def test_set_lowest_energy_conformer():
from autode.mol_graphs import make_graph
hb = Atom('H', z=0.7)
hydrogen = Species(name='H2', atoms=[h1, hb], charge=0, mult=1)
make_graph(hydrogen)
hydrogen_wo_e = Species(name='H2', atoms=[h1, hb], charge=0, mult=1)
hydrogen_with_e = Species(name='H2', atoms=[h1, hb], charge=0, mult=1)
hydrogen_with_e.energy = -1
hydrogen.conformers = [hydrogen_wo_e, hydrogen_with_e]
hydrogen._set_lowest_energy_conformer()
# Conformers without energy should be skipped
assert hydrogen.energy == -1
# Conformers with a different molecular graph should be skipped
h_atom = Species(name='H', atoms=[Atom('H')], charge=0, mult=1)
h_atom.energy = -2
hydrogen.conformers = [hydrogen_with_e, h_atom]
assert hydrogen.energy == -1
def test_species_isomorphism():
h2.graph = None
h2_copy = Species(name='H2', atoms=[h_a, h_b], charge=0, mult=1)
h2_copy.graph = None
with pytest.raises(NoMolecularGraph):
assert mol_graphs.species_are_isomorphic(h2, h2_copy)
# With molecular graphs the species should be isomorphic
mol_graphs.make_graph(h2)
mol_graphs.make_graph(h2_copy)
assert mol_graphs.species_are_isomorphic(h2, h2_copy)
# Shift one of the atoms far away and remake the graph
h2_copy.atoms[1].translate(vec=np.array([10, 0, 0]))
mol_graphs.make_graph(h2_copy)
assert mol_graphs.species_are_isomorphic(h2, h2_copy) is False
# Generating a pair of conformers that are isomporhpic should return that
# the species are again isomorphic
h2.conformers = [
Conformer(name='h2_conf', atoms=[h_a, h_b], charge=0, mult=1)
]
h2_copy.conformers = [
Conformer(name='h2_conf', atoms=[h_a, h_b], charge=0, mult=1)
]
assert mol_graphs.species_are_isomorphic(h2, h2_copy)