covert smiles to .mol files

smiles2molfile.py

import pandas as pd
from rdkit.Chem import AllChem as Chem

import argparse
 
def smiles2molfile(smiles):
    """ smiles to mol file
    @parma molecule_name
    @return None
    @obtain a file
    """
    m = Chem.MolFromSmiles(smiles)
    m2 = Chem.AddHs(m)
    print(Chem.MolToMolBlock(m2),file=open("data/"+str(smiles)+".mol",'w+'))


def main():
    parser = argparse.ArgumentParser(description='filename')
    parser.add_argument('filename')
    args = parser.parse_args()
    data = pd.read_csv(args.filename)
    smiles_lst=data["smiles"]

    for i in range(len(smiles_lst)):
        smiles = smiles_lst[i]
        smiles2molfile(smiles)


if __name__ == "__main__":
    main()