FIX: Handle a non-linear FrameIterator in HydrogenBondAnalysis (#5202)

* Fixes #5200
* Refactor count_by_time() to handle returning values on a non-linear FrameIterator
  - refactored whole function
  - returned counts array is now guaranteed to have the same shape as frames and elements correspond
    directly to each other
* add test
* update changelog

Author: BradyAJohnston

package/AUTHORS

@@ -266,6 +266,7 @@ Chronological list of authors
   - Pranay Pelapkar
   - Shreejan Dolai
   - Tanisha Dubey
+  - Brady Johnston
 
 External code
 -------------

package/CHANGELOG

@@ -15,11 +15,13 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
-         spyke7, talagayev, tanii1125
+         spyke7, talagayev, tanii1125, BradyAJohnston
 
  * 2.11.0
 
 Fixes
+ * HydrogenBondAnalysis: Fixed `count_by_time()` when using `run(FrameIterator)` that
+   results in `self.start` and `self.end` being None (Issue #5200, PR #5202)
  * NoJump shows a more informative message and fails  when applied
    outside of the first frame (Issue #4915, PR #5201)
  * DSSP now explicitly checks for a minimum of 6 residues and raises a clear

package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py

@@ -911,17 +911,13 @@ def count_by_time(self):
              Can be used along with :attr:`HydrogenBondAnalysis.times` to plot
              the number of hydrogen bonds over time.
         """
+        hbond_frames = self.results.hbonds[:, 0].astype(int)
+        frame_unique, frame_counts = np.unique(hbond_frames, return_counts=True)
+        frame_min, frame_max = self.frames.min(), self.frames.max()
 
-        indices, tmp_counts = np.unique(self.results.hbonds[:, 0], axis=0,
-                                        return_counts=True)
-
-        indices -= self.start
-        indices /= self.step
-
-        counts = np.zeros_like(self.frames)
-        counts[indices.astype(np.intp)] = tmp_counts
-
-        return counts
+        counts = np.zeros(frame_max - frame_min + 1, dtype=int)
+        counts[frame_unique - frame_min] = frame_counts
+        return counts[self.frames - frame_min]
 
     def count_by_type(self):
         """Counts the total number of each unique type of hydrogen bond.

testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py

@@ -760,3 +760,23 @@ def test_hbond_analysis(self, universe, client_HydrogenBondAnalysis):
         assert h.hydrogens_sel == ""
         assert h.acceptors_sel == ""
         assert h.results.hbonds.size == 0
+
+
+class TestHydrogenBondAnalysisFrameIterator:
+    @staticmethod
+    @pytest.fixture(scope="class")
+    def universe():
+        return MDAnalysis.Universe(waterPSF, waterDCD)
+
+    def test_frame_iterator(self, universe):
+        frames = np.array([0, 1, 2, 5, 6, 7, 8])
+        hbonds = HydrogenBondAnalysis(
+            universe=universe,
+            hydrogens_sel="name H1 H2",
+            acceptors_sel="name OH2",
+            update_selections=False,
+        )
+        hbonds.run(frames=frames)
+        assert np.array_equal(
+            hbonds.count_by_time(), np.array([2, 1, 4, 3, 3, 2, 2])
+        )