def save_structures(cfg, log, db, listItem):
try:
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateCandidate)
for item in listItem:
log.info('Saving Candidate: %s...' % item)
if PDB.get_file(cfg, log, item):
pdb = PDB.parse_header(cfg, item)
db.executeCommand(
cfg.sqlInsertCandidate,
(item, MySQLdb.escape_string(
PDB.get_content()), MySQLdb.escape_string(
pdb['name']), MySQLdb.escape_string(
pdb['author']), pdb['deposition_date'],
pdb['release_date'], '0', pdb['resolution'], pdb['head'],
pdb['structure_method'], pdb['compound']['1']['chain']
if 'chain' in pdb['compound']['1'] else '',
pdb['compound']['1']['ec_number']
if 'ec_number' in pdb['compound']['1'] else '',
pdb['source']['1']['organism_taxid']
if 'organism_taxid' in pdb['source']['1'] else '',
pdb['source']['1']['organism_scientific']
if 'organism_scientific' in pdb['source']['1'] else '',
pdb['source']['1']['expression_system_taxid'] if
'expression_system_taxid' in pdb['source']['1'] else '',
pdb['source']['1']['expression_system']
if 'expression_system' in pdb['source']['1'] else ''))
db.commit()
except:
log.error(traceback.format_exc())
db.rollback()
def save_structures(cfg,log,db,listItem):
try:
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateCandidate)
for item in listItem:
log.info('Saving Candidate: %s...' % item)
if PDB.get_file(cfg,log,item):
pdb = PDB.parse_header(cfg,item)
db.executeCommand(cfg.sqlInsertCandidate,(item, MySQLdb.escape_string(PDB.get_content()), MySQLdb.escape_string(pdb['name']), MySQLdb.escape_string(pdb['author']), pdb['deposition_date'], pdb['release_date'], pdb['version'], pdb['resolution'], pdb['head'], pdb['structure_method'], pdb['compound']['1']['chain'], pdb['compound']['1']['ec_number'], pdb['source']['1']['organism_taxid'],pdb['source']['1']['organism_scientific'],pdb['source']['1']['expression_system_taxid'],pdb['source']['1']['expression_system']))
db.commit()
except:
log.error(traceback.format_exc())
db.rollback()
