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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")
# Loop over SMILES
for smi in df["Smiles_molvs"]:
mol = Chem.MolFromSmiles(smi)
if mol is None:
# if parsing fails, append NaN
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
# compute and append
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) )
# Attach back to DataFrame
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) |