def test_2_atoms(self): smi = 'CCC' mol = Molecule().from_smiles(smi) atom_indices = [1, 2] distances = compute_atom_distance(atom_indices, mol) expected = {(1, 2): 1} self.assertEquals(distances, expected)
def _compute_agglomerate_distance(agglomerates, mol): """ Iterates over a list of lists containing atom indices. For each list the distances between the atoms is computed. A list of distances is returned. """ cython.declare( distances=list, agglomerate=list, dist=dict, ) distances = [] for agglomerate in agglomerates: dist = pathfinder.compute_atom_distance(agglomerate, mol) distances.append(dist) return distances
def _compute_agglomerate_distance(agglomerates, mol): """ Iterates over a list of lists containing atom indices. For each list the distances between the atoms is computed. A list of distances is returned. """ cython.declare( distances=list, agglomerate=list, dist=dict, ) distances = [] for agglomerate in agglomerates: dist = pathfinder.compute_atom_distance(agglomerate, mol) distances.append(dist) return distances