old_contents: # propka 3.1
  # (Module renamed from original Source to propka to facilitate setuptools installation)
  
  __all__ = ['coupled_residues', 'lib', 'parameters', 'residue', 'bonds', 'debug', 'ligand', 'pdb', 'calculator', 'determinants', 'mutate', 'protein', 'chain', 'iterative', 'output', 'protonate']
  
  
new_contents: """PROPKA 3.1
  
  See https://github.com/jensengroup/propka-3.1 for more information.
  
  Please cite these PROPKA references in publications:
  
  * Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen.
  "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and
  Rationalization of pKa Values." Journal of Chemical Theory and Computation 7,
  no. 7 (2011): 2284-2295.
  
  * Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen.
  "PROPKA3: consistent treatment of internal and surface residues in empirical pKa
  predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
  """
  __all__ = ["atom", "bonds", "calculations", "conformation_container",
             "coupled_groups", "determinant", "determinants", "group",
             "hybrid36", "iterative", "lib", "ligand_pka_values", "ligand",
             "molecular_container", "output", "parameters", "pdb", "protonate",
             "run", "vector_algebra", "version"]
subject: Update __init__.py.