import statements in unit tests outdated.

rmgpy/species.pxd

@@ -55,6 +55,7 @@ cdef class Species:
     cpdef bint isIsomorphic(self, other)
 
     cpdef fromAdjacencyList(self, adjlist)
+    cpdef fromSMILES(self, smiles)
 
     cpdef toAdjacencyList(self)
 

rmgpy/species.py

@@ -220,6 +220,17 @@ def fromAdjacencyList(self, adjlist):
             self.label = label.strip()
         # Return a reference to itself so we can use e.g. Species().fromAdjacencyList()
         return self
+
+    def fromSMILES(self, smiles):
+        """
+        Load the structure of a species as a :class:`Molecule` object from the
+        given SMILES string `smiles` and store it as the first entry of a 
+        list in the `molecule` attribute. Does not generate resonance isomers
+        of the loaded molecule.
+        """
+        self.molecule = [Molecule().fromSMILES(smiles)]
+        # Return a reference to itself so we can use e.g. Species().fromAdjacencyList()
+        return self
 
     def toAdjacencyList(self):
         """

unittest/atomtypeTest.py

@@ -9,6 +9,7 @@
 
 import rmgpy.atomtype
 from rmgpy.atomtype import AtomType, getAtomType
+from rmgpy.molecule import Molecule
 
 ################################################################################
 
@@ -55,7 +56,137 @@ def testPickle(self):
         self.assertEqual(len(self.atomType.decrementRadical), len(atomType.decrementRadical))
         for item1, item2 in zip(self.atomType.decrementRadical, atomType.decrementRadical):
             self.assertEqual(item1.label, item2.label)
-
+
+    def testOutput(self):
+        """
+        Test that we can reconstruct an AtomType object from its repr()
+        with no loss of information.
+        """
+        exec('atomType = rmgpy.atomtype.atomTypes[{0!r}]'.format(
+                                    self.atomType.__repr__().split('"')[1]))
+        return self.atomType.equivalent(atomType)
+
+    def testEquivalent(self):
+        """
+        Test the AtomType.equivalent() method.
+        """
+        return self.atomType.equivalent(rmgpy.atomtype.atomTypes['Cd'])
+
+    def testIsSpecficCaseOf(self):
+        """
+        Test the AtomType.isSpecificCaseOf() method.
+        """
+        return self.atomType.isSpecificCaseOf(rmgpy.atomtype.atomTypes['C'])
+
+    def testSetActions(self):
+        """
+        Test the AtomType.setActions() method.
+        """
+        other = rmgpy.atomtype.atomTypes['R']
+        other.setActions(self.atomType.incrementBond,
+                               self.atomType.decrementBond,
+                               self.atomType.formBond,
+                               self.atomType.breakBond,
+                               self.atomType.incrementRadical,
+                               self.atomType.decrementRadical)
+        self.assertEqual(self.atomType.incrementBond, other.incrementBond)
+        self.assertEqual(self.atomType.decrementBond, other.decrementBond)
+        self.assertEqual(self.atomType.formBond, other.formBond)
+        self.assertEqual(self.atomType.breakBond, other.breakBond)
+        self.assertEqual(self.atomType.incrementRadical, other.incrementRadical)
+        self.assertEqual(self.atomType.decrementRadical, other.decrementRadical)
+
+################################################################################
+
+class TestGetAtomType(unittest.TestCase):
+    """
+    Contains unit tests of the getAtomType() method.
+    """
+
+    def setUp(self):
+        """
+        A function run before each unit test in this class.
+        """
+        self.mol1 = Molecule().fromSMILES('COO=CC=C=CC#C')
+        self.mol2 = Molecule().fromSMILES('c1ccccc1')
+        self.mol3 = Molecule().fromSMILES('[H]')
+        self.mol4 = Molecule().fromSMILES(
+                                'O=[Si][Si][Si]=[Si]=[Si][Si]#[Si]SS=S')
+        self.mol5 = Molecule().fromSMILES('[N]')
+        self.mol6 = Molecule().fromSMILES('[Ar]')
+        self.mol7 = Molecule().fromSMILES('[He]')
+        self.mol8 = Molecule().fromSMILES('[Ne]')
+
+    def testCarbonTypes(self):
+        """
+        Test that getAtomType() returns appropriate carbon atom types.
+        """
+        self.assertEqual(getAtomType(self.mol1.atoms[0],
+            self.mol1.getBonds(self.mol1.atoms[0])).label, 'Cs')
+        self.assertEqual(getAtomType(self.mol1.atoms[4],
+            self.mol1.getBonds(self.mol1.atoms[4])).label, 'Cd')
+        self.assertEqual(getAtomType(self.mol1.atoms[5],
+            self.mol1.getBonds(self.mol1.atoms[5])).label, 'Cdd')
+        self.assertEqual(getAtomType(self.mol1.atoms[7],
+            self.mol1.getBonds(self.mol1.atoms[7])).label, 'Ct')
+        self.assertEqual(getAtomType(self.mol1.atoms[3],
+            self.mol1.getBonds(self.mol1.atoms[3])).label, 'CO')
+        self.assertEqual(getAtomType(self.mol2.atoms[0],
+            self.mol2.getBonds(self.mol2.atoms[0])).label, 'Cb')
+
+    def testHydrogenType(self):
+        """
+        Test that getAtomType() returns the hydrogen atom type.
+        """
+        self.assertEqual(getAtomType(self.mol3.atoms[0],
+            self.mol3.getBonds(self.mol3.atoms[0])).label, 'H')
+
+    def testOxygenTypes(self):
+        """
+        Test that getAtomType() returns appropriate oxygen atom types.
+        """
+        self.assertEqual(getAtomType(self.mol1.atoms[1],
+            self.mol1.getBonds(self.mol1.atoms[1])).label, 'Os')
+        self.assertEqual(getAtomType(self.mol1.atoms[2],
+            self.mol1.getBonds(self.mol1.atoms[2])).label, 'Od')
+
+    def testSiliconTypes(self):
+        """
+        Test that getAtomType() returns appropriate silicon atom types.
+        """
+        self.assertEqual(getAtomType(self.mol4.atoms[2],
+            self.mol4.getBonds(self.mol4.atoms[2])).label, 'Sis')
+        self.assertEqual(getAtomType(self.mol4.atoms[3],
+            self.mol4.getBonds(self.mol4.atoms[3])).label, 'Sid')
+        self.assertEqual(getAtomType(self.mol4.atoms[4],
+            self.mol4.getBonds(self.mol4.atoms[4])).label, 'Sidd')
+        self.assertEqual(getAtomType(self.mol4.atoms[6],
+            self.mol4.getBonds(self.mol4.atoms[6])).label, 'Sit')
+        self.assertEqual(getAtomType(self.mol4.atoms[1],
+            self.mol4.getBonds(self.mol4.atoms[1])).label, 'SiO')
+
+    def testSulfurTypes(self):
+        """
+        Test that getAtomType() returns appropriate sulfur atom types.
+        """
+        self.assertEqual(getAtomType(self.mol4.atoms[8],
+            self.mol4.getBonds(self.mol4.atoms[8])).label, 'Ss')
+        self.assertEqual(getAtomType(self.mol4.atoms[9],
+            self.mol4.getBonds(self.mol4.atoms[9])).label, 'Sd')
+
+    def testNoneTypes(self):
+        """
+        Test that getAtomType() returns appropriate NoneTypes.
+        """
+        self.assertIsNone(getAtomType(self.mol5.atoms[0],
+            self.mol5.getBonds(self.mol5.atoms[0])))
+        self.assertIsNone(getAtomType(self.mol6.atoms[0],
+            self.mol6.getBonds(self.mol6.atoms[0])))
+        self.assertIsNone(getAtomType(self.mol7.atoms[0],
+            self.mol7.getBonds(self.mol7.atoms[0])))
+        self.assertIsNone(getAtomType(self.mol8.atoms[0],
+            self.mol8.getBonds(self.mol8.atoms[0])))
+
 ################################################################################
 
 if __name__ == '__main__':

unittest/cantherm/gaussianTest.py

@@ -3,6 +3,7 @@
 
 import numpy
 import unittest
+import os
 
 from rmgpy.cantherm.gaussian import *
 from rmgpy.statmech import *
@@ -21,7 +22,7 @@ def testLoadEthyleneFromGaussianLog(self):
         molecular degrees of freedom can be properly read.
         """
 
-        log = GaussianLog('unittest/cantherm/ethylene.log')
+        log = GaussianLog(os.path.join(os.path.dirname(__file__),'ethylene.log'))
         s = log.loadStates()
         E0 = log.loadEnergy()
 
@@ -47,7 +48,7 @@ def testLoadOxygenFromGaussianLog(self):
         molecular degrees of freedom can be properly read.
         """
 
-        log = GaussianLog('unittest/cantherm/oxygen.log')
+        log = GaussianLog(os.path.join(os.path.dirname(__file__),'oxygen.log'))
         s = log.loadStates()
         E0 = log.loadEnergy()
 

unittest/data/datatest.py

@@ -7,9 +7,11 @@
 sys.path.append('.')
 
 from rmgpy.data.base import *
-from rmgpy.chem.pattern import MoleculePattern
+from rmgpy.group import Group
 
-thermoDatabase = 'database/output/RMG_Database/thermo_groups'
+from rmgpy import settings
+
+thermoDatabase = os.path.join(settings['database.directory'],'../output/RMG_Database/thermo_groups')
 
 ################################################################################
 
@@ -24,7 +26,7 @@ def testDatabaseLoad(self):
 		libstr = thermoDatabase + '/Group_Library.txt'
 
 		database = Database()
-		database.load(dictstr, treestr, libstr)
+		database.loadOld(dictstr, treestr, libstr, 12)
 
 		# All nodes in library should be in tree and dictionary
 		# All nodes in tree should be in dictionary
@@ -55,7 +57,7 @@ def testDatabaseLoad(self):
 
 		# All values in dictionary should be chemical structures
 		for node in database.dictionary:
-			self.assertTrue(isinstance(database.dictionary[node], MoleculePattern))
+			self.assertTrue(isinstance(database.dictionary[node], Group))
 
 ################################################################################
 

unittest/data/thermoTest.py

@@ -6,13 +6,16 @@
 import sys
 sys.path.append('.')
 
-from rmgpy.data.thermo import loadThermoDatabase, ThermoEntry, generateThermoData
+import rmgpy.data.thermo
+
 from rmgpy.data.base import LogicNode
 from rmgpy.chem.molecule import Molecule
 from rmgpy.chem.pattern import MoleculePattern
 from rmgpy.chem.thermo import ThermoData
 from rmgpy.chem.species import Species
 
+from rmgpy import settings
+
 ################################################################################
 
 class ThermoDatabaseCheck(unittest.TestCase):
@@ -21,7 +24,7 @@ def testOldThermoDatabase(self):
         """
         Check the database load functions.
         """
-
+        
         thermoDatabase = loadThermoDatabase('database/output/RMG_Database/thermo_groups', group=True, old=True)
 
         for database in [thermoDatabase.groupDatabase,
@@ -75,15 +78,15 @@ def testThermoDatabase(self):
         """
         Check the database load functions.
         """
-
-        thermoDatabase = loadThermoDatabase('database/input/RMG_database/thermo_groups', group=True, old=False)
+        thermoDatabase = rmgpy.data.thermo.ThermoDatabase()
+        thermoDatabase.load(os.path.join(settings['database.path'],'RMG_Database'))
 
         for database in [thermoDatabase.groupDatabase,
-            thermoDatabase.int15Database,
-            thermoDatabase.gaucheDatabase,
-            thermoDatabase.otherDatabase,
-            thermoDatabase.radicalDatabase,
-            thermoDatabase.ringDatabase]:
+                thermoDatabase.int15Database,
+                thermoDatabase.gaucheDatabase,
+                thermoDatabase.otherDatabase,
+                thermoDatabase.radicalDatabase,
+                thermoDatabase.ringDatabase]:
 
             # All nodes in library should be in tree and dictionary
             # All nodes in tree should be in dictionary

unittest/kineticsTest.py

@@ -115,7 +115,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the KineticsData.isPressureDependent() method.
-
         """
         self.assertFalse(self.kinetics.isPressureDependent())
 
@@ -195,7 +194,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the Arrhenius.isPressureDependent() method.
-
         """
         self.assertFalse(self.kinetics.isPressureDependent())
 
@@ -226,7 +224,7 @@ def testFitToData(self):
         """
         Tdata = numpy.array([300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500], numpy.float)
         kdata = numpy.array([self.kinetics.getRateCoefficient(T) for T in Tdata], numpy.float)
-        kinetics = Arrhenius().fitToData(Tdata, kdata, kunits="m^3/(mol*s)")
+        kinetics = Arrhenius().fitToData(Tdata, kdata, kunits="m^3/(mol*s)", T0=300)
         self.assertEqual(self.kinetics.T0.value, 300)
         self.assertEqual(self.kinetics.T0.units, "K")
         for T, k in zip(Tdata, kdata):
@@ -305,7 +303,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the ArrheniusEP.isPressureDependent() method.
-
         """
         self.assertFalse(self.kinetics.isPressureDependent())
 
@@ -429,7 +426,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the MultiKinetics.isPressureDependent() method.
-
         """
         self.assertFalse(self.kinetics.isPressureDependent())
 
@@ -536,7 +532,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the PDepArrhenius.isPressureDependent() method.
-
         """
         self.assertTrue(self.kinetics.isPressureDependent())
 
@@ -669,7 +664,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the Chebyshev.isPressureDependent() method.
-
         """
         self.assertTrue(self.kinetics.isPressureDependent())
 
@@ -804,7 +798,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the ThirdBody.isPressureDependent() method.
-
         """
         self.assertTrue(self.kinetics.isPressureDependent())
 
@@ -937,7 +930,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the Lindemann.isPressureDependent() method.
-
         """
         self.assertTrue(self.kinetics.isPressureDependent())
 
@@ -1072,7 +1064,6 @@ def setUp(self):
     def testIsPressureDependent(self):
         """
         Test the Troe.isPressureDependent() method.
-
         """
         self.assertTrue(self.kinetics.isPressureDependent())
 

unittest/rmg/atomtest.py

@@ -6,7 +6,7 @@
 import sys
 sys.path.append('.')
 
-from rmg.chem import *
+from rmgpy.molecule import *
 
 ################################################################################
 

unittest/rmg/bondtest.py

@@ -6,7 +6,7 @@
 import sys
 sys.path.append('.')
 
-from rmg.chem import *
+from rmgpy.molecule import *
 
 ################################################################################
 

unittest/rmg/datatest.py

@@ -6,8 +6,8 @@
 import sys
 sys.path.append('.')
 
-from rmg.data import *
-from rmg.structure import *
+from rmgpy.data import *
+from rmgpy.molecule import *
 
 thermoDatabase = 'data/RMG_database/thermo_groups'