emdb v3.4.1
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
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