def remove_anomalous_suffix_if_necessary(miller_array=None,
column_root_label=None):
# if the miller array is anomalous and the suffix is "(+)", remove it
if column_root_label and column_root_label.endswith("(+)") and \
miller_array.anomalous_flag():
column_root_label = column_root_label[:-3]
return column_root_label
def remove_anomalous_suffix_if_necessary(
miller_array=None,
column_root_label=None):
# if the miller array is anomalous and the suffix is "(+)", remove it
if column_root_label and column_root_label.endswith("(+)") and \
miller_array.anomalous_flag():
column_root_label=column_root_label[:-3]
return column_root_label
def exercise_reflection_file_as_miller_array():
refl_1 = """\
NREFlection= 3
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=PHASE DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
DECLare NAME=FOM DOMAin=RECIprocal TYPE=REAL END
INDE 1 1 2 FOBS= 713.650 PHASE= 0.000 SIGMA= 3.280
TEST= 0 FOM= -1.000
INDE -2 0 3 FOBS= 539.520 PHASE= 0.000 SIGMA= 4.140
TEST= 1 FOM= -1.000
INDE 0 2 1 FOBS= 268.140 PHASE= 0.000 SIGMA= 1.690
TEST= 0 FOM= -1.000
"""
refl_2 = """\
{ sg=C2 a=97.37 b=46.64 c=65.47 alpha=90 beta=115.4 gamma=90 }
NREFlection= 3
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
DECLare NAME=FOM DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PB DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PC DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PD DOMAin=RECIprocal TYPE=REAL END
GROUp TYPE=HL
OBJEct=PA
OBJEct=PB
OBJEct=PC
OBJEct=PD
END
INDE 1 1 2 FOBS= 713.650 44.854 SIGMA= 3.280 TEST= 0
FOM= 0.044 PA= 0.066 PB= 0.065 PC= -0.001
PD= -0.099
INDE -2 0 3 FOBS= 539.520 0.000 SIGMA= 4.140 TEST= 1
FOM= 0.994 PA= 2.893 PB= 0.000 PC= 0.000
PD= 0.000
INDE 0 2 1 FOBS= 268.140 184.247 SIGMA= 1.690 TEST= 0
FOM= 0.890 PA= -46.660 PB= -3.465 PC= -12.988
PD= -1.940
"""
crystal_symmetry = crystal.symmetry(unit_cell=(97.37, 46.64, 65.47, 90,
115.4, 90),
space_group_symbol="C 1 2 1")
all_arrays = [
iotbx.cns.reflection_reader.cns_reflection_file(
file_handle=StringIO(refl)).as_miller_arrays(crystal_symmetry=cs)
for refl, cs in [(refl_1, crystal_symmetry), (refl_2, None)]
]
for miller_arrays in all_arrays:
for miller_array in miller_arrays:
assert miller_array.crystal_symmetry().is_similar_symmetry(
other=crystal_symmetry,
relative_length_tolerance=1.e-10,
absolute_angle_tolerance=1.e-10)
assert not miller_array.anomalous_flag()
assert list(miller_array.indices()) == [(1, 1, 2), (-2, 0, 3),
(0, 2, 1)]
lbl = miller_array.info().label_string()
if (lbl == "FOBS,SIGMA"):
assert str(miller_array.observation_type()) == "xray.amplitude"
assert approx_equal(miller_array.data(),
[713.65, 539.52, 268.14])
assert approx_equal(miller_array.sigmas(), [3.28, 4.14, 1.69])
else:
assert miller_array.observation_type() is None
if (lbl == "TEST"):
assert list(miller_array.data()) == [0, 1, 0]
elif (lbl == "PHASE"):
assert approx_equal(miller_array.data(), [0, 0, 0])
elif (lbl == "FOM"):
if (miller_array.data()[0] < 0):
assert approx_equal(miller_array.data(), [-1, -1, -1])
else:
assert approx_equal(miller_array.data(),
[0.044, 0.994, 0.890])
elif (lbl == "PA,PB,PC,PD"):
assert approx_equal(miller_array.data(),
[(0.066, 0.065, -0.001, -0.099),
(2.893, 0.000, 0.000, 0.000),
(-46.660, -3.465, -12.988, -1.940)])
else:
raise RuntimeError
def exercise_reflection_file_as_miller_array():
refl_1 = """\
NREFlection= 3
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=PHASE DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
DECLare NAME=FOM DOMAin=RECIprocal TYPE=REAL END
INDE 1 1 2 FOBS= 713.650 PHASE= 0.000 SIGMA= 3.280
TEST= 0 FOM= -1.000
INDE -2 0 3 FOBS= 539.520 PHASE= 0.000 SIGMA= 4.140
TEST= 1 FOM= -1.000
INDE 0 2 1 FOBS= 268.140 PHASE= 0.000 SIGMA= 1.690
TEST= 0 FOM= -1.000
"""
refl_2 = """\
{ sg=C2 a=97.37 b=46.64 c=65.47 alpha=90 beta=115.4 gamma=90 }
NREFlection= 3
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
DECLare NAME=FOM DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PB DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PC DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=PD DOMAin=RECIprocal TYPE=REAL END
GROUp TYPE=HL
OBJEct=PA
OBJEct=PB
OBJEct=PC
OBJEct=PD
END
INDE 1 1 2 FOBS= 713.650 44.854 SIGMA= 3.280 TEST= 0
FOM= 0.044 PA= 0.066 PB= 0.065 PC= -0.001
PD= -0.099
INDE -2 0 3 FOBS= 539.520 0.000 SIGMA= 4.140 TEST= 1
FOM= 0.994 PA= 2.893 PB= 0.000 PC= 0.000
PD= 0.000
INDE 0 2 1 FOBS= 268.140 184.247 SIGMA= 1.690 TEST= 0
FOM= 0.890 PA= -46.660 PB= -3.465 PC= -12.988
PD= -1.940
"""
crystal_symmetry = crystal.symmetry(
unit_cell=(97.37, 46.64, 65.47, 90, 115.4, 90),
space_group_symbol="C 1 2 1")
all_arrays = [iotbx.cns.reflection_reader.cns_reflection_file(
file_handle=StringIO(refl)).as_miller_arrays(
crystal_symmetry=cs)
for refl,cs in [(refl_1,crystal_symmetry), (refl_2,None)]]
for miller_arrays in all_arrays:
for miller_array in miller_arrays:
assert miller_array.crystal_symmetry().is_similar_symmetry(
other=crystal_symmetry,
relative_length_tolerance=1.e-10,
absolute_angle_tolerance=1.e-10)
assert not miller_array.anomalous_flag()
assert list(miller_array.indices()) == [(1,1,2), (-2,0,3), (0,2,1)]
lbl = miller_array.info().label_string()
if (lbl == "FOBS,SIGMA"):
assert str(miller_array.observation_type()) == "xray.amplitude"
assert approx_equal(miller_array.data(), [713.65, 539.52, 268.14])
assert approx_equal(miller_array.sigmas(), [3.28, 4.14, 1.69])
else:
assert miller_array.observation_type() is None
if (lbl == "TEST"):
assert list(miller_array.data()) == [0, 1, 0]
elif (lbl == "PHASE"):
assert approx_equal(miller_array.data(), [0, 0, 0])
elif (lbl == "FOM"):
if (miller_array.data()[0] < 0):
assert approx_equal(miller_array.data(), [-1, -1, -1])
else:
assert approx_equal(miller_array.data(), [0.044, 0.994, 0.890])
elif (lbl == "PA,PB,PC,PD"):
assert approx_equal(miller_array.data(), [
(0.066, 0.065, -0.001, -0.099),
(2.893, 0.000, 0.000, 0.000),
(-46.660, -3.465, -12.988, -1.940)])
else:
raise RuntimeError