def exercise_is_simple_interaction():
for space_group_symbol in ["P1", "P41"]:
for shifts in flex.nested_loop((-2,-2,-2),(2,2,2),False):
shifts = matrix.col(shifts)
structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(10,10,20,90,90,90),
space_group_symbol=space_group_symbol),
scatterers=flex.xray_scatterer([
xray.scatterer(label="O", site=shifts+matrix.col((0,0,0))),
xray.scatterer(label="N", site=shifts+matrix.col((0.5,0.5,0))),
xray.scatterer(label="C", site=shifts+matrix.col((0.25,0.25,0)))]))
asu_mappings = structure.asu_mappings(buffer_thickness=7)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=7)
simple_interactions = {}
for i_pair,pair in enumerate(pair_generator):
if (asu_mappings.is_simple_interaction(pair)):
assert asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
key = (pair.i_seq,pair.j_seq)
assert simple_interactions.get(key, None) is None
simple_interactions[key] = 1
else:
assert not asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
assert len(simple_interactions) == 2
assert simple_interactions[(0,2)] == 1
assert simple_interactions[(1,2)] == 1
def exercise_is_simple_interaction():
for space_group_symbol in ["P1", "P41"]:
for shifts in flex.nested_loop((-2, -2, -2), (2, 2, 2), False):
shifts = matrix.col(shifts)
structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(10, 10, 20, 90, 90, 90),
space_group_symbol=space_group_symbol),
scatterers=flex.xray_scatterer([
xray.scatterer(label="O",
site=shifts + matrix.col((0, 0, 0))),
xray.scatterer(label="N",
site=shifts + matrix.col((0.5, 0.5, 0))),
xray.scatterer(label="C",
site=shifts + matrix.col((0.25, 0.25, 0)))
]))
asu_mappings = structure.asu_mappings(buffer_thickness=7)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=7)
simple_interactions = {}
for i_pair, pair in enumerate(pair_generator):
if (asu_mappings.is_simple_interaction(pair)):
assert asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
key = (pair.i_seq, pair.j_seq)
assert simple_interactions.get(key, None) is None
simple_interactions[key] = 1
else:
assert not asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
assert len(simple_interactions) == 2
assert simple_interactions[(0, 2)] == 1
assert simple_interactions[(1, 2)] == 1
def run():
for elements in flex.nested_loop([-1] * 9, [1 + 1] * 9):
r = sgtbx.rot_mx(elements)
if (r.determinant() != 1): continue
if (not r.multiply(r).is_unit_mx()): continue
if (r.is_unit_mx()): continue
print(elements, r.info().ev(), r.transpose().info().ev())
print("OK")
def run():
for elements in flex.nested_loop([-1]*9,[1+1]*9):
r = sgtbx.rot_mx(elements)
if (r.determinant() != 1): continue
if (not r.multiply(r).is_unit_mx()): continue
if (r.is_unit_mx()): continue
print elements, r.info().ev(), r.transpose().info().ev()
print "OK"
def enumerate_reduced_cell_two_folds():
result = []
for elements in flex.nested_loop([-1]*9,[1+1]*9):
r = sgtbx.rot_mx(elements)
if (r.determinant() != 1): continue
if (r.inverse() != r): continue
if (r.is_unit_mx()): continue
result.append(r)
return result
def enumerate_reduced_cell_two_folds():
result = []
for elements in flex.nested_loop([-1] * 9, [1 + 1] * 9):
r = sgtbx.rot_mx(elements)
if (r.determinant() != 1): continue
if (r.inverse() != r): continue
if (r.is_unit_mx()): continue
result.append(r)
return result
def exercise_float_asu(space_group_info, n_grid=6):
unit_cell = space_group_info.any_compatible_unit_cell(volume=1000)
ref_asu = reference_table.get_asu(space_group_info.type().number())
exercise_cut_planes(ref_asu.cuts)
inp_asu = space_group_info.direct_space_asu()
assert sgtbx.space_group(inp_asu.hall_symbol) == space_group_info.group()
exercise_cut_planes(inp_asu.cuts)
exercise_shape_vertices(inp_asu, unit_cell)
float_asu = inp_asu.add_buffer(unit_cell=unit_cell, thickness=0.001)
cb_mx_ref_inp = space_group_info.type().cb_op().c_inv().as_rational()
n = n_grid
for ref_n in flex.nested_loop((-n // 2, -n // 2, -n // 2), (n, n, n),
False):
# check correctness of space_group_info.direct_space_asu()
ref_r = matrix.col([rational.int(g, n) for g in ref_n])
inp_r = cb_mx_ref_inp * ref_r
assert ref_asu.is_inside(ref_r.elems) == inp_asu.is_inside(inp_r.elems)
# check correctness of cut_plane.add_buffer()
inp_r = inp_r.elems
inp_f = [float(r) for r in inp_r]
for cut in inp_asu.cuts:
r_cut = cut.strip()
r_inside = r_cut.is_inside(inp_r)
for buffer_thickness in [0.001, 1, -1][:1]:
f_cut = cut.as_float_cut_plane().add_buffer(
unit_cell=unit_cell, thickness=buffer_thickness)
f_inside = f_cut.is_inside(inp_f)
if (buffer_thickness < 0):
if (r_inside != f_inside):
assert r_inside
elif (buffer_thickness < 0.01):
assert r_inside == f_inside
elif (r_inside != f_inside):
assert f_inside
# check correctness of float_asu.add_buffer()
assert float_asu.is_inside(inp_f) == inp_asu.shape_only().is_inside(
inp_r)
asu_with_metric = inp_asu.define_metric(unit_cell)
assert asu_with_metric.hall_symbol is inp_asu.hall_symbol
assert len(asu_with_metric.cuts) == len(inp_asu.cuts)
assert asu_with_metric.unit_cell is unit_cell
asu_tight = asu_with_metric.as_float_asu()
asu_buffer = asu_with_metric.add_buffer(thickness=2)
asu_shrunk = asu_with_metric.add_buffer(relative_thickness=-1.e-5)
vertices = facet_analysis.shape_vertices(inp_asu)
for vertex in vertices:
assert inp_asu.shape_only().is_inside(vertex)
for vertex in vertices:
assert asu_tight.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert asu_buffer.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert not asu_shrunk.is_inside(matrix.col(vertex).as_float().elems)
def exercise_float_asu(space_group_info, n_grid=6):
unit_cell = space_group_info.any_compatible_unit_cell(volume=1000)
ref_asu = reference_table.get_asu(space_group_info.type().number())
exercise_cut_planes(ref_asu.cuts)
inp_asu = space_group_info.direct_space_asu()
assert sgtbx.space_group(inp_asu.hall_symbol) == space_group_info.group()
exercise_cut_planes(inp_asu.cuts)
exercise_shape_vertices(inp_asu, unit_cell)
float_asu = inp_asu.add_buffer(unit_cell=unit_cell, thickness=0.001)
cb_mx_ref_inp = space_group_info.type().cb_op().c_inv().as_rational()
n = n_grid
for ref_n in flex.nested_loop((-n//2,-n//2,-n//2),(n,n,n),False):
# check correctness of space_group_info.direct_space_asu()
ref_r = matrix.col([rational.int(g,n) for g in ref_n])
inp_r = cb_mx_ref_inp * ref_r
assert ref_asu.is_inside(ref_r.elems) == inp_asu.is_inside(inp_r.elems)
# check correctness of cut_plane.add_buffer()
inp_r = inp_r.elems
inp_f = [float(r) for r in inp_r]
for cut in inp_asu.cuts:
r_cut = cut.strip()
r_inside = r_cut.is_inside(inp_r)
for buffer_thickness in [0.001, 1, -1][:1]:
f_cut = cut.as_float_cut_plane().add_buffer(
unit_cell=unit_cell,
thickness=buffer_thickness)
f_inside = f_cut.is_inside(inp_f)
if (buffer_thickness < 0):
if (r_inside != f_inside):
assert r_inside
elif (buffer_thickness < 0.01):
assert r_inside == f_inside
elif (r_inside != f_inside):
assert f_inside
# check correctness of float_asu.add_buffer()
assert float_asu.is_inside(inp_f) == inp_asu.shape_only().is_inside(inp_r)
asu_with_metric = inp_asu.define_metric(unit_cell)
assert asu_with_metric.hall_symbol is inp_asu.hall_symbol
assert len(asu_with_metric.cuts) == len(inp_asu.cuts)
assert asu_with_metric.unit_cell is unit_cell
asu_tight = asu_with_metric.as_float_asu()
asu_buffer = asu_with_metric.add_buffer(thickness=2)
asu_shrunk = asu_with_metric.add_buffer(relative_thickness=-1.e-5)
vertices = facet_analysis.shape_vertices(inp_asu)
for vertex in vertices:
assert inp_asu.shape_only().is_inside(vertex)
for vertex in vertices:
assert asu_tight.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert asu_buffer.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert not asu_shrunk.is_inside(matrix.col(vertex).as_float().elems)
def exercise_asu_eight_point_interpolation():
map = flex.double(flex.grid(2,3,5), 10)
cs = crystal.symmetry(
unit_cell=(1,1,1,90,90,90),
space_group="P1")
asu_mappings=cs.asu_mappings(buffer_thickness=0)
for shift in [0,1,-1]:
for index in flex.nested_loop(map.focus()):
x_frac = [float(i)/n+shift for i,n in zip(index, map.focus())]
assert approx_equal(
maptbx.asu_eight_point_interpolation(map, asu_mappings, x_frac), 10)
assert approx_equal(
maptbx.asu_eight_point_interpolation(map, asu_mappings, (10,11,12)), 10)
def exercise_eight_point_interpolation():
map = flex.double(flex.grid(2,3,5), 10)
for shift in [0,1,-1]:
for index in flex.nested_loop(map.focus()):
x_frac = [float(i)/n+shift for i,n in zip(index, map.focus())]
assert approx_equal(maptbx.eight_point_interpolation(map, x_frac), 10)
assert approx_equal(
maptbx.eight_point_interpolation_with_gradients(map, x_frac,[1,1,1])[0], 10)
assert maptbx.closest_grid_point(map.accessor(), x_frac) == index
for i in xrange(100):
x_frac = [3*random.random()-1 for i in xrange(3)]
assert approx_equal(map.eight_point_interpolation(x_frac), 10)
assert approx_equal(
map.eight_point_interpolation_with_gradients(x_frac,[1,1,1])[0], 10)
map = flex.double(range(30))
map.resize(flex.grid(2,3,5))
for shift in [0,1,-1]:
v = 0
for index in flex.nested_loop(map.focus()):
x_frac = [float(i)/n+shift for i,n in zip(index, map.focus())]
assert approx_equal(map.eight_point_interpolation(x_frac), v)
assert approx_equal(
map[maptbx.closest_grid_point(map.accessor(), x_frac)], v)
assert approx_equal(map.value_at_closest_grid_point(x_frac), v)
v += 1
map = flex.double()
for i in xrange(48): map.append(i%2)
map.resize(flex.grid(2,4,6))
for shift in [0,1,-1]:
for offs in [.0,.5,.25,.75]:
v = offs
for index in flex.nested_loop(map.focus()):
x_frac = [(i+offs)/n+shift for i,n in zip(index, map.focus())]
assert approx_equal(map.eight_point_interpolation(x_frac), v)
if (offs != .5):
assert maptbx.closest_grid_point(map.accessor(), x_frac) == tuple(
[int(i+offs+.5)%n for i,n in zip(index,map.focus())])
v = 1-v
def exercise_comprehensive(args):
if ("--verbose" in args):
out = sys.stdout
else:
out = StringIO()
if ("--paranoid" in args):
cb_range = 2
else:
cb_range = 1
for symbol in bravais_types.acentric:
print("bravais type:", symbol)
sym = sgtbx.space_group_info(symbol=symbol) \
.any_compatible_crystal_symmetry(volume=1000) \
.niggli_cell()
abc = list(sym.unit_cell().parameters()[:3])
abc.sort()
for cb_elements in flex.nested_loop([-cb_range] * 9,
[cb_range + 1] * 9):
r = sgtbx.rot_mx(cb_elements)
if (r.determinant() != 1): continue
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r))
sym_cb = sym.change_basis(cb_op)
abc_cb = list(sym_cb.unit_cell().parameters()[:3])
abc_cb.sort()
for x, y in zip(abc, abc_cb):
assert y - x > -1.e-6
if (y - x > 1.e-4): break
else:
print("cb_ob:", cb_op.c(), cb_elements, file=out)
assert min(cb_elements) >= -1
assert max(cb_elements) <= 1
for s in sym_cb.space_group():
assert s.r().den() == 1
r_num = s.r().num()
print("r:", r_num, file=out)
assert min(r_num) >= -1
assert max(r_num) <= 1
for enforce in [False, True]:
lattice_group = sgtbx.lattice_symmetry.group(
reduced_cell=sym_cb.unit_cell(),
max_delta=1.4,
enforce_max_delta_for_generated_two_folds=enforce)
assert lattice_group == sym_cb.space_group()
sys.stdout.flush()
print(file=out)
def exercise_comprehensive(args):
if ("--verbose" in args):
out = sys.stdout
else:
out = StringIO()
if ("--paranoid" in args):
cb_range = 2
else:
cb_range = 1
for symbol in bravais_types.acentric:
print "bravais type:", symbol
sym = sgtbx.space_group_info(symbol=symbol) \
.any_compatible_crystal_symmetry(volume=1000) \
.niggli_cell()
abc = list(sym.unit_cell().parameters()[:3])
abc.sort()
for cb_elements in flex.nested_loop([-cb_range]*9,[cb_range+1]*9):
r = sgtbx.rot_mx(cb_elements)
if (r.determinant() != 1): continue
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r))
sym_cb = sym.change_basis(cb_op)
abc_cb = list(sym_cb.unit_cell().parameters()[:3])
abc_cb.sort()
for x,y in zip(abc, abc_cb):
assert y-x > -1.e-6
if (y-x > 1.e-4): break
else:
print >> out, "cb_ob:", cb_op.c(), cb_elements
assert min(cb_elements) >= -1
assert max(cb_elements) <= 1
for s in sym_cb.space_group():
assert s.r().den() == 1
r_num = s.r().num()
print >> out, "r:", r_num
assert min(r_num) >= -1
assert max(r_num) <= 1
for enforce in [False, True]:
lattice_group = sgtbx.lattice_symmetry.group(
reduced_cell=sym_cb.unit_cell(),
max_delta=1.4,
enforce_max_delta_for_generated_two_folds=enforce)
assert lattice_group == sym_cb.space_group()
sys.stdout.flush()
print >> out
# Actual data via member; no work done here.
rmap = sampled_density.real_map()
# Convert the cctbx flex array to EMData. Better done in C++, or
# work with EMData after getting the `coords` above.
from EMAN2_cppwrap import *
ed = EMData()
# .focus() is logical array size
# .all() is the allocated size (padding etc.)
n = rmap.focus()
ed.set_size(n[2],n[1],n[0])
print "Entering slow loop...", # should be implemented in C++
sys.stdout.flush()
for i in flex.nested_loop(rmap.focus()):
ee[i[2],i[1],i[0]] = rmap[i]
print "done."
sys.stdout.flush()
# Save.
drop_image(ed, image_file_name)
#
#* Example from Pawel Afonine
# Also see
# $SPXROOT/cctbx/cctbx_sources/cctbx/cctbx/xray/structure.py
from cctbx.array_family import flex
from iotbx import pdb
# Actual data via member; no work done here.
rmap = sampled_density.real_map()
# Convert the cctbx flex array to EMData. Better done in C++, or
# work with EMData after getting the `coords` above.
from EMAN2_cppwrap import *
ed = EMData()
# .focus() is logical array size
# .all() is the allocated size (padding etc.)
n = rmap.focus()
ed.set_size(n[2], n[1], n[0])
print("Entering slow loop...", end=' ') # should be implemented in C++
sys.stdout.flush()
for i in flex.nested_loop(rmap.focus()):
ee[i[2], i[1], i[0]] = rmap[i]
print("done.")
sys.stdout.flush()
# Save.
drop_image(ed, image_file_name)
#
#* Example from Pawel Afonine
# Also see
# $SPXROOT/cctbx/cctbx_sources/cctbx/cctbx/xray/structure.py
from cctbx.array_family import flex
from iotbx import pdb
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 rho_stats(xray_structure, d_min, resolution_factor, electron_sum_radius,
zero_out_f000):
n_real = []
n_half_plus = []
n_half_minus = []
s2 = d_min * resolution_factor * 2
for l in xray_structure.unit_cell().parameters()[:3]:
nh = ifloor(l / s2)
n_real.append(2 * nh + 1)
n_half_plus.append(nh)
n_half_minus.append(-nh)
n_real = tuple(n_real)
n_real_product = matrix.col(n_real).product()
crystal_gridding = maptbx.crystal_gridding(
unit_cell=xray_structure.unit_cell(),
space_group_info=xray_structure.space_group_info(),
pre_determined_n_real=n_real)
miller_indices = flex.miller_index()
miller_indices.reserve(n_real_product)
for h in flex.nested_loop(n_half_minus, n_half_plus, open_range=False):
miller_indices.append(h)
assert miller_indices.size() == n_real_product
#
miller_set = miller.set(crystal_symmetry=xray_structure,
anomalous_flag=True,
indices=miller_indices).sort(by_value="resolution")
assert miller_set.indices()[0] == (0, 0, 0)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure, algorithm="direct",
cos_sin_table=False).f_calc()
if (zero_out_f000):
f_calc.data()[0] = 0j
#
unit_cell_volume = xray_structure.unit_cell().volume()
voxel_volume = unit_cell_volume / n_real_product
number_of_miller_indices = []
rho_max = []
electron_sums_around_atoms = []
densities_along_x = []
for f in [f_calc, f_calc.resolution_filter(d_min=d_min)]:
assert f.indices()[0] == (0, 0, 0)
number_of_miller_indices.append(f.indices().size())
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f)
assert fft_map.n_real() == n_real
rho = fft_map.real_map_unpadded() / unit_cell_volume
assert approx_equal(voxel_volume * flex.sum(rho), f_calc.data()[0])
if (xray_structure.scatterers().size() == 1):
assert flex.max_index(rho) == 0
rho_max.append(rho[0])
else:
rho_max.append(flex.max(rho))
site_cart = xray_structure.sites_cart()[0]
gias = maptbx.grid_indices_around_sites(
unit_cell=xray_structure.unit_cell(),
fft_n_real=n_real,
fft_m_real=n_real,
sites_cart=flex.vec3_double([site_cart]),
site_radii=flex.double([electron_sum_radius]))
electron_sums_around_atoms.append(
flex.sum(rho.as_1d().select(gias)) * voxel_volume)
#
a = xray_structure.unit_cell().parameters()[0]
nx = n_real[0]
nxh = nx // 2
x = []
y = []
for ix in range(-nxh, nxh + 1):
x.append(a * ix / nx)
y.append(rho[(ix % nx, 0, 0)])
densities_along_x.append((x, y))
#
print(
"%3.1f %4.2f %-12s %5d %5d | %6.3f %6.3f | %6.3f %6.3f | %4.2f %5.1f" %
(d_min, resolution_factor, n_real, number_of_miller_indices[0],
number_of_miller_indices[1], electron_sums_around_atoms[0],
electron_sums_around_atoms[1], rho_max[0], rho_max[1],
f_calc.data()[0].real, u_as_b(xray_structure.scatterers()[0].u_iso)))
#
return densities_along_x
def hcp_fill_box(cb_op_original_to_sampling, float_asu, continuous_shift_flags,
point_distance,
buffer_thickness=-1, all_twelve_neighbors=False,
exercise_cpp=True):
if (exercise_cpp):
cpp = close_packing.hexagonal_sampling_generator(
cb_op_original_to_sampling=cb_op_original_to_sampling,
float_asu=float_asu,
continuous_shift_flags=continuous_shift_flags,
point_distance=point_distance,
buffer_thickness=buffer_thickness,
all_twelve_neighbors=all_twelve_neighbors)
assert point_distance > 0
if (buffer_thickness < 0):
buffer_thickness = point_distance * (2/3. * (.5 * math.sqrt(3)))
if (exercise_cpp):
assert cpp.cb_op_original_to_sampling().c()==cb_op_original_to_sampling.c()
assert cpp.float_asu().unit_cell().is_similar_to(float_asu.unit_cell())
assert cpp.continuous_shift_flags() == continuous_shift_flags
assert approx_equal(cpp.point_distance(), point_distance)
assert approx_equal(cpp.buffer_thickness(), buffer_thickness)
assert cpp.all_twelve_neighbors() == all_twelve_neighbors
float_asu_buffer = float_asu.add_buffer(thickness=buffer_thickness)
hex_cell = hexagonal_sampling_cell(point_distance=point_distance)
hex_box = hexagonal_box(
hex_cell=hex_cell,
vertices_cart=float_asu.shape_vertices(cartesian=True))
hex_box_buffer = hexagonal_box(
hex_cell=hex_cell,
vertices_cart=float_asu_buffer.shape_vertices(cartesian=True))
box_lower = []
box_upper = []
for i in xrange(3):
if (continuous_shift_flags[i]):
box_lower.append(0)
box_upper.append(0)
else:
n = iceil(abs(hex_box.max[i]-hex_box.pivot[i]))
box_lower.append(min(-2,ifloor(hex_box_buffer.min[i]-hex_box.pivot[i])))
box_upper.append(n+max(2,iceil(hex_box_buffer.max[i]-hex_box.max[i])))
if (exercise_cpp):
assert list(cpp.box_lower()) == box_lower
assert list(cpp.box_upper()) == box_upper
hex_to_frac_matrix = (
matrix.sqr(float_asu.unit_cell().fractionalization_matrix())
* matrix.sqr(hex_cell.orthogonalization_matrix()))
sites_frac = flex.vec3_double()
for point in flex.nested_loop(begin=box_lower,
end=box_upper,
open_range=False):
site_hex = matrix.col(hex_box.pivot) \
+ matrix.col(hex_indices_as_site(point))
site_frac = hex_to_frac_matrix * site_hex
if (float_asu_buffer.is_inside(site_frac)):
sites_frac.append(site_frac)
elif (all_twelve_neighbors):
for offset in [(1,0,0),(1,1,0),(0,1,0),(-1,0,0),(-1,-1,0),(0,-1,0),
(0,0,1),(-1,-1,1),(0,-1,1),
(0,0,-1),(-1,-1,-1),(0,-1,-1)]:
offset_hex = hex_indices_as_site(offset, layer=point[2])
offset_frac = hex_to_frac_matrix * matrix.col(offset_hex)
other_site_frac = site_frac + offset_frac
if (float_asu.is_inside(other_site_frac)):
sites_frac.append(site_frac)
break
assert sites_frac.size() > 0
rt = cb_op_original_to_sampling.c_inv().as_double_array()
sites_frac = rt[:9] * sites_frac
sites_frac += rt[9:]
if (exercise_cpp):
assert not cpp.at_end()
cpp_sites_frac = cpp.all_sites_frac()
assert cpp.at_end()
assert cpp_sites_frac.size() == sites_frac.size()
assert approx_equal(cpp_sites_frac, sites_frac)
cpp.restart()
assert not cpp.at_end()
assert approx_equal(cpp.next_site_frac(), sites_frac[0])
assert cpp.count_sites() == sites_frac.size()-1
assert cpp.at_end()
cpp.restart()
n = 0
for site in cpp: n += 1
assert n == sites_frac.size()
return sites_frac
def exercise_copy():
for flex_type in flex_types():
m = flex_type((1,2,3,4))
m.resize(flex.grid(2,2))
c = maptbx.copy(map=m, result_grid=m.accessor())
assert tuple(m) == tuple(c)
c = maptbx.copy(map=m, result_grid=flex.grid(2,3).set_focus(2,2))
assert approx_equal(tuple(c), (1,2,0,3,4,0))
n = maptbx.copy(c, result_grid=m.accessor())
assert approx_equal(tuple(m), tuple(n))
c = maptbx.copy(m, flex.grid(3,2).set_focus(2,2))
assert approx_equal(tuple(c), (1,2,3,4,0,0))
n = maptbx.copy(c, m.accessor())
assert approx_equal(tuple(m), tuple(n))
m = flex_type((1,2,3,4,5,6))
m.resize(flex.grid((1,2),(3,5)))
c = maptbx.copy(m, m.accessor())
assert approx_equal(tuple(m), tuple(c))
c = maptbx.copy(m, flex.grid((1,2),(3,6)).set_focus(3,5))
assert approx_equal(tuple(c), (1,2,3,0,4,5,6,0))
n = maptbx.copy(c, m.accessor())
assert approx_equal(tuple(m), tuple(n))
c = maptbx.copy(m, flex.grid((1,2),(4,5)).set_focus(3,5))
assert approx_equal(tuple(c), (1,2,3,4,5,6,0,0,0))
n = maptbx.copy(c, m.accessor())
assert approx_equal(tuple(m), tuple(n))
#
m = flex_type()
for i in xrange(2):
for j in xrange(3):
for k in xrange(5):
m.append(i*100+j*10+k)
m.resize(flex.grid(2,3,5).set_focus((2,3,4)))
for i in xrange(-5,5):
for j in xrange(-5,5):
for k in xrange(-5,5):
c = maptbx.copy(map_unit_cell=m, first=(i,j,k), last=(i,j,k))
assert c.size() == 1
assert c[(i,j,k)] == m[(i%2,j%3,k%4)]
c = maptbx.copy(map_unit_cell=m, first=(-1,1,-2), last=(1,2,0))
assert list(c) == [112, 113, 110, 122, 123, 120, 12, 13, 10,
22, 23, 20, 112, 113, 110, 122, 123, 120]
#
m2 = m.deep_copy()
grid = flex.grid( (-1,-1,-1), (1,2,4) ).set_focus( (1,2,3) )
m2.resize(grid)
for i in xrange(-1,1):
for j in xrange(-1,2):
for k in xrange(-1,3):
# aperiodic copy
c = maptbx.copy_box(map=m2, first=(i,j,k), last=(i,j,k))
assert c.size() == 1
ind = ((i+1)%2-1,(j+1)%3-1,(k+1)%4-1)
assert c[(i,j,k)] == m2[ind]
c = maptbx.copy_box(map=m2, first=(-1,0,-1), last=(0,1,2))
assert list(c) == [10, 11, 12, 13, 20, 21, 22, 23, 110,
111, 112, 113, 120, 121, 122, 123]
#
for n0 in xrange(4):
for n1 in xrange(4):
for n2 in xrange(4):
for d2 in xrange(3):
g = flex.grid((n0,n1,n2+d2)).set_focus((n0,n1,n2))
map1 = flex_type(range(1,1+g.size_1d()))
map1.resize(g)
map2 = map1.deep_copy()
maptbx.unpad_in_place(map=map2)
assert map2.all() == (n0,n1,n2)
assert not map2.is_padded()
if (n0*n1*n2 != 0):
for i in flex.nested_loop((n0,n1,n2)):
assert map2[i] == map1[i]
n0,n1,n2,d2 = 2,3,4,1
g = flex.grid((n0,n1,n2+d2)).set_focus((n0,n1,n2))
map1 = flex_type(range(1,1+g.size_1d()))
map1.resize(g)
map2 = map1.deep_copy()
maptbx.unpad_in_place(map=map2)
assert map2.all() == (n0,n1,n2)
assert not map2.is_padded()
assert list(map2) == [
1, 2, 3, 4,
6, 7, 8, 9,
11,12,13,14,
16,17,18,19,
21,22,23,24,
26,27,28,29]
def rho_stats(
xray_structure,
d_min,
resolution_factor,
electron_sum_radius,
zero_out_f000):
n_real = []
n_half_plus = []
n_half_minus = []
s2 = d_min * resolution_factor * 2
for l in xray_structure.unit_cell().parameters()[:3]:
nh = ifloor(l / s2)
n_real.append(2*nh+1)
n_half_plus.append(nh)
n_half_minus.append(-nh)
n_real = tuple(n_real)
n_real_product = matrix.col(n_real).product()
crystal_gridding = maptbx.crystal_gridding(
unit_cell=xray_structure.unit_cell(),
space_group_info=xray_structure.space_group_info(),
pre_determined_n_real=n_real)
miller_indices = flex.miller_index()
miller_indices.reserve(n_real_product)
for h in flex.nested_loop(n_half_minus, n_half_plus, open_range=False):
miller_indices.append(h)
assert miller_indices.size() == n_real_product
#
miller_set = miller.set(
crystal_symmetry=xray_structure,
anomalous_flag=True,
indices=miller_indices).sort(by_value="resolution")
assert miller_set.indices()[0] == (0,0,0)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure,
algorithm="direct",
cos_sin_table=False).f_calc()
if (zero_out_f000):
f_calc.data()[0] = 0j
#
unit_cell_volume = xray_structure.unit_cell().volume()
voxel_volume = unit_cell_volume / n_real_product
number_of_miller_indices = []
rho_max = []
electron_sums_around_atoms = []
densities_along_x = []
for f in [f_calc, f_calc.resolution_filter(d_min=d_min)]:
assert f.indices()[0] == (0,0,0)
number_of_miller_indices.append(f.indices().size())
fft_map = miller.fft_map(
crystal_gridding=crystal_gridding,
fourier_coefficients=f)
assert fft_map.n_real() == n_real
rho = fft_map.real_map_unpadded() / unit_cell_volume
assert approx_equal(voxel_volume*flex.sum(rho), f_calc.data()[0])
if (xray_structure.scatterers().size() == 1):
assert flex.max_index(rho) == 0
rho_max.append(rho[0])
else:
rho_max.append(flex.max(rho))
site_cart = xray_structure.sites_cart()[0]
gias = maptbx.grid_indices_around_sites(
unit_cell=xray_structure.unit_cell(),
fft_n_real=n_real,
fft_m_real=n_real,
sites_cart=flex.vec3_double([site_cart]),
site_radii=flex.double([electron_sum_radius]))
electron_sums_around_atoms.append(
flex.sum(rho.as_1d().select(gias))*voxel_volume)
#
a = xray_structure.unit_cell().parameters()[0]
nx = n_real[0]
nxh = nx//2
x = []
y = []
for ix in xrange(-nxh,nxh+1):
x.append(a*ix/nx)
y.append(rho[(ix%nx,0,0)])
densities_along_x.append((x,y))
#
print \
"%3.1f %4.2f %-12s %5d %5d | %6.3f %6.3f | %6.3f %6.3f | %4.2f %5.1f" % (
d_min,
resolution_factor,
n_real,
number_of_miller_indices[0],
number_of_miller_indices[1],
electron_sums_around_atoms[0],
electron_sums_around_atoms[1],
rho_max[0],
rho_max[1],
f_calc.data()[0].real,
u_as_b(xray_structure.scatterers()[0].u_iso))
#
return densities_along_x
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 hcp_fill_box(cb_op_original_to_sampling,
float_asu,
continuous_shift_flags,
point_distance,
buffer_thickness=-1,
all_twelve_neighbors=False,
exercise_cpp=True):
if (exercise_cpp):
cpp = close_packing.hexagonal_sampling_generator(
cb_op_original_to_sampling=cb_op_original_to_sampling,
float_asu=float_asu,
continuous_shift_flags=continuous_shift_flags,
point_distance=point_distance,
buffer_thickness=buffer_thickness,
all_twelve_neighbors=all_twelve_neighbors)
assert point_distance > 0
if (buffer_thickness < 0):
buffer_thickness = point_distance * (2 / 3. * (.5 * math.sqrt(3)))
if (exercise_cpp):
assert cpp.cb_op_original_to_sampling().c(
) == cb_op_original_to_sampling.c()
assert cpp.float_asu().unit_cell().is_similar_to(float_asu.unit_cell())
assert cpp.continuous_shift_flags() == continuous_shift_flags
assert approx_equal(cpp.point_distance(), point_distance)
assert approx_equal(cpp.buffer_thickness(), buffer_thickness)
assert cpp.all_twelve_neighbors() == all_twelve_neighbors
float_asu_buffer = float_asu.add_buffer(thickness=buffer_thickness)
hex_cell = hexagonal_sampling_cell(point_distance=point_distance)
hex_box = hexagonal_box(
hex_cell=hex_cell,
vertices_cart=float_asu.shape_vertices(cartesian=True))
hex_box_buffer = hexagonal_box(
hex_cell=hex_cell,
vertices_cart=float_asu_buffer.shape_vertices(cartesian=True))
box_lower = []
box_upper = []
for i in range(3):
if (continuous_shift_flags[i]):
box_lower.append(0)
box_upper.append(0)
else:
n = iceil(abs(hex_box.max[i] - hex_box.pivot[i]))
box_lower.append(
min(-2, ifloor(hex_box_buffer.min[i] - hex_box.pivot[i])))
box_upper.append(
n + max(2, iceil(hex_box_buffer.max[i] - hex_box.max[i])))
if (exercise_cpp):
assert list(cpp.box_lower()) == box_lower
assert list(cpp.box_upper()) == box_upper
hex_to_frac_matrix = (
matrix.sqr(float_asu.unit_cell().fractionalization_matrix()) *
matrix.sqr(hex_cell.orthogonalization_matrix()))
sites_frac = flex.vec3_double()
for point in flex.nested_loop(begin=box_lower,
end=box_upper,
open_range=False):
site_hex = matrix.col(hex_box.pivot) \
+ matrix.col(hex_indices_as_site(point))
site_frac = hex_to_frac_matrix * site_hex
if (float_asu_buffer.is_inside(site_frac)):
sites_frac.append(site_frac)
elif (all_twelve_neighbors):
for offset in [(1, 0, 0), (1, 1, 0), (0, 1, 0), (-1, 0, 0),
(-1, -1, 0), (0, -1, 0), (0, 0, 1), (-1, -1, 1),
(0, -1, 1), (0, 0, -1), (-1, -1, -1), (0, -1, -1)]:
offset_hex = hex_indices_as_site(offset, layer=point[2])
offset_frac = hex_to_frac_matrix * matrix.col(offset_hex)
other_site_frac = site_frac + offset_frac
if (float_asu.is_inside(other_site_frac)):
sites_frac.append(site_frac)
break
assert sites_frac.size() > 0
rt = cb_op_original_to_sampling.c_inv().as_double_array()
sites_frac = rt[:9] * sites_frac
sites_frac += rt[9:]
if (exercise_cpp):
assert not cpp.at_end()
cpp_sites_frac = cpp.all_sites_frac()
assert cpp.at_end()
assert cpp_sites_frac.size() == sites_frac.size()
assert approx_equal(cpp_sites_frac, sites_frac)
cpp.restart()
assert not cpp.at_end()
assert approx_equal(cpp.next_site_frac(), sites_frac[0])
assert cpp.count_sites() == sites_frac.size() - 1
assert cpp.at_end()
cpp.restart()
n = 0
for site in cpp:
n += 1
assert n == sites_frac.size()
return sites_frac
