diffusionmap faster test

MDAnalysis · Jul 7, 2016 · b6f8632 · b6f8632
1 parent 6f8e8cc
commit b6f8632
Showing 1 changed file with 16 additions and 10 deletions.
diff --git a/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py b/testsuite/MDAnalysisTests/analysis/test_diffusionmap.py
@@ -17,9 +17,6 @@
 
 import MDAnalysis
 
-import MDAnalysis.analysis.align as align
-import MDAnalysis.analysis.rms as rms
-import MDAnalysis.lib.qcprot as qcp
 import MDAnalysis.analysis.diffusionmap as diffusionmap
 from MDAnalysis import SelectionError
 
@@ -31,27 +28,36 @@
 import tempdir
 from os import path
 
-from MDAnalysisTests.datafiles import PSF, DCD, FASTA
+from MDAnalysisTests.datafiles import PDB,XTC
 from MDAnalysisTests import executable_not_found, parser_not_found
 
 
 class TestDiffusionmap(object):
     def __init__(self):
-        u = MDAnalysis.Universe(PSF,DCD)
-        eg,ev=diffusionmap.diffusionmap(u)
+        #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
+        u = MDAnalysis.Universe(PDB, XTC)
+        eg,ev=diffusionmap.diffusionmap(u, select='backbone', k=5)
         self.eg=eg
         self.ev=ev
 
 
     def test_eg(self):
-        assert_equal(self.eg.shape, (98,))
+        assert_equal(self.eg.shape, (10,))
         assert_almost_equal(self.eg[0], 1.0)
-        assert_almost_equal(self.eg[-1],0.03174182)
+        assert_almost_equal(self.eg[-1],0.03661048812801191)
 
 
     def test_ev(self):
-        assert_equal(self.ev.shape, (98,98))
-        assert_almost_equal(self.ev[0,0], .095836037343022831)
+        assert_equal(self.ev.shape, (10,10))
+        assert_almost_equal(self.ev[0,0], -0.30796900898350615)