How to use the cclib.io.xyzwriter.XYZ 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 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 test_outputclass(self):
        """Does the function determine output class as expected."""
        outputtype = "xyz"
        outputdest = "file.xyz"
        self.assertEqual(self._determine_output_format(outputtype, outputdest),
                         cclib.io.xyzwriter.XYZ)
        # Must raise a KeyError for unsuported extensions
        self.assertRaises(self.UnknownOutputFormatError,
                          self._determine_output_format, 'ext', outputdest)
        self.assertRaises(self.UnknownOutputFormatError,
                          self._determine_output_format, None, None)

def test_roundtrip_two(self):
        """Does a written XYZ file with two structures match a reference
        output?

        Perform a roundtrip test, reading an XYZ file into a ccData
        instance then writing it out again.
        """
        orig_fpath = os.path.join(__filedir__, "data/uracil_two.xyz")
        reader = cclib.io.xyzreader.XYZ(orig_fpath)
        data = reader.parse()
        orig_repr = reader.filecontents

        # If not `allgeom`, only the last structure present in a
        # `ccData` will be written out.
        writer = cclib.io.xyzwriter.XYZ(data, allgeom=True)
        new_repr = writer.generate_repr()

        ref_fpath = os.path.join(__filedir__, "data/uracil_two_ref.xyz")
        with open(ref_fpath) as ref:
            # Compare the contents of the reference file (left) with
            # the string representation generated by the writer
            # (right).
            assert ref.read() == new_repr

def test_subclass(self):
        """Is the writer a subclass of the abstract file writer?"""
        fpath = os.path.join(__datadir__, "data/ADF/basicADF2007.01/dvb_gopt.adfout")
        self.assertTrue(os.path.exists(fpath))
        data = cclib.io.ccread(fpath)
        writer = cclib.io.xyzwriter.XYZ(data)
        self.assertTrue(isinstance(writer, cclib.io.filewriter.Writer))
        self.assertTrue(issubclass(type(writer), cclib.io.filewriter.Writer))

def test_roundtrip_one(self):
        """Does a written XYZ file with a single structure match a reference
        output?

        Perform a roundtrip test, reading an XYZ file into a ccData
        instance then writing it out again.
        """
        orig_fpath = os.path.join(__datadir__, "test/bridge/uracil.xyz")
        reader = cclib.io.xyzreader.XYZ(orig_fpath)
        data = reader.parse()
        orig_repr = reader.filecontents

        writer = cclib.io.xyzwriter.XYZ(data)
        new_repr = writer.generate_repr()

        ref_fpath = os.path.join(__filedir__, "data/uracil_one_ref.xyz")
        with open(ref_fpath) as ref:
            # Compare the contents of the reference file (left) with
            # the string representation generated by the writer
            # (right).
            assert ref.read() == new_repr

firstgeom=False, lastgeom=False, allgeom=False,
                 *args, **kwargs):
        """Initialize the XYZ writer object.

        Inputs:
          ccdata - An instance of ccData, parse from a logfile.
          splitfiles - Boolean to write multiple files if multiple files are requested. [TODO]
          firstgeom - Boolean to write the first available geometry from the logfile.
          lastgeom - Boolean to write the last available geometry from the logfile.
          allgeom - Boolean to write all available geometries from the logfile.
        """

        self.required_attrs = ('natom', 'atomcoords', 'atomnos')

        # Call the __init__ method of the superclass
        super(XYZ, self).__init__(ccdata, *args, **kwargs)

        self.do_firstgeom = firstgeom
        self.do_lastgeom = lastgeom
        self.do_allgeom = allgeom

        self.natom = str(self.ccdata.natom)
        self.element_list = [self.pt.element[Z] for Z in self.ccdata.atomnos]