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import pandas as pd
from molvs import Standardizer
from rdkit import Chem
def standardize_smiles(smiles):
mol = Chem.MolFromSmiles(smiles)
if mol is None:
return None
std = Standardizer()
try:
std_mol = std.standardize(mol)
return Chem.MolToSmiles(std_mol)
except:
return None
# Load and manually parse .txt file
data = []
with open("EDC_data.txt", "r") as f:
for line in f:
parts = line.strip().split()
if len(parts) < 6:
continue # skip malformed lines
sample_id = parts[0]
smiles = parts[1]
name = parts[3]
label = parts[-2] # sometimes it's merged, so this may need refining
source = parts[-1]
data.append((sample_id, smiles, name, label, source))
df = pd.DataFrame(data, columns=["id", "smiles", "name", "label", "source"])
# Sanitize
df["standardized_smiles"] = df["smiles"].apply(standardize_smiles)
df.dropna(subset=["standardized_smiles"], inplace=True)
# Save
df.to_csv("EDC_data_sanitized.csv", index=False)
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