def test_parity_property(self):
mdata = MoleculeData()
mdata.parities = 1,
self.assertEqual(len(mdata.pars), 1)
mdata.parities = 1, 0
self.assertCountEqual(mdata.pars, [0, 1])
mdata.parities = 0
self.assertEqual(len(mdata.pars), 1)
def test_exp_data_shape1(self):
mdata = MoleculeData()
mdata.jvalues = 2.5,
exp_data_string = u"""1 \n
1 0 2.5 0.000000000 1 5.0e-03 1 5
"""
data_stream = io.StringIO(exp_data_string)
mdata.set_exp_data(data_stream, markers=[1])
self.assertEqual(mdata.exp_data.shape[0], 1)
def test_exp_data_shape2(self):
mdata = MoleculeData()
mdata.jvalues = 2.5, 3.5
exp_data_string = u"""2 \n
1 0 2.5 0.000000000 1 5.0e-03 1 5
2 0 3.5 27.92907799 1 2.554E-03 1 5
"""
data_stream = io.StringIO(exp_data_string)
mdata.set_exp_data(data_stream, markers=[1])
self.assertEqual(mdata.exp_data.shape[0], 2)
def test_exp_data_markers_None(self):
mdata = MoleculeData()
mdata.jvalues = 2.5, 3.5, 4.5
exp_data_string = u"""3 \n
1 0 2.5 0.000000000 1 5.0e-03 1 5
2 0 3.5 27.92907799 1 2.554E-03 1 5
3 0 4.5 63.82044637 1 2.589E-03 1 5
"""
data_stream = io.StringIO(exp_data_string)
mdata.set_exp_data(data_stream)
self.assertEqual(mdata.exp_data.shape[0], 3)
def test_exp_data_jnumbers_wrong_values(self):
mdata = MoleculeData()
mdata.jvalues = 8.5, 9.5, 6.5
exp_data_string = u"""3 \n
1 0 2.5 0.000000000 1 5.0e-03 1 5
2 0 3.5 27.92907799 1 2.554E-03 1 5
3 0 4.5 63.82044637 1 2.589E-03 1 5
"""
data_stream = io.StringIO(exp_data_string)
self.assertRaises(
SystemExit, mdata.set_exp_data, data_stream, markers=[1]
)
def test_exp_data_missing_column(self):
mdata = MoleculeData()
mdata.jvalues = 2.5, 3.5, 4.5
exp_data_string = u"""3 \n
1 0 2.5 0.000000000 1 5.0e-03 1
2 0 3.5 27.92907799 1 2.554E-03 1
3 0 4.5 63.82044637 1 2.589E-03 1
"""
data_stream = io.StringIO(exp_data_string)
self.assertRaises(
SystemExit, mdata.set_exp_data, data_stream, markers=[1]
)
def test_masses_property(self):
mdata = MoleculeData()
# number or string should not work
try:
mdata.masses = 1.0
except TypeError:
pass
# tuple or list of numbers should work
mdata.masses = 1.0,
self.assertEqual(len(mdata.imasses), 1)
mdata.masses = [1.0]
self.assertEqual(len(mdata.imasses), 1)
def test_molecule_property(self):
mdata = MoleculeData()
# string should not work
try:
mdata.molecule = '58Ni1H'
except SystemExit:
pass
# tuple or list of strings should work
mdata.molecule = '58Ni1H',
self.assertTrue(len(mdata.reduced_masses) == 1)
mdata.molecule = ['58Ni1H']
self.assertTrue(len(mdata.reduced_masses) == 1)
def test_exp_data_shape_large(self):
mdata = MoleculeData()
mdata.jvalues = 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5
exp_data_string = u"""8 \n
1 0 2.5 0.000000000 1 5.0e-03 1 5
2 0 3.5 27.92907799 1 2.554E-03 1 5
3 0 4.5 63.82044637 1 2.589E-03 1 5
4 0 5.5 107.6598777 1 2.993E-03 1 5
5 0 6.5 159.4241657 1 3.105E-03 1 5
6 0 7.5 219.0977590 1 3.052E-03 1 5
7 0 8.5 286.6573545 1 3.059E-03 1 5
8 0 9.5 362.0793175 1 3.108E-03 1 5
"""
data_stream = io.StringIO(exp_data_string)
mdata.set_exp_data(data_stream, markers=[1])
self.assertEqual(mdata.exp_data.shape[0], 8)
def test_exp_data_comments(self):
mdata = MoleculeData()
mdata.jvalues = 2.5, 3.5, 4.5
exp_data_string = u"""3 \n # comment
# comment
# comment
1 0 2.5 0.000000000 1 5.0e-03 1 5 # comment
# comment
2 0 3.5 27.92907799 1 2.554E-03 1 5
3 0 4.5 63.82044637 1 2.589E-03 1 5
#4 0 4.5 64.82044637 1 2.589E-03 1 5 # skip commented lines
#5 0 4.5 65.82044637 1 2.589E-03 1 5 # skip commented lines
# comment
# comment
"""
data_stream = io.StringIO(exp_data_string)
mdata.set_exp_data(data_stream)
self.assertEqual(mdata.exp_data.shape[0], 3)
def test_molecule_symbol_fail(self):
mdata = MoleculeData()
# pass
self.assert_is_instance_of_float(mdata, '1H 1H')
self.assert_is_instance_of_float(mdata, '1 H 1 H')
self.assert_is_instance_of_float(mdata, '1 H 1H')
self.assert_is_instance_of_float(mdata, '1H 1 H')
self.assert_is_instance_of_float(mdata, ' 1H1H')
self.assert_is_instance_of_float(mdata, '1H1H ')
# fail
self.assert_raised_error(mdata, 'H1H1')
self.assert_raised_error(mdata, '1HH')
self.assert_raised_error(mdata, 'H1H1H')
self.assertTrue(mdata._calculate_molecule_reduced_mass('1H1H') < 1.0)
self.assertRaises(AttributeError,
mdata._calculate_molecule_reduced_mass, 1)
def test_exp_data_both_parities(self):
mdata = MoleculeData()
mdata.jvalues = 2.5, 3.5, 4.5
mdata.parities = 0, 1
exp_data_string = u"""6 \n
1 0 2.5 0.000000000 1 5.0e-03 1 5
2 0 3.5 27.92907799 1 2.554E-03 1 5
3 0 4.5 63.82044637 1 2.589E-03 1 5
4 0 2.5 0.000000000 0 5.0e-03 2 5
5 0 3.5 27.92907799 0 2.554E-03 2 5
6 0 4.5 63.82044637 0 2.589E-03 2 5
"""
data_stream = io.StringIO(exp_data_string)
mdata.set_exp_data(data_stream, markers=[1, 2])
self.assertTrue(mdata.exp_data.shape[0] == 6)
def test_existing_exp_file(self):
mdata = MoleculeData()
self.assertRaises(
SystemExit, mdata.set_exp_data, 'some_file', markers=[1]
)
def test_jrange_and_jvalues_property(self):
mdata = MoleculeData()
mdata.jrange = 1, 5
self.assertCountEqual(mdata.jqnumbers, np.array([1, 2, 3, 4, 5]))
mdata.jqnumbers = np.array([], dtype=np.float64)
mdata.jrange = 1, 1
self.assertCountEqual(mdata.jqnumbers, np.array([1]))
mdata.jqnumbers = np.array([], dtype=np.float64)
mdata.jrange = 1, 0
self.assertEqual(mdata.jqnumbers.shape[0], 0)
mdata.jqnumbers = np.array([], dtype=np.float64)
mdata.jvalues = 1, 12, 15, 3, 12, 4
self.assertCountEqual(mdata.jqnumbers, np.array([1, 3, 4, 12, 15]))
mdata.jrange = 1, 4
self.assertCountEqual(mdata.jqnumbers, np.array([1, 2, 3, 4, 12, 15]))
mdata.referencej = 2
self.assertEqual(mdata.jqnumbers[0], 2)
self.assertCountEqual(mdata.jqnumbers, set(mdata.jqnumbers))