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()
class Scaffold(Featurizer):
"""
Molecular scaffolds.
Parameters
----------
Parameters
----------
include_chirality : : bool, optional (default False)
Include chirality in scaffolds.
"""
name = 'scaffold'
def __init__(self, include_chirality=False):
self.include_chirality = include_chirality
self.engine = ScaffoldGenerator(include_chirality=include_chirality)
def _featurize(self, mol):
"""
Generate a 2D depiction of a molecule.
Parameters
----------
mol : RDKit Mol
Molecule.
"""
return self.engine.get_scaffold(mol)
class TestScaffoldGenerator(unittest.TestCase):
"""
Test ScaffoldGenerator.
"""
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 test_scaffolds(self):
"""
Test scaffold generation.
"""
scaffolds = [self.engine.get_scaffold(mol) for mol in self.mols]
scaffold_mols = [
Chem.MolFromSmiles(scaffold) for scaffold in scaffolds
]
for mol, ref_mol in zip(scaffold_mols, self.mols):
assert mol.GetNumAtoms() < ref_mol.GetNumAtoms()
assert scaffold_mols[0].GetNumAtoms() == 6
assert scaffold_mols[1].GetNumAtoms() == 20
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 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())
class TestScaffoldGenerator(unittest.TestCase):
"""
Test ScaffoldGenerator.
"""
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 test_scaffolds(self):
"""
Test scaffold generation.
"""
scaffolds = [self.engine.get_scaffold(mol) for mol in self.mols]
scaffold_mols = [Chem.MolFromSmiles(scaffold)
for scaffold in scaffolds]
for mol, ref_mol in zip(scaffold_mols, self.mols):
assert mol.GetNumAtoms() < ref_mol.GetNumAtoms()
assert scaffold_mols[0].GetNumAtoms() == 6
assert scaffold_mols[1].GetNumAtoms() == 20
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 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 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 generate_scaffold(smiles, include_chirality=False): """Compute the Bemis-Murcko scaffold for a SMILES string.""" mol = Chem.MolFromSmiles(smiles) engine = ScaffoldGenerator(include_chirality=include_chirality) scaffold = engine.get_scaffold(mol) return scaffold
def __init__(self, include_chirality=False):
self.include_chirality = include_chirality
self.engine = ScaffoldGenerator(include_chirality=include_chirality)