def test_double_quotes_and_underscore_data(self):
cif_str = """data_test
_symmetry_space_group_name_H-M "P -3 m 1"
_thing '_annoying_data'"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_symmetry_space_group_name_H-M"], "P -3 m 1")
self.assertEqual(cb["_thing"], "_annoying_data")
self.assertEqual(str(cb), cif_str.replace('"', "'"))
def test_double_quotes_and_underscore_data(self):
cif_str = """data_test
_symmetry_space_group_name_H-M "P -3 m 1"
_thing '_annoying_data'"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_symmetry_space_group_name_H-M"], "P -3 m 1")
self.assertEqual(cb["_thing"], "_annoying_data")
self.assertEqual(str(cb), cif_str.replace('"', "'"))
def test_double_quoted_data(self):
cif_str = """data_test
_thing ' '_annoying_data''
_other " "_more_annoying_data""
_more ' "even more" ' """
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " '_annoying_data'")
self.assertEqual(cb["_other"], ' "_more_annoying_data"')
self.assertEqual(cb["_more"], ' "even more" ')
def test_double_quoted_data(self):
cif_str = """data_test
_thing ' '_annoying_data''
_other " "_more_annoying_data""
_more ' "even more" ' """
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " '_annoying_data'")
self.assertEqual(cb["_other"], ' "_more_annoying_data"')
self.assertEqual(cb["_more"], ' "even more" ')
def test_nested_fake_multiline_quotes(self):
cif_str = """data_test
_thing
;
long quotes
;
still in the quote
;
actually going to end now
;"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " long quotes ; still in the quote"
" ; actually going to end now")
def test_nested_fake_multiline_quotes(self):
cif_str = """data_test
_thing
;
long quotes
;
still in the quote
;
actually going to end now
;"""
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_thing"], " long quotes ; still in the quote"
" ; actually going to end now")
def test_long_loop(self):
data = {'_stuff1': ['A' * 30] * 2,
'_stuff2': ['B' * 30] * 2,
'_stuff3': ['C' * 30] * 2}
loops = [['_stuff1', '_stuff2', '_stuff3']]
cif_str = """data_test
loop_
_stuff1
_stuff2
_stuff3
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"""
self.assertEqual(str(CifBlock(data, loops, 'test')), cif_str)
def test_to_string(self):
with open(os.path.join(test_dir, 'Graphite.cif')) as f:
s = f.read()
c = CifBlock.from_string(s)
cif_str_2 = str(CifBlock.from_string(str(c)))
cif_str = """data_28417-ICSD
_database_code_ICSD 28417
_audit_creation_date 1980-01-01
_audit_update_record 2003-04-01
_chemical_name_systematic Carbon
_chemical_formula_structural C
_chemical_formula_sum C1
_chemical_name_mineral 'Graphite, nitrated'
_exptl_crystal_density_diffrn 1.36
_publ_section_title
'Order-disorder transformations in graphite nitrates'
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary
;
Proceedings of the Royal Society of London, Series A: Mathematical and
Physical Sciences (76,1906-)
;
1966 291 324 339 PRLAAZ
loop_
_publ_author_name
'Nixon, D.E.'
'Parry, G.S.'
'Ubbelohde, A.R.'
_cell_length_a 2.46
_cell_length_b 2.46
_cell_length_c 33.45
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 175.31
_cell_formula_units_Z 12
_symmetry_space_group_name_H-M 'R -3 m H'
_symmetry_Int_Tables_number 166
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x-y, -y, -z'
2 '-x, -x+y, -z'
3 'y, x, -z'
4 'x-y, x, -z'
5 'y, -x+y, -z'
6 '-x, -y, -z'
7 '-x+y, y, z'
8 'x, x-y, z'
9 '-y, -x, z'
10 '-x+y, -x, z'
11 '-y, x-y, z'
12 'x, y, z'
13 'x-y+2/3, -y+1/3, -z+1/3'
14 '-x+2/3, -x+y+1/3, -z+1/3'
15 'y+2/3, x+1/3, -z+1/3'
16 'x-y+2/3, x+1/3, -z+1/3'
17 'y+2/3, -x+y+1/3, -z+1/3'
18 '-x+2/3, -y+1/3, -z+1/3'
19 '-x+y+2/3, y+1/3, z+1/3'
20 'x+2/3, x-y+1/3, z+1/3'
21 '-y+2/3, -x+1/3, z+1/3'
22 '-x+y+2/3, -x+1/3, z+1/3'
23 '-y+2/3, x-y+1/3, z+1/3'
24 'x+2/3, y+1/3, z+1/3'
25 'x-y+1/3, -y+2/3, -z+2/3'
26 '-x+1/3, -x+y+2/3, -z+2/3'
27 'y+1/3, x+2/3, -z+2/3'
28 'x-y+1/3, x+2/3, -z+2/3'
29 'y+1/3, -x+y+2/3, -z+2/3'
30 '-x+1/3, -y+2/3, -z+2/3'
31 '-x+y+1/3, y+2/3, z+2/3'
32 'x+1/3, x-y+2/3, z+2/3'
33 '-y+1/3, -x+2/3, z+2/3'
34 '-x+y+1/3, -x+2/3, z+2/3'
35 '-y+1/3, x-y+2/3, z+2/3'
36 'x+1/3, y+2/3, z+2/3'
loop_
_atom_type_symbol
_atom_type_oxidation_number
C0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
C1 C0+ 6 c 0 0 0.05 0. 1. 0
C2 C0+ 6 c 0 0 0.283 0. 1. 0"""
for l1, l2, l3 in zip(str(c).split("\n"), cif_str.split("\n"),
cif_str_2.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
self.assertEqual(l2.strip(), l3.strip())
def test_double_quotes(self):
cif_str = 'data_test\n_symmetry_space_group_name_H-M "P -3 m 1"'
cb = CifBlock.from_string(cif_str)
self.assertEqual(cb["_symmetry_space_group_name_H-M"], "P -3 m 1")
self.assertEqual(str(cb), cif_str.replace('"', "'") )
def test_to_string(self):
with open(os.path.join(test_dir, 'Graphite.cif')) as f:
s = f.read()
c = CifBlock.from_string(s)
cif_str_2 = str(CifBlock.from_string(str(c)))
cif_str = """data_28417-ICSD
_database_code_ICSD 28417
_audit_creation_date 1980-01-01
_audit_update_record 2003-04-01
_chemical_name_systematic Carbon
_chemical_formula_structural C
_chemical_formula_sum C1
_chemical_name_mineral 'Graphite, nitrated'
_exptl_crystal_density_diffrn 1.36
_publ_section_title
'Order-disorder transformations in graphite nitrates'
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary
;
Proceedings of the Royal Society of London, Series A: Mathematical and
Physical Sciences (76,1906-)
;
1966 291 324 339 PRLAAZ
loop_
_publ_author_name
'Nixon, D.E.'
'Parry, G.S.'
'Ubbelohde, A.R.'
_cell_length_a 2.46
_cell_length_b 2.46
_cell_length_c 33.45
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 120.
_cell_volume 175.31
_cell_formula_units_Z 12
_symmetry_space_group_name_H-M 'R -3 m H'
_symmetry_Int_Tables_number 166
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x-y, -y, -z'
2 '-x, -x+y, -z'
3 'y, x, -z'
4 'x-y, x, -z'
5 'y, -x+y, -z'
6 '-x, -y, -z'
7 '-x+y, y, z'
8 'x, x-y, z'
9 '-y, -x, z'
10 '-x+y, -x, z'
11 '-y, x-y, z'
12 'x, y, z'
13 'x-y+2/3, -y+1/3, -z+1/3'
14 '-x+2/3, -x+y+1/3, -z+1/3'
15 'y+2/3, x+1/3, -z+1/3'
16 'x-y+2/3, x+1/3, -z+1/3'
17 'y+2/3, -x+y+1/3, -z+1/3'
18 '-x+2/3, -y+1/3, -z+1/3'
19 '-x+y+2/3, y+1/3, z+1/3'
20 'x+2/3, x-y+1/3, z+1/3'
21 '-y+2/3, -x+1/3, z+1/3'
22 '-x+y+2/3, -x+1/3, z+1/3'
23 '-y+2/3, x-y+1/3, z+1/3'
24 'x+2/3, y+1/3, z+1/3'
25 'x-y+1/3, -y+2/3, -z+2/3'
26 '-x+1/3, -x+y+2/3, -z+2/3'
27 'y+1/3, x+2/3, -z+2/3'
28 'x-y+1/3, x+2/3, -z+2/3'
29 'y+1/3, -x+y+2/3, -z+2/3'
30 '-x+1/3, -y+2/3, -z+2/3'
31 '-x+y+1/3, y+2/3, z+2/3'
32 'x+1/3, x-y+2/3, z+2/3'
33 '-y+1/3, -x+2/3, z+2/3'
34 '-x+y+1/3, -x+2/3, z+2/3'
35 '-y+1/3, x-y+2/3, z+2/3'
36 'x+1/3, y+2/3, z+2/3'
loop_
_atom_type_symbol
_atom_type_oxidation_number
C0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
C1 C0+ 6 c 0 0 0.05 0. 1. 0
C2 C0+ 6 c 0 0 0.283 0. 1. 0"""
for l1, l2, l3 in zip(str(c).split("\n"), cif_str.split("\n"),
cif_str_2.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
self.assertEqual(l2.strip(), l3.strip())
