scripts/clean_data.py

from rdkit import Chem
from molvs import Standardizer
import pandas as pd
df0 = pd.read_csv("data/negative.csv")
df1 = pd.read_csv("data/positive.csv")
s = Standardizer()

def standardize_smiles(smiles):
    try:
        mol = Chem.MolFromSmiles(smiles)  
        if mol:
            clean_mol = s.fragment_parent(mol)  
            standardized_mol = s.standardize(clean_mol)  
            return Chem.MolToSmiles(standardized_mol)  
    except:
        return None

df0["Standardized_SMILES"] = df0.iloc[:,0].apply(standardize_smiles)
df0 = df0.dropna(subset=["Standardized_SMILES"])
df0.to_csv("intermediate/cleaned_negative.csv", index=False)

df1["Standardized_SMILES"] = df1.iloc[:,0].apply(standardize_smiles)
df1 = df1.dropna(subset=["Standardized_SMILES"])
df1.to_csv("intermediate/cleaned_positive.csv", index=False)