nmr-parser
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 foler (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
// 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
// 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 PATH_TO_BRUKER_FOLDER = './'
const fileCollection = fileCollectionFromPath(PATH_TO_BRUKER_FOLDER);
let data = await fromBruker(fileCollection);
//or
const zipBuffer = await getBrukerData('aspirin-1h.zip');
const fileCollection2 = await fileCollectionFromZip(zipBuffer);
let data2 = await fromBruker(fileCollection2);JEOL
// import JEOL parser
import { fromJEOL } from 'nmr-parser';
// import test data
import { experiments } from 'jeol-data-test';
let data = fromJEOL(
experiments['Rutin_3080ug200uL_DMSOd6_qHNMR_400MHz_Jeol.jdf'],
);
// result is a JSON object
// {
// timeStamp: 1593098292162,
// version: '1.0.0'
// description: {
// title: 'title: Rutin_RUTI01_3080u200u / comment: qHNMR Spinning GARP Gated 13C Decoupled 20p 9pCntr 32K 90deg aq+d1=60s NS=128 / author:gfp / site: UIC ECZ400',
// nucleus: [ '1H' ],
// sampleName: 'Rutin_RUTI01_308',
// date: '{"year":2016,"month":12,"day":21}',
// ...
// spectralWidth: 25.05370594702938,
// metadata: {...