def tst_twin_completion():
uc = uctbx.unit_cell("40,40,70,90,90,90")
xs = crystal.symmetry(unit_cell=uc, space_group="P1")
miller_set = miller.build_set(crystal_symmetry=xs,
anomalous_flag=False,
d_min=3.0).map_to_asu()
select = flex.bool(miller_set.indices().size(), True)
select[300] = False
miller_set_mod = miller_set.select(select)
# make sure we threw away a reflection
assert not miller_set_mod.indices().all_eq(miller_set.indices())
checker = xray.twin_completion(miller_set_mod.indices(), xs.space_group(),
False, [0, 1, 0, 1, 0, 0, 0, 0, -1])
new_hkl = checker.twin_complete()
miller_set_mod = miller_set_mod.customized_copy(indices=new_hkl)
miller_set_mod = miller_set_mod.map_to_asu()
a, b = miller_set_mod.common_sets(miller_set)
assert a.indices().size() == miller_set_mod.indices().size()
assert a.indices().size() == miller_set.indices().size()
assert miller_set_mod.is_unique_set_under_symmetry()
checker = xray.twin_completion(miller_set.indices(), xs.space_group(),
False, [0, 1, 0, 1, 0, 0, 0, 0, -1])
basic_flags = miller_set.generate_r_free_flags_basic()
lattice_flags = miller_set.generate_r_free_flags_on_lattice_symmetry()
assert not checker.check_free_flags(
basic_flags.data()) # this should give False
assert checker.check_free_flags(
lattice_flags.data()) # this should give True
selection_array = checker.get_free_model_selection(lattice_flags.indices(),
lattice_flags.data())
assert selection_array.all_eq(lattice_flags.data())
def tst_twin_completion():
uc = uctbx.unit_cell( "40,40,70,90,90,90" )
xs = crystal.symmetry( unit_cell=uc, space_group="P1" )
miller_set = miller.build_set( crystal_symmetry=xs,
anomalous_flag=False,
d_min=3.0 ).map_to_asu()
select = flex.bool( miller_set.indices().size(), True )
select[300]=False
miller_set_mod = miller_set.select( select )
# make sure we threw away a reflection
assert not miller_set_mod.indices().all_eq( miller_set.indices() )
checker = xray.twin_completion(
miller_set_mod.indices(),
xs.space_group(),
False,
[0,1,0,1,0,0,0,0,-1]
)
new_hkl = checker.twin_complete()
miller_set_mod = miller_set_mod.customized_copy(
indices=new_hkl)
miller_set_mod = miller_set_mod.map_to_asu()
a,b = miller_set_mod.common_sets( miller_set )
assert a.indices().size() == miller_set_mod.indices().size()
assert a.indices().size() == miller_set.indices().size()
assert miller_set_mod.is_unique_set_under_symmetry()
checker = xray.twin_completion(
miller_set.indices(),
xs.space_group(),
False,
[0,1,0,1,0,0,0,0,-1]
)
basic_flags = miller_set.generate_r_free_flags_basic()
lattice_flags = miller_set.generate_r_free_flags_on_lattice_symmetry()
assert not checker.check_free_flags( basic_flags.data() ) # this should give False
assert checker.check_free_flags( lattice_flags.data() ) # this should give True
selection_array = checker.get_free_model_selection( lattice_flags.indices(), lattice_flags.data() )
assert selection_array.all_eq( lattice_flags.data() )
def __init__(self):
self.structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(7.6338, 7.6338, 9.8699, 90, 90, 120),
space_group_symbol='hall: P 3 -2c'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='LI',
site=(0.032717, 0.241544, 0.254924),
u=(0.000544, 0.000667, 0.000160,
0.000326, 0.000072, -0.000030)),
xray.scatterer( #1
label='NA',
site=(0.033809, 0.553123, 0.484646),
u=(0.000554, 0.000731, 0.000174,
0.000212, 0.000032, -0.000015)),
xray.scatterer( #2
label='S1',
site=(0.000000, 0.000000, -0.005908),
u=(0.000370, 0.000370, 0.000081,
0.000185, 0.000000, 0.000000)),
xray.scatterer( #3
label='S2',
site=(0.333333, 0.666667, 0.211587),
u=(0.000244, 0.000244, 0.000148,
0.000122, 0.000000, 0.000000)),
xray.scatterer( #4
label='S3',
site=(0.666667, 0.333333, 0.250044),
u=(0.000349, 0.000349, 0.000094,
0.000174, 0.000000, 0.000000)),
xray.scatterer( #5
label='O1',
site=(0.000000, -0.000000, 0.154207),
u=(0.000360, 0.000360, 0.000149,
0.000180, 0.000000, 0.000000),
occupancy=0.999000),
xray.scatterer( #6
label='O2',
site=(0.333333, 0.666667, 0.340665),
u=(0.000613, 0.000613, 0.000128,
0.000306, 0.000000, 0.000000)),
xray.scatterer( #7
label='O3',
site=(0.666667, 0.333333, 0.112766),
u=(0.000724, 0.000724, 0.000118,
0.000362, 0.000000, 0.000000)),
xray.scatterer( #8
label='O4',
site=(0.225316, 0.110088, -0.035765),
u=(0.000477, 0.000529, 0.000213,
0.000230, 0.000067, -0.000013)),
xray.scatterer( #9
label='O5',
site=(0.221269, 0.442916, 0.153185),
u=(0.000767, 0.000286, 0.000278,
0.000210, 0.000016, -0.000082)),
xray.scatterer( #10
label='O6',
site=(0.487243, 0.169031, 0.321690),
u=(0.000566, 0.000582, 0.000354,
0.000007, 0.000022, 0.000146))
)))
self.twin_laws = (sgtbx.rot_mx((0,1,0,1,0,0,0,0,-1)),)
self.twin_fractions = flex.double((flex.random_double(),))
self.scale_factor = 0.05 + 10 * flex.random_double()
self.crystal_symmetry = self.structure.crystal_symmetry()
mi = self.crystal_symmetry.build_miller_set(anomalous_flag=False,
d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
self.structure, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(
data=fo_sq.data()*self.scale_factor,
sigmas=flex.double(fo_sq.size(), 1))
twin_completion = xray.twin_completion(
mi.indices(),
mi.space_group(),
mi.anomalous_flag(),
self.twin_laws[0].as_double())
sigmas = flex.double(fo_sq.size(), 1)
from cctbx import miller
twin_complete_set = miller.set(
crystal_symmetry=self.crystal_symmetry,
indices=twin_completion.twin_complete(),
anomalous_flag=mi.anomalous_flag()).map_to_asu()
detwinner = xray.hemihedral_detwinner(
hkl_obs=fo_sq.indices(),
hkl_calc=twin_complete_set.indices(),
space_group=mi.space_group(),
anomalous_flag=mi.anomalous_flag(),
twin_law=self.twin_laws[0].as_double())
twinned_i, twinned_s = detwinner.twin_with_twin_fraction(
fo_sq.data(),
sigmas,
twin_fraction=self.twin_fractions[0])
self.fo_sq = fo_sq.customized_copy(data=twinned_i, sigmas=twinned_s)
