# Rfd4 Proteina Generate

Use when generating RFD4-Proteina designs from annotated inputs with task, sampling...

- Repository: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit (503 stars)
- Category: Design
- License: CC-BY-4.0
- Last updated: 2026-10-28
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill rfd4-proteina-generate -g -a claude-code -y`
Codex: `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill rfd4-proteina-generate -g -a codex -y`
Cursor: `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill rfd4-proteina-generate -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill rfd4-proteina-generate -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA-BioNeMo/bionemo-agent-toolkit`

## Description

Use when generating RFD4-Proteina designs from annotated inputs with task, sampling, batch, and inline-metric choices.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# RFD4-Proteína Generate

## Purpose

Single-shot generation for RFD4-Proteína. One entry point drives every design task, unconditional monomers/complexes, folding & inverse folding, motif scaffolding,
enzyme design, small-molecule binders, protein binders, and DNA binders. The
skill's job is to **route** the request to the right example input and the right
overrides, then run one command. Deep input construction, reward-guided search,
and oracle metrics live in sibling skills; this skill points at them.

Run everything from the repository root (the directory containing `.project-root`). All model arguments
are Hydra `key=value`, **never** `--key value`.

## Prerequisites

A model environment that passes setup preflight, supported GPU, checkpoints, and a validated annotated input or benchmark example.

Use the user-selected model checkout at `RFPROTEINA_ROOT` for model commands,
configs, and upstream manuals. This catalog contains the skills, not that checkout.
In helper examples, resolve `open-models-skills/rfd4-proteina/<name>/...` to its absolute installed path
when the catalog and model checkout are separate.

## Inputs

Required: the user's task, input CIF or benchmark path, output directory, and design count. Optional: batch size, seed, sampling overrides, and metric tags. Preserve explicit choices and use the documented defaults only for unspecified values.

## Instructions

### Step 1, Preflight

Never launch a long run against a broken environment. Confirm venv, GPU, and
checkpoints first:

```bash
bash open-models-skills/rfd4-proteina/rfd4-proteina-setup/scripts/preflight.sh
```

Fix every `FAIL` (see **rfd4-proteina-setup**) before generating.
`scripts/download_example_data.sh` fetches the release pair composed by
`configs/inference.yaml`, so the default run needs no checkpoint override.

## Step 2, Route the task

Pick the design case, then open its reference for the exact command, example
input, task-specific overrides, and gotchas:

The rest: https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/blob/HEAD/skills/bionemo-agent-toolkit/skills/rfd4-proteina-generate/SKILL.md