MBAR verbosity and some bug fixes

craabreu · Nov 23, 2018 · 49bbf88 · 49bbf88
1 parent bbd4414
commit 49bbf88
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/src/mics/MBAR.py b/src/mics/MBAR.py
@@ -39,7 +39,8 @@ def __initialize__(self, mixture):
 
         mb = self.MBAR = mbar.MBAR(np.hstack(mixture.u), n,
                                    relative_tolerance=self.tol,
-                                   initial_f_k=mixture.f)
+                                   initial_f_k=mixture.f,
+                                   verbose=mics.verbose)
 
         mixture.f = mb.f_k
         mics.verbose and info("Free energies after convergence:", mixture.f)

diff --git a/src/mics/mixtures.py b/src/mics/mixtures.py
@@ -251,10 +251,9 @@ def pmf(self, potential, property, bins=10, interval=None, **constants):
             zc = zmin + delta*(i + 0.5)
             mics.verbose and info("Bin[%d]:" % (i + 1), "%s = %s" % (property, str(zc)))
             y = [np.equal(x, i).astype(np.float) for x in ibin]
-            yu, Theta = self.__reweight__(u, y)
+            (yu, Theta) = self.engine.__reweight__(self, u, y)
             if yu[1] > 0.0:
                 dyu = np.sqrt(Theta[1, 1])
-                print([zc, -np.log(yu[1]), dyu/yu[1]])
                 results.append([zc, -np.log(yu[1]), dyu/yu[1]])
 
         return pd.DataFrame(results, columns=[property, "pmf", errorTitle("pmf")])
@@ -270,7 +269,7 @@ def histograms(self, property="u0", bins=100, **constants):
         elif property == "potential":
             y = [self.u[i][i, :] for i in range(self.m)]
         else:
-            y = self.compute(property, constants)
+            y = self.__compute__(property, constants)
         ymin = min([np.amin(x) for x in y])
         ymax = max([np.amax(x) for x in y])
         delta = (ymax - ymin)/bins

diff --git a/src/mics/samples.py b/src/mics/samples.py
@@ -116,7 +116,7 @@ def subsampling(self, integratedACF=True):
         """
         n = len(self.dataset)
         if mics.verbose:
-            info("\n=== Subsampling via %s ===" % "integrated ACF" if integratedACF else "OBM")
+            info("\n=== Subsampling via %s ===" % ("integrated ACF" if integratedACF else "OBM"))
             info("Original sample size:", n)
         if integratedACF:
             y = multimap([self.acfun.lambdify()], self.dataset)