def test_occupancy(self):
"""
Test ShapeGrid with occupancy featurization.
"""
self.engine = ShapeGrid(featurization='occupancy')
features = self.engine(self.mols)
assert features.shape == (len(self.mols), self.max_confs, 81, 81, 81)
def test_distance(self):
"""
Test ShapeGrid with distances featurization.
"""
self.engine = ShapeGrid(featurization='distance')
features = self.engine(self.mols)
assert features.shape == (len(self.mols), self.max_confs, 81, 81, 81)
def test_embed_mol_in_grid_hydrogens(self):
"""
Test ShapeGrid.embed_mol_in_grid with hydrogens=True.
"""
self.engine = ShapeGrid(hydrogens=True)
grid_mol = self.engine.embed_mol_in_grid(self.mols[0], conf_id=0)
num_atoms = self.mols[0].GetNumAtoms()
assert grid_mol.get_num_atoms() == num_atoms
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
mol = Chem.MolFromSmiles(smiles)
engine = conformers.ConformerGenerator(max_conformers=3)
self.mols = [engine.generate_conformers(mol)]
for mol in self.mols:
assert mol.GetNumConformers() > 0
self.max_confs = max([mol.GetNumConformers() for mol in self.mols])
self.engine = ShapeGrid()
class TestShapeGrid(unittest.TestCase):
"""
Tests for ShapeGrid featurizer.
"""
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
mol = Chem.MolFromSmiles(smiles)
engine = conformers.ConformerGenerator(max_conformers=3)
self.mols = [engine.generate_conformers(mol)]
for mol in self.mols:
assert mol.GetNumConformers() > 0
self.max_confs = max([mol.GetNumConformers() for mol in self.mols])
self.engine = ShapeGrid()
def test_distance(self):
"""
Test ShapeGrid with distances featurization.
"""
self.engine = ShapeGrid(featurization='distance')
features = self.engine(self.mols)
assert features.shape == (len(self.mols), self.max_confs, 81, 81, 81)
def test_occupancy(self):
"""
Test ShapeGrid with occupancy featurization.
"""
self.engine = ShapeGrid(featurization='occupancy')
features = self.engine(self.mols)
assert features.shape == (len(self.mols), self.max_confs, 81, 81, 81)
def test_embed_mol_in_grid(self):
"""
Test ShapeGrid.embed_mol_in_grid.
"""
grid_mol = self.engine.embed_mol_in_grid(self.mols[0], conf_id=0)
num_atoms = Chem.RemoveHs(self.mols[0]).GetNumAtoms()
assert num_atoms < self.mols[0].GetNumAtoms()
assert grid_mol.get_num_atoms() == num_atoms
def test_embed_mol_in_grid_hydrogens(self):
"""
Test ShapeGrid.embed_mol_in_grid with hydrogens=True.
"""
self.engine = ShapeGrid(hydrogens=True)
grid_mol = self.engine.embed_mol_in_grid(self.mols[0], conf_id=0)
num_atoms = self.mols[0].GetNumAtoms()
assert grid_mol.get_num_atoms() == num_atoms