Constant epsilon tests

MDAnalysis · Jun 6, 2016 · 5e24b3a · 5e24b3a
1 parent c3f5564
commit 5e24b3a
Showing 1 changed file with 25 additions and 11 deletions.
diff --git a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py
@@ -17,23 +17,23 @@
 import numpy as np
 import MDAnalysis
 import MDAnalysis.analysis.diffusionmap as diffusionmap
-from numpy.testing import (assert_almost_equal, assert_equal)
+from numpy.testing import (assert_almost_equal, assert_equal, raises)
 
 
 from MDAnalysisTests.datafiles import PDB, XTC
 
 
 class TestDiffusionmap(object):
     def __init__(self):
-        #slow 6s test
-        #u = MDAnalysis.Universe(PSF,DCD)
-        #eg,ev=diffusionmap.diffusionmap(u)
-        #assert_equal(self.eg.shape, (98,))
-        #assert_almost_equal(self.eg[0], 1.0)
-        #assert_almost_equal(self.eg[-1],0.03174182)
-        #assert_equal(self.ev.shape, (98,98))
-        #assert_almost_equal(self.ev[0,0], .095836037343022831)
-        #faster
+        # slow 6s test
+        # u = MDAnalysis.Universe(PSF,DCD)
+        # eg,ev=diffusionmap.diffusionmap(u)
+        # assert_equal(self.eg.shape, (98,))
+        # assert_almost_equal(self.eg[0], 1.0)
+        # assert_almost_equal(self.eg[-1],0.03174182)
+        # assert_equal(self.ev.shape, (98,98))
+        # assert_almost_equal(self.ev[0,0], .095836037343022831)
+        # faster
         self.u = MDAnalysis.Universe(PDB, XTC)
         self.dmap = diffusionmap.DiffusionMap(self.u, select='backbone', k=5)
         self.dmap.run()
@@ -42,7 +42,7 @@ def __init__(self):
         self.weights = np.ones((self.dmap.nframes, ))
 
     def test_eg(self):
-        #number of frames is trajectory is now 10?
+        # number of frames is trajectory is now 10 vs. 98
         assert_equal(self.eigvals.shape, (self.dmap.nframes, ))
         assert_almost_equal(self.eigvals[0], 1.0, decimal=5)
         assert_almost_equal(self.eigvals[-1], 0.0142, decimal=3)
@@ -57,3 +57,17 @@ def test_weights(self):
         dmap2.run()
         assert_almost_equal(self.eigvals, dmap2.eigenvalues, decimal=5)
         assert_almost_equal(self.eigvects, dmap2.eigenvectors, decimal=6)
+        assert_raised
+
+    @raises(ValueError)
+    def test_wrong_weights(self):
+        dmap2 = diffusionmap.DiffusionMap(self.u, select='backbone',
+                                          weights=np.ones((2,)),
+                                          k=5)
+
+    def test_constant_epsilon(self):
+        dmap3 = diffusionmap.DiffusionMap(self.u, select='backbone', k=5,
+                                          epsilon=4.62827648)
+        dmap3.run()
+        assert_almost_equal(self.eigvals, dmap3.eigenvalues, decimal=5)
+        assert_almost_equal(self.eigvects, dmap3.eigenvectors, decimal=5)