# 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.