Schema
======

The BioSim schema defines a shared metadata model for biomolecular simulation
data. It provides a consistent structure for describing simulation setup,
execution context, system composition, observables, topology, trajectory, and
related computational details.

Why this schema exists
----------------------

Different simulation engines expose similar concepts using different names and
formats. This schema provides a canonical vocabulary so metadata can be:

- compared across engines
- validated consistently
- transformed into downstream artefacts for extraction and web forms
- reused by other BioSimDR tools

How the schema is organized
---------------------------

The schema uses a top-level ``SimulationMetadata`` model and is split into
domain-focused component files (for example settings, stages, observables,
topology, and trajectory). This keeps the structure modular while preserving
one coherent metadata object.

The autogenerated LinkML pages below are the authoritative reference for all
classes, slots, enums, and types.

How to read the autogenerated reference
---------------------------------------

Use the pages under ``linkml/index`` to inspect:

- classes: object structure and nested fields
- slots: field-level definitions and constraints
- enums: controlled vocabularies
- types: scalar and custom value types

.. toctree::
   :maxdepth: 2
   :caption: Autogenerated Reference

   linkml/index