def update_loops(pdb_ids):
"""
"""
try:
"""extract all loops and import into the database"""
e = LoopExtractor()
e.extract_and_import_loops(pdb_ids)
"""do loop qa, create a new loop release. It only makes sense
to do this if loop extraction worked"""
q = LoopQualityChecker()
q.check_loop_quality(pdb_ids)
except:
logging.warning(traceback.format_exc(sys.exc_info()))
logging.warning('Loop extraction or loop QA failed')
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
