def testNumOfMolecules(self): # fold>>
xyz = XYZFile.XYZFile(os.path.join(moduleDir(), "testfile_simple.xyz"))
self.assertEqual(xyz.numOfMolecules(), 1)
xyz = XYZFile.XYZFile(
os.path.join(moduleDir(), "testfile_multiple.xyz"))
self.assertEqual(xyz.numOfMolecules(), 2)
def testCreateMolecule(self):
xyz = XYZFile.XYZFile()
self.assertEqual(xyz.createMolecule(), 0)
self.assertEqual(xyz.createMolecule(), 1)
self.assertEqual(xyz.createMolecule(1), 1)
self.assertEqual(xyz.numOfMolecules(), 3)
def testSaveTo(self):
xyz = XYZFile.XYZFile()
xyz.createMolecule()
xyz.setComment("hello 1")
xyz.addAtom((PeriodicTable.Hydrogen,
Measure.Measure((1.0, 2.0, 3.0), Units.angstrom)))
xyz.addAtom((PeriodicTable.Carbon,
Measure.Measure((1.0, 2.0, 3.0), Units.angstrom)))
xyz.createMolecule()
xyz.setComment("hello 2")
xyz.addAtom((PeriodicTable.Oxygen,
Measure.Measure((4.0, 6.0, 8.0), Units.angstrom)))
xyz.addAtom((PeriodicTable.Fluorine,
Measure.Measure((5.0, 7.0, 9.0), Units.angstrom)))
xyz.saveTo(os.path.join(moduleDir(), "testfile_saveTo.xyz"))
f1 = file(os.path.join(moduleDir(), "testfile_saveTo.xyz")).read()
f2 = file(os.path.join(moduleDir(), "saveTo.expected")).read()
md1 = hashlib.md5(f1)
md2 = hashlib.md5(f2)
self.assertEqual(md1.hexdigest(), md2.hexdigest())
os.unlink(os.path.join(moduleDir(), "testfile_saveTo.xyz"))
def testGetData2(self):
xyz = XYZFile.XYZFile(os.path.join(moduleDir(),"testfile_multiple.xyz"))
self.assertEqual(xyz.numOfAtoms(0),2)
self.assertEqual(xyz.comment(0), "benzene single")
self.assertEqual(xyz.atom(0,1)[0], PeriodicTable.Hydrogen)
self.assertEqual(xyz.atom(0,1)[1].__class__, Measure.Measure)
self.assertEqual(xyz.atom(0,1)[1].value(), (0.0000, 2.49029, 0.00000 ))
self.assertEqual(xyz.atom(0,1)[1].unit(), Units.angstrom)
xyz = XYZFile.XYZFile(os.path.join(moduleDir(),"testfile_multiple.xyz"))
self.assertEqual(xyz.numOfAtoms(),12)
self.assertEqual(xyz.comment(), "benzene example")
self.assertEqual(xyz.atom(3)[0], PeriodicTable.Hydrogen)
self.assertEqual(xyz.atom(3)[1].__class__, Measure.Measure)
self.assertEqual(xyz.atom(3)[1].value(), (-2.15666, 1.24515, 0.00000 ))
self.assertEqual(xyz.atom(3)[1].unit(), Units.angstrom)
def testAddAtom(self):
xyz = XYZFile.XYZFile()
xyz.createMolecule()
xyz.setComment("hello")
xyz.addAtom((PeriodicTable.Hydrogen, Measure.Measure( (1.0, 2.0, 3.0), Units.angstrom)))
xyz.addAtom((PeriodicTable.Carbon, Measure.Measure( (1.0, 2.0, 3.0), Units.angstrom)))
self.assertEqual(xyz.atom(0)[0], PeriodicTable.Hydrogen)
self.assertEqual(xyz.atom(1)[0], PeriodicTable.Carbon)
def main(argv): # fold>>
options = _getOptions(argv)
infile = XYZFile.XYZFile(options.input_filename)
outfile = XYZFile.XYZFile()
for mol_idx in xrange(infile.numOfMolecules()):
atom_list = []
for atom_idx in xrange(infile.numOfAtoms(mol_idx)):
atom_list.append(infile.atom(mol_idx, atom_idx))
molecule = XYZMolecule.XYZMolecule(atom_list)
molecule.translate(-XYZMolecule.centerOfMass(molecule))
new_mol_index = outfile.createMolecule()
for atom in zip(molecule.elements(), molecule.atomPos()):
outfile.addAtom(new_mol_index,atom)
outfile.saveTo(options.output_filename)
def testSetComment(self):
xyz = XYZFile.XYZFile()
xyz.createMolecule()
xyz.setComment("hello")
self.assertEqual(xyz.comment(), "hello")
xyz.createMolecule()
xyz.setComment("hello 2")
self.assertEqual(xyz.comment(), "hello 2")
xyz.setComment(0, "hello 1")
self.assertEqual(xyz.comment(0), "hello 1")
self.assertEqual(xyz.comment(1), "hello 2")
self.assertEqual(xyz.comment(), "hello 2")
self.assertRaises(IndexError, xyz.setComment, 2, "hello")
def testCommentReturnsNone(self):
xyz = XYZFile.XYZFile()
self.assertEqual(xyz.comment(), None)
self.assertEqual(xyz.comment(1), None)
def testInit2(self): # fold>>
xyz = XYZFile.XYZFile(
os.path.join(moduleDir(), "testfile_multiple.xyz"))
self.assertEqual(xyz.__class__, XYZFile.XYZFile)