def test_nmrmol_read_structure():
mol = nmrmol(molid='ethane')
mol.read_structure('tests/test_store/ethane.xyz', 'xyz')
assert mol_is_ethane(mol)
def test_save_pickle():
mol = nmrmol(molid='ethane')
file = 'TMP_mol.pkl'
mol.save_pickle(file)
assert os.path.isfile(file)
os.remove(file)
def test_nmrmol_read_opt():
mol = nmrmol(molid='ethane')
mol.read_opt('tests/test_store/TST_pass_orca_opt.log', 'orca')
assert mol.energy == -1072.556525704736
mol.read_opt('tests/test_store/TST_pass_g09_opt.log', 'g09')
assert mol.energy == -1419.091348
def test_nmrmol():
mol = nmrmol(molid='ethane')
for attr in [
mol.types, mol.xyz, mol.conn, mol.shift, mol.shift_var,
mol.coupling, mol.coupling_var, mol.coupling_len
]:
assert attr == []
assert mol.path == ''
assert mol.molid == 'ethane'
assert mol.energy == -404.404
def test_scale_shifts():
mol = nmrmol(molid='ethane')
mol.read_structure('tests/test_store/ethane.xyz', 'xyz')
mol.read_nmr('tests/test_store/ethane_orca_nmr.log', 'orca')
mol.scale_shifts(scaling_factors={'H': [-1.1, 30.0], 'C': [-1.2, 30.2]})
print(mol.shift)
assert np.allclose(
mol.shift,
[-161.341, -161.341, -1.820, -1.820, -1.822, -1.820, -1.822, -1.820],
0.001)
def get_ethane_mol():
mol = nmrmol(molid='ethane')
mol.types = np.asarray([6, 6, 1, 1, 1, 1, 1, 1])
size = len(mol.types)
mol.xyz = np.asarray([[-0.4125, 0.0000, 0.0000], [0.4125, 0.0000, 0.0000],
[-0.9475, 0.9266,
0.0000], [-0.9475, -0.9266, 0.0000],
[-1.4825, -0.0000, 0.0000],
[0.9475, -0.9266, 0.0000], [0.9475, 0.9266, 0.0000],
[1.4825, 0.0000, 0.0000]])
mol.conn = np.asarray([[0, 1, 1, 1, 1, 0, 0, 0], [1, 0, 0, 0, 0, 1, 1, 1],
[1, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0]])
mol.coupling_len = np.asarray([[0, 1, 1, 1, 1, 2, 2, 2],
[1, 0, 2, 2, 2, 1, 1, 1],
[1, 2, 0, 2, 2, 3, 3, 3],
[1, 2, 2, 0, 2, 3, 3, 3],
[1, 2, 2, 2, 0, 3, 3, 3],
[2, 1, 3, 3, 3, 0, 2, 2],
[2, 1, 3, 3, 3, 2, 0, 2],
[2, 1, 3, 3, 3, 2, 2, 0]])
mol.shift = np.asarray(
[223.81, 223.81, 32.002, 32.002, 32.005, 32.002, 32.005, 32.002])
mol.shift_var = np.zeros(size, dtype=np.float64)
mol.coupling = np.asarray(
[[0.0000, 38.796, 114.462, 115.871, 113.801, -4.644, -4.576, -4.558],
[38.796, 0.000, -4.558, -4.644, -4.576, 115.87, 113.801, 114.462],
[114.462, -4.558, 0.000, -13.961, -13.644, 3.174, 3.161, 12.579],
[115.871, -4.644, -13.961, 0.000, -13.906, 12.673, 3.181, 3.182],
[113.801, -4.576, -13.644, -13.906, 0.000, 3.178, 12.524, 3.167],
[-4.644, 115.87, 3.174, 12.673, 3.178, 0.000, -13.906, -13.971],
[-4.576, 113.801, 3.161, 3.181, 12.524, -13.906, 0.000, -13.658],
[-4.558, 114.462, 12.579, 3.182, 3.167, -13.971, -13.658, 0.000]])
mol.coupling_var = np.zeros((size, size), dtype=np.float64)
return mol
def test_nmrmol_read_nmr():
mol = nmrmol(molid='ethane')
mol.read_nmr('tests/test_store/ethane_orca_nmr.log', 'orca')
assert np.array_equal(
mol.shift,
[223.81, 223.81, 32.002, 32.002, 32.005, 32.002, 32.005, 32.002])
assert np.array_equal(
mol.coupling,
[[0.0000, 38.796, 114.462, 115.871, 113.801, -4.644, -4.576, -4.558],
[38.796, 0.000, -4.558, -4.644, -4.576, 115.87, 113.801, 114.462],
[114.462, -4.558, 0.000, -13.961, -13.644, 3.174, 3.161, 12.579],
[115.871, -4.644, -13.961, 0.000, -13.906, 12.673, 3.181, 3.182],
[113.801, -4.576, -13.644, -13.906, 0.000, 3.178, 12.524, 3.167],
[-4.644, 115.87, 3.174, 12.673, 3.178, 0.000, -13.906, -13.971],
[-4.576, 113.801, 3.161, 3.181, 12.524, -13.906, 0.000, -13.658],
[-4.558, 114.462, 12.579, 3.182, 3.167, -13.971, -13.658, 0.000]])
'''
mol.read_nmr('tests/test_store/ethane_g09_nmr.log', 'g09')
assert mol_is_ethane(mol)
assert np.array_equal(mol.shift, [223.81, 223.81, 32.002, 32.002, 32.005, 32.002, 32.005, 32.002])
assert np.array_equal(mol.coupling, [[ 0.0000, 38.796, 114.462, 115.871, 113.801, -4.644 , -4.576, -4.558],
[ 38.796, 0.000, -4.558, -4.644, -4.576, 115.87 , 113.801, 114.462],
[114.462, -4.558, 0.000, -13.961, -13.644, 3.174, 3.161, 12.579],
[115.871, -4.644, -13.961, 0.000, -13.906, 12.673, 3.181, 3.182],
[113.801, -4.576, -13.644, -13.906, 0.000, 3.178, 12.524, 3.167],
[ -4.644, 115.87 , 3.174, 12.673, 3.178, 0.000, -13.906, -13.971],
[ -4.576, 113.801, 3.161, 3.181, 12.524, -13.906, 0.000, -13.658],
[ -4.558, 114.462, 12.579, 3.182, 3.167, -13.971, -13.658, 0.000]])
mol.read_nmr('tests/test_store/ethane_g16_nmr.log', 'g09')
assert mol_is_ethane(mol)
assert np.array_equal(mol.shift, [223.81, 223.81, 32.002, 32.002, 32.005, 32.002, 32.005, 32.002])
assert np.array_equal(mol.coupling, [[ 0.0000, 38.796, 114.462, 115.871, 113.801, -4.644 , -4.576, -4.558],
[ 38.796, 0.000, -4.558, -4.644, -4.576, 115.87 , 113.801, 114.462],
[114.462, -4.558, 0.000, -13.961, -13.644, 3.174, 3.161, 12.579],
[115.871, -4.644, -13.961, 0.000, -13.906, 12.673, 3.181, 3.182],
[113.801, -4.576, -13.644, -13.906, 0.000, 3.178, 12.524, 3.167],
[ -4.644, 115.87 , 3.174, 12.673, 3.178, 0.000, -13.906, -13.971],
[ -4.576, 113.801, 3.161, 3.181, 12.524, -13.906, 0.000, -13.658],
[ -4.558, 114.462, 12.579, 3.182, 3.167, -13.971, -13.658, 0.000]])
'''
mol.read_nmr('tests/test_store/ethane.nmredata.sdf', 'nmredata')
assert np.allclose(
mol.shift,
[223.849, 223.849, 32.006, 32.003, 32.012, 32.006, 32.004, 32.011],
0.001)
assert np.allclose(
mol.coupling,
[[0.000, 38.849, 114.872, 115.641, 114.354, -4.636, -4.627, -4.609],
[38.849, 0.000, -4.607, -4.65, -4.615, 115.341, 114.951, 114.575],
[114.872, -4.607, 0.000, -14.014, -13.691, 9.479, 3.178, 6.319],
[115.641, -4.650, -14.014, 0.000, -13.953, 6.348, 9.489, 3.185],
[114.354, -4.615, -13.691, -13.953, 0.000, 3.187, 6.302, 9.464],
[-4.636, 115.341, 9.479, 6.348, 3.187, 0.000, -13.996, -13.800],
[-4.627, 114.951, 3.178, 9.489, 6.302, -13.996, 0.000, -13.870],
[-4.609, 114.575, 6.319, 3.185, 9.464, -13.800, -13.870, 0.000]],
0.001)