japanfold

Command-line client for JapanFold, a hosted API for protein structure prediction, binder design and protein embeddings. No GPU and no model weights on your side; the models run on JapanFold's servers in Japan.

pip install japanfold
export JAPANFOLD_API_KEY=jf_live_...       # from https://japanfold.aiand.com/account/token
japanfold fold --sequence MKTAYIAKQRQISFVKSHFSRQ --wait --out ./out

It has no dependencies beyond the Python standard library (3.9+).

Key and endpoint

Every call needs a key. Sign in at japanfold.aiand.com/account/token to get one; a new account comes with $100 of credit. The CLI reads it from --api-key, then $JAPANFOLD_API_KEY, then ~/.config/japanfold/config.json (written by japanfold auth login).

The API lives at https://api.japanfold.aiand.com. Set JAPANFOLD_BASE_URL or --base-url to point somewhere else.

Commands

japanfold models                                   # every model and design protocol
japanfold fold --sequence MKTAYIAK... --model boltz2 --wait --out ./out
japanfold design spec.yaml --model boltzgen --protocol nanobody-anything --wait --out ./out
japanfold design --model rfd3 --protocol rfd3-binder --structure target.pdb \
    --contig 'A1-150,60-80' --wait --out ./out
japanfold design --model pxdesign --protocol pxdesign-binder --structure target.pdb \
    --chains A --binder-length 80 --hotspots A64,A65,A66 --wait --out ./out
japanfold embed --sequence MKTAYIAK... --model esmc-600m --wait --out ./out
japanfold wait JOB_ID --out ./out                  # wait for a job and download it
japanfold credits                                  # balance left on the key
japanfold jobs list

--wait submits, waits for the job and downloads the results in one foreground command. Without it a command prints the job id and returns; japanfold wait JOB_ID picks it up later and is safe to re-run. fold is the same command as predict, and wait the same as download.

For agents

--json on any command prints machine-readable JSON on stdout and keeps human messages on stderr. japanfold schema prints the OpenAPI 3.1 contract. Exit codes say what went wrong without parsing text:

Agents that prefer plain HTTP can skip the CLI: the docs cover the REST API, and the agent skill lives at github.com/japanfold/japanfold.