Fix/typed cv virtual atoms - #3
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Vendor the origin RESP, QM, bundled-I/O, and Lipid17/Lipid21 compatibility modules and packaged lipid manifests. Extend frcmod, legacy runtime, CLI, PSF, and force-field parsing behavior while aligning the native RESP grid orientation. Add regression coverage for PSF residue grouping and constrained RESP compatibility.
Run every public XpongeCPP and legacy Xponge force-field module in a fresh interpreter so mutually exclusive force-field families are tested without contaminating one another. Restore package-relative GLYCAM tool imports and add legacy EDIP and Martini namespace shims.
Clear synthetic O0/C0 head metadata in native, bundled, and reference GLYCAM registries. Add four-family parity and PDB export coverage, update release contracts and CI assertions, and bump XpongeCPP to 0.2.1.
Synchronize legacy AtomType and residue-link APIs with native registries, align GAFF/GAFF2 and PDB export behavior with Xponge 1.7b9, and remove obsolete Python-side CONECT rewriting. Ship non-Amber reference force-field assets in wheels, add fail-closed capability metadata and provider-neutral performance coverage, and make the full test suite valid against installed runtimes.
Align the native template, force-field, export, and legacy compatibility layers with Xponge-origin 1.7b9 across Mokda-used workflows. Preserve mmCIF template pseudobonds, synchronize temporary residue linkage overrides, normalize CMAP scientific identities, and close protein, GAFF, nucleic-acid, glycan, lipid, metal-patch, raw, and bundle parity gaps. Add installed-wheel, release-contract, real-system scientific-manifest, and regression coverage; publish the 0.2.3 version metadata and release evidence.
Preserve residue-link bonds in MOL2 exports and keep mixed standard/GAFF systems intact during parameterization. Align the legacy MDAnalysis raw reader with Xponge format hints, add focused regressions, and advance package and CI release metadata to 0.2.4.
Expose the native SPONGE save permutation and apply it to compatibility-layer source atom IDs before raw serialization. This keeps Mokda atom-order mappings and trajectory CIF topology aligned when linked residue components are made contiguous, including repeated solvent residues.\n\nBump XpongeCPP to 0.2.5, update release automation and notes, and add focused mapping regression coverage.
Completes the integration-branch port of 9a7ce58 without replaying its obsolete 0.1.7 release metadata.
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This pull request delivers the XpongeCPP 0.2.6 release, targeting compatibility with Xponge-origin 1.7b10. The main highlights are a more robust QM backend selection mechanism, improved CMake and CI packaging for better wheel distribution, and several bugfixes and enhancements for molecule assembly and force field handling. It also introduces a new provider-neutral benchmarking script and updates documentation and release notes accordingly.
Backend selection and packaging improvements:
0.2.6, addedauditwheelanddelvewheelrepair commands for Linux and Windows wheel builds, and updated test cohorts to match the new release. [1] [2] [3]Core molecule and force field enhancements:
Algorithm and bugfixes:
Documentation and benchmarking:
Documentation and minor clarifications: