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)
