def test_two_particle_vsite(self):
""" Tests assignment of 2-particle virtual site """
struct = pmd.Structure()
struct.add_atom(pmd.Atom(name='C', atomic_number=6), 'RES', 1)
struct.add_atom(pmd.Atom(name='C', atomic_number=6), 'RES', 1)
struct.add_atom(pmd.ExtraPoint(name='EP', atomic_number=0), 'RES', 1)
struct.bond_types.append(pmd.BondType(10, 1.0))
struct.bond_types.append(pmd.BondType(10, 0.5))
struct.bond_types.claim()
struct.bonds.append(pmd.Bond(struct[0], struct[1],
type=struct.bond_types[0])
)
struct.bonds.append(pmd.Bond(struct[1], struct[2],
type=struct.bond_types[1])
)
# This should be a two-particle virtual site
struct.coordinates = [[0, 0, 0], [0, 0, 1], [0, 0, 1.5]]
system = mm.System()
system.addParticle(struct[0].mass)
system.addParticle(struct[1].mass)
system.addParticle(struct[2].mass)
struct.omm_set_virtual_sites(system)
# Make sure the third atom is a virtual site
self.assertTrue(system.isVirtualSite(2))
self.assertIsInstance(system.getVirtualSite(2), mm.TwoParticleAverageSite)
def createStructureFromResidue(residue):
# Create ParmEd structure for residue.
structure = parmed.Structure()
for a in residue.atoms():
if a.element is None:
atom = parmed.ExtraPoint(name=a.name)
else:
atom = parmed.Atom(atomic_number=a.element.atomic_number, name=a.name, mass=a.element.mass)
structure.add_atom(atom, residue.name, residue.index, 'A')
atommap[a] = atom
for a1, a2 in topology.bonds():
structure.bonds.append(Bond(atommap[a1], atommap[a2]))
return structure
