Reference

Reference pages are for lookup. Use this section when you need commands, configuration fields, plugin settings, API signatures, or benchmark data.

Tip

For a guided walkthrough, go to Tutorials. For a task-oriented solution, go to How-To Guides.

CLI Commands

All polyzymd commands, flags, and options.

CLI Reference

Configuration YAML

Every key in config.yaml — types, defaults, and constraints.

Configuration Reference

Analysis Plugin Reference

Per-plugin settings, comparison YAML schema, and post-hoc testing options.

Analysis Plugin Settings Reference

API Documentation

Module-level Python API for config, builders, simulation, workflow, and analysis.

API Reference

CLI, Configuration & Data

• CLI Reference
• Configuration Reference
• Data Requirements & Directory Layout
• Benchmarks

Analysis Plugin Reference

• Comparison YAML Schema
• Analysis Plugin Settings Reference
• Comparison and Plotting Reference
• RMSD Plugin Reference
• Rg Plugin Reference
• RMSF Plugin Reference
• Catalytic Triad Plugin Reference
• Distances Plugin Reference
• Contacts Plugin Reference
• Secondary Structure Plugin Reference
• SASA Plugin Reference
• Hydrogen Bonds Plugin Reference
• Post-Hoc Testing Reference
• Experimental Analyses Archive

API Reference

Full Python API documentation.

• API Reference
• Package and workflow APIs
  • API Overview
  • Configuration Module
  • Builders Module
  • Simulation Module
  • Workflow Module
  • Core Module
• Analysis APIs
  • Analyses Plugin System API
  • Analysis Base Classes
  • Analysis Shared Utilities
• MDAnalysis extension-layer APIs
  • MDAnalysis Extension-Layer API
  • Public facade
  • Job execution
  • Frame selection
  • Plugin lifecycle and collectors
  • Artifact envelopes and store
  • Aggregation and comparison
  • Universe provenance and shared MDAnalysis primitives