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 sysimport MolecularSystemms = 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.