def ligands(self):
if (self._ligands is None):
return dummy_validation()
return self._ligands
def as_table1_column (self,
label,
wavelength,
log,
re_compute_r_factors=Auto) :
"""
Extract information for display in the traditional 'Table 1' of
crystallographic statistics in structure articles.
"""
outer_shell = None
data_stats = self.data_stats
if (data_stats is None) :
data_stats = dummy_validation()
merging_stats = dummy_validation()
merging_outer = dummy_validation()
n_refl_uniq = data_stats.n_refl
n_refl_refine = data_stats.n_refl_refine
n_free = data_stats.n_free
completeness = data_stats.completeness
completeness_outer = data_stats.completeness_outer
d_max_min = self.d_max_min()
d_max, d_min = d_max_min
if (self.merging is not None) :
merging_stats = self.merging.overall
merging_outer = self.merging.bins[-1]
n_refl_uniq = merging_stats.n_uniq
epsilon = 0.001
if ((merging_stats.d_min > d_min + 2*epsilon) or
(merging_stats.d_max < d_max - 2*epsilon)) :
raise Sorry(("Resolution limits for unmerged data in the structure "+
"'%s' do not cover the "+
"full range present in the merged data: %g - %g (merged) versus "+
"%g - %g (unmerged)") % (label, d_max, d_min,
merging_stats.d_max, merging_stats.d_min))
r_work = self.r_work()
r_free = self.r_free()
n_tls_groups = None
if (self.header_info is not None) :
if (self.header_info.n_tls_groups > 0) :
n_tls_groups = self.header_info.n_tls_groups
use_header_values = (not re_compute_r_factors or
(not self.header_info.is_phenix_refinement() and
(re_compute_r_factors is Auto)))
r_work, r_free, warned = rfactor_sanity_check(
r_work_pdb=self.header_info.r_work,
r_free_pdb=self.header_info.r_free,
r_work_fmodel=r_work,
r_free_fmodel=r_free,
out=log,
structure_name=label,
re_compute_r_factors=not use_header_values)
if (use_header_values) :
n_refl_refine = data_stats.n_refl
return iotbx.table_one.column(
label=label,
space_group=self.space_group_info(),
unit_cell=self.unit_cell().parameters(),
# data properties
wavelength=wavelength,
d_max_min=d_max_min,
n_refl_all=merging_stats.n_obs,
n_refl=n_refl_uniq,
multiplicity=merging_stats.mean_redundancy,
completeness=completeness * 100.0,
i_over_sigma=merging_stats.i_over_sigma_mean,
wilson_b=data_stats.wilson_b,
r_sym=merging_stats.r_merge,
r_meas=merging_stats.r_meas,
r_pim=merging_stats.r_pim,
cc_one_half=merging_stats.cc_one_half,
cc_star=merging_stats.cc_star,
# refinement
n_refl_refine=n_refl_refine,
n_free=n_free,
r_work=r_work,
r_free=r_free,
cc_work=merging_stats.cc_work,
cc_free=merging_stats.cc_free,
# model properties
n_atoms=self.model_stats.all.n_non_hd,
n_macro_atoms=self.model_stats.macromolecules.n_non_hd,
n_ligand_atoms=self.model_stats.ligands.n_non_hd,
n_waters=self.model_stats.water.n_non_hd,
n_residues=self.model_stats.n_protein,
bond_rmsd=self.rms_bonds(),
angle_rmsd=self.rms_angles(),
rama_favored=self.rama_favored(),
rama_allowed=self.rama_allowed(),
rama_outliers=self.rama_outliers(),
rota_outliers=self.rota_outliers(),
clashscore=self.clashscore(),
adp_mean=self.model_stats.all.b_mean,
adp_mean_mm=self.model_stats.macromolecules.b_mean,
adp_mean_lig=self.model_stats.ligands.b_mean,
adp_mean_wat=self.model_stats.water.b_mean,
n_tls_groups=n_tls_groups,
anomalous_flag=data_stats.anomalous_flag,
).add_outer_shell(
# XXX we need a consistency check here as well
d_max_min=(data_stats.d_max_outer, data_stats.d_min_outer),
n_refl=data_stats.n_refl_outer,
n_refl_all=merging_outer.n_obs,
n_refl_refine=data_stats.n_refl_refine_outer,
n_free=data_stats.n_free_outer,
cc_one_half=merging_outer.cc_one_half,
cc_star=merging_outer.cc_star,
r_sym=merging_outer.r_merge,
r_meas=merging_outer.r_meas,
r_pim=merging_outer.r_pim,
i_over_sigma=merging_outer.i_over_sigma_mean,
multiplicity=merging_outer.mean_redundancy,
completeness=completeness_outer * 100,
cc_work=merging_outer.cc_work,
cc_free=merging_outer.cc_free,
r_work=data_stats.r_work_outer,
r_free=data_stats.r_free_outer)
def water(self):
if (self._water is None):
return dummy_validation()
return self._water
def macromolecules(self):
if (self._macromolecules is None):
return dummy_validation()
return self._macromolecules
def ligands (self) :
if (self._ligands is None) :
return dummy_validation()
return self._ligands
def water (self) :
if (self._water is None) :
return dummy_validation()
return self._water
def macromolecules (self) :
if (self._macromolecules is None) :
return dummy_validation()
return self._macromolecules
