def restore_selected(self):
items = [item for item in self.tree.selectedItems()]
model_dict = self.session.filereader_manager.filereader_dict
models = list(model_dict.keys())
for item in items:
parent = item.parent()
mdl = models[self.tree.indexOfTopLevelItem(parent)]
if parent is None:
fr = model_dict[mdl][-1]
else:
fr = model_dict[mdl][parent.indexOfChild(item)]
fr_rescol = ResidueCollection(fr)
fr_rescol.update_chix(mdl)
if fr.all_geom is not None and len(fr.all_geom) > 1:
coordsets = fr_rescol.all_geom_coordsets(fr)
mdl.remove_coordsets()
mdl.add_coordsets(coordsets)
for i, coordset in enumerate(coordsets):
mdl.active_coordset_id = i + 1
for atom, coord in zip(mdl.atoms, coordset):
atom.coord = coord
mdl.active_coordset_id = 1
def job_finished(self, trigger_name, job):
"""when a job is finished, open or update the structure as requested"""
if self.session.seqcrow_settings.settings.JOB_FINISHED_NOTIFICATION == \
'log and popup notifications' and self.session.ui.is_gui:
#it's just an error message for now
#TODO: make my own logger
self.session.logger.error("%s: %s" % (trigger_name, job))
else:
job.session.logger.info("%s: %s" % (trigger_name, job))
if isinstance(job, LocalJob):
self._thread = None
if not hasattr(job, "output_name") or \
not os.path.exists(job.output_name):
job.error = True
else:
fr = FileReader(job.output_name, just_geom=False)
#XXX: finished is not added to the FileReader for ORCA and Psi4 when finished = False
if 'finished' not in fr.other or not fr.other['finished']:
job.error = True
if job.auto_update and (
job.theory.geometry.chix_atomicstructure is not None
and not job.theory.geometry.chix_atomicstructure.deleted):
if os.path.exists(job.output_name):
finfo = job.output_name
try:
finfo = (job.output_name, job.format_name, None)
fr = FileReader(finfo, get_all=True, just_geom=False)
if len(fr.atoms) > 0:
job.session.filereader_manager.triggers.activate_trigger(
ADD_FILEREADER,
([job.theory.geometry.chix_atomicstructure], [fr]))
rescol = ResidueCollection(fr)
rescol.update_chix(
job.theory.geometry.chix_atomicstructure)
except:
job.update_structure()
if fr.all_geom is not None and len(fr.all_geom) > 1:
coordsets = rescol.all_geom_coordsets(fr)
job.theory.geometry.chix_atomicstructure.remove_coordsets()
job.theory.geometry.chix_atomicstructure.add_coordsets(
coordsets)
for i, coordset in enumerate(coordsets):
job.theory.geometry.chix_atomicstructure.active_coordset_id = i + 1
for atom, coord in zip(
job.theory.geometry.chix_atomicstructure.atoms,
coordset):
atom.coord = coord
job.theory.geometry.chix_atomicstructure.active_coordset_id = job.theory.geometry.chix_atomicstructure.num_coordsets
elif job.auto_open or job.auto_update:
if hasattr(job, "output_name") and os.path.exists(job.output_name):
if job.format_name:
run(
job.session, "open \"%s\" coordsets true format %s" %
(job.output_name, job.format_name))
else:
run(job.session,
"open \"%s\" coordsets true" % job.output_name)
else:
self.session.logger.error("could not open output of %s" %
repr(job))
self.triggers.activate_trigger(JOB_QUEUED, trigger_name)
pass