def test3MDLParsers(self):
fileN = os.path.join(self.dataDir, 'AmideBond.rxn')
rxn = rdChemReactions.ReactionFromRxnFile(fileN)
self.failUnless(rxn)
self.failIf(rxn._getImplicitPropertiesFlag())
self.failUnless(rxn.GetNumReactantTemplates() == 2)
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)
rxnBlock = file(fileN, 'r').read()
rxn = rdChemReactions.ReactionFromRxnBlock(rxnBlock)
self.failUnless(rxn)
self.failUnless(rxn.GetNumReactantTemplates() == 2)
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)
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 testV3000Reactions(self):
reaction = rdChemReactions.ReactionFromSmarts(
'[cH:1]1[cH:2][cH:3][cH:4][cH:5][c:6]1-[Br].[#6:7]B(O)O>>[cH:1]1[cH:2][cH:3][cH:4][cH:5][c:6]1-[#6:7]'
)
self.assertIsNotNone(reaction)
mb1 = rdChemReactions.ReactionToRxnBlock(reaction, forceV3000=True)
mb2 = rdChemReactions.ReactionToV3KRxnBlock(reaction)
self.assertEqual(mb1, mb2)
reaction2 = rdChemReactions.ReactionFromRxnBlock(mb1)
self.assertIsNotNone(reaction2)
self.assertEqual(reaction.GetNumReactantTemplates(), reaction2.GetNumReactantTemplates())
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 test21CheckRawIters(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)
reactants = rxn.GetReactants()
self.assertEquals(len(reactants), rxn.GetNumReactantTemplates())
products = rxn.GetProducts()
self.assertEquals(len(products), rxn.GetNumProductTemplates())
agents = rxn.GetAgents()
self.assertEquals(len(agents), rxn.GetNumAgentTemplates())
for i in range(rxn.GetNumReactantTemplates()):
p = rxn.GetReactantTemplate(i)
mb1 = Chem.MolToMolBlock(p)
mb2 = Chem.MolToMolBlock(reactants[i])
self.assertEquals(mb1, mb2)
def test4ErrorHandling(self):
self.failUnlessRaises(
ValueError,
lambda x='[C:1](=[O:2])Q.[N:3]>>[C:1](=[O:2])[N:3]':
rdChemReactions.ReactionFromSmarts(x))
self.failUnlessRaises(
ValueError,
lambda x='[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]Q':
rdChemReactions.ReactionFromSmarts(x))
self.failUnlessRaises(
ValueError,
lambda x='[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]>>CC':
rdChemReactions.ReactionFromSmarts(x))
block = """$RXN
ISIS 082120061354
3 1
$MOL
-ISIS- 08210613542D
3 2 0 0 0 0 0 0 0 0999 V2000
-1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0
-0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
M END
$MOL
-ISIS- 08210613542D
1 0 0 0 0 0 0 0 0 0999 V2000
2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
M END
$MOL
-ISIS- 08210613542D
3 2 0 0 0 0 0 0 0 0999 V2000
9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0
8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
M END
"""
self.failUnlessRaises(
ValueError,
lambda x=block: rdChemReactions.ReactionFromRxnBlock(x))
block = """$RXN
ISIS 082120061354
2 1
$MOL
-ISIS- 08210613542D
4 2 0 0 0 0 0 0 0 0999 V2000
-1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0
-0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
M END
$MOL
-ISIS- 08210613542D
1 0 0 0 0 0 0 0 0 0999 V2000
2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
M END
$MOL
-ISIS- 08210613542D
3 2 0 0 0 0 0 0 0 0999 V2000
9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0
8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
M END
"""
#self.failUnlessRaises(ValueError,lambda x=block:rdChemReactions.ReactionFromRxnBlock(x))
block = """$RXN
def test_rxnblock_removehs(self):
rxnblock = """$RXN
Dummy 0
Dummy 0123456789
1 1
$MOL
Dummy 01234567892D
10 10 0 0 0 0 999 V2000
7.0222 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
8.0615 -11.7783 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
7.0222 -9.6783 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
5.7231 -8.9283 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
5.7231 -7.7283 0.0000 A 0 0 0 0 0 0 0 0 0 5 0 0
4.4242 -9.6783 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0
4.4242 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
3.3849 -11.7783 0.0000 A 0 0 0 0 0 0 0 0 0 8 0 0
5.7231 -11.9283 0.0000 N 0 0 0 0 0 0 0 0 0 9 0 0
5.7231 -13.1094 0.0000 H 0 0
1 2 2 0 0 0 8
1 3 1 0 0 0 8
3 4 2 0 0 0 8
4 5 1 0 0 0 2
4 6 1 0 0 0 8
6 7 2 0 0 0 8
7 8 1 0 0 0 2
7 9 1 0 0 0 8
9 1 1 0 0 0 8
9 10 1 0
M SUB 1 9 2
M END
$MOL
Dummy 01234567892D
9 9 0 0 0 0 999 V2000
17.0447 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
18.0840 -11.7783 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
17.0447 -9.6783 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
15.7457 -8.9283 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
15.7457 -7.7283 0.0000 A 0 0 0 0 0 0 0 0 0 5 0 0
14.4467 -9.6783 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0
14.4467 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
13.4074 -11.7783 0.0000 A 0 0 0 0 0 0 0 0 0 8 0 0
15.7457 -11.9283 0.0000 N 0 0 0 0 0 0 0 0 0 9 0 0
1 2 1 0 0 0 8
1 3 1 0 0 0 8
3 4 2 0 0 0 8
4 5 1 0 0 0 2
4 6 1 0 0 0 8
6 7 2 0 0 0 8
7 8 1 0 0 0 2
7 9 1 0 0 0 8
9 1 2 0 0 0 8
M END
"""
mol = Chem.MolFromSmiles("c1(=O)nc([Cl])cc([F])[nH]1")
rxn = rdChemReactions.ReactionFromRxnBlock(rxnblock)
self.assertIsNotNone(rxn)
prods = rxn.RunReactants((mol, ))
# if the explicit hydrogen is not removed and the reactant template
# is not sanitized, the reactant template is not aromatic and our
# aromatic reactant won't match
self.assertEqual(len(prods), 0)
rxn = rdChemReactions.ReactionFromRxnBlock(rxnblock,
removeHs=True,
sanitize=True)
self.assertIsNotNone(rxn)
prods = rxn.RunReactants((mol, ))
self.assertEqual(len(prods), 2)
