def test4OnBitsInCommon(self):
sz = 100
bv1 = DataStructs.ExplicitBitVect(sz)
bv2 = DataStructs.ExplicitBitVect(sz)
for i in range(0, sz, 2):
bv1.SetBit(i)
if i < 3 * sz / 4:
bv2.SetBit(i)
self.failUnless(DataStructs.AllProbeBitsMatch(bv1, bv1.ToBinary()))
self.failUnless(DataStructs.AllProbeBitsMatch(bv2, bv1.ToBinary()))
self.failIf(DataStructs.AllProbeBitsMatch(bv1, bv2.ToBinary()))
self.failUnless(DataStructs.AllProbeBitsMatch(bv2, bv2.ToBinary()))
def _molge(x, y):
"""Allows for substructure check using the >= operator (X has substructure Y -> X >= Y) by
monkey-patching the __ge__ function
This has the effect that the pandas/numpy rowfilter can be used for substructure filtering (filtered = dframe[dframe['RDKitColumn'] >= SubstructureMolecule])
"""
if x is None or y is None: return False
if hasattr(x, '_substructfp'):
if not hasattr(y, '_substructfp'):
y._substructfp = _fingerprinter(y, True)
if not DataStructs.AllProbeBitsMatch(y._substructfp, x._substructfp):
return False
return x.HasSubstructMatch(y)
def test_basic(self):
mol = Chem.MolFromSmiles("O=C1CCCCC1")
tautomer_query = rdTautomerQuery.TautomerQuery(mol)
self.assertEqual(2, len(tautomer_query.GetTautomers()))
modified_bonds = tautomer_query.GetModifiedBonds()
self.assertEqual(3, len(modified_bonds))
modified_atoms = tautomer_query.GetModifiedAtoms()
self.assertEqual(3, len(modified_atoms))
target = Chem.MolFromSmiles("OC1=CCCC(CC)C1")
self.assertTrue(
target.HasSubstructMatch(tautomer_query.GetTemplateMolecule()))
match = tautomer_query.IsSubstructOf(target)
self.assertTrue(match)
self.assertTrue(
target.HasSubstructMatch(tautomer_query.GetTemplateMolecule()))
#self.assertTrue(target.HasSubstructMatch(tautomer_query.GetTautomers()[1]))
match = tautomer_query.GetSubstructMatch(target)
self.assertEqual(7, len(match))
matches = tautomer_query.GetSubstructMatches(target)
self.assertEqual(1, len(matches))
tautomer_matches = tautomer_query.GetSubstructMatchesWithTautomers(
target)
self.assertEqual(1, len(tautomer_matches))
self.assertEqual(len(tautomer_matches[0][0]), 7)
matching_tautomer = tautomer_matches[0][1]
self.assertTrue(target.HasSubstructMatch(matching_tautomer))
tautomer_fingerprint = tautomer_query.PatternFingerprintTemplate()
target_fingerprint = rdTautomerQuery.PatternFingerprintTautomerTarget(
target)
matching_fingerprints = DataStructs.AllProbeBitsMatch(
tautomer_fingerprint, target_fingerprint)
self.assertTrue(matching_fingerprints)
file = os.environ[
'RDBASE'] + '/Code/GraphMol/MolStandardize/test_data/tautomerTransforms.in'
tautomer_query2 = rdTautomerQuery.TautomerQuery(mol, file)
self.assertEqual(2, len(tautomer_query.GetTautomers()))
logger.info(f'Results{len(ts)}: {t2-t1 : .2f} seconds')
for nm, qs, qfps in [('frags', frags, fragsfps), ('leads', leads, leadsfps),
('pieces', pieces, piecesfps)]:
logger.info(f'testing {nm} queries')
t1 = time.time()
nPossible = 0
nTested = 0
nFound = 0
nErrors = 0
for i, fragfp in enumerate(qfps):
for j, mfp in enumerate(mfps):
nPossible += 1
if args.validateResults:
matched = mols[j].HasSubstructMatch(qs[i])
fpMatch = DataStructs.AllProbeBitsMatch(fragfp, mfp)
if fpMatch:
nTested += 1
if matched:
nFound += 1
if not fpMatch:
nErrors += 1
logger.error(f"ERROR: mol {j} query {i}")
else:
if DataStructs.AllProbeBitsMatch(fragfp, mfp):
nTested += 1
if mols[j].HasSubstructMatch(qs[i]):
nFound += 1
t2 = time.time()
ts.append(t2 - t1)
logger.info(
