def test_can_copy_chain_with_atoms(self, mock_ligands, mock_residues):
residues = [Mock(), Mock()]
mock_residues.return_value = residues
ligands = [Mock(), Mock()]
mock_ligands.return_value = ligands
residues[0].copy.return_value, residues[1].copy.return_value = Mock(), Mock()
ligands[0].copy.return_value, ligands[1].copy.return_value = Mock(), Mock()
chain = Chain(rep="ABC")
atoms = [Mock(_residue=None), Mock(_ligand=None), Mock(_ligand=None, _residue=None)]
chain._atoms = set(atoms)
patcher = patch("atomium.models.molecules.Chain")
mock_chain = patcher.start()
mock_chain.return_value = Mock(_atoms=set(atoms[:-1]))
try:
new_chain = chain.copy()
mock_chain.assert_called_with(
ligands[0].copy.return_value, ligands[1].copy.return_value,
residues[0].copy.return_value, residues[1].copy.return_value, rep="ABC"
)
atoms[-1].copy.assert_called_with()
self.assertFalse(atoms[0].called)
self.assertFalse(atoms[0].called)
self.assertEqual(new_chain._atoms, set(atoms[:-1] + [atoms[-1].copy.return_value]))
finally:
patcher.stop()
def setUp(self):
self.atom1, self.atom2 = Mock(), Mock()
self.atom3, self.atom4 = Mock(), Mock()
self.atom5, self.atom6 = Mock(), Mock()
self.atom7, self.atom8 = Mock(), Mock()
self.residue1, self.residue2 = Mock(), Mock()
self.residue3, self.residue4 = Mock(), Mock()
self.residue1.next = self.residue2
self.residue2.next = self.residue3
self.residue3.next = self.residue4
self.residue4.next = None
self.residue1.previous = None
self.residue2.previous = self.residue1
self.residue3.previous = self.residue2
self.residue4.previous = self.residue3
self.atom1.residue = self.residue1
self.atom2.residue = self.residue1
self.atom3.residue = self.residue2
self.atom4.residue = self.residue2
self.atom5.residue = self.residue3
self.atom6.residue = self.residue3
self.atom7.residue = self.residue4
self.atom8.residue = self.residue4
self.chain = Chain()
self.chain._atoms = set([
self.atom1, self.atom2, self.atom3, self.atom4,
self.atom5, self.atom6, self.atom7, self.atom8
])
def test_can_copy_chain(self, mock_ligands, mock_residues):
residues = [Mock(), Mock()]
mock_residues.return_value = residues
ligands = [Mock(), Mock()]
mock_ligands.return_value = ligands
residues[0].copy.return_value, residues[1].copy.return_value = Mock(), Mock()
ligands[0].copy.return_value, ligands[1].copy.return_value = Mock(), Mock()
chain = Chain(rep="ABC")
patcher = patch("atomium.models.molecules.Chain")
mock_chain = patcher.start()
try:
new_chain = chain.copy()
mock_chain.assert_called_with(
ligands[0].copy.return_value, ligands[1].copy.return_value,
residues[0].copy.return_value, residues[1].copy.return_value, rep="ABC"
)
finally:
patcher.stop()
class ChainCorrectCheckingTests(TestCase):
def setUp(self):
self.atom1, self.atom2 = Mock(), Mock()
self.atom3, self.atom4 = Mock(), Mock()
self.atom5, self.atom6 = Mock(), Mock()
self.atom7, self.atom8 = Mock(), Mock()
self.residue1, self.residue2 = Mock(), Mock()
self.residue3, self.residue4 = Mock(), Mock()
self.residue1.next = self.residue2
self.residue2.next = self.residue3
self.residue3.next = self.residue4
self.residue4.next = None
self.residue1.previous = None
self.residue2.previous = self.residue1
self.residue3.previous = self.residue2
self.residue4.previous = self.residue3
self.atom1.residue = self.residue1
self.atom2.residue = self.residue1
self.atom3.residue = self.residue2
self.atom4.residue = self.residue2
self.atom5.residue = self.residue3
self.atom6.residue = self.residue3
self.atom7.residue = self.residue4
self.atom8.residue = self.residue4
self.chain = Chain()
self.chain._atoms = set([
self.atom1, self.atom2, self.atom3, self.atom4,
self.atom5, self.atom6, self.atom7, self.atom8
])
def test_can_verify_conected_residues(self):
self.chain._atoms = set([self.atom1, self.atom2])
self.assertTrue(self.chain.verify())
self.chain._atoms = set([self.atom3, self.atom4])
self.assertTrue(self.chain.verify())
self.chain._atoms = set([self.atom5, self.atom6])
self.assertTrue(self.chain.verify())
self.chain._atoms = set([self.atom7, self.atom8])
self.assertTrue(self.chain.verify())
self.chain._atoms = set([
self.atom1, self.atom2, self.atom3, self.atom4
])
self.assertTrue(self.chain.verify())
self.chain._atoms = set([
self.atom3, self.atom4, self.atom5, self.atom6
])
self.assertTrue(self.chain.verify())
self.chain._atoms = set([
self.atom5, self.atom6, self.atom7, self.atom8
])
self.assertTrue(self.chain.verify())
def test_can_reject_unconnected_residues(self):
self.chain._atoms = set([
self.atom3, self.atom4, self.atom7, self.atom8
])
with self.assertRaises(SequenceConnectivityError):
self.chain.verify()
def test_empty_sequences_pass(self):
self.chain._atoms = set()
self.assertTrue(self.chain.verify())
def test_can_get_len(self, mock_residues):
chain = Chain()
mock_residues.return_value = [1, 2, 4]
self.assertEqual(chain[0], 1)
self.assertEqual(chain[1], 2)
self.assertEqual(chain[2], 4)
def test_can_get_len(self, mock_residues):
chain = Chain()
mock_residues.return_value = [1, 2, 4]
self.assertEqual(len(chain), 3)
def test_can_create_chain_with_rep_sequence(self, mock_veriy, mock_init):
chain = Chain("a", b="c", rep="ABC")
self.assertIsInstance(chain, AtomStructure)
mock_init.assert_called_with(chain, "a", b="c")
mock_veriy.assert_called_with()
self.assertEqual(chain._rep_sequence, "ABC")
def test_can_update_chain_rep_sequence(self):
chain = Chain(rep="ABC")
chain.rep_sequence = "DEF"
self.assertEqual(chain._rep_sequence, "DEF")
def test_chain_rep_sequence_property(self):
chain = Chain(rep="ABC")
self.assertIs(chain._rep_sequence, chain.rep_sequence)
def test_can_get_sequence(self, mock_residues):
chain = Chain()
mock_residues.return_value = (Mock(code="Y"), Mock(code="T"))
self.assertEqual(chain.sequence, "YT")
def test_can_get_len(self, mock_len):
chain = Chain()
mock_len.return_value = 100
self.assertEqual(chain.length, 100)