def run():
show_times = libtbx.utils.show_times()
from scitbx.python_utils import command_line
flags = command_line.parse_options(sys.argv[1:], [
"RandomSeed",
"Verbose",
])
if (not flags.RandomSeed): random.seed(0)
assert fftpack.adjust_gridding(13, 5) == 15
assert fftpack.adjust_gridding(13, 5, 6) == 18
assert fftpack.adjust_gridding_triple((13, 22, 34), 5) == (15, 24, 36)
assert fftpack.adjust_gridding_triple((13, 22, 34), 5,
(6, 10, 8)) == (18, 30, 40)
f = fftpack.factorization(30, False)
assert f.n() == 30
assert tuple(f.factors()) == (2, 3, 5)
test_complex_to_complex(flags.Verbose)
test_real_to_complex(flags.Verbose)
test_complex_to_complex_2d(flags.Verbose)
test_complex_to_complex_3d(flags.Verbose)
test_real_to_complex_3d(flags.Verbose)
exercise_real_to_complex_padding_area()
max_transform_size = 300
test_comprehensive_cc_1d(max_transform_size)
test_comprehensive_rc_1d(max_transform_size)
show_times()
def run():
show_times = libtbx.utils.show_times()
from scitbx.python_utils import command_line
flags = command_line.parse_options(sys.argv[1:], [
"RandomSeed",
"Verbose",
])
if (not flags.RandomSeed): random.seed(0)
assert fftpack.adjust_gridding(13, 5) == 15
assert fftpack.adjust_gridding(13, 5, 6) == 18
assert fftpack.adjust_gridding_triple((13,22,34), 5) == (15,24,36)
assert fftpack.adjust_gridding_triple((13,22,34), 5, (6,10,8)) == (18,30,40)
f = fftpack.factorization(30, False)
assert f.n() == 30
assert tuple(f.factors()) == (2, 3, 5)
test_complex_to_complex(flags.Verbose)
test_real_to_complex(flags.Verbose)
test_complex_to_complex_2d(flags.Verbose)
test_complex_to_complex_3d(flags.Verbose)
test_real_to_complex_3d(flags.Verbose)
exercise_real_to_complex_padding_area()
max_transform_size = 300
test_comprehensive_cc_1d(max_transform_size)
test_comprehensive_rc_1d(max_transform_size)
show_times()
def region_density_correlation(large_unit_cell, large_d_min, large_density_map,
sites_cart, site_radii, work_scatterers):
sites_frac_large = large_unit_cell.fractionalize(sites_cart)
large_frac_min = sites_frac_large.min()
large_frac_max = sites_frac_large.max()
large_n_real = large_density_map.focus()
from scitbx import fftpack
from libtbx.math_utils import ifloor, iceil
large_ucp = large_unit_cell.parameters()
small_n_real = [0, 0, 0]
small_origin_in_large_grid = [0, 0, 0]
small_abc = [0, 0, 0]
sites_frac_shift = [0, 0, 0]
for i in xrange(3):
grid_step = large_ucp[i] / large_n_real[i]
buffer = large_d_min / grid_step
grid_min = ifloor(large_frac_min[i] * large_n_real[i] - buffer)
grid_max = iceil(large_frac_max[i] * large_n_real[i] + buffer)
min_grid = grid_max - grid_min + 1
small_n_real[i] = fftpack.adjust_gridding(min_grid=min_grid,
max_prime=5)
if (small_n_real[i] < large_n_real[i]):
shift_min = (small_n_real[i] - min_grid) // 2
small_origin_in_large_grid[i] = grid_min - shift_min
small_abc[i] = small_n_real[i] * grid_step
sites_frac_shift[
i] = small_origin_in_large_grid[i] / large_n_real[i]
else:
small_n_real[i] = large_n_real[i]
small_origin_in_large_grid[i] = 0
small_abc[i] = large_ucp[i]
sites_frac_shift[i] = 0
sites_cart_shift = large_unit_cell.orthogonalize(sites_frac_shift)
sites_cart_small = sites_cart - sites_cart_shift
from cctbx import xray
small_xray_structure = xray.structure(crystal_symmetry=crystal.symmetry(
unit_cell=tuple(small_abc) + large_ucp[3:], space_group_symbol="P1"),
scatterers=work_scatterers)
small_xray_structure.set_sites_cart(sites_cart=sites_cart_small)
small_f_calc = small_xray_structure.structure_factors(
d_min=large_d_min).f_calc()
small_gridding = crystal_gridding(
unit_cell=small_f_calc.unit_cell(),
space_group_info=small_f_calc.space_group_info(),
pre_determined_n_real=small_n_real)
from cctbx import miller
small_fft_map = miller.fft_map(crystal_gridding=small_gridding,
fourier_coefficients=small_f_calc)
small_fft_map.apply_sigma_scaling()
small_map = small_fft_map.real_map_unpadded()
grid_indices = grid_indices_around_sites(
unit_cell=small_xray_structure.unit_cell(),
fft_n_real=small_n_real,
fft_m_real=small_n_real,
sites_cart=sites_cart_small,
site_radii=site_radii)
small_copy_from_large_map = copy(
map_unit_cell=large_density_map,
first=small_origin_in_large_grid,
last=matrix.col(small_origin_in_large_grid) +
matrix.col(small_n_real) - matrix.col((1, 1, 1)))
assert small_copy_from_large_map.all() == small_map.all()
corr = flex.linear_correlation(
x=small_map.select(grid_indices),
y=small_copy_from_large_map.select(grid_indices))
if (not corr.is_well_defined()):
return None
return corr.coefficient()
def region_density_correlation(
large_unit_cell,
large_d_min,
large_density_map,
sites_cart,
site_radii,
work_scatterers):
sites_frac_large = large_unit_cell.fractionalize(sites_cart)
large_frac_min = sites_frac_large.min()
large_frac_max = sites_frac_large.max()
large_n_real = large_density_map.focus()
from scitbx import fftpack
from libtbx.math_utils import ifloor, iceil
large_ucp = large_unit_cell.parameters()
small_n_real = [0,0,0]
small_origin_in_large_grid = [0,0,0]
small_abc = [0,0,0]
sites_frac_shift = [0,0,0]
for i in xrange(3):
grid_step = large_ucp[i] / large_n_real[i]
buffer = large_d_min / grid_step
grid_min = ifloor(large_frac_min[i] * large_n_real[i] - buffer)
grid_max = iceil(large_frac_max[i] * large_n_real[i] + buffer)
min_grid = grid_max - grid_min + 1
small_n_real[i] = fftpack.adjust_gridding(min_grid=min_grid, max_prime=5)
if (small_n_real[i] < large_n_real[i]):
shift_min = (small_n_real[i] - min_grid) // 2
small_origin_in_large_grid[i] = grid_min - shift_min
small_abc[i] = small_n_real[i] * grid_step
sites_frac_shift[i] = small_origin_in_large_grid[i] / large_n_real[i]
else:
small_n_real[i] = large_n_real[i]
small_origin_in_large_grid[i] = 0
small_abc[i] = large_ucp[i]
sites_frac_shift[i] = 0
sites_cart_shift = large_unit_cell.orthogonalize(sites_frac_shift)
sites_cart_small = sites_cart - sites_cart_shift
from cctbx import xray
small_xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=tuple(small_abc)+large_ucp[3:],
space_group_symbol="P1"),
scatterers=work_scatterers)
small_xray_structure.set_sites_cart(sites_cart=sites_cart_small)
small_f_calc = small_xray_structure.structure_factors(
d_min=large_d_min).f_calc()
small_gridding = crystal_gridding(
unit_cell=small_f_calc.unit_cell(),
space_group_info=small_f_calc.space_group_info(),
pre_determined_n_real=small_n_real)
from cctbx import miller
small_fft_map = miller.fft_map(
crystal_gridding=small_gridding,
fourier_coefficients=small_f_calc)
small_fft_map.apply_sigma_scaling()
small_map = small_fft_map.real_map_unpadded()
grid_indices = grid_indices_around_sites(
unit_cell=small_xray_structure.unit_cell(),
fft_n_real=small_n_real,
fft_m_real=small_n_real,
sites_cart=sites_cart_small,
site_radii=site_radii)
small_copy_from_large_map = copy(
map_unit_cell=large_density_map,
first=small_origin_in_large_grid,
last=matrix.col(small_origin_in_large_grid)
+ matrix.col(small_n_real)
- matrix.col((1,1,1)))
assert small_copy_from_large_map.all() == small_map.all()
corr = flex.linear_correlation(
x=small_map.select(grid_indices),
y=small_copy_from_large_map.select(grid_indices))
if (not corr.is_well_defined()):
return None
return corr.coefficient()