MDAnalysis 2.9.0: native stochastic proximity embedding, shrinkage covariance, HES bootstrap.
Actual existing 51-frame 76-C-alpha ubiquitin data. First/last26 overlap one real middle frame; no new MD.
Run bash setup.sh, bash run.sh, bash verify.sh, bash plot.sh.
Native C SPE seeds with time and process id. NumPy seed does not fix it; SPE coordinates and pictures change on repeat. verify checks mathematical consistency and frozen quality gates, not equality to old coordinates.
HES four-bootstrap spread is a demonstration of resampling, not a confidence interval or trajectory convergence.
bash plot.sh --reference regenerates archived-source figures into reference-plots; normal plot.sh visualizes this run.
