def test_classify():
# Can do this with integers are in classify there is no check on their
# contents, only their length
addition = classify([0, 0], [0])
assert addition.name == 'addition'
dissociation = classify([0], [0, 0])
assert dissociation.name == 'dissociation'
substitution = classify([0, 0], [0, 0])
assert substitution.name == 'substitution'
elimination = classify([0, 0], [0, 0, 0])
assert elimination.name == 'elimination'
rearrangement = classify([0], [0])
assert rearrangement.name == 'rearrangement'
# Needs to have at least some reactants and products
with pytest.raises(ReactionFormationFalied):
_ = classify([], [])
_ = classify([0], [])
_ = classify([], [0])
# 3 -> 3 reactions are not currently supported
with pytest.raises(NotImplementedError):
_ = classify([0, 1, 2], [3, 4, 5])
def __init__(self,
*args,
name='reaction',
solvent_name=None,
smiles=None,
temp=298.15):
"""
Reaction containing reactants and products. reaction.reactant is the
reactant complex which is the same as reacs[0] if there is only
reactant
Arguments:
args (autode.species.Molecule) or (str): Reactant and Product
objects or a SMILES string of the whole reaction
name (str):
solvent_name (str):
smiles (str):
temp (float): Temperature in Kelvin
"""
logger.info(f'Generating a Reaction object for {name}')
self.name = name
self.reacs = [mol for mol in args if isinstance(mol, Reactant)]
self.prods = [mol for mol in args if isinstance(mol, Product)]
# If there is only one string argument assume it's a SMILES
if len(args) == 1 and type(args[0]) is str:
smiles = args[0]
if smiles is not None:
self._init_from_smiles(smiles)
self.reactant, self.product = None, None
self.ts, self.tss = None, None
self.type = reaction_types.classify(self.reacs, self.prods)
self.solvent = get_solvent(solvent_name=solvent_name)
self.temp = float(temp)
self._check_solvent()
self._check_balance()
def test_classify():
# Can do this with integers are in classify there is no check on their
# contents, only their length
addition = classify([0, 0], [0])
assert addition.name == 'addition'
dissociation = classify([0], [0, 0])
assert dissociation.name == 'dissociation'
substitution = classify([0, 0], [0, 0])
assert substitution.name == 'substitution'
elimination = classify([0, 0], [0, 0, 0])
assert elimination.name == 'elimination'
rearrangement = classify([0], [0])
assert rearrangement.name == 'rearrangement'
with pytest.raises(ReactionFormationFalied):
classify([], [])