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pip install rdkit
pip install molvs
import pandas as pd
import numpy as np
import rdkit
import molvs
from rdkit import Chem
standardizer = molvs.Standardizer()
fragment_remover = molvs.fragment.FragmentRemover()
from rdkit.Chem import PandasTools
sdfFile = 'Redox_training_set_curated.sdf'
dataframe = PandasTools.LoadSDF(sdfFile)
dataframe.to_csv('Nano Luciferase.csv', index=False)
df = pd.read_csv('redox.csv')
# Some of the 'Raw_SMILES' rows contain TWO smiles separated by ;
# These cause smiles parse error (which means they cannot be read)
# So I separated the smiles
df.rename(columns = {'PUBCHEM_EXT_DATASOURCE_REGID': 'REGID_1'}, inplace = True)
df.rename(columns = {'Other REGIDs': 'REGID_2'}, inplace = True)
df.insert(3, 'SMILES_2', np.NaN)
df['SMILES_2'] = df['Raw_SMILES'].str.split(';').str[1]
df['Raw_SMILES'] = df['Raw_SMILES'].str.split(';').str[0]
df.rename(columns= {'Raw_SMILES' : 'SMILES_1'}, inplace = True)
df.insert(10, 'AC50_uM_2', np.NaN)
df['AC50_uM_2'] = df['AC50_uM'].str.split(';').str[1]
df['AC50_uM'] = df['AC50_uM'].str.split(';').str[0]
df.rename(columns = {'AC50_uM': 'AC50_uM_1'}, inplace = True)
df['X_1'] = [ \
rdkit.Chem.MolToSmiles(
fragment_remover.remove(
standardizer.standardize(
rdkit.Chem.MolFromSmiles(
smiles))))
for smiles in df['SMILES_1']]
def process_smiles(smiles):
if pd.isna(smiles):
return None
try:
return rdkit.Chem.MolToSmiles(
fragment_remover.remove(
standardizer.standardize(
rdkit.Chem.MolFromSmiles(smiles))))
except Exception as e:
print(f"Error processing SMILES {smiles}: {e}")
return None
df['X_2'] = df['SMILES_2'].apply(process_smiles)
df.rename(columns={'X_1' : 'newSMILES_1', 'X_2' : 'newSMILES_2'}, inplace = True)
df[['REGID_1',
'REGID_2',
'newSMILES_1',
'newSMILES_2',
'log_AC50_M',
'Efficacy',
'CC-v2',
'Outcome',
'InChIKey',
'AC50_uM_1',
'AC50_uM_2',
'ID',
'ROMol']].to_csv('redox_sanitized.csv', index = False) |