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Contributing

Proteus is most useful when it captures real structural-biology workflow knowledge: command-line patterns, gotchas, reproducible helper scripts, and small tests that keep agents from repeating common mistakes.

Good Contributions

  • a PyMOL, ChimeraX, AlphaFold, RCSB, UniProt, or Rosetta gotcha with a tested fix
  • a small stdlib-only helper workflow that returns JSON
  • focused docs that help agents choose the right tool
  • tiny fixtures and tests for edge cases

Development

make test
python3 scripts/proteus_doctor.py --json

Keep helper scripts dependency-free unless there is a clear reason not to. Prefer deterministic JSON output in --json mode:

{"status": "ok", "data": {}}

Errors should remain parseable:

{"status": "error", "error": "message"}

Pull Requests

  • Keep changes scoped.
  • Add or update tests for script behavior.
  • Do not commit downloaded structures, private data, generated AlphaFold files, caches, or local machine artifacts.
  • Document any external API or local binary assumptions.