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())