g# This is a combination of 6 commits.

Test group selections

Reverted back to save.
Updated test coverage for exceptions.
Found some errors with logging requiring a message.

Reverted inclusion of unnecessary RMSD array

Fixed a small error and combined save and mass_weighted test

No Data Error

Cover save

package/CHANGELOG

@@ -25,7 +25,6 @@ Fixes
     next (Issue #869)
   * Display of Deprecation warnings doesn't affect other modules anymore (Issue #754)
   * Changed nframes to n_frames in analysis modules for consistency (Issue #890)
-  * Removed call to protected process_selection function in RMSD
 
 Changes
   * Added protected variable _frame_index to to keep track of frame iteration

package/MDAnalysis/analysis/rms.py

@@ -83,7 +83,7 @@
 
    import matplotlib.pyplot as plt
    rmsd = R.rmsd.T   # transpose makes it easier for plotting
-   time = rmsd[1]
+   time = rmsd[1]facebook.com
    fig = plt.figure(figsize=(4,4))
    ax = fig.add_subplot(111)
    ax.plot(time, rmsd[2], 'k-',  label="all")
@@ -351,7 +351,7 @@ def __init__(self, traj, reference=None, select='all',
         self.ref_atoms = self.reference.select_atoms(*self.select['reference'])
         self.traj_atoms = self.universe.select_atoms(*self.select['mobile'])
         if len(self.ref_atoms) != len(self.traj_atoms):
-            logger.exception()
+            logger.exception('SelectionError: ref_atoms, traj_atoms unequal')
             raise SelectionError("Reference and trajectory atom selections do "
                                  "not contain the same number of atoms: "
                                  "N_ref={0:d}, N_traj={1:d}".format(
@@ -386,7 +386,7 @@ def __init__(self, traj, reference=None, select='all',
         for igroup, (sel, atoms) in enumerate(zip(self.groupselections,
                                                   self.groupselections_atoms)):
             if len(atoms['mobile']) != len(atoms['reference']):
-                logger.exception()
+                logger.exception('SelectionError: Group Selection')
                 raise SelectionError(
                     "Group selection {0}: {1} | {2}: Reference and trajectory "
                     "atom selections do not contain the same number of atoms: "
@@ -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.save(filename, self.rmsd)
+            np.savetxt(filename, self.rmsd)
             logger.info("Wrote RMSD timeseries  to file %r", filename)
         return filename
 

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -26,7 +26,8 @@
 
 import os
 
-from MDAnalysisTests.datafiles import GRO, XTC, rmsfArray, rmsdArray, PSF, DCD
+from MDAnalysis.exceptions import SelectionError, NoDataError
+from MDAnalysisTests.datafiles import GRO, XTC, rmsfArray, PSF, DCD
 from MDAnalysisTests import tempdir
 
 
@@ -130,7 +131,7 @@ def test_with_superposition_equal(self):
 
 class TestRMSD(object):
     def setUp(self):
-        self.universe = MDAnalysis.Universe(GRO, XTC)
+        self.universe = MDAnalysis.Universe(PSF, DCD)
         self.tempdir = tempdir.TempDir()
         self.outfile = os.path.join(self.tempdir.name, 'rmsd.npy')
 
@@ -140,26 +141,58 @@ def tearDown(self):
 
     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,
+        RMSD.run(step=49)
+        correct_values = [[  0, 0, 0],
+                          [  49, 48.9999, 4.68953]]
+        assert_almost_equal(RMSD.rmsd, correct_values, 4,
                             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)
 
-    def test_rmsd_save(self):
+
+    def test_mass_weighted_and_save(self):
         RMSD = MDAnalysis.analysis.rms.RMSD(self.universe, select='name CA')
-        RMSD.run()
-        RMSD.save(self.outfile)
-        saved_file = np.load(self.outfile)
-        test_rmsds = np.load(rmsdArray)
-        assert_almost_equal(saved_file, test_rmsds, 5,
-                            err_msg="error: rmsd profile should match test " +
-                            "values")
+        RMSD.run(step=49, mass_weighted= True)
+        RMSD.save()
+
+    def test_rmsd_group_selections(self):
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe,
+                                            groupselections=
+                                            ['backbone','name CA'])
+        RMSD.run(step=49)
+
+
+    @raises(SelectionError)
+    def test_ref_length_unequal_len(self):
+        reference = MDAnalysis.Universe(PSF, DCD)
+        reference.atoms = reference.atoms[:-1]
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe,
+                                            reference=reference)
+
+    @raises(SelectionError)
+    def test_mass_mismatches(self):
+        reference = MDAnalysis.Universe(PSF, DCD)
+        reference.atoms.masses = 10
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe,
+                                            reference=reference)
+
+
+    @raises(SelectionError)
+    def test_group_selections_unequal_len(self):
+        reference = MDAnalysis.Universe(PSF, DCD)
+        reference.atoms[0].resname='NOTMET'
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe,
+                                            reference=reference,
+                                            groupselections=
+                                            ['resname MET','type NH3'])
+    @raises(NoDataError)
+    def test_save_before_run(self):
+        RMSD = MDAnalysis.analysis.rms.RMSD(self.universe)
+        RMSD.save('blah')
 
 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","rmsdArray",
+    "waterPSF","waterDCD","rmsfArray",
     "HoomdXMLdata",
     "Make_Whole",  # for testing the function lib.mdamath.make_whole, has 9 atoms
     "Plength",
@@ -318,7 +318,6 @@
 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')