fix: missing root tag bug fix

resources/scripts/python/3d/extract_3d.py

@@ -0,0 +1,51 @@
+import os
+import json
+import pandas as pd
+from rdkit import Chem
+from rdkit.Chem import SDWriter
+from tqdm import tqdm  # For progress bar
+
+# === CONFIGURATION ===
+csv_file = "/Users/chandu-jena/Development/nfdi4chem/coconut/resources/scripts/python/3d/coconut_30_01_2025.csv"
+input_folder = "/Users/chandu-jena/Development/nfdi4chem/coconut/resources/scripts/python/3d/molecules_3d"
+output_sdf = "coconut_30_01_2025_3D.sdf"
+
+# === STEP 1: READ CSV & GET IDENTIFIERS ===
+df = pd.read_csv(csv_file, usecols=["identifier"])  # Load only necessary column
+identifiers = set(df["identifier"].astype(str))  # Convert to string & store as a set for fast lookup
+print(f"✅ Loaded {len(identifiers)} unique identifiers from CSV")
+
+# === STEP 2: PROCESS JSON FILES ===
+json_files = [os.path.join(input_folder, f) for f in os.listdir(input_folder) if f.endswith(".json")]
+writer = SDWriter(output_sdf)
+
+matched_count = 0
+failed_count = 0
+
+for json_path in tqdm(json_files, desc="Processing JSON Files", unit="file"):
+    try:
+        with open(json_path, "r", encoding="utf-8") as file:
+            data = json.load(file)
+    except (json.JSONDecodeError, FileNotFoundError) as e:
+        print(f"⚠️ Skipping {json_path}: {e}")
+        continue
+
+    # Filter JSON keys to only those present in CSV
+    matched_keys = identifiers.intersection(data.keys())
+
+    for key in matched_keys:
+        mol_block = data[key]
+        mol = Chem.MolFromMolBlock(mol_block, sanitize=False, removeHs=False)
+
+        if mol:
+            mol.SetProp("coconut_id", key)  # Store key as a property
+            writer.write(mol)
+            matched_count += 1
+        else:
+            failed_count += 1
+
+# === STEP 3: CLOSE WRITER & SUMMARY ===
+writer.close()
+print(f"\n✅ Exported {matched_count} molecules to {output_sdf}")
+if failed_count:
+    print(f"⚠️ {failed_count} molecules failed to parse.")