def test_can_translate_atoms_with_iterable(self, mock_trim):
atom = Atom("C", 20, 30, 50)
atom.translate((5, -4, 12))
self.assertEqual(atom._x, 25)
self.assertEqual(atom._y, 26)
self.assertEqual(atom._z, 62)
mock_trim.assert_called_with(12)
def test_can_unbond_from_atom(self):
atom = Atom("C")
atom2 = Mock(_bonded_atoms={atom})
atom._bonded_atoms = {atom2}
atom.unbond_from(atom2)
self.assertEqual(atom._bonded_atoms, set())
self.assertEqual(atom2._bonded_atoms, set())
def test_can_transform_atoms(self, mock_trim):
atom = Atom("C", 20, 30, 50)
atom.transform([[1, 0, 0], [0, 0.7071, -0.7071], [0, 0.7071, 0.7071]],
trim=12)
self.assertEqual(atom._x, 20)
self.assertAlmostEqual(atom._y, -14.142, delta=3)
self.assertAlmostEqual(atom._z, 56.569, delta=3)
mock_trim.assert_called_with(12)
def test_atom_mass_case_insensitive(self):
atom = Atom("he", 2, 3, 5)
self.assertAlmostEqual(atom.mass, 4, delta=0.1)
atom = Atom("He", 2, 3, 5)
self.assertAlmostEqual(atom.mass, 4, delta=0.1)
atom = Atom("hE", 2, 3, 5)
self.assertAlmostEqual(atom.mass, 4, delta=0.1)
atom = Atom("HE", 2, 3, 5)
self.assertAlmostEqual(atom.mass, 4, delta=0.1)
def test_can_get_nearby_atoms(self, mock_loc):
model = Mock()
mock_loc.return_value = (1, 2, 3)
atom = Atom("C", 4, 8, 3)
atom._model = model
model.atoms_in_sphere.return_value = [1, 2, atom, 4]
atoms = atom.nearby_atoms(4, a=1, b=2)
model.atoms_in_sphere.assert_called_with(1, 2, 3, 4, a=1, b=2)
self.assertEqual(atoms, [1, 2, 4])
def test_can_round_atom_location(self):
atom = Atom("C", 0.1111, 0.4444, 0.8888)
atom.trim(3)
self.assertEqual((atom._x, atom._y, atom._z), (0.111, 0.444, 0.889))
atom.trim(2)
self.assertEqual((atom._x, atom._y, atom._z), (0.11, 0.44, 0.89))
atom.trim(1)
self.assertEqual((atom._x, atom._y, atom._z), (0.1, 0.4, 0.9))
atom.trim(0)
self.assertEqual((atom._x, atom._y, atom._z), (0, 0, 1))
def test_can_make_atom_copy(self):
atom = Atom("he", 2, 3, 5, 10, "H1", 0.5, 0.4, (1, 1, 1, 1, 1, 1))
patcher = patch("atomium.models.atoms.Atom")
mock_atom = patcher.start()
try:
copy = atom.copy()
self.assertIs(copy, mock_atom.return_value)
mock_atom.assert_called_with(element="he",
x=2,
y=3,
z=5,
id=10,
name="H1",
charge=0.5,
bfactor=0.4,
anisotropy=[1, 1, 1, 1, 1, 1])
finally:
patcher.stop()
def test_can_create_atom(self):
atom = Atom("C")
self.assertEqual(atom._element, "C")
self.assertEqual((atom._x, atom._y, atom._z), (0, 0, 0))
self.assertEqual(atom._id, 0)
self.assertEqual(atom._name, None)
self.assertEqual(atom._charge, 0)
self.assertEqual(atom._bfactor, 0)
self.assertEqual(atom._anisotropy, [0, 0, 0, 0, 0, 0])
self.assertEqual(atom._bonded_atoms, set())
self.assertEqual(atom._residue, None)
self.assertEqual(atom._ligand, None)
self.assertEqual(atom._chain, None)
self.assertEqual(atom._model, None)
def test_can_rotate_atoms(self, mock_transform):
atom = Atom("C", 20, 30, 50)
atom.rotate(math.pi / 2, "x", 10, a=20)
self.assertEqual(mock_transform.call_args_list[0][0][1], 10)
self.assertEqual(mock_transform.call_args_list[0][1], {"a": 20})
matrix_used = mock_transform.call_args_list[0][0][0]
self.assertEqual([[round(val, 12) for val in row]
for row in matrix_used],
[[1, 0, 0], [0, 0, -1], [0, 1, 0]])
atom.rotate(math.pi / 18, "y")
matrix_used = mock_transform.call_args_list[1][0][0]
self.assertEqual([[round(val, 3) for val in row]
for row in matrix_used],
[[0.985, 0, 0.174], [0, 1, 0], [-0.174, 0, 0.985]])
atom.rotate(math.pi / -36, "z")
matrix_used = mock_transform.call_args_list[2][0][0]
self.assertEqual([[round(val, 3) for val in row]
for row in matrix_used],
[[0.996, 0.087, 0], [-0.087, 0.996, 0], [0, 0, 1]])
def test_atom_str(self):
atom = Atom("C", 2, 3, 5, id=15, name="CA")
self.assertEqual(str(atom), "<Atom 15 (CA)>")
def test_basic_atom_repr(self):
atom = Atom("C")
self.assertEqual(repr(atom), "<C Atom at (0, 0, 0)>")
def test_atom_repr(self):
atom = Atom("C", 2, 3, 5, id=15, name="CA")
self.assertEqual(repr(atom), "<C (CA) Atom 15 at (2, 3, 5)>")
def test_model_property(self):
model = Mock()
atom = Atom("C", 2, 3, 5)
atom._model = model
self.assertIs(atom.model, model)
def test_x_property(self):
atom = Atom("C", 2, 3, 5)
self.assertIs(atom._x, atom.x)
def test_y_property(self):
atom = Atom("C", 2, 3, 5)
self.assertIs(atom._y, atom.y)
def test_atom_with_no_model_has_no_nearby_atoms(self):
atom = Atom("C", 4, 8, 3)
self.assertEqual(atom.nearby_atoms(cutoff=1), set())
self.assertEqual(atom.nearby_atoms(cutoff=100), set())
def test_can_handle_unbonding_from_unconnected_atom(self):
atom = Atom("C")
atom2 = Mock(_bonded_atoms=set())
atom.unbond_from(atom2)
self.assertEqual(atom._bonded_atoms, set())
self.assertEqual(atom2._bonded_atoms, set())
def test_can_create_atom_with_bfactor(self):
atom = Atom("C", bfactor=1.1)
self.assertEqual(atom._bfactor, 1.1)
def test_can_create_atom_with_charge(self):
atom = Atom("C", charge=-1)
self.assertEqual(atom._charge, -1)
def test_can_bond_to_atom(self):
atom = Atom("C")
atom2 = Mock(_bonded_atoms=set())
atom.bond_to(atom2)
self.assertEqual(atom._bonded_atoms, {atom2})
self.assertEqual(atom2._bonded_atoms, {atom})
def test_bonded_atoms_property(self):
atom = Atom("C", 2, 3, 5)
atom._bonded_atoms = [1, 2, 3]
self.assertEqual(atom.bonded_atoms, {1, 2, 3})
def test_basic_atom_str(self):
atom = Atom("C")
self.assertEqual(str(atom), "<Atom (C)>")
def test_element_property(self):
atom = Atom("C", 2, 3, 5)
self.assertIs(atom._element, atom.element)
def test_can_get_nearby_residues(self, mock_atoms):
mock_atoms.return_value = self.atoms
atom = Atom("C", 4, 8, 3)
self.assertEqual(atom.nearby_residues(3, a=1), set(self.residues))
mock_atoms.assert_called_with(3, a=1)
def test_can_update_element(self):
atom = Atom("C", 2, 3, 5)
atom.element = "N"
self.assertEqual(atom._element, "N")
def test_can_get_nearby_residues_and_ligands(self, mock_atoms):
mock_atoms.return_value = self.atoms
atom = Atom("C", 4, 8, 3)
self.assertEqual(atom.nearby_residues(3, ligands=True, a=1),
set(self.residues + ["LIG"]))
mock_atoms.assert_called_with(3, a=1)
def test_can_update_x(self):
atom = Atom("C", 2, 3, 5)
atom.x = 6
self.assertEqual(atom._x, 6)
def test_chain_property(self):
chain = Mock()
atom = Atom("C", 2, 3, 5)
atom._chain = chain
self.assertIs(atom.chain, chain)
def test_can_update_y(self):
atom = Atom("C", 2, 3, 5)
atom.y = 6
self.assertEqual(atom._y, 6)
def test_can_create_atom_with_anisotropy(self):
atom = Atom("C", anisotropy=[2, 5, 3, 2, 5, 6])
self.assertEqual(atom._anisotropy, [2, 5, 3, 2, 5, 6])