def test_get_virtual_site(self):
"""Test Topology.virtual_site function (get virtual site from index)"""
topology = Topology()
topology.add_molecule(self.ethane_from_smiles_w_vsites)
assert topology.n_topology_virtual_sites == 2
topology.add_molecule(self.propane_from_smiles_w_vsites)
assert topology.n_topology_virtual_sites == 4
with self.assertRaises(Exception) as context:
topology_vsite = topology.virtual_site(-1)
with self.assertRaises(Exception) as context:
topology_vsite = topology.virtual_site(4)
topology_vsite1 = topology.virtual_site(0)
topology_vsite2 = topology.virtual_site(1)
topology_vsite3 = topology.virtual_site(2)
topology_vsite4 = topology.virtual_site(3)
assert topology_vsite1.type == "BondChargeVirtualSite"
assert topology_vsite2.type == "MonovalentLonePairVirtualSite"
assert topology_vsite3.type == "MonovalentLonePairVirtualSite"
assert topology_vsite4.type == "BondChargeVirtualSite"
n_equal_atoms = 0
for topology_atom in topology.topology_atoms:
for vsite in topology.topology_virtual_sites:
for vsite_atom in vsite.atoms:
if topology_atom == vsite_atom:
n_equal_atoms += 1
# There are four virtual sites -- Two BondCharges with 2 atoms, and two MonovalentLonePairs with 3 atoms
assert n_equal_atoms == 10
def test_topology_virtual_site_particle_start_index(self):
topology = Topology()
topology.add_molecule(self.propane_from_smiles_w_vsites)
assert topology.virtual_site(
0).topology_virtual_particle_start_index == 11
assert topology.virtual_site(
1).topology_virtual_particle_start_index == 13
def test_topology_virtual_site_n_particles(self):
"""
Test if the virtual sites report the correct number of particles
"""
topology = Topology()
topology.add_molecule(self.propane_from_smiles_w_vsites)
assert topology.virtual_site(0).n_particles == 2
assert topology.virtual_site(1).n_particles == 1
topology = Topology()
topology.add_molecule(self.tip5_water)
assert topology.virtual_site(0).n_particles == 2