def reference_setting_choices(space_group):
# we used to have
cyclic_permutations = ['x,y,z',
'y,z,x',
'z,x,y' ]
adams_group = sgtbx.space_group_info(
group=space_group.build_derived_group(False, False))
space_group = sgtbx.space_group_info(group=space_group)
# please check that we have something in reference setting
# just to make sure that thne thing is used for it's original purpose
assert space_group.is_reference_setting()
info = []
identity_op = sgtbx.change_of_basis_op('x,y,z').c().r()
for cyclic_permutation in cyclic_permutations:
cob_op = sgtbx.change_of_basis_op(cyclic_permutation)
transformed_adams_group = adams_group.change_basis(cob_op)
transformed_space_group = space_group.change_basis(cob_op)
cob_to_ref_sg = transformed_space_group.\
change_of_basis_op_to_reference_setting()
cob_to_ref_pg = transformed_adams_group.\
change_of_basis_op_to_reference_setting()
adams_norm = False
space_norm = False
# check if the rotation part of the cb_op to ref is
# the identity operator
# if hall symbols are equal, sg's are equal
if (identity_op == cob_to_ref_pg.c().r()):
adams_norm=True
if (identity_op == cob_to_ref_sg.c().r()):
space_norm=True
info_tuple = (cob_op, cob_to_ref_sg, adams_norm, space_norm)
info.append(info_tuple)
possible_additional_transforms = []
# we have to of course take into account the identity operator
possible_additional_transforms.append(info[0][0]*info[0][1])
for ii in info:
if ii[2]: # should fall in the adams normalizer
if not ii[3]: # should NOT fall in the space normalizer
# cob should ONLY be applied on unit cell, not to the sg.
possible_additional_transforms.append(ii[0])
return possible_additional_transforms
def exercise_double_coset_decomposition(
crystal_symmetry_ri,
lattice_group,
miller_array_subs,
miller_array_sub_as,
miller_array_sub_bs,
coset_decompositions,
i,
j,
verbose,
):
group_a = miller_array_subs[i].space_group_info().group()
group_b = miller_array_subs[j].space_group_info().group()
miller_array_sub_a = miller_array_sub_as[i]
miller_array_sub_b = miller_array_sub_bs[j]
single_coset_ccs = {}
for partition in coset_decompositions[i].partitions:
cb_op = sgtbx.change_of_basis_op(partition[0])
cb = miller_array_sub_a.change_basis(cb_op).map_to_asu()
cc = cb.correlation(other=miller_array_sub_b).coefficient()
key = "%.6f" % cc
single_coset_ccs.setdefault(key, []).append(str(partition[0]))
double_coset_ccs = {}
for c in sgtbx.cosets.double_unique(lattice_group, group_a, group_b):
cb_op = sgtbx.change_of_basis_op(c)
cb = miller_array_sub_b.change_basis(cb_op).map_to_asu()
cc = cb.correlation(other=miller_array_sub_a).coefficient()
key = "%.6f" % cc
double_coset_ccs.setdefault(key, []).append(str(c))
double_coset_repetitions = [len(v) for v in double_coset_ccs.values()]
failure = max(double_coset_repetitions) > 1
if failure or verbose:
print [str(sgtbx.space_group_info(group=g)) for g in (group_a, group_b)]
def construct_nice_cb_op(coset,
sym_transform_1_to_2,
to_niggli_1,
to_niggli_2):
best_choice = None
best_choice_as_hkl = None
to_niggli_2 = to_niggli_2.new_denominators( to_niggli_1 )
sym_transform_1_to_2 = sym_transform_1_to_2.new_denominators( to_niggli_1 )
for coset_element in coset:
tmp_coset_element = sgtbx.change_of_basis_op(coset_element)
tmp_coset_element = tmp_coset_element.new_denominators( to_niggli_1 )
tmp_op = to_niggli_1.inverse() \
* (tmp_coset_element * sym_transform_1_to_2) \
* to_niggli_2
if (best_choice_as_hkl is None
or sgtbx.compare_cb_op_as_hkl(
best_choice_as_hkl, tmp_op.as_hkl()) > 0):
best_choice = tmp_op
best_choice_as_hkl = tmp_op.as_hkl()
assert best_choice is not None
tmptmp = sgtbx.change_of_basis_op(coset[0])
return best_choice
def exercise_monoclinic_cell_choices_core(space_group_number, verbose):
# transformation matrices for cell choices
# columns are basis vectors "new in terms of old"
# see Int. Tab. Vol. A, p. 22, Fig. 2.2.6.4.
b1 = (1, 0, 0,
0, 1, 0,
0, 0, 1)
b2 = (-1, 0, 1,
0, 1, 0,
-1, 0, 0)
b3 = (0, 0, -1,
0, 1, 0,
1, 0, -1)
flip = (0, 0, 1,
0, -1, 0,
1, 0, 0)
p3s = sgtbx.space_group("P 3*")
done = {}
ref = sgtbx.space_group_info(number=space_group_number)
ref_uhm = ref.type().universal_hermann_mauguin_symbol()
for i_fl,fl in enumerate([b1, flip]):
rfl = sgtbx.rot_mx(fl)
cfl = sgtbx.change_of_basis_op(sgtbx.rt_mx(rfl))
for i_rt,rt in enumerate(p3s):
rp3 = rt.r()
cp3 = sgtbx.change_of_basis_op(sgtbx.rt_mx(rp3))
for i_cs,cs in enumerate([b1,b2,b3]):
rcs = sgtbx.rot_mx(cs).inverse()
ccs = sgtbx.change_of_basis_op(sgtbx.rt_mx(rcs))
cb_all = cp3 * cfl * ccs
refcb = ref.change_basis(cb_all)
refcb2 = sgtbx.space_group_info(symbol=ref_uhm+"("+str(cb_all.c())+")")
assert refcb2.group() == refcb.group()
s = sgtbx.space_group_symbols(str(refcb))
q = s.qualifier()
hm = str(refcb)
if (0 or verbose): print hm, q, cb_all.c()
if (i_fl == 0):
assert q[0] == "bca"[i_rt]
if (len(q) == 2): assert q[1] == "123"[i_cs]
elif (q[0] == "-"):
assert q[1] == "bca"[i_rt]
if (len(q) == 3): assert q[2] == "123"[i_cs]
else:
assert q[0] == "bca"[i_rt]
if (len(q) == 2 and q[1] != "123"[i_cs]):
assert done[hm] == 1
done.setdefault(hm, 0)
done[hm] += 1
assert len(done) in [3, 9, 18]
assert done.values() == [18/len(done)]*len(done)
if (0 or verbose): print
return done
def exercise_orthorhombic_hm_qualifier_as_cb_symbol():
cb_symbols = {
"cab": ["c,a,b", "z,x,y"],
"a-cb": ["a,-c,b", "x,-z,y"],
"-cba": ["-c,b,a", "-z,y,x"],
"bca": ["b,c,a", "y,z,x"],
"ba-c": ["b,a,-c", "y,x,-z"]}
for sgsyms1 in sgtbx.space_group_symbol_iterator():
n = sgsyms1.number()
if (n < 16 or n > 74): continue
q = sgsyms1.qualifier()
if (len(q) == 0): continue
e = sgsyms1.extension()
if (e == "\0"): e = ""
ehm = sgtbx.space_group_symbols(
space_group_number=n, extension=e).universal_hermann_mauguin()
cabc, cxyz = cb_symbols[q]
assert sgtbx.change_of_basis_op(cxyz).as_abc() == cabc
assert sgtbx.change_of_basis_op(cabc).as_xyz() == cxyz
uhm_xyz = ehm + " ("+cxyz+")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_xyz)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g1 = sgtbx.space_group(space_group_symbols=sgsyms1)
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
g2 = sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm)).change_basis(
sgtbx.change_of_basis_op(sgtbx.rt_mx(cxyz)))
assert g2 == g1
for c in [cxyz, cabc]:
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm))).change_basis(c).group()
assert g2 == g1
cit = sgtbx.rt_mx(cxyz).r().inverse().transpose()
cit_xyz = cit.as_xyz()
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm))).change_basis(cit_xyz).group()
assert g2 == g1
assert cit.as_xyz(False, "abc") == cabc
uhm_abc = ehm + " ("+cabc+")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_abc)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
def show_rfactors_targets_scales_overall(self, header = None, out=None):
from cctbx import sgtbx
if(out is None): out = sys.stdout
out.flush()
p = " "
self._header_resolutions_nreflections(header=header, out=out)
print("| "+" "*38+"|", file=out)
self._rfactors_and_bulk_solvent_and_scale_params(out=out)
line7="| normalized target function (%s) (work): %s"% (
self.target_name, n_as_s("%15.6f",self.target_work))
np = 79 - (len(line7) + 1)
line7 = line7 + " "*np + "|"
print(line7, file=out)
# no norm - work
line71="| target function (%s) not normalized (work): %s"% (
self.target_name, n_as_s("%15.6f",self.target_work_no_norm))
np = 79 - (len(line71) + 1)
line71 = line71 + " "*np + "|"
print(line71, file=out)
# no norm - free
line71="| target function (%s) not normalized (free): %s"% (
self.target_name, n_as_s("%15.6f",self.target_free_no_norm))
np = 79 - (len(line71) + 1)
line71 = line71 + " "*np + "|"
print(line71, file=out)
#
if(self.twin_fraction is not None):
line8="| twin fraction: "+format_value("%-4.2f",self.twin_fraction)+\
" twin operator: "+\
format_value("%-s",sgtbx.change_of_basis_op(self.twin_law).as_hkl())
np = 79 - (len(line8) + 1)
line8 = line8 + " "*np + "|"
print(line8, file=out)
print("|"+"-"*77+"|", file=out)
out.flush()
def _apply_reindexing_operators(self, reindexing_ops, subgroup=None):
"""Apply the reindexing operators to the reflections and experiments."""
unique_ids = set(self.cosym_analysis.dataset_ids)
for cb_op, dataset_id in zip(reindexing_ops, unique_ids):
cb_op = sgtbx.change_of_basis_op(cb_op)
logger.debug("Applying reindexing op %s to dataset %i",
cb_op.as_xyz(), dataset_id)
expt = self._experiments[dataset_id]
refl = self._reflections[dataset_id]
expt.crystal = expt.crystal.change_basis(cb_op)
if subgroup is not None:
cb_op = subgroup["cb_op_inp_best"] * cb_op
expt.crystal = expt.crystal.change_basis(cb_op)
expt.crystal.set_space_group(
subgroup["best_subsym"].space_group(
).build_derived_acentric_group())
else:
expt.crystal = expt.crystal.change_basis(cb_op)
expt.crystal.set_unit_cell(
expt.crystal.get_space_group().average_unit_cell(
expt.crystal.get_unit_cell()))
refl["miller_index"] = cb_op.apply(refl["miller_index"])
# Allow for the case where some datasets are filtered out.
if len(reindexing_ops) < len(self._experiments):
to_delete = [
i for i in range(len(self._experiments)) if i not in unique_ids
]
for idx in sorted(to_delete, reverse=True):
logger.info(
f"Removing dataset {idx} as unable to determine reindexing operator"
)
del self._experiments[idx]
del self._reflections[idx]
def run():
settings = [0]
for i in xrange(1, 231): settings.append({})
list_cb_op = []
for xyz in ("x,y,z", "z,x,y", "y,z,x"):
list_cb_op.append(sgtbx.change_of_basis_op(sgtbx.rt_mx(xyz)))
n_built = 0
for i in sgtbx.space_group_symbol_iterator():
hall_symbol = i.hall()
for z in "PABCIRHF":
hall_z = hall_symbol[0] + z + hall_symbol[2:]
for cb_op in list_cb_op:
group = sgtbx.space_group(hall_z).change_basis(cb_op)
sg_type = group.type()
settings[sg_type.number()][sg_type.lookup_symbol()] = 0
n_built += 1
print "# n_built =", n_built
n_non_redundant = 0
print "settings = ("
for i in xrange(1, 231):
print "#", i
symbols = settings[i].keys()
symbols.sort()
for s in symbols:
print "'" + s + "',"
n_non_redundant += 1
print ")"
print "# n_non_redundant =", n_non_redundant
def show_rfactors_targets_scales_overall(self, header = None, out=None):
from cctbx import sgtbx
if(out is None): out = sys.stdout
out.flush()
p = " "
self._header_resolutions_nreflections(header=header, out=out)
print >> out, "| "+" "*38+"|"
self._rfactors_and_bulk_solvent_and_scale_params(out=out)
line7="| normalized target function (%s) (work): %s"% (
self.target_name, n_as_s("%15.6f",self.target_work))
np = 79 - (len(line7) + 1)
line7 = line7 + " "*np + "|"
print >> out, line7
# no norm - work
line71="| target function (%s) not normalized (work): %s"% (
self.target_name, n_as_s("%15.6f",self.target_work_no_norm))
np = 79 - (len(line71) + 1)
line71 = line71 + " "*np + "|"
print >> out, line71
# no norm - free
line71="| target function (%s) not normalized (free): %s"% (
self.target_name, n_as_s("%15.6f",self.target_free_no_norm))
np = 79 - (len(line71) + 1)
line71 = line71 + " "*np + "|"
print >> out, line71
#
if(self.twin_fraction is not None):
line8="| twin fraction: "+format_value("%-4.2f",self.twin_fraction)+\
" twin operator: "+\
format_value("%-s",sgtbx.change_of_basis_op(self.twin_law).as_hkl())
np = 79 - (len(line8) + 1)
line8 = line8 + " "*np + "|"
print >> out, line8
print >> out, "|"+"-"*77+"|"
out.flush()
def difference_rotation_matrix_axis_angle(crystal_a, crystal_b):
from cctbx import sgtbx
#assert crystal_a.get_space_group() == crystal_b.get_space_group()
space_group = crystal_b.get_space_group()
best_R_ab = None
best_cb_op = None
best_axis = None
best_angle = 1e8
# iterate over space group ops to find smallest differences
for i_op, op in enumerate(
space_group.build_derived_laue_group().all_ops()):
if op.r().determinant() < 0:
continue
elif not op.t().is_zero():
continue
cb_op = sgtbx.change_of_basis_op(op.inverse())
crystal_b_sym = crystal_b.change_basis(cb_op)
U_a = crystal_a.get_U()
U_b = crystal_b_sym.get_U()
assert U_a.is_r3_rotation_matrix()
assert U_b.is_r3_rotation_matrix()
# the rotation matrix to transform from U_a to U_b
R_ab = U_b * U_a.transpose()
axis_angle = r3_rotation_axis_and_angle_from_matrix(R_ab)
axis = axis_angle.axis
angle = axis_angle.angle() * 180.0 / math.pi
if abs(angle) < abs(best_angle):
best_angle = angle
best_axis = axis
best_R_ab = R_ab
best_cb_op = cb_op
return best_R_ab, best_axis, best_angle, best_cb_op
def generate_twin_operators(self, lattice_symmetry_max_delta=3.0):
# see also mmtbx.scaling.twin_analyses.twin_laws
cb_op_to_niggli_cell = \
self._data.change_of_basis_op_to_niggli_cell()
if self._lattice_group is None:
minimum_cell_symmetry = self._data.crystal_symmetry().change_basis(
cb_op=cb_op_to_niggli_cell)
self._lattice_group = sgtbx.lattice_symmetry.group(
reduced_cell=minimum_cell_symmetry.unit_cell(),
max_delta=lattice_symmetry_max_delta)
intensity_symmetry = minimum_cell_symmetry.reflection_intensity_symmetry(
anomalous_flag=self._data.anomalous_flag())
cb_op = cb_op_to_niggli_cell.inverse()
else:
cb_op = sgtbx.change_of_basis_op()
intensity_symmetry = self._data.reflection_intensity_symmetry()
operators = []
for partition in sgtbx.cosets.left_decomposition(
g = self._lattice_group,
h = intensity_symmetry.space_group()
.build_derived_acentric_group()
.make_tidy()).partitions[1:] :
if (partition[0].r().determinant() > 0):
operators.append(cb_op.apply(partition[0]))
return operators
def __init__(self, f_in_p1, **kwds):
isinstance(f_in_p1, miller.array)
assert f_in_p1.space_group().type().hall_symbol() == ' P 1'
self.f_in_p1 = f_in_p1
adopt_optional_init_args(self, kwds)
self.search_parameters = maptbx.peak_search_parameters(
peak_search_level=3,
interpolate=True,
min_distance_sym_equiv=0.25,
)
self.space_group = sgtbx.space_group('P 1', t_den=sg_t_den)
self.origin = None
self.symmetry_pool = []
self.find_centring_translations()
if self.space_group.order_z() > 1:
f_in_centered = self.f_in_p1.customized_copy(
space_group_info=sgtbx.space_group_info(group=self.space_group)
).eliminate_sys_absent().merge_equivalents().array()
self.cb_op_to_primitive = \
f_in_centered.change_of_basis_op_to_primitive_setting()
self.f_in_p1 = f_in_centered.change_basis(self.cb_op_to_primitive)
self.space_group = self.f_in_p1.space_group()
else:
self.cb_op_to_primitive = sgtbx.change_of_basis_op()
self.f_in_p1 = self.f_in_p1.generate_bijvoet_mates()
self.find_space_group()
self.space_group = sgtbx.space_group(self.space_group.type().hall_symbol(),
t_den=sgtbx.sg_t_den)
self.space_group_info = sgtbx.space_group_info(group=self.space_group)
def find_space_group(self):
decorated_symmetry_pool = []
denominator = 12**3
for i, (r, d) in enumerate(self.cross_correlation_peaks()):
t = sgtbx.tr_vec((d*denominator).as_int(), tr_den=denominator)
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r, t))
phi_sym = self.f_in_p1.symmetry_agreement_factor(
cb_op, assert_is_similar_symmetry=False)
if phi_sym < self.phi_sym_acceptance_cutoff:
status = possible_symmetry.accepted
elif phi_sym < self.phi_sym_rejection_cutoff:
status = possible_symmetry.unsure
else:
status = possible_symmetry.rejected
decorated_symmetry_pool.append(
(-status, i, possible_symmetry(r, d, phi_sym, status)))
decorated_symmetry_pool.sort()
self.symmetry_pool = [ item[-1] for item in decorated_symmetry_pool ]
self.origin = mat.mutable_zeros(3)
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.set_components_of_global_origin(self.origin)
if self.origin.elems.count(0) == 0: break
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.change_origin(self.origin)
self.space_group.expand_smx(symm.rt)
def subgroups_table(d):
header = (
"Patterson group",
"",
"Likelihood",
"NetZcc",
"Zcc+",
"Zcc-",
"delta",
"Reindex operator",
)
rows = [header]
for score in d["subgroup_scores"]:
rows.append((
str(
sgtbx.space_group(
hall_symbol=str(score["patterson_group"])).info()),
score["stars"],
"%.3f" % score["likelihood"],
"% .2f" % score["z_cc_net"],
"% .2f" % score["z_cc_for"],
"% .2f" % score["z_cc_against"],
"%.1f" % score["max_angular_difference"],
str(sgtbx.change_of_basis_op(str(score["cb_op"]))),
))
return rows
def test_experimentlist_change_basis(dials_data):
experiments = ExperimentList()
for i in range(4):
experiments.extend(
ExperimentList.from_file(
dials_data("vmxi_proteinase_k_sweeps") /
("experiments_%i.expt" % i),
check_format=False,
))
reindexed_uc = (68.368, 103.968, 68.368, 90.000, 90.000, 90.000)
reindexed_sg = sgtbx.space_group_info("P 4 2 2 (b,c,a)").group()
cb_op = sgtbx.change_of_basis_op("-a,-c,-b")
for cb_op in (cb_op, [cb_op] * len(experiments)):
expts_rdx = experiments.change_basis(cb_op)
for expt in expts_rdx:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
reindexed_uc, abs=0.1)
assert expt.crystal.get_space_group() == reindexed_sg
experiments.change_basis(cb_op, in_place=True)
for expt in experiments:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
reindexed_uc, abs=0.1)
assert expt.crystal.get_space_group() == reindexed_sg
with pytest.raises(AssertionError):
experiments.change_basis([cb_op, cb_op])
def assign_operators(self, reidx_ops=None):
arrays = self.arrays
self.best_operators = None
if reidx_ops is None: reidx_ops = self.find_reindex_ops()
print >>self.log_out, "Reindex operators:", map(lambda x: str(x.as_hkl()), reidx_ops)
print >>self.log_out, ""
reidx_ops.sort(key=lambda x: not x.is_identity_op()) # identity op to first
data = None
latt_id = flex.int([])
for i, a in enumerate(arrays):
if data is None: data = a
else: data = data.concatenate(a, assert_is_similar_symmetry=False)
latt_id.extend(flex.int(a.size(), i))
latt_id = data.customized_copy(data=latt_id.as_double())
result = brehm_diederichs.run(L=[data, latt_id], nproc=self.nproc, verbose=True)
self.best_operators = map(lambda x: None, xrange(len(arrays)))
for op in result:
idxes = map(int, result[op])
print >>self.log_out, " %s num=%3d idxes= %s" %(op, len(result[op]), idxes)
for idx in idxes:
self.best_operators[idx] = sgtbx.change_of_basis_op(op)
def __init__(self, crystal_symmetry, symmetry_flags):
self.cb_op_original_to_sampling = crystal_symmetry \
.change_of_basis_op_to_reference_setting()
point_group_type = crystal_symmetry.space_group().point_group_type()
add_cb_op = {"2": "z,x,y",
"m": "y,z,x"}.get(point_group_type, None)
if (add_cb_op is not None):
self.cb_op_original_to_sampling = sgtbx.change_of_basis_op(add_cb_op) \
* self.cb_op_original_to_sampling
sampling_symmetry = crystal_symmetry.change_basis(
self.cb_op_original_to_sampling)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=sampling_symmetry.space_group_info().type(),
seminvariant=sampling_symmetry.space_group_info()
.structure_seminvariants())
expanded_symmetry = crystal.symmetry(
unit_cell=sampling_symmetry.unit_cell(),
space_group=search_symmetry.projected_subgroup())
self.rational_asu = expanded_symmetry.space_group_info().direct_space_asu()
self.rational_asu.add_planes(
normal_directions=search_symmetry.continuous_shifts(),
both_directions=True)
self.float_asu=self.rational_asu.define_metric(
unit_cell=expanded_symmetry.unit_cell()).as_float_asu()
self.continuous_shift_flags=search_symmetry.continuous_shift_flags()
def difference_rotation_matrix_and_euler_angles(crystal_a, crystal_b):
from cctbx import sgtbx
#assert crystal_a.get_space_group() == crystal_b.get_space_group()
space_group = crystal_b.get_space_group()
min_sum_euler_angles = 1e8
best_R_ab = None
best_cb_op = None
# iterate over space group ops to find smallest differences
for i_op, op in enumerate(space_group.build_derived_laue_group().all_ops()):
if op.r().determinant() < 0:
continue
elif not op.t().is_zero():
continue
cb_op = sgtbx.change_of_basis_op(op.inverse())
crystal_b_sym = crystal_b.change_basis(cb_op)
U_a = crystal_a.get_U()
U_b = crystal_b_sym.get_U()
assert U_a.is_r3_rotation_matrix()
assert U_b.is_r3_rotation_matrix()
# the rotation matrix to transform from U_a to U_b
R_ab = U_b * U_a.transpose()
euler_angles = euler.xyz_angles(R_ab)
sum_euler_angles = sum(abs(ea) for ea in euler_angles)
if sum_euler_angles < min_sum_euler_angles:
min_sum_euler_angles = sum_euler_angles
best_R_ab = R_ab
best_cb_op = cb_op
best_euler_angles = euler.xyz_angles(best_R_ab)
return best_R_ab, best_euler_angles, best_cb_op
def exercise():
ma = miller.array(
miller.set(crystal.symmetry(unit_cell=(5,5,5, 90, 90, 90),
space_group=sgtbx.space_group('P 2x')),
indices=flex.miller_index(
[(1,0,0), (0,1,0), (0,0,1),
(-1,0,0), (0,-1,0), (0,0,-1),
(1,1,0), (1,0,1), (0,1,1),
(-1,-1,0), (-1,0,-1), (0,-1,-1),
(1,-1,0), (1,0,-1), (0,1,-1),
(-1,1,0), (-1,0,1), (0,-1,1),
(1,1,1), (-1,1,1), (1,-1,1), (1,1,-1),
(-1,-1,-1), (1,-1,-1), (-1,1,-1), (-1,-1,1)])),
data=flex.complex_double(flex.random_double(26), flex.random_double(26)))
f_at_h = dict(zip(ma.indices(), ma.data()))
for op in ("-x, y+1/2, -z", "x+1/2, -y, z-1/2"):
op = sgtbx.rt_mx(op)
original, transformed = ma.common_sets(
ma.change_basis(sgtbx.change_of_basis_op(op.inverse())))
for h, f in original:
assert f == f_at_h[h]
for h, op_f in transformed:
assert approx_equal(
op_f,
f_at_h[h*op.r()]*exp(1j*2*pi*row(h).dot(col(op.t().as_double()))))
def reindex(self, reflections, experiments, solution):
''' Reindex with newly-determined space group / unit cell '''
# Update space group / unit cell
experiment = experiments[0]
print "Old crystal:"
print experiment.crystal
print
experiment.crystal.update(solution.refined_crystal)
print "New crystal:"
print experiment.crystal
print
# Change basis
cb_op = solution['cb_op_inp_best'].as_abc()
change_of_basis_op = sgtbx.change_of_basis_op(cb_op)
miller_indices = reflections['miller_index']
non_integral_indices = change_of_basis_op.apply_results_in_non_integral_indices(
miller_indices)
if non_integral_indices.size() > 0:
print "Removing {}/{} reflections (change of basis results in non-integral indices)" \
"".format(non_integral_indices.size(), miller_indices.size())
sel = flex.bool(miller_indices.size(), True)
sel.set_selected(non_integral_indices, False)
miller_indices_reindexed = change_of_basis_op.apply(
miller_indices.select(sel))
reflections['miller_index'].set_selected(sel, miller_indices_reindexed)
reflections['miller_index'].set_selected(~sel, (0, 0, 0))
return experiments, reflections
def loop_over_super_cells(max_index, all_subgroups, subgroup):
assert subgroup.n_ltr() == 1
for ia in xrange(1,max_index+1):
for ib in xrange(1,max_index+1):
for ic in xrange(1,max_index+1):
cb_op = sgtbx.change_of_basis_op("x/%d,y/%d,z/%d" % (ia,ib,ic))
try:
scsubgroup = subgroup.change_basis(cb_op=cb_op)
except RuntimeError, e:
if (str(e).endswith(
"Unsuitable value for rational rotation matrix.")):
all_subgroups["incompatible_rotation_denominator"] += 1
elif (str(e).endswith(
"Unsuitable value for rational translation vector.")):
all_subgroups["incompatible_translation_denominator"] += 1
else:
raise RuntimeError
else:
def remove_lattice_translations(g):
result = sgtbx.space_group(
hall_symbol="P1", t_den=subgroup.t_den())
for i_inv in xrange(g.f_inv()):
for i_smx in xrange(g.n_smx()):
result.expand_smx(g(0, i_inv, i_smx))
return result
subsubgroup = remove_lattice_translations(scsubgroup)
uhm = sgtbx.space_group_type(group=subsubgroup) \
.universal_hermann_mauguin_symbol()
all_subgroups[uhm] += 1
def test_twin_r_value(twin_operator):
miller_array = random_data(35).map_to_asu()
miller_array = miller_array.f_as_f_sq()
for twin_fraction, expected_r_abs,expected_r_sq in zip(
[0,0.1,0.2,0.3,0.4,0.5],
[0.50,0.40,0.30,0.20,0.10,0.0],
[0.333,0.213,0.120,0.0533,0.0133,0.00]):
cb_op = sgtbx.change_of_basis_op( twin_operator )
miller_array_mod, miller_array_twin = miller_array.common_sets(
miller_array.change_basis( cb_op ).map_to_asu() )
twinned_miller = miller_array_mod.customized_copy(
data = (1.0-twin_fraction)*miller_array_mod.data()
+ twin_fraction*miller_array_twin.data(),
sigmas = flex.sqrt(
flex.pow( ((1.0-twin_fraction)*miller_array_mod.sigmas()),2.0)+\
flex.pow( ((twin_fraction)*miller_array_twin.sigmas()),2.0))
)
twinned_miller.set_observation_type( miller_array.observation_type())
twin_r = scaling.twin_r( twinned_miller.indices(),
twinned_miller.data(),
twinned_miller.space_group(),
twinned_miller.anomalous_flag(),
cb_op.c().r().as_double()[0:9] )
assert approx_equal(twin_r.r_abs_value(), expected_r_abs, 0.08)
assert approx_equal(twin_r.r_sq_value(), expected_r_sq, 0.08)
def find_space_group(self):
decorated_symmetry_pool = []
denominator = 12**3
for i, (r, d) in enumerate(self.cross_correlation_peaks()):
t = sgtbx.tr_vec((d*denominator).as_int(), tr_den=denominator)
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r, t))
phi_sym = self.f_in_p1.symmetry_agreement_factor(
cb_op, assert_is_similar_symmetry=False)
if phi_sym < self.phi_sym_acceptance_cutoff:
status = possible_symmetry.accepted
elif phi_sym < self.phi_sym_rejection_cutoff:
status = possible_symmetry.unsure
else:
status = possible_symmetry.rejected
decorated_symmetry_pool.append(
(-status, i, possible_symmetry(r, d, phi_sym, status)))
decorated_symmetry_pool.sort()
self.symmetry_pool = [ item[-1] for item in decorated_symmetry_pool ]
self.origin = mat.mutable_zeros(3)
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.set_components_of_global_origin(self.origin)
if self.origin.elems.count(0) == 0: break
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.change_origin(self.origin)
self.space_group.expand_smx(symm.rt)
def run(args):
if "--full" in args:
to_do = range(1, 230 + 1)
elif "--special" in args:
to_do = sorted(special.keys())
else:
to_do = [75, 151]
for space_group_number in to_do:
sgi = sgtbx.space_group_info(number=space_group_number)
sgi.show_summary(prefix="")
sys.stdout.flush()
n_special = 0
for m in scitbx.math.unimodular_generator(range=1).all():
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(m, 1), 1)).new_denominators(12, 144)
cb_sgi = sgi.change_basis(cb_op=cb_op)
cb_op_ref = cb_sgi.change_of_basis_op_to_reference_setting()
ref_sgi = cb_sgi.change_basis(cb_op=cb_op_ref)
assert ref_sgi.group() == sgi.group()
c = cb_op_ref.c()
if c.r().is_unit_mx() and c.t().num() != (0, 0, 0):
n_special += 1
cb_ref_sgi = sgi.change_basis(cb_op=cb_op_ref)
print " cb_op=%s -> %s" % (str(cb_op.c()), cb_ref_sgi.type().universal_hermann_mauguin_symbol())
sys.stdout.flush()
# verify that c.t() is not an allowed origin shift
assert cb_ref_sgi.group() != sgi.group()
assert special.get(space_group_number, 0) == n_special
print format_cpu_times()
def get_symop_correlation_coefficients(miller_array, use_binning=False):
from copy import deepcopy
from scitbx.array_family import flex
from cctbx import miller
corr_coeffs = flex.double()
n_refs = flex.int()
space_group = miller_array.space_group()
for smx in space_group.smx():
reindexed_array = miller_array.change_basis(sgtbx.change_of_basis_op(smx))
intensity, intensity_rdx = reindexed_array.common_sets(miller_array)
if use_binning:
intensity.use_binning_of(miller_array)
intensity_rdx.use_binning_of(miller_array)
cc = intensity.correlation(intensity_rdx, use_binning=use_binning)
corr_coeffs.append(
flex.mean_weighted(
flex.double(i for i in cc.data if i is not None),
flex.double(j for i, j in zip(cc.data, cc.binner.counts()) if i is not None),
)
)
else:
corr_coeffs.append(intensity.correlation(intensity_rdx, use_binning=use_binning).coefficient())
n_refs.append(intensity.size())
return corr_coeffs, n_refs
def __init__(self, f_in_p1, **kwds):
isinstance(f_in_p1, miller.array)
assert f_in_p1.space_group().type().hall_symbol() == ' P 1'
self.f_in_p1 = f_in_p1
adopt_optional_init_args(self, kwds)
self.search_parameters = maptbx.peak_search_parameters(
peak_search_level=3,
interpolate=True,
min_distance_sym_equiv=0.25,
)
self.space_group = sgtbx.space_group('P 1', t_den=sg_t_den)
self.origin = None
self.symmetry_pool = []
self.find_centring_translations()
if self.space_group.order_z() > 1:
f_in_centered = self.f_in_p1.customized_copy(
space_group_info=sgtbx.space_group_info(group=self.space_group)
).eliminate_sys_absent().merge_equivalents().array()
self.cb_op_to_primitive = \
f_in_centered.change_of_basis_op_to_primitive_setting()
self.f_in_p1 = f_in_centered.change_basis(self.cb_op_to_primitive)
self.space_group = self.f_in_p1.space_group()
else:
self.cb_op_to_primitive = sgtbx.change_of_basis_op()
self.f_in_p1 = self.f_in_p1.generate_bijvoet_mates()
self.find_space_group()
self.space_group = sgtbx.space_group(self.space_group.type().hall_symbol(),
t_den=sgtbx.sg_t_den)
self.space_group_info = sgtbx.space_group_info(group=self.space_group)
def difference_rotation_matrix_axis_angle(crystal_a, crystal_b, target_angle=0):
from cctbx import sgtbx
# assert crystal_a.get_space_group() == crystal_b.get_space_group()
space_group = crystal_b.get_space_group()
best_R_ab = None
best_cb_op = None
best_axis = None
best_angle = 1e8
# iterate over space group ops to find smallest differences
for i_op, op in enumerate(space_group.build_derived_laue_group().all_ops()):
if op.r().determinant() < 0:
continue
elif not op.t().is_zero():
continue
cb_op = sgtbx.change_of_basis_op(op.inverse())
crystal_b_sym = crystal_b.change_basis(cb_op)
U_a = crystal_a.get_U()
U_b = crystal_b_sym.get_U()
assert U_a.is_r3_rotation_matrix()
assert U_b.is_r3_rotation_matrix()
# the rotation matrix to transform from U_a to U_b
R_ab = U_b * U_a.transpose()
axis_angle = r3_rotation_axis_and_angle_from_matrix(R_ab)
axis = axis_angle.axis
angle = axis_angle.angle() * 180.0 / math.pi
for sign in (+1, -1):
if abs(sign * angle - target_angle) < abs(best_angle - target_angle):
best_angle = sign * angle
best_axis = tuple(sign * a for a in axis)
best_R_ab = R_ab if sign > 0 else R_ab.inverse()
best_cb_op = cb_op if sign > 0 else cb_op.inverse()
return best_R_ab, best_axis, best_angle, best_cb_op
def detwin_miller_array(miller_obs,
twin_law,
twin_fraction):
# for the moment, ignore incompleten twin pairs please
cb_op = sgtbx.change_of_basis_op( twin_law )
twin_related_miller = miller_obs.change_basis( cb_op ).set_observation_type(
miller_obs )
set1, set2 = miller_obs.common_sets( twin_related_miller )\
.set_observation_type(miller_obs )
assert miller_obs.observation_type() is not None
assert miller_obs.sigmas() is not None
if set1.is_xray_amplitude_array():
set1 = set1.f_as_f_sq()
set2 = set1.f_as_f_sq()
detwinned_f = flex.double()
detwinned_sigma = flex.double()
if set1.is_xray_intensity_array():
if set2.is_xray_intensity_array():
for i1,s1,i2,s2 in zip( set1.data(), set1.sigmas(),
set2.data(), set2.sigmas() ):
tmp_detwinner = detwin(i1,s1,i2,s2)
# we do some double work here actually
ni1 = tmp_detwinner.xm
ns1 = math.sqrt( math.abs(self.vcv[0]) )
detwinned_f.append( ni1 )
detwinned_s.append( ns1 )
set1 = set1.f_sq_as_f()
new_f = set1.customized_copy
def assign_operators(self, reidx_ops=None):
arrays = self.arrays
self.best_operators = None
if reidx_ops is None: reidx_ops = self.find_reindex_ops()
print >>self.log_out, "Reindex operators:", map(lambda x: str(x.as_hkl()), reidx_ops)
print >>self.log_out, ""
reidx_ops.sort(key=lambda x: not x.is_identity_op()) # identity op to first
data = None
latt_id = flex.int([])
for i, a in enumerate(arrays):
if data is None: data = a
else: data = data.concatenate(a, assert_is_similar_symmetry=False)
latt_id.extend(flex.int(a.size(), i))
latt_id = data.customized_copy(data=latt_id.as_double())
result = brehm_diederichs.run(L=[data, latt_id], nproc=self.nproc, plot=True, verbose=True)
self.best_operators = map(lambda x: None, xrange(len(arrays)))
for op in result:
idxes = map(int, result[op])
print >>self.log_out, " %s num=%3d idxes= %s" %(op, len(result[op]), idxes)
for idx in idxes:
self.best_operators[idx] = sgtbx.change_of_basis_op(op)
def exercise_space_group_contains():
g = sgtbx.space_group("P 2")
for s in ["x,y,z", "-x,-y,z", "-x+1,-y-2,z+3"]:
assert g.contains(sgtbx.rt_mx(s))
for s in ["x,y,-z", "x+1/2,y,z"]:
assert not g.contains(sgtbx.rt_mx(s))
for symbols in sgtbx.space_group_symbol_iterator():
g = sgtbx.space_group(symbols.hall())
for s in g:
assert g.contains(s)
rnd = flex.mersenne_twister(seed=0)
n_c = 0
n_nc = 0
for symbol in sgtbx.bravais_types.centric:
g = sgtbx.space_group_info(symbol=symbol, space_group_t_den=144).group()
for s in g.change_basis(sgtbx.change_of_basis_op("x+1/12,y-1/12,z+1/12")):
if (rnd.random_double() < 0.9): continue # avoid long runtime
gc = sgtbx.space_group(g)
gc.expand_smx(s)
if (gc.order_z() == g.order_z()):
assert g.contains(s)
n_c += 1
else:
assert not g.contains(s)
n_nc += 1
assert n_c == 11, n_c
assert n_nc == 53, n_nc
def exercise_double_coset_decomposition(crystal_symmetry_ri, lattice_group,
miller_array_subs, miller_array_sub_as,
miller_array_sub_bs,
coset_decompositions, i, j, verbose):
group_a = miller_array_subs[i].space_group_info().group()
group_b = miller_array_subs[j].space_group_info().group()
miller_array_sub_a = miller_array_sub_as[i]
miller_array_sub_b = miller_array_sub_bs[j]
single_coset_ccs = {}
for partition in coset_decompositions[i].partitions:
cb_op = sgtbx.change_of_basis_op(partition[0])
cb = miller_array_sub_a.change_basis(cb_op).map_to_asu()
cc = cb.correlation(other=miller_array_sub_b).coefficient()
key = "%.6f" % cc
single_coset_ccs.setdefault(key, []).append(str(partition[0]))
double_coset_ccs = {}
for c in sgtbx.cosets.double_unique(lattice_group, group_a, group_b):
cb_op = sgtbx.change_of_basis_op(c)
cb = miller_array_sub_b.change_basis(cb_op).map_to_asu()
cc = cb.correlation(other=miller_array_sub_a).coefficient()
key = "%.6f" % cc
double_coset_ccs.setdefault(key, []).append(str(c))
double_coset_repetitions = [len(v) for v in double_coset_ccs.values()]
failure = (max(double_coset_repetitions) > 1)
if (failure or verbose):
print(
[str(sgtbx.space_group_info(group=g)) for g in (group_a, group_b)])
print("single_coset ops:", list(single_coset_ccs.values()))
print("double_coset ops:", list(double_coset_ccs.values()))
if (failure):
for cc, ops in double_coset_ccs.items():
if (len(ops) > 1):
print(cc, ops)
for op in ops:
ri = sgtbx.rt_mx(op).r().info()
print(" ", ri.type(), ri.sense(), ri.ev())
raise RuntimeError("max(double_coset_repetitions) > 1")
single_coset_ccs = list(single_coset_ccs.keys())
double_coset_ccs = list(double_coset_ccs.keys())
single_coset_ccs.sort()
double_coset_ccs.sort()
failure = (double_coset_ccs != single_coset_ccs)
if (failure or verbose):
print("single_coset_ccs:", single_coset_ccs)
print("double_coset_ccs:", double_coset_ccs)
if (failure):
raise RuntimeError("double_coset_ccs != single_coset_ccs")
def exercise_find_matching_symmetry():
from cctbx import crystal, sgtbx, uctbx
from dials.algorithms.indexing import symmetry
def run_once(crystal_symmetry):
cs = crystal_symmetry
#print
cs.show_summary()
from cctbx.sgtbx import lattice_symmetry
subgroups = lattice_symmetry.metric_subgroups(cs, max_delta=5)
for op in ('x,y,z', 'z,x,y', 'y,z,x', '-x,z,y', 'y,x,-z', 'z,-y,x')[:]:
cb_op = sgtbx.change_of_basis_op(op)
uc_inp = cs.unit_cell().change_basis(cb_op)
for ref_uc, ref_sg in [(cs.unit_cell(), cs.space_group()),
(None, cs.space_group())][:]:
best_subgroup = symmetry.find_matching_symmetry(
uc_inp, target_space_group=ref_sg)
cb_op_inp_best = best_subgroup['cb_op_inp_best']
assert uc_inp.change_basis(cb_op_inp_best).is_similar_to(
cs.as_reference_setting().best_cell().unit_cell())
# 1) known unit cell and space group
# -> cb op for test unit cell to best match for reference symmetry
# 2) known unit cell
# -> cb op for test unit cell to best match for given unit cell
# 3) known space group
# -> cb op for test unit cell to best match for given space group
# Assumptions:
# 1) test unit cell is minimum cell
uc = uctbx.unit_cell("76, 115, 134, 90, 99.07, 90")
sgi = sgtbx.space_group_info(symbol="I2")
cs = crystal.symmetry(unit_cell=uc, space_group_info=sgi)
uc_inp = uc.minimum_cell()
cs_min = crystal.symmetry(unit_cell=cs.minimum_cell().unit_cell(),
space_group=sgtbx.space_group())
uc = uctbx.unit_cell("42,42,40,90,90,90")
sgi = sgtbx.space_group_info(symbol="P41212")
cs = crystal.symmetry(unit_cell=uc, space_group_info=sgi)
cb_op = sgtbx.change_of_basis_op("c,a,b")
uc_inp = uc.change_basis(cb_op)
run_once(cs.change_basis(cb_op))
from cctbx.sgtbx import bravais_types
for symbol in bravais_types.acentric:
sgi = sgtbx.space_group_info(symbol=symbol)
uc = sgi.any_compatible_unit_cell(volume=1000)
cs = crystal.symmetry(unit_cell=uc, space_group_info=sgi)
cs = cs.niggli_cell().as_reference_setting().primitive_setting()
run_once(cs)
def show_remark_3(self, out=None):
from cctbx import sgtbx
if (out is None): out = sys.stdout
pr = "REMARK 3 "
print >> out, pr + "REFINEMENT TARGET : %s" % self.target_name.upper()
print >> out, pr
print >> out, pr + "DATA USED IN REFINEMENT."
print >> out, pr + " RESOLUTION RANGE HIGH (ANGSTROMS) : %s" % format_value(
"%-8.3f", self.d_min)
print >> out, pr + " RESOLUTION RANGE LOW (ANGSTROMS) : %s" % format_value(
"%-8.3f", self.d_max)
print >> out, pr + " MIN(FOBS/SIGMA_FOBS) : %s" % format_value(
"%-6.2f", self.min_f_obs_over_sigma)
print >> out,pr+" COMPLETENESS FOR RANGE (%s) : %-6.2f"%\
("%", self.completeness_in_range*100.0)
print >> out, pr + " NUMBER OF REFLECTIONS : %-10d" % self.number_of_reflections
print >> out, pr + " NUMBER OF REFLECTIONS (NON-ANOMALOUS) : %-10d" % self.number_of_reflections_merged
print >> out, pr
print >> out, pr + "FIT TO DATA USED IN REFINEMENT."
print >> out, pr + " R VALUE (WORKING + TEST SET) : %s" % format_value(
"%-6.4f", self.r_all)
print >> out, pr + " R VALUE (WORKING SET) : %s" % format_value(
"%-6.4f", self.r_work)
print >> out, pr + " FREE R VALUE : %s" % format_value(
"%-6.4f", self.r_free)
print >> out, pr + " FREE R VALUE TEST SET SIZE (%s) : %-6.2f" % (
"%", float(self.number_of_test_reflections) /
self.number_of_reflections * 100.)
print >> out, pr + " FREE R VALUE TEST SET COUNT : %-10d" % self.number_of_test_reflections
print >> out, pr
self.show_rwork_rfree_number_completeness(
prefix=pr,
title="FIT TO DATA USED IN REFINEMENT (IN BINS).",
out=out)
print >> out, pr
print >> out, pr + "BULK SOLVENT MODELLING."
print >> out, pr + " METHOD USED : FLAT BULK SOLVENT MODEL"
print >> out, pr + " SOLVENT RADIUS : %s" % format_value(
"%-8.2f", self.mask_solvent_radius)
print >> out, pr + " SHRINKAGE RADIUS : %s" % format_value(
"%-8.2f", self.mask_shrink_radius)
print >> out, pr + " GRID STEP FACTOR : %s" % format_value(
"%-8.2f", self.mask_grid_step_factor)
print >> out, pr
if (self.twin_fraction is not None):
print >> out, pr + "TWINNING INFORMATION."
print >> out, pr + " FRACTION: %s" % format_value(
"%-8.3f", self.twin_fraction)
print >> out,pr+" OPERATOR: %s"%\
format_value("%-s", sgtbx.change_of_basis_op(self.twin_law).as_hkl())
print >> out, pr + "ERROR ESTIMATES."
print >> out,pr+" COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : %s"%\
format_value("%-8.2f", self.ml_coordinate_error)
print >> out,pr+" PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : %s"%\
format_value("%-8.2f", self.ml_phase_error)
print >> out, pr
print >> out,pr+"STRUCTURE FACTORS CALCULATION ALGORITHM : %-s"%\
self.sf_algorithm.upper()
out.flush()
def get_hkl_offset_correlation_coefficients(
dials_reflections, dials_crystal, map_to_asu=False,
grid_h=0, grid_k=0, grid_l=0, reference=None):
# N.B. deliberately ignoring d_min, d_max as these are inconsistent with
# changing the miller indices
from dials.array_family import flex
from cctbx.miller import set as miller_set
from cctbx import sgtbx
cs = cctbx_crystal_from_dials(dials_crystal)
ms = cctbx_i_over_sigi_ms_from_dials_data(dials_reflections, cs)
if reference:
reference_ms = cctbx_i_over_sigi_ms_from_dials_data(reference, cs)
else:
reference_ms = None
ccs = flex.double()
offsets = flex.vec3_int()
nref = flex.size_t()
if reference:
cb_op = sgtbx.change_of_basis_op('x,y,z')
else:
cb_op = sgtbx.change_of_basis_op('-x,-y,-z')
hkl_test = [(h, k, l) for h in range(-grid_h, grid_h + 1) \
for k in range(-grid_k, grid_k + 1) \
for l in range(-grid_l, grid_l + 1)]
for hkl in hkl_test:
indices = offset_miller_indices(ms.indices(), hkl)
reindexed_indices = cb_op.apply(indices)
rms = miller_set(cs, reindexed_indices).array(ms.data())
if reference_ms:
_ms = reference_ms
else:
_ms = miller_set(cs, indices).array(ms.data())
n, cc = compute_miller_set_correlation(_ms, rms, map_to_asu=map_to_asu)
ccs.append(cc)
offsets.append(hkl)
nref.append(n)
return offsets, ccs, nref
def convert_operator(change_of_basis):
from cctbx import sgtbx
try:
c_o_b = sgtbx.change_of_basis_op(change_of_basis)
except RuntimeError as e:
raise Sorry(str(e))
else:
return c_o_b
def exercise_monoclinic_cell_choices_core(space_group_number, verbose):
# transformation matrices for cell choices
# columns are basis vectors "new in terms of old"
# see Int. Tab. Vol. A, p. 22, Fig. 2.2.6.4.
b1 = (1, 0, 0, 0, 1, 0, 0, 0, 1)
b2 = (-1, 0, 1, 0, 1, 0, -1, 0, 0)
b3 = (0, 0, -1, 0, 1, 0, 1, 0, -1)
flip = (0, 0, 1, 0, -1, 0, 1, 0, 0)
p3s = sgtbx.space_group("P 3*")
done = {}
ref = sgtbx.space_group_info(number=space_group_number)
ref_uhm = ref.type().universal_hermann_mauguin_symbol()
for i_fl, fl in enumerate([b1, flip]):
rfl = sgtbx.rot_mx(fl)
cfl = sgtbx.change_of_basis_op(sgtbx.rt_mx(rfl))
for i_rt, rt in enumerate(p3s):
rp3 = rt.r()
cp3 = sgtbx.change_of_basis_op(sgtbx.rt_mx(rp3))
for i_cs, cs in enumerate([b1, b2, b3]):
rcs = sgtbx.rot_mx(cs).inverse()
ccs = sgtbx.change_of_basis_op(sgtbx.rt_mx(rcs))
cb_all = cp3 * cfl * ccs
refcb = ref.change_basis(cb_all)
refcb2 = sgtbx.space_group_info(symbol=ref_uhm + "(" +
str(cb_all.c()) + ")")
assert refcb2.group() == refcb.group()
s = sgtbx.space_group_symbols(str(refcb))
q = s.qualifier()
hm = str(refcb)
if (0 or verbose): print(hm, q, cb_all.c())
if (i_fl == 0):
assert q[0] == "bca"[i_rt]
if (len(q) == 2): assert q[1] == "123"[i_cs]
elif (q[0] == "-"):
assert q[1] == "bca"[i_rt]
if (len(q) == 3): assert q[2] == "123"[i_cs]
else:
assert q[0] == "bca"[i_rt]
if (len(q) == 2 and q[1] != "123"[i_cs]):
assert done[hm] == 1
done.setdefault(hm, 0)
done[hm] += 1
assert len(done) in [3, 9, 18]
assert list(done.values()) == [18 / len(done)] * len(done)
if (0 or verbose): print()
return done
def get_hkl_offset_correlation_coefficients(
dials_reflections, dials_crystal, map_to_asu=False,
grid_h=0, grid_k=0, grid_l=0, reference=None):
# N.B. deliberately ignoring d_min, d_max as these are inconsistent with
# changing the miller indices
from dials.array_family import flex
from cctbx.miller import set as miller_set
from cctbx import sgtbx
cs = cctbx_crystal_from_dials(dials_crystal)
ms = cctbx_i_over_sigi_ms_from_dials_data(dials_reflections, cs)
if reference:
reference_ms = cctbx_i_over_sigi_ms_from_dials_data(reference, cs)
else:
reference_ms = None
ccs = flex.double()
offsets = flex.vec3_int()
nref = flex.size_t()
if reference:
cb_op = sgtbx.change_of_basis_op('x,y,z')
else:
cb_op = sgtbx.change_of_basis_op('-x,-y,-z')
hkl_test = [(h, k, l) for h in range(-grid_h, grid_h + 1) \
for k in range(-grid_k, grid_k + 1) \
for l in range(-grid_l, grid_l + 1)]
for hkl in hkl_test:
indices = offset_miller_indices(ms.indices(), hkl)
reindexed_indices = cb_op.apply(indices)
rms = miller_set(cs, reindexed_indices).array(ms.data())
if reference_ms:
_ms = reference_ms
else:
_ms = miller_set(cs, indices).array(ms.data())
n, cc = compute_miller_set_correlation(_ms, rms, map_to_asu=map_to_asu)
ccs.append(cc)
offsets.append(hkl)
nref.append(n)
return offsets, ccs, nref
def generate_unimodular_cells(cell):
Amat = sqr(cell.orthogonalization_matrix()).transpose()
for m in unimodular_generator(range=1).all():
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(m))
orientation_similarity_cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
new_cell = cell.change_basis(orientation_similarity_cb_op)
yield new_cell,orientation_similarity_cb_op
def generate_unimodular_cells(cell):
Amat = sqr(cell.orthogonalization_matrix()).transpose()
for m in unimodular_generator(range=1).all():
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(m))
orientation_similarity_cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
new_cell = cell.change_basis(orientation_similarity_cb_op)
yield new_cell,orientation_similarity_cb_op
def _reindexing_ops(
self,
coords: np.ndarray,
sym_ops: List[sgtbx.rt_mx],
cosets: sgtbx.cosets.left_decomposition,
) -> List[sgtbx.change_of_basis_op]:
"""Identify the reindexing operator for each dataset.
Args:
coords (np.ndarray):
A flattened list of the N-dimensional vectors, i.e. coordinates in
the first dimension are stored first, followed by the coordinates in
the second dimension, etc.
sym_ops (List[sgtbx.rt_mx]): List of cctbx.sgtbx.rt_mx used for the cosym
symmetry analysis
cosets (sgtbx.cosets.left_decomposition): The left coset decomposition of the
lattice group with respect to the proposed Patterson group
Returns:
List[sgtbx.change_of_basis_op]: A list of reindexing operators corresponding
to each dataset.
"""
reindexing_ops = []
n_datasets = len(self.input_intensities)
n_sym_ops = len(sym_ops)
coord_ids = np.arange(n_datasets * n_sym_ops)
dataset_ids = coord_ids % n_datasets
# choose a high density point as seed
X = coords
nbrs = NearestNeighbors(n_neighbors=min(11, len(X)),
algorithm="brute",
metric="cosine").fit(X)
distances, indices = nbrs.kneighbors(X)
average_distance = np.array([dist[1:].mean() for dist in distances])
i = average_distance.argmin()
xis = np.array([X[i]])
for j in range(n_datasets):
sel = np.where(dataset_ids == j)
X = coords[sel]
# Find nearest neighbour in cosine-space to the current cluster centroid
nbrs = NearestNeighbors(n_neighbors=min(1, len(X)),
algorithm="brute",
metric="cosine").fit(X)
distances, indices = nbrs.kneighbors([xis.mean(axis=0)])
k = indices[0][0]
xis = np.append(xis, [X[k]], axis=0)
for partition in cosets.partitions:
if sym_ops[k] in partition:
cb_op = sgtbx.change_of_basis_op(
partition[0]).new_denominators(self.cb_op_inp_min)
reindexing_ops.append(
(self.cb_op_inp_min.inverse() * cb_op *
self.cb_op_inp_min).as_xyz())
break
return reindexing_ops
def test_symmetry_basis_changes_for_C2(tmpdir):
"""Test the correctness of change of basis operations in dials.symmetry
Supply the unit cell of beta-lactamase, which triggers a change of
basis from input to minimum during symmetry analysis."""
os.chdir(tmpdir.strpath)
unit_cell = (53.173, 61.245, 69.292, 90.0, 93.04675, 90.0)
space_group = sgtbx.space_group_info("C 2").group()
experiments, reflections, _ = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
sample_size=1,
map_to_minimum=False,
)
experiments.as_json("tmp.expt")
expt_file = tmpdir.join("tmp.expt").strpath
joint_table = flex.reflection_table()
for r in reflections:
joint_table.extend(r)
joint_table.as_file("tmp.refl")
refl_file = tmpdir.join("tmp.refl").strpath
command = ["dials.symmetry", expt_file, refl_file, "json=symmetry.json"]
result = procrunner.run(command, working_directory=tmpdir.strpath)
assert not result.returncode and not result.stderr
assert tmpdir.join("symmetrized.refl").check(file=1)
assert tmpdir.join("symmetrized.expt").check(file=1)
expts = load.experiment_list(tmpdir.join("symmetrized.expt").strpath,
check_format=False)
for v, expected in zip(expts[0].crystal.get_unit_cell().parameters(),
unit_cell):
assert v == pytest.approx(expected)
# Using the change of basis ops from the json output we should be able to
# reindex the input experiments to match the output experiments
with tmpdir.join("symmetry.json").open() as f:
d = json.load(f)
cs = experiments[0].crystal.get_crystal_symmetry()
cb_op_inp_min = sgtbx.change_of_basis_op(str(d["cb_op_inp_min"][0]))
cb_op_min_best = sgtbx.change_of_basis_op(
str(d["subgroup_scores"][0]["cb_op"]))
assert cs.change_basis(cb_op_min_best *
cb_op_inp_min).is_similar_symmetry(
expts[0].crystal.get_crystal_symmetry())
def get_indexing_offset_correlation_coefficients(
reflections, crystal, grid_search_scope, d_min=None, d_max=None, map_to_asu=False
):
from copy import deepcopy
from dials.array_family import flex
space_group = crystal.get_space_group()
unit_cell = crystal.get_unit_cell()
from cctbx.crystal import symmetry as crystal_symmetry
cs = crystal_symmetry(unit_cell, space_group.type().lookup_symbol())
from cctbx.miller import set as miller_set
data = reflections["intensity.sum.value"] / flex.sqrt(reflections["intensity.sum.variance"])
ccs = flex.double()
offsets = flex.vec3_int()
nref = flex.size_t()
original_miller_indices = reflections["miller_index"]
ms = miller_set(cs, original_miller_indices)
ms = ms.array(data)
if d_min is not None or d_max is not None:
ms = ms.resolution_filter(d_min=d_min, d_max=d_max)
if map_to_asu:
ms = ms.map_to_asu()
g = grid_search_scope
for h in range(-g, g + 1):
for k in range(-g, g + 1):
for l in range(-g, g + 1):
for smx in ["-x,-y,-z"]:
# reindexed = deepcopy(reflections)
# hkl offset doubled as equivalent of h0 + 1, hI - 1
miller_indices = offset_miller_indices(ms.indices(), (2 * h, 2 * k, 2 * l))
reindexed_miller_indices = sgtbx.change_of_basis_op(smx).apply(miller_indices)
rms = miller_set(cs, reindexed_miller_indices)
rms = rms.array(data)
# if params.d_min or params.d_max:
# rms = rms.resolution_filter(d_min=params.d_min, d_max=params.d_max)
# if map_to_asu:
# rms = rms.map_to_asu()
intensity, intensity_rdx = rms.common_sets(ms)
cc = intensity.correlation(intensity_rdx).coefficient()
ccs.append(cc)
offsets.append((h, k, l))
nref.append(intensity.size())
return offsets, ccs, nref
def generate_reindex_sets(self, obs_in):
ops = self.generate_twin_operators(obs_in)
alternates = {'h,k,l': obs_in}
for op in ops:
hkl = obs_in.indices()
cb_op = sgtbx.change_of_basis_op(op.operator.r().as_hkl())
hklrev = cb_op.apply(hkl)
alternates[op.operator.r().as_hkl()] = obs_in.customized_copy(indices = hklrev).map_to_asu()
return alternates
def generate_reindex_sets(self):
ops = self.generate_twin_operators()
alternates = {}
for op in ops:
hkl = self.data.indices()
cb_op = sgtbx.change_of_basis_op(op.operator.r().as_hkl())
hklrev = cb_op.apply(hkl)
alternates[op.operator.r().as_hkl()] = self.data.customized_copy(indices = hklrev).map_to_asu()
return alternates
def create_shelx_reflection_data_source(self,
format,
indices_transform=None,
change_of_basis_op=None,
data_scale=1):
""" format is one of 3, 4, 5, etc.
data_scale scales the data and their standard deviations
"""
assert [indices_transform, change_of_basis_op].count(None) == 1
if change_of_basis_op is None:
if indices_transform.is_unit_mx():
change_of_basis_op = sgtbx.change_of_basis_op()
else:
r = sgtbx.rt_mx(indices_transform.new_denominator(24).transpose())
change_of_basis_op = sgtbx.change_of_basis_op(r).inverse()
self.reflection_file_format = "hklf%i" % format
self.data_change_of_basis_op = change_of_basis_op
self.data_scale = data_scale
def __call__(self, params, options):
''' Import the integrate.hkl file. '''
from iotbx.xds import integrate_hkl
from dials.array_family import flex
from dials.util.command_line import Command
from cctbx import sgtbx
# Get the unit cell to calculate the resolution
uc = self._experiment.crystal.get_unit_cell()
# Read the INTEGRATE.HKL file
Command.start('Reading INTEGRATE.HKL')
handle = integrate_hkl.reader()
handle.read_file(self._integrate_hkl)
hkl = flex.miller_index(handle.hkl)
xyzcal = flex.vec3_double(handle.xyzcal)
xyzobs = flex.vec3_double(handle.xyzobs)
iobs = flex.double(handle.iobs)
sigma = flex.double(handle.sigma)
rlp = flex.double(handle.rlp)
peak = flex.double(handle.peak) * 0.01
Command.end('Read %d reflections from INTEGRATE.HKL file.' % len(hkl))
# Derive the reindex matrix
rdx = self.derive_reindex_matrix(handle)
print 'Reindex matrix:\n%d %d %d\n%d %d %d\n%d %d %d' % (rdx.elems)
# Reindex the reflections
Command.start('Reindexing reflections')
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(rdx.elems)))
hkl = cb_op.apply(hkl)
Command.end('Reindexed %d reflections' % len(hkl))
# Create the reflection list
Command.start('Creating reflection table')
table = flex.reflection_table()
table['id'] = flex.int(len(hkl), 0)
table['panel'] = flex.size_t(len(hkl), 0)
table['miller_index'] = hkl
table['xyzcal.px'] = xyzcal
table['xyzobs.px.value'] = xyzobs
table['intensity.cor.value'] = iobs
table['intensity.cor.variance'] = sigma**2
table['intensity.prf.value'] = iobs * peak / rlp
table['intensity.prf.variance'] = (sigma * peak / rlp)**2
table['lp'] = 1.0 / rlp
table['d'] = flex.double(uc.d(h) for h in hkl)
Command.end('Created table with {0} reflections'.format(len(table)))
# Output the table to pickle file
if params.output.filename is None:
params.output.filename = 'integrate_hkl.pickle'
Command.start('Saving reflection table to %s' % params.output.filename)
table.as_pickle(params.output.filename)
Command.end('Saved reflection table to %s' % params.output.filename)
def _change_of_basis(self):
if(self.params.change_of_basis is not None):
print("Applying change-of-basis operator '%s'" % \
self.params.change_of_basis, file=self.log)
from cctbx import sgtbx
cb_op = sgtbx.change_of_basis_op(self.params.change_of_basis)
self.xray_structure = self.xray_structure.change_basis(cb_op)
self.pdb_hierarchy.atoms().set_xyz(self.xray_structure.sites_cart())
print("New symmetry:", file=self.log)
self.xray_structure.crystal_symmetry().show_summary(f=self.log, prefix=" ")
self.crystal_symmetry = self.xray_structure.crystal_symmetry()
def exercise():
from dials.algorithms.indexing import compare_orientation_matrices
from dxtbx.model import Crystal
from cctbx import sgtbx
from scitbx import matrix
from scitbx.math import euler_angles as euler
# try and see if we can get back the original rotation matrix and euler angles
real_space_a = matrix.col((10, 0, 0))
real_space_b = matrix.col((0, 10, 10))
real_space_c = matrix.col((0, 0, 10))
euler_angles = (1.3, 5.6, 7.8)
R = matrix.sqr(
euler.xyz_matrix(euler_angles[0], euler_angles[1], euler_angles[2]))
crystal_a = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('P 1'))
crystal_b = Crystal(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('P 1'))
assert approx_equal(
matrix.sqr(crystal_b.get_U()) *
matrix.sqr(crystal_a.get_U()).transpose(), R)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.is_identity_op()
assert approx_equal(best_R_ab, R)
# now see if we can deconvolute the original euler angles after applying
# a change of basis to one of the crystals
crystal_a = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('I 2 3'))
crystal_b = Crystal(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('I 2 3'))
cb_op = sgtbx.change_of_basis_op('z,x,y')
crystal_b = crystal_b.change_basis(cb_op)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.c() == cb_op.inverse().c()
assert approx_equal(best_R_ab, R)
def get_observations_non_polar(self, observations_original, pickle_filename, iparams):
#return observations with correct polarity
if iparams.indexing_ambiguity.index_basis_in is None:
return observations_original.map_to_asu(), 'h,k,l'
ind_pickle = pickle.load(open(iparams.indexing_ambiguity.index_basis_in, "rb"))
if pickle_filename not in ind_pickle:
return observations_original.map_to_asu(), 'Not Found'
from cctbx import sgtbx
cb_op = sgtbx.change_of_basis_op(ind_pickle[pickle_filename])
observations_alt = observations_original.map_to_asu().change_basis(cb_op).map_to_asu()
return observations_alt, ind_pickle[pickle_filename]
def construct_rational_point_group( space_group, cb_op=None ):
gr = rat_rot_group()
if cb_op is None:
cb_op = sgtbx.change_of_basis_op( "a,b,c" )
cb_op = cb_op_as_rational( cb_op )
for s in space_group:
tmp_r = rt_mx_as_rational( s.r() )
gr.expand( tmp_r )
gr.change_basis( cb_op )
gr.expand(show=False)
return gr
def get_observations_non_polar(self, observations_original, pickle_filename, iparams):
#return observations with correct polarity
if iparams.indexing_ambiguity.index_basis_in is None:
return observations_original.map_to_asu(), 'h,k,l'
ind_pickle = pickle.load(open(iparams.indexing_ambiguity.index_basis_in, "rb"))
if pickle_filename not in ind_pickle:
return observations_original.map_to_asu(), 'Not Found'
from cctbx import sgtbx
cb_op = sgtbx.change_of_basis_op(ind_pickle[pickle_filename])
observations_alt = observations_original.map_to_asu().change_basis(cb_op).map_to_asu()
return observations_alt, ind_pickle[pickle_filename]
def construct_rational_point_group(space_group, cb_op=None):
gr = rat_rot_group()
if cb_op is None:
cb_op = sgtbx.change_of_basis_op("a,b,c")
cb_op = cb_op_as_rational(cb_op)
for s in space_group:
tmp_r = rt_mx_as_rational(s.r())
gr.expand(tmp_r)
gr.change_basis(cb_op)
gr.expand(show=False)
return gr
def combined_cb_op(self, other, cb_op):
sc = self.change_of_basis_op_to_minimum_cell
oc = other.change_of_basis_op_to_minimum_cell
cb_op = cb_op.new_denominators(sc)
best_choice = None
best_choice_as_hkl = None
for s_symop in self.minimum_cell_symmetry.space_group():
s_symop = sgtbx.change_of_basis_op(sgtbx.rt_mx(
s_symop.r())).new_denominators(sc)
for o_symop in other.minimum_cell_symmetry.space_group():
o_symop = sgtbx.change_of_basis_op(sgtbx.rt_mx(
o_symop.r())).new_denominators(sc)
possible_choice = sc.inverse() * s_symop * cb_op * o_symop * oc
possible_choice_as_hkl = possible_choice.as_hkl()
if (best_choice_as_hkl is None or sgtbx.compare_cb_op_as_hkl(
best_choice_as_hkl, possible_choice_as_hkl) > 0):
best_choice = possible_choice
best_choice_as_hkl = possible_choice_as_hkl
assert best_choice is not None
return best_choice
def main(mtz, index_basis):
# read in mtz
reflection_file = reflection_file_reader.any_reflection_file(mtz)
miller_arrays = reflection_file.as_miller_arrays()
# apply new basis
cb_op = sgtbx.change_of_basis_op(index_basis)
miller_array_new = miller_arrays[0].change_basis(cb_op)
# write out new mtz
hklout = os.path.splitext(mtz)[0] + "_modified.mtz"
mtz_dataset = miller_array_new.as_mtz_dataset(column_root_label="IOBS")
mtz_dataset.mtz_object().write(file_name=hklout)
print("Output file saved to", hklout)
def combined_cb_op(self, other, cb_op):
sc = self.change_of_basis_op_to_minimum_cell
oc = other.change_of_basis_op_to_minimum_cell
cb_op = cb_op.new_denominators(sc)
best_choice = None
best_choice_as_hkl = None
for s_symop in self.minimum_cell_symmetry.space_group():
s_symop = sgtbx.change_of_basis_op(sgtbx.rt_mx(s_symop.r())).new_denominators(sc)
for o_symop in other.minimum_cell_symmetry.space_group():
o_symop = sgtbx.change_of_basis_op(sgtbx.rt_mx(o_symop.r())).new_denominators(sc)
possible_choice = sc.inverse() * s_symop * cb_op * o_symop * oc
possible_choice_as_hkl = possible_choice.as_hkl()
if (
best_choice_as_hkl is None
or sgtbx.compare_cb_op_as_hkl(best_choice_as_hkl, possible_choice_as_hkl) > 0
):
best_choice = possible_choice
best_choice_as_hkl = possible_choice_as_hkl
assert best_choice is not None
return best_choice
def change_basis(self, cb_op):
if (not isinstance(cb_op, sgtbx.change_of_basis_op)):
cb_op = sgtbx.change_of_basis_op(cb_op)
cb_hall_symbol = None
if (self.hall_symbol is not None):
space_group_info = sgtbx.space_group_info("Hall: " + self.hall_symbol)
cb_space_group_info = space_group_info.change_basis(cb_op)
cb_hall_symbol = cb_space_group_info.type().hall_symbol()
cb_asu = direct_space_asu(cb_hall_symbol)
for cut in self.cuts:
cb_asu.cuts.append(cut.change_basis(cb_op))
return cb_asu
def exercise_inversion_centring():
cb = sgtbx.change_of_basis_op("x+1/12,y+1/12,z-1/12")
for symb in sgtbx.space_group_symbol_iterator():
sg = sgtbx.space_group(space_group_symbols=symb)
sg1 = sg.change_basis(cb)
icb = sg1.change_of_origin_realising_origin_centricity()
if sg1.is_centric():
assert not sg1.is_origin_centric()
sg2 = sg1.change_basis(icb)
assert sg2.is_origin_centric()
else:
assert str(icb) == "a,b,c"
