Download skills/bionemo-molmim-nim/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does molmim-nim live?
The publisher keeps it at https://github.com/NVIDIA/skills.
Which agents can use molmim-nim?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.
>
name: molmim-nim
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.
license: Apache-2.0 AND CC-BY-4.0
compatibility: "requests>=2.28; rdkit"
allowed-tools: Bash, Read, Write, AskUserQuestion
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:
See 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 under Local Docker verbatim.
Readiness check:
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:
Use hosted /generate for seed-SMILES generation or optimization. Use
algorithm: "CMA-ES" for guided property optimization and algorithm: "none"
for unguided sampling around the seed.
num_molecules is 1-100. iterations is 1-1000. particles is 2-1000.
min_similarity is 0-1 in the hosted API reference; local docs emphasize
common values up to 0.7 for constrained optimization.
scaled_radius is 0-2 and is mainly used with algorithm: "none" or local
/sampling.
Local Latent Workflow
Use local-only endpoints for embedding, hidden-state manipulation, and decode.
This is also the surface used by the guided optimization example package.
For local latent workflows, state explicitly that the hosted API reference
exposes /generate; /embedding, /hidden, /decode, and /sampling are
local-only in the current docs.
Save generated SMILES and validate before using them downstream.
from pathlib import Path
import json
def molmim_smiles(result):
values = []
if isinstance(result.get("generated"), list):
for item in result["generated"]:
if isinstance(item, str):
values.append(item)
elif isinstance(item, list):
values.extend(x for x in item if isinstance(x, str))
molecules = result.get("molecules")
if isinstance(molecules, str):
molecules = json.loads(molecules)
if isinstance(molecules, list):
for item in molecules:
if isinstance(item, dict) and isinstance(item.get("sample"), str):
values.append(item["sample"])
return values
generated = molmim_smiles(result)
if not generated:
raise RuntimeError(f"MolMIM returned no generated molecules: {result}")
Path("molmim_response.json").write_text(json.dumps(result, indent=2))
Path("molmim_generated.smi").write_text("\n".join(generated) + "\n")
for i, smiles in enumerate(generated, start=1):
print(i, smiles)
Use RDKit when available to check parseability, uniqueness, simple property
ranges, and whether seed similarity constraints are plausible. Generated
molecules are candidates, not validated hits; use downstream property, docking,
affinity, toxicity, and synthetic-feasibility checks before prioritization.
Troubleshooting
Hosted 404 on /embedding, /hidden, /decode, or /sampling: those
endpoints are local-only in the docs.
401: missing or unauthorized NGC key for hosted requests.
Hosted response parsing: live hosted /generate may return molecules as
a JSON string of {sample, score} objects, while local endpoints may return
generated; parse both.
Local startup auth: set NGC_CLI_API_KEY, or set NGC_API_KEY/NVIDIA_API_KEY
and map it as shown above.
Local startup cache misses: mount LOCAL_NIM_CACHE to /home/nvs/.cache/nim,
not /opt/nim/.cache.
How do I install molmim-nim?
Download skills/bionemo-molmim-nim/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does molmim-nim live?
The publisher keeps it at https://github.com/NVIDIA/skills.
Which agents can use molmim-nim?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.