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Docking poses and reference frames

dockingmt.view(result, reference=reference, view=existing_view) replaces the displayed docking complex. Reusing a viewer therefore does not accumulate duplicate receptors and poses. A result's structures correspond to pose ranks: frame 0 is rank 1. Reconstruction still requires checked source atom identity. The receptor and each reconstructed pose must contain exactly one structure; select the receptor conformation through MolSysMT before rendering a result.

The independently usable public operation molsysviewer_dockingmt.build_docking_reference_system(reference, n_poses) prepares a detached reference through public MolSysMT conversion, copy and extraction:

  • One static structure is explicitly repeated to the pose count.
  • Exactly N reference structures are copied in their existing order, comparing reference frame k with pose frame k.
  • Other counts and non-positive/non-integer pose counts raise ValueError.

No alignment, interpolation, inferred atom correspondence or chemical preparation is performed. Source coordinates, units and declared structure attributes remain owned by MolSysMT; input systems are not mutated. Repetition preserves the static reference's declarations, including time when present. It does not invent a time axis to match arbitrary trajectories.

The reference count is checked before replacing the scene. Provider load and initial-player failures propagate, retaining the original exception. No render success event or completed result state is published on failure. Multiple provider calls are not a transaction: if reference addition or player movement fails after replacement, the scene may be partially changed. Correct the input and reload explicitly; the runtime retains the last completed result.

Provider contract and temporary compatibility

The reference is loaded with mode='add' and structure_pairing='by_index' when that parameter is explicitly present in the public view.load signature. Arbitrary **kwargs does not advertise support. There is no catch-and-retry on TypeError or other provider errors. The unchanged CI-pinned legacy viewer receives its existing load signature.

This bounded compatibility branch is tracked by DockingMT #37 and MolSysViewer #151. DockingMT maintainers will review it by 2026-11-03 and remove it when published explicit pairing support is qualified across the supported provider profiles. The provider owns time/cell compatibility and loading behavior. No minimum published version or committed delivery of the candidate is asserted here. The consumer handoff requests an inspectable public signature and exact committed/published migration identity. No sibling source files were changed.

Measured integration — 2026-10-03

The editable molsyssuite@uibcdf_3.14 environment uses Python 3.14.7 and Vina 1.2.7. The full suite passes 706 tests without skips in 133.23 s, using MolSysMT c19a47ada0c2279029abfa296cf915560610ad9a and MolSysViewer ec4c71e574d798b7c8675b7e7e983da878ce9889, the unchanged Python 3.14 CI pins. tests/test_viewer_reference.py adds 22 cases covering counts, source ownership, time/box and non-default pm/fs units, explicit/legacy signatures, original loading/player failures, reload and frame correspondence. Existing addon and native 181L redocking controls remain included.

The same 32 focused cases pass in 30.16 s against an isolated snapshot of the in-progress MolSysViewer tree, retaining the pinned MolSysMT provider. Its HEAD is 924da3a32111d8994639e8a72cb901ebeb8f870a with uncommitted changes. Source evidence records the 633-file Python source inventory digest and individual boundary file hashes. This is candidate integration evidence, not released viewer qualification.

The executed notebook uses real seeded Vina poses from 181L with explicitly provisional preparation. Four code cells check public reference preparation, molecular coordinate correspondence, player movement, repeated result loading and rejection before scene mutation. Its saved outputs use the CI-pinned viewer. Candidate execution is recorded separately in the notebook receipt. Neither execution certifies browser graphics or docking accuracy.

The legacy viewer emits RegionWithoutOwnVisualWarning when visibility is toggled on the reference region without its own representation. These tests verify the DockingMT command/runtime boundary; they do not claim that legacy visibility changes browser graphics. The candidate supports masking such regions through the whole representation. This distinction is handed off in MolSysViewer #151 rather than bypassing its representation policy here. Provider H5MSM deprecation, pandas future and structural-attribute-drop warnings also remain visible; molecular field completeness is not inferred from a successful display. The full stable run reports 57 warnings, the candidate focused run 27.

Reproduce the test boundary with:

python -m pytest tests/test_viewer_reference.py tests/test_viewer_addon.py \
    tests/test_redocking.py --receptor=llm

Set PYTHONPATH to the qualified provider archives for exact-source evidence. The notebook records actual import origins and the original 181L SHA-256. Its kernel is the shared Conda environment, not the launching shell's Python.