--- a/remove_protonation_state.py	Tue Jul 28 08:41:13 2020 -0400
+++ b/remove_protonation_state.py	Mon Oct 19 14:48:13 2020 +0000
@@ -4,32 +4,37 @@
     Output: Molecule file with removed ions and fragments.
     Copyright 2013, Bjoern Gruening and Xavier Lucas
 """
-import sys, os
 import argparse
 
 from openbabel import openbabel, pybel
 openbabel.obErrorLog.StopLogging()
 
+
 def parse_command_line():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--iformat', default='sdf' , help='input file format')
+    parser.add_argument('--iformat', default='sdf', help='input file format')
     parser.add_argument('-i', '--input', required=True, help='input file name')
     parser.add_argument('-o', '--output', required=True, help='output file name')
     return parser.parse_args()
 
-def remove_protonation( args ):
+
+def remove_protonation(args):
     outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
     for mol in pybel.readfile(args.iformat, args.input):
         [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms]
-        outfile.write( mol )
+        if 'inchi' in mol.data:
+            del mol.data['inchi']  # remove inchi cache so modified mol is saved
+        outfile.write(mol)
     outfile.close()
 
+
 def __main__():
     """
         Remove any protonation state from each atom in each molecule.
     """
     args = parse_command_line()
-    remove_protonation( args )
+    remove_protonation(args)
+
 
-if __name__ == "__main__" :
+if __name__ == "__main__":
     __main__()