Added tests for RMSD, added a testfile.

Changed RMSD class to save rmsd array as numpy file instead of text.

package/MDAnalysis/analysis/rms.py

@@ -527,7 +527,7 @@ def save(self, filename=None):
         if filename is not None:
             if self.rmsd is None:
                 raise NoDataError("rmsd has not been calculated yet")
-            np.savetxt(filename, self.rmsd)
+            np.save(filename, self.rmsd)
             logger.info("Wrote RMSD timeseries  to file %r", filename)
         return filename
 

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -26,11 +26,11 @@
 
 import os
 
-from MDAnalysisTests.datafiles import GRO, XTC, rmsfArray, PSF, DCD
+from MDAnalysisTests.datafiles import GRO, XTC, rmsfArray, rmsdArray, PSF, DCD
 from MDAnalysisTests import tempdir
 
 
-class TestRMSD(object):
+class Testrmsd(object):
     def __init__(self):
         shape = (5, 3)
         # vectors with length one
@@ -128,6 +128,30 @@ def test_with_superposition_equal(self):
         rmsd_superposition = rms.rmsd(A, B, center=True, superposition=True)
         assert_almost_equal(rmsd, rmsd_superposition)
 
+class TestRMSD(object):
+    def setUp(self):
+        self.universe = MDAnalysis.Universe(GRO, XTC)
+        self.tempdir = tempdir.TempDir()
+        self.outfile = os.path.join(self.tempdir.name, 'rmsd.xtc')
+
+    def tearDown(self):
+        del self.universe
+        del self.tempdir
+
+    def test_rmsd(self):
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe, select='name CA')
+        RMSD.run()
+        test_rmsds = np.load(rmsdArray)
+
+        assert_almost_equal(RMSD.rmsd, test_rmsds, 5,
+                            err_msg="error: rmsd profile should match test " +
+                            "values")
+
+    def test_rmsd_single_frame(self):
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe, select='name CA')
+        RMSD.run(start=5, stop=6)
+
+
 
 class TestRMSF(TestCase):
     def setUp(self):

testsuite/MDAnalysisTests/datafiles.py

@@ -104,7 +104,7 @@
     "two_water_gro_widebox",  # Issue #548
     "DLP_CONFIG", "DLP_CONFIG_order", "DLP_CONFIG_minimal",  # dl_poly 4 config file
     "DLP_HISTORY", "DLP_HISTORY_order", "DLP_HISTORY_minimal",  # dl_poly 4 history file
-    "waterPSF","waterDCD","rmsfArray",
+    "waterPSF","waterDCD","rmsfArray","rmsdArray",
     "HoomdXMLdata",
     "Make_Whole",  # for testing the function lib.mdamath.make_whole, has 9 atoms
     "Plength",
@@ -318,6 +318,7 @@
 waterDCD = resource_filename(__name__, 'data/watdyn.dcd')
 
 rmsfArray = resource_filename(__name__, 'data/adk_oplsaa_CA_rmsf.npy')
+rmsdArray = resource_filename(__name__, 'data/adk_oplsaa_CA_rmsd.npy')
 
 HoomdXMLdata = resource_filename(__name__, 'data/C12x64.xml.bz2')