Analysis API

This page is the entry point for the analysis-side API.

All analysis code lives in polyzymd.analyses:

Package	Role
polyzymd.analyses	Plugin system — unified analysis lifecycle (compute → aggregate → compare → plot → format)
polyzymd.analyses.shared	Reusable utilities (trajectory loading, alignment, autocorrelation, statistics)
polyzymd.analyses.<name>._results	Pydantic result models for serialization (existing plugins)

Plugin System

For the unified analysis lifecycle, see the Analyses Plugin API.

Related Documentation

• Analyses Plugin API

• Configuration API

• API Overview

• Extending the Analysis Framework

Notes

• Stable plugins (9): RMSD, Rg, RMSF, catalytic triad, secondary structure, SASA, distances, contacts, and hydrogen bonds.

• Experimental plugins (4): exposure, binding free energy, polymer affinity, and polymer bridging — metric definitions and interpretation may still change. See individual plugin docs for details.