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
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
