def run(args):
if "--fix_random_seeds" in args:
random.seed(1)
flex.set_random_seed(1)
scitbx.random.set_random_seed(1)
libtbx.utils.show_times_at_exit()
for i in range(10):
exercise_optimise_shelxl_weights()
exercise_weighting_schemes()
def run(args):
if "--fix_random_seeds" in args:
random.seed(1)
flex.set_random_seed(1)
scitbx.random.set_random_seed(1)
libtbx.utils.show_times_at_exit()
for i in range(10):
exercise_optimise_shelxl_weights()
exercise_weighting_schemes()
def generate_test_data(
space_group,
lattice_group=None,
unit_cell=None,
unit_cell_volume=1000,
seed=0,
d_min=1,
sigma=0.1,
sample_size=100,
map_to_p1=False,
twin_fractions=None,
map_to_minimum=True,
):
import random
if seed is not None:
flex.set_random_seed(seed)
random.seed(seed)
assert [unit_cell, lattice_group].count(None) > 0
sgi = space_group.info()
if unit_cell is not None:
cs = crystal.symmetry(unit_cell=unit_cell, space_group_info=sgi)
elif lattice_group is not None:
subgrps = subgroups(lattice_group).groups_parent_setting()
assert space_group in subgrps
cs = lattice_group.any_compatible_crystal_symmetry(
volume=unit_cell_volume).customized_copy(space_group_info=sgi)
else:
cs = sgi.any_compatible_crystal_symmetry(volume=unit_cell_volume)
if map_to_minimum:
cs = cs.minimum_cell()
intensities = generate_intensities(cs, d_min=d_min)
intensities.show_summary()
twin_ops = generate_twin_operators(intensities)
twin_ops = [
sgtbx.change_of_basis_op(op.operator.as_xyz()) for op in twin_ops
]
if twin_fractions is not None:
assert len(twin_fractions) == len(twin_ops)
assert len(
twin_fractions) == 1, "Only 1 twin component currently supported"
twin_op = twin_ops[0]
twin_fraction = twin_fractions[0]
intensities, intensities_twin = intensities.common_sets(
intensities.change_basis(twin_op).map_to_asu())
twinned_miller = intensities.customized_copy(
data=(1.0 - twin_fraction) * intensities.data() +
twin_fraction * intensities_twin.data(),
sigmas=flex.sqrt(
flex.pow2((1.0 - twin_fraction) * intensities.sigmas()) +
flex.pow2(twin_fraction * intensities_twin.sigmas())),
)
intensities = twinned_miller
cb_ops = twin_ops
cb_ops.insert(0, sgtbx.change_of_basis_op())
reindexing_ops = {}
datasets = []
rand_norm = scitbx.random.normal_distribution(mean=0, sigma=sigma)
g = scitbx.random.variate(rand_norm)
for i in range(sample_size):
cb_op = random.choice(cb_ops)
if cb_op.as_xyz() not in reindexing_ops:
reindexing_ops[cb_op.as_xyz()] = set()
reindexing_ops[cb_op.as_xyz()].add(i)
d = intensities.change_basis(cb_op).customized_copy(
crystal_symmetry=intensities.crystal_symmetry())
if map_to_p1:
cb_op_to_primitive = d.change_of_basis_op_to_primitive_setting()
d = d.change_basis(cb_op_to_primitive)
d = d.expand_to_p1()
d = d.customized_copy(data=d.data() + g(d.size()))
datasets.append(d)
return datasets, reindexing_ops
def exercise(space_group_info,
fixed_random_seed=True,
shifted_origin=None,
elements=None,
d_min=0.8,
grid_resolution_factor=1/3.,
verbose=False,
**kwds):
if elements is None:
n_C = 5
n_O = 1
n_N = 1
elements = ["C"]*n_C + ["O"]*n_O + ["N"]*n_N
if verbose:
print elements
target_space_group_type = space_group_info.type()
hall = sgtbx.space_group_symbols(
target_space_group_type.lookup_symbol()).hall()
print hall
if fixed_random_seed:
random.seed(1)
flex.set_random_seed(1)
# Generate a random structure in real space,
# compute its structure factors,
# that we will try to recover the symmetry of
target_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=elements,
use_u_iso=True,
random_u_iso=True,
random_u_iso_scale=0.04,
use_u_aniso=False,
)
if shifted_origin is None:
shifted_origin = flex.random_double(3)
shifted_origin = mat.col(shifted_origin)
if verbose:
print "new origin = (%.3f, %.3f, %.3f)" % shifted_origin.elems
print
target_structure_in_p1 = target_structure\
.expand_to_p1().apply_shift(shifted_origin)
target_f_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=False,
d_min=d_min
).structure_factors_from_scatterers(
xray_structure=target_structure_in_p1,
algorithm="direct").f_calc()
# Recover space group?
sf_symm = symmetry_search.structure_factor_symmetry(target_f_in_p1)
if verbose:
print sf_symm
solution_hall, target_hall = [
sgi.as_reference_setting().type().hall_symbol()
for sgi in (sf_symm.space_group_info,
target_structure.space_group_info()) ]
assert solution_hall == target_hall, (solution_hall, target_hall)
# Shift maximises goodness of symmetry?
gos, solution_f = sf_symm.symmetrised_structure_factors()
if space_group_info.type().hall_symbol() != ' P 1':
assert gos.correlation > 0.99
assert gos.gradient == (0, 0, 0)
gos_away_from_max = sf_symm.symmetrised_structure_factors(
delta=mat.col((0.1, 0.1, 0.1)))[0]
assert gos_away_from_max.correlation < 0.9, gos_away_from_max.correlation
# Recovered origin
"""The sequence of transform read:
----->target structure
^ V
^ V (1, shifted_origin=sigma)
^ V
^ shifted target
^ V
^ V sf_symm.cb_op_to_primitive = (P, 0)
^ V
^ shifted target in primitive cell = shifted solution in primitive cell
^ V
^ V (1, -sf_symm.origin=-s)
^ V
^ solution in primitive cell
^ V
^ V solution_to_target_cb_op = (Q, q)
^ V
^------------
The total transfrom from the target structure back to it reads
(QP, q') with q' = (Q,q)(-s + P sigma) = (Q,q)delta_o
with
delta_o = sf_symm.cb_op_to_primitive(shifted_origin) - sf_symm.origin
(Q, q') must leave the target structure space group invariant.
Most of the time Q is the unit matrix and the test boils down to check
whether delta is an allowed origin shift after changing to the input cell
but it does not hurt to do the more general test all the time.
"""
solution_to_target_cb_op = (
target_structure.space_group_info()
.change_of_basis_op_to_reference_setting().inverse()
*
sf_symm.space_group_info
.change_of_basis_op_to_reference_setting())
if verbose:
print
print "solution -> target: %s" % solution_to_target_cb_op.as_xyz()
delta_o = (mat.col(sf_symm.cb_op_to_primitive(shifted_origin))
- sf_symm.origin)
delta = mat.col(solution_to_target_cb_op(delta_o))
stabilising_cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(
(solution_to_target_cb_op*sf_symm.cb_op_to_primitive).c().r(),
sgtbx.tr_vec((delta*72).as_int()*2, tr_den=144)))
# guarding against rounding errors on some platforms (e.g. FC8)
# meaning that (delta*144).as_int() would not work.
target_sg = target_structure.space_group()
assert target_sg == target_sg.change_basis(stabilising_cb_op)
def run(args):
master_phil = libtbx.phil.parse("""
d_min = 0.5
.type = float
constrained_refinement = True
.type = bool
random_seed = 1
.type = int
shake_sites_rmsd = 0.5
.type = float
shake_adp_spread = 20
.type = float
grad_site=True
.type = bool
grad_u_iso=False
.type = bool
grad_u_aniso=False
.type = bool
grad_occupancy=False
.type = bool
grad_fp_fdp=False
.type = bool
lbfgs_m = 5
.type = int
lbfgs_max_iterations = 1000
.type = int
verbose = 0
.type = int
""")
argument_interpreter = master_phil.command_line_argument_interpreter()
phil_objects = []
remaining_args = []
for arg in args:
if (arg.find("=") >= 0):
phil_objects.append(argument_interpreter.process(arg=arg))
else:
remaining_args.append(arg)
work_phil = master_phil.fetch(sources=phil_objects)
work_phil.show()
params = work_phil.extract()
if params.random_seed is not None:
import scitbx.random
import random
scitbx.random.set_random_seed(params.random_seed)
flex.set_random_seed(params.random_seed)
random.seed(params.random_seed)
if len(remaining_args):
assert len(remaining_args) == 1
file_path = remaining_args[0]
root, ext = os.path.splitext(file_path)
if ext == ".cif":
xs_dict = xray.structure.from_cif(file_path=file_path)
assert len(
xs_dict) == 1, "CIF should contain only one xray structure"
xs = xs_dict.values()[0]
xs.show_summary().show_scatterers()
print
constraints_list = None
t_celsius = 20
else:
raise RuntimeError("Only CIF format currently supported!")
else:
test_case = tst_constrained_structure.sucrose_test_case(None)
t_celsius = test_case.t_celsius
xs = test_case.xray_structure
constraints_list = test_case.constraints
#from cctbx import adptbx
#for sc in xs.scatterers():
#if sc.flags.use_u_aniso():
#sc.u_iso = adptbx.u_star_as_u_iso(xs.unit_cell(), sc.u_star)
#sc.set_use_u_iso_only()
if not params.constrained_refinement:
constraints_list = []
exercise_constrained_lbfgs(
xray_structure=xs,
constraints_list=constraints_list,
t_celsius=t_celsius,
d_min=params.d_min,
shake_sites_rmsd=params.shake_sites_rmsd,
shake_u_iso_spread=params.shake_adp_spread,
grad_site=params.grad_site,
grad_u_iso=params.grad_u_iso,
grad_u_aniso=params.grad_u_aniso,
grad_occupancy=params.grad_occupancy,
grad_fp_fdp=params.grad_fp_fdp,
lbfgs_m=params.lbfgs_m,
lbfgs_max_iterations=params.lbfgs_max_iterations,
verbose=params.verbose)
def exercise(space_group_info,
fixed_random_seed=True,
shifted_origin=None,
elements=None,
d_min=0.8,
grid_resolution_factor=1/3.,
verbose=False,
**kwds):
if elements is None:
n_C = 5
n_O = 1
n_N = 1
elements = ["C"]*n_C + ["O"]*n_O + ["N"]*n_N
if verbose:
print(elements)
target_space_group_type = space_group_info.type()
hall = sgtbx.space_group_symbols(
target_space_group_type.lookup_symbol()).hall()
print(hall)
if fixed_random_seed:
random.seed(1)
flex.set_random_seed(1)
# Generate a random structure in real space,
# compute its structure factors,
# that we will try to recover the symmetry of
target_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=elements,
use_u_iso=True,
random_u_iso=True,
random_u_iso_scale=0.04,
use_u_aniso=False,
)
if shifted_origin is None:
shifted_origin = flex.random_double(3)
shifted_origin = mat.col(shifted_origin)
if verbose:
print("new origin = (%.3f, %.3f, %.3f)" % shifted_origin.elems)
print()
target_structure_in_p1 = target_structure\
.expand_to_p1().apply_shift(shifted_origin)
target_f_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=False,
d_min=d_min
).structure_factors_from_scatterers(
xray_structure=target_structure_in_p1,
algorithm="direct").f_calc()
# Recover space group?
sf_symm = symmetry_search.structure_factor_symmetry(target_f_in_p1)
if verbose:
print(sf_symm)
solution_hall, target_hall = [
sgi.as_reference_setting().type().hall_symbol()
for sgi in (sf_symm.space_group_info,
target_structure.space_group_info()) ]
assert solution_hall == target_hall, (solution_hall, target_hall)
# Shift maximises goodness of symmetry?
gos, solution_f = sf_symm.symmetrised_structure_factors()
if space_group_info.type().hall_symbol() != ' P 1':
assert gos.correlation > 0.99
assert gos.gradient == (0, 0, 0)
gos_away_from_max = sf_symm.symmetrised_structure_factors(
delta=mat.col((0.1, 0.1, 0.1)))[0]
assert gos_away_from_max.correlation < 0.9, gos_away_from_max.correlation
# Recovered origin
"""The sequence of transform read:
----->target structure
^ V
^ V (1, shifted_origin=sigma)
^ V
^ shifted target
^ V
^ V sf_symm.cb_op_to_primitive = (P, 0)
^ V
^ shifted target in primitive cell = shifted solution in primitive cell
^ V
^ V (1, -sf_symm.origin=-s)
^ V
^ solution in primitive cell
^ V
^ V solution_to_target_cb_op = (Q, q)
^ V
^------------
The total transfrom from the target structure back to it reads
(QP, q') with q' = (Q,q)(-s + P sigma) = (Q,q)delta_o
with
delta_o = sf_symm.cb_op_to_primitive(shifted_origin) - sf_symm.origin
(Q, q') must leave the target structure space group invariant.
Most of the time Q is the unit matrix and the test boils down to check
whether delta is an allowed origin shift after changing to the input cell
but it does not hurt to do the more general test all the time.
"""
solution_to_target_cb_op = (
target_structure.space_group_info()
.change_of_basis_op_to_reference_setting().inverse()
*
sf_symm.space_group_info
.change_of_basis_op_to_reference_setting())
if verbose:
print()
print("solution -> target: %s" % solution_to_target_cb_op.as_xyz())
delta_o = (mat.col(sf_symm.cb_op_to_primitive(shifted_origin))
- sf_symm.origin)
delta = mat.col(solution_to_target_cb_op(delta_o))
stabilising_cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(
(solution_to_target_cb_op*sf_symm.cb_op_to_primitive).c().r(),
sgtbx.tr_vec((delta*72).as_int()*2, tr_den=144)))
# guarding against rounding errors on some platforms (e.g. FC8)
# meaning that (delta*144).as_int() would not work.
target_sg = target_structure.space_group()
assert target_sg == target_sg.change_basis(stabilising_cb_op)
def run(args):
master_phil = libtbx.phil.parse("""
d_min = 0.5
.type = float
constrained_refinement = True
.type = bool
random_seed = 1
.type = int
shake_sites_rmsd = 0.5
.type = float
shake_adp_spread = 20
.type = float
grad_site=True
.type = bool
grad_u_iso=False
.type = bool
grad_u_aniso=False
.type = bool
grad_occupancy=False
.type = bool
grad_fp_fdp=False
.type = bool
lbfgs_m = 5
.type = int
lbfgs_max_iterations = 1000
.type = int
verbose = 0
.type = int
""")
argument_interpreter = master_phil.command_line_argument_interpreter()
phil_objects = []
remaining_args = []
for arg in args:
if (arg.find("=") >= 0):
phil_objects.append(argument_interpreter.process(arg=arg))
else:
remaining_args.append(arg)
work_phil = master_phil.fetch(sources=phil_objects)
work_phil.show()
params = work_phil.extract()
if params.random_seed is not None:
import scitbx.random
import random
scitbx.random.set_random_seed(params.random_seed)
flex.set_random_seed(params.random_seed)
random.seed(params.random_seed)
if len(remaining_args):
assert len(remaining_args) == 1
file_path = remaining_args[0]
root, ext = os.path.splitext(file_path)
if ext == ".cif":
xs_dict = xray.structure.from_cif(file_path=file_path)
assert len(xs_dict) == 1, "CIF should contain only one xray structure"
xs = xs_dict.values()[0]
xs.show_summary().show_scatterers()
print
constraints_list = None
t_celsius = 20
else:
raise RuntimeError("Only CIF format currently supported!")
else:
test_case = tst_constrained_structure.sucrose_test_case(None)
t_celsius = test_case.t_celsius
xs = test_case.xray_structure
constraints_list = test_case.constraints
#from cctbx import adptbx
#for sc in xs.scatterers():
#if sc.flags.use_u_aniso():
#sc.u_iso = adptbx.u_star_as_u_iso(xs.unit_cell(), sc.u_star)
#sc.set_use_u_iso_only()
if not params.constrained_refinement:
constraints_list = []
exercise_constrained_lbfgs(xray_structure=xs,
constraints_list=constraints_list,
t_celsius=t_celsius,
d_min=params.d_min,
shake_sites_rmsd=params.shake_sites_rmsd,
shake_u_iso_spread=params.shake_adp_spread,
grad_site=params.grad_site,
grad_u_iso=params.grad_u_iso,
grad_u_aniso=params.grad_u_aniso,
grad_occupancy=params.grad_occupancy,
grad_fp_fdp=params.grad_fp_fdp,
lbfgs_m=params.lbfgs_m,
lbfgs_max_iterations=params.lbfgs_max_iterations,
verbose=params.verbose)