Fix hbond autocorrel

package/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py

@@ -212,6 +212,7 @@
 from MDAnalysis.lib.log import ProgressBar
 from MDAnalysis.lib.distances import capped_distance, calc_angles, calc_bonds
 from MDAnalysis.core.groups import requires
+from MDAnalysis.analysis.base import AnalysisBase
 
 from MDAnalysis.due import due, Doi
 
@@ -243,7 +244,7 @@ def find_hydrogen_donors(hydrogens):
     return sum(h.bonded_atoms[0] for h in hydrogens)
 
 
-class HydrogenBondAutoCorrel(object):
+class HydrogenBondAutoCorrel(AnalysisBase):
     """Perform a time autocorrelation of the hydrogen bonds in the system.
 
     Parameters
@@ -306,16 +307,8 @@ def __init__(
         pbc=True,
     ):
 
-        # warnings.warn("This class is deprecated, use analysis.hbonds.HydrogenBondAnalysis "
-        #              "which has .autocorrelation function",
-        #              category=DeprecationWarning)
-
+        super(HydrogenBondAutoCorrel, self).__init__(universe.trajectory)
         self.u = universe
-        # check that slicing is possible
-        try:
-            self.u.trajectory[0]
-        except Exception:
-            raise ValueError("Trajectory must support slicing") from None
 
         self.h = hydrogens
         self.a = acceptors
@@ -361,6 +354,12 @@ def __init__(
         }
 
     def _slice_traj(self, sample_time):
+
+        try:
+            self.u.trajectory[0]
+        except TypeError:
+            raise ValueError("Trajectory is unable to be sliced")
+
         """Set up start and end points in the trajectory for the
         different passes
         """
@@ -400,17 +399,21 @@ def _slice_traj(self, sample_time):
             )
             self._skip = 1
 
-    def run(self, force=False):
+    def run(self, start=None, stop=None, step=None, verbose=None, **kwargs):
         """Run all the required passes
 
         Parameters
         ----------
-        force : bool, optional
-            Will overwrite previous results if they exist
+        start : int, optional
+            start frame of trajectory (ignored, uses nruns logic)
+        stop : int, optional
+            end frame of trajectory (ignored, uses nruns logic)
+        step : int, optional
+            step size (ignored, uses nruns logic)
+        verbose : bool, optional
+            Show the progress bar
         """
-        # if results exist, don't waste any time
-        if self.solution["results"] is not None and not force:
-            return
+        self._slice_traj(self.sample_time)
 
         main_results = np.zeros_like(
             np.arange(self._starts[0], self._stops[0], self._skip),
@@ -423,6 +426,7 @@ def run(self, force=False):
             enumerate(zip(self._starts, self._stops)),
             total=self.nruns,
             desc="Performing run",
+            verbose=verbose,
         ):
 
             # needed else trj seek thinks a np.int64 isn't an int?
@@ -445,6 +449,8 @@ def run(self, force=False):
         )
         self.solution["results"] = main_results
 
+        return self
+
     def _single_run(self, start, stop):
         """Perform a single pass of the trajectory"""
         self.u.trajectory[start]

testsuite/MDAnalysisTests/analysis/conftest.py

@@ -15,6 +15,9 @@
 from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import (
     HydrogenBondAnalysis,
 )
+from MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel import (
+    HydrogenBondAutoCorrel,
+)
 from MDAnalysis.analysis.nucleicacids import NucPairDist
 from MDAnalysis.analysis.contacts import Contacts
 from MDAnalysis.analysis.density import DensityAnalysis
@@ -217,3 +220,34 @@ def client_InterRDF_s(request):
 @pytest.fixture(scope="module", params=params_for_cls(DistanceMatrix))
 def client_DistanceMatrix(request):
     return request.param
+
+
+# MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel
+
+
+@pytest.fixture(
+    scope="module",
+    params=params_for_cls(HydrogenBondAutoCorrel, exclude=["multiprocessing"]),
+)
+def client_HydrogenBondAutoCorrel(request):
+    return request.param
+
+
+@pytest.fixture(scope="module")
+def hbond_autocorrel(trajectory):
+    """Fixture for HydrogenBondAutoCorrel analysis"""
+    u = trajectory
+    h = u.select_atoms("name H1")
+    n = u.select_atoms("name N")
+    o = u.select_atoms("name O")
+
+    return HydrogenBondAutoCorrel(
+        u,
+        hydrogens=h,
+        donors=n,
+        acceptors=o,
+        bond_type="continuous",
+        sample_time=10.0,
+        nruns=2,
+        nsamples=10,
+    )

testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py

@@ -58,6 +58,10 @@ def nitrogens(self, u):
     def oxygens(self, u):
         return u.atoms.select_atoms("name O")
 
+    @pytest.fixture(autouse=True)
+    def client(self, client_HydrogenBondAutoCorrel):
+        self.client = client_HydrogenBondAutoCorrel
+
     # regression tests for different conditions
     def test_continuous(self, u, hydrogens, oxygens, nitrogens):
         hbond = HBAC(