def correctDegeneracyOfReverseReactions(reactionList, reactants):
"""
This method corrects the degeneracy of reactions found when the backwards
template is used. Given the following parameters:
reactionList - list of reactions with their degeneracies already counted
reactants - list/tuple of species used in the generateReactions method
This method modifies reactionList in place and returns nothing
This does not adjust for identical reactants, you need to use `reduceSameReactantDegeneracy`
to adjust for that.
"""
from rmgpy.reaction import _isomorphicSpeciesList
from rmgpy.reaction import ReactionError
for rxn in reactionList:
if _isomorphicSpeciesList(rxn.reactants, reactants):
# was forward reaction so ignore
continue
elif _isomorphicSpeciesList(rxn.products, reactants):
# was reverse reaction so should find degeneracy
family = getDB('kinetics').families[rxn.family]
if not family.ownReverse:
rxn.degeneracy = family.calculateDegeneracy(
rxn, ignoreSameReactants=True)
else:
# wrong reaction was sent here
raise ReactionError(
'Reaction in reactionList did not match reactants. Reaction: {}, Reactants: {}'
.format(rxn, reactants))
def test_degeneracy_same_reactant_different_resonance_structure(self):
"""Test if degeneracy is correct when reacting different resonance structures."""
from rmgpy.reaction import _isomorphicSpeciesList
spc = Species().fromSMILES('CC=C[CH2]')
# reactSpecies will label reactants and generate resonance structures
reactions = reactSpecies((spc, spc))
# these products are only possible if the reacting structures are CC=C[CH2] and C[CH2]C=C
products = [
Species().fromSMILES('CC=CC'),
Species().fromSMILES('C=CC=C')
]
# search for the desired products
desired_rxn = None
for rxn in reactions:
if rxn.family == 'Disproportionation' and _isomorphicSpeciesList(
rxn.products, products):
if desired_rxn is None:
desired_rxn = rxn
else:
self.fail(
'Found two reactions which should be isomorphic.')
self.assertEqual(desired_rxn.degeneracy, 3)
self.assertEqual(set(desired_rxn.template),
{'C_rad/H2/Cd', 'Cmethyl_Csrad/H/Cd'})