def test_as_dict(self):
index = 11
in_site = 4
c = np.array([0.1, 0.2, 0.3])
atom = Atom(index=index)
atom.in_site = in_site
atom._frac_coords = c
d = atom.as_dict()
self.assertEqual(d['index'], index)
self.assertEqual(d['in_site'], in_site)
np.testing.assert_array_equal(d['frac_coords'], c)
def test_reset(self):
atom = Atom(index=12)
atom.in_site = 3
atom._frac_coords = np.array( [0,0, 0.0, 0.0] )
atom.trajectory = [1,2,3]
atom.reset()
self.assertEqual( atom.in_site, None )
self.assertEqual( atom._frac_coords, None )
self.assertEqual( atom.trajectory, [] )
def test_atom_is_initialised(self):
atom = Atom(index=22)
self.assertEqual(atom.index, 22)
self.assertEqual(atom.in_site, None)
self.assertEqual(atom._frac_coords, None)
self.assertEqual(atom.trajectory, [])
def test_frac_coords_getter(self):
atom = Atom(index=12)
c = np.array([0.3, 0.4, 0.5])
atom._frac_coords = c
np.testing.assert_array_equal(atom.frac_coords, c)
def test_frac_coords_getter_raises_atttribute_error_if_frac_coords_is_none(self):
atom = Atom(index=1)
atom._frac_coords = None
with self.assertRaises(AttributeError):
atom.frac_coords
def test_assign_coords(self):
atom = Atom(index=1)
structure = example_structure()
atom.assign_coords(structure=structure)
np.testing.assert_array_equal(atom._frac_coords, structure[1].frac_coords )
def test___repr__(self):
atom = Atom(index=12)
self.assertEqual(atom.__repr__(), 'site_analysis.Atom(index=12, in_site=None, frac_coords=None)')
def test___str__(self):
atom = Atom(index=12)
self.assertEqual(str(atom), 'Atom: 12')