def testCCLibParser(self):
#Tests to check whether the CCLibParser wrapper around CCLib works fine
name = 'AAAOFKFEDKWQNN-UHFFFAOYAY'
InChIaug = 'InChI=1/C9H14O2/c1-6(2)9-5-8(11-10)4-7(9)3/h4-6,8,10H,1-3H3'
molecule = mol.Molecule().fromInChI(InChIaug)
inputFileExtension = '.log'
driver = qm.QMTP('gaussian03', 'pm3')
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles',
'G03')
parsingTool = pars.CCLibParser(
os.path.join(directory, name + inputFileExtension), driver)
data = parsingTool.parse(molecule)
self.assertEqual(data.groundStateDegeneracy, 1)
self.assertEqual(data.cclib_data.natom, 25)
self.assertEqual(data.cclib_data.molmass, 154.09938)
self.assertEqual(len(data.cclib_data.atomcoords[-1]),
data.cclib_data.natom)
self.assertEqual(len(data.atomCoords), data.numberOfAtoms)
self.assertEqual(len(data.cclib_data.rotcons[-1]), 3)
self.assertEqual(len(data.cclib_data.atomnos), data.cclib_data.natom)
print 'Z-coord Atom coord of 1st atom: ' + str(
data.cclib_data.atomcoords[-1][0][2])
def testSymmetryJob(self):
"""
Check whether external call to symmetry tool works fine.
"""
name = 'AAAOFKFEDKWQNN-UHFFFAOYAY'
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles',
'G03')
InChIaug = 'InChI=1/C9H14O2/c1-6(2)9-5-8(11-10)4-7(9)3/h4-6,8,10H,1-3H3'
molecule = mol.Molecule().fromInChI(InChIaug)
molfile = qm.molFile(molecule, name, directory, InChIaug)
inputFileExtension = '.log'
driver = qm.QMTP('gaussian03', 'pm3')
parsingTool = pars.CCLibParser(
os.path.join(directory, name + inputFileExtension), driver)
iqmdata = parsingTool.parse(molecule)
symm_job = job.SymmetryJob(molfile, iqmdata)
pointGroup = symm_job.calculate()
self.assertTrue(
os.path.exists(
os.path.join(directory, 'AAAOFKFEDKWQNN-UHFFFAOYAY.symm')))
self.assertEqual(pointGroup.symmetryNumber, 1)
self.assertTrue(
pointGroup.chiral
) #the chiral flag is set to True for C1 symmetry groups!
self.assertFalse(pointGroup.linear)
def testVerifierDoesNotExist(self):
molecule = mol.Molecule()
name = 'UMRZSTCPUPJPOJ-UHFFFAOYSA'
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles')
InChIaug = 'InChI=1S/C7H12/c1-2-7-4-3-6(1)5-7/h6-7H,1-5H2'
molfile = qm.molFile(molecule, name, directory, InChIaug)
verifier = verif.QMVerifier(molfile)
verifier.verify()
self.assertFalse(verifier.succesfulJobExists())
def testMOPAC_PM3_Parser(self):
driver = qm.QMTP('mopac')
name = 'GRWFGVWFFZKLTI-UHFFFAOYAF'
InChIaug = 'InChI=1/C10H16/c1-7-4-5-8-6-9(7)10(8,2)3/h4,8-9H,5-6H2,1-3H3'
molecule = mol.Molecule().fromInChI(InChIaug)
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles',
'MOPAC')
mf = qm.molFile(molecule, name, directory)
parser = pars.MOPACPM3Parser(mf, driver)
result = parser.parse()
assert isinstance(result, ThermoData)
def testVerifierMOPACResultExists(self):
molecule = mol.Molecule()
name = 'GRWFGVWFFZKLTI-UHFFFAOYAF'
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles',
'MOPAC')
InChIaug = 'InChI=1/C10H16/c1-7-4-5-8-6-9(7)10(8,2)3/h4,8-9H,5-6H2,1-3H3'
molfile = qm.molFile(molecule, name, directory, InChIaug)
verifier = verif.QMVerifier(molfile)
verifier.verify()
self.assertTrue(verifier.succesfulJobExists())
self.assertTrue(verifier.mopacResultExists)
self.assertFalse(verifier.gaussianResultExists)
def testMOPACJob(self):
molecule = mol.Molecule()
name = 'UMRZSTCPUPJPOJ-UHFFFAOYAR'
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles',
'MOPAC')
InChIAug = ''
molfile = qm.molFile(molecule, name, directory, InChIAug)
mj = MOPACJob(molfile)
success = mj.run()
self.assertTrue(success)
#remove generated output files
os.remove(os.path.join(directory, name + '.out'))
os.remove(os.path.join(directory, name + '.arc'))
def testG03InputWriter(self):
"""
Checks whether the .gjf output file has been written based on the 3D coords file (.mol)
"""
name = 'WTARULDDTDQWMU-UHFFFAOYAW'
inchi = 'InChI=1/C10H16/c1-7-4-5-8-6-9(7)10(8,2)3/h8-9H,1,4-6H2,2-3H3'
directory = os.path.join(os.path.dirname(__file__), 'data', 'QMfiles',
'3DMolfiles')
target_file = os.path.join(directory, name + '.gjf')
if os.path.exists(target_file): os.remove(target_file)
molecule = mol.Molecule().fromInChI(inchi)
mf = qm.molFile(molecule, name, directory)
writer = writers.GaussianPM3InputWriter(mf,
attemptNumber=1,
multiplicity=1)
writer.write()
time.sleep(3) #otherwise assertion fails before the file is written!
self.assertTrue(os.path.exists(target_file))
def testPointGroupCalculator(self):
"""
Tests PointGroupCalculator
"""
name = 'AAAOFKFEDKWQNN-UHFFFAOYAY'
InChIaug = 'InChI=1/C9H14O2/c1-6(2)9-5-8(11-10)4-7(9)3/h4-6,8,10H,1-3H3'
molecule = mol.Molecule().fromInChI(InChIaug)
inputFileExtension = '.log'
directory = os.path.join(os.path.dirname(__file__),'data/QMfiles/G03')
driver = qm.QMTP('gaussian03', 'pm3')
parsingTool = pars.CCLibParser(os.path.join(directory, name+inputFileExtension), driver)
data = parsingTool.parse(molecule)
mf = qm.molFile(molecule, name, directory)
pgc = symm.PointGroupCalculator(mf, data)
pg = pgc.calculate()
self.assertTrue(isinstance(pg, symm.PointGroup))
self.assertFalse(pg.linear)
self.assertTrue(pg.chiral)#the chiral flag is set to True for C1 symmetry groups!
self.assertEqual(pg.symmetryNumber, 1)