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()