nmr-cli Service
The nmr-cli container (nmr-converter) packages the nmr-load-save toolchain and related NMR processing utilities. NMRKit invokes it via docker exec for spectra parsing, format conversion, and structure-based prediction.
Docker image
| Registry | Image | Tags |
|---|---|---|
| Docker Hub | nfdi4chem/nmr-cli | dev-latest, latest |
In docker-compose.yml the service is named nmr-load-save with container name nmr-converter.
Commands used by NMRKit
| nmr-cli command | API endpoint | Description |
|---|---|---|
parse-spectra | POST /spectra/parse/url, POST /spectra/parse/file | Parse Bruker, JCAMP-DX, zipped archives into NMRium JSON |
parse-publication-string | POST /spectra/parse/publication-string | Reconstruct spectrum from ACS publication string |
peaks-to-nmrium | POST /spectra/parse/peaks | Generate spectrum from a peak list |
predict | POST /predict/, POST /predict/file | Predict spectra via nmrdb.org or nmrshift |
-u <url> | GET /convert/spectra | Legacy URL-based conversion |
parse-spectra flags
| Flag | API parameter | Description |
|---|---|---|
-u | url | Remote URL to spectra file |
-p | file / auto_processing | File path or enable FID → FT processing |
-s | capture_snapshot | Capture spectra image snapshot |
-d | auto_detection | Automatic range/zone detection |
-r | raw_data | Include raw data in output |
Manual testing
Build and run the container locally:
bash
docker pull nfdi4chem/nmr-cli:dev-latest
docker run -it --name nmr-converter nfdi4chem/nmr-cli:dev-latest bashInside the container:
bash
nmr-cli parse-spectra -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
nmr-cli predict -s "<mol block>" --engine nmrshift --spectra protonShared volume
The /shared volume is mounted in both nmrkit-api and nmr-converter so uploaded MOL files can be passed to nmr-cli predict without docker cp.
Timeouts
| Operation | Timeout |
|---|---|
| Spectra parsing | 120 s |
| nmrshift prediction | 120 s |
| nmrdb.org prediction | 300 s |