MDAnalysis2.9.0 ENCORE: native PCA, DRES, CES/DRES increasing-window checks, KMeans/DBSCAN/AffinityPropagation wrappers.
Real owned ubiquitin51frames76CA; first/last26frames share their middle frame. No newMD.
PCA explicitly converts the exact read coordinates to double before native fullSVD; nearest-exemplar checks accept ties. Initial float32/self and first-index tie oracle failures are kept privately.
1000/10000 KDE MonteCarlo integration draws are not new physical MD frames. The final convergence value is zero because the full trajectory is compared with itself; not proof of physical equilibrium.
DBSCAN .35A/min2 returns50 noise frames and a two-member cluster from the duplicated shared middle frame; not a real metastable state.
bash setup.sh
bash run.sh
bash verify.sh
bash plot.sh
Read-only local dependency links, no sharedenvironment changes.
