Experimental analyses

PolyzyMD v1.3 ships the stable analysis plugins documented in the analysis reference pages. The following experimental analyses were removed from the shipped v1.3 code and are not available as active plugins:

• contacts binding preference

• exposure dynamics

• binding free energy

• polymer affinity

• polymer bridging

These archived features are retained only for historical review. They are not maintained as part of the v1.3 analysis workflow, and this page intentionally does not reproduce the old how-to content.

This is an intentional breaking change for v1.3. The archived plugins were experimental, had no known external users, and did not yet have stable result or cache contracts. PolyzyMD therefore does not migrate their old configuration blocks, cached intermediates, or result files forward into the active analysis workflow.

Archived names and migration path

Remove these names from plugins: and plot_settings: in new comparison.yaml files. If you need a related stable analysis, recompute from the original trajectories with the active plugin listed below; do not reuse old experimental caches as input to v1.3 comparisons.

Archived request names	Active replacement path
binding_preference, contacts_binding_preference, contact_binding_preference, bp	No one-to-one replacement. Recompute contacts and perform project-specific post-processing outside the plugin if you need binding-preference summaries.
exposure, exposure_dynamics, surface_exposure	No direct replacement. Recompute sasa for solvent exposure observables when SASA answers the scientific question.
binding_free_energy, bfe	No active PolyzyMD replacement. Use a dedicated free-energy workflow outside v1.3, or inspect the archived implementation for historical context only.
polymer_affinity, pa	No one-to-one replacement. Recompute active contacts and/or distances metrics when those observables are sufficient.
polymer_bridging, bridging	No one-to-one replacement. Recompute active contacts and/or distances metrics and implement bridging-specific logic externally if required.

If you previously ran one of the archived plugins, keep those outputs as historical artifacts. For v1.3 analyses, remove the archived plugin settings, clear any experimental cache directories for those plugins, and rerun the active replacement analysis from trajectories so the result metadata, cache identity, and comparison statistics all come from the current code.

Current workflow

The active v1.3 workflow is comparison.yaml plus canonical plugin names. Run polyzymd compare validate, then polyzymd compare run <analysis>, and use polyzymd compare plot-all for figures. Requests for removed plugin names are handled as ordinary unknown analysis names.