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()