INNER CODE UNIT · Python

run_propka

Electrostatics/pdb2pqr · pdb2pqr/main.py:530

def run_propka(args, biomolecule):
    """Run a PROPKA calculation.

    :param args:  command-line arguments
    :type args:  argparse.Namespace
    :param biomolecule:  biomolecule object
    :type biomolecule:  Biomolecule
    :return:  (DataFrame-convertible table of assigned pKa values,
               pKa information from PROPKA)
    :rtype:  (list, str)
    """
    lines = io.print_biomolecule_atoms(
        atomlist=biomolecule.atoms, chainflag=args.keep_chain, pdbfile=True
    )

    with StringIO() as fpdb:
        fpdb.writelines(lines)
        parameters = Parameters()

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