def test_trajectory_change_atoms_for_single_ideal_mof():
""" Test trajectory class change atoms method for non-interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
assert traj.get_unique_atoms() == ['1']
traj.change_atoms({'1': 'C'})
assert traj.get_unique_atoms() == ['C']
ref_atoms = ['C'] * traj.n_atoms
assert [line.split()[0] for line in traj.xyz[0][2:]] == ref_atoms
assert traj.atoms[0] == ref_atoms
def test_trajectory_change_atoms_for_interpenetrated_ideal_mof():
""" Test trajectory class change atoms method for interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(ipmof_trial_dir, 'Run1', 'traj.xyz'))
assert Counter(traj.get_unique_atoms()) == Counter(['1', '2'])
traj.change_atoms({'1': 'C', '2': 'O'})
assert Counter(traj.get_unique_atoms()) == Counter(['C', 'O'])
ref_atoms = ['C'] * int(traj.n_atoms / 2) + ['O'] * int(traj.n_atoms / 2)
assert [line.split()[0] for line in traj.xyz[0][2:]] == ref_atoms
assert traj.atoms[0] == ref_atoms
def test_center_of_mass_for_interpenetrated_ideal_mof():
""" Test trajectory class read method for interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(ipmof_trial_dir, 'Run1', 'traj.xyz'))
traj.change_atoms({'1': 'C', '2': 'O'})
traj.calculate_com()
assert np.isclose(traj.com[0][0], traj.com[0][1], traj.com[0][2])