def test_square_with_bridge(self):
mytop = Topology()
s1 = Atom(name="1")
s2 = Atom(name="2")
s3 = Atom(name="3")
s4 = Atom(name="4")
c12 = Bond(connection_members=[s1, s2])
c23 = Bond(connection_members=[s2, s3])
c34 = Bond(connection_members=[s3, s4])
c41 = Bond(connection_members=[s4, s1])
c24 = Bond(connection_members=[s2, s4])
mytop.add_site(s1, update_types=False)
mytop.add_site(s2, update_types=False)
mytop.add_site(s3, update_types=False)
mytop.add_site(s4, update_types=False)
mytop.add_connection(c12, update_types=False)
mytop.add_connection(c23, update_types=False)
mytop.add_connection(c34, update_types=False)
mytop.add_connection(c41, update_types=False)
mytop.add_connection(c24, update_types=False)
assert mytop.n_bonds == 5
assert mytop.n_angles == 0
assert mytop.n_dihedrals == 0
assert mytop.n_impropers == 0
mytop.identify_connections()
assert mytop.n_bonds == 5
assert mytop.n_angles == 8
assert mytop.n_dihedrals == 6
assert mytop.n_impropers == 2
def test_square(self):
mytop = Topology()
s1 = Atom(name="1")
s2 = Atom(name="2")
s3 = Atom(name="3")
s4 = Atom(name="4")
c12 = Bond(connection_members=[s1, s2])
c23 = Bond(connection_members=[s2, s3])
c34 = Bond(connection_members=[s3, s4])
c41 = Bond(connection_members=[s4, s1])
for site in [s1, s2, s3, s4]:
mytop.add_site(site, update_types=False)
for conn in [c12, c23, c34, c41]:
mytop.add_connection(conn, update_types=False)
assert mytop.n_bonds == 4
assert mytop.n_angles == 0
assert mytop.n_dihedrals == 0
assert mytop.n_impropers == 0
mytop.identify_connections()
assert mytop.n_bonds == 4
assert mytop.n_angles == 4
assert mytop.n_dihedrals == 4
assert mytop.n_impropers == 0
