def testTokenizerFileHeader(self): # fold>>
data = FileSnippets.fileHeader()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.FileHeaderToken)
def testTokenizerIsotopicMasses(self): # fold>>
data = FileSnippets.isotopicMasses()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.IsotopicMassesToken)
def testTokenizerDipoleMomentComponents(self): # fold>>
data = FileSnippets.dipoleMomentComponents()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.DipoleMomentComponentsToken)
def testTokenizerHOMOLUMOSeparation(self): # fold>>
data = FileSnippets.HomoLumoSeparation()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.HOMOLUMOSeparationToken)
def testTokenizerAtomsAndBasisSetsTable(self): # fold>>
data = FileSnippets.atomsAndBasisSetsTable()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.AtomsAndBasisSetsToken)
def testTokenizerNormalModesEigenvalues(self): # fold>>
data = FileSnippets.normalModesEigenvalues()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.NormalModesEigenvaluesToken)
def testTokenizerOptimizationInfo(self): # fold>>
data = FileSnippets.optimizationInfo()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.OptimizationInfoToken)
def testTokenizerGeometryConvergenceNumIterations(self): # fold>>
data = FileSnippets.geometryConvergenceNumIterations()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.GeometryConvergenceNumIterationsToken)
def testTokenizer(self): # fold>>
data = FileSnippets.fileHeader()+"\n"+ FileSnippets.centerOfMass()+"\n"+FileSnippets.isotopicMasses()+"\n"+FileSnippets.totalMass()+"\n"+FileSnippets.momentsOfInertia()+"\n"
writeToTestFile(data)
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 5)
self.assertEqual(tokens[0].__class__, Tokens.FileHeaderToken)
self.assertEqual(tokens[1].__class__, Tokens.CenterOfMassToken)
self.assertEqual(tokens[2].__class__, Tokens.IsotopicMassesToken)
self.assertEqual(tokens[3].__class__, Tokens.TotalMassToken)
self.assertEqual(tokens[4].__class__, Tokens.MomentsOfInertiaToken)
def main(filename):
tokens = Dalton.tokenizeOutFile(filename)
try:
bond_length_token = filter(
lambda x: x.__class__ == Tokens.BondLengthsToken, tokens)[-1]
except:
print "Sorry, looks like there are no bond length entries in the file"
sys.exit(1)
atom_list = bond_length_token.atomList()
print "# %s" % (filename, )
for entry in atom_list:
if entry[0][0][0] == "C" and entry[1][0][0] == "C":
print "%s %s %s %s %s" % (entry[0][0], entry[0][1], entry[1][0],
entry[1][1], entry[2])
def main(dalton_out):
tokenlist = Dalton.tokenizeOutFile(dalton_out)
atom_basis_set_token = getAtomsAndBasisSetsToken(tokenlist)
geometry_token = getFinalGeometry(tokenlist)
datalist = atom_basis_set_token.atomDataList()
final_geometry = geometry_token.atomList()
doc = minidom.parseString(
"<cml xmlns=\"http://www.xml-cml.org/schema\" xmlns:sb=\"http://forthescience.org/NS/mycml\"/>"
)
namespace = "http://www.xml-cml.org/schema"
molecule = doc.createElementNS(namespace, "molecule")
doc.documentElement.appendChild(molecule)
name = doc.createElementNS(namespace, "name")
molecule.appendChild(name)
text = doc.createTextNode(os.path.splitext(dalton_out)[0])
name.appendChild(text)
atomarray = doc.createElementNS(namespace, "atomArray")
molecule.appendChild(atomarray)
for id, atom_entry in enumerate(final_geometry):
label, group, coords = atom_entry
x, y, z = coords
atomic_number = labelToAtomicNumber(label, datalist)
atom = doc.createElementNS(namespace, "atom")
atom.setAttribute("id", "a" + str(id + 1))
atom.setAttribute("x3", str(x))
atom.setAttribute("y3", str(y))
atom.setAttribute("z3", str(z))
atom.setAttributeNS("http://forthescience.org/NS/mycml",
"sb:atomicNumber", str(atomic_number))
label_node = doc.createElementNS(namespace, "label")
label_node.setAttribute("value", label)
atom.appendChild(label_node)
atomarray.appendChild(atom)
print doc.toprettyxml()
def testTokenizerEmptyFile(self): # fold>>
writeToTestFile("")
tokens = Dalton.tokenizeOutFile(testFilePath())
self.assertEqual(tokens, [])