def test_position_units(self, typed_ar_system):
typed_ar_system.box = Box(lengths=[1,1,1])
n_topology_sites = len(typed_ar_system.sites)
omm_top = to_openmm(typed_ar_system, openmm_object='modeller')
assert isinstance(omm_top.positions.unit, type(simtk_unit.nanometer))
def test_n_atoms(self, topology_site):
top = topology_site(sites=10)
n_topology_sites = len(top.sites)
modeller = to_openmm(top, openmm_object='modeller')
n_modeller_atoms = len([i for i in modeller.topology.atoms()])
assert n_topology_sites == n_modeller_atoms
def test_box_dims(self, typed_ar_system):
n_topology_sites = len(typed_ar_system.sites)
omm_top = to_openmm(typed_ar_system)
topology_lengths = typed_ar_system.box.lengths
omm_lengths = omm_top.getUnitCellDimensions()
assert_allclose_units(topology_lengths.value, omm_lengths._value, rtol=1e-5, atol=1e-8)
def test_box_dims(self, topology_site):
top = topology_site(sites=10)
n_topology_sites = len(top.sites)
omm_top = to_openmm(top)
topology_lengths = top.box.lengths
omm_lengths = omm_top.getUnitCellDimensions()
assert np.allclose(topology_lengths.value, omm_lengths._value)
def test_particle_positions(self, typed_ar_system):
typed_ar_system.sites[0].position = (1, 1, 1) * u.nanometer
omm_top = to_openmm(typed_ar_system, openmm_object="modeller")
assert_allclose_units(
omm_top.positions._value,
typed_ar_system.positions.value,
rtol=1e-5,
atol=1e-8,
)
def test_n_atoms(self, typed_ar_system):
n_topology_sites = len(typed_ar_system.sites)
modeller = to_openmm(typed_ar_system, openmm_object='modeller')
n_modeller_atoms = len([i for i in modeller.topology.atoms()])
assert n_topology_sites == n_modeller_atoms
def test_openmm_topology(self, typed_ar_system):
to_openmm(typed_ar_system, openmm_object='topology')
def test_openmm_modeller(self, typed_ar_system):
to_openmm(typed_ar_system, openmm_object='modeller')
def test_particle_positions(self, typed_ar_system):
typed_ar_system.sites[0].position = (1,1,1) * u.nanometer
omm_top = to_openmm(typed_ar_system, openmm_object='modeller')
assert np.allclose(omm_top.positions._value,
typed_ar_system.positions.value)
def test_particle_positions(self, topology_site):
top = topology_site()
top.sites[0].position = (1, 1, 1) * u.nanometer
omm_top = to_openmm(top, openmm_object='modeller')
assert np.allclose(omm_top.positions._value, top.positions.value)
def test_openmm_topology(self, topology_site):
to_openmm(topology_site(), openmm_object='topology')
def test_openmm_modeller(self, topology_site):
to_openmm(topology_site(), openmm_object='modeller')