def exercise_quick():
for space_group_symbol in ("P-1",
"P2/m",
"C2/m",
"Pmmm",
"Cmmm",
"Fmmm",
"Immm",
"P4/mmm",
"I4/mmm",
"R-3m",
"P6/mmm",
"Pm-3m",
"Im-3m",
"Fm-3m"):
parent_group_info = sgtbx.space_group_info(space_group_symbol)
non_centric = sgtbx.space_group()
for i_ltr in xrange(parent_group_info.group().n_ltr()):
for i_smx in xrange(parent_group_info.group().n_smx()):
s = parent_group_info.group()(i_ltr,0,i_smx)
non_centric.expand_smx(s)
assert non_centric.f_inv() == 1
assert non_centric.order_z() * 2 == parent_group_info.group().order_z()
non_centric_info = sgtbx.space_group_info(group=non_centric)
unit_cell = non_centric_info.any_compatible_unit_cell(volume=1000)
crystal_symmetry = crystal.symmetry(
unit_cell=unit_cell,
space_group_info=non_centric_info)
minimum_symmetry = crystal_symmetry.minimum_cell()
lattice_group = lattice_symmetry.group(
minimum_symmetry.unit_cell(), max_delta=0.5)
lattice_group_info = sgtbx.space_group_info(group=lattice_group)
assert lattice_group_info.group() == minimum_symmetry.space_group()
subgrs = subgroups.subgroups(lattice_group_info).groups_parent_setting()
for group in subgrs:
subsym = crystal.symmetry(
unit_cell=minimum_symmetry.unit_cell(),
space_group=group,
assert_is_compatible_unit_cell=False)
assert subsym.unit_cell().is_similar_to(minimum_symmetry.unit_cell())
assert lattice_symmetry.find_max_delta(
reduced_cell=minimum_symmetry.unit_cell(),
space_group=group) < 0.6
minimum_symmetry = crystal.symmetry(
unit_cell="106.04, 181.78, 110.12, 90, 90, 90",
space_group_symbol="P 1").minimum_cell()
for max_delta in xrange(10,100,10):
lattice_group = lattice_symmetry.group(
minimum_symmetry.unit_cell(), max_delta=max_delta)
lattice_group_info = sgtbx.space_group_info(group=lattice_group)
assert str(lattice_group_info) == "P 4 2 2"
def possible_point_group_generators(self):
lattice_group = lattice_symmetry.group(self.f_in_p1.unit_cell(),
max_delta=1)
lattice_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
rot_parts = set()
decorated_rot_parts = []
for op in lattice_group:
r = op.r()
if r.is_unit_mx(): continue
if op.inverse() in rot_parts: continue
r_info = sgtbx.rot_mx_info(r)
if r_info.type() < -2: continue
rot_parts.add(op)
decorated_rot_parts.append((
r_info.type() == -1, # inversion shall come first,
list(r_info.ev()).count(
0), # axes // to unit cell shall come first
# note Python 2.5- compatibility
r_info.type() == -2, # mirrors preferred.
r.order(), # higher order preferred
op))
decorated_rot_parts.sort()
decorated_rot_parts.reverse()
for item in decorated_rot_parts:
yield item[-1]
def run(mtz, mtz_out, fraction, flag_name=None, ccp4=True, use_lattice_symmetry=True, n_shells=20):
# Open mtz
miller_arrays = iotbx.mtz.object(mtz).as_miller_arrays()
print "Opening", mtz
print " Using information from", miller_arrays[0].info().label_string()
input_symm = crystal.symmetry(
unit_cell=miller_arrays[0].unit_cell(),
space_group_info=miller_arrays[0].space_group().info(),
assert_is_compatible_unit_cell=False,
force_compatible_unit_cell=False)
d_max, d_min = get_best_resolution(miller_arrays, input_symm)
print " d_max, d_min=", d_max, d_min
print " Symm:", input_symm.space_group_info(), input_symm.unit_cell()
print
# Extend flag
complete_set = make_joined_set(miller_arrays).complete_set()
if use_lattice_symmetry:
from cctbx.sgtbx import lattice_symmetry
print "Lattice symmetry:"
cb_op_to_niggli = complete_set.change_of_basis_op_to_niggli_cell()
tmp_ma = complete_set.change_basis( cb_op_to_niggli )
lattice_group = lattice_symmetry.group(tmp_ma.unit_cell(), max_delta=5.0)
print " ", tmp_ma.unit_cell(), lattice_group.laue_group_type()
print
new_r_free_array = complete_set.generate_r_free_flags(fraction=fraction,
max_free=None,
lattice_symmetry_max_delta=5.0,
use_lattice_symmetry=use_lattice_symmetry,
n_shells=n_shells)
print new_r_free_array.show_r_free_flags_info()
if ccp4:
new_r_free_array = new_r_free_array.customized_copy(data=r_free_utils.export_r_free_flags_for_ccp4(flags=new_r_free_array.data(), test_flag_value=True))
print
# Write mtz file
mtz_object = iotbx.mtz.object(mtz).add_crystal("crystal", "project", new_r_free_array.unit_cell()). \
add_dataset(name="dataset", wavelength=0). \
add_miller_array(miller_array=new_r_free_array, column_root_label=flag_name).mtz_object()
#mtz_object.show_summary(out=sys.stdout, prefix=" ")
mtz_object.write(file_name=mtz_out)
print
print "Writing:", mtz_out
print
def run(mtz, mtz_out, fraction, flag_name=None, ccp4=True, use_lattice_symmetry=True, n_shells=20):
# Open mtz
miller_arrays = iotbx.mtz.object(mtz).as_miller_arrays()
print "Opening", mtz
print " Using information from", miller_arrays[0].info().label_string()
input_symm = crystal.symmetry(
unit_cell=miller_arrays[0].unit_cell(),
space_group_info=miller_arrays[0].space_group().info(),
assert_is_compatible_unit_cell=False,
force_compatible_unit_cell=False)
d_max, d_min = get_best_resolution(miller_arrays, input_symm)
print " d_max, d_min=", d_max, d_min
print " Symm:", input_symm.space_group_info(), input_symm.unit_cell()
print
# Extend flag
complete_set = make_joined_set(miller_arrays).complete_set()
if use_lattice_symmetry:
from cctbx.sgtbx import lattice_symmetry
print "Lattice symmetry:"
cb_op_to_niggli = complete_set.change_of_basis_op_to_niggli_cell()
tmp_ma = complete_set.change_basis( cb_op_to_niggli )
lattice_group = lattice_symmetry.group(tmp_ma.unit_cell(), max_delta=5.0)
print " ", tmp_ma.unit_cell(), lattice_group.laue_group_type()
print
new_r_free_array = complete_set.generate_r_free_flags(fraction=fraction,
max_free=None,
lattice_symmetry_max_delta=5.0,
use_lattice_symmetry=use_lattice_symmetry,
n_shells=n_shells)
print new_r_free_array.show_r_free_flags_info()
if ccp4:
new_r_free_array = new_r_free_array.customized_copy(data=r_free_utils.export_r_free_flags_for_ccp4(flags=new_r_free_array.data(), test_flag_value=True))
print
# Write mtz file
mtz_object = iotbx.mtz.object(mtz).add_crystal("crystal", "project", new_r_free_array.unit_cell()). \
add_dataset(name="dataset", wavelength=0). \
add_miller_array(miller_array=new_r_free_array, column_root_label=flag_name).mtz_object()
#mtz_object.show_summary(out=sys.stdout, prefix=" ")
mtz_object.write(file_name=mtz_out)
print
print "Writing:", mtz_out
print
def exercise_quick():
for space_group_symbol in ("P-1", "P2/m", "C2/m", "Pmmm", "Cmmm", "Fmmm",
"Immm", "P4/mmm", "I4/mmm", "R-3m", "P6/mmm",
"Pm-3m", "Im-3m", "Fm-3m"):
parent_group_info = sgtbx.space_group_info(space_group_symbol)
non_centric = sgtbx.space_group()
for i_ltr in range(parent_group_info.group().n_ltr()):
for i_smx in range(parent_group_info.group().n_smx()):
s = parent_group_info.group()(i_ltr, 0, i_smx)
non_centric.expand_smx(s)
assert non_centric.f_inv() == 1
assert non_centric.order_z() * 2 == parent_group_info.group().order_z()
non_centric_info = sgtbx.space_group_info(group=non_centric)
unit_cell = non_centric_info.any_compatible_unit_cell(volume=1000)
crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group_info=non_centric_info)
minimum_symmetry = crystal_symmetry.minimum_cell()
lattice_group = lattice_symmetry.group(minimum_symmetry.unit_cell(),
max_delta=0.5)
lattice_group_info = sgtbx.space_group_info(group=lattice_group)
assert lattice_group_info.group() == minimum_symmetry.space_group()
subgrs = subgroups.subgroups(
lattice_group_info).groups_parent_setting()
for group in subgrs:
subsym = crystal.symmetry(unit_cell=minimum_symmetry.unit_cell(),
space_group=group,
assert_is_compatible_unit_cell=False)
assert subsym.unit_cell().is_similar_to(
minimum_symmetry.unit_cell())
assert lattice_symmetry.find_max_delta(
reduced_cell=minimum_symmetry.unit_cell(),
space_group=group) < 0.6
minimum_symmetry = crystal.symmetry(
unit_cell="106.04, 181.78, 110.12, 90, 90, 90",
space_group_symbol="P 1").minimum_cell()
for max_delta in range(10, 100, 10):
lattice_group = lattice_symmetry.group(minimum_symmetry.unit_cell(),
max_delta=max_delta)
lattice_group_info = sgtbx.space_group_info(group=lattice_group)
assert str(lattice_group_info) == "P 4 2 2"
def possible_point_group_generators(self):
lattice_group = lattice_symmetry.group(self.f_in_p1.unit_cell(),
max_delta=1)
lattice_group.expand_inv(sgtbx.tr_vec((0,0,0)))
rot_parts = set()
decorated_rot_parts = []
for op in lattice_group:
r = op.r()
if r.is_unit_mx(): continue
if op.inverse() in rot_parts: continue
r_info = sgtbx.rot_mx_info(r)
if r_info.type() < -2: continue
rot_parts.add(op)
decorated_rot_parts.append(
(r_info.type() == -1, # inversion shall come first,
list(r_info.ev()).count(0), # axes // to unit cell shall come first
# note Python 2.5- compatibility
r_info.type() == -2, # mirrors preferred.
r.order(), # higher order preferred
op))
decorated_rot_parts.sort()
decorated_rot_parts.reverse()
for item in decorated_rot_parts: yield item[-1]
def __init__(self,
xs1,
xs2,
relative_length_tolerance=0.05,
absolute_angle_tolerance=10,
max_delta=3.0,
anomalous_flag=True,
out=None):
# first we have to go to the niggli setting
self.cb_op_to_n_1 = xs1.change_of_basis_op_to_niggli_cell()
self.cb_op_to_n_2 = xs2.change_of_basis_op_to_niggli_cell()
nxs1 = xs1.change_basis( self.cb_op_to_n_1 )
nxs2 = xs2.change_basis( self.cb_op_to_n_2 )
# get the lattice symmetry please
lat_sym_1 = lattice_symmetry.group( nxs1.unit_cell(), max_delta )
lat_sym_2 = lattice_symmetry.group( nxs2.unit_cell(), max_delta )
# and the intensity symmetry please
int_sym_1 = nxs1.reflection_intensity_symmetry( anomalous_flag ).space_group()
int_sym_2 = nxs2.reflection_intensity_symmetry( anomalous_flag ).space_group()
# Now we have to find a similarity transform that maps the two niggli cells onto each other
c_inv_rs = nxs1.unit_cell().similarity_transformations(
other=nxs2.unit_cell(),
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance)
min_bases_msd = None
self.similarity_cb_op = None
for c_inv_r in c_inv_rs:
# make the similarity transform into a cb_op
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r))
cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
# compute the mean square difference for the bases
bases_msd = nxs1.unit_cell() \
.bases_mean_square_difference(
other=nxs2.unit_cell().change_basis(cb_op=cb_op))
# and find cb_op correspondiong to the the minimum rmsd
if (min_bases_msd is None
or min_bases_msd > bases_msd):
min_bases_msd = bases_msd
self.similarity_cb_op = cb_op
# if nothing is found, do not continue
self.double_cosets = None
if (self.similarity_cb_op is not None):
# make the common lattice group please
common_lattice_group = lat_sym_1
for s in lat_sym_2.build_derived_acentric_group().change_basis(
self.similarity_cb_op ):
try: common_lattice_group.expand_smx(s)
except RuntimeError:
common_lattice_group=None
if common_lattice_group is not None:
common_lattice_group.make_tidy()
h1 = int_sym_1.build_derived_acentric_group().make_tidy()
h2 = int_sym_2.build_derived_acentric_group().change_basis( self.similarity_cb_op ).make_tidy()
# do the double coset decomposition
self.double_cosets = cosets.double_cosets( common_lattice_group,
h1,
h2,
)
