emdb

emdb

Database manager for molecular formula with various query feature.

Installation

npm install --save emdb

Using the project

There are 2 parts:

• adding databases in the database manager
• checking the databases
• searching the databases

Adding database in the database manager

const emdb = require('emdb');

emdb.loadTest(); // add a database named test containing all the molecular formula from C1 to C100

loadTest

A method that allows to create a database named 'test' and that contains all the molecular formula from C1 to C100

loadKnapSack

loadCommercials

loadContaminants

fromMonoisotopicMass(em, options)

fromArray

A method that creates a database (by default named generated) that contains all the posible combination based on an array of strings.

  emdb.fromArray( ['C1-10','N1-10']);

This method use the project 'mf-generator'

The following fields in the json are expected to be returned

• id
• url: optional external link
• mf
• em
• mw
• msem: calculated from em and charge
• charge
• ocl: either a string or an object with value / coordinates
• comment: if in the molecular formula there is a '$' this will end-up in this field
• parts: array of mf if the mf is the result of a combination of mf
• info: object of free information
• filter: optional information about the kind of mass spectra that yields to this mass
  • ESI
  • MALDI
  • positive
  • negative

loadGoogleSheet

Static methods

EMDB.Util.MF

Example:

var mf = new EMDB.Util.MF('Et3N');

EMDB.Util.IsotopicDistribution

EMDB.Util.Peptide

EMDB.Util.Peptide.sequenceToMF

Generates a molecular formula from a peptidic sequence.

Example:

const Peptide = require('emdb').Util.Peptide;
let mf = Peptide.mfFromSequence('AAA');
// mf = HAlaAlaAlaOH

EMDB.Util.Nucleotide

EMDB.Util.Nucleotide.sequenceToMF

Generates a molecular formula from a nucleotide sequence. Will correctly deal with dna, rna and ds-dna.

By default if the sequence contains a 'U' it is rna otherwise it is ds-dna. You can force the type by using the option kind. A nucleotide sequence may also be either circular or non circular (default value).

Example:

const Nucleotide = require('emdb').Util.Nucleotide;
let mf = Nucleotide.mfFromSequence('AAA', {circular: false, kind: 'dna'});
// mf = HODampDampDampH

License

MIT