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MolDynX Tools 0.3 (part 2): complex analyses, annotations, MM-GBSA/PBSA, documents, datasets - #3
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- contact_lifetime, water_bridges, porcupine ported from the validated legacy pipeline, generalised (partners from persisted chain identity; porcupine uses its own aligned copy and an SVD instead of a 3N x 3N covariance). - core/annotations.py: display names, biological numbering offsets, domain transfer by global alignment (BLOSUM62, gap -10/-0.5) with uncertain-edge flags, motif location (exact, then local alignment, partial matches). - annotation analysis: domains/motifs/docking site in biological numbering and their interface involvement; says so when no annotations are given. - analysis_window: Chodera equilibration detection, drift and half-vs-half tests; no silent choice of the primary averaging window. - statistics.autocorr: statistical inefficiency, corrected SEM, detection. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Built on gmx_MMPBSA (https://github.com/Valdes-Tresanca-MS/gmx_MMPBSA; Valdes-Tresanca et al. 2021) and AmberTools MMPBSA.py; both cited in outputs. - binding/prepare.py: protein-only complex.tpr (convert-tpr on Protein), complex.top with solute molecule types only, complex.ndx from persisted chain identity (0 = receptor, 1 = ligand), no Amber forcefields line, ionic strength derived from ions and box volume, explicit print_res from residues ever within 6 A of the partner (fallback: all), run script with a probe gate (bonded deltas must be zero; decomposition coverage checked). - binding/analyse.py: autocorrelation-corrected means per window, drift, GB vs PB, per-residue hotspots in biological numbering, closure check, entropy validity gate (IE < 3.6, C2 < 6.0 kcal/mol). - analysis/mmpbsa.py: analyses existing outputs or prepares the package; never reports numbers it did not compute. New 'moldynx binding-energy'. - Reproduces a manual analysis of real gmx_MMPBSA outputs exactly. Co-Authored-By: Claude Opus 5.5 <[email protected]>
- report/documents.py: PBC_VALIDATION, EQUILIBRATION and BINDING_ENERGY written from the results files (Observations / Interpretation / Limitations), wording rules enforced (no stability claim from an RMSD plateau, binding energies are end-point estimates, entropy only if valid, gmx_MMPBSA credited and cited). - Markdown rendered with python-markdown to self-contained HTML (contents, embedded images); replaces the renderer that only deleted '**'. - generator: links the companion documents, reports PBC proof, interface, preparation, stationarity and binding-energy results. Co-Authored-By: Claude Opus 5.5 <[email protected]>
- moldynx.dataset: numbered dataset layout from a run (report + companion documents re-linked, results, solute trajectory, validation, workflow, binding energy), raw-file manifest (files + SHA-256 with --include-raw, otherwise a stub), generated README. - verify_dataset.py shipped inside each dataset (layout, links, manifest, PBC proof, Rg smoke test); package() zips, extracts and re-verifies. - CLI: moldynx dataset / verify / package. Co-Authored-By: Claude Opus 5.5 <[email protected]>
…, next steps - README rewritten for MolDynX Tools: run stages, input-file contract, annotations schema, gmx_MMPBSA credit and citation, verification. - docs/WHATS_NEW_0.3.md: every change compared with mdforge 0.2. - QUICKSTART: intake, binding energy, datasets; conda env renamed to moldynx. - Example config: pbc, annotations, binding_energy. - CHANGELOG and NEXT_STEPS updated. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Co-Authored-By: Claude Opus 5.5 <[email protected]>
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Completes the 0.3 plan: contact lifetimes, water bridges, porcupine; annotations (numbering, homology domains, motifs, docking site) and analysis-window selection; MM-GBSA/MM-PBSA built on gmx_MMPBSA (https://github.com/Valdes-Tresanca-MS/gmx_MMPBSA) with prepare/probe-gate/run/analyse; data-driven documents with self-contained HTML; dataset/verify/package commands; README, WHATS_NEW_0.3 and quickstart. 66 tests pass; MM-GBSA/PBSA analysis reproduces a manual analysis of real outputs exactly.
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