def test_detect_bonds_cyclopropene_exceptions():
system = get_system_cyclopropene()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between all hydrogen and carbon atoms (unrealistic but useful for testing)
system.detect_bonds({(1,6): 8.0*angstrom})
assert system.nbond == 3+4*3
def test_detect_bonds_cyclopropene_exceptions():
system = get_system_cyclopropene()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between all hydrogen and carbon atoms (unrealistic but useful for testing)
system.detect_bonds({(1, 6): 8.0 * angstrom})
assert system.nbond == 3 + 4 * 3
def test_iter_matches_cyclopropene_cyclopropene():
system = get_system_cyclopropene()
result = sorted(system.iter_matches(system))
assert result == [
(0, 1, 2, 3, 4, 5, 6),
(0, 1, 2, 4, 3, 5, 6),
(0, 2, 1, 3, 4, 6, 5),
(0, 2, 1, 4, 3, 6, 5),
]
def test_iter_matches_cyclopropene_cyclopropene():
system = get_system_cyclopropene()
result = sorted(system.iter_matches(system))
assert result == [
(0, 1, 2, 3, 4, 5, 6),
(0, 1, 2, 4, 3, 5, 6),
(0, 2, 1, 3, 4, 6, 5),
(0, 2, 1, 4, 3, 6, 5),
]
def test_iter_matches_cyclopropene_ch():
system0 = get_system_cyclopropene()
system1 = system0.subsystem([0, 4])
result = sorted(system0.iter_matches(system1))
assert result == [(0, 3), (0, 4), (1, 5), (2, 6)]
def test_iter_bonds_empty():
system = get_system_cyclopropene()
system.bonds = None
assert len(list(system.iter_bonds())) == 0
assert len(list(system.iter_angles())) == 0
assert len(list(system.iter_dihedrals())) == 0
def test_iter_bonds_empty():
system = get_system_cyclopropene()
system.bonds = None
assert len(list(system.iter_bonds())) == 0
assert len(list(system.iter_angles())) == 0
assert len(list(system.iter_dihedrals())) == 0
def test_iter_matches_cyclopropene_ch():
system0 = get_system_cyclopropene()
system1 = system0.subsystem([0, 4])
result = sorted(system0.iter_matches(system1))
assert result == [(0, 3), (0, 4), (1, 5), (2, 6)]