def __init__(self, model, params, log):
"""
model is changed in place
params - those in master_phil_str without scope name
"""
self.model = model
self.params = params
self.log = log
self.outliers = None
self.cablam_contours = fetch_peptide_expectations()
self.ca_contours = fetch_ca_expectations()
self.motif_contours = fetch_motif_contours()
self.n_tried_residues = 0
self.n_rotated_residues = 0
self.cablam_fixed_minimized = None
if not self.params.enabled:
return
self.model.process_input_model(make_restraints=True)
print("CaBLAM idealization", file=self.log)
if self.model.get_hierarchy().models_size() > 1:
raise Sorry("Multi-model files are not supported")
self.model.search_for_ncs()
print(self.model.get_ncs_obj().show_phil_format(), file=self.log)
self.outliers_by_chain = self.identify_outliers()
# idealization
# TODO: verify if outliers by chain is dict
for chain, outliers in six.iteritems(self.outliers_by_chain):
b_selection = self.model.selection("chain %s" % chain)
self.atoms_around = self.model.get_xray_structure(
).selection_within(7, b_selection).iselection()
for outlier in outliers:
self.fix_cablam_outlier(chain, outlier)
if self.params.find_ss_after_fixes:
ss_manager = ss_manager_class(
pdb_hierarchy=self.model.get_hierarchy(),
geometry_restraints_manager=self.model.get_restraints_manager(
).geometry,
sec_str_from_pdb_file=None,
params=None,
mon_lib_srv=self.model.get_mon_lib_srv,
verbose=-1,
log=self.log)
self.model.get_restraints_manager(
).geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.model.get_hierarchy(),
log=self.log)
self.model.set_ss_annotation(ann=ss_manager.actual_sec_str)
if params.do_gm:
self.cablam_fixed_minimized = self._minimize()
def __init__(self, model, params, log):
"""
model is changed in place
params - those in master_phil_str without scope name
"""
self.model = model
self.params = params
self.log = log
self.outliers = None
self.cablam_contours = fetch_peptide_expectations()
self.ca_contours = fetch_ca_expectations()
self.motif_contours = fetch_motif_contours()
self.n_tried_residues = 0
self.n_rotated_residues = 0
# with open("in.pdb",'w') as f:
# f.write(self.model.model_as_pdb())
if self.model.get_hierarchy().models_size() > 1:
raise Sorry("Multi-model files are not supported")
self.outliers_by_chain = self.identify_outliers()
# idealization
for chain, outliers in self.outliers_by_chain.iteritems():
for outlier in outliers:
self.fix_cablam_outlier(chain, outlier)
if self.params.find_ss_after_fixes:
ss_manager = ss_manager_class(
pdb_hierarchy=self.model.get_hierarchy(),
geometry_restraints_manager=self.model.get_restraints_manager().geometry,
sec_str_from_pdb_file=None,
params=None,
mon_lib_srv=self.model.get_mon_lib_srv,
verbose=-1,
log=self.log)
self.model.get_restraints_manager().geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.model.get_hierarchy(),
log=self.log)
self.model.set_ss_annotation(ann=ss_manager.actual_sec_str)
self.cablam_fixed_minimized = None
if params.do_gm:
self.cablam_fixed_minimized = self._minimize()