--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/remove_protonation_state.py	Sat May 20 08:40:31 2017 -0400
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+"""
+    Input: molecular input file.
+    Output: Molecule file with removed ions and fragments.
+    Copyright 2013, Bjoern Gruening and Xavier Lucas
+"""
+import sys, os
+import argparse
+import openbabel
+openbabel.obErrorLog.StopLogging()
+import pybel
+
+def parse_command_line():
+    parser = argparse.ArgumentParser()
+    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 ):
+    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 )
+    outfile.close()
+
+def __main__():
+    """
+        Remove any protonation state from each atom in each molecule.
+    """
+    args = parse_command_line()
+    remove_protonation( args )
+
+if __name__ == "__main__" :
+    __main__()