Capability Map

agentic-proteins preserves historical access to runtime capabilities while applications move to bijux-proteomics-runtime. It is a compatibility distribution, not an independent execution platform.

flowchart LR
    U[Historical caller] --> A[agentic_proteins]
    A --> R[bijux_proteomics_runtime]
    R --> C[bijux_proteomics core operations]
    R --> O[run state and artifacts]

Supported compatibility surfaces

Surface	Historical entry	Canonical owner
Python root	agentic_proteins.AppConfig, RunManager, create_app, cli	bijux_proteomics_runtime
Command line	agentic-proteins	Runtime CLI implementation
HTTP application	agentic_proteins.interfaces.http	Runtime HTTP interfaces
Agents and tools	agentic_proteins.agents, agentic_proteins.tools	Runtime execution families
Providers	local, remote, and experimental provider paths	Runtime provider selection and implementations
State	historical state models and helpers	Runtime run, artifact, and persistence owners
Execution	compiler, evaluation, and runtime paths	Runtime execution and orchestration owners

Optional extras such as api, nl, local-esmfold, and local-rosettafold forward the corresponding runtime capability. Installing an extra changes available providers or interfaces; it does not transfer their ownership into this package.

Deliberate limits

New scheduling, provider, state, API, workflow, or artifact behavior belongs in runtime first. New scientific calculations belong in core. The compatibility package may add forwarding required to preserve an established historical path, but it must not acquire a competing implementation or a stronger behavior contract than the canonical owner.

Consumers can therefore use the bridge for controlled migration while treating the runtime handbook as the authoritative capability description.