def test0FilterCatalogEntry(self):
matcher = FilterCatalog.SmartsMatcher("Aromatic carbon chain")
self.assertTrue(not matcher.IsValid())
pat = Chem.MolFromSmarts("c:c:c:c:c")
matcher.SetPattern(pat)
matcher.SetMinCount(1)
entry = FilterCatalog.FilterCatalogEntry("Bar", matcher)
if FilterCatalog.FilterCatalogCanSerialize():
pickle = entry.Serialize()
else:
pickle = None
self.assertTrue(entry.GetDescription() == "Bar")
self.assertTrue(matcher.GetMinCount() == 1)
self.assertTrue(matcher.GetMaxCount() == 2**32 - 1)
self.assertTrue(matcher.IsValid())
entry.SetDescription("Foo")
self.assertTrue(entry.GetDescription() == "Foo")
mol = Chem.MolFromSmiles("c1ccccc1")
self.assertTrue(matcher.HasMatch(mol))
matcher = FilterCatalog.SmartsMatcher(pat)
self.assertEqual(str(matcher), "Unnamed SmartsMatcher")
self.assertTrue(matcher.GetMinCount() == 1)
self.assertTrue(matcher.HasMatch(mol))
matches = matcher.GetMatches(mol)
matcher = FilterCatalog.ExclusionList()
matcher.SetExclusionPatterns([matcher])
self.assertTrue(not matcher.HasMatch(mol))
def testFunctionalGroupHierarchy(self):
fc = FilterCatalog.GetFunctionalGroupHierarchy()
matches = [(Chem.MolFromSmiles("CCl"), ['Halogen.Aliphatic', 'Halogen.NotFluorine.Aliphatic']),
(Chem.MolFromSmiles("c1ccccc1Cl"),
['Halogen.Aromatic', 'Halogen.NotFluorine.Aromatic']),
(Chem.MolFromSmiles("c1ccccc1F"), ['Halogen.Aromatic']), (
Chem.MolFromSmiles("CBr"), ['Halogen.Aliphatic', 'Halogen.NotFluorine.Aliphatic',
'Halogen.Bromine.Aliphatic'])]
catalogs = [fc]
if FilterCatalog.FilterCatalogCanSerialize():
pickle = fc.Serialize()
fc2 = FilterCatalog.FilterCatalog(pickle)
catalogs.append(fc2)
for fc in catalogs:
# test GetMatches API
for mol, res in matches:
entries = list(fc.GetMatches(mol))
for entry in entries:
hits = [match.filterMatch.GetName() for match in entry.GetFilterMatches(mol)]
self.assertEquals(res, hits)
# test GetFilterMatches API
for mol, res in matches:
self.assertEquals(res, [match.filterMatch.GetName() for match in fc.GetFilterMatches(mol)])
def test2FilterCatalogTest(self):
tests = ((FilterCatalogParams.FilterCatalogs.PAINS_A,
16), (FilterCatalogParams.FilterCatalogs.PAINS_B,
55), (FilterCatalogParams.FilterCatalogs.PAINS_C, 409),
(FilterCatalogParams.FilterCatalogs.PAINS, 409 + 16 + 55))
for catalog_idx, num in tests:
params = FilterCatalog.FilterCatalogParams()
print("*" * 44)
print("Testing:", catalog_idx, int(catalog_idx))
self.assertTrue(params.AddCatalog(catalog_idx))
catalog1 = FilterCatalog.FilterCatalog(params)
if FilterCatalog.FilterCatalogCanSerialize():
pickle = catalog1.Serialize()
catalog2 = FilterCatalog.FilterCatalog(pickle)
catalogs = [catalog1, catalog2]
else:
catalogs = [catalog1]
catalogs.append(FilterCatalog.FilterCatalog(catalog_idx))
for index, catalog in enumerate(catalogs):
self.assertEqual(catalog.GetNumEntries(), num)
if catalog_idx in [
FilterCatalogParams.FilterCatalogs.PAINS_A,
FilterCatalogParams.FilterCatalogs.PAINS
]:
# http://chemistrycompass.com/chemsearch/58909/
mol = Chem.MolFromSmiles(
"O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2"
)
entry = catalog.GetFirstMatch(mol)
for key in entry.GetPropList():
if key == "Reference":
self.assertEquals(
entry.GetProp(key),
"Baell JB, Holloway GA. New Substructure Filters for "
"Removal of Pan Assay Interference Compounds (PAINS) "
"from Screening Libraries and for Their Exclusion in "
"Bioassays. J Med Chem 53 (2010) 2719D40. "
"doi:10.1021/jm901137j.")
elif key == "Scope":
self.assertEquals(entry.GetProp(key),
"PAINS filters (family A)")
self.assertEqual(entry.GetDescription(),
"hzone_phenol_A(479)")
result = catalog.GetMatches(mol)
self.assertEquals(len(result), 1)
for entry in result:
for filtermatch in entry.GetFilterMatches(mol):
self.assertEquals(str(filtermatch.filterMatch),
"hzone_phenol_A(479)")
atomPairs = [
tuple(x) for x in filtermatch.atomPairs
]
self.assertEquals(atomPairs, [(0, 23), (1, 22),
(2, 20), (3, 19),
(4, 25), (5, 24),
(6, 18), (7, 17),
(8, 16), (9, 21)])
elif catalog_idx == FilterCatalogParams.FilterCatalogs.PAINS_B:
mol = Chem.MolFromSmiles(
"FC(F)(F)Oc1ccc(NN=C(C#N)C#N)cc1") # CHEMBL457504
entry = catalog.GetFirstMatch(mol)
self.assertTrue(entry)
self.assertEquals(entry.GetDescription(),
"cyano_imine_B(17)")
elif catalog_idx == FilterCatalogParams.FilterCatalogs.PAINS_C:
mol = Chem.MolFromSmiles(
"O=C1C2OC2C(=O)c3cc4CCCCc4cc13") # CHEMBL476649
entry = catalog.GetFirstMatch(mol)
self.assertTrue(entry)
self.assertEquals(entry.GetDescription(),
"keto_keto_gamma(5)")