def rfree(self, override=False):
if not override:
for m_a in self.miller_arrays:
if looks_like_r_free_flags_info(m_a.info()):
raise RuntimeError(
"R-free column already found in {0}. Set override to true to generate a new"
"R-free column.")
for m_a in self.miller_arrays:
if looks_like_r_free_flags_info(m_a.info()):
self.delete(m_a.info().labels)
rfree_m_a = self.miller_arrays[0].generate_r_free_flags(format='ccp4')
self.miller_arrays['FreeR_flag'] = rfree_m_a
def get_array_description(miller_array):
from iotbx import reflection_file_utils
info = miller_array.info()
labels = info.label_string()
if labels in ["PHI", "PHIB", "PHIM", "PHIC"]:
return "Phases"
if labels in ["FOM", "FOMM"]:
return "Weights"
if ((miller_array.is_integer_array() or miller_array.is_bool_array())
and reflection_file_utils.looks_like_r_free_flags_info(info)):
return "R-free flag"
methods_and_meanings = [
("is_complex_array", "Map coeffs"),
("is_xray_amplitude_array", "Amplitude"),
("is_xray_intensity_array", "Intensity"),
("is_hendrickson_lattman_array", "HL coeffs"),
("is_bool_array", "Boolean"),
("is_integer_array", "Integer"),
("is_real_array", "Floating-point"),
]
for method, desc in methods_and_meanings:
test = getattr(miller_array, method)
if test():
return desc
return "Unknown"
def get_array_description(miller_array):
from iotbx import reflection_file_utils
info = miller_array.info()
labels = info.label_string()
if labels in ["PHI", "PHIB", "PHIM", "PHIC"]:
return "Phases"
if labels in ["FOM", "FOMM"]:
return "Weights"
if ((miller_array.is_integer_array() or miller_array.is_bool_array())
and reflection_file_utils.looks_like_r_free_flags_info(info)):
return "R-free flag"
methods_and_meanings = [("is_complex_array", "Map coeffs"),
("is_xray_amplitude_array", "Amplitude"),
("is_xray_reconstructed_amplitude_array",
"Amplitude"),
("is_xray_intensity_array", "Intensity"),
("is_hendrickson_lattman_array", "HL coeffs"),
("is_bool_array", "Boolean"),
("is_integer_array", "Integer"),
("is_real_array", "Floating-point"),
("is_string_array", "String")]
for method, desc in methods_and_meanings:
test = getattr(miller_array, method)
if test():
return desc
# resort to the name of the python data type if not matching any of the above
return type(miller_array.data()).__name__
def detect_Rfree(self, array):
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
info = array.info()
if (array.is_integer_array()) and (looks_like_r_free_flags_info(info)) :
from iotbx.reflection_file_utils import get_r_free_flags_scores
score_array = get_r_free_flags_scores([array], None)
test_flag_value = score_array.test_flag_values[0]
array = array.customized_copy(data=(array.data() == test_flag_value))
array.set_info(info)
return array
def process_miller_array(self, array):
if (array is None): return
if (array.is_hendrickson_lattman_array()):
raise Sorry("Hendrickson-Lattman coefficients are not supported.")
info = array.info()
if isinstance(info, str):
labels = "TEST DATA"
else:
labels = info.label_string()
if self.settings.unit_cell is not None:
symm = crystal.symmetry(unit_cell=self.settings.unit_cell,
space_group=array.space_group())
array = array.customized_copy(crystal_symmetry=symm).set_info(info)
if self.settings.space_group is not None:
symm = crystal.symmetry(
unit_cell=array.unit_cell(),
space_group=self.settings.space_group.group())
array = array.customized_copy(crystal_symmetry=symm).set_info(info)
if (array.unit_cell() is None) or (array.space_group() is None):
dlg = wxtbx.symmetry_dialog.SymmetryDialog(self, -1,
"Enter symmetry")
dlg.SetUnitCell(array.unit_cell())
dlg.SetSpaceGroup(array.space_group_info())
if (dlg.ShowModal() == wx.ID_OK):
symm = dlg.GetSymmetry()
array = array.customized_copy(
crystal_symmetry=symm).set_info(info)
wx.CallAfter(dlg.Destroy)
details = []
merge = True
details.append("merged")
self.update_settings_for_merged(True)
if array.is_complex_array():
array = array.amplitudes().set_info(info)
details.append("as amplitudes")
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
if (array.is_integer_array()) and (looks_like_r_free_flags_info(info)):
from iotbx.reflection_file_utils import get_r_free_flags_scores
score_array = get_r_free_flags_scores([array], None)
test_flag_value = score_array.test_flag_values[0]
array = array.customized_copy(
data=(array.data() == test_flag_value))
array.set_info(info)
sg = "%s" % array.space_group_info()
uc = "a=%g b=%g c=%g angles=%g,%g,%g" % array.unit_cell().parameters()
details_str = ""
if (len(details) > 0):
details_str = "(%s)" % ", ".join(details)
array_info = group_args(labels=labels,
details_str=details_str,
merge=merge,
sg=sg,
uc=uc)
return array, array_info
def detect_Rfree(self, array):
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
info = array.info()
if (array.is_integer_array()) and (looks_like_r_free_flags_info(info)) :
from iotbx.reflection_file_utils import get_r_free_flags_scores
score_array = get_r_free_flags_scores([array], None)
test_flag_value = score_array.test_flag_values[0]
if test_flag_value not in array.data():
return array # for the few cases where a miller array cannot be considered as a valid Rfree array
array = array.customized_copy(data=(array.data() == test_flag_value))
array.set_info(info)
array._data = array.data().as_int()
return array
def run(self, mtz_file):
reflection_file = reflection_file_reader.any_reflection_file(
file_name=mtz_file)
if not reflection_file.file_type() == "ccp4_mtz":
msg = "File is not of type ccp4_mtz: {0}".format(mtz_file)
logging.critical(msg)
raise RuntimeError(msg)
miller_arrays = reflection_file.as_miller_arrays()
for m_a in miller_arrays:
if looks_like_r_free_flags_info(m_a.info()) and not self.free:
self.free = m_a.info().labels[0]
elif self.check_anomalous(m_a):
if self.check_for_dano_labels(m_a):
if len(m_a.info().labels) == 5:
self.f, self.sigf, self.dano, self.sigdano, isym = m_a.info(
).labels
elif len(m_a.info().labels) == 4:
self.f, self.sigf, self.dano, self.sigdano = m_a.info(
).labels
elif len(m_a.info().labels) == 2:
self.dano, self.sigdano = m_a.info().labels
else:
msg = "Unexpected number of columns found in anomalous miller array"
logging.debug(msg)
elif self.check_for_plus_minus_labels(m_a):
if m_a.is_xray_amplitude_array():
self.fplus, self.sigfplus, self.fminus, self.sigfminus = m_a.info(
).labels
elif m_a.is_xray_intensity_array():
self.iplus, self.sigiplus, self.iminus, self.sigiminus = m_a.info(
).labels
else:
msg = "Type of anomalous miller array unknown"
logging.debug(msg)
else:
msg = "Type of anomalous miller array unknown"
logging.debug(msg)
elif m_a.is_xray_intensity_array() and len(
m_a.info().labels) == 2 and not self.i:
self.i, self.sigi = m_a.info().labels
elif m_a.is_xray_amplitude_array() and len(
m_a.info().labels) == 2 and not self.f:
self.f, self.sigf = m_a.info().labels
else:
pass
def __init__(self, file_name=None, miller_arrays=()):
assert (file_name is not None) or (len(miller_arrays) > 0)
self.file_name = file_name
self.miller_arrays = miller_arrays
if (len(self.miller_arrays) == 0):
from iotbx import file_reader
f = file_reader.any_file(file_name, force_type="hkl")
f.assert_file_type("hkl")
self.miller_arrays = f.file_server.miller_arrays
assert (len(self.miller_arrays) > 0)
self.map_coeffs = []
self.array_labels = []
self.data_arrays = []
self.phase_arrays = []
self.weight_arrays = []
self.rfree_arrays = []
self.fcalc_arrays = []
self._pdb_cache = {}
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
for array in self.miller_arrays:
labels = array.info().label_string()
self.array_labels.append(labels)
if (array.is_xray_amplitude_array()
or array.is_xray_intensity_array()):
if (labels.startswith("FC")):
self.fcalc_arrays.append(array)
else:
self.data_arrays.append(array)
elif (array.is_complex_array()):
if (labels.startswith("FC") or labels.startswith("FMODEL")
or labels.startswith("F-model")):
self.fcalc_arrays.append(array)
else:
self.map_coeffs.append(array)
elif (array.is_real_array()):
if (labels.startswith("PH")):
self.phase_arrays.append(array)
elif (labels.startswith("FOM")):
self.weight_arrays.append(array)
elif (array.is_bool_array()):
self.rfree_arrays.append(array)
elif (array.is_integer_array()):
if (looks_like_r_free_flags_info(array.info())):
self.rfree_arrays.append(array)
def __init__ (self, file_name=None, miller_arrays=()) :
assert (file_name is not None) or (len(miller_arrays) > 0)
self.file_name = file_name
self.miller_arrays = miller_arrays
if (len(self.miller_arrays) == 0) :
from iotbx import file_reader
f = file_reader.any_file(file_name, force_type="hkl")
f.assert_file_type("hkl")
self.miller_arrays = f.file_server.miller_arrays
assert (len(self.miller_arrays) > 0)
self.map_coeffs = []
self.array_labels = []
self.data_arrays = []
self.phase_arrays = []
self.weight_arrays = []
self.rfree_arrays = []
self.fcalc_arrays = []
self._pdb_cache = {}
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
for array in self.miller_arrays :
labels = array.info().label_string()
self.array_labels.append(labels)
if (array.is_xray_amplitude_array() or array.is_xray_intensity_array()) :
if (labels.startswith("FC")) :
self.fcalc_arrays.append(array)
else :
self.data_arrays.append(array)
elif (array.is_complex_array()) :
if (labels.startswith("FC") or labels.startswith("FMODEL") or
labels.startswith("F-model")) :
self.fcalc_arrays.append(array)
else :
self.map_coeffs.append(array)
elif (array.is_real_array()) :
if (labels.startswith("PH")) :
self.phase_arrays.append(array)
elif (labels.startswith("FOM")) :
self.weight_arrays.append(array)
elif (array.is_bool_array()) :
self.rfree_arrays.append(array)
elif (array.is_integer_array()) :
if (looks_like_r_free_flags_info(array.info())) :
self.rfree_arrays.append(array)
def get_array_description (miller_array) :
from iotbx import reflection_file_utils
info = miller_array.info()
labels = info.label_string()
if labels in ["PHI", "PHIB", "PHIM", "PHIC"] :
return "Phases"
if labels in ["FOM", "FOMM"] :
return "Weights"
if ((miller_array.is_integer_array() or miller_array.is_bool_array()) and
reflection_file_utils.looks_like_r_free_flags_info(info)) :
return "R-free flag"
methods_and_meanings = [ ("is_complex_array", "Map coeffs"),
("is_xray_amplitude_array", "Amplitude"),
("is_xray_intensity_array", "Intensity"),
("is_hendrickson_lattman_array", "HL coeffs"),
("is_bool_array", "Boolean"),
("is_integer_array", "Integer"),
("is_real_array", "Floating-point"), ]
for method, desc in methods_and_meanings :
test = getattr(miller_array, method)
if test() :
return desc
return "Unknown"
def __init__(self,
mtz_object,
custom_cif_labels_dict=None,
log=None,
test_flag_value=None):
self.cif_blocks = {'xray': None, 'neutron': None}
if log is None: log = sys.stdout
miller_arrays = mtz_object.as_miller_arrays()
miller_arrays_as_cif_block = None
input_observations_xray = None
input_observations_neutron = None
r_free_xray = None
r_free_neutron = None
f_obs_filtered_xray = None
f_obs_filtered_neutron = None
mtz_to_cif_labels_dict = {}
mtz_to_cif_labels_dict.update(phenix_to_cif_labels_dict)
mtz_to_cif_labels_dict.update(ccp4_to_cif_labels_dict)
if custom_cif_labels_dict is not None:
mtz_to_cif_labels_dict.update(custom_cif_labels_dict)
unknown_mtz_labels = []
for array in miller_arrays:
labels = array.info().labels
label = labels[0]
if reflection_file_utils.looks_like_r_free_flags_info(
array.info()):
if "(+)" in label:
array = array.average_bijvoet_mates()
labels = [label.replace("(+)", "")]
if label.endswith(("neutron", "_N")):
r_free_neutron = array
else:
r_free_xray = array
continue # deal with these later
elif label.startswith("F-obs-filtered"):
if label.endswith(("neutron", "_N")):
f_obs_filtered_neutron = array
else:
f_obs_filtered_xray = array
elif label.startswith("F-obs") or label.startswith("I-obs"):
if label.strip("(+)").endswith(("neutron", "_N")):
input_observations_neutron = array
else:
input_observations_xray = array
#elif label.startswith("R-free-flags"):
column_names = []
for mtz_label in labels:
cif_label = mtz_to_cif_label(mtz_to_cif_labels_dict, mtz_label)
column_names.append(cif_label)
if column_names.count(None) > 0:
# I don't know what to do with this array
for i, mtz_label in enumerate(labels):
if column_names[i] is None:
unknown_mtz_labels.append(mtz_label)
continue
assert column_names.count(None) == 0
if labels[0].strip("(+)").endswith(("neutron", "_N")):
data_type = "neutron"
else:
data_type = "xray"
if column_names[0].startswith(
("_refln.F_meas", "_refln.F_squared_meas", "_refln.pdbx_F_",
"_refln.pdbx_I_")):
if data_type == "neutron":
input_observations_neutron = array
else:
input_observations_xray = array
if self.cif_blocks.get(data_type) is None:
self.cif_blocks[
data_type] = iotbx.cif.miller_arrays_as_cif_block(
array=array, column_names=column_names, format="mmcif")
else:
self.cif_blocks[data_type].add_miller_array(
array, column_names=column_names)
if len(unknown_mtz_labels):
print >> log, "Warning: Unknown mtz label%s: %s" % (plural_s(
len(unknown_mtz_labels))[1], ", ".join(unknown_mtz_labels))
print >> log, " Use mtz_labels and cif_labels keywords to provide translation for custom labels."
data_types = set(["xray"])
if self.cif_blocks['neutron'] is not None:
data_types.add("neutron")
if input_observations_xray is None and f_obs_filtered_xray is not None:
self.cif_blocks["xray"].add_miller_array(
array=f_obs_filtered_xray,
column_names=('_refln.F_meas_au', '_refln.F_meas_sigma_au'))
if input_observations_neutron is None and f_obs_filtered_neutron is not None:
self.cif_blocks["neutron"].add_miller_array(
array=f_obs_filtered_neutron,
column_names=('_refln.F_meas_au', '_refln.F_meas_sigma_au'))
for data_type in data_types:
if data_type == "xray":
r_free = r_free_xray
input_obs = input_observations_xray
f_obs_filtered = f_obs_filtered_xray
if (self.cif_blocks["xray"] is None and r_free_xray is not None
and self.cif_blocks["neutron"] is not None
and r_free_neutron is None):
r_free_neutron = r_free_xray
elif data_type == "neutron":
r_free = r_free_neutron
input_obs = input_observations_neutron
f_obs_filtered = f_obs_filtered_neutron
if self.cif_blocks[data_type] is not None and r_free is not None:
self.cif_blocks[data_type].add_miller_array(
array=r_free, column_name='_refln.pdbx_r_free_flag')
if input_obs is None or r_free is None: continue
if (test_flag_value is None):
test_flag_value = reflection_file_utils.guess_r_free_flag_value(
miller_array=r_free)
assert (test_flag_value is not None)
refln_status = r_free.array(
data=flex.std_string(r_free.size(), "."))
input_obs_non_anom = input_obs.average_bijvoet_mates()
match = r_free.match_indices(input_obs_non_anom)
refln_status.data().set_selected(match.pair_selection(0), "o")
refln_status.data().set_selected(r_free.data() == test_flag_value,
"f")
if f_obs_filtered is not None:
f_obs_filtered_non_anom = f_obs_filtered.average_bijvoet_mates(
)
match = r_free.match_indices(f_obs_filtered_non_anom)
refln_status.data().set_selected(match.single_selection(0),
"<") # XXX
self.cif_blocks[data_type].add_miller_array(
array=refln_status, column_name="_refln.status")
def process_miller_array(self, array):
if (array is None): return
if (array.is_hendrickson_lattman_array()):
raise Sorry("Hendrickson-Lattman coefficients are not supported.")
info = array.info()
if isinstance(info, str):
labels = "TEST DATA"
else:
labels = info.label_string()
if (array.unit_cell() is None) or (array.space_group() is None):
dlg = wxtbx.symmetry_dialog.SymmetryDialog(self, -1,
"Enter symmetry")
dlg.SetUnitCell(array.unit_cell())
dlg.SetSpaceGroup(array.space_group_info())
if (dlg.ShowModal() == wx.ID_OK):
symm = dlg.GetSymmetry()
array = array.customized_copy(
crystal_symmetry=symm).set_info(info)
wx.CallAfter(dlg.Destroy)
details = []
merge = None
if (not array.is_unique_set_under_symmetry()):
merge = wx.MessageBox(
"The data in the selected array are not symmetry-" +
"unique, which usually means they are unmerged (but could also be due "
+
"to different indexing conventions). Do you want to merge equivalent "
+
"observations (preserving anomalous data if present), or view the "
+
"array unmodified? (Note that if you do not merge the array, the "
+
"options to expand to P1 or generate Friedel pairs will be be disabled"
+
", and the 2D view will only show indices present in the file, rather "
+ "than a full pseudo-precession view.)",
style=wx.YES_NO)
if (merge == wx.YES):
merge = True
#array = array.merge_equivalents().array().set_info(info)
details.append("merged")
self.update_settings_for_merged(True)
else:
merge = False
details.append("unmerged data")
self.update_settings_for_unmerged()
else:
self.update_settings_for_merged()
if array.is_complex_array():
array = array.amplitudes().set_info(info)
details.append("as amplitudes")
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
if (array.is_integer_array()) and (looks_like_r_free_flags_info(info)):
from iotbx.reflection_file_utils import get_r_free_flags_scores
score_array = get_r_free_flags_scores([array], None)
test_flag_value = score_array.test_flag_values[0]
array = array.customized_copy(
data=(array.data() == test_flag_value))
array.set_info(info)
sg = "%s" % array.space_group_info()
uc = "a=%g b=%g c=%g angles=%g,%g,%g" % array.unit_cell().parameters()
details_str = ""
if (len(details) > 0):
details_str = "(%s)" % ", ".join(details)
array_info = group_args(labels=labels,
details_str=details_str,
merge=merge,
sg=sg,
uc=uc)
return array, array_info
def process_miller_array (self, array) :
if (array is None) : return
if (array.is_hendrickson_lattman_array()) :
raise Sorry("Hendrickson-Lattman coefficients are not supported.")
info = array.info()
if isinstance(info, str) :
labels = "TEST DATA"
else :
labels = info.label_string()
if (array.unit_cell() is None) or (array.space_group() is None) :
dlg = wxtbx.symmetry_dialog.SymmetryDialog(self, -1, "Enter symmetry")
dlg.SetUnitCell(array.unit_cell())
dlg.SetSpaceGroup(array.space_group_info())
if (dlg.ShowModal() == wx.ID_OK) :
symm = dlg.GetSymmetry()
array = array.customized_copy(crystal_symmetry=symm).set_info(info)
wx.CallAfter(dlg.Destroy)
details = []
merge = None
if (not array.is_unique_set_under_symmetry()) :
merge = wx.MessageBox("The data in the selected array are not symmetry-"+
"unique, which usually means they are unmerged (but could also be due "+
"to different indexing conventions). Do you want to merge equivalent "+
"observations (preserving anomalous data if present), or view the "+
"array unmodified? (Note that if you do not merge the array, the "+
"options to expand to P1 or generate Friedel pairs will be be disabled"+
", and the 2D view will only show indices present in the file, rather "+
"than a full pseudo-precession view.)",
style=wx.YES_NO)
if (merge == wx.YES) :
merge = True
#array = array.merge_equivalents().array().set_info(info)
details.append("merged")
self.update_settings_for_merged(True)
else :
merge = False
details.append("unmerged data")
self.update_settings_for_unmerged()
else :
self.update_settings_for_merged()
if array.is_complex_array() :
array = array.amplitudes().set_info(info)
details.append("as amplitudes")
from iotbx.reflection_file_utils import looks_like_r_free_flags_info
if (array.is_integer_array()) and (looks_like_r_free_flags_info(info)) :
from iotbx.reflection_file_utils import get_r_free_flags_scores
score_array = get_r_free_flags_scores([array], None)
test_flag_value = score_array.test_flag_values[0]
array = array.customized_copy(data=(array.data() == test_flag_value))
array.set_info(info)
sg = "%s" % array.space_group_info()
uc = "a=%g b=%g c=%g angles=%g,%g,%g" % array.unit_cell().parameters()
details_str = ""
if (len(details) > 0) :
details_str = "(%s)" % ", ".join(details)
array_info = group_args(
labels=labels,
details_str=details_str,
merge=merge,
sg=sg,
uc=uc)
return array, array_info
def __init__(self, mtz_object, custom_cif_labels_dict=None, log=None,
test_flag_value=None):
self.cif_blocks = {
'xray': None,
'neutron': None
}
if log is None: log = sys.stdout
miller_arrays = mtz_object.as_miller_arrays()
miller_arrays_as_cif_block = None
input_observations_xray = None
input_observations_neutron = None
r_free_xray = None
r_free_neutron = None
f_obs_filtered_xray = None
f_obs_filtered_neutron = None
mtz_to_cif_labels_dict = {}
mtz_to_cif_labels_dict.update(phenix_to_cif_labels_dict)
mtz_to_cif_labels_dict.update(ccp4_to_cif_labels_dict)
if custom_cif_labels_dict is not None:
mtz_to_cif_labels_dict.update(custom_cif_labels_dict)
unknown_mtz_labels = []
for array in miller_arrays:
labels = array.info().labels
label = labels[0]
if reflection_file_utils.looks_like_r_free_flags_info(array.info()):
if "(+)" in label:
array = array.average_bijvoet_mates()
labels = [label.replace("(+)", "")]
if label.endswith(("neutron", "_N")):
r_free_neutron = array
else:
r_free_xray = array
continue # deal with these later
elif label.startswith("F-obs-filtered"):
if label.endswith(("neutron", "_N")):
f_obs_filtered_neutron = array
else:
f_obs_filtered_xray = array
elif label.startswith("F-obs") or label.startswith("I-obs"):
if label.strip("(+)").endswith(("neutron", "_N")):
input_observations_neutron = array
else:
input_observations_xray = array
#elif label.startswith("R-free-flags"):
column_names = []
for mtz_label in labels:
cif_label = mtz_to_cif_label(mtz_to_cif_labels_dict, mtz_label)
column_names.append(cif_label)
if column_names.count(None) > 0:
# I don't know what to do with this array
for i, mtz_label in enumerate(labels):
if column_names[i] is None:
unknown_mtz_labels.append(mtz_label)
continue
assert column_names.count(None) == 0
if labels[0].strip("(+)").endswith(("neutron", "_N")):
data_type = "neutron"
else:
data_type = "xray"
if column_names[0].startswith(("_refln.F_meas",
"_refln.F_squared_meas",
"_refln.pdbx_F_",
"_refln.pdbx_I_")):
if data_type == "neutron":
input_observations_neutron = array
else:
input_observations_xray = array
if self.cif_blocks.get(data_type) is None:
self.cif_blocks[data_type] = iotbx.cif.miller_arrays_as_cif_block(
array=array, column_names=column_names, format="mmcif")
else:
self.cif_blocks[data_type].add_miller_array(array, column_names=column_names)
if len(unknown_mtz_labels):
print >> log, "Warning: Unknown mtz label%s: %s" %(
plural_s(len(unknown_mtz_labels))[1], ", ".join(unknown_mtz_labels))
print >> log, " Use mtz_labels and cif_labels keywords to provide translation for custom labels."
data_types = set(["xray"])
if self.cif_blocks['neutron'] is not None:
data_types.add("neutron")
if input_observations_xray is None and f_obs_filtered_xray is not None:
self.cif_blocks["xray"].add_miller_array(
array=f_obs_filtered_xray,
column_names=('_refln.F_meas_au','_refln.F_meas_sigma_au'))
if input_observations_neutron is None and f_obs_filtered_neutron is not None:
self.cif_blocks["neutron"].add_miller_array(
array=f_obs_filtered_neutron,
column_names=('_refln.F_meas_au','_refln.F_meas_sigma_au'))
for data_type in data_types:
if data_type == "xray":
r_free = r_free_xray
input_obs = input_observations_xray
f_obs_filtered = f_obs_filtered_xray
if (self.cif_blocks["xray"] is None and r_free_xray is not None and
self.cif_blocks["neutron"] is not None and r_free_neutron is None):
r_free_neutron = r_free_xray
elif data_type == "neutron":
r_free = r_free_neutron
input_obs = input_observations_neutron
f_obs_filtered = f_obs_filtered_neutron
if self.cif_blocks[data_type] is not None and r_free is not None:
self.cif_blocks[data_type].add_miller_array(
array=r_free, column_name='_refln.pdbx_r_free_flag')
if input_obs is None or r_free is None: continue
if (test_flag_value is None) :
test_flag_value = reflection_file_utils.guess_r_free_flag_value(
miller_array=r_free)
assert (test_flag_value is not None)
refln_status = r_free.array(data=flex.std_string(r_free.size(), "."))
input_obs_non_anom = input_obs.average_bijvoet_mates()
match = r_free.match_indices(input_obs_non_anom)
refln_status.data().set_selected(match.pair_selection(0), "o")
refln_status.data().set_selected(r_free.data() == test_flag_value, "f")
if f_obs_filtered is not None:
f_obs_filtered_non_anom = f_obs_filtered.average_bijvoet_mates()
match = r_free.match_indices(f_obs_filtered_non_anom)
refln_status.data().set_selected(match.single_selection(0), "<") # XXX
self.cif_blocks[data_type].add_miller_array(
array=refln_status, column_name="_refln.status")
def reindex(self, sg):
for m_a in self.miller_arrays:
if not looks_like_r_free_flags_info(m_a.info()):
m_a.change_symmetry(sg)
