assign, ref_macro_assign = tlp._metastable_system() fig1 = plt.figure() plt.plot(assign, 'o') plt.title('microstate assignments') plt.savefig('/home/shenglan/TryMSMbuilder/output/test_microassign.png') plt.close(fig1) print assign.shape print ref_macro_assign.shape print assign[0] test = PCCA(2).fit(assign) macro_assign = test.fit_transform(assign)[0] print test.n_states_ print test.mapping_ print macro_assign.shape print np.sum(macro_assign) print len(np.unique(macro_assign)) == 2 fig2 = plt.figure() plt.plot(macro_assign, 'o') plt.title('macro assignments') plt.savefig('/home/shenglan/TryMSMbuilder/output/test_macroassign.png') plt.close(fig2) macro_msm = MarkovStateModel().fit(macro_assign)