convert data from https://pubs.acs.org/doi/10.1021/ci049802u si to SMILES using RDKit

haloalkane_smiles.csv

haloalkane_smiles.py

# convert data from https://pubs.acs.org/doi/10.1021/ci049802u si to SMILES using RDKit
# preprocessed the file by converting all tabs and double spaces to spaces for easier parsing

import pandas as pd
from rdkit import Chem

def read_haloalkane(str):
    original = str
    # deal with the unusual structures first
    str = str.replace("(CH3)2","(C)(C)")
    str = str.replace("(CH2Cl)2","(CCl)(CCl)")
    str = str.replace("(CF3)3","(CFFF)(CFFF)(CFFF)") # bracks get added a few lines down
    str = str.replace("(CF3)2","(CFFF)(CFFF)")
    # remove hydrogen
    str = str.replace("H3","")
    str = str.replace("H2","")
    str = str.replace("H","")
    # add brackets to halogens and expand
    str = str.replace("F","(F)")
    str = str.replace("(F)4","(F)(F)(F)F")
    str = str.replace("(F)3","(F)(F)(F)")
    str = str.replace("(F)2","(F)(F)")
    str = str.replace("Br","(Br)")
    str = str.replace("(Br)4","(Br)(Br)(Br)Br")
    str = str.replace("(Br)3","(Br)(Br)(Br)")
    str = str.replace("(Br)2","(Br)(Br)")
    str = str.replace("Cl","(Cl)")
    str = str.replace("(Cl)4","(Cl)(Cl)(Cl)Cl")
    str = str.replace("(Cl)3","(Cl)(Cl)(Cl)")
    str = str.replace("(Cl)2","(Cl)(Cl)")
    smi = Chem.MolToSmiles(Chem.MolFromSmiles(str))
    return smi

df = pd.read_csv("raw.txt",sep=' ')
df["smiles"] = df["Structure"].apply(read_haloalkane)
df.to_csv("haloalkane_smiles.csv",index=False)