class TestCELL(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_volume(self):
self.assertEqual(4493.0474, round(self.shx.cell.volume, 4))
class TestRESI(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_get_resi_1_tol(self):
r = RESI(None, 'RESI 1 TOL'.split())
self.assertEqual(
('TOL', 1, None, None),
(r.residue_class, r.residue_number, r.chain_id, r.alias))
def test_tol_1(self):
r = RESI(None, 'RESI TOL 1'.split())
self.assertEqual(
('TOL', 1, None, None),
(r.residue_class, r.residue_number, r.chain_id, r.alias))
def test_resi_chainid_tol(self):
r = RESI(None, 'RESI A:100 TOL'.split())
self.assertEqual(
('TOL', 100, 'A', None),
(r.residue_class, r.residue_number, r.chain_id, r.alias))
def test_resi__negative_chain_tol(self):
r = RESI(None, 'RESI -10 TOL'.split())
self.assertEqual(
('TOL', -10, None, None),
(r.residue_class, r.residue_number, r.chain_id, r.alias))
def test_resi_b_chain_tol(self):
r = RESI(None, 'RESI b:-10 TOL'.split())
self.assertEqual(
('TOL', -10, 'b', None),
(r.residue_class, r.residue_number, r.chain_id, r.alias))
class TestLSCycles(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
self.ref = ShelxlRefine(self.shx, Path('./resources/p21c.res'))
def test_set_refine_cycles(self):
self.shx.cycles.set_refine_cycles(44)
self.assertEqual('L.S. 44',
self.shx._reslist[self.shx.cycles.index].__repr__())
class TestWGHT(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_wght(self):
self.assertEqual('WGHT 0.049 0.0', self.shx.wght.__repr__())
def test_wght_differene(self):
self.assertEqual([0.0, 0.0], self.shx.wght.difference())
class TestSADI(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/I-43d.res')
def test_sadi_normal(self):
a = SADI(self.shx, 'SADI C1 C2 C2 C3 C3 C4'.split())
self.assertEqual([['C1', 'C2'], ['C2', 'C3'], ['C3', 'C4']], a.atoms)
self.assertEqual('', a.residue_class)
self.assertEqual([0], a.residue_number)
def test_sadi_normal_with_resinum(self):
a = SADI(self.shx, 'SADI_1 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual([['C1', 'C2'], ['C2', 'C3'], ['C3', 'C4']], a.atoms)
self.assertEqual('', a.residue_class)
self.assertEqual([1], a.residue_number)
def test_sadi_normal_with_resinum_on_atoms(self):
a = SADI(self.shx, 'SADI C1_1 C2_1 C2_2 C3_2 C3_2 C4_2'.split())
self.assertEqual(
[['C1_1', 'C2_1'], ['C2_2', 'C3_2'], ['C3_2', 'C4_2']], a.atoms)
self.assertEqual('', a.residue_class)
self.assertEqual([0], a.residue_number)
def test_sadi_normal_with_name(self):
a = SADI(self.shx, 'SADI_CCF3 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual([['C1', 'C2'], ['C2', 'C3'], ['C3', 'C4']], a.atoms)
def test_sadi_with_name_2(self):
a = SADI(self.shx, 'SADI_CCF3 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual('', a.residue_class)
self.assertEqual([0], a.residue_number)
def test_sadi_with_name_3(self):
a = SADI(self.shx, 'SADI_CCF3 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual(0.02, a.s)
def test_sadi_with_name_4(self):
a = SADI(self.shx, 'SADI_CCF3 0.001 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual(0.001, a.s)
class TestSymmetryElement(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_to_shelxl(self):
self.assertEqual(
'[+X, +Y, +Z, -X, -Y, -Z, -X, 0.5+Y, 0.5-Z, +X, -0.5-Y, -0.5+Z]',
self.shx.symmcards._symmcards.__repr__())
def test_repr(self):
self.assertEqual(SymmetryElement(['-X', '-Y', '-Z']),
self.shx.symmcards[1])
def test_string(self):
self.assertEqual(
"|-1 0 0| | 0.0|\n"
"| 0 1 0| + | 0.5|\n"
"| 0 0 -1| | 0.5|\n", self.shx.symmcards[2].__str__())
def test_equals_false(self):
self.assertEqual(False, self.shx.symmcards[0] == self.shx.symmcards[1])
def test_equals_True(self):
self.assertEqual(True, self.shx.symmcards[1] == self.shx.symmcards[1])
def test_s12_equals(self):
s1 = SymmetryElement(['0.5', '0.5', '0.5'])
s2 = SymmetryElement(['0.5', '0.5', '0.5'])
self.assertEqual(True, s1 == s2)
def test_s12_equals2(self):
s1 = SymmetryElement(['1.5', '1.5', '1.5'])
s2 = SymmetryElement(['0.5', '0.5', '0.5'])
self.assertEqual(True, s1 == s2)
def test_s34_not_equals(self):
s3 = SymmetryElement(['1', '0.5', '0.5'])
s4 = SymmetryElement(['0.5', '0.5', '0.5'])
self.assertEqual(False, s3 == s4)
class TestSFACTable(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_sfac_table(self):
self.assertEqual('SFAC C H O F Al Ga', str(self.shx.sfac_table))
def test_unit_table(self):
self.assertEqual('UNIT 1 2 3 4 5 6', str(self.shx.unit))
def test_sfac_add_element(self):
self.shx.sfac_table.add_element('Au')
self.assertEqual('SFAC C H O F Al Ga Au',
str(self.shx.sfac_table))
def test_unit_add_element(self):
self.shx.sfac_table.add_element('Au')
self.assertEqual('UNIT 1 2 3 4 5 6 1', self.shx.unit.__repr__())
def test_unit_add_element_string_repr(self):
self.shx.sfac_table.add_element('Au')
self.assertEqual('UNIT 1 2 3 4 5 6 1', str(self.shx.unit))
class TestACTA(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
self.ref = ShelxlRefine(self.shx, Path('./tests/resources/p21c.res'))
def test_acta(self):
self.assertEqual('ACTA 45', self.shx._reslist[12].__repr__())
self.assertEqual('ACTA 45', self.shx.acta.__repr__())
def test_remove_acta(self):
self.ref.remove_acta_card(self.shx.acta)
self.assertEqual('SIZE 0.12 0.23 0.33',
self.shx._reslist[12].__repr__())
def test_restore_acta(self):
self.ref.remove_acta_card(self.shx.acta)
self.ref.restore_acta_card()
self.assertEqual(8, self.shx.index_of(self.shx.acta))
self.assertEqual([
'UNIT 1 2 3 4 5 6', 'ACTA 45',
'LIST 4 ! automatically inserted. Change 6 to 4 for CHECKCIF!!'
], [str(x) for x in self.shx._reslist[7:10]])
class TestwithDEFS(TestCase):
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def test_sadi_with_s(self):
a = SADI(self.shx, 'SADI_CCF3 0.001 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual(0.001, a.s)
def test_sadi_without_s(self):
a = SADI(self.shx, 'SADI C1 C2 C2 C3 C3 C4'.split())
self.assertEqual(0.0234, a.s)
def test_DFIX_without_s(self):
a = DFIX(self.shx, 'DFIX 1.45 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual(1.45, a.d)
self.assertEqual(0.0234, a.s)
self.assertEqual(0.0234, self.shx.defs.sd)
def test_DFIX_with_s(self):
a = DFIX(self.shx, 'DFIX 1.45 0.022 C1 C2 C2 C3 C3 C4'.split())
self.assertEqual(1.45, a.d)
self.assertEqual(0.022, a.s)
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
def setUp(self) -> None:
self.shx = Shelxfile()
self.shx.read_file('tests/resources/p21c.res')
self.ref = ShelxlRefine(self.shx, Path('./resources/p21c.res'))
def test_fmap_number(self):
shx = Shelxfile()
shx.read_file('tests/resources/p21c.res')
self.assertEqual(2.0, shx.fmap.code)
def test_abin(self):
a = ABIN(Shelxfile(), 'ABIN 1.234 4'.split())
self.assertEqual(1.234, a.n1)
self.assertEqual(4, a.n2)
def test_anis_atoms(self):
a = ANIS(Shelxfile(), 'ANIS C12 C23 Al3a'.split())
self.assertEqual(['C12', 'C23', 'Al3a'], a.atoms)
self.assertEqual(False, hasattr(a, 'n'))
def test_anis_n(self):
a = ANIS(Shelxfile(), 'ANIS 12'.split())
self.assertEqual([], a.atoms)
self.assertEqual(12, a.n)
astar = (b * c * sin(radians(alpha))) / V
bstar = (c * a * sin(radians(beta))) / V
cstar = (a * b * sin(radians(gamma))) / V
# matrix with the reciprocal lattice vectors:
N = Matrix([[astar, 0, 0],
[0, bstar, 0],
[0, 0, cstar]])
# Finally transform Uij values from fractional to cartesian axis system:
Ucart = A * N * Uij * N.T * A.T
return Ucart
if __name__ == "__main__":
from shelxfile.shelx.shelx import Shelxfile
shx = Shelxfile()
shx.read_file('shelxfile/tests/resources/p-31c.res')
t1 = time.perf_counter()
sdm = SDMR(shx)
needsymm = sdm.calc_sdm()
print('Zeit für sdm:', round(time.perf_counter() - t1, 3), 's')
print(needsymm)
packed_atoms = sdm.packer(sdm, needsymm)
print(len(shx.atoms))
print(len(packed_atoms))
assert str(packed_atoms[90]) == 'H2>>1_b 2 0.557744 0.080938 0.300634 21.00000 -1.30000'
assert str(packed_atoms[
129]) == 'C15>>2_a 1 1.145639 0.497216 0.299794 11.00000 0.01803 0.01661 0.03458 0.00038 -0.00408 0.01187'
# [[1, 5, 5, 5, 4], [1, 5, 5, 5, 5], [2, 6, 5, 5, 5], [3, 6, 6, 5, 5], [1, 5, 5, 5, 3], [2, 6, 6, 5, 3],
# 88
# 208