def as_miller_arrays(self,
crystal_symmetry=None,
force_symmetry=False,
merge_equivalents=True,
base_array_info=None,
include_unmerged_data=False,
anomalous=None,
reconstruct_amplitudes=True
):
assert not include_unmerged_data, "Unmerged data not supported in MTZ"
other_symmetry = crystal_symmetry
if (base_array_info is None):
base_array_info = miller.array_info(source_type="ccp4_mtz")
result = []
for crystal in self.crystals():
try :
unit_cell = crystal.unit_cell()
except ValueError as e :
raise Sorry(str(e))
crystal_symmetry_from_file = cctbx.crystal.symmetry(
unit_cell=unit_cell,
space_group_info=self.space_group_info(),
raise_sorry_if_incompatible_unit_cell=True)
crystal_symmetry = crystal_symmetry_from_file.join_symmetry(
other_symmetry=other_symmetry,
force=force_symmetry)
for dataset in crystal.datasets():
base_dataset_info = base_array_info.customized_copy(
wavelength=dataset.wavelength())
column_groups = self.group_columns(
crystal_symmetry_from_file=crystal_symmetry_from_file,
crystal_symmetry=crystal_symmetry,
base_array_info=base_dataset_info,
dataset=dataset,
anomalous=anomalous,
reconstruct_amplitudes=reconstruct_amplitudes
)
for column_group in column_groups:
if (merge_equivalents
and isinstance(column_group.data(), flex.double)
and isinstance(column_group.sigmas(), flex.double)
and column_group.sigmas().size() != 0
and flex.min(column_group.sigmas()) > 0):
merged_column_group = column_group.merge_equivalents().array()
if (merged_column_group.indices().size()
!= column_group.indices().size()):
merged_column_group.set_info(
column_group.info().customized_copy(merged=True))
column_group = merged_column_group
result.append(column_group)
return result
def show_summary(self, out=None, prefix=""):
if (out is None): out = sys.stdout
p = prefix
print >> out, p+"Title:", self.title()
print >> out, p+"Space group symbol from file:", self.space_group_name()
print >> out, p+"Space group number from file:", self.space_group_number()
self.space_group_info().show_summary(
f=out, prefix=p+"Space group from matrices: ")
print >> out, p+"Point group symbol from file:", self.point_group_name()
if (self.n_batches() > 0):
print >> out, p+"Number of batches:", self.n_batches()
print >> out, p+"Number of crystals:", self.n_crystals()
print >> out, p+"Number of Miller indices:", self.n_reflections()
if (self.n_crystals() > 0 and self.n_reflections() > 0):
print >> out, p+"Resolution range: %.6g %.6g" % self.max_min_resolution()
print >> out, p+"History:"
for line in self.history():
print >> out, p+" ", line.rstrip()
for i_crystal,crystal in enumerate(self.crystals()):
print >> out, p+"Crystal %d:" % (i_crystal+1)
print >> out, p+" Name:", crystal.name()
print >> out, p+" Project:", crystal.project_name()
print >> out, p+" Id:", crystal.id()
crystal.unit_cell().show_parameters(f=out, prefix=p+" Unit cell: ")
print >> out, p+" Number of datasets:", crystal.n_datasets()
for i_dataset,dataset in enumerate(crystal.datasets()):
print >> out, p+" Dataset %d:" % (i_dataset+1)
print >> out, p+" Name:", dataset.name()
print >> out, p+" Id:", dataset.id()
print >> out, p+" Wavelength: %.6g" % dataset.wavelength()
print >> out, p+" Number of columns:", dataset.n_columns()
if (dataset.n_columns() > 0):
fields_list = [[
"label", "#valid", "%valid", "min", "max", "type", ""]]
max_field_lengths = [len(field) for field in fields_list[0]]
max_field_lengths[-2] = 0
for i_column,column in enumerate(dataset.columns()):
fields = column.format_fields_for_mtz_dump(
n_refl=self.n_reflections())
fields_list.append(fields)
for i,field in enumerate(fields):
max_field_lengths[i] = max(max_field_lengths[i], len(field))
format = " %%-%ds %%%ds %%%ds %%%ds %%%ds %%%ds %%s" % tuple(
max_field_lengths[:6])
for fields in fields_list:
print >> out, p+(format % tuple(fields)).rstrip()
return self
def as_miller_arrays(self,
crystal_symmetry=None,
force_symmetry=False,
merge_equivalents=True,
base_array_info=None,
include_unmerged_data=False,
):
assert not include_unmerged_data, "Unmerged data not supported in MTZ"
other_symmetry = crystal_symmetry
if (base_array_info is None):
base_array_info = miller.array_info(source_type="ccp4_mtz")
result = []
for crystal in self.crystals():
try :
unit_cell = crystal.unit_cell()
except ValueError, e :
raise Sorry(str(e))
crystal_symmetry_from_file = cctbx.crystal.symmetry(
unit_cell=unit_cell,
space_group_info=self.space_group_info(),
raise_sorry_if_incompatible_unit_cell=True)
crystal_symmetry = crystal_symmetry_from_file.join_symmetry(
other_symmetry=other_symmetry,
force=force_symmetry)
for dataset in crystal.datasets():
base_dataset_info = base_array_info.customized_copy(
wavelength=dataset.wavelength())
column_groups = self.group_columns(
crystal_symmetry_from_file=crystal_symmetry_from_file,
crystal_symmetry=crystal_symmetry,
base_array_info=base_dataset_info,
dataset=dataset)
for column_group in column_groups:
if (merge_equivalents
and isinstance(column_group.data(), flex.double)
and isinstance(column_group.sigmas(), flex.double)
and column_group.sigmas().size() != 0
and flex.min(column_group.sigmas()) > 0):
merged_column_group = column_group.merge_equivalents().array()
if (merged_column_group.indices().size()
!= column_group.indices().size()):
merged_column_group.set_info(
column_group.info().customized_copy(merged=True))
column_group = merged_column_group
result.append(column_group)
def measure(hklin, spacegroup):
'''Look at HKLIN, see how strong the absences (according to the given
spacegroup) are... looking for IPR / SIGIPR.'''
mtz_obj = mtz.object(hklin)
sg = sgtbx.space_group(sgtbx.space_group_symbols(spacegroup).hall())
mi = mtz_obj.extract_miller_indices()
sg_m = mtz_obj.space_group()
ipr_column = None
sigipr_column = None
for crystal in mtz_obj.crystals():
for dataset in crystal.datasets():
for column in dataset.columns():
if column.label() == 'IPR':
ipr_column = column
elif column.label() == 'SIGIPR':
sigipr_column = column
assert(ipr_column != None)
assert(sigipr_column != None)
ipr_values = ipr_column.extract_values(not_a_number_substitute = 0.0)
sigipr_values = sigipr_column.extract_values(not_a_number_substitute = 0.0)
present = []
absent = []
for j in range(mi.size()):
hkl = mi[j]
if sg.is_sys_absent(hkl):
absent.append(ipr_values[j] / sigipr_values[j])
else:
present.append(ipr_values[j] / sigipr_values[j])
print 'A: %f' % (sum(absent) / len(absent))
print 'P: %f' % (sum(present) / len(present))
def as_miller_arrays_dict(self,
crystal_symmetry=None,
force_symmetry=False,
merge_equivalents=True,
base_array_info=None,
anomalous=None):
"""
Returns a python dictionary with keys of tuples containing
(crystal name, dataset name, column label) and values of
the Miller arrays from :func:`as_miller_arrays`.
The arguments to :func:`as_miller_arrays_dict` are the same
as :func:`as_miller_arrays`.
>>> miller_dict = mtz_file.as_miller_arrays_dict()
>>> miller_dict[('NATIVE', 'NATIVE', 'FTOXD3')]
<cctbx.miller.array at 0x108a87b90>
>>> miller_dict[('NATIVE', 'NATIVE', 'SIGFTOXD3')]
<cctbx.miller.array at 0x108a87b90>
"""
miller_arrays = self.as_miller_arrays(
crystal_symmetry,
force_symmetry,
merge_equivalents,
base_array_info,
anomalous=anomalous
)
keys = []
for crystal in self.crystals():
for dataset in crystal.datasets():
for label in dataset.column_labels():
keys.append((crystal.name(), dataset.name(), label))
miller_dict = {}
ikeys = iter(keys)
for miller_array in miller_arrays:
for label in miller_array.info().labels:
for key in ikeys:
if label == key[2]:
miller_dict[key] = miller_array
break
return miller_dict
def measure(hklin, spacegroup):
'''Look at HKLIN, see how strong the absences (according to the given
spacegroup) are... looking for IPR / SIGIPR.'''
mtz_obj = mtz.object(hklin)
sg = sgtbx.space_group(sgtbx.space_group_symbols(spacegroup).hall())
mi = mtz_obj.extract_miller_indices()
sg_m = mtz_obj.space_group()
ipr_column = None
sigipr_column = None
for crystal in mtz_obj.crystals():
for dataset in crystal.datasets():
for column in dataset.columns():
if column.label() == 'IPR':
ipr_column = column
elif column.label() == 'SIGIPR':
sigipr_column = column
assert (ipr_column is not None)
assert (sigipr_column is not None)
ipr_values = ipr_column.extract_values(not_a_number_substitute=0.0)
sigipr_values = sigipr_column.extract_values(not_a_number_substitute=0.0)
present = []
absent = []
for j in range(mi.size()):
hkl = mi[j]
if sg.is_sys_absent(hkl):
absent.append(ipr_values[j] / sigipr_values[j])
else:
present.append(ipr_values[j] / sigipr_values[j])
print 'A: %f' % (sum(absent) / len(absent))
print 'P: %f' % (sum(present) / len(present))
def as_miller_arrays_dict(self,
crystal_symmetry=None,
force_symmetry=False,
merge_equivalents=True,
base_array_info=None):
"""
Returns a python dictionary with keys of tuples containing
(crystal name, dataset name, column label) and values of
the Miller arrays from :func:`as_miller_arrays`.
The arguments to :func:`as_miller_arrays_dict` are the same
as :func:`as_miller_arrays`.
>>> miller_dict = mtz_file.as_miller_arrays_dict()
>>> miller_dict[('NATIVE', 'NATIVE', 'FTOXD3')]
<cctbx.miller.array at 0x108a87b90>
>>> miller_dict[('NATIVE', 'NATIVE', 'SIGFTOXD3')]
<cctbx.miller.array at 0x108a87b90>
"""
miller_arrays = self.as_miller_arrays(crystal_symmetry,
force_symmetry,
merge_equivalents,
base_array_info)
keys = []
for crystal in self.crystals():
for dataset in crystal.datasets():
for label in dataset.column_labels():
keys.append((crystal.name(), dataset.name(), label))
miller_dict = {}
ikeys = iter(keys)
for miller_array in miller_arrays:
for label in miller_array.info().labels:
for key in ikeys:
if label == key[2]:
miller_dict[key] = miller_array
break
return miller_dict
def columns(self):
for crystal in self.crystals():
for dataset in crystal.datasets():
for column in dataset.columns():
yield column
def n_columns(self):
result = 0
for crystal in self.crystals():
for dataset in crystal.datasets():
result += dataset.n_columns()
return result