src/05_sanitize_data.py

from molvs import standardize_smiles
import pandas as pd

file_path = "./checkpoints_merged/all_data_merged.parquet"
df = pd.read_parquet(file_path)
smiles_column_key = df.columns[2]

sanatized_rows = []
std_smile_list=[]
failed_to_sanatize_row = []

for index, row in df.iterrows():
    smile = row[smiles_column_key]
    std_smile = standardize_smiles(smile)
    std_smile_list.append(std_smile)

df["Smiles_molvs"]=std_smile_list
col = df.columns[-1]           # name of the last column
df.insert(3, col, df.pop(col)) # remove it then re‑insert at index 2
df.drop('SMILES_GDB17', axis=1, inplace=True)
df.to_parquet("./clean_checkpoints/all_data_merged-cleaned.parquet", index=False)