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Open Source Science

https://github.com/cheminfo/nmr-parser

read and convert any NMR file

https://github.com/cheminfo/nmr-parser

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 9 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary

Keywords

bruker jcamp jcamp-dx jeol nmr nmr-parser nmr-spectroscopy parser

Keywords from Contributors

chemistry
Last synced: 5 months ago · JSON representation

Repository

read and convert any NMR file

Basic Info
  • Host: GitHub
  • Owner: cheminfo
  • License: mit
  • Language: JavaScript
  • Default Branch: main
  • Homepage:
  • Size: 1.54 MB
Statistics
  • Stars: 7
  • Watchers: 4
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Topics
bruker jcamp jcamp-dx jeol nmr nmr-parser nmr-spectroscopy parser
Created almost 6 years ago · Last pushed over 3 years ago
Metadata Files
Readme Changelog License

README.md

nmr-parser

NPM version build status Test coverage npm download

This package has born from the necessity to find a common data structure for NMR spectra (1D and 2D) originally stored in different formats as an entry point for processing pipelines. Reading and parsing data in original format represents an important work load for open source projects that usually seek to propose improved data analysis pipelines. This package aims at reading any NMR format and create a JSON object that is human readable, with a scientifically meaningful structure and variable names, strongly inspired by the work by Grandinetti and coworkers, but with a few liberties. For instance, camelCase variable naming has been preferred over the one proposed in the original work.

supported input formats

  • JCAMP-DX (may include several spectra)
  • Bruker data folder (as a zip file)
  • JEOL data format (.jdf)

data formats under development

What this package isn't?

  • This package is not promoting a new format
  • This package is not a JavaScript implementation of CSDM
  • This data structure in not intended for storage
  • This package is not intended to be a converter between formats

Installation

$ npm i nmr-parser

Usage

JCAMP

```js // import JCAMP parser import { fromJCAMP } from 'nmr-parser';

// import test data import { getData: getJcampData } from 'jcamp-data-test';

let data = fromJCAMP(await getJcampData('aspirin-1h.fid.dx')); ```

Bruker

```js // import Bruker parser import { fromBruker } from 'nmr-parser'; import { fileCollectionFromPath, fileCollectionFromZip } from 'filelist-utils';

// import bruker data import { getData: getBrukerData } from 'bruker-data-test'; const PATHTOBRUKERFOLDER = './' const fileCollection = fileCollectionFromPath(PATHTOBRUKERFOLDER); let data = await fromBruker(fileCollection);

//or

const zipBuffer = await getBrukerData('aspirin-1h.zip'); const fileCollection2 = await fileCollectionFromZip(zipBuffer); let data2 = await fromBruker(fileCollection2); ```

JEOL

```js // import JEOL parser import { fromJEOL } from 'nmr-parser';

// import test data import { experiments } from 'jeol-data-test';

let data = fromJEOL( experiments['Rutin3080ug200uLDMSOd6qHNMR400MHzJeol.jdf'], ); // result is a JSON object // { // timeStamp: 1593098292162, // version: '1.0.0' // description: { // title: 'title: RutinRUTI013080u200u / comment: qHNMR Spinning GARP Gated 13C Decoupled 20p 9pCntr 32K 90deg aq+d1=60s NS=128 / author:gfp / site: UIC ECZ400', // nucleus: [ '1H' ], // sampleName: 'RutinRUTI01_308', // date: '{"year":2016,"month":12,"day":21}', // ... // spectralWidth: 25.05370594702938, // metadata: {... ```

API Documentation

License

MIT

Owner

  • Name: Cheminfo
  • Login: cheminfo
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 178
  • Total Committers: 9
  • Avg Commits per committer: 19.778
  • Development Distribution Score (DDS): 0.674
Top Committers
Name Email Commits
jobo322 j****s@c****o 58
cheminfo-bot 1****t@u****m 42
jul j****t@c****o 42
Luc Patiny l****c@p****m 17
Michaël Zasso t****s@p****m 9
Luc Patiny l****y@u****m 4
cheminfo bot a****n@c****g 3
Michael Wenk m****k@u****e 2
Julien Wist j****t@u****m 1
Committer Domains (Top 20 + Academic)
correounivalle.edu.co: 2 uni-jena.de: 1 cheminfo.org: 1 patiny.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 14
  • Total pull requests: 62
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 0.71
  • Average comments per pull request: 1.32
  • Merged pull requests: 61
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lpatiny (5)
  • jobo322 (4)
  • michaelwenk (2)
  • targos (2)
  • mgreiner79 (1)
Pull Request Authors
  • cheminfo-bot (42)
  • jobo322 (18)
  • michaelwenk (2)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
autorelease: tagged (42) hacktoberfest-accepted (1)

Packages

  • Total packages: 1
  • Total downloads:
    • npm 88 last-month
  • Total dependent packages: 6
  • Total dependent repositories: 9
  • Total versions: 52
  • Total maintainers: 5
npmjs.org: nmr-parser

Read and convert any NMR file

  • Versions: 52
  • Dependent Packages: 6
  • Dependent Repositories: 9
  • Downloads: 88 Last month
Rankings
Dependent packages count: 3.2%
Dependent repos count: 3.9%
Average: 8.3%
Downloads: 11.4%
Stargazers count: 11.6%
Forks count: 11.7%
Maintainers (5)
cheminfo-bot targos lpatiny stropitek jwist
Last synced: 6 months ago

Dependencies

package.json npm
  • @babel/plugin-transform-modules-commonjs ^7.17.9 development
  • @rollup/plugin-json ^4.1.0 development
  • @types/jest ^27.5.0 development
  • bruker-data-test ^0.2.1 development
  • cheminfo-build ^1.1.11 development
  • eslint ^8.15.0 development
  • eslint-config-cheminfo ^7.3.0 development
  • jcamp-data-test ^0.0.5 development
  • jeol-data-test ^0.2.3 development
  • jest ^28.1.0 development
  • prettier ^2.6.2 development
  • rollup ^2.72.1 development
  • brukerconverter ^4.1.0
  • filelist-from ^0.3.0
  • filelist-utils ^0.5.0
  • is-any-array ^2.0.0
  • jcampconverter ^9.0.1
  • jeolconverter ^1.0.1
  • nmr-processing ^8.0.0
.github/workflows/documentationjs.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/checkout v3 composite
  • zakodium/documentationjs-action v1 composite
.github/workflows/lactame.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • zakodium/lactame-action v1 composite