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fix: normalize PersistenceLength by n_frames instead of trajectory n_frames #5456

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fix: normalize PersistenceLength by n_frames instead of trajectory n_frames #5456

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8d59a08
fix: normalize PersistenceLength by n_frames instead of trajectory n_…
shubhrai23 Aug 11, 2026
720cf66
test: add test for PersistenceLength with partial trajectory run
shubhrai23 Aug 14, 2026
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2 changes: 1 addition & 1 deletion package/MDAnalysis/analysis/polymer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
)
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4 changes: 4 additions & 0 deletions testsuite/MDAnalysisTests/analysis/test_persistencelength.py
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Expand Up @@ -72,6 +72,10 @@ def test_ag_ValueError(self, u):
def test_run(self, p_run):
assert len(p_run.results.bond_autocorrelation) == 280

def test_run_partial(self, p):
p.run(start=0, stop=2)
assert_almost_equal(p.results.bond_autocorrelation[0], 1.0, 3)

def test_lb(self, p_run):
assert_almost_equal(p_run.results.lb, 1.485, 3)

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