def import_redundant_nucleotides(self, pdbs, recalculate=False):
"""
"""
try:
logging.info("Importing redundant nucleotides")
if not recalculate:
recalculate = self.config["recalculate"]["redundant_nts"]
if recalculate:
pdb_list = pdbs
self.__delete_old_data(pdbs)
else:
pdb_list = self.filter_out_analyzed_pdbs(pdbs, "redundant_nts")
if pdb_list:
MotifAtlasBaseClass._setup_matlab(self)
for pdb_file in pdb_list:
logging.info("Running matlab on %s", pdb_file)
ifn, err_msg = self.mlab.loadRedundantNucleotides(pdb_file, nout=2)
if err_msg == "":
self.__import_temporary_file(ifn, pdb_file)
else:
MotifAtlasBaseClass._crash(self, err_msg)
self.mark_pdb_as_analyzed(pdb_file, "redundant_nts")
logging.info("%s", "=" * 40)
except:
e = sys.exc_info()[1]
MotifAtlasBaseClass._crash(self, e)
def import_best_chains_and_models(self, pdbs, recalculate=False):
"""
"""
try:
logging.info("Importing best chains and models")
if not recalculate:
recalculate = self.config["recalculate"]["best_chains_and_models"]
if recalculate:
pdb_list = pdbs
self.__delete_old_data(pdbs)
else:
pdb_list = self.filter_out_analyzed_pdbs(pdbs, "best_chains_and_models")
if pdb_list:
MotifAtlasBaseClass._setup_matlab(self)
for pdb_file in pdb_list:
logging.info("Running matlab on %s", pdb_file)
# 'ABC', '1,2', ''
best_chains, best_models, err_msg = self.mlab.loadBestChainsAndModels(pdb_file, nout=3)
best_chains = ",".join(list(best_chains))
if err_msg == "":
self.__import_into_db(pdb_file, best_chains, best_models)
else:
MotifAtlasBaseClass._crash(self, err_msg)
self.mark_pdb_as_analyzed(pdb_file, "best_chains_and_models")
logging.info("%s", "=" * 40)
except:
e = sys.exc_info()[1]
MotifAtlasBaseClass._crash(self, e)
def save_mat_files(self,Loops):
"""Pass the Loops structure array back to matlab so that it can
save the .mat files in the specified location."""
MotifAtlasBaseClass._setup_matlab(self)
[status, err_msg] = self.mlab.aSaveLoops(Loops,
self.config['locations']['loops_mat_files'],
nout=2)
if status == 0:
logging.info('mat files saved')
else:
MotifAtlasBaseClass._crash(self,err_msg)
def loop_qa(self, pdb_id, release_id):
"""
"""
logging.info('QA on %s', pdb_id)
MotifAtlasBaseClass._setup_matlab(self)
[ifn, err_msg] = self.mlab.aLoopQualityAssurance(pdb_id, nout=2)
if err_msg != '':
logging.warning('Error %s in pdb %s' % (err_msg, pdb_id))
else:
self.__import_qa_from_csv(ifn, release_id)
self.mark_pdb_as_analyzed(pdb_id,'qa')
def extract_loops(self, pdb_id, loop_type):
"""
"""
try:
MotifAtlasBaseClass._setup_matlab(self)
"""Loops - array of FR3D File structures. l - its length"""
[Loops, l, err_msg] = self.mlab.extractLoops(pdb_id, loop_type, nout=3)
if err_msg != '':
MotifAtlasBaseClass._crash(self,err_msg)
if Loops == 0:
logging.info('No %s in %s', loop_type, pdb_id)
return (0, 0)
else:
logging.info('Found %i loops', l)
return (Loops, l)
except:
e = sys.exc_info()[1]
MotifAtlasBaseClass._crash(self,e)
def import_interactions(self, pdbs, recalculate=False):
"""Determines what files need to be analyzed, deletes stored data if
necessary, loops over the pdbs, runs matlab on each of them
independently, matlab generates a temporary csv file, it's imported
and immediately deleted."""
try:
logging.info('Inside import_interactions')
if not recalculate:
recalculate = self.config['recalculate']['interactions']
if recalculate:
pdb_list = pdbs
self.__delete_interactions(pdbs)
else:
pdb_list = self.filter_out_analyzed_pdbs(pdbs,'interactions')
if pdb_list:
MotifAtlasBaseClass._setup_matlab(self)
for pdb_file in pdb_list:
logging.info('Running matlab on %s', pdb_file)
ifn, status, err_msg = self.mlab.loadInteractions(pdb_file,nout=3)
status = status[0][0]
if status == 0:
self.__import_interactions_from_csv(ifn, pdb_file)
elif status == 2: # no nucleotides in the pdb file
logging.info('Pdb file %s has no nucleotides', pdb_file)
else:
logging.warning('Matlab error code %i when analyzing %s',
status, pdb_file)
MotifAtlasBaseClass._crash(self,err_msg)
self.mark_pdb_as_analyzed(pdb_file,'interactions')
self.success = True
logging.info('%s', '='*40)
except:
e = sys.exc_info()[1]
MotifAtlasBaseClass._crash(self,e)
