def testFlattenedFunctionalGroupHierarchy(self):
queryDefs = FilterCatalog.GetFlattenedFunctionalGroupHierarchy()
items = sorted(queryDefs.items())
matches = [(Chem.MolFromSmiles("CCl"), [
'Halogen', 'Halogen.Aliphatic', 'Halogen.NotFluorine',
'Halogen.NotFluorine.Aliphatic'
]),
(Chem.MolFromSmiles("c1ccccc1Cl"), [
'Halogen', 'Halogen.Aromatic', 'Halogen.NotFluorine',
'Halogen.NotFluorine.Aromatic'
]),
(Chem.MolFromSmiles("c1ccccc1F"),
['Halogen', 'Halogen.Aromatic']),
(Chem.MolFromSmiles("CBr"), [
'Halogen',
'Halogen.Aliphatic',
'Halogen.Bromine',
'Halogen.Bromine.Aliphatic',
'Halogen.NotFluorine',
'Halogen.NotFluorine.Aliphatic',
])]
# test the normalized groups
for mol, res in matches:
hits = [name for name, pat in items if mol.HasSubstructMatch(pat)]
self.assertEquals(hits, res)
queryDefs = FilterCatalog.GetFlattenedFunctionalGroupHierarchy(
normalized=True)
items = sorted(queryDefs.items())
matches = [(Chem.MolFromSmiles("CCl"), [
'halogen', 'halogen.aliphatic', 'halogen.notfluorine',
'halogen.notfluorine.aliphatic'
]),
(Chem.MolFromSmiles("c1ccccc1Cl"), [
'halogen', 'halogen.aromatic', 'halogen.notfluorine',
'halogen.notfluorine.aromatic'
]),
(Chem.MolFromSmiles("c1ccccc1F"),
['halogen', 'halogen.aromatic']),
(Chem.MolFromSmiles("CBr"), [
'halogen',
'halogen.aliphatic',
'halogen.bromine',
'halogen.bromine.aliphatic',
'halogen.notfluorine',
'halogen.notfluorine.aliphatic',
])]
for mol, res in matches:
hits = [name for name, pat in items if mol.HasSubstructMatch(pat)]
self.assertEquals(hits, res)
def test17bAddRecursiveQueriesToReaction(self):
from rdkit.Chem import FilterCatalog
rxn = rdChemReactions.ReactionFromSmarts("[C:1][O:2].[N:3]>>[C:1][N:2]")
self.assertTrue(rxn)
rxn.Initialize()
rxn.GetReactantTemplate(0).GetAtomWithIdx(0).SetProp('query', 'carboxylicacid')
querydefs = {k.lower(): v
for k, v in FilterCatalog.GetFlattenedFunctionalGroupHierarchy().items()}
self.assertTrue('CarboxylicAcid' in FilterCatalog.GetFlattenedFunctionalGroupHierarchy())
rxn.AddRecursiveQueriesToReaction(querydefs, 'query')
q = rxn.GetReactantTemplate(0)
m = Chem.MolFromSmiles('C(=O)[O-].N')
self.assertTrue(m.HasSubstructMatch(q))
m = Chem.MolFromSmiles('C.N')
self.assertFalse(m.HasSubstructMatch(q))
