Proton Related

You can protonate unprotonated proteins, and there is a hydrogen bond calculator.

""" Protonate a protein. Add the hydrogens to the protein. i.e. create a list of possible donors and all of their hydrogens 'atomsHydList': {'atom','hydAtoms'}
    """
protonate (pchain,protonFile,redo=False)

There is an active site calculator in this file. I think all of this work was done by Paul Anderson.

You can calculate pI through "import pH" and "calculate_pI_from_sequence(sequence)", and there is a hydrogen bond calculator:

import sys
import MolecularSystem

ms = MolecularSystem.System ("test_pdbs/1c7k.pdb")

"""
Test the protonation and hbond functionality
"""
ms.create_hbonds(None,None,True)
ms.print_hbonds()
ms.save_pdb("output.pdb")

Also by Paul Anderson.