def test1Basics(self):
rxna = rdChemReactions.ChemicalReaction()
# also tests empty copy constructor
for rxn in [rxna, rdChemReactions.ChemicalReaction(rxna)]:
self.assertTrue(rxn.GetNumReactantTemplates() == 0)
self.assertTrue(rxn.GetNumProductTemplates() == 0)
r1 = Chem.MolFromSmarts('[C:1](=[O:2])O')
rxn.AddReactantTemplate(r1)
self.assertTrue(rxn.GetNumReactantTemplates() == 1)
r1 = Chem.MolFromSmarts('[N:3]')
rxn.AddReactantTemplate(r1)
self.assertTrue(rxn.GetNumReactantTemplates() == 2)
r1 = Chem.MolFromSmarts('[C:1](=[O:2])[N:3]')
rxn.AddProductTemplate(r1)
self.assertTrue(rxn.GetNumProductTemplates() == 1)
reacts = (Chem.MolFromSmiles('C(=O)O'), Chem.MolFromSmiles('N'))
ps = rxn.RunReactants(reacts)
self.assertTrue(len(ps) == 1)
self.assertTrue(len(ps[0]) == 1)
self.assertTrue(ps[0][0].GetNumAtoms() == 3)
ps = rxn.RunReactants(list(reacts))
self.assertTrue(len(ps) == 1)
self.assertTrue(len(ps[0]) == 1)
self.assertTrue(ps[0][0].GetNumAtoms() == 3)
def test1Basics(self):
rxn = rdChemReactions.ChemicalReaction()
self.failUnless(rxn.GetNumReactantTemplates() == 0)
self.failUnless(rxn.GetNumProductTemplates() == 0)
r1 = Chem.MolFromSmarts('[C:1](=[O:2])O')
rxn.AddReactantTemplate(r1)
self.failUnless(rxn.GetNumReactantTemplates() == 1)
r1 = Chem.MolFromSmarts('[N:3]')
rxn.AddReactantTemplate(r1)
self.failUnless(rxn.GetNumReactantTemplates() == 2)
r1 = Chem.MolFromSmarts('[C:1](=[O:2])[N:3]')
rxn.AddProductTemplate(r1)
self.failUnless(rxn.GetNumProductTemplates() == 1)
reacts = (Chem.MolFromSmiles('C(=O)O'), Chem.MolFromSmiles('N'))
ps = rxn.RunReactants(reacts)
self.failUnless(len(ps) == 1)
self.failUnless(len(ps[0]) == 1)
self.failUnless(ps[0][0].GetNumAtoms() == 3)
ps = rxn.RunReactants(list(reacts))
self.failUnless(len(ps) == 1)
self.failUnless(len(ps[0]) == 1)
self.failUnless(ps[0][0].GetNumAtoms() == 3)
def testRandomSample(self):
log("testRandomSample")
rgroups = [[Chem.MolFromSmiles("C")] * 10,
[Chem.MolFromSmiles("N")] * 5,
[Chem.MolFromSmiles("O")] * 6]
rxn = rdChemReactions.ChemicalReaction()
randProd = rdChemReactions.RandomSampleStrategy()
randProd.Initialize(rxn, rgroups)
self.assertEquals(randProd.GetNumPermutations(), 10 * 5 * 6)
groups = []
for i in range(10 * 5 * 6):
groups.append(tuple(randProd.next()))
print(len(set(groups)), "out of", 10 * 5 * 6)
randProd = rdChemReactions.RandomSampleStrategy()
randProd.Initialize(rxn, rgroups)
self.assertEquals(randProd.GetNumPermutations(), 10 * 5 * 6)
groups = []
for i in range(10):
groups.append(tuple(randProd.next()))
for i in range(3):
print(i, len(set([g[i] for g in groups])), "out of", [10, 5, 6][i])
copy.copy(randProd)
def test3MDLParsers(self):
fileN = os.path.join(self.dataDir, 'AmideBond.rxn')
rxna = rdChemReactions.ReactionFromRxnFile(fileN)
print("*" * 44)
print(fileN)
print(rxna)
for rxn in [rxna, rdChemReactions.ChemicalReaction(rxna)]:
self.assertTrue(rxn)
self.assertFalse(rxn._getImplicitPropertiesFlag())
self.assertTrue(rxn.GetNumReactantTemplates() == 2)
self.assertTrue(rxn.GetNumProductTemplates() == 1)
reacts = (Chem.MolFromSmiles('C(=O)O'), Chem.MolFromSmiles('N'))
ps = rxn.RunReactants(reacts)
self.assertTrue(len(ps) == 1)
self.assertTrue(len(ps[0]) == 1)
self.assertTrue(ps[0][0].GetNumAtoms() == 3)
with open(fileN, 'r') as rxnF:
rxnBlock = rxnF.read()
rxn = rdChemReactions.ReactionFromRxnBlock(rxnBlock)
self.assertTrue(rxn)
self.assertTrue(rxn.GetNumReactantTemplates() == 2)
self.assertTrue(rxn.GetNumProductTemplates() == 1)
reacts = (Chem.MolFromSmiles('C(=O)O'), Chem.MolFromSmiles('N'))
ps = rxn.RunReactants(reacts)
self.assertTrue(len(ps) == 1)
self.assertTrue(len(ps[0]) == 1)
self.assertTrue(ps[0][0].GetNumAtoms() == 3)
def testCartesianProduct(self):
log("testCartesianProduct")
rxn = rdChemReactions.ChemicalReaction()
rgroups = [[Chem.MolFromSmiles("C")] * 10,
[Chem.MolFromSmiles("N")] * 5,
[Chem.MolFromSmiles("O")] * 6]
cartProd = rdChemReactions.CartesianProductStrategy()
cartProd.Initialize(rxn, rgroups)
self.assertEquals(cartProd.GetNumPermutations(), 10 * 5 * 6)
groups = []
count = 0
print(cartProd.__bool__())
while cartProd:
groups.append(tuple(cartProd.next()))
# count += 1
# assert count <= cartProd.GetNumPermutations()
self.assertEquals(len(groups), 10 * 5 * 6)
# see if we are equal to the Python implementation
g = list(
itertools.product(list(range(10)), list(range(5)), list(range(6))))
self.assertEquals(set(g), set(groups))
copy.copy(cartProd)
def testProperties(self):
smirks_thiourea = "[N;$(N-[#6]):3]=[C;$(C=S):1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);!$([ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[N:3]-[C:1]-[N+0:2]"
rxn = rdChemReactions.ReactionFromSmarts(smirks_thiourea)
self.assertFalse(rxn.HasProp("fooprop"))
rxn.SetProp("fooprop", "bar", computed=True)
rxn.SetIntProp("intprop", 3)
self.assertTrue(rxn.HasProp("fooprop"))
self.assertTrue(rxn.HasProp("intprop"))
self.assertEquals(rxn.GetIntProp("intprop"), 3)
nrxn = rdChemReactions.ChemicalReaction(rxn.ToBinary())
self.assertFalse(nrxn.HasProp("fooprop"))
nrxn = rdChemReactions.ChemicalReaction(rxn.ToBinary(Chem.PropertyPickleOptions.AllProps))
self.assertTrue(nrxn.HasProp("fooprop"))
nrxn.ClearComputedProps()
self.assertFalse(nrxn.HasProp("fooprop"))
self.assertTrue(nrxn.HasProp("intprop"))
self.assertEquals(nrxn.GetIntProp("intprop"), 3)
def test_github_4162(self):
rxn = rdChemReactions.ReactionFromSmarts(
"[C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3]")
rxn_copy = rdChemReactions.ChemicalReaction(rxn)
rdChemReactions.SanitizeRxn(rxn)
rdChemReactions.SanitizeRxn(rxn_copy)
pkl = rxn.ToBinary()
rxn_from_pickle = rdChemReactions.ChemicalReaction(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = pickle.dumps(rxn)
rxn_from_pickle = pickle.loads(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = rxn_from_pickle.ToBinary()
rxn_from_pickle = rdChemReactions.ChemicalReaction(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = pickle.dumps(rxn_from_pickle)
rxn_from_pickle = pickle.loads(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
def test20CheckCopyConstructedReactionAtomProps(self):
RLABEL = "_MolFileRLabel"
amine_rxn = '$RXN\n\n ISIS 090220091541\n\n 2 1\n$MOL\n\n -ISIS- 09020915412D\n\n 3 2 0 0 0 0 0 0 0 0999 V2000\n -2.9083 -0.4708 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0\n -2.3995 -0.1771 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n -2.4042 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 2 0 0 0 0\nV 2 aldehyde\nM RGP 1 1 1\nM END\n$MOL\n\n -ISIS- 09020915412D\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n 2.8375 -0.2500 0.0000 R# 0 0 0 0 0 0 0 0 0 3 0 0\n 3.3463 0.0438 0.0000 N 0 0 0 0 0 0 0 0 0 4 0 0\n 1 2 1 0 0 0 0\nV 2 amine\nM RGP 1 1 2\nM END\n$MOL\n\n -ISIS- 09020915412D\n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n 13.3088 0.9436 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n 13.8206 1.2321 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0\n 13.3028 0.3561 0.0000 N 0 0 0 0 0 0 0 0 0 4 0 0\n 12.7911 0.0676 0.0000 R# 0 0 0 0 0 0 0 0 0 3 0 0\n 1 3 1 0 0 0 0\n 1 2 1 0 0 0 0\n 3 4 1 0 0 0 0\nM RGP 2 2 1 4 2\nM END\n'
rxn = rdChemReactions.ReactionFromRxnBlock(amine_rxn)
res = []
for atom in rxn.GetReactantTemplate(0).GetAtoms():
if atom.HasProp(RLABEL):
res.append((atom.GetIdx(), atom.GetProp(RLABEL)))
rxn2 = rdChemReactions.ChemicalReaction(rxn)
res2 = []
for atom in rxn2.GetReactantTemplate(0).GetAtoms():
if atom.HasProp(RLABEL):
res2.append((atom.GetIdx(), atom.GetProp(RLABEL)))
self.assertEquals(res, res2)
def testTimings(self):
log("testTimings")
rxn = rdChemReactions.ChemicalReaction()
rgroups = [[Chem.MolFromSmiles("C")] * 17000,
[Chem.MolFromSmiles("N")] * 50000,
[Chem.MolFromSmiles("O")] * 4000]
cartProd = rdChemReactions.CartesianProductStrategy()
randProd = rdChemReactions.RandomSampleStrategy()
randAllBBs = rdChemReactions.RandomSampleAllBBsStrategy()
for r in [cartProd, randProd, randAllBBs]:
r.Initialize(rxn, rgroups)
num = 10000000
t1 = time.time()
r.Skip(num)
t2 = time.time()
print("%s Skipped %s in %s seconds" % (r, num, t2 - t1))
def test2DaylightParser(self):
rxna = rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]')
for rxn in [rxna, rdChemReactions.ChemicalReaction(rxna)]:
self.assertTrue(rxn)
self.assertTrue(rxn.GetNumReactantTemplates()==2)
self.assertTrue(rxn.GetNumProductTemplates()==1)
self.assertTrue(rxn._getImplicitPropertiesFlag())
reacts = (Chem.MolFromSmiles('C(=O)O'),Chem.MolFromSmiles('N'))
ps = rxn.RunReactants(reacts)
self.assertTrue(len(ps)==1)
self.assertTrue(len(ps[0])==1)
self.assertTrue(ps[0][0].GetNumAtoms()==3)
reacts = (Chem.MolFromSmiles('CC(=O)OC'),Chem.MolFromSmiles('CN'))
ps = rxn.RunReactants(reacts)
self.assertTrue(len(ps)==1)
self.assertTrue(len(ps[0])==1)
self.assertTrue(ps[0][0].GetNumAtoms()==5)
def test12Pickles(self):
rxn = rdChemReactions.ReactionFromSmarts(
'[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1')
pkl = cPickle.dumps(rxn)
rxn = cPickle.loads(pkl)
mol = Chem.MolFromSmiles('C1ON1')
products = rxn.RunReactants([mol])
self.failUnlessEqual(len(products), 1)
for p in products:
self.failUnlessEqual(len(p), 1)
self.failUnlessEqual(p[0].GetNumAtoms(), 3)
self.failUnlessEqual(p[0].GetNumBonds(), 2)
rxn = rdChemReactions.ChemicalReaction(rxn.ToBinary())
products = rxn.RunReactants([mol])
self.failUnlessEqual(len(products), 1)
for p in products:
self.failUnlessEqual(len(p), 1)
self.failUnlessEqual(p[0].GetNumAtoms(), 3)
self.failUnlessEqual(p[0].GetNumBonds(), 2)
def test12Pickles(self):
# 08/05/14
# This test is changed due to a new behavior of the smarts
# reaction parser which now allows using parenthesis in products
# as well. original smiles: '[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1'
rxn = rdChemReactions.ReactionFromSmarts('[C:1]1[O:2][N:3]1>>([C:1]1[O:2].[N:3]1)')
pkl = cPickle.dumps(rxn)
rxn = cPickle.loads(pkl)
mol = Chem.MolFromSmiles('C1ON1')
products = rxn.RunReactants([mol])
self.assertEqual(len(products),1)
for p in products:
self.assertEqual(len(p),1)
self.assertEqual(p[0].GetNumAtoms(),3)
self.assertEqual(p[0].GetNumBonds(),2)
rxn = rdChemReactions.ChemicalReaction(rxn.ToBinary())
products = rxn.RunReactants([mol])
self.assertEqual(len(products),1)
for p in products:
self.assertEqual(len(p),1)
self.assertEqual(p[0].GetNumAtoms(),3)
self.assertEqual(p[0].GetNumBonds(),2)
def testEvenPairsSampling(self):
rxn = rdChemReactions.ChemicalReaction()
rgroups = [[Chem.MolFromSmiles("C")] * 10,
[Chem.MolFromSmiles("N")] * 10,
[Chem.MolFromSmiles("O")] * 10]
rxn = rdChemReactions.ChemicalReaction()
count = 0
pairs01 = {}
pairs12 = {}
pairs02 = {}
strategy = rdChemReactions.EvenSamplePairsStrategy()
strategy.Initialize(rxn, rgroups)
# try 100 samples
while count < 100:
v = strategy.next()
p01 = (v[0], v[1])
p12 = (v[1], v[2])
p02 = (v[0], v[2])
pairs01[p01] = pairs01.get(p01, 0) + 1
pairs12[p01] = pairs12.get(p12, 0) + 1
pairs02[p01] = pairs02.get(p02, 0) + 1
count += 1
# each pair should be used rougly once
self.assertEquals(np.median(list(pairs01.values())), 1.0)
self.assertEquals(np.median(list(pairs02.values())), 1.0)
self.assertEquals(np.median(list(pairs12.values())), 1.0)
# now try 1000
pairs01 = {}
pairs12 = {}
pairs02 = {}
strategy = rdChemReactions.EvenSamplePairsStrategy()
strategy.Initialize(rxn, rgroups)
count = 0
while count < 1000:
v = strategy.next()
p01 = (v[0], v[1])
p12 = (v[1], v[2])
p02 = (v[0], v[2])
pairs01[p01] = pairs01.get(p01, 0) + 1
pairs12[p01] = pairs12.get(p12, 0) + 1
pairs02[p01] = pairs02.get(p02, 0) + 1
count += 1
# each pair should be used roughly 10 times
self.assertTrue(9 <= np.median(list(pairs01.values())) <= 11)
self.assertTrue(9 <= np.median(list(pairs02.values())) <= 11)
self.assertTrue(9 <= np.median(list(pairs12.values())) <= 11)
# now try 500
pairs01 = {}
pairs12 = {}
pairs02 = {}
strategy = rdChemReactions.EvenSamplePairsStrategy()
strategy.Initialize(rxn, rgroups)
count = 0
while count < 500:
v = strategy.next()
p01 = (v[0], v[1])
p12 = (v[1], v[2])
p02 = (v[0], v[2])
pairs01[p01] = pairs01.get(p01, 0) + 1
pairs12[p01] = pairs12.get(p12, 0) + 1
pairs02[p01] = pairs02.get(p02, 0) + 1
count += 1
# each pair should be used roughly 5 times
self.assertTrue(4 <= np.median(list(pairs01.values())) <= 6)
self.assertTrue(4 <= np.median(list(pairs02.values())) <= 6)
self.assertTrue(4 <= np.median(list(pairs12.values())) <= 6)
self.assertTrue("PAIRSTAT" in strategy.Stats())