MDAnalysis2.9.0 / NetworkX3.6.1 RNA andbilayer geometry. Run bash run.sh innewdirectory: sourceenvironment uses existingqvasp2.26 Python forMDAnalysis only and creates own.dep links to existingread-onlyNetworkX frompymatgen2026.9.24, no publicinstallationchanged. SingleofficialMDAnalysisTests2.9 snapshots, notnewMDorownMD generation. RNA739atoms23residues fromPDB1K5I-derivedPSF/PDB, exactnativePSFmasses andcoordinates retained; RNAfilewas subsetexported, massesnotguessed. Native2-rowfields useproper90degrotation as algebraiccheck only, notphysicaltimeseries. TwoG-Ccandidategeometries selected deterministically; distancesalonearenotbasepairassignment. Membrane450lipids/360PO4, originalcoordinateunitsconverted byMDAnalysisGROreader. Independentfullgraph verifies nativeLeafletFinder andcutoffprofile; leafletlabelIDs arbitrary. FullnativeandlegacyNAgeometryinterfaces andall147backbonetorsions independentlychecked. SourceURLs,h ahes andupstreamLICENSEincluded; no copiedvendorcode/binary orprivateserverpath.
