| import numpy as np |
| import pandas as pd |
| from rdkit import Chem |
| from rdkit.Chem import Descriptors |
|
|
|
|
| mw_list=[] |
| logp_list=[] |
| TPSA_list=[] |
| HBD_list=[] |
| HBA_list=[] |
| rot_bond_list=[] |
| ring_count_list=[] |
| frac_sp3_list=[] |
|
|
| df=pd.read_parquet("./ecfp/all_data_merged-cleaned-ecfp4.parquet") |
| |
|
|
| for smi in df["Smiles_molvs"]: |
| mol = Chem.MolFromSmiles(smi) |
| if mol is None: |
| |
| mw_list.append(np.nan) |
| logp_list.append(np.nan) |
| TPSA_list.append(np.nan) |
| HBD_list.append(np.nan) |
| HBA_list.append(np.nan) |
| rot_bond_list.append(np.nan) |
| ring_count_list.append(np.nan) |
| frac_sp3_list.append(np.nan) |
| print(smi,"this smile failed") |
| continue |
|
|
| |
| mw_list.append( Descriptors.MolWt(mol) ) |
| logp_list.append( Descriptors.MolLogP(mol) ) |
| TPSA_list.append( Descriptors.TPSA(mol) ) |
| HBD_list.append( Descriptors.NumHDonors(mol) ) |
| HBA_list.append( Descriptors.NumHAcceptors(mol) ) |
| rot_bond_list.append(Descriptors.NumRotatableBonds(mol) ) |
| ring_count_list.append(Descriptors.RingCount(mol) ) |
| frac_sp3_list.append(Descriptors.FractionCSP3(mol) ) |
|
|
| |
| df["MolWt"] = mw_list |
| df["ClogP"] = logp_list |
| df["TPSA"] = TPSA_list |
| df["HBD"] = HBD_list |
| df["HBA"] = HBA_list |
| df["NumRotatableBonds"] = rot_bond_list |
| df["RingCount"] = ring_count_list |
| df["FractionCSP3"] = frac_sp3_list |
|
|
| output_file="./ecfp_and_properties/all_data_merged-cleaned-ecfp4-properties.parquet" |
|
|
| df.to_parquet(output_file, index=False) |
