bagel-script-builder - Interactively build reviewable BAGEL scripts
Interactively turns natural-language protein-design goals into runnable, reviewable BAGEL scripts, smoke tests, and execution harnesses.
Tags
Updated: 2026-09-29Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Draft BAGEL design scripts
- Interview unresolved design choices
- Define states, chains, and energy terms
- Generate commented design scripts
- Generate smoke-test scripts
- Generate execution harnesses
- Run Modal smoke tests
- Create parallel or serial sweeps
- Save scripts for review
Inputs
- Natural-language design goal
- Protein and target sequences
- State and chain definitions
- Mutable and protected residues
- Energy terms and weights
- Oracle and optimizer choices
- Execution backend and sweep parameters
- Output directory
- Modal credentials
Outputs
- BAGEL design script files
- Smoke-test script files
- Execution harness files
- Per-run output directories
- Smoke-test results
Requirements
- Python environment with biobagel
- BAGEL API and reference files
- Access to selected oracles or backends
- Modal credentials for Modal execution
- SLURM or PBS cluster for cluster sweeps