def test_creating_restraint_should_raise_if_ramp_is_wrong_type(self):
scaler = restraints.ConstantScaler()
ramp = restraints.ConstantScaler()
with self.assertRaises(ValueError):
_rest = self.manager.create_restraint(
"distance",
scaler,
ramp=ramp,
atom1=self.system.index.atom(0, "CA"),
atom2=self.system.index.atom(1, "CA"),
r1=0.0,
r2=1.0,
r3=3.0,
r4=4.0,
k=1.0,
)
def test_creating_restraint_should_raise_if_ramp_is_wrong_type(self):
scaler = restraints.ConstantScaler()
ramp = restraints.ConstantScaler()
self.mock_system.index_of_atom.side_effect = [0, 1]
with self.assertRaises(ValueError):
_rest = self.manager.create_restraint(
"distance",
scaler,
ramp=ramp,
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,
)
def test_create_restraint_without_specifying_ramp_should_use_constant_ramp(
self):
scaler = restraints.ConstantScaler()
rest = self.manager.create_restraint(
"distance",
scaler,
atom1=self.system.index.atom(0, "CA"),
atom2=self.system.index.atom(1, "CA"),
r1=0.0 * u.nanometer,
r2=1.0 * u.nanometer,
r3=3.0 * u.nanometer,
r4=4.0 * u.nanometer,
k=1.0 * u.kilojoule_per_mole / u.nanometer**2,
)
self.assertTrue(isinstance(rest.ramp, restraints.ConstantRamp))
def test_create_restraint_without_specifying_ramp_should_use_constant_ramp(
self):
scaler = restraints.ConstantScaler()
self.mock_system.index_of_atom.side_effect = [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.ramp, restraints.ConstantRamp))
def test_should_raise_if_alpha_is_greater_than_one(self):
scaler = restraints.ConstantScaler()
with self.assertRaises(RuntimeError):
scaler(2.0)
def test_should_raise_if_alpha_is_less_than_zero(self):
scaler = restraints.ConstantScaler()
with self.assertRaises(RuntimeError):
scaler(-1.0)
def test_should_return_1_when_alpha_is_1(self):
scaler = restraints.ConstantScaler()
self.assertAlmostEqual(scaler(1.0), 1.0)
def setUp(self):
p = SubSystemFromSequence("GLY GLY GLY GLY")
b = SystemBuilder()
self.system = b.build_system([p])
self.scaler = restraints.ConstantScaler()
self.ramp = restraints.ConstantRamp()
def setUp(self):
self.mock_system = mock.Mock()
self.scaler = restraints.ConstantScaler()
self.ramp = restraints.ConstantRamp()
def setUp(self):
p = system.ProteinMoleculeFromSequence("GLY GLY GLY GLY")
b = system.SystemBuilder()
self.system = b.build_system_from_molecules([p])
self.scaler = restraints.ConstantScaler()
self.ramp = restraints.ConstantRamp()
