<commit_before># 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']
<commit_msg>Update __init__.py.<commit_after>"""PROPKA 3.1

See https://github.com/jensengroup/propka-3.1 for more information.

Please cite these PROPKA references in publications:

* Sondergaard, <NAME>., <NAME> Olsson, <NAME>, and <NAME>.
"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, <NAME>, <NAME>, <NAME>, and <NAME>.
"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"]
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