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()