def get_pd_from_molecule(molecule_name, structures):
    """
    INPUT:
        molecule_name: name of the molecule as given in the structres file
        structures: structures file containing information (x, y, z coordinates) for all molecules

    OUTPUT:
        X_scaled: scaled persistence diagrams
    """
    m = structures[structures['molecule_name'] == molecule_name][['x', 'y', 'z']].to_numpy()
    m = m.reshape((1, m.shape[0], m.shape[1]))
    homology_dimensions = [0, 1, 2]
    persistenceDiagram = VietorisRipsPersistence(metric='euclidean',
                                                homology_dimensions=homology_dimensions, n_jobs=1)
    persistenceDiagram.fit(m)
    X_diagrams = persistenceDiagram.transform(m)

    diagram_scaler = diag.Scaler()
    diagram_scaler.fit(X_diagrams)
    X_scaled = diagram_scaler.transform(X_diagrams)

    return X_scaled
def test_vrp_not_fitted():
    vrp = VietorisRipsPersistence()

    with pytest.raises(NotFittedError):
        vrp.transform(X)