Merge pull request #954 from ReactionMechanismGenerator/Thermo_Test_AMP

Add Unit Tests to rmgpy/data/thermo.py

Author: KEHANG

rmgpy/data/thermoTest.py

@@ -69,6 +69,40 @@ def setUp(self):
             ['C1C=CC=C1',       2,    32.5, 65.5, 18.16, 24.71, 30.25, 34.7, 41.25, 45.83, 52.61],
         ]
 
+    def testPickle(self):
+        """
+        Test that a ThermoDatabase object can be successfully pickled and
+        unpickled with no loss of information.
+        """
+        import cPickle
+        thermodb0 = cPickle.loads(cPickle.dumps(self.database))
+        
+        self.assertEqual(thermodb0.libraryOrder, self.database.libraryOrder)
+        self.assertEqual(sorted(thermodb0.depository.keys()), \
+                        sorted(self.database.depository.keys()))
+
+        self.assertEqual(sorted(thermodb0.libraries.keys()), \
+                        sorted(self.database.libraries.keys()))
+        self.assertEqual(sorted(thermodb0.groups.keys()), \
+                        sorted(self.database.groups.keys()))
+
+        for key, depository0 in thermodb0.depository.iteritems():
+            depository = self.database.depository[key]
+            self.assertTrue(type(depository0), type(depository))
+            self.assertEqual(sorted(depository0.entries.keys()), sorted(depository.entries.keys()))
+
+        for key, library0 in thermodb0.libraries.iteritems():
+            library = self.database.libraries[key]
+            self.assertTrue(type(library0), type(library))
+            self.assertEqual(sorted(library0.entries.keys()), sorted(library.entries.keys()))
+
+        for key, group0 in thermodb0.groups.iteritems():
+            group = self.database.groups[key]
+            self.assertTrue(type(group0), type(group))
+            self.assertEqual(sorted(group0.entries.keys()), sorted(group.entries.keys()))
+
+
+
     @work_in_progress
     def testNewThermoGeneration(self):
         """
@@ -108,7 +142,6 @@ def testSymmetryContributionRadicals(self):
         thermoData_ga = self.database.getThermoDataFromGroups(spc)
 
         self.assertAlmostEqual(thermoData_lib.getEntropy(298.), thermoData_ga.getEntropy(298.), 0)
-
 
     @work_in_progress
     def testSymmetryNumberGeneration(self):
@@ -613,6 +646,22 @@ def testConvertRingToSubMolecule(self):
         self.assertEqual(len(bonds2), 11)
         self.assertEqual(len(bonds3), 15)
 
+    def testGetCopyForOneRing(self):
+        """
+        This method tests the getCopyForOneRing method, which returns
+        an atom object list that contains deep copies of the atoms
+        """
+
+        testAtomList=Molecule(SMILES='C1CCCCC1').atoms
+        copiedAtomList=getCopyForOneRing(testAtomList)
+
+        testMolecule=Molecule(atoms=testAtomList)
+        copiedMolecule=Molecule(atoms=copiedAtomList)
+
+        self.assertTrue(testAtomList!=copiedAtomList)
+        self.assertTrue(len(testAtomList)==len(copiedAtomList))
+        self.assertTrue(testMolecule.is_equal(copiedMolecule))
+
     def testToFailCombineTwoRingsIntoSubMolecule(self):
         """
         Test that if two non-overlapped rings lead to AssertionError
@@ -833,6 +882,17 @@ def testBicyclicDecompositionForPolyringUsingAlkaneTricyclic(self):
         expectedAromaticBondNumInBicyclics = [0, 0, 0]
         self.assertEqual(aromaticBondNumInBicyclics, expectedAromaticBondNumInBicyclics)
 
+    def testCombineCycles(self):
+        """
+        This method tests the combineCycles method, which simply joins two lists
+        together without duplication.
+        """
+        mainCycle=Molecule(SMILES='C1CCC2CCCCC2C1').atoms
+        testCycle1=mainCycle[0:8]
+        testCycle2=mainCycle[6:]
+        joinedCycle=combineCycles(testCycle1,testCycle2)
+        self.assertTrue(sorted(mainCycle)==sorted(joinedCycle))
+
 
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