How to use the mdtraj.formats.XTCTrajectoryFile function in mdtraj

def test_write_1(tmpdir):
    xyz = np.asarray(np.around(np.random.randn(100, 10, 3), 3), dtype=np.float32)
    time = np.asarray(np.random.randn(100), dtype=np.float32)
    step = np.arange(100)
    box = np.asarray(np.random.randn(100, 3, 3), dtype=np.float32)

    tmpfn = '{}/traj.xtc'.format(tmpdir)
    with XTCTrajectoryFile(tmpfn, 'w') as f:
        f.write(xyz, time=time, step=step, box=box)
    with XTCTrajectoryFile(tmpfn) as f:
        xyz2, time2, step2, box2 = f.read()

    eq(xyz, xyz2)
    eq(time, time2)
    eq(step, step2)
    eq(box, box2)

def test_read_stride(get_fn, fn_xtc):
    # read xtc with stride
    iofile = io.loadh(get_fn('frame0.xtc.h5'), deferred=False)
    with XTCTrajectoryFile(fn_xtc) as f:
        xyz, time, step, box = f.read(stride=3)
    assert eq(xyz, iofile['xyz'][::3])
    assert eq(step, iofile['step'][::3])
    assert eq(box, iofile['box'][::3])
    assert eq(time, iofile['time'][::3])

def test_write_0(tmpdir, fn_xtc):
    with XTCTrajectoryFile(fn_xtc) as f:
        xyz = f.read()[0]

    tmpfn = '{}/traj.xtc'.format(tmpdir)
    f = XTCTrajectoryFile(tmpfn, 'w')
    f.write(xyz)
    f.close()

    with XTCTrajectoryFile(tmpfn) as f:
        xyz2, time2, step2, box2 = f.read()
    eq(xyz, xyz2)

def test_xtc_write_wierd_0(tmpdir):
    x0 = np.asarray(np.random.randn(100, 3, 3), dtype=np.float32)
    x1 = np.asarray(np.random.randn(100, 9, 3), dtype=np.float32)
    tmpfn = '{}/traj.xtc'.format(tmpdir)
    with XTCTrajectoryFile(tmpfn, 'w') as f:
        f.write(x0)
        with pytest.raises(ValueError):
            f.write(x1)

    xr = XTCTrajectoryFile(tmpfn).read()[0]
    print(xr.shape)

def test_short_traj(tmpdir):
    tmpfn = '{}/traj.xtc'.format(tmpdir)
    with XTCTrajectoryFile(tmpfn, 'w') as f:
        f.write(np.random.uniform(size=(5, 100000, 3)))
    with XTCTrajectoryFile(tmpfn, 'r') as f:
        assert len(f) == 5, len(f)

def test_flush(tmpdir):
    tmpfn = '{}/traj.xtc'.format(tmpdir)
    data = np.random.random((5, 100, 3))
    with XTCTrajectoryFile(tmpfn, 'w') as f:
        f.write(data)
        f.flush()
        # note that f is still open, so we can now try to read the contents flushed to disk.
        with XTCTrajectoryFile(tmpfn, 'r') as f2:
            out = f2.read()
        np.testing.assert_allclose(out[0], data, atol=1E-3)

def test_read_chunk1(get_fn, fn_xtc):
    with XTCTrajectoryFile(fn_xtc, 'r', chunk_size_multiplier=0.5) as f:
        xyz, time, step, box = f.read()

    iofile = io.loadh(get_fn('frame0.xtc.h5'), deferred=False)
    assert eq(xyz, iofile['xyz'])
    assert eq(step, iofile['step'])
    assert eq(box, iofile['box'])
    assert eq(time, iofile['time'])

def _regroup_DISK_subset(states, trajs, topology_file, disctrajs, path, stride):
    writer = [None] * (max(states) + 1)
    out_fnames = []
    for i in states:
        out_fname = path + os.sep + ('%d.xtc' % i)
        out_fnames.append(out_fname)
        writer[i] = XTCTrajectoryFile(out_fname, 'w', force_overwrite=True)

    for disctraj, traj in zip(disctrajs, trajs):
        reader = md.iterload(traj, top=topology_file, stride=stride)
        start = 0
        for chunk in reader:
            chunk_length = chunk.xyz.shape[0]
            for i in xrange(chunk_length):
                cl = disctraj[i + start]
                if cl in states:
                    writer[cl].write(chunk.xyz[i, :, :])
            start += chunk_length
    for i in states:
        writer[i].close()

    return out_fnames

def save_xtc(self, filename, force_overwrite=True):
        """Save trajectory to Gromacs XTC format

        Parameters
        ----------
        filename : str
            filesystem path in which to save the trajectory
        force_overwrite : bool, default=True
            Overwrite anything that exists at filename, if its already there
        """
        with XTCTrajectoryFile(filename, 'w', force_overwrite=force_overwrite) as f:
            f.write(xyz=in_units_of(self.xyz, Trajectory._distance_unit, f.distance_unit),
                    time=self.time,
                    box=in_units_of(self.unitcell_vectors, Trajectory._distance_unit, f.distance_unit))

def save_xtc(self, filename, force_overwrite=True):
        """Save trajectory to Gromacs XTC format

        Parameters
        ----------
        filename : str
            filesystem path in which to save the trajectory
        force_overwrite : bool, default=True
            Overwrite anything that exists at filename, if its already there
        """
        with XTCTrajectoryFile(filename, 'w', force_overwrite=force_overwrite) as f:
            f.write(xyz=self.xyz, time=self.time, box=self.unitcell_vectors)