convert RMSF to AnalysisBase

package/MDAnalysis/analysis/rms.py

@@ -537,32 +537,8 @@ def save(self, filename=None):
         return filename
 
 
-class RMSF(object):
-    """Class to perform RMSF analysis on a set of atoms across a trajectory.
-
-    Run the analysis with :meth:`RMSF.run`, which stores the results
-    in the array :attr:`RMSF.rmsf`.
-
-    This class performs no coordinate transforms; RMSFs are obtained from atom
-    coordinates as-is.
-
-    .. versionadded:: 0.11.0
-    """
-
-    def __init__(self, atomgroup):
-        """Calculate RMSF of given atoms across a trajectory.
-
-        Parameters
-        ----------
-        atomgroup : mda.AtomGroup
-                AtomGroup to obtain RMSF for
-
-        """
-        self.atomgroup = atomgroup
-        self._rmsf = None
-
-    def run(self, start=None, stop=None, step=None, progout=10, quiet=False):
-        """Calculate RMSF of given atoms across a trajectory.
+class RMSF(AnalysisBase):
+    """Calculate RMSF of given atoms across a trajectory.
 
         This method implements an algorithm for computing sums of squares while
         avoiding overflows and underflows [Welford1962]_.
@@ -589,40 +565,27 @@ def run(self, start=None, stop=None, step=None, progout=10, quiet=False):
         .. [Welford1962] B. P. Welford (1962). "Note on a Method for
            Calculating Corrected Sums of Squares and Products." Technometrics
            4(3):419-420.
-        """
-        traj = self.atomgroup.universe.trajectory
-        start, stop, step = traj.check_slice_indices(start, stop, step)
-        sumsquares = np.zeros((self.atomgroup.n_atoms, 3))
-        means = np.array(sumsquares)
-
-        if quiet:
-            progout = None
-
-        # set up progress output
-        if progout:
-            percentage = ProgressMeter(self.atomgroup.universe.trajectory.n_frames,
-                                       interval=progout)
-        else:
-            percentage = ProgressMeter(self.atomgroup.universe.trajectory.n_frames,
-                                       quiet=True)
+    """
+    def __init__(self, atomgroup, weights=None, **kwargs):
+        super(RMSF, self).__init__(atomgroup.universe.trajectory, **kwargs)
+        self.atomgroup = atomgroup
+        if weights == 'mass':
+            weights = self.atomgroup.masses
+        self.weights = weights
 
-        for k, ts in enumerate(self.atomgroup.universe.trajectory[start:stop:step]):
-            sumsquares += (k/(k + 1.0)) * (self.atomgroup.positions - means)**2
-            means = (k * means + self.atomgroup.positions)/(k + 1)
+    def _prepare(self):
+        self.sumsquares = np.zeros((self.atomgroup.n_atoms, 3))
+        self.mean = self.sumsquares.copy()
 
-            percentage.echo(ts.frame)
+    def _single_frame(self):
+        k = self._frame_index
+        self.sumsquares += (k / (k+1.0)) * (self.atomgroup.positions - self.mean) ** 2
+        self.mean = (k * self.mean + self.atomgroup.positions) / (k + 1)
 
-        rmsf = np.sqrt(sumsquares.sum(axis=1)/(k + 1))
+    def _conclude(self):
+        k = self._frame_index
+        self.rmsf = np.sqrt(self.sumsquares.sum(axis=1) / (k + 1))
 
-        if not (rmsf >= 0).all():
+        if not (self.rmsf >= 0).all():
             raise ValueError("Some RMSF values negative; overflow " +
                              "or underflow occurred")
-
-        self._rmsf = rmsf
-
-    @property
-    def rmsf(self):
-        """RMSF data; only available after using :meth:`RMSF.run`
-
-        """
-        return self._rmsf

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -140,6 +140,7 @@ 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):
     @dec.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
@@ -227,6 +228,7 @@ def test_save_before_run(self):
         RMSD = MDAnalysis.analysis.rms.RMSD(self.universe)
         RMSD.save('blah')
 
+
 class TestRMSF(TestCase):
     def setUp(self):
         self.universe = MDAnalysis.Universe(GRO, XTC)
@@ -239,16 +241,16 @@ def tearDown(self):
 
     def test_rmsf(self):
         rmsfs = MDAnalysis.analysis.rms.RMSF(self.universe.select_atoms('name CA'))
-        rmsfs.run(quiet=True)
+        rmsfs.run()
         test_rmsfs = np.load(rmsfArray)
 
         assert_almost_equal(rmsfs.rmsf, test_rmsfs, 5,
                             err_msg="error: rmsf profile should match test " +
                             "values")
 
     def test_rmsf_single_frame(self):
-        rmsfs = MDAnalysis.analysis.rms.RMSF(self.universe.select_atoms('name CA'))
-        rmsfs.run(start=5, stop=6, quiet=True)
+        rmsfs = MDAnalysis.analysis.rms.RMSF(self.universe.select_atoms('name CA'), start=5, stop=6)
+        rmsfs.run()
 
         assert_almost_equal(rmsfs.rmsf, 0, 5,
                             err_msg="error: rmsfs should all be zero")
@@ -261,7 +263,7 @@ def test_rmsf_identical_frames(self):
 
         self.universe = MDAnalysis.Universe(GRO, self.outfile)
         rmsfs = MDAnalysis.analysis.rms.RMSF(self.universe.select_atoms('name CA'))
-        rmsfs.run(quiet=True)
+        rmsfs.run()
 
         assert_almost_equal(rmsfs.rmsf, 0, 5,
                             err_msg="error: rmsfs should all be 0")