How to use the cclib.io function in cclib

def test_init(self):
        """Does the class initialize correctly?"""
        fpath = os.path.join(__datadir__, "data/ADF/basicADF2007.01/dvb_gopt.adfout")
        data = cclib.io.ccread(fpath)
        xyz = cclib.io.xyzwriter.XYZ(data)

        # The object should keep the ccData instance passed to its constructor.
        self.assertEqual(xyz.ccdata, data)

def setUp(self):
        self._determine_output_format = cclib.io.ccio._determine_output_format
        self.UnknownOutputFormatError = cclib.io.ccio.UnknownOutputFormatError

def test_data_stdin(self):
        """Check that the same attributes are parsed when a file is piped through standard input."""
        logfiles = [
            "data/ADF/basicADF2007.01/dvb_gopt.adfout",
            "data/GAMESS/basicGAMESS-US2017/C_bigbasis.out",
        ]
        get_attributes = lambda data: [a for a in data._attrlist if hasattr(data, a)]
        for lf in logfiles:
            path = "%s/%s" % (__datadir__, lf)
            expected_attributes = get_attributes(cclib.io.ccread(path))
            with open(path) as handle:
                contents = handle.read()
            # This is fix strings not being unicode in Python2.
            try:
                stdin = io.StringIO(contents)
            except TypeError:
                stdin = io.StringIO(unicode(contents))
            stdin.seek = sys.stdin.seek
            data = cclib.io.ccread(stdin)
            self.assertEqual(get_attributes(data), expected_attributes)

def test_attributes_one(self):
        """Is an XYZ file with a single geometry read into a ccData properly?
        """
        fpath = os.path.join(__datadir__, "test/bridge/uracil.xyz")
        xyz = cclib.io.xyzreader.XYZ(fpath)
        data = xyz.parse()

        self.assertEqual(data.natom, 12)

        atomnos = np.array([7, 6, 1, 8, 7, 6, 8, 6, 6, 1, 1, 1], dtype=int)
        np.testing.assert_equal(data.atomnos, atomnos)

        self.assertEqual(data.atomcoords.shape, (1, 12, 3))

def import_cclib(self, fname):
        """
        Imports any cclib parsable file as a Molecule class instance

        Parameters
        -----------
        fname : string
            cclib parsable output file name
        """
        try:
            self.ftype = 'cclib'
            data = cclib.io.ccread(fname)
            self.n_atom = data.natom
            self.at_num = data.atomnos
            # This gets the atomic symbols by looking up the keys of the
            # atomic numbers. It looks somewhat crazy but it is looking
            # through a list of the values stored in the dictionary,
            # matching the value to the atomic number and returning
            # the key that corresponds to that atomic number. It works
            # with this dictionary because the keys to values are 1 to 1.
            self.sym = []
            for i in data.atomnos:
                self.sym.append(qcel.periodictable.to_E(i))
            # cclib stores the atomic coordinates in a array of shape
            # [molecule, num atoms, 3 for xyz] because I think they might
            # have many "molecules" from each step of an optimization or
            # something. Here we are taking just the last one.
            self.xyz = data.atomcoords[-1]