def GOQLtoFindDrugs(TargetIds: list,
TargetType='Protein',
drugEffect=['negative']):
if TargetType == 'Protein':
return OQL.get_drugs(for_targets_with_ids=TargetIds)
elif TargetType == 'Small Molecule':
REL_TYPES = ['Regulation', 'MolSynthesis']
OQLquery = OQL.expand_entity(PropertyValues=TargetIds,
SearchByProperties=['id'],
expand_by_rel_types=REL_TYPES,
expand2neighbors=['Small Molecule'],
direction='upstream')
OQLquery += ' AND Effect = (' + ','.join(drugEffect) + ')'
return OQLquery
else:
REL_TYPES = ['Regulation']
OQLquery = OQL.expand_entity(PropertyValues=TargetIds,
SearchByProperties=['id'],
expand_by_rel_types=REL_TYPES,
expand2neighbors=['Small Molecule'],
direction='upstream')
OQLquery += ' AND Effect = (' + ','.join(drugEffect) + ')'
return OQLquery
IdToNames = ps_api.Graph.get_properties(PPIids, 'Name')
sorted_centrality_byName = list()
for t in sorted_centrality:
idx = t[0]
# if idx in IdToNames.keys():
name = IdToNames[idx][0]
sorted_centrality_byName.append((name, t[1]))
print(sorted_centrality_byName)
DiseaseProteins = set(ps_api.Graph.get_entity_ids(['Protein']))
print("Finding Drugs for Proteins containing GeneticVariants linked to %s" %
InputDiseaseNames)
ps_api.add_dump_file(foutDrugsForDiseaseProteins, replace_main_dump=True)
start_time = time.time()
ps_api.process_oql(GOQL.get_drugs(for_targets_with_ids=list(DiseaseProteins)),
flush_dump=True)
DrugCount = set([
x for x, y in ps_api.Graph.nodes(data=True)
if ((ps_api.Graph.out_degree(x) > 0)
& (y['ObjTypeName'][0] in ['Small Molecule', 'SmallMol']))
])
FoundTargets = set([
x for x, y in ps_api.Graph.nodes(data=True)
if ((ps_api.Graph.in_degree(x) > 1) & (y['ObjTypeName'][0] in ['Protein']))
])
execution_time = ps_api.execution_time(start_time)
print("%d drugs for %d proteins linked to %s were retrieved in %s ---" %
(len(DrugCount), len(FoundTargets), InputDiseaseNames, execution_time))
# find RMC compounds for non-druggable targets