def load_traj(): "Load up a 3 frame, 4 atom trajectory for testing" empty = np.array([]) frame0 = np.array([[1, 1, 1], [2, 2, 2], [3, 3, 3], [4, 4, 4]]) frame1 = np.array([[-1, -1, -1], [-2, -2, -2], [-3, -3, -3], [-4, -4, -4]]) frame2 = np.array([[1, 2, 1], [3, 2, 2], [3, 4, 3], [5, 4, 4]]) traj = Trajectory({ 'ChainID': empty, 'AtomNames': empty, 'ResidueNames': empty, 'ResidueID': empty, 'AtomID': empty, 'XYZList': np.empty(shape=(3, 4, 3)) }) traj['XYZList'][0] = frame0 traj['XYZList'][1] = frame1 traj['XYZList'][2] = frame2 return traj import functools import nose