def d_max_min (self, file_name=None, file_param_name=None,
array_name=None, array_names=None) :
from iotbx.reflection_file_editor import get_best_resolution
miller_arrays = []
if (file_name is None) and (file_param_name is None) :
for phil_name, file_name in self._param_files.iteritems() :
input_file = self.get_file(file_name)
if (input_file is not None) :
miller_arrays.extend(input_file.file_server.miller_arrays)
else :
hkl_file = self.get_file(file_name, file_param_name)
if (hkl_file is None) :
return (None, None)
for miller_array in hkl_file.file_server.miller_arrays :
label = miller_array.info().label_string()
if (array_name is not None) :
if (label == array_name) :
miller_arrays = [miller_array]
break
elif (array_names is not None) :
if (label in array_names) :
miller_arrays.append(miller_array)
else :
miller_arrays.append(miller_array)
(d_max, d_min) = get_best_resolution(miller_arrays)
return (d_max, d_min)
def d_max_min(self, file_name=None, file_param_name=None,
array_name=None, array_names=None):
from iotbx.reflection_file_editor import get_best_resolution
miller_arrays = []
if (file_name is None) and (file_param_name is None):
for phil_name, file_name in six.iteritems(self._param_files):
input_file = self.get_file(file_name)
if (input_file is not None):
miller_arrays.extend(input_file.file_server.miller_arrays)
else :
hkl_file = self.get_file(file_name, file_param_name)
if (hkl_file is None):
return (None, None)
for miller_array in hkl_file.file_server.miller_arrays :
label = miller_array.info().label_string()
if (array_name is not None):
if (label == array_name):
miller_arrays = [miller_array]
break
elif (array_names is not None):
if (label in array_names):
miller_arrays.append(miller_array)
else :
miller_arrays.append(miller_array)
(d_max, d_min) = get_best_resolution(miller_arrays)
return (d_max, d_min)
def run(mtz, mtz_out, fraction, flag_name=None, ccp4=True, use_lattice_symmetry=True, n_shells=20):
# Open mtz
miller_arrays = iotbx.mtz.object(mtz).as_miller_arrays()
print "Opening", mtz
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()
if use_lattice_symmetry:
from cctbx.sgtbx import lattice_symmetry
print "Lattice symmetry:"
cb_op_to_niggli = complete_set.change_of_basis_op_to_niggli_cell()
tmp_ma = complete_set.change_basis( cb_op_to_niggli )
lattice_group = lattice_symmetry.group(tmp_ma.unit_cell(), max_delta=5.0)
print " ", tmp_ma.unit_cell(), lattice_group.laue_group_type()
print
new_r_free_array = complete_set.generate_r_free_flags(fraction=fraction,
max_free=None,
lattice_symmetry_max_delta=5.0,
use_lattice_symmetry=use_lattice_symmetry,
n_shells=n_shells)
print new_r_free_array.show_r_free_flags_info()
if ccp4:
new_r_free_array = new_r_free_array.customized_copy(data=r_free_utils.export_r_free_flags_for_ccp4(flags=new_r_free_array.data(), test_flag_value=True))
print
# Write mtz file
mtz_object = iotbx.mtz.object(mtz).add_crystal("crystal", "project", new_r_free_array.unit_cell()). \
add_dataset(name="dataset", wavelength=0). \
add_miller_array(miller_array=new_r_free_array, column_root_label=flag_name).mtz_object()
#mtz_object.show_summary(out=sys.stdout, prefix=" ")
mtz_object.write(file_name=mtz_out)
print
print "Writing:", mtz_out
print
def run(mtz, mtz_out, fraction, flag_name=None, ccp4=True, use_lattice_symmetry=True, n_shells=20):
# Open mtz
miller_arrays = iotbx.mtz.object(mtz).as_miller_arrays()
print "Opening", mtz
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()
if use_lattice_symmetry:
from cctbx.sgtbx import lattice_symmetry
print "Lattice symmetry:"
cb_op_to_niggli = complete_set.change_of_basis_op_to_niggli_cell()
tmp_ma = complete_set.change_basis( cb_op_to_niggli )
lattice_group = lattice_symmetry.group(tmp_ma.unit_cell(), max_delta=5.0)
print " ", tmp_ma.unit_cell(), lattice_group.laue_group_type()
print
new_r_free_array = complete_set.generate_r_free_flags(fraction=fraction,
max_free=None,
lattice_symmetry_max_delta=5.0,
use_lattice_symmetry=use_lattice_symmetry,
n_shells=n_shells)
print new_r_free_array.show_r_free_flags_info()
if ccp4:
new_r_free_array = new_r_free_array.customized_copy(data=r_free_utils.export_r_free_flags_for_ccp4(flags=new_r_free_array.data(), test_flag_value=True))
print
# Write mtz file
mtz_object = iotbx.mtz.object(mtz).add_crystal("crystal", "project", new_r_free_array.unit_cell()). \
add_dataset(name="dataset", wavelength=0). \
add_miller_array(miller_array=new_r_free_array, column_root_label=flag_name).mtz_object()
#mtz_object.show_summary(out=sys.stdout, prefix=" ")
mtz_object.write(file_name=mtz_out)
print
print "Writing:", mtz_out
print
def copy_flag_to_mtz(flag_array,
flag_name,
flag_value,
mtz_in,
mtz_out,
log_out=sys.stdout):
# Open mtz
miller_arrays = iotbx.mtz.object(mtz_in).as_miller_arrays()
print >> log_out, "Opening", mtz_in
if flag_name in [arr.info().label_string() for arr in miller_arrays]:
print >> log_out, "Error: The column %s already exists in the mtz file: %s" % (
flag_name, mtz_in)
return
print >> log_out, " 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 >> log_out, " d_max, d_min=", d_max, d_min
print >> log_out, " Symm:", input_symm.space_group_info(
), input_symm.unit_cell()
print >> log_out
# 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=log_out).common_set(
complete_set) #resolution_filter(d_min=d_min-0.01)
print >> log_out
r_free_flags.customized_copy(
data=r_free_flags.data() == flag_value).show_r_free_flags_info(
out=log_out)
# Write mtz file
mtz_object = iotbx.mtz.object(mtz_in).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.write(file_name=mtz_out)
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
flag_array, flag_name = get_flag_array(ref_arrays, flag_name)
# 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
copy_flag_to_mtz(flag_array, flag_name, flag_value, mtz, mtz_out)
print
print "Written:", mtz_out
print
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
