def get_UBlattsymm_from_sweep_info(self, sweep_info):
"""Calculate U, B and lattice symmetry from experiment."""
expt = load.experiment_list(sweep_info.get_experiments())[0]
uc = expt.crystal.get_unit_cell()
umatrix = expt.crystal.get_U()
lattice_symm = lattice_symmetry_group(uc, max_delta=0.0)
return tuple(umatrix), mosflm_B_matrix(uc), lattice_symm
def lattice_group_info(self):
# Get highest symmetry compatible with lattice
lattice_group = sgtbx.lattice_symmetry_group(
self.minimum_symmetry.unit_cell(),
max_delta=self.max_delta,
enforce_max_delta_for_generated_two_folds=self.
enforce_max_delta_for_generated_two_folds)
return sgtbx.space_group_info(group=lattice_group)
def lattice_group_info(self):
# Get highest symmetry compatible with lattice
lattice_group = sgtbx.lattice_symmetry_group(
self.minimum_symmetry.unit_cell(),
max_delta=self.max_delta,
enforce_max_delta_for_generated_two_folds
=self.enforce_max_delta_for_generated_two_folds)
return sgtbx.space_group_info(group=lattice_group)
def lattice_symmetry_group(self,
max_delta=3,
enforce_max_delta_for_generated_two_folds=True):
from cctbx import sgtbx
return sgtbx.lattice_symmetry_group(
reduced_cell=self,
max_delta=max_delta,
enforce_max_delta_for_generated_two_folds
=enforce_max_delta_for_generated_two_folds)
def lattice_symmetry_group(self,
max_delta=3,
enforce_max_delta_for_generated_two_folds=True):
from cctbx import sgtbx
return sgtbx.lattice_symmetry_group(
reduced_cell=self,
max_delta=max_delta,
enforce_max_delta_for_generated_two_folds
=enforce_max_delta_for_generated_two_folds)
def get_umat_bmat_lattice_symmetry_from_mtz(mtz_file):
"""Get the U matrix and lattice symmetry derived from the unit cell
constants from an MTZ file."""
m = mtz.object(mtz_file)
# assert first U matrix from batches is OK
uc = m.crystals()[0].unit_cell()
lattice_symm = lattice_symmetry_group(uc, max_delta=0.0)
return tuple(m.batches()[0].umat()), mosflm_B_matrix(uc), lattice_symm
def get_umat_bmat_lattice_symmetry_from_mtz(mtz_file):
'''Get the U matrix and lattice symmetry derived from the unit cell
constants from an MTZ file.'''
from iotbx import mtz
m = mtz.object(mtz_file)
# assert first U matrix from batches is OK
uc = m.crystals()[0].unit_cell()
from cctbx.sgtbx import lattice_symmetry_group
lattice_symm = lattice_symmetry_group(uc, max_delta=0.0)
return tuple(m.batches()[0].umat()), mosflm_B_matrix(uc), lattice_symm
def run(args):
import libtbx.load_env
from scitbx import matrix
from cctbx.sgtbx import lattice_symmetry_group
from scitbx.math import r3_rotation_axis_and_angle_from_matrix
usage = "%s [options] experiment_0.expt ..." % libtbx.env.dispatcher_name
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_experiments=True,
check_format=False,
epilog=help_message,
)
params, options = parser.parse_args(show_diff_phil=True)
experiments = params.input.experiments
# check input
space_group = None
for experiment in experiments:
assert len(experiment.data.goniometers()) == 1
assert len(experiment.data.crystals()) == 1
crystal = experiment.data.crystals()[0]
if space_group is None:
space_group = crystal.get_space_group()
else:
assert crystal.get_space_group() == space_group
reference_U = None
reference_space_group = None
for j, experiment in enumerate(experiments):
goniometer = experiment.data.goniometers()[0]
F = matrix.sqr(goniometer.get_fixed_rotation())
crystal = experiment.data.crystals()[0]
U = matrix.sqr(crystal.get_U())
B = matrix.sqr(crystal.get_B())
UB = F * U * B
UBt = UB.transpose().elems
a, b, c = matrix.col(UBt[0:3]), matrix.col(UBt[3:6]), matrix.col(
UBt[6:9])
axis = matrix.col(goniometer.get_rotation_axis())
from math import pi
r2d = 180 / pi
abc = [a, b, c]
abc_names = "abc"
distances = [(r2d * (min(axis.angle(_a), pi - axis.angle(_a))), k)
for k, _a in enumerate(abc)]
close = sorted(distances)[0]
if reference_U is None:
reference_U = U
reference_space_group = lattice_symmetry_group(
crystal.get_unit_cell(), max_delta=0.0)
print("%s possible lattice ops" %
len(reference_space_group.all_ops()))
print("Experiment %d" % j)
print("Closest (original) axis: %s* %.2f" %
(abc_names[close[1]], close[0]))
results = []
for op in reference_space_group.all_ops():
R = B * matrix.sqr(op.r().as_double()).transpose() * B.inverse()
relative = (U * R).inverse() * reference_U
rot = r3_rotation_axis_and_angle_from_matrix(relative)
results.append((abs(rot.angle()), op.r().as_hkl(), rot))
results.sort()
print("Best reindex op for experiment %d: %12s (%.3f)" %
(j, results[0][1], 180.0 * results[0][2].angle() / pi))
if results[0][0] > (5 * pi / 180.0):
print("Rotation: axis: %.4f %.4f %.4f" % results[0][2].axis)
print(" angle: %.4f degrees" %
(180.0 * results[0][2].angle() / pi))
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 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
}
def run(args):
import libtbx.load_env
from scitbx import matrix
from cctbx.sgtbx import lattice_symmetry_group
from scitbx.math import r3_rotation_axis_and_angle_from_matrix
usage = "%s [options] experiment_0.json ..." % \
libtbx.env.dispatcher_name
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_experiments=True,
check_format=False,
epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
experiments = params.input.experiments
# check input
space_group = None
for experiment in experiments:
assert(len(experiment.data.goniometers()) == 1)
assert(len(experiment.data.crystals()) == 1)
crystal = experiment.data.crystals()[0]
if space_group is None:
space_group = crystal.get_space_group()
else:
assert(crystal.get_space_group() == space_group)
reference_U = None
reference_space_group = None
for j, experiment in enumerate(experiments):
goniometer = experiment.data.goniometers()[0]
F = matrix.sqr(goniometer.get_fixed_rotation())
crystal = experiment.data.crystals()[0]
U = matrix.sqr(crystal.get_U())
B = matrix.sqr(crystal.get_B())
UB = F * U * B
UBt = UB.transpose().elems
a, b, c = matrix.col(UBt[0:3]), matrix.col(UBt[3:6]), matrix.col(UBt[6:9])
axis = matrix.col(goniometer.get_rotation_axis())
from math import pi
r2d = 180 / pi
abc = [a, b, c]
abc_names = 'abc'
distances = [(r2d * (min(axis.angle(_a), pi - axis.angle(_a))), k)
for k, _a in enumerate(abc)]
close = sorted(distances)[0]
if reference_U is None:
reference_U = U
reference_space_group = lattice_symmetry_group(crystal.get_unit_cell(),
max_delta=0.0)
print '%s possible lattice ops' % len(reference_space_group.all_ops())
print 'Experiment %d' % j
print 'Closest (original) axis: %s* %.2f' % \
(abc_names[close[1]], close[0])
results = []
for op in reference_space_group.all_ops():
R = B * matrix.sqr(op.r().as_double()).transpose() * B.inverse()
relative = (U * R).inverse() * reference_U
rot = r3_rotation_axis_and_angle_from_matrix(relative)
results.append((abs(rot.angle()), op.r().as_hkl(), rot))
results.sort()
print 'Best reindex op for experiment %d: %12s (%.3f)' % \
(j, results[0][1], 180.0 * results[0][2].angle() / pi)
if results[0][0] > (5 * pi / 180.0):
print 'Rotation: axis: %.4f %.4f %.4f' % results[0][2].axis
print ' angle: %.4f degrees' % \
(180.0 * results[0][2].angle() / pi)