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