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 testSmartsMatcherAPI(self):
sm = FilterCatalog.SmartsMatcher("Too many carbons", "[#6]", 40 + 1)
sm2 = FilterCatalog.SmartsMatcher("ok # carbons", "[#6]", 0, 40)
sm3 = FilterCatalog.FilterMatchOps.Not(sm2)
m = Chem.MolFromSmiles("C" * 40)
self.assertFalse(sm.HasMatch(m))
self.assertTrue(sm2.HasMatch(m))
self.assertFalse(sm3.HasMatch(m))
m = Chem.MolFromSmiles("C" * 41)
self.assertTrue(sm.HasMatch(m))
self.assertFalse(sm2.HasMatch(m))
self.assertTrue(sm3.HasMatch(m))
def test4CountTests(self):
matcher = FilterCatalog.SmartsMatcher("Carbon", "[#6]", 0, 2)
m = Chem.MolFromSmiles("N")
self.assertTrue(matcher.HasMatch(m))
m = Chem.MolFromSmiles("C")
self.assertTrue(matcher.HasMatch(m))
m = Chem.MolFromSmiles("CC")
self.assertTrue(matcher.HasMatch(m))
m = Chem.MolFromSmiles("CCC")
self.assertFalse(matcher.HasMatch(m))
matcher = FilterCatalog.SmartsMatcher("Carbon", "[#6]", 1, 2)
m = Chem.MolFromSmiles("N")
self.assertFalse(matcher.HasMatch(m))
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 test3ExclusionFilter(self):
mol = Chem.MolFromSmiles("c1ccccc1")
pat = Chem.MolFromSmarts("c:c:c:c:c")
matcher = FilterCatalog.SmartsMatcher("Five aromatic carbons", pat)
self.assertTrue(matcher.GetMinCount() == 1)
self.assertTrue(matcher.HasMatch(mol))
matches = matcher.GetMatches(mol)
exclusionFilter = FilterCatalog.ExclusionList()
exclusionFilter.AddPattern(matcher)
self.assertFalse(exclusionFilter.HasMatch(mol))
matches2 = exclusionFilter.GetMatches(mol)
self.assertTrue(matches)
self.assertFalse(matches2)
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 test1FilterMatchOps(self):
mol = Chem.MolFromSmiles("c1ccccc1")
pat = Chem.MolFromSmarts("c:c:c:c:c")
matcher = FilterCatalog.SmartsMatcher("Five aromatic carbons", pat)
self.assertTrue(matcher.GetMinCount() == 1)
self.assertTrue(matcher.HasMatch(mol))
matches = matcher.GetMatches(mol)
matcher2 = FilterCatalog.ExclusionList()
matcher2.SetExclusionPatterns([matcher])
self.assertTrue(not matcher2.HasMatch(mol))
and_match = FilterMatchOps.And(matcher, matcher2)
self.assertTrue(not and_match.HasMatch(mol))
not_match = FilterMatchOps.Not(and_match)
self.assertTrue(not_match.HasMatch(mol))
or_match = FilterMatchOps.Or(matcher, matcher2)
self.assertTrue(or_match.HasMatch(mol))
print(and_match)
print(or_match)
print(not_match)
def testFilterHierarchyMatcher(self):
# test
root = FilterCatalog.FilterHierarchyMatcher()
sm = h = FilterCatalog.SmartsMatcher(
"Halogen", "[$([F,Cl,Br,I]-!@[#6]);!$([F,Cl,Br,I]"
"-!@C-!@[F,Cl,Br,I]);!$([F,Cl,Br,I]-[C,S]"
"(=[O,S,N]))]", 1)
root.SetPattern(sm)
def hierarchy(matcher):
node = FilterCatalog.FilterHierarchyMatcher(matcher)
self.assertEquals(matcher.GetName(), node.GetName())
return node
sm = FilterCatalog.SmartsMatcher("Halogen.Aromatic",
"[F,Cl,Br,I;$(*-!@c)]")
root.AddChild(hierarchy(sm))
sm = FilterCatalog.SmartsMatcher(
"Halogen.NotFluorine", "[$([Cl,Br,I]-!@[#6]);!$([Cl,Br,I]"
"-!@C-!@[F,Cl,Br,I]);!$([Cl,Br,I]-[C,S]"
"(=[O,S,N]))]")
node = hierarchy(sm)
halogen_notf_children = [
hierarchy(x) for x in [
FilterCatalog.SmartsMatcher(
"Halogen.NotFluorine.Aliphatic",
"[$([Cl,Br,I]-!@C);!$([Cl,Br,I]"
"-!@C-!@[F,Cl,Br,I]);!$([Cl,Br,I]-[C,S](=[O,S,N]))]"),
FilterCatalog.SmartsMatcher("Halogen.NotFluorine.Aromatic",
"[$([Cl,Br,I]-!@c)]")
]
]
for child in halogen_notf_children:
node.AddChild(child)
root.AddChild(node)
sm = FilterCatalog.SmartsMatcher(
"Halogen.Bromine", "[Br;$([Br]-!@[#6]);!$([Br]-!@C-!@[F,Cl,Br,I])"
";!$([Br]-[C,S](=[O,S,N]))]", 1)
node = hierarchy(sm)
halogen_bromine_children = [
hierarchy(x) for x in [
FilterCatalog.SmartsMatcher(
"Halogen.Bromine.Aliphatic",
"[Br;$(Br-!@C);!$(Br-!@C-!@[F,Cl,Br,I]);"
"!$(Br-[C,S](=[O,S,N]))]"),
FilterCatalog.SmartsMatcher("Halogen.Bromine.Aromatic",
"[Br;$(Br-!@c)]"),
FilterCatalog.SmartsMatcher("Halogen.Bromine.BromoKetone",
"[Br;$(Br-[CH2]-C(=O)-[#6])]")
]
]
for child in halogen_bromine_children:
node.AddChild(child)
root.AddChild(node)
m = Chem.MolFromSmiles("CCl")
assert h.HasMatch(m)
res = root.GetMatches(m)
self.assertEquals(len(res), 1)
self.assertEquals([match.filterMatch.GetName() for match in res],
['Halogen.NotFluorine.Aliphatic'])
m = Chem.MolFromSmiles("c1ccccc1Cl")
assert h.HasMatch(m)
res = root.GetMatches(m)
self.assertEquals(len(res), 2)
m = Chem.MolFromSmiles("c1ccccc1Br")
assert h.HasMatch(m)
res = root.GetMatches(m)
self.assertEquals(len(res), 3)
self.assertEquals([match.filterMatch.GetName() for match in res], [
'Halogen.Aromatic', 'Halogen.NotFluorine.Aromatic',
'Halogen.Bromine.Aromatic'
])
m = Chem.MolFromSmiles("c1ccccc1F")
assert h.HasMatch(m)
res = root.GetMatches(m)
self.assertEquals(len(res), 1)
self.assertEquals([match.filterMatch.GetName() for match in res],
['Halogen.Aromatic'])
m = Chem.MolFromSmiles("CBr")
assert h.HasMatch(m)
res = root.GetMatches(m)
self.assertEquals(
[match.filterMatch.GetName() for match in res],
['Halogen.NotFluorine.Aliphatic', 'Halogen.Bromine.Aliphatic'])
