def test_position_velocities_protein(self, molecule_protein: Molecule):
"""
Test for the atom position and velocities get and setter for the
molecule with multiple residues.
"""
test_protein_pos = np.array([
[2.490, 3.850, 5.330],
[2.310, 4.040, 5.170],
[2.190, 4.380, 5.220],
[2.480, 3.530, 5.200],
[2.280, 3.350, 5.350],
[2.180, 3.040, 5.290],
[2.700, 3.410, 5.120],
[2.770, 3.370, 4.800],
[2.900, 3.290, 5.390],
[3.220, 3.190, 5.390],
[3.440, 3.130, 5.540],
[2.700, 3.030, 5.470],
[2.490, 3.060, 5.730],
[2.430, 3.160, 6.050],
[2.710, 2.860, 5.200],
[2.550, 2.950, 4.940],
[3.040, 2.820, 5.150],
[3.110, 2.980, 4.860],
[3.090, 2.690, 5.460],
[3.280, 2.580, 5.720],
[3.120, 2.490, 5.990],
[2.830, 2.450, 5.450],
[2.750, 2.270, 5.670],
[2.460, 2.210, 5.800],
[2.910, 2.280, 5.170],
[2.850, 2.430, 4.850],
[3.210, 2.310, 5.160],
[3.250, 2.010, 5.010],
[3.330, 1.820, 5.160],
[3.220, 2.140, 5.500],
[3.550, 2.070, 5.510],
[3.830, 2.170, 5.540],
[3.050, 1.870, 5.590],
[2.790, 1.770, 5.390]
])
assert np.isclose(test_protein_pos, molecule_protein.atoms_positions).all()
assert molecule_protein.atoms_velocities is None
test_protein_pos[1] = np.array((1, 1, 1))
molecule_protein.atoms_positions = test_protein_pos
assert np.isclose(test_protein_pos, molecule_protein.atoms_positions).all()
change_atom = np.array((2, 3, 4))
test_protein_pos[3] = change_atom
molecule_protein[3].position = change_atom
assert np.isclose(molecule_protein[3].position, change_atom).all()
assert np.isclose(test_protein_pos, molecule_protein.atoms_positions).all()
geom_test = np.mean(test_protein_pos, axis=0)
assert np.isclose(geom_test, molecule_protein.geometric_center).all()
with pytest.raises(ValueError):
molecule_protein.atoms_positions = change_atom
with pytest.raises(ValueError):
molecule_protein.atoms_velocities = change_atom
molecule_protein.atoms_velocities = test_protein_pos
assert np.isclose(test_protein_pos, molecule_protein.atoms_velocities).all()
change_atom = np.array((5, 1, 3))
test_protein_pos[5] = change_atom
assert np.isclose(molecule_protein[5].velocity, change_atom).all()
assert np.isclose(test_protein_pos, molecule_protein.atoms_velocities).all()
def test_position_velocities_bmim(self, molecule_bmim: Molecule):
"""
Test for the atom position and velocities get and setter for bmim
molecule.
"""
test_bmim_pos = np.array([
[1.593, 1.896, 0.729],
[1.706, 1.984, 0.708],
[1.807, 1.892, 0.660],
[1.755, 1.761, 0.652],
[1.626, 1.764, 0.693],
[1.738, 2.029, 0.805],
[1.809, 1.674, 0.618],
[1.559, 1.679, 0.698],
[1.464, 1.937, 0.778],
[1.942, 1.930, 0.624],
[2.044, 1.858, 0.713],
[2.188, 1.899, 0.677],
[2.289, 1.828, 0.765],
[1.463, 2.046, 0.799],
[1.441, 1.883, 0.872],
[1.385, 1.914, 0.703],
[1.960, 1.904, 0.517],
[1.955, 2.039, 0.636],
[2.024, 1.884, 0.819],
[2.034, 1.748, 0.701],
[2.200, 2.009, 0.689],
[2.208, 1.872, 0.571],
[2.392, 1.859, 0.737],
[2.273, 1.854, 0.872],
[2.281, 1.718, 0.753]
])
assert np.isclose(test_bmim_pos, molecule_bmim.atoms_positions).all()
assert molecule_bmim.atoms_velocities is None
test_bmim_pos[1] = np.array((1, 1, 1))
molecule_bmim.atoms_positions = test_bmim_pos
assert np.isclose(test_bmim_pos, molecule_bmim.atoms_positions).all()
change_atom = np.array((2, 3, 4))
test_bmim_pos[3] = change_atom
molecule_bmim[3].position = change_atom
assert np.isclose(molecule_bmim[3].position, change_atom).all()
assert np.isclose(test_bmim_pos, molecule_bmim.atoms_positions).all()
geom_test = np.mean(test_bmim_pos, axis=0)
assert np.isclose(geom_test, molecule_bmim.geometric_center).all()
with pytest.raises(ValueError):
molecule_bmim.atoms_positions = change_atom
with pytest.raises(ValueError):
molecule_bmim.atoms_velocities = change_atom
molecule_bmim.atoms_velocities = test_bmim_pos
assert np.isclose(test_bmim_pos, molecule_bmim.atoms_velocities).all()
change_atom = np.array((5, 1, 3))
test_bmim_pos[5] = change_atom
assert np.isclose(molecule_bmim[5].velocity, change_atom).all()
assert np.isclose(test_bmim_pos, molecule_bmim.atoms_velocities).all()