def setUp(self) -> None:
if not find_shelxl_exe():
self.skipTest('SHELXL not found')
os.chdir(Path(__file__).parent.parent)
res = Path('tests/resources/complete_run/p21c.res')
shutil.copy(res, '.')
self.shx = Shelxfile()
self.shx.read_file('./p21c.res')
def test_read_file_to_list(self):
shx = Shelxfile()
shx.read_file('tests/resources/p21c.res')
self.assertEqual(['TITL p21c in P2(1)/c',
' created by SHELXL-2018/3 at 16:18:25 on 03-May-2018',
'CELL 0.71073 10.5086 20.9035 20.5072 90 94.13 90',
'ZERR 4 0.0003 0.0005 0.0005 0 0.001 0',
'LATT 1'],
[str(x) for x in shx._reslist[:5]])
class TestShelxfileElementToSfac(TestCase):
"""
SFAC C H O F Al Ga
"""
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_elem2sfac_oxygen(self):
self.assertEqual(3, self.shx.elem2sfac('O'))
def test_elem2sfac_carbon(self):
self.assertEqual(1, self.shx.elem2sfac('c'))
def test_elem2sfac_Argon(self):
self.assertEqual(None, self.shx.elem2sfac('Ar'))
def test_SDM_rustversion(self):
from shelxfile.shelx.sdm_rust import SDMR
shx = Shelxfile()
shx.read_file('tests/resources/p-31c.res')
sdm = SDMR(shx)
needsymm = sdm.calc_sdm()
packed_atoms = sdm.packer(sdm, needsymm)
for at in packed_atoms:
if at.qpeak:
print(at)
continue
self.head += wrap_line(str(at)) + '\n'
self.head += self.tail
p = Path('tests/resources/test-sdm1.res')
print('Zeit für sdm:', round(sdm.sdmtime, 3), 's')
self.assertEqual(p.read_text(), self.head)
class TestShelxfileGoodModel(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/model_finished/p21c.res')
def test_atom_representation(self):
a = self.shx._reslist[39]
self.assertEqual(
'C1 1 -0.187504 0.282782 0.527531 11.00000 0.01807 0.02353 0.01797 0.00008 -0.00179 0.00036',
str(a))
def test_atom_object(self):
a = self.shx._reslist[39]
self.assertEqual(
'C1 1 -0.187504 0.282782 0.527531 11.00000 0.01807 0.02353 0.01797 0.00008 -0.00179 0.00036',
a)
def test_SDM(self):
shx = Shelxfile()
shx.read_file('tests/resources/p-31c.res')
sdm = SDM(shx)
needsymm = sdm.calc_sdm()
packed_atoms = sdm.packer(sdm, needsymm)
# print(needsymm)
# [[8, 5, 5, 5, 1], [16, 5, 5, 5, 1], [7, 4, 5, 5, 3]]
# print(len(shx.atoms))
# print(len(packed_atoms))
for at in packed_atoms:
if at.qpeak:
continue
# print(wrap_line(str(at)))
self.head += wrap_line(str(at)) + '\n'
self.head += self.tail
p = Path('tests/resources/test-sdm1.res')
print('Zeit für sdm:', round(sdm.sdmtime, 3), 's')
self.assertEqual(p.read_text(), self.head)
class TestRefine(TestCase):
def setUp(self) -> None:
if not find_shelxl_exe():
self.skipTest('SHELXL not found')
os.chdir(Path(__file__).parent.parent)
res = Path('tests/resources/complete_run/p21c.res')
shutil.copy(res, '.')
self.shx = Shelxfile()
self.shx.read_file('./p21c.res')
def tearDown(self) -> None:
os.chdir(Path(__file__).parent.parent)
clean_refine_files('p21c')
def test_get_xl_version_string_with_no_path(self):
self.assertEqual('', get_xl_version_string(''))
def test_get_xl_version_string_with_real_path(self):
shx = which('shelxl') if which('shelxl') else which('xl')
self.assertEqual('2019/2', get_xl_version_string(shx))
def test_check_cycle_numbers(self):
self.assertEqual('L.S. 10', str(self.shx.cycles))
def test_set_cycle_numbers_directly(self):
self.shx.cycles.number = 3
self.assertEqual('L.S. 3', str(self.shx.cycles))
def test_set_cycle_numbers_by_set_function(self):
self.shx.cycles.set_refine_cycles(4)
self.assertEqual('L.S. 4', str(self.shx.cycles))
self.assertEqual('L.S. 4',
self.shx._reslist[self.shx.cycles.index].__repr__())
def test_set_cycle_numbers_negative(self):
self.shx.cycles.set_refine_cycles(-1)
self.assertEqual('L.S. -1', str(self.shx.cycles))
def test_set_cycle_numbers_directly2(self):
self.shx.cycles.cycles = 3
self.assertEqual('L.S. 10', str(self.shx.cycles))
class TestShelxfile(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_sfac2elem_C(self):
self.assertEqual('C', self.shx.sfac2elem(1))
def test_sfac2elem_H(self):
self.assertEqual('H', self.shx.sfac2elem(2))
def test_sfac2elem_O(self):
self.assertEqual('O', self.shx.sfac2elem(3))
def test_sfac2elem_Al(self):
self.assertEqual('Al', self.shx.sfac2elem(5))
def test_sfac2elem_not_existent(self):
self.assertEqual('', self.shx.sfac2elem(8))
def test_sfac2elem_zero(self):
self.assertEqual('', self.shx.sfac2elem(0))
def test_sum_formula(self):
self.assertEqual('C0.25 H0.5 O0.75 F1 AL1.25 GA1.5', self.shx.sum_formula)
def test_read_file_to_list(self):
shx = Shelxfile()
shx.read_file('tests/resources/p21c.res')
self.assertEqual(['TITL p21c in P2(1)/c',
' created by SHELXL-2018/3 at 16:18:25 on 03-May-2018',
'CELL 0.71073 10.5086 20.9035 20.5072 90 94.13 90',
'ZERR 4 0.0003 0.0005 0.0005 0 0.001 0',
'LATT 1'],
[str(x) for x in shx._reslist[:5]])
def test_read_file(self):
shx = Shelxfile()
with self.assertRaises(FileNotFoundError):
shx.read_file('tests/resources/foobar.res')
def test_is_an_atom_short(self):
is_atom = Shelxfile.is_atom('O1 3 0.120080 0.336659 0.494426')
self.assertEqual(True, is_atom)
def test_is_no_atom_because_its_a_command2(self):
is_atom = Shelxfile.is_atom("AFIX")
self.assertEqual(False, is_atom)
def test_is_no_atom_because_coordinate_is_missing(self):
is_an_atom = Shelxfile.is_atom(atomline='O1 4 0.120080 0.494426 11.00000 0.01445 ...')
self.assertEqual(False, is_an_atom)
self.append([])
for _ in range(self.height):
self[i].append(" ")
def set(self, index, val):
x = index[0]
y = index[1]
self[x][y] = val
def show(self):
for row in self:
print("".join(row))
if __name__ == "__main__":
shx = Shelxfile()
shx.read_file('./tests/resources/p21c.res')
try:
width = sys.argv[2]
height = sys.argv[3]
dims = (int(width), int(height) - 1)
except IndexError:
dims = None
angle = 0
angle_incr = (2 * pi) * (1 / 40) # 40th of a circle
while True:
Molecule(shx.atoms).draw(plane=[Coordinate(0, 1, 0), Coordinate(sin(angle), 0, cos(angle))], dimensions=dims)
angle = angle + angle_incr
time.sleep(0.5)
print("\33[H")
def test_parse_hklf_after_uncloded_resi(self):
shx = Shelxfile()
shx.read_file(r'tests/resources/unclosed_resi.res')
self.assertEqual('HKLF 4 1 1 0 0 0 1 0 0 0 1 1 0',
shx.hklf.__repr__()) # add assertion here
class TestRefineFinishedmodel(TestCase):
def setUp(self) -> None:
if not find_shelxl_exe():
self.skipTest('SHELXL not found')
os.chdir(Path(__file__).parent.parent)
res = Path('tests/resources/model_finished/p21c.res')
hkl = Path('tests/resources/model_finished/p21c.hkl')
shutil.copy(res, '.')
shutil.copy(hkl, '.')
self.shx = Shelxfile()
self.shx.read_file('./p21c.res')
def tearDown(self) -> None:
os.chdir(Path(__file__).parent.parent)
clean_refine_files('p21c')
def test_refine_with_cycle_number_set_to_4_in_LScycles(self):
self.assertTrue('L.S. 10' in Path('p21c.res').read_text())
self.shx.cycles.set_refine_cycles(4)
self.shx.refine(backup_before=False)
txt = Path('p21c.res').read_text()
self.assertTrue('L.S. 4' in txt)
def test_refine_with_cycle_number_set_to_4_in_refine(self):
self.assertTrue('L.S. 10' in Path('p21c.res').read_text())
self.shx.refine(4, backup_before=False)
txt = Path('p21c.res').read_text()
self.assertTrue('L.S. 4' in txt)
def test_refine_with_ANIS_inserted_and_cycle_number_set_to_4_in_refine(
self):
self.assertFalse('ANIS' in Path('p21c.res').read_text())
self.shx.insert_anis()
self.shx.refine(3, backup_before=False)
self.assertTrue('ANIS' in Path('p21c.ins').read_text())
self.assertFalse('ANIS' in Path('p21c.res').read_text())
def test_refine_with_cycle_number_set_to_0_in_refine(self):
self.assertTrue('L.S. 10' in Path('p21c.res').read_text())
self.refine = self.shx.refine(0, backup_before=False)
txt = Path('p21c.res').read_text()
self.assertTrue('L.S. 0' in txt)
def test_vector_length(self):
shx = Shelxfile()
shx.read_string(self.head + self.tail)
sdm = SDM(shx)
self.assertEqual(7.343581289102655, sdm.vector_length(-0.3665069999999999, 0.293439, -0.06597900000000001))
def test_is_atom_long_line_true(self):
"""
"""
is_an_atom = Shelxfile.is_atom(atomline='O1 3 0.120080 0.336659 0.494426 11.00000 0.01445 ...')
self.assertEqual(True, is_an_atom)
def test_hkl_checksum(self) -> bool:
"""
A method to check whether the checksums in the cif file fit to the content.
"""
cif_hkl_ckecksum = 0
hkl_checksum_calcd = self.hkl_checksum_calcd
if hkl_checksum_calcd > 0:
cif_hkl_ckecksum = self['_shelx_hkl_checksum'] or -1
try:
cif_hkl_ckecksum = int(cif_hkl_ckecksum)
except ValueError:
cif_hkl_ckecksum = -1
if cif_hkl_ckecksum > 0 and cif_hkl_ckecksum != hkl_checksum_calcd:
return False
else:
return True
if __name__ == '__main__':
c = CifContainer('test-data/p21c.cif')
# print(c.hkl_file)
# print(c.hkl_as_cif)
# print(c.test_hkl_checksum())
s = Shelxfile()
# print(c.res_file_data)
s.read_string(c.res_file_data)
print(s.hklf.n)
# print(CifContainer('tests/examples/1979688.cif').hkl_as_cif[-250:])
def test_read_file(self):
shx = Shelxfile()
with self.assertRaises(FileNotFoundError):
shx.read_file('tests/resources/foobar.res')
def hklf_number_from_shelxl_file(self) -> int:
shx = Shelxfile()
shx.read_string(self.res_file_data)
return shx.hklf.n if shx.hklf.n != 0 else 4
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/model_finished/p21c.res')
def test_is_no_atoms_because_type_is_missing(self):
is_an_atom = Shelxfile.is_atom(atomline='O1 0.120080 0.336659 0.494426 11.00000 0.01445 ...')
self.assertEqual(False, is_an_atom)