Click here to go to the corresponding page for the latest version of DIALS
Source code for dials.algorithms.indexing.symmetry
from __future__ import absolute_import, division, print_function
import logging
import scitbx.matrix
from cctbx import crystal, sgtbx
from cctbx.crystal_orientation import crystal_orientation
from cctbx.sgtbx import change_of_basis_op, subgroups
from cctbx.sgtbx.bravais_types import bravais_lattice
from rstbx.dps_core.lepage import iotbx_converter
from scitbx.array_family import flex
from dxtbx.model import Crystal
logger = logging.getLogger(__name__)
[docs]def metric_supergroup(group):
return (
sgtbx.space_group_info(group=group)
.type()
.expand_addl_generators_of_euclidean_normalizer(True, True)
.build_derived_acentric_group()
)
[docs]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_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, reverse=True)
for i_subgr in perm:
acentric_subgroup = subgrs[i_subgr]
acentric_supergroup = metric_supergroup(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=minimum_symmetry.unit_cell(),
space_group=acentric_subgroup,
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_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 = sgtbx.lattice_symmetry_find_max_delta(
reduced_cell=minimum_symmetry.unit_cell(), space_group=acentric_supergroup
)
if max_angular_difference < best_angular_difference:
best_angular_difference = max_angular_difference
best_subgroup = {
"subsym": subsym,
"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
[docs]class SymmetryHandler(object):
def __init__(self, unit_cell=None, space_group=None, max_delta=5):
self._max_delta = max_delta
self.target_symmetry_primitive = None
self.target_symmetry_reference_setting = None
self.cb_op_inp_ref = None
self.cb_op_inp_best = None
target_space_group = space_group
if target_space_group is not None:
target_space_group = target_space_group.build_derived_patterson_group()
if unit_cell is not None:
assert (
space_group
), "space_group must be provided in combination with unit_cell"
if target_space_group:
self.target_symmetry_inp = crystal.symmetry(
unit_cell=unit_cell, space_group=target_space_group
)
self.cb_op_inp_ref = (
self.target_symmetry_inp.change_of_basis_op_to_reference_setting()
)
self.target_symmetry_reference_setting = self.target_symmetry_inp.change_basis(
self.cb_op_inp_ref
)
self.cb_op_inp_best = (
self.target_symmetry_reference_setting.change_of_basis_op_to_best_cell()
* self.cb_op_inp_ref
)
elif target_space_group is not None:
self.target_symmetry_inp = crystal.symmetry(space_group=target_space_group)
self.cb_op_inp_ref = (
target_space_group.info().change_of_basis_op_to_reference_setting()
)
self.target_symmetry_reference_setting = crystal.symmetry(
space_group=target_space_group.change_basis(self.cb_op_inp_ref)
)
cb_op_reference_to_primitive = (
self.target_symmetry_reference_setting.change_of_basis_op_to_primitive_setting()
)
if unit_cell:
self.target_symmetry_primitive = self.target_symmetry_reference_setting.change_basis(
cb_op_reference_to_primitive
)
else:
self.target_symmetry_primitive = crystal.symmetry(
space_group=self.target_symmetry_reference_setting.space_group().change_basis(
cb_op_reference_to_primitive
)
)
self.cb_op_ref_inp = self.cb_op_inp_ref.inverse()
self.cb_op_primitive_inp = (
self.cb_op_ref_inp * cb_op_reference_to_primitive.inverse()
)
if self.target_symmetry_reference_setting:
logger.debug(
"Target symmetry (reference setting):\n%s",
self.target_symmetry_reference_setting,
)
if self.target_symmetry_primitive:
logger.debug(
"Target symmetry (primitive cell):\n%s", self.target_symmetry_primitive,
)
logger.debug("cb_op primitive->input: %s", self.cb_op_primitive_inp)
[docs] def apply_symmetry(self, crystal_model):
"""Apply symmetry constraints to a crystal model.
Returns the crystal model (with symmetry constraints applied) in the same
setting as provided as input. The cb_op returned by the method is
that necessary to transform that model to the user-provided
target symmetry.
Args:
crystal_model (dxtbx.model.Crystal): The input crystal model to which to
apply symmetry constraints.
Returns: (dxtbx.model.Crystal, cctbx.sgtbx.change_of_basis_op):
The crystal model with symmetry constraints applied, and the change_of_basis_op
that transforms the returned model to the user-specified target symmetry.
"""
if not (
self.target_symmetry_primitive
and self.target_symmetry_primitive.space_group()
):
return crystal, sgtbx.change_of_basis_op()
target_space_group = self.target_symmetry_primitive.space_group()
A = crystal_model.get_A()
max_delta = self._max_delta
items = iotbx_converter(crystal_model.get_unit_cell(), max_delta=max_delta)
target_sg_ref = target_space_group.info().reference_setting().group()
best_angular_difference = 1e8
for item in items:
if bravais_lattice(group=target_sg_ref) != item["bravais"]:
continue
if item["max_angular_difference"] < best_angular_difference:
best_angular_difference = item["max_angular_difference"]
best_subgroup = item
if best_subgroup is None:
return None, None
cb_op_inp_best = best_subgroup["cb_op_inp_best"]
best_subsym = best_subgroup["best_subsym"]
ref_subsym = best_subgroup["ref_subsym"]
cb_op_ref_best = ref_subsym.change_of_basis_op_to_best_cell()
cb_op_best_ref = cb_op_ref_best.inverse()
cb_op_inp_ref = cb_op_best_ref * cb_op_inp_best
cb_op_ref_inp = cb_op_inp_ref.inverse()
orient = crystal_orientation(A, True)
orient_ref = orient.change_basis(
scitbx.matrix.sqr((cb_op_inp_ref).c().as_double_array()[0:9]).transpose()
)
constrain_orient = orient_ref.constrain(best_subgroup["system"])
direct_matrix = constrain_orient.direct_matrix()
a = scitbx.matrix.col(direct_matrix[:3])
b = scitbx.matrix.col(direct_matrix[3:6])
c = scitbx.matrix.col(direct_matrix[6:9])
model = Crystal(a, b, c, space_group=target_sg_ref)
assert target_sg_ref.is_compatible_unit_cell(model.get_unit_cell())
model = model.change_basis(cb_op_ref_inp)
if self.cb_op_inp_best is not None:
# Then the unit cell has been provided: this is the cb_op to map to the
# user-provided input unit cell
return model, self.cb_op_inp_best.inverse() * cb_op_inp_best
if not self.cb_op_ref_inp.is_identity_op():
if self.target_symmetry_inp.space_group() == best_subsym.space_group():
# Handle where e.g. the user has requested I2 instead of the reference C2
return model, cb_op_inp_best
# The user has specified a setting that is not the reference setting
return model, self.cb_op_ref_inp * cb_op_inp_ref
# Default to reference setting
# This change of basis op will ensure that we get the best beta angle without
# changing the centring (e.g. from C2 to I2)
cb_op_ref_best = ref_subsym.change_of_basis_op_to_best_cell(
best_monoclinic_beta=False
)
return model, cb_op_ref_best * cb_op_inp_ref
