def setUp(self):
p = SubSystemFromSequence("NALA ALA CALA")
b = SystemBuilder(explicit_solvent=True)
self.system = b.build_system([p])
def setUp(self):
p = SubSystemFromSequence("NALA ALA CALA")
b = SystemBuilder(
explicit_solvent=True, explicit_ions=True, p_ioncount=3, n_ioncount=3
)
self.system = b.build_system([p])
def setUp(self):
p = SubSystemFromSequence("NALA ALA CALA")
b = SystemBuilder()
sys = b.build_system([p])
self.bonds = amber.ParmTopReader(sys.top_string).get_bonds()
def setUp(self):
p = SubSystemFromSequence("NALA ALA CALA")
b = SystemBuilder()
self.system = b.build_system([p])
def setUp(self):
p = SubSystemFromSequence("GLY GLY GLY GLY")
b = SystemBuilder()
self.system = b.build_system([p])
self.manager = restraints.RestraintManager(self.system)
def setUp(self):
p = SubSystemFromSequence("GLY GLY GLY GLY")
b = SystemBuilder()
self.system = b.build_system([p])
self.scaler = mock.Mock()
self.ramp = mock.Mock()
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()