def testIntraHmigration(self):
"""An intra-H migration reaction"""
self.loadDatabase(only_families=['intra_H_migration'])
structure1 = Structure()
structure1.fromSMILES("[CH](CCCc1ccccc1)CCCCCC")
species1 = makeNewSpecies(structure1)
structure2 = Structure()
structure2.fromSMILES("C(CCCC[CH]c1ccccc1)CCCC")
species2 = makeNewSpecies(structure2)
# wipe the reaction list
reaction.reactionList=[]
rxns = reaction.kineticsDatabase.getReactions([species1])
#for rxn in rxns:
# print 'Reaction family:',rxn.family
# print 'Reaction:',rxn
# print 'Kinetics:',rxn.kinetics
# print 'bestKinetics:',rxn.bestKinetics
# print
all_products = []
for rxn in rxns:
self.assertEqual(rxn.family.label,'Intra H migration',"Was trying to test 'Intra H migration' but made a reaction from family %s"%rxn.family)
self.assertEqual(len(rxn.reactants),1,"Reaction %s wasn't unimolecular"%rxn)
all_products.extend(rxn.products)
self.assertTrue(species2 in all_products, "None of the reactions made %s"%(species2))
def testEthaneExtrusionFromEther(self):
"""A reaction that was giving trouble in a diesel simulation"""
self.loadDatabase(only_families=['1,3_Insertion_ROR'])
structure1 = Structure()
structure1.fromSMILES("c1c([CH]C(C=CCCCCCC)OOCc2c3ccccc3ccc2)cccc1")
species1 = makeNewSpecies(structure1)
structure2 = Structure()
structure2.fromSMILES("c1ccc(c2ccccc12)COO")
species2 = makeNewSpecies(structure2)
structure3 = Structure()
structure3.fromSMILES("c1cc(C=C[C]=CCCCCCC)ccc1")
species3 = makeNewSpecies(structure3)
# wipe the reaction list
reaction.reactionList=[]
#print "FORWARD"
rxns = reaction.kineticsDatabase.getReactions([species2,species3])
#for rxn in rxns:
# print 'Reaction family:',rxn.family
# print 'Reaction:',rxn
# print 'Kinetics:',rxn.kinetics
# print 'bestKinetics:',rxn.bestKinetics
# print
self.assertEqual(len(rxns),18, "Was expecting to make 18 reactions for %s + %s"%(species2,species3))
# wipe the reaction list
reaction.reactionList=[]
#print "REVERSE"
rxns = reaction.kineticsDatabase.getReactions([species1])
#for rxn in rxns:
# print 'Reaction family:',rxn.family
# print 'Reaction:',rxn
# print 'Kinetics:',rxn.kinetics
# print 'bestKinetics:',rxn.bestKinetics
# print
self.assertEqual(len(rxns),1, "Was expecting to make 1 reaction for %s"%(species1))
rxn = rxns[0]
self.assertEqual(len(rxn.reactants),2,"Reaction wasn't bimolecular")
self.assertTrue(species2 in rxn.reactants, "Didn't make %s"%species2)
self.assertTrue(species3 in rxn.reactants, "Didn't make %s"%species3)
