fix hbond iterator

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
 
  * 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 #****)
  * DSSP now explicitly checks for a minimum of 6 residues and raises a clear
    error message, unlike the previous behavior where it would fail with an
    incomprehensible broadcasting error at execution time (Issue #5046, PR #5163)

package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py

@@ -912,8 +912,16 @@ def count_by_time(self):
              the number of hydrogen bonds over time.
         """
 
-        indices, tmp_counts = np.unique(self.results.hbonds[:, 0], axis=0,
-                                        return_counts=True)
+        indices, tmp_counts = np.unique(
+            self.results.hbonds[:, 0], axis=0, return_counts=True
+        )
+
+        # if we pass a specific subset of frames there won't be a start / end frame
+        # so we do a manual lookup and return instead. some frames might be zero
+        # so they would be missing from the np.unique return
+        if self.start is None:
+            count_lookup = {idx: count for idx, count in zip(indices, tmp_counts)}
+            return np.array([count_lookup.get(i, 0) for i in range(len(self.frames))])
 
         indices -= self.start
         indices /= self.step

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, 0, 0, 3, 3])
+        )