def exercise_value(f_c_in_p1, f_o, flags, n_sampled):
""" where we check against the trusted correlation map implemented
in cctbx.translation_search """
crystal_gridding = f_o.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False),
resolution_factor=1/3)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_o.space_group(),
anomalous_flag=f_o.anomalous_flag(),
miller_indices_f_obs=f_o.indices(),
f_obs=f_o.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_c_in_p1.indices(),
p1_f_calc=f_c_in_p1.data()).target_map()
nx, ny, nz = n = crystal_gridding.n_real()
def sampled_indices():
from random import randrange
yield (0,0,0)
for i in xrange(n_sampled - 1):
yield randrange(0, n[0]), randrange(0, n[1]), randrange(0, n[2])
f_o_sq = f_o.as_intensity_array()
for i,j,k in sampled_indices():
x = (i/nx, j/ny, k/nz)
if random.random() > 0.5: f_o_or_f_o_sq = f_o
else: f_o_or_f_o_sq = f_o_sq
gos = symmetrised_shifted_structure_factors(
f_o_or_f_o_sq, f_c_in_p1, x).misfit(f_o_or_f_o_sq)
assert approx_equal(gos.correlation, correlation_map[i,j,k]), (i,j,k)
def exercise_value(f_c_in_p1, f_o, flags, n_sampled):
""" where we check against the trusted correlation map implemented
in cctbx.translation_search """
crystal_gridding = f_o.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False, have_f_part=False),
resolution_factor=1 / 3)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_o.space_group(),
anomalous_flag=f_o.anomalous_flag(),
miller_indices_f_obs=f_o.indices(),
f_obs=f_o.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_c_in_p1.indices(),
p1_f_calc=f_c_in_p1.data()).target_map()
nx, ny, nz = n = crystal_gridding.n_real()
def sampled_indices():
from random import randrange
yield (0, 0, 0)
for i in xrange(n_sampled - 1):
yield randrange(0, n[0]), randrange(0, n[1]), randrange(0, n[2])
f_o_sq = f_o.as_intensity_array()
for i, j, k in sampled_indices():
x = (i / nx, j / ny, k / nz)
if random.random() > 0.5: f_o_or_f_o_sq = f_o
else: f_o_or_f_o_sq = f_o_sq
gos = symmetrised_shifted_structure_factors(f_o_or_f_o_sq, f_c_in_p1,
x).misfit(f_o_or_f_o_sq)
assert approx_equal(gos.correlation, correlation_map[i, j,
k]), (i, j, k)
def run():
target_structure = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("I432"),
elements=['C']*6+['O'],
use_u_iso=False,
use_u_aniso=True,
)
shift = tuple(flex.random_double(3))
print "shift to be found: (%.3f, %.3f, %.3f)" % shift
target_structure_in_p1 = target_structure.expand_to_p1().apply_shift(shift)
miller_indices = miller.build_set(
crystal_symmetry=target_structure,
anomalous_flag=True,
d_min=0.8)
f_obs = miller_indices.structure_factors_from_scatterers(
xray_structure=target_structure,
algorithm="direct").f_calc().amplitudes()
miller_indices_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=True,
d_min=0.8)
f_calc = miller_indices_in_p1.structure_factors_from_scatterers(
xray_structure=target_structure_in_p1,
algorithm="direct").f_calc()
crystal_gridding = f_calc.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False),
resolution_factor=1/2
)
omptbx.env.num_threads = 1
t_fast_tf = show_times()
fast_tf_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc.indices(),
p1_f_calc=f_calc.data()).target_map()
print
print "Fast translation function"
t_fast_tf()
t_cross_corr = show_times()
for op in target_structure.space_group():
f, op_times_f = f_calc.original_and_transformed(op)
cross_corr_map = miller.fft_map(crystal_gridding,
f * op_times_f.conjugate().data())
print
print "Traditional cross-correlation"
t_cross_corr()
def exercise_symmetry_flags():
for i_flags in xrange(4):
is_isotropic_search_model = (i_flags % 2 != 0)
have_f_part = ((i_flags // 2) % 2 != 0)
f = translation_search.symmetry_flags(
is_isotropic_search_model=is_isotropic_search_model,
have_f_part=have_f_part)
assert f.is_isotropic_search_model() == is_isotropic_search_model
assert f.have_f_part() == have_f_part
assert f.use_space_group_symmetry() == is_isotropic_search_model
assert f.use_normalizer_k2l() \
== (is_isotropic_search_model and (not have_f_part))
assert f.use_seminvariants() == (not have_f_part)
def exercise_symmetry_flags():
for i_flags in xrange(4):
is_isotropic_search_model = (i_flags % 2 != 0)
have_f_part = ((i_flags//2) % 2 != 0)
f = translation_search.symmetry_flags(
is_isotropic_search_model=is_isotropic_search_model,
have_f_part=have_f_part)
assert f.is_isotropic_search_model() == is_isotropic_search_model
assert f.have_f_part() == have_f_part
assert f.use_space_group_symmetry() == is_isotropic_search_model
assert f.use_normalizer_k2l() \
== (is_isotropic_search_model and (not have_f_part))
assert f.use_seminvariants() == (not have_f_part)
def f_calc_symmetrisations(f_obs, f_calc_in_p1, min_cc_peak_height):
# The fast correlation map as per cctbx.translation_search.fast_nv1995
# is computed and its peaks studied.
# Inspiration from phenix.substructure.hyss for the parameters tuning.
if 0: # Display f_calc_in_p1
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="f_calc in P1 before fast CC",
fft_map=f_calc_in_p1.fft_map(),
iso_level_positive_range_fraction=0.8)
crystal_gridding = f_obs.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False),
resolution_factor=1/3
)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc_in_p1.indices(),
p1_f_calc=f_calc_in_p1.data()).target_map()
if 0: # Display correlation_map
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="Fast CC map",
raw_map=correlation_map,
unit_cell=f_calc_in_p1.unit_cell(),
positive_iso_level=0.8)
search_parameters = maptbx.peak_search_parameters(
peak_search_level=1,
peak_cutoff=0.5,
interpolate=True,
min_distance_sym_equiv=1e-6,
general_positions_only=False,
min_cross_distance=f_obs.d_min()/2)
## The correlation map is not a miller.fft_map, just a 3D flex.double
correlation_map_peaks = crystal_gridding.tags().peak_search(
map=correlation_map,
parameters=search_parameters)
# iterate over the strong peak; for each, shift and symmetrised f_calc
for peak in correlation_map_peaks:
if peak.height < min_cc_peak_height: break
sr = symmetry_search.shift_refinement(
f_obs, f_calc_in_p1, peak.site)
yield sr.symmetrised_shifted_sf.f_x, sr.shift, sr.goos.correlation
def run():
target_structure = random_structure.xray_structure(
space_group_info=sgtbx.space_group_info("I432"),
elements=['C'] * 6 + ['O'],
use_u_iso=False,
use_u_aniso=True,
)
shift = tuple(flex.random_double(3))
print "shift to be found: (%.3f, %.3f, %.3f)" % shift
target_structure_in_p1 = target_structure.expand_to_p1().apply_shift(shift)
miller_indices = miller.build_set(crystal_symmetry=target_structure,
anomalous_flag=True,
d_min=0.8)
f_obs = miller_indices.structure_factors_from_scatterers(
xray_structure=target_structure,
algorithm="direct").f_calc().amplitudes()
miller_indices_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=True,
d_min=0.8)
f_calc = miller_indices_in_p1.structure_factors_from_scatterers(
xray_structure=target_structure_in_p1, algorithm="direct").f_calc()
crystal_gridding = f_calc.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False, have_f_part=False),
resolution_factor=1 / 2)
omptbx.env.num_threads = 1
t_fast_tf = show_times()
fast_tf_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc.indices(),
p1_f_calc=f_calc.data()).target_map()
print
print "Fast translation function"
t_fast_tf()
t_cross_corr = show_times()
for op in target_structure.space_group():
f, op_times_f = f_calc.original_and_transformed(op)
cross_corr_map = miller.fft_map(crystal_gridding,
f * op_times_f.conjugate().data())
print
print "Traditional cross-correlation"
t_cross_corr()
def f_calc_symmetrisations(f_obs, f_calc_in_p1, min_cc_peak_height):
# The fast correlation map as per cctbx.translation_search.fast_nv1995
# is computed and its peaks studied.
# Inspiration from phenix.substructure.hyss for the parameters tuning.
if 0: # Display f_calc_in_p1
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="f_calc in P1 before fast CC",
fft_map=f_calc_in_p1.fft_map(),
iso_level_positive_range_fraction=0.8)
crystal_gridding = f_obs.crystal_gridding(
symmetry_flags=translation_search.symmetry_flags(
is_isotropic_search_model=False, have_f_part=False),
resolution_factor=1 / 3)
correlation_map = translation_search.fast_nv1995(
gridding=crystal_gridding.n_real(),
space_group=f_obs.space_group(),
anomalous_flag=f_obs.anomalous_flag(),
miller_indices_f_obs=f_obs.indices(),
f_obs=f_obs.data(),
f_part=flex.complex_double(), ## no sub-structure is already fixed
miller_indices_p1_f_calc=f_calc_in_p1.indices(),
p1_f_calc=f_calc_in_p1.data()).target_map()
if 0: # Display correlation_map
from crys3d.qttbx import map_viewer
map_viewer.display(window_title="Fast CC map",
raw_map=correlation_map,
unit_cell=f_calc_in_p1.unit_cell(),
positive_iso_level=0.8)
search_parameters = maptbx.peak_search_parameters(
peak_search_level=1,
peak_cutoff=0.5,
interpolate=True,
min_distance_sym_equiv=1e-6,
general_positions_only=False,
min_cross_distance=f_obs.d_min() / 2)
## The correlation map is not a miller.fft_map, just a 3D flex.double
correlation_map_peaks = crystal_gridding.tags().peak_search(
map=correlation_map, parameters=search_parameters)
# iterate over the strong peak; for each, shift and symmetrised f_calc
for peak in correlation_map_peaks:
if peak.height < min_cc_peak_height: break
sr = symmetry_search.shift_refinement(f_obs, f_calc_in_p1, peak.site)
yield sr.symmetrised_shifted_sf.f_x, sr.shift, sr.goos.correlation
def test_shift(space_group_info,
d_min=0.8, grid_resolution_factor=0.48, max_prime=5,
verbose=0):
n = 12 // len(space_group_info.group()) or 1
target_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=['C']*n,
use_u_iso=False,
use_u_aniso=False,
)
f_target = miller.build_set(
crystal_symmetry=target_structure,
anomalous_flag=False,
d_min=d_min
).structure_factors_from_scatterers(
xray_structure=target_structure,
algorithm="direct").f_calc()
f_obs = abs(f_target)
indices_in_p1 = miller.set.expand_to_p1(f_target)
target_structure_in_p1 = target_structure.expand_to_p1()
reference_translation = matrix.col((0.1, 0.2, 0.7))
structure_in_p1 = target_structure_in_p1.apply_shift(reference_translation)
f_structure_in_p1 = indices_in_p1.structure_factors_from_scatterers(
xray_structure=structure_in_p1,
algorithm="direct").f_calc()
symmetry_flags = translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=False)
gridding = f_target.crystal_gridding(
symmetry_flags=symmetry_flags,
resolution_factor=grid_resolution_factor,
max_prime=max_prime).n_real()
grid_tags = maptbx.grid_tags(gridding)
for f_calc_in_p1 in (f_structure_in_p1,):
peak_list = run_fast_nv1995(
f_obs=f_obs, f_calc_fixed=None, f_calc_p1=f_calc_in_p1,
symmetry_flags=symmetry_flags, gridding=gridding,
grid_tags=grid_tags, verbose=verbose)
assert peak_list.heights()[0] > 0.9
shift = matrix.col(peak_list.sites()[0])
assert f_target.space_group_info().is_allowed_origin_shift(
shift + reference_translation, tolerance=0.04)
def test_molecule(space_group_info, use_primitive_setting, flag_f_part,
d_min=3., grid_resolution_factor=0.48, max_prime=5,
verbose=0):
if (use_primitive_setting):
space_group_info = space_group_info.primitive_setting()
elements = ("N", "C", "C", "O", "N", "C", "C", "O")
structure = random_structure.xray_structure(
space_group_info,
elements=elements,
volume_per_atom=50,
min_distance=1.,
general_positions_only=True,
random_u_iso=True,
random_occupancy=True)
if (0 or verbose):
structure.show_summary().show_scatterers()
miller_set_f_obs = miller.build_set(
crystal_symmetry=structure,
anomalous_flag=(random.random() < 0.5),
d_min=d_min)
f_obs = abs(miller_set_f_obs.structure_factors_from_scatterers(
xray_structure=structure,
algorithm="direct").f_calc())
if (0 or verbose):
f_obs.show_summary()
if (0 or verbose):
f_obs.show_array()
miller_set_p1 = miller.set.expand_to_p1(f_obs)
special_position_settings_p1 = crystal.special_position_settings(
crystal_symmetry=miller_set_p1)
structure_p1 = xray.structure(
special_position_settings=special_position_settings_p1)
structure_fixed = xray.structure(special_position_settings=structure)
for scatterer in structure.scatterers():
if (flag_f_part and structure_fixed.scatterers().size()
< structure.scatterers().size()//2):
structure_fixed.add_scatterer(scatterer)
else:
structure_p1.add_scatterer(scatterer)
if (0 or verbose):
if (flag_f_part):
structure_fixed.show_summary().show_scatterers()
structure_p1.show_summary().show_scatterers()
f_calc_fixed = None
if (flag_f_part):
f_calc_fixed = f_obs.structure_factors_from_scatterers(
xray_structure=structure_fixed,
algorithm="direct").f_calc()
f_calc_p1 = miller_set_p1.structure_factors_from_scatterers(
xray_structure=structure_p1,
algorithm="direct").f_calc()
symmetry_flags = translation_search.symmetry_flags(
is_isotropic_search_model=False,
have_f_part=flag_f_part)
gridding = miller_set_f_obs.crystal_gridding(
symmetry_flags=symmetry_flags,
resolution_factor=grid_resolution_factor,
max_prime=max_prime).n_real()
grid_tags = maptbx.grid_tags(gridding)
run_fast_terms(
structure_fixed, structure_p1,
f_obs, f_calc_fixed, f_calc_p1,
symmetry_flags, gridding, grid_tags,
test_origin=True,
verbose=verbose)
peak_list = run_fast_nv1995(
f_obs, f_calc_fixed, f_calc_p1,
symmetry_flags, gridding, grid_tags, verbose)
assert peak_list.heights()[0] > 0.99
def test_atom(space_group_info, use_primitive_setting,
n_elements=3, d_min=3.,
grid_resolution_factor=0.48, max_prime=5, verbose=0):
if (use_primitive_setting):
space_group_info = space_group_info.primitive_setting()
structure = random_structure.xray_structure(
space_group_info,
n_scatterers=n_elements,
volume_per_atom=150,
min_distance=1.,
general_positions_only=True)
miller_set_f_obs = miller.build_set(
crystal_symmetry=structure,
anomalous_flag=(random.random() < 0.5),
d_min=d_min)
symmetry_flags = translation_search.symmetry_flags(
is_isotropic_search_model=True,
have_f_part=(n_elements>=2))
gridding = miller_set_f_obs.crystal_gridding(
symmetry_flags=symmetry_flags,
resolution_factor=grid_resolution_factor,
max_prime=max_prime).n_real()
structure.build_scatterers(
elements=["Se"]*n_elements,
grid=gridding)
if (0 or verbose):
structure.show_summary().show_scatterers()
f_obs = abs(miller_set_f_obs.structure_factors_from_scatterers(
xray_structure=structure,
algorithm="direct").f_calc())
if (0 or verbose):
f_obs.show_summary()
if (0 or verbose):
f_obs.show_array()
miller_set_p1 = miller.set.expand_to_p1(f_obs)
special_position_settings_p1 = crystal.special_position_settings(
crystal_symmetry=miller_set_p1)
structure_fixed = xray.structure(special_position_settings=structure)
for scatterer in structure.scatterers():
structure_p1 = xray.structure(
special_position_settings=special_position_settings_p1)
scatterer_at_origin = scatterer.customized_copy(site=(0,0,0))
structure_p1.add_scatterer(scatterer_at_origin)
if (0 or verbose):
structure_p1.show_summary().show_scatterers()
f_calc_p1 = miller_set_p1.structure_factors_from_scatterers(
xray_structure=structure_p1,
algorithm="direct").f_calc()
if (0 or verbose):
f_calc_p1.show_array()
f_calc_fixed = None
if (structure_fixed.scatterers().size() > 0):
f_calc_fixed = f_obs.structure_factors_from_scatterers(
xray_structure=structure_fixed,
algorithm="direct").f_calc()
symmetry_flags = translation_search.symmetry_flags(
is_isotropic_search_model=True,
have_f_part=(f_calc_fixed is not None))
if (structure_fixed.scatterers().size() <= 1):
gridding = miller_set_f_obs.crystal_gridding(
symmetry_flags=symmetry_flags,
resolution_factor=grid_resolution_factor,
max_prime=max_prime).n_real()
grid_tags = maptbx.grid_tags(gridding)
run_fast_terms(
structure_fixed, structure_p1,
f_obs, f_calc_fixed, f_calc_p1,
symmetry_flags, gridding, grid_tags,
verbose=verbose)
peak_list = run_fast_nv1995(
f_obs, f_calc_fixed, f_calc_p1,
symmetry_flags, gridding, grid_tags, verbose)
structure_fixed.add_scatterer(scatterer)
if (0 or verbose):
structure_fixed.show_summary().show_scatterers()
if (structure_fixed.scatterers().size() < n_elements):
assert peak_list.heights()[0] < 1
else:
assert peak_list.heights()[0] > 0.99
assert peak_list.heights()[0] > 0.99