def run(mtz_data_file, d_col, mtz_template_file, t_col, mtz_out_file):
# READ DATA MTZ
miller_arrays_data = reflection_file_reader.any_reflection_file(file_name=mtz_data_file).as_miller_arrays()
labels = [ma.info().labels[0] for ma in miller_arrays_data]
try:
F_data = miller_arrays_data[labels.index(d_col)]
except:
print "ERROR: column label not found in input data file"
sys.exit()
# READ TEMPLATE MTZ
miller_arrays_template = reflection_file_reader.any_reflection_file(file_name=mtz_template_file).as_miller_arrays()
labels = [ma.info().labels[0] for ma in miller_arrays_template]
try:
F_template = miller_arrays_template[labels.index(t_col)]
except:
print "ERROR: column label not found in reference template file"
sys.exit()
# SELECT REFLECTIONS
# ~ print F_template.size()
# ~ print F_data.size()
F_data, tmp = F_data.common_sets(F_template)
# ~ print tmp.size()
# ~ print F_data.size()
# WRITE NEW MTZ
mtz_dataset = F_data.as_mtz_dataset(column_root_label="FP")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name=mtz_out_file)
def exercise_get_experimental_phases():
crystal_symmetry = crystal.symmetry(
unit_cell=(30,31,32,85,95,100),
space_group_symbol="P 1")
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=3)
input_array = miller_set.array(
data=flex.hendrickson_lattman(miller_set.indices().size(), (0,0,0,0)))
mtz_dataset = input_array.as_mtz_dataset(column_root_label="P")
mtz_dataset.mtz_object().write("tmp.mtz")
reflection_files = [reflection_file_reader.any_reflection_file(
file_name="tmp.mtz")]
err = StringIO()
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=err)
experimental_phases = reflection_file_srv.get_experimental_phases(
file_name=None,
labels=None,
ignore_all_zeros=False,
parameter_scope="experimental_phases")
assert str(experimental_phases.info()) == "tmp.mtz:PA,PB,PC,PD"
try:
reflection_file_srv.get_experimental_phases(
file_name=None,
labels=None,
ignore_all_zeros=True,
parameter_scope="experimental_phases")
except Sorry, e:
assert str(e) == "No array of experimental phases found."
assert err.getvalue() == """\
def extract_miller_array_from_file(file_name, label=None, type=None, log=None):
if(log is None): log = sys.stdout
assert type in ["complex", "real", None]
result = None
miller_arrays = reflection_file_reader.any_reflection_file(file_name =
file_name).as_miller_arrays()
def get_flag(ma):
return (type == "complex" and ma.is_complex_array()) or \
(type == "real" and ma.is_real_array()) or \
type is None
print >> log, " Available suitable arrays:"
suitable_arrays = []
suitable_labels = []
for ma in miller_arrays:
if(get_flag(ma=ma)):
print >> log, " ", ma.info().label_string()
suitable_arrays.append(ma)
suitable_labels.append(ma.info().label_string())
print >> log
if( len(suitable_arrays) == 0): raise Sorry("No suitable arrays.")
elif(len(suitable_arrays) == 1): result = suitable_arrays[0]
elif(len(suitable_arrays) > 1):
if(label is None):
msg='''Multiple choices available. No map coefficients array selected.
See choices listed above and use "label=" to select one.
Example: label="2FOFCWT,PH2FOFCWT"'''
raise Sorry(msg)
else:
for ma in miller_arrays:
if(get_flag(ma=ma) and (ma.info().label_string() == label)):
print >> log, " Selected:", ma.info().label_string()
result = ma
return result
def load_reflections_file (self, file_name, **kwds) :
if (isinstance(file_name, unicode)) :
file_name = str(file_name)
if (file_name != "") :
from iotbx.reflection_file_reader import any_reflection_file
from cctbx import miller
from scitbx.array_family import flex
try :
hkl_file = any_reflection_file(file_name)
except Exception, e :
raise Sorry(str(e))
arrays = hkl_file.as_miller_arrays(merge_equivalents=True)
f_obs = f_model = None
for array in arrays :
labels = array.info().label_string()
if labels.startswith("F-obs-filtered") :
f_obs = array
elif labels.startswith("F-model") :
f_model = array
if (f_obs is None) or (f_model is None) :
raise Sorry("This does not appear to be a phenix.refine output "+
"file. The MTZ file should contain data arrays for the filtered "+
"amplitudes (F-obs) and F-model.")
f_delta = f_obs.customized_copy(sigmas=None,
data=flex.abs(f_obs.data()-abs(f_model).data())).set_info(
miller.array_info(labels=["abs(F_obs - F_model)"]))
self.set_miller_array(f_delta)
def _try_as_hkl (self) : from iotbx.reflection_file_reader import any_reflection_file # XXX this is unfortunate, but unicode breaks Boost.Python extensions hkl_file = any_reflection_file(str(self.file_name)) assert (hkl_file.file_type() is not None), "Not a valid reflections file." self._file_type = "hkl" self._file_object = hkl_file
def check(tuple_calc, selection, prefix):
miller_arrays = reflection_file_reader.any_reflection_file(file_name =
prefix+"polder_map_coeffs.mtz").as_miller_arrays()
mc_polder = None
for ma in miller_arrays:
lbl = ma.info().label_string()
if(lbl == "mFo-DFc_polder,PHImFo-DFc_polder"):
mc_polder = ma.deep_copy()
assert (mc_polder is not None)
cg = maptbx.crystal_gridding(
unit_cell = mc_polder.unit_cell(),
d_min = mc_polder.d_min(),
resolution_factor = 0.25,
space_group_info = mc_polder.space_group_info())
map_polder = get_map(cg=cg, mc=mc_polder)
pdb_hierarchy = iotbx.pdb.input(
source_info=None, lines=pdb_str).construct_hierarchy()
sel = pdb_hierarchy.atom_selection_cache().selection(string = selection)
sites_cart_lig = pdb_hierarchy.atoms().extract_xyz().select(sel)
sites_frac_lig = mc_polder.unit_cell().fractionalize(sites_cart_lig)
mp = get_map_stats(
map = map_polder,
sites_frac = sites_frac_lig)
#
mmm_mp = mp.min_max_mean().as_tuple()
print "Polder map : %7.3f %7.3f %7.3f" % mmm_mp
assert approx_equal(mmm_mp, tuple_calc, eps=1.0), "\
calculated is %s and expected is %s" % (mmm_mp, tuple_calc)
def run(params):
hkl_in = reflection_file_reader.any_reflection_file(params.hklin)
miller_arrays = hkl_in.as_miller_arrays(merge_equivalents=False)
miller_arrays = filter(lambda x: x.is_xray_intensity_array(), miller_arrays)
print "Reading intensity data from %s" % params.hklin
for ma in miller_arrays:
print " %s" % ma.info()
if len(miller_arrays) > 1:
print "Using %s for analysis" % miller_arrays[0].info()
elif len(miller_arrays) == 0:
print "Error: No intensity data!"
return
iobs = miller_arrays[0]
est = estimate_resolution_based_on_cc_half(iobs, params.cc_one_half_min,
params.cc_half_tol, params.n_bins,
params.anomalous, sys.stdout)
print
print "Suggested cutoff= %.2f A (CC1/2= %.4f)" %(est.d_min, est.cc_at_d_min)
print "# Treated as *%s* data" % ("anomalous" if params.anomalous else "non-anomalous")
if params.show_plot:
est.show_plot(filename="cchalf_plot.pdf")
def get_miller_f_from_reflection_file(hklin):
flag_hklin_found = False
miller_array_f = None
if hklin is not None:
flag_hklin_found = True
reflection_file = reflection_file_reader.any_reflection_file(hklin)
miller_arrays = reflection_file.as_miller_arrays()
is_found_as_intensity_array = False
is_found_as_amplitude_array = False
is_found_as_complex_array = False
for miller_array in miller_arrays:
if miller_array.is_xray_amplitude_array():
miller_array_f = miller_array.deep_copy()
is_found_as_amplitude_array = True
break
elif miller_array.is_xray_intensity_array():
is_found_as_intensity_array = True
miller_array_converted_to_amplitude = miller_array.enforce_positive_amplitudes()
elif miller_array.is_complex_array():
is_found_as_complex_array = True
miller_array_converted_to_amplitude = miller_array.amplitudes()
if is_found_as_amplitude_array == False:
if is_found_as_intensity_array or is_found_as_complex_array:
miller_array_f = miller_array_converted_to_amplitude.deep_copy()
else:
flag_hklin_found = False
return flag_hklin_found, miller_array_f
def run(args, command_name="iotbx.r_free_flags_accumulation"):
def raise_usage():
raise Usage("%s reflection_file [label=value]" % command_name)
if (len(args) == 0 or "--help" in args or "-h" in args):
raise_usage()
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="r_free_flags_accumulation")
reflection_files = []
for arg in args:
if (os.path.isfile(arg)):
refl_file = reflection_file_reader.any_reflection_file(
file_name=arg)
if (refl_file.file_type() is not None):
reflection_files.append(refl_file)
arg = None
if (arg is not None):
try: command_line_params = argument_interpreter.process(arg=arg)
except KeyboardInterrupt: raise
except Exception: raise Sorry("Unknown file or keyword: %s" % arg)
else: phil_objects.append(command_line_params)
params_scope = master_params.fetch(sources=phil_objects).extract()
params = params_scope.r_free_flags_accumulation
srv = reflection_file_utils.reflection_file_server(
reflection_files=reflection_files)
r_free_flags, test_flag_value = srv.get_r_free_flags(
file_name=params.file_name,
label=params.label,
test_flag_value=params.test_flag_value,
disable_suitability_test=params.disable_suitability_test,
parameter_scope="r_free_flags_accumulation")
params.file_name = r_free_flags.info().source
params.label = r_free_flags.info().label_string()
params.test_flag_value = test_flag_value
if (params.output is None):
params.output = os.path.basename(params.file_name) \
+ ".r_free_flags_accumulation"
working_params = master_params.format(python_object=params_scope)
working_params.show()
print
print "#phil __OFF__"
r_free_flags = r_free_flags.array(
data=r_free_flags.data()==params.test_flag_value)
r_free_flags.show_r_free_flags_info()
print
accu = r_free_flags \
.sort(by_value="resolution") \
.r_free_flags_accumulation()
print "Writing file: %s" % show_string(params.output)
print " 1. column: reflection counts, sorted by resolution"
print " 2. column: number of free reflections / total number of reflections"
sys.stdout.flush()
out = open(params.output, "w")
for line in params.plot_header:
print >> out, line
for c,f in zip(accu.reflection_counts, accu.free_fractions):
print >> out, c, f
out.close()
print
sys.stdout.flush()
def mtz2ccp4maps(filename, prefix, amplitudes, phases):
'''
Creates a temporary directory and dumps all maps from the given MTZ file
into this directory as CCP4 maps files. Returns the path of the temporary
directory.
'''
import tempfile
from iotbx.reflection_file_reader import any_reflection_file
hkl_in = any_reflection_file(file_name=filename)
temp_dir = tempfile.mkdtemp()
for i_map, array in enumerate(hkl_in.as_miller_arrays()):
if not array.is_complex_array():
continue
labels = array.info().labels
if amplitudes and [amplitudes, phases] != labels:
continue
fft_map = array.fft_map(resolution_factor=0.25).apply_sigma_scaling()
map_filename = os.path.join(temp_dir, prefix + '_' + '_'.join(labels))
if hasattr(fft_map, 'as_ccp4_map'):
fft_map.as_ccp4_map(file_name=map_filename + '.ccp4')
else:
fft_map.as_xplor_map(file_name=map_filename + '.xplor')
return temp_dir
def get_f_obs_and_flags(reflection_file_name,
crystal_symmetry,
f_obs_label = None,
r_free_flags_label = None,
log = None):
reflection_files = []
reflection_files.append(reflection_file_reader.any_reflection_file(
file_name = reflection_file_name, ensure_read_access = False))
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry = crystal_symmetry,
force_symmetry = True,
reflection_files = reflection_files,
err = log)
parameters = mmtbx.utils.data_and_flags_master_params().extract()
if(f_obs_label is not None):
parameters.labels = command_line.options.f_obs_label
if(r_free_flags_label is not None):
parameters.r_free_flags.label = command_line.options.r_free_flags_label
determine_data_and_flags_result = mmtbx.utils.determine_data_and_flags(
reflection_file_server = reflection_file_server,
parameters = parameters,
keep_going = True,
log = log)
f_obs = determine_data_and_flags_result.f_obs
r_free_flags = determine_data_and_flags_result.r_free_flags
return f_obs, r_free_flags
def get_miller_array_from_mtz(mtz_filename):
flag_hklisoin_found = False
miller_array_iso = None
if mtz_filename is not None:
flag_hklisoin_found = True
reflection_file_iso = reflection_file_reader.any_reflection_file(mtz_filename)
miller_arrays_iso=reflection_file_iso.as_miller_arrays()
is_found_iso_as_intensity_array = False
is_found_iso_as_amplitude_array = False
for miller_array in miller_arrays_iso:
if miller_array.is_xray_intensity_array():
miller_array_iso = miller_array.deep_copy()
is_found_iso_as_intensity_array = True
break
elif miller_array.is_xray_amplitude_array():
is_found_iso_as_amplitude_array = True
miller_array_converted_to_intensity = miller_array.as_intensity_array()
if is_found_iso_as_intensity_array == False:
if is_found_iso_as_amplitude_array:
miller_array_iso = miller_array_converted_to_intensity.deep_copy()
else:
flag_hklisoin_found = False
if miller_array_iso is not None:
perm = miller_array_iso.sort_permutation(by_value="resolution", reverse=True)
miller_array_iso = miller_array_iso.select(perm)
return flag_hklisoin_found, miller_array_iso
def __init__(self, mtz_file, params=None):
print 'Reading reflections from %s' %mtz_file
from iotbx.reflection_file_reader import any_reflection_file
result = any_reflection_file(mtz_file)
assert result.file_type() == 'ccp4_mtz'
mtz_object = result.file_content()
mtz_object.show_summary()
intensities = None
for ma in result.as_miller_arrays(merge_equivalents=False):
if (params.anomalous and
ma.info().labels == ['I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)']):
assert ma.anomalous_flag()
intensities = ma.merge_equivalents().array() # XXX why is this necessary?
elif (not params.anomalous and ma.info().labels == ['IMEAN', 'SIGIMEAN']):
assert not ma.anomalous_flag()
intensities = ma
assert intensities.is_xray_intensity_array()
amplitudes = intensities.french_wilson(params=params)
assert amplitudes.is_xray_amplitude_array()
mtz_dataset = mtz_object.crystals()[1].datasets()[0]
mtz_dataset.add_miller_array(amplitudes, column_root_label='F')
mtz_object.add_history('cctbx.french_wilson analysis')
print 'Writing reflections to %s' %(params.hklout)
mtz_object.show_summary()
mtz_object.write(params.hklout)
def get_array(file_name=None,labels=None):
print "Reading from %s" %(file_name)
from iotbx import reflection_file_reader
reflection_file = reflection_file_reader.any_reflection_file(
file_name=file_name)
array_to_use=None
if labels:
for array in reflection_file.as_miller_arrays():
if ",".join(array.info().labels)==labels:
array_to_use=array
break
else:
for array in reflection_file.as_miller_arrays():
if array.is_complex_array() or array.is_xray_amplitude_array() or\
array.is_xray_intensity_array():
array_to_use=array
break
if not array_to_use:
text=""
for array in reflection_file.as_miller_arrays():
text+=" %s " %(",".join(array.info().labels))
raise Sorry("Cannot identify array to use...possibilities: %s" %(text))
print "Using the array %s" %(",".join(array_to_use.info().labels))
return array_to_use
def get_rfree(file_name):
"""Return the Rfree label"""
reflection_file = reflection_file_reader.any_reflection_file(file_name=file_name)
if not reflection_file.file_type()=="ccp4_mtz":
raise RuntimeError("File is not of type ccp4_mtz: {0}".format(file_name))
return _get_rfree(reflection_file.file_content())
def _import(self, event):
self._gauge.Show()
self._gauge_label.Show()
self.Fit()
pdb = str(self._pdb_entry.GetValue())
if not os.path.exists(self._root + '/temp'):
os.mkdir(self._root + '/temp')
self._set_status(0, 'Downloading PDB')
urllib.urlretrieve('http://www.rcsb.org/pdb/files/' + pdb.lower() + '.pdb.gz', self._root + '/temp/' + pdb.lower() + '.pdb.gz')
self._set_status(1, 'Uncompressing PDB')
out = open(self._root + '/temp/' + pdb.lower() + '.pdb', 'wb')
out.write(gzip.open(self._root + '/temp/' + pdb.lower() + '.pdb.gz', 'rb').read())
out.close()
self._set_status(2, 'Converting PDB to INS')
PDBImporter(self._root + '/temp/' + pdb.lower() + '.pdb', self._root)
self._set_status(3, 'Downloading SFs')
urllib.urlretrieve('http://www.rcsb.org/pdb/files/r' + pdb.upper() + 'sf.ent.gz', self._root + '/temp/r' + pdb.upper() + 'sf.ent.gz')
self._set_status(4, 'Uncompressing SFs')
sff = self._root + '/temp/' + pdb.lower() + '.cif'
out = open(sff, 'wb')
out.write(gzip.open(self._root + '/temp/r' + pdb.upper() + 'sf.ent.gz', 'rb').read())
out.close()
self._set_status(5, 'Finding Columns')
if os.path.exists(sff):
m = reflection_file_reader.any_reflection_file(sff)
fs = []
rs = []
for col in m.as_miller_arrays():
if (col.is_xray_intensity_array() or col.is_xray_amplitude_array()) and not col.anomalous_flag():
fs.append(col.info().label_string())
elif col.info().label_string().find('status') > -1:
rs.append(col.info().label_string())
self._set_status(6, 'Converting CIF to HKL')
if len(fs) > 0:
for f in fs:
if len(rs) > 0:
CIFImporter(sff, f, rs[0], self._root)
else:
CIFImporter(sff, f, '', self._root, True)
self._set_status(7, 'Cleaning Up...')
os.remove(self._root + '/temp/' + pdb.lower() + '.pdb.gz')
os.remove(self._root + '/temp/' + pdb.lower() + '.pdb')
os.remove(self._root + '/temp/r' + pdb.upper() + 'sf.ent.gz')
os.remove(self._root + '/temp/' + pdb.lower() + '.cif')
self._set_status(8, 'Finished')
self._close('')
wx.MessageBox('Input files successfully generated for ' + pdb, 'Sucess', style=wx.OK | wx.CENTRE)
def change_space_group (file_name, space_group_info) : """ Update the space group in an MTZ file, writing it in place. """ mtz_in = reflection_file_reader.any_reflection_file(file_name) assert (mtz_in.file_type() == "ccp4_mtz") mtz_object = mtz_in.file_content() mtz_new = mtz_object.set_space_group_info(space_group_info) mtz_new.write(file_name)
def get_target_map(reflection_file_name, log=sys.stderr) :
miller_arrays = reflection_file_reader.any_reflection_file(file_name =
reflection_file_name).as_miller_arrays()
ma = miller_arrays[0]
fft_map = ma.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
print >> log, "\nUsing sigma scaled map.\n"
target_map = fft_map.real_map_unpadded()
return target_map
def resolve_indexing_ambiguity_using_reference(dirs, reidx_ops, reference_file):
from iotbx import reflection_file_reader
hkl_ref = filter(lambda x: x.is_xray_intensity_array(),
reflection_file_reader.any_reflection_file(reference_file).as_miller_arrays(merge_equivalents=False))
if len(hkl_ref) == 0:
raise Exception("No intensity data in %s"%reference_file)
ref_data = hkl_ref[0].merge_equivalents(use_internal_variance=False).array()
data = {}
# Read all (strong) data
for wd in dirs:
print "reading", wd
tmp = read_strong_i_from_xds_ascii(os.path.join(wd, "XDS_ASCII.HKL"))
if tmp is None:
continue
data[wd] = tmp
# Compare with reference
best_op = map(lambda x: 0, xrange(len(dirs)))
for i in xrange(len(dirs)):
if dirs[i] not in data:
continue
data_i = data[dirs[i]]
cc_list = []
idx_max = 0
for k, rop in enumerate(reidx_ops):
if k == 0:
data_i_ = data_i
else:
data_i_ = data_i.customized_copy(indices=rop.apply(data_i.indices()))
cc_list.append(get_cc(data_i_, ref_data))
if cc_list[k] is not None:
if cc_list[k] > cc_list[idx_max]: idx_max = k
if len(cc_list) - cc_list.count(None) < 2:
print i,"skip"
continue
cc_max = cc_list[idx_max]
print i,
for cc in cc_list: print cc,
print
best_op[i] = idx_max
print "\n Best reindexing operators"
print "=================================\n"
for i in xrange(len(dirs)):
print "%.3d op= %d %s" % (i, best_op[i], dirs[i])
print "\nApplying.."
for i, opi in enumerate(best_op):
if opi == 0: continue
# XXX treat!!
print "Done."
def __init__(self,
refinement_type = 'None'):
self.pdb_structure = pdb.hierarchy.input(command_line_args.pdb_input)
self.get_crystal_symmetry()
self.xray_structure = self.pdb_structure.input.xray_structure_simple()
self.miller_arrays = any_reflection_file(command_line_args.reflection_input).as_miller_arrays()
self.miller_arrays_work_test_partition()
return
def run(processed_args, params):
if(params.scattering_table not in ["n_gaussian","wk1995",
"it1992","neutron"]):
raise Sorry("Incorrect scattering_table.")
crystal_symmetry = None
crystal_symmetries = []
for f in [str(params.pdb_file_name), str(params.reflection_file_name)]:
cs = crystal_symmetry_from_any.extract_from(f)
if(cs is not None): crystal_symmetries.append(cs)
if(len(crystal_symmetries) == 1): crystal_symmetry = crystal_symmetries[0]
elif(len(crystal_symmetries) == 0):
raise Sorry("No crystal symmetry found.")
else:
if(not crystal_symmetries[0].is_similar_symmetry(crystal_symmetries[1])):
raise Sorry("Crystal symmetry mismatch between different files.")
crystal_symmetry = crystal_symmetries[0]
f_obs = None
r_free_flags = None
if(params.reflection_file_name is not None):
reflection_file = reflection_file_reader.any_reflection_file(
file_name = params.reflection_file_name, ensure_read_access = True)
rfs = reflection_file_server(
crystal_symmetry = crystal_symmetry,
reflection_files = [reflection_file])
parameters = utils.data_and_flags_master_params().extract()
if(params.data_labels is not None):
parameters.labels = [processed_args.data_labels]
determine_data_and_flags_result = utils.determine_data_and_flags(
reflection_file_server = rfs,
parameters = parameters,
keep_going = True,
log = StringIO())
f_obs = determine_data_and_flags_result.f_obs
r_free_flags = determine_data_and_flags_result.r_free_flags
if(r_free_flags is None):
r_free_flags=f_obs.array(data=flex.bool(f_obs.data().size(), False))
test_flag_value=None
xray_structure = iotbx.pdb.input(file_name =
params.pdb_file_name).xray_structure_simple()
xray_structure_da = None
if(params.external_da_pdb_file_name is not None):
xray_structure_da = iotbx.pdb.input(file_name =
params.external_da_pdb_file_name).xray_structure_simple()
if(f_obs is not None):
f_obs = f_obs.resolution_filter(d_min = params.high_resolution,
d_max = params.low_resolution)
r_free_flags = r_free_flags.resolution_filter(d_min = params.high_resolution,
d_max = params.low_resolution)
#
assert params.mode in ["build", "build_and_refine"]
grow_density(f_obs = f_obs,
r_free_flags = r_free_flags,
xray_structure = xray_structure,
xray_structure_da = xray_structure_da,
params = params)
def _refresh(self):
m = reflection_file_reader.any_reflection_file(self._browse.file())
self._inputs[3].Clear()
self._inputs[5].Clear()
for col in m.as_miller_arrays():
if col.is_xray_intensity_array() or col.is_xray_amplitude_array():
self._inputs[3].Append(col.info().label_string())
else:
self._inputs[5].Append(col.info().label_string())
def npp(hklin):
from iotbx.reflection_file_reader import any_reflection_file
from xia2.Toolkit.NPP import npp_ify, mean_variance
from scitbx.array_family import flex
import math
import sys
reader = any_reflection_file(hklin)
mtz_object = reader.file_content()
intensities = [ma for ma in reader.as_miller_arrays(merge_equivalents=False)
if ma.info().labels == ['I', 'SIGI']][0]
indices = intensities.indices()
# merging: use external variance i.e. variances derived from SIGI column
merger = intensities.merge_equivalents(use_internal_variance=False)
mult = merger.redundancies().data()
imean = merger.array()
unique = imean.indices()
iobs = imean.data()
# scale up variance to account for sqrt(multiplicity) effective scaling
variobs = (imean.sigmas() ** 2) * mult.as_double()
all = flex.double()
cen = flex.double()
for hkl, i, v, m in zip(unique, iobs, variobs, mult):
# only consider if meaningful number of observations
if m < 3:
continue
sel = indices == hkl
data = intensities.select(sel).data()
assert(m == len(data))
_x, _y = npp_ify(data, input_mean_variance=(i,v))
# perform linreg on (i) all data and (ii) subset between +/- 2 sigma
sel = (flex.abs(_x) < 2)
_x_ = _x.select(sel)
_y_ = _y.select(sel)
fit_all = flex.linear_regression(_x, _y)
fit_cen = flex.linear_regression(_x_, _y_)
all.append(fit_all.slope())
cen.append(fit_cen.slope())
print '%3d %3d %3d' % hkl, '%.2f %.2f %.2f' % (i, v, i/math.sqrt(v)), \
'%.2f %.2f' % (fit_all.slope(), fit_cen.slope()), '%d' % m
sys.stderr.write('Mean gradients: %.2f %.2f\n' % (flex.sum(all) / all.size(),
flex.sum(cen) / cen.size()))
def process_other (self, arg) :
if ("=" in arg) :
fields = arg.split("=")
if (len(fields) == 2) and (fields[1] in ["amplitudes", "intensities",
"hklf3", "hklf4"]) :
from iotbx import reflection_file_reader
hkl_in = reflection_file_reader.any_reflection_file(arg)
if (hkl_in.file_type() is not None) :
return iotbx.phil.parse("%s=%s" % (self.reflection_file_def,
arg))
return False
def get_map_coeffs_from_file(
map_coeffs_file=None,
map_coeffs_labels=None):
from iotbx import reflection_file_reader
reflection_file=reflection_file_reader.any_reflection_file(
map_coeffs_file)
mtz_content=reflection_file.file_content()
for ma in reflection_file.as_miller_arrays(merge_equivalents=True):
if not ma.is_complex_array(): continue
labels=",".join(ma.info().labels)
if not map_coeffs_labels or labels==map_coeffs_labels: # take it
return ma
def read_data(file_name, labels, xs, log=None):
if log is None:
log=sys.stdout
if not os.path.isfile(file_name):
raise Sorry("No such file: >%s<"%(file_name) )
reflection_file = reflection_file_reader.any_reflection_file(
file_name= file_name)
miller_arrays = reflection_file.as_miller_arrays(crystal_symmetry=xs)
label_table = reflection_file_utils.label_table(miller_arrays)
return label_table.select_array(
label=labels,
command_line_switch="xray_data.labels",
f=log)
def read_reference(mtz_file):
from iotbx import reflection_file_reader
reflection_file = reflection_file_reader.any_reflection_file(
file_name=mtz_file)
reference = None
for miller_array in reflection_file.as_miller_arrays():
label = miller_array.info().labels[0].lower()
if label.find('imean') >= 0:
reference = miller_array
break
assert reference is not None
return reference.map_to_asu()
def smtbx_refinement_model_from(cls, ins_or_res=None, hkl=None,
fo_sq=None, strictly_shelxl=True):
import os
from iotbx.reflection_file_reader import any_reflection_file
import iotbx.builders
if ins_or_res is None:
assert hkl is not None
root, _ = os.path.splitext(hkl)
ins = "%s.ins" % root
res = "%s.res" % root
ins_exists = os.path.isfile(ins)
res_exists = os.path.isfile(res)
assert ins_exists or res_exists
if res_exists: ins_or_res = res
elif ins_exists: ins_or_res = ins
builder = iotbx.builders.mixin_builder_class(
"smtbx_builder",
iotbx.builders.weighted_constrained_restrained_crystal_structure_builder,
iotbx.builders.reflection_data_source_builder,
iotbx.builders.twinning_builder)()
stream = command_stream(filename=ins_or_res)
stream = crystal_symmetry_parser(stream, builder)
stream = afix_parser(stream.filtered_commands(), builder)
stream = atom_parser(stream.filtered_commands(), builder,
strictly_shelxl=strictly_shelxl)
stream = restraint_parser(stream.filtered_commands(), builder)
stream = instruction_parser(stream.filtered_commands(), builder)
stream.parse()
if fo_sq is None:
if hkl is None:
assert ins_or_res is not None
root, _ = os.path.splitext(ins_or_res)
hkl = "%s.hkl" % root
assert os.path.isfile(hkl)
fo_sq = any_reflection_file("%s=hklf4" % hkl)\
.as_miller_arrays(crystal_symmetry=builder.structure)[0]\
.merge_equivalents().array()
else:
assert hkl is None
return cls(fo_sq.as_xray_observations(),
builder.structure,
builder.constraints,
builder.restraints_manager,
builder.weighting_scheme)
def get_map_coeffs(map_coeffs_file=None, map_coeffs_labels=None):
if not map_coeffs_file:
return
if not os.path.isfile(map_coeffs_file):
raise Sorry("Unable to find the map coeffs file %s" % (map_coeffs_file))
from iotbx import reflection_file_reader
reflection_file = reflection_file_reader.any_reflection_file(map_coeffs_file)
miller_arrays = reflection_file.as_miller_arrays()
for ma in miller_arrays:
if not ma.is_complex_array:
continue
if not map_coeffs_labels or map_coeffs_labels == ma.info().labels[0]:
return ma
raise Sorry("Unable to find map coeffs in the file %s with labels %s" % (map_coeffs_file, str(map_coeffs_labels)))
def run(args):
if(len(args)!=1):
raise Sorry("Reflection file expected.")
reflection_file = reflection_file_reader.any_reflection_file(
file_name = args[0])
miller_arrays = reflection_file.as_miller_arrays(
force_symmetry=True,
merge_equivalents=False)
if(miller_arrays is None):
raise Sorry("Warning: unknown file format:", file_name)
for ma in miller_arrays:
if(type(ma.data()) == type(flex.double())):
print "Processing data array with labels:", ma.info().label_string()
compute(miller_array=ma)
print
def exercise_cif():
# .cif input
cif_in = """\
data_r2etdsf
#
_cell.entry_id 2etd
_cell.length_a 80.4540
_cell.length_b 85.2590
_cell.length_c 53.3970
_cell.angle_alpha 90.0000
_cell.angle_beta 90.0000
_cell.angle_gamma 90.0000
#
_symmetry.entry_id 2etd
_symmetry.space_group_name_H-M 'C 2 2 2'
#
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.intensity_meas
_refln.intensity_sigma
1 1 1 0 2 -8 o 1544.6 130.4
1 1 1 0 2 9 o 3450.1 264.9
1 1 1 0 -2 9 o 3243.5 268.5
1 1 1 0 -2 -9 o 3475.4 265.0
1 1 1 0 2 -9 o 3420.1 260.3
1 1 1 0 2 10 o 58.8 31.8
1 1 1 0 -2 -10 o 131.7 50.7
1 1 1 0 2 -10 o 97.9 48.7
1 1 1 0 -2 11 o 9808.3 953.5
1 1 1 0 -2 -11 o 11486.1 970.3
1 1 1 0 2 -11 o 11278.1 967.8
1 1 1 0 2 12 o 1368.9 150.7
1 1 1 0 -2 12 o 1620.9 148.7
1 1 1 0 -2 -12 o 1293.5 147.6
1 1 1 0 2 -12 o 1619.5 155.7
1 1 1 0 -2 13 o 47438.3 4104.1
1 1 1 0 2 14 o 8577.5 1188.0
1 1 1 0 -2 14 o 7996.7 1179.9
1 1 1 0 -2 -14 o 9333.7 1178.1
1 1 1 0 2 -14 o 9642.3 1197.6
1 1 1 0 2 15 o 13577.7 1852.4
1 1 1 0 -2 15 o 14100.9 1852.8
1 1 1 0 -2 -15 o 14184.2 1871.6
1 1 1 0 2 16 o 135.6 76.3
1 1 1 0 -2 16 o 117.0 60.4
"""
cif_file = prefix + "_in.cif"
open(cif_file, "w").write(cif_in)
hkl_orig = any_reflection_file(cif_file).file_content()
i_obs_orig = hkl_orig.as_miller_arrays(merge_equivalents=False)[0]
ofn = export_scalepack_unmerged.run(args=[cif_file], out=null_out())[0]
assert (ofn == "tst_export_scalepack_unmerged_in_w1_unmerged.sca")
hkl_new = any_reflection_file(ofn).file_content()
i_obs_new = hkl_new.as_miller_arrays(merge_equivalents=False)[0]
assert (not i_obs_new.is_unique_set_under_symmetry())
assert i_obs_new.indices().all_eq(i_obs_orig.indices())
def exercise_mosflm_integrate():
if not have_dials_regression:
print(
"Skipping exercise_mosflm_integrate(): dials_regression not configured"
)
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template % 1)
indexer = MosflmIndex()
indexer.set_images((1, 45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1, 3), (21, 23), (43, 45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads()) / len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1, 45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.39, 0.39, 0.39, 0.39, 0.39
]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0,
'full': 507.0,
'dist': 158.6,
'ccx': -0.01,
'yscale': 1.0,
'sdrat': 7.5,
'tilt': 25.0,
'rsym': 0.027,
'bad': 0.0,
'i/sigi': 18.1,
'i/sigi_out': 1.6,
'twist': 13.0,
'resid': 0.021,
'wresid': 1.1,
'part': 1309.0,
'nsym': 18.0,
'neg': 158.0,
'ccy': -0.01,
'ccom': -0.01,
'toff': 0.0,
'roff': 0.0
}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0,
1.0, 0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9,
0.8, 0.8, 0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9,
0.8, 0.9, 1.0
]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'
def exercise(prefix="tst_polder_3"):
"""
Test for phenix.polder sphere radius and box buffer.
"""
f = open("%s.pdb" % prefix, "w")
f.write(pdb_str + pdb_str_ligand)
f.close()
# get mtz file from model using fmodel
cmd = " ".join([
"phenix.fmodel",
"%s.pdb" % prefix, "high_res=2.0", "type=real", "label=f-obs",
"k_sol=0.4", "b_sol=50",
"output.file_name=%s.mtz" % prefix,
"> %s.log" % prefix
])
print(cmd)
easy_run.call(cmd)
params_line = master_params_str
params = iotbx.phil.parse(input_string=params_line,
process_includes=True).extract()
pdb_inp = iotbx.pdb.input(file_name='tst_polder_3.pdb')
model = mmtbx.model.manager(model_input=pdb_inp)
pdb_hierarchy = model.get_hierarchy()
selection_bool = pdb_hierarchy.atom_selection_cache().selection(
string='chain A')
miller_arrays = reflection_file_reader.any_reflection_file(
file_name="tst_polder_3.mtz").as_miller_arrays()
fobs = [None]
for ma in miller_arrays:
if (ma.info().label_string() == "f-obs"):
fobs = ma.deep_copy()
mmm_list = []
mask_mmm = [[0.0, 1.0, 0.9083055555555556], [0.0, 1.0, 0.8901388888888889],
[0.0, 1.0, 0.9083055555555556], [0.0, 1.0, 0.8583379629629629],
[0.0, 1.0, 0.9083055555555556], [0.0, 1.0, 0.8025601851851852]]
for radius in [3, 5, 7]:
params.polder.sphere_radius = radius
polder_object = mmtbx.maps.polder.compute_polder_map(
f_obs=fobs,
r_free_flags=None,
model=model,
params=params.polder,
selection_bool=selection_bool)
polder_object.validate()
polder_object.run()
results = polder_object.get_results()
mmm_list.append(
polder_object.mask_data_omit.as_1d().min_max_mean().as_tuple())
mmm_list.append(
polder_object.mask_data_polder.as_1d().min_max_mean().as_tuple())
for i in range(6):
assert approx_equal(mask_mmm[i], mmm_list[i], eps=0.1)
#print mask_mmm[i], mmm_list[i]
#-------------------------------------------------------------------------
mmm_list = []
mask_mmm = [[0.0, 1.0, 0.898712962962963], [0.0, 1.0, 0.8642268518518519],
[0.0, 1.0, 0.898712962962963], [0.0, 1.0, 0.7957083333333334],
[0.0, 1.0, 0.898712962962963], [0.0, 1.0, 0.6772777777777778]]
for box_buffer in [3, 5, 7]:
params.polder.box_buffer = box_buffer
params.polder.compute_box = True
polder_object = mmtbx.maps.polder.compute_polder_map(
f_obs=fobs,
r_free_flags=None,
model=model,
params=params.polder,
selection_bool=selection_bool)
polder_object.validate()
polder_object.run()
results = polder_object.get_results()
mmm_list.append(
polder_object.mask_data_omit.as_1d().min_max_mean().as_tuple())
mmm_list.append(
polder_object.mask_data_polder.as_1d().min_max_mean().as_tuple())
for i in range(6):
assert approx_equal(mask_mmm[i], mmm_list[i], eps=0.1)
def _integrate_finish(self):
"""
Finish off the integration.
If in high-pressure mode run dials.anvil_correction.
Run dials.export.
"""
# FIXME - do we want to export every time we call this method
# (the file will not have changed) and also (more important) do
# we want a different exported MTZ file every time (I do not think
# that we do; these can be very large) - was exporter.get_xpid() ->
# now dials
if self._output_format == "hkl":
exporter = self.ExportMtz()
exporter.set_reflections_filename(
self._intgr_integrated_reflections)
mtz_filename = os.path.join(self.get_working_directory(),
"%s_integrated.mtz" % "dials")
exporter.set_mtz_filename(mtz_filename)
exporter.run()
self._intgr_integrated_filename = mtz_filename
# record integrated MTZ file
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
"%s %s %s %s INTEGRATE" % (pname, xname, dname, sweep),
mtz_filename)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(
self._intgr_integrated_filename).as_miller_arrays()
# look for profile-fitted intensities
intensities = [
ma for ma in miller_arrays
if ma.info().labels == ["IPR", "SIGIPR"]
]
if len(intensities) == 0:
# look instead for summation-integrated intensities
intensities = [
ma for ma in miller_arrays
if ma.info().labels == ["I", "SIGI"]
]
assert len(intensities)
self._intgr_n_ref = intensities[0].size()
if not os.path.isfile(self._intgr_integrated_filename):
raise RuntimeError("dials.export failed: %s does not exist." %
self._intgr_integrated_filename)
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice())):
logger.debug("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == 0):
logger.debug("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
logger.debug(
"Reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number, self._intgr_reindex_operator))
hklin = mtz_filename
from xia2.Wrappers.CCP4.Reindex import Reindex
reindex = Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
reindex.set_operator(self._intgr_reindex_operator)
if self._intgr_spacegroup_number:
reindex.set_spacegroup(self._intgr_spacegroup_number)
else:
reindex.set_spacegroup(
lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()))
hklout = "%s_reindex.mtz" % hklin[:-4]
reindex.set_hklin(hklin)
reindex.set_hklout(hklout)
reindex.reindex()
self._intgr_integrated_filename = hklout
self._intgr_cell = reindex.get_cell()
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_experiments(),
)
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_reflections(),
)
return hklout
elif self._output_format == "pickle":
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice())):
logger.debug("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return self._intgr_integrated_reflections
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == 0):
logger.debug("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return self._intgr_integrated_reflections
logger.debug(
"Reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number, self._intgr_reindex_operator))
from xia2.Wrappers.Dials.Reindex import Reindex
reindex = Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
reindex.set_cb_op(self._intgr_reindex_operator)
if self._intgr_spacegroup_number:
reindex.set_space_group(self._intgr_spacegroup_number)
else:
reindex.set_space_group(
lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()))
reindex.set_experiments_filename(self.get_integrated_experiments())
reindex.set_indexed_filename(self.get_integrated_reflections())
reindex.run()
self._intgr_integrated_reflections = (
reindex.get_reindexed_reflections_filename())
self._intgr_integrated_filename = (
reindex.get_reindexed_reflections_filename())
self._intgr_experiments_filename = (
reindex.get_reindexed_experiments_filename())
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_experiments(),
)
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_reflections(),
)
return None # this will be set to intgr_hklout - better to cause failure
def run(args):
def vdw_radii_callback(option, opt_str, value, parser):
# create a dict from space separated string of element types and radii
radii = {}
items = value.split()
assert len(items) % 2 == 0
for i in range(int(len(items) / 2)):
radii.setdefault(items[i*2], float(items[i*2+1]))
setattr(parser.values, option.dest, radii)
command_line = (option_parser(
usage="smtbx.masks structure reflections [options]")
.enable_symmetry_comprehensive()
.option(None, "--solvent_radius",
action="store",
type="float",
default=1.3)
.option(None, "--shrink_truncation_radius",
action="store",
type="float",
default=1.3)
.option(None, "--debug",
action="store_true")
.option(None, "--verbose",
action="store_true")
.option(None, "--resolution_factor",
action="store",
type="float",
default=1/4)
.option(None, "--grid_step",
action="store",
type="float")
.option(None, "--d_min",
action="store",
type="float")
.option(None, "--two_theta_max",
action="store",
type="float")
.option(None, "--cb_op",
action="store",
type="string")
.option(None, "--vdw_radii",
action="callback",
callback=vdw_radii_callback,
type="string",
nargs=1)
.option(None, "--use_space_group_symmetry",
action="store_true")).process(args=args)
structure_file = command_line.args[0]
ext = os.path.splitext(structure_file)[-1].lower()
if ext in ('.res', '.ins'):
xs = xray.structure.from_shelx(filename=structure_file)
elif ext == '.cif':
xs = xray.structure.from_cif(filename=structure_file)
else:
print("%s: unsupported structure file format {shelx|cif}" %ext)
return
reflections_server = reflection_file_utils.reflection_file_server(
crystal_symmetry = xs.crystal_symmetry(),
reflection_files = [
reflection_file_reader.any_reflection_file(command_line.args[1])
]
)
fo_sq = reflections_server.get_miller_arrays(None)[0]
if command_line.options.cb_op is not None:
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(command_line.options.cb_op))
fo_sq = fo_sq.change_basis(cb_op).customized_copy(
crystal_symmetry=xs)
print("structure file: %s" %command_line.args[0])
print("reflection file: %s" %command_line.args[1])
if command_line.options.debug:
print("debug: %s" %command_line.options.debug)
print()
xs.show_summary()
print()
d_min = command_line.options.d_min
two_theta_max = command_line.options.two_theta_max
assert [d_min, two_theta_max].count(None) > 0
if two_theta_max is not None:
d_min = uctbx.two_theta_as_d(two_theta_max, wavelength=0.71073, deg=True)
exercise_masks(
xs, fo_sq,
solvent_radius=command_line.options.solvent_radius,
shrink_truncation_radius=command_line.options.shrink_truncation_radius,
resolution_factor=command_line.options.resolution_factor,
grid_step=command_line.options.grid_step,
resolution_cutoff=d_min,
atom_radii_table=command_line.options.vdw_radii,
use_space_group_symmetry=command_line.options.use_space_group_symmetry,
debug=command_line.options.debug,
verbose=command_line.options.verbose)
print("OK")
from iotbx import reflection_file_reader
import sys
import matplotlib.pyplot as plt
import numpy as np
from cctbx.array_family import flex
hklin = sys.argv[1]
reflection_file = reflection_file_reader.any_reflection_file(hklin)
miller_arrays = reflection_file.as_miller_arrays()
num_bins = 20
for miller_array in miller_arrays:
if miller_array.sigmas() is not None:
miller_array.show_summary()
mean_sigI = np.mean(miller_array.sigmas())
mean_I = np.mean(miller_array.data())
std_I = np.std(miller_array.data())
ma_1 = miller_array.select((miller_array.sigmas() > 0) & (miller_array.sigmas() <= mean_sigI))
ma_2 = miller_array.select((miller_array.sigmas() > mean_sigI))
ma_3 = miller_array.select((miller_array.data() < (mean_I - (0*std_I))))
#plot
plt.subplot(321)
x = miller_array.sigmas().as_numpy_array()
mu = np.mean(x)
med = np.median(x)
sigma = np.std(x)
plt.hist(x, num_bins, normed=0, facecolor='green', alpha=0.5)
plt.ylabel('Frequencies')
plt.title('sigI distribution\nmean %5.3f median %5.3f sigma %5.3f' %(mu, med, sigma))
plt.subplot(322)
plt.scatter(miller_array.data(), miller_array.sigmas(), s=10, c='b', marker='o')
plt.subplot(323)
def exercise_get_amplitudes_and_get_phases_deg():
crystal_symmetry = crystal.symmetry(unit_cell=(10, 11, 12, 85, 95, 100),
space_group_symbol="P 1")
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=3)
input_arrays = [
miller_set.array(data=flex.random_double(size=miller_set.indices(
).size())).set_observation_type_xray_amplitude() for i in [0, 1]
]
mtz_dataset = input_arrays[0].as_mtz_dataset(column_root_label="F0")
mtz_dataset.mtz_object().write("tmp_rfu1.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp_rfu1.mtz")
]
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files)
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=None,
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
assert str(ampl.info()) == "tmp_rfu1.mtz:F0"
ampl = reflection_file_srv.get_miller_array(labels="F0")
assert str(ampl.info()) == "tmp_rfu1.mtz:F0"
mtz_dataset.add_miller_array(miller_array=input_arrays[1],
column_root_label="F1")
mtz_dataset.mtz_object().write("tmp_rfu2.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp_rfu2.mtz")
]
err = StringIO()
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=err)
try:
reflection_file_srv.get_amplitudes(
file_name=None,
labels=None,
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
except Sorry:
assert not show_diff(
err.getvalue(), """\
Multiple equally suitable arrays of amplitudes found.
Possible choices:
tmp_rfu2.mtz:F0
tmp_rfu2.mtz:F1
Please use amplitudes.labels
to specify an unambiguous substring of the target label.
""")
err = reflection_file_srv.err = StringIO()
else:
raise Exception_expected
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=["F1"],
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
assert str(ampl.info()) == "tmp_rfu2.mtz:F1"
try:
reflection_file_srv.get_amplitudes(
file_name=None,
labels=["F2"],
convert_to_amplitudes_if_necessary=True,
parameter_name="labels",
parameter_scope=None)
except Sorry:
assert not show_diff(
err.getvalue(), """\
No matching array: labels=F2
Possible choices:
tmp_rfu2.mtz:F0
tmp_rfu2.mtz:F1
Please use labels
to specify an unambiguous substring of the target label.
""")
err = reflection_file_srv.err = StringIO()
else:
raise Exception_expected
assert len(reflection_file_srv.file_name_miller_arrays) == 1
ampl = reflection_file_srv.get_amplitudes(
file_name="tmp_rfu1.mtz",
labels=None,
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
assert len(reflection_file_srv.file_name_miller_arrays) == 2
assert str(ampl.info()) == "tmp_rfu1.mtz:F0"
ampl = reflection_file_srv.get_amplitudes(
file_name=os.path.abspath("tmp_rfu1.mtz"),
labels=["f0"],
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
assert len(reflection_file_srv.file_name_miller_arrays) == 2
assert str(ampl.info()) == "tmp_rfu1.mtz:F0"
try:
reflection_file_srv.get_amplitudes(
file_name=None,
labels=None,
convert_to_amplitudes_if_necessary=True,
parameter_scope=None,
parameter_name=None)
except Sorry:
assert not show_diff(
err.getvalue(), """\
Multiple equally suitable arrays of amplitudes found.
Possible choices:
tmp_rfu2.mtz:F0
tmp_rfu2.mtz:F1
Please specify an unambiguous substring of the target label.
""")
err = reflection_file_srv.err = StringIO()
else:
raise Exception_expected
#
mtz_dataset.add_miller_array(miller_array=miller_set.array(
data=flex.polar(flex.random_double(size=miller_set.indices().size()),
flex.random_double(size=miller_set.indices().size()))),
column_root_label="F2")
mtz_dataset.add_miller_array(miller_array=miller_set.array(
data=flex.random_double(size=miller_set.indices().size()),
sigmas=flex.random_double(size=miller_set.indices().size()) /
10).set_observation_type_xray_intensity(),
column_root_label="F3")
mtz_dataset.add_miller_array(miller_array=miller_set.array(
data=flex.hendrickson_lattman(miller_set.indices().size(), (0, 0, 0,
0))),
column_root_label="P")
mtz_dataset.mtz_object().write("tmp_rfu3.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp_rfu3.mtz")
]
err = StringIO()
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=err)
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=["f2"],
convert_to_amplitudes_if_necessary=False,
parameter_scope="amplitudes",
parameter_name="labels")
assert str(ampl.info()) == "tmp_rfu3.mtz:F2,PHIF2"
assert ampl.is_complex_array()
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=["f2"],
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
assert str(ampl.info()) == "tmp_rfu3.mtz:F2"
assert ampl.is_real_array()
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=["f3"],
convert_to_amplitudes_if_necessary=False,
parameter_scope="amplitudes",
parameter_name="labels")
assert str(ampl.info()) == "tmp_rfu3.mtz:F3,SIGF3"
assert ampl.is_xray_intensity_array()
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=["f3"],
convert_to_amplitudes_if_necessary=True,
parameter_scope="amplitudes",
parameter_name="labels")
assert str(ampl.info()) == "tmp_rfu3.mtz:F3,as_amplitude_array"
assert ampl.is_real_array()
ampl = reflection_file_srv.get_amplitudes(
file_name=None,
labels=None,
convert_to_amplitudes_if_necessary=False,
parameter_scope="amplitudes",
parameter_name="labels",
return_all_valid_arrays=True,
strict=True)
assert (len(ampl) == 2)
for f in ampl:
assert (not f.is_xray_intensity_array()) and (not f.is_complex_array())
#
phases = reflection_file_srv.get_phases_deg(
file_name=None,
labels=["f2"],
convert_to_phases_if_necessary=False,
original_phase_units=None,
parameter_scope="phases",
parameter_name="labels")
assert str(phases.info()) == "tmp_rfu3.mtz:F2,PHIF2"
assert phases.is_complex_array()
phases = reflection_file_srv.get_phases_deg(
file_name=None,
labels=["f2"],
convert_to_phases_if_necessary=True,
original_phase_units=None,
parameter_scope=None,
parameter_name="labels")
assert str(phases.info()) == "tmp_rfu3.mtz:PHIF2"
assert phases.is_real_array()
assert flex.mean(phases.data()) > 5
phases = reflection_file_srv.get_phases_deg(
file_name=None,
labels=["PA"],
convert_to_phases_if_necessary=False,
original_phase_units=None,
parameter_scope="phases",
parameter_name="labels")
assert str(phases.info()) == "tmp_rfu3.mtz:PA,PB,PC,PD"
phases = reflection_file_srv.get_phases_deg(
file_name=None,
labels=["PA"],
convert_to_phases_if_necessary=True,
original_phase_units=None,
parameter_scope="phases",
parameter_name="labels")
assert str(phases.info()) \
== "tmp_rfu3.mtz:PA,PB,PC,PD,converted_to_centroid_phases"
assert phases.is_real_array()
for original_phase_units in [None, "deg", "rad"]:
phases = reflection_file_srv.get_phases_deg(
file_name=None,
labels=["F0"],
convert_to_phases_if_necessary=False,
original_phase_units=original_phase_units,
parameter_scope=None,
parameter_name="labels")
if (original_phase_units != "rad"):
assert str(phases.info()) == "tmp_rfu3.mtz:F0"
else:
assert str(phases.info()) == "tmp_rfu3.mtz:F0,converted_to_deg"
def exercise_get_r_free_flags():
crystal_symmetry = crystal.symmetry(unit_cell=(30, 31, 32, 85, 95, 100),
space_group_symbol="P 1")
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=3)
n = miller_set.indices().size()
exercise_flag_arrays = []
exercise_flag_arrays.append(
flex.int(list(flex.random_permutation(size=n) % 10)))
exercise_flag_arrays.append(flex.int(xrange(n)))
exercise_flag_arrays.append(flex.int(n, 0))
for style in ["ccp4", "cns", "shelx", "bool"]:
for i_exercise, exercise_flag_array in enumerate(exercise_flag_arrays):
for reversed in [False, True]:
if (style == "ccp4"):
if (reversed): break
data = exercise_flag_array
test_flag_value = 3
else:
if (not reversed):
data = (exercise_flag_array == 0)
test_flag_value = True
else:
data = (exercise_flag_array != 0)
test_flag_value = False
if (style == "cns"):
data = data.as_int()
test_flag_value = int(test_flag_value)
elif (style == "shelx"):
data = -data.as_int()
data.set_selected((data == 0), 1)
if (not reversed): test_flag_value = -1
else: test_flag_value = 1
input_array = miller_set.array(data=data)
mtz_dataset = input_array.as_mtz_dataset(
column_root_label="FreeRflags")
mtz_dataset.mtz_object().write("tmp.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(
file_name="tmp.mtz")
]
err = StringIO()
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=err)
for trial_test_flag_value in [None, test_flag_value]:
for trial_label in [None, "free", "foo"]:
try:
r_free_flags, actual_test_flag_value = \
reflection_file_srv.get_r_free_flags(
file_name=None,
label=trial_label,
test_flag_value=trial_test_flag_value,
disable_suitability_test=False,
parameter_scope="r_free_flags")
except Sorry, e:
if (trial_label != "foo"):
assert i_exercise > 0
if (trial_label is None):
assert str(e) == """\
No array of R-free flags found.
For manual selection define:
r_free_flags.label
r_free_flags.test_flag_value
r_free_flags.disable_suitability_test=True"""
else:
assert str(e) == \
"Not a suitable array of R-free flags:" \
+ " r_free_flags.label=free\n" \
+ "To override the suitability test define:" \
+ " r_free_flags.disable_suitability_test=True"
else:
assert str(
e
) == "No matching array: r_free_flags.label=foo"
if (i_exercise == 0):
assert err.getvalue() == """\
No matching array: r_free_flags.label=foo
Possible choices:
tmp.mtz:FreeRflags
Please use r_free_flags.label
to specify an unambiguous substring of the target label.
"""
else:
assert err.getvalue() == """\
No matching array: r_free_flags.label=foo
"""
err = reflection_file_srv.err = StringIO()
else:
assert i_exercise == 0
actual_test_flag_value_2 = guess_r_free_flag_value(
miller_array=r_free_flags,
test_flag_value=trial_test_flag_value)
assert (actual_test_flag_value_2 ==
actual_test_flag_value)
def __init__(self, _parameters):
'''Instantiate class and perform initial processing needed before the
real work is done. This includes assessment of the anomalous signal,
the signal to noise and conversion to pseudo-scalepack format of the
data for input into shelxc, which is used to compute FA values.'''
self._hklin = _parameters.get_data()
self._native_hklin = _parameters.get_native()
self._native = None
self._cpu = _parameters.get_cpu()
self._machines = _parameters.get_machines()
self._atom = _parameters.get_atom()
self._ntry = _parameters.get_ntry()
self._ncycle = _parameters.get_ncycle()
self._ano_rlimits = _parameters.get_rlims()
self._trace = _parameters.get_trace()
self._mode = _parameters.get_mode()
self._sge_project = _parameters.get_sge_project()
self._data = None
self._spacegroups = [
_parameters.get_spg(),
] if _parameters.get_spg() else None
self._nsites = [
_parameters.get_nsites(),
] if _parameters.get_nsites() else None
self._xml_name = _parameters.get_xml()
self._json_name = _parameters.get_json()
self._start_time = datetime.now().strftime("%c")
if self._machines == 1:
self._cluster = False
else:
self._cluster = True
self._wd = os.getcwd()
logging.info('Using %d cpus / %d machines' %
(self._cpu, self._machines))
self._full_command_line = ' '.join(sys.argv)
# pull information we'll need from the input MTZ file - the unit cell,
# the pointgroup and the number of reflections in the file. select
# first Miller array in file which has anomalous data
# --- SAD DATA ---
reader = any_reflection_file(self._hklin)
self._file_type = reader.file_type()
if self._file_type == 'ccp4_mtz':
self._file_content = reader.file_content()
self._is_merged = False if self._file_content.n_batches(
) > 0 else True
self._all_data = [
m for m in reader.as_miller_arrays(
merge_equivalents=self._is_merged)
if type(m.observation_type()) is observation_types.intensity
and (m.anomalous_flag() if self._is_merged else True)
]
if not self._all_data:
raise RuntimeError, 'no intensity data found in %s' % self._hklin
if self._native_hklin:
native_reader = any_reflection_file(self._native_hklin)
try:
self._native = next(
m for m in native_reader.as_miller_arrays(
merge_equivalents=True)
if (type(m.observation_type()) is observation_types.
intensity and not m.anomalous_flag()))
except StopIteration:
self._native = None
else:
raise RuntimeError, 'Unsupported input file type: %s' % self._file_type
self._nrefl = self._file_content.n_reflections()
self._pointgroup = self._file_content.space_group_number()
self._dmax, self._dmin = self._file_content.max_min_resolution()
self._xml_results = {}
self._xml_results['LOWRES'] = self._dmax
self._xml_results['HIGHRES'] = self._dmin
return
except AssertionError, e:
if ("No unit cell and symmetry information supplied" in str(e)):
raise Sorry(
"Missing or incomplete symmetry information. This program " +
"will only work with reflection file formats that contain both "
+ "unit cell and space group records, such as MTZ files.")
#
reflection_files = []
reflection_file_names = []
for rfn in [
params.maps.input.reflection_data.file_name,
params.maps.input.reflection_data.r_free_flags.file_name
]:
if (os.path.isfile(str(rfn))) and (not rfn in reflection_file_names):
reflection_files.append(
reflection_file_reader.any_reflection_file(
file_name=rfn, ensure_read_access=False))
reflection_file_names.append(rfn)
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files, #[],
err=log)
#
reflection_data_master_params = mmtbx.utils.data_and_flags_master_params(
master_scope_name="reflection_data")
reflection_data_input_params = processed_args.params.get(
"maps.input.reflection_data")
reflection_data_params = reflection_data_master_params.fetch(
reflection_data_input_params).extract().reflection_data
#
determine_data_and_flags_result = mmtbx.utils.determine_data_and_flags(
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
self.viewer.isnewfile = True
#self.params.NGL_HKLviewer.mergedata = None
self.params.NGL_HKLviewer.viewer.scene_id = None
self.viewer.colour_scene_id = None
self.viewer.radii_scene_id = None
self.viewer.match_valarrays = []
self.viewer.proc_arrays = []
self.spacegroup_choices = []
display.reset_settings()
self.settings = display.settings()
self.viewer.settings = self.params.NGL_HKLviewer.viewer
self.viewer.mapcoef_fom_dict = {}
try:
hkl_file = any_reflection_file(file_name)
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
except Exception as e:
self.NewFileLoaded = False
self.mprint(to_str(e))
arrays = []
valid_arrays = []
self.viewer.array_infostrs = []
self.viewer.array_infotpls = []
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()) \
and (not array.is_integer_array()) and (not array.is_bool_array()) :
self.mprint('Ignoring miller array \"%s\" of %s' \
%(array.info().label_string(), type(array.data()[0]) ) )
continue
self.viewer.array_infostrs.append(
ArrayInfo(array, self.mprint).infostr)
self.viewer.array_infotpls.append(
ArrayInfo(array, self.mprint).infotpl)
valid_arrays.append(array)
self.valid_arrays = valid_arrays
self.mprint("Miller arrays in this file:")
for e in self.viewer.array_infostrs:
self.mprint("%s" % e)
self.NewFileLoaded = True
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
self.mprint(msg)
self.NewFileLoaded = False
return False
elif (len(valid_arrays) >= 1):
if (set_array):
self.set_miller_array()
mydict = {
"info":
self.infostr,
"array_infotpls":
self.viewer.array_infotpls,
"bin_infotpls":
self.viewer.bin_infotpls,
"html_url":
self.viewer.url,
"merge_data":
self.params.NGL_HKLviewer.merge_data,
"spacegroups":
[e.symbol_and_number() for e in self.spacegroup_choices],
"NewFileLoaded":
self.NewFileLoaded
}
self.SendInfoToGUI(mydict)
return True
def run(args):
if len(args) == 0:
master_params.show(expert_level=0)
elif ("--help" in args):
print "no help available as yet"
elif ("--h" in args):
print "no help availableas yet"
elif ("--show_defaults" in args):
master_params.show(expert_level=0)
elif ("--show_defaults_all" in args):
master_params.show(expert_level=10)
else:
log = multi_out()
if (not "--quiet" in args):
log.register(label="stdout", file_object=sys.stdout)
string_buffer = StringIO()
string_buffer_plots = StringIO()
log.register(label="log_buffer", file_object=string_buffer)
log_plots = StringIO()
print >> log, "#phil __OFF__"
print >> log
print >> log, date_and_time()
print >> log
print >> log
phil_objects = []
argument_interpreter = master_params.command_line_argument_interpreter(
home_scope="scaling")
reflection_file = None
for arg in args:
command_line_params = None
arg_is_processed = False
if arg == '--quiet':
arg_is_processed = True
## The associated action with this keyword is implemented above
if (os.path.isfile(arg)): ## is this a file name?
## Check if this is a phil file
try:
command_line_params = iotbx.phil.parse(file_name=arg)
except KeyboardInterrupt:
raise
except Exception:
pass
if command_line_params is not None:
phil_objects.append(command_line_params)
arg_is_processed = True
## Check if this file is a reflection file
if command_line_params is None:
reflection_file = reflection_file_reader.any_reflection_file(
file_name=arg, ensure_read_access=False)
if (reflection_file is not None):
reflection_file = arg
arg_is_processed = True
## If it is not a file, it must be a phil command
else:
try:
command_line_params = argument_interpreter.process(arg=arg)
if command_line_params is not None:
phil_objects.append(command_line_params)
arg_is_processed = True
except KeyboardInterrupt:
raise
except Exception:
pass
if not arg_is_processed:
print >> log, "##----------------------------------------------##"
print >> log, "## Unknown phil-file or phil-command:", arg
print >> log, "##----------------------------------------------##"
print >> log
raise Sorry("Unknown file format or phil command: %s" % arg)
effective_params = master_params.fetch(sources=phil_objects)
params = effective_params.extract()
effective_params = master_params.fetch(sources=phil_objects)
new_params = master_params.format(python_object=params)
## Now please read in the reflections files
## get symmetry and cell data first please
## By default, the native cell and symmetry are used
## as reference
crystal_symmetry_nat = None
crystal_symmetry_nat = crystal_symmetry_from_any.extract_from(
file_name=params.scaling.input.xray_data.reference.file_name)
if params.scaling.input.xray_data.space_group is None:
params.scaling.input.xray_data.space_group =\
crystal_symmetry_nat.space_group_info()
print >> log, "Using symmetry of native data"
if params.scaling.input.xray_data.unit_cell is None:
params.scaling.input.xray_data.unit_cell =\
crystal_symmetry_nat.unit_cell()
print >> log, "Using cell of native data"
## Check if a unit cell is defined
if params.scaling.input.xray_data.space_group is None:
raise Sorry("No space group defined")
if params.scaling.input.xray_data.unit_cell is None:
raise Sorry("No unit cell defined")
crystal_symmetry = crystal_symmetry = crystal.symmetry(
unit_cell=params.scaling.input.xray_data.unit_cell,
space_group_symbol=str(params.scaling.input.xray_data.space_group))
effective_params = master_params.fetch(sources=phil_objects)
new_params = master_params.format(python_object=params)
print >> log, "Effective parameters"
print >> log, "#phil __ON__"
new_params.show(out=log,
expert_level=params.scaling.input.expert_level)
print >> log, "#phil __END__"
print >> log
## define a xray data server
xray_data_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=[])
## Read in native data and make appropriatre selections
miller_array_native = None
miller_array_native = xray_data_server.get_xray_data(
file_name=params.scaling.input.xray_data.reference.file_name,
labels=params.scaling.input.xray_data.reference.labels,
ignore_all_zeros=True,
parameter_scope='scaling.input.SIR_scale.xray_data.native')
info_native = miller_array_native.info()
miller_array_native = miller_array_native.map_to_asu().select(
miller_array_native.indices() != (0, 0, 0))
miller_array_native = miller_array_native.select(
miller_array_native.data() > 0)
## Convert to amplitudes
if (miller_array_native.is_xray_intensity_array()):
miller_array_native = miller_array_native.f_sq_as_f()
elif (miller_array_native.is_complex_array()):
miller_array_native = abs(miller_array_native)
if not miller_array_native.is_real_array():
raise Sorry("miller_array_native is not a real array")
miller_array_native.set_info(info=info_native)
## Print info
print >> log
print >> log, "Reference data"
print >> log, "=============="
miller_array_native.show_comprehensive_summary(f=log)
print >> log
native_pre_scale = pre_scale.pre_scaler(
miller_array_native,
params.scaling.input.scaling_strategy.pre_scaler_protocol,
params.scaling.input.basic)
miller_array_native = native_pre_scale.x1.deep_copy()
del native_pre_scale
scaler = fa_estimation.ano_scaling(
miller_array_native,
params.scaling.input.scaling_strategy.ano_protocol)
positive_miller = scaler.x1p.deep_copy()
negative_miller = scaler.x1n.deep_copy()
print >> log
print >> log, "Making delta f's"
print >> log, "----------------"
print >> log
delta_gen = pair_analyses.delta_generator(positive_miller,
negative_miller)
print >> log
print >> log, "writing mtz file"
print >> log, "----------------"
print >> log
## some assertions to make sure nothing went weerd
assert positive_miller.observation_type() is not None
assert negative_miller.observation_type() is not None
assert delta_gen.abs_delta_f.observation_type() is not None
## Please write out the abs_delta_f array
mtz_dataset = delta_gen.abs_delta_f.as_mtz_dataset(
column_root_label='F' + params.scaling.input.output.outlabel)
mtz_dataset.mtz_object().write(
file_name=params.scaling.input.output.hklout)
if params.scaling.input.omit.perform_omit:
print >> log
print >> log, "writing omit files"
print >> log, "------------------"
print >> log
omit_object = random_omit.random_omit_data(
delta_gen.abs_delta_f, params.scaling.input.omit)
omit_object.write_datasets()
def run(prefix="tst_00"):
# Poor model that we want to refine so it matches the answer
pdb_file = libtbx.env.find_in_repositories(
relative_path="mmtbx/regression/real_space_refine_chain/poor_model.pdb",
test=os.path.isfile)
mtz_file = libtbx.env.find_in_repositories(
relative_path="mmtbx/regression/real_space_refine_chain/poor_map.mtz",
test=os.path.isfile)
pdb_inp = iotbx.pdb.input(file_name=pdb_file)
ph_poor = pdb_inp.construct_hierarchy()
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp.xray_structure_simple()
# Initialize states accumulator
states = mmtbx.utils.states(pdb_hierarchy=ph_poor, xray_structure=xrs_poor)
states.add(sites_cart=xrs_poor.sites_cart())
# Compute target map
mas = reflection_file_reader.any_reflection_file(
file_name=mtz_file).as_miller_arrays()
assert len(mas) == 1
fc = mas[0]
fft_map = fc.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
target_map_data = fft_map.real_map_unpadded()
ccp4_map(crystal_symmetry=fc.crystal_symmetry(),
file_name="map.ccp4",
map_data=target_map_data)
# Build geometry restraints
params = monomer_library.pdb_interpretation.master_params.extract()
params.nonbonded_weight = 200
#params.peptide_link.ramachandran_restraints=True
#params.peptide_link.rama_potential="oldfield"
#print dir(params)
#STOP()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
file_name=pdb_file,
params=params,
#crystal_symmetry = fc.crystal_symmetry(),
strict_conflict_handling=True,
force_symmetry=True,
log=None)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False,
plain_pairs_radius=5,
assume_hydrogens_all_missing=True)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
#for a in ph_answer.atoms():
# print a.i_seq, a.name, a.xyz
#STOP()
#ref_xyz = flex.vec3_double([(14.323, 35.055, 14.635), (16.099, 12.317, 16.37)])
#selection = flex.size_t([1,76])
#
#restraints_manager.geometry.adopt_reference_coordinate_restraints_in_place(
# reference.add_coordinate_restraints(
# sites_cart = ref_xyz,
# selection = selection,
# sigma = 0.1))
# Do real-space refinement
t0 = time.time()
ear = mmtbx.refinement.real_space.explode_and_refine.run(
xray_structure=xrs_poor,
pdb_hierarchy=ph_poor,
map_data=target_map_data,
restraints_manager=restraints_manager,
states=states)
print("Time: %6.4f" % (time.time() - t0))
ear.pdb_hierarchy.write_pdb_file(file_name="%s_refined.pdb" % prefix)
states.write(file_name="%s_refined_all_states.pdb" % prefix)
def load_reflections_file(self, file_name):
file_name = to_str(file_name)
ret = False
if (file_name != ""):
self.mprint("Reading file...")
from iotbx.reflection_file_reader import any_reflection_file
self.viewer.isnewfile = True
#self.params.NGL_HKLviewer.mergedata = None
self.params.NGL_HKLviewer.viewer.scene_id = None
self.viewer.colour_scene_id = None
self.viewer.radii_scene_id = None
self.viewer.match_valarrays = []
self.viewer.proc_arrays = []
self.spacegroup_choices = []
display.reset_settings()
self.settings = display.settings()
self.viewer.settings = self.params.NGL_HKLviewer.viewer
self.viewer.mapcoef_fom_dict = {}
self.hklfile_history = []
self.tncsvec = None
try :
hkl_file = any_reflection_file(file_name)
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
if hkl_file._file_type == 'ccp4_mtz':
self.hklfile_history = list(hkl_file._file_content.history())
for e in self.hklfile_history:
if "TNCS NMOL" in e and "VECTOR" in e:
svec = e.split()[-3:]
t1 = float(svec[0])
t2 = float(svec[1])
t3 = float(svec[2])
if (t1*t1 + t2*t2 + t3*t3) > 0.0:
self.tncsvec = [ t1, t2, t3 ]
self.mprint("tNCS vector found in header of mtz file: %s" %str(svec) )
except Exception as e :
self.NewFileLoaded=False
self.mprint(to_str(e))
arrays = []
valid_arrays = []
self.viewer.array_infostrs = []
self.viewer.array_infotpls = []
for array in arrays :
if (not array.is_real_array()) and (not array.is_complex_array()) \
and (not array.is_integer_array()) and (not array.is_bool_array()) :
self.mprint('Ignoring miller array \"%s\" of %s' \
%(array.info().label_string(), type(array.data()[0]) ) )
continue
self.viewer.array_infostrs.append( ArrayInfo(array, self.mprint).infostr )
self.viewer.array_infotpls.append( ArrayInfo(array, self.mprint).infotpl )
valid_arrays.append(array)
self.valid_arrays = valid_arrays
self.mprint("%d Miller arrays in this file:" %len(arrays))
for e in self.viewer.array_infostrs:
self.mprint("%s" %e)
self.mprint("\n")
self.NewFileLoaded = True
if (len(valid_arrays) == 0):
msg = "No arrays of the supported types in this file."
self.mprint(msg)
self.NewFileLoaded=False
elif (len(valid_arrays) >= 1):
self.set_miller_array()
mydict = { "info": self.infostr,
"array_infotpls": self.viewer.array_infotpls,
"bin_infotpls": self.viewer.bin_infotpls,
"html_url": self.viewer.url,
"tncsvec": self.tncsvec,
"merge_data": self.params.NGL_HKLviewer.merge_data,
"spacegroups": [e.symbol_and_number() for e in self.spacegroup_choices],
"NewFileLoaded": self.NewFileLoaded,
"file_name": self.params.NGL_HKLviewer.openfilename
}
self.SendInfoToGUI(mydict)
ret = True
self.params.NGL_HKLviewer.openfilename = None
return ret
def convert_scaled_intensities_to_structure_factors(
scaled_intensity_mtz_filename):
cwd = os.getcwd()
scaled_intensity_mtz_fullpath = os.path.join(
cwd, scaled_intensity_mtz_filename)
scaled_structure_factor_mtz_prefix = scaled_intensity_mtz_filename.split(
'.')[-2]
hkl_file = any_reflection_file(scaled_intensity_mtz_fullpath)
info = hkl_file.file_content()
xtals = info.crystals()
if len(xtals) > 1:
xtal = xtals[0]
else:
xtal = xtals
space_group = info.space_group_number()
unit_cell = xtal.unit_cell_parameters()
uc_a, uc_b, uc_c, uc_al, uc_be, uc_ga = unit_cell
uc_str = str(unit_cell)[1:-1]
RFE_def_file_fullpath = os.path.join(cwd, "reflection_file_editor.def")
RFE_def_file = open(RFE_def_file_fullpath, 'w')
RFE_def_text = """show_arrays = False
dry_run = False
verbose = True
mtz_file {
crystal_symmetry {
unit_cell = %s
space_group = %s
output_unit_cell = None
output_space_group = None
change_of_basis = None
eliminate_invalid_indices = False
expand_to_p1 = False
disable_unit_cell_check = True
disable_space_group_check = False
eliminate_sys_absent = True
}
d_max = None
d_min = None
wavelength = None
output_file = %s/%s_asF.mtz
job_title = None
resolve_label_conflicts = True
exclude_reflection = None
miller_array {
file_name = %s
labels = Iobs,SIGIobs
output_labels = FOBS SIGFOBS
column_root_label = None
d_min = None
d_max = None
output_as = auto intensities amplitudes_fw *amplitudes
anomalous_data = *Auto merged anomalous
force_type = *auto amplitudes intensities
scale_max = None
scale_factor = None
remove_negatives = False
massage_intensities = False
filter_by_signal_to_noise = None
add_b_iso = None
add_b_aniso = 0 0 0 0 0 0
shuffle_values = False
reset_values_to = None
}
r_free_flags {
generate = False
force_generate = False
new_label = "FreeR_flag"
fraction = 0.1
max_free = 2000
lattice_symmetry_max_delta = 5
use_lattice_symmetry = True
use_dataman_shells = False
n_shells = 20
random_seed = None
extend = True
old_test_flag_value = None
export_for_ccp4 = False
preserve_input_values = True
warn_if_all_same_value = True
adjust_fraction = False
d_eps = 0.0001
relative_to_complete_set = False
remediate_mismatches = False
}
}
""" % (uc_str, space_group, cwd, scaled_structure_factor_mtz_prefix,
scaled_intensity_mtz_fullpath)
RFE_def_file.write(RFE_def_text)
RFE_def_file.close()
print "Wrote RFE def file successfully! - Now converting intensities to structure factor amplitudes with RFE."
subprocess.call(
['iotbx.reflection_file_editor', 'reflection_file_editor.def'])
output_mtz_filename = "%s_asF.mtz" % (scaled_structure_factor_mtz_prefix)
return output_mtz_filename
print "Conversion to Structure Factors is finished!"
def run(args, command_name="phenix.fobs_minus_fobs_map", log=None):
if (len(args) == 0): args = ["--help"]
examples = """Examples:
phenix.fobs_minus_fobs_map f_obs_1_file=data1.mtz f_obs_2_file=data2.sca \
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 model.pdb
phenix.fobs_minus_fobs_map f_obs_1_file=data.mtz f_obs_2_file=data.mtz \
f_obs_1_label=FOBS1 f_obs_2_label=FOBS2 phase_source=model.pdb \
high_res=2.0 sigma_cutoff=2 scattering_table=neutron"""
command_line = (iotbx_option_parser(
usage="%s [options]" % command_name,
description=examples).option("--silent",
action="store_true",
help="Suppress output to the screen.").
enable_symmetry_comprehensive()).process(args=args)
#
if (log is None):
log = sys.stdout
if (not command_line.options.silent):
utils.print_header("phenix.fobs_minus_fobs_map", out=log)
print("Command line arguments: ", file=log)
print(args, file=log)
print(file=log)
#
processed_args = utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=fo_minus_fo_master_params(),
absolute_angle_tolerance=5,
absolute_length_tolerance=1,
log=log,
suppress_symmetry_related_errors=True)
working_phil = processed_args.params
if (not command_line.options.silent):
print("*** Parameters:", file=log)
working_phil.show(out=log)
print(file=log)
params = working_phil.extract()
consensus_symmetry = None
if (params.ignore_non_isomorphous_unit_cells):
if (None in [
params.f_obs_1_file_name, params.f_obs_2_file_name,
params.phase_source
]):
raise Sorry(
"The file parameters (f_obs_1_file_name, f_obs_2_file_name, " +
"phase_source) must be specified explicitly when " +
"ignore_non_isomorphous_unit_cells=True.")
symm_manager = iotbx.symmetry.manager()
pdb_in = iotbx.file_reader.any_file(params.phase_source,
force_type="pdb")
symm_manager.process_pdb_file(pdb_in)
hkl_in_1 = iotbx.file_reader.any_file(params.f_obs_1_file_name,
force_type="hkl")
sg_err_1, uc_err_1 = symm_manager.process_reflections_file(hkl_in_1)
hkl_in_2 = iotbx.file_reader.any_file(params.f_obs_2_file_name,
force_type="hkl")
sg_err_2, uc_err_2 = symm_manager.process_reflections_file(hkl_in_2)
out = StringIO()
symm_manager.show(out=out)
if (sg_err_1) or (sg_err_2):
raise Sorry((
"Incompatible space groups in input files:\n%s\nAll files " +
"must have the same point group (and ideally the same space group). "
+
"Please note that any symmetry information in the PDB file will be "
+ "used first.") % out.getvalue())
elif (uc_err_1) or (uc_err_2):
libtbx.call_back(
message="warn",
data=
("Crystal symmetry mismatch:\n%s\nCalculations will continue "
+
"using the symmetry in the PDB file (or if not available, the "
+
"first reflection file), but the maps should be treated with "
+ "extreme suspicion.") % out.getvalue())
crystal_symmetry = symm_manager.as_symmetry_object()
else:
processed_args = utils.process_command_line_args(
args=command_line.args,
cmd_cs=command_line.symmetry,
master_params=fo_minus_fo_master_params(),
suppress_symmetry_related_errors=False,
absolute_angle_tolerance=5,
absolute_length_tolerance=1,
log=StringIO())
crystal_symmetry = processed_args.crystal_symmetry
#
pdb_file_names = processed_args.pdb_file_names
if (len(processed_args.pdb_file_names) == 0):
if (params.phase_source is not None):
pdb_file_names = [params.phase_source]
else:
raise Sorry("No PDB file found.")
# Extaract Fobs1, Fobs2
f_obss = []
if (len(processed_args.reflection_files) == 2):
for reflection_file in processed_args.reflection_files:
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=[reflection_file],
err=null_out())
# XXX UGLY !!!
try:
parameters = extract_xtal_data.data_and_flags_master_params(
).extract()
if (params.f_obs_1_label is not None):
parameters.labels = [params.f_obs_1_label]
determine_data_and_flags_result = extract_xtal_data.run(
reflection_file_server=reflection_file_server,
keep_going=True,
parameters=parameters,
log=null_out())
except: # intentional
parameters = extract_xtal_data.data_and_flags_master_params(
).extract()
if (params.f_obs_2_label is not None):
parameters.labels = [params.f_obs_2_label]
determine_data_and_flags_result = extract_xtal_data.run(
reflection_file_server=reflection_file_server,
keep_going=True,
parameters=parameters,
log=null_out())
f_obss.append(determine_data_and_flags_result.f_obs)
else:
if ([params.f_obs_1_file_name,
params.f_obs_2_file_name].count(None) == 2):
raise Sorry("No reflection data file found.")
for file_name, label in zip(
[params.f_obs_1_file_name, params.f_obs_2_file_name],
[params.f_obs_1_label, params.f_obs_2_label]):
reflection_file = reflection_file_reader.any_reflection_file(
file_name=file_name, ensure_read_access=False)
reflection_file_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=[reflection_file],
err=null_out())
parameters = extract_xtal_data.data_and_flags_master_params(
).extract()
if (label is not None):
parameters.labels = [label]
determine_data_and_flags_result = extract_xtal_data.run(
reflection_file_server=reflection_file_server,
parameters=parameters,
keep_going=True,
log=null_out())
f_obss.append(determine_data_and_flags_result.f_obs)
if (len(f_obss) != 2):
raise Sorry(" ".join(errors))
if (not command_line.options.silent):
for ifobs, fobs in enumerate(f_obss):
print("*** Summary for data set %d:" % ifobs, file=log)
fobs.show_comprehensive_summary(f=log)
print(file=log)
pdb_combined = combine_unique_pdb_files(file_names=pdb_file_names)
pdb_combined.report_non_unique(out=log)
if (len(pdb_combined.unique_file_names) == 0):
raise Sorry("No coordinate file given.")
#
raw_recs = flex.std_string()
for rec in pdb_combined.raw_records:
if (rec.upper().count("CRYST1") == 0):
raw_recs.append(rec)
raw_recs.append(
iotbx.pdb.format_cryst1_record(crystal_symmetry=crystal_symmetry))
#
pdb_in = iotbx.pdb.input(source_info=None, lines=raw_recs)
model = mmtbx.model.manager(model_input=pdb_in)
d_min = min(f_obss[0].d_min(), f_obss[1].d_min())
model.setup_scattering_dictionaries(
scattering_table=params.scattering_table, d_min=d_min)
xray_structure = model.get_xray_structure()
hierarchy = model.get_hierarchy()
#
omit_sel = flex.bool(hierarchy.atoms_size(), False)
if (params.advanced.omit_selection is not None):
print("Will omit selection from phasing model:", file=log)
print(" " + params.advanced.omit_selection, file=log)
omit_sel = hierarchy.atom_selection_cache().selection(
params.advanced.omit_selection)
print("%d atoms selected for removal" % omit_sel.count(True), file=log)
del hierarchy
xray_structure = xray_structure.select(~omit_sel)
if (not command_line.options.silent):
print("*** Model summary:", file=log)
xray_structure.show_summary(f=log)
print(file=log)
info0 = f_obss[0].info()
info1 = f_obss[1].info()
f_obss[0] = f_obss[0].resolution_filter(
d_min=params.high_resolution,
d_max=params.low_resolution).set_info(info0)
f_obss[1] = f_obss[1].resolution_filter(
d_min=params.high_resolution,
d_max=params.low_resolution).set_info(info1)
if (params.sigma_cutoff is not None):
for i in [0, 1]:
if (f_obss[i].sigmas() is not None):
sel = f_obss[i].data(
) > f_obss[i].sigmas() * params.sigma_cutoff
f_obss[i] = f_obss[i].select(sel).set_info(info0)
for k, f_obs in enumerate(f_obss):
if (f_obs.indices().size() == 0):
raise Sorry(
"No data left in array %d (labels=%s) after filtering!" %
(k + 1, f_obs.info().label_string()))
output_file_name = params.output_file
if (output_file_name is None) and (params.file_name_prefix is not None):
output_file_name = "%s_%s.mtz" % (params.file_name_prefix,
params.job_id)
output_files = compute_fo_minus_fo_map(
data_arrays=f_obss,
xray_structure=xray_structure,
log=log,
silent=command_line.options.silent,
output_file=output_file_name,
peak_search=params.find_peaks_holes,
map_cutoff=params.map_cutoff,
peak_search_params=params.peak_search,
multiscale=params.advanced.multiscale,
anomalous=params.advanced.anomalous).file_names
return output_files
def exercise_get_xtal_data():
crystal_symmetry = crystal.symmetry(unit_cell=(10, 11, 12, 85, 95, 100),
space_group_symbol="P 1")
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=3)
input_arrays = [
miller_set.array(
data=flex.random_double(size=miller_set.indices().size()),
sigmas=flex.random_double(size=miller_set.indices().size()) /
10).set_observation_type_xray_intensity() for i in [0, 1]
]
mtz_dataset = input_arrays[0].as_mtz_dataset(column_root_label="F0")
mtz_dataset.mtz_object().write("tmp_rfu1.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp_rfu1.mtz")
]
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files)
f_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=False,
parameter_scope="xray_data")
assert str(f_obs.info()) == "tmp_rfu1.mtz:F0,SIGF0"
mtz_dataset.add_miller_array(miller_array=input_arrays[1],
column_root_label="F1")
mtz_dataset.mtz_object().write("tmp_rfu2.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp_rfu2.mtz")
]
err = StringIO()
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=err)
try:
f_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=True,
parameter_scope="xray_data")
except Sorry:
assert err.getvalue() == """\
Multiple equally suitable arrays of observed xray data found.
Possible choices:
tmp_rfu2.mtz:F0,SIGF0
tmp_rfu2.mtz:F1,SIGF1
Please use xray_data.labels
to specify an unambiguous substring of the target label.
"""
err = reflection_file_srv.err = StringIO()
else:
raise Exception_expected
f_obs_list = reflection_file_srv.get_xray_data(
file_name=None,
labels=None,
ignore_all_zeros=True,
parameter_scope="xray_data",
return_all_valid_arrays=True,
minimum_score=1)
assert len(f_obs_list) == 2
f_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=["F1", "SIGF1"],
ignore_all_zeros=True,
parameter_scope="xray_data")
assert str(f_obs.info()) == "tmp_rfu2.mtz:F1,SIGF1"
try:
f_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=["F1", "SIGF0"],
ignore_all_zeros=True,
parameter_scope="xray_data")
except Sorry:
assert err.getvalue() == """\
No matching array: xray_data.labels=F1 SIGF0
Possible choices:
tmp_rfu2.mtz:F0,SIGF0
tmp_rfu2.mtz:F1,SIGF1
Please use xray_data.labels
to specify an unambiguous substring of the target label.
"""
err = reflection_file_srv.err = StringIO()
else:
raise Exception_expected
assert len(reflection_file_srv.file_name_miller_arrays) == 1
f_obs = reflection_file_srv.get_xray_data(file_name="tmp_rfu1.mtz",
labels=None,
ignore_all_zeros=True,
parameter_scope="xray_data")
assert len(reflection_file_srv.file_name_miller_arrays) == 2
assert str(f_obs.info()) == "tmp_rfu1.mtz:F0,SIGF0"
f_obs = reflection_file_srv.get_xray_data(
file_name=os.path.abspath("tmp_rfu1.mtz"),
labels=["sigf0"],
ignore_all_zeros=True,
parameter_scope="xray_data")
assert len(reflection_file_srv.file_name_miller_arrays) == 2
assert str(f_obs.info()) == "tmp_rfu1.mtz:F0,SIGF0"
try:
f_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=True,
parameter_scope="xray_data")
except Sorry:
assert err.getvalue() == """\
Multiple equally suitable arrays of observed xray data found.
Possible choices:
tmp_rfu2.mtz:F0,SIGF0
tmp_rfu2.mtz:F1,SIGF1
Please use xray_data.labels
to specify an unambiguous substring of the target label.
"""
err = reflection_file_srv.err = StringIO()
else:
raise Exception_expected
# test preference for anomalous (or merged) data
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=True,
d_min=3)
i_obs = miller_set.array(
data=flex.random_double(size=miller_set.indices().size()),
sigmas=flex.random_double(size=miller_set.indices().size()) /
10).set_observation_type_xray_intensity()
i_mean = i_obs.average_bijvoet_mates()
mtz_data = i_obs.as_mtz_dataset(column_root_label="I")
mtz_data.add_miller_array(i_mean, column_root_label="I")
mtz_data.mtz_object().write("tmp_rfu3.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp_rfu3.mtz")
]
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files)
err = reflection_file_srv.err = StringIO()
try:
i_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=False,
parameter_scope="xray_data")
except Sorry:
pass
i_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=False,
parameter_scope="xray_data",
prefer_anomalous=True)
assert (i_obs.info().label_string() == "I(+),SIGI(+),I(-),SIGI(-)")
i_obs = reflection_file_srv.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=False,
parameter_scope="xray_data",
prefer_anomalous=False)
assert (i_obs.info().label_string() == "I,SIGI")
'''
return self._cchalf
def delta_cchalf_i(self):
'''
Return the Delta CC 1/2 for each image excluded
'''
return dict((k, v - self._cchalf_mean) for k, v in self._cchalf.iteritems())
if __name__ == '__main__':
# Read the mtz file
reader = any_reflection_file(sys.argv[1])
# Get the columns as miller arrays
miller_arrays = reader.as_miller_arrays(merge_equivalents=False)
# Select the desired columns
intensities = None
batches = None
for array in miller_arrays:
if array.info().labels == ['I', 'SIGI']:
intensities = array
if array.info().labels == ['BATCH']:
batches = array
assert intensities is not None
assert batches is not None
assert len(batches.data()) == len(intensities.data())
def exercise(prefix="tst_polder_ccs"):
"""
Test for phenix.polder correlation coefficients.
"""
# write pdb string to file
f = open("%s.pdb" % prefix, "w")
f.write(pdb_str)
f.close()
# get mtz file from model using fmodel
cmd = " ".join([
"phenix.fmodel",
"%s.pdb" % prefix, "high_res=2.0", "type=real", "label=f-obs",
"k_sol=0.4", "b_sol=50",
"output.file_name=%s.mtz" % prefix,
"> %s.log" % prefix
])
print cmd
easy_run.call(cmd)
# get params.polder
params_line = master_params_str
params = iotbx.phil.parse(input_string=params_line,
process_includes=True).extract()
pdb_input = iotbx.pdb.input(file_name='tst_polder_ccs.pdb')
pdb_hierarchy = pdb_input.construct_hierarchy()
crystal_symmetry = crystal_symmetry_from_any.extract_from(
'tst_polder_ccs.pdb')
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=crystal_symmetry)
selection_bool = pdb_hierarchy.atom_selection_cache().selection(
string='resseq 88')
#f_obs = abs(xray_structure.structure_factors(d_min=2).f_calc())
#mtz = f_obs.as_mtz_dataset(column_root_label = "Fobs")
#mtz.mtz_object().write("bla.mtz")
miller_arrays = reflection_file_reader.any_reflection_file(
file_name="tst_polder_ccs.mtz").as_miller_arrays()
fobs = [None]
for ma in miller_arrays:
if (ma.info().label_string() == "f-obs"):
fobs = ma.deep_copy()
# Calculate polder map and get results
polder_object = mmtbx.maps.polder_lib.compute_polder_map(
f_obs=fobs,
r_free_flags=None,
xray_structure=xray_structure,
pdb_hierarchy=pdb_hierarchy,
params=params.polder,
selection_bool=selection_bool)
polder_object.validate()
polder_object.run()
results = polder_object.get_results()
#mtz_dataset = results.mc_polder.as_mtz_dataset(
# column_root_label = "mFo-DFc_polder")
#mtz_dataset.add_miller_array(
# miller_array = results.mc_omit,
# column_root_label = "mFo-DFc_omit")
#mtz_object = mtz_dataset.mtz_object()
#mtz_object.write(file_name = "bla.mtz")
box_1 = results.box_1
box_2 = results.box_2
box_3 = results.box_3
sites_cart_box = box_1.xray_structure_box.sites_cart()
sel = maptbx.grid_indices_around_sites(
unit_cell=box_1.xray_structure_box.unit_cell(),
fft_n_real=box_1.map_box.focus(),
fft_m_real=box_1.map_box.all(),
sites_cart=sites_cart_box,
site_radii=flex.double(sites_cart_box.size(), 2.0))
b1 = box_1.map_box.select(sel).as_1d()
b2 = box_2.map_box.select(sel).as_1d()
b3 = box_3.map_box.select(sel).as_1d()
#print "Map 1: calculated Fobs with ligand", "CC(1,2): %6.4f" % cc12
#print "Map 2: calculated Fobs without ligand", "CC(1,3): %6.4f" % cc13
#print "Map 3: real Fobs data", "CC(2,3): %6.4f" % cc23
cc12 = flex.linear_correlation(x=b1, y=b2).coefficient()
cc13 = flex.linear_correlation(x=b1, y=b3).coefficient()
cc23 = flex.linear_correlation(x=b2, y=b3).coefficient()
#print "CC(1,2): %6.4f" % cc12
#print "CC(1,3): %6.4f" % cc13
#print "CC(2,3): %6.4f" % cc23
#### D-function
b1 = maptbx.volume_scale_1d(map=b1, n_bins=10000).map_data()
b2 = maptbx.volume_scale_1d(map=b2, n_bins=10000).map_data()
b3 = maptbx.volume_scale_1d(map=b3, n_bins=10000).map_data()
#print "Peak CC:"
cc12p = flex.linear_correlation(x=b1, y=b2).coefficient()
cc13p = flex.linear_correlation(x=b1, y=b3).coefficient()
cc23p = flex.linear_correlation(x=b2, y=b3).coefficient()
#print "CC(1,2): %6.4f" % cc12p
#print "CC(1,3): %6.4f" % cc13p
#print "CC(2,3): %6.4f" % cc23p
assert approx_equal([cc12, cc13, cc23], [0.4153, 0.9980, 0.4213], eps=0.1)
assert approx_equal([cc12p, cc13p, cc23p], [0.4310, 0.9966, 0.4379],
eps=0.1)
else:
assert i_exercise == 0
actual_test_flag_value_2 = guess_r_free_flag_value(
miller_array=r_free_flags,
test_flag_value=trial_test_flag_value)
assert (actual_test_flag_value_2 ==
actual_test_flag_value)
for second_label in ["test", "foo"]:
input_array = miller_set.array(data=exercise_flag_arrays[0])
mtz_dataset = input_array.as_mtz_dataset(
column_root_label="FreeRflags")
mtz_dataset.add_miller_array(miller_array=input_array,
column_root_label=second_label)
mtz_dataset.mtz_object().write("tmp.mtz")
reflection_files = [
reflection_file_reader.any_reflection_file(file_name="tmp.mtz")
]
err = StringIO()
reflection_file_srv = reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=err)
try:
reflection_file_srv.get_r_free_flags(
file_name=None,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope="r_free_flags")
except Sorry, e:
