def exercise_space_group_contains():
g = sgtbx.space_group("P 2")
for s in ["x,y,z", "-x,-y,z", "-x+1,-y-2,z+3"]:
assert g.contains(sgtbx.rt_mx(s))
for s in ["x,y,-z", "x+1/2,y,z"]:
assert not g.contains(sgtbx.rt_mx(s))
for symbols in sgtbx.space_group_symbol_iterator():
g = sgtbx.space_group(symbols.hall())
for s in g:
assert g.contains(s)
rnd = flex.mersenne_twister(seed=0)
n_c = 0
n_nc = 0
for symbol in sgtbx.bravais_types.centric:
g = sgtbx.space_group_info(symbol=symbol,
space_group_t_den=144).group()
for s in g.change_basis(
sgtbx.change_of_basis_op("x+1/12,y-1/12,z+1/12")):
if (rnd.random_double() < 0.9): continue # avoid long runtime
gc = sgtbx.space_group(g)
gc.expand_smx(s)
if (gc.order_z() == g.order_z()):
assert g.contains(s)
n_c += 1
else:
assert not g.contains(s)
n_nc += 1
assert n_c == 11, n_c
assert n_nc == 53, n_nc
def exercise_space_group_contains():
g = sgtbx.space_group("P 2")
for s in ["x,y,z", "-x,-y,z", "-x+1,-y-2,z+3"]:
assert g.contains(sgtbx.rt_mx(s))
for s in ["x,y,-z", "x+1/2,y,z"]:
assert not g.contains(sgtbx.rt_mx(s))
for symbols in sgtbx.space_group_symbol_iterator():
g = sgtbx.space_group(symbols.hall())
for s in g:
assert g.contains(s)
rnd = flex.mersenne_twister(seed=0)
n_c = 0
n_nc = 0
for symbol in sgtbx.bravais_types.centric:
g = sgtbx.space_group_info(symbol=symbol, space_group_t_den=144).group()
for s in g.change_basis(sgtbx.change_of_basis_op("x+1/12,y-1/12,z+1/12")):
if (rnd.random_double() < 0.9): continue # avoid long runtime
gc = sgtbx.space_group(g)
gc.expand_smx(s)
if (gc.order_z() == g.order_z()):
assert g.contains(s)
n_c += 1
else:
assert not g.contains(s)
n_nc += 1
assert n_c == 11, n_c
assert n_nc == 53, n_nc
def generate_enantiomorph_unique_spacegroups(pointgroup):
'''Generate an enantiomorph unique list of chiral spacegroups which
share a pointgroup with this pointgroup.'''
sg = space_group(space_group_symbols(pointgroup).hall())
pg = sg.build_derived_patterson_group()
eu_list = []
for j in space_group_symbol_iterator():
sg_test = space_group(j)
if not sg_test.is_chiral():
continue
pg_test = sg_test.build_derived_patterson_group()
if pg_test == pg:
enantiomorph = sg_test.change_basis(
sg_test.type().change_of_hand_op())
if not sg_test in eu_list and not \
enantiomorph in eu_list:
eu_list.append(sg_test)
return [
sg_test.type().lookup_symbol().replace(' ', '') \
for sg_test in eu_list]
def __init__(self, f_in_p1, **kwds):
isinstance(f_in_p1, miller.array)
assert f_in_p1.space_group().type().hall_symbol() == ' P 1'
self.f_in_p1 = f_in_p1
adopt_optional_init_args(self, kwds)
self.search_parameters = maptbx.peak_search_parameters(
peak_search_level=3,
interpolate=True,
min_distance_sym_equiv=0.25,
)
self.space_group = sgtbx.space_group('P 1', t_den=sg_t_den)
self.origin = None
self.symmetry_pool = []
self.find_centring_translations()
if self.space_group.order_z() > 1:
f_in_centered = self.f_in_p1.customized_copy(
space_group_info=sgtbx.space_group_info(group=self.space_group)
).eliminate_sys_absent().merge_equivalents().array()
self.cb_op_to_primitive = \
f_in_centered.change_of_basis_op_to_primitive_setting()
self.f_in_p1 = f_in_centered.change_basis(self.cb_op_to_primitive)
self.space_group = self.f_in_p1.space_group()
else:
self.cb_op_to_primitive = sgtbx.change_of_basis_op()
self.f_in_p1 = self.f_in_p1.generate_bijvoet_mates()
self.find_space_group()
self.space_group = sgtbx.space_group(
self.space_group.type().hall_symbol(), t_den=sgtbx.sg_t_den)
self.space_group_info = sgtbx.space_group_info(group=self.space_group)
def __init__(self, f_in_p1, **kwds):
isinstance(f_in_p1, miller.array)
assert f_in_p1.space_group().type().hall_symbol() == ' P 1'
self.f_in_p1 = f_in_p1
adopt_optional_init_args(self, kwds)
self.search_parameters = maptbx.peak_search_parameters(
peak_search_level=3,
interpolate=True,
min_distance_sym_equiv=0.25,
)
self.space_group = sgtbx.space_group('P 1', t_den=sg_t_den)
self.origin = None
self.symmetry_pool = []
self.find_centring_translations()
if self.space_group.order_z() > 1:
f_in_centered = self.f_in_p1.customized_copy(
space_group_info=sgtbx.space_group_info(group=self.space_group)
).eliminate_sys_absent().merge_equivalents().array()
self.cb_op_to_primitive = \
f_in_centered.change_of_basis_op_to_primitive_setting()
self.f_in_p1 = f_in_centered.change_basis(self.cb_op_to_primitive)
self.space_group = self.f_in_p1.space_group()
else:
self.cb_op_to_primitive = sgtbx.change_of_basis_op()
self.f_in_p1 = self.f_in_p1.generate_bijvoet_mates()
self.find_space_group()
self.space_group = sgtbx.space_group(self.space_group.type().hall_symbol(),
t_den=sgtbx.sg_t_den)
self.space_group_info = sgtbx.space_group_info(group=self.space_group)
def exercise():
from dials.algorithms.indexing import compare_orientation_matrices
from dxtbx.model import Crystal
from cctbx import sgtbx
from scitbx import matrix
from scitbx.math import euler_angles as euler
# try and see if we can get back the original rotation matrix and euler angles
real_space_a = matrix.col((10, 0, 0))
real_space_b = matrix.col((0, 10, 10))
real_space_c = matrix.col((0, 0, 10))
euler_angles = (1.3, 5.6, 7.8)
R = matrix.sqr(
euler.xyz_matrix(euler_angles[0], euler_angles[1], euler_angles[2]))
crystal_a = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('P 1'))
crystal_b = Crystal(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('P 1'))
assert approx_equal(
matrix.sqr(crystal_b.get_U()) *
matrix.sqr(crystal_a.get_U()).transpose(), R)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.is_identity_op()
assert approx_equal(best_R_ab, R)
# now see if we can deconvolute the original euler angles after applying
# a change of basis to one of the crystals
crystal_a = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('I 2 3'))
crystal_b = Crystal(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('I 2 3'))
cb_op = sgtbx.change_of_basis_op('z,x,y')
crystal_b = crystal_b.change_basis(cb_op)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.c() == cb_op.inverse().c()
assert approx_equal(best_R_ab, R)
def exercise_compatible_symmetries():
pg = sgtbx.space_group('P 2x')
ops = [op.as_xyz() for op in pt.compatible_symmetries(pg)]
assert ops == ['x,-y,-z', 'x+1/2,-y,-z']
pg = sgtbx.space_group('P 2x 2y')
ops = [op.as_xyz() for op in pt.compatible_symmetries(pg)]
assert ops == [
'x,-y,-z', 'x+1/2,-y,-z', '-x,y,-z', '-x,y+1/2,-z', '-x,-y,z',
'-x,-y,z+1/2'
]
pg = sgtbx.space_group('P 2x 3*')
ops = [op.as_xyz() for op in pt.compatible_symmetries(pg)]
assert 'x,-y,-z' in ops
assert 'x+1/2,-y,-z' in ops
assert '-x,y,-z' in ops
assert '-x,y+1/2,-z' in ops
assert '-x,-y,z' in ops
assert '-x,-y,z+1/2' in ops
assert 'z,x,y' in ops
assert 'z+1/3,x+1/3,y+1/3' in ops
assert 'y,z,x' in ops
assert 'y+1/3,z+1/3,x+1/3' in ops
assert 'z,-x,-y' in ops
assert 'z+1/3,-x-1/3,-y+1/3' in ops
assert '-y,z,-x' in ops
assert '-y-1/3,z+1/3,-x+1/3' in ops
assert '-y,-z,x' in ops
assert '-y+1/3,-z-1/3,x+1/3' in ops
assert 'y,-z,-x' in ops
assert 'y-1/3,-z-1/3,-x+1/3' in ops
assert '-z,-x,y' in ops
assert '-z-1/3,-x+1/3,y+1/3' in ops
assert '-z,x,-y' in ops
assert '-z-1/3,x-1/3,-y+1/3' in ops
pg = sgtbx.space_group('-P -2y')
ops = [op.as_xyz() for op in pt.compatible_symmetries(pg)]
assert ops == [
'x,-y,z', 'x+1/2,-y,z', 'x,-y,z+1/2', 'x+1/2,-y,z+1/2', '-x,-y,-z',
'-x,y,-z', '-x,y+1/2,-z'
]
def exercise():
from dials.algorithms.indexing import compare_orientation_matrices
from dxtbx.model.crystal import crystal_model
from cctbx import sgtbx
from scitbx import matrix
from scitbx.math import euler_angles as euler
# try and see if we can get back the original rotation matrix and euler angles
real_space_a = matrix.col((10,0,0))
real_space_b = matrix.col((0,10,10))
real_space_c = matrix.col((0,0,10))
euler_angles = (1.3, 5.6, 7.8)
R = matrix.sqr(
euler.xyz_matrix(euler_angles[0], euler_angles[1], euler_angles[2]))
crystal_a = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('P 1'))
crystal_b = crystal_model(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('P 1'))
assert approx_equal(crystal_b.get_U() * crystal_a.get_U().transpose(), R)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.is_identity_op()
assert approx_equal(best_R_ab, R)
# now see if we can deconvolute the original euler angles after applying
# a change of basis to one of the crystals
crystal_a = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('I 2 3'))
crystal_b = crystal_model(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('I 2 3'))
cb_op = sgtbx.change_of_basis_op('z,x,y')
crystal_b = crystal_b.change_basis(cb_op)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.c() == cb_op.inverse().c()
assert approx_equal(best_R_ab, R)
def exercise_compatible_symmetries():
pg = sgtbx.space_group('P 2x')
ops = [ op.as_xyz() for op in pt.compatible_symmetries(pg) ]
assert ops == [ 'x,-y,-z', 'x+1/2,-y,-z' ]
pg = sgtbx.space_group('P 2x 2y')
ops = [ op.as_xyz() for op in pt.compatible_symmetries(pg) ]
assert ops == [ 'x,-y,-z', 'x+1/2,-y,-z',
'-x,y,-z', '-x,y+1/2,-z',
'-x,-y,z', '-x,-y,z+1/2' ]
pg = sgtbx.space_group('P 2x 3*')
ops = [ op.as_xyz() for op in pt.compatible_symmetries(pg) ]
assert 'x,-y,-z' in ops
assert 'x+1/2,-y,-z' in ops
assert '-x,y,-z' in ops
assert '-x,y+1/2,-z' in ops
assert '-x,-y,z' in ops
assert '-x,-y,z+1/2' in ops
assert 'z,x,y' in ops
assert 'z+1/3,x+1/3,y+1/3' in ops
assert 'y,z,x' in ops
assert 'y+1/3,z+1/3,x+1/3' in ops
assert 'z,-x,-y' in ops
assert 'z+1/3,-x-1/3,-y+1/3' in ops
assert '-y,z,-x' in ops
assert '-y-1/3,z+1/3,-x+1/3' in ops
assert '-y,-z,x' in ops
assert '-y+1/3,-z-1/3,x+1/3' in ops
assert 'y,-z,-x' in ops
assert 'y-1/3,-z-1/3,-x+1/3' in ops
assert '-z,-x,y' in ops
assert '-z-1/3,-x+1/3,y+1/3' in ops
assert '-z,x,-y' in ops
assert '-z-1/3,x-1/3,-y+1/3' in ops
pg = sgtbx.space_group('-P -2y')
ops = [ op.as_xyz() for op in pt.compatible_symmetries(pg) ]
assert ops == ['x,-y,z', 'x+1/2,-y,z', 'x,-y,z+1/2', 'x+1/2,-y,z+1/2',
'-x,-y,-z', '-x,y,-z', '-x,y+1/2,-z']
def main(filenames,
map_file,
npoints=192,
max_resolution=6,
reverse_phi=False):
rec_range = 1 / max_resolution
image = ImageFactory(filenames[0])
panel = image.get_detector()[0]
beam = image.get_beam()
s0 = beam.get_s0()
pixel_size = panel.get_pixel_size()
xlim, ylim = image.get_raw_data().all()
xy = recviewer.get_target_pixels(panel, s0, xlim, ylim, max_resolution)
s1 = panel.get_lab_coord(xy * pixel_size[0]) # FIXME: assumed square pixel
s1 = s1 / s1.norms() * (1 / beam.get_wavelength()) # / is not supported...
S = s1 - s0
grid = flex.double(flex.grid(npoints, npoints, npoints), 0)
cnts = flex.int(flex.grid(npoints, npoints, npoints), 0)
for filename in filenames:
print "Processing image", filename
try:
fill_voxels(ImageFactory(filename), grid, cnts, S, xy, reverse_phi,
rec_range)
except:
print " Failed to process. Skipped this."
recviewer.normalize_voxels(grid, cnts)
uc = uctbx.unit_cell((npoints, npoints, npoints, 90, 90, 90))
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"), (0, 0, 0),
grid.all(), grid,
flex.std_string(["cctbx.miller.fft_map"]))
return
from scitbx import fftpack
fft = fftpack.complex_to_complex_3d(grid.all())
grid_complex = flex.complex_double(reals=flex.pow2(grid),
imags=flex.double(grid.size(), 0))
grid_transformed = flex.abs(fft.backward(grid_complex))
print flex.max(grid_transformed), flex.min(
grid_transformed), grid_transformed.all()
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"), (0, 0, 0),
grid.all(), grid_transformed,
flex.std_string(["cctbx.miller.fft_map"]))
def __init__(self, parent_group_info):
self._p_groups = []
self.z2p_op = parent_group_info.group().z2p_op()
p_parent_group_info = parent_group_info.change_basis(self.z2p_op)
p_parent_group = p_parent_group_info.group()
assert p_parent_group.order_p() == p_parent_group.order_z()
p_parent_group.make_tidy()
for i_smx in xrange(p_parent_group.order_p()):
group_i = sgtbx.space_group()
group_i.expand_smx(p_parent_group(i_smx))
for j_smx in xrange(i_smx,p_parent_group.order_p()):
subgroup = sgtbx.space_group(group_i)
subgroup.expand_smx(p_parent_group(j_smx))
subgroup.make_tidy()
self._add(subgroup)
def test_compare_orientation_matrices():
# try and see if we can get back the original rotation matrix and euler angles
real_space_a = matrix.col((10, 0, 0))
real_space_b = matrix.col((0, 10, 10))
real_space_c = matrix.col((0, 0, 10))
euler_angles = (1.3, 5.6, 7.8)
R = matrix.sqr(
euler.xyz_matrix(euler_angles[0], euler_angles[1], euler_angles[2]))
crystal_a = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('P 1'))
crystal_b = Crystal(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('P 1'))
assert (matrix.sqr(crystal_b.get_U()) *
matrix.sqr(crystal_a.get_U()).transpose()).elems == pytest.approx(
R.elems)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert best_euler_angles == pytest.approx(euler_angles)
assert best_cb_op.is_identity_op()
assert best_R_ab.elems == pytest.approx(R.elems)
# now see if we can deconvolute the original euler angles after applying
# a change of basis to one of the crystals
crystal_a = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('I 2 3'))
crystal_b = Crystal(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('I 2 3'))
cb_op = sgtbx.change_of_basis_op('z,x,y')
crystal_b = crystal_b.change_basis(cb_op)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert best_euler_angles == pytest.approx(euler_angles)
assert best_cb_op.c() == cb_op.inverse().c()
assert best_R_ab.elems == pytest.approx(R.elems)
def __init__(self, with_special_position_pivot):
self.with_special_position_pivot = with_special_position_pivot
self.uc = uctbx.unit_cell((1, 2, 3))
self.sg = sgtbx.space_group("P 6")
self.c0 = xray.scatterer("C0", site=(1e-5, 0., 0.1))
self.site_symm = sgtbx.site_symmetry(self.uc, self.sg, self.c0.site)
self.c0.flags.set_grad_site(True)
self.c1 = xray.scatterer("C1", site=(0.09, 0.11, 0.))
self.c1.flags.set_grad_site(True)
self.h = xray.scatterer("H")
self.reparam = constraints.ext.reparametrisation(self.uc)
if with_special_position_pivot:
x0 = self.reparam.add(constraints.special_position_site_parameter,
self.site_symm, self.c0)
else:
x0 = self.reparam.add(constraints.independent_site_parameter, self.c0)
x1 = self.reparam.add(constraints.independent_site_parameter, self.c1)
l = self.reparam.add(constraints.independent_scalar_parameter,
self.bond_length, variable=False)
x_h = self.reparam.add(constraints.terminal_linear_ch_site,
pivot=x0,
pivot_neighbour=x1,
length=l,
hydrogen=self.h)
self.reparam.finalise()
self.x0, self.x1, self.x_h, self.l = [ x.index for x in (x0, x1, x_h, l) ]
if self.with_special_position_pivot:
self.y0 = x0.independent_params.index
def convert(file_object):
""" Examplify the direct use of the tool from shelx.lexer
In practice, one is strongly encouraged to make use of the tools
from shelx.parsers: that is to say, for the task handled here,
crystal_symmetry_parser (the code to follow just parrots
the implementation of crystal_symmetry_parser).
"""
space_group = None
for command, line in shelx.command_stream(file=file_object):
cmd, args = command[0], command[-1]
if cmd == "LATT":
assert space_group is None
assert len(args) == 1
space_group = sgtbx.space_group()
n = int(args[0])
if n > 0:
space_group.expand_inv(sgtbx.tr_vec((0,0,0)))
z = "*PIRFABC"[abs(n)]
space_group.expand_conventional_centring_type(z)
elif cmd == "SYMM":
assert space_group is not None
assert len(args) == 1
s = sgtbx.rt_mx(args[0])
space_group.expand_smx(s)
elif cmd == "SFAC":
return sgtbx.space_group_info(group=space_group)
def __init__(self, file_name, header_only=False):
self.file_name = os.path.normpath(file_name)
f = open(file_name)
line = f.readline()
assert line[5] == " "
n_sym_ops_from_file = int(line[:5].strip())
assert n_sym_ops_from_file > 0
self.space_group_symbol = line[6:].strip()
self.space_group_from_ops = sgtbx.space_group()
for i in xrange(n_sym_ops_from_file):
line = f.readline().rstrip()
assert len(line) == 27
r = sgtbx.rot_mx([int(line[j*3:(j+1)*3]) for j in xrange(9)], 1)
line = f.readline().rstrip()
assert len(line) == 9
t = sgtbx.tr_vec([int(line[j*3:(j+1)*3]) for j in xrange(3)], 12)
self.space_group_from_ops.expand_smx(sgtbx.rt_mx(r, t))
f.close()
if (header_only):
self.original_indices = None
return
all_arrays = scalepack_ext.no_merge_original_index_arrays(
file_name, n_sym_ops_from_file*2+1)
self.original_indices = all_arrays.original_indices()
self.unique_indices = all_arrays.unique_indices()
self.batch_numbers = all_arrays.batch_numbers()
self.centric_tags = all_arrays.centric_tags()
self.spindle_flags = all_arrays.spindle_flags()
self.asymmetric_unit_indices = all_arrays.asymmetric_unit_indices()
self.i_obs = all_arrays.i_obs()
self.sigmas = all_arrays.sigmas()
def list(self):
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(
space_group_symbols=symbols))
if self.comparator(sgi):
if (self.chiral is None) or (self.chiral == sgi.group().is_chiral()):
yield sgi
def run():
settings = [0]
for i in xrange(1, 231): settings.append({})
list_cb_op = []
for xyz in ("x,y,z", "z,x,y", "y,z,x"):
list_cb_op.append(sgtbx.change_of_basis_op(sgtbx.rt_mx(xyz)))
n_built = 0
for i in sgtbx.space_group_symbol_iterator():
hall_symbol = i.hall()
for z in "PABCIRHF":
hall_z = hall_symbol[0] + z + hall_symbol[2:]
for cb_op in list_cb_op:
group = sgtbx.space_group(hall_z).change_basis(cb_op)
sg_type = group.type()
settings[sg_type.number()][sg_type.lookup_symbol()] = 0
n_built += 1
print "# n_built =", n_built
n_non_redundant = 0
print "settings = ("
for i in xrange(1, 231):
print "#", i
symbols = settings[i].keys()
symbols.sort()
for s in symbols:
print "'" + s + "',"
n_non_redundant += 1
print ")"
print "# n_non_redundant =", n_non_redundant
def exercise_f000():
miller_indices = flex.miller_index([(0,0,0)])
data = flex.complex_double([1-2j])
n_real = [1,2,3]
conjugate_flag = True
for hall_symbol in ["P 1", "P 3", "R 3*"]:
for is_centric in [False, True]:
if (not is_centric):
space_group = sgtbx.space_group(hall_symbol)
else:
space_group.expand_smx("-x,-y,-z")
for anomalous_flag in [False, True]:
if (not anomalous_flag):
rfft = fftpack.real_to_complex_3d(n_real)
n_complex = rfft.n_complex()
else:
cfft = fftpack.complex_to_complex_3d(n_real)
n_complex = cfft.n()
for treat_restricted in [False, True]:
map = maptbx.structure_factors.to_map(
space_group=space_group,
anomalous_flag=anomalous_flag,
miller_indices=miller_indices,
structure_factors=data,
n_real=n_real,
map_grid=flex.grid(n_complex),
conjugate_flag=conjugate_flag,
treat_restricted=treat_restricted)
if (treat_restricted):
assert approx_equal(
map.complex_map()[0], data[0])
else:
assert approx_equal(
map.complex_map()[0], data[0]*space_group.order_p())
def remove_lattice_translations(g):
result = sgtbx.space_group(
hall_symbol="P1", t_den=subgroup.t_den())
for i_inv in xrange(g.f_inv()):
for i_smx in xrange(g.n_smx()):
result.expand_smx(g(0, i_inv, i_smx))
return result
def exercise():
ma = miller.array(
miller.set(crystal.symmetry(unit_cell=(5,5,5, 90, 90, 90),
space_group=sgtbx.space_group('P 2x')),
indices=flex.miller_index(
[(1,0,0), (0,1,0), (0,0,1),
(-1,0,0), (0,-1,0), (0,0,-1),
(1,1,0), (1,0,1), (0,1,1),
(-1,-1,0), (-1,0,-1), (0,-1,-1),
(1,-1,0), (1,0,-1), (0,1,-1),
(-1,1,0), (-1,0,1), (0,-1,1),
(1,1,1), (-1,1,1), (1,-1,1), (1,1,-1),
(-1,-1,-1), (1,-1,-1), (-1,1,-1), (-1,-1,1)])),
data=flex.complex_double(flex.random_double(26), flex.random_double(26)))
f_at_h = dict(zip(ma.indices(), ma.data()))
for op in ("-x, y+1/2, -z", "x+1/2, -y, z-1/2"):
op = sgtbx.rt_mx(op)
original, transformed = ma.common_sets(
ma.change_basis(sgtbx.change_of_basis_op(op.inverse())))
for h, f in original:
assert f == f_at_h[h]
for h, op_f in transformed:
assert approx_equal(
op_f,
f_at_h[h*op.r()]*exp(1j*2*pi*row(h).dot(col(op.t().as_double()))))
def generate_table(complex_data, indices, numpy_args=False, anom=True):
"""
:param complex_data: structure factors
:param indices: miller indices in a list, Nx3
:param numpy_args: are the complex data and indices numpy type, if not
assume flex
:param anom: return a miller array with +H and -H ?
:return: dictionary whose keys are miller index tuple and values are structure fact
"""
sg = sgtbx.space_group(" P 4nw 2abw")
Symm = crystal.symmetry(unit_cell=(79, 79, 38, 90, 90, 90), space_group=sg)
if numpy_args:
assert type(indices) == tuple
assert (type(indices[0]) == tuple)
indices = flex.miller_index(indices)
mil_set = miller.set(crystal_symmetry=Symm,
indices=indices,
anomalous_flag=anom)
if numpy_args:
complex_data = flex.complex_double(np.ascontiguousarray(complex_data))
mil_ar = miller.array(mil_set, data=complex_data)
mil_dict = {h: val for h, val in izip(mil_ar.indices(), mil_ar.data())}
return mil_dict
def to_crystal(filename):
''' Get the crystal model from the xparm file
Params:
filename The xparm/or integrate filename
Return:
The crystal model
'''
from rstbx.cftbx.coordinate_frame_converter import \
coordinate_frame_converter
from dxtbx.model.crystal import crystal_model
from cctbx.sgtbx import space_group, space_group_symbols
# Get the real space coordinate frame
cfc = coordinate_frame_converter(filename)
real_space_a = cfc.get('real_space_a')
real_space_b = cfc.get('real_space_b')
real_space_c = cfc.get('real_space_c')
sg = cfc.get('space_group_number')
space_group = space_group(space_group_symbols(sg).hall())
mosaicity = cfc.get('mosaicity')
# Return the crystal model
return crystal_model(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=space_group,
mosaicity=mosaicity)
def anomalous_reflection_intensity_primitive_cell(space_group):
assert space_group.n_ltr() == 1
assert not space_group.is_centric()
subgroup = sgtbx.space_group(space_group)
subgroup.make_tidy()
result = [subgroup]
for s1 in space_group:
assert s1.t().num() == (0,0,0)
for s2 in space_group:
subgroup = sgtbx.space_group()
subgroup.expand_smx(s1)
subgroup.expand_smx(s2)
subgroup.make_tidy()
if (not subgroup in result):
result.append(subgroup)
return result
def test_correct(space_group_symbol):
sgi = sgtbx.space_group_info(space_group_symbol)
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
ms = cs.build_miller_set(anomalous_flag=True, d_min=1).expand_to_p1()
# the reciprocal matrix
B = scitbx.matrix.sqr(cs.unit_cell().fractionalization_matrix()).transpose()
crystal = Crystal(B, sgtbx.space_group())
expts = ExperimentList([Experiment(crystal=crystal)])
refl = flex.reflection_table()
refl["miller_index"] = ms.indices()
refl["rlp"] = B.elems * ms.indices().as_vec3_double()
refl["imageset_id"] = flex.int(len(refl))
refl["xyzobs.mm.value"] = flex.vec3_double(len(refl))
non_primitive_basis.correct(expts, refl, assign_indices.AssignIndicesGlobal())
cs_corrected = expts.crystals()[0].get_crystal_symmetry()
assert cs_corrected.change_of_basis_op_to_primitive_setting().is_identity_op()
assert (
cs.change_of_basis_op_to_primitive_setting().apply(ms.indices())
== refl["miller_index"]
)
def assemble_symops(self):
t_den = self.sg_low.t_den()
r_den = self.sg_low.r_den()
# loop over all symops
for item, symop in enumerate(self.symops):
tmp_symops = []
tmp_indices = []
# multiply in the symop in the space group
check_sg = sgtbx.space_group(self.sg_low)
check_sg.expand_smx(symop.new_denominators(r_den, t_den))
# Check if this SG is already in the list
assert check_sg != self.sg_low
if check_sg not in self.sg_groups:
# add sg to list
self.sg_groups.append(check_sg)
tmp_symops.append(symop)
tmp_indices.append(item)
# check if the other symops generate the same sg please
for check_item, check_op in enumerate(self.symops):
if check_sg.contains(check_op.new_denominators(r_den,t_den)):
# add symop to list if it is not in there yet
if check_op not in tmp_symops:
tmp_symops.append(check_op)
# add index to list
if check_item not in tmp_indices:
tmp_indices.append(check_item)
self.grouped_symops.append(tmp_symops)
self.grouped_index.append(tmp_indices)
def compare_hall_symops_with_sgtbx(self, hall, existing_group=True):
cctbx_sg = sgtbx.space_group(hall)
cctbx_triplets = set(m.as_xyz() for m in cctbx_sg.all_ops(mod=1))
gemmi_gops = gemmi.symops_from_hall(hall)
self.assertEqual(len(gemmi_gops.sym_ops), cctbx_sg.order_p())
self.assertEqual(len(gemmi_gops.cen_ops), cctbx_sg.n_ltr())
self.assertEqual(len(gemmi_gops), cctbx_sg.order_z())
self.assertEqual(gemmi_gops.is_centric(), cctbx_sg.is_centric())
ctr = gemmi_gops.find_centering()
self.assertEqual(ctr, cctbx_sg.conventional_centring_type_symbol())
gemmi_triplets = set(m.triplet() for m in gemmi_gops)
self.assertEqual(cctbx_triplets, gemmi_triplets)
gemmi_sg = gemmi.find_spacegroup_by_ops(gemmi_gops)
if existing_group:
self.assertEqual(gemmi_sg.point_group_hm(),
cctbx_sg.point_group_type())
self.assertEqual(gemmi_sg.crystal_system_str(),
cctbx_sg.crystal_system().lower())
self.assertEqual(gemmi_sg.is_sohncke(), cctbx_sg.is_chiral())
self.assertEqual(gemmi_sg.is_enantiomorphic(),
cctbx_sg.type().is_enantiomorphic())
self.assertEqual(gemmi_sg.is_symmorphic(),
cctbx_sg.type().is_symmorphic())
self.assertEqual(gemmi_sg.centring_type(), ctr)
else:
self.assertIsNone(gemmi_sg)
def reindex_old(self):
self.set_executable(os.path.join(os.environ.get('CBIN', ''),
'reindex'))
self.check_hklin()
self.check_hklout()
if not self._spacegroup and not self._operator:
raise RuntimeError, 'reindex requires spacegroup or operator'
self.start()
# look up the space group number to cope with complex symbols
# that old fashioned CCP4 reindex does not understand...
from cctbx.sgtbx import space_group, space_group_symbols
sg_t = space_group(space_group_symbols(str(self._spacegroup))).type()
if self._operator:
self.input('reindex %s' % str(self._operator))
if self._spacegroup:
self.input('symmetry %d' % sg_t.number())
self.close_wait()
# check for errors
try:
self.check_for_errors()
except RuntimeError, e:
try:
os.remove(self.get_hklout())
except:
pass
raise e
def reindex_experiments(experiments, cb_op, space_group=None):
reindexed_experiments = copy.deepcopy(experiments)
for crystal in reindexed_experiments.crystals():
cryst_reindexed = copy.deepcopy(crystal)
if space_group is not None:
# See also https://github.com/cctbx/cctbx_project/issues/424
cryst_reindexed.set_space_group(sgtbx.space_group("P 1"))
cryst_reindexed = cryst_reindexed.change_basis(cb_op)
cryst_reindexed.set_space_group(space_group)
S = parameter_reduction.symmetrize_reduce_enlarge(
cryst_reindexed.get_space_group()
)
S.set_orientation(cryst_reindexed.get_B())
S.symmetrize()
# Cache the scan-varying A matrices if applicable as these get lost
# when we call crystal.set_B()
A_varying = [
cryst_reindexed.get_A_at_scan_point(i)
for i in range(cryst_reindexed.num_scan_points)
]
# Update the symmetrized B matrix
cryst_reindexed.set_B(S.orientation.reciprocal_matrix())
# Reapply the scan-varying A matrices
cryst_reindexed.set_A_at_scan_points(A_varying)
else:
cryst_reindexed = cryst_reindexed.change_basis(cb_op)
crystal.update(cryst_reindexed)
return reindexed_experiments
def test_symmetry_handler_c2_i2(crystal_symmetry):
cs_ref = crystal_symmetry.as_reference_setting()
cs_ref = cs_ref.change_basis(
cs_ref.change_of_basis_op_to_best_cell(best_monoclinic_beta=False)
)
cs_best = cs_ref.best_cell()
# best -> ref is different to cs_ref above
cs_best_ref = cs_best.as_reference_setting()
assert not cs_ref.is_similar_symmetry(cs_best_ref)
B = scitbx.matrix.sqr(
crystal_symmetry.unit_cell().fractionalization_matrix()
).transpose()
cryst = Crystal(B, sgtbx.space_group())
for cs in (crystal_symmetry, cs_ref, cs_best):
print(cs)
handler = symmetry.SymmetryHandler(space_group=cs.space_group())
new_cryst, cb_op = handler.apply_symmetry(cryst)
assert (
new_cryst.change_basis(cb_op).get_crystal_symmetry().is_similar_symmetry(cs)
)
for cs in (crystal_symmetry, cs_ref, cs_best, cs_best_ref):
print(cs)
handler = symmetry.SymmetryHandler(
unit_cell=cs.unit_cell(), space_group=cs.space_group()
)
new_cryst, cb_op = handler.apply_symmetry(cryst)
assert (
new_cryst.change_basis(cb_op).get_crystal_symmetry().is_similar_symmetry(cs)
)
def exercise_generator_set():
sgi = sgtbx.space_group_info('P1')
sg_generator_set = sgtbx.any_generator_set(sgi.group())
assert sg_generator_set.non_primitive_generators == ()
sgi = sgtbx.space_group_info('P21')
sg_generator_set = sgtbx.any_generator_set(sgi.group())
assert (list(map(
str, sg_generator_set.non_primitive_generators)) == ['-x,y+1/2,-z'])
sgi = sgtbx.space_group_info('Pmmm')
sg_generator_set = sgtbx.any_generator_set(sgi.group())
assert (list(map(str, sg_generator_set.non_primitive_generators)) == [
'-x,-y,-z', 'x,-y,-z', '-x,y,-z'
])
for i in range(1, 231):
sgi = sgtbx.space_group_info(number=i)
sg = sgi.group()
sg_gen = sgtbx.any_generator_set(sg)
if sg.z2p_op().is_identity_op():
assert sg_gen.non_primitive_generators == sg_gen.primitive_generators
for i in range(1, 231):
sgi = sgtbx.space_group_info(number=i)
sg = sgi.group()
sg_gen = sgtbx.any_generator_set(sg)
sg1 = sgtbx.space_group("P1")
for op in sg_gen.non_primitive_generators:
sg1.expand_smx(op)
for t in sg.ltr():
sg1.expand_ltr(t)
assert sg1.type().number() == sg.type().number()
def test_table(self):
for sg in gemmi.spacegroup_table():
if sg.ccp4 != 0:
self.assertEqual(sg.ccp4 % 1000, sg.number)
if sg.operations().is_centric():
self.assertEqual(sg.laue_str(), sg.point_group_hm())
else:
self.assertNotEqual(sg.laue_str(), sg.point_group_hm())
if sgtbx:
hall = sg.hall.encode()
cctbx_sg = sgtbx.space_group(hall)
cctbx_info = sgtbx.space_group_info(group=cctbx_sg)
self.assertEqual(sg.is_reference_setting(),
cctbx_info.is_reference_setting())
#to_ref = cctbx_info.change_of_basis_op_to_reference_setting()
#from_ref = '%s' % cob_to_ref.inverse().c()
c2p_sg = gemmi.Op(cctbx_sg.z2p_op().c().inverse().as_xyz())
self.assertEqual(sg.centred_to_primitive(), c2p_sg)
ops = gemmi.get_spacegroup_reference_setting(sg.number).operations()
ops.change_basis_forward(sg.basisop)
self.assertEqual(ops, sg.operations())
itb = gemmi.spacegroup_table_itb()
if sgtbx:
for s in sgtbx.space_group_symbol_iterator():
self.assertEqual(s.hall().strip(), next(itb).hall)
with self.assertRaises(StopIteration):
next(itb)
def map_sites_to_asu(spacegroup, pdb_in, pdb_out, invert=False):
'''Map sites to asu of input spacegroup (as sites from shelxd claim
P1 in CRYST1 record) inverting if necessary. N.B. if inverting sites
also need to invert spacegroup.'''
from cctbx.crystal import symmetry, direct_space_asu
from iotbx.pdb import hierarchy
from scitbx.array_family import flex
sg = space_group(space_group_symbols(spacegroup).hall())
coords = hierarchy.input(file_name=pdb_in)
cs = coords.input.crystal_symmetry()
uc = cs.unit_cell()
cs2 = symmetry(unit_cell=uc, space_group=sg)
xs = coords.xray_structure_simple().customized_copy(crystal_symmetry=cs2)
if invert:
xs = xs.change_hand()
am = xs.crystal_symmetry().asu_mappings(0.0)
xyz = xs.sites_cart()
am.process_sites_cart(xyz)
xyz = flex.vec3_double()
for m in am.mappings():
xyz.append(m[0].mapped_site())
xs.set_sites_cart(xyz)
open(pdb_out, 'w').write(xs.as_pdb_file())
return
def modify_ins_text(_ins_text, _spacegroup, _nsites, _rlimit):
'''Update the text in a SHELXD .ins file to handle the correct number
of sites and spacegroup symmetry operations.'''
new_text = []
symm = [
op.as_xyz().upper()
for op in space_group(space_group_symbols(_spacegroup).hall()).smx()
]
for record in _ins_text:
if 'SYMM' in record:
if not symm:
continue
for op in symm:
if op == 'X,Y,Z':
continue
new_text.append(('SYMM %s' % op))
symm = None
elif 'FIND' in record:
new_text.append(('FIND %d' % _nsites))
elif 'SHEL' in record:
new_text.append(('SHEL 999 %.1f' % _rlimit))
else:
new_text.append(record.strip())
return new_text
def __init__(self, file_name, header_only=False):
self.file_name = os.path.normpath(file_name)
f = open(file_name)
line = f.readline()
assert line[5] == " "
n_sym_ops_from_file = int(line[:5].strip())
assert n_sym_ops_from_file > 0
self.space_group_symbol = line[6:].strip()
self.space_group_from_ops = sgtbx.space_group()
for i in range(n_sym_ops_from_file):
line = f.readline().rstrip()
assert len(line) == 27
r = sgtbx.rot_mx([int(line[j*3:(j+1)*3]) for j in range(9)], 1)
line = f.readline().rstrip()
assert len(line) == 9
t = sgtbx.tr_vec([int(line[j*3:(j+1)*3]) for j in range(3)], 12)
self.space_group_from_ops.expand_smx(sgtbx.rt_mx(r, t))
f.close()
if (header_only):
self.original_indices = None
return
all_arrays = scalepack_ext.no_merge_original_index_arrays(
file_name, n_sym_ops_from_file*2+1)
self.original_indices = all_arrays.original_indices()
self.unique_indices = all_arrays.unique_indices()
self.batch_numbers = all_arrays.batch_numbers()
self.centric_tags = all_arrays.centric_tags()
self.spindle_flags = all_arrays.spindle_flags()
self.asymmetric_unit_indices = all_arrays.asymmetric_unit_indices()
self.i_obs = all_arrays.i_obs()
self.sigmas = all_arrays.sigmas()
def cosym(self):
logger.debug("Running cosym analysis")
cosym = DialsCosym()
auto_logfiler(cosym)
experiments_filename = self._data_manager.export_experiments("tmp.expt")
reflections_filename = self._data_manager.export_reflections("tmp.refl")
cosym.add_experiments_json(experiments_filename)
cosym.add_reflections_file(reflections_filename)
if self._params.symmetry.space_group is not None:
cosym.set_space_group(self._params.symmetry.space_group.group())
cosym.run()
self._cosym_analysis = cosym.get_cosym_analysis()
self._experiments_filename = cosym.get_reindexed_experiments()
self._reflections_filename = cosym.get_reindexed_reflections()
self._data_manager.experiments = load.experiment_list(
self._experiments_filename, check_format=False
)
self._data_manager.reflections = flex.reflection_table.from_file(
self._reflections_filename
)
if self._params.symmetry.space_group is None:
best_solution = cosym.get_best_solution()
best_space_group = sgtbx.space_group(
str(best_solution["patterson_group"])
).build_derived_acentric_group()
self._params.symmetry.space_group = best_space_group.info()
logger.info(
"Space group determined by dials.cosym: %s" % best_space_group.info()
)
return
def run(server_info, inp, status):
print "<pre>"
symbols_inp = None
lookup_symbol = inp.sgsymbol
if (lookup_symbol == ""): lookup_symbol = "P 1"
if (inp.convention == "Hall"):
hall_symbol = lookup_symbol
else:
symbols_inp = sgtbx.space_group_symbols(lookup_symbol, inp.convention)
hall_symbol = symbols_inp.hall()
if (symbols_inp.number() == 0):
symbols_inp = None
inp.convention = "Hall"
else:
print "Result of symbol lookup:"
show_symbols(symbols_inp)
print
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError, e:
print "-->" + ps.string() + "<--"
print ("-" * (ps.where() + 3)) + "^"
raise
def generate_reflections(self):
# Build a mock scan for a 3 degree sweep
from dxtbx.model.scan import scan_factory
sf = scan_factory()
self.scan = sf.make_scan(image_range = (1,1),
exposure_times = 0.1,
oscillation = (0, 3.0),
epochs = range(1),
deg = True)
sweep_range = self.scan.get_oscillation_range(deg=False)
# Create a scans ExperimentList, only for generating reflections
experiments = ExperimentList()
experiments.append(Experiment(
beam=self.beam, detector=self.detector, goniometer=self.gonio, scan=self.scan,
crystal=self.crystal, imageset=None))
# Create a ScansRayPredictor
ray_predictor = ScansRayPredictor(experiments, sweep_range)
# Generate rays - only to work out which hkls are predicted
resolution = 2.0
index_generator = IndexGenerator(self.crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution)
indices = index_generator.to_array()
rays = ray_predictor.predict(indices)
# Make a standard reflection_table and copy in the ray data
self.reflections = flex.reflection_table.empty_standard(len(rays))
self.reflections.update(rays)
return
def ref_gen_static(experiments):
"""Generate some reflections using the static predictor"""
beam = experiments[0].beam
crystal = experiments[0].crystal
detector = experiments[0].detector
scan = experiments[0].scan
# All indices to the detector max resolution
dmin = detector.get_max_resolution(beam.get_s0())
index_generator = IndexGenerator(
crystal.get_unit_cell(), space_group(space_group_symbols(1).hall()).type(), dmin
)
indices = index_generator.to_array()
# Predict rays within the sequence range
sequence_range = scan.get_oscillation_range(deg=False)
ray_predictor = ScansRayPredictor(experiments, sequence_range)
refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(detector, refs)
refs = refs.select(intersects)
# Make a reflection predictor and re-predict for these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
refs["id"] = flex.int(len(refs), 0)
refs = ref_predictor(refs)
return refs
def mock_cif():
"""Mock a cif file for testing loading data from a cif."""
cif = Mock()
cif.intensities = flex.double([1.0, 1.0])
cif.indices = flex.miller_index([(1, 0, 0), (0, 0, 1)])
cif.space_group = space_group("C 2y")
return cif
def remove_lattice_translations(g):
result = sgtbx.space_group(hall_symbol="P1",
t_den=subgroup.t_den())
for i_inv in range(g.f_inv()):
for i_smx in range(g.n_smx()):
result.expand_smx(g(0, i_inv, i_smx))
return result
def __init__(self, with_special_position_pivot):
self.with_special_position_pivot = with_special_position_pivot
self.uc = uctbx.unit_cell((1, 2, 3))
self.sg = sgtbx.space_group("P 6")
self.c0 = xray.scatterer("C0", site=(1e-5, 0., 0.1))
self.site_symm = sgtbx.site_symmetry(self.uc, self.sg, self.c0.site)
self.c0.flags.set_grad_site(True)
self.c1 = xray.scatterer("C1", site=(0.09, 0.11, 0.))
self.c1.flags.set_grad_site(True)
self.h = xray.scatterer("H")
self.reparam = constraints.ext.reparametrisation(self.uc)
if with_special_position_pivot:
x0 = self.reparam.add(constraints.special_position_site_parameter,
self.site_symm, self.c0)
else:
x0 = self.reparam.add(constraints.independent_site_parameter,
self.c0)
x1 = self.reparam.add(constraints.independent_site_parameter, self.c1)
l = self.reparam.add(constraints.independent_scalar_parameter,
self.bond_length,
variable=False)
x_h = self.reparam.add(constraints.terminal_linear_ch_site,
pivot=x0,
pivot_neighbour=x1,
length=l,
hydrogen=self.h)
self.reparam.finalise()
self.x0, self.x1, self.x_h, self.l = [
x.index for x in (x0, x1, x_h, l)
]
if self.with_special_position_pivot:
self.y0 = x0.independent_params.index
def exercise_expand():
sg = sgtbx.space_group("P 41 (1,-1,0)")
h = flex.miller_index(((3,1,-2), (1,-2,0)))
assert tuple(sg.is_centric(h)) == (0, 1)
p1 = miller.expand_to_p1_iselection(
space_group=sg, anomalous_flag=False, indices=h, build_iselection=False)
p1_i0 = ((-3,-1,2), (-1, 3,2),(3,1,2),(1,-3,2),(1,-2, 0),(2,1,0))
assert tuple(p1.indices) == p1_i0
assert p1.iselection.size() == 0
p1 = miller.expand_to_p1_iselection(
space_group=sg, anomalous_flag=True, indices=h, build_iselection=False)
assert tuple(p1.indices) \
== ((3,1,-2), (1,-3,-2), (-3,-1,-2), (-1,3,-2),
(1,-2,0), (-2,-1,0), (-1,2,0), (2,1,0))
p1 = miller.expand_to_p1_iselection(
space_group=sg, anomalous_flag=False, indices=h, build_iselection=True)
assert tuple(p1.indices) == p1_i0
assert tuple(p1.iselection) == (0,0,0,0,1,1)
a = flex.double((1,2))
p = flex.double((10,90))
p1 = miller.expand_to_p1_phases(
space_group=sg, anomalous_flag=False, indices=h, data=p, deg=True)
assert approx_equal(tuple(p1.data), (-10,110,110,-10, 90,30))
p1 = miller.expand_to_p1_phases(
space_group=sg, anomalous_flag=True, indices=h, data=p, deg=True)
assert approx_equal(tuple(p1.data), (10,-110,-110,10, 90,-30,-90,30))
p = flex.double([x * math.pi/180 for x in p])
v = [x * math.pi/180 for x in p1.data]
p1 = miller.expand_to_p1_phases(
space_group=sg, anomalous_flag=True, indices=h, data=p, deg=False)
assert approx_equal(tuple(p1.data), v)
f = flex.polar(a, p)
p1 = miller.expand_to_p1_complex(
space_group=sg, anomalous_flag=True, indices=h, data=f)
assert approx_equal(tuple(flex.abs(p1.data)), (1,1,1,1,2,2,2,2))
assert approx_equal(tuple(flex.arg(p1.data)), v)
hl = flex.hendrickson_lattman([(1,2,3,4), (5,6,7,8)])
p1 = miller.expand_to_p1_hendrickson_lattman(
space_group=sg, anomalous_flag=True, indices=h, data=hl)
assert approx_equal(p1.data, [
[1,2,3,4],
[1.232051,-1.866025,-4.964102,0.5980762],
[1.232051,-1.866025,-4.964102,0.5980762],
[1,2,3,4],
[5,6,7,8],
[2.696152,-7.330127,-10.4282,2.062178],
[-5,-6,7,8],
[7.696152,-1.330127,3.428203,-10.06218]])
b = flex.bool([True,False])
p1 = miller.expand_to_p1_iselection(
space_group=sg, anomalous_flag=True, indices=h, build_iselection=True)
assert b.select(p1.iselection).all_eq(
flex.bool([True, True, True, True, False, False, False, False]))
i = flex.int([13,17])
p1 = miller.expand_to_p1_iselection(
space_group=sg, anomalous_flag=True, indices=h, build_iselection=True)
assert i.select(p1.iselection).all_eq(flex.int([13,13,13,13,17,17,17,17]))
#
assert approx_equal(miller.statistical_mean(sg, False, h, a), 4/3.)
assert approx_equal(miller.statistical_mean(sg, True, h, a), 3/2.)
def run():
for space_group_symbol in ("P-1",
"P2/m",
"C2/m",
"Pmmm",
"Cmmm",
"Fmmm",
"Immm",
"P4/mmm",
"I4/mmm",
"R-3m",
"P6/mmm",
"Pm-3m",
"Im-3m",
"Fm-3m"):
centric_info = sgtbx.space_group_info(space_group_symbol)
non_centric = sgtbx.space_group()
for i_ltr in xrange(centric_info.group().n_ltr()):
for i_smx in xrange(centric_info.group().n_smx()):
s = centric_info.group()(i_ltr,0,i_smx)
non_centric.expand_smx(s)
assert non_centric.f_inv() == 1
assert non_centric.order_z() * 2 == centric_info.group().order_z()
non_centric_info = sgtbx.space_group_info(group=non_centric)
centric_stats = subgroup_stats(centric_info)
non_centric_stats = subgroup_stats(non_centric_info)
assert len(centric_stats.subgroups) >= 2*len(non_centric_stats.subgroups)
assert centric_stats.n_non_centric >= non_centric_stats.n_non_centric
assert centric_stats.n_chiral == non_centric_stats.n_chiral
assert non_centric_stats.n_non_centric == len(non_centric_stats.subgroups)
assert non_centric_stats.n_non_centric == non_centric_stats.n_chiral
print "OK"
def subgroups_table(d):
header = (
"Patterson group",
"",
"Likelihood",
"NetZcc",
"Zcc+",
"Zcc-",
"delta",
"Reindex operator",
)
rows = [header]
for score in d["subgroup_scores"]:
rows.append((
str(
sgtbx.space_group(
hall_symbol=str(score["patterson_group"])).info()),
score["stars"],
f"{score['likelihood']:.3f}",
f"{score['z_cc_net']: .2f}",
f"{score['z_cc_for']: .2f}",
f"{score['z_cc_against']: .2f}",
f"{score['max_angular_difference']:.1f}",
str(sgtbx.change_of_basis_op(str(score["cb_op"]))),
))
return rows
def exercise_generator_set():
sgi = sgtbx.space_group_info('P1')
sg_generator_set = sgtbx.any_generator_set(sgi.group())
assert sg_generator_set.non_primitive_generators == ()
sgi = sgtbx.space_group_info('P21')
sg_generator_set = sgtbx.any_generator_set(sgi.group())
assert (map(str, sg_generator_set.non_primitive_generators)
== ['-x,y+1/2,-z'])
sgi = sgtbx.space_group_info('Pmmm')
sg_generator_set = sgtbx.any_generator_set(sgi.group())
assert (map(str, sg_generator_set.non_primitive_generators)
== ['-x,-y,-z', 'x,-y,-z', '-x,y,-z'])
for i in xrange(1, 231):
sgi = sgtbx.space_group_info(number=i)
sg = sgi.group()
sg_gen = sgtbx.any_generator_set(sg)
if sg.z2p_op().is_identity_op():
assert sg_gen.non_primitive_generators == sg_gen.primitive_generators
for i in xrange(1, 231):
sgi = sgtbx.space_group_info(number=i)
sg = sgi.group()
sg_gen = sgtbx.any_generator_set(sg)
sg1 = sgtbx.space_group("P1")
for op in sg_gen.non_primitive_generators:
sg1.expand_smx(op)
for t in sg.ltr():
sg1.expand_ltr(t)
assert sg1.type().number() == sg.type().number()
def ref_gen_static(experiments):
"""Generate some reflections using the static predictor"""
beam = experiments[0].beam
crystal = experiments[0].crystal
goniometer = experiments[0].goniometer
detector = experiments[0].detector
scan = experiments[0].scan
# All indices to the detector max resolution
dmin = detector.get_max_resolution(beam.get_s0())
index_generator = IndexGenerator(crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(), dmin)
indices = index_generator.to_array()
# Predict rays within the sweep range
sweep_range = scan.get_oscillation_range(deg=False)
ray_predictor = ScansRayPredictor(experiments, sweep_range)
refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(detector, refs)
refs = refs.select(intersects)
# Make a reflection predictor and re-predict for these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ExperimentsPredictor(experiments)
refs['id'] = flex.int(len(refs), 0)
refs = ref_predictor(refs)
return refs
def set_correct_lattice(self, lattice):
"""In a rerunning situation, set the correct lattice, which will
assert a correct lauegroup based on the previous run of the
program..."""
if self._lattice_to_laue == {}:
raise RuntimeError("no lattice to lauegroup mapping")
if lattice not in self._lattice_to_laue:
raise RuntimeError("lattice %s not possible" % lattice)
self._input_laue_group = self._lattice_to_laue[lattice]
with open(self._json, "rb") as f:
d = json.load(f)
for soln in d["subgroup_scores"]:
patterson_group = sgtbx.space_group(
str(soln["patterson_group"]))
if PhilIndex.params.xia2.settings.symmetry.chirality in (
None,
"chiral",
):
patterson_group = patterson_group.build_derived_acentric_group(
)
if patterson_group == self._input_laue_group:
# set this as correct solution
self.set_best_solution(d, soln)
break
def run(server_info, inp, status):
print "<pre>"
symbols_inp = None
lookup_symbol = inp.sgsymbol
if (lookup_symbol == ""): lookup_symbol = "P 1"
if (inp.convention == "Hall"):
hall_symbol = lookup_symbol
else:
symbols_inp = sgtbx.space_group_symbols(lookup_symbol, inp.convention)
hall_symbol = symbols_inp.hall()
if (symbols_inp.number() == 0):
symbols_inp = None
inp.convention = "Hall"
else:
print "Result of symbol lookup:"
show_symbols(symbols_inp)
print
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError, e:
print "-->" + ps.string() + "<--"
print("-" * (ps.where() + 3)) + "^"
raise
def load_sfall(fname):
"""
special script for loading the structure factor file generated in main()
:param fname: file generated in the main method above..
:return: mil_ar, energies
mil_ar: dict of miller arrays (complex)
energies: array of xray energies in electron volts
such that mil_ar[0] is Fhkl at energy energies[0]
"""
f = h5py.File(fname, "r")
data = f["data"][()]
indices = f["indices"][()]
hall = f["hall_symbol"][()]
ucell_param = f["ucell_tuple"][()]
energies = f["energies"][()]
sg = sgtbx.space_group(hall)
Symm = crystal.symmetry(unit_cell=ucell_param, space_group=sg)
indices_flex = tuple(map(tuple, indices))
mil_idx = flex.miller_index(indices_flex)
mil_set = miller.set(crystal_symmetry=Symm,
indices=mil_idx,
anomalous_flag=True)
mil_ar = {} # load a dict of "sfall at each energy"
for i_chan, data_chan in enumerate(data):
data_flex = flex.complex_double(np.ascontiguousarray(data_chan))
mil_ar[i_chan] = miller.array(mil_set, data=data_flex)
return mil_ar, energies
def combine_symops_and_symbol(space_group_from_ops, space_group_symbol):
space_group_symbol = space_group_symbol.replace(" ", "").upper()
z = space_group_symbol[:1]
if ("PABCIFRH".find(z) < 0):
raise RuntimeError(
"Cannot determine lattice centring type given space group symbol"
" %s" % show_string(space_group_symbol))
if (z == "P"):
return sgtbx.space_group_info(group=space_group_from_ops)
if (z == "H"):
space_group_symbol = "R" + space_group_symbol[1:] + ":H"
z = "R"
elif (z == "R" and not space_group_symbol.endswith(":H")):
if (space_group_symbol.endswith(":R")):
z = None
else:
for s in space_group_from_ops:
r_info = s.r().info()
if (abs(r_info.type()) == 3):
if (r_info.ev() == (0, 0, 1)):
space_group_symbol = "R" + space_group_symbol[1:] + ":H"
break
elif (r_info.ev() == (1, 1, 1)):
space_group_symbol += ":R"
z = None
break
space_group_exp = sgtbx.space_group(space_group_from_ops)
if (z is not None):
try:
space_group_exp.expand_conventional_centring_type(z)
except RuntimeError:
space_group_exp = None
if (space_group_exp is not None):
try:
space_group_from_symbol = sgtbx.space_group_info(
symbol=space_group_symbol).group()
except RuntimeError:
space_group_from_symbol = None
if (space_group_exp is None or space_group_from_symbol is None
or space_group_exp != space_group_from_symbol):
if space_group_from_symbol:
warnings.warn(
"""
WARNING:
Symmetry operations in input file are for space group %(space_group_exp)s
However space group symbol is: %(space_group_symbol)s
This may be a format error in the Scalepack file!
Using %(space_group_symbol)s
""" % {
"space_group_exp": str(space_group_exp.info()),
"space_group_symbol": show_string(space_group_symbol),
},
UserWarning,
stacklevel=10)
space_group_exp = space_group_from_symbol
else:
raise RuntimeError(
"Symmetry operations in unmerged SCALEPACK file incompatible with"
" space group symbol %s" % show_string(space_group_symbol))
return sgtbx.space_group_info(group=space_group_exp)
def _export_experiments_reflections(self, experiments, reflections,
result):
from dxtbx.serialize import dump
from rstbx.symmetry.constraints import parameter_reduction
reindexed_experiments = copy.deepcopy(experiments)
reindexed_reflections = flex.reflection_table()
cb_op_inp_best = (result.best_solution.subgroup["cb_op_inp_best"] *
result.cb_op_inp_min)
best_subsym = result.best_solution.subgroup["best_subsym"]
for i, expt in enumerate(reindexed_experiments):
expt.crystal = expt.crystal.change_basis(result.cb_op_inp_min)
expt.crystal.set_space_group(sgtbx.space_group("P 1"))
expt.crystal = expt.crystal.change_basis(
result.best_solution.subgroup["cb_op_inp_best"])
expt.crystal.set_space_group(
best_subsym.space_group().build_derived_acentric_group())
S = parameter_reduction.symmetrize_reduce_enlarge(
expt.crystal.get_space_group())
S.set_orientation(expt.crystal.get_B())
S.symmetrize()
expt.crystal.set_B(S.orientation.reciprocal_matrix())
reindexed_refl = copy.deepcopy(reflections[i])
reindexed_refl["miller_index"] = cb_op_inp_best.apply(
reindexed_refl["miller_index"])
reindexed_reflections.extend(reindexed_refl)
logger.info("Saving reindexed experiments to %s" %
self._params.output.experiments)
dump.experiment_list(reindexed_experiments,
self._params.output.experiments)
logger.info(
"Saving %s reindexed reflections to %s" %
(len(reindexed_reflections), self._params.output.reflections))
reindexed_reflections.as_file(self._params.output.reflections)
def combine_symops_and_symbol(space_group_from_ops, space_group_symbol):
space_group_symbol = space_group_symbol.replace(" ","").upper()
z = space_group_symbol[:1]
if ("PABCIFRH".find(z) < 0):
raise RuntimeError(
"Cannot determine lattice centring type given space group symbol"
" %s" % show_string(space_group_symbol))
if (z == "P"):
return sgtbx.space_group_info(group=space_group_from_ops)
if (z == "H"):
space_group_symbol = "R" + space_group_symbol[1:] + ":H"
z = "R"
elif (z == "R" and not space_group_symbol.endswith(":H")):
if (space_group_symbol.endswith(":R")):
z = None
else:
for s in space_group_from_ops:
r_info = s.r().info()
if (abs(r_info.type()) == 3):
if (r_info.ev() == (0,0,1)):
space_group_symbol = "R" + space_group_symbol[1:] + ":H"
break
elif (r_info.ev() == (1,1,1)):
space_group_symbol += ":R"
z = None
break
space_group_exp = sgtbx.space_group(space_group_from_ops)
if (z is not None):
try:
space_group_exp.expand_conventional_centring_type(z)
except RuntimeError:
space_group_exp = None
if (space_group_exp is not None):
try:
space_group_from_symbol = sgtbx.space_group_info(
symbol=space_group_symbol).group()
except RuntimeError:
space_group_from_symbol = None
if ( space_group_exp is None
or space_group_from_symbol is None
or space_group_exp != space_group_from_symbol):
if space_group_from_symbol:
warnings.warn("""
WARNING:
Symmetry operations in input file are for space group %(space_group_exp)s
However space group symbol is: %(space_group_symbol)s
This may be a format error in the Scalepack file!
Using %(space_group_symbol)s
""" % {"space_group_exp" : str(space_group_exp.info()),
"space_group_symbol" : show_string(space_group_symbol), },
UserWarning, stacklevel=10)
space_group_exp = space_group_from_symbol
else:
raise RuntimeError(
"Symmetry operations in unmerged SCALEPACK file incompatible with"
" space group symbol %s"
% show_string(space_group_symbol))
return sgtbx.space_group_info(group=space_group_exp)
def run(args):
if (len(args) != 2):
raise Usage("""\
cctbx.python space_subgroups.py max_index space_group_symbol
Example: cctbx.python space_subgroups.py 2 P41212""")
#
max_index = int(args[0])
print "max_index:", max_index
assert max_index >= 1
print
space_group_t_den = 144
sginfo = sgtbx.space_group_info(
symbol=args[1], space_group_t_den=space_group_t_den)
sginfo.show_summary()
print
cb_op_to_p = sginfo.change_of_basis_op_to_primitive_setting()
sginfo_p = sginfo.change_basis(cb_op=cb_op_to_p)
if (sginfo_p.group() != sginfo.group()):
print "Primitive setting:"
sginfo_p.show_summary()
print
#
all_subgroups = dict_with_default_0()
sg_p = sginfo_p.group()
sg_p_a = sg_p.build_derived_acentric_group()
if (sg_p.is_centric()):
inv_mx = sg_p(0, 1, 0).t()
else:
inv_mx = None
for symx1 in sg_p_a:
subgr1 = sgtbx.space_group(hall_symbol="P1", t_den=space_group_t_den)
subgr1.expand_smx(symx1)
for symx2 in sg_p_a:
subgr2 = sgtbx.space_group(subgr1)
subgr2.expand_smx(symx2)
loop_over_super_cells(
max_index=max_index, all_subgroups=all_subgroups, subgroup=subgr2)
if (inv_mx is not None):
subgr3 = sgtbx.space_group(subgr2)
subgr3.expand_inv(inv_mx)
loop_over_super_cells(
max_index=max_index, all_subgroups=all_subgroups, subgroup=subgr3)
#
show_sorted_by_counts(label_count_pairs=all_subgroups.items())
def main(filenames, map_file, npoints=192, max_resolution=6, reverse_phi=False):
rec_range = 1 / max_resolution
image = ImageFactory(filenames[0])
panel = image.get_detector()[0]
beam = image.get_beam()
s0 = beam.get_s0()
pixel_size = panel.get_pixel_size()
xlim, ylim = image.get_raw_data().all()
xy = recviewer.get_target_pixels(panel, s0, xlim, ylim, max_resolution)
s1 = panel.get_lab_coord(xy * pixel_size[0]) # FIXME: assumed square pixel
s1 = s1 / s1.norms() * (1 / beam.get_wavelength()) # / is not supported...
S = s1 - s0
grid = flex.double(flex.grid(npoints, npoints, npoints), 0)
cnts = flex.int(flex.grid(npoints, npoints, npoints), 0)
for filename in filenames:
print "Processing image", filename
try:
fill_voxels(ImageFactory(filename), grid, cnts, S, xy, reverse_phi, rec_range)
except:
print " Failed to process. Skipped this."
recviewer.normalize_voxels(grid, cnts)
uc = uctbx.unit_cell((npoints, npoints, npoints, 90, 90, 90))
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"),
(0, 0, 0), grid.all(), grid,
flex.std_string(["cctbx.miller.fft_map"]))
return
from scitbx import fftpack
fft = fftpack.complex_to_complex_3d(grid.all())
grid_complex = flex.complex_double(
reals=flex.pow2(grid),
imags=flex.double(grid.size(), 0))
grid_transformed = flex.abs(fft.backward(grid_complex))
print flex.max(grid_transformed), flex.min(grid_transformed), grid_transformed.all()
ccp4_map.write_ccp4_map(map_file, uc, sgtbx.space_group("P1"),
(0, 0, 0), grid.all(), grid_transformed,
flex.std_string(["cctbx.miller.fft_map"]))
def is_centred(space_group_number):
'''Test if space group # corresponds to a centred space group.'''
sg_hall = sgtbx.space_group_symbols(space_group_number).hall()
sg = sgtbx.space_group(sg_hall)
if (sg.n_ltr() - 1):
return True
return False
def save_CIF(self, fpath):
"""Saving model into cif file"""
cif_object = model.cif()
cif_block = model.block()
cif_object["BEA"] = cif_block
space_group = sgtbx.space_group(self.iucr_structure.space_group())
#unit cell:
cell_pars = self.iucr_structure.unit_cell().parameters()
cif_block["_cell_length_a"] = cell_pars[0]
cif_block["_cell_length_b"] = cell_pars[1]
cif_block["_cell_length_c"] = cell_pars[2]
cif_block["_cell_angle_alpha"] = cell_pars[3]
cif_block["_cell_angle_beta"] = cell_pars[4]
cif_block["_cell_angle_gamma"] = cell_pars[5]
space_group_type = self.iucr_structure.space_group_info().type()
cif_block["_symmetry_cell_setting"] = \
space_group.crystal_system().lower()
cif_block["_symmetry_Int_Tables_number"] = space_group_type.number()
cif_block["_symmetry_space_group_name_H-M"] = \
space_group_type.lookup_symbol()
#cif_block["_space_group.name_Hall"] = space_group_type.hall_symbol()
symop_loop = model.loop(
header = ("_symmetry_equiv_pos_as_xyz",)
)
for symop_id, symop in enumerate(space_group):
symop_loop.add_row(("'{}'".format(symop.as_xyz()),))
struct_loop = model.loop(
header = ("_atom_site_label",
"_atom_site_type_symbol",
"_atom_site_fract_x",
"_atom_site_fract_y",
"_atom_site_fract_z",
"_atom_site_U_iso_or_equiv"))
for scatterer in self.iucr_structure.scatterers():
struct_loop.add_row(
(scatterer.label,
scatterer.scattering_type,
scatterer.site[0],
scatterer.site[1],
scatterer.site[2],
scatterer.u_iso))
cif_block.add_loop(symop_loop)
cif_block.add_loop(struct_loop)
with open(fpath,'w') as fobj:
fobj.write(cif_object.__str__())
def browse(self):
for self.symbol in sgtbx.space_group_symbol_iterator():
self.sg = sgtbx.space_group(self.symbol.hall()).make_tidy()
self.z2p_op = self.sg.z2p_op()
self.sg_p = self.sg.change_basis(self.z2p_op)
self.on_new_space_group()
for self.op in self.sg_p:
self.rot_info = self.op.r().info()
self.tr_info = sgtbx.translation_part_info(self.op)
if self.tr_info.origin_shift().is_zero(): continue
self.on_new_symmetry()
def symopSymList(sgNr):
"""For a S.G. Returns list of symmetry operations in symbolic form"""
sg_hall = sgtbx.space_group_symbols(sgNr).hall()
sg = sgtbx.space_group(sg_hall)
print "\nGENERATING LIST OF SYMMETRY OPERATIONS FOR S.G. %d..." % (sgNr)
symop_list = []
sg_order = sg.order_z()
for i in range(0, sg_order):
symop_list.append(sg(i).as_xyz())
print "A LIST OF %d SYMMETRY OPERATIONS WAS CREATED!\n" % (sg_order)
return symop_list