def testAppend(self):
try:
fname = tempfile.mktemp() + ".smi"
fname2 = tempfile.mktemp() + "-2.smi"
storefname = tempfile.mktemp() + ".store"
with open(fname, 'w') as f:
f.write(one_smiles)
opts = make_store.MakeStorageOptions(storage=storefname,
smilesfile=fname,
hasHeader=False,
batchsize=1,
smilesColumn=0,
nameColumn=1,
seperator=" ",
descriptors="RDKit2DSubset",
index_inchikey=True)
make_store.make_store(opts)
with contextlib.closing(DescriptaStore(storefname)) as store:
self.assertEqual(store.lookupName("0"), 0)
self.assertEqual(
store.lookupInchiKey("UHOVQNZJYSORNB-UHFFFAOYSA-N"), [0])
self.assertEqual(store.descriptors().get(0),
(True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
# now append some junk
with open(fname2, 'w') as f:
f.write(two_smiles)
opts.smilesfile = fname2
append_store.append_store(opts)
with contextlib.closing(DescriptaStore(storefname)) as store:
self.assertEqual(len(store), 2)
self.assertEqual(store.lookupName("0"), 0)
self.assertEqual(
store.lookupInchiKey("UHOVQNZJYSORNB-UHFFFAOYSA-N"),
[0, 1])
self.assertEqual(store.descriptors().get(0),
(True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.lookupName("1"), 1)
self.assertEqual(
store.lookupInchiKey("UHOVQNZJYSORNB-UHFFFAOYSA-N"),
[0, 1])
self.assertEqual(store.descriptors().get(1),
(True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
finally:
if os.path.exists(fname):
os.unlink(fname)
if os.path.exists(fname2):
os.unlink(fname2)
if os.path.exists(storefname):
shutil.rmtree(storefname)
def main():
opts = parser.parse_args()
if opts.verbose:
logging.getLogger().setLevel(logging.INFO)
if not opts.append:
d = vars(opts)
del d['append']
make_store.make_store(make_store.MakeStorageOptions(**d))
else:
append_store.append_store(
append_store.AppendStorageOptions(**vars(opts)))
def main():
opts = parser.parse_args()
if opts.verbose:
logging.getLogger().setLevel(logging.INFO)
if opts.append and opts.append_store:
logging.error("Use one of --append --append-store")
if opts.append:
append_store.append_smiles(append_store.AppendStorageOptions(**vars(opts)))
elif opts.append_store:
append_store.append_store(append_store.AppendStorageOptions(**vars(opts)))
else:
d = vars(opts)
del d['append']
make_store.make_store(make_store.MakeStorageOptions(**d))
def testAppendStore(self):
fname = tempfile.mktemp()+".smi"
fname2 = tempfile.mktemp()+"2.smi"
storefname = tempfile.mktemp()+".store"
with open(fname, 'w') as f:
f.write(many_smiles)
with open(fname2, 'w') as f:
f.write(many_smiles2)
# make the first store
args = ["--index-inchikey",
"--smilesColumn", "0",
"--nameColumn", "1",
"--seperator", " ",
"--numprocs", "1",
"--descriptors", "RDKit2DSubset",
fname, storefname]
args2 = ["--append",
"--index-inchikey",
"--smilesColumn", "0",
"--nameColumn", "1",
"--seperator", " ",
"--numprocs", "1",
"--descriptors", "RDKit2DSubset",
fname2, storefname]
try:
opts = storus.parser.parse_args(args)
make_store.make_store(make_store.MakeStorageOptions(**vars(opts)))
opts = storus.parser.parse_args(args2)
append_store.append_store(append_store.AppendStorageOptions(**vars(opts)))
with contextlib.closing(DescriptaStore(storefname)) as store:
for i in range(20):
m = store.molIndex().getRDMol(i)
if m:
sm = AllChem.MolToSmiles(m)
inchi = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
logging.info("%s: %s %s"%(i, sm, inchi))
else:
logging.info("%s: nostruct"%i)
for i in range(10):
self.assertEqual( store.lookupName(str(i)), i)
for i in range(10):
m = store.molIndex().getRDMol(i)
inchi = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
self.assertEqual( store.lookupInchiKey(inchi), [i, i+11])
self.assertEqual(store.descriptors().get(0), (True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(1), (True, 92.062600256, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(2), (True, 106.07825032, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(3), (True, 120.093900384, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(4), (True, 134.109550448, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(5), (True, 148.125200512, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(6), (True, 162.140850576, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(7), (True, 176.15650064, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(8), (True, 190.172150704, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(9), (True, 204.187800768, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(10), (False, 0.0, 0.0, 0.0, 0.0, 0.0))
self.assertEqual(store.descriptors().getDict(7), toDict((True, 176.15650064, 0.0, 1.0, 0.0, 1.0)))
calc = store.getDescriptorCalculator()
for i in range(10):
m = store.molIndex().getRDMol(i)
if m:
sm = AllChem.MolToSmiles(m)
inchi = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
logging.info("%s: %s"%(i, inchi))
self.assertEqual( store.lookupInchiKey(inchi), [i, i+11])
v = store.descriptors().get(i)
sv = tuple(calc.process(sm))
self.assertEqual(v, sv)
for i in range(10):
m = store.molIndex().getRDMol(i)
if not m: continue
inchi = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
m = store.molIndex().getRDMol(i+11)
self.assertTrue(m!=None)
inchi2 = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
self.assertEqual(inchi, inchi2)
self.assertEqual( store.lookupInchiKey(inchi), [i, i+11])
for i in range(2):
self.assertEqual(store.descriptors().get(11+0), (True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+1), (True, 92.062600256, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+2), (True, 106.07825032, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+3), (True, 120.093900384, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+4), (True, 134.109550448, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+5), (True, 148.125200512, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+6), (True, 162.140850576, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+7), (True, 176.15650064, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+8), (True, 190.172150704, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+9), (True, 204.187800768, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11+10), (False, 0.0, 0.0, 0.0, 0.0, 0.0))
finally:
if os.path.exists(fname):
os.unlink(fname)
if os.path.exists(storefname):
shutil.rmtree(storefname)
def testAppend(self):
try:
fname = tempfile.mktemp() + ".smi"
storefname = tempfile.mktemp() + ".store"
with open(fname, 'w') as f:
f.write(many_smiles)
opts = make_store.MakeStorageOptions(storage=storefname,
smilesfile=fname,
hasHeader=False,
smilesColumn=0,
nameColumn=1,
seperator=" ",
descriptors="RDKit2DSubset",
index_inchikey=True)
make_store.make_store(opts)
with contextlib.closing(DescriptaStore(storefname)) as store:
for i in range(10):
self.assertEqual(store.lookupName(str(i)), i)
for i in range(10):
m = store.molIndex().getRDMol(i)
inchi = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
self.assertEqual(store.lookupInchiKey(inchi), [i])
self.assertEqual(store.descriptors().get(0),
(True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(1),
(True, 92.062600256, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(2),
(True, 106.07825032, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(3),
(True, 120.093900384, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(4),
(True, 134.109550448, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(5),
(True, 148.125200512, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(6),
(True, 162.140850576, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(7),
(True, 176.15650064, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(8),
(True, 190.172150704, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(9),
(True, 204.187800768, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(10),
(False, 0.0, 0.0, 0.0, 0.0, 0.0))
fname = tempfile.mktemp() + ".smi"
with open(fname, 'w') as f:
f.write(many_smiles2)
opts.smilesfile = fname
append_store.append_store(opts)
with contextlib.closing(DescriptaStore(storefname)) as store:
for i in range(10):
self.assertEqual(store.lookupName(str(i)), i)
for i in range(10):
m = store.molIndex().getRDMol(i)
inchi = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
m = store.molIndex().getRDMol(i + 11)
self.assertTrue(m != None)
inchi2 = AllChem.InchiToInchiKey(AllChem.MolToInchi(m))
self.assertEqual(inchi, inchi2)
self.assertEqual(store.lookupInchiKey(inchi), [i, i + 11])
for i in range(2):
self.assertEqual(store.descriptors().get(11 + 0),
(True, 78.046950192, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 1),
(True, 92.062600256, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 2),
(True, 106.07825032, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 3),
(True, 120.093900384, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 4),
(True, 134.109550448, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 5),
(True, 148.125200512, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 6),
(True, 162.140850576, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 7),
(True, 176.15650064, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 8),
(True, 190.172150704, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 9),
(True, 204.187800768, 0.0, 1.0, 0.0, 1.0))
self.assertEqual(store.descriptors().get(11 + 10),
(False, 0.0, 0.0, 0.0, 0.0, 0.0))
finally:
if os.path.exists(fname):
os.unlink(fname)
if os.path.exists(storefname):
shutil.rmtree(storefname)