def main(self):
# get current crawl number
crawldata_row = models.CrawlData.query.first()
current_crawl_number = crawldata_row.current_crawl_number
print 'Current crawl number: %d' % current_crawl_number
# Get list of uniprot accession numbers that are in the rows of current crawl number
uniprot_acs = [str(uniprot_ac[0]) for uniprot_ac in models.UniProt.query.filter_by(crawl_number=current_crawl_number).values(models.UniProt.ac)]
# Iterate through Uniprot ACs
for uniprot_ac in uniprot_acs:
# get ChEMBL target id using bioservices
chembl=ChEMBL(verbose=False)
target_info = chembl.get_target_by_uniprotId(uniprot_ac)
target_chembl_id=target_info['chemblId']
print "ChEMBL ID of target protein:", target_chembl_id
target = models.ChemblTarget(crawl_number=current_crawl_number, target_chembl_id=target_chembl_id)
db.session.add(target)
# Updata datestamp for Chembl
now = datetime.datetime.utcnow()
current_crawl_datestamp_row = models.DateStamps.query.filter_by(crawl_number=current_crawl_number).first()
current_crawl_datestamp_row.chembl_datestamp = now
db.session.commit()
print 'Done.'
from bioservices import ChEMBL chembl=ChEMBL(verbose=False) acc = 'P00519' target_info = chembl.get_target_by_uniprotId(acc) print target_info target_chembl_id=target_info['chemblId'] bioactivities=chembl.get_target_bioactivities(str(target_chembl_id)) compound_chemblids = [ entry['ingredient_cmpd_chemblid'] for entry in bioactivities ] print "# of compound chemblids:", len(compound_chemblids) resjson = chembl.get_compounds_by_chemblId(chembl._chemblId_example) print "Example compound retrieved by compound chemblid: \n", resjson