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    chemcalc

    3.4.1 • Public • Published

    chemcalc-js

    NPM version build status npm download

    Library allowing to manipulate and find molecular formula.
    This library contains 2 main functions: analyseMF and mfFromMonoisotopicMass.
    In all the molecular formula you are allowed to use groups like Phe, Ala, Gly, Ph, ...

    Installation

    npm install chemcalc --save
    OR
    bower install chemcalc
    OR just include in a script tag

    Usage

    In NodeJS

    var chemcalc = require('chemcalc');
    var result = chemcalc.analyseMF('CaSO4.1/2H2O');

    In the browser

    By default

    var result = CI.Chemcalc.analyseMF('PhNH2.HCl');

    Using an AMD loader

    require(['lib/chemcalc'], function(Chemcalc) { 
        var result = Chemcalc.analyseMF('Ph(CO)C(CH3)3');
    });

    Documentation

    General

    getInfo()

    Get information about elements, isotopes and special groups.

    Molecular formula

    analyseMF(mf, [options])

    Get various information about a molecular formula as an object.
    From a molecular formula and different options, this function will return an object that may contain the monoisotopic mass, molecular weight, element analysis, isotopic distribution (as a JDX of XY).
    Molecular formula can be entered using groups, parenthesis, isotopes, combinatorial elements, enriched isotopic elements, ...

    Arguments

    • mf - string with the molecular formula to analyse

    Options

    • isotopomers - Should we calculate the isotompers, possible values are xy, jcamp, array or any comma-separated combination (default: false). The use of "arrayXYXY" or "arrayXXYY" allows to get back a javascript array for further processing.
    • fwhm - Specify the FWHM to calculate the information (default: 0.001)
    • threshold - Intensity cutoff (default: 1e-5)
    • gaussianWidth - Define the number of point (default: 0). A good value is 10 which means that the width at half the height will be 10 points.
    • joiningAlgorithm - May take 2 values: "center" (center of mass) or "main" (keep the main peak) (default: main)
    • typedResult - The result field will be typed like "mf" "jcamp" ... so instead of having "mf":"C10H12" the json will contain "mf":{type:"mf",value:"C10H12"} (default: false)
    • defaultUnsaturationContribution - Allow to have a default value for the isotope with undefined unsaturation contribution. By default it is null and therefore if you use element like Ru, V, ... the unsaturation will not be calculated.
    • groups - a comma separated string containing abbreviation : molecular formula that can be used further in the definiation of molecular formula. It should always ba an uppercase followed by 2 to 5 lowercase. Example: Ala:C3H5NO,Gly:C2H3NO

    Examples

    Chemcalc.analyseMF("CH3CH2Cl") Retrieve a JSON containing the information about all the parts of this molecular formula. In this case there is only one part.
    Chemcalc.analyseMF("CH3CH2Cl",{isotopomers:"xy,jcamp",fwhm:0.0001}) Retrieve a JSON containing the information for a molecular formula with a FWHM of 0.0001 and calculate also the isotopomers as a jcamp and xy.
    Chemcalc.analyseMF("RuClH(CO)(PPh3)3") MF containing groups (like "Ph") and parenthesis.
    Chemcalc.analyseMF("CuSO4.5H2O") MF containing many parts.
    Chemcalc.analyseMF("{Ph,Me}Me") MF containing a mixture of groups (like in combinatorial chemistry), ie 0.5PhMe+0.5MeMe.
    Chemcalc.analyseMF("HAla(H-1Ph)OH") MF containing a negative atom count. Funny way to represent the phenyl alanine but very practical to describe peptide side-chain modification.
    Chemcalc.analyseMF("C{50,50}10C10") MF containing atoms with non natural isotopic ratio. ie 10 atoms of enriched C (50% 12C and 50% 13C) and 10 natural abundance carbons.
    Chemcalc.analyseMF("HAla10OH+.HAla10OH++.HAla10OH+++") MF containing many parts and charges. ie a mixure of mono, di and tri- charged decapeptide, perfect for mass spectra simulation.

    mfFromMonoisotopicMass(mass, [options])

    Find molecular formulas from a monoisotopic mass.
    This general method allow to retrieve the possible molecular formula based on a monoisotopic mass and a range of atoms or groups. Various options may be specified.
    This method is well optimized and can provide possible molecular formula even with huge ranges.
    It also allows to provide groups of atoms. For example you may allow a possible sequence of amino acids: H2OAla0-20Arg0-20Asn0-20Asp0-20Cys0-20Gln0-20Glu0-20Gly0-20His0-20Ile0-20Leu0-20Lys0-20Met0-20Phe0-20Pro0-20Ser0-20Val0-20Thr0-20Trp0-20Tyr0-20.

    Arguments

    • mass - Target monoisotopic mass

    Options

    • mfRange - Molecular formula range like for example: 'C1-30H1-60' (default: C0-20H0-40N0-5O0-8F0-3Cl0-3Br0-1). The range may also include groups or non natural isotopic ratio.
    • minUnsaturation - Minimal number of unsaturation (default: 0)
    • maxUnsaturation - Maximal number of unsaturation (default: 50)
    • integerUnsaturation - Integer number of unsaturation (default: true)
    • useUnsaturation - Should we use unsaturation as a filter if possible (default: true)
    • numberOfResultsOnly - Returns only the number of results found (default: false)
    • massRange - Range of mass to analyse (default: 0.5)
    • maxNumberRows - Maximum number of results (rows) to retrieve (default: 1000)
    • typedResult - The result field will be typed like "mf" "jcamp" ... so instead of having "mf":"C10H12" the json will contain "mf":{type:"mf",value:"C10H12"}
    • defaultUnsaturationContribution - Allow to have a default value for the isotope with undefined unsaturation contribution. By default it is null and therefore if you use element like Ru, V, ... the unsaturation will not be calculated and therefore filtering is not possible.
    • groups - a comma separated string containing abbreviation : molecular formula that can be used further in the definiation of molecular formula. It should always ba an uppercase followed by 2 to 5 lowercase. Example: Ala:C3H5NO,Gly:C2H3NO

    Examples

    Chemcalc.mfFromMonoisotopicMass(397.17,{'mfRange':'C1-30F0-10H1-60N0-10O0-10'}) Retrieve all the molecular formula close to 397.17 and within a range of C1-30F0-10H1-60N0-10O0-10. The other options will be used by default. Only integer unsaturation from 0 to 50 and a massRange of +/- 0.5.
    Chemcalc.mfFromMonoisotopicMass(1000,{'mfRange':'H2OAla0-20Arg0-20Asn0-20Asp0-20Cys0-20Gln0-20Glu0-20Gly0-20His0-20Ile0-20Leu0-20Lys0-20Met0-20Phe0-20Pro0-20Ser0-20Val0-20Thr0-20Trp0-20Tyr0-20'}) Find a peptide with monoisotopic mass close to 1000. You should note the H2O that is added in order to add the H on the N-terminal and OH on the C-terminal. All the groups like Ala, Gly, Thr, etc. are diradicals.

    Peptides

    All the methods has been moved to chemcalc-extented.

    Development

    To build the project, run gulp build:min
    To test the build, run npm test

    License

    BSD

    Install

    npm i chemcalc

    DownloadsWeekly Downloads

    25

    Version

    3.4.1

    License

    BSD

    Last publish

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