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,
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 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 change_basis_in_place(self,
cb_op,
new_space_group_info=None,
assert_is_compatible_unit_cell=False):
assert len(column_type_legend) == 17 # programmer alert
# force update if column_type_legend is changed
for column_type in self.column_types():
if (column_type == "P"):
raise RuntimeError(
"In-place transformation of phase angles not implemented.")
if (column_type == "A"):
raise RuntimeError(
"In-place transformation of Hendrickson-Lattman coefficients"
" not implemented.")
if (new_space_group_info is None):
new_space_group_info = self.space_group_info().change_basis(cb_op)
if "M_ISYM" in self.column_labels():
original_miller_indices = self.extract_original_index_miller_indices()
indices = cb_op.apply(original_miller_indices)
isym = flex.int(len(indices))
self.replace_original_index_miller_indices(indices)
else:
self.replace_miller_indices(cb_op.apply(self.extract_miller_indices()))
self.set_space_group_info(space_group_info=new_space_group_info)
for crystal in self.crystals():
crystal_symmetry = cctbx.crystal.symmetry(
unit_cell=crystal.unit_cell().change_basis(cb_op=cb_op),
space_group_info=new_space_group_info,
assert_is_compatible_unit_cell=assert_is_compatible_unit_cell,
raise_sorry_if_incompatible_unit_cell=True)
crystal.set_unit_cell_parameters(
crystal_symmetry.unit_cell().parameters())
# transform & symmetrize per-batch unit cell to support Scala 6.0 (NKS)
# re-zero the U-matrix so nobody tries to use it downstream
for batch in self.batches():
batch_uc = uctbx.unit_cell(list(batch.cell()))
batch_crystal_symmetry = cctbx.crystal.symmetry(
unit_cell=batch_uc.change_basis(cb_op=cb_op),
space_group_info=new_space_group_info,
assert_is_compatible_unit_cell=assert_is_compatible_unit_cell)
batch.set_cell(flex.float(
batch_crystal_symmetry.unit_cell().parameters()))
batch.set_umat(flex.float(
(0,0,0,0,0,0,0,0,0)))
def change_basis_in_place(self,
cb_op,
new_space_group_info=None,
assert_is_compatible_unit_cell=False):
assert len(column_type_legend) == 17 # programmer alert
# force update if column_type_legend is changed
for column_type in self.column_types():
if (column_type == "P"):
raise RuntimeError(
"In-place transformation of phase angles not implemented.")
if (column_type == "A"):
raise RuntimeError(
"In-place transformation of Hendrickson-Lattman coefficients"
" not implemented.")
if (new_space_group_info is None):
new_space_group_info = self.space_group_info().change_basis(cb_op)
if "M_ISYM" in self.column_labels():
original_miller_indices = self.extract_original_index_miller_indices()
indices = cb_op.apply(original_miller_indices)
isym = flex.int(len(indices))
self.replace_original_index_miller_indices(indices)
else:
self.replace_miller_indices(cb_op.apply(self.extract_miller_indices()))
self.set_space_group_info(space_group_info=new_space_group_info)
for crystal in self.crystals():
crystal_symmetry = cctbx.crystal.symmetry(
unit_cell=crystal.unit_cell().change_basis(cb_op=cb_op),
space_group_info=new_space_group_info,
assert_is_compatible_unit_cell=assert_is_compatible_unit_cell,
raise_sorry_if_incompatible_unit_cell=True)
crystal.set_unit_cell_parameters(
crystal_symmetry.unit_cell().parameters())
# transform & symmetrize per-batch unit cell to support Scala 6.0 (NKS)
# MTZ stores umat corresponding to Busing & Levy convention
def mosflm_B(unit_cell):
from math import cos, sin, radians
params = unit_cell.parameters()
rparams = unit_cell.reciprocal_parameters()
a, b, c = params[:3]
alpha, beta, gamma = [radians(a) for a in params[3:]]
ra, rb, rc = rparams[:3]
ralpha, rbeta, rgamma = [radians(a) for a in rparams[3:]]
B = (ra, rb * cos(rgamma), rc * cos(rbeta),
0, rb * sin(rgamma), -rc * sin(rbeta) * cos(alpha),
0, 0, 1/c)
return B
from scitbx import matrix
for batch in self.batches():
batch_uc = uctbx.unit_cell(list(batch.cell()))
B = matrix.sqr(mosflm_B(batch_uc))
U = matrix.sqr(batch.umat()).transpose()
A = U * B
direct_matrix = A.inverse()
M = cb_op.c_inv().r().transpose().as_rational()
new_direct_matrix = M * direct_matrix
new_uc = batch_uc.change_basis(cb_op=cb_op)
new_B = matrix.sqr(mosflm_B(new_uc))
new_U = (new_direct_matrix.inverse() * new_B.inverse()).transpose()
batch_crystal_symmetry = cctbx.crystal.symmetry(
unit_cell=new_uc,
space_group_info=new_space_group_info,
assert_is_compatible_unit_cell=assert_is_compatible_unit_cell)
batch.set_cell(flex.float(
batch_crystal_symmetry.unit_cell().parameters()))
batch.set_umat(flex.float(new_U))