def exercise_systematic(verbose):
from cctbx import miller
from cctbx import crystal
from cctbx.array_family import flex
cs = crystal.symmetry(
unit_cell=(13,15,14,90,90,100),
space_group_symbol="P112")
ms = miller.set(
crystal_symmetry=cs,
indices=flex.miller_index([
(0,0,1),(0,0,-1),
(0,1,1),
(1,0,0),
(-1,-1,-1)]),
anomalous_flag=True).map_to_asu()
cf = ms.centric_flags().data()
assert cf.count(True) == 1
mt = flex.mersenne_twister(seed=0)
ma = ms.array(
data=mt.random_double(size=5)+0.1,
sigmas=mt.random_double(size=5)+0.1)
def recycle(expected_column_data):
mtz_obj = ma.as_mtz_dataset(column_root_label="X").mtz_object()
sio = StringIO()
mtz_obj.show_column_data_human_readable(out=sio)
from libtbx.test_utils import show_diff
if (verbose): sys.stdout.write(sio.getvalue())
assert not show_diff(sio.getvalue(), expected_column_data)
ma_2 = only_element(mtz_obj.as_miller_arrays())
assert_equal_data_and_sigmas(ma, ma_2)
recycle("""\
Column data:
-------------------------------------------------------------------------------
X(+) SIGX(+) X(-) SIGX(-)
0 0 1 0.517022 0.192339 0.820324 0.28626
0 1 1 0.100114 0.445561 None None
1 0 0 0.402333 0.496767 None None
1 1 1 None None 0.246756 0.638817
-------------------------------------------------------------------------------
""")
from cctbx.xray import observation_types
ma.set_observation_type(observation_types.reconstructed_amplitude())
recycle("""\
Column data:
-------------------------------------------------------------------------------
X SIGX DANOX SIGDANOX
ISYMX
0 0 1 0.668673 0.172438 -0.303302 0.344875
0
0 1 1 0.100114 0.445561 None None
1
1 0 0 0.402333 0.496767 None None
0
1 1 1 0.246756 0.638817 None None
2
-------------------------------------------------------------------------------
""")
def recycle_one_dano(missing, verbose):
assert missing in [None, "+", "-"]
from cctbx import crystal
cs = crystal.symmetry(
unit_cell=(13,17,19,85,95,105),
space_group_symbol="P1")
from cctbx.array_family import flex
mi = flex.miller_index([(1,2,3), (-1,-2,-3)])
fpm = flex.double([2.5, 5.5])
spm = flex.double([0.1, 0.3])
from cctbx import miller
ms = miller.set(crystal_symmetry=cs, indices=mi, anomalous_flag=True)
ma = ms.array(data=fpm, sigmas=spm)
mtz_dataset = ma.as_mtz_dataset(column_root_label="X")
if (missing is not None):
for col in mtz_dataset.columns():
if (col.label() in ["X(%s)" % missing, "SIGX(%s)" % missing]):
col.set_values(
values=flex.float([0]),
selection_valid=flex.bool([False]))
if (missing == "+"): i = 1
else: i = 0
ma = ma.select(flex.size_t([i]))
mtz_obj = mtz_dataset.mtz_object()
from cctbx.xray import observation_types
ma.set_observation_type(observation_types.reconstructed_amplitude())
mtz_obj_reco = ma.as_mtz_dataset(column_root_label="R").mtz_object()
sio = StringIO()
print >> sio, "Resulting mtz from .as_mtz_dataset():"
mtz_obj_reco.show_column_data_human_readable(out=sio)
print >> sio
ma_reco = mtz_obj_reco.as_miller_arrays()[0]
print >> sio, "mtz_obj_reco.as_miller_arrays result:"
ma_reco.show_array(f=sio)
print >> sio
if (verbose):
sys.stdout.write(sio.getvalue())
if (missing is None):
expected = """\
Resulting mtz from .as_mtz_dataset():
Column data:
-------------------------------------------------------------------------------
R SIGR DANOR SIGDANOR
ISYMR
1 2 3 4 0.158114 -3 0.316228
0
-------------------------------------------------------------------------------
mtz_obj_reco.as_miller_arrays result:
(1, 2, 3) 2.5 0.223606796247
(-1, -2, -3) 5.5 0.223606796247
"""
elif (missing == "+"):
expected = """\
Resulting mtz from .as_mtz_dataset():
Column data:
-------------------------------------------------------------------------------
R SIGR DANOR SIGDANOR
ISYMR
1 2 3 5.5 0.3 None None
2
-------------------------------------------------------------------------------
mtz_obj_reco.as_miller_arrays result:
(-1, -2, -3) 5.5 0.300000011921
"""
elif (missing == "-"):
expected = """\
Resulting mtz from .as_mtz_dataset():
Column data:
-------------------------------------------------------------------------------
R SIGR DANOR SIGDANOR
ISYMR
1 2 3 2.5 0.1 None None
1
-------------------------------------------------------------------------------
mtz_obj_reco.as_miller_arrays result:
(1, 2, 3) 2.5 0.10000000149
"""
else:
raise RuntimeError("Unreachable.")
from libtbx.test_utils import show_diff
assert not show_diff(sio.getvalue(), expected)
