def possible_twin_laws(self):
cosets = sgtbx.cosets.left_decomposition_point_groups_only(
g=self.lattice_group,
h=self.intensity_symmetry.space_group(
).build_derived_acentric_group().make_tidy())
return cosets.best_partition_representatives(
cb_op=self.change_of_basis_op_to_minimum_cell.inverse(),
omit_first_partition=True,
omit_negative_determinants=True)
def possible_twin_laws(self):
cosets = sgtbx.cosets.left_decomposition_point_groups_only(
g=self.lattice_group, h=self.intensity_symmetry.space_group().build_derived_acentric_group().make_tidy()
)
return cosets.best_partition_representatives(
cb_op=self.change_of_basis_op_to_minimum_cell.inverse(),
omit_first_partition=True,
omit_negative_determinants=True,
)
def __init__(O, lattice_group, intensity_group, miller_indices):
O.lattice_group = lattice_group
O.intensity_group = intensity_group
O.miller_indices = miller_indices
import cctbx.miller
import cctbx.sgtbx.cosets
cosets = cctbx.sgtbx.cosets.left_decomposition_point_groups_only(
g=lattice_group,
h=intensity_group)
reps = cosets.best_partition_representatives(omit_first_partition=False)
O.cb_ops = []
O.perms = []
O.inv_perms = []
for rep in reps:
assert rep.t().is_zero()
cb_op = cctbx.sgtbx.change_of_basis_op(rep)
O.cb_ops.append(cb_op)
mi_cb = cb_op.apply(miller_indices)
matches = cctbx.miller.match_indices(mi_cb, miller_indices)
assert not matches.have_singles()
perm = matches.permutation()
O.perms.append(perm)
O.inv_perms.append(perm.inverse_permutation())
lookup_dict = {}
for i_part,part in enumerate(cosets.partitions):
for s in part:
assert s.t().is_zero()
key = str(s.r().as_hkl())
lookup_dict[key] = i_part
def multiplication_table(reps_i, reps_j):
result = []
for rep_i in reps_i:
row = []
for rep_j in reps_j:
s = rep_i.multiply(rep_j)
assert s.t().is_zero()
key = str(s.r().as_hkl())
row.append(lookup_dict[key])
result.append(row)
return result
reps_inv = [_.inverse() for _ in reps]
O.i_j_multiplication_table = multiplication_table(reps, reps)
O.i_inv_j_multiplication_table = multiplication_table(reps_inv, reps)
O.i_j_inv_multiplication_table = multiplication_table(reps, reps_inv)
def __init__(O, lattice_group, intensity_group, miller_indices):
O.lattice_group = lattice_group
O.intensity_group = intensity_group
O.miller_indices = miller_indices
import cctbx.miller
import cctbx.sgtbx.cosets
cosets = cctbx.sgtbx.cosets.left_decomposition_point_groups_only(
g=lattice_group,
h=intensity_group)
reps = cosets.best_partition_representatives(omit_first_partition=False)
O.cb_ops = []
O.perms = []
O.inv_perms = []
for rep in reps:
assert rep.t().is_zero()
cb_op = cctbx.sgtbx.change_of_basis_op(rep)
O.cb_ops.append(cb_op)
mi_cb = cb_op.apply(miller_indices)
matches = cctbx.miller.match_indices(mi_cb, miller_indices)
assert not matches.have_singles()
perm = matches.permutation()
O.perms.append(perm)
O.inv_perms.append(perm.inverse_permutation())
lookup_dict = {}
for i_part,part in enumerate(cosets.partitions):
for s in part:
assert s.t().is_zero()
key = str(s.r().as_hkl())
lookup_dict[key] = i_part
def multiplication_table(reps_i, reps_j):
result = []
for rep_i in reps_i:
row = []
for rep_j in reps_j:
s = rep_i.multiply(rep_j)
assert s.t().is_zero()
key = str(s.r().as_hkl())
row.append(lookup_dict[key])
result.append(row)
return result
reps_inv = [_.inverse() for _ in reps]
O.i_j_multiplication_table = multiplication_table(reps, reps)
O.i_inv_j_multiplication_table = multiplication_table(reps_inv, reps)
O.i_j_inv_multiplication_table = multiplication_table(reps, reps_inv)
def exercise_unmerged(space_group_info):
import random
from cctbx import sgtbx
# shuffle the
space_group = sgtbx.space_group('P 1', no_expand=True)
perm = list(range(len(space_group_info.group())))
random.shuffle(perm)
for i in perm:
space_group.expand_smx(space_group_info.group()[i])
unit_cell = space_group_info.any_compatible_unit_cell(volume=1000)
for cb_op in (None,
space_group.info().change_of_basis_op_to_primitive_setting(),
unit_cell.change_of_basis_op_to_niggli_cell()):
miller_set = crystal.symmetry(
unit_cell=unit_cell,
space_group=space_group).build_miller_set(d_min=1,
anomalous_flag=True)
miller_set = miller_set.expand_to_p1().customized_copy(
space_group_info=miller_set.space_group_info())
if cb_op is not None:
miller_set = miller_set.change_basis(cb_op)
m = mtz.object()
m.set_title('This is a title')
m.set_space_group_info(miller_set.space_group_info())
x = m.add_crystal('XTAL', 'CCTBX', miller_set.unit_cell().parameters())
d = x.add_dataset('TEST', 1)
indices = miller_set.indices()
original_indices = indices.deep_copy()
# map the miller indices to one hemisphere (i.e. just I+)
miller.map_to_asu(m.space_group().type(), False, indices)
h, k, l = [i.iround() for i in indices.as_vec3_double().parts()]
m.adjust_column_array_sizes(len(h))
m.set_n_reflections(len(h))
# assign H, K, L
d.add_column('H', 'H').set_values(h.as_double().as_float())
d.add_column('K', 'H').set_values(k.as_double().as_float())
d.add_column('L', 'H').set_values(l.as_double().as_float())
d.add_column('M_ISYM', 'Y').set_values(flex.float(len(indices)))
m.replace_original_index_miller_indices(original_indices)
assert (m.extract_original_index_miller_indices() == original_indices
).count(False) == 0
# check the indices in the mtz file are actually in the asu
extracted_indices = m.extract_miller_indices()
miller.map_to_asu(m.space_group().type(), False, extracted_indices)
assert (
extracted_indices == m.extract_miller_indices()).count(False) == 0
# test change_basis_in_place if appropriate for current space group
import cctbx.sgtbx.cosets
cb_op_to_niggli_cell \
= miller_set.change_of_basis_op_to_niggli_cell()
minimum_cell_symmetry = crystal.symmetry.change_basis(
miller_set.crystal_symmetry(), cb_op=cb_op_to_niggli_cell)
lattice_group = sgtbx.lattice_symmetry.group(
minimum_cell_symmetry.unit_cell(), max_delta=3.0)
lattice_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
lattice_group.make_tidy()
cosets = sgtbx.cosets.left_decomposition_point_groups_only(
g=lattice_group,
h=minimum_cell_symmetry.reflection_intensity_symmetry(
anomalous_flag=True).space_group(
).build_derived_acentric_group().make_tidy())
possible_twin_laws = cosets.best_partition_representatives(
cb_op=cb_op_to_niggli_cell.inverse(),
omit_first_partition=True,
omit_negative_determinants=True)
for twin_law in possible_twin_laws:
cb_op = sgtbx.change_of_basis_op(twin_law.as_xyz())
#print cb_op.as_hkl()
# forward direction
m.change_basis_in_place(cb_op)
assert (m.extract_original_index_miller_indices() == cb_op.apply(
original_indices)).count(False) == 0
## check the indices in the mtz file are actually in the asu
#extracted_indices = m.extract_miller_indices()
#miller.map_to_asu(m.space_group().type(), False, extracted_indices)
#assert (extracted_indices == m.extract_miller_indices()).count(False) == 0
# and back again
m.change_basis_in_place(cb_op.inverse())
assert (m.extract_original_index_miller_indices() ==
original_indices).count(False) == 0
def exercise_unmerged(space_group_info):
import random
from cctbx import sgtbx
# shuffle the
space_group = sgtbx.space_group("P 1", no_expand=True)
perm = list(range(len(space_group_info.group())))
random.shuffle(perm)
for i in perm:
space_group.expand_smx(space_group_info.group()[i])
unit_cell = space_group_info.any_compatible_unit_cell(volume=1000)
for cb_op in (
None,
space_group.info().change_of_basis_op_to_primitive_setting(),
unit_cell.change_of_basis_op_to_niggli_cell(),
):
miller_set = crystal.symmetry(unit_cell=unit_cell, space_group=space_group).build_miller_set(
d_min=1, anomalous_flag=True
)
miller_set = miller_set.expand_to_p1().customized_copy(space_group_info=miller_set.space_group_info())
if cb_op is not None:
miller_set = miller_set.change_basis(cb_op)
m = mtz.object()
m.set_title("This is a title")
m.set_space_group_info(miller_set.space_group_info())
x = m.add_crystal("XTAL", "CCTBX", miller_set.unit_cell().parameters())
d = x.add_dataset("TEST", 1)
indices = miller_set.indices()
original_indices = indices.deep_copy()
# map the miller indices to one hemisphere (i.e. just I+)
miller.map_to_asu(m.space_group().type(), False, indices)
h, k, l = [i.iround() for i in indices.as_vec3_double().parts()]
m.adjust_column_array_sizes(len(h))
m.set_n_reflections(len(h))
# assign H, K, L
d.add_column("H", "H").set_values(h.as_double().as_float())
d.add_column("K", "H").set_values(k.as_double().as_float())
d.add_column("L", "H").set_values(l.as_double().as_float())
d.add_column("M_ISYM", "Y").set_values(flex.float(len(indices)))
m.replace_original_index_miller_indices(original_indices)
assert (m.extract_original_index_miller_indices() == original_indices).count(False) == 0
# check the indices in the mtz file are actually in the asu
extracted_indices = m.extract_miller_indices()
miller.map_to_asu(m.space_group().type(), False, extracted_indices)
assert (extracted_indices == m.extract_miller_indices()).count(False) == 0
# test change_basis_in_place if appropriate for current space group
import cctbx.sgtbx.cosets
cb_op_to_niggli_cell = miller_set.change_of_basis_op_to_niggli_cell()
minimum_cell_symmetry = crystal.symmetry.change_basis(miller_set.crystal_symmetry(), cb_op=cb_op_to_niggli_cell)
lattice_group = sgtbx.lattice_symmetry.group(minimum_cell_symmetry.unit_cell(), max_delta=3.0)
lattice_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
lattice_group.make_tidy()
cosets = sgtbx.cosets.left_decomposition_point_groups_only(
g=lattice_group,
h=minimum_cell_symmetry.reflection_intensity_symmetry(anomalous_flag=True)
.space_group()
.build_derived_acentric_group()
.make_tidy(),
)
possible_twin_laws = cosets.best_partition_representatives(
cb_op=cb_op_to_niggli_cell.inverse(), omit_first_partition=True, omit_negative_determinants=True
)
for twin_law in possible_twin_laws:
cb_op = sgtbx.change_of_basis_op(twin_law.as_xyz())
# print cb_op.as_hkl()
# forward direction
m.change_basis_in_place(cb_op)
assert (m.extract_original_index_miller_indices() == cb_op.apply(original_indices)).count(False) == 0
## check the indices in the mtz file are actually in the asu
# extracted_indices = m.extract_miller_indices()
# miller.map_to_asu(m.space_group().type(), False, extracted_indices)
# assert (extracted_indices == m.extract_miller_indices()).count(False) == 0
# and back again
m.change_basis_in_place(cb_op.inverse())
assert (m.extract_original_index_miller_indices() == original_indices).count(False) == 0
