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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) |