Fix PersistenceLength normalization for sliced run (Issue #5453)

PersistenceLength._conclude() normalized bond_autocorrelation using
the total number of frames in the trajectory instead of the number
of frames actually analyzed. This gave wrong results whenever run()
was called with start, stop, or step. Now uses self.n_frames, which
AnalysisBase already tracks for this purpose. Added a regression
test comparing full trajectory and sliced runs against manually
computed normalization values.

Author: srikarjy

package/AUTHORS

@@ -284,6 +284,7 @@ Chronological list of authors
   - Sai Udayagiri
   - Apoorva Verma
   - Aryaman Chaudhri
+  - Srikar JY
 
 External code
 -------------

package/CHANGELOG

@@ -18,11 +18,12 @@ The rules for this file:
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
          ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
-         raulloiscuns, Aryaman-Chaudhri
+         raulloiscuns, Aryaman-Chaudhri, srikarjy
 
  * 2.11.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
  * `AtomGroup.rotate()` and the `rotateby` trajectory transformation now
    also rotate velocities and forces besides positions. This also affects
    `MDAnalysis.analysis.align.alignto()` and `AlignTraj`, since they
@@ -120,6 +121,7 @@ Deprecations
  * 2.10.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
  * Fix incorrect conversion factors for speed units A/fs, A/us, A/ms
    in MDAnalysis.units (Issue #5051, PR #5053)
  * `analysis.polymer.sort_backbone` is now working for discontinuous polymers
@@ -212,6 +214,7 @@ Deprecations
  * 2.9.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
  * Add support for TPR files produced by GROMACS 2024.4 and GROMACS 2025.0
  * Fixes invalid default unit from Angstrom to Angstrom^{-3} for
    convert_density() function. (Issue #4829)
@@ -254,6 +257,7 @@ Changes
  * 2.8.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
  * Fix `test_imd.py` test failures after imdclient 0.2.4
    increased default timeout by ensuring EOF sent (Issue #5442, PR #5443)
  * Allows bond/angle/dihedral connectivity to be guessed additively with
@@ -389,6 +393,7 @@ Deprecations
  * 2.7.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fix doctest errors of lib/transformations.py (Issue #3925, PR #4370)
   * Fix documentation building errors due to `html_static_path` and unindented
     block of code (Issue #4362, PR #4365)
@@ -458,6 +463,7 @@ Deprecations
  * 2.6.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fix Atom type guessing error (PR #4168, Issue #4167)
 
 Enhancements
@@ -482,6 +488,7 @@ Deprecations
  * 2.6.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fix AtomGroup.center_of_charge(..., unwrap=True) giving
     inconsistent (but scientifically correct) results on Intel macOS
     (Issue #4211)
@@ -541,6 +548,7 @@ Deprecations
  * 2.5.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed using 'rb' mode inside GSDReader to avoid FutureWarning from GSDFile (Issue #4152)
   * Fixed ChainReader performing transformations correctly across boundaries in the individual trajectories
     (Issue #3657 #4008 PR #3906)
@@ -631,6 +639,7 @@ Changes
  * 2.4.3
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed DCD reading for large (>2Gb) files (Issue #4039).  This was broken
     for versions 2.4.0, 2.4.1 and 2.4.2
   * Fix element parsing from PSF files tests read via Parmed (Issue #4015)
@@ -641,6 +650,7 @@ Fixes
  * 2.4.2
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * np.histogramdd calls in :class:`DensityAnalysis` now pass the `density`
     argument rather than the NumPy 1.24 removed `normed` (PR #3976)
   * visualization.streamlines_3D and visualization.streamlines no longer
@@ -653,6 +663,7 @@ Fixes
  * 2.4.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
 * Fixes pyproject.toml minimum pin for biopython
 
 
@@ -662,6 +673,7 @@ Fixes
  * 2.4.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Update hbond analysis doc string to use exclusive bound language
     (Issue #3847)
   * XTC and TRR readers now fail with IOError when a status except EOK (=0) is
@@ -755,6 +767,7 @@ Deprecations
  * 2.3.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixes awk call in deploy.yaml tests for macos runners (Issue #3693)
   * add a 0.5 for correct midpoints in hole analysis (Issue #3715)
   * Fix reading error when PDB CONECT records are corrupt. (Issue #988)
@@ -798,6 +811,7 @@ Deprecations
  * 2.2.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed issue where Reader.copy() did not preserve optional arguments
     and kwargs passed to the original class (Issue #3664, PR #3685)
   * Iterating a SingleFrameReaderBase trajectory now rewinds the
@@ -895,6 +909,7 @@ Deprecations
  * 2.1.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Use uint64_t loop counters in C level distance functions to avoid overflow
     for large arrays (Issue #3512, PR #3513).
   * Prevents attempts to close an already closed NamedStream (Issue #3386)
@@ -946,6 +961,7 @@ Deprecations
   * 2.0.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Added an `rdkit_kwargs` parameter to pass arguments to the RDKitConverter
     from the `select_atoms` method (Issue #3319, PR #3324)
   * Fixes AtomGroup.unique, ResidueGroup.unique, SegmentGroup.unique not
@@ -1309,6 +1325,7 @@ Deprecations
   * 1.1.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Remove absolute paths from package upload to pypi.
 
 
@@ -1318,6 +1335,7 @@ Fixes
   * 1.1.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Removes use of absolute paths in setup.py to avoid Windows installation
     failures (Issue #3129)
   * Adds test for crashes caused by small box NSGrid searches (Issue #2670)
@@ -1361,6 +1379,7 @@ Enhancements
   * 1.0.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Due to issues with the reliability/accuracy of `nsgrid`, this method is
     currently not recommended for use. It has also been removed as an option
     from lib.capped_distance and lib.self_capped_distance. Please use PKDTree
@@ -1423,6 +1442,7 @@ Deprecations
   * 1.0.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * MOL2Writer now accepts both Universes and AtomgGroups (Issue #2717)
   * Use user-provided `remark` in `XYZWriter` (Issue #2692)
   * Added more informative error messages about topology attributes
@@ -1625,6 +1645,7 @@ Deprecations
   * 0.20.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * The NetCDF writer now writes `cell_angle` units as `degree` instead of
     `degrees` in accordance with the AMBER NetCDF convention (Issue #2327).
   * Fixed installation without Cython (Issue #2337)
@@ -1698,6 +1719,7 @@ Changes
   * changed the water bridge analysis output format (PR #2087)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * fixed ChainReader setting format with format keyword (Issue #2334)
   * fixed lack of check for scaling of NCDFReader velocities (Issue #2323)
   * fixed PDBReader and PDBWriter newlines for PDB header (Issue #2324)
@@ -1769,6 +1791,7 @@ Changes
   * 0.19.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
    * limit output of Chainreader __repr__ (#2109)
    * added missing docs for lib.pkdtree (#2104)
    * Added sphinx markup for FrameIterator (#2106)
@@ -1857,6 +1880,7 @@ Enhancements
     (where possible) (Issue #1041 PR #2080)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Rewind in the SingleFrameReader now reads the frame from the file (Issue #1929)
   * Fixed order of indices in Angle/Dihedral/Improper repr
   * coordinates.memory.MemoryReader now takes np.ndarray only (Issue #1685)
@@ -1956,6 +1980,7 @@ Enhancements
   * Added AtomGroup, ResidueGroup and SegmentGroup to the top module namespace
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed MPI fork() warning when importing MDAnalysis in an Infiniband-enabled
     MPI environment (PR #1794)
   * Fixed waterdynamics SurvivalProbability ignoring the t0 start time
@@ -2034,6 +2059,7 @@ Deprecations
   * timeseries keyword format is replaced by order. The format keyword is marked for deprecation in 1.0
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed analysis.psa.dist_mat_to_vec not returning int values (Issue #1507)
   * Fixed triclinic PBC transform for a- and b- axes (Issue #1697)
   * Fixed nuclinfo.tors() not converting delta (Issue #1572)
@@ -2098,6 +2124,7 @@ Deprecations
   * deprecated the core.flag registry for 1.0 (Issue #782)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * fixed GROWriter truncating long resids from the wrong end (Issue #1395)
   * Fixed dtype of numpy arrays to accomodate 32 bit architectures (Issue #1362)
   * Groups are hashable on python 3 (Issue #1397)
@@ -2129,6 +2156,7 @@ Enhancements
   * made online docs responsive with the Alabaster Sphinx theme (#378)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * In Universe.transfer_to_memory(): dt is now adjusted with step (Issue #1310)
   * Various documentation sphinx errors (PR #1312)
   * Bugfix in confdistmatrix.get_distance_matrix; now works on all trajectory types.
@@ -2222,6 +2250,7 @@ Enhancements
     weights="size") by about 5x (partially Issue #1191)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Trajectory slicing made completely Pythonic (Issue #918 PR #1195)
   * Argument validation of dist_mat_to_vec is fixed (#597 PR #1183)
   * Give correct error when the topology file format is not recognized (Issue #982)
@@ -2357,6 +2386,7 @@ Enhancements
   * Iteration and seeking in PDB files made faster (Issue #848)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed TypeError in PSAnalysis heatmap-dendrogram plotting (Issue #1018)
   * ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
   * rmsd now returns proper value when given array of weights (Issue #814)
@@ -2451,6 +2481,7 @@ Changes
     before trying to deduce the format from file extension. (Issue #712)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
 
   * Syntax error corrected in psa.py (Issue #738)
   * XDR file seeking and telling working again for large files (Issue #677).
@@ -2530,6 +2561,7 @@ Changes
   * MOL2Writer.write now only writes a single frame (Issue #521)
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
 
   * Fixed select_atoms requiring a trajectory be loaded (Issue #270)
   * AtomGroup timesteps no longer cached (Issue #606)
@@ -2577,6 +2609,7 @@ Enhancements
 Changes
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed OpenMP detection on Linux/OSX #459
   * Fixed reading of LAMMPS trajectory times: default unit ought
     to be fs and not ps
@@ -2631,6 +2664,7 @@ Changes
   * To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * Fixed minor issue in lib.mdamath.make_whole where if all bonds
     were correctly sized, it wouldn't notice that multiple fragments
     had been given. (Issue #445)
@@ -3227,6 +3261,7 @@ Testsuite
   * 0.7.5.1
 
 Fixes
+ * `PersistenceLength._conclude()` now normalizes `results.bond_autocorrelation` using the number of frames actually analyzed instead of the total trajectory frame count, fixing incorrect results when `run()` is called with `start`/`stop`/`step` (Issue #5453).
   * added: missing files (Issue 95)
   * removed: unused delaunay-related files
 

package/MDAnalysis/analysis/polymer.py

@@ -317,7 +317,7 @@ def fit(self):
 
     def _conclude(self):
         norm = np.linspace(self.chainlength - 1, 1, self.chainlength - 1)
-        norm *= len(self._atomgroups) * self._trajectory.n_frames
+        norm *= len(self._atomgroups) * self.n_frames
         self.results.bond_autocorrelation = (
             self.results.raw_bond_autocorr / norm
         )