def test0SubstructLibrary(self):
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
for holder in [
rdSubstructLibrary.MolHolder(),
rdSubstructLibrary.CachedMolHolder(),
rdSubstructLibrary.CachedSmilesMolHolder()
]:
if fpholderCls: fpholder = fpholderCls()
else: fpholder = None
slib = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
for i in range(100):
m = Chem.MolFromSmiles("c1ccccc1")
self.assertEqual(slib.AddMol(m), i)
res = slib.GetMatches(m)
t2 = time.time()
self.assertTrue(len(res) == 100)
res = slib.GetMatches(m)
self.assertEqual(len(res), 100)
self.assertTrue(set(res) == set(list(range(100))))
res = slib.GetMatches(m, maxResults=100)
self.assertEqual(len(res), 100)
self.assertEqual(
len(slib.GetMatches(m, startIdx=0, endIdx=100)), 100)
self.assertTrue(slib.HasMatch(m))
self.assertEqual(slib.CountMatches(m), 100)
def test0SubstructLibrary(self):
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
for holder in [rdSubstructLibrary.MolHolder(), rdSubstructLibrary.CachedMolHolder(),
rdSubstructLibrary.CachedSmilesMolHolder()]:
if fpholderCls: fpholder = fpholderCls()
else: fpholder = None
slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
for i in range(100):
m = Chem.MolFromSmiles("c1ccccc1")
self.assertEqual(slib_.AddMol(m), i)
libs = [slib_]
if rdSubstructLibrary.SubstructLibraryCanSerialize():
serialized1 = pickle.loads(pickle.dumps(slib_))
serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
libs.append(serialized1)
libs.append(serialized2)
for slib in libs:
res = slib.GetMatches(m)
t2 = time.time()
self.assertTrue(len(res) == 100)
res = slib.GetMatches(m)
self.assertEqual(len(res), 100)
self.assertTrue(set(res) == set(list(range(100))))
res = slib.GetMatches(m, maxResults=100);
self.assertEqual(len(res), 100)
self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=100)), 100)
self.assertTrue(slib.HasMatch(m))
self.assertEqual(slib.CountMatches(m), 100)
def test1SubstructLibrary(self):
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
for holder in [
rdSubstructLibrary.MolHolder(),
rdSubstructLibrary.CachedMolHolder(),
rdSubstructLibrary.CachedSmilesMolHolder()
]:
if fpholderCls: fpholder = fpholderCls()
else: fpholder = None
slib = rdSubstructLibrary.SubstructLibrary(holder, fpholder)
mols = []
for i in range(100):
m = Chem.MolFromSmiles("c1ccccc1")
self.assertEqual(slib.AddMol(m), i * 2)
mols.append(m)
m2 = Chem.MolFromSmiles("CCCC")
self.assertEqual(slib.AddMol(m2), i * 2 + 1)
mols.append(m2)
res = slib.GetMatches(m)
self.assertEqual(len(res), 100)
self.assertEqual(set(res), set(list(range(0, 200, 2))))
res = slib.GetMatches(m2)
self.assertEqual(len(res), 100)
self.assertTrue(set(res) == set(list(range(1, 200, 2))))
res = slib.GetMatches(m)
self.assertEqual(len(res), 100)
res = slib.GetMatches(m, maxResults=100)
self.assertEqual(len(res), 100)
self.assertEqual(
len(slib.GetMatches(m, startIdx=0, endIdx=50 * 2)), 50)
self.assertEqual(
len(slib.GetMatches(m2, startIdx=1, endIdx=50 * 2 + 1)),
50)
self.assertTrue(slib.HasMatch(m))
self.assertTrue(slib.HasMatch(m2))
self.assertEqual(slib.CountMatches(m), 100)
self.assertEqual(slib.CountMatches(m2), 100)
def testSearchOrder(self):
for keyholder in [None, rdSubstructLibrary.KeyFromPropHolder()]:
ssl = rdSubstructLibrary.SubstructLibrary(
rdSubstructLibrary.MolHolder(), keyholder)
for idx, smi in enumerate(
("CCCOC", "CCCCOCC", "CCOC", "COC", "CCCCCOC")):
m = Chem.MolFromSmiles(smi)
m.SetProp("_Name", str(idx))
ssl.AddMol(m)
ssl.SetSearchOrder((3, 2, 0, 1, 4))
self.assertEqual(ssl.GetSearchOrder(), (3, 2, 0, 1, 4))
qm = Chem.MolFromSmiles('COC')
self.assertEqual(list(ssl.GetMatches(qm, maxResults=2)), [3, 2])
self.assertEqual(list(ssl.GetMatches(qm, maxResults=2)), [3, 2])
if keyholder:
self.assertEqual(keyholder.GetPropName(), "_Name")
self.assertEqual(
list(ssl.GetKeyHolder().GetKeys(
ssl.GetMatches(qm, maxResults=2))), ['3', '2'])
def testPropHolder(self):
for propname in [None, 'foo']:
if propname is None:
keyholder = rdSubstructLibrary.KeyFromPropHolder()
else:
keyholder = rdSubstructLibrary.KeyFromPropHolder(propname)
library = rdSubstructLibrary.SubstructLibrary(
rdSubstructLibrary.MolHolder(), keyholder)
m = Chem.MolFromSmiles('CCC')
if propname is None:
self.assertEqual(keyholder.GetPropName(), "_Name")
else:
self.assertEqual(keyholder.GetPropName(), propname)
if propname:
m.SetProp(propname, 'Z11234')
else:
m.SetProp("_Name", 'Z11234')
library.AddMol(m)
indices = library.GetMatches(m)
self.assertEqual(['Z11234'],
list(library.GetKeyHolder().GetKeys(indices)))
def test1SubstructLibrary(self):
for keyholderCls in [None, rdSubstructLibrary.KeyFromPropHolder]:
for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
for holder in [
rdSubstructLibrary.MolHolder(),
rdSubstructLibrary.CachedMolHolder(),
rdSubstructLibrary.CachedSmilesMolHolder()
]:
if fpholderCls: fpholder = fpholderCls()
else: fpholder = None
if keyholderCls:
keyholder = keyholderCls()
self.assertEqual(keyholder.GetPropName(), "_Name")
else:
keyholder = None
slib_ = rdSubstructLibrary.SubstructLibrary(
holder, fpholder, keyholder)
mols = []
for i in range(100):
m = Chem.MolFromSmiles("c1ccccc1")
m.SetProp("_Name", str(i * 2))
self.assertEqual(slib_.AddMol(m), i * 2)
mols.append(m)
m2 = Chem.MolFromSmiles("CCCC")
m2.SetProp("_Name", str(i * 2 + 1))
self.assertEqual(slib_.AddMol(m2), i * 2 + 1)
mols.append(m2)
libs = [slib_]
if rdSubstructLibrary.SubstructLibraryCanSerialize():
serialized1 = pickle.loads(pickle.dumps(slib_))
serialized2 = rdSubstructLibrary.SubstructLibrary(
slib_.Serialize())
libs.append(serialized1)
libs.append(serialized2)
for slib in libs:
res = slib.GetMatches(m)
self.assertEqual(len(res), 100)
self.assertEqual(set(res), set(list(range(0, 200, 2))))
if keyholderCls:
self.assertEqual(
[str(idx) for idx in res],
[str(idx) for idx in range(0, 200, 2)])
res = slib.GetMatches(m2)
self.assertEqual(len(res), 100)
self.assertTrue(
set(res) == set(list(range(1, 200, 2))))
if keyholderCls:
self.assertEqual(
[str(idx) for idx in res],
[str(idx) for idx in range(1, 200, 2)])
res = slib.GetMatches(m)
self.assertEqual(len(res), 100)
res = slib.GetMatches(m, maxResults=100)
self.assertEqual(len(res), 100)
self.assertEqual(
len(slib.GetMatches(m, startIdx=0, endIdx=50 * 2)),
50)
self.assertEqual(
len(
slib.GetMatches(m2,
startIdx=1,
endIdx=50 * 2 + 1)), 50)
self.assertTrue(slib.HasMatch(m))
self.assertTrue(slib.HasMatch(m2))
self.assertEqual(slib.CountMatches(m), 100)
self.assertEqual(slib.CountMatches(m2), 100)
