def get_spacegroup(facet, parent_sg, O):
"""
Get reduced symmetry spacegroup for crystal aligned on `facet`.
"""
e_field_direction = np.linalg.inv(O) @ (np.linalg.inv(O).T @ facet)
e_field_unit_vector = np.array(e_field_direction) / np.linalg.norm(
e_field_direction)
parent = sgtbx.space_group_info(parent_sg)
subgrs = subgroups.subgroups(parent).groups_parent_setting()
possible = []
for subgroup in subgrs:
subgroup_info = sgtbx.space_group_info(group=subgroup)
valid = True
for op in subgroup.smx():
rot_mat = np.array(op.r().as_double()).reshape((3, 3))
valid &= np.allclose(rot_mat @ e_field_unit_vector,
e_field_unit_vector)
if valid:
possible.append([
subgroup.n_smx(),
subgroup_info.symbol_and_number(), subgroup
])
possible = sorted(possible)
return possible[-1][1], possible[-1][0]
def generate_mtz_files(space_group_info, anomalous_flag):
crystal_symmetry = crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(volume=1000),
space_group_info=space_group_info)
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=anomalous_flag,
d_min=1)
miller_array = miller.array(
miller_set=miller_set,
data=flex.random_double(size=miller_set.indices().size()))
miller_array_p1 = miller_array.expand_to_p1()
miller_arrays = []
file_names = []
subgrs = subgroups.subgroups(space_group_info).groups_parent_setting()
for i_subgroup, subgroup in enumerate(subgrs):
subgroup_miller_array = miller_array_p1.customized_copy(
space_group_info=sgtbx.space_group_info(group=subgroup)) \
.merge_equivalents() \
.array() \
.as_reference_setting() \
.set_observation_type_xray_intensity()
file_name = "tmp_refl_stats%d.mtz" % i_subgroup
mtz_object = subgroup_miller_array.as_mtz_dataset(
column_root_label="FOBS").mtz_object().write(file_name=file_name)
miller_arrays.append(
subgroup_miller_array.f_sq_as_f().expand_to_p1().map_to_asu())
file_names.append(file_name)
return miller_arrays, file_names
def generate_mtz_files(space_group_info, anomalous_flag):
crystal_symmetry = crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(volume=1000),
space_group_info=space_group_info)
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry,
anomalous_flag=anomalous_flag,
d_min=1)
miller_array = miller.array(
miller_set=miller_set,
data=flex.random_double(size=miller_set.indices().size()))
miller_array_p1 = miller_array.expand_to_p1()
miller_arrays = []
file_names = []
subgrs = subgroups.subgroups(space_group_info).groups_parent_setting()
for i_subgroup, subgroup in enumerate(subgrs):
subgroup_miller_array = miller_array_p1.customized_copy(
space_group_info=sgtbx.space_group_info(group=subgroup)) \
.merge_equivalents() \
.array() \
.as_reference_setting() \
.set_observation_type_xray_intensity()
file_name = "tmp_refl_stats%d.mtz" % i_subgroup
mtz_object = subgroup_miller_array.as_mtz_dataset(
column_root_label="FOBS").mtz_object().write(file_name=file_name)
miller_arrays.append(
subgroup_miller_array.f_sq_as_f().expand_to_p1().map_to_asu())
file_names.append(file_name)
return miller_arrays, file_names
def update_space_group_choices(self):
if self.viewer.miller_array is None or \
self.params.NGL_HKLviewer.using_space_subgroup:
return
current_miller_array_idx = self.viewer.hkl_scenes_info[
self.viewer.scene_id][1]
matching_valid_array = self.valid_arrays[current_miller_array_idx]
from cctbx.sgtbx.subgroups import subgroups
from cctbx import sgtbx
sg_info = matching_valid_array.space_group_info()
subgrs = subgroups(sg_info).groups_parent_setting()
self.spacegroup_choices = []
for i, subgroup in enumerate(subgrs):
subgroup_info = sgtbx.space_group_info(group=subgroup)
self.spacegroup_choices.append(subgroup_info)
if (sg_info in self.spacegroup_choices):
self.current_spacegroup = self.spacegroup_choices.index(sg_info)
else:
self.spacegroup_choices.insert(0, sg_info)
self.current_spacegroup = sg_info
mydict = {
"spacegroups":
[e.symbol_and_number() for e in self.spacegroup_choices]
}
self.SendInfoToGUI(mydict)
def update_space_group_choices(self, col=None) :
if (self.viewer.miller_array is None and col is None) or \
self.params.using_space_subgroup:
return
if col is None:
current_miller_array_idx = self.viewer.HKLInfo_from_dict()[1]
else:
current_miller_array_idx = col
matching_valid_array = self.procarrays[ current_miller_array_idx ]
from cctbx.sgtbx.subgroups import subgroups
from cctbx import sgtbx
sg_info = matching_valid_array.space_group_info()
subgrs = subgroups(sg_info).groups_parent_setting()
self.spacegroup_choices = []
for i,subgroup in enumerate(subgrs) :
subgroup_info = sgtbx.space_group_info(group=subgroup)
self.spacegroup_choices.append(subgroup_info)
for i,e in enumerate(self.spacegroup_choices):
c = None
if str(sg_info) == str(e):
self.current_spacegroup = self.spacegroup_choices[i]
c = i
break
if c is None:
c = 0
self.spacegroup_choices.insert(c, sg_info)
self.current_spacegroup = sg_info
self.params.spacegroup_choice = c
spglst = [e.symbol_and_number() for e in self.spacegroup_choices] + ["original spacegroup"]
mydict = { "spacegroups": spglst }
self.SendInfoToGUI(mydict)
def __init__(self, parent_group_info):
self.subgroups = subgroups.subgroups(
parent_group_info).groups_parent_setting()
self.n_non_centric = 0
self.n_chiral = 0
for subgroup in self.subgroups:
if (not subgroup.is_centric()): self.n_non_centric += 1
if (subgroup.is_chiral()): self.n_chiral += 1
def test_double_coset_decomposition():
from cctbx.sgtbx import subgroups
for space_group_number in xrange(17, 44):
parent_group_info = sgtbx.space_group_info(space_group_number)
subgrs = subgroups.subgroups(parent_group_info).groups_parent_setting()
g = parent_group_info.group()
for h1 in subgrs:
for h2 in subgrs:
tmp_new = double_cosets(g, h1, h2)
assert not tmp_new.have_duplicates()
def test_double_coset_decomposition():
from cctbx.sgtbx import subgroups
for space_group_number in xrange(17,44):
parent_group_info = sgtbx.space_group_info(space_group_number)
subgrs = subgroups.subgroups(parent_group_info).groups_parent_setting()
g = parent_group_info.group()
for h1 in subgrs:
for h2 in subgrs:
tmp_new = double_cosets(g, h1, h2)
assert not tmp_new.have_duplicates()
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 update_space_group_choices(self):
from cctbx.sgtbx.subgroups import subgroups
from cctbx import sgtbx
sg_info = self.miller_array.space_group_info()
subgrs = subgroups(sg_info).groups_parent_setting()
self.spacegroup_choices = []
for i, subgroup in enumerate(subgrs):
subgroup_info = sgtbx.space_group_info(group=subgroup)
self.spacegroup_choices.append(subgroup_info)
self.mprint("%d, %s" % (i, subgroup_info.symbol_and_number()))
if (sg_info in self.spacegroup_choices):
self.current_spacegroup = self.spacegroup_choices.index(sg_info)
else:
self.spacegroup_choices.insert(0, sg_info)
self.current_spacegroup = sg_info
def update_space_group_choices(self, miller_array):
from cctbx.sgtbx.subgroups import subgroups
from cctbx import sgtbx
sg_info = miller_array.space_group_info()
subgrs = subgroups(sg_info).groups_parent_setting()
choices = []
for subgroup in subgrs:
subgroup_info = sgtbx.space_group_info(group=subgroup)
choices.append(str(subgroup_info))
if (str(sg_info) in choices):
current = choices.index(str(sg_info))
else:
choices.insert(0, str(sg_info))
current = 0
self.sg_ctrl.SetItems(choices)
self.sg_ctrl.SetSelection(current)
self._last_sg_sel = str(sg_info)
def update_space_group_choices (self, miller_array) :
from cctbx.sgtbx.subgroups import subgroups
from cctbx import sgtbx
sg_info = miller_array.space_group_info()
subgrs = subgroups(sg_info).groups_parent_setting()
choices = []
for subgroup in subgrs :
subgroup_info = sgtbx.space_group_info(group=subgroup)
choices.append(str(subgroup_info))
if (str(sg_info) in choices) :
current = choices.index(str(sg_info))
else :
choices.insert(0, str(sg_info))
current = 0
self.sg_ctrl.SetItems(choices)
self.sg_ctrl.SetSelection(current)
self._last_sg_sel = str(sg_info)
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 tst_bravais_types(verbose):
from cctbx import sgtbx
from cctbx.sgtbx.subgroups import subgroups
bravais_types_reference = {"aP":2,"mP":8,"mC":5,"mA":0,"mI":0,"mB":0,"oP":30,"oC":11,
"oA":4,"oB":0,"oI":9,"oF":5,"tP":49,"tI":19,"hP":45,"hR":7,
"cP":15,"cI":10,"cF":11}
bravais_types_tally = {}
for key in bravais_types_reference: bravais_types_tally[key]=0
crystal_systems_reference = {"Triclinic":2,"Monoclinic":13,"Orthorhombic":59,"Tetragonal":68,
"Trigonal":25,"Hexagonal":27,"Cubic":36}
crystal_systems_tally = {}
for key in crystal_systems_reference: crystal_systems_tally[key]=0
for space_group_number in xrange(1,231):
space_group_info = sgtbx.space_group_info(number=space_group_number)
GC = bravais_lattice(number=space_group_number)
GC_1 = bravais_lattice(group=space_group_info.group())
GC_2 = bravais_lattice(symbol=str(space_group_info))
assert GC == GC_1
assert GC == GC_2
bravais_types_tally[str(GC)]+=1
crystal_systems_tally[GC.crystal_system]+=1
if verbose:
GC.space_group_info.show_summary()
print str(GC), GC.crystal_system
# idea, not fully implemented--more extensive testing by generating all subgroups
if False:
subgrs = subgroups(parent_group_info).groups_parent_setting()
for subgroup in subgrs:
subgroup_info = sgtbx.space_group_info(group=subgroup)
subgroup_info.show_summary()
bravais_lattice(subgroup_info.type().lookup_symbol())
return (bravais_types_tally==bravais_types_reference and
crystal_systems_tally==crystal_systems_reference)
def tst_bravais_types(verbose):
from cctbx import sgtbx
from cctbx.sgtbx.subgroups import subgroups
bravais_types_reference = {
"aP": 2,
"mP": 8,
"mC": 5,
"mA": 0,
"mI": 0,
"mB": 0,
"oP": 30,
"oC": 11,
"oA": 4,
"oB": 0,
"oI": 9,
"oF": 5,
"tP": 49,
"tI": 19,
"hP": 45,
"hR": 7,
"cP": 15,
"cI": 10,
"cF": 11
}
bravais_types_tally = {}
for key in bravais_types_reference:
bravais_types_tally[key] = 0
crystal_systems_reference = {
"Triclinic": 2,
"Monoclinic": 13,
"Orthorhombic": 59,
"Tetragonal": 68,
"Trigonal": 25,
"Hexagonal": 27,
"Cubic": 36
}
crystal_systems_tally = {}
for key in crystal_systems_reference:
crystal_systems_tally[key] = 0
for space_group_number in xrange(1, 231):
space_group_info = sgtbx.space_group_info(number=space_group_number)
GC = bravais_lattice(number=space_group_number)
GC_1 = bravais_lattice(group=space_group_info.group())
GC_2 = bravais_lattice(symbol=str(space_group_info))
assert GC == GC_1
assert GC == GC_2
bravais_types_tally[str(GC)] += 1
crystal_systems_tally[GC.crystal_system] += 1
if verbose:
GC.space_group_info.show_summary()
print str(GC), GC.crystal_system
# idea, not fully implemented--more extensive testing by generating all subgroups
if False:
subgrs = subgroups(parent_group_info).groups_parent_setting()
for subgroup in subgrs:
subgroup_info = sgtbx.space_group_info(group=subgroup)
subgroup_info.show_summary()
bravais_lattice(subgroup_info.type().lookup_symbol())
return (bravais_types_tally == bravais_types_reference
and crystal_systems_tally == crystal_systems_reference)
def generate_test_data(
space_group,
lattice_group=None,
unit_cell=None,
unit_cell_volume=1000,
seed=0,
d_min=1,
sigma=0.1,
sample_size=100,
map_to_p1=False,
twin_fractions=None,
map_to_minimum=True,
):
import random
if seed is not None:
flex.set_random_seed(seed)
random.seed(seed)
assert [unit_cell, lattice_group].count(None) > 0
sgi = space_group.info()
if unit_cell is not None:
cs = crystal.symmetry(unit_cell=unit_cell, space_group_info=sgi)
elif lattice_group is not None:
subgrps = subgroups(lattice_group).groups_parent_setting()
assert space_group in subgrps
cs = lattice_group.any_compatible_crystal_symmetry(
volume=unit_cell_volume).customized_copy(space_group_info=sgi)
else:
cs = sgi.any_compatible_crystal_symmetry(volume=unit_cell_volume)
if map_to_minimum:
cs = cs.minimum_cell()
intensities = generate_intensities(cs, d_min=d_min)
intensities.show_summary()
twin_ops = generate_twin_operators(intensities)
twin_ops = [
sgtbx.change_of_basis_op(op.operator.as_xyz()) for op in twin_ops
]
if twin_fractions is not None:
assert len(twin_fractions) == len(twin_ops)
assert len(
twin_fractions) == 1, "Only 1 twin component currently supported"
twin_op = twin_ops[0]
twin_fraction = twin_fractions[0]
intensities, intensities_twin = intensities.common_sets(
intensities.change_basis(twin_op).map_to_asu())
twinned_miller = intensities.customized_copy(
data=(1.0 - twin_fraction) * intensities.data() +
twin_fraction * intensities_twin.data(),
sigmas=flex.sqrt(
flex.pow2((1.0 - twin_fraction) * intensities.sigmas()) +
flex.pow2(twin_fraction * intensities_twin.sigmas())),
)
intensities = twinned_miller
cb_ops = twin_ops
cb_ops.insert(0, sgtbx.change_of_basis_op())
reindexing_ops = {}
datasets = []
rand_norm = scitbx.random.normal_distribution(mean=0, sigma=sigma)
g = scitbx.random.variate(rand_norm)
for i in range(sample_size):
cb_op = random.choice(cb_ops)
if cb_op.as_xyz() not in reindexing_ops:
reindexing_ops[cb_op.as_xyz()] = set()
reindexing_ops[cb_op.as_xyz()].add(i)
d = intensities.change_basis(cb_op).customized_copy(
crystal_symmetry=intensities.crystal_symmetry())
if map_to_p1:
cb_op_to_primitive = d.change_of_basis_op_to_primitive_setting()
d = d.change_basis(cb_op_to_primitive)
d = d.expand_to_p1()
d = d.customized_copy(data=d.data() + g(d.size()))
datasets.append(d)
return datasets, reindexing_ops
def derive_result_group_list_original_input(self,group_of_interest):
# more-or-less a capitulation to code duplication. Don't want to copy code
# from cctbx.sgtbx.lattice_symmetry but can't figure out a quick way around it.
# Get list of sub-spacegroups
subgrs = subgroups.subgroups(group_of_interest).groups_parent_setting()
# Order sub-groups
sort_values = flex.double()
for group in subgrs:
order_z = group.order_z()
space_group_number = sgtbx.space_group_type(group, False).number()
assert 1 <= space_group_number <= 230
sort_values.append(order_z*1000+space_group_number)
perm = flex.sort_permutation(sort_values, True)
for i_subgr in perm:
acentric_subgroup = subgrs[i_subgr]
acentric_supergroup = metric_supergroup(acentric_subgroup)
# Add centre of inversion to acentric lattice symmetry
centric_group = sgtbx.space_group(acentric_subgroup)
# Make symmetry object: unit-cell + space-group
# The unit cell is potentially modified to be exactly compatible
# with the space group symmetry.
subsym = crystal.symmetry(
unit_cell=self.minimum_symmetry.unit_cell(),
space_group=centric_group,
assert_is_compatible_unit_cell=False)
supersym = crystal.symmetry(
unit_cell=self.minimum_symmetry.unit_cell(),
space_group=acentric_supergroup,
assert_is_compatible_unit_cell=False)
# Convert subgroup to reference setting
cb_op_minimum_ref = subsym.space_group_info().type().cb_op()
ref_subsym = subsym.change_basis(cb_op_minimum_ref)
# Ignore unwanted groups
if (self.bravais_types_only and
not str(ref_subsym.space_group_info()) in bravais_types.centric):
continue
# Choose best setting for monoclinic and orthorhombic systems
cb_op_best_cell = self.change_of_basis_op_to_best_cell(ref_subsym)
best_subsym = ref_subsym.change_basis(cb_op_best_cell)
# Total basis transformation
cb_op_best_cell = change_of_basis_op(str(cb_op_best_cell),stop_chars='',r_den=144,t_den=144)
cb_op_minimum_ref=change_of_basis_op(str(cb_op_minimum_ref),stop_chars='',r_den=144,t_den=144)
self.cb_op_inp_minimum=change_of_basis_op(str(self.cb_op_inp_minimum),stop_chars='',r_den=144,t_den=144)
cb_op_inp_best = cb_op_best_cell * (cb_op_minimum_ref * self.cb_op_inp_minimum)
# Use identity change-of-basis operator if possible
if (best_subsym.unit_cell().is_similar_to(self.input_symmetry.unit_cell())):
cb_op_corr = cb_op_inp_best.inverse()
try:
best_subsym_corr = best_subsym.change_basis(cb_op_corr)
except RuntimeError, e:
if (str(e).find("Unsuitable value for rational rotation matrix.") < 0):
raise
else:
if (best_subsym_corr.space_group() == best_subsym.space_group()):
cb_op_inp_best = cb_op_corr * cb_op_inp_best
"""Note: The following call does not work if n_ltr >1 for the space group"""
if acentric_subgroup.n_ltr() == 1:
m_a_d = find_max_delta(
reduced_cell=self.minimum_symmetry.unit_cell(),
space_group=acentric_subgroup)
else:
m_a_d = 0.0
self.result_groups.append({'subsym':subsym,
'supersym':supersym,
'ref_subsym':ref_subsym,
'best_subsym':best_subsym,
'cb_op_inp_best':cb_op_inp_best,
'max_angular_difference':m_a_d
})
def find_matching_symmetry(unit_cell, target_space_group, max_delta=5):
cs = crystal.symmetry(unit_cell=unit_cell, space_group=sgtbx.space_group())
target_bravais_t = bravais_types.bravais_lattice(
group=target_space_group.info().reference_setting().group())
best_subgroup = None
best_angular_difference = 1e8
# code based on cctbx/sgtbx/lattice_symmetry.py but optimised to only
# look at subgroups with the correct bravais type
input_symmetry = cs
# Get cell reduction operator
cb_op_inp_minimum = input_symmetry.change_of_basis_op_to_minimum_cell()
# New symmetry object with changed basis
minimum_symmetry = input_symmetry.change_basis(cb_op_inp_minimum)
# Get highest symmetry compatible with lattice
lattice_group = sgtbx.lattice_symmetry_group(
minimum_symmetry.unit_cell(),
max_delta=max_delta,
enforce_max_delta_for_generated_two_folds=True)
# Get list of sub-spacegroups
subgrs = subgroups.subgroups(lattice_group.info()).groups_parent_setting()
# Order sub-groups
sort_values = flex.double()
for group in subgrs:
order_z = group.order_z()
space_group_number = sgtbx.space_group_type(group, False).number()
assert 1 <= space_group_number <= 230
sort_values.append(order_z * 1000 + space_group_number)
perm = flex.sort_permutation(sort_values, True)
for i_subgr in perm:
acentric_subgroup = subgrs[i_subgr]
acentric_supergroup = metric_supergroup(acentric_subgroup)
## Add centre of inversion to acentric lattice symmetry
#centric_group = sgtbx.space_group(acentric_subgroup)
#centric_group.expand_inv(sgtbx.tr_vec((0,0,0)))
# Make symmetry object: unit-cell + space-group
# The unit cell is potentially modified to be exactly compatible
# with the space group symmetry.
subsym = crystal.symmetry(unit_cell=minimum_symmetry.unit_cell(),
space_group=acentric_subgroup,
assert_is_compatible_unit_cell=False)
#supersym = crystal.symmetry(
#unit_cell=minimum_symmetry.unit_cell(),
#space_group=acentric_supergroup,
#assert_is_compatible_unit_cell=False)
# Convert subgroup to reference setting
cb_op_minimum_ref = subsym.space_group_info().type().cb_op()
ref_subsym = subsym.change_basis(cb_op_minimum_ref)
# Ignore unwanted groups
bravais_t = bravais_types.bravais_lattice(
group=ref_subsym.space_group())
if bravais_t != target_bravais_t:
continue
# Choose best setting for monoclinic and orthorhombic systems
cb_op_best_cell = ref_subsym.change_of_basis_op_to_best_cell(
best_monoclinic_beta=True)
best_subsym = ref_subsym.change_basis(cb_op_best_cell)
# Total basis transformation
cb_op_best_cell = change_of_basis_op(str(cb_op_best_cell),
stop_chars='',
r_den=144,
t_den=144)
cb_op_minimum_ref = change_of_basis_op(str(cb_op_minimum_ref),
stop_chars='',
r_den=144,
t_den=144)
cb_op_inp_minimum = change_of_basis_op(str(cb_op_inp_minimum),
stop_chars='',
r_den=144,
t_den=144)
cb_op_inp_best = cb_op_best_cell * cb_op_minimum_ref * cb_op_inp_minimum
# Use identity change-of-basis operator if possible
if best_subsym.unit_cell().is_similar_to(input_symmetry.unit_cell()):
cb_op_corr = cb_op_inp_best.inverse()
try:
best_subsym_corr = best_subsym.change_basis(cb_op_corr)
except RuntimeError as e:
if str(e).find(
"Unsuitable value for rational rotation matrix.") < 0:
raise
else:
if best_subsym_corr.space_group() == best_subsym.space_group():
cb_op_inp_best = cb_op_corr * cb_op_inp_best
max_angular_difference = find_max_delta(
reduced_cell=minimum_symmetry.unit_cell(),
space_group=acentric_supergroup)
if max_angular_difference < best_angular_difference:
#best_subgroup = subgroup
best_angular_difference = max_angular_difference
best_subgroup = {
'subsym': subsym,
#'supersym':supersym,
'ref_subsym': ref_subsym,
'best_subsym': best_subsym,
'cb_op_inp_best': cb_op_inp_best,
'max_angular_difference': max_angular_difference
}
if best_subgroup is not None:
return best_subgroup
def derive_result_group_list(self, group_of_interest):
# Get list of sub-spacegroups
subgrs = subgroups.subgroups(group_of_interest).groups_parent_setting()
# Order sub-groups
sort_values = flex.double()
for group in subgrs:
order_z = group.order_z()
space_group_number = sgtbx.space_group_type(group, False).number()
assert 1 <= space_group_number <= 230
sort_values.append(order_z * 1000 + space_group_number)
perm = flex.sort_permutation(sort_values, True)
for i_subgr in perm:
acentric_subgroup = subgrs[i_subgr]
acentric_supergroup = metric_supergroup(acentric_subgroup)
# Add centre of inversion to acentric lattice symmetry
centric_group = sgtbx.space_group(acentric_subgroup)
centric_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
# Make symmetry object: unit-cell + space-group
# The unit cell is potentially modified to be exactly compatible
# with the space group symmetry.
subsym = crystal.symmetry(
unit_cell=self.minimum_symmetry.unit_cell(),
space_group=centric_group,
assert_is_compatible_unit_cell=False)
supersym = crystal.symmetry(
unit_cell=self.minimum_symmetry.unit_cell(),
space_group=acentric_supergroup,
assert_is_compatible_unit_cell=False)
# Convert subgroup to reference setting
cb_op_minimum_ref = subsym.space_group_info().type().cb_op()
ref_subsym = subsym.change_basis(cb_op_minimum_ref)
# Ignore unwanted groups
if (self.bravais_types_only and not str(
ref_subsym.space_group_info()) in bravais_types.centric):
continue
# Choose best setting for monoclinic and orthorhombic systems
cb_op_best_cell = self.change_of_basis_op_to_best_cell(ref_subsym)
best_subsym = ref_subsym.change_basis(cb_op_best_cell)
# Total basis transformation
cb_op_best_cell = change_of_basis_op(str(cb_op_best_cell),
stop_chars='',
r_den=144,
t_den=144)
cb_op_minimum_ref = change_of_basis_op(str(cb_op_minimum_ref),
stop_chars='',
r_den=144,
t_den=144)
self.cb_op_inp_minimum = change_of_basis_op(str(
self.cb_op_inp_minimum),
stop_chars='',
r_den=144,
t_den=144)
cb_op_inp_best = cb_op_best_cell * cb_op_minimum_ref * self.cb_op_inp_minimum
# Use identity change-of-basis operator if possible
if (best_subsym.unit_cell().is_similar_to(
self.input_symmetry.unit_cell())):
cb_op_corr = cb_op_inp_best.inverse()
try:
best_subsym_corr = best_subsym.change_basis(cb_op_corr)
except RuntimeError, e:
if (str(e).find(
"Unsuitable value for rational rotation matrix.") <
0):
raise
else:
if (best_subsym_corr.space_group() ==
best_subsym.space_group()):
cb_op_inp_best = cb_op_corr * cb_op_inp_best
self.result_groups.append({
'subsym':
subsym,
'supersym':
supersym,
'ref_subsym':
ref_subsym,
'best_subsym':
best_subsym,
'cb_op_inp_best':
cb_op_inp_best,
'max_angular_difference':
find_max_delta(reduced_cell=self.minimum_symmetry.unit_cell(),
space_group=acentric_supergroup)
})
def find_matching_symmetry(unit_cell, target_space_group, max_delta=5):
cs = crystal.symmetry(unit_cell=unit_cell, space_group=sgtbx.space_group())
target_bravais_t = bravais_types.bravais_lattice(
group=target_space_group.info().reference_setting().group())
best_subgroup = None
best_angular_difference = 1e8
# code based on cctbx/sgtbx/lattice_symmetry.py but optimised to only
# look at subgroups with the correct bravais type
input_symmetry = cs
# Get cell reduction operator
cb_op_inp_minimum = input_symmetry.change_of_basis_op_to_minimum_cell()
# New symmetry object with changed basis
minimum_symmetry = input_symmetry.change_basis(cb_op_inp_minimum)
# Get highest symmetry compatible with lattice
lattice_group = sgtbx.lattice_symmetry_group(
minimum_symmetry.unit_cell(),
max_delta=max_delta,
enforce_max_delta_for_generated_two_folds=True)
# Get list of sub-spacegroups
subgrs = subgroups.subgroups(lattice_group.info()).groups_parent_setting()
# Order sub-groups
sort_values = flex.double()
for group in subgrs:
order_z = group.order_z()
space_group_number = sgtbx.space_group_type(group, False).number()
assert 1 <= space_group_number <= 230
sort_values.append(order_z*1000+space_group_number)
perm = flex.sort_permutation(sort_values, True)
for i_subgr in perm:
acentric_subgroup = subgrs[i_subgr]
acentric_supergroup = metric_supergroup(acentric_subgroup)
## Add centre of inversion to acentric lattice symmetry
#centric_group = sgtbx.space_group(acentric_subgroup)
#centric_group.expand_inv(sgtbx.tr_vec((0,0,0)))
# Make symmetry object: unit-cell + space-group
# The unit cell is potentially modified to be exactly compatible
# with the space group symmetry.
subsym = crystal.symmetry(
unit_cell=minimum_symmetry.unit_cell(),
space_group=acentric_subgroup,
assert_is_compatible_unit_cell=False)
#supersym = crystal.symmetry(
#unit_cell=minimum_symmetry.unit_cell(),
#space_group=acentric_supergroup,
#assert_is_compatible_unit_cell=False)
# Convert subgroup to reference setting
cb_op_minimum_ref = subsym.space_group_info().type().cb_op()
ref_subsym = subsym.change_basis(cb_op_minimum_ref)
# Ignore unwanted groups
bravais_t = bravais_types.bravais_lattice(
group=ref_subsym.space_group())
if bravais_t != target_bravais_t:
continue
# Choose best setting for monoclinic and orthorhombic systems
cb_op_best_cell = ref_subsym.change_of_basis_op_to_best_cell(
best_monoclinic_beta=True)
best_subsym = ref_subsym.change_basis(cb_op_best_cell)
# Total basis transformation
cb_op_best_cell = change_of_basis_op(str(cb_op_best_cell),stop_chars='',r_den=144,t_den=144)
cb_op_minimum_ref=change_of_basis_op(str(cb_op_minimum_ref),stop_chars='',r_den=144,t_den=144)
cb_op_inp_minimum=change_of_basis_op(str(cb_op_inp_minimum),stop_chars='',r_den=144,t_den=144)
cb_op_inp_best = cb_op_best_cell * cb_op_minimum_ref * cb_op_inp_minimum
# Use identity change-of-basis operator if possible
if (best_subsym.unit_cell().is_similar_to(input_symmetry.unit_cell())):
cb_op_corr = cb_op_inp_best.inverse()
try:
best_subsym_corr = best_subsym.change_basis(cb_op_corr)
except RuntimeError, e:
if (str(e).find("Unsuitable value for rational rotation matrix.") < 0):
raise
else:
if (best_subsym_corr.space_group() == best_subsym.space_group()):
cb_op_inp_best = cb_op_corr * cb_op_inp_best
max_angular_difference = find_max_delta(
reduced_cell=minimum_symmetry.unit_cell(),
space_group=acentric_supergroup)
if max_angular_difference < best_angular_difference:
#best_subgroup = subgroup
best_angular_difference = max_angular_difference
best_subgroup = {'subsym':subsym,
#'supersym':supersym,
'ref_subsym':ref_subsym,
'best_subsym':best_subsym,
'cb_op_inp_best':cb_op_inp_best,
'max_angular_difference':max_angular_difference
}