Asserted everywhere, fixed error messages.

MDAnalysis · Jul 10, 2016 · 91ba82a · 91ba82a
1 parent 40eb01c
commit 91ba82a
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Showing 2 changed files with 32 additions and 19 deletions.
diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py
@@ -351,13 +351,12 @@ 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):
-            errmsg = "Reference and trajectory atom selections do "
-                                 "not contain the same number of atoms: "
-                                 "N_ref={0:d}, N_traj={1:d}".format(
-                                     self.ref_atoms.n_atoms,
-                                     self.traj_atoms.n_atoms)
+            errmsg = ("Reference and trajectory atom selections do "+
+                      "not contain the same number of atoms: "+
+                      "N_ref={0:d}, N_traj={1:d}".format(self.ref_atoms.n_atoms,
+                                                        self.traj_atoms.n_atoms))
             logger.exception(errmsg)
-            raise SelectionError(errormsg)
+            raise SelectionError(errmsg)
         logger.info("RMS calculation for {0:d} atoms.".format(len(self.ref_atoms)))
         mass_mismatches = (np.absolute(self.ref_atoms.masses - self.traj_atoms.masses) > self.tol_mass)
         if np.any(mass_mismatches):
@@ -367,9 +366,9 @@ def __init__(self, traj, reference=None, select='all',
                 if ar.name != at.name:
                     logger.error("{0!s:>4} {1:3d} {2!s:>3} {3!s:>3} {4:6.3f}  |  {5!s:>4} {6:3d} {7!s:>3} {8!s:>3} {9:6.3f}".format(ar.segid, ar.resid, ar.resname, ar.name, ar.mass,
                                  at.segid, at.resid, at.resname, at.name, at.mass))
-            errmsg = "Inconsistent selections, masses differ by more than"
+            errmsg = ("Inconsistent selections, masses differ by more than"
                      + "{0:f}; mis-matching atoms are shown above.".format(
-                     self.tol_mass)
+                     self.tol_mass))
             logger.error(errmsg)
             raise SelectionError(errmsg)
         del mass_mismatches

diff --git a/testsuite/MDAnalysisTests/analysis/test_rms.py b/testsuite/MDAnalysisTests/analysis/test_rms.py
@@ -21,7 +21,9 @@
 import MDAnalysis as mda
 from MDAnalysis.analysis import rms, align
 
-from numpy.testing import TestCase, assert_almost_equal, raises, assert_
+from numpy.testing import (TestCase, assert_almost_equal, raises, assert_,
+                           assert_array_almost_equal)
+
 import numpy as np
 
 import os
@@ -133,7 +135,11 @@ class TestRMSD(object):
     def setUp(self):
         self.universe = MDAnalysis.Universe(PSF, DCD)
         self.tempdir = tempdir.TempDir()
-        self.outfile = os.path.join(self.tempdir.name, 'rmsd.npy')
+        self.outfile = os.path.join(self.tempdir.name, 'rmsd.txt')
+        self.correct_values = [[0, 0, 0], [49, 48.9999, 4.68953]]
+        self.correct_values_group = [[0 , 0, 0, 0, 0],
+                                     [49, 48.9999, 4.7857, 4.7002,
+                                      4.68981]]
 
     def tearDown(self):
         del self.universe
@@ -142,29 +148,37 @@ def tearDown(self):
     def test_rmsd(self):
         RMSD = MDAnalysis.analysis.rms.RMSD(self.universe, select='name CA')
         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")
-
+        assert_array_almost_equal(RMSD.rmsd, self.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)
-
+        single_frame = [[ 5, 5, 0.91544906]]
+        assert_array_almost_equal(RMSD.rmsd, single_frame, 4,
+                                  err_msg="error: rmsd profile should match" +
+                                  "test values")
 
     def test_mass_weighted_and_save(self):
         RMSD = MDAnalysis.analysis.rms.RMSD(self.universe, select='name CA')
         RMSD.run(step=49, mass_weighted= True)
-        RMSD.save()
-
+        RMSD.save(self.outfile)
+        saved = np.loadtxt(self.outfile)
+        assert_array_almost_equal(RMSD.rmsd, saved, 4,
+                                  err_msg="error: rmsd profile should match " +
+                                          "test values")
+
     def test_rmsd_group_selections(self):
         RMSD = MDAnalysis.analysis.rms.RMSD(self.universe,
                                             groupselections=
                                             ['backbone','name CA'])
         RMSD.run(step=49)
 
+        assert_array_almost_equal(RMSD.rmsd, self.correct_values_group, 4,
+                                  err_msg="error: rmsd profile should match" +
+                                  "test values")
+
 
     @raises(SelectionError)
     def test_ref_length_unequal_len(self):