def fastrocs_query(self, qmol, numHits, host):
with self.logger("fastrocs_query") as logger:
ofs = oechem.oemolostream()
ofs.SetFormat(oechem.OEFormat_OEB)
ofs.openstring()
oechem.OEWriteMolecule(ofs, qmol)
bytes = ofs.GetString()
s = ServerProxy("http://" + host)
data = Binary(bytes)
# idx = s.SubmitQuery(data, numHits)
dargs = {
'altStarts': 'random',
'tversky': False,
'shapeOnly': False
}
assert (numHits is not None)
assert (data is not None)
assert (dargs is not None)
idx = s.SubmitQuery(data, numHits, 'oeb', 'oeb', dargs)
first = False
while True:
try:
current, total = s.QueryStatus(idx, True)
except Fault as e:
logger.error((str(e)))
return 1
if total == 0:
continue
if first:
# logger.log("%s/%s" % ("current", "total"))
first = False
# logger.log("%i/%i" % (current, total))
if total <= current:
break
results = s.QueryResults(idx)
ifs = oechem.oemolistream()
ifs.openstring(results.data)
ifs.SetFormat(oechem.OEFormat_OEB)
mols = []
for mol in ifs.GetOEMols():
good_mol = oechem.OEMol(mol)
oechem.OEAddExplicitHydrogens(good_mol)
oechem.OEClearSDData(good_mol)
oeshape.OEDeleteCompressedColorAtoms(good_mol)
oeshape.OEClearCachedSelfColor(good_mol)
oeshape.OEClearCachedSelfShape(good_mol)
oeshape.OERemoveColorAtoms(good_mol)
mols.append(good_mol)
return mols
def __call__(self,
smiles,
receptor_name,
receptor=None,
receptor_path=None):
receptor = self.get_receptor_from_request(receptor, receptor_path)
s = ServerProxy("http://" + f'{self.hostname}:{self.port}')
opts = OEOptions()
opts.high_resolution = False
idx = s.SubmitQuery(smiles, receptor, receptor_name, opts)
not_done = True
while not_done:
try:
not_done = not s.QueryStatus(idx)
time.sleep(2)
except Fault as e:
print(str(e), file=sys.stderr)
return 1
results = s.QueryResults(idx)
return results