def test_modify_topology(self, ethane_system_topology):
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
residues = [*ethane_system_topology[1].residues()]
ethane_system_topology[1].addAtom('added', None, residues[0])
my_ommp.populate_ommperator()
assert len(my_ommp.atoms) == 9
def test_clear_ommperator(self, ethane_system_topology):
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_ommp.clear_ommperator()
assert not hasattr('self', 'atoms')
assert not hasattr('self', 'bonds')
assert not hasattr('self', 'angles')
assert not hasattr('self', 'dihedrals')
assert not hasattr('self', 'nonbonds')
assert not hasattr('self', 'custom_bonds')
assert not hasattr('self', 'custom_nonbonds')
def test_modify_omm(self, ethane_system_topology):
periodic_torsion = openmm.PeriodicTorsionForce()
periodic_torsion.addTorsion(0, 1, 2, 3, 10, 20, 30)
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_dih_ommp = PeriodicTorsionForceOmmperator(my_ommp, periodic_torsion,
0)
periodic_torsion.setTorsionParameters(0, 1, 2, 3, 4, 20, 30, 40)
assert my_dih_ommp.particle1 == periodic_torsion.getTorsionParameters(
0)[0]
assert my_dih_ommp.particle1 == 1
assert my_dih_ommp.particle2 == periodic_torsion.getTorsionParameters(
0)[1]
assert my_dih_ommp.particle2 == 2
assert my_dih_ommp.particle3 == periodic_torsion.getTorsionParameters(
0)[2]
assert my_dih_ommp.particle3 == 3
assert my_dih_ommp.particle4 == periodic_torsion.getTorsionParameters(
0)[3]
assert my_dih_ommp.particle4 == 4
assert my_dih_ommp.n == periodic_torsion.getTorsionParameters(0)[4]
assert my_dih_ommp.phase == periodic_torsion.getTorsionParameters(0)[5]
assert my_dih_ommp.k == periodic_torsion.getTorsionParameters(0)[6]
def test_setting(self, ethane_system_topology):
nb_force = openmm.NonbondedForce()
nb_force.addParticle(1, 2, 3)
my_ommp = Ommperator(ethane_system_topology[0], ethane_system_topology[1])
my_nb_ommp = NonbondedForceOmmperator(my_ommp, nb_force, 0)
my_nb_ommp.charge = 10*unit.elementary_charge
my_nb_ommp.sigma = 20*unit.nanometer
my_nb_ommp.epsilon = 30*unit.kilojoule_per_mole
assert my_nb_ommp.charge == nb_force.getParticleParameters(0)[0]
assert my_nb_ommp.sigma == nb_force.getParticleParameters(0)[1]
assert my_nb_ommp.epsilon == nb_force.getParticleParameters(0)[2]
assert is_close(my_nb_ommp.charge, 10*unit.elementary_charge)
assert is_close(my_nb_ommp.sigma, 20*unit.nanometer)
assert is_close(my_nb_ommp.epsilon, 30*unit.kilojoule_per_mole)
my_nb_ommp.set_params(charge=100*unit.elementary_charge,
sigma=200*unit.nanometer,
epsilon=300*unit.kilojoule_per_mole)
assert my_nb_ommp.charge == nb_force.getParticleParameters(0)[0]
assert my_nb_ommp.sigma == nb_force.getParticleParameters(0)[1]
assert my_nb_ommp.epsilon == nb_force.getParticleParameters(0)[2]
assert is_close(my_nb_ommp.charge, 100*unit.elementary_charge)
assert is_close(my_nb_ommp.sigma, 200*unit.nanometer)
assert is_close(my_nb_ommp.epsilon, 300*unit.kilojoule_per_mole)
def test_setting(self, ethane_system_topology):
harmonic_bond = openmm.HarmonicBondForce()
harmonic_bond.addBond(0, 1, 10, 20)
my_ommp = Ommperator(ethane_system_topology[0], ethane_system_topology[1])
my_bond_ommp = HarmonicBondForceOmmperator(my_ommp, harmonic_bond, 0)
my_bond_ommp.particle1 = 5
my_bond_ommp.particle2 = 6
my_bond_ommp.k = 100
my_bond_ommp.length = 200
assert my_bond_ommp.particle1 == harmonic_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 5
assert my_bond_ommp.particle2 == harmonic_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 6
assert my_bond_ommp.length == harmonic_bond.getBondParameters(0)[2]
assert my_bond_ommp.k == harmonic_bond.getBondParameters(0)[3]
my_bond_ommp.set_params(p1=100, p2=200,
k=300, length=400)
assert my_bond_ommp.particle1 == harmonic_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 100
assert my_bond_ommp.particle2 == harmonic_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 200
assert my_bond_ommp.length == harmonic_bond.getBondParameters(0)[2]
assert my_bond_ommp.k == harmonic_bond.getBondParameters(0)[3]
def test_update_kwarg(self, geometric_ethane_system_topology):
my_ommp = Ommperator(geometric_ethane_system_topology[0],
geometric_ethane_system_topology[1])
my_ommp.custom_nonbond_types['opls_135'].update(sigma=5 *
unit.nanometer)
param_index = my_ommp.custom_nonbonds[0].parameter_index['sigma']
for nonbond in my_ommp.custom_nonbond_types['opls_135']:
assert nonbond.parameters[param_index] == 5
def test_setting(self, ethane_system_topology):
rb_torsion = openmm.RBTorsionForce()
rb_torsion.addTorsion(0, 1, 2, 3, 10, 20, 30, 40, 50, 60)
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_dih_ommp = RBTorsionForceOmmperator(my_ommp, rb_torsion, 0)
my_dih_ommp.particle1 = 10
my_dih_ommp.particle2 = 20
my_dih_ommp.particle3 = 30
my_dih_ommp.particle4 = 40
my_dih_ommp.c0 = 100
my_dih_ommp.c1 = 200
my_dih_ommp.c2 = 300
my_dih_ommp.c3 = 400
my_dih_ommp.c4 = 500
my_dih_ommp.c5 = 600
assert my_dih_ommp.particle1 == rb_torsion.getTorsionParameters(0)[0]
assert my_dih_ommp.particle1 == 10
assert my_dih_ommp.particle2 == rb_torsion.getTorsionParameters(0)[1]
assert my_dih_ommp.particle2 == 20
assert my_dih_ommp.particle3 == rb_torsion.getTorsionParameters(0)[2]
assert my_dih_ommp.particle3 == 30
assert my_dih_ommp.particle4 == rb_torsion.getTorsionParameters(0)[3]
assert my_dih_ommp.particle4 == 40
assert my_dih_ommp.c0 == rb_torsion.getTorsionParameters(0)[4]
assert my_dih_ommp.c1 == rb_torsion.getTorsionParameters(0)[5]
assert my_dih_ommp.c2 == rb_torsion.getTorsionParameters(0)[6]
assert my_dih_ommp.c3 == rb_torsion.getTorsionParameters(0)[7]
assert my_dih_ommp.c4 == rb_torsion.getTorsionParameters(0)[8]
assert my_dih_ommp.c5 == rb_torsion.getTorsionParameters(0)[9]
my_dih_ommp.set_params(p1=100,
p2=200,
p3=300,
p4=400,
c0=1000,
c1=2000,
c2=3000,
c3=4000,
c4=5000,
c5=6000)
assert my_dih_ommp.particle1 == rb_torsion.getTorsionParameters(0)[0]
assert my_dih_ommp.particle1 == 100
assert my_dih_ommp.particle2 == rb_torsion.getTorsionParameters(0)[1]
assert my_dih_ommp.particle2 == 200
assert my_dih_ommp.particle3 == rb_torsion.getTorsionParameters(0)[2]
assert my_dih_ommp.particle3 == 300
assert my_dih_ommp.particle4 == rb_torsion.getTorsionParameters(0)[3]
assert my_dih_ommp.particle4 == 400
assert my_dih_ommp.c0 == rb_torsion.getTorsionParameters(0)[4]
assert my_dih_ommp.c1 == rb_torsion.getTorsionParameters(0)[5]
assert my_dih_ommp.c2 == rb_torsion.getTorsionParameters(0)[6]
assert my_dih_ommp.c3 == rb_torsion.getTorsionParameters(0)[7]
assert my_dih_ommp.c4 == rb_torsion.getTorsionParameters(0)[8]
assert my_dih_ommp.c5 == rb_torsion.getTorsionParameters(0)[9]
def test_update_arg(self, geometric_ethane_system_topology):
my_ommp = Ommperator(geometric_ethane_system_topology[0],
geometric_ethane_system_topology[1])
my_ommp.custom_nonbond_types['opls_135'].update(
10 * unit.kilojoule_per_mole, 5 * unit.nanometer)
sigma_index = my_ommp.custom_nonbonds[0].parameter_index['sigma']
epsilon_index = my_ommp.custom_nonbonds[0].parameter_index['epsilon']
for nonbond in my_ommp.custom_nonbond_types['opls_135']:
assert nonbond.parameters[sigma_index] == 5
assert nonbond.parameters[epsilon_index] == 10
def test_parsing(self, ethane_system_topology):
harmonic_bond = openmm.HarmonicBondForce()
harmonic_bond.addBond(0, 1, 10, 20)
my_ommp = Ommperator(ethane_system_topology[0], ethane_system_topology[1])
my_bond_ommp = HarmonicBondForceOmmperator(my_ommp, harmonic_bond, 0)
assert my_bond_ommp.particle1 == harmonic_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle2 == harmonic_bond.getBondParameters(0)[1]
assert my_bond_ommp.length == harmonic_bond.getBondParameters(0)[2]
assert my_bond_ommp.k == harmonic_bond.getBondParameters(0)[3]
def test_parsing(self, ethane_system_topology):
custom_bond = openmm.CustomBondForce('a+b*r')
custom_bond.addPerBondParameter('a')
custom_bond.addPerBondParameter('b')
custom_bond.addBond(0, 1, (10, 20))
my_ommp = Ommperator(ethane_system_topology[0], ethane_system_topology[1])
my_bond_ommp = CustomBondForceOmmperator(my_ommp, custom_bond, 0)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
def test_setting(self, ethane_system_topology):
periodic_torsion = openmm.PeriodicTorsionForce()
periodic_torsion.addTorsion(0, 1, 2, 3, 10, 20, 30)
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_dih_ommp = PeriodicTorsionForceOmmperator(my_ommp, periodic_torsion,
0)
my_dih_ommp.particle1 = 10
my_dih_ommp.particle2 = 20
my_dih_ommp.particle3 = 30
my_dih_ommp.particle4 = 40
my_dih_ommp.n == 50
my_dih_ommp.phase == 60
my_dih_ommp.k == 70
assert my_dih_ommp.particle1 == periodic_torsion.getTorsionParameters(
0)[0]
assert my_dih_ommp.particle1 == 10
assert my_dih_ommp.particle2 == periodic_torsion.getTorsionParameters(
0)[1]
assert my_dih_ommp.particle2 == 20
assert my_dih_ommp.particle3 == periodic_torsion.getTorsionParameters(
0)[2]
assert my_dih_ommp.particle3 == 30
assert my_dih_ommp.particle4 == periodic_torsion.getTorsionParameters(
0)[3]
assert my_dih_ommp.particle4 == 40
assert my_dih_ommp.n == periodic_torsion.getTorsionParameters(0)[4]
assert my_dih_ommp.phase == periodic_torsion.getTorsionParameters(0)[5]
assert my_dih_ommp.k == periodic_torsion.getTorsionParameters(0)[6]
my_dih_ommp.set_params(p1=100,
p2=200,
p3=300,
p4=400,
n=500,
phase=600,
k=700)
assert my_dih_ommp.particle1 == periodic_torsion.getTorsionParameters(
0)[0]
assert my_dih_ommp.particle1 == 100
assert my_dih_ommp.particle2 == periodic_torsion.getTorsionParameters(
0)[1]
assert my_dih_ommp.particle2 == 200
assert my_dih_ommp.particle3 == periodic_torsion.getTorsionParameters(
0)[2]
assert my_dih_ommp.particle3 == 300
assert my_dih_ommp.particle4 == periodic_torsion.getTorsionParameters(
0)[3]
assert my_dih_ommp.particle4 == 400
assert my_dih_ommp.n == periodic_torsion.getTorsionParameters(0)[4]
assert my_dih_ommp.phase == periodic_torsion.getTorsionParameters(0)[5]
assert my_dih_ommp.k == periodic_torsion.getTorsionParameters(0)[6]
def test_setting(self, geometric_ethane_system_topology):
nb_force = openmm.CustomNonbondedForce('epsilon1*epsilon2*(sigr6^2-sigr6); sigr6=sigr2*sigr2*sigr2; '
'sigr2=(sigc/r)^2; sigc=sigma1*sigma2')
nb_force.addPerParticleParameter('epsilon')
nb_force.addPerParticleParameter('sigma')
nb_force.addParticle((1*unit.kilojoule_per_mole, 2*unit.nanometer))
my_ommp = Ommperator(geometric_ethane_system_topology[0],
geometric_ethane_system_topology[1])
my_nb_ommp = CustomNonbondedForceOmmperator(my_ommp, nb_force, 0)
my_nb_ommp.set_params(10*unit.kilojoule_per_mole, -1)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 10
assert my_nb_ommp.parameters[1] == 2
my_nb_ommp.set_params(-1, 20*unit.nanometer)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 10
assert my_nb_ommp.parameters[1] == 20
my_nb_ommp.set_params(epsilon=100*unit.kilojoule_per_mole)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 100
assert my_nb_ommp.parameters[1] == 20
my_nb_ommp.set_params(sigma=200*unit.nanometer)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 100
assert my_nb_ommp.parameters[1] == 200
my_nb_ommp.set_params(1000*unit.kilojoule_per_mole, 2000*unit.nanometer)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 1000
assert my_nb_ommp.parameters[1] == 2000
my_nb_ommp.set_params(epsilon=10000*unit.kilojoule_per_mole,
sigma=20000*unit.nanometer)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 10000
assert my_nb_ommp.parameters[1] == 20000
with pytest.raises(ValueError):
my_nb_ommp.set_params(1,2,epsilon=3, sigma=4)
def test_parsing(self, ethane_system_topology):
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
assert len(my_ommp.atoms) == 8
assert len(my_ommp.bonds) == 7
assert len(my_ommp.angles) == 12
assert len(my_ommp.dihedrals) == 9
assert len(my_ommp.nonbonds) == 8
assert len(my_ommp.bond_types) == 2
assert len(my_ommp.angle_types) == 2
assert len(my_ommp.dihedral_types) == 1
assert len(my_ommp.nonbond_types) == 2
def test_parsing(self, geometric_ethane_system_topology):
nb_force = openmm.CustomNonbondedForce('epsilon1*epsilon2*(sigr6^2-sigr6); sigr6=sigr2*sigr2*sigr2; '
'sigr2=(sigc/r)^2; sigc=sigma1*sigma2')
nb_force.addPerParticleParameter('epsilon')
nb_force.addPerParticleParameter('sigma')
nb_force.addParticle((1*unit.kilojoule_per_mole, 2*unit.nanometer))
my_ommp = Ommperator(geometric_ethane_system_topology[0],
geometric_ethane_system_topology[1])
my_nb_ommp = CustomNonbondedForceOmmperator(my_ommp, nb_force, 0)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.energy_function == nb_force.getEnergyFunction()
assert my_nb_ommp.parameter_index['epsilon'] == 0
assert my_nb_ommp.parameter_index['sigma'] == 1
def test_parsing(self, ethane_system_topology):
harmonic_Angle = openmm.HarmonicAngleForce()
harmonic_Angle.addAngle(0, 1, 2, 10, 20)
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_Angle_ommp = HarmonicAngleForceOmmperator(my_ommp, harmonic_Angle,
0)
assert my_Angle_ommp.particle1 == harmonic_Angle.getAngleParameters(
0)[0]
assert my_Angle_ommp.particle2 == harmonic_Angle.getAngleParameters(
0)[1]
assert my_Angle_ommp.particle3 == harmonic_Angle.getAngleParameters(
0)[2]
assert my_Angle_ommp.angle == harmonic_Angle.getAngleParameters(0)[3]
assert my_Angle_ommp.k == harmonic_Angle.getAngleParameters(0)[4]
def test_modify_omm(self, geometric_ethane_system_topology):
nb_force = openmm.CustomNonbondedForce('epsilon1*epsilon2*(sigr6^2-sigr6); sigr6=sigr2*sigr2*sigr2; '
'sigr2=(sigc/r)^2; sigc=sigma1*sigma2')
nb_force.addPerParticleParameter('epsilon')
nb_force.addPerParticleParameter('sigma')
nb_force.addParticle((1*unit.kilojoule_per_mole, 2*unit.nanometer))
nb_force.setParticleParameters(0, (10*unit.kilojoule_per_mole,
20*unit.nanometer))
my_ommp = Ommperator(geometric_ethane_system_topology[0],
geometric_ethane_system_topology[1])
my_nb_ommp = CustomNonbondedForceOmmperator(my_ommp, nb_force, 0)
assert my_nb_ommp.parameters == nb_force.getParticleParameters(0)
assert my_nb_ommp.parameters[0] == 10
assert my_nb_ommp.parameters[1] == 20
def test_parsing(self, ethane_system_topology):
rb_torsion = openmm.RBTorsionForce()
rb_torsion.addTorsion(0, 1, 2, 3, 10, 20, 30, 40, 50, 60)
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_dih_ommp = RBTorsionForceOmmperator(my_ommp, rb_torsion, 0)
assert my_dih_ommp.particle1 == rb_torsion.getTorsionParameters(0)[0]
assert my_dih_ommp.particle2 == rb_torsion.getTorsionParameters(0)[1]
assert my_dih_ommp.particle3 == rb_torsion.getTorsionParameters(0)[2]
assert my_dih_ommp.particle4 == rb_torsion.getTorsionParameters(0)[3]
assert my_dih_ommp.c0 == rb_torsion.getTorsionParameters(0)[4]
assert my_dih_ommp.c1 == rb_torsion.getTorsionParameters(0)[5]
assert my_dih_ommp.c2 == rb_torsion.getTorsionParameters(0)[6]
assert my_dih_ommp.c3 == rb_torsion.getTorsionParameters(0)[7]
assert my_dih_ommp.c4 == rb_torsion.getTorsionParameters(0)[8]
assert my_dih_ommp.c5 == rb_torsion.getTorsionParameters(0)[9]
def test_setting(self, ethane_system_topology):
harmonic_Angle = openmm.HarmonicAngleForce()
harmonic_Angle.addAngle(0, 1, 2, 10, 20)
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_Angle_ommp = HarmonicAngleForceOmmperator(my_ommp, harmonic_Angle,
0)
my_Angle_ommp.particle1 = 5
my_Angle_ommp.particle2 = 6
my_Angle_ommp.particle3 = 7
my_Angle_ommp.angle = 100
my_Angle_ommp.length = 200
assert my_Angle_ommp.particle1 == harmonic_Angle.getAngleParameters(
0)[0]
assert my_Angle_ommp.particle1 == 5
assert my_Angle_ommp.particle2 == harmonic_Angle.getAngleParameters(
0)[1]
assert my_Angle_ommp.particle2 == 6
assert my_Angle_ommp.particle3 == harmonic_Angle.getAngleParameters(
0)[2]
assert my_Angle_ommp.particle3 == 7
assert my_Angle_ommp.angle == harmonic_Angle.getAngleParameters(0)[3]
assert my_Angle_ommp.k == harmonic_Angle.getAngleParameters(0)[4]
my_Angle_ommp.set_params(p1=100, p2=200, p3=800, k=300, angle=400)
assert my_Angle_ommp.particle1 == harmonic_Angle.getAngleParameters(
0)[0]
assert my_Angle_ommp.particle1 == 100
assert my_Angle_ommp.particle2 == harmonic_Angle.getAngleParameters(
0)[1]
assert my_Angle_ommp.particle2 == 200
assert my_Angle_ommp.particle3 == harmonic_Angle.getAngleParameters(
0)[2]
assert my_Angle_ommp.particle3 == 800
assert my_Angle_ommp.angle == harmonic_Angle.getAngleParameters(0)[3]
assert my_Angle_ommp.k == harmonic_Angle.getAngleParameters(0)[4]
def test_setting(self, ethane_system_topology):
custom_bond = openmm.CustomBondForce('a+b*r')
custom_bond.addPerBondParameter('a')
custom_bond.addPerBondParameter('b')
custom_bond.addBond(0, 1, (10, 20))
my_ommp = Ommperator(ethane_system_topology[0], ethane_system_topology[1])
my_bond_ommp = CustomBondForceOmmperator(my_ommp, custom_bond, 0)
my_bond_ommp.particle1 = 2
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 1
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
my_bond_ommp.particle2 = 3
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
my_bond_ommp.set_params(100, -1)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
assert my_bond_ommp.parameters[0] == 100
assert my_bond_ommp.parameters[1] == 20
my_bond_ommp.set_params(-1, 200)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
assert my_bond_ommp.parameters[0] == 100
assert my_bond_ommp.parameters[1] == 200
my_bond_ommp.set_params(1000, 2000)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
assert my_bond_ommp.parameters[0] == 1000
assert my_bond_ommp.parameters[1] == 2000
my_bond_ommp.set_params(a=10)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
assert my_bond_ommp.parameters[0] == 10
assert my_bond_ommp.parameters[1] == 2000
my_bond_ommp.set_params(b=20)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
assert my_bond_ommp.parameters[0] == 10
assert my_bond_ommp.parameters[1] == 20
my_bond_ommp.set_params(a=100, b=200)
assert my_bond_ommp.particle1 == custom_bond.getBondParameters(0)[0]
assert my_bond_ommp.particle1 == 2
assert my_bond_ommp.particle2 == custom_bond.getBondParameters(0)[1]
assert my_bond_ommp.particle2 == 3
assert my_bond_ommp.parameters == custom_bond.getBondParameters(0)[2]
assert my_bond_ommp.parameters[0] == 100
assert my_bond_ommp.parameters[1] == 200
with pytest.raises(ValueError):
my_bond_ommp.set_params(100, 200, a=100, b=200)
def test_update_kwarg(self, ethane_system_topology):
my_ommp = Ommperator(ethane_system_topology[0],
ethane_system_topology[1])
my_ommp.nonbond_types['opls_135'].update(sigma=5 * unit.nanometer)
for nonbond in my_ommp.nonbond_types['opls_135']:
assert nonbond.sigma == 5 * unit.nanometer
