Update unit tests.

rmgpy/rmg/modelTest.py

@@ -396,7 +396,7 @@ def testInflate(self):
         """
         spcA = Species().fromSMILES('[OH]')
         spcs = [Species().fromSMILES('CC'), Species().fromSMILES('[CH3]')]
-        spcTuples = [(spcA, spc) for spc in spcs]
+        spcTuples = [((spcA, spc), 'H_Abstraction') for spc in spcs]
 
         rxns = list(react(*spcTuples))
 

rmgpy/rmg/reactTest.py

@@ -38,7 +38,7 @@
 from rmgpy.species import Species
 
 from rmgpy.rmg.main import RMG
-from rmgpy.rmg.react import react, react_all, deflate, deflateReaction
+from rmgpy.rmg.react import react, react_all
 
 ###################################################
 
@@ -85,68 +85,6 @@ def testReactMultiproc(self):
         self.assertIsNotNone(reactionList)
         self.assertTrue(all([isinstance(rxn, TemplateReaction) for rxn in reactionList]))
 
-    def testDeflate(self):
-        """
-        Test that reaction deflate function works.
-        """
-        molA = Species().fromSMILES('[OH]')
-        molB = Species().fromSMILES('CC')
-        molC = Species().fromSMILES('[CH3]')
-
-        reactants = [molA, molB]
-
-        # both reactants were already part of the core:
-        reactantIndices = [1, 2]
-
-        rxn = Reaction(reactants=[molA, molB], products=[molC],
-        pairs=[(molA, molC), (molB, molC)])
-
-        deflate([rxn], reactants, reactantIndices)
-
-        for spc, t in zip(rxn.reactants, [int, int]):
-            self.assertTrue(isinstance(spc, t))
-        self.assertEquals(rxn.reactants, reactantIndices)
-        for spc in rxn.products:
-            self.assertTrue(isinstance(spc, Species))
-
-        # one of the reactants was not yet part of the core:
-        reactantIndices = [-1, 2]
-
-        rxn = Reaction(reactants=[molA, molB], products=[molC],
-                pairs=[(molA, molC), (molB, molC)])
-
-        deflate([rxn], reactants, reactantIndices)
-
-        for spc, t in zip(rxn.reactants, [Species, int]):
-            self.assertTrue(isinstance(spc, t))
-        for spc in rxn.products:
-            self.assertTrue(isinstance(spc, Species))
-
-    def testReactStoreIndices(self):
-        """
-        Test that reaction generation keeps track of the original species indices.
-        """
-
-        indices = {'[OH]':1, 'CC':2, '[CH3]':3}
-
-        # make it bidirectional so that we can look-up indices as well:
-        revd=dict([reversed(i) for i in indices.items()])
-        indices.update(revd)
-
-        spcA = Species(index=indices['[OH]']).fromSMILES('[OH]')
-        spcs = [Species(index=indices['CC']).fromSMILES('CC'),
-                Species(index=indices['[CH3]']).fromSMILES('[CH3]')]
-
-        spcTuples = [(spcA, spc) for spc in spcs]
-
-        reactionList = list(react(*spcTuples))
-        self.assertIsNotNone(reactionList)
-        self.assertEquals(len(reactionList), 3)
-        for rxn in reactionList:
-            for i, reactant in enumerate(rxn.reactants):
-                rxn.reactants[i] = Molecule().fromSMILES(indices[reactant])
-            self.assertTrue(rxn.isBalanced())
-
     def testReactAll(self):
         """
         Test that the reactAll function works.
@@ -166,44 +104,6 @@ def testReactAll(self):
         self.assertIsNotNone(rxns)
         self.assertTrue(all([isinstance(rxn, TemplateReaction) for rxn in rxns]))
 
-    def testDeflateReaction(self):
-        """
-        Test if the deflateReaction function works.
-        """
-
-        molA = Species().fromSMILES('[OH]')
-        molB = Species().fromSMILES('CC')
-        molC = Species().fromSMILES('[CH3]')
-
-        # both reactants were already part of the core:
-        reactantIndices = [1, 2]
-        molDict = {molA.molecule[0]: 1, molB.molecule[0]: 2}
-
-        rxn = Reaction(reactants=[molA, molB], products=[molC],
-        pairs=[(molA, molC), (molB, molC)])
-
-        deflateReaction(rxn, molDict)
-
-        for spc, t in zip(rxn.reactants, [int, int]):
-            self.assertTrue(isinstance(spc, t))
-        self.assertEquals(rxn.reactants, reactantIndices)
-        for spc in rxn.products:
-            self.assertTrue(isinstance(spc, Species))
-
-        # one of the reactants was not yet part of the core:
-        reactantIndices = [-1, 2]
-        molDict = {molA.molecule[0]: molA, molB.molecule[0]: 2}
-
-        rxn = Reaction(reactants=[molA, molB], products=[molC],
-                pairs=[(molA, molC), (molB, molC)])
-
-        deflateReaction(rxn, molDict)
-
-        for spc, t in zip(rxn.reactants, [Species, int]):
-            self.assertTrue(isinstance(spc, t), 'Species {} is not of type {}'.format(spc,t))
-        for spc in rxn.products:
-            self.assertTrue(isinstance(spc, Species))
-
     def tearDown(self):
         """
         Reset the loaded database