def get_flag_array(arrays, flag_name=None, log_out=sys.stdout):
flag_array = None
if flag_name is None:
flags = filter(lambda x: is_rfree_array(x, x.info()), arrays)
if len(flags) == 0:
print >> log_out, " No R free flags like column found."
return None, None
elif len(flags) > 1:
print >> log_out, " More than one column which looks like R free flag:"
for f in flags:
print >> log_out, " ", f.info().label_string()
return None, None
else:
flag_name = flags[0].info().label_string()
flag_array = flags[0]
print >> log_out, " Guessing R free flag:", flag_name
else:
flags = filter(lambda x: flag_name == x.info().label_string(), arrays)
if len(flags) == 0:
print >> log_out, " Specified flag name not found:", flag
return None, None
else:
print >> log_out, " Use specified flag:", flag
flag_array = flags[0]
return flag_array, flag_name
def guess_flag_name_and_value(mtzin, name=None, val=None):
arrays = iotbx.mtz.object(mtzin).as_miller_arrays()
if name is None:
flags = filter(lambda x: is_rfree_array(x, x.info()), arrays)
name = flags[0].info().label_string()
flag_array = flags[0]
else:
flags = filter(lambda x: name==x.info().label_string(), arrays)
flag_array = flags[0]
if val is None:
flag_scores = get_r_free_flags_scores(miller_arrays=[flag_array], test_flag_value=val)
val = flag_scores.test_flag_values[0]
return name, val
def guess_flag_name_and_value(mtzin, name=None, val=None):
arrays = iotbx.mtz.object(mtzin).as_miller_arrays()
if name is None:
flags = filter(lambda x: is_rfree_array(x, x.info()), arrays)
name = flags[0].info().label_string()
flag_array = flags[0]
else:
flags = filter(lambda x: name == x.info().label_string(), arrays)
flag_array = flags[0]
if val is None:
flag_scores = get_r_free_flags_scores(miller_arrays=[flag_array],
test_flag_value=val)
val = flag_scores.test_flag_values[0]
return name, val
def get_flag(arrays, flag_name=None, flag_value=None):
flag_array = None
# Get flag array
if flag_name is None:
flags = filter(lambda x: is_rfree_array(x, x.info()), arrays)
if len(flags) == 0:
print " No R free flags like column found."
return None
elif len(flags) > 1:
print " More than one column which looks like R free flag:"
for f in flags:
print " ", f.info().label_string()
return None
else:
flag_name = flags[0].info().label_string()
flag_array = flags[0]
print "# Guessing R free flag:", flag_name
else:
flags = filter(lambda x: flag_name==x.info().label_string(), arrays)
if len(flags) == 0:
print " Specified flag name not found:", flag
quit()
else:
print "# Use specified flag:", flag
flag_array = flags[0]
# Get flag number
if flag_value is None:
flag_scores = get_r_free_flags_scores(miller_arrays=[flag_array], test_flag_value=flag_value)
flag_value = flag_scores.test_flag_values[0]
print "# Guessing flag number:", flag_value
else:
print "# Specified flag number:", flag_value
return flag_array.customized_copy(data=flag_array.data() == flag_value)
def run(mtz, mtz_out, mtz_ref, flag_name=None, flag_value=None):
ref_arrays = iotbx.mtz.object(mtz_ref).as_miller_arrays()
print "Opening reference:", mtz_ref
# Get flag array
flag_array = None
if flag_name is None:
flags = filter(lambda x: is_rfree_array(x, x.info()), ref_arrays)
if len(flags) == 0:
print " No R free flags like column found."
quit()
elif len(flags) > 1:
print " More than one column which looks like R free flag:"
for f in flags:
print " ", f.info().label_string()
quit()
else:
flag_name = flags[0].info().label_string()
flag_array = flags[0]
print " Guessing R free flag:", flag_name
else:
flags = filter(lambda x: flag_name==x.info().label_string(), ref_arrays)
if len(flags) == 0:
print " Specified flag name not found:", flag
quit()
else:
print " Use specified flag:", flag
flag_array = flags[0]
# Get flag number
if flag_value is None:
flag_scores = get_r_free_flags_scores(miller_arrays=[flag_array], test_flag_value=flag_value)
flag_value = flag_scores.test_flag_values[0]
print " Guessing flag number:", flag_value
else:
print " Specified flag number:", flag_value
print " d_max, d_min=", get_best_resolution([flag_array], flag_array.crystal_symmetry())
print " Symm:", flag_array.space_group().info(), flag_array.unit_cell()
print
# Open mtz
miller_arrays = iotbx.mtz.object(mtz).as_miller_arrays()
print "Opening", mtz
if flag_name in [arr.info().label_string() for arr in miller_arrays]:
print "Error: The column %s already exists in the mtz file: %s" % (flag_name, mtz)
quit()
print " Using information from", miller_arrays[0].info().label_string()
input_symm = crystal.symmetry(
unit_cell=miller_arrays[0].unit_cell(),
space_group_info=miller_arrays[0].space_group().info(),
assert_is_compatible_unit_cell=False,
force_compatible_unit_cell=False)
d_max, d_min = get_best_resolution(miller_arrays, input_symm)
print " d_max, d_min=", d_max, d_min
print " Symm:", input_symm.space_group_info(), input_symm.unit_cell()
print
# Extend flag
complete_set = make_joined_set(miller_arrays).complete_set()
r_free_flags = r_free_utils.extend_flags(
r_free_flags=flag_array.customized_copy(crystal_symmetry=input_symm),
test_flag_value=flag_value,
array_label=flag_name,
complete_set=complete_set,
accumulation_callback=None,
preserve_input_values=True,
d_max=d_max,
d_min=d_min,
log=sys.stdout).common_set(complete_set) #resolution_filter(d_min=d_min-0.01)
print
print r_free_flags.customized_copy(data=r_free_flags.data()==flag_value).show_r_free_flags_info()
# Write mtz file
#mtz_dataset = create_mtz_dataset(miller_arrays)
#mtz_dataset.add_miller_array(miller_array=r_free_flags, column_root_label=flag_name)
#mtz_object = mtz_dataset.mtz_object()
mtz_object = iotbx.mtz.object(mtz).add_crystal("crystal", "project", r_free_flags.unit_cell()). \
add_dataset(name="dataset", wavelength=0). \
add_miller_array(miller_array=r_free_flags, column_root_label=flag_name).mtz_object()
#mtz_object.add_history("copy and extend test flag from "+mtz_ref)
#mtz_object.show_summary(out=sys.stdout, prefix=" ")
mtz_object.write(file_name=mtz_out)
print
print "Writing:", mtz_out
print
def run(args=(), params=None, out=None):
if (out is None):
out = sys.stdout
validate_params(params)
from iotbx import reflection_file_editor
from iotbx import reflection_file_utils
from iotbx import file_reader
data_in = file_reader.any_file(params.import_data.data_file,
force_type="hkl")
data_in.check_file_type("hkl")
miller_arrays = data_in.file_server.miller_arrays
new_arrays = []
labels = ["H","K","L"]
warnings = []
have_r_free = False
for array in miller_arrays :
if (reflection_file_editor.is_rfree_array(array, array.info())):
have_r_free = True
if (params.import_data.flags_file is not None):
raise Sorry("The data file (%s) already contains R-free flags." %
params.import_data.data_file)
if (array.is_xray_reconstructed_amplitude_array()):
if ("F(+)" in labels):
labels.extend(["F_rec(+)", "SIGF_rec(+)", "F_rec(-)", "SIGF_rec(-)"])
else :
labels.extend(["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"])
else :
labels.extend(array.info().labels)
array = array.map_to_asu()
if (not array.is_unique_set_under_symmetry()):
array = array.merge_equivalents().array()
new_arrays.append(array)
complete_set = reflection_file_utils.make_joined_set(
new_arrays).complete_set()
if (not have_r_free):
if (params.import_data.flags_file is not None):
flags_in = file_reader.any_file(params.import_data.flags_file,
force_type="hkl")
flags_in.check_file_type("hkl")
flags_and_values = flags_in.file_server.get_r_free_flags(
file_name=flags_in.file_name,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope=None,
return_all_valid_arrays=True)
if (len(flags_and_values) == 0):
raise Sorry("No R-free flags were found in the file %s." %
params.import_data.flags_file)
elif (len(flags_and_values) > 1):
raise Sorry(("Multiple valid sets of R-free flags were found in the "+
"file %s. Please use the reflection file editor to select a "+
"single set of flags.") % params.import_data.flags_file)
old_flags, test_flag_value = flags_and_values[0]
labels.extend(old_flags.info().labels)
old_flags = old_flags.map_to_asu().merge_equivalents().array()
old_flags = old_flags.customized_copy(
data=old_flags.data()==test_flag_value)
missing_set = complete_set.lone_set(old_flags)
n_missing = missing_set.indices().size()
fraction_free = old_flags.data().count(True) / old_flags.data().size()
if (n_missing != 0):
(n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats(
miller_array=old_flags,
test_flag_value=True)
min_bins = int(old_flags.indices().size() * 0.005)
if (n_bins < (n_free / 100)) or (sse > 0.005) or (n_bins < min_bins):
if (not params.import_data.ignore_shells):
raise Sorry(("The R-free flags in %s appear to have been "+
"assigned in thin resolution shells. PHENIX is unable to "+
"properly extend flags created in this manner. If you "+
"prefer to ignore this check and want to create new flags using "+
"random assignment, or if you think this message is in error, "+
"you can use the reflection file editor instead. "+
"(To view the distribution of R-free flags, click the "+
"toolbar button \"Other tools\" and select \"Inspect R-free "+
"flags\".)") % params.import_data.flags_file)
else :
print >> out, "WARNING: ignoring thin shells"
if (n_missing <= 20) : # XXX hack
from scitbx.array_family import flex
missing_flags = missing_set.array(data=flex.bool(n_missing, False))
else :
missing_flags = missing_set.generate_r_free_flags(
fraction_free=fraction_free,
max_free=None,
use_lattice_symmetry=True)
new_flags = old_flags.concatenate(other=missing_flags)
else :
new_flags = old_flags
new_arrays.append(new_flags)
mtz_out = new_arrays[0].as_mtz_dataset(
column_root_label="A")
for i, array in enumerate(new_arrays[1:]):
mtz_out.add_miller_array(
miller_array=array,
column_root_label="%s" % string.uppercase[i+1])
mtz_obj = mtz_out.mtz_object()
for i, column in enumerate(mtz_obj.columns()):
column.set_label(labels[i])
if (params.import_data.output_file is None):
base,ext = os.path.splitext(params.import_data.data_file)
params.import_data.output_file = base + "_flags.mtz"
mtz_obj.write(file_name=params.import_data.output_file)
print >> out, "Data and flags written to %s" % params.import_data.output_file
return params.import_data.output_file
def run (args=(), params=None, out=None) :
if (out is None) :
out = sys.stdout
validate_params(params)
from iotbx import reflection_file_editor
from iotbx import reflection_file_utils
from iotbx import file_reader
data_in = file_reader.any_file(params.import_data.data_file,
force_type="hkl")
data_in.check_file_type("hkl")
miller_arrays = data_in.file_server.miller_arrays
new_arrays = []
labels = ["H","K","L"]
warnings = []
have_r_free = False
for array in miller_arrays :
if (reflection_file_editor.is_rfree_array(array, array.info())) :
have_r_free = True
if (params.import_data.flags_file is not None) :
raise Sorry("The data file (%s) already contains R-free flags." %
params.import_data.data_file)
if (array.is_xray_reconstructed_amplitude_array()) :
if ("F(+)" in labels) :
labels.extend(["F_rec(+)", "SIGF_rec(+)", "F_rec(-)", "SIGF_rec(-)"])
else :
labels.extend(["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"])
else :
labels.extend(array.info().labels)
array = array.map_to_asu()
if (not array.is_unique_set_under_symmetry()) :
array = array.merge_equivalents().array()
new_arrays.append(array)
complete_set = reflection_file_utils.make_joined_set(
new_arrays).complete_set()
if (not have_r_free) :
if (params.import_data.flags_file is not None) :
flags_in = file_reader.any_file(params.import_data.flags_file,
force_type="hkl")
flags_in.check_file_type("hkl")
flags_and_values = flags_in.file_server.get_r_free_flags(
file_name=flags_in.file_name,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope=None,
return_all_valid_arrays=True)
if (len(flags_and_values) == 0) :
raise Sorry("No R-free flags were found in the file %s." %
params.import_data.flags_file)
elif (len(flags_and_values) > 1) :
raise Sorry(("Multiple valid sets of R-free flags were found in the "+
"file %s. Please use the reflection file editor to select a "+
"single set of flags.") % params.import_data.flags_file)
old_flags, test_flag_value = flags_and_values[0]
labels.extend(old_flags.info().labels)
old_flags = old_flags.map_to_asu().merge_equivalents().array()
old_flags = old_flags.customized_copy(
data=old_flags.data()==test_flag_value)
missing_set = complete_set.lone_set(old_flags)
n_missing = missing_set.indices().size()
fraction_free = old_flags.data().count(True) / old_flags.data().size()
if (n_missing != 0) :
(n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats(
miller_array=old_flags,
test_flag_value=True)
min_bins = int(old_flags.indices().size() * 0.005)
if (n_bins < (n_free / 100)) or (sse > 0.005) or (n_bins < min_bins) :
if (not params.import_data.ignore_shells) :
raise Sorry(("The R-free flags in %s appear to have been "+
"assigned in thin resolution shells. PHENIX is unable to "+
"properly extend flags created in this manner. If you "+
"prefer to ignore this check and want to create new flags using "+
"random assignment, or if you think this message is in error, "+
"you can use the reflection file editor instead. "+
"(To view the distribution of R-free flags, click the "+
"toolbar button \"Other tools\" and select \"Inspect R-free "+
"flags\".)") % params.import_data.flags_file)
else :
print >> out, "WARNING: ignoring thin shells"
if (n_missing <= 20) : # XXX hack
from scitbx.array_family import flex
missing_flags = missing_set.array(data=flex.bool(n_missing, False))
else :
missing_flags = missing_set.generate_r_free_flags(
fraction_free=fraction_free,
max_free=None,
use_lattice_symmetry=True)
new_flags = old_flags.concatenate(other=missing_flags)
else :
new_flags = old_flags
new_arrays.append(new_flags)
mtz_out = new_arrays[0].as_mtz_dataset(
column_root_label="A")
for i, array in enumerate(new_arrays[1:]) :
mtz_out.add_miller_array(
miller_array=array,
column_root_label="%s" % string.uppercase[i+1])
mtz_obj = mtz_out.mtz_object()
for i, column in enumerate(mtz_obj.columns()) :
column.set_label(labels[i])
if (params.import_data.output_file is None) :
base,ext = os.path.splitext(params.import_data.data_file)
params.import_data.output_file = base + "_flags.mtz"
mtz_obj.write(file_name=params.import_data.output_file)
print >> out, "Data and flags written to %s" % params.import_data.output_file
return params.import_data.output_file
print "Provide pdb and mtz"
quit()
arrays = iotbx.mtz.object(mtzfile).as_miller_arrays()
col_free = []
col_target = []
col_ph = []
wavelengths = []
for array in arrays:
wavelengths.append(array.info().wavelength)
labs = tuple(array.info().labels)
if is_rfree_array(array, array.info()):
flag_scores = get_r_free_flags_scores(miller_arrays=[array], test_flag_value=None)
flag_value = flag_scores.test_flag_values[0]
col_free.append(("FREE="+array.info().label_string(), flag_value))
elif array.is_xray_intensity_array():
if "(+)" in array.info().label_string(): #array.anomalous_flag():
col_target.append("I+=%s SIGI+=%s I-=%s SIGI-=%s" % tuple(array.info().labels))
else:
if len(labs) < 2:
col_target.append("IP=%s" % labs)
else:
col_target.append("IP=%s SIGIP=%s" % labs)
elif array.is_xray_amplitude_array():
if array.sigmas() is None:
