/bionemo-proteinmpnn-nim

name: proteinmpnn-nim
description: >
  Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided PDB files and design parameters to NVIDIA's hosted API, authenticated with an environment API key, or to a user-selected local NIM. Use for sequence design, backbone redesign, fixed chains and residues, omit_AAs, sampling temperature, soluble model, local Docker, and multi-FASTA output.
license: Apache-2.0 AND CC-BY-4.0
compatibility: "Python >=3.10; requests>=2.28"
allowed-tools: Bash, Read, Write, AskUserQuestion
permissions:
  - network
  - env

ProteinMPNN NIM

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Design protein sequences for a supplied backbone PDB. Use this guide for first-pass hosted/local usage; load supplemental files only when needed:

• `references/api.md`: exact endpoints, schemas, Docker flags, response fields.
• `references/science.md`: inverse-folding uses, limits, and validation.
• `references/parameters.md`: design controls, fixed positions, sampling.
• `references/validation.md`: FASTA, score, and structure checks.
• `references/examples.md`: compact hosted/local request patterns.

Choose Mode

Honor the user's explicit mode; otherwise use the configured runtime. `NIM_API_MODE=local` selects the local service at `PROTEINMPNN_NIM_URL`; the URL defaults to `http://localhost:8000` for a NIM running in the same host or container. Ask only when neither the environment nor the user's request makes the mode clear:

> Hosted NVIDIA API or local Docker NIM?

• Hosted: `https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict`
• Local: append `/biology/ipd/proteinmpnn/predict` to `PROTEINMPNN_NIM_URL`

(default base URL: `http://localhost:8000`).

Local inference paths do not include `/v1/`. Hosted requests use `Authorization: Bearer $NGC_API_KEY`. Supported local Docker startup uses `NGC_API_KEY` (or `NVIDIA_API_KEY` via the preflight) for registry login, entitlement checks, and first-run model downloads; pass it into the container with `-e NGC_API_KEY`. Local inference requests use no auth header after readiness. Warm-cache key-free startup varies by image/version and should not be assumed.

Data Transfer and Authorization

Before a hosted request, tell the user that the **entire PDB file and design parameters will be uploaded to NVIDIA's hosted API** at the endpoint above. Proceed if the user has explicitly requested hosted processing of that PDB or already approved the transfer; otherwise ask for confirmation before submitting. For confidential structures, recommend a local NIM in the user's approved environment. A configured local URL may point to another machine; use only the configured or user-selected destination. Do not switch from local to hosted processing without the user's authorization.

The client reads `NIM_API_MODE`, `PROTEINMPNN_NIM_URL`, and, for hosted mode, `NGC_API_KEY` from the environment. It sends the key only in the HTTPS Authorization header to the hosted endpoint; local inference sends no key. Keep credentials out of logs and saved artifacts. The output directory contains the full input PDB in `request.json` and the returned sequences and scores, so use a location appropriate for the input's sensitivity. See [`references/api.md`](references/api.md) for endpoint and data-handling details.

Local Docker

For local setup, run the full sequence — env preflight, `docker login`, `docker run`, readiness loop, then the no-auth localhost request; do not answer with only a localhost Python request. For the exact preflight (`.env` sourcing, `NGC_API_KEY`/`NVIDIA_API_KEY` handling, and the `docker run` for `nvcr.io/nim/ipd/proteinmpnn:latest`), copy the command block in [`references/api.md`](references/api.md) under **Docker Reference** verbatim. This NIM's cache mount is `/home/nvs/.cache/nim`, not `/opt/nim/.cache`. When `PROTEINMPNN_NIM_URL` is supplied, the service is already managed elsewhere; use that URL and do not start another Docker container.

Readiness:

proteinmpnn_nim_url="${PROTEINMPNN_NIM_URL:-http://localhost:8000}"
until curl -sf "${proteinmpnn_nim_url%/}/v1/health/ready"; do sleep 5; done

Instructions

For a request to execute a design, run [`scripts/design.py`](scripts/design.py) and inspect its results. Writing a request script alone does not complete an execution request. If the user asks only for code or setup instructions, provide those without submitting an inference request.

1. Use the user's PDB path and requested sequence count. The client reads the entire PDB into `input_pdb`; do not replace or truncate the supplied backbone. 2. Select `--mode hosted` or `--mode local` and follow **Data Transfer and Authorization** above before submitting. Hosted mode uploads the PDB to the documented NVIDIA endpoint and requires `NGC_API_KEY` in the environment. Check only whether the key is set; do not print it, dump the environment, or save authentication headers. Local inference sends no authorization header. 3. Choose a new `--output-dir` for each request. The client reserves it before submitting, preserves the raw response for diagnostics, and validates the designed sequence count and score alignment before reporting completion. 4. Read `summary.json` and report the actual results described below. If the request or validation fails, report the failure and diagnostic path; do not substitute example sequences or repeatedly resubmit the same request.

Examples

Run from this skill's directory, or use an absolute path to `scripts/design.py`. Substitute the user's input path and a new output directory:

python scripts/design.py --mode hosted \
  --pdb /path/to/backbone.pdb --num-sequences 10 \
  --temperature 0.1 --output-dir /path/to/new-design-run

For a running local NIM, use `--mode local`; the client honors `PROTEINMPNN_NIM_URL`. To design only chain A, exclude cysteine, or reques