def test_topology_get_index(self):
top = Topology()
conn_members = [Site(), Site(), Site(), Site()]
for i in range(5):
top.add_site(Site())
top.add_connection(Bond(
connection_members=[conn_members[0], conn_members[1]]))
top.add_connection(Angle(
connection_members=[conn_members[0], conn_members[1], conn_members[2]]))
top.add_connection(Dihedral(
connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]]))
top.add_connection(Improper(
connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]]))
a_bond = Bond(connection_members=[conn_members[0], conn_members[1]])
an_angle = Angle(connection_members=[conn_members[0], conn_members[1], conn_members[2]])
a_site = Site()
a_dihedral = Dihedral(connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]])
an_improper = Improper(connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]])
top.add_site(a_site)
top.add_connection(a_bond)
top.add_connection(an_angle)
top.add_connection(a_dihedral)
top.add_connection(an_improper)
assert top.get_index(a_site) == 9
assert top.get_index(a_bond) == 5
assert top.get_index(an_angle) == 5
assert top.get_index(a_dihedral) == 5
assert top.get_index(an_improper) == 5
def test_topology_get_index(self):
top = Topology()
conn_members = [Atom() for _ in range(10)]
for atom in conn_members:
top.add_site(atom)
for i in range(5):
top.add_connection(
Bond(connection_members=[conn_members[i], conn_members[i +
1]]))
top.add_connection(
Angle(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2]
]))
top.add_connection(
Dihedral(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2],
conn_members[i + 3]
]))
top.add_connection(
Improper(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2],
conn_members[i + 3]
]))
a_atom = Atom()
a_bond = Bond(connection_members=[conn_members[6], conn_members[7]])
an_angle = Angle(connection_members=[
conn_members[6], conn_members[7], conn_members[8]
])
a_dihedral = Dihedral(connection_members=[
conn_members[6], conn_members[7], conn_members[8], conn_members[9]
])
an_improper = Improper(connection_members=[
conn_members[6], conn_members[7], conn_members[8], conn_members[9]
])
top.add_site(a_atom)
top.add_connection(a_bond)
top.add_connection(an_angle)
top.add_connection(a_dihedral)
top.add_connection(an_improper)
assert top.get_index(a_atom) == 10
assert top.get_index(a_bond) == 5
assert top.get_index(an_angle) == 5
assert top.get_index(a_dihedral) == 5
assert top.get_index(an_improper) == 5
def test_topology_get_index_non_existing_member(self):
top = Topology()
site = Site()
with pytest.raises(ValueError):
top.get_index(site)
def test_topology_get_index_wrong_member_type(self):
top = Topology()
with pytest.raises(TypeError):
top.get_index(object())
