def setUp(self):
# create a tri-ala molecule
p = protein.ProteinMoleculeFromSequence('NALA ALA CALA')
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p, p])
# mock openmm system to recieve the new cmap torsion force
self.mock_openmm_system = mock.Mock(spec=openmm.System)
# patch out CMAPTorsionForce so we can see how it is called
self.patcher = mock.patch(
'meld.system.openmm_runner.cmap.openmm.CMAPTorsionForce',
spec=openmm.CMAPTorsionForce)
self.MockCMAP = self.patcher.start()
self.mock_cmap = mock.Mock(spec=openmm.CMAPTorsionForce)
self.MockCMAP.return_value = self.mock_cmap
def setUp(self):
# create a tri-ala molecule
p = protein.ProteinMoleculeFromSequence("NALA ALA CALA")
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
# create eight 24x24 maps filled with 0, 1, ..7
self.maps = [np.zeros((24, 24)) + i for i in range(8)]
# mock openmm system to recieve the new cmap torsion force
self.mock_openmm_system = mock.Mock(spec=openmm.System)
# patch out CMAPTorsionForce so we can see how it is called
self.patcher = mock.patch(
"meld.system.openmm_runner.cmap.openmm.CMAPTorsionForce",
spec=openmm.CMAPTorsionForce,
)
self.MockCMAP = self.patcher.start()
self.mock_cmap = mock.Mock(spec=openmm.CMAPTorsionForce)
self.MockCMAP.return_value = self.mock_cmap
def make_system(self, restype):
sequence = f"NALA {restype} CALA"
p = protein.ProteinMoleculeFromSequence(sequence)
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
def make_system(self, restype):
sequence = 'NALA {0} CALA'.format(restype)
p = protein.ProteinMoleculeFromSequence(sequence)
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
def setUp(self):
p = protein.ProteinMoleculeFromSequence("NALA ALA CALA")
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
self.system.temperature_scaler = ConstantTemperatureScaler(300.)
def setUp(self):
p = protein.ProteinMoleculeFromSequence('NALA ALA CALA')
b = builder.SystemBuilder()
sys = b.build_system_from_molecules([p])
self.bonds = ParmTopReader(sys.top_string).get_bonds()
def setUp(self):
p = protein.ProteinMoleculeFromSequence('NALA ALA CALA')
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
def setUp(self):
p = protein.ProteinMoleculeFromSequence("NALA ALA CALA")
b = builder.SystemBuilder(explicit_solvent=True)
self.system = b.build_system_from_molecules([p])