def testFindStringNotFound(self): # fold>>
"Findstring functionality/not found case"
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
self.assertEqual(f.findString('notfound'), '')
self.assertEqual(f.isAtEOF(), True)
self.assertEqual(f.findString('notfound', backward=True), '')
self.assertEqual(f.isAtBOF(), True)
def parseFile(self, infile): # fold>>
self.__infile = FileReader.FileReader(infile)
self.__parameters = _parseParametersSection(self.__infile)
self.__zmatrix, self.__distance_units, self.__angle_units = _parseZMatrixSection(
self.__infile, self.__parameters)
self.__basis = _parseBasisSection(self.__infile, self.__zmatrix)
self.__symmetries = _parseSymmetrySection(self.__infile)
def testOptimizationNextGeometryToken(self): # fold>>
data = FileSnippets.optimizationNextGeometry()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.OptimizationNextGeometryToken.match(reader)
self.assertEqual(token.__class__, Tokens.OptimizationNextGeometryToken)
self.assertEqual(reader.currentPos(), start_pos + 8)
atom_list = token.atomList()
self.assertEqual(len(atom_list), 4)
self.assertEqual(atom_list[0][0], "O1")
self.assertEqual(atom_list[0][1], "")
self.assertEqual(atom_list[0][2],
("0.0000000000", "0.0000000000", "0.0680928675"))
self.assertEqual(atom_list[1][0], "H1")
self.assertEqual(atom_list[1][1], "1")
self.assertEqual(atom_list[1][2],
("0.0000000000", "-1.7554324515", "3.4700805319"))
self.assertEqual(atom_list[2][0], "H1")
self.assertEqual(atom_list[2][1], "2")
self.assertEqual(atom_list[2][2],
("0.0000000000", "1.7554324515", "3.4700805319"))
self.assertEqual(atom_list[3][0], "C1")
self.assertEqual(atom_list[3][1], "")
self.assertEqual(atom_list[3][2],
("0.0000000000", "0.0000000000", "2.3521294415"))
def testEmptyFileRegexpNotFound(self): # fold>>
f = FileReader.FileReader(
os.path.join(moduleDir(), "emptytestfile.txt"))
self.assertEqual(f.findRegexp('notfound'), None)
self.assertEqual(f.isAtEOF(), True)
self.assertEqual(f.findRegexp('notfound', backward=True), None)
self.assertEqual(f.isAtBOF(), True)
def testCartesianCoordinatesToken(self): # fold>>
data = FileSnippets.cartesianCoordinates()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.CartesianCoordinatesToken.match(reader)
self.assertEqual(token.__class__, Tokens.CartesianCoordinatesToken)
self.assertEqual(reader.currentPos(), start_pos + 22)
atom_list = token.atomList()
self.assertEqual(len(atom_list), 4)
self.assertEqual(atom_list[0][0], "O1")
self.assertEqual(atom_list[0][1], "")
self.assertEqual(atom_list[0][2],
("0.0000000000", "0.0000000000", "0.3000000000"))
self.assertEqual(atom_list[1][0], "H1")
self.assertEqual(atom_list[1][1], "1")
self.assertEqual(atom_list[1][2],
("0.0000000000", "-1.7597098488", "3.3775957364"))
self.assertEqual(atom_list[2][0], "H1")
self.assertEqual(atom_list[2][1], "2")
self.assertEqual(atom_list[2][2],
("0.0000000000", "1.7597098488", "3.3775957364"))
self.assertEqual(atom_list[3][0], "C1")
self.assertEqual(atom_list[3][1], "")
self.assertEqual(atom_list[3][2],
("0.0000000000", "0.0000000000", "2.3051919000"))
def testEmptyFileSkipLines(self): # fold>>
f = FileReader.FileReader(
os.path.join(moduleDir(), "emptytestfile.txt"))
self.assertEqual(f.currentPos(), -1)
f.skipLines(10)
self.assertEqual(f.isAtEOF(), True)
f.skipLines(-10)
self.assertEqual(f.isAtBOF(), True)
def testRegexpCurlineNeverEvaluated(self): # fold>>
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
f.toPos(0)
self.assertEqual(f.findRegexp('line'), ("2nd line\n", ))
self.assertEqual(f.currentLine(), "2nd line\n")
f.toPos(2)
self.assertEqual(f.findRegexp('line', backward=True), ("2nd line\n", ))
self.assertEqual(f.currentLine(), "2nd line\n")
def testGetItem(self): # fold>>
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
self.assertEqual(f[0], "1st line\n")
self.assertEqual(f[1], "2nd line\n")
self.assertEqual(f[2], "3rd line\n")
f.close()
def testRegexpBasic(self): # fold>>
"Findregexp functionality/basic search"
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
self.assertEqual(f.findRegexp("3rd"), ("3rd line\n", ))
self.assertEqual(f.currentLine(), "3rd line\n")
f.toEOF()
self.assertEqual(f.findRegexp("1st", backward=True), ("1st line\n", ))
self.assertEqual(f.currentLine(), "1st line\n")
def testFindStringCounted(self): # fold>>
"Findstring functionality/counted search"
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
self.assertEqual(f.findString("line", 2), "2nd line\n")
self.assertEqual(f.currentLine(), "2nd line\n")
f.toEOF()
self.assertEqual(f.findString("line", 2, backward=True), "2nd line\n")
self.assertEqual(f.currentLine(), "2nd line\n")
def testFindStringCurlineNeverEvaluated(self): # fold>>
"Findstring functionality/curline never evaluated"
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
f.toPos(0)
self.assertEqual(f.findString('line'), "2nd line\n")
self.assertEqual(f.currentLine(), "2nd line\n")
f.toPos(2)
self.assertEqual(f.findString('line', backward=True), "2nd line\n")
self.assertEqual(f.currentLine(), "2nd line\n")
def testFileHeaderToken(self): # fold>>
data = FileSnippets.fileHeader()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.FileHeaderToken.match(reader)
self.assertEqual(token.__class__, Tokens.FileHeaderToken)
self.assertEqual(reader.currentPos(), start_pos + 1)
def testEndOfOptimizationHeaderTokenNotMatching(self): # fold>>
data = FileSnippets.fileHeader()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.EndOfOptimizationHeaderToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testIsotopicMassesTokenNotMatching(self): # fold>>
data = FileSnippets.isotopicMasses()
writeToTestFile("\n" + data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.IsotopicMassesToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testMomentsOfInertiaTokenNotMatching(self): # fold>>
data = FileSnippets.momentsOfInertia()
writeToTestFile("\n" + data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.MomentsOfInertiaToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testHOMOLUMOSeparationTokenNotMatching(self): # fold>>
data = FileSnippets.optimizationNextGeometry()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.HOMOLUMOSeparationToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testAtomsAndBasisSetsTokenNotMatching(self): # fold>>
data = FileSnippets.fileHeader()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.AtomsAndBasisSetsToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testNormalModesEigenvaluesTokenNotMatching(self): # fold>>
data = FileSnippets.fileHeader()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.NormalModesEigenvaluesToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testGeometryConvergenceNumIterationsTokenNotMatching(self): # fold>>
data = FileSnippets.fileHeader()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.GeometryConvergenceNumIterationsToken.match(reader)
self.assertEqual(token, None)
self.assertEqual(reader.currentPos(), start_pos)
def testParseSymmetrySection(self): # fold>>
filename = os.path.join(moduleDir(), "HSO2POEtg3.zmat")
f = FileReader.FileReader(filename)
sym = zmatmodule._parseSymmetrySection(f)
valid_data = ['X', 'Z']
self.assertEqual(len(sym), len(valid_data))
for index in xrange(len(sym)):
self.assertEqual(sym[index], valid_data[index])
f.close()
def tokenize(self, filename):
reader = FileReader.FileReader(filename)
token_list = []
while not reader.isAtEOF():
token = self._resolveNextToken(reader)
if token is None:
reader.readline()
else:
token_list.append(token)
return token_list
def testEmptyFileSeeks(self): # fold>>
f = FileReader.FileReader(
os.path.join(moduleDir(), "emptytestfile.txt"))
self.assertEqual(f.currentPos(), -1)
self.assertEqual(f.isAtBOF(), True)
f.toEOF()
self.assertEqual(f.currentPos(), 0)
self.assertEqual(f.isAtEOF(), True)
f.toBOF()
self.assertEqual(f.currentPos(), -1)
self.assertEqual(f.isAtBOF(), True)
def testSkipLines(self): # fold>>
"Seeking with relative jumps"
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
self.assertEqual(f.currentPos(), -1)
f.skipLines(3)
self.assertEqual(f.currentPos(), 2)
f.skipLines(-1)
self.assertEqual(f.currentPos(), 1)
f.skipLines(10)
self.assertEqual(f.isAtEOF(), True)
f.skipLines(-10)
self.assertEqual(f.isAtBOF(), True)
def testFileReadlineBackward(self): # fold>>
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
f.toEOF()
l = f.readbackline()
self.assertEqual(l, "3rd line\n")
l = f.readbackline()
self.assertEqual(l, "2nd line\n")
l = f.readbackline()
self.assertEqual(l, "1st line\n")
# now the pointer is at begin of file
self.assertEqual(f.readbackline(), '')
def testTotalMassToken(self): # fold>>
data = FileSnippets.totalMass()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.TotalMassToken.match(reader)
self.assertEqual(token.__class__, Tokens.TotalMassToken)
self.assertEqual(reader.currentPos(), start_pos + 1)
self.assertEqual(type(token.totalMass()), type(""))
self.assertEqual(token.totalMass(), "30.010565")
def testFileReadLine(self): # fold>>
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
l = f.readline()
self.assertEqual(l, "1st line\n")
l = f.readline()
self.assertEqual(l, "2nd line\n")
l = f.readline()
self.assertEqual(l, "3rd line\n")
# now the pointer is at end of file
self.assertEqual(f.readline(), '')
f.close()
def testOccurrences(self): # fold>>
"Seeking with relative jumps"
f = FileReader.FileReader(os.path.join(moduleDir(), "testfile.txt"))
f.skipLines(1)
self.assertEqual(f.isAtPos(0), True)
self.assertEqual(f.occurrences('line'), [1, 2])
self.assertEqual(f.isAtPos(0), True)
f.skipLines(2)
self.assertEqual(f.isAtPos(2), True)
self.assertEqual(f.occurrences('line', backward=True), [1, 0])
self.assertEqual(f.isAtPos(2), True)
f.toBOF()
self.assertEqual(f.occurrences('not found'), [])
def testFinalGeometryEnergyToken(self): # fold>>
data = FileSnippets.finalGeometryEnergy()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.FinalGeometryEnergyToken.match(reader)
self.assertEqual(token.__class__, Tokens.FinalGeometryEnergyToken)
self.assertEqual(reader.currentPos(), start_pos + 1)
energy = token.energy()
self.assertEqual(type(energy), type(""))
self.assertEqual(energy, "-113.984888")
def testDipoleMomentToken(self): # fold>>
data = FileSnippets.dipoleMoment()
writeToTestFile(data)
reader = FileReader.FileReader(testFilePath())
start_pos = reader.currentPos()
token = Tokens.DipoleMomentToken.match(reader)
self.assertEqual(token.__class__, Tokens.DipoleMomentToken)
self.assertEqual(reader.currentPos(), start_pos + 4)
dipole = token.dipole()
self.assertAlmostEqual(dipole, 3.141592)
def testEmptyFileGetItemOutOfBounds(self): # fold>>
f = FileReader.FileReader(
os.path.join(moduleDir(), "emptytestfile.txt"))
# move at BOF with big negative num
self.assertEqual(f[-999999], '')
self.assertEqual(f.isAtBOF(), True)
# move at EOF with big positive num
self.assertEqual(f[9999999], '')
self.assertEqual(f.isAtEOF(), True)
# move at BOF with -1
self.assertEqual(f[-1], '')
self.assertEqual(f.isAtBOF(), True)
# move at EOF with len
self.assertEqual(f[len(f)], '')
self.assertEqual(f.isAtEOF(), True)
