# Molmim Nim

Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule...

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: DevOps
- License: Apache-2.0 AND CC-BY-4.0
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add NVIDIA/skills --skill molmim-nim -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill molmim-nim -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill molmim-nim -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill molmim-nim -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization. Invoke for MolMIM, molecular embeddings, hidden states, latent decoding, sampling around a seed SMILES, CMA-ES guided molecule generation, QED or plogP optimization, hosted NVIDIA API calls, or local Docker deployment.

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

# MolMIM NIM

Generate, sample, embed, and decode small molecules with MolMIM. Use this
guide for first-pass hosted/local usage; load supplemental files only when
needed:

- `references/api.md`: endpoints, schema, Docker flags, response fields.
- `references/science.md`: use cases, strengths, limits, and handoffs.
- `references/parameters.md`: generation, sampling, and optimization effects.
- `references/validation.md`: SMILES/property/artifact checks.
- `references/examples.md`: compact hosted/local request patterns.

## Choose Mode

Ask only when context is unclear:

> Hosted NVIDIA API or local Docker NIM?

See [`references/api.md`](references/api.md) under **Endpoints** for the full
hosted/local endpoint list.

Mode difference: the hosted API reference exposes `/generate`; the local
container exposes the broader latent-space workflow (`/embedding`, `/hidden`,
`/decode`, `/sampling`, `/generate`). Do not invent hosted latent endpoints.

Hosted requests use `Authorization: Bearer $NGC_API_KEY`. Local inference uses
no auth header after readiness.

## Local Docker

Use shell env first; source repo-root `.env` only if present. Do not print keys.
MolMIM docs use `NGC_CLI_API_KEY` for the local container; this repo accepts
`NGC_API_KEY` or `NVIDIA_API_KEY` and maps to `NGC_CLI_API_KEY` for startup.
Mount `LOCAL_NIM_CACHE` at `/home/nvs/.cache/nim`.

For the exact startup preflight (the `NGC_API_KEY`/`NVIDIA_API_KEY` →
`NGC_CLI_API_KEY` mapping, `docker login`, and the `docker run` for
`nvcr.io/nim/nvidia/molmim:1.0.0`), copy the command block in
[`references/api.md`](references/api.md) under **Local Docker** verbatim.

Readiness check:

```bash
until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done
```

Local embedding smoke test after readiness. Local inference uses no
`Authorization` header:

```python
import requests

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-molmim-nim/SKILL.md