nmrxiv-downloader: NMR Dataset Search & Download

CLI tool for searching and downloading NMR spectroscopy datasets from nmrxiv.org.

Setup

bash
1# Install from PyPI
2pip install nmrxiv-downloader
3
4# Verify installation
5nmrxiv --help

Quick Reference

Common Experiment Types

bash
1nmrxiv search --type hsqc      # 1H-13C HSQC
2nmrxiv search --type hmbc      # HMBC
3nmrxiv search --type cosy      # COSY
4nmrxiv search --type dept      # DEPT
5nmrxiv search --type "1d-13c"  # 1D 13C
6nmrxiv search --type noesy     # NOESY
7nmrxiv search --type tocsy     # TOCSY

Key Facts

• All output is JSON by default (add --no-json for human-readable)
• Projects have download URLs, datasets don't - download via parent project
• Data hierarchy: Project → Study → Dataset → Files (Bruker, JCAMP-DX)
• Pagination: Use --page N for large result sets

Workflow: Find and Download NMR Data

bash
1# 1. Search for experiment type
2nmrxiv search --type hsqc
3
4# 2. Get dataset details (shows parent project)
5nmrxiv show D410
6
7# 3. Download parent project
8nmrxiv download P11 --output ./data --extract
9
10# 4. Data is now in ./data/P11/

Workflow: Search by Compound

bash
1# 1. Search by name
2nmrxiv search --query "quercetin"
3
4# 2. Or by SMILES substructure
5nmrxiv search --smiles "c1ccc(O)cc1"
6
7# 3. Find related projects
8nmrxiv list --type project | jq '.items[] | select(.name | test("quercetin"; "i"))'

Error Handling

If download fails with "No download URL":

json
1{"error": true, "message": "No download URL for D410. Try downloading parent project: P11", "code": 1}

→ Use the suggested parent project ID to download.

Parsing Examples

bash
1# Get first project identifier
2nmrxiv list --type project | jq -r '.items[0].identifier'
3
4# Get all HSQC dataset IDs
5nmrxiv search --type hsqc | jq -r '.results[].identifier'
6
7# Get download URL for a project
8nmrxiv show P5 | jq -r '.item.download_url'