def show(self, out=None):
def format_p(p_value):
if p_value is None: return "n/a"
elif p_value >= 1e-2: return "%.3f" % p_value
else: return "%.3e" % p_value
if out is None: out = sys.stdout
print("Bijvoet pair analysis using %s distribution" %
self.distribution,
file=out)
print("Bijvoet pairs (all): %i" % self.n_bijvoet_pairs, file=out)
print("Bijvoet pairs (used): %i" % self.delta_fo2.size(), file=out)
print("Bijvoet pairs coverage: %.2f" %
(self.n_bijvoet_pairs / self.delta_fo2.customized_copy(
anomalous_flag=True).complete_set().n_bijvoet_pairs()),
file=out)
print("G: %s" % format_float_with_su(self.G, self.sigma_G), file=out)
print("P2(true): %s" % format_p(self.p2_true), file=out)
print("P2(false): %s" % format_p(self.p2_false), file=out)
print("P3(true): %s" % format_p(self.p3_true), file=out)
print("P3(false): %s" % format_p(self.p3_false), file=out)
print("P3(racemic twin): %s" % format_p(self.p3_racemic_twin),
file=out)
print("Hooft y: %s" % format_float_with_su(self.hooft_y, self.sigma_y),
file=out)
def __init__(self,
crystal_symmetry,
cell_covariance_matrix=None,
format="coreCIF"):
self.format = format.lower()
assert self.format in ("corecif", "mmcif")
if self.format == "mmcif": self.separator = '.'
else: self.separator = '_'
self.cif_block = model.block()
cell_prefix = '_cell%s' % self.separator
if crystal_symmetry.space_group() is not None:
sym_loop = model.loop(data=OrderedDict((
('_space_group_symop' + self.separator + 'id',
range(1,
len(crystal_symmetry.space_group()) + 1)),
('_space_group_symop' + self.separator + 'operation_xyz',
[s.as_xyz() for s in crystal_symmetry.space_group()]))))
self.cif_block.add_loop(sym_loop)
sg_prefix = '_space_group%s' % self.separator
sg_type = crystal_symmetry.space_group_info().type()
sg = sg_type.group()
self.cif_block[sg_prefix +
'crystal_system'] = sg.crystal_system().lower()
self.cif_block[sg_prefix + 'IT_number'] = sg_type.number()
self.cif_block[sg_prefix +
'name_H-M_alt'] = sg_type.lookup_symbol()
self.cif_block[sg_prefix + 'name_Hall'] = sg_type.hall_symbol()
sg_prefix = '_symmetry%s' % self.separator
self.cif_block[sg_prefix +
'space_group_name_H-M'] = sg_type.lookup_symbol()
self.cif_block[sg_prefix +
'space_group_name_Hall'] = sg_type.hall_symbol()
self.cif_block[sg_prefix + 'Int_Tables_number'] = sg_type.number()
if crystal_symmetry.unit_cell() is not None:
uc = crystal_symmetry.unit_cell()
params = list(uc.parameters())
volume = uc.volume()
if cell_covariance_matrix is not None:
diag = cell_covariance_matrix.matrix_packed_u_diagonal()
for i in range(6):
if diag[i] > 0:
params[i] = format_float_with_su(
params[i], math.sqrt(diag[i]))
d_v_d_params = matrix.row(uc.d_volume_d_params())
vcv = matrix.sqr(
cell_covariance_matrix.matrix_packed_u_as_symmetric())
var_v = (d_v_d_params * vcv).dot(d_v_d_params)
volume = format_float_with_su(volume, math.sqrt(var_v))
a, b, c, alpha, beta, gamma = params
self.cif_block[cell_prefix + 'length_a'] = a
self.cif_block[cell_prefix + 'length_b'] = b
self.cif_block[cell_prefix + 'length_c'] = c
self.cif_block[cell_prefix + 'angle_alpha'] = alpha
self.cif_block[cell_prefix + 'angle_beta'] = beta
self.cif_block[cell_prefix + 'angle_gamma'] = gamma
self.cif_block[cell_prefix + 'volume'] = volume
def __init__(self,
pair_asu_table,
site_labels,
sites_frac=None,
sites_cart=None,
covariance_matrix=None,
cell_covariance_matrix=None,
parameter_map=None,
include_bonds_to_hydrogen=False,
fixed_angles=None,
conformer_indices=None,
eps=2e-16):
assert [sites_frac, sites_cart].count(None) == 1
fmt = "%.1f"
asu_mappings = pair_asu_table.asu_mappings()
space_group_info = sgtbx.space_group_info(
group=asu_mappings.space_group())
unit_cell = asu_mappings.unit_cell()
if sites_cart is not None:
sites_frac = unit_cell.fractionalize(sites_cart)
self.loop = model.loop(header=("_geom_angle_atom_site_label_1",
"_geom_angle_atom_site_label_2",
"_geom_angle_atom_site_label_3",
"_geom_angle",
"_geom_angle_site_symmetry_1",
"_geom_angle_site_symmetry_3"))
angles = crystal.calculate_angles(
pair_asu_table,
sites_frac,
covariance_matrix=covariance_matrix,
cell_covariance_matrix=cell_covariance_matrix,
parameter_map=parameter_map,
conformer_indices=conformer_indices)
for a in angles:
i_seq, j_seq, k_seq = a.i_seqs
if (not include_bonds_to_hydrogen
and (site_labels[i_seq].startswith('H')
or site_labels[k_seq].startswith('H'))):
continue
sym_code_ji = space_group_info.cif_symmetry_code(a.rt_mx_ji)
sym_code_ki = space_group_info.cif_symmetry_code(a.rt_mx_ki)
if sym_code_ji == "1": sym_code_ji = "."
if sym_code_ki == "1": sym_code_ki = "."
if (a.variance is not None and a.variance > eps
and not (fixed_angles is not None and
((i_seq, j_seq, k_seq) in fixed_angles or
(k_seq, j_seq, i_seq) in fixed_angles))):
angle = format_float_with_su(a.angle, math.sqrt(a.variance))
else:
angle = fmt % a.angle
self.loop.add_row((
site_labels[i_seq],
site_labels[j_seq],
site_labels[k_seq],
angle,
sym_code_ji,
sym_code_ki,
))
self.angles = angles.angles
self.variances = angles.variances
def __init__(self,
pair_asu_table,
site_labels,
sites_frac=None,
sites_cart=None,
covariance_matrix=None,
cell_covariance_matrix=None,
parameter_map=None,
include_bonds_to_hydrogen=False,
fixed_angles=None,
conformer_indices=None,
eps=2e-16):
assert [sites_frac, sites_cart].count(None) == 1
fmt = "%.1f"
asu_mappings = pair_asu_table.asu_mappings()
space_group_info = sgtbx.space_group_info(group=asu_mappings.space_group())
unit_cell = asu_mappings.unit_cell()
if sites_cart is not None:
sites_frac = unit_cell.fractionalize(sites_cart)
self.loop = model.loop(header=(
"_geom_angle_atom_site_label_1",
"_geom_angle_atom_site_label_2",
"_geom_angle_atom_site_label_3",
"_geom_angle",
"_geom_angle_site_symmetry_1",
"_geom_angle_site_symmetry_3"
))
angles = crystal.calculate_angles(
pair_asu_table, sites_frac,
covariance_matrix=covariance_matrix,
cell_covariance_matrix=cell_covariance_matrix,
parameter_map=parameter_map,
conformer_indices=conformer_indices)
for a in angles:
i_seq, j_seq, k_seq = a.i_seqs
if (not include_bonds_to_hydrogen
and (site_labels[i_seq].startswith('H') or
site_labels[k_seq].startswith('H'))):
continue
sym_code_ji = space_group_info.cif_symmetry_code(a.rt_mx_ji)
sym_code_ki = space_group_info.cif_symmetry_code(a.rt_mx_ki)
if sym_code_ji == "1": sym_code_ji = "."
if sym_code_ki == "1": sym_code_ki = "."
if (a.variance is not None and a.variance > eps
and not(fixed_angles is not None and
((i_seq, j_seq, k_seq) in fixed_angles or
(k_seq, j_seq, i_seq) in fixed_angles))):
angle = format_float_with_su(a.angle, math.sqrt(a.variance))
else:
angle = fmt % a.angle
self.loop.add_row((site_labels[i_seq],
site_labels[j_seq],
site_labels[k_seq],
angle,
sym_code_ji,
sym_code_ki,
))
self.angles = angles.angles
self.variances = angles.variances
def show(self, out=None):
def format_p(p_value):
if p_value is None: return "n/a"
elif p_value >= 1e-2: return "%.3f" %p_value
else: return "%.3e" %p_value
if out is None: out=sys.stdout
print >> out, "Bijvoet pair analysis using %s distribution" %self.distribution
print >> out, "Bijvoet pairs (all): %i" %self.n_bijvoet_pairs
print >> out, "Bijvoet pairs (used): %i" %self.delta_fo2.size()
print >> out, "Bijvoet pairs coverage: %.2f" %(
self.n_bijvoet_pairs/self.delta_fo2.customized_copy(
anomalous_flag=True).complete_set().n_bijvoet_pairs())
print >> out, "G: %s" %format_float_with_su(self.G, self.sigma_G)
print >> out, "P2(true): %s" %format_p(self.p2_true)
print >> out, "P2(false): %s" %format_p(self.p2_false)
print >> out, "P3(true): %s" %format_p(self.p3_true)
print >> out, "P3(false): %s" %format_p(self.p3_false)
print >> out, "P3(racemic twin): %s" %format_p(self.p3_racemic_twin)
print >> out, "Hooft y: %s" %format_float_with_su(
self.hooft_y, self.sigma_y)
def __init__(self,
pair_asu_table,
site_labels,
sites_frac=None,
sites_cart=None,
covariance_matrix=None,
cell_covariance_matrix=None,
parameter_map=None,
include_bonds_to_hydrogen=False,
fixed_distances=None,
eps=2e-16):
assert [sites_frac, sites_cart].count(None) == 1
fmt = "%.4f"
asu_mappings = pair_asu_table.asu_mappings()
space_group_info = sgtbx.space_group_info(group=asu_mappings.space_group())
unit_cell = asu_mappings.unit_cell()
if sites_cart is not None:
sites_frac = unit_cell.fractionalize(sites_cart)
self.loop = model.loop(header=(
"_geom_bond_atom_site_label_1",
"_geom_bond_atom_site_label_2",
"_geom_bond_distance",
"_geom_bond_site_symmetry_2"
))
distances = crystal.calculate_distances(
pair_asu_table, sites_frac,
covariance_matrix=covariance_matrix,
cell_covariance_matrix=cell_covariance_matrix,
parameter_map=parameter_map)
for d in distances:
if (not include_bonds_to_hydrogen
and (site_labels[d.i_seq].startswith('H') or
site_labels[d.j_seq].startswith('H'))):
continue
if (d.variance is not None and d.variance > eps
and not(fixed_distances is not None and
((d.i_seq, d.j_seq) in fixed_distances or
(d.j_seq, d.i_seq) in fixed_distances))):
distance = format_float_with_su(d.distance, math.sqrt(d.variance))
else:
distance = fmt % d.distance
sym_code = space_group_info.cif_symmetry_code(d.rt_mx_ji)
if sym_code == "1": sym_code = "."
self.loop.add_row((site_labels[d.i_seq],
site_labels[d.j_seq],
distance,
sym_code))
self.distances = distances.distances
self.variances = distances.variances
self.pair_counts = distances.pair_counts
def formatted_angle(self, i_seq, j_seq, k_seq, angle, rt_mx_ki):
if rt_mx_ki is None: rt_mx_ki = unit_mx
if self.covariance_matrix_cart is not None:
cov = covariance.extract_covariance_matrix_for_sites(
flex.size_t((i_seq,j_seq,k_seq)),
self.covariance_matrix_cart,
self.parameter_map)
if self.cell_covariance_matrix is not None:
var = angle.variance(cov, self.cell_covariance_matrix, self.unit_cell,
(unit_mx, unit_mx, rt_mx_ki))
else:
var = angle.variance(cov, self.unit_cell, (unit_mx, unit_mx, rt_mx_ki))
if var > self.eps:
return format_float_with_su(angle.angle_model, math.sqrt(var))
return "%.1f" %angle.angle_model
def formatted_distance(self, i_seq, j_seq, distance, rt_mx_ji):
if rt_mx_ji is None: rt_mx_ji = unit_mx
if self.covariance_matrix_cart is not None:
cov = covariance.extract_covariance_matrix_for_sites(
flex.size_t((i_seq,j_seq)),
self.covariance_matrix_cart,
self.parameter_map)
if self.cell_covariance_matrix is not None:
var = distance.variance(
cov, self.cell_covariance_matrix, self.unit_cell, rt_mx_ji)
else:
var = distance.variance(cov, self.unit_cell, rt_mx_ji)
if var > self.eps:
return format_float_with_su(distance.distance_model, math.sqrt(var))
return "%.4f" %distance.distance_model
def __init__(self,
angles,
space_group_info,
site_labels,
include_bonds_to_hydrogen=False,
eps=2e-16):
fmt = "%.1f"
self.loop = model.loop(header=(
"_geom_torsion_atom_site_label_1",
"_geom_torsion_atom_site_label_2",
"_geom_torsion_atom_site_label_3",
"_geom_torsion_atom_site_label_4",
"_geom_torsion",
"_geom_torsion_site_symmetry_1",
"_geom_torsion_site_symmetry_2",
"_geom_torsion_site_symmetry_3",
"_geom_torsion_site_symmetry_4"
))
for a in angles:
i_seq, j_seq, k_seq, l_seq = a.i_seqs
if (not include_bonds_to_hydrogen
and (site_labels[i_seq].startswith('H') or
site_labels[j_seq].startswith('H') or
site_labels[k_seq].startswith('H') or
site_labels[l_seq].startswith('H'))):
continue
sym_code_i = space_group_info.cif_symmetry_code(a.rt_mxs[0])
sym_code_j = space_group_info.cif_symmetry_code(a.rt_mxs[1])
sym_code_k = space_group_info.cif_symmetry_code(a.rt_mxs[2])
sym_code_l = space_group_info.cif_symmetry_code(a.rt_mxs[3])
if sym_code_i == "1": sym_code_i = "."
if sym_code_j == "1": sym_code_j = "."
if sym_code_k == "1": sym_code_k = "."
if sym_code_l == "1": sym_code_l = "."
if a.variance is not None and a.variance > eps:
angle = format_float_with_su(a.angle, math.sqrt(a.variance))
else:
angle = fmt % a.angle
self.loop.add_row((site_labels[i_seq],
site_labels[j_seq],
site_labels[k_seq],
site_labels[l_seq],
angle,
sym_code_i,
sym_code_j,
sym_code_k,
sym_code_l,
))
def __init__(self,
xray_structure,
covariance_matrix=None,
cell_covariance_matrix=None):
crystal_symmetry_as_cif_block.__init__(
self,
xray_structure.crystal_symmetry(),
cell_covariance_matrix=cell_covariance_matrix)
scatterers = xray_structure.scatterers()
uc = xray_structure.unit_cell()
if covariance_matrix is not None:
param_map = xray_structure.parameter_map()
covariance_diagonal = covariance_matrix.matrix_packed_u_diagonal()
u_star_to_u_cif_linear_map_pow2 = flex.pow2(
flex.double(uc.u_star_to_u_cif_linear_map()))
u_star_to_u_iso_linear_form = matrix.row(
uc.u_star_to_u_iso_linear_form())
fmt = "%.6f"
# _atom_site_* loop
atom_site_loop = model.loop(
header=('_atom_site_label', '_atom_site_type_symbol',
'_atom_site_fract_x', '_atom_site_fract_y',
'_atom_site_fract_z', '_atom_site_U_iso_or_equiv',
'_atom_site_adp_type', '_atom_site_occupancy'))
for i_seq, sc in enumerate(scatterers):
# site
if covariance_matrix is not None and sc.flags.grad_site():
site = []
for i in range(3):
idx = param_map[i_seq].site
if idx > -1:
var = covariance_diagonal[idx + i]
else:
var = 0
if var > 0:
site.append(
format_float_with_su(sc.site[i], math.sqrt(var)))
else:
site.append(fmt % sc.site[i])
else:
site = [fmt % sc.site[i] for i in range(3)]
# u_eq
if (covariance_matrix is not None
and (sc.flags.grad_u_iso() or sc.flags.grad_u_aniso())):
if sc.flags.grad_u_iso():
u_iso_or_equiv = format_float_with_su(
sc.u_iso,
math.sqrt(
covariance.variance_for_u_iso(
i_seq, covariance_matrix, param_map)))
else:
cov = covariance.extract_covariance_matrix_for_u_aniso(
i_seq, covariance_matrix,
param_map).matrix_packed_u_as_symmetric()
var = (u_star_to_u_iso_linear_form *
matrix.sqr(cov)).dot(u_star_to_u_iso_linear_form)
u_iso_or_equiv = format_float_with_su(
sc.u_iso_or_equiv(uc), math.sqrt(var))
else:
u_iso_or_equiv = fmt % sc.u_iso_or_equiv(uc)
if sc.flags.use_u_aniso():
adp_type = 'Uani'
else:
adp_type = 'Uiso'
atom_site_loop.add_row(
(sc.label, sc.scattering_type, site[0], site[1], site[2],
u_iso_or_equiv, adp_type, fmt % sc.occupancy))
self.cif_block.add_loop(atom_site_loop)
# _atom_site_aniso_* loop
aniso_scatterers = scatterers.select(scatterers.extract_use_u_aniso())
if aniso_scatterers.size():
labels = list(scatterers.extract_labels())
aniso_loop = model.loop(
header=('_atom_site_aniso_label', '_atom_site_aniso_U_11',
'_atom_site_aniso_U_22', '_atom_site_aniso_U_33',
'_atom_site_aniso_U_12', '_atom_site_aniso_U_13',
'_atom_site_aniso_U_23'))
for sc in aniso_scatterers:
u_cif = adptbx.u_star_as_u_cif(uc, sc.u_star)
if covariance_matrix is not None:
row = [sc.label]
idx = param_map[labels.index(sc.label)].u_aniso
if idx > -1:
var = covariance_diagonal[
idx:idx + 6] * u_star_to_u_cif_linear_map_pow2
for i in range(6):
if var[i] > 0:
row.append(
format_float_with_su(
u_cif[i], math.sqrt(var[i])))
else:
row.append(fmt % u_cif[i])
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
aniso_loop.add_row(row)
self.cif_block.add_loop(aniso_loop)
self.cif_block.add_loop(atom_type_cif_loop(xray_structure))
def run(args):
# adjust file names
in_root, in_ext = os.path.splitext(args.ref_structure)
# Check that input files exist
for filename in (args.ref_structure, args.reflections):
if not os.path.isfile(filename):
raise command_line_error("No such file %s" % filename)
# Check output file
if args.outfile and os.path.isfile(args.outfile) and not args.overwrite:
raise command_line_error("Output file {} exists.".format(args.outfile))
# Load input model and reflections
if in_ext == '.cif':
xm = refinement.model.from_cif(model=args.ref_structure,
reflections=args.reflections + '=hklf4')
else:
xm = refinement.model.from_shelx(ins_or_res=args.ref_structure,
hkl=args.reflections,
strictly_shelxl=False)
# Look for beam energy
if args.energy:
energy = args.energy
wvl = 12398 / energy
elif args.energy_in_fname:
estart,elength = args.energy_in_fname.split(',')
estart = int(estart)
elength = int(elength)
energy = float(args.reflections[estart:estart+elength])
wvl = 12398 / energy
else:
energy = None
sys.stderr.write('''WARNING: Using beam energy from reference model. \
Inelastic form factors for \n non-refined atoms may be inaccurate.\n''')
wvl = xm.wavelength
# Load default anomalous scattering factors if wavelength is available
if wvl:
xm.xray_structure.set_inelastic_form_factors(wvl, 'sasaki')
else:
raise energy_missing_error()
# At last...
anom_sc_list=[]
for i, sc in enumerate(xm.xray_structure.scatterers()):
sc.flags.set_grad_site(False)
sc.flags.set_grad_u_iso(False)
sc.flags.set_grad_u_aniso(False)
sc.flags.set_grad_occupancy(False)
if sc.element_symbol().lower() == args.anom_atom.lower():
sc.flags.set_use_fp_fdp(True)
sc.flags.set_grad_fp(True)
sc.flags.set_grad_fdp(True)
anom_sc_list.append((i, sc))
ls = xm.least_squares()
steps = lstbx.normal_eqns_solving.levenberg_marquardt_iterations(
non_linear_ls=ls,
n_max_iterations=args.max_cycles,
gradient_threshold=args.stop_deriv,
step_threshold=args.stop_shift)
cov = ls.covariance_matrix()
cov_diag = cov.matrix_packed_u_diagonal()
param_map = xm.xray_structure.parameter_map()
# Prepare output
result = ''
if args.table or args.table_with_su:
if energy: label = "{:.1f} ".format(energy)
else: label = "{} ".format(args.reflections)
result += label
for i, sc in anom_sc_list:
result += "{:6.3f} ".format(sc.fp)
for i, sc in anom_sc_list:
result += "{:6.3f} ".format(sc.fdp)
result += '\n'
if args.table_with_su:
result += ' ' * len(label)
for i, sc in anom_sc_list:
sigma_fp = None
params = param_map[i]
if params.fp >= 0:
sigma_fp = sqrt(cov_diag[params.fp])
result += "{:6.3f} ".format(sigma_fp)
else:
result += " "
for i, sc in anom_sc_list:
sigma_fdp = None
params = param_map[i]
if params.fdp >= 0:
sigma_fdp = sqrt(cov_diag[params.fdp])
result += "{:6.3f} ".format(sigma_fdp)
else:
result += " "
result += '\n'
if not (args.table or args.table_with_su):
from libtbx.utils import format_float_with_standard_uncertainty \
as format_float_with_su
result += "\n### REFINE ANOMALOUS SCATTERING FACTORS ###\n"
result += "Reflections: {}\n\n".format(args.reflections)
for i, sc in anom_sc_list:
sigma_fp = sigma_fdp = None
params = param_map[i]
if params.fp >= 0:
sigma_fp = sqrt(cov_diag[params.fp])
if params.fdp >= 0:
sigma_fdp = sqrt(cov_diag[params.fdp])
result += "{}:\n\tfp: {}\n\tfdp: {}\n".format(
sc.label,
format_float_with_su(sc.fp, sigma_fp),
format_float_with_su(sc.fdp, sigma_fdp))
# Write to file or stdout
if args.outfile:
with open(args.outfile, 'w') as f:
f.write(result)
else:
print(result)
def show(self, out=None):
if out is None: out = sys.stdout
print("Flack x: %s" %format_float_with_su(self.flack_x, self.sigma_x), file=out)
def show(self, out=None): if out is None: out = sys.stdout print >> out, "Flack x: %s" %format_float_with_su(self.flack_x, self.sigma_x)
def __init__(self, xray_structure, covariance_matrix=None, cell_covariance_matrix=None):
crystal_symmetry_as_cif_block.__init__(
self, xray_structure.crystal_symmetry(), cell_covariance_matrix=cell_covariance_matrix
)
scatterers = xray_structure.scatterers()
uc = xray_structure.unit_cell()
if covariance_matrix is not None:
param_map = xray_structure.parameter_map()
covariance_diagonal = covariance_matrix.matrix_packed_u_diagonal()
u_star_to_u_cif_linear_map_pow2 = flex.pow2(flex.double(uc.u_star_to_u_cif_linear_map()))
u_star_to_u_iso_linear_form = matrix.row(uc.u_star_to_u_iso_linear_form())
fmt = "%.6f"
# _atom_site_* loop
atom_site_loop = model.loop(
header=(
"_atom_site_label",
"_atom_site_type_symbol",
"_atom_site_fract_x",
"_atom_site_fract_y",
"_atom_site_fract_z",
"_atom_site_U_iso_or_equiv",
"_atom_site_adp_type",
"_atom_site_occupancy",
)
)
for i_seq, sc in enumerate(scatterers):
site = occu = u_iso_or_equiv = None
# site
if covariance_matrix is not None:
params = param_map[i_seq]
if sc.flags.grad_site() and params.site >= 0:
site = []
for i in range(3):
site.append(format_float_with_su(sc.site[i], math.sqrt(covariance_diagonal[params.site + i])))
# occupancy
if sc.flags.grad_occupancy() and params.occupancy >= 0:
occu = format_float_with_su(sc.occupancy, math.sqrt(covariance_diagonal[params.occupancy]))
# Uiso/eq
if sc.flags.grad_u_iso() or sc.flags.grad_u_aniso():
if sc.flags.grad_u_iso():
u_iso_or_equiv = format_float_with_su(
sc.u_iso, math.sqrt(covariance.variance_for_u_iso(i_seq, covariance_matrix, param_map))
)
else:
cov = covariance.extract_covariance_matrix_for_u_aniso(
i_seq, covariance_matrix, param_map
).matrix_packed_u_as_symmetric()
var = (u_star_to_u_iso_linear_form * matrix.sqr(cov)).dot(u_star_to_u_iso_linear_form)
u_iso_or_equiv = format_float_with_su(sc.u_iso_or_equiv(uc), math.sqrt(var))
if site is None:
site = [fmt % sc.site[i] for i in range(3)]
if occu is None:
occu = fmt % sc.occupancy
if u_iso_or_equiv is None:
u_iso_or_equiv = fmt % sc.u_iso_or_equiv(uc)
if sc.flags.use_u_aniso():
adp_type = "Uani"
else:
adp_type = "Uiso"
atom_site_loop.add_row(
(sc.label, sc.scattering_type, site[0], site[1], site[2], u_iso_or_equiv, adp_type, occu)
)
self.cif_block.add_loop(atom_site_loop)
# _atom_site_aniso_* loop
aniso_scatterers = scatterers.select(scatterers.extract_use_u_aniso())
if aniso_scatterers.size():
labels = list(scatterers.extract_labels())
aniso_loop = model.loop(
header=(
"_atom_site_aniso_label",
"_atom_site_aniso_U_11",
"_atom_site_aniso_U_22",
"_atom_site_aniso_U_33",
"_atom_site_aniso_U_12",
"_atom_site_aniso_U_13",
"_atom_site_aniso_U_23",
)
)
for sc in aniso_scatterers:
u_cif = adptbx.u_star_as_u_cif(uc, sc.u_star)
if covariance_matrix is not None:
row = [sc.label]
idx = param_map[labels.index(sc.label)].u_aniso
if idx > -1:
var = covariance_diagonal[idx : idx + 6] * u_star_to_u_cif_linear_map_pow2
for i in range(6):
if var[i] > 0:
row.append(format_float_with_su(u_cif[i], math.sqrt(var[i])))
else:
row.append(fmt % u_cif[i])
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
aniso_loop.add_row(row)
self.cif_block.add_loop(aniso_loop)
self.cif_block.add_loop(atom_type_cif_loop(xray_structure))
def __init__(self, crystal_symmetry, cell_covariance_matrix=None, format="coreCIF", numeric_format="%.3f"):
self.format = format.lower()
assert self.format in ("corecif", "mmcif")
if self.format == "mmcif":
self.separator = "."
else:
self.separator = "_"
assert numeric_format.startswith("%")
self.cif_block = model.block()
cell_prefix = "_cell%s" % self.separator
if crystal_symmetry.space_group() is not None:
sym_loop = model.loop(
data=OrderedDict(
(
(
"_space_group_symop" + self.separator + "id",
range(1, len(crystal_symmetry.space_group()) + 1),
),
(
"_space_group_symop" + self.separator + "operation_xyz",
[s.as_xyz() for s in crystal_symmetry.space_group()],
),
)
)
)
self.cif_block.add_loop(sym_loop)
sg_prefix = "_space_group%s" % self.separator
sg_type = crystal_symmetry.space_group_info().type()
sg = sg_type.group()
self.cif_block[sg_prefix + "crystal_system"] = sg.crystal_system().lower()
self.cif_block[sg_prefix + "IT_number"] = sg_type.number()
self.cif_block[sg_prefix + "name_H-M_alt"] = sg_type.lookup_symbol()
self.cif_block[sg_prefix + "name_Hall"] = sg_type.hall_symbol()
sg_prefix = "_symmetry%s" % self.separator
self.cif_block[sg_prefix + "space_group_name_H-M"] = sg_type.lookup_symbol()
self.cif_block[sg_prefix + "space_group_name_Hall"] = sg_type.hall_symbol()
self.cif_block[sg_prefix + "Int_Tables_number"] = sg_type.number()
if crystal_symmetry.unit_cell() is not None:
uc = crystal_symmetry.unit_cell()
params = list(uc.parameters())
volume = uc.volume()
if cell_covariance_matrix is not None:
diag = cell_covariance_matrix.matrix_packed_u_diagonal()
for i in range(6):
if diag[i] > 0:
params[i] = format_float_with_su(params[i], math.sqrt(diag[i]))
d_v_d_params = matrix.row(uc.d_volume_d_params())
vcv = matrix.sqr(cell_covariance_matrix.matrix_packed_u_as_symmetric())
var_v = (d_v_d_params * vcv).dot(d_v_d_params)
volume = format_float_with_su(volume, math.sqrt(var_v))
numeric_format = "%s"
a, b, c, alpha, beta, gamma = params
self.cif_block[cell_prefix + "length_a"] = numeric_format % a
self.cif_block[cell_prefix + "length_b"] = numeric_format % b
self.cif_block[cell_prefix + "length_c"] = numeric_format % c
self.cif_block[cell_prefix + "angle_alpha"] = numeric_format % alpha
self.cif_block[cell_prefix + "angle_beta"] = numeric_format % beta
self.cif_block[cell_prefix + "angle_gamma"] = numeric_format % gamma
self.cif_block[cell_prefix + "volume"] = numeric_format % volume
def atom_type_cif_loop(xray_structure, format="mmcif", covariance_matrix=None):
format = format.lower()
assert format in ("corecif", "mmcif")
if format == "mmcif": separator = '.'
else: separator = '_'
sources = {
"it1992": "International Tables Volume C Table 6.1.1.4 (pp. 500-502)",
"wk1995": "Waasmaier & Kirfel (1995), Acta Cryst. A51, 416-431",
}
inelastic_references = {
"henke":
"Henke, Gullikson and Davis, At. Data and Nucl. Data Tables, 1993, 54, 2",
"sasaki": "Sasaki, KEK Report, 1989, 88-14, 1",
}
scattering_type_registry = xray_structure.scattering_type_registry()
unique_gaussians = scattering_type_registry.unique_gaussians_as_list()
max_n_gaussians = max(
[gaussian.n_terms() for gaussian in unique_gaussians])
max_n_gaussians = max(max_n_gaussians,
4) # Need for compliance with mmcif_pdbx_v50
# _atom_type_* loop
header = [
'_atom_type%ssymbol' % separator,
'_atom_type%sscat_dispersion_real' % separator,
'_atom_type%sscat_dispersion_imag' % separator
]
header.extend([
'_atom_type%sscat_Cromer_Mann_a%i' % (separator, i + 1)
for i in range(max_n_gaussians)
])
header.extend([
'_atom_type%sscat_Cromer_Mann_b%i' % (separator, i + 1)
for i in range(max_n_gaussians)
])
header.extend([
'_atom_type%sscat_Cromer_Mann_c' % separator,
'_atom_type%sscat_source' % separator,
'_atom_type%sscat_dispersion_source' % separator
])
atom_type_loop = model.loop(header=header)
gaussian_dict = scattering_type_registry.as_type_gaussian_dict()
scattering_type_registry = xray_structure.scattering_type_registry()
params = xray_structure.scattering_type_registry_params
if covariance_matrix:
param_map = xray_structure.parameter_map()
covariance_diagonal = covariance_matrix.matrix_packed_u_diagonal()
fp_fdp_table = {}
for i_seq, sc in enumerate(xray_structure.scatterers()):
covariance_diagonal
sc_params = param_map[i_seq]
fp, fdp = sc.fp, sc.fdp
if covariance_matrix:
if sc.flags.grad_fp():
fp = format_float_with_su(
sc.fp, math.sqrt(covariance_diagonal[sc_params.fp]))
if sc.flags.grad_fdp():
fdp = format_float_with_su(
sc.fdp, math.sqrt(covariance_diagonal[sc_params.fdp]))
fp_fdp_table.setdefault(sc.scattering_type, (fp, fdp))
disp_source = inelastic_references.get(
xray_structure.inelastic_form_factors_source)
# custom?
if disp_source is None:
disp_source = xray_structure.inelastic_form_factors_source
if disp_source is None:
disp_source = "."
for atom_type, gaussian in six.iteritems(
scattering_type_registry.as_type_gaussian_dict()):
scat_source = sources.get(params.table)
if params.custom_dict and atom_type in params.custom_dict:
scat_source = "Custom %i-Gaussian" % gaussian.n_terms()
elif scat_source is None:
scat_source = """\
%i-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD:
Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31."""
scat_source = scat_source % gaussian.n_terms()
if disp_source == ".":
fp, fdp = ".", "."
else:
fp, fdp = fp_fdp_table[atom_type]
if not isinstance(fp, str):
fp = "%.5f" % fp
if not isinstance(fdp, str):
fdp = "%.5f" % fdp
row = [atom_type, fp, fdp]
#gaussian = gaussian_dict[sc.scattering_type]
gaussian_a = ["%.5f" % a for a in gaussian.array_of_a()]
gaussian_b = ["%.5f" % a for a in gaussian.array_of_b()]
gaussian_c = "%.5f" % gaussian.c()
gaussian_a.extend(["."] * (max_n_gaussians - gaussian.n_terms()))
gaussian_b.extend(["."] * (max_n_gaussians - gaussian.n_terms()))
row.extend(gaussian_a + gaussian_b)
row.extend([gaussian_c, scat_source, disp_source])
atom_type_loop.add_row(row)
return atom_type_loop
