Retire remaining consumer implementations of general molecular operations

This is a cross-repository ownership tracker, not a single task: most rows wait on MolSysMT provider issues (#222, #223, #214, #226, #348). Start by reading the consumer files named in the table, preparation/ligand.py, preparation/receptor.py and molsysviewer_dockingmt/adapters/complex.py, and identify which local operation each one performs. Done means each reviewed duplicate is replaced by a public MolSysMT call, or carries a bounded, owner-linked exception with a removal condition.

What

Retire DockingMT's remaining implementations of general molecular operations and consume the public tools owned by MolSysMT. The maintainer reaffirmed this boundary on 2026-10-10: an uncovered reusable molecular operation must be proposed in MolSysMT, rather than implemented in DockingMT. Apply the same ownership rule to pharmacophoric operations in PharmacophoreMT.

This is a bounded consumer migration, linked to #5, #28 and #33. Provider work remains owned by the existing issues below. It does not authorize sibling source edits or a new chemistry implementation in DockingMT.

Inspected state and authority — original 2026-10-10 review

• DockingMT implementation inspected at b793075e8a06bea6d8704eb0db24239b16671e57.
• Suite governance inspected at de01c5f55e9dcafca8e67f4eb36be38d4c4ea476, including modular reusable tools, cross-component feedback and repository ownership. MOLI inspected at 6ebbf4b064f12f6d53204ef41b4cbad22ebf6395, including its guide, component registry and Architecture 1.0 ecosystem boundary. MOLI governs the platform boundary; MolSysSuite owns member governance and providers own implementation.
• MolSysMT checkout is 8ae160fc93ed5bc815bcc24b37c2875ba735623d; fetched origin/main is 970fd28e374f3dda58eda0a5ab259bbdf7629402. Read-only source inspection includes the remote implementation, not merely the checkout's older version.
• Executed consumer profile remains the qualified source 5bd893c85fe8d211663b2b1f865f5f1d2c382a90, Python 3.14.7 and Vina 1.2.7. Inspection of newer source does not establish its runtime compatibility or authorize a dependency upgrade.
• Refreshed suite inventory preserves all sibling worktrees, including human changes in PharmacophoreMT, TopoMT, ElastNetMT and OpenCASTP, and behind checkouts. No sibling source, environment or native extension was changed.

Actual delegation already present

DockingProblem normalizes, selects and extracts through msm.convert/select/extract. Preparation consumes public stored chemistry/coverage and delegates explicitly requested H addition, partial charges and AutoDock types through msm.build.add_missing_hydrogens/assign_partial_charges/assign_autodock_atom_types. Torsion chemistry and fragment partition use msm.topology.get_rotatable_bonds/get_rigid_fragments. Pose reconstruction uses msm.copy/extract/set; positional RMSD uses msm.structure.get_rmsd. Scientific controls call public dihedral setters, fitting, translation and distance tools. These are actual call paths, not an architectural inference from dependency declarations.

DockingMT retains docking protocol choices, explicitly selected cuts/ROOT orientation, engine execution, score semantics, ranking, result accounting and provenance. Public provider validation and failures must continue to propagate; general chemistry must not be recovered through implicit consumer fallbacks.

Remaining consumer duplicates and migration ownership

Reference bridges and independent verification

The original unversioned 5X72 heavy-only SDF references still enter some developer workflows through Chem.SDMolSupplier followed by public MolSysMT conversion. This is an explicitly tracked reference bridge under MolSysMT uibcdf/molsysmt#215; its consumer evidence is already reported there. The native H-bearing 5X72 route uses public msm.convert with explicit stereo/property-loss choices. Do not add another reader or silently normalize the original files. Qualify provider admission before replacing the bridge; preserve historical producer/source bytes.

Finite NumPy distances, dihedral checks and proper-fit checks in developer controls independently verify public MolSysMT outputs. They are not molecular transformations used instead of the provider, and must not become a second reusable geometry API. The pending seven-point translation control calls msm.structure.translate for all 39 atoms, public distances and public RMSD. Its original 112 evaluations and producer were preserved; it has not yet been admitted as a completed/tested repository change.

PharmacophoreMT boundary

Read-only inspection finds public feature extraction, feature correspondence/evaluation and rigid pharmacophore placement tools in PharmacophoreMT. DockingMT currently implements no pharmacophore perception, feature matcher or pharmacophore pose evaluator. Simple saved-input pair-distance summaries do not classify hydrogen bonds, hydrophobic sites or pharmacophoric interactions. Therefore no new missing PharmacophoreMT capability is established by this review and no speculative issue or dependency is warranted. The first accepted feature-guided scoring/filtering workflow must call its public tools and file any actual missing contract in that provider.

Ordered acceptance

1. Retain qualified compatible MolSysMT 3502232d802ee2927f6b6f5d19f0ae045777ecb5, including delivered permutation and canonical form-owned readers. Its source, ordinary installed candidate and exact-head gates remain distinct from public file/pair admission. Original earlier artifacts and provider revisions retain their identities.
2. Retire available consumer duplicates: molecular writers, fallback construction and coordinate composition. Select the explicit compatibility policy for heuristic typing separately, preserving safe failure and original scientific evidence.
3. Receive the already delivered provider tools under uibcdf/molsysmt#223, uibcdf/molsysmt#226 and uibcdf/molsysmt#348 at an explicitly qualified revision. Connectivity, H projection/charge transfer in both roles, source-free reconstruction and preparation stage-map composition are delegated; finish mapped native writing/reading with actual public calls and behavioral consumer tests. Later provider namespace/stage composition changes require separate receiving evidence. Provider maintainers own implementation and prioritization.
4. Keep protocol interpretation, search/score execution and provenance in DockingMT. Preserve declared units, index spaces, named preparation attribution, original input/producer bytes, unsupported-input failures and source immutability in each migration.
5. Close this issue only when the reviewed general operations are delegated or have a current bounded owner-linked exception with a removal condition. Passing current consumer tests alone is not architectural acceptance or chemical validation.

The original review made no runtime edits; subsequent migrations are recorded above and in the dated comments. Existing provider issues cover the discovered needs; do not create duplicates for the same themes.