def __init__(self, model, fmodel_x=None, fmodel_n=None, refinement_params=None, use_molprobity=True): ref_par = refinement_params self.wilson_b = None self.model = model if fmodel_x is not None: self.wilson_b = fmodel_x.wilson_b() elif fmodel_n is not None: self.wilson_b = fmodel_n.wilson_b() self.geometry = model.geometry_statistics() self.adp = model.adp_statistics() self.data_x, self.data_n = None, None if (fmodel_x is not None): self.data_x = fmodel_x.info( free_reflections_per_bin=ref_par.alpha_beta. free_reflections_per_bin, max_number_of_bins=ref_par.main.max_number_of_resolution_bins) if (fmodel_n is not None): self.data_n = fmodel_n.info( free_reflections_per_bin=ref_par.alpha_beta. free_reflections_per_bin, max_number_of_bins=ref_par.main.max_number_of_resolution_bins)
def __init__(self, model, fmodel_x = None, fmodel_n = None, refinement_params = None): ref_par = refinement_params self.wilson_b = None self.model = model if fmodel_x is not None: self.wilson_b = fmodel_x.wilson_b() elif fmodel_n is not None: self.wilson_b = fmodel_n.wilson_b() self.geometry = model.geometry_statistics() self.adp = model.adp_statistics() self.data_x, self.data_n = None, None if(fmodel_x is not None): self.data_x = fmodel_x.info( free_reflections_per_bin = ref_par.alpha_beta.free_reflections_per_bin, max_number_of_bins = ref_par.main.max_number_of_resolution_bins) if(fmodel_n is not None): self.data_n = fmodel_n.info( free_reflections_per_bin = ref_par.alpha_beta.free_reflections_per_bin, max_number_of_bins = ref_par.main.max_number_of_resolution_bins) self._pdbx_refine_id = '' if self.data_x is not None: self._pdbx_refine_id = 'X-RAY DIFFRACTION' if self.data_n is not None: # !!! Warning: "X-ray+Neutron" is not compliant with mmCIF dictionary: # http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_exptl.method.html self._pdbx_refine_id = 'NEUTRON DIFFRACTION' if self.data_x is None else 'X-ray+Neutron' if self._pdbx_refine_id == '': # most likely electron microscopy, but checking scattering table anyway if self.model.get_xray_structure().scattering_type_registry().last_table() == "electron": self._pdbx_refine_id = 'ELECTRON MICROSCOPY'
def __init__(self, model, ignore_hd, use_molprobity=True, ncs_manager=None, cdl_restraints=False, general_selection=None, ): self.geometry = model.geometry_statistics( ignore_hd = ignore_hd, molprobity_scores=use_molprobity, cdl_restraints=cdl_restraints, general_selection=general_selection, ) self.content = model_content(model) self.adp = adp(model) self.tls_groups = model.tls_groups self.anomalous_scatterer_groups = model.anomalous_scatterer_groups self.ncs_groups = model.extract_ncs_groups() self.ncs_manager = ncs_manager self.pdb_hierarchy = model.pdb_hierarchy(sync_with_xray_structure=True) self.cdl_restraints = cdl_restraints