def test_chiral_scaffolds(self):
"""
Test chiral scaffold generation.
"""
achiral_scaffold = self.engine.get_scaffold(self.mols[1])
self.engine = ScaffoldGenerator(include_chirality=True)
chiral_scaffold = self.engine.get_scaffold(self.mols[1])
assert '@' not in achiral_scaffold
assert '@' in chiral_scaffold
assert (Chem.MolFromSmiles(achiral_scaffold).GetNumAtoms() ==
Chem.MolFromSmiles(chiral_scaffold).GetNumAtoms())
def setUp(self):
"""
Set up tests.
"""
smiles = [
'CC(=O)OC1=CC=CC=C1C(=O)O',
'CN1C=C(C2=CC=CC=C21)C(=O)[C@@H]3CCC4=C(C3)NC=N4'
]
names = ['aspirin', 'ramosetron']
self.mols = []
for this_smiles, name in zip(smiles, names):
mol = Chem.MolFromSmiles(this_smiles)
mol.SetProp('_Name', name)
self.mols.append(mol)
self.engine = ScaffoldGenerator()
def get_scaffolds(mols, include_chirality=False):
"""
Get Murcko scaffolds for molecules.
Murcko scaffolds are described in DOI: 10.1021/jm9602928. They are
essentially that part of the molecule consisting of rings and the linker
atoms between them.
Parameters
----------
mols : array_like
Molecules.
include_chirality : bool, optional (default False)
Whether to include chirality in scaffolds.
"""
print "Generating molecule scaffolds..."
engine = ScaffoldGenerator(include_chirality=include_chirality)
scaffolds = []
for mol in mols:
scaffolds.append(engine.get_scaffold(mol))
scaffolds = np.asarray(scaffolds)
return scaffolds
def __init__(self, include_chirality=False):
self.include_chirality = include_chirality
self.engine = ScaffoldGenerator(include_chirality=include_chirality)
