def test_from_msm():
assignments, _ = _metastable_system()
msm = MarkovStateModel()
msm.fit(assignments)
pcca = PCCA.from_msm(msm, 2)
msm = MarkovStateModel()
msm.fit(assignments)
pccaplus = PCCAPlus.from_msm(msm, 2)
def test_from_msm():
assignments, _ = _metastable_system()
msm = MarkovStateModel()
msm.fit(assignments)
pcca = PCCA.from_msm(msm, 2)
msm = MarkovStateModel()
msm.fit(assignments)
pccaplus = PCCAPlus.from_msm(msm, 2)
for this_assign in geo_assign:
this_list = []
for this_item in this_assign:
try:
this_list.append(partial_raw_to_micro_mapping[this_item])
except KeyError:
pass
partial_micro_assign.append(this_list)
unique_assign = []
for this_assign in partial_micro_assign:
unique_assign.extend(np.unique(this_assign))
unique_assign = np.unique(np.array(unique_assign))
N_MACRO = 10
pcca = PCCA.from_msm(micro_msm,N_MACRO)
micro_to_macro_mapping = {}
for ii in range(len(pcca.microstate_mapping_)):
micro_to_macro_mapping[ii] = pcca.microstate_mapping_[ii]
# for n macrostates, any frame that does not belong to any microstate and thus macrostate is labeled to be in the nth macrostate
for ii in range(len(raw_clusters)):
if ii in micro_to_macro_mapping.keys():
pass
else:
micro_to_macro_mapping[ii] = N_MACRO
# assignments to macro states
macro_assign = []
for this_assign in geo_assign:
for this_assign in geo_assign:
this_list = []
for this_item in this_assign:
try:
this_list.append(partial_raw_to_micro_mapping[this_item])
except KeyError:
pass
partial_micro_assign.append(this_list)
unique_assign = []
for this_assign in partial_micro_assign:
unique_assign.extend(np.unique(this_assign))
unique_assign = np.unique(np.array(unique_assign))
N_MACRO = 5
pcca = PCCA.from_msm(micro_msm, N_MACRO)
micro_to_macro_mapping = {}
for ii in range(len(pcca.microstate_mapping_)):
micro_to_macro_mapping[ii] = pcca.microstate_mapping_[ii]
# for n macrostates, any frame that does not belong to any microstate and thus macrostate is labeled to be in the nth macrostate
for ii in range(len(raw_clusters)):
if ii in micro_to_macro_mapping.keys():
pass
else:
micro_to_macro_mapping[ii] = N_MACRO
# assignments to macro states
macro_assign = []
for this_assign in geo_assign:
