def test_flexibleConstraints(self):
""" Test the flexibleConstraints keyword """
topology = self.pdb1.topology
system1 = self.forcefield1.createSystem(topology, constraints=HAngles,
rigidWater=True)
system2 = self.forcefield1.createSystem(topology, constraints=HAngles,
rigidWater=True, flexibleConstraints=True)
system3 = self.forcefield1.createSystem(topology, constraints=None, rigidWater=False)
validateConstraints(self, topology, system1, HAngles, True)
# validateConstraints fails for system2 since by definition atom pairs can be in both bond
# and constraint lists. So just check that the number of constraints is the same for both
# system1 and system2
self.assertEqual(system1.getNumConstraints(), system2.getNumConstraints())
for force in system1.getForces():
if isinstance(force, HarmonicBondForce):
bf1 = force
elif isinstance(force, HarmonicAngleForce):
af1 = force
for force in system2.getForces():
if isinstance(force, HarmonicBondForce):
bf2 = force
elif isinstance(force, HarmonicAngleForce):
af2 = force
for force in system3.getForces():
if isinstance(force, HarmonicAngleForce):
af3 = force
# Make sure we picked up extra bond terms with flexibleConstraints
self.assertGreater(bf2.getNumBonds(), bf1.getNumBonds())
# Make sure flexibleConstraints yields just as many angles as no constraints
self.assertEqual(af2.getNumAngles(), af3.getNumAngles())
def test_flexibleConstraints(self):
""" Test the flexibleConstraints keyword """
topology = self.pdb1.topology
system1 = self.forcefield1.createSystem(topology, constraints=HAngles,
rigidWater=True)
system2 = self.forcefield1.createSystem(topology, constraints=HAngles,
rigidWater=True, flexibleConstraints=True)
system3 = self.forcefield1.createSystem(topology, constraints=None, rigidWater=False)
validateConstraints(self, topology, system1, HAngles, True)
# validateConstraints fails for system2 since by definition atom pairs can be in both bond
# and constraint lists. So just check that the number of constraints is the same for both
# system1 and system2
self.assertEqual(system1.getNumConstraints(), system2.getNumConstraints())
for force in system1.getForces():
if isinstance(force, HarmonicBondForce):
bf1 = force
elif isinstance(force, HarmonicAngleForce):
af1 = force
for force in system2.getForces():
if isinstance(force, HarmonicBondForce):
bf2 = force
elif isinstance(force, HarmonicAngleForce):
af2 = force
for force in system3.getForces():
if isinstance(force, HarmonicAngleForce):
af3 = force
# Make sure we picked up extra bond terms with flexibleConstraints
self.assertGreater(bf2.getNumBonds(), bf1.getNumBonds())
# Make sure flexibleConstraints yields just as many angles as no constraints
self.assertEqual(af2.getNumAngles(), af3.getNumAngles())
def test_RigidWaterAndConstraints(self):
"""Test all eight options for the constraints and rigidWater parameters."""
topology = self.prmtop1.topology
for constraints_value in [None, HBonds, AllBonds, HAngles]:
for rigidWater_value in [True, False]:
system = self.prmtop1.createSystem(constraints=constraints_value, rigidWater=rigidWater_value)
validateConstraints(self, topology, system, constraints_value, rigidWater_value)
def test_RigidWaterAndConstraints(self):
"""Test all eight options for the constraints and rigidWater parameters."""
topology = prmtop1.topology
for constraints_value in [None, HBonds, AllBonds, HAngles]:
for rigidWater_value in [True, False]:
system = prmtop1.createSystem(constraints=constraints_value,
rigidWater=rigidWater_value)
validateConstraints(self, topology, system, constraints_value,
rigidWater_value)