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Open Source Science

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

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

Science Score: 36.0%

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    CITATION.cff file
  • ✓
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    2 of 6 committers (33.3%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary

Keywords from Contributors

nmr nmr-spectroscopy chemistry
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 1
  • Open Issues: 2
  • Releases: 31
Created over 5 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

nmr-correlation

NPM version npm download

This package provides methods to build correlation data from NMR spectra. The NMR dataset has to be already processed and given in a certain format (see below).

Mainly, this is done by a grouping of signals with same nuclei between 1D and 2D or 2D and 2D NMR spectra. Each group is then represented by one correlation.

If a molecular formula is given, then missing correlations will be added as placeholder to complete the list.

Another feature is to determine the number of attached protons by using information from DEPT 90/135 or multiplicity-edited HSQC.

Input

Spectra

  • array of 1D, 2D, DEPT 90/135 spectra, e.g. obtained by nmr-load-save
  • each spectrum has to be processed, e.g. via nmr-processing
  • declared type for spectra is

ts type Spectra = Array<Spectrum1D | Spectrum2D>;

  • further type definitions are available in src/types

Options

  • tolerances (must be given for each occurring atom type in spectra)
  • molecular formula (optional)

Values

  • optional, previously built correlations
  • useful to not override the following information if it is set to true in edited property:
    • hybridization, equivalence, protonsCount

Output

State

  • for each atom type with at least one correlation
  • current number of correlations
  • some error information according to a given molecular formula

Values

An array of correlations with following content:

  • link (array)
    • signal, axis (1D/2D signal and current axis which links to signals in another spectra)
    • match (indices of correlations with signal shift matches)
    • pseudo (whether this link is artificial)
    • some further meta information
  • attachment (contains indices of each attached correlation/atom)
  • protonsCount (array of possible numbers of attached protons)
  • equivalence (number of equivalences, default is 1)
  • hybridization (not set, except a CH3 group was detected)
  • pseudo (whether this is a placeholder, e.g. if molecular formula is given)
  • some further meta information, e.g. the group representing signal

Installation

$ npm i nmr-correlation

Usage

```js import { fromJCAMP } from 'nmr-parser'; import { buildCorrelationData } from 'nmr-correlation';

// parse spectra (symbolic example) const data1H = fromJCAMP('1h.dx'); const data13C = fromJCAMP('13C.dx'); const dataHSQC = fromJCAMP('hsqc.dx'); const dataHMBC = fromJCAMP('hmbc.dx'); const dataCOSY = fromJCAMP('cosy.dx'); const dataDEPT90 = fromJCAMP('dept90.dx'); const dataDEPT135 = fromJCAMP('dept135.dx');

// process data (ranges/zones picking) // ... // put all the information together into specified format // ...

// combine spectra into one array const spectra = [ data1H, data13C, dataHSQC, dataHMBC, dataCOSY, dataDEPT90, dataDEPT135, ]; // create options const options = { tolerance: { C: 0.25, H: 0.02, }, mf: 'C11H14N2O', // molecular formula }; // build correlation data const correlationData = buildCorrelationData(spectra, options); ```

License

MIT

Owner

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

GitHub Events

Total
  • Release event: 3
  • Delete event: 7
  • Issue comment event: 8
  • Push event: 14
  • Pull request event: 12
  • Create event: 9
Last Year
  • Release event: 3
  • Delete event: 7
  • Issue comment event: 8
  • Push event: 14
  • Pull request event: 12
  • Create event: 9

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 163
  • Total Committers: 6
  • Avg Commits per committer: 27.167
  • Development Distribution Score (DDS): 0.239
Top Committers
Name Email Commits
michaelwenk m****k@u****e 124
cheminfo-bot 1****t@u****m 23
Luc Patiny l****c@p****m 6
Luc Patiny l****y@u****m 4
Michaël Zasso t****s@p****m 4
Jose Alejandro Bolanos Arroyave j****s@c****o 2
Committer Domains (Top 20 + Academic)
correounivalle.edu.co: 1 patiny.com: 1 uni-jena.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 3
  • Total pull requests: 56
  • Average time to close issues: 7 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 1.0
  • Average comments per pull request: 1.21
  • Merged pull requests: 53
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 14
  • Average time to close issues: N/A
  • Average time to close pull requests: 13 minutes
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 1.07
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jobo322 (2)
  • targos (1)
Pull Request Authors
  • cheminfo-bot (32)
  • michaelwenk (14)
  • targos (8)
  • jobo322 (2)
Top Labels
Issue Labels
Pull Request Labels
autorelease: tagged (26) autorelease: pending (6)

Packages

  • Total packages: 1
  • Total downloads:
    • npm 4,315 last-month
  • Total dependent packages: 6
  • Total dependent repositories: 10
  • Total versions: 34
  • Total maintainers: 4
npmjs.org: nmr-correlation

Build and manipulation of correlations from 1D and 2D NMR data

  • Versions: 34
  • Dependent Packages: 6
  • Dependent Repositories: 10
  • Downloads: 4,315 Last month
Rankings
Downloads: 3.0%
Dependent packages count: 3.2%
Dependent repos count: 3.7%
Average: 8.5%
Forks count: 11.6%
Stargazers count: 21.0%
Maintainers (4)
cheminfo-bot targos lpatiny michaelwenk
Last synced: 11 months ago

Dependencies

package.json npm
  • @types/jest ^28.1.6 development
  • @types/lodash ^4.14.182 development
  • eslint ^8.21.0 development
  • eslint-config-cheminfo-typescript ^11.0.1 development
  • jest ^28.1.3 development
  • prettier ^2.7.1 development
  • rimraf ^3.0.2 development
  • ts-jest ^28.0.7 development
  • typescript ^4.7.4 development
  • cheminfo-types ^1.4.0
  • lodash ^4.17.21
  • ml-matrix-peaks-finder ^1.0.0
  • ml-peak-shape-generator ^4.1.1
.github/workflows/typedoc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • zakodium/typedoc-action v2 composite
.github/workflows/nodejs.yml actions
.github/workflows/release.yml actions