chemcalc-extended

Extend the project chemcalc with new functionnalities

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chemcalc-extended

NPM version build status Test coverage David deps npm download

chemcalc-extended project - Extend chemcalc-js to allow experimental spectra similarity search

Configuration

mfFromMonoisotopicMassSimilarity(mass, experimental, options)

  • experimental : an array of [[x1,y1],[x2,y2],...] or [[x1,x2,x3,...][y1,y2,y3,...]]

options are the same as mfFromMonoisotopicMass with the following added possibilities:

  • widthTop : top width of the trapezoid
  • widthBottom : bottom width of the trapezoid
  • widthFunction : code that allows to calculate the widthBottom and widthTop from mass and charge.
var widthTop=mass*0.005;
var widthBottom=mass*0.010;
  • from : mass "from" which calculate the similarity
  • to : mass "to" which calculate the similarity
  • decimalsPPM : number of decimals for PPM
  • decimalsMass : number decimals for the mass

analyseMF(mf, options)

Extends analyseMF from chemcalc to return a property atoms that contains the number of each of the atoms.

Arguments

  • mf - string with a molecular formula to charge
  • options

matchMFs

We will try to find the molecular formula that match

matchMFs(mfs, experimental, options)

  • experimental : an array of [[x1,y1],[x2,y2],...] or [[x1,x2,x3,...][y1,y2,y3,...]]
  • mfs: array of array (or simple array) of all the possibilities to test / combine
  • options
    • widthTop : top width of the trapezoid
    • widthBottom : bottom width of the trapezoid
    • from : mass "from" which calculate the similarity
    • to : mass "to" which calculate the similarity
    • decimalsPPM : number of decimals for PPM
    • decimalsMass : number of decimals for the mass
    • zone : zone on which to calculate similarity. It is based on monoisotopic mass. It is an object that contains "low" and "high". Those values will be divided by the charge of the current molecular formula. Default: zone: {low: -0.5, high: 4.5}
    • bestOf : keep only the best result in the defined range of mass. By default, 0 = not used
    • maxResults : keep only the best similarity. This process is done after "bestOf". By default: 500
    • minSimilarity : minimal similarity value (between 0 and 1). By default: 50
    • common : only consider the common part for similarity calculation based on the widthBottom value (Default: '', possible values: '', 'first', 'second', 'both')

combineMFs(array)

We may have array of array of string and we combine to get all the possible MFs

ex:

  • combineMFs([["C","H$YY"],[],[""],["Cl","Br$XX"]])
  • combineMFs(["C.H.O","+,++",['Cl','Br$XX']])

enumerateMF(string|regexp, options)

Enumerate molecules given a regular expression:

Example:

var result = CE.enumerateMF('HCys(C(Gly|Ala10)|C{50,50}|C{90,10})OH');
 /* 
 result should be: 
 [
    'HCys(C(Ala10))OH',
    'HCys(C(Gly))OH',
    'HCys(C{50,50})OH',
    'HCys(C{90,10})OH'
 ]
 */

The options are the same as regexp-enumerator library

getEutrophicationPotential

getEutrophicationPotential(mf)

Returns an object containing the eutrophication potential of the given molecular formula.

Peptides

convertAASequence(sequence)

Returns a peptidic sequence from a PDB or one letter code to the internal molecular formula format

Arguments

  • sequence - string with the amino acids sequence

chargePeptide(mf, options)

Charge the peptide at a specific pH. 'mf' is either a 3 letter peptide sequence or an array of peptide sequences.

Arguments

  • mf - string with a molecular formula to charge
  • options:
  • pH : you may specify the pH to calculate the protonation state. By default: 0, it has the consequence to add a positive charge on Arg, His and Lys.

allowNeutralLoss(mf, options)

Allow neutral loss for the follow residues:

  • H2O for S, T, E, D
  • NH3 for R, K, Q, N

The residues may not be side-chain modified.

generatePeptideFragments(mf, [options])

Generate peptide fragmentation. Returns an array of molecular formulas with the different fragments.

Arguments

  • mf - string with the molecular formula
  • options - object with requested fragments. Default: {a:false, b:true, c:false, x:false, y:true, z:false, i:false}

splitPeptide(sequence)

Split a 3 letter code sequence respecting uppercase, lowercase in an array of residu.

Arguments

  • sequence - string with the amino acids sequence

digestPeptide(sequence, options)

Allows to digest virtually a peptide

Arguments

  • sequence - string with the amino acids sequence
  • options
    • minMissed - minimal missed cleavage (default: 0)
    • maxMissed - maximal missed cleavage (default: 0)
    • minResidue - minimal number of residues (default: 0)
    • maxResidue - maximal number of residues (default: infinity)
    • enzyme - enzyme used for digestion
      • chymotrypsin : (Phe|Tyr|Trp)(?!Pro)
      • trypsin : (Lys|Arg)(?!Pro)
      • lysc : (Lys)(?!Pro)
      • glucph4 : (Glu)(?!Pro|Glu)
      • glucph8 : (Asp|Glu)(?!Pro|Glu)
      • thermolysin : (Leu|Ile|Met|Phe|Trp)
      • cyanogenbromide : (Met)

Development

Install dev dependencies

npm install

Execute test suite

npm test

License

MIT

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