diffdock-nim

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 under Docker Reference verbatim.

Readiness:

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.

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")