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 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 lex_scatterer(self, args, scatterer_index):
name = args[0]
n = int(args[1])
n_vars = len(args) - 2
if n_vars == 5 or (not self.strictly_shelxl and n_vars == 6):
values, behaviours = self.decode_variables(args[2:7],
u_iso_idx=n_vars - 1)
u = values[4]
isotropic = True
elif n_vars == 10:
unit_cell = self.builder.crystal_symmetry.unit_cell()
values, behaviours = self.decode_variables(
args[2:-3] + (args[-1], args[-2], args[-3]), u_iso_idx=None)
u = adptbx.u_cif_as_u_star(unit_cell, values[-6:])
isotropic = False
else:
raise shelx_error("wrong number of parameters for scatterer",
self.line)
site = values[0:3]
occ = values[3]
scattering_type = eltbx.xray_scattering.get_standard_label(
self.label_for_sfac[n], # works thank to (a) above
exact=True)
scatterer = xray.scatterer(label=name,
site=site,
occupancy=occ,
u=u,
scattering_type=scattering_type)
if (not isotropic or not isinstance(behaviours[-1], tuple)
or behaviours[-1][0] != constant_times_u_eq):
self.scatterer_to_bind_u_eq_to = (scatterer, scatterer_index)
return scatterer, behaviours
def run():
symmetry = crystal.symmetry(unit_cell=(10.67, 10.67, 4.68, 90, 90, 120),
space_group_symbol="P 3")
special_position_settings = crystal.special_position_settings(
crystal_symmetry=symmetry, min_distance_sym_equiv=0.5)
site = (0, 0, 0.236)
u_cif = ((0.17, 0.17, 0.19, 0.09, 0, 0))
site_symmetry = special_position_settings.site_symmetry(site)
print "Input Ucif:", u_cif
u_star = adptbx.u_cif_as_u_star(symmetry.unit_cell(), u_cif)
if (not site_symmetry.is_compatible_u_star(u_star)):
print "Warning: ADP tensor is incompatible with site symmetry."
u_star = site_symmetry.average_u_star(u_star)
u_cif = adptbx.u_star_as_u_cif(symmetry.unit_cell(), u_star)
print "Averaged Ucif:", u_cif
u_cart = adptbx.u_star_as_u_cart(symmetry.unit_cell(), u_star)
eigenvalues = adptbx.eigenvalues(u_cart)
if (not adptbx.is_positive_definite(eigenvalues)):
print "ADP tensor is not positive definite."
print "Eigenvectors and values:"
eigensystem = adptbx.eigensystem(u_cart)
for i in xrange(3):
print " v=(%.5f %.5f %.5f) " % eigensystem.vectors(i),
print "lambda=%.4f" % (eigensystem.values()[i], )
def run():
symmetry = crystal.symmetry(
unit_cell=(10.67, 10.67, 4.68, 90, 90, 120),
space_group_symbol="P 3")
special_position_settings = crystal.special_position_settings(
crystal_symmetry=symmetry,
min_distance_sym_equiv=0.5)
site = (0, 0, 0.236)
u_cif = ((0.17, 0.17, 0.19, 0.09, 0, 0))
site_symmetry = special_position_settings.site_symmetry(site)
print "Input Ucif:", u_cif
u_star = adptbx.u_cif_as_u_star(symmetry.unit_cell(), u_cif)
if (not site_symmetry.is_compatible_u_star(u_star)):
print "Warning: ADP tensor is incompatible with site symmetry."
u_star = site_symmetry.average_u_star(u_star)
u_cif = adptbx.u_star_as_u_cif(symmetry.unit_cell(), u_star)
print "Averaged Ucif:", u_cif
u_cart = adptbx.u_star_as_u_cart(symmetry.unit_cell(), u_star)
eigenvalues = adptbx.eigenvalues(u_cart)
if (not adptbx.is_positive_definite(eigenvalues)):
print "ADP tensor is not positive definite."
print "Eigenvectors and values:"
eigensystem = adptbx.eigensystem(u_cart)
for i in xrange(3):
print " v=(%.5f %.5f %.5f) " % eigensystem.vectors(i),
print "lambda=%.4f" % (eigensystem.values()[i],)
def lex_scatterer(self, args, scatterer_index):
name = args[0]
n = int(args[1])
n_vars = len(args) - 2
if n_vars == 5 or (not self.strictly_shelxl and n_vars == 6):
values, behaviours = self.decode_variables(
args[2:7],
u_iso_idx=n_vars-1)
u = values[4]
isotropic = True
elif n_vars == 10:
unit_cell = self.builder.crystal_symmetry.unit_cell()
values, behaviours = self.decode_variables(
args[2:-3] + (args[-1], args[-2], args[-3]),
u_iso_idx=None)
u = adptbx.u_cif_as_u_star(unit_cell, values[-6:])
isotropic = False
else:
raise shelx_error("wrong number of parameters for scatterer",
self.line)
site = values[0:3]
occ = values[3]
scattering_type = eltbx.xray_scattering.get_standard_label(
self.label_for_sfac[n], # works thank to (a) above
exact=True)
scatterer = xray.scatterer(
label = name,
site = site,
occupancy = occ,
u = u,
scattering_type = scattering_type)
if (not isotropic
or not isinstance(behaviours[-1], tuple)
or behaviours[-1][0] != constant_times_u_eq):
self.scatterer_to_bind_u_eq_to = (scatterer, scatterer_index)
return scatterer, behaviours
def u_cif_as_u_star(self, u_cif): return adptbx.u_cif_as_u_star(self.crystal_symmetry.unit_cell(), u_cif)
class crystal_structure_builder(crystal_symmetry_builder):
def __init__(self, cif_block):
# XXX To do: interpret _atom_site_refinement_flags
crystal_symmetry_builder.__init__(self, cif_block, strict=True)
atom_sites_frac = [
as_double_or_none_if_all_question_marks(
_, column_name='_atom_site_fract_%s' % axis) for _ in [
cif_block.get('_atom_site_fract_%s' % axis)
for axis in ('x', 'y', 'z')
]
]
if atom_sites_frac.count(None) == 3:
atom_sites_cart = [
as_double_or_none_if_all_question_marks(
_, column_name='_atom_site_Cartn_%s' % axis) for _ in [
cif_block.get('_atom_site_Cartn_%s' % axis)
for axis in ('x', 'y', 'z')
]
]
if atom_sites_cart.count(None) != 0:
raise CifBuilderError("No atomic coordinates could be found")
atom_sites_cart = flex.vec3_double(*atom_sites_cart)
# XXX do we need to take account of _atom_sites_Cartn_tran_matrix_ ?
atom_sites_frac = self.crystal_symmetry.unit_cell().fractionalize(
atom_sites_cart)
else:
if atom_sites_frac.count(None) != 0:
raise CifBuilderError("No atomic coordinates could be found")
atom_sites_frac = flex.vec3_double(*atom_sites_frac)
labels = cif_block.get('_atom_site_label')
type_symbol = cif_block.get('_atom_site_type_symbol')
U_iso_or_equiv = flex_double_else_none(
cif_block.get('_atom_site_U_iso_or_equiv',
cif_block.get('_atom_site_U_equiv_geom_mean')))
if U_iso_or_equiv is None:
B_iso_or_equiv = flex_double_else_none(
cif_block.get('_atom_site_B_iso_or_equiv',
cif_block.get('_atom_site_B_equiv_geom_mean')))
adp_type = cif_block.get('_atom_site_adp_type')
occupancy = flex_double_else_none(
cif_block.get('_atom_site_occupancy'))
scatterers = flex.xray_scatterer()
atom_site_aniso_label = flex_std_string_else_none(
cif_block.get('_atom_site_aniso_label'))
if atom_site_aniso_label is not None:
atom_site_aniso_label = atom_site_aniso_label
adps = [
cif_block.get('_atom_site_aniso_U_%i' % i)
for i in (11, 22, 33, 12, 13, 23)
]
have_Bs = False
if adps.count(None) > 0:
adps = [
cif_block.get('_atom_site_aniso_B_%i' % i)
for i in (11, 22, 33, 12, 13, 23)
]
have_Bs = True
if adps.count(None) == 6:
adps = None
elif adps.count(None) > 0:
CifBuilderError("Some ADP items are missing")
else:
sel = None
for adp in adps:
f = (adp == "?")
if (sel is None): sel = f
else: sel &= f
sel = ~sel
atom_site_aniso_label = atom_site_aniso_label.select(sel)
try:
adps = [flex.double(adp.select(sel)) for adp in adps]
except ValueError, e:
raise CifBuilderError("Error interpreting ADPs: " + str(e))
adps = flex.sym_mat3_double(*adps)
for i in range(len(atom_sites_frac)):
kwds = {}
if labels is not None:
kwds.setdefault('label', str(labels[i]))
if type_symbol is not None:
kwds.setdefault('scattering_type', str(type_symbol[i]))
if (atom_site_aniso_label is not None and adps is not None
and labels is not None
and labels[i] in atom_site_aniso_label):
adp = adps[flex.first_index(atom_site_aniso_label, labels[i])]
if have_Bs: adp = adptbx.b_as_u(adp)
kwds.setdefault(
'u',
adptbx.u_cif_as_u_star(self.crystal_symmetry.unit_cell(),
adp))
elif U_iso_or_equiv is not None:
kwds.setdefault('u', float_from_string(U_iso_or_equiv[i]))
elif B_iso_or_equiv is not None:
kwds.setdefault('b', float_from_string(B_iso_or_equiv[i]))
if occupancy is not None:
kwds.setdefault('occupancy', float_from_string(occupancy[i]))
scatterers.append(xray.scatterer(**kwds))
scatterers.set_sites(atom_sites_frac)
special_position_settings = crystal.special_position_settings(
crystal_symmetry=self.crystal_symmetry,
min_distance_sym_equiv=0.0001)
self.structure = xray.structure(
special_position_settings=special_position_settings,
scatterers=scatterers)
def u_cif_as_u_star(self, u_cif): return adptbx.u_cif_as_u_star(self.crystal_symmetry.unit_cell(), u_cif)
