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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) |