def as_cif_block(self, cif_block=None, pdbx_refine_id=''):
if cif_block is None:
cif_block = iotbx.cif.model.block()
cif_block["_refine.pdbx_stereochemistry_target_values"] = \
self.restraints_source if self.restraints_source is not None else '?'
loop = iotbx.cif.model.loop(header=(
"_refine_ls_restr.pdbx_refine_id",
"_refine_ls_restr.type",
"_refine_ls_restr.number",
"_refine_ls_restr.dev_ideal",
#"_refine_ls_restr.dev_ideal_target",
"_refine_ls_restr.weight",
#"_refine_ls_restr.pdbx_refine_id",
"_refine_ls_restr.pdbx_restraint_function",
))
res = self.result()
a,b,c,d,p,n = res.angle, res.bond, res.chirality, res.dihedral, \
res.planarity, res.nonbonded
loop.add_row((pdbx_refine_id, "f_bond_d", b.n, round_4_for_cif(b.mean), "?", "?"))
loop.add_row((pdbx_refine_id, "f_angle_d", a.n, round_4_for_cif(a.mean), "?", "?"))
loop.add_row((pdbx_refine_id, "f_chiral_restr", c.n, round_4_for_cif(c.mean), "?", "?"))
loop.add_row((pdbx_refine_id, "f_plane_restr", p.n, round_4_for_cif(p.mean), "?", "?"))
loop.add_row((pdbx_refine_id, "f_dihedral_angle_d", d.n, round_4_for_cif(d.mean), "?", "?"))
cif_block.add_loop(loop)
return cif_block
def as_cif_block(self,
cif_block=None,
scattering_type="X-RAY DIFFRACTION"):
import iotbx.cif.model
if cif_block is None:
cif_block = iotbx.cif.model.block()
cif_block["_refine.pdbx_refine_id"] = scattering_type
cif_block["_refine.ls_d_res_low"] = round_2_for_cif(self.d_max)
cif_block["_refine.ls_d_res_high"] = round_2_for_cif(self.d_min)
cif_block["_refine.pdbx_ls_sigma_F"] = round_2_for_cif(
self.min_f_obs_over_sigma)
cif_block["_refine.ls_percent_reflns_obs"] = round_2_for_cif(
self.completeness_in_range * 100.0)
cif_block["_refine.ls_number_reflns_obs"] = self.number_of_reflections
#_refine.ls_number_reflns_all
cif_block["_refine.ls_number_reflns_R_work"] = (
self.number_of_reflections - self.number_of_test_reflections)
cif_block[
"_refine.ls_number_reflns_R_free"] = self.number_of_test_reflections
cif_block["_refine.ls_R_factor_obs"] = round_4_for_cif(self.r_all)
cif_block["_refine.ls_R_factor_R_work"] = round_4_for_cif(self.r_work)
cif_block["_refine.ls_R_factor_R_free"] = round_4_for_cif(self.r_free)
cif_block["_refine.ls_percent_reflns_R_free"] = round_2_for_cif(
self.number_of_test_reflections / self.number_of_reflections * 100)
loop = iotbx.cif.model.loop(header=(
"_refine_ls_shell.pdbx_refine_id",
#"_refine_ls_shell.pdbx_total_number_of_bins_used",
"_refine_ls_shell.d_res_high",
"_refine_ls_shell.d_res_low",
"_refine_ls_shell.number_reflns_R_work",
"_refine_ls_shell.R_factor_R_work",
"_refine_ls_shell.percent_reflns_obs",
"_refine_ls_shell.R_factor_R_free",
#"_refine_ls_shell.R_factor_R_free_error",
#"_refine_ls_shell.percent_reflns_R_free",
"_refine_ls_shell.number_reflns_R_free",
#"_refine_ls_shell.number_reflns_all",
#"_refine_ls_shell.R_factor_all",
#"_refine_ls_shell.redundancy_reflns_obs",
#"_refine_ls_shell.number_reflns_obs",
))
for bin in self.bins:
d_max, d_min = [float(d) for d in bin.d_range.split('-')]
loop.add_row((scattering_type, round_2_for_cif(d_min),
round_2_for_cif(d_max), bin.n_work,
round_4_for_cif(bin.r_work),
round_2_for_cif(bin.completeness * 100),
round_4_for_cif(bin.r_free), bin.n_free))
cif_block.add_loop(loop)
cif_block["_refine.solvent_model_details"] = "FLAT BULK SOLVENT MODEL"
#_refine.solvent_model_param_ksol
#_refine.solvent_model_param_bsol
cif_block["_refine.pdbx_solvent_vdw_probe_radii"] = round_4_for_cif(
self.mask_solvent_radius)
cif_block["_refine.pdbx_solvent_shrinkage_radii"] = round_4_for_cif(
self.mask_shrink_radius)
# twinning?
cif_block["_refine.overall_SU_ML"] = round_4_for_cif(
self.ml_coordinate_error)
cif_block["_refine.pdbx_overall_phase_error"] = round_4_for_cif(
self.ml_phase_error)
return cif_block
