| 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) |
| DataStructs.ConvertToNumpyArray(fp, arr) |
| 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) |
