def begin(self):
self.in_orion = config_from_env() is not None
if self.in_orion:
#self.stream = stream_file(988)
self.stream = stream_file(self.args.data_in)
else:
self.stream = open(str(self.args.data_in), 'rb')
def begin(self):
if self.args.method == 'Fingerprint':
fptypes = {102 : 'path', 104 : 'circular', 105 : 'tree'}
self.FPType = fptypes[self.args.fptype]
self.name_ext = 'FP_' + self.FPType
elif self.args.method == 'FastROCS':
self.name_ext = 'FR'
self.in_orion = config_from_env() is not None
if self.in_orion:
self.stream = tempfile.NamedTemporaryFile()
else:
path = self.args.name + "ranking_" + self.name_ext + ".txt"
self.stream = open(path, 'wb')
def __iter__(self):
max_idx = self.args.limit
if max_idx is not None:
max_idx = int(max_idx)
count = 0
self.config = config_from_env()
in_orion = self.config is not None
if not in_orion:
with oechem.oemolistream(str(self.args.data_in)) as ifs:
for mol in ifs.GetOEMols():
mol.SetData(oechem.OEGetTag('prefix'), self.opt['prefix'])
mol.SetData(oechem.OEGetTag('suffix'), self.opt['suffix'])
for at in mol.GetAtoms():
residue = oechem.OEAtomGetResidue(at)
residue.SetName(self.opt['type'])
oechem.OEAtomSetResidue(at, residue)
if self.opt['IDTag']:
mol.SetData(oechem.OEGetTag('IDTag'), 'l' + mol.GetTitle()[0:12] + '_' + str(count))
yield mol
count += 1
if max_idx is not None and count == max_idx:
break
else:
stream = StreamingDataset(self.args.data_in,
input_format=self.args.download_format)
for mol in stream:
mol.SetData(oechem.OEGetTag('prefix'), self.opt['prefix'])
mol.SetData(oechem.OEGetTag('suffix'), self.opt['suffix'])
for at in mol.GetAtoms():
residue = oechem.OEAtomGetResidue(at)
residue.SetName(self.opt['type'])
oechem.OEAtomSetResidue(at, residue)
if self.opt['IDTag']:
mol.SetData(oechem.OEGetTag('IDTag'), 'l' + mol.GetTitle()[0:12] + '_'+str(count))
yield mol
count += 1
if max_idx is not None and count == max_idx:
break
def __iter__(self):
max_idx = self.args.limit
if max_idx is not None:
max_idx = int(max_idx)
count = 0
self.config = config_from_env()
in_orion = self.config is not None
if not in_orion:
with oechem.oemolistream(str(self.args.data_in)) as ifs:
for mol in ifs.GetOEMols():
mol.SetTitle(self.opt['protein_prefix'])
yield mol
count += 1
if max_idx is not None and count == max_idx:
break
else:
stream = StreamingDataset(self.args.data_in,
input_format=self.args.download_format)
for mol in stream:
mol.SetTitle(self.opt['protein_prefix'])
yield mol
count += 1
if max_idx is not None and count == max_idx:
break
def begin(self):
self.in_orion = config_from_env() is not None
if self.in_orion:
self.stream = tempfile.NamedTemporaryFile()
def begin(self):
self.in_orion = config_from_env() is not None
if self.in_orion:
self.stream = tempfile.NamedTemporaryFile()
else:
self.stream = open(self.args.name, 'w')
def __iter__(self):
max_idx = self.args.limit
if max_idx is not None:
max_idx = int(max_idx)
count = 0
self.config = config_from_env()
in_orion = self.config is not None
if not in_orion:
with oechem.oemolistream(str(self.args.data_in)) as ifs:
for mol in ifs.GetOEMols():
mol.SetTitle(self.opt['protein_prefix'])
yield mol
count += 1
if max_idx is not None and count == max_idx:
break
else:
stream = StreamingDataset(self.args.data_in,
input_format=self.args.download_format)
for mol in stream:
mol.SetTitle(self.opt['protein_prefix'])
yield mol
count += 1
if max_idx is not None and count == max_idx:
break
# class SimOutputCube(OEMolOStreamCube):
# """
# A sink cube that writes molecules to a file
# """
# classification = [["Output"]]
# title = "Output Writer"
#
# intake = BinaryMoleculeInputPort('intake')
# data_out = DataSetOutputParameter('data_out',
# required=True,
# title='Name of Dataset to create',
# description='The dataset to output')
# backend = DataSetOutputParameter(
# 'backend',
# default="auto",
# choices=["db", "s3", "auto"],
# description="The Orion storage backend to use")
#
# def begin(self):
# self.in_orion = config_from_env() is not None
# self.decoder = MoleculeSerializerMixin()
# self.need_decode = not self.args.data_out.endswith(".oeb.gz")
# if self.in_orion:
# self.ofs = MultipartDatasetUploader(self.args.data_out,
# tags=[self.name],
# backend=self.args.backend)
# elif self.need_decode:
# self.ofs = oechem.oemolostream(str(self.args.data_out))
# else:
# self.ofs = open(str(self.args.data_out), 'wb')
#
# def write(self, mol, port):
# if self.in_orion or not self.need_decode:
# self.ofs.write(mol)
# else:
# oechem.OEWriteMolecule(self.ofs, self.decoder.decode(mol))
#
# def end(self):
# if self.in_orion:
# self.ofs.complete()
# else:
# self.ofs.close()