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 __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 __init__(self, space_group_info, use_k2l, use_l2n):
adopt_init_args(self, locals())
search_symmetry = sgtbx.search_symmetry(
flags=sgtbx.search_symmetry_flags(use_space_group_symmetry=False,
use_space_group_ltr=-1,
use_seminvariants=True,
use_normalizer_k2l=use_k2l,
use_normalizer_l2n=use_l2n),
space_group_type=space_group_info.type(),
seminvariant=space_group_info.structure_seminvariants())
self.rt_mx = search_symmetry.subgroup()
self.continuous_shifts = search_symmetry.continuous_shifts()
assert search_symmetry.continuous_shifts_are_principal()
self.continuous_shift_flags = search_symmetry.continuous_shift_flags()
def __init__(self, space_group_info, use_k2l, use_l2n):
adopt_init_args(self, locals())
search_symmetry = sgtbx.search_symmetry(
flags=sgtbx.search_symmetry_flags(
use_space_group_symmetry=False,
use_space_group_ltr=-1,
use_seminvariants=True,
use_normalizer_k2l=use_k2l,
use_normalizer_l2n=use_l2n),
space_group_type=space_group_info.type(),
seminvariant=space_group_info.structure_seminvariants())
self.rt_mx = search_symmetry.subgroup()
self.continuous_shifts = search_symmetry.continuous_shifts()
assert search_symmetry.continuous_shifts_are_principal()
self.continuous_shift_flags = search_symmetry.continuous_shift_flags()
def check_with_grid_tags(inp_symmetry, symmetry_flags, sites_cart,
point_distance, strictly_inside, flag_write_pdb,
verbose):
cb_op_inp_ref = inp_symmetry.change_of_basis_op_to_reference_setting()
if (verbose):
print("cb_op_inp_ref.c():", cb_op_inp_ref.c())
ref_symmetry = inp_symmetry.change_basis(cb_op_inp_ref)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=ref_symmetry.space_group_info().type(),
seminvariant=ref_symmetry.space_group_info().structure_seminvariants())
assert search_symmetry.continuous_shifts_are_principal()
continuous_shift_flags = search_symmetry.continuous_shift_flags()
if (flag_write_pdb):
tag_sites_frac = flex.vec3_double()
else:
tag_sites_frac = None
if (strictly_inside):
inp_tags = inp_symmetry.gridding(step=point_distance * .7,
symmetry_flags=symmetry_flags).tags()
if (tag_sites_frac is not None):
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [
float(n) / d for n, d in zip(point, inp_tags.n_real())
]
tag_sites_frac.append(point_frac_inp)
if (inp_tags.tags().n_independent() < sites_cart.size()):
print("FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size())
raise AssertionError
else:
inp_tags = inp_symmetry.gridding(step=point_distance / 2.,
symmetry_flags=symmetry_flags).tags()
sites_frac_inp = inp_symmetry.unit_cell().fractionalize(
sites_cart=sites_cart)
rt = cb_op_inp_ref.c().as_double_array()
sites_frac_ref = rt[:9] * sites_frac_inp
sites_frac_ref += rt[9:]
max_distance = 2 * ((.5 * math.sqrt(3) * point_distance) * 2 / 3.)
if (verbose):
print("max_distance:", max_distance)
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [
float(n) / d for n, d in zip(point, inp_tags.n_real())
]
if (tag_sites_frac is not None):
tag_sites_frac.append(point_frac_inp)
point_frac_ref = cb_op_inp_ref.c() * point_frac_inp
equiv_points = sgtbx.sym_equiv_sites(
unit_cell=ref_symmetry.unit_cell(),
space_group=search_symmetry.subgroup(),
original_site=point_frac_ref,
minimum_distance=2.e-6,
tolerance=1.e-6)
min_dist = sgtbx.min_sym_equiv_distance_info(
reference_sites=equiv_points,
others=sites_frac_ref,
principal_continuous_allowed_origin_shift_flags=
continuous_shift_flags).dist()
if (min_dist > max_distance):
print("FAIL:", inp_symmetry.space_group_info(), \
point_frac_ref, min_dist)
raise AssertionError
if (inp_tags.tags().n_independent() + 10 < sites_cart.size()):
print("FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size())
raise AssertionError
if (tag_sites_frac is not None):
dump_pdb(file_name="tag_sites.pdb",
crystal_symmetry=inp_symmetry,
sites_cart=inp_symmetry.unit_cell().orthogonalize(
sites_frac=tag_sites_frac))
def check_with_grid_tags(inp_symmetry, symmetry_flags,
sites_cart, point_distance,
strictly_inside, flag_write_pdb, verbose):
cb_op_inp_ref = inp_symmetry.change_of_basis_op_to_reference_setting()
if (verbose):
print "cb_op_inp_ref.c():", cb_op_inp_ref.c()
ref_symmetry = inp_symmetry.change_basis(cb_op_inp_ref)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=ref_symmetry.space_group_info().type(),
seminvariant=ref_symmetry.space_group_info().structure_seminvariants())
assert search_symmetry.continuous_shifts_are_principal()
continuous_shift_flags = search_symmetry.continuous_shift_flags()
if (flag_write_pdb):
tag_sites_frac = flex.vec3_double()
else:
tag_sites_frac = None
if (strictly_inside):
inp_tags = inp_symmetry.gridding(
step=point_distance*.7,
symmetry_flags=symmetry_flags).tags()
if (tag_sites_frac is not None):
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp=[float(n)/d for n,d in zip(point, inp_tags.n_real())]
tag_sites_frac.append(point_frac_inp)
if (inp_tags.tags().n_independent() < sites_cart.size()):
print "FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size()
raise AssertionError
else:
inp_tags = inp_symmetry.gridding(
step=point_distance/2.,
symmetry_flags=symmetry_flags).tags()
sites_frac_inp = inp_symmetry.unit_cell().fractionalize(
sites_cart=sites_cart)
rt = cb_op_inp_ref.c().as_double_array()
sites_frac_ref = rt[:9] * sites_frac_inp
sites_frac_ref += rt[9:]
max_distance = 2 * ((.5 * math.sqrt(3) * point_distance) * 2/3.)
if (verbose):
print "max_distance:", max_distance
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [float(n)/d for n,d in zip(point, inp_tags.n_real())]
if (tag_sites_frac is not None):
tag_sites_frac.append(point_frac_inp)
point_frac_ref = cb_op_inp_ref.c() * point_frac_inp
equiv_points = sgtbx.sym_equiv_sites(
unit_cell=ref_symmetry.unit_cell(),
space_group=search_symmetry.subgroup(),
original_site=point_frac_ref,
minimum_distance=2.e-6,
tolerance=1.e-6)
min_dist = sgtbx.min_sym_equiv_distance_info(
reference_sites=equiv_points,
others=sites_frac_ref,
principal_continuous_allowed_origin_shift_flags
=continuous_shift_flags).dist()
if (min_dist > max_distance):
print "FAIL:", inp_symmetry.space_group_info(), \
point_frac_ref, min_dist
raise AssertionError
if (inp_tags.tags().n_independent()+10 < sites_cart.size()):
print "FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size()
raise AssertionError
if (tag_sites_frac is not None):
dump_pdb(
file_name="tag_sites.pdb",
crystal_symmetry=inp_symmetry,
sites_cart=inp_symmetry.unit_cell().orthogonalize(
sites_frac=tag_sites_frac))