("params", {}) # Determine ref style: map-num (new) or raw idx (old) has_maps = any(k in params for k in ("atom_map", "anchor_map", "atom1_map", "atom2_map")) def atom_ref(map_key, idx_key): if has_maps and map_key in params: return {"map_num": params[map_key]} return {"idx": params[idx_key]} def bond_ref(map1, idx1, map2, idx2): return {"atom1": atom_ref(map1, idx1), "atom2": atom_ref(map2, idx2)} if old_type == "change_atom_element": return { "type": "ChangeAtom", "atom": atom_ref("atom_map", "atom_idx"), "element": params["to_elem"], } if old_type == "change_charge": return { "type": "ChangeAtom", "atom": atom_ref("atom_map", "atom_idx"), "charge": params["to_charge"], } if old_type == "add_atom": return { "type": "AddAtom", "anchor": atom_ref("anchor_map", "anchor_idx"), "element": params["new_elem"], "bond_order": params.get("bond_type", "SINGLE"), } if old_type == "remove_atom": return { "type": "RemoveAtom", "atom": atom_ref("atom_map", "atom_idx"), } if old_type == "change_bond_order": return { "type": "ChangeBond", "bond": bond_ref("atom1_map", "atom_idx1", "atom2_map", "atom_idx2"), "order": params["to_order"], } if old_type == "add_bond": return { "type": "AddBond", "bond": bond_ref("atom1_map", "atom_idx1", "atom2_map", "atom_idx2"), "order": params.get("bond_type", "SINGLE"), } if old_type == "remove_bond": return { "type": "RemoveBond", "bond": bond_ref("atom1_map", "atom_idx1", "atom2_map", "atom_idx2"), } if old_type == "add_functional_group": return { "type": "AddGroup", "anchor": atom_ref("anchor_map", "anchor_idx"), "group": params["group_name"], } if old_type == "remove_functional_group": return { "type": "RemoveGroup", "anchor": atom_ref("anchor_map", "anchor_idx"), "group": params["group_name"], } if old_type == "flip_chirality": return { "type": "FlipChirality", "atom": atom_ref("atom_map", "atom_idx"), } if old_type == "flip_ez": # SMILES-level op — find the double bond automatically return {"type": "FlipEZ"} if old_type == "move_substituent": return { "type": "MoveSubstituent", "substituent": {"map_num": params["substituent_map"]}, "from_atom": {"map_num": params["from_map"]}, "to_atom": {"map_num": params["to_map"]}, } if old_type == "swap_substituents": return { "type": "SwapSubstituents", "atom1": {"map_num": params["ring1_map"]}, "atom2": {"map_num": params["ring2_map"]}, } raise ValueError(f"Unhandled old type: {old_type!r}") # --------------------------------------------------------------------------- # Validation # --------------------------------------------------------------------------- def validate(records, verbose=False): ex = ActionExecutor() results = defaultdict(lambda: {"pass": 0, "fail": 0, "error": 0}) failures = [] for r in records: op_type = r["operation"]["type"] # Prefer mapped SMILES (new format) so map_num refs work correctly wrong = r.get("wrong_smiles_mapped") or r.get("wrong_smiles", "") correct = r["correct_smiles"] try: action = translate_operation(r["operation"]) except Exception as e: results[op_type]["error"] += 1 failures.append({"id": r.get("id"), "op": op_type, "kind": "translate_error", "msg": str(e)}) continue try: restored = ex.execute(wrong, action) except ActionError as e: results[op_type]["error"] += 1 failures.append({ "id": r.get("id"), "op": op_type, "kind": "executor_error", "msg": str(e), "wrong": wrong, "action": action, }) continue except Exception as e: results[op_type]["error"] += 1 failures.append({ "id": r.get("id"), "op": op_type, "kind": "unexpected_error", "msg": str(e), "wrong": wrong, }) continue # Canonicalize both for fair comparison mol_r = Chem.MolFromSmiles(restored) if restored else None mol_c = Chem.MolFromSmiles(correct) canon_r = Chem.MolToSmiles(mol_r) if mol_r else None canon_c = Chem.MolToSmiles(mol_c) if mol_c else None if canon_r == canon_c: results[op_type]["pass"] += 1 else: results[op_type]["fail"] += 1 failures.append({ "id": r.get("id"), "op": op_type, "kind": "mismatch", "wrong": wrong, "expected": correct, "got": restored, "action": action, }) return results, failures # --------------------------------------------------------------------------- # Report # --------------------------------------------------------------------------- def report(results, failures, verbose=False): print("=" * 76) print(f"{'Op Type':<35} {'Total':>6} {'Pass':>5} {'Fail':>5} {'Error':>6} {'Rate':>6}") print("-" * 76) total_p = total_f = total_e = 0 for op in sorted(results): r = results[op] p, f, e = r["pass"], r["fail"], r["error"] n = p + f + e rate = p / n * 100 if n else 0 mark = "" if (f + e) == 0 else " āœ—" print(f"{op:<35} {n:>6} {p:>5} {f:>5} {e:>6} {rate:>5.0f}%{mark}") total_p += p; total_f += f; total_e += e total = total_p + total_f + total_e print("-" * 76) rate = total_p / total * 100 if total else 0 print(f"{'TOTAL':<35} {total:>6} {total_p:>5} {total_f:>5} {total_e:>6} {rate:>5.0f}%") print("=" * 76) if failures: show = failures if verbose else failures[:5] print(f"\n--- {len(failures)} failure(s){' (showing first 5)' if not verbose and len(failures) > 5 else ''} ---") for fl in show: print(f"\n [{fl['op']}] id={fl.get('id')} kind={fl['kind']}") if fl["kind"] == "mismatch": print(f" wrong : {fl['wrong']}") print(f" action : {fl['action']}") print(f" expected : {fl['expected']}") print(f" got : {fl['got']}") elif fl["kind"] in ("executor_error", "translate_error", "unexpected_error"): print(f" wrong : {fl.get('wrong', '')}") print(f" action : {fl.get('action', '')}") print(f" error : {fl['msg']}") else: print("\nāœ“ All records pass validation.") def main(): parser = argparse.ArgumentParser() parser.add_argument("--dataset", default="./data/pubchem_dataset") parser.add_argument("--verbose", action="store_true", help="Show all failures") args = parser.parse_args() for name in ("dataset.json", "roundtrip_test.json"): p = os.path.join(args.dataset, name) if os.path.exists(p): json_path = p break else: print(f"No dataset JSON found in {args.dataset}") sys.exit(1) with open(json_path) as f: records = json.load(f) print(f"Loaded {len(records)} records from {json_path}\n") results, failures = validate(records, verbose=args.verbose) report(results, failures, verbose=args.verbose) if __name__ == "__main__": main()