class CrystalStructureBuilderTestAtoms(unittest.TestCase):
def setUp(self):
self.builder = CrystalStructureBuilder()
self._baseData = dict([(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
def _getData(self, additionalData):
data = self._baseData.copy()
data.update(additionalData)
return data
def test_getAtoms_required_keys(self):
mandatoryKeys = dict([(u'_atom_site_label', [u'Si']),
(u'_atom_site_fract_x', [u'1/8']),
(u'_atom_site_fract_y', [u'1/8']),
(u'_atom_site_fract_z', [u'1/8'])])
for key in mandatoryKeys:
tmp = mandatoryKeys.copy()
del tmp[key]
self.assertRaises(RuntimeError,
self.builder._getAtoms,
cifData=tmp)
def test_getAtoms_correct(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_atom_type_symbol(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Fake1', u'Fake2']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(
self.builder._getAtoms(data),
'Fake 1/8 1/8 1/8 1.0 0.01;Fake 0.34 0.56 0.23 1.0 0.02')
data[u'_atom_site_type_symbol'] = [u'Si', u'Al']
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_B_iso(self):
data = self._getData(
dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_b_iso_or_equiv', [u'1.0', u'2.0'])]))
self.assertEqual(
self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0 0.0253302959106'
)
class CrystalStructureBuilderTestUnitCell(unittest.TestCase):
def setUp(self):
self.builder = CrystalStructureBuilder()
def test_getUnitCell_invalid(self):
invalid_no_a = {u'_cell_length_b': u'5.6'}
self.assertRaises(RuntimeError, self.builder._getUnitCell, cifData={})
self.assertRaises(RuntimeError, self.builder._getUnitCell, cifData=invalid_no_a)
def test_getUnitCell_cubic(self):
cell = {u'_cell_length_a': u'5.6'}
self.assertEqual(self.builder._getUnitCell(cell), '5.6 5.6 5.6 90.0 90.0 90.0')
def test_getUnitCell_tetragonal(self):
cell = {u'_cell_length_a': u'5.6', u'_cell_length_c': u'2.3'}
self.assertEqual(self.builder._getUnitCell(cell), '5.6 5.6 2.3 90.0 90.0 90.0')
def test_getUnitCell_orthorhombic(self):
cell = {u'_cell_length_a': u'5.6', u'_cell_length_b': u'1.6', u'_cell_length_c': u'2.3'}
self.assertEqual(self.builder._getUnitCell(cell), '5.6 1.6 2.3 90.0 90.0 90.0')
def test_getUnitCell_hexagonal(self):
cell = {u'_cell_length_a': u'5.6', u'_cell_length_c': u'2.3', u'_cell_angle_gamma': u'120.0'}
cell_errors = {u'_cell_length_a': u'5.6(1)', u'_cell_length_c': u'2.3(1)', u'_cell_angle_gamma': u'120.0'}
self.assertEqual(self.builder._getUnitCell(cell), '5.6 5.6 2.3 90.0 90.0 120.0')
self.assertEqual(self.builder._getUnitCell(cell_errors), '5.6 5.6 2.3 90.0 90.0 120.0')
class CrystalStructureBuilderTestAtoms(unittest.TestCase):
def setUp(self):
self.builder = CrystalStructureBuilder()
self._baseData = dict([
(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
def _getData(self, additionalData):
data = self._baseData.copy()
data.update(additionalData)
return data
def test_getAtoms_required_keys(self):
mandatoryKeys = dict([(u'_atom_site_label', [u'Si']),
(u'_atom_site_fract_x', [u'1/8']),
(u'_atom_site_fract_y', [u'1/8']),
(u'_atom_site_fract_z', [u'1/8'])])
for key in mandatoryKeys:
tmp = mandatoryKeys.copy()
del tmp[key]
self.assertRaises(RuntimeError, self.builder._getAtoms, cifData=tmp)
def test_getAtoms_correct(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_atom_type_symbol(self):
data = self._getData(dict([(u'_atom_site_label', [u'Fake1', u'Fake2']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
self.assertEqual(self.builder._getAtoms(data), 'Fake 1/8 1/8 1/8 1.0 0.01;Fake 0.34 0.56 0.23 1.0 0.02')
data[u'_atom_site_type_symbol'] = [u'Si', u'Al']
self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
def test_getAtoms_B_iso(self):
data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
(u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
(u'_atom_site_b_iso_or_equiv', [u'1.0', u'2.0'])]))
self.assertEqual(self.builder._getAtoms(data),
'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0 0.0253302959106')
class CrystalStructureBuilderTestUnitCell(unittest.TestCase):
def setUp(self):
self.builder = CrystalStructureBuilder()
def test_getUnitCell_invalid(self):
invalid_no_a = {u'_cell_length_b': u'5.6'}
self.assertRaises(RuntimeError, self.builder._getUnitCell, cifData={})
self.assertRaises(RuntimeError,
self.builder._getUnitCell,
cifData=invalid_no_a)
def test_getUnitCell_cubic(self):
cell = {u'_cell_length_a': u'5.6'}
self.assertEqual(self.builder._getUnitCell(cell),
'5.6 5.6 5.6 90.0 90.0 90.0')
def test_getUnitCell_tetragonal(self):
cell = {u'_cell_length_a': u'5.6', u'_cell_length_c': u'2.3'}
self.assertEqual(self.builder._getUnitCell(cell),
'5.6 5.6 2.3 90.0 90.0 90.0')
def test_getUnitCell_orthorhombic(self):
cell = {
u'_cell_length_a': u'5.6',
u'_cell_length_b': u'1.6',
u'_cell_length_c': u'2.3'
}
self.assertEqual(self.builder._getUnitCell(cell),
'5.6 1.6 2.3 90.0 90.0 90.0')
def test_getUnitCell_hexagonal(self):
cell = {
u'_cell_length_a': u'5.6',
u'_cell_length_c': u'2.3',
u'_cell_angle_gamma': u'120.0'
}
cell_errors = {
u'_cell_length_a': u'5.6(1)',
u'_cell_length_c': u'2.3(1)',
u'_cell_angle_gamma': u'120.0'
}
self.assertEqual(self.builder._getUnitCell(cell),
'5.6 5.6 2.3 90.0 90.0 120.0')
self.assertEqual(self.builder._getUnitCell(cell_errors),
'5.6 5.6 2.3 90.0 90.0 120.0')
class CrystalStructureBuilderTestSpaceGroup(unittest.TestCase):
def setUp(self):
self.builder = CrystalStructureBuilder()
def test_getSpaceGroupFromString_valid_no_exceptions(self):
valid_new = {u'_space_group_name_h-m_alt': u'P m -3 m'}
valid_old = {u'_symmetry_space_group_name_h-m': u'P m -3 m'}
assertRaisesNothing(self, self.builder._getSpaceGroupFromString, cifData=valid_old)
assertRaisesNothing(self, self.builder._getSpaceGroupFromString, cifData=valid_new)
assertRaisesNothing(self, self.builder._getSpaceGroupFromString, cifData=merge_dicts(valid_new, valid_old))
def test_getSpaceGroupFromString_valid_correct_value(self):
valid_new = {u'_space_group_name_h-m_alt': u'P m -3 m'}
valid_old = {u'_symmetry_space_group_name_h-m': u'P m -3 m'}
valid_old_different = {u'_symmetry_space_group_name_h-m': u'F d d d'}
invalid_old = {u'_symmetry_space_group_name_h-m': u'invalid'}
self.assertEqual(self.builder._getSpaceGroupFromString(valid_new), 'P m -3 m')
self.assertEqual(self.builder._getSpaceGroupFromString(valid_old), 'P m -3 m')
self.assertEqual(self.builder._getSpaceGroupFromString(merge_dicts(valid_new, valid_old)), 'P m -3 m')
self.assertEqual(self.builder._getSpaceGroupFromString(merge_dicts(valid_new, valid_old_different)), 'P m -3 m')
self.assertEqual(self.builder._getSpaceGroupFromString(merge_dicts(valid_new, invalid_old)), 'P m -3 m')
def test_getSpaceGroupFromString_invalid(self):
valid_old = {u'_symmetry_space_group_name_h-m': u'P m -3 m'}
invalid_new = {u'_space_group_name_h-m_alt': u'invalid'}
invalid_old = {u'_symmetry_space_group_name_h-m': u'invalid'}
self.assertRaises(RuntimeError, self.builder._getSpaceGroupFromString, cifData={})
self.assertRaises(ValueError, self.builder._getSpaceGroupFromString, cifData=invalid_new)
self.assertRaises(ValueError, self.builder._getSpaceGroupFromString, cifData=invalid_old)
self.assertRaises(ValueError, self.builder._getSpaceGroupFromString,
cifData=merge_dicts(invalid_new, valid_old))
def test_getCleanSpaceGroupSymbol(self):
fn = self.builder._getCleanSpaceGroupSymbol
self.assertEqual(fn('P m -3 m :1'), 'P m -3 m')
self.assertEqual(fn('P m -3 m :H'), 'P m -3 m')
def test_getSpaceGroupFromNumber_invalid(self):
invalid_old = {u'_symmetry_int_tables_number': u'400'}
invalid_new = {u'_space_group_it_number': u'400'}
self.assertRaises(RuntimeError, self.builder._getSpaceGroupFromNumber, cifData={})
self.assertRaises(RuntimeError, self.builder._getSpaceGroupFromNumber, cifData=invalid_old)
self.assertRaises(RuntimeError, self.builder._getSpaceGroupFromNumber, cifData=invalid_new)
def setUp(self):
self.builder = CrystalStructureBuilder()
class CrystalStructureBuilderTestSpaceGroup(unittest.TestCase):
def setUp(self):
self.builder = CrystalStructureBuilder()
def test_getSpaceGroupFromString_valid_no_exceptions(self):
valid_new = {u'_space_group_name_h-m_alt': u'P m -3 m'}
valid_old = {u'_symmetry_space_group_name_h-m': u'P m -3 m'}
assertRaisesNothing(self,
self.builder._getSpaceGroupFromString,
cifData=valid_old)
assertRaisesNothing(self,
self.builder._getSpaceGroupFromString,
cifData=valid_new)
assertRaisesNothing(self,
self.builder._getSpaceGroupFromString,
cifData=merge_dicts(valid_new, valid_old))
def test_getSpaceGroupFromString_valid_correct_value(self):
valid_new = {u'_space_group_name_h-m_alt': u'P m -3 m'}
valid_old = {u'_symmetry_space_group_name_h-m': u'P m -3 m'}
valid_old_different = {u'_symmetry_space_group_name_h-m': u'F d d d'}
invalid_old = {u'_symmetry_space_group_name_h-m': u'invalid'}
self.assertEqual(self.builder._getSpaceGroupFromString(valid_new),
'P m -3 m')
self.assertEqual(self.builder._getSpaceGroupFromString(valid_old),
'P m -3 m')
self.assertEqual(
self.builder._getSpaceGroupFromString(
merge_dicts(valid_new, valid_old)), 'P m -3 m')
self.assertEqual(
self.builder._getSpaceGroupFromString(
merge_dicts(valid_new, valid_old_different)), 'P m -3 m')
self.assertEqual(
self.builder._getSpaceGroupFromString(
merge_dicts(valid_new, invalid_old)), 'P m -3 m')
def test_getSpaceGroupFromString_invalid(self):
valid_old = {u'_symmetry_space_group_name_h-m': u'P m -3 m'}
invalid_new = {u'_space_group_name_h-m_alt': u'invalid'}
invalid_old = {u'_symmetry_space_group_name_h-m': u'invalid'}
self.assertRaises(RuntimeError,
self.builder._getSpaceGroupFromString,
cifData={})
self.assertRaises(ValueError,
self.builder._getSpaceGroupFromString,
cifData=invalid_new)
self.assertRaises(ValueError,
self.builder._getSpaceGroupFromString,
cifData=invalid_old)
self.assertRaises(ValueError,
self.builder._getSpaceGroupFromString,
cifData=merge_dicts(invalid_new, valid_old))
def test_getCleanSpaceGroupSymbol(self):
fn = self.builder._getCleanSpaceGroupSymbol
self.assertEqual(fn('P m -3 m :1'), 'P m -3 m')
self.assertEqual(fn('P m -3 m :H'), 'P m -3 m')
def test_getSpaceGroupFromNumber_invalid(self):
invalid_old = {u'_symmetry_int_tables_number': u'400'}
invalid_new = {u'_space_group_it_number': u'400'}
self.assertRaises(RuntimeError,
self.builder._getSpaceGroupFromNumber,
cifData={})
self.assertRaises(RuntimeError,
self.builder._getSpaceGroupFromNumber,
cifData=invalid_old)
self.assertRaises(RuntimeError,
self.builder._getSpaceGroupFromNumber,
cifData=invalid_new)
def setUp(self):
self.builder = CrystalStructureBuilder()
self._baseData = dict([(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
def setUp(self):
self.builder = CrystalStructureBuilder()
self._baseData = dict([
(u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
(u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
(u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
def setUp(self):
self.builder = CrystalStructureBuilder()