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Implementing the full StructAgent system

This document describes how to reproduce the Annika/Maria/A2A design without using private configuration from the original deployment.

1. Requirements

  • OpenClaw or an equivalent multi-agent runtime with:
    • separate agent workspaces;
    • tool/skill loading;
    • a message bus or A2A JSON-RPC endpoint;
    • filesystem access for structural-biology tools.
  • Structural-biology tools as needed:
    • ChimeraX;
    • ISOLDE;
    • PHENIX;
    • Coot;
    • CCP4 / REFMAC5 / Servalcat;
    • gemmi;
    • Python scientific stack.
  • Model providers or local models chosen by the implementer.

2. Create the agents

Create two agent workspaces.

workspace-maria/
  AGENTS.md
  skills/
  memory/ or project database/

workspace-annika/
  AGENTS.md
  skills/
  runs/
  tools/

Recommended division:

  • install skills/maria/* into Maria's skills/ directory;
  • install skills/annika/* into Annika's skills/ directory.

3. Minimal agent role prompts

Maria:

You are Maria, the domain-reasoning agent for StructAgent. Your job is to read literature, maintain the project knowledge base, propose structural-biology workflows, critique results, identify risks, and decide whether evidence supports a claim. You do not leak private data or raw unpublished datasets. You ask Annika to execute when tool work is needed.

Annika:

You are Annika, the execution orchestrator for StructAgent. Your job is to run structural-biology tools, maintain provenance, capture metrics, recover from failures, and report concise results. You ask Maria for scientific planning or review when choices depend on domain judgment.

4. Configure A2A messaging

Use a local A2A gateway or equivalent JSON-RPC endpoint. Do not hard-code tokens in scripts. Use environment variables.

export STRUCTAGENT_A2A_URL="http://127.0.0.1:18800"
export STRUCTAGENT_A2A_TOKEN="replace-with-generated-token"

A sanitized sender template is provided at ../scripts/a2a-send-template.sh.

Example:

./scripts/a2a-send-template.sh --to maria --message "Review this refinement plan and define stop criteria."
./scripts/a2a-send-template.sh --to annika --message "Run PHENIX validation and return MolProbity, clashscore and rotamer outliers."

5. Recommended task loop

  1. User asks for a structural-biology task.
  2. Annika captures inputs, constraints and success criteria.
  3. Annika asks Maria for a scientific plan when needed.
  4. Annika executes tool steps and records provenance.
  5. Maria reviews outputs and flags scientific concerns.
  6. Annika reports final status and artifacts.

6. Privacy and release hygiene

Never publish:

  • private identities/persona files;
  • raw chat transcripts;
  • API tokens or A2A bearer tokens;
  • private routing config;
  • unpublished structure IDs or coordinates unless cleared;
  • full PDFs unless license permits redistribution.

Publishable material should be protocols, wrappers, derived notes, citations, BibTeX, and sanitized provenance summaries.