def __init__(self, millarr, mprint=sys.stdout.write):
from iotbx.gui_tools.reflections import get_array_description
data = millarr.data()
if (isinstance(data, flex.int)):
data = [e for e in data if e != display.inanval]
if millarr.is_complex_array():
data = flex.abs(millarr.data())
data = [e for e in data if not math.isnan(e)]
self.maxdata = max(data)
self.mindata = min(data)
self.maxsigmas = self.minsigmas = None
if millarr.sigmas() is not None:
data = millarr.sigmas()
data = [e for e in data if not math.isnan(e)]
self.maxsigmas = max(data)
self.minsigmas = min(data)
self.minmaxdata = (roundoff(self.mindata), roundoff(self.maxdata))
self.minmaxsigs = (roundoff(self.minsigmas), roundoff(self.maxsigmas))
self.labels = self.desc = ""
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
if millarr.info():
self.labels = millarr.info().label_string()
self.desc = get_array_description(millarr)
self.span = ("?", "?")
dmin = 0.0
dmax = 0.0
try:
self.span = (millarr.index_span().min(),
millarr.index_span().max())
dmin = millarr.d_max_min()[1]
dmax = millarr.d_max_min()[0]
except Exception, e:
mprint(to_str(e))
def run(args):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
reflection_file_def="data",
pdb_file_def="symmetry_file",
usage_string="xia2.plot_multiplicity scaled_unmerged.mtz [options]",
)
settings = pcl.work.extract()
file_name = settings.data
try:
hkl_file = any_reflection_file(file_name)
except Exception as e:
raise Sorry(str(e))
arrays = hkl_file.as_miller_arrays(merge_equivalents=False)
valid_arrays = []
array_info = []
for array in arrays:
if array.is_hendrickson_lattman_array():
continue
if (not array.is_real_array()) and (not array.is_complex_array()):
continue
labels = array.info().label_string()
desc = get_array_description(array)
array_info.append(f"{labels} ({desc})")
valid_arrays.append(array)
if len(valid_arrays) == 0:
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
miller_array = valid_arrays[0]
plot_multiplicity(miller_array, settings)
def load_reflections_file(self, file_name, set_array=True, data_only=True):
if (file_name != ""):
from iotbx.reflection_file_reader import any_reflection_file
from iotbx.gui_tools.reflections import get_array_description
try:
hkl_file = any_reflection_file(file_name)
except Exception as e:
raise Sorry(str(e))
arrays = hkl_file.as_miller_arrays(
merge_equivalents=False,
) #observation_type_callback=misc_dialogs.get_shelx_file_data_type)
#arrays = f.file_server.miller_arrays
valid_arrays = []
array_info = []
for array in arrays:
if array.is_hendrickson_lattman_array():
continue
elif (data_only):
if (not array.is_real_array()) and (
not array.is_complex_array()):
continue
labels = array.info().label_string()
desc = get_array_description(array)
array_info.append("%s (%s)" % (labels, desc))
valid_arrays.append(array)
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
elif (len(valid_arrays) >= 1):
if (set_array):
self.set_miller_array(valid_arrays[0])
return valid_arrays[0]
raise Abort()
def __init__(self, millarr):
from iotbx.gui_tools.reflections import get_array_description
data = millarr.data()
if (isinstance(data, flex.int)):
data = [e for e in data if e!= display.inanval]
if millarr.is_complex_array():
data = flex.abs(millarr.data())
self.maxdata =max( data )
self.mindata =min( data )
self.maxsigmas = self.minsigmas = display.nanval
if millarr.sigmas() is not None:
data = millarr.sigmas()
self.maxsigmas =max( data )
self.minsigmas =min( data )
self.minmaxstr = "MinMaxValues:[%s; %s], MinMaxSigmaValues:[%s; %s]" \
%(roundoff(self.mindata), roundoff(self.maxdata), \
roundoff(self.minsigmas), roundoff(self.maxsigmas))
else:
self.minmaxstr = "MinMaxValues:[%s; %s]" %(roundoff(self.mindata), roundoff(self.maxdata))
self.labels = self.desc = ""
if millarr.info():
self.labels = millarr.info().label_string()
self.desc = get_array_description(millarr)
self.span = "HKLs: %s to %s" % \
( millarr.index_span().min(), millarr.index_span().max())
self.infostr = "%s (%s), %s %s, %s, d_min: %s" % \
(self.labels, self.desc, millarr.size(), self.span, self.minmaxstr, roundoff(millarr.d_min()))
def load_reflections_file(self,
file_name,
set_array=True,
data_only=False):
file_name = to_str(file_name)
if (file_name != ""):
from iotbx.reflection_file_reader import any_reflection_file
from iotbx.gui_tools.reflections import get_array_description
try:
hkl_file = any_reflection_file(file_name)
except Exception as e:
raise Sorry(to_str(e))
arrays = hkl_file.as_miller_arrays(
merge_equivalents=False,
) #observation_type_callback=misc_dialogs.get_shelx_file_data_type)
#arrays = f.file_server.miller_arrays
valid_arrays = []
array_info = []
for array in arrays:
if array.is_hendrickson_lattman_array():
continue
elif (data_only):
if (not array.is_real_array()) and (
not array.is_complex_array()):
continue
labels = array.info().label_string()
desc = get_array_description(array)
array_info.append("%s (%s)" % (labels, desc))
valid_arrays.append(array)
self.valid_arrays = valid_arrays
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
elif (len(valid_arrays) == 1):
if (set_array):
self.set_miller_array(valid_arrays[0])
return valid_arrays[0]
else:
#dlg = SelectArrayDialog(self, -1, "Select data")
dlg = wx.SingleChoiceDialog(
parent=None,
message="Please select the data you wish to view:",
caption="Select data",
choices=array_info)
# print("kau labels info is", array_info) #Kau added
# print("Kau printing array_info from calling ", array_info)
if (dlg.ShowModal() == wx.ID_OK):
sel = dlg.GetSelection()
if (set_array):
self.set_miller_array(valid_arrays[sel])
wx.CallAfter(dlg.Destroy)
self.settings_panel.update_column_choices(
array_info, valid_arrays, sel) # kau added
# self.settings_panel.update_column_choices(array_info,valid_arrays,sel) # kau added
return valid_arrays[sel]
wx.CallAfter(dlg.Destroy)
raise Abort()
def run(args):
from libtbx.utils import Sorry
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
reflection_file_def="data",
pdb_file_def="symmetry_file",
usage_string="%s scaled_unmerged.mtz [options]" %
libtbx.env.dispatcher_name)
settings = pcl.work.extract()
file_name = settings.data
data_only = True
from iotbx.reflection_file_reader import any_reflection_file
from iotbx.gui_tools.reflections import get_array_description
try:
hkl_file = any_reflection_file(file_name)
except Exception as e:
raise Sorry(str(e))
arrays = hkl_file.as_miller_arrays(merge_equivalents=False)
valid_arrays = []
array_info = []
for array in arrays:
if array.is_hendrickson_lattman_array():
continue
elif (data_only):
if (not array.is_real_array()) and (not array.is_complex_array()):
continue
labels = array.info().label_string()
desc = get_array_description(array)
array_info.append("%s (%s)" % (labels, desc))
valid_arrays.append(array)
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
miller_array = valid_arrays[0]
settings.scale_colors_multiplicity = True
settings.scale_radii_multiplicity = True
settings.expand_to_p1 = True
settings.expand_anomalous = True
settings.slice_mode = True
if settings.plot.filename is not None:
view = MultiplicityViewPng(scene(miller_array, settings, merge=True),
settings=settings)
if settings.json.filename is not None:
view = MultiplicityViewJson(scene(miller_array, settings, merge=True),
settings=settings)
def load_reflections_file (self, file_name, set_array=True,
data_only=False) :
if (isinstance(file_name, unicode)) :
file_name = str(file_name)
if (file_name != "") :
from iotbx.reflection_file_reader import any_reflection_file
from iotbx.gui_tools.reflections import get_array_description
try :
hkl_file = any_reflection_file(file_name)
except Exception, e :
raise Sorry(str(e))
arrays = hkl_file.as_miller_arrays(merge_equivalents=False,
)#observation_type_callback=misc_dialogs.get_shelx_file_data_type)
#arrays = f.file_server.miller_arrays
valid_arrays = []
array_info = []
for array in arrays :
if array.is_hendrickson_lattman_array() :
continue
elif (data_only) :
if (not array.is_real_array()) and (not array.is_complex_array()) :
continue
labels = array.info().label_string()
desc = get_array_description(array)
array_info.append("%s (%s)" % (labels, desc))
valid_arrays.append(array)
if (len(valid_arrays) == 0) :
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
elif (len(valid_arrays) == 1) :
if (set_array) :
self.set_miller_array(valid_arrays[0])
return valid_arrays[0]
else :
#dlg = SelectArrayDialog(self, -1, "Select data")
dlg = wx.SingleChoiceDialog(parent=None,
message="Please select the data you wish to view:",
caption="Select data",
choices=array_info)
if (dlg.ShowModal() == wx.ID_OK) :
sel = dlg.GetSelection()
if (set_array) :
self.set_miller_array(valid_arrays[sel])
wx.CallAfter(dlg.Destroy)
return valid_arrays[sel]
wx.CallAfter(dlg.Destroy)
def __init__(self, millarr, mprint=sys.stdout.write):
from iotbx.gui_tools.reflections import get_array_description
data = millarr.data()
if (isinstance(data, flex.int)):
data = [e for e in data if e != display.inanval]
if millarr.is_complex_array():
data = flex.abs(millarr.data())
data = [e for e in data if not math.isnan(e)]
self.maxdata = max(data)
self.mindata = min(data)
self.maxsigmas = self.minsigmas = None
if millarr.sigmas() is not None:
data = millarr.sigmas()
data = [e for e in data if not math.isnan(e)]
self.maxsigmas = max(data)
self.minsigmas = min(data)
self.minmaxdata = (roundoff(self.mindata), roundoff(self.maxdata))
self.minmaxsigs = (roundoff(self.minsigmas), roundoff(self.maxsigmas))
self.labels = self.desc = ""
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
if millarr.info():
self.labels = millarr.info().label_string()
self.desc = get_array_description(millarr)
self.span = ("?", "?")
dmin = 0.0
dmax = 0.0
try:
self.span = (millarr.index_span().min(),
millarr.index_span().max())
dmin = millarr.d_max_min()[1]
dmax = millarr.d_max_min()[0]
except Exception as e:
mprint(to_str(e))
issymunique = millarr.is_unique_set_under_symmetry()
self.infotpl = (self.labels, self.desc, millarr.indices().size(),
self.span, self.minmaxdata, self.minmaxsigs,
(roundoff(dmin), roundoff(dmax)), issymunique)
self.infostr = "%s (%s), %s HKLs: %s, MinMax: %s, MinMaxSigs: %s, d_minmax: %s, SymUnique: %d" % self.infotpl
def exercise_reflections():
hkl_handler = reflections.reflections_handler(
allowed_param_names=phil_names)
from cctbx import miller
from cctbx import crystal
from cctbx.array_family import flex
symm = crystal.symmetry(unit_cell=(30, 30, 40, 90, 90, 120),
space_group_symbol="P 61 2 2")
miller_set = miller.build_set(crystal_symmetry=symm,
anomalous_flag=True,
d_min=1.5)
n_refl = miller_set.indices().size()
data = flex.random_double(n_refl)
sigmas = flex.random_double(n_refl)
f_obs = miller_set.array(data=data, sigmas=sigmas)
f_obs_merged = f_obs.average_bijvoet_mates()
flags = f_obs_merged.generate_r_free_flags()
# single dataset
mtz_dataset = f_obs_merged.as_mtz_dataset(column_root_label="F-obs",
wavelength=1.54)
mtz_dataset.add_miller_array(flags, column_root_label="R-free-flags")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(
file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
assert (hkl_handler.set_param_file(
file_name=file_name,
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) ==
['R-free-flags'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=False) ==
hkl_handler.get_rfree_labels(file_name=file_name,
neutron=True) == ['R-free-flags'])
assert approx_equal(
1.54,
hkl_handler.get_wavelength(file_name=file_name,
labels="F-obs,SIGF-obs"))
# join X/N datasets
hkl_handler = reflections.reflections_handler(
allowed_param_names=phil_names)
data_neutron = flex.random_double(n_refl)
sigmas_neutron = flex.random_double(n_refl)
f_obs_neutron = miller_set.array(data=data_neutron, sigmas=sigmas_neutron)
mtz_dataset = f_obs_merged.as_mtz_dataset(column_root_label="F-obs-xray")
mtz_dataset.add_miller_array(f_obs_neutron,
column_root_label="F-obs-neutron")
mtz_dataset.add_miller_array(flags, column_root_label="R-free-flags-xray")
mtz_dataset.add_miller_array(flags.deep_copy(),
column_root_label="R-free-flags-neutron")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(
file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
for i, phil_name in enumerate(phil_names[1:4]):
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name=phil_name) == False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) ==
['R-free-flags-xray', 'R-free-flags-neutron'])
assert (hkl_handler.get_rfree_labels(
file_name=file_name, neutron=False) == ['R-free-flags-xray'])
assert (hkl_handler.get_rfree_labels(
file_name=file_name, neutron=True) == ['R-free-flags-neutron'])
hkl_handler.check_symmetry(file_name=file_name)
assert (hkl_handler.get_data_labels(
file_param_name="refinement.input.xray_data.file_name") ==
hkl_handler.get_data_labels(file_name=file_name) ==
hkl_handler.get_amplitude_labels(file_name=file_name) == [
"F-obs-xray,SIGF-obs-xray",
"F-obs-neutron(+),SIGF-obs-neutron(+)," +
"F-obs-neutron(-),SIGF-obs-neutron(-)"
])
assert (hkl_handler.get_anomalous_data_labels(
file_param_name="refinement.input.xray_data.file_name") == [
"F-obs-neutron(+),SIGF-obs-neutron(+)," +
"F-obs-neutron(-),SIGF-obs-neutron(-)"
])
assert (hkl_handler.has_anomalous_data(
file_param_name="refinement.input.xray_data.file_name"))
assert (hkl_handler.get_rfree_flag_value(
array_name="F-obs-xray,SIGF-obs-xray",
file_param_name="refinement.input.xray_data.file_name") is None)
assert (hkl_handler.get_rfree_flag_value(
array_name='R-free-flags-xray',
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
1)
(d_max, d_min) = hkl_handler.d_max_min()
assert approx_equal(d_max, 25.98, eps=0.01)
assert approx_equal(d_min, 1.5, eps=0.01)
assert hkl_handler.space_group_as_str() == "P 61 2 2"
assert (hkl_handler.unit_cell_as_str() == "30 30 40 90 90 120")
assert (hkl_handler.unit_cell_as_str(
separator=",") == "30,30,40,90,90,120")
n_refl_merged = len(f_obs_merged.indices())
phi_array = f_obs_merged.random_phases_compatible_with_phase_restrictions(
deg=True)
fom_array = phi_array.array(data=flex.random_double(n_refl_merged))
hl_data = flex.hendrickson_lattman(n_refl_merged, (0, 0, 0, 0))
hl_coeffs = phi_array.array(data=hl_data)
assert (hl_coeffs.is_hendrickson_lattman_array())
from iotbx.mtz import label_decorator
import iotbx.mtz
class resolve_label_decorator(label_decorator):
def phases(self, *args, **kwds):
return label_decorator.phases(self, *args, **kwds) + "M"
def hendrickson_lattman(self, *args, **kwds):
return label_decorator.hendrickson_lattman(self, *args, **
kwds) + "M"
mtz_dataset = f_obs_merged.as_mtz_dataset(column_root_label="FP")
mtz_dataset.add_miller_array(phi_array,
column_root_label="PHIM",
label_decorator=resolve_label_decorator(),
column_types="P")
mtz_dataset.add_miller_array(fom_array,
column_root_label="FOMM",
column_types="W")
mtz_dataset.add_miller_array(hl_coeffs,
column_root_label="HL",
label_decorator=resolve_label_decorator())
fwt_map = f_obs_merged.customized_copy(
sigmas=None).phase_transfer(phi_array)
mtz_dataset.add_miller_array(
fwt_map,
column_root_label="FWT",
label_decorator=iotbx.mtz.ccp4_label_decorator())
mtz_dataset.add_miller_array(flags, column_root_label="FreeR_flag")
resolve_file = "tst_iotbx_gui_tools_resolve.mtz"
mtz_dataset.mtz_object().write(resolve_file)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["map_coeffs"])
hkl_handler.set_param_file(file_name=resolve_file,
file_param_name="map_coeffs")
assert hkl_handler.has_data(file_name=resolve_file)
l1 = hkl_handler.get_map_coeff_labels(file_name=resolve_file)
assert (l1 == ['FWT,PHWT', 'FP,PHIM,FOMM'])
l2 = hkl_handler.get_phase_deg_labels(file_name=resolve_file)
assert (l2 == [
'HLAM,HLBM,HLCM,HLDM',
'FWT,PHWT',
'PHIM',
]), l2
l3 = hkl_handler.get_experimental_phase_labels(file_name=resolve_file)
#print l3
l4 = hkl_handler.get_data_labels_for_wizard(file_name=resolve_file)
assert (l4 == ['FP SIGFP'])
l5 = hkl_handler.get_map_coeff_labels_for_build(file_name=resolve_file)
assert (l5 == ['FWT,PHWT', 'FP,PHIM,FOMM']), l5
hkl_in = hkl_handler.get_file(file_name=resolve_file)
assert (reflections.get_mtz_label_prefix(hkl_in) == "/crystal/dataset")
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file,
f_label="FP,SIGFP")
assert map_coeffs.is_complex_array()
try:
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file)
except Sorry:
pass
else:
raise Exception_expected
assert (hkl_handler.get_map_coeff_labels_for_fft(
file_name=resolve_file) == ['FWT,PHWT', 'FP,SIGFP PHIM FOMM'])
# miscellaneous utilities
file_name = resolve_file
hkl_in = file_reader.any_file(file_name)
hkl_server = hkl_in.file_server
assert approx_equal(reflections.get_high_resolution(hkl_server),
1.5,
eps=0.0001)
descriptions = []
for miller_array in hkl_server.miller_arrays:
(sg, uc) = reflections.get_miller_array_symmetry(miller_array)
assert (uc == "30 30 40 90 90 120")
assert (str(sg) == "P 61 2 2")
descriptions.append(reflections.get_array_description(miller_array))
assert (descriptions == [
'Amplitude', 'Phases', 'Weights', 'HL coeffs', 'Map coeffs',
'R-free flag'
]), descriptions
handler = reflections.reflections_handler()
handler.save_file(input_file=hkl_in)
assert (not handler.has_anomalous_data())
assert (handler.get_resolution_range(
file_name=file_name) == "(25.981 - 1.500)")
assert (handler.get_resolution_limits(file_name=file_name) == ('(25.981)',
'(1.500)'))
fmodel = phi_array.array(
data=flex.complex_double(n_refl_merged, complex(0.5, 0.8)))
m1 = phi_array.array(
data=flex.complex_double(n_refl_merged, complex(1, 0)))
m2 = phi_array.array(
data=flex.complex_double(n_refl_merged, complex(0.5, 0)))
m3 = phi_array.array(flex.complex_double(n_refl_merged, complex(1, 1)))
dec = label_decorator(phases_prefix="PH")
mtz_dataset = fmodel.as_mtz_dataset(column_root_label="F-model",
label_decorator=dec)
mtz_dataset.add_miller_array(m1,
column_root_label="2FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m2,
column_root_label="FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m3,
column_root_label="2FOFCWT_no_fill",
label_decorator=dec)
file_name = "tst_iotbx_gui_tools_map_coeffs.mtz"
mtz_dataset.mtz_object().write(file_name)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["fmodel", "map_coeffs"])
hkl_handler.set_param_file(file_name=file_name, file_param_name="fmodel")
assert (hkl_handler.get_fmodel_labels(file_name=file_name) == [
'F-model,PHF-model'
])
assert (hkl_handler.get_amplitude_labels(file_name=file_name) == [])
phi_labels = hkl_handler.get_phase_deg_labels(file_name=file_name)
assert (len(phi_labels) == 4)
phi_cols = hkl_handler.get_phase_column_labels(file_name=file_name)
assert (phi_cols == [
'PHF-model', 'PH2FOFCWT', 'PHFOFCWT', 'PH2FOFCWT_no_fill'
])
assert (len(
hkl_handler.get_amplitude_column_labels(file_name=file_name,
allow_conversion=True)) == 0)
fc_cols = hkl_handler.get_fmodel_labels(file_name=file_name,
first_column_only=True)
assert (fc_cols == ['F-model'])
hkl_server = file_reader.any_file(file_name).file_server
map_labels = reflections.get_map_coeff_labels(hkl_server)
assert (map_labels == [
'2FOFCWT,PH2FOFCWT',
'FOFCWT,PHFOFCWT',
'2FOFCWT_no_fill,PH2FOFCWT_no_fill',
])
map_labels = reflections.get_map_coeffs_for_build(hkl_server)
assert map_labels == [
'2FOFCWT,PH2FOFCWT', '2FOFCWT_no_fill,PH2FOFCWT_no_fill'
]
map_coeffs = reflections.extract_phenix_refine_map_coeffs(file_name)
assert (len(map_coeffs) == 3)
hkl_file = file_reader.any_file(file_name)
assert reflections.get_mtz_label_prefix(hkl_file) == "/crystal/dataset"
# other stuff
(fp, fpp) = reflections.get_fp_fpp_from_sasaki("Se", 0.979)
assert fp is not None and fpp is not None
from iotbx.gui_tools.reflections import get_array_description
try :
hkl_file = any_reflection_file(file_name)
except Exception, e :
raise Sorry(str(e))
arrays = hkl_file.as_miller_arrays(merge_equivalents=False)
valid_arrays = []
array_info = []
for array in arrays :
if array.is_hendrickson_lattman_array() :
continue
elif (data_only) :
if (not array.is_real_array()) and (not array.is_complex_array()) :
continue
labels = array.info().label_string()
desc = get_array_description(array)
array_info.append("%s (%s)" % (labels, desc))
valid_arrays.append(array)
if (len(valid_arrays) == 0) :
msg = "No arrays of the supported types in this file."
raise Sorry(msg)
miller_array = valid_arrays[0]
settings.scale_colors_multiplicity = True
settings.scale_radii_multiplicity = True
settings.expand_to_p1 = True
settings.expand_anomalous = True
settings.slice_mode = True
view = MultiplicityViewPng(
scene(miller_array, settings, merge=True), settings=settings)
def exercise_reflections () :
hkl_handler = reflections.reflections_handler(allowed_param_names=phil_names)
from cctbx import miller
from cctbx import crystal
from cctbx.array_family import flex
symm = crystal.symmetry(
unit_cell=(30,30,40,90,90,120),
space_group_symbol="P 61 2 2")
miller_set = miller.build_set(
crystal_symmetry=symm,
anomalous_flag=True,
d_min=1.5)
n_refl = miller_set.indices().size()
data = flex.random_double(n_refl)
sigmas = flex.random_double(n_refl)
f_obs = miller_set.array(data=data, sigmas=sigmas)
f_obs_merged = f_obs.average_bijvoet_mates()
flags = f_obs_merged.generate_r_free_flags()
# single dataset
mtz_dataset = f_obs_merged.as_mtz_dataset(
column_root_label="F-obs",
wavelength=1.54)
mtz_dataset.add_miller_array(flags,
column_root_label="R-free-flags")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name="refinement.input.xray_data.r_free_flags.file_name")
== False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) == ['R-free-flags'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=False) ==
hkl_handler.get_rfree_labels(file_name=file_name, neutron=True) ==
['R-free-flags'])
assert approx_equal(1.54, hkl_handler.get_wavelength(file_name=file_name,
labels="F-obs,SIGF-obs"))
# join X/N datasets
hkl_handler = reflections.reflections_handler(allowed_param_names=phil_names)
data_neutron = flex.random_double(n_refl)
sigmas_neutron = flex.random_double(n_refl)
f_obs_neutron = miller_set.array(data=data_neutron, sigmas=sigmas_neutron)
mtz_dataset = f_obs_merged.as_mtz_dataset(
column_root_label="F-obs-xray")
mtz_dataset.add_miller_array(f_obs_neutron,
column_root_label="F-obs-neutron")
mtz_dataset.add_miller_array(flags,
column_root_label="R-free-flags-xray")
mtz_dataset.add_miller_array(flags.deep_copy(),
column_root_label="R-free-flags-neutron")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
for i, phil_name in enumerate(phil_names[1:4]) :
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name=phil_name) == False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) ==
['R-free-flags-xray', 'R-free-flags-neutron'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=False) ==
['R-free-flags-xray'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=True) ==
['R-free-flags-neutron'])
hkl_handler.check_symmetry(file_name=file_name)
assert (hkl_handler.get_data_labels(
file_param_name="refinement.input.xray_data.file_name") ==
hkl_handler.get_data_labels(file_name=file_name) ==
hkl_handler.get_amplitude_labels(file_name=file_name) ==
["F-obs-xray,SIGF-obs-xray", "F-obs-neutron(+),SIGF-obs-neutron(+),"+
"F-obs-neutron(-),SIGF-obs-neutron(-)"])
assert (hkl_handler.get_anomalous_data_labels(
file_param_name="refinement.input.xray_data.file_name") ==
["F-obs-neutron(+),SIGF-obs-neutron(+)," +
"F-obs-neutron(-),SIGF-obs-neutron(-)"])
assert (hkl_handler.has_anomalous_data(
file_param_name="refinement.input.xray_data.file_name"))
assert (hkl_handler.get_rfree_flag_value(
array_name="F-obs-xray,SIGF-obs-xray",
file_param_name="refinement.input.xray_data.file_name") is None)
assert (hkl_handler.get_rfree_flag_value(array_name='R-free-flags-xray',
file_param_name="refinement.input.xray_data.r_free_flags.file_name") == 1)
(d_max, d_min) = hkl_handler.d_max_min()
assert approx_equal(d_max, 25.98, eps=0.01)
assert approx_equal(d_min, 1.5, eps=0.01)
assert hkl_handler.space_group_as_str() == "P 61 2 2"
assert (hkl_handler.unit_cell_as_str() ==
"30 30 40 90 90 120")
assert (hkl_handler.unit_cell_as_str(separator=",") ==
"30,30,40,90,90,120")
n_refl_merged = len(f_obs_merged.indices())
phi_array = f_obs_merged.random_phases_compatible_with_phase_restrictions(
deg=True)
fom_array = phi_array.array(data=flex.random_double(n_refl_merged))
hl_data = flex.hendrickson_lattman(n_refl_merged, (0,0,0,0))
hl_coeffs = phi_array.array(data=hl_data)
assert (hl_coeffs.is_hendrickson_lattman_array())
from iotbx.mtz import label_decorator
import iotbx.mtz
class resolve_label_decorator (label_decorator) :
def phases (self, *args, **kwds) :
return label_decorator.phases(self, *args, **kwds) + "M"
def hendrickson_lattman (self, *args, **kwds) :
return label_decorator.hendrickson_lattman(self, *args, **kwds) + "M"
mtz_dataset = f_obs_merged.as_mtz_dataset(
column_root_label="FP")
mtz_dataset.add_miller_array(phi_array,
column_root_label="PHIM",
label_decorator=resolve_label_decorator(),
column_types="P")
mtz_dataset.add_miller_array(fom_array,
column_root_label="FOMM",
column_types="W")
mtz_dataset.add_miller_array(hl_coeffs,
column_root_label="HL",
label_decorator=resolve_label_decorator())
fwt_map = f_obs_merged.customized_copy(sigmas=None).phase_transfer(phi_array)
mtz_dataset.add_miller_array(fwt_map,
column_root_label="FWT",
label_decorator=iotbx.mtz.ccp4_label_decorator())
mtz_dataset.add_miller_array(flags,
column_root_label="FreeR_flag")
resolve_file = "tst_iotbx_gui_tools_resolve.mtz"
mtz_dataset.mtz_object().write(resolve_file)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["map_coeffs"])
hkl_handler.set_param_file(
file_name=resolve_file,
file_param_name="map_coeffs")
assert hkl_handler.has_data(file_name=resolve_file)
l1 = hkl_handler.get_map_coeff_labels(file_name=resolve_file)
assert (l1 == ['FWT,PHWT', 'FP,PHIM,FOMM'])
l2 = hkl_handler.get_phase_deg_labels(file_name=resolve_file)
assert (l2 == ['HLAM,HLBM,HLCM,HLDM', 'FWT,PHWT', 'PHIM',]), l2
l3 = hkl_handler.get_experimental_phase_labels(file_name=resolve_file)
#print l3
l4 = hkl_handler.get_data_labels_for_wizard(file_name=resolve_file)
assert (l4 == ['FP SIGFP'])
l5 = hkl_handler.get_map_coeff_labels_for_build(file_name=resolve_file)
assert (l5 == ['FWT,PHWT', 'FP,PHIM,FOMM']), l5
hkl_in = hkl_handler.get_file(file_name=resolve_file)
assert (reflections.get_mtz_label_prefix(hkl_in) == "/crystal/dataset")
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file,
f_label="FP,SIGFP")
assert map_coeffs.is_complex_array()
try :
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file)
except Sorry :
pass
else :
raise Exception_expected
assert (hkl_handler.get_map_coeff_labels_for_fft(file_name=resolve_file) ==
['FWT,PHWT', 'FP,SIGFP PHIM FOMM'])
# miscellaneous utilities
file_name = resolve_file
hkl_in = file_reader.any_file(file_name)
hkl_server = hkl_in.file_server
assert approx_equal(reflections.get_high_resolution(hkl_server), 1.5,
eps=0.0001)
descriptions = []
for miller_array in hkl_server.miller_arrays :
(sg, uc) = reflections.get_miller_array_symmetry(miller_array)
assert (uc == "30 30 40 90 90 120")
assert (str(sg) == "P 61 2 2")
descriptions.append(reflections.get_array_description(miller_array))
assert (descriptions == [
'Amplitude', 'Phases', 'Weights', 'HL coeffs', 'Map coeffs',
'R-free flag']), descriptions
handler = reflections.reflections_handler()
handler.save_file(input_file=hkl_in)
assert (not handler.has_anomalous_data())
assert (handler.get_resolution_range(file_name=file_name)=="(25.981 - 1.500)")
assert (handler.get_resolution_limits(file_name=file_name) ==
('(25.981)', '(1.500)'))
fmodel = phi_array.array(data=flex.complex_double(n_refl_merged,
complex(0.5,0.8)))
m1 = phi_array.array(data=flex.complex_double(n_refl_merged, complex(1,0)))
m2 = phi_array.array(data=flex.complex_double(n_refl_merged, complex(0.5,0)))
m3 = phi_array.array(flex.complex_double(n_refl_merged, complex(1,1)))
dec = label_decorator(phases_prefix="PH")
mtz_dataset = fmodel.as_mtz_dataset(
column_root_label="F-model",
label_decorator=dec)
mtz_dataset.add_miller_array(m1,
column_root_label="2FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m2,
column_root_label="FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m3,
column_root_label="2FOFCWT_no_fill",
label_decorator=dec)
file_name = "tst_iotbx_gui_tools_map_coeffs.mtz"
mtz_dataset.mtz_object().write(file_name)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["fmodel", "map_coeffs"])
hkl_handler.set_param_file(
file_name=file_name,
file_param_name="fmodel")
assert (hkl_handler.get_fmodel_labels(file_name=file_name) ==
['F-model,PHF-model'])
assert (hkl_handler.get_amplitude_labels(file_name=file_name) == [])
phi_labels = hkl_handler.get_phase_deg_labels(file_name=file_name)
assert (len(phi_labels) == 4)
phi_cols = hkl_handler.get_phase_column_labels(file_name=file_name)
assert (phi_cols == ['PHF-model','PH2FOFCWT','PHFOFCWT','PH2FOFCWT_no_fill'])
assert (len(hkl_handler.get_amplitude_column_labels(file_name=file_name,
allow_conversion=True)) == 0)
fc_cols = hkl_handler.get_fmodel_labels(file_name=file_name,
first_column_only=True)
assert (fc_cols == ['F-model'])
hkl_server = file_reader.any_file(file_name).file_server
map_labels = reflections.get_map_coeff_labels(hkl_server)
assert (map_labels == ['2FOFCWT,PH2FOFCWT', 'FOFCWT,PHFOFCWT',
'2FOFCWT_no_fill,PH2FOFCWT_no_fill',])
map_labels = reflections.get_map_coeffs_for_build(hkl_server)
assert map_labels == ['2FOFCWT,PH2FOFCWT','2FOFCWT_no_fill,PH2FOFCWT_no_fill']
map_coeffs = reflections.extract_phenix_refine_map_coeffs(file_name)
assert (len(map_coeffs) == 3)
hkl_file = file_reader.any_file(file_name)
assert reflections.get_mtz_label_prefix(hkl_file) == "/crystal/dataset"
# other stuff
(fp, fpp) = reflections.get_fp_fpp_from_sasaki("Se", 0.979)
assert fp is not None and fpp is not None
