def test_can_load_crystal_data_from_multi_data_block_cif(self):
p = CIFParser("tests/functional/static/valid_cifs/multi_data_block.cif")
p.parse()
# basic checks that correct number of data items were caught
assert len(p.data_blocks) == 20
assert p.data_blocks[0].header == "data_CSD_CIF_ACAGUG"
assert p.data_blocks[11].header == "data_CSD_CIF_AHUKOD"
data_items_1 = p.data_blocks[0].data_items
data_items_2 = p.data_blocks[11].data_items
assert len(data_items_1) == 39
assert len(data_items_2) == 41
# check loops operated correctly
assert len(data_items_1["atom_site_label"]) == 119
assert len(data_items_2["atom_site_label"]) == 69
assert data_items_1["atom_type_radius_bond"] == \
["0.68", "0.23", "1.35", "0.68", "1.02"]
assert data_items_2["atom_type_radius_bond"] == \
["0.68", "0.23", "1.21", "0.64", "1.40", "1.02"]
# check semicolon text fields assigned correctly
assert data_items_1["refine_special_details"] == \
"One of the water molecules is disordered over two sites."
assert data_items_2["chemical_name_systematic"] == \
("tris(bis(Ethylenedithio)tetrathiafulvalene) \n"
"2,5-difluoro-1,4-bis(iodoethynyl)benzene bromide")
# check a few inline data items
assert data_items_1["journal_year"] == "2001"
assert data_items_1["exptl_crystal_colour"] == "dark brown"
assert data_items_2["journal_name_full"] == "J.Mater.Chem. "
assert data_items_2["cell_angle_gamma"] == "76.35(2)"
def test_parse_method_calls_in_correct_order(self):
p = mock.Mock(spec=CIFParser)
data_block = mock.Mock(spec=DataBlock)
p.data_blocks = [data_block]
CIFParser.parse(p)
expected_calls = [
mock.call._strip_comments_and_blank_lines(),
mock.call._extract_data_blocks(),
mock.call.extract_data_items(SEMICOLON_DATA_ITEM),
mock.call.extract_data_items(INLINE_DATA_ITEM),
mock.call.extract_loop_data_items()
]
assert p.method_calls + data_block.method_calls == expected_calls
def test_can_load_crystal_data_from_vesta_cif(self):
p = CIFParser("tests/functional/static/valid_cifs/calcite_vesta.cif")
p.parse()
# basic checks that correct number of data items were caught
assert p.data_blocks[0].header == 'data_VESTA_phase_1'
assert len(p.data_blocks) == 1
data_items = p.data_blocks[0].data_items
assert len(data_items) == 25
# check the loops operated correctly
pos = data_items["symmetry_equiv_pos_as_xyz"]
assert len(pos) == 36
assert data_items["atom_site_occupancy"] == ["1.0", "1.0", "1.0"]
assert data_items["atom_site_aniso_label"] == ["Ca1", "C1", "O1"]
# check a few inline data items
assert data_items["cell_length_a"] == "4.9900(2)"
assert data_items["symmetry_space_group_name_H-M"] == "R -3 c"
assert data_items["symmetry_Int_Tables_number"] == "167"
def test_can_load_crystal_data_from_icsd_cif(self):
p = CIFParser("tests/functional/static/valid_cifs/calcite_icsd.cif")
p.parse()
# basic checks that correct number of data items were caught
assert p.data_blocks[0].header == "data_18166-ICSD"
assert len(p.data_blocks) == 1
data_items = p.data_blocks[0].data_items
assert len(data_items) == 51
# check the loops operated correctly
ids = data_items["symmetry_equiv_pos_site_id"]
assert ids == [str(i) for i in range(1, 37)]
assert data_items["atom_site_label"] == ["Ca1", "C1", "O1"]
assert data_items["atom_site_aniso_U_22"] == ["0.01775(90)"]
assert data_items["publ_author_name"] == \
["Chessin, H.", "Hamilton, W.C.", "Post, B."]
# check a few inline data items
assert data_items["cell_length_a"] == "4.9900(2)"
assert data_items["chemical_name_mineral"] == "Calcite"
assert data_items["cell_formula_units_Z"] == "6"
