def test2Bug28(self):
smi = 'Cc([s]1)nnc1SCC(\CS2)=C(/C([O-])=O)N3C(=O)[C@H]([C@@H]23)NC(=O)C[n]4cnnn4'
mol = Chem.MolFromSmiles(smi)
factory = Gobbi_Pharm2D.factory
factory.SetBins([(2, 3), (3, 4), (4, 5), (5, 8), (8, 100)])
sig = Generate.Gen2DFingerprint(mol, factory)
onBits = sig.GetOnBits()
for bit in onBits:
atoms = Matcher.GetAtomsMatchingBit(factory, bit, mol, justOne=1)
self.assertTrue(len(atoms))
def test3Roundtrip(self):
# longer-running Bug 28 test
nToDo = 20
with open(os.path.join(RDConfig.RDDataDir, 'NCI', 'first_5K.smi'), 'r') as inF:
inD = inF.readlines()[:nToDo]
factory = Gobbi_Pharm2D.factory
factory.SetBins([(2, 3), (3, 4), (4, 5), (5, 8), (8, 100)])
for line in inD:
smi = line.split('\t')[0]
mol = Chem.MolFromSmiles(smi)
sig = Generate.Gen2DFingerprint(mol, factory)
onBits = sig.GetOnBits()
for bit in onBits:
atoms = Matcher.GetAtomsMatchingBit(factory, bit, mol, justOne=1)
assert len(atoms), f'bit {bit} failed to match for smi {smi}'
def test1_simple(self):
mol = Chem.MolFromSmiles('OCC(=O)CCCN')
self.factory.skipFeats = ['Donor']
self.factory.Init()
self.assertEqual(self.factory.GetSigSize(), 510)
Generate._verbose = False
sig = Generate.Gen2DFingerprint(mol, self.factory)
Generate._verbose = False
tgt = (1, 2, 11, 52, 117)
onBits = sig.GetOnBits()
self.assertEqual(tuple(onBits), tgt)
self.assertEqual(len(onBits), len(tgt))
bitMatches = ([((0, ), (3, ))],
[((0, ), (7, )), ((3, ), (7, ))],
[((0, ), (3, ), (7, ))], )
for i, bit in enumerate(onBits):
matches = Matcher.GetAtomsMatchingBit(self.factory, bit, mol)
def GetBit(self,idx):
""" returns a bool indicating whether or not the bit is set
"""
if idx < 0 or idx >= self.sig.GetSize():
raise IndexError('Index %d invalid'%(idx))
if self.bits is not None and self.bits.has_key(idx):
return self.bits[idx]
tmp = Matcher.GetAtomsMatchingBit(self.sig,idx,self.mol,
dMat=self.dMat,justOne=1,
matchingAtoms=self.pattMatches)
if not tmp or len(tmp)==0: res = 0
else: res = 1
if self.bits is not None:
self.bits[idx] = res
return res
def test_exampleCode(self):
# We make sure that the example code runs
f = StringIO()
with redirect_stdout(f):
Matcher._exampleCode()
self.assertIn('finished', f.getvalue())
def test_exampleCode(self):
# We make sure that the example code runs
f = StringIO()
with redirect_stdout(f):
Matcher._exampleCode()
self.assertIn('finished', f.getvalue())