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Rename mdforge to MolDynX Tools (moldynx) - #2
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- git mv mdforge -> moldynx; imports, CLI, output folder, manifest key and plugin entry-point group renamed; prose and citation metadata use the display name "MolDynX Tools (formerly mdforge)". - Distribution renamed to moldynx-tools; version 0.3.0. - Compatibility for one minor version: an mdforge shim package aliases every mdforge.* import to the same moldynx module objects (one registry) with a DeprecationWarning; the mdforge console script is kept; plugins under the legacy mdforge.plugins entry-point group are still loaded, with a warning. - tests/test_rename.py covers the new identity and the shim. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Discovery used to pick the largest file per role, which on real CHARMM-GUI folders selects an equilibration .tpr as the topology and a minimisation crash dump as the structure. Files are now classified by simulation stage; earlier analysis outputs, backups and caches are ignored; the production trajectory is the longest complete one whose atom count matches the run input, verified from file headers, and ambiguities are reported instead of resolved silently. - moldynx.io.gromacs: read-only log/mdp/xtc/tpr readers and a gmx runner with WSL fallback (the XTC scanner writes no offset cache into the data folder). - moldynx.io.validation: capability matrix, atom-count consistency check. - moldynx.io.intake + `moldynx intake`: INTAKE_REPORT.md / intake_manifest.json with per-stage summaries, temperature changes, clock offset, run extension and job-script inputs that are absent. - SystemInfo gains per-chain records and ion counts; the manifest records the evidence chain and fingerprints of every input. - Tests on real trimmed logs and miniature copies of two real folder layouts. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Co-Authored-By: Claude Opus 5.5 <[email protected]>
- moldynx.core.pbc.PBCProcessor: per frame, measure the raw coordinates (split molecules, COM continuity, PBC-aware partner distance), apply none/whole/nojump (auto: nojump for multi-molecule solutes, first-frame clustering), then prove the result against the raw frame (whole-box translations only, bonds short, partner distances preserved, two translation vectors exactly where a molecule was split). - AnalysisContext: no more silent try/except around unwrap; the solute cache is keyed on input fingerprints, PBC mode, slice and selection; chain identity persisted as atom-index ranges (chain_groups()). - interface: partners from persisted chain identity (PDB truncates CHARMM-GUI segids to 'seg_', collapsing both chains into one segment). - New pbc_validation analysis. - Reproduces an independent manual audit of two 100 ns complexes exactly. Co-Authored-By: Claude Opus 5.5 <[email protected]>
…ext steps - analysis/equilibration.py: stage parameters, minimisation outcome and Fmax location, crash dumps, energy statistics, position restraints (gmx dump), protonation, chain of custody (io/jobscripts.py), timeline, figure. - io/gromacs.py: filtered gmx dump pipeline and position-restraint reader. - analysis/interface.py: legacy-validated suite with full core lists, residues ever within 6 A, buried area, iRMSD, trends. - core/surface.py: frame-by-frame Shrake-Rupley (mdtraj 1.11.1 multi-frame calls return wrong values for some frames); sasa and interface stride 10. - docs/NEXT_STEPS.md: remaining phases 5-10 and acceptance values. Co-Authored-By: Claude Opus 5.5 <[email protected]>
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plugin entry-point group renamed; prose and citation metadata use the
display name "MolDynX Tools (formerly mdforge)".
mdforge.* import to the same moldynx module objects (one registry) with a
DeprecationWarning; the mdforge console script is kept; plugins under the
legacy mdforge.plugins entry-point group are still loaded, with a warning.
Co-Authored-By: Claude Opus 5.5 [email protected]