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)
def test_species_conformers_isomorphic():
h2_a = Molecule(name='H2', atoms=[Atom('H'), Atom('H', x=0.7)])
h2_b = Molecule(name='H2', atoms=[Atom('H'), Atom('H', x=1.5)])
assert not mol_graphs.species_are_isomorphic(h2_a, h2_b)
# Should raise an exception for two non-isomorphic graphs
with pytest.raises(NoMapping):
mol_graphs.get_mapping(h2_a.graph, h2_b.graph)
h2_a.conformers = None
h2_b.conformers = [
Conformer(name='H2', atoms=[Atom('H'), Atom('H', x=0.7)])
]
assert mol_graphs.species_are_isomorphic(h2_a, h2_b)
def f_b_isomorphic_to_r_p(forwards, backwards, reactant, product):
"""Is the forward/backward displacement to reactants/products?"""
if any(mol.atoms is None for mol in (forwards, backwards)):
logger.warning(
'Atoms not set in the output. Cannot calculate isomorphisms')
return False
if species_are_isomorphic(backwards, reactant) and species_are_isomorphic(
forwards, product):
logger.info(
'Forwards displacement lead to products and backwards reactants')
return True
if species_are_isomorphic(forwards, reactant) and species_are_isomorphic(
backwards, product):
logger.info(
'Backwards displacement lead to products and forwards to reactants'
)
return True
return False
def find_tss(reaction):
"""Find all the possible the transition states of a reaction
Arguments:
reaction (list(autode.reaction.Reaction)): Reaction
Returns:
list: list of transition state objects
"""
logger.info('Finding possible transition states')
reactant, product = reaction.reactant, reaction.product
if species_are_isomorphic(reactant, product):
logger.error('Reactant and product complexes are isomorphic. Cannot'
' find a TS')
return None
bond_rearrs = get_bond_rearrangs(reactant, product, name=str(reaction))
if bond_rearrs is None:
logger.error('Could not find a set of forming/breaking bonds')
return None
tss = []
for bond_rearrangement in bond_rearrs:
logger.info(f'Locating transition state using active bonds '
f'{bond_rearrangement.all}')
ts = get_ts(reaction, reactant, bond_rearrangement)
if ts is not None:
tss.append(ts)
if len(tss) == 0:
logger.error('Did not find any transition state(s)')
return None
logger.info(
f'Found *{len(tss)}* transition state(s) that lead to products')
return tss
