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workflow/07.pubchem_exploration_fingerprints.py

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+import os
+
+# Data Manipulation
+import pickle
+import numpy as np
+import pandas as pd
+from tqdm import tqdm
+
+
+# Rdkit
+from rdkit import Chem
+from rdkit.Chem import Descriptors
+from rdkit.Chem import Draw
+from rdkit.Chem import AllChem
+
+from rdkit.Chem import DataStructs
+
+
+RAW_DATA_DIR = "../raw_data"
+
+OUTPUT_DIR = "../data/07.pubchem_exploration"
+os.makedirs(OUTPUT_DIR, exist_ok=True)
+
+def main():
+
+    # Read complete data
+    pchem_df = pd.read_csv(os.path.join(RAW_DATA_DIR, "pubchem_random", "pubchem_100k_selected_smiles.tsv.gz"), sep='\t')
+
+
+    # Convert all chemicals into fingerprints
+    fps_dictionary = {cid:AllChem.GetMorganFingerprintAsBitVect(Chem.MolFromSmiles(pchem_df.loc[pchem_df["chem_id"]==cid, "smiles"].values[0]), 
+                                                            radius=2,
+                                                            nBits=1024) for cid in tqdm(pchem_df.chem_id)}
+    
+    # Save dictionary
+    with open(os.path.join(OUTPUT_DIR, "fps_dictionary.pkl"), "wb") as file:
+        pickle.dump(fps_dictionary, file)
+
+
+if __name__ == "__main__":
+    main()
+