class TestQMSettings(unittest.TestCase): """ Contains unit tests for the QMSettings class. """ def setUp(self): """ A function run before each unit test in this class. """ rmg_path = os.path.normpath(os.path.join(get_path(), '..')) self.settings1 = QMSettings( software='mopac', method='pm3', fileStore=os.path.join(rmg_path, 'testing', 'qm', 'QMfiles'), scratchDirectory=None, onlyCyclics=False, maxRadicalNumber=0, ) self.settings2 = QMSettings() def test_check_all_set(self): """ Test that check_all_set() works correctly. """ try: self.settings1.check_all_set() except AssertionError: self.fail("check_all_set() raised unexpected AssertionError.") with self.assertRaises(AssertionError): self.settings2.check_all_set()
class TestQMSettings(unittest.TestCase): """ Contains unit tests for the QMSettings class. """ def setUp(self): """ A function run before each unit test in this class. """ RMGpy_path = os.path.normpath(os.path.join(getPath(),'..')) self.settings1 = QMSettings(software = 'mopac', method = 'pm3', fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'), scratchDirectory = None, onlyCyclics = False, maxRadicalNumber = 0, ) self.settings2 = QMSettings() def testCheckAllSet(self): """ Test that checkAllSet() works correctly. """ try: self.settings1.checkAllSet() except AssertionError: self.fail("checkAllSet() raised unexpected AssertionError.") with self.assertRaises(AssertionError): self.settings2.checkAllSet()
def setUp(self): """ A function run before each unit test in this class. """ RMGpy_path = os.path.normpath(os.path.join(getPath(),'..')) self.settings1 = QMSettings(software = 'mopac', method = 'pm3', fileStore = os.path.join(RMGpy_path, 'testing', 'qm', 'QMfiles'), scratchDirectory = None, onlyCyclics = False, maxRadicalNumber = 0, ) self.settings2 = QMSettings()
atLblsP = dict([(lbl[0], False) for lbl in reaction.labeledAtoms]) for reactant in reaction.reactants: reactant = reactant.molecule[0] reactant.clearLabeledAtoms() for atom in reactant.atoms: for atomLabel in reaction.labeledAtoms: if atom == atomLabel[1]: atom.label = atomLabel[0] atLblsR[atomLabel[0]] = True for product in reaction.products: product = product.molecule[0] product.clearLabeledAtoms() for atom in product.atoms: for atomLabel in reaction.labeledAtoms: if atom == atomLabel[1]: atom.label = atomLabel[0] atLblsP[atomLabel[0]] = True if all(atLblsR.values()) and all(atLblsP.values()): gotOne = True break qmSettings = QMSettings( software='gaussian', method='m062x', fileStore=os.getcwd(), scratchDirectory='/gss_gpfs_scratch/slakman.b/QMscratch') qmReac = GaussianTSM062X(reaction, qmSettings, tsDatabase) qmReac.generateTSGeometryDirectGuess()