patch to support APBS 3.1

[mokurin000]

def computeAPBS(vertices, pdb_file, tmp_file_base, mol2_file=None):
    """
        Calls APBS, pdb2pqr, and multivalue and returns the charges per vertex
    """
    fields = tmp_file_base.split("/")[0:-1]
    directory = "/".join(fields) + "/"
    filename_base = tmp_file_base.split("/")[-1]
    pdbname = pdb_file.split("/")[-1]
    args = [
        pdb2pqr_bin,
        "--ff=PARSE",
        "--whitespace",
        "--noopt",
        "--apbs-input",
        pdbname,
        filename_base,
    ]

Simply different call convention