def u_base(self):
if (self._u_base is None):
self._u_base = xray.calc_u_base(
self.d_min(),
self.grid_resolution_factor(),
self.quality_factor())
return self._u_base
def exercise(space_group_info,
const_gaussian,
negative_gaussian,
anomalous_flag,
allow_mix,
use_u_iso,
use_u_aniso,
d_min=1.,
resolution_factor=1. / 3,
max_prime=5,
quality_factor=100,
wing_cutoff=1.e-6,
exp_table_one_over_step_size=-100,
force_complex=False,
verbose=0):
if (const_gaussian):
elements = ["const"] * 8
elif (negative_gaussian):
elements = ["H"] * 8
else:
elements = ["N", "C", "C", "O", "N", "C", "C", "O"]
if (random.random() < 0.5):
random_f_prime_scale = 0.6
else:
random_f_prime_scale = 0
structure = random_structure.xray_structure(
space_group_info,
elements=elements,
random_f_prime_d_min=1,
random_f_prime_scale=random_f_prime_scale,
random_f_double_prime=anomalous_flag,
use_u_aniso=True,
use_u_iso=False,
random_u_cart_scale=0.3,
random_u_iso=True,
random_occupancy=True)
random_structure.random_modify_adp_and_adp_flags_2(
scatterers=structure.scatterers(),
use_u_iso=use_u_iso,
use_u_aniso=use_u_aniso,
allow_mix=allow_mix,
random_u_iso_scale=0.3,
random_u_iso_min=0.0)
sampled_density_must_be_positive = True
if (negative_gaussian):
reg = structure.scattering_type_registry(
custom_dict={"H": eltbx.xray_scattering.gaussian(-1)})
assert reg.gaussian("H").n_terms() == 0
assert reg.gaussian("H").c() == -1
sampled_density_must_be_positive = False
elif (not const_gaussian and random.random() < 0.5):
if (random.random() < 0.5):
sampled_density_must_be_positive = False
assign_custom_gaussians(
structure, negative_a=not sampled_density_must_be_positive)
f_direct = structure.structure_factors(anomalous_flag=anomalous_flag,
d_min=d_min,
algorithm="direct").f_calc()
crystal_gridding = f_direct.crystal_gridding(
resolution_factor=resolution_factor, d_min=d_min, max_prime=max_prime)
assert crystal_gridding.symmetry_flags() is None
rfft = fftpack.real_to_complex_3d(crystal_gridding.n_real())
u_base = xray.calc_u_base(d_min, resolution_factor, quality_factor)
omptbx.env.num_threads = libtbx.introspection.number_of_processors()
sampled_density = xray.sampled_model_density(
unit_cell=structure.unit_cell(),
scatterers=structure.scatterers(),
scattering_type_registry=structure.scattering_type_registry(),
fft_n_real=rfft.n_real(),
fft_m_real=rfft.m_real(),
u_base=u_base,
wing_cutoff=wing_cutoff,
exp_table_one_over_step_size=exp_table_one_over_step_size,
force_complex=force_complex,
sampled_density_must_be_positive=sampled_density_must_be_positive,
tolerance_positive_definite=1.e-5,
use_u_base_as_u_extra=False)
focus = sampled_density.real_map_unpadded().focus()
all = sampled_density.real_map_unpadded().all()
last = sampled_density.real_map_unpadded().last()
assert approx_equal(focus, last)
assert approx_equal(all, last)
assert sampled_density.anomalous_flag() == (anomalous_flag
or force_complex)
if (0 or verbose):
print("const_gaussian:", const_gaussian)
print("negative_gaussian:", negative_gaussian)
print("number of scatterers passed:", \
sampled_density.n_scatterers_passed())
print("number of contributing scatterers:", \
sampled_density.n_contributing_scatterers())
print("number of anomalous scatterers:", \
sampled_density.n_anomalous_scatterers())
print("wing_cutoff:", sampled_density.wing_cutoff())
print("exp_table_one_over_step_size:", \
sampled_density.exp_table_one_over_step_size())
print("exp_table_size:", sampled_density.exp_table_size())
print("max_sampling_box_edges:",
sampled_density.max_sampling_box_edges(),
end=' ')
print("(%.4f, %.4f, %.4f)" %
sampled_density.max_sampling_box_edges_frac())
if (not sampled_density.anomalous_flag()):
print("map min:", flex.min(sampled_density.real_map()))
print("map max:", flex.max(sampled_density.real_map()))
else:
print("map min:",
flex.min(flex.real(sampled_density.complex_map())),
end=' ')
print(flex.min(flex.imag(sampled_density.complex_map())))
print("map max:",
flex.max(flex.real(sampled_density.complex_map())),
end=' ')
print(flex.max(flex.imag(sampled_density.complex_map())))
if (not sampled_density.anomalous_flag() and negative_gaussian):
assert flex.min(sampled_density.real_map()) < 0
assert flex.max(sampled_density.real_map()) == 0
if (not sampled_density.anomalous_flag()):
map = sampled_density.real_map()
assert map.all() == rfft.m_real()
assert map.focus() == rfft.n_real()
sf_map = rfft.forward(map)
assert sf_map.all() == rfft.n_complex()
assert sf_map.focus() == rfft.n_complex()
collect_conj = True
else:
cfft = fftpack.complex_to_complex_3d(rfft.n_real())
map = sampled_density.complex_map()
assert map.all() == cfft.n()
assert map.focus() == cfft.n()
sf_map = cfft.backward(map)
assert sf_map.all() == cfft.n()
assert sf_map.focus() == cfft.n()
collect_conj = False
f_fft_data = maptbx.structure_factors.from_map(
space_group=f_direct.space_group(),
anomalous_flag=sampled_density.anomalous_flag(),
miller_indices=f_direct.indices(),
complex_map=sf_map,
conjugate_flag=collect_conj).data()
sampled_density.eliminate_u_extra_and_normalize(f_direct.indices(),
f_fft_data)
structure_factor_utils.check_correlation("direct/fft_regression",
f_direct.indices(),
0,
f_direct.data(),
f_fft_data,
min_corr_ampl=1 * 0.99,
max_mean_w_phase_error=1 * 3.,
verbose=verbose)
f_fft = xray.structure_factors.from_scatterers(
miller_set=f_direct,
grid_resolution_factor=resolution_factor,
quality_factor=quality_factor,
wing_cutoff=wing_cutoff,
exp_table_one_over_step_size=exp_table_one_over_step_size,
sampled_density_must_be_positive=sampled_density_must_be_positive,
max_prime=max_prime)(xray_structure=structure,
miller_set=f_direct,
algorithm="fft").f_calc()
structure_factor_utils.check_correlation("direct/fft_xray",
f_direct.indices(),
0,
f_direct.data(),
f_fft.data(),
min_corr_ampl=1 * 0.99,
max_mean_w_phase_error=1 * 3.,
verbose=verbose)
def exercise(space_group_info, const_gaussian, negative_gaussian,
anomalous_flag,
allow_mix,
use_u_iso,
use_u_aniso,
d_min=1., resolution_factor=1./3, max_prime=5,
quality_factor=100, wing_cutoff=1.e-6,
exp_table_one_over_step_size=-100,
force_complex=False,
verbose=0):
if (const_gaussian):
elements=["const"]*8
elif (negative_gaussian):
elements=["H"]*8
else:
elements=["N", "C", "C", "O", "N", "C", "C", "O"]
if (random.random() < 0.5):
random_f_prime_scale=0.6
else:
random_f_prime_scale=0
structure = random_structure.xray_structure(
space_group_info,
elements=elements,
random_f_prime_d_min=1,
random_f_prime_scale=random_f_prime_scale,
random_f_double_prime=anomalous_flag,
use_u_aniso= True,
use_u_iso= False,
random_u_cart_scale=0.3,
random_u_iso=True,
random_occupancy=True)
random_structure.random_modify_adp_and_adp_flags_2(
scatterers = structure.scatterers(),
use_u_iso = use_u_iso,
use_u_aniso = use_u_aniso,
allow_mix = allow_mix,
random_u_iso_scale = 0.3,
random_u_iso_min = 0.0)
sampled_density_must_be_positive = True
if (negative_gaussian):
reg = structure.scattering_type_registry(
custom_dict={"H": eltbx.xray_scattering.gaussian(-1)})
assert reg.gaussian("H").n_terms() == 0
assert reg.gaussian("H").c() == -1
sampled_density_must_be_positive = False
elif (not const_gaussian and random.random() < 0.5):
if (random.random() < 0.5):
sampled_density_must_be_positive = False
assign_custom_gaussians(
structure,
negative_a=not sampled_density_must_be_positive)
f_direct = structure.structure_factors(
anomalous_flag=anomalous_flag,
d_min=d_min,
algorithm="direct").f_calc()
crystal_gridding = f_direct.crystal_gridding(
resolution_factor=resolution_factor,
d_min=d_min,
max_prime=max_prime)
assert crystal_gridding.symmetry_flags() is None
rfft = fftpack.real_to_complex_3d(crystal_gridding.n_real())
u_base = xray.calc_u_base(d_min, resolution_factor, quality_factor)
omptbx.env.num_threads = libtbx.introspection.number_of_processors()
sampled_density = xray.sampled_model_density(
unit_cell=structure.unit_cell(),
scatterers=structure.scatterers(),
scattering_type_registry=structure.scattering_type_registry(),
fft_n_real=rfft.n_real(),
fft_m_real=rfft.m_real(),
u_base=u_base,
wing_cutoff=wing_cutoff,
exp_table_one_over_step_size=exp_table_one_over_step_size,
force_complex=force_complex,
sampled_density_must_be_positive=sampled_density_must_be_positive,
tolerance_positive_definite=1.e-5,
use_u_base_as_u_extra=False)
focus = sampled_density.real_map_unpadded().focus()
all = sampled_density.real_map_unpadded().all()
last = sampled_density.real_map_unpadded().last()
assert approx_equal(focus, last)
assert approx_equal(all, last)
assert sampled_density.anomalous_flag() == (anomalous_flag or force_complex)
if (0 or verbose):
print "const_gaussian:", const_gaussian
print "negative_gaussian:", negative_gaussian
print "number of scatterers passed:", \
sampled_density.n_scatterers_passed()
print "number of contributing scatterers:", \
sampled_density.n_contributing_scatterers()
print "number of anomalous scatterers:", \
sampled_density.n_anomalous_scatterers()
print "wing_cutoff:", sampled_density.wing_cutoff()
print "exp_table_one_over_step_size:", \
sampled_density.exp_table_one_over_step_size()
print "exp_table_size:", sampled_density.exp_table_size()
print "max_sampling_box_edges:", sampled_density.max_sampling_box_edges(),
print "(%.4f, %.4f, %.4f)" % sampled_density.max_sampling_box_edges_frac()
if (not sampled_density.anomalous_flag()):
print "map min:", flex.min(sampled_density.real_map())
print "map max:", flex.max(sampled_density.real_map())
else:
print "map min:", flex.min(flex.real(sampled_density.complex_map())),
print flex.min(flex.imag(sampled_density.complex_map()))
print "map max:", flex.max(flex.real(sampled_density.complex_map())),
print flex.max(flex.imag(sampled_density.complex_map()))
if (not sampled_density.anomalous_flag() and negative_gaussian):
assert flex.min(sampled_density.real_map()) < 0
assert flex.max(sampled_density.real_map()) == 0
if (not sampled_density.anomalous_flag()):
map = sampled_density.real_map()
assert map.all() == rfft.m_real()
assert map.focus() == rfft.n_real()
sf_map = rfft.forward(map)
assert sf_map.all() == rfft.n_complex()
assert sf_map.focus() == rfft.n_complex()
collect_conj = True
else:
cfft = fftpack.complex_to_complex_3d(rfft.n_real())
map = sampled_density.complex_map()
assert map.all() == cfft.n()
assert map.focus() == cfft.n()
sf_map = cfft.backward(map)
assert sf_map.all() == cfft.n()
assert sf_map.focus() == cfft.n()
collect_conj = False
f_fft_data = maptbx.structure_factors.from_map(
space_group=f_direct.space_group(),
anomalous_flag=sampled_density.anomalous_flag(),
miller_indices=f_direct.indices(),
complex_map=sf_map,
conjugate_flag=collect_conj).data()
sampled_density.eliminate_u_extra_and_normalize(
f_direct.indices(),
f_fft_data)
structure_factor_utils.check_correlation(
"direct/fft_regression", f_direct.indices(), 0,
f_direct.data(), f_fft_data,
min_corr_ampl=1*0.99, max_mean_w_phase_error=1*3.,
verbose=verbose)
f_fft = xray.structure_factors.from_scatterers(
miller_set=f_direct,
grid_resolution_factor=resolution_factor,
quality_factor=quality_factor,
wing_cutoff=wing_cutoff,
exp_table_one_over_step_size=exp_table_one_over_step_size,
sampled_density_must_be_positive=sampled_density_must_be_positive,
max_prime=max_prime)(
xray_structure=structure,
miller_set=f_direct,
algorithm="fft").f_calc()
structure_factor_utils.check_correlation(
"direct/fft_xray", f_direct.indices(), 0,
f_direct.data(), f_fft.data(),
min_corr_ampl=1*0.99, max_mean_w_phase_error=1*3.,
verbose=verbose)