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 testAddEntry(self):
sm = FilterCatalog.SmartsMatcher("Too many carbons", "[#6]", 40 + 1)
entry = FilterCatalog.FilterCatalogEntry("Bar", sm)
fc = FilterCatalog.FilterCatalog()
fc.AddEntry(entry)
del entry
del fc
def testThreadedPythonFilter(self):
class MWFilter(FilterCatalog.FilterMatcher):
def __init__(self, minMw, maxMw):
FilterCatalog.FilterMatcher.__init__(self, "MW violation")
self.minMw = minMw
self.maxMw = maxMw
def IsValid(self):
return True
def HasMatch(self, mol):
mw = rdMolDescriptors.CalcExactMolWt(mol)
res = not self.minMw <= mw <= self.maxMw
Chem.MolFromSmiles("---")
Chem.LogErrorMsg("dasfsadf")
return res
path = os.path.join(os.environ['RDBASE'], 'Code', 'GraphMol',
'test_data', 'pains.smi')
with open(path) as f:
smiles = [f.strip() for f in f.readlines()][1:]
print("1")
self.assertEqual(len(smiles), 3)
print("2")
entry = FilterCatalog.FilterCatalogEntry("MW Violation",
MWFilter(100, 500))
fc = FilterCatalog.FilterCatalog()
fc.AddEntry(entry)
self.assertTrue(entry.GetDescription() == "MW Violation")
print("running")
results = FilterCatalog.RunFilterCatalog(fc, smiles * 10, numThreads=3)
def testPyFilter(self):
class MyFilterMatcher(FilterCatalog.FilterMatcher):
def IsValid(self):
return True
def HasMatch(self, mol):
return True
def GetMatches(self, mol, vect):
v = FilterCatalog.MatchTypeVect()
v.append(FilterCatalog.IntPair(1, 1))
match = FilterCatalog.FilterMatch(self, v)
vect.append(match)
return True
func = MyFilterMatcher("FilterMatcher")
self.assertEquals(func.GetName(), "FilterMatcher")
mol = Chem.MolFromSmiles("c1ccccc1")
self.assertEquals(func.HasMatch(mol), True)
or_match = FilterMatchOps.Or(func, func)
self.assertEquals([[tuple(x) for x in filtermatch.atomPairs]
for filtermatch in or_match.GetMatches(mol)],
[[(1, 1)], [(1, 1)]])
not_match = FilterMatchOps.Not(func)
print(not_match)
self.assertEquals(not_match.HasMatch(mol), False)
# test memory
del func
self.assertEquals(not_match.HasMatch(mol), False)
self.assertEquals([[tuple(x) for x in filtermatch.atomPairs]
for filtermatch in not_match.GetMatches(mol)], [])
entry = FilterCatalog.FilterCatalogEntry(
"Bar", MyFilterMatcher("FilterMatcher"))
fc = FilterCatalog.FilterCatalog()
fc.AddEntry(entry)
catalogEntry = fc.GetFirstMatch(mol)
print(catalogEntry.GetDescription())
def buildFilterCatalog():
inhousefilter = pd.read_csv(
'SubstructureFilter_HitTriaging_wPubChemExamples.csv')
inhouseFiltersCat = FilterCatalog.FilterCatalog()
for i in range(inhousefilter.shape[0]):
mincount = 1
if inhousefilter['MIN_COUNT'][i] != 0:
mincount = int(inhousefilter['MIN_COUNT'][i])
pname = inhousefilter['PATTERN_NAME'][i]
sname = inhousefilter['SET_NAME'][i]
pname_final = '{0}_min({1})__{2}__{3}__{4}'.format(
pname, mincount, inhousefilter['SEVERITY_SCORE'][i],
inhousefilter['COVALENT'][i], inhousefilter['SPECIAL_MOL'][i])
fil = FilterCatalog.SmartsMatcher(pname_final,
inhousefilter['SMARTS'][i], mincount)
inhouseFiltersCat.AddEntry(
FilterCatalog.FilterCatalogEntry(pname_final, fil))
inhouseFiltersCat.GetEntry(i).SetProp('Scope', sname)
return inhouseFiltersCat
def testMWFilter(self):
class MWFilter(FilterCatalog.FilterMatcher):
def __init__(self, minMw, maxMw):
FilterCatalog.FilterMatcher.__init__(self, "MW violation")
self.minMw = minMw
self.maxMw = maxMw
def IsValid(self):
return True
def HasMatch(self, mol):
mw = rdMolDescriptors.CalcExactMolWt(mol)
return not self.minMw <= mw <= self.maxMw
entry = FilterCatalog.FilterCatalogEntry("MW Violation",
MWFilter(100, 500))
fc = FilterCatalog.FilterCatalog()
fc.AddEntry(entry)
self.assertTrue(entry.GetDescription() == "MW Violation")
mol = Chem.MolFromSmiles("c1ccccc1")
catalogEntry = fc.GetFirstMatch(mol)
