def setUp(self):
p = system.protein.ProteinMoleculeFromSequence(
'NALA ALA ALA ALA ALA ALA ALA ALA ALA CALA')
b = system.builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
self.ss = 'HHHHHEEEEE'
self.scaler = restraints.LinearScaler(0, 1)
def setUp(self):
p = system.subsystem.SubSystemFromSequence(
"NALA ALA ALA ALA ALA ALA ALA ALA ALA CALA"
)
b = system.builder.SystemBuilder()
self.scaler = restraints.LinearScaler(0, 1)
self.patcher = patchers.RdcAlignmentPatcher(n_tensors=1)
self.system = b.build_system([p], patchers=[self.patcher])
def setUp(self):
p = system.protein.ProteinMoleculeFromSequence(
"NALA ALA ALA ALA ALA ALA ALA ALA ALA CALA")
b = system.builder.SystemBuilder()
self.scaler = restraints.LinearScaler(0, 1)
self.patcher = patchers.RdcAlignmentPatcher(n_tensors=1)
self.system = b.build_system_from_molecules([p],
patchers=[self.patcher])
def setUp(self):
p = system.subsystem.SubSystemFromSequence(
"NALA ALA ALA ALA ALA ALA ALA ALA ALA CALA"
)
b = system.builder.SystemBuilder()
self.system = b.build_system([p])
self.ss = "HHHHHEEEEE"
self.scaler = restraints.LinearScaler(0, 1)
def test_creating_restraint_with_scaler_should_use_it(self):
scaler = restraints.LinearScaler(0, 1)
rest = self.manager.create_restraint(
"distance",
scaler,
atom1=self.system.index.atom(0, "CA"),
atom2=self.system.index.atom(1, "CA"),
r1=0 * u.nanometer,
r2=1 * u.nanometer,
r3=3 * u.nanometer,
r4=4 * u.nanometer,
k=1.0 * u.kilojoule_per_mole / u.nanometer**2,
)
self.assertTrue(isinstance(rest.scaler, restraints.LinearScaler))
def test_creating_restraint_with_scaler_should_use_it(self):
self.mock_system.index_of_atom.side_effect = [0, 1]
scaler = restraints.LinearScaler(0, 1)
rest = self.manager.create_restraint(
"distance",
scaler,
atom_1_res_index=1,
atom_1_name="CA",
atom_2_res_index=2,
atom_2_name="CA",
r1=0,
r2=1,
r3=3,
r4=4,
k=1.0,
)
self.assertTrue(isinstance(rest.scaler, restraints.LinearScaler))
def test_should_return_correct_value_in_middle(self):
scaler = restraints.LinearScaler(0.0, 1.0, 1.0, 0.0)
self.assertAlmostEqual(scaler(0.3), 0.7)
def test_should_return_0_above_alpha_max(self):
scaler = restraints.LinearScaler(0.2, 0.8, 1.0, 0.0)
self.assertAlmostEqual(scaler(0.9), 0.0)
def test_should_return_1_below_alpha_min(self):
scaler = restraints.LinearScaler(0.2, 0.8, 1.0, 0.0)
self.assertAlmostEqual(scaler(0.1), 1.0)
def test_should_raise_if_alpha_is_above_one(self):
scaler = restraints.LinearScaler(0.2, 0.8)
with self.assertRaises(RuntimeError):
scaler(2)
def test_should_raise_if_alpha_is_below_zero(self):
scaler = restraints.LinearScaler(0.2, 0.8)
with self.assertRaises(RuntimeError):
scaler(-1)
def test_should_raise_if_alpha_max_less_than_alpha_min(self):
with self.assertRaises(RuntimeError):
restraints.LinearScaler(0.7, 0.6)
def test_should_raise_when_alpha_max_above_one(self):
with self.assertRaises(RuntimeError):
restraints.LinearScaler(1, 2)
def test_should_raise_when_alpha_max_below_zero(self):
with self.assertRaises(RuntimeError):
restraints.LinearScaler(1, -1)
