def update_pdb_cache(self):
"""
get a list of pdb files, loop over them, refresh cache
"""
self._refresh_cache('pdb')
P = PdbInfoLoader()
P.get_all_rna_pdbs()
for pdb_id in P.pdbs:
logging.info(pdb_id)
subpages = [pdb_id, pdb_id + '/motifs']
for subpage in subpages:
self._refresh_cache('pdb/' + subpage)
def main(argv):
"""
"""
Q = LoopQualityChecker()
Q.start_logging()
# pdbs = ['1FG0']
p = PdbInfoLoader()
p.get_all_rna_pdbs()
pdbs = p.pdbs
Q.check_loop_quality(pdbs)
def main(argv):
"""
"""
logging.basicConfig(level=logging.DEBUG)
B = BestChainsAndModelsLoader()
from PdbInfoLoader import PdbInfoLoader
P = PdbInfoLoader()
P.get_all_rna_pdbs()
B.import_best_chains_and_models(P.pdbs)
def main(argv):
"""
"""
logging.basicConfig(level=logging.DEBUG)
R = RedundantNucleotidesLoader()
# pdbs = ['1J5E', '1KOG']
from PdbInfoLoader import PdbInfoLoader
P = PdbInfoLoader()
P.get_all_rna_pdbs()
R.import_redundant_nucleotides(P.pdbs)
def main(argv):
"""
"""
logging.basicConfig(level=logging.DEBUG)
pdbs = ['3V11', '1J5E']
from PdbInfoLoader import PdbInfoLoader
p = PdbInfoLoader()
p.get_all_rna_pdbs()
pdbs = p.pdbs
A = PairwiseInteractionsLoader()
for pdb_id in pdbs:
A.import_interactions([pdb_id], recalculate=True)
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
def main(argv):
"""
"""
U = UnitIdLoader()
U.start_logging()
pdbs = argv
if not pdbs:
from PdbInfoLoader import PdbInfoLoader
P = PdbInfoLoader()
P.get_all_rna_pdbs()
pdbs = P.pdbs
try:
U.import_unit_ids(pdbs, recalculate=True)
except:
e = sys.exc_info()[1]
U.set_email_subject('Unit id update failed')
U._crash(e)
U.set_email_subject('Unit ids successfully updated')
U.send_report()
def get_pdb_info():
"""
get new pdb files, import descriptions into the database.
Return an empty list if something goes wrong, then all following
steps that rely on pdb_ids will be skipped.
"""
try:
p = PdbInfoLoader()
p.get_all_rna_pdbs()
pdb_ids = p.pdbs
p.update_rna_containing_pdbs()
p.check_obsolete_structures()
except:
logging.warning(traceback.format_exc(sys.exc_info()))
pdb_ids = []
return pdb_ids
