Updated tests, updated docs

MDAnalysis · Jul 16, 2016 · cc384f1 · cc384f1
1 parent b299d89
commit cc384f1
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Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py
@@ -280,7 +280,7 @@ class DiffusionMap(object):
 
     Attributes
     ----------
-    eigenvalues: array
+    eigenvalues: array ()
         Eigenvalues of the diffusion map
 
     Methods
@@ -357,7 +357,7 @@ def transform(self, n_eigenvectors, time):
             values, more dominant eigenvectors determine diffusion distance.
         Return
         ------
-        diffusion_space : array
+        diffusion_space : array (n_frames, n_eigenvectors)
             The diffusion map embedding as defined by [Ferguson1]_.
         """
         return (self._eigenvectors[1:n_eigenvectors+1,].T *

diff --git a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py
@@ -42,12 +42,22 @@ def test_dist_weights(self):
         backbone = self.u.select_atoms('backbone')
         weights_atoms = np.ones(len(backbone.atoms))
         self.dist = diffusionmap.DistanceMatrix(self.u, select='backbone',
-                                                weights=weights_atoms)
+                                                weights=weights_atoms,
+                                                step=3)
         self.dist.run()
+        self.dmap = diffusionmap.DiffusionMap(self.dist)
+        self.dmap.run()
+        assert_array_almost_equal(self.dmap.eigenvalues, [1,1,1,1], 4)
+        assert_array_almost_equal(self.dmap._eigenvectors,
+                                  ([[ 0, 0, 1, 0],
+                                    [ 0, 0, 0, 1],
+                                    [ -.707,-.707, 0, 0],
+                                    [  .707,-.707, 0, 0]]) ,2)
 
     def test_different_steps(self):
         self.dmap = diffusionmap.DiffusionMap(self.u, select='backbone', step=3)
         self.dmap.run()
+        assert_equal(self.dmap._eigenvectors.shape, (4,4))
 
     def test_transform(self):
         self.n_eigenvectors = 4