def exercise_monoclinic_cell_choices_core(space_group_number, verbose):
# transformation matrices for cell choices
# columns are basis vectors "new in terms of old"
# see Int. Tab. Vol. A, p. 22, Fig. 2.2.6.4.
b1 = (1, 0, 0,
0, 1, 0,
0, 0, 1)
b2 = (-1, 0, 1,
0, 1, 0,
-1, 0, 0)
b3 = (0, 0, -1,
0, 1, 0,
1, 0, -1)
flip = (0, 0, 1,
0, -1, 0,
1, 0, 0)
p3s = sgtbx.space_group("P 3*")
done = {}
ref = sgtbx.space_group_info(number=space_group_number)
ref_uhm = ref.type().universal_hermann_mauguin_symbol()
for i_fl,fl in enumerate([b1, flip]):
rfl = sgtbx.rot_mx(fl)
cfl = sgtbx.change_of_basis_op(sgtbx.rt_mx(rfl))
for i_rt,rt in enumerate(p3s):
rp3 = rt.r()
cp3 = sgtbx.change_of_basis_op(sgtbx.rt_mx(rp3))
for i_cs,cs in enumerate([b1,b2,b3]):
rcs = sgtbx.rot_mx(cs).inverse()
ccs = sgtbx.change_of_basis_op(sgtbx.rt_mx(rcs))
cb_all = cp3 * cfl * ccs
refcb = ref.change_basis(cb_all)
refcb2 = sgtbx.space_group_info(symbol=ref_uhm+"("+str(cb_all.c())+")")
assert refcb2.group() == refcb.group()
s = sgtbx.space_group_symbols(str(refcb))
q = s.qualifier()
hm = str(refcb)
if (0 or verbose): print hm, q, cb_all.c()
if (i_fl == 0):
assert q[0] == "bca"[i_rt]
if (len(q) == 2): assert q[1] == "123"[i_cs]
elif (q[0] == "-"):
assert q[1] == "bca"[i_rt]
if (len(q) == 3): assert q[2] == "123"[i_cs]
else:
assert q[0] == "bca"[i_rt]
if (len(q) == 2 and q[1] != "123"[i_cs]):
assert done[hm] == 1
done.setdefault(hm, 0)
done[hm] += 1
assert len(done) in [3, 9, 18]
assert done.values() == [18/len(done)]*len(done)
if (0 or verbose): print
return done
def run(args):
if "--full" in args:
to_do = range(1, 230 + 1)
elif "--special" in args:
to_do = sorted(special.keys())
else:
to_do = [75, 151]
for space_group_number in to_do:
sgi = sgtbx.space_group_info(number=space_group_number)
sgi.show_summary(prefix="")
sys.stdout.flush()
n_special = 0
for m in scitbx.math.unimodular_generator(range=1).all():
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(m, 1), 1)).new_denominators(12, 144)
cb_sgi = sgi.change_basis(cb_op=cb_op)
cb_op_ref = cb_sgi.change_of_basis_op_to_reference_setting()
ref_sgi = cb_sgi.change_basis(cb_op=cb_op_ref)
assert ref_sgi.group() == sgi.group()
c = cb_op_ref.c()
if c.r().is_unit_mx() and c.t().num() != (0, 0, 0):
n_special += 1
cb_ref_sgi = sgi.change_basis(cb_op=cb_op_ref)
print " cb_op=%s -> %s" % (str(cb_op.c()), cb_ref_sgi.type().universal_hermann_mauguin_symbol())
sys.stdout.flush()
# verify that c.t() is not an allowed origin shift
assert cb_ref_sgi.group() != sgi.group()
assert special.get(space_group_number, 0) == n_special
print format_cpu_times()
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 __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 run(args):
if ("--full" in args):
to_do = range(1, 230 + 1)
elif ("--special" in args):
to_do = sorted(special.keys())
else:
to_do = [75, 151]
for space_group_number in to_do:
sgi = sgtbx.space_group_info(number=space_group_number)
sgi.show_summary(prefix="")
sys.stdout.flush()
n_special = 0
for m in scitbx.math.unimodular_generator(range=1).all():
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(m,1), 1)) \
.new_denominators(12, 144)
cb_sgi = sgi.change_basis(cb_op=cb_op)
cb_op_ref = cb_sgi.change_of_basis_op_to_reference_setting()
ref_sgi = cb_sgi.change_basis(cb_op=cb_op_ref)
assert ref_sgi.group() == sgi.group()
c = cb_op_ref.c()
if (c.r().is_unit_mx() and c.t().num() != (0, 0, 0)):
n_special += 1
cb_ref_sgi = sgi.change_basis(cb_op=cb_op_ref)
print " cb_op=%s -> %s" % (str(cb_op.c()), cb_ref_sgi.type().
universal_hermann_mauguin_symbol())
sys.stdout.flush()
# verify that c.t() is not an allowed origin shift
assert cb_ref_sgi.group() != sgi.group()
assert special.get(space_group_number, 0) == n_special
print format_cpu_times()
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 algebraic(self):
op = self.operation()
# eliminate minus signs to make the expression look more like
# what people are used to see
r = op.r().num()
d = op.r().den()
signs = [None, None, None]
for j in xrange(3):
for i in xrange(3):
rij = r[i * 3 + j]
if (signs[i] is None and rij != 0):
if (rij < 0): signs[i] = -1
else: signs[i] = 1
m = list(sgtbx.rot_mx(d, d).num())
for i in xrange(3):
if (signs[i] == -1): m[i * 4] *= -1
return str(sgtbx.rt_mx(op.r().multiply(sgtbx.rot_mx(m, d)), op.t()))
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 generate_unimodular_cells(cell):
Amat = sqr(cell.orthogonalization_matrix()).transpose()
for m in unimodular_generator(range=1).all():
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(m))
orientation_similarity_cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
new_cell = cell.change_basis(orientation_similarity_cb_op)
yield new_cell,orientation_similarity_cb_op
def exercise_monoclinic_cell_choices_core(space_group_number, verbose):
# transformation matrices for cell choices
# columns are basis vectors "new in terms of old"
# see Int. Tab. Vol. A, p. 22, Fig. 2.2.6.4.
b1 = (1, 0, 0, 0, 1, 0, 0, 0, 1)
b2 = (-1, 0, 1, 0, 1, 0, -1, 0, 0)
b3 = (0, 0, -1, 0, 1, 0, 1, 0, -1)
flip = (0, 0, 1, 0, -1, 0, 1, 0, 0)
p3s = sgtbx.space_group("P 3*")
done = {}
ref = sgtbx.space_group_info(number=space_group_number)
ref_uhm = ref.type().universal_hermann_mauguin_symbol()
for i_fl, fl in enumerate([b1, flip]):
rfl = sgtbx.rot_mx(fl)
cfl = sgtbx.change_of_basis_op(sgtbx.rt_mx(rfl))
for i_rt, rt in enumerate(p3s):
rp3 = rt.r()
cp3 = sgtbx.change_of_basis_op(sgtbx.rt_mx(rp3))
for i_cs, cs in enumerate([b1, b2, b3]):
rcs = sgtbx.rot_mx(cs).inverse()
ccs = sgtbx.change_of_basis_op(sgtbx.rt_mx(rcs))
cb_all = cp3 * cfl * ccs
refcb = ref.change_basis(cb_all)
refcb2 = sgtbx.space_group_info(symbol=ref_uhm + "(" +
str(cb_all.c()) + ")")
assert refcb2.group() == refcb.group()
s = sgtbx.space_group_symbols(str(refcb))
q = s.qualifier()
hm = str(refcb)
if (0 or verbose): print(hm, q, cb_all.c())
if (i_fl == 0):
assert q[0] == "bca"[i_rt]
if (len(q) == 2): assert q[1] == "123"[i_cs]
elif (q[0] == "-"):
assert q[1] == "bca"[i_rt]
if (len(q) == 3): assert q[2] == "123"[i_cs]
else:
assert q[0] == "bca"[i_rt]
if (len(q) == 2 and q[1] != "123"[i_cs]):
assert done[hm] == 1
done.setdefault(hm, 0)
done[hm] += 1
assert len(done) in [3, 9, 18]
assert list(done.values()) == [18 / len(done)] * len(done)
if (0 or verbose): print()
return done
def algebraic(self):
op = self.operation()
# eliminate minus signs to make the expression look more like
# what people are used to see
r = op.r().num()
d = op.r().den()
signs = [None,None,None]
for j in xrange(3):
for i in xrange(3):
rij = r[i*3+j]
if (signs[i] is None and rij != 0):
if (rij < 0): signs[i] = -1
else: signs[i] = 1
m = list(sgtbx.rot_mx(d, d).num())
for i in xrange(3):
if (signs[i] == -1): m[i*4] *= -1
return str(sgtbx.rt_mx(op.r().multiply(sgtbx.rot_mx(m,d)), op.t()))
def generate_unimodular_cells(cell):
Amat = sqr(cell.orthogonalization_matrix()).transpose()
for m in unimodular_generator(range=1).all():
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(m))
orientation_similarity_cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
new_cell = cell.change_basis(orientation_similarity_cb_op)
yield new_cell,orientation_similarity_cb_op
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 __call__(self, params, options):
''' Import the integrate.hkl file. '''
from iotbx.xds import integrate_hkl
from dials.array_family import flex
from dials.util.command_line import Command
from cctbx import sgtbx
# Get the unit cell to calculate the resolution
uc = self._experiment.crystal.get_unit_cell()
# Read the INTEGRATE.HKL file
Command.start('Reading INTEGRATE.HKL')
handle = integrate_hkl.reader()
handle.read_file(self._integrate_hkl)
hkl = flex.miller_index(handle.hkl)
xyzcal = flex.vec3_double(handle.xyzcal)
xyzobs = flex.vec3_double(handle.xyzobs)
iobs = flex.double(handle.iobs)
sigma = flex.double(handle.sigma)
rlp = flex.double(handle.rlp)
peak = flex.double(handle.peak) * 0.01
Command.end('Read %d reflections from INTEGRATE.HKL file.' % len(hkl))
# Derive the reindex matrix
rdx = self.derive_reindex_matrix(handle)
print 'Reindex matrix:\n%d %d %d\n%d %d %d\n%d %d %d' % (rdx.elems)
# Reindex the reflections
Command.start('Reindexing reflections')
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(rdx.elems)))
hkl = cb_op.apply(hkl)
Command.end('Reindexed %d reflections' % len(hkl))
# Create the reflection list
Command.start('Creating reflection table')
table = flex.reflection_table()
table['id'] = flex.int(len(hkl), 0)
table['panel'] = flex.size_t(len(hkl), 0)
table['miller_index'] = hkl
table['xyzcal.px'] = xyzcal
table['xyzobs.px.value'] = xyzobs
table['intensity.cor.value'] = iobs
table['intensity.cor.variance'] = sigma**2
table['intensity.prf.value'] = iobs * peak / rlp
table['intensity.prf.variance'] = (sigma * peak / rlp)**2
table['lp'] = 1.0 / rlp
table['d'] = flex.double(uc.d(h) for h in hkl)
Command.end('Created table with {0} reflections'.format(len(table)))
# Output the table to pickle file
if params.output.filename is None:
params.output.filename = 'integrate_hkl.pickle'
Command.start('Saving reflection table to %s' % params.output.filename)
table.as_pickle(params.output.filename)
Command.end('Saved reflection table to %s' % params.output.filename)
def __init__(self,
xray_structure,
obs_,
exti=None,
connectivity_table=None):
if exti is None:
exti = xray.dummy_extinction_correction()
adopt_init_args(self, locals())
assert obs_.fo_sq.anomalous_flag()
assert not (obs_.twin_fractions and obs_.merohedral_components)
xray_structure = xray_structure.deep_copy_scatterers()
for sc in xray_structure.scatterers():
f = xray.scatterer_flags()
f.set_use_u_aniso(sc.flags.use_u_aniso())
f.set_use_u_iso(sc.flags.use_u_iso())
f.set_use_fp_fdp(True)
sc.flags = f
twin_fractions = ()
it = xray.twin_component(sgtbx.rot_mx((-1, 0, 0, 0, -1, 0, 0, 0, -1)),
0.2, True)
twin_components = (it, )
obs = observations.customized_copy(obs_, twin_fractions,
twin_components)
# reparameterisation needs all fractions
twin_fractions += twin_components
if connectivity_table is None:
connectivity_table = smtbx.utils.connectivity_table(xray_structure)
reparametrisation = constraints.reparametrisation(
xray_structure, [],
connectivity_table,
twin_fractions=twin_fractions,
extinction=exti)
normal_eqns = least_squares.crystallographic_ls(obs, reparametrisation)
cycles = normal_eqns_solving.naive_iterations(normal_eqns,
n_max_iterations=10,
gradient_threshold=1e-7,
step_threshold=1e-4)
self.flack_x = it.value
self.sigma_x = math.sqrt(
normal_eqns.covariance_matrix(
jacobian_transpose=reparametrisation.
jacobian_transpose_matching(
reparametrisation.mapping_to_grad_fc_independent_scalars))
[0])
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 derive_change_of_basis_op(from_hkl, to_hkl):
# exclude those reflections that we couldn't index
sel = (to_hkl != (0, 0, 0)) & (from_hkl != (0, 0, 0))
assert sel.count(True) >= 3 # need minimum of 3 equations ?
to_hkl = to_hkl.select(sel)
from_hkl = from_hkl.select(sel)
# for each miller index, solve a system of linear equations to find the
# change of basis operator
h, k, l = to_hkl.as_vec3_double().parts()
r = []
from scitbx.lstbx import normal_eqns
for i in range(3):
eqns = normal_eqns.linear_ls(3)
for index, hkl in zip((h, k, l)[i], from_hkl):
eqns.add_equation(
right_hand_side=index, design_matrix_row=flex.double(hkl), weight=1
)
eqns.solve()
r.extend(eqns.solution())
from scitbx import matrix
from scitbx.math import continued_fraction
denom = 12
r = [
int(denom * continued_fraction.from_real(r_, eps=1e-2).as_rational())
for r_ in r
]
r = matrix.sqr(r).transpose()
# print (1/denom)*r
# now convert into a cctbx change_of_basis_op object
change_of_basis_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(r, denominator=denom))
).inverse()
print("discovered change_of_basis_op=%s" % (str(change_of_basis_op)))
# sanity check that this is the right cb_op
assert (change_of_basis_op.apply(from_hkl) == to_hkl).count(False) == 0
return change_of_basis_op
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
def __init__(self, xray_structure, obs_, exti=None, connectivity_table=None):
if exti is None:
exti = xray.dummy_extinction_correction()
adopt_init_args(self, locals())
assert obs_.fo_sq.anomalous_flag()
xray_structure = xray_structure.deep_copy_scatterers()
flags = xray_structure.scatterer_flags()
for sc in xray_structure.scatterers():
f = xray.scatterer_flags()
f.set_use_u_aniso(sc.flags.use_u_aniso())
f.set_use_u_iso(sc.flags.use_u_iso())
f.set_use_fp_fdp(True)
sc.flags = f
twin_fractions = obs_.twin_fractions
twin_components = obs_.merohedral_components
for tw in twin_fractions: tw.grad = False
for tc in twin_components: tc.grad = False
it = xray.twin_component(sgtbx.rot_mx((-1,0,0,0,-1,0,0,0,-1)), 0.2, True)
twin_components += (it,)
obs = observations.customized_copy(obs_, twin_fractions, twin_components)
# reparameterisation needs all fractions
twin_fractions += twin_components
if connectivity_table is None:
connectivity_table = smtbx.utils.connectivity_table(xray_structure)
reparametrisation = constraints.reparametrisation(
xray_structure, [], connectivity_table,
twin_fractions=twin_fractions,
extinction=exti
)
normal_eqns = least_squares.crystallographic_ls(obs,
reparametrisation)
cycles = normal_eqns_solving.naive_iterations(
normal_eqns, n_max_iterations=10,
gradient_threshold=1e-7,
step_threshold=1e-4)
self.flack_x = it.value
self.sigma_x = math.sqrt(normal_eqns.covariance_matrix(
jacobian_transpose=reparametrisation.jacobian_transpose_matching(
reparametrisation.mapping_to_grad_fc_independent_scalars))[0])
def derive_change_of_basis_op(from_hkl, to_hkl):
# exclude those reflections that we couldn't index
sel = (to_hkl != (0,0,0)) & (from_hkl != (0,0,0))
assert sel.count(True) >= 3 # need minimum of 3 equations ?
to_hkl = to_hkl.select(sel)
from_hkl = from_hkl.select(sel)
# for each miller index, solve a system of linear equations to find the
# change of basis operator
h, k, l = to_hkl.as_vec3_double().parts()
r = []
from scitbx.lstbx import normal_eqns
for i in range(3):
eqns = normal_eqns.linear_ls(3)
for index, hkl in zip((h,k,l)[i], from_hkl):
eqns.add_equation(right_hand_side=index,
design_matrix_row=flex.double(hkl),
weight=1)
eqns.solve()
r.extend(eqns.solution())
from scitbx.math import continued_fraction
from scitbx import matrix
denom = 12
r = [int(denom * continued_fraction.from_real(r_, eps=1e-2).as_rational())
for r_ in r]
r = matrix.sqr(r).transpose()
#print (1/denom)*r
# now convert into a cctbx change_of_basis_op object
change_of_basis_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(r, denominator=denom))).inverse()
print "discovered change_of_basis_op=%s" %(str(change_of_basis_op))
# sanity check that this is the right cb_op
assert (change_of_basis_op.apply(from_hkl) == to_hkl).count(False) == 0
return change_of_basis_op
def __init__(self, lf):
self.symbol = None
l = lf.next()
print l.strip()
if (lf.eof): return
no, number, symbol, m = l.split()
assert no == "NO."
number = int(number)
assert int(float(m)) == float(m)
m = int(float(m))
space_group = sgtbx.space_group()
if (m < 0):
space_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
space_group.expand_conventional_centring_type(symbol[0])
t_den = space_group.t_den()
matrices = []
for i in xrange(abs(m)):
l = lf.next()
assert not lf.eof
flds = l.split()
assert len(flds) == 12
r = [int(e) for e in flds[1:4] + flds[5:8] + flds[9:12]]
t = [
int(round(float(e) * t_den))
for e in (flds[0], flds[4], flds[8])
]
try:
s = sgtbx.rt_mx(sgtbx.rot_mx(r), sgtbx.tr_vec(t))
except RuntimeError, e:
print e
print l
else:
try:
matrices.append(s)
space_group.expand_smx(s)
except RuntimeError, e:
print e
print l
print s
def run():
lines = iter(matrices_from_email.splitlines())
while True:
for line in lines:
if (line.rstrip() == "S:"): break
else:
break
s = []
for i in xrange(3):
s.extend([float(v) for v in lines.next().split()])
for line in lines:
if (line.rstrip() == "M:"): break
else:
raise RuntimeError("S: found but not M:")
m = []
for i in xrange(3):
m.extend([int(v) for v in lines.next().split()])
for line in lines:
if (line.rstrip() == "Score:"): break
else:
raise RuntimeError("S: and M: found but not Score:")
score = float(lines.next().strip())
s = matrix.sqr(s)
m = matrix.sqr(m)
print s.mathematica_form(label="s", one_row_per_line=True)
print m.mathematica_form(label="m", one_row_per_line=True)
r = sgtbx.rot_mx(m, 1)
print "rotation type:", r.info().type()
print "axis direction:", r.info().ev()
u = uctbx.unit_cell(metrical_matrix=s.as_sym_mat3())
p = r.lebedev_2005_perturbation(reduced_cell=u)
print "score given: ", score
print "score reproduced:", p
assert abs(p-score) < 1.e-6
delta = r.le_page_1982_delta(reduced_cell=u)
print "Le Page delta: ", delta
print
print "OK"
def run():
lines = iter(matrices_from_email.splitlines())
while True:
for line in lines:
if (line.rstrip() == "S:"): break
else:
break
s = []
for i in range(3):
s.extend([float(v) for v in lines.next().split()])
for line in lines:
if (line.rstrip() == "M:"): break
else:
raise RuntimeError("S: found but not M:")
m = []
for i in range(3):
m.extend([int(v) for v in lines.next().split()])
for line in lines:
if (line.rstrip() == "Score:"): break
else:
raise RuntimeError("S: and M: found but not Score:")
score = float(lines.next().strip())
s = matrix.sqr(s)
m = matrix.sqr(m)
print(s.mathematica_form(label="s", one_row_per_line=True))
print(m.mathematica_form(label="m", one_row_per_line=True))
r = sgtbx.rot_mx(m, 1)
print("rotation type:", r.info().type())
print("axis direction:", r.info().ev())
u = uctbx.unit_cell(metrical_matrix=s.as_sym_mat3())
p = r.lebedev_2005_perturbation(reduced_cell=u)
print("score given: ", score)
print("score reproduced:", p)
assert abs(p-score) < 1.e-6
delta = r.le_page_1982_delta(reduced_cell=u)
print("Le Page delta: ", delta)
print()
print("OK")
def __init__(self, lf):
self.symbol = None
l = lf.next()
print l.strip()
if (lf.eof): return
no, number, symbol, m = l.split()
assert no == "NO."
number = int(number)
assert int(float(m)) == float(m)
m = int(float(m))
space_group = sgtbx.space_group()
if (m < 0):
space_group.expand_inv(sgtbx.tr_vec((0,0,0)))
space_group.expand_conventional_centring_type(symbol[0])
t_den = space_group.t_den()
matrices = []
for i in xrange(abs(m)):
l = lf.next()
assert not lf.eof
flds = l.split()
assert len(flds) == 12
r = [int(e) for e in flds[1:4] + flds[5:8] + flds[9:12]]
t = [int(round(float(e)*t_den)) for e in (flds[0],flds[4],flds[8])]
try:
s = sgtbx.rt_mx(sgtbx.rot_mx(r), sgtbx.tr_vec(t))
except RuntimeError, e:
print e
print l
else:
try:
matrices.append(s)
space_group.expand_smx(s)
except RuntimeError, e:
print e
print l
print s
def excersise():
s = """\
-1 -6 9624.8650 54.9190 1
-1 6 9749.5660 52.1870 -2
1 6 -9749.5660 52.1870 1
1 -6 -8695.6020 53.8100 -2
-1 -6 8695.6020 53.8100 1
-1 6 8746.7970 51.3980 -2
1 6 -8746.7970 51.3980 1
-1 -6 -12281.3590 49.5060 1
1 6 12185.9370 47.3950 1
-1 -6 -1316.0700044.01400 1
1 6 13 4.7500043.54900 1
-1 -6 -1479.6380048.66400 2
1 6 1432.7830051.51700 2
"""
sg = sgtbx.space_group("P 1")
uc = uctbx.unit_cell((11, 11, 13, 90, 90, 120))
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
ma = hklf.reader(file_object=StringIO(s))\
.as_miller_arrays(crystal_symmetry=cs, merge_equivalents=False)
fo_sq = ma[0]
batch_numbers = ma[1]
obs = fo_sq.as_xray_observations(scale_indices=batch_numbers.data(),
twin_fractions=(xray.twin_fraction(
0.4, True), ))
measured_cnt = 0
measured_scale_indices = obs.measured_scale_indices
for bn in batch_numbers.data():
if bn > 0:
assert (measured_scale_indices[measured_cnt] == bn)
measured_cnt = measured_cnt + 1
assert (measured_cnt == obs.indices.size())
itr = obs.iterator(0)
assert (not itr.has_next())
itr = obs.iterator(1)
assert (itr.next().h == (-1, 6, 9))
itr = obs.iterator(2)
assert (itr.next().h == (1, -6, -8))
# this is supposed to fail for now until somebody re-implements
# mixed HKLF 5 + merohedral twinning in a meaningful way...
try:
obs = observations.customized_copy(
obs,
twin_fractions=(xray.twin_fraction(0.7, True), ),
twin_components=(xray.twin_component(
sgtbx.rot_mx((-1, 0, 0, 0, -1, 0, 0, 0, -1)), 0.25, True), ))
itr = obs.iterator(0)
assert (itr.has_next())
assert (itr.next().h == (1, 6, -9))
assert (not itr.has_next())
itr = obs.iterator(1)
assert (itr.next().h == (-1, -6, 9))
assert (itr.next().h == (-1, 6, 9))
assert (itr.next().h == (1, -6, -9))
assert (not itr.has_next())
ts = 1 - obs.ref_twin_components[0].value
ps = 1 - obs.ref_twin_fractions[0].value
itr = obs.iterator(0)
assert obs.scale(0) == ts * ps
nv = next(itr)
assert nv.scale == obs.ref_twin_components[0].value * ps
except RuntimeError as e:
pass
def __call__(self, params, options):
''' Import the integrate.hkl file. '''
from iotbx.xds import integrate_hkl
from dials.array_family import flex
from dials.util.command_line import Command
from cctbx import sgtbx
# Get the unit cell to calculate the resolution
uc = self._experiment.crystal.get_unit_cell()
# Read the INTEGRATE.HKL file
Command.start('Reading INTEGRATE.HKL')
handle = integrate_hkl.reader()
handle.read_file(self._integrate_hkl)
hkl = flex.miller_index(handle.hkl)
xyzcal = flex.vec3_double(handle.xyzcal)
xyzobs = flex.vec3_double(handle.xyzobs)
iobs = flex.double(handle.iobs)
sigma = flex.double(handle.sigma)
rlp = flex.double(handle.rlp)
peak = flex.double(handle.peak) * 0.01
if len(handle.iseg):
panel = flex.size_t(handle.iseg) - 1
else:
panel = flex.size_t(len(hkl), 0)
Command.end('Read %d reflections from INTEGRATE.HKL file.' % len(hkl))
if len(self._experiment.detector) > 1:
for p_id, p in enumerate(self._experiment.detector):
sel = (panel == p_id)
offset = p.get_raw_image_offset()
xyzcal.set_selected(
sel,
xyzcal.select(sel) - (offset[0], offset[1], 0))
xyzobs.set_selected(
sel,
xyzobs.select(sel) - (offset[0], offset[1], 0))
# Derive the reindex matrix
rdx = self.derive_reindex_matrix(handle)
print('Reindex matrix:\n%d %d %d\n%d %d %d\n%d %d %d' % (rdx.elems))
# Reindex the reflections
Command.start('Reindexing reflections')
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(rdx.elems)))
hkl = cb_op.apply(hkl)
Command.end('Reindexed %d reflections' % len(hkl))
# Create the reflection list
Command.start('Creating reflection table')
table = flex.reflection_table()
table['id'] = flex.int(len(hkl), 0)
table['panel'] = panel
table['miller_index'] = hkl
table['xyzcal.px'] = xyzcal
table['xyzobs.px.value'] = xyzobs
table['intensity.cor.value'] = iobs
table['intensity.cor.variance'] = sigma**2
table['intensity.prf.value'] = iobs * peak / rlp
table['intensity.prf.variance'] = (sigma * peak / rlp)**2
table['lp'] = 1.0 / rlp
table['d'] = flex.double(uc.d(h) for h in hkl)
Command.end('Created table with {0} reflections'.format(len(table)))
# Output the table to pickle file
if params.output.filename is None:
params.output.filename = 'integrate_hkl.pickle'
Command.start('Saving reflection table to %s' % params.output.filename)
table.as_pickle(params.output.filename)
Command.end('Saved reflection table to %s' % params.output.filename)
def __init__(self,
xs_a,
xs_b,
max_delta=2.0,
out=None,
relative_length_tolerance=0.05,
absolute_angle_tolerance=10.0,
order=1):
self.relative_length_tolerance = relative_length_tolerance
self.absolute_angle_tolerance = absolute_angle_tolerance
self.order = order
self.max_delta = max_delta
self.out = out
if self.out is None:
self.out = sys.stdout
self.xs_a = xs_a
self.xs_b = xs_b
# Go to niggli cell
self.xs_a_n = self.xs_a.niggli_cell()
self.xs_b_n = self.xs_b.niggli_cell()
if (self.xs_a.niggli_cell().unit_cell().volume() >
self.xs_b.niggli_cell().unit_cell().volume()):
self.xs_a = xs_b
self.xs_b = xs_a
# go to niggli cell please
self.xs_a_n = self.xs_a.niggli_cell()
self.xs_b_n = self.xs_b.niggli_cell()
volume_ratio = self.xs_b_n.unit_cell().volume(
) / self.xs_a_n.unit_cell().volume()
n_volume_ratio = math.floor(volume_ratio + 1)
self.show_basic_info()
self.basis_a = matrix.sqr(
self.xs_a_n.unit_cell().orthogonalization_matrix())
print("Cartesian basis (column) vectors of lego cell:", file=self.out)
tmp_bas = self.basis_a.as_list_of_lists()
print(" / %5.1f %5.1f %5.1f \\ " %
(tmp_bas[0][0], tmp_bas[0][1], tmp_bas[0][2]),
file=self.out)
print(" | %5.1f %5.1f %5.1f | " %
(tmp_bas[1][0], tmp_bas[1][1], tmp_bas[1][2]),
file=self.out)
print(" \\ %5.1f %5.1f %5.1f / " %
(tmp_bas[2][0], tmp_bas[2][1], tmp_bas[2][2]),
file=self.out)
print(file=self.out)
self.basis_b = matrix.sqr(
self.xs_b_n.unit_cell().orthogonalization_matrix())
print("Cartesian basis (column) vectors of target cell:",
file=self.out)
tmp_bas = self.basis_b.as_list_of_lists()
print(" / %5.1f %5.1f %5.1f \\ " %
(tmp_bas[0][0], tmp_bas[0][1], tmp_bas[0][2]),
file=self.out)
print(" | %5.1f %5.1f %5.1f | " %
(tmp_bas[1][0], tmp_bas[1][1], tmp_bas[1][2]),
file=self.out)
print(" \\ %5.1f %5.1f %5.1f / " %
(tmp_bas[2][0], tmp_bas[2][1], tmp_bas[2][2]),
file=self.out)
print(file=self.out)
self.lattice_symm_a = sgtbx.lattice_symmetry.group(
self.xs_a_n.unit_cell(), self.max_delta)
self.lattice_symm_b = sgtbx.lattice_symmetry.group(
self.xs_b_n.unit_cell(), self.max_delta)
self.xs_ref = crystal.symmetry(unit_cell=self.xs_b_n.unit_cell(),
space_group=self.lattice_symm_b,
assert_is_compatible_unit_cell=False)
# make a list of matrices
self.matrix_list = generate_matrix_up_to_order(
n_volume_ratio, max(n_volume_ratio - 1, 1))
self.uc_and_symm_list = []
self.possible_solutions = []
print(
"A total of %4i matrices in the hermite normal form have been generated."
% (len(self.matrix_list)),
file=self.out)
print("The volume changes they cause lie between %4i and %4i." %
(n_volume_ratio, max(n_volume_ratio - 1, 1)),
file=self.out)
count = 0
print(file=self.out)
print("Trying all matrices", file=self.out)
print(file=self.out)
print(" 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0", file=self.out)
print(" ", end=' ', file=self.out)
for mat in self.matrix_list:
count += 1
found_it = False
tmp_xs = self.make_new_cell_and_symmetry(mat)
self.uc_and_symm_list.append(tmp_xs)
tmp_gen = self.xs_b_n.unit_cell().similarity_transformations(
tmp_xs[2].unit_cell(), self.relative_length_tolerance,
self.absolute_angle_tolerance, self.order)
if tmp_gen.size() > 0:
found_it = True
cb_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(tmp_gen[0]))).inverse()
tmp_sol = (mat, cb_op, tmp_xs[2].change_basis(cb_op), tmp_xs[3]
) # matrix, corresponding cb_op, cell + lattice sym
self.possible_solutions.append(tmp_sol)
#self.show_solution(tmp_sol)
if found_it:
print("*", end=' ', file=self.out)
self.out.flush()
else:
if count % 10 == 0:
print("|", end=' ', file=self.out)
self.out.flush()
else:
print(".", end=' ', file=self.out)
self.out.flush()
if count % 20 == 0:
print(file=self.out)
print(" ", end=' ', file=self.out)
self.out.flush()
print(file=self.out)
print(" Listing all possible solutions", file=self.out)
count = 0
if len(self.possible_solutions) == 0:
print(file=out)
print(
"No relations found for this particular sublattice of the specified target cell.",
file=out)
print(" ", file=out)
print(file=out)
for tmp_sol in self.possible_solutions:
count += 1
print(file=self.out)
print("Solution %4i" % (count), file=self.out)
self.show_solution(tmp_sol)
def __init__(self, lf):
self.symbol = None
l = next(lf)
print(l.strip())
if (lf.eof): return
no, number, symbol, m = l.split()
assert no == "NO."
number = int(number)
assert int(float(m)) == float(m)
m = int(float(m))
space_group = sgtbx.space_group()
if (m < 0):
space_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
space_group.expand_conventional_centring_type(symbol[0])
t_den = space_group.t_den()
matrices = []
for i in range(abs(m)):
l = next(lf)
assert not lf.eof
flds = l.split()
assert len(flds) == 12
r = [int(e) for e in flds[1:4] + flds[5:8] + flds[9:12]]
t = [
int(round(float(e) * t_den))
for e in (flds[0], flds[4], flds[8])
]
try:
s = sgtbx.rt_mx(sgtbx.rot_mx(r), sgtbx.tr_vec(t))
except RuntimeError as e:
print(e)
print(l)
else:
try:
matrices.append(s)
space_group.expand_smx(s)
except RuntimeError as e:
print(e)
print(l)
print(s)
space_group_info = sgtbx.space_group_info(group=space_group)
if (space_group_info.type().number() != number):
print("Space group number mismatch:")
print(" from file:", number)
print(" operations:", space_group_info.type().number())
for s in matrices:
space_group = sgtbx.space_group_info(symbol=number).group()
order_z = space_group.order_z()
space_group.expand_smx(s)
if (space_group.order_z() != order_z):
print(" misfit:", s)
space_group = sgtbx.space_group_info(symbol=number).group()
for i_smx in range(space_group.n_smx()):
OK = False
for i_inv in range(space_group.f_inv()):
for i_ltr in range(space_group.n_ltr()):
sg = space_group(i_ltr, i_inv, i_smx).mod_positive()
for sm in matrices:
sm = sm.mod_positive()
if (sm == sg):
OK = True
break
if (OK): break
if (OK): break
if (not OK):
print(" missing:", sg)
self.number = number
self.symbol = symbol
self.space_group_info = space_group_info
def exercise_change_basis():
assert approx_equal(O1.unit_cell().parameters(),
(47.659, 47.6861, 49.6444, 62.9615, 73.8222, 73.5269),
1E-3)
reindex = (0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0
) # swap a & b and take inverse
O2 = O1.change_basis(reindex)
assert approx_equal(O2.unit_cell().parameters(),
(47.6861, 47.659, 49.6444, 73.8222, 62.9615, 73.5269),
1E-3)
rhombohedral_test = crystal_orientation(
(0.002737747939994224, -0.0049133768326561278, 0.0023634556852316566,
0.0062204242383498082, 0.006107332242442573, 0.0047036576949967112,
-0.0057640198753891566, -0.0025891042237382953,
0.0023674924674260264), basis_type.reciprocal)
rhombohedral_reference = crystal_orientation(
(-0.0076361080646872997, 0.0049061665572297979, 0.0023688116121433865,
-0.00011109895272056645, -0.0061110173438898583,
0.0047062769738302939, 0.0031790372319626674, 0.0025876279220667518,
0.0023669727051432361), basis_type.reciprocal)
# Find a similarity transform that maps the two cells onto each other
c_inv_r_best = rhombohedral_test.best_similarity_transformation(
other=rhombohedral_reference,
fractional_length_tolerance=1.00,
unimodular_generator_range=1)
c_inv_r_int = tuple([int(round(ij, 0)) for ij in c_inv_r_best])
assert c_inv_r_int == (-1, 0, 0, 1, -1, 0, 0, 0, 1)
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r_int))
cb_op = sgtbx.change_of_basis_op(c_inv)
rhombohedral_reindex = rhombohedral_test.change_basis(cb_op)
assert rhombohedral_reindex.difference_Z_score(
rhombohedral_reference) < 0.40
assert rhombohedral_reindex.direct_mean_square_difference(
rhombohedral_reference) < 0.1
#an alternative test from ana that should fail (gives high msd~0.22; cell axes don't match):
ana_reference = crystal_orientation(
(0.0023650364919947241, 0.012819317075171401, 0.003042762222847376,
0.0081242553464681254, 0.0050052660206998077, -0.01472465697193685,
-0.01373896574061278, 0.0083781530252581681, -0.0035301340829149005),
basis_type.reciprocal)
ana_current = crystal_orientation(
(-0.014470153848927263, 0.0095185368147633793, 0.00087746490483763798,
-0.0049989006573928716, -0.0079714727432991222, 0.014778692772530192,
0.0051268914129933571, 0.010264066188909109, 0.0044244589492769002),
basis_type.reciprocal)
c_inv_r_best = ana_current.best_similarity_transformation(
other=ana_reference,
fractional_length_tolerance=200.0,
unimodular_generator_range=1)
c_inv_r_int = tuple([int(round(ij, 0)) for ij in c_inv_r_best])
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r_int))
cb_op = sgtbx.change_of_basis_op(c_inv)
ana_reindex = ana_reference.change_basis(cb_op.inverse())
assert 200.0 > ana_reindex.difference_Z_score(ana_current) > 20.
u = uctbx.unit_cell((10., 10., 10., 90., 90., 90.))
CO = crystal_orientation(u.fractionalization_matrix(), True)
assert approx_equal(
CO.unit_cell().parameters(),
CO.change_basis((1, 0, 0, 0, 1, 0, 0, 0, 1)).unit_cell().parameters())
u = uctbx.unit_cell((2, 3, 5))
CO = crystal_orientation(u.fractionalization_matrix(), True)
assert approx_equal(
CO.change_basis((0, 1, 0, 0, 0, 1, 1, 0, 0)).unit_cell().parameters(),
(5, 2, 3, 90, 90, 90))
cb_op = sgtbx.change_of_basis_op("y,z,x")
assert approx_equal(
CO.change_basis(cb_op).unit_cell().parameters(), (5, 2, 3, 90, 90, 90))
import scitbx.math
from scitbx import matrix
fmx = matrix.sqr(
uctbx.unit_cell((10, 13, 17, 85, 95, 105)).fractionalization_matrix())
crm = matrix.sqr(
scitbx.math.r3_rotation_axis_and_angle_as_matrix(axis=(-3, 5, -7),
angle=37,
deg=True))
co = crystal_orientation(crm * fmx.transpose(), True)
assert approx_equal(co.crystal_rotation_matrix(), crm)
def filtered_commands(self):
from scitbx.math import continued_fraction
temperature = 20
for command, line in self.command_stream:
cmd, args = command[0], command[-1]
n_args = len(args)
if cmd == 'OMIT':
if n_args == 3 and isinstance(args[0], float):
self.instructions.setdefault('omit_hkl', [])
self.instructions['omit_hkl'].append([int(i) for i in args])
elif n_args == 2 and isinstance(args[0], float):
self.instructions['omit'] = {
's': args[0],
'two_theta': args[1]}
else:
yield command, line
elif cmd == 'SHEL':
if args:
shel = {'lowres': args[0]}
if n_args > 1:
shel['highres'] = args[1]
elif cmd == 'MERG':
if args:
self.instructions['merg'] = args[0]
elif cmd == 'TEMP':
if len(args) > 1:
raise shelx_error("TEMP takes at most 1 argument")
if args: temperature = args[0]
self.instructions['temp'] = temperature
self.builder.temperature_in_celsius = temperature
elif cmd == 'WGHT':
if n_args > 6:
raise shelx_error("Too many argument for %s" % cmd, line)
default_weighting_scheme = { 'a': 0.1,
'b': 0,
'c': 0,
'd': 0,
'e': 0,
'f': 1/3 }
weighting_scheme = dict([
(key, (arg is not None and arg) or default_weighting_scheme[key])
for key, arg in itertools.izip_longest('abcdef', args) ])
self.instructions['wght'] = weighting_scheme
self.builder.make_shelx_weighting_scheme(**weighting_scheme)
elif cmd == 'HKLF':
# only ONE HKLF instruction allowed
assert 'hklf' not in self.instructions
hklf = {'s': 1, 'matrix': sgtbx.rot_mx()}
hklf['n'] = args[0]
if n_args > 1:
hklf['s'] = args[1]
if n_args > 2:
assert n_args > 10
mx = [ continued_fraction.from_real(e, eps=1e-3).as_rational()
for e in args[2:11] ]
den = reduce(rational.lcm, [ r.denominator() for r in mx ])
nums = [ r.numerator()*(den//r.denominator()) for r in mx ]
hklf['matrix'] = sgtbx.rot_mx(nums, den)
if n_args > 11:
hklf['wt'] = args[11]
if n_args == 13:
hklf['m'] = args[12]
self.instructions['hklf'] = hklf
assert not self.builder or ('wt' not in hklf and 'm' not in hklf)
self.builder.create_shelx_reflection_data_source(
format=hklf['n'],
indices_transform=hklf['matrix'],
data_scale=hklf['s'])
if 'basf' in self.instructions and hklf['n'] == 5:
self.builder.make_non_merohedral_twinning_with_transformed_hkl(
fractions=self.instructions['basf'])
elif cmd == 'TWIN':
# only ONE twin instruction allowed
assert 'twin' not in self.instructions
twin = {}
if n_args > 0:
assert n_args >= 9
twin['matrix'] = sgtbx.rt_mx(
sgtbx.rot_mx([int(i) for i in args[0:9]]))
if n_args > 9:
twin['n'] = args[9]
self.instructions['twin'] = twin
if 'basf' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'BASF':
self.instructions['basf'] = args
if 'twin' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'EXTI':
if len(args) == 1:
self.instructions['exti'] = args[0]
else:
yield command, line
else:
# All token have been read without errors or early bailout
assert 'hklf' in self.instructions, "Missing HKLF instruction"
def __init__(
self,
xs_a,
xs_b,
max_delta=2.0,
out=None,
relative_length_tolerance=0.05,
absolute_angle_tolerance=10.0,
order=1,
):
self.relative_length_tolerance = relative_length_tolerance
self.absolute_angle_tolerance = absolute_angle_tolerance
self.order = order
self.max_delta = max_delta
self.out = out
if self.out is None:
self.out = sys.stdout
self.xs_a = xs_a
self.xs_b = xs_b
# Go to niggli cell
self.xs_a_n = self.xs_a.niggli_cell()
self.xs_b_n = self.xs_b.niggli_cell()
if self.xs_a.niggli_cell().unit_cell().volume() > self.xs_b.niggli_cell().unit_cell().volume():
self.xs_a = xs_b
self.xs_b = xs_a
# go to niggli cell please
self.xs_a_n = self.xs_a.niggli_cell()
self.xs_b_n = self.xs_b.niggli_cell()
volume_ratio = self.xs_b_n.unit_cell().volume() / self.xs_a_n.unit_cell().volume()
n_volume_ratio = math.floor(volume_ratio + 1)
self.show_basic_info()
self.basis_a = matrix.sqr(self.xs_a_n.unit_cell().orthogonalization_matrix())
print >> self.out, "Cartesian basis (column) vectors of lego cell:"
tmp_bas = self.basis_a.as_list_of_lists()
print >> self.out, " / %5.1f %5.1f %5.1f \ " % (tmp_bas[0][0], tmp_bas[0][1], tmp_bas[0][2])
print >> self.out, " | %5.1f %5.1f %5.1f | " % (tmp_bas[1][0], tmp_bas[1][1], tmp_bas[1][2])
print >> self.out, " \ %5.1f %5.1f %5.1f / " % (tmp_bas[2][0], tmp_bas[2][1], tmp_bas[2][2])
print >> self.out
self.basis_b = matrix.sqr(self.xs_b_n.unit_cell().orthogonalization_matrix())
print >> self.out, "Cartesian basis (column) vectors of target cell:"
tmp_bas = self.basis_b.as_list_of_lists()
print >> self.out, " / %5.1f %5.1f %5.1f \ " % (tmp_bas[0][0], tmp_bas[0][1], tmp_bas[0][2])
print >> self.out, " | %5.1f %5.1f %5.1f | " % (tmp_bas[1][0], tmp_bas[1][1], tmp_bas[1][2])
print >> self.out, " \ %5.1f %5.1f %5.1f / " % (tmp_bas[2][0], tmp_bas[2][1], tmp_bas[2][2])
print >> self.out
self.lattice_symm_a = sgtbx.lattice_symmetry.group(self.xs_a_n.unit_cell(), self.max_delta)
self.lattice_symm_b = sgtbx.lattice_symmetry.group(self.xs_b_n.unit_cell(), self.max_delta)
self.xs_ref = crystal.symmetry(
unit_cell=self.xs_b_n.unit_cell(), space_group=self.lattice_symm_b, assert_is_compatible_unit_cell=False
)
# make a list of matrices
self.matrix_list = generate_matrix_up_to_order(n_volume_ratio, max(n_volume_ratio - 1, 1))
self.uc_and_symm_list = []
self.possible_solutions = []
print >> self.out, "A total of %4i matrices in the hermite normal form have been generated." % (
len(self.matrix_list)
)
print >> self.out, "The volume changes they cause lie between %4i and %4i." % (
n_volume_ratio,
max(n_volume_ratio - 1, 1),
)
count = 0
print >> self.out
print >> self.out, "Trying all matrices"
print >> self.out
print >> self.out, " 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0"
print >> self.out, " ",
for mat in self.matrix_list:
count += 1
found_it = False
tmp_xs = self.make_new_cell_and_symmetry(mat)
self.uc_and_symm_list.append(tmp_xs)
tmp_gen = self.xs_b_n.unit_cell().similarity_transformations(
tmp_xs[2].unit_cell(), self.relative_length_tolerance, self.absolute_angle_tolerance, self.order
)
if tmp_gen.size() > 0:
found_it = True
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(tmp_gen[0]))).inverse()
tmp_sol = (
mat,
cb_op,
tmp_xs[2].change_basis(cb_op),
tmp_xs[3],
) # matrix, corresponding cb_op, cell + lattice sym
self.possible_solutions.append(tmp_sol)
# self.show_solution(tmp_sol)
if found_it:
print >> self.out, "*",
self.out.flush()
else:
if count % 10 == 0:
print >> self.out, "|",
self.out.flush()
else:
print >> self.out, ".",
self.out.flush()
if count % 20 == 0:
print >> self.out
print >> self.out, " ",
self.out.flush()
print >> self.out
print >> self.out, " Listing all possible solutions"
count = 0
if len(self.possible_solutions) == 0:
print >> out
print >> out, "No relations found for this particular sublattice of the specified target cell."
print >> out, " "
print >> out
for tmp_sol in self.possible_solutions:
count += 1
print >> self.out
print >> self.out, "Solution %4i" % (count)
self.show_solution(tmp_sol)
def __call__(self, params, options):
"""Import the integrate.hkl file."""
# Get the unit cell to calculate the resolution
uc = self._experiment.crystal.get_unit_cell()
# Read the INTEGRATE.HKL file
Command.start("Reading INTEGRATE.HKL")
handle = integrate_hkl.reader()
handle.read_file(self._integrate_hkl)
hkl = flex.miller_index(handle.hkl)
xyzcal = flex.vec3_double(handle.xyzcal)
xyzobs = flex.vec3_double(handle.xyzobs)
iobs = flex.double(handle.iobs)
sigma = flex.double(handle.sigma)
rlp = flex.double(handle.rlp)
peak = flex.double(handle.peak) * 0.01
if len(handle.iseg):
panel = flex.size_t(handle.iseg) - 1
else:
panel = flex.size_t(len(hkl), 0)
Command.end(f"Read {len(hkl)} reflections from INTEGRATE.HKL file.")
if len(self._experiment.detector) > 1:
for p_id, p in enumerate(self._experiment.detector):
sel = panel == p_id
offset = p.get_raw_image_offset()
xyzcal.set_selected(sel, xyzcal.select(sel) - (offset[0], offset[1], 0))
xyzobs.set_selected(sel, xyzobs.select(sel) - (offset[0], offset[1], 0))
# Derive the reindex matrix
rdx = self.derive_reindex_matrix(handle)
print("Reindex matrix:\n%d %d %d\n%d %d %d\n%d %d %d" % (rdx.elems))
# Reindex the reflections
Command.start("Reindexing reflections")
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(rdx.elems)))
hkl = cb_op.apply(hkl)
Command.end(f"Reindexed {len(hkl)} reflections")
# Create the reflection list
Command.start("Creating reflection table")
table = flex.reflection_table()
table["id"] = flex.int(len(hkl), 0)
table["panel"] = panel
table["miller_index"] = hkl
table["xyzcal.px"] = xyzcal
table["xyzobs.px.value"] = xyzobs
table["intensity.cor.value"] = iobs
table["intensity.cor.variance"] = flex.pow2(sigma)
table["intensity.prf.value"] = iobs * peak / rlp
table["intensity.prf.variance"] = flex.pow2(sigma * peak / rlp)
table["lp"] = 1.0 / rlp
table["d"] = flex.double(uc.d(h) for h in hkl)
Command.end(f"Created table with {len(table)} reflections")
# Output the table to pickle file
if params.output.filename is None:
params.output.filename = "integrate_hkl.refl"
Command.start(f"Saving reflection table to {params.output.filename}")
table.as_file(params.output.filename)
Command.end(f"Saved reflection table to {params.output.filename}")
def change_of_basis_op(self):
from cctbx import sgtbx
return sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(self._r_inv.elems, 1))).inverse()
def excersise():
s = """\
-1 -6 9624.8650 54.9190 1
-1 6 9749.5660 52.1870 -2
1 6 -9749.5660 52.1870 1
1 -6 -8695.6020 53.8100 -2
-1 -6 8695.6020 53.8100 1
-1 6 8746.7970 51.3980 -2
1 6 -8746.7970 51.3980 1
-1 -6 -12281.3590 49.5060 1
1 6 12185.9370 47.3950 1
-1 -6 -1316.0700044.01400 1
1 6 13 4.7500043.54900 1
-1 -6 -1479.6380048.66400 2
1 6 1432.7830051.51700 2
"""
sg = sgtbx.space_group("P 1")
uc = uctbx.unit_cell((11,11,13,90,90,120))
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
ma = hklf.reader(file_object=StringIO(s))\
.as_miller_arrays(crystal_symmetry=cs, merge_equivalents=False)
fo_sq = ma[0]
batch_numbers = ma[1]
obs = fo_sq.as_xray_observations(
scale_indices=batch_numbers.data(),
twin_fractions=(xray.twin_fraction(0.4,True),))
measured_cnt = 0
measured_scale_indices = obs.measured_scale_indices
for bn in batch_numbers.data():
if bn > 0:
assert(measured_scale_indices[measured_cnt]==bn)
measured_cnt = measured_cnt+1
assert(measured_cnt == obs.indices.size())
itr = obs.iterator(0)
assert(not itr.has_next())
itr = obs.iterator(1)
assert(itr.next().h==(-1,6,9))
itr = obs.iterator(2)
assert(itr.next().h==(1,-6,-8))
obs = observations.customized_copy(obs,
twin_fractions=(xray.twin_fraction(0.7,True),),
twin_components=(xray.twin_component(
sgtbx.rot_mx((-1,0,0,0,-1,0,0,0,-1)), 0.25, True),))
itr = obs.iterator(0)
assert(itr.has_next())
assert(itr.next().h==(1,6,-9))
assert(not itr.has_next())
itr = obs.iterator(1)
assert(itr.next().h==(-1,-6,9))
assert(itr.next().h==(-1,6,9))
assert(itr.next().h==(1,-6,-9))
assert(not itr.has_next())
ts = 1-obs.ref_twin_components[0].value
ps = 1-obs.ref_twin_fractions[0].value
itr = obs.iterator(0)
assert obs.scale(0) == ts*ps
nv = itr.next()
assert nv.scale == obs.ref_twin_components[0].value*ps
def __init__(self,
xs1,
xs2,
relative_length_tolerance=0.05,
absolute_angle_tolerance=10,
max_delta=3.0,
anomalous_flag=True,
out=None):
# first we have to go to the niggli setting
self.cb_op_to_n_1 = xs1.change_of_basis_op_to_niggli_cell()
self.cb_op_to_n_2 = xs2.change_of_basis_op_to_niggli_cell()
nxs1 = xs1.change_basis( self.cb_op_to_n_1 )
nxs2 = xs2.change_basis( self.cb_op_to_n_2 )
# get the lattice symmetry please
lat_sym_1 = lattice_symmetry.group( nxs1.unit_cell(), max_delta )
lat_sym_2 = lattice_symmetry.group( nxs2.unit_cell(), max_delta )
# and the intensity symmetry please
int_sym_1 = nxs1.reflection_intensity_symmetry( anomalous_flag ).space_group()
int_sym_2 = nxs2.reflection_intensity_symmetry( anomalous_flag ).space_group()
# Now we have to find a similarity transform that maps the two niggli cells onto each other
c_inv_rs = nxs1.unit_cell().similarity_transformations(
other=nxs2.unit_cell(),
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance)
min_bases_msd = None
self.similarity_cb_op = None
for c_inv_r in c_inv_rs:
# make the similarity transform into a cb_op
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r))
cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
# compute the mean square difference for the bases
bases_msd = nxs1.unit_cell() \
.bases_mean_square_difference(
other=nxs2.unit_cell().change_basis(cb_op=cb_op))
# and find cb_op correspondiong to the the minimum rmsd
if (min_bases_msd is None
or min_bases_msd > bases_msd):
min_bases_msd = bases_msd
self.similarity_cb_op = cb_op
# if nothing is found, do not continue
self.double_cosets = None
if (self.similarity_cb_op is not None):
# make the common lattice group please
common_lattice_group = lat_sym_1
for s in lat_sym_2.build_derived_acentric_group().change_basis(
self.similarity_cb_op ):
try: common_lattice_group.expand_smx(s)
except RuntimeError:
common_lattice_group=None
if common_lattice_group is not None:
common_lattice_group.make_tidy()
h1 = int_sym_1.build_derived_acentric_group().make_tidy()
h2 = int_sym_2.build_derived_acentric_group().change_basis( self.similarity_cb_op ).make_tidy()
# do the double coset decomposition
self.double_cosets = cosets.double_cosets( common_lattice_group,
h1,
h2,
)
def exercise_change_basis():
assert approx_equal(O1.unit_cell().parameters(),
(47.659, 47.6861, 49.6444, 62.9615, 73.8222, 73.5269),1E-3)
reindex = (0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0) # swap a & b and take inverse
O2 = O1.change_basis(reindex)
assert approx_equal(O2.unit_cell().parameters(),
(47.6861, 47.659, 49.6444, 73.8222, 62.9615, 73.5269),1E-3)
rhombohedral_test = crystal_orientation((
0.002737747939994224, -0.0049133768326561278, 0.0023634556852316566,
0.0062204242383498082, 0.006107332242442573, 0.0047036576949967112,
-0.0057640198753891566, -0.0025891042237382953, 0.0023674924674260264),basis_type.reciprocal)
rhombohedral_reference = crystal_orientation((
-0.0076361080646872997, 0.0049061665572297979, 0.0023688116121433865,
-0.00011109895272056645, -0.0061110173438898583, 0.0047062769738302939,
0.0031790372319626674, 0.0025876279220667518, 0.0023669727051432361),basis_type.reciprocal)
# Find a similarity transform that maps the two cells onto each other
c_inv_r_best = rhombohedral_test.best_similarity_transformation(
other = rhombohedral_reference, fractional_length_tolerance = 1.00,
unimodular_generator_range=1)
c_inv_r_int = tuple([int(round(ij,0)) for ij in c_inv_r_best])
assert c_inv_r_int == (-1, 0, 0, 1, -1, 0, 0, 0, 1)
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r_int))
cb_op = sgtbx.change_of_basis_op(c_inv)
rhombohedral_reindex = rhombohedral_test.change_basis(cb_op)
assert rhombohedral_reindex.difference_Z_score(rhombohedral_reference) < 0.40
assert rhombohedral_reindex.direct_mean_square_difference(rhombohedral_reference) < 0.1
#an alternative test from ana that should fail (gives high msd~0.22; cell axes don't match):
ana_reference = crystal_orientation((
0.0023650364919947241, 0.012819317075171401, 0.003042762222847376,
0.0081242553464681254, 0.0050052660206998077, -0.01472465697193685,
-0.01373896574061278, 0.0083781530252581681, -0.0035301340829149005),basis_type.reciprocal)
ana_current = crystal_orientation((
-0.014470153848927263, 0.0095185368147633793, 0.00087746490483763798,
-0.0049989006573928716, -0.0079714727432991222, 0.014778692772530192,
0.0051268914129933571, 0.010264066188909109, 0.0044244589492769002),basis_type.reciprocal)
c_inv_r_best = ana_current.best_similarity_transformation(
other = ana_reference,
fractional_length_tolerance = 200.0,
unimodular_generator_range=1)
c_inv_r_int = tuple([int(round(ij,0)) for ij in c_inv_r_best])
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r_int))
cb_op = sgtbx.change_of_basis_op(c_inv)
ana_reindex = ana_reference.change_basis(cb_op.inverse())
assert 200.0 > ana_reindex.difference_Z_score(ana_current) > 20.
u = uctbx.unit_cell((10., 10., 10., 90., 90., 90.))
CO = crystal_orientation(u.fractionalization_matrix(),True)
assert approx_equal(
CO.unit_cell().parameters(),
CO.change_basis((1,0,0, 0,1,0, 0,0,1)).unit_cell().parameters())
u = uctbx.unit_cell((2,3,5))
CO = crystal_orientation(u.fractionalization_matrix(),True)
assert approx_equal(
CO.change_basis((0,1,0, 0,0,1, 1,0,0)).unit_cell().parameters(),
(5,2,3,90,90,90))
cb_op = sgtbx.change_of_basis_op("y,z,x")
assert approx_equal(
CO.change_basis(cb_op).unit_cell().parameters(),
(5,2,3,90,90,90))
import scitbx.math
from scitbx import matrix
fmx = matrix.sqr(
uctbx.unit_cell((10, 13, 17, 85, 95, 105)).fractionalization_matrix())
crm = matrix.sqr(scitbx.math.r3_rotation_axis_and_angle_as_matrix(
axis=(-3,5,-7), angle=37, deg=True))
co = crystal_orientation(crm * fmx.transpose(), True)
assert approx_equal(co.crystal_rotation_matrix(), crm)
def filtered_commands(self):
from scitbx.math import continued_fraction
temperature = 20
for command, line in self.command_stream:
cmd, args = command[0], command[-1]
n_args = len(args)
if cmd == 'OMIT':
if n_args == 3 and isinstance(args[0], float):
self.instructions.setdefault('omit_hkl', [])
self.instructions['omit_hkl'].append([int(i) for i in args])
elif n_args == 2 and isinstance(args[0], float):
self.instructions['omit'] = {
's': args[0],
'two_theta': args[1]}
else:
yield command, line
elif cmd == 'SHEL':
if args:
shel = {'lowres': args[0]}
if n_args > 1:
shel['highres'] = args[1]
elif cmd == 'MERG':
if args:
self.instructions['merg'] = args[0]
elif cmd == 'TEMP':
if len(args) > 1:
raise shelx_error("TEMP takes at most 1 argument")
if args: temperature = args[0]
self.instructions['temp'] = temperature
self.builder.temperature_in_celsius = temperature
elif cmd == 'WGHT':
if n_args > 6:
raise shelx_error("Too many argument for %s" % cmd, line)
default_weighting_scheme = { 'a': 0.1,
'b': 0,
'c': 0,
'd': 0,
'e': 0,
'f': 1/3 }
weighting_scheme = dict([
(key, (arg is not None and arg) or default_weighting_scheme[key])
for key, arg in itertools.izip_longest('abcdef', args) ])
self.instructions['wght'] = weighting_scheme
self.builder.make_shelx_weighting_scheme(**weighting_scheme)
elif cmd == 'HKLF':
# only ONE HKLF instruction allowed
assert 'hklf' not in self.instructions
hklf = {'s': 1, 'matrix': sgtbx.rot_mx()}
hklf['n'] = args[0]
if n_args > 1:
hklf['s'] = args[1]
if n_args > 2:
assert n_args > 10
mx = [ continued_fraction.from_real(e, eps=1e-3).as_rational()
for e in args[2:11] ]
den = reduce(rational.lcm, [ r.denominator() for r in mx ])
nums = [ r.numerator()*(den//r.denominator()) for r in mx ]
hklf['matrix'] = sgtbx.rot_mx(nums, den)
if n_args > 11:
hklf['wt'] = args[11]
if n_args == 13:
hklf['m'] = args[12]
self.instructions['hklf'] = hklf
assert not self.builder or ('wt' not in hklf and 'm' not in hklf)
self.builder.create_shelx_reflection_data_source(
format=hklf['n'],
indices_transform=hklf['matrix'],
data_scale=hklf['s'])
if 'basf' in self.instructions and hklf['n'] == 5:
self.builder.make_non_merohedral_twinning_with_transformed_hkl(
fractions=self.instructions['basf'])
elif cmd == 'TWIN':
# only ONE twin instruction allowed
assert 'twin' not in self.instructions
twin = {}
if n_args > 0:
assert n_args >= 9
twin['matrix'] = sgtbx.rt_mx(
sgtbx.rot_mx([int(i) for i in args[0:9]]))
if n_args > 9:
twin['n'] = args[9]
self.instructions['twin'] = twin
if 'basf' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'BASF':
self.instructions['basf'] = args
if 'twin' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'EXTI':
if len(args) == 1:
self.instructions['exti'] = args[0]
else:
yield command, line
else:
# All token have been read without errors or early bailout
assert 'hklf' in self.instructions, "Missing HKLF instruction"
def __init__(self):
self.structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(7.6338, 7.6338, 9.8699, 90, 90, 120),
space_group_symbol='hall: P 3 -2c'),
scatterers=flex.xray_scatterer((
xray.scatterer( #0
label='LI',
site=(0.032717, 0.241544, 0.254924),
u=(0.000544, 0.000667, 0.000160,
0.000326, 0.000072, -0.000030)),
xray.scatterer( #1
label='NA',
site=(0.033809, 0.553123, 0.484646),
u=(0.000554, 0.000731, 0.000174,
0.000212, 0.000032, -0.000015)),
xray.scatterer( #2
label='S1',
site=(0.000000, 0.000000, -0.005908),
u=(0.000370, 0.000370, 0.000081,
0.000185, 0.000000, 0.000000)),
xray.scatterer( #3
label='S2',
site=(0.333333, 0.666667, 0.211587),
u=(0.000244, 0.000244, 0.000148,
0.000122, 0.000000, 0.000000)),
xray.scatterer( #4
label='S3',
site=(0.666667, 0.333333, 0.250044),
u=(0.000349, 0.000349, 0.000094,
0.000174, 0.000000, 0.000000)),
xray.scatterer( #5
label='O1',
site=(0.000000, -0.000000, 0.154207),
u=(0.000360, 0.000360, 0.000149,
0.000180, 0.000000, 0.000000),
occupancy=0.999000),
xray.scatterer( #6
label='O2',
site=(0.333333, 0.666667, 0.340665),
u=(0.000613, 0.000613, 0.000128,
0.000306, 0.000000, 0.000000)),
xray.scatterer( #7
label='O3',
site=(0.666667, 0.333333, 0.112766),
u=(0.000724, 0.000724, 0.000118,
0.000362, 0.000000, 0.000000)),
xray.scatterer( #8
label='O4',
site=(0.225316, 0.110088, -0.035765),
u=(0.000477, 0.000529, 0.000213,
0.000230, 0.000067, -0.000013)),
xray.scatterer( #9
label='O5',
site=(0.221269, 0.442916, 0.153185),
u=(0.000767, 0.000286, 0.000278,
0.000210, 0.000016, -0.000082)),
xray.scatterer( #10
label='O6',
site=(0.487243, 0.169031, 0.321690),
u=(0.000566, 0.000582, 0.000354,
0.000007, 0.000022, 0.000146))
)))
self.twin_laws = (sgtbx.rot_mx((0,1,0,1,0,0,0,0,-1)),)
self.twin_fractions = flex.double((flex.random_double(),))
self.scale_factor = 0.05 + 10 * flex.random_double()
self.crystal_symmetry = self.structure.crystal_symmetry()
mi = self.crystal_symmetry.build_miller_set(anomalous_flag=False,
d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
self.structure, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(
data=fo_sq.data()*self.scale_factor,
sigmas=flex.double(fo_sq.size(), 1))
twin_completion = xray.twin_completion(
mi.indices(),
mi.space_group(),
mi.anomalous_flag(),
self.twin_laws[0].as_double())
sigmas = flex.double(fo_sq.size(), 1)
from cctbx import miller
twin_complete_set = miller.set(
crystal_symmetry=self.crystal_symmetry,
indices=twin_completion.twin_complete(),
anomalous_flag=mi.anomalous_flag()).map_to_asu()
detwinner = xray.hemihedral_detwinner(
hkl_obs=fo_sq.indices(),
hkl_calc=twin_complete_set.indices(),
space_group=mi.space_group(),
anomalous_flag=mi.anomalous_flag(),
twin_law=self.twin_laws[0].as_double())
twinned_i, twinned_s = detwinner.twin_with_twin_fraction(
fo_sq.data(),
sigmas,
twin_fraction=self.twin_fractions[0])
self.fo_sq = fo_sq.customized_copy(data=twinned_i, sigmas=twinned_s)
def filter_known_symmetry(
crystal_models,
target_symmetry,
relative_length_tolerance=0.1,
absolute_angle_tolerance=5,
max_delta=5,
):
"""Filter crystal models for known symmetry.
Args:
crystal_models (list): A list of :class:`dxtbx.model.Crystal` objects.
target_symmetry (cctbx.crystal.symmetry): The target symmetry for filtering.
relative_length_tolerance (float): Relative tolerance for unit cell lengths in
unit cell comparision (default value is 0.1).
absolute_angle_tolerance (float): Angular tolerance (in degrees) in unit cell
comparison (default value is 5).
max_delta (float): Maximum allowed Le Page delta used in searching for basis
vector combinations that are consistent with the given symmetry (default
value is 5).
"""
cb_op_ref_to_primitive = target_symmetry.change_of_basis_op_to_primitive_setting(
)
if target_symmetry.unit_cell() is not None:
target_symmetry_primitive = target_symmetry.change_basis(
cb_op_ref_to_primitive)
target_min_cell = target_symmetry_primitive.minimum_cell().unit_cell()
else:
target_symmetry_primitive = target_symmetry.customized_copy(
space_group_info=target_symmetry.space_group_info().change_basis(
cb_op_ref_to_primitive))
target_min_cell = None
transformations = [
sgtbx.change_of_basis_op(
str(sgtbx.rt_mx(sgtbx.rot_mx(T["trans"].transpose().as_int()))))
for T in tools.R if T["mod"] < 5
]
transformations = [] # XXX temporarily disable cell doubling checks
transformations.insert(0, sgtbx.change_of_basis_op())
for model in crystal_models:
best_model = None
for T in transformations:
uc = model.get_unit_cell()
det = T.c().r().determinant()
if target_symmetry_primitive.unit_cell() is None:
if det > 1:
break
else:
primitive_volume = target_symmetry_primitive.unit_cell(
).volume()
if det > 1 and abs(uc.volume() / primitive_volume - det) < 1e-1:
uc = uc.change_basis(T)
best_subgroup = find_matching_symmetry(
uc,
target_symmetry_primitive.space_group(),
max_delta=max_delta)
cb_op_extra = None
if best_subgroup is None:
if not cb_op_ref_to_primitive.is_identity_op():
# if we have been told we have a centred unit cell check that
# indexing hasn't found the centred unit cell instead of the
# primitive cell
best_subgroup = find_matching_symmetry(
uc,
target_symmetry.space_group().
build_derived_point_group(),
max_delta=max_delta,
)
cb_op_extra = cb_op_ref_to_primitive
if best_subgroup is None:
continue
else:
continue
cb_op_inp_best = best_subgroup["cb_op_inp_best"]
best_subsym = best_subgroup["best_subsym"]
cb_op_best_ref = best_subsym.change_of_basis_op_to_reference_setting(
)
ref_subsym = best_subsym.change_basis(cb_op_best_ref)
cb_op_ref_primitive = ref_subsym.change_of_basis_op_to_primitive_setting(
)
cb_op_to_primitive = (cb_op_ref_primitive * cb_op_best_ref *
cb_op_inp_best * T)
if cb_op_extra is not None:
cb_op_to_primitive = cb_op_extra * cb_op_to_primitive
best_model = model.change_basis(cb_op_to_primitive)
if target_symmetry_primitive.unit_cell(
) is not None and not (best_model.get_unit_cell().is_similar_to(
target_symmetry_primitive.unit_cell(),
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance,
) or best_model.get_unit_cell().minimum_cell().is_similar_to(
target_min_cell,
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance,
)):
best_model = None
continue
else:
break
if best_model is not None:
yield best_model
def image_case_factory(item_no):
mosflm = sqr(
(1, 0, 0, 0, 1, 0, 0, 0, 1)) # mosflm lab vectors in their own frame
labelit = sqr(
(0, 0, -1, -1, 0, 0, 0, 1, 0)) # mosflm basis vectors in labelit frame
MLx = (0, 0, -1)
MLy = (-1, 0, 0)
MLz = (0, 1, 0) # "virtual" rotation axis being used by cctbx.xfel for CXI
LM = mosflm * labelit.inverse(
) # converts labelit frame coords to mosflm frame
SWAPXY = sqr((0, 1, 0, 1, 0, 0, 0, 0, 1)) # in labelit frame
SWAPZ = sqr((1, 0, 0, 0, 1, 0, 0, 0, -1)) # in labelit frame
R90 = sqr((0, -1, 0, 1, 0, 0, 0, 0,
1)) # in labelit frame, rotation 90 on beam axis
CONTAINER_SZ = 1000
WAVELENGTH = 1.32 # given by James Holton
container_no = item // CONTAINER_SZ
filename = "/net/viper/raid1/sauter/fake/result/basic00/"
filename = os.path.join(filename, "r%02d" % container_no, TRIAL,
"integration", "int-data_%05d.pickle" % item_no)
trial_results = pickle.load(open(filename, "rb"))
current_hexagonal_ori = trial_results["current_orientation"][0]
current_cb_op_to_primitive = trial_results["current_cb_op_to_primitive"][0]
current_triclinic_ori = current_hexagonal_ori.change_basis(
current_cb_op_to_primitive)
filename = "/net/viper/raid1/sauter/fake/holton/mosflm_matrix"
filename = os.path.join(filename, "%02d" % container_no,
"%05d.mat" % item_no)
lines = open(filename).readlines()
A0 = lines[0].strip().split()
A1 = lines[1].strip().split()
A2 = lines[2].strip().split()
A = sqr(
(float(A0[0]), float(A0[1]), float(A0[2]), float(A1[0]), float(A1[1]),
float(A1[2]), float(A2[0]), float(A2[1]), float(A2[2])))
A = A / WAVELENGTH
Holton_hexagonal_ori = crystal_orientation(SWAPZ * SWAPXY * R90 * LM * A,
True)
Holton_triclinic_ori = Holton_hexagonal_ori.change_basis(
current_cb_op_to_primitive)
c_inv_r_best = Holton_triclinic_ori.best_similarity_transformation(
other=current_triclinic_ori,
fractional_length_tolerance=50.,
unimodular_generator_range=1)
c_inv_r_int = tuple([int(round(ij, 0)) for ij in c_inv_r_best])
from cctbx import sgtbx
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r_int))
cb_op = sgtbx.change_of_basis_op(c_inv)
comparison_triclinic = Holton_triclinic_ori.change_basis(cb_op)
comparison_hexagonal = comparison_triclinic.change_basis(
current_cb_op_to_primitive.inverse())
print(
sqr(current_hexagonal_ori.direct_matrix()) -
sqr(comparison_hexagonal.direct_matrix()))
print("item %d" % item_no)
SC = ScoringContainer()
SC.model = current_hexagonal_ori
SC.reference = comparison_hexagonal
return SC
gamma = ground_truth_ori.unit_cell().parameters()[5]
alpha = ground_truth_ori.unit_cell().parameters()[3]
beta = ground_truth_ori.unit_cell().parameters()[4]
if gamma < 80 or gamma > 85 or alpha < 73 or alpha > 77 or beta < 73 or beta > 77:
continue
c_inv_r_best = ground_truth_ori.best_similarity_transformation(
other=refined_triclinic_ori,
fractional_length_tolerance=50.,
unimodular_generator_range=1)
print((sqr(c_inv_r_best)).determinant())
#c_inv_r_int = tuple([int(round(ij,0)) for ij in c_inv_r_best])
c_inv_r_int = tuple([int(round(ij, 0)) for ij in c_inv_r_best])
from cctbx import sgtbx
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(c_inv_r_int))
cb_op = sgtbx.change_of_basis_op(c_inv)
print(cb_op)
comparison_triclinic = ground_truth_ori.change_basis(cb_op)
print("comparison---> %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f" %
(comparison_triclinic.unit_cell().parameters()))
missetting_rot = sqr(refined_ori.direct_matrix()) * sqr(
ground_truth_ori.direct_matrix()).inverse()
print("deter", missetting_rot.determinant())
from LS49.missetting.mark0 import ScoringContainer
SC = ScoringContainer()
SC.model = refined_triclinic_ori
SC.reference = ground_truth_ori
angle_deg = SC.angular_rotation() * 180. / math.pi
#print missetting_rot.elems
def change_of_basis_op(self):
from cctbx import sgtbx
return sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(self._r_inv.elems, 1))).inverse()
