fixed MSM coarse-graining

markovmodel · Feb 18, 2016 · 82dd713 · 82dd713
1 parent ff0c55b
commit 82dd713
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/pyemma/msm/estimators/maximum_likelihood_hmsm.py b/pyemma/msm/estimators/maximum_likelihood_hmsm.py
@@ -200,6 +200,7 @@ def _estimate(self, dtrajs):
 
         # INIT HMM
         from bhmm import init_discrete_hmm
+        from pyemma.msm.estimators import MaximumLikelihoodMSM
         if self.msm_init=='largest-strong':
             hmm_init = init_discrete_hmm(dtrajs_lagged_strided, self.nstates, lag=1,
                                          reversible=self.reversible, stationary=True, regularize=True,
@@ -208,7 +209,7 @@ def _estimate(self, dtrajs):
             hmm_init = init_discrete_hmm(dtrajs_lagged_strided, self.nstates, lag=1,
                                          reversible=self.reversible, stationary=True, regularize=True,
                                          method='spectral', separate=self.separate)
-        elif issubclass(self.msm_init.__class__, MaximumLikelihoodHMSM):  # initial MSM given.
+        elif issubclass(self.msm_init.__class__, MaximumLikelihoodMSM):  # initial MSM given.
             from bhmm.init.discrete import init_discrete_hmm_spectral
             p0, P0, pobs0 = init_discrete_hmm_spectral(self.msm_init.count_matrix_full, self.nstates,
                                                        reversible=self.reversible, stationary=True,

diff --git a/pyemma/msm/estimators/maximum_likelihood_msm.py b/pyemma/msm/estimators/maximum_likelihood_msm.py
@@ -703,7 +703,7 @@ def hmm(self, nhidden):
         # if hmm.nstates = msm.nstates there is no problem. Otherwise, check spectral gap
         if self.nstates > nhidden:
             timescale_ratios = self.timescales()[:-1] / self.timescales()[1:]
-            if timescale_ratios[self.nstates-2] < 1.5:
+            if timescale_ratios[nhidden-2] < 1.5:
                 self.logger.warning('Requested coarse-grained model with ' + str(nhidden) + ' metastable states at ' +
                                  'lag=' + str(self.lag) + '.' + 'The ratio of relaxation timescales between ' +
                                  str(nhidden) + ' and ' + str(nhidden+1) + ' states is only ' +