def main(argv):
"""
RNA 3D Hub update entry point.
"""
try:
m = MotifAtlasBaseClass()
m.start_logging()
pdb_ids = get_pdb_info()
update_loops(pdb_ids)
update_pairwise_annotations(pdb_ids)
update_unit_ids(pdb_ids)
update_unit_ordering(pdb_ids)
update_coordinates(pdb_ids)
update_redundant_nucleotides(pdb_ids)
update_best_chains_and_models(pdb_ids)
# must follow best chain and model update
cluster_motifs('IL')
import_motifs('IL')
cluster_motifs('HL')
import_motifs('HL')
# must follow motif clustering
update_loop_annotations()
# must follow unit id updates
export_data(pdb_ids)
# TODO annotate all pdb files with motifs
# TODO compute new non-redundant lists, import into the database
update_cache()
logging.info('Update completed')
m.send_report()
except:
try:
logging.critical('Update failed')
logging.critical(traceback.format_exc(sys.exc_info()))
m.set_email_subject('RNA 3D Hub update failed')
m.send_report()
except:
pass
def setUp(self):
"""runs the entire pipeline"""
self.success = False
self.clean_up_database()
m = MotifAtlasBaseClass()
m.start_logging()
logging.info('Initializing update')
"""get new pdb files"""
p = PdbInfoLoader()
p.get_all_rna_pdbs()
"""override pdb files with a smaller set"""
p.pdbs = ['1FG0','1HLX']
"""extract all loops and import into the database"""
e = LoopExtractor()
e.extract_and_import_loops(p.pdbs)
"""do loop QA, import into the database. Create a new loop release."""
q = LoopQualityChecker()
q.check_loop_quality(p.pdbs)
"""import pairwise interactions annotated by FR3D"""
i = PairwiseInteractionsLoader()
i.import_interactions(p.pdbs)
"""import coordinates and distances into the database"""
d = DistancesAndCoordinatesLoader()
d.import_distances(p.pdbs)
d.import_coordinates(p.pdbs)
"""import info about redundant nucleotides"""
r = RedundantNucleotidesLoader()
r.import_redundant_nucleotides(p.pdbs)
"""import best chains and models"""
b = BestChainsAndModelsLoader()
b.import_best_chains_and_models(p.pdbs)
self.success = True
