added tests, fixed logger issue

MDAnalysis · May 30, 2016 · 0671f02 · 0671f02
1 parent f1dd6e2
commit 0671f02
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Showing 3 changed files with 10 additions and 11 deletions.
diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
@@ -242,7 +242,6 @@ def rotation_matrix(a, b, weights=None):
 
     rot = np.zeros(9, dtype=np.float64)
     rmsd = qcp.CalcRMSDRotationalMatrix(a.T, b.T, N, rot, weights)
-    logger.info("qcp: %d", rmsd)
     return np.matrix(rot.reshape(3, 3)), rmsd
 
 

diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py
@@ -182,15 +182,14 @@ def _prepare(self):
         self.rot = np.zeros(9)
 
     def _single_frame(self):
-        logger.info("_ts.frame {0}, numframes{1}".format(self._ts.frame, self.nframes))
         traj_index = self._ts.frame
         i_ref = np.copy(self.u.trajectory[traj_index].positions-self.atoms.center_of_mass())
 
         #diagonal entries need not be calculated due to metric(x,x) == 0 in theory
         for j in range(self.nframes-1, self._ts.frame-1, -1):
             j_ref = np.copy(self.u.trajectory[j].positions-self.atoms.center_of_mass())
             self.rmsd_matrix[traj_index, j] = self.metric(i_ref.T.astype(np.float64),\
-                j_ref.T.astype(np.float64), self.natoms, self.rot, self.weights)
+                j_ref.T.astype(np.float64), self.natoms, self.rot, None)
 
     def _conclude(self):
         self.rmsd_matrix = self.rmsd_matrix + self.rmsd_matrix.T - \

diff --git a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py
@@ -34,20 +34,21 @@ def __init__(self):
         #assert_almost_equal(self.ev[0,0], .095836037343022831)
         #faster
         u = MDAnalysis.Universe(PDB, XTC)
-        eg, ev = diffusionmap.diffusionmap(u, select = 'backbone', k = 5)
-        self.eg = eg
-        self.ev = ev
+        dmap = diffusionmap.DiffusionMap(u, select='backbone', k = 5)
+        dmap.run()
+        self.eigvals = dmap.eigenvalues
+        self.eigvects = dmap.eigenvectors
 
 
     def test_eg(self):
-        assert_equal(self.eg.shape, (10, ))
-        assert_almost_equal(self.eg[0], 1.0, decimal=5)
-        assert_almost_equal(self.eg[-1], 0.0142, decimal = 3)
+        assert_equal(self.eigvals.shape, (10, ))
+        assert_almost_equal(self.eigvals[0], 1.0, decimal=5)
+        assert_almost_equal(self.eigvals[-1], 0.0142, decimal = 3)
 
 
     def test_ev(self):
-        assert_equal(self.ev.shape, (10, 10))
-        assert_almost_equal(self.ev[0, 0], -0.3019, decimal = 2)
+        assert_equal(self.eigvects.shape, (10, 10))
+        assert_almost_equal(self.eigvects[0, 0], -0.3019, decimal = 2)