def test_can_remove_previous_residue(self):
res = Residue(self.atom1, self.atom2, self.atom3)
previous_res = Mock(Residue)
res._previous = previous_res
previous_res._next = res
res.previous = None
self.assertIsNone(res._previous)
self.assertIsNone(previous_res._next)
def test_can_remove_next_residue(self):
res = Residue(self.atom1, self.atom2, self.atom3)
next_res = Mock(Residue)
res._next = next_res
next_res._previous = res
res.next = None
self.assertIsNone(res._next)
self.assertIsNone(next_res._previous)
def test_can_get_no_chain(self, mock_atoms):
mock_atoms.return_value = set(self.atoms)
self.atom1.chain = None
self.atom2.chain = None
self.atom3.chain = None
res = Residue(self.atom1, self.atom2, self.atom3)
self.assertIs(res.chain, None)
def test_can_get_chain(self, mock_atoms):
mock_atoms.return_value = set(self.atoms)
chain = Mock()
self.atom1.chain = chain
self.atom2.chain = chain
self.atom3.chain = chain
res = Residue(self.atom1, self.atom2, self.atom3)
self.assertIs(res.chain, chain)
def test_can_create_residue(self, mock_init):
mock_init.side_effect = self.mock_init
res = Residue(self.atom1, self.atom2, self.atom3, a=1, b=2)
self.assertIsInstance(res, Molecule)
mock_init.assert_called_with(res,
self.atom1,
self.atom2,
self.atom3,
a=1,
b=2)
self.assertIsNone(res._next)
self.assertIsNone(res._previous)
def is_residue_nearby(fragment_positions: List[Tuple[float, float, float]],
residue: Residue, radius: float) -> bool:
residue_positions = [a.location() for a in residue.atoms()]
residue_bounding_box = bounding_box(residue_positions)
fragment_bounding_box = bounding_box(fragment_positions)
if not bounding_boxes_overlap(fragment_bounding_box, radius,
residue_bounding_box):
return False
square_radius = radius * radius
for fragment_atom_position in fragment_positions:
for residue_atom_position in residue_positions:
x = residue_atom_position[0] - fragment_atom_position[0]
y = residue_atom_position[1] - fragment_atom_position[1]
z = residue_atom_position[2] - fragment_atom_position[2]
dist = x * x + y * y + z * z
if dist < square_radius:
return True
return False
def test_molecule_repr_id_no_name(self):
res = Residue(self.atom1, self.atom2, self.atom3)
res._id = "C10A"
self.assertEqual(str(res), "<Residue C10A (3 atoms)>")
def test_next_residue_must_be_residue(self):
res = Residue(self.atom1, self.atom2, self.atom3)
mol = Mock(Molecule)
with self.assertRaises(TypeError):
res.next = mol
def test_next_res_cannot_be_self(self):
res = Residue(self.atom1, self.atom2, self.atom3)
with self.assertRaises(ValueError):
res.next = res
def test_next_gets_next(self):
res = Residue(self.atom1, self.atom2, self.atom3)
res._next = Mock(Residue)
self.assertIs(res.next, res._next)
def test_can_assign_next(self):
res = Residue(self.atom1, self.atom2, self.atom3)
next_res = Mock(Residue)
res.next = next_res
self.assertIs(res._next, next_res)
self.assertIs(next_res._previous, res)
def test_can_get_name(self):
res = Residue(self.atom1, self.atom2, self.atom3)
self.assertIsNone(res.full_name)
res._name = "XMP"
self.assertEqual(res.full_name, "XMP")
def test_can_lookup_full_name(self):
res = Residue(self.atom1, self.atom2, self.atom3)
res._name = "met"
self.assertEqual(res.full_name, "methionine")
def test_molecule_repr_name_no_id(self):
res = Residue(self.atom1, self.atom2, self.atom3)
res._name = "GLY"
self.assertEqual(str(res), "<Residue (GLY, 3 atoms)>")
def test_molecule_repr_id_and_name(self):
res = Residue(self.atom1, self.atom2)
res._id, res._name = "C10B", "GLY"
self.assertEqual(str(res), "<Residue C10B (GLY, 2 atoms)>")
def test_previous_gets_previous(self):
res = Residue(self.atom1, self.atom2, self.atom3)
res._previous = Mock(Residue)
self.assertIs(res.previous, res._previous)
def test_molecule_repr_no_id_or_name(self):
res = Residue(self.atom1, self.atom2, self.atom3)
self.assertEqual(str(res), "<Residue (3 atoms)>")
def test_atoms_are_linked_to_residue(self):
res = Residue(self.atom1, self.atom2, self.atom3)
self.assertIs(self.atom1._residue, res)
self.assertIs(self.atom2._residue, res)
self.assertIs(self.atom3._residue, res)
def test_can_assign_previous(self):
res = Residue(self.atom1, self.atom2, self.atom3)
previous_res = Mock(Residue)
res.previous = previous_res
self.assertIs(res._previous, previous_res)
self.assertIs(previous_res._next, res)
def test_previous_res_cannot_be_self(self):
res = Residue(self.atom1, self.atom2, self.atom3)
with self.assertRaises(ValueError):
res.previous = res