def run_pcca_plus(num_macrostates, assignments, tProb, output_dir, flux_cutoff=0.0, objective_function="crispness", do_minimization=True): MacroAssignmentsFn = os.path.join(output_dir, "MacroAssignments.h5") MacroMapFn = os.path.join(output_dir, "MacroMapping.dat") ChiFn = os.path.join(output_dir, 'Chi.dat') AFn = os.path.join(output_dir, 'A.dat') arglib.die_if_path_exists([MacroAssignmentsFn, MacroMapFn, ChiFn, AFn]) logger.info("Running PCCA+...") A, chi, vr, MAP = lumping.pcca_plus(tProb, num_macrostates, flux_cutoff=flux_cutoff, do_minimization=do_minimization, objective_function=objective_function) MSMLib.apply_mapping_to_assignments(assignments, MAP) np.savetxt(ChiFn, chi) np.savetxt(AFn, A) np.savetxt(MacroMapFn, MAP, "%d") msmbuilder.io.saveh(MacroAssignmentsFn, assignments) logger.info('Saved output to: %s, %s, %s, %s', ChiFn, AFn, MacroMapFn, MacroAssignmentsFn)
def run_pcca_plus(num_macrostates, assignments, tProb, flux_cutoff=0.0, objective_function="crispness",do_minimization=True): logger.info("Running PCCA+...") A, chi, vr, MAP = lumping.pcca_plus(tProb, num_macrostates, flux_cutoff=flux_cutoff, do_minimization=do_minimization, objective_function=objective_function) MSMLib.apply_mapping_to_assignments(assignments, MAP) return chi, A, MAP, assignments
def run_pcca_plus(num_macrostates, assignments, tProb, output_dir, flux_cutoff=0.0,objective_function="crispness",do_minimization=True): MacroAssignmentsFn = os.path.join(output_dir, "MacroAssignments.h5") MacroMapFn = os.path.join(output_dir, "MacroMapping.dat") ChiFn = os.path.join(output_dir, 'Chi.dat') AFn = os.path.join(output_dir, 'A.dat') arglib.die_if_path_exists([MacroAssignmentsFn, MacroMapFn, ChiFn, AFn]) logger.info("Running PCCA+...") A, chi, vr, MAP = lumping.pcca_plus(tProb, num_macrostates, flux_cutoff=flux_cutoff, do_minimization=do_minimization, objective_function=objective_function) MSMLib.apply_mapping_to_assignments(assignments, MAP) np.savetxt(ChiFn, chi) np.savetxt(AFn, A) np.savetxt(MacroMapFn, MAP,"%d") msmbuilder.io.saveh(MacroAssignmentsFn, assignments) logger.info('Saved output to: %s, %s, %s, %s', ChiFn, AFn, MacroMapFn, MacroAssignmentsFn)