def finite_differences_scalar(parameter_name,
target_ftor,
structure,
delta=0.00001):
derivatives = flex.double()
for i_scatterer in range(structure.scatterers().size()):
target_values = []
for d_sign in (-1, 1):
modified_structure = structure.deep_copy_scatterers()
ms = modified_structure.scatterers()[i_scatterer]
if (parameter_name == "u_iso" and ms.flags.use_u_iso()):
ms.u_iso += d_sign * delta
elif (parameter_name == "tan_u_iso" and ms.flags.use_u_iso()):
assert ms.u_iso >= 0
x = math.tan(ms.u_iso * math.pi /
adptbx.b_as_u(ms.flags.param) -
math.pi / 2) + d_sign * delta
ms.u_iso = adptbx.b_as_u(
ms.flags.param) / math.pi * (math.atan(x) + math.pi / 2)
elif (parameter_name == "occupancy"):
ms.occupancy += d_sign * delta
elif (parameter_name == "fp"):
ms.fp = ms.fp + d_sign * delta
elif (parameter_name == "fdp"):
ms.fdp = ms.fdp + d_sign * delta
else:
raise RuntimeError
f_calc = target_ftor.f_obs().structure_factors_from_scatterers(
xray_structure=modified_structure,
algorithm="direct").f_calc()
target_result = target_ftor(f_calc, compute_derivatives=False)
target_values.append(target_result.target())
derivative = (target_values[1] - target_values[0]) / (2 * delta)
derivatives.append(derivative)
return derivatives
def read_scatterer(flds, default_b_iso=3.0):
scatterer = xray.scatterer(scattering_type="const")
# Label [ScatFact] x y z [Occ [Biso]]
try:
scatterer.label = flds[0]
try:
float(flds[1])
except Exception:
offs = 2
scatterer.scattering_type = eltbx.xray_scattering.get_standard_label(label=flds[1], exact=True)
else:
offs = 1
scatterer.scattering_type = eltbx.xray_scattering.get_standard_label(label=flds[0], exact=False)
site = flds[offs : offs + 3]
for i in xrange(3):
site[i] = float(site[i])
scatterer.site = site
scatterer.occupancy = 1.0
scatterer.set_use_u_iso_only()
scatterer.u_iso = adptbx.b_as_u(default_b_iso)
if len(flds) >= offs + 4:
scatterer.occupancy = float(flds[offs + 3])
if len(flds) == offs + 5:
scatterer.u_iso = adptbx.b_as_u(float(flds[offs + 4]))
else:
assert len(flds) < offs + 5
except Exception:
raise cgi_utils.FormatError, flds
return scatterer
def finite_differences_scalar(parameter_name, target_ftor, structure,
delta=0.00001):
derivatives = flex.double()
for i_scatterer in xrange(structure.scatterers().size()):
target_values = []
for d_sign in (-1, 1):
modified_structure = structure.deep_copy_scatterers()
ms = modified_structure.scatterers()[i_scatterer]
if (parameter_name == "u_iso" and ms.flags.use_u_iso()):
ms.u_iso += d_sign * delta
elif (parameter_name == "tan_u_iso" and ms.flags.use_u_iso()):
assert ms.u_iso >= 0
x = math.tan(ms.u_iso*math.pi/adptbx.b_as_u(ms.flags.param)-math.pi/2) + d_sign * delta
ms.u_iso = adptbx.b_as_u(ms.flags.param)/math.pi*(math.atan(x)+math.pi/2)
elif (parameter_name == "occupancy"):
ms.occupancy += d_sign * delta
elif (parameter_name == "fp"):
ms.fp = ms.fp + d_sign * delta
elif (parameter_name == "fdp"):
ms.fdp = ms.fdp + d_sign * delta
else:
raise RuntimeError
f_calc = target_ftor.f_obs().structure_factors_from_scatterers(
xray_structure=modified_structure,
algorithm="direct").f_calc()
target_result = target_ftor(f_calc, compute_derivatives=False)
target_values.append(target_result.target())
derivative = (target_values[1] - target_values[0]) / (2 * delta)
derivatives.append(derivative)
return derivatives
def read_scatterer(flds, default_b_iso=3.0):
scatterer = xray.scatterer(scattering_type="const")
# Label [ScatFact] x y z [Occ [Biso]]
try:
scatterer.label = flds[0]
try:
float(flds[1])
except Exception:
offs = 2
scatterer.scattering_type = eltbx.xray_scattering.get_standard_label(
label=flds[1], exact=True)
else:
offs = 1
scatterer.scattering_type = eltbx.xray_scattering.get_standard_label(
label=flds[0], exact=False)
site = flds[offs:offs + 3]
for i in xrange(3):
site[i] = float(site[i])
scatterer.site = site
scatterer.occupancy = 1.
scatterer.set_use_u_iso_only()
scatterer.u_iso = adptbx.b_as_u(default_b_iso)
if (len(flds) >= offs + 4):
scatterer.occupancy = float(flds[offs + 3])
if (len(flds) == offs + 5):
scatterer.u_iso = adptbx.b_as_u(float(flds[offs + 4]))
else:
assert (len(flds) < offs + 5)
except Exception:
raise cgi_utils.FormatError, flds
return scatterer
def apply_aniso_correction(self, f_array=None):
if self.b_cart is None or self.b_cart_aniso_removed is None:
return f_array # nothing to do
from mmtbx.scaling import absolute_scaling
from cctbx import adptbx
u_star = adptbx.u_cart_as_u_star(f_array.unit_cell(),
adptbx.b_as_u(self.b_cart))
u_star_aniso_removed = adptbx.u_cart_as_u_star(
f_array.unit_cell(), adptbx.b_as_u(self.b_cart_aniso_removed))
no_aniso_array = absolute_scaling.anisotropic_correction(
f_array, 0.0, u_star, must_be_greater_than=-0.0001)
no_aniso_array = absolute_scaling.anisotropic_correction(
no_aniso_array,
0.0,
u_star_aniso_removed,
must_be_greater_than=-0.0001)
no_aniso_array = no_aniso_array.set_observation_type(f_array)
return no_aniso_array
def __init__(self,
label="",
site=(0, 0, 0),
u=None,
occupancy=1,
scattering_info="",
b=None):
assert u is None or b is None
if (b is not None): u = adptbx.b_as_u(b)
elif (u is None): u = 0
if (type(scattering_info) == type("")):
if (scattering_info == ""):
scattering_info = neutron_news_1992_table(label, 0)
else:
scattering_info = neutron_news_1992_table(scattering_info, 1)
self.label = label
self.site = site
try:
self.u_iso = float(u)
self.anisotropic_flag = False
except Exception:
assert len(u) == 6
self.anisotropic_flag = True
self.u_star = tuple([float(uij) for uij in u])
self.occupancy = occupancy
self.scattering_info = scattering_info
self._multiplicity = 0
self._weight = 0
def iass_as_xray_structure(self, iass):
ias_xray_structure = xray.structure(
crystal_symmetry = self.xray_structure.crystal_symmetry())
for ias in iass:
assert ias.status is not None
if(ias.status):
if(self.params.use_map):
site_cart = ias.peak_position_cart
b_iso = ias.b_iso
q = ias.q
else:
site_cart = ias.site_cart_predicted
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
q = self.params.initial_ias_occupancy
if(b_iso is None):
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
if(q is None):
q = self.params.initial_ias_occupancy
if(site_cart is None):
site_cart = ias.site_cart_predicted
assert [b_iso, q].count(None) == 0
if(site_cart is not None):
ias_scatterer = xray.scatterer(
label = ias.name,
scattering_type = ias.name,
site = self.xray_structure.unit_cell().fractionalize(site_cart),
u = adptbx.b_as_u(b_iso),
occupancy = q)
ias_xray_structure.add_scatterer(ias_scatterer)
ias_xray_structure.scattering_type_registry(
custom_dict = ias_scattering_dict)
return ias_xray_structure
def ml_normalisation(self, aniso=False):
# estimate number of residues per unit cell
mr = matthews.matthews_rupp(self.intensities.crystal_symmetry())
n_residues = mr.n_residues
# estimate B-factor and scale factors for normalisation
if aniso:
normalisation = absolute_scaling.ml_aniso_absolute_scaling(
self.intensities, n_residues=n_residues)
u_star = normalisation.u_star
else:
normalisation = absolute_scaling.ml_iso_absolute_scaling(
self.intensities, n_residues=n_residues)
u_star = adptbx.b_as_u(
adptbx.u_iso_as_u_star(
self.intensities.unit_cell(), normalisation.b_wilson))
# apply scales
self.intensities = self.intensities.customized_copy(
data=scaling.ml_normalise_aniso(
self.intensities.indices(), self.intensities.data(),
normalisation.p_scale, self.intensities.unit_cell(),
u_star),
sigmas=scaling.ml_normalise_aniso(
self.intensities.indices(), self.intensities.sigmas(),
normalisation.p_scale, self.intensities.unit_cell(),
u_star)).set_info(self.intensities.info())
# record output in log file
s = StringIO()
mr.show(out=s)
normalisation.show(out=s)
logger.info(s.getvalue())
def __init__(self, label="",
site=(0,0,0),
u=None,
occupancy=1,
scattering_info="",
b=None):
assert u is None or b is None
if (b is not None): u = adptbx.b_as_u(b)
elif (u is None): u = 0
if (type(scattering_info) == type("")):
if (scattering_info == ""):
scattering_info = neutron_news_1992_table(label, 0)
else:
scattering_info = neutron_news_1992_table(scattering_info, 1)
self.label = label
self.site = site
try:
self.u_iso = float(u)
self.anisotropic_flag = False
except Exception:
assert len(u) == 6
self.anisotropic_flag = True
self.u_star = tuple([float(uij) for uij in u])
self.occupancy = occupancy
self.scattering_info = scattering_info
self._multiplicity = 0
self._weight = 0
def _find_peaks(self, min_peak_peak_distance=1.5):
cg = maptbx.crystal_gridding(
space_group_info=self.model.crystal_symmetry().space_group_info(),
symmetry_flags=maptbx.use_space_group_symmetry,
unit_cell=self.unit_cell,
pre_determined_n_real=self.map_data.accessor().all())
cgt = maptbx.crystal_gridding_tags(gridding=cg)
peak_search_parameters = maptbx.peak_search_parameters(
peak_search_level=3,
max_peaks=0,
peak_cutoff=self.cutoff,
interpolate=True,
min_distance_sym_equiv=0,
general_positions_only=False, # ???????XXXXXXXXXXXXXX
min_cross_distance=min_peak_peak_distance,
min_cubicle_edge=5)
psr = cgt.peak_search(parameters=peak_search_parameters,
map=self.map_data).all(max_clusters=99999999)
# Convert peaks into water xray.structure
mean_b = flex.mean(self.model.get_hierarchy().atoms().extract_b())
sp = crystal.special_position_settings(self.model.crystal_symmetry())
scatterers = flex.xray_scatterer()
for site_frac in psr.sites():
sc = xray.scatterer(label="O",
site=site_frac,
u=adptbx.b_as_u(mean_b),
occupancy=1.0)
scatterers.append(sc)
self.xrs_water = xray.structure(sp, scatterers)
#
self.ma.add(" total peaks found: %d" %
self.xrs_water.scatterers().size())
self.ma.add(" B factors set to : %8.3f" % mean_b)
if (self.debug): self._write_pdb_file(file_name_prefix="hoh_all_peaks")
def debye_waller_factors(self,
miller_index=None,
miller_indices=None,
u_iso=None,
b_iso=None,
u_cart=None,
b_cart=None,
u_cif=None,
u_star=None,
exp_arg_limit=50,
truncate_exp_arg=False):
assert [miller_index, miller_indices].count(None) == 1
assert [u_iso, b_iso, u_cart, b_cart, u_cif, u_star].count(None) == 5
from cctbx import adptbx
h = miller_index
if (h is None): h = miller_indices
if (u_iso is not None):
b_iso = adptbx.u_as_b(u_iso)
if (b_iso is not None):
return adptbx.debye_waller_factor_b_iso(
self.stol_sq(h),
b_iso, exp_arg_limit, truncate_exp_arg)
if (b_cart is not None):
u_cart = adptbx.b_as_u(b_cart)
if (u_cart is not None):
u_star = adptbx.u_cart_as_u_star(self, u_cart)
if (u_cif is not None):
u_star = adptbx.u_cif_as_u_star(self, u_cif)
assert u_star is not None
return adptbx.debye_waller_factor_u_star(
h, u_star, exp_arg_limit, truncate_exp_arg)
def _append_to_model(self):
mean_b = flex.mean(self.model.get_hierarchy().atoms().extract_b())
self.ma.add(" new water B factors will be set to mean B: %8.3f" %
mean_b)
sp = crystal.special_position_settings(self.model.crystal_symmetry())
scatterers = flex.xray_scatterer()
for site_frac in self.sites_frac_water:
sc = xray.scatterer(label="O",
site=site_frac,
u=adptbx.b_as_u(mean_b),
occupancy=1.0)
scatterers.append(sc)
xrs_water = xray.structure(sp, scatterers)
#
chain_ids_taken = []
for chain in self.model.get_hierarchy().chains():
chain_ids_taken.append(chain.id)
unique_taken = list(set(chain_ids_taken))
if (len(unique_taken) == 1):
solvent_chain = unique_taken[0]
else:
for solvent_chain in all_chain_ids():
if (not solvent_chain in chain_ids_taken):
break
self.ma.add(" new water will have chain ID: '%s'" % solvent_chain)
#
self.model.add_solvent(solvent_xray_structure=xrs_water,
atom_name="O",
residue_name="HOH",
chain_id=solvent_chain,
refine_adp="isotropic")
def get_sf(k_sol,
b_sol,
b_cart,
xrs,
miller_set=None,
d_min=None,
twin_law=None,
sfg_params=None):
random.seed(0)
flex.set_random_seed(0)
if (miller_set is None):
assert d_min is not None
f_dummy = abs(
xrs.structure_factors(d_min=d_min, anomalous_flag=False).f_calc())
else:
f_dummy = miller_set
assert d_min is None
r_free_flags = f_dummy.generate_r_free_flags(fraction=0.1)
fmodel = mmtbx.f_model.manager(r_free_flags=r_free_flags,
f_obs=f_dummy,
sf_and_grads_accuracy_params=sfg_params,
xray_structure=xrs,
twin_law=twin_law)
ss = 1. / flex.pow2(r_free_flags.d_spacings().data()) / 4.
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(r_free_flags.indices(),
u_star)
fmodel.update_xray_structure(xray_structure=xrs,
update_f_calc=True,
update_f_mask=True)
fmodel.update_core(k_mask=k_mask, k_anisotropic=k_anisotropic)
f_obs = abs(fmodel.f_model())
return f_obs, r_free_flags
def iass_as_xray_structure(self, iass):
ias_xray_structure = xray.structure(
crystal_symmetry = self.xray_structure.crystal_symmetry())
for ias in iass:
assert ias.status is not None
if(ias.status):
if(self.params.use_map):
site_cart = ias.peak_position_cart
b_iso = ias.b_iso
q = ias.q
else:
site_cart = ias.site_cart_predicted
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
q = self.params.initial_ias_occupancy
if(b_iso is None):
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
if(q is None):
q = self.params.initial_ias_occupancy
if(site_cart is None):
site_cart = ias.site_cart_predicted
assert [b_iso, q].count(None) == 0
if(site_cart is not None):
ias_scatterer = xray.scatterer(
label = ias.name,
scattering_type = ias.name,
site = self.xray_structure.unit_cell().fractionalize(site_cart),
u = adptbx.b_as_u(b_iso),
occupancy = q)
ias_xray_structure.add_scatterer(ias_scatterer)
ias_xray_structure.scattering_type_registry(
custom_dict = ias_scattering_dict)
return ias_xray_structure
def debye_waller_factors(self,
miller_index=None,
miller_indices=None,
u_iso=None,
b_iso=None,
u_cart=None,
b_cart=None,
u_cif=None,
u_star=None,
exp_arg_limit=50,
truncate_exp_arg=False):
assert [miller_index, miller_indices].count(None) == 1
assert [u_iso, b_iso, u_cart, b_cart, u_cif, u_star].count(None) == 5
from cctbx import adptbx
h = miller_index
if (h is None): h = miller_indices
if (u_iso is not None):
b_iso = adptbx.u_as_b(u_iso)
if (b_iso is not None):
return adptbx.debye_waller_factor_b_iso(
self.stol_sq(h),
b_iso, exp_arg_limit, truncate_exp_arg)
if (b_cart is not None):
u_cart = adptbx.b_as_u(b_cart)
if (u_cart is not None):
u_star = adptbx.u_cart_as_u_star(self, u_cart)
if (u_cif is not None):
u_star = adptbx.u_cif_as_u_star(self, u_cif)
assert u_star is not None
return adptbx.debye_waller_factor_u_star(
h, u_star, exp_arg_limit, truncate_exp_arg)
def print_atom_statisitics(self,
selection_string='name CA',
selection_bool_array=None,
model=None):
if model == None:
model = self.ensemble_obj.model
pdb_hierarchy = model.get_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
if selection_bool_array == None:
selection_bool_array = pdb_hierarchy.atom_selection_cache(
).selection(selection_string)
xrs = model.get_xray_structure().deep_copy_scatterers()
xrs.convert_to_isotropic()
b_iso_atoms = xrs.scatterers().extract_u_iso() / adptbx.b_as_u(1)
q_atoms = xrs.scatterers().extract_occupancies()
for i_seq, x in enumerate(selection_bool_array):
if x:
atom_info = pdb_atoms[i_seq].fetch_labels()
if self.ensemble_obj.er_data.ke_protein_running == None:
print(' {0:6} {1:6} {2:6} {3:6} {4:6d} {5:6.3f} {6:6.3f} '.
format(atom_info.name, atom_info.resseq,
atom_info.resname, atom_info.chain_id, i_seq,
b_iso_atoms[i_seq], q_atoms[i_seq]),
file=self.ensemble_obj.log)
else:
print(
' {0:6} {1:6} {2:6} {3:6} {4:6d} {5:6.3f} {6:6.3f} {7:6.3f}'
.format(
atom_info.name, atom_info.resseq,
atom_info.resname, atom_info.chain_id, i_seq,
b_iso_atoms[i_seq], q_atoms[i_seq], self.
ensemble_obj.er_data.ke_protein_running[i_seq]),
file=self.ensemble_obj.log)
def exercise_05_k_sol_b_sol_only(d_min=2.0):
xray_structure = get_xray_structure_from_file()
k_sol = 0.33
b_sol = 34.0
b_cart = [1, 2, 3, 0, 4, 0]
f_obs, r_free_flags = get_f_obs_freer(d_min=d_min,
k_sol=k_sol,
b_sol=b_sol,
b_cart=b_cart,
xray_structure=xray_structure)
fmodel = mmtbx.f_model.manager(r_free_flags=r_free_flags,
f_obs=f_obs,
xray_structure=xray_structure)
params = bss.master_params.extract()
params.anisotropic_scaling = False
params.number_of_macro_cycles = 5
u_star = adptbx.u_cart_as_u_star(fmodel.f_obs().unit_cell(),
adptbx.b_as_u(b_cart))
fmodel_kbu = mmtbx.f_model.manager_kbu(f_obs=fmodel.f_obs(),
f_calc=fmodel.f_calc(),
f_masks=fmodel.arrays.core.f_masks,
f_part1=fmodel.arrays.core.f_part1,
f_part2=fmodel.arrays.core.f_part2,
ss=fmodel.ss,
u_star=u_star)
r_work_start = fmodel_kbu.r_factor()
result = bss.bulk_solvent_and_scales(fmodel_kbu=fmodel_kbu, params=params)
r_work = result.fmodel_kbu.r_factor() * 100.
assert r_work_start > 0.05
#
assert approx_equal(r_work, 0.0, eps=1.e-4)
assert approx_equal(result.k_sols()[0], k_sol, eps=1.e-4)
assert approx_equal(result.b_sols()[0], b_sol, eps=1.e-4)
assert approx_equal(result.b_cart(), b_cart, eps=1.e-4)
def run_00():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol=symbol)
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["N"] * 100,
volume_per_atom=50.0,
random_u_iso=True)
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group, reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(
xrs.unit_cell(), adptbx.random_u_cart(u_scale=1, u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start = adptbx.u_as_b(
adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0] + b_cart_start[1] + b_cart_start[2]) / 3
b_cart_start = [
b_cart_start[0] - tr, b_cart_start[1] - tr, b_cart_start[2] - tr,
b_cart_start[3], b_cart_start[4], b_cart_start[5]
]
tr = (b_cart_start[0] + b_cart_start[1] + b_cart_start[2]) / 3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
F = xrs.structure_factors(d_min=2.0).f_calc()
u_star = adptbx.u_cart_as_u_star(F.unit_cell(),
adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data=flex.abs(fc.data() * fbc))
t0 = time.time()
#
obj = bulk_solvent.aniso_u_scaler(
f_model_abs=flex.abs(fc.data()),
f_obs=f_obs.data(),
miller_indices=f_obs.indices(),
adp_constraint_matrix=adp_constraints.gradient_sum_matrix())
time_aniso_u_scaler += (time.time() - t0)
b_cart_final = adptbx.u_as_b(
adptbx.u_star_as_u_cart(
f_obs.unit_cell(),
adp_constraints.all_params(tuple(obj.u_star_independent))))
#
obj = bulk_solvent.aniso_u_scaler(f_model_abs=flex.abs(fc.data()),
f_obs=f_obs.data(),
miller_indices=f_obs.indices())
b_cart_final2 = adptbx.u_as_b(
adptbx.u_star_as_u_cart(f_obs.unit_cell(), tuple(obj.u_star)))
#
assert approx_equal(b_cart_final, b_cart_final2)
#print "Output b_cart:", " ".join(["%8.4f"%i for i in b_cart_final])
assert approx_equal(b_cart_start, b_cart_final, 1.e-4)
print("Time (aniso_u_scaler only): %6.4f" % time_aniso_u_scaler)
def _ml_normalisation(intensities, aniso):
# estimate number of residues per unit cell
mr = matthews.matthews_rupp(intensities.crystal_symmetry())
n_residues = mr.n_residues
# estimate B-factor and scale factors for normalisation
if aniso:
normalisation = absolute_scaling.ml_aniso_absolute_scaling(
intensities, n_residues=n_residues
)
u_star = normalisation.u_star
else:
normalisation = absolute_scaling.ml_iso_absolute_scaling(
intensities, n_residues=n_residues
)
u_star = adptbx.b_as_u(
adptbx.u_iso_as_u_star(intensities.unit_cell(), normalisation.b_wilson)
)
# record output in log file
if aniso:
b_cart = normalisation.b_cart
logger.info("ML estimate of overall B_cart value:")
logger.info(
"""\
%5.2f, %5.2f, %5.2f
%12.2f, %5.2f
%19.2f"""
% (b_cart[0], b_cart[3], b_cart[4], b_cart[1], b_cart[5], b_cart[2])
)
else:
logger.info("ML estimate of overall B value:")
logger.info(" %5.2f A**2" % normalisation.b_wilson)
logger.info("ML estimate of -log of scale factor:")
logger.info(" %5.2f" % (normalisation.p_scale))
s = StringIO()
mr.show(out=s)
normalisation.show(out=s)
logger.debug(s.getvalue())
# apply scales
return intensities.customized_copy(
data=scaling.ml_normalise_aniso(
intensities.indices(),
intensities.data(),
normalisation.p_scale,
intensities.unit_cell(),
u_star,
),
sigmas=scaling.ml_normalise_aniso(
intensities.indices(),
intensities.sigmas(),
normalisation.p_scale,
intensities.unit_cell(),
u_star,
),
)
def __init__(self, label="", site=(0, 0, 0), u=None, occupancy=1, scattering_type=None, fp=0, fdp=0, b=None):
assert u is None or b is None
if b is not None:
u = adptbx.b_as_u(b)
elif u is None:
u = 0
if scattering_type is None:
scattering_type = eltbx.xray_scattering.get_standard_label(label=label, exact=False)
ext.scatterer.__init__(self, label, site, u, occupancy, scattering_type, fp, fdp)
def exercise(space_group_info, anomalous_flag,
d_min=1.0, reflections_per_bin=200, n_bins=10, verbose=0):
elements = ("N", "C", "C", "O") * 5
structure_factors = random_structure.xray_structure(
space_group_info,
elements=elements,
volume_per_atom=50.,
min_distance=1.5,
general_positions_only=True,
use_u_aniso=False,
u_iso=adptbx.b_as_u(10)
).structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct")
if (0 or verbose):
structure_factors.xray_structure().show_summary()
asu_contents = dicts.with_default_value(0)
for elem in elements: asu_contents[elem] += 1
f_calc = abs(structure_factors.f_calc())
f_calc.setup_binner(
auto_binning=True,
reflections_per_bin=reflections_per_bin,
n_bins=n_bins)
if (0 or verbose):
f_calc.binner().show_summary()
for k_given in [1,0.1,0.01,10,100]:
f_obs = miller.array(
miller_set=f_calc,
data=f_calc.data()*k_given).set_observation_type_xray_amplitude()
f_obs.use_binner_of(f_calc)
wp = statistics.wilson_plot(f_obs, asu_contents, e_statistics=True)
if (0 or verbose):
print "wilson_k, wilson_b:", wp.wilson_k, wp.wilson_b
print "space group:", space_group_info.group().type().hall_symbol()
print "<E^2-1>:", wp.mean_e_sq_minus_1
assert 0.8 < wp.wilson_k/k_given < 1.2
assert 0.64 < wp.wilson_intensity_scale_factor/(k_given*k_given) < 1.44
assert 9 < wp.wilson_b < 11
assert wp.xy_plot_info().fit_correlation == wp.fit_correlation
if space_group_info.group().is_centric():
assert 0.90 < wp.mean_e_sq_minus_1 < 1.16
assert 3.15 < wp.percent_e_sq_gt_2 < 6.5
else:
assert 0.65 < wp.mean_e_sq_minus_1 < 0.90
assert 1.0 < wp.percent_e_sq_gt_2 < 3.15
assert wp.normalised_f_obs.size() == f_obs.size()
f_obs = f_calc.array(data=flex.double(f_calc.indices().size(), 0))
f_obs.use_binner_of(f_calc)
n_bins = f_obs.binner().n_bins_used()
try:
statistics.wilson_plot(f_obs, asu_contents)
except RuntimeError, e:
assert not show_diff(str(e), """\
wilson_plot error: %d empty bins:
Number of bins: %d
Number of f_obs > 0: 0
Number of f_obs <= 0: %d""" % (n_bins, n_bins, f_obs.indices().size()))
def run_00():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*100,
volume_per_atom = 50.0,
random_u_iso = True)
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group,
reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(),
adptbx.random_u_cart(u_scale=1,u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start=adptbx.u_as_b(adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
b_cart_start = [b_cart_start[0]-tr,b_cart_start[1]-tr,b_cart_start[2]-tr,
b_cart_start[3],b_cart_start[4],b_cart_start[5]]
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
F = xrs.structure_factors(d_min = 2.0).f_calc()
u_star = adptbx.u_cart_as_u_star(
F.unit_cell(), adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data = flex.abs(fc.data()*fbc))
t0 = time.time()
#
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = flex.abs(fc.data()),
f_obs = f_obs.data(),
miller_indices = f_obs.indices(),
adp_constraint_matrix = adp_constraints.gradient_sum_matrix())
time_aniso_u_scaler += (time.time()-t0)
b_cart_final = adptbx.u_as_b(adptbx.u_star_as_u_cart(f_obs.unit_cell(),
adp_constraints.all_params(tuple(obj.u_star_independent))))
#
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = flex.abs(fc.data()),
f_obs = f_obs.data(),
miller_indices = f_obs.indices())
b_cart_final2 = adptbx.u_as_b(adptbx.u_star_as_u_cart(f_obs.unit_cell(),
tuple(obj.u_star)))
#
assert approx_equal(b_cart_final, b_cart_final2)
#print "Output b_cart:", " ".join(["%8.4f"%i for i in b_cart_final])
assert approx_equal(b_cart_start, b_cart_final, 1.e-4)
print "Time (aniso_u_scaler only): %6.4f"%time_aniso_u_scaler
def run_group(symbol):
group = space_group_info(symbol);
print "\n=="
elements = ('C', 'N', 'O', 'H')*11
xrs = random_structure.xray_structure(
space_group_info = group,
volume_per_atom = 25.,
general_positions_only = False,
elements = elements,
min_distance = 1.0)
fo = abs(xrs.structure_factors(d_min=2).f_calc())
fmodel = mmtbx.f_model.manager(
f_obs = fo,
xray_structure = xrs)
#
k_sol=flex.double([10.35,5.34])
b_sol=flex.double([30.0, 24.0])
b_cart = [10,20,30,40,50,60]
u_star = flex.double(adptbx.b_as_u(
adptbx.u_cart_as_u_star(xrs.unit_cell(), b_cart)))
#
TGO = cpp_tg(fmodel=fmodel)
tg = TGO.get_tg(k_sol=k_sol, b_sol=b_sol, u_star=u_star)
# k_sol
gk_a=list(tg.grad_k_sols())
ck_a=list(tg.curv_k_sols())
gk_fd, ck_fd=fd(TGO=TGO, k_sol=k_sol, b_sol=b_sol, u_star=u_star, param="k_sol")
# b_sol
gb_a=list(tg.grad_b_sols())
cb_a=list(tg.curv_b_sols())
gb_fd, cb_fd=fd(TGO=TGO, k_sol=k_sol, b_sol=b_sol, u_star=u_star, param="b_sol")
# u_star
gu_a=list(tg.grad_u_star())
gu_fd, junk=fd(TGO=TGO, k_sol=k_sol, b_sol=b_sol, u_star=u_star, param="u_star")
print "u_star:",gu_a
print "u_star:",gu_fd
TGO2 = cpp_tg_u_star_only(fmodel=fmodel)
tg2 = TGO2.get_tg(k_sol=k_sol, b_sol=b_sol, u_star=u_star)
gu_a2=list(tg2.grad_u_star())
gu_fd2, junk=fd(TGO=TGO2, k_sol=k_sol, b_sol=b_sol, u_star=u_star, param="u_star")
print "u_star:",gu_a2
print "u_star:",gu_fd2
#
print "k_sol:", gk_a, ck_a
print "k_sol:", gk_fd, ck_fd
print "b_sol:", gb_a, cb_a
print "b_sol:", gb_fd, cb_fd
#
assert approx_equal(gk_a, gk_fd, eps=1.e-4)
assert approx_equal(gb_a, gb_fd, eps=1.e-4)
assert approx_equal(ck_a, ck_fd, eps=1.e-4)
assert approx_equal(cb_a, cb_fd, eps=1.e-4)
assert approx_equal(gu_a, gu_fd, eps=1.e-4)
assert approx_equal(gu_a2, gu_fd2, eps=1.e-6)
def dummy_structure(space_group_info, volume, n_scatterers):
structure = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(volume=volume),
space_group_info=space_group_info)))
b_iso = 20
u_iso = adptbx.b_as_u(b_iso)
u_star = adptbx.u_iso_as_u_star(structure.unit_cell(), u_iso)
scatterer = xray.scatterer(label="C", site=(0.123,0.234,0.345), u=u_star)
for i in xrange(n_scatterers):
structure.add_scatterer(scatterer)
return structure
def add_new_solvent(self):
if (self.params.b_iso is None):
sol_sel = self.model.solvent_selection()
xrs_mac_h = self.model.get_xray_structure().select(~sol_sel)
hd_mac = self.model.get_hd_selection().select(~sol_sel)
xrs_mac = xrs_mac_h.select(~hd_mac)
b = xrs_mac.extract_u_iso_or_u_equiv() * math.pi**2 * 8
b_solv = flex.mean_default(b, None)
if (b_solv is not None and b_solv < self.params.b_iso_min
or b_solv > self.params.b_iso_max):
b_solv = (self.params.b_iso_min + self.params.b_iso_max) / 2.
else:
b_solv = self.params.b_iso
if (self.params.new_solvent == "isotropic"):
new_scatterers = flex.xray_scatterer(
self.sites.size(),
xray.scatterer(occupancy=self.params.occupancy,
b=b_solv,
scattering_type=self.params.scattering_type))
elif (self.params.new_solvent == "anisotropic"):
u_star = adptbx.u_iso_as_u_star(
self.model.get_xray_structure().unit_cell(),
adptbx.b_as_u(b_solv))
new_scatterers = flex.xray_scatterer(
self.sites.size(),
xray.scatterer(occupancy=self.params.occupancy,
u=u_star,
scattering_type=self.params.scattering_type))
else:
raise RuntimeError
new_scatterers.set_sites(self.sites)
solvent_xray_structure = xray.structure(
special_position_settings=self.model.get_xray_structure(),
scatterers=new_scatterers)
xrs_sol = self.model.get_xray_structure().select(
self.model.solvent_selection())
xrs_mac = self.model.get_xray_structure().select(
~self.model.solvent_selection())
xrs_sol = xrs_sol.concatenate(other=solvent_xray_structure)
sol_sel = flex.bool(xrs_mac.scatterers().size(), False)
sol_sel.extend(flex.bool(xrs_sol.scatterers().size(), True))
self.model.add_solvent(
solvent_xray_structure=solvent_xray_structure,
residue_name=self.params.output_residue_name,
atom_name=self.params.output_atom_name,
chain_id=self.params.output_chain_id,
refine_occupancies=self.params.refine_occupancies,
refine_adp=self.params.new_solvent)
self.fmodel.update_xray_structure(
xray_structure=self.model.get_xray_structure(), update_f_calc=True)
def as_xray_scatterer(self, unit_cell=None):
scattering_type = eltbx.xray_scattering.get_standard_label(
label=self.type, exact=False, optional=True)
if (scattering_type is None):
scattering_type = eltbx.xray_scattering.get_standard_label(
label=self.segid, exact=False, optional=True)
if (scattering_type is None): scattering_type = "unknown"
site = (self.x, self.y, self.z)
if (unit_cell is not None): site = unit_cell.fractionalize(site)
return xray.scatterer(label="_".join((self.segid, self.type)),
site=site,
u=adptbx.b_as_u(self.b),
occupancy=self.q,
scattering_type=scattering_type)
def customized_copy(
self,
label=None,
site=None,
u=None,
b=None,
occupancy=None,
scattering_type=None,
fp=None,
fdp=None,
flags=None,
u_iso=None,
u_star=None,
):
assert u is None or b is None
if b is not None:
u = adptbx.b_as_u(b)
del b
if u is not None:
assert u_iso is None and u_star is None
if flags is None:
assert self.flags.use_u_iso() ^ self.flags.use_u_aniso()
else:
assert flags.use_u_iso() ^ flags.use_u_aniso()
result = ext.scatterer(other=self)
if label is not None:
result.label = label
if site is not None:
result.site = site
if flags is not None:
result.flags = flags
if u is not None:
if result.flags.use_u_iso():
result.u_iso = u
else:
result.u_star = u
if u_iso is not None:
result.u_iso = u_iso
if u_star is not None:
result.u_star = u_star
if occupancy is not None:
result.occupancy = occupancy
if scattering_type is not None:
result.scattering_type = scattering_type
if fp is not None:
result.fp = fp
if fdp is not None:
result.fdp = fdp
return result
def as_xray_scatterer(self, unit_cell=None):
scattering_type = eltbx.xray_scattering.get_standard_label(
label=self.type, exact=False, optional=True)
if (scattering_type is None):
scattering_type = eltbx.xray_scattering.get_standard_label(
label=self.segid, exact=False, optional=True)
if (scattering_type is None): scattering_type = "unknown"
site = (self.x, self.y, self.z)
if (unit_cell is not None): site = unit_cell.fractionalize(site)
return xray.scatterer(
label="_".join((self.segid, self.type)),
site=site,
u=adptbx.b_as_u(self.b),
occupancy=self.q,
scattering_type=scattering_type)
def exercise_cumulative_intensity_distribution(space_group_info,
anomalous_flag,
d_min=1.0,
reflections_per_bin=200,
n_bins=10,
verbose=0):
elements = ("N", "C", "C", "O") * 5
structure_factors = random_structure.xray_structure(
space_group_info,
elements=elements,
volume_per_atom=50.,
min_distance=1.5,
general_positions_only=True,
use_u_aniso=False,
u_iso=adptbx.b_as_u(10)).structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct")
if (0 or verbose):
structure_factors.xray_structure().show_summary()
for n_bins in [10, 20]:
f_calc = abs(structure_factors.f_calc())
f_calc.setup_binner(auto_binning=True,
reflections_per_bin=reflections_per_bin,
n_bins=n_bins)
f_obs = miller.array(
miller_set=f_calc,
data=f_calc.data()).set_observation_type_xray_amplitude()
f_obs.use_binner_of(f_calc)
f_obs_sq = f_obs.f_as_f_sq()
f_obs_sq.use_binner_of(f_obs)
for ma in (f_obs, f_obs_sq):
if ma.is_xray_amplitude_array():
dist = statistics.cumulative_intensity_distribution(f_obs=ma)
else:
dist = statistics.cumulative_intensity_distribution(
f_obs_sq=ma)
n_bins_used = f_obs.binner().n_bins_used()
x_index = {}
x_index[0.1] = n_bins_used // 10
x_index[0.5] = n_bins_used // 2
x_index[0.9] = 9 * n_bins_used // 10
if space_group_info.group().is_centric():
assert 0.23 < dist.y[x_index[0.1]] < 0.32
assert 0.49 < dist.y[x_index[0.5]] < 0.57
assert 0.65 < dist.y[x_index[0.9]] < 0.70
else:
assert 0.08 < dist.y[x_index[0.1]] < 0.21
assert 0.37 < dist.y[x_index[0.5]] < 0.49
assert 0.57 < dist.y[x_index[0.9]] < 0.65
def add_new_solvent(self):
if(self.params.b_iso is None):
sol_sel = self.model.solvent_selection()
xrs_mac_h = self.model.xray_structure.select(~sol_sel)
hd_mac = self.model.xray_structure.hd_selection().select(~sol_sel)
xrs_mac = xrs_mac_h.select(~hd_mac)
b = xrs_mac.extract_u_iso_or_u_equiv() * math.pi**2*8
b_solv = flex.mean_default(b, None)
if(b_solv is not None and b_solv < self.params.b_iso_min or
b_solv > self.params.b_iso_max):
b_solv = (self.params.b_iso_min + self.params.b_iso_max) / 2.
else:
b_solv = self.params.b_iso
if(self.params.new_solvent == "isotropic"):
new_scatterers = flex.xray_scatterer(
self.sites.size(),
xray.scatterer(occupancy = self.params.occupancy,
b = b_solv,
scattering_type = self.params.scattering_type))
elif(self.params.new_solvent == "anisotropic"):
u_star = adptbx.u_iso_as_u_star(self.model.xray_structure.unit_cell(),
adptbx.b_as_u(b_solv))
new_scatterers = flex.xray_scatterer(
self.sites.size(),
xray.scatterer(
occupancy = self.params.occupancy,
u = u_star,
scattering_type = self.params.scattering_type))
else: raise RuntimeError
new_scatterers.set_sites(self.sites)
solvent_xray_structure = xray.structure(
special_position_settings = self.model.xray_structure,
scatterers = new_scatterers)
xrs_sol = self.model.xray_structure.select(self.model.solvent_selection())
xrs_mac = self.model.xray_structure.select(~self.model.solvent_selection())
xrs_sol = xrs_sol.concatenate(other = solvent_xray_structure)
sol_sel = flex.bool(xrs_mac.scatterers().size(), False)
sol_sel.extend( flex.bool(xrs_sol.scatterers().size(), True) )
self.model.add_solvent(
solvent_xray_structure = solvent_xray_structure,
residue_name = self.params.output_residue_name,
atom_name = self.params.output_atom_name,
chain_id = self.params.output_chain_id,
refine_occupancies = self.params.refine_occupancies,
refine_adp = self.params.new_solvent)
self.fmodel.update_xray_structure(
xray_structure = self.model.xray_structure,
update_f_calc = True)
def __init__(self,
label="",
site=(0, 0, 0),
u=None,
occupancy=1,
scattering_type=None,
fp=0,
fdp=0,
b=None):
assert u is None or b is None
if (b is not None): u = adptbx.b_as_u(b)
elif (u is None): u = 0
if (scattering_type is None):
scattering_type = eltbx.xray_scattering.get_standard_label(
label=label, exact=False)
ext.scatterer.__init__(self, label, site, u, occupancy,
scattering_type, fp, fdp)
def exercise_cumulative_intensity_distribution(space_group_info, anomalous_flag,
d_min=1.0, reflections_per_bin=200, n_bins=10, verbose=0):
elements = ("N", "C", "C", "O") * 5
structure_factors = random_structure.xray_structure(
space_group_info,
elements=elements,
volume_per_atom=50.,
min_distance=1.5,
general_positions_only=True,
use_u_aniso=False,
u_iso=adptbx.b_as_u(10)
).structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct")
if (0 or verbose):
structure_factors.xray_structure().show_summary()
for n_bins in [10,20]:
f_calc = abs(structure_factors.f_calc())
f_calc.setup_binner(
auto_binning=True,
reflections_per_bin=reflections_per_bin,
n_bins=n_bins)
f_obs = miller.array(
miller_set=f_calc,
data=f_calc.data()).set_observation_type_xray_amplitude()
f_obs.use_binner_of(f_calc)
f_obs_sq = f_obs.f_as_f_sq()
f_obs_sq.use_binner_of(f_obs)
for ma in (f_obs,f_obs_sq):
if ma.is_xray_amplitude_array():
dist = statistics.cumulative_intensity_distribution(f_obs=ma)
else:
dist = statistics.cumulative_intensity_distribution(f_obs_sq=ma)
n_bins_used = f_obs.binner().n_bins_used()
x_index = {}
x_index[0.1] = n_bins_used//10
x_index[0.5] = n_bins_used//2
x_index[0.9] = 9*n_bins_used//10
if space_group_info.group().is_centric():
assert 0.23 < dist.y[x_index[0.1]] < 0.32
assert 0.49 < dist.y[x_index[0.5]] < 0.57
assert 0.65 < dist.y[x_index[0.9]] < 0.70
else:
assert 0.08 < dist.y[x_index[0.1]] < 0.21
assert 0.37 < dist.y[x_index[0.5]] < 0.49
assert 0.57 < dist.y[x_index[0.9]] < 0.65
def run(refine_xyz=True, refine_adp=False):
# get xray_structure from PDB file
inp = get_inputs(pdb_str=pdb_str)
if (1):
inp.pdb_hierarchy.adopt_xray_structure(inp.xray_structure)
inp.pdb_hierarchy.write_pdb_file(file_name="start.pdb")
# simulate poor starting model: shake coordinates and B-factors
xrs_poor = inp.xray_structure.deep_copy_scatterers()
if (refine_xyz):
xrs_poor.shake_sites_in_place(mean_distance=0.3)
if (refine_adp):
for sc in xrs_poor.scatterers():
sc.u_iso = adptbx.b_as_u(random.choice([7, 8, 9, 11, 12, 13]))
if (1):
inp.pdb_hierarchy.adopt_xray_structure(xrs_poor)
inp.pdb_hierarchy.write_pdb_file(file_name="poor.pdb")
# simulate Fobs
f_obs = abs(
inp.xray_structure.structure_factors(d_min=1.0,
algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
# get fmodel
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
fmodel = mmtbx.f_model.manager(f_obs=f_obs,
r_free_flags=r_free_flags,
xray_structure=xrs_poor,
sf_and_grads_accuracy_params=params,
target_name="ls_wunit_kunit")
# refinement loop
print "start r_factor: %6.4f" % fmodel.r_work()
for macro_cycle in xrange(100):
# refine coordinates
if (refine_xyz):
minimized = minimizer(fmodel=fmodel, sites=True)
print " macro_cycle %3d (sites) r_factor: %6.4f" % (
macro_cycle, fmodel.r_work())
# refine ADPs
if (refine_adp):
minimized = minimizer(fmodel=fmodel, u_iso=True)
print " macro_cycle %3d (adp) r_factor: %6.4f" % (
macro_cycle, fmodel.r_work())
if (1):
inp.pdb_hierarchy.adopt_xray_structure(fmodel.xray_structure)
inp.pdb_hierarchy.write_pdb_file(file_name="refined.pdb")
def anisotropic_correction(self):
if not self.params.anisotropic_correction: return
self.aniso_scale_and_b = None
n_copies_solc = self.params.asu_contents.n_copies_per_asu
n_residues = self.params.asu_contents.n_residues
n_bases = self.params.asu_contents.n_bases
self.aniso_scale_and_b = absolute_scaling.ml_aniso_absolute_scaling(
miller_array=self.f_obs,
n_residues=n_residues*self.f_obs.space_group().order_z()*n_copies_solc,
n_bases=n_bases*self.f_obs.space_group().order_z()*n_copies_solc)
self.aniso_scale_and_b.show(out=self.log)
b_cart = self.aniso_scale_and_b.b_cart
trace = sum(b_cart[:3])/3
b_cart = [b_cart[0]-trace, b_cart[1]-trace, b_cart[2]-trace,
b_cart[3], b_cart[4], b_cart[5]]
u_star = adptbx.u_cart_as_u_star(self.f_obs.unit_cell(), adptbx.b_as_u(b_cart))
self.f_obs = absolute_scaling.anisotropic_correction(
self.f_obs, 0.0, u_star).set_observation_type(self.f_obs)
def anisotropic_correction(self):
if not self.params.anisotropic_correction: return
self.aniso_scale_and_b = None
n_copies_solc = self.params.asu_contents.n_copies_per_asu
n_residues = self.params.asu_contents.n_residues
n_bases = self.params.asu_contents.n_bases
self.aniso_scale_and_b = absolute_scaling.ml_aniso_absolute_scaling(
miller_array=self.f_obs,
n_residues=n_residues*self.f_obs.space_group().order_z()*n_copies_solc,
n_bases=n_bases*self.f_obs.space_group().order_z()*n_copies_solc)
self.aniso_scale_and_b.show(out=self.log)
b_cart = self.aniso_scale_and_b.b_cart
trace = sum(b_cart[:3])/3
b_cart = [b_cart[0]-trace, b_cart[1]-trace, b_cart[2]-trace,
b_cart[3], b_cart[4], b_cart[5]]
u_star = adptbx.u_cart_as_u_star(self.f_obs.unit_cell(), adptbx.b_as_u(b_cart))
self.f_obs = absolute_scaling.anisotropic_correction(
self.f_obs, 0.0, u_star).set_observation_type(self.f_obs)
def exercise_packed(structure_ideal, f_obs,
anomalous_flag,
verbose=0):
sh, ls = shift_all(structure_ideal, f_obs, anomalous_flag)
flag = (random.random() > 0.5)
gradient_flags = randomize_gradient_flags(
xray.structure_factors.gradient_flags(site=flag, u=not flag),
f_obs.anomalous_flag(),
thresholds=(1/2.,0))
u_iso_refinable_params = flex.double()
for scatterer in sh.structure_shifted.scatterers():
scatterer.flags.set_grad_site(gradient_flags.site)
scatterer.flags.set_grad_u_iso(gradient_flags.u_iso)
scatterer.flags.set_grad_u_aniso(gradient_flags.u_aniso)
scatterer.flags.set_grad_occupancy(gradient_flags.occupancy)
scatterer.flags.set_grad_fp(gradient_flags.fp)
scatterer.flags.set_grad_fdp(gradient_flags.fdp)
scatterer.flags.set_tan_u_iso(True)
param = random.randint(90,120)
scatterer.flags.param= param
value = math.tan(scatterer.u_iso*math.pi/adptbx.b_as_u(param)-math.pi/2)
u_iso_refinable_params.append(value)
n_parameters = xray.scatterer_grad_flags_counts(
sh.structure_shifted.scatterers()).n_parameters()
assert n_parameters == sh.structure_shifted.n_parameters()
if (n_parameters > 0):
sfd = xray.structure_factors.gradients_direct(
xray_structure=sh.structure_shifted,
u_iso_refinable_params=u_iso_refinable_params,
miller_set=f_obs,
d_target_d_f_calc=ls.derivatives(),
n_parameters=n_parameters)
assert sfd.packed().size() == n_parameters
re = resampling(miller_set=f_obs)
map0 = re(
xray_structure=sh.structure_shifted,
u_iso_refinable_params=u_iso_refinable_params,
dp=miller.array(miller_set=f_obs, data=ls.derivatives()),
n_parameters=n_parameters,
verbose=verbose)
assert map0.packed().size() == n_parameters
correlation = flex.linear_correlation(sfd.packed(), map0.packed())
assert correlation.is_well_defined()
assert correlation.coefficient() > 0.999
def run():
# get xray_structure from PDB file
inp = get_inputs()
if(1):
inp.pdb_hierarchy.adopt_xray_structure(inp.xray_structure)
inp.pdb_hierarchy.write_pdb_file(file_name="start.pdb")
# simulate poor starting model
xrs_poor = inp.xray_structure.deep_copy_scatterers()
xrs_poor.shake_sites_in_place(mean_distance = 0.3)
for sc in xrs_poor.scatterers():
# what is that for? why 7-13?
# isn't adptbx.b_as_u(_) retruns 1.0?
sc.u_iso = adptbx.b_as_u(random.choice([7,8,9,11,12,13]))
if(1):
inp.pdb_hierarchy.adopt_xray_structure(xrs_poor)
inp.pdb_hierarchy.write_pdb_file(file_name="poor.pdb")
# simulate Fobs
f_obs = abs(inp.xray_structure.structure_factors(
d_min = 1.0,
algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
# get fmodel
params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
params.algorithm = "direct"
fmodel = mmtbx.f_model.manager(
f_obs = f_obs,
r_free_flags = r_free_flags,
xray_structure = xrs_poor,
sf_and_grads_accuracy_params = params,
target_name = "ls_wunit_kunit")
# refinement loop
print "start r_factor: %6.4f" % fmodel.r_work()
for macro_cycle in xrange(100):
# refine coordinates
minimized = minimizer(fmodel = fmodel, sites = True)
print " macro_cycle %3d (sites) r_factor: %6.4f"%(macro_cycle, fmodel.r_work())
# refine ADPs (atomic displacement parameter)
minimized = minimizer(fmodel = fmodel, u_iso = True)
print " macro_cycle %3d (adp) r_factor: %6.4f"%(macro_cycle, fmodel.r_work())
if fmodel.r_work() < 0.03: break
if(1):
inp.pdb_hierarchy.adopt_xray_structure(fmodel.xray_structure)
inp.pdb_hierarchy.write_pdb_file(file_name="refined.pdb")
def __init__(self, space_group_info, **kwds):
libtbx.adopt_optional_init_args(self, kwds)
self.space_group_info = space_group_info
self.structure = random_structure.xray_structure(
space_group_info,
elements=self.elements,
volume_per_atom=20.,
min_distance=1.5,
general_positions_only=True,
use_u_aniso=False,
u_iso=adptbx.b_as_u(10),
)
self.structure.set_inelastic_form_factors(1.54, "sasaki")
self.scale_factor = 0.05 + 10 * flex.random_double()
fc = self.structure.structure_factors(anomalous_flag=True,
d_min=self.d_min,
algorithm="direct").f_calc()
fo = fc.as_amplitude_array()
fo.set_observation_type_xray_amplitude()
if self.use_students_t_errors:
nu = random.uniform(1, 10)
normal_g = variate(normal_distribution())
gamma_g = variate(gamma_distribution(0.5 * nu, 2))
errors = normal_g(fc.size()) / flex.sqrt(2 * gamma_g(fc.size()))
else:
# use gaussian errors
g = variate(normal_distribution())
errors = g(fc.size())
fo2 = fo.as_intensity_array()
self.fo2 = fo2.customized_copy(
data=(fo2.data() + errors) * self.scale_factor,
sigmas=flex.double(fc.size(), 1),
)
self.fc = fc
xs_i = self.structure.inverse_hand()
self.fc_i = xs_i.structure_factors(anomalous_flag=True,
d_min=self.d_min,
algorithm="direct").f_calc()
fo2_twin = self.fc.customized_copy(
data=self.fc.data() + self.fc_i.data()).as_intensity_array()
self.fo2_twin = fo2_twin.customized_copy(
data=(errors + fo2_twin.data()) * self.scale_factor,
sigmas=self.fo2.sigmas())
def run(d_min=2.0, radius_max=5, radius_step=0.01):
for i, mxp in enumerate([0, 6]):
o = maptbx.atom_curves(scattering_type="C", scattering_table="wk1995")
b = o.bcr_approx(
d_min=d_min,
radius_max=radius_max,
radius_step=radius_step,
mxp=mxp,
epsc=0.001,
kpres=0 # BCR params
)
r = rfactor(b.image_values, b.bcr_approx_values)
if (i == 0): assert r > 10, r
else: assert r < 0.4, r
#
# b_iso is not 0
#
b_iso = 50
im = o.image(d_min=d_min,
b_iso=b_iso,
radius_max=radius_max,
radius_step=radius_step)
bcr_approx_values = flex.double()
bcr_approx_values_cpp = flex.double()
# c++
sc = xray.scatterer("c", site=(0, 0, 0), u=adptbx.b_as_u(b_iso))
bcr_cpp = ext.bcr_model(scatterer=sc, B=b.B, C=b.C, R=b.R)
calc = ext.calculator(bcr_model=bcr_cpp)
#
for r in im.radii:
first = 0
second = 0
for B, C, R in zip(b.B, b.C, b.R):
if (abs(R) < 1.e-6):
first += bcr.gauss(B=B, C=C, r=r, b_iso=b_iso)
else:
second += C * bcr.chi(B=B, R=R, r=r, b_iso=b_iso)
bcr_approx_values.append(first + second)
bcr_approx_values_cpp.append(calc.rho(r))
r = rfactor(im.image_values, bcr_approx_values)
if (i == 0): assert r > 10, r
else: assert r < 0.4, r
assert approx_equal(bcr_approx_values, bcr_approx_values_cpp)
def __init__(self, space_group_info, **kwds):
libtbx.adopt_optional_init_args(self, kwds)
self.space_group_info = space_group_info
self.structure = random_structure.xray_structure(
space_group_info,
elements=self.elements,
volume_per_atom=20.,
min_distance=1.5,
general_positions_only=True,
use_u_aniso=False,
u_iso=adptbx.b_as_u(10),
)
self.structure.set_inelastic_form_factors(1.54, "sasaki")
self.scale_factor = 0.05 + 10 * flex.random_double()
fc = self.structure.structure_factors(
anomalous_flag=True, d_min=self.d_min, algorithm="direct").f_calc()
fo = fc.as_amplitude_array()
fo.set_observation_type_xray_amplitude()
if self.use_students_t_errors:
nu = random.uniform(1, 10)
normal_g = variate(normal_distribution())
gamma_g = variate(gamma_distribution(0.5*nu, 2))
errors = normal_g(fc.size())/flex.sqrt(2*gamma_g(fc.size()))
else:
# use gaussian errors
g = variate(normal_distribution())
errors = g(fc.size())
fo2 = fo.as_intensity_array()
self.fo2 = fo2.customized_copy(
data=(fo2.data()+errors)*self.scale_factor,
sigmas=flex.double(fc.size(), 1),
)
self.fc = fc
xs_i = self.structure.inverse_hand()
self.fc_i = xs_i.structure_factors(
anomalous_flag=True, d_min=self.d_min, algorithm="direct").f_calc()
fo2_twin = self.fc.customized_copy(
data=self.fc.data()+self.fc_i.data()).as_intensity_array()
self.fo2_twin = fo2_twin.customized_copy(
data=(errors + fo2_twin.data()) * self.scale_factor,
sigmas=self.fo2.sigmas())
def adjust_stp(O,
stp,
csd,
large_shift_site=0.1,
large_shift_u_iso_factor=0.5,
min_large_shift_u_iso=b_as_u(1)):
print "adjust_stp", stp
assert csd.size() == O.x.size()
max_stp = 100
ix = 0
uc = O.xray_structure.unit_cell()
sstab = O.xray_structure.site_symmetry_table()
for i_sc, sc in enumerate(O.xray_structure.scatterers()):
site_symmetry = sstab.get(i_sc)
if (site_symmetry.is_point_group_1()):
np = 3
for i, ucp in enumerate(uc.parameters()[:3]):
lsx = large_shift_site / ucp \
* O.p_as_x[ix+i]
if (abs(stp * csd[ix + i]) > lsx):
max_stp = min(max_stp, abs(lsx / csd[ix]))
else:
constr = site_symmetry.site_constraints()
np = constr.n_independent_params()
raise RuntimeError(
"SPECIAL POSITION LARGE SHIFT NOT IMPLEMENTED.")
ix += np
u_iso = O.x[ix] / O.p_as_x[ix]
lux = max(min_large_shift_u_iso, abs(u_iso) * large_shift_u_iso_factor) \
* O.p_as_x[ix]
if (abs(stp * csd[ix]) > lux):
max_stp = min(max_stp, abs(lux / csd[ix]))
ix += 1
assert ix == O.x.size()
print "max_stp:", max_stp
sys.stdout.flush()
if (O.params.use_max_stp):
return min(max_stp, stp)
return stp
def apply_back_trace_of_overall_exp_scale_matrix(self,
xray_structure=None):
if (xray_structure is None): return None
k_sol, b_sol, b_cart = self.k_sols(), self.b_sols(), self.b_cart()
assert len(k_sol) == 1 # XXX Only one mask!
k_sol = k_sol[0]
b_sol = b_sol[0]
#
xrs = xray_structure
if (xrs is None): return
b_min = min(b_sol, xrs.min_u_cart_eigenvalue() * adptbx.u_as_b(1.))
if (b_min < 0): xrs.tidy_us()
b_iso = (b_cart[0] + b_cart[1] + b_cart[2]) / 3.0
b_test = b_min + b_iso
if (b_test < 0.0): b_adj = b_iso + abs(b_test) + 0.001
else: b_adj = b_iso
b_cart_new = [
b_cart[0] - b_adj, b_cart[1] - b_adj, b_cart[2] - b_adj, b_cart[3],
b_cart[4], b_cart[5]
]
b_sol_new = b_sol + b_adj
xrs.shift_us(b_shift=b_adj)
b_min = min(b_sol_new, xrs.min_u_cart_eigenvalue() * adptbx.u_as_b(1.))
assert b_min >= 0.0
xrs.tidy_us()
#
assert self.fmodel_kbu
k_masks = [ext.k_mask(self.fmodel_kbu.ss, k_sol, b_sol_new)]
u_star = adptbx.u_cart_as_u_star(self.fmodel_kbu.f_obs.unit_cell(),
adptbx.b_as_u(b_cart_new))
k_anisotropic = ext.k_anisotropic(self.fmodel_kbu.f_obs.indices(),
u_star)
self.fmodel_kbu = self.fmodel_kbu.update(b_sols=[b_sol_new],
b_cart=b_cart_new)
return group_args(xray_structure=xrs,
b_adj=b_adj,
b_sol=b_sol_new,
b_cart=b_cart_new)
def customized_copy(self,
label=None,
site=None,
u=None,
b=None,
occupancy=None,
scattering_type=None,
fp=None,
fdp=None,
flags=None,
u_iso=None,
u_star=None):
assert u is None or b is None
if (b is not None): u = adptbx.b_as_u(b)
del b
if (u is not None):
assert u_iso is None and u_star is None
if (flags is None):
assert self.flags.use_u_iso() ^ self.flags.use_u_aniso()
else:
assert flags.use_u_iso() ^ flags.use_u_aniso()
result = ext.scatterer(other=self)
if (label is not None): result.label = label
if (site is not None): result.site = site
if (flags is not None): result.flags = flags
if (u is not None):
if (result.flags.use_u_iso()):
result.u_iso = u
else:
result.u_star = u
if (u_iso is not None): result.u_iso = u_iso
if (u_star is not None): result.u_star = u_star
if (occupancy is not None): result.occupancy = occupancy
if (scattering_type is not None):
result.scattering_type = scattering_type
if (fp is not None): result.fp = fp
if (fdp is not None): result.fdp = fdp
return result
def split_u(xray_structure, tls_selections, offset):
global time_split_u
timer = user_plus_sys_time()
uc = xray_structure.unit_cell()
u_iso = xray_structure.scatterers().extract_u_iso()
u_eq_1 = xray_structure.extract_u_iso_or_u_equiv()
for tls_selection in tls_selections:
u_iso_sel = u_iso.select(tls_selection)
u_iso_min = flex.min(u_iso_sel)
if (offset):
offset_ = adptbx.b_as_u(5.0)
else:
offset_ = 0.0
if u_iso_min >= offset_:
u_iso_min = u_iso_min - offset_
t = adptbx.u_iso_as_u_star(uc, u_iso_min)
for i_seq in tls_selection:
sc = xray_structure.scatterers()[i_seq]
assert sc.u_iso == u_iso[i_seq]
u_iso_new = sc.u_iso - u_iso_min
assert u_iso_new >= 0.0
sc.u_iso = u_iso_new
assert sc.flags.use_u_aniso()
assert sc.flags.use_u_iso()
if (sc.u_star == (-1.0, -1.0, -1.0, -1.0, -1.0, -1.0)):
sc.u_star = t
else:
x = flex.double(sc.u_star)
y = flex.double(t)
z = list(x + y)
sc.u_star = z
u_iso = xray_structure.scatterers().extract_u_iso().select(
xray_structure.use_u_iso())
assert (u_iso < 0.0).count(True) == 0
u_eq_2 = xray_structure.extract_u_iso_or_u_equiv()
assert approx_equal(u_eq_1, u_eq_2)
time_split_u += timer.elapsed()
def print_atom_statisitics(self,
selection_string = 'name CA',
selection_bool_array = None,
model = None):
if model == None:
model = self.ensemble_obj.model
pdb_hierarchy = model.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
if selection_bool_array == None:
selection_bool_array = pdb_hierarchy.atom_selection_cache().selection(selection_string)
xrs = model.xray_structure.deep_copy_scatterers()
xrs.convert_to_isotropic()
b_iso_atoms = xrs.scatterers().extract_u_iso()/adptbx.b_as_u(1)
q_atoms = xrs.scatterers().extract_occupancies()
for i_seq, x in enumerate(selection_bool_array):
if x:
atom_info = pdb_atoms[i_seq].fetch_labels()
if self.ensemble_obj.er_data.ke_protein_running == None:
print >> self.ensemble_obj.log, ' {0:6} {1:6} {2:6} {3:6} {4:6d} {5:6.3f} {6:6.3f} '.format(
atom_info.name,
atom_info.resseq,
atom_info.resname,
atom_info.chain_id,
i_seq,
b_iso_atoms[i_seq],
q_atoms[i_seq])
else:
print >> self.ensemble_obj.log, ' {0:6} {1:6} {2:6} {3:6} {4:6d} {5:6.3f} {6:6.3f} {7:6.3f}'.format(
atom_info.name,
atom_info.resseq,
atom_info.resname,
atom_info.chain_id,
i_seq,
b_iso_atoms[i_seq],
q_atoms[i_seq],
self.ensemble_obj.er_data.ke_protein_running[i_seq])
def split_u(u_eq, xray_structure, tls_selections, offset):
global time_split_u
timer = user_plus_sys_time()
uc = xray_structure.unit_cell()
for tls_selection in tls_selections:
if (offset):
offset_ = adptbx.b_as_u(5.0)
else:
offset_ = 0.0
for i_seq in tls_selection:
sc = xray_structure.scatterers()[i_seq]
u_nm = sc.u_star
u_nm_iso = adptbx.u_star_as_u_iso(uc, u_nm)
u_iso_new = u_eq[i_seq] - u_nm_iso
if u_iso_new < 0.0:
u_iso_new = 0.0
assert u_iso_new >= 0.0
sc.u_iso = u_iso_new
assert sc.flags.use_u_aniso()
assert sc.flags.use_u_iso()
u_iso = xray_structure.scatterers().extract_u_iso().select(
xray_structure.use_u_iso())
assert (u_iso < 0.0).count(True) == 0
time_split_u += timer.elapsed()
def split_u(xray_structure, tls_selections, offset):
global time_split_u
timer = user_plus_sys_time()
uc = xray_structure.unit_cell()
u_iso = xray_structure.scatterers().extract_u_iso()
u_eq_1 = xray_structure.extract_u_iso_or_u_equiv()
for tls_selection in tls_selections:
u_iso_sel = u_iso.select(tls_selection)
u_iso_min = flex.min(u_iso_sel)
if(offset):
offset_ = adptbx.b_as_u(5.0)
else: offset_ = 0.0
if u_iso_min >= offset_:
u_iso_min = u_iso_min - offset_
t = adptbx.u_iso_as_u_star(uc, u_iso_min)
for i_seq in tls_selection:
sc = xray_structure.scatterers()[i_seq]
assert sc.u_iso == u_iso[i_seq]
u_iso_new = sc.u_iso - u_iso_min
assert u_iso_new >= 0.0
sc.u_iso = u_iso_new
assert sc.flags.use_u_aniso()
assert sc.flags.use_u_iso()
if(sc.u_star == (-1.0,-1.0,-1.0,-1.0,-1.0,-1.0)):
sc.u_star = t
else:
x = flex.double(sc.u_star)
y = flex.double(t)
z = list(x + y)
sc.u_star = z
u_iso = xray_structure.scatterers().extract_u_iso().select(
xray_structure.use_u_iso())
assert (u_iso < 0.0).count(True) == 0
u_eq_2 = xray_structure.extract_u_iso_or_u_equiv()
assert approx_equal(u_eq_1, u_eq_2)
time_split_u += timer.elapsed()
def adjust_stp(O, stp, csd,
large_shift_site=0.1,
large_shift_u_iso_factor=0.5,
min_large_shift_u_iso=b_as_u(1)):
print "adjust_stp", stp
assert csd.size() == O.x.size()
max_stp = 100
ix = 0
uc = O.xray_structure.unit_cell()
sstab = O.xray_structure.site_symmetry_table()
for i_sc,sc in enumerate(O.xray_structure.scatterers()):
site_symmetry = sstab.get(i_sc)
if (site_symmetry.is_point_group_1()):
np = 3
for i,ucp in enumerate(uc.parameters()[:3]):
lsx = large_shift_site / ucp \
* O.p_as_x[ix+i]
if (abs(stp*csd[ix+i]) > lsx):
max_stp = min(max_stp, abs(lsx/csd[ix]))
else:
constr = site_symmetry.site_constraints()
np = constr.n_independent_params()
raise RuntimeError("SPECIAL POSITION LARGE SHIFT NOT IMPLEMENTED.")
ix += np
u_iso = O.x[ix]/O.p_as_x[ix]
lux = max(min_large_shift_u_iso, abs(u_iso) * large_shift_u_iso_factor) \
* O.p_as_x[ix]
if (abs(stp*csd[ix]) > lux):
max_stp = min(max_stp, abs(lux/csd[ix]))
ix += 1
assert ix == O.x.size()
print "max_stp:", max_stp
sys.stdout.flush()
if (O.params.use_max_stp):
return min(max_stp, stp)
return stp
def apply_back_trace_of_overall_exp_scale_matrix(self, xray_structure=None):
if(xray_structure is None): return None
k_sol, b_sol, b_cart = self.k_sols(), self.b_sols(), self.b_cart()
assert len(k_sol)==1 # XXX Only one mask!
k_sol = k_sol[0]
b_sol = b_sol[0]
#
xrs = xray_structure
if(xrs is None): return
b_min = min(b_sol, xrs.min_u_cart_eigenvalue()*adptbx.u_as_b(1.))
if(b_min < 0): xrs.tidy_us()
b_iso = (b_cart[0]+b_cart[1]+b_cart[2])/3.0
b_test = b_min+b_iso
if(b_test < 0.0): b_adj = b_iso + abs(b_test) + 0.001
else: b_adj = b_iso
b_cart_new = [b_cart[0]-b_adj,b_cart[1]-b_adj,b_cart[2]-b_adj,
b_cart[3], b_cart[4], b_cart[5]]
b_sol_new = b_sol + b_adj
xrs.shift_us(b_shift = b_adj)
b_min = min(b_sol_new, xrs.min_u_cart_eigenvalue()*adptbx.u_as_b(1.))
assert b_min >= 0.0
xrs.tidy_us()
#
assert self.fmodel_kbu
k_masks = [ext.k_mask(self.fmodel_kbu.ss, k_sol, b_sol_new)]
u_star=adptbx.u_cart_as_u_star(
self.fmodel_kbu.f_obs.unit_cell(), adptbx.b_as_u(b_cart_new))
k_anisotropic = ext.k_anisotropic(self.fmodel_kbu.f_obs.indices(), u_star)
self.fmodel_kbu = self.fmodel_kbu.update(
b_sols = [b_sol_new],
b_cart = b_cart_new)
return group_args(
xray_structure = xrs,
b_adj = b_adj,
b_sol = b_sol_new,
b_cart = b_cart_new)
def exercise_05_k_sol_b_sol_only(d_min = 2.0):
xray_structure = get_xray_structure_from_file()
k_sol = 0.33
b_sol = 34.0
b_cart = [1,2,3,0,4,0]
f_obs, r_free_flags = get_f_obs_freer(
d_min = d_min,
k_sol = k_sol,
b_sol = b_sol,
b_cart = b_cart,
xray_structure = xray_structure)
fmodel = mmtbx.f_model.manager(
r_free_flags = r_free_flags,
f_obs = f_obs,
xray_structure = xray_structure)
params = bss.master_params.extract()
params.anisotropic_scaling = False
u_star = adptbx.u_cart_as_u_star(
fmodel.f_obs().unit_cell(),adptbx.b_as_u(b_cart))
fmodel_kbu = mmtbx.f_model.manager_kbu(
f_obs = fmodel.f_obs(),
f_calc = fmodel.f_calc(),
f_masks = fmodel.arrays.core.f_masks,
f_part1 = fmodel.arrays.core.f_part1,
f_part2 = fmodel.arrays.core.f_part2,
ss = fmodel.ss,
u_star = u_star)
r_work_start = fmodel_kbu.r_factor()
result = bss.bulk_solvent_and_scales(
fmodel_kbu = fmodel_kbu, params = params)
r_work = result.fmodels.r_factor()*100.
assert r_work_start > 0.05
assert approx_equal(r_work, 0.0, eps = 1.e-6)
assert approx_equal(result.k_sol(0), k_sol, eps = 1.e-6)
assert approx_equal(result.b_sol(), b_sol, eps = 1.e-6)
assert approx_equal(result.b_cart(), b_cart, eps = 1.e-6)
def exercise(small=1.e-9):
for symbol in ["P 1"]:
space_group_info = sgtbx.space_group_info(symbol=symbol)
random_xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["N"] * 10,
volume_per_atom=50.0,
random_u_iso=False,
u_iso=adptbx.b_as_u(20.0))
sg = random_xray_structure.space_group()
uc = random_xray_structure.unit_cell()
print(symbol, uc)
print()
sys.stdout.flush()
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
counter += 1
r = random.random()
if (r < 0.333):
m = adptbx.random_u_cart(u_scale=20. * random.random(),
u_min=0)
n = adptbx.random_u_cart(u_scale=20. * random.random(),
u_min=0)
while 1:
for ind in range(6):
r = random.random()
m = flex.double(m)
if (r > 0.5):
m[ind] = n[ind]
m = list(m)
if (adptbx.is_positive_definite(m, 0)
and adptbx.is_positive_definite(n, 0)):
break
elif (r >= 0.333 and r < 0.66):
m, n = branch_3_mn()
else:
m, n = branch_2_mn(0)
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
m = factor(list(m), i)
n = factor(list(n), i)
qq = tools.common(n, m, small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if (qq.branch_0()): branch_0 += 1
if (qq.branch_1()): branch_1 += 1
if (qq.branch_1_1()): branch_1_1 += 1
if (qq.branch_1_2()): branch_1_2 += 1
if (qq.branch_1_2_1()): branch_1_2_1 += 1
if (qq.branch_1_2_2()): branch_1_2_2 += 1
if (qq.branch_1_2_3()): branch_1_2_3 += 1
if (qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if (qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print("." * 30, symbol)
print("i= ", i, "out of ", trials)
print("branch_0 = ", branch_0)
print("branch_1 = ", branch_1)
print("branch_1_1 = ", branch_1_1)
print("branch_1_2 = ", branch_1_2)
print("branch_1_2_1 = ", branch_1_2_1)
print("branch_1_2_2 = ", branch_1_2_2)
print("branch_1_2_3 = ", branch_1_2_3)
print("branch_1_2_3_1 = ", branch_1_2_3_1)
print("branch_1_2_3_2 = ", branch_1_2_3_2)
sys.stdout.flush()
def __init__(self, fmodels,
restraints_manager = None,
model = None,
is_neutron_scat_table = None,
target_weights = None,
tan_b_iso_max = None,
refine_xyz = False,
refine_adp = False,
lbfgs_termination_params = None,
use_fortran = False,
verbose = 0,
correct_special_position_tolerance = 1.0,
iso_restraints = None,
h_params = None,
qblib_params = None,
macro_cycle = None,
u_min = adptbx.b_as_u(-5.0),
u_max = adptbx.b_as_u(999.99),
collect_monitor = True,
log = None):
timer = user_plus_sys_time()
adopt_init_args(self, locals())
self.f=None
self.xray_structure = self.fmodels.fmodel_xray().xray_structure
self.fmodels.create_target_functors()
self.fmodels.prepare_target_functors_for_minimization()
if(self.refine_adp and fmodels.fmodel_neutron() is None):
self.xray_structure.tidy_us()
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
self.weights = None
# QBLIB INSERT
self.qblib_params = qblib_params
if(self.qblib_params is not None and self.qblib_params.qblib):
self.macro = macro_cycle
self.qblib_cycle_count = 0
self.tmp_XYZ = None
self.XYZ_diff_curr=None
# QBLIB END
self.correct_special_position_tolerance = correct_special_position_tolerance
if(refine_xyz and target_weights is not None):
self.weights = target_weights.xyz_weights_result
elif(refine_adp and target_weights is not None):
self.weights = target_weights.adp_weights_result
else:
from phenix.refinement import weight_xray_chem
self.weights = weight_xray_chem.weights(wx = 1,
wx_scale = 1,
angle_x = None,
wn = 1,
wn_scale = 1,
angle_n = None,
w = 0,
wxn = 1)
if(self.collect_monitor):
self.monitor = monitor(
weights = self.weights,
fmodels = fmodels,
model = model,
iso_restraints = iso_restraints,
refine_xyz = refine_xyz,
refine_adp = refine_adp,
refine_occ = False)
if(self.collect_monitor): self.monitor.collect()
self.neutron_refinement = (self.fmodels.fmodel_n is not None)
self.x = flex.double(self.xray_structure.n_parameters(), 0)
self._scatterers_start = self.xray_structure.scatterers()
self.minimizer = scitbx.lbfgs.run(
target_evaluator = self,
termination_params = lbfgs_termination_params,
use_fortran = use_fortran,
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True))
self.apply_shifts()
del self._scatterers_start
self.compute_target(compute_gradients = False,u_iso_refinable_params = None)
if(self.refine_adp and self.fmodels.fmodel_neutron() is None):
self.xray_structure.tidy_us()
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
if(self.collect_monitor):
self.monitor.collect(iter = self.minimizer.iter(),
nfun = self.minimizer.nfun())
self.fmodels.create_target_functors()
# QBLIB INSERT
if(self.qblib_params is not None and self.qblib_params.qblib):
print >>self.qblib_params.qblib_log,'{:-^80}'.format("")
print >>self.qblib_params.qblib_log
def exercise_6_instantiate_consistency(symbol = "C 2"):
random.seed(0)
flex.set_random_seed(0)
for scale in [1.e-4, 1.0, 1.e+4]:
for k_sol in [0, 0.3]:
for b_sol in [0, 50]:
for set_h_occ_to_zero in [True, False]:
for update_f_part1 in [True, False]:
for apply_scale_to in ["f_obs", "f_model"]:
# Simulate Fobs START
x = random_structure.xray_structure(
space_group_info = sgtbx.space_group_info(symbol=symbol),
elements =(("O","N","C")*3+("H",)*10),
volume_per_atom = 50,
min_distance = 3,
general_positions_only = True,
random_u_iso = True,
random_occupancy = False)
x.scattering_type_registry(table="wk1995")
x.set_occupancies(value=0.8, selection = x.hd_selection())
f_calc = x.structure_factors(d_min = 2.0).f_calc()
mask_manager = mmtbx.masks.manager(miller_array = f_calc)
f_mask = mask_manager.shell_f_masks(xray_structure = x)[0]
assert flex.mean(abs(f_mask).data()) > 0
b_cart=adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=x.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(x.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(f_calc.indices(), u_star)
ss = 1./flex.pow2(f_calc.d_spacings().data()) / 4.
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
if(apply_scale_to=="f_model"):
k_isotropic = flex.double(f_calc.data().size(), scale)
else:
k_isotropic = flex.double(f_calc.data().size(), 1)
f_model_data = scale*k_anisotropic*(f_calc.data()+k_mask*f_mask.data())
f_model = f_calc.customized_copy(data = f_model_data)
f_obs = abs(f_model)
if(apply_scale_to=="f_obs"):
f_obs = f_obs.customized_copy(data = f_obs.data()*scale)
r_free_flags = f_obs.generate_r_free_flags()
# Simulate Fobs END
if(set_h_occ_to_zero):
x.set_occupancies(value=0.0, selection = x.hd_selection())
x.shake_sites_in_place(mean_distance=5)
sel = x.random_remove_sites_selection(fraction=0.3)
x = x.select(sel)
fmodel = mmtbx.f_model.manager(
xray_structure = x,
f_obs = f_obs,
r_free_flags = r_free_flags)
fmodel.update_all_scales(fast=True, show=False,
update_f_part1=update_f_part1)
f_part1_data = fmodel.f_calc().data()*flex.random_double(
fmodel.f_calc().data().size())
f_part1 = fmodel.f_calc().customized_copy(data = f_part1_data)
fmodel.update(f_part1 = f_part1)
r1 = fmodel.r_work()
#
zero=fmodel.f_calc().customized_copy(data=fmodel.f_calc().data()*0)
fmodel_dc = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
k_isotropic = fmodel.k_isotropic(),
k_anisotropic = fmodel.k_anisotropic(),
f_calc = fmodel.f_model_no_scales(),
f_part1 = fmodel.f_part1(),
f_part2 = fmodel.f_part2(),
f_mask = zero)
r2 = fmodel_dc.r_work()
if(0):
print "r1=%8.6f r2=%8.6f fp1=%6.3f fp2=%6.3f fc=%6.3f"%(r1, r2,
flex.mean(abs(fmodel.f_part1()).data()), \
flex.mean(abs(fmodel.f_part2()).data()), \
flex.mean(abs(fmodel.f_calc()).data())), \
"set_h_occ_to_zero=", set_h_occ_to_zero,\
"update_f_part1=", update_f_part1
assert approx_equal(r1, r2), [r1, r2]
def u_iso(structure_ideal, d_min, f_obs, tan_u_iso, verbose=0):
sh = shifted_u_iso(f_obs, structure_ideal, 0, 0.05)
if (0 or verbose):
print "u_iso"
sh.structure_shifted.show_summary().show_scatterers()
print
ls = xray.targets_least_squares_residual(
f_obs.data(), sh.f_calc.data(), True, 1)
gradient_flags = randomize_gradient_flags(
xray.structure_factors.gradient_flags(u_iso=True),
f_obs.anomalous_flag())
if(tan_u_iso):
u_iso_refinable_params = flex.double()
else:
u_iso_refinable_params = None
for scatterer in sh.structure_shifted.scatterers():
scatterer.flags.set_grad_site(gradient_flags.site)
scatterer.flags.set_grad_u_iso(gradient_flags.u_iso)
scatterer.flags.set_grad_u_aniso(gradient_flags.u_aniso)
scatterer.flags.set_grad_occupancy(gradient_flags.occupancy)
scatterer.flags.set_grad_fp(gradient_flags.fp)
scatterer.flags.set_grad_fdp(gradient_flags.fdp)
if(tan_u_iso):
scatterer.flags.set_tan_u_iso(True)
param = random.randint(90,120)
scatterer.flags.param= param
value=math.tan(scatterer.u_iso*math.pi/adptbx.b_as_u(param)-math.pi/2)
u_iso_refinable_params.append(value)
if (0):
print "u_iso"
print "gradient_flags.site ", gradient_flags.site
print "gradient_flags.u_iso ", gradient_flags.u_iso
print "gradient_flags.u_aniso ", gradient_flags.u_aniso
print "gradient_flags.occupancy ", gradient_flags.occupancy
print "gradient_flags.fp ", gradient_flags.fp
print "gradient_flags.fdp ", gradient_flags.fdp
cntr_use_u_iso = 0
cntr_use_u_aniso = 0
cntr_grad_u_iso = 0
cntr_grad_u_aniso = 0
for scatterer in sh.structure_shifted.scatterers():
if (scatterer.flags.use_u_iso()): cntr_use_u_iso += 1
if (scatterer.flags.use_u_aniso()): cntr_use_u_aniso += 1
if (scatterer.flags.grad_u_iso()): cntr_grad_u_iso += 1
if (scatterer.flags.grad_u_aniso()): cntr_grad_u_aniso += 1
print "use_u_iso ", cntr_use_u_iso,cntr_grad_u_iso
print "use_u_aniso ", cntr_use_u_aniso,cntr_grad_u_aniso
grad_flags_counts = \
xray.scatterer_grad_flags_counts(sh.structure_shifted.scatterers())
if(grad_flags_counts.n_parameters() > 0):
sfd = xray.structure_factors.gradients_direct(
xray_structure=sh.structure_shifted,
u_iso_refinable_params=u_iso_refinable_params,
miller_set=f_obs,
d_target_d_f_calc=ls.derivatives(),
n_parameters=0)
re = resampling(miller_set=f_obs)
map0 = re(
xray_structure=sh.structure_shifted,
u_iso_refinable_params=u_iso_refinable_params,
dp=miller.array(miller_set=f_obs, data=ls.derivatives()),
n_parameters=0,
verbose=verbose)
if(grad_flags_counts.u_aniso > 0):
sfd_d_target_d_u_cart = sfd.d_target_d_u_cart()
map0_d_target_d_u_cart = map0.d_target_d_u_cart()
top_gradient = None
gradients_1 = []
for i_scatterer,scatterer in enumerate(sh.structure_shifted.scatterers()):
if(0):
print "i_scatterer= ", i_scatterer,scatterer.flags.use_u_iso(),\
scatterer.flags.grad_u_iso(), scatterer.flags.use_u_aniso(),\
scatterer.flags.grad_u_aniso(), scatterer.u_iso, scatterer.u_star
if(scatterer.flags.use_u_iso()): parameter_name = "u_iso"
if(scatterer.flags.use_u_aniso()): parameter_name = "u_star"
if(parameter_name == "u_iso" and scatterer.flags.grad_u_iso() and
scatterer.flags.use_u_iso()):
direct_summ = sfd.d_target_d_u_iso()[i_scatterer]
if (top_gradient is None): top_gradient = direct_summ
fast_gradie = map0.d_target_d_u_iso()[i_scatterer]
sys.stdout.flush()
gradients_1.append([direct_summ, fast_gradie])
match = judge(scatterer, parameter_name, direct_summ, fast_gradie,
top_gradient)
if (0 or verbose):
print "direct summ[%d]: " % i_scatterer, direct_summ
print "fast gradie[%d]: " % i_scatterer, fast_gradie, match
print
assert not match.is_bad
if(parameter_name == "u_star" and scatterer.flags.grad_u_aniso() and
scatterer.flags.use_u_aniso()):
sfd_star = sfd.d_target_d_u_star()[i_scatterer]
sfd_cart = adptbx.grad_u_star_as_u_cart(
structure_ideal.unit_cell(), sfd_star)
assert approx_equal(
sfd_star,
adptbx.grad_u_cart_as_u_star(structure_ideal.unit_cell(), sfd_cart))
for ij in xrange(6):
direct_summ = sfd_d_target_d_u_cart[i_scatterer][ij]
if (top_gradient is None): top_gradient = direct_summ
fast_gradie = map0_d_target_d_u_cart[i_scatterer][ij]
gradients_1.append([direct_summ, fast_gradie])
match =judge(scatterer,"u_star",direct_summ,fast_gradie,top_gradient)
if (0 or verbose or match.is_bad):
print "direct summ[%d][%d]: " % (i_scatterer, ij), direct_summ
print "fast gradie[%d][%d]: " % (i_scatterer, ij),fast_gradie,match
print
assert not match.is_bad
# Making sure that gradients_1 = gradients_2
for i_scatterer,scatterer in enumerate(sh.structure_shifted.scatterers()):
if(not scatterer.flags.use_u_iso()):
scatterer.u_iso = -12345.0
if(not scatterer.flags.use_u_aniso()):
scatterer.u_star =(-999.,-999.,-999.,-999.,-999.,-999.)
sfd = xray.structure_factors.gradients_direct(
xray_structure=sh.structure_shifted,
u_iso_refinable_params=u_iso_refinable_params,
miller_set=f_obs,
d_target_d_f_calc=ls.derivatives(),
n_parameters=0)
re = resampling(miller_set=f_obs)
map0 = re(
xray_structure=sh.structure_shifted,
u_iso_refinable_params=u_iso_refinable_params,
dp=miller.array(miller_set=f_obs, data=ls.derivatives()),
n_parameters=0,
verbose=verbose)
grad_flags_counts = \
xray.scatterer_grad_flags_counts(sh.structure_shifted.scatterers())
if(grad_flags_counts.u_aniso):
sfd_d_target_d_u_cart = sfd.d_target_d_u_cart()
map0_d_target_d_u_cart = map0.d_target_d_u_cart()
gradients_2 = []
for i_scatterer,scatterer in enumerate(sh.structure_shifted.scatterers()):
if(scatterer.flags.use_u_iso()): parameter_name = "u_iso"
if(scatterer.flags.use_u_aniso()): parameter_name = "u_star"
if(parameter_name == "u_iso" and scatterer.flags.grad_u_iso() and
scatterer.flags.use_u_iso()):
direct_summ = sfd.d_target_d_u_iso()[i_scatterer]
fast_gradie = map0.d_target_d_u_iso()[i_scatterer]
gradients_2.append([direct_summ, fast_gradie])
if(parameter_name == "u_star" and scatterer.flags.grad_u_aniso() and
scatterer.flags.use_u_aniso()):
sfd_star = sfd.d_target_d_u_star()[i_scatterer]
sfd_cart = adptbx.grad_u_star_as_u_cart(structure_ideal.unit_cell(),
sfd_star)
assert approx_equal(
sfd_star,
adptbx.grad_u_cart_as_u_star(structure_ideal.unit_cell(), sfd_cart))
for ij in xrange(6):
direct_summ = sfd_d_target_d_u_cart[i_scatterer][ij]
fast_gradie = map0_d_target_d_u_cart[i_scatterer][ij]
gradients_2.append([direct_summ, fast_gradie])
for g1,g2 in zip(gradients_1, gradients_2):
assert approx_equal(g1, g2)
sys.stdout.flush()
def exercise(space_group_info,
n_elements = 10,
table = "wk1995",
d_min = 2.0,
k_sol = 0.35,
b_sol = 45.0,
b_cart = None,
quick=False,
verbose=0):
xray_structure = random_structure.xray_structure(
space_group_info = space_group_info,
elements =(("O","N","C")*(n_elements//3+1))[:n_elements],
volume_per_atom = 100,
min_distance = 1.5,
general_positions_only = True,
random_u_iso = False,
random_occupancy = False)
xray_structure.scattering_type_registry(table = table)
sg = xray_structure.space_group()
uc = xray_structure.unit_cell()
u_cart_1 = adptbx.random_u_cart(u_scale=5, u_min=5)
u_star_1 = adptbx.u_cart_as_u_star(uc, u_cart_1)
b_cart = adptbx.u_star_as_u_cart(uc, sg.average_u_star(u_star = u_star_1))
for anomalous_flag in [False, True]:
scatterers = xray_structure.scatterers()
if (anomalous_flag):
assert scatterers.size() >= 7
for i in [1,7]:
scatterers[i].fp = -0.2
scatterers[i].fdp = 5
have_non_zero_fdp = True
else:
for i in [1,7]:
scatterers[i].fp = 0
scatterers[i].fdp = 0
have_non_zero_fdp = False
f_obs = abs(xray_structure.structure_factors(
d_min = d_min,
anomalous_flag = anomalous_flag,
cos_sin_table = sfg_params.cos_sin_table,
algorithm = sfg_params.algorithm).f_calc())
f_obs_comp = f_obs.structure_factors_from_scatterers(
xray_structure = xray_structure,
algorithm = sfg_params.algorithm,
cos_sin_table = sfg_params.cos_sin_table).f_calc()
f_obs = abs(f_obs_comp)
flags = f_obs.generate_r_free_flags(fraction = 0.1,
max_free = 99999999)
#flags = flags.array(data = flex.bool(f_obs.data().size(), False))
xrs = xray_structure.deep_copy_scatterers()
xrs.shake_sites_in_place(rms_difference=0.3)
for target in mmtbx.refinement.targets.target_names:
if (quick):
if (target not in ["ls_wunit_k1", "ml", "mlhl", "ml_sad"]):
continue
if (target == "mlhl"):
if (have_non_zero_fdp): continue # XXX gradients not correct!
experimental_phases = generate_random_hl(miller_set=f_obs)
else:
experimental_phases = None
if (target == "ml_sad"
and (not anomalous_flag or mmtbx.refinement.targets.phaser is None)):
continue
print " ",target
xray.set_scatterer_grad_flags(
scatterers = xrs.scatterers(),
site = True)
ss = 1./flex.pow2(f_obs.d_spacings().data()) / 4.
u_star = adptbx.u_cart_as_u_star(
f_obs.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), u_star)
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
fmodel = mmtbx.f_model.manager(
xray_structure = xrs,
f_obs = f_obs,
r_free_flags = flags,
target_name = target,
abcd = experimental_phases,
sf_and_grads_accuracy_params = sfg_params,
k_mask = k_mask,
k_anisotropic = k_anisotropic,
mask_params = masks.mask_master_params.extract())
fmodel.update_xray_structure(
xray_structure=xrs,
update_f_calc=True,
update_f_mask=True)
xray.set_scatterer_grad_flags(
scatterers=fmodel.xray_structure.scatterers(),
site=True)
fmodel.update_xray_structure(update_f_calc=True)
t_f = fmodel.target_functor()
t_f.prepare_for_minimization()
gs = t_f(compute_gradients=True).d_target_d_site_cart().as_double()
gfd = finite_differences_site(target_functor=t_f)
cc = flex.linear_correlation(gs, gfd).coefficient()
if (0 or verbose):
print "ana:", list(gs)
print "fin:", list(gfd)
print "rat:", [f/a for a,f in zip(gs,gfd)]
print target, "corr:", cc, space_group_info
print
diff = gs - gfd
diff /= max(1, flex.max(flex.abs(gfd)))
tolerance = 1.2e-5
assert approx_equal(abs(flex.min(diff) ), 0.0, tolerance)
assert approx_equal(abs(flex.mean(diff)), 0.0, tolerance)
assert approx_equal(abs(flex.max(diff) ), 0.0, tolerance)
assert approx_equal(cc, 1.0, tolerance)
fmodel.model_error_ml()
def run_0(symbol = "C 2"):
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*50,
volume_per_atom = 100.0,
random_u_iso = True)
#
b_cart = adptbx.random_traceless_symmetry_constrained_b_cart(
crystal_symmetry=xrs.crystal_symmetry())
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(), adptbx.b_as_u(b_cart))
#
F = xrs.structure_factors(d_min = 1.5).f_calc()
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
#
bin_selections = []
F.setup_binner(reflections_per_bin=50)
for i_bin in F.binner().range_used():
sel = F.binner().selection(i_bin)
bin_selections.append(sel)
#
d_spacings = F.d_spacings().data()
ss = 1./flex.pow2(d_spacings) / 4.
k_mask_tmp = mmtbx.f_model.ext.k_mask(ss, 0.35, 80.)
k_mask = flex.double(F.data().size(), 0)
k_isotropic = flex.double(F.data().size(), 0)
for s in bin_selections:
d = d_spacings.select(s)
k_mask.set_selected(s, flex.mean(k_mask_tmp.select(s)))
k_isotropic.set_selected(s, random.randint(1,10))
#
fmodel = mmtbx.f_model.manager(
xray_structure = xrs,
f_obs = abs(F),
k_isotropic = k_isotropic,
k_anisotropic = k_anisotropic,
k_mask = k_mask)
f_calc = fmodel.f_calc()
f_masks = fmodel.f_masks()
f_model = fmodel.f_model()
f_obs = abs(f_model)
r_free_flags = f_obs.generate_r_free_flags(use_lattice_symmetry=False)
#
assert approx_equal(bulk_solvent.r_factor(f_obs.data(), f_model.data()), 0)
aso = scaler.run(
f_obs = f_obs,
f_calc = f_calc,
f_mask = f_masks,
r_free_flags = r_free_flags,
bin_selections = bin_selections,
number_of_cycles = 500,
auto_convergence_tolerance = 1.e-9,
ss = ss,
try_poly = True,
try_expanal = True,
try_expmin = True,
verbose = False)
assert approx_equal(aso.r_final, 0.00037, 0.00001)
assert approx_equal(aso.r_low, 0.00002, 0.00001)
assert approx_equal(aso.r_high, 0.00006, 0.00001)
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data(), 1),
bulk_solvent.r_factor(f_obs.data(), abs(aso.core.f_model).data()))
def run_02():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*100,
volume_per_atom = 50.0,
random_u_iso = True)
xrs.scattering_type_registry(table = "wk1995")
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group,
reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(),
adptbx.random_u_cart(u_scale=1,u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start=adptbx.u_as_b(adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
b_cart_start = [b_cart_start[0]-tr,b_cart_start[1]-tr,b_cart_start[2]-tr,
b_cart_start[3],b_cart_start[4],b_cart_start[5]]
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
reg = xrs.scattering_type_registry(table="wk1995", d_min=1/12)
f_000 = reg.sum_of_scattering_factors_at_diffraction_angle_0()
F = xrs.structure_factors(d_min = 2.0).f_calc()
i = F.indices()
i.append([0,0,0])
d = F.data()
d.append(f_000)
F = F.customized_copy(indices = i, data = d)
u_star = adptbx.u_cart_as_u_star(
F.unit_cell(), adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data = flex.abs(fc.data()*fbc))
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
obj = bulk_solvent.aniso_u_scaler(
f_model = fc.data(),
f_obs = f_obs.data(),
miller_indices = f_obs.indices(),
unit_cell = f_obs.unit_cell())
a = obj.a
####
#print "Input a :", " ".join(["%7.3f"%i for i in a])
overall_anisotropic_scale = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), a, f_obs.unit_cell())
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data()*overall_anisotropic_scale)
f_obs = abs(fc)
f_obs = f_obs.customized_copy(data = f_obs.data() * overall_anisotropic_scale)
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
t0 = time.time()
obj = bulk_solvent.aniso_u_scaler(
f_model = fc.data(),
f_obs = f_obs.data(),
miller_indices = f_obs.indices(),
unit_cell = f_obs.unit_cell())
time_aniso_u_scaler += (time.time()-t0)
overall_anisotropic_scale = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), obj.a, f_obs.unit_cell())
assert approx_equal(bulk_solvent.r_factor(f_obs.data(),
fc.data()*overall_anisotropic_scale), 0.0, 1.e-2) # XXX seems to be low
#print "Output a:", " ".join(["%7.3f"%i for i in obj.a])
assert approx_equal(a, obj.a, 1.e-4) # XXX can it be smaller?
assert overall_anisotropic_scale[len(overall_anisotropic_scale)-1]==1
print "Time (aniso_u_scaler only): %6.4f"%time_aniso_u_scaler
def energies_adp_iso(self,
xray_structure,
parameters,
use_u_local_only,
use_hd,
wilson_b=None,
compute_gradients=False,
tan_b_iso_max=None,
u_iso_refinable_params=None,
gradients=None):
"""
Compute target and gradients for isotropic ADPs/B-factors relative to
restraints.
:returns: scitbx.restraints.energies object
"""
result = scitbx.restraints.energies(
compute_gradients=compute_gradients,
gradients=gradients,
gradients_size=xray_structure.scatterers().size(),
gradients_factory=flex.double,
normalization=self.normalization)
if (self.geometry is None):
result.geometry = None
else:
result.geometry = cctbx.adp_restraints.energies_iso(
geometry_restraints_manager=self.geometry,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=wilson_b,
use_hd = use_hd,
use_u_local_only=use_u_local_only,
compute_gradients=compute_gradients,
gradients=result.gradients)
result += result.geometry
if (self.ncs_groups is not None and \
self.torsion_ncs_groups is not None):
raise Sorry("Cannot have both Cartesian and torsion NCS restraints"+\
" at the same time.")
if (self.ncs_groups is None):
result.ncs_groups = None
else:
result.ncs_groups = self.ncs_groups.energies_adp_iso(
u_isos=xray_structure.extract_u_iso_or_u_equiv(),
average_power=parameters.average_power,
compute_gradients=compute_gradients,
gradients=result.gradients)
result += result.ncs_groups
if (self.torsion_ncs_groups is None):
result.torsion_ncs_groups = None
else:
result.torsion_ncs_groups = self.torsion_ncs_groups.energies_adp_iso(
u_isos=xray_structure.extract_u_iso_or_u_equiv(),
average_power=parameters.average_power,
compute_gradients=compute_gradients,
gradients=result.gradients)
result += result.torsion_ncs_groups
result.finalize_target_and_gradients()
if(compute_gradients):
#XXX highly inefficient code: do something asap by adopting new scatters flags
if(tan_b_iso_max is not None and tan_b_iso_max != 0):
u_iso_max = adptbx.b_as_u(tan_b_iso_max)
if(u_iso_refinable_params is not None):
chain_rule_scale = u_iso_max / math.pi / (flex.pow2(u_iso_refinable_params)+1.0)
else:
u_iso_refinable_params = flex.tan(math.pi*(xray_structure.scatterers().extract_u_iso()/u_iso_max-1./2.))
chain_rule_scale = u_iso_max / math.pi / (flex.pow2(u_iso_refinable_params)+1.0)
else:
chain_rule_scale = 1.0
result.gradients = result.gradients * chain_rule_scale
return result
