def _parseUDCTokenList(self):
tokenizer = grrm.ListOutputTokenizer()
tokens = tokenizer.tokenize(self._filename)
current_molecule = None
header_found = False
for t in tokens:
if t.__class__ == tokentypes.HeaderDissociatedToken:
header_found = True
if t.__class__ == tokentypes.StructureHeaderToken:
if not header_found:
raise Exception("Header not found")
current_molecule = grrm2.BarrierlessDissociated.new(
self._graph,
rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
self._molecules.append(current_molecule)
grrm2.structureNumber(current_molecule).set(int(t.number()))
self._struct_label_to_molecule_mapper[(
"uDC", t.number())] = current_molecule
if t.__class__ == tokentypes.GeometryToken:
if not header_found:
raise Exception("Header not found")
grrm2.geometry(current_molecule).set(
helperfuncs.parseGeometryToken(t))
if t.__class__ == tokentypes.EnergyToken:
if not header_found:
raise Exception("Header not found")
grrm2.energy(current_molecule).set(
helperfuncs.parseEnergyToken(t))
if t.__class__ == tokentypes.SpinToken:
if not header_found:
raise Exception("Header not found")
grrm2.spin(current_molecule).set(
int(t.spin().rescale(units.hbar).magnitude))
if t.__class__ == tokentypes.ZPVEToken:
if not header_found:
raise Exception("Header not found")
grrm2.zeroPointVibrationalEnergy(current_molecule).set(
helperfuncs.parseZPVEToken(t))
if t.__class__ == tokentypes.NormalModesToken:
if not header_found:
raise Exception("Header not found")
grrm2.normalModesEigenvalues(current_molecule).set(
helperfuncs.parseNormalModesEigenvalues(t))
if t.__class__ == tokentypes.ConnectionToken:
if not header_found:
raise Exception("Header not found")
self._connections.append(
(("uDC", grrm2.structureNumber(current_molecule).get()),
("EQ", t.first())))
if t.__class__ == tokentypes.DissociationFragmentsToken:
if not header_found:
raise Exception("Header not found")
grrm2.fragments(current_molecule).set(t.fragments())
def testHeaderDissociatedToken(self): # fold>>
data = filesnippets.headerDissociated()+"\n"
writeToTestFile(data)
tokenizer = grrm.ListOutputTokenizer()
token_gen = tokenizer.tokenize(testFilePath())
token_list = list(token_gen)
self.assertEqual(len(token_list), 1)
self.assertEqual(token_list[0].__class__, tokentypes.HeaderDissociatedToken)
def testGeometryToken(self): # fold>>
data = filesnippets.geometry()+"\n"
writeToTestFile(data)
tokenizer = grrm.ListOutputTokenizer()
token_gen = tokenizer.tokenize(testFilePath())
token_list = list(token_gen)
self.assertEqual(len(token_list), 1)
self.assertEqual(token_list[0].__class__, tokentypes.GeometryToken)
def testTokenizerEmptyFile(self): # fold>>
writeToTestFile("")
tokenizer = grrm.ListOutputTokenizer()
token_gen = tokenizer.tokenize(testFilePath())
self.assertEqual(list(token_gen), [])