diffdock-nim

Files (14)

• BENCHMARK.md
• SKILL.md
• skillspector-baseline.yml · config/
• config.yml · evals/
• evals.json · evals/
• protein.pdb · evals/files/
• trigger_evals.json · evals/
• api.md · references/
• examples.md · references/
• parameters.md · references/
• science.md · references/
• validation.md · references/
• skill-card.md
• skill.oms.sig

SKILL.md (first lines)

# DiffDock NIM

Predict protein-ligand binding poses with blind docking. Use this guide for
first-pass hosted/local usage; load supplemental files only when needed:

- `references/api.md`: exact hosted/local endpoints, schemas, Docker flags.
- `references/science.md`: docking use cases, limits, and handoffs.
- `references/parameters.md`: ligand formats, pose counts, diffusion controls.
- `references/validation.md`: receptor, ligand, pose, and confidence checks.
- `references/examples.md`: compact hosted/local and pose-saving patterns.

## Choose Mode

Ask only when context is unclear:

> Hosted NVIDIA API or local Docker NIM?

- Hosted: `https://health.api.nvidia.com/v1/biology/mit/diffdock`
- Local: `http://localhost:8000/molecular-docking/diffdock/generate`

The hosted and local paths differ. Local has no `/v1/` prefix and uses the
`/molecular-docking/` route. 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.

## Local Docker

For the exact local preflight (`.env` load, `NVIDIA_API_KEY` fallback,
`LOCAL_NIM_CACHE`, `NVIDIA_VISIBLE_DEVICES=0`, `--shm-size=2G`, both `--ulimit`
flags, `docker login`, and the `docker run` for `nvcr.io/nim/mit/diffdock:2.2.0`),
copy the command block in [`references/api.md`](references/api.md) under
**Docker Reference** verbatim.

Readiness:

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

## Prepare Inputs

Protein receptor must be ATOM records only. Strip headers, water, and HETATM.

```python
from pathlib import Path
raw_pdb = Path("protein.pdb").read_text()
protein = "\n".join(line for line in raw_pdb.splitlines() if line.startswith("ATOM"))
if not protein:
    raise ValueError("protein.pdb has no ATOM records")
```

Ligand options:

- SMILES: `ligand = "CC(=O)OC1=CC=CC=C1C(=O)O"`; `ligand_file_type = "txt"`.
- SDF: `ligand = Path("ligand.sdf").read_text()`; `ligand_file_type = "sdf"`.
- MOL2: `ligand_file_type = "mol2"`.

Do not use `"smiles"` as `ligand_file_type`; SMILES is `"txt"`.

## Request Pattern

```python
import os
import requests

HOSTED = True
url = (
    "https://health.api.nvidia.com/v1/biology/mit/diffdock"
    if HOSTED else "http://localhost:8000/molecular-docking/diffdock/generate"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
    headers["Authorization"] = f"Bearer {os.getenv('NGC_API_KEY')}"

payload = {
    "protein": protein,
    "ligand": ligand,
    "ligand_file_type": ligand_file_type,
    "num_poses": 10,
    "time_divisions": 20,
    "steps": 18,
    "save_trajectory": False,
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()
```

## Save And Report Output

`ligand_positions` and `position_confidence` are parallel ranked lists.
`position_confidence[0]` is the rank-1 pose confidence.

Save the ranked pose SDFs using the snippet in
[`references/examples.md`](references/examples.md) under **Save Ranked Poses**.

View pose SDF files with the receptor in PyMOL, ChimeraX, or UCSF Chimera. For
pose sanity checks and confidence caveats, read `references/validation.md`.

## Limits And Troubleshooting

- Max `num_poses`: 100. Max `time_divisions`: 20. Max `steps`: 18.
- Single GPU; local minimum is about 24 GB VRAM.
- `422`: invalid `ligand_file_type`, invalid SMILES/SDF, or no ATOM records.
- Empty poses: validate receptor ATOM records and ligand parseability.
- Local URL 404 usually means the wrong hosted path or an accidental `/v1/`.

From NVIDIA/skills, Apache-2.0 AND CC-BY-4.0.

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