def multiDomain(pfamDict, chemblTargets, winners, threshold, release, user,
pword, host, port):
import getLigands
import filterForTarget
import pickle
multi = {}
for target in chemblTargets:
candidates = {}
if target in pfamDict:
for domain in pfamDict[target]['domains']:
domain = str(domain)
if domain in winners:
candidates[domain] = 0
if len(candidates.keys()) == 1 and len(
pfamDict[target]['domains']) > 1:
ligands = getLigands.getLigandsForTarget(target, release, user,
pword, host, port)
ligands = filterForTarget.filterForTarget(ligands, threshold)
domain = candidates.keys()[0]
for ligand in ligands:
smiles = ligand[0]
aff = ligand[1]
molregno = ligand[2]
actId = ligand[3]
try:
multi[domain][molregno]['pAfnty'].append(aff)
multi[domain][molregno]['target'].append(target)
multi[domain][molregno]['actId'].append(actId)
multi[domain][molregno]['smiles'] = smiles
except KeyError:
try:
multi[domain][molregno] = {}
multi[domain][molregno]['pAfnty'] = []
multi[domain][molregno]['target'] = []
multi[domain][molregno]['actId'] = []
multi[domain][molregno]['smiles'] = smiles
multi[domain][molregno]['pAfnty'].append(aff)
multi[domain][molregno]['target'].append(target)
multi[domain][molregno]['actId'].append(actId)
except KeyError:
multi[domain] = {}
multi[domain][molregno] = {}
multi[domain][molregno]['pAfnty'] = []
multi[domain][molregno]['target'] = []
multi[domain][molregno]['actId'] = []
multi[domain][molregno]['smiles'] = smiles
multi[domain][molregno]['pAfnty'].append(aff)
multi[domain][molregno]['target'].append(target)
multi[domain][molregno]['actId'].append(actId)
outfile = open('data/multiDict_pKi%s_%s.pkl' % (int(threshold), release),
'w')
pickle.dump(multi, outfile)
outfile.close()
return multi
def toSam(conflicts, threshold, user, pword, host, release, port):
import parse
import getLigands
import filterForTarget
import queryDevice
conf = {}
for confStr in conflicts.keys():
for target in conflicts[confStr]:
ligands = getLigands.getLigandsForTarget(target, release, user,
pword, host, port)
ligands = filterForTarget.filterForTarget(ligands, threshold)
for ligand in ligands:
molregno = ligand[2]
actId = ligand[3]
pubmed = queryDevice.queryDevice(
"SELECT pubmed_id FROM docs JOIN activities act ON act.doc_id = docs.doc_id WHERE activity_id = %s"
% actId, release, user, pword, host, port)[0][0]
pubmed = pubmed
try:
conf[confStr][molregno]['actId'].append(actId)
conf[confStr][molregno]['pubmed'].append(pubmed)
conf[confStr][molregno]['pubmed'] = []
conf[confStr][molregno]['pubmed'].append(pubmed)
except KeyError:
try:
conf[confStr][molregno] = {}
conf[confStr][molregno]['actId'] = []
conf[confStr][molregno]['actId'].append(actId)
conf[confStr][molregno]['pubmed'] = []
conf[confStr][molregno]['pubmed'].append(pubmed)
except KeyError:
conf[confStr] = {}
conf[confStr][molregno] = {}
conf[confStr][molregno]['actId'] = []
conf[confStr][molregno]['actId'].append(actId)
conf[confStr][molregno]['pubmed'] = []
conf[confStr][molregno]['pubmed'].append(pubmed)
confLkp = {}
for confStr in conf.keys():
confLkp[confStr] = 0
for confStr in confLkp.keys():
out = open('data/forSam_%s.pred' % confStr, 'w')
out.write('molregno\tpubmed\tprediction\tactivity_id\n')
for conflict in conf[confStr]:
for molregno in conf[confStr].keys():
pubmed = conf[confStr][molregno]['pubmed']
domain = 'None'
actId = conf[confStr][molregno]['actId']
for act in actId:
out.write('%s\t%s\t%s\t%s\n' %
(molregno, pubmed[0], domain, act))
out.close()
def multiDomain(pfamDict, chemblTargets, winners, threshold, release, user, pword, host, port):
import getLigands
import filterForTarget
import pickle
multi = {}
for target in chemblTargets:
candidates = {}
if target in pfamDict:
for domain in pfamDict[target]['domains']:
domain = str(domain)
if domain in winners:
candidates[domain]=0
if len(candidates.keys()) == 1 and len(pfamDict[target]['domains']) >1:
ligands = getLigands.getLigandsForTarget(target, release, user, pword, host, port)
ligands = filterForTarget.filterForTarget(ligands, threshold)
domain = candidates.keys()[0]
for ligand in ligands:
smiles = ligand[0]
aff = ligand[1]
molregno = ligand[2]
actId = ligand[3]
try:
multi[domain][molregno]['pAfnty'].append(aff)
multi[domain][molregno]['target'].append(target)
multi[domain][molregno]['actId'].append(actId)
multi[domain][molregno]['smiles']=smiles
except KeyError:
try:
multi[domain][molregno] = {}
multi[domain][molregno]['pAfnty']=[]
multi[domain][molregno]['target']=[]
multi[domain][molregno]['actId'] = []
multi[domain][molregno]['smiles']=smiles
multi[domain][molregno]['pAfnty'].append(aff)
multi[domain][molregno]['target'].append(target)
multi[domain][molregno]['actId'].append(actId)
except KeyError:
multi[domain]={}
multi[domain][molregno] = {}
multi[domain][molregno]['pAfnty']=[]
multi[domain][molregno]['target']=[]
multi[domain][molregno]['actId'] = []
multi[domain][molregno]['smiles']=smiles
multi[domain][molregno]['pAfnty'].append(aff)
multi[domain][molregno]['target'].append(target)
multi[domain][molregno]['actId'].append(actId)
outfile = open('data/multiDict_pKi%s_%s.pkl'%(int(threshold), release),'w')
pickle.dump(multi, outfile)
outfile.close()
return multi
def toSam(conflicts, threshold, user, pword, host, release, port):
import parse
import getLigands
import filterForTarget
import queryDevice
conf = {}
for confStr in conflicts.keys():
for target in conflicts[confStr]:
ligands = getLigands.getLigandsForTarget(target, release, user, pword, host, port)
ligands = filterForTarget.filterForTarget(ligands, threshold)
for ligand in ligands:
molregno = ligand[2]
actId = ligand[3]
pubmed = queryDevice.queryDevice("SELECT pubmed_id FROM docs JOIN activities act ON act.doc_id = docs.doc_id WHERE activity_id = %s"%actId,release, user, pword, host, port)[0][0]
pubmed = pubmed
try:
conf[confStr][molregno]['actId'].append(actId)
conf[confStr][molregno]['pubmed'].append(pubmed)
conf[confStr][molregno]['pubmed'] = []
conf[confStr][molregno]['pubmed'].append(pubmed)
except KeyError:
try:
conf[confStr][molregno] = {}
conf[confStr][molregno]['actId'] = []
conf[confStr][molregno]['actId'].append(actId)
conf[confStr][molregno]['pubmed'] = []
conf[confStr][molregno]['pubmed'].append(pubmed)
except KeyError:
conf[confStr]={}
conf[confStr][molregno] = {}
conf[confStr][molregno]['actId'] = []
conf[confStr][molregno]['actId'].append(actId)
conf[confStr][molregno]['pubmed'] = []
conf[confStr][molregno]['pubmed'].append(pubmed)
confLkp = {}
for confStr in conf.keys():
confLkp[confStr] = 0
for confStr in confLkp.keys():
out = open('data/forSam_%s.pred'%confStr, 'w')
out.write('molregno\tpubmed\tprediction\tactivity_id\n')
for conflict in conf[confStr]:
for molregno in conf[confStr].keys():
pubmed = conf[confStr][molregno]['pubmed']
domain = 'None'
actId = conf[confStr][molregno]['actId']
for act in actId:
out.write('%s\t%s\t%s\t%s\n'%(molregno, pubmed[0], domain, act))
out.close()
def singleDomains(pfamDict, chemblTargets,threshold, release, user, pword, host, port):
import pickle
import getLigands
import filterForTarget
single = {}
for target in chemblTargets:
if target in pfamDict:
if len(pfamDict[target]['domains']) == 1:
domain = pfamDict[target]['domains'][0]
ligands = getLigands.getLigandsForTarget(target, release, user, pword, host, port)
ligands = filterForTarget.filterForTarget(ligands, threshold)
for ligand in ligands:
smiles = ligand[0]
aff = ligand[1]
molregno = ligand[2]
actId = ligand[3]
try:
single[domain][molregno]['pAfnty'].append(aff)
single[domain][molregno]['target'].append(target)
single[domain][molregno]['actId'].append(actId)
single[domain][molregno]['smiles']=smiles
except KeyError:
try:
single[domain][molregno] = {}
single[domain][molregno]['pAfnty']=[]
single[domain][molregno]['target']=[]
single[domain][molregno]['actId'] = []
single[domain][molregno]['smiles']=smiles
single[domain][molregno]['pAfnty'].append(aff)
single[domain][molregno]['target'].append(target)
single[domain][molregno]['actId'].append(actId)
except KeyError:
single[domain]={}
single[domain][molregno] = {}
single[domain][molregno]['pAfnty']=[]
single[domain][molregno]['target']=[]
single[domain][molregno]['actId'] = []
single[domain][molregno]['smiles']=smiles
single[domain][molregno]['pAfnty'].append(aff)
single[domain][molregno]['target'].append(target)
single[domain][molregno]['actId'].append(actId)
outfile = open('data/singleDict_pKi%s_%s.pkl' %(int(threshold), release),'w')
pickle.dump(single, outfile)
outfile.close()
return single
