src/06_calculate_ecfp.py

from rdkit import Chem
from rdkit.Chem import rdFingerprintGenerator
from rdkit.Chem.Draw import IPythonConsole
from rdkit import DataStructs
import rdkit
import pandas as pd

df=pd.read_parquet("./clean_checkpoints/all_data_merged-cleaned.parquet")

smiles_list=df["Smiles_molvs"]
ecfp_list=[]

mfpgen = rdFingerprintGenerator.GetMorganGenerator(radius=2,fpSize=2048)
for i, smile in enumerate(smiles_list):
    mol = Chem.MolFromSmiles(smile)
    if mol is None:
        raise ValueError(f"Invalid SMILES: {smile}, at item", {i})
    else:
        fp = mfpgen.GetFingerprint(mol)
        arr = np.zeros((2048,), dtype=int)            # make empty array
        DataStructs.ConvertToNumpyArray(fp, arr)      # fill it
        ecfp_list.append(arr)

df["Ecfp_4"]=ecfp_list
col = df.columns[-1]          
df.insert(3, col, df.pop(col)) 

output_file="./ecfp/all_data_merged-cleaned-ecfp4.parquet"
df.to_parquet(output_file, index=False)