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_list_of_arrays():
X_2 = np.array([[0., 1.], [1., 2.]])
X_list = [X[0].copy(), X_2]
vrp = VietorisRipsPersistence()
vrp.fit(X_list)