How to use the mdtraj.testing.eq function in mdtraj

def test_4():
    # using a really big box, we should get the same results with and without
    # pbcs
    box = np.array([[100, 0, 0], [0, 200, 0], [0, 0, 300]])
    box = np.zeros((N_FRAMES, 3, 3)) + box  # broadcast it out
    a = _displacement_mic(xyz, pairs, box, False)
    b = _displacement(xyz, pairs)
    eq(a, b, decimal=3)

def test_multiread(get_fn):
    reference = md.load(get_fn('frame0.mdcrd'), top=get_fn('native.pdb'))
    with MDCRDTrajectoryFile(get_fn('frame0.mdcrd'), n_atoms=22) as f:
        xyz0, box0 = f.read(n_frames=1)
        xyz1, box1 = f.read(n_frames=1)

    eq(reference.xyz[0], xyz0[0] / 10)
    eq(reference.xyz[1], xyz1[0] / 10)

def test_read_0(get_fn):
    with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
        xyz = f.read()
    with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
        xyz3 = f.read(stride=3)
    eq(xyz[::3], xyz3)

def test_box(get_fn):
    t = md.load(get_fn('native.pdb'))
    assert eq(t.unitcell_vectors, None)
    assert eq(t.unitcell_lengths, None)
    assert eq(t.unitcell_angles, None)
    assert eq(t.unitcell_volumes, None)

    t.unitcell_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]).reshape(1, 3, 3)
    assert eq(np.array([1.0, 1.0, 1.0]), t.unitcell_lengths[0])
    assert eq(np.array([90.0, 90.0, 90.0]), t.unitcell_angles[0])
    assert eq(np.array([1.0]), t.unitcell_volumes)

def test_seek(get_fn):
    reference = md.load(get_fn('frame0.xyz'), top=get_fn('native.pdb'))

    with XYZTrajectoryFile(get_fn('frame0.xyz')) as f:
        f.seek(1)
        eq(1, f.tell())
        xyz1 = f.read(n_frames=1)
        eq(reference.xyz[1], xyz1[0] / 10)

        f.seek(10)
        eq(10, f.tell())
        xyz10 = f.read(n_frames=1)
        eq(reference.xyz[10], xyz10[0] / 10)
        eq(11, f.tell())

        f.seek(-8, 1)
        xyz3 = f.read(n_frames=1)
        eq(reference.xyz[3], xyz3[0] / 10)

        f.seek(4, 1)
        xyz8 = f.read(n_frames=1)
        eq(reference.xyz[8], xyz8[0] / 10)

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 test_restrict_atoms(get_fn):
    traj = md.load(get_fn('traj.h5'))
    time_address = traj.time.ctypes.data

    desired_atom_indices = [0, 1, 2, 5]
    traj.restrict_atoms(desired_atom_indices)
    atom_indices = [a.index for a in traj.top.atoms]
    eq([0, 1, 2, 3], atom_indices)
    eq(traj.xyz.shape[1], 4)
    eq(traj.n_atoms, 4)
    eq(traj.n_residues, 1)
    eq(len(traj.top._bonds), 2)
    eq(traj.n_residues, traj.topology._numResidues)
    eq(traj.n_atoms, traj.topology._numAtoms)
    eq(np.array([a.index for a in traj.topology.atoms]), np.arange(traj.n_atoms))

    # assert that the time field was not copied
    assert traj.time.ctypes.data == time_address

def test_read_write_4(get_fn):
    traj = md.load(get_fn('frame0.nc'), top=get_fn('native.pdb'))
    traj[0].save(temp2)
    assert os.path.exists(temp2)
    rsttraj = md.load(temp2, top=get_fn('native.pdb'))
    eq(rsttraj.xyz, traj[0].xyz)
    os.unlink(temp2)
    traj.save(temp2)
    for i in range(traj.n_frames):
        assert os.path.exists('%s.%03d' % (temp2, i + 1))
        os.unlink('%s.%03d' % (temp2, i + 1))

# HETATM19787  S   SO4 D 804      -4.788  -9.395  22.515  1.00121.87           S  
    # HETATM19788  O1  SO4 D 804      -3.815  -9.511  21.425  1.00105.97           O  
    # HETATM19789  O2  SO4 D 804      -5.989  -8.733  21.999  1.00116.13           O  
    # HETATM19790  O3  SO4 D 804      -5.130 -10.726  23.043  1.00108.74           O  
    # HETATM19791  O4  SO4 D 804      -4.210  -8.560  23.575  1.00112.54           O  
    t1 = load_pdb(get_fn('3nch.pdb.gz'))
    top, bonds = t1.top.to_dataframe()
    
    top2 = Topology.from_dataframe(top, bonds)
    eq(t1.top, top2)
    
    top = top.set_index('serial')  # Index by the actual data in the PDB
    eq(str(top.ix[19791]["name"]), "O4")
    eq(str(top.ix[19787]["name"]), "S")
    eq(str(top.ix[19787]["resName"]), "SO4")
    eq(int(top.ix[19787]["resSeq"]), 804)

integrator = LangevinIntegrator(300 * kelvin, 1.0 / picoseconds, 2.0 * femtoseconds)
    integrator.setConstraintTolerance(0.00001)

    platform = Platform.getPlatformByName('Reference')
    simulation = Simulation(pdb.topology, system, integrator, platform)
    simulation.loadCheckpoint(checkpoint)
    reporter = XTCReporter(xtcfile, 2, append=True)
    simulation.reporters.append(reporter)
    simulation.step(10)
    reporter.close()
    xtc_traj = md.load(xtcfile, top=get_fn('native.pdb'))
    xtc_traj_cp = md.load(xtcfile_cp, top=get_fn('native.pdb'))
    eq(xtc_traj.xyz[:5], xtc_traj_cp.xyz)
    eq(xtc_traj.n_frames, 10)
    eq(xtc_traj_cp.n_frames, 5)
    eq(xtc_traj.time[:5], xtc_traj_cp.time)