def testPreprocess(self):
testFile = os.path.join(RDConfig.RDCodeDir, 'Chem', 'SimpleEnum', 'test_data', 'boronic1.rxn')
rxn = rdChemReactions.ReactionFromRxnFile(testFile)
rxn.Initialize()
res = rdChemReactions.PreprocessReaction(rxn)
self.assertEquals(res,
(0, 0, 2, 1, (((0, 'halogen.bromine.aromatic'), ), ((1, 'boronicacid'), ))))
def testGitHub1868(self):
fileN = os.path.join(self.dataDir, 'v3k.AmideBond.rxn')
for i in range(100):
_rxn = rdChemReactions.ReactionFromRxnFile(fileN)
_rxn.Initialize()
_reacts = [Chem.MolToSmarts(r) for r in _rxn.GetReactants()]
_prods = [Chem.MolToSmarts(p) for p in _rxn.GetProducts()]
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 getReaction(rfile):
rxn = rdChemReactions.ReactionFromRxnFile(rfile)
smi = rdChemReactions.ReactionToSmiles(rxn)
return storeReaction(smi, rfile), smi
def create_reaction_image(rxn_path, image_path):
from rdkit.Chem import rdChemReactions as Reactions
react = Reactions.ReactionFromRxnFile(rxn_path)
from rdkit.Chem.Draw import ReactionToImage
image = ReactionToImage(react, subImgSize=(150, 150))
image.save(image_path)
