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Extend chemcalc-js to allow experimental spectra similarity search\n\n## Configuration\n\n### mfFromMonoisotopicMassSimilarity(mass, experimental, options)\n\n* experimental : an array of [[x1,y1],[x2,y2],...] or [[x1,x2,x3,...][y1,y2,y3,...]]\n\noptions are the same as mfFromMonoisotopicMass with the following added possibilities:\n* widthTop : top width of the trapezoid\n* widthBottom : bottom width of the trapezoid\n* widthFunction : code that allows to calculate the `widthBottom` and `widthTop` from `mass` and `charge`.\n```js\nvar widthTop=mass*0.005;\nvar widthBottom=mass*0.010;\n```\n* from : mass \"from\" which calculate the similarity\n* to : mass \"to\" which calculate the similarity\n* decimalsPPM : number of decimals for PPM\n* decimalsMass : number decimals for the mass\n\n#### analyseMF(mf, options)\n\nExtends analyseMF from chemcalc to return a property atoms that contains the number of each of the atoms.\n\n__Arguments__\n\n* mf - string with a molecular formula to charge\n* options\n\n\n\n\n### matchMFs\n\nWe will try to find the molecular formula that match \n\nmatchMFs(mfs, experimental, options)\n* experimental : an array of [[x1,y1],[x2,y2],...] or [[x1,x2,x3,...][y1,y2,y3,...]]\n* mfs: array of array (or simple array) of all the possibilities to test / combine\n* options\n  * widthTop : top width of the trapezoid\n  * widthBottom : bottom width of the trapezoid\n  * from : mass \"from\" which calculate the similarity\n  * to : mass \"to\" which calculate the similarity\n  * decimalsPPM : number of decimals for PPM\n  * decimalsMass : number of decimals for the mass\n  * 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}\n  * bestOf : keep only the best result in the defined range of mass. By default, 0 = not used\n  * maxResults : keep only the best similarity. This process is done after \"bestOf\". By default: 500\n  * minSimilarity : minimal similarity value (between 0 and 1). By default: 50\n  * common : only consider the common part for similarity calculation based on the widthBottom value (Default: '', possible values: '', 'first', 'second', 'both')\n\n### combineMFs(array)\n\nWe may have array of array of string and we combine to get all the possible MFs\n\nex:\n* combineMFs([[\"C\",\"H$YY\"],[],[\"\"],[\"Cl\",\"Br$XX\"]])\n* combineMFs([\"C.H.O\",\"+,++\",['Cl','Br$XX']])\n\n### enumerateMF(string|regexp, options)\n\nEnumerate molecules given a regular expression:\n\nExample: \n\n```js\nvar result = CE.enumerateMF('HCys(C(Gly|Ala10)|C{50,50}|C{90,10})OH');\n /* \n result should be: \n [\n    'HCys(C(Ala10))OH',\n    'HCys(C(Gly))OH',\n    'HCys(C{50,50})OH',\n    'HCys(C{90,10})OH'\n ]\n */\n```\n\nThe options are the same as [regexp-enumerator](https://github.com/cheminfo-js/regexp-enumerator) library\n\n### getEutrophicationPotential\n\ngetEutrophicationPotential(mf)\n\nReturns an object containing the eutrophication potential of the given molecular formula.\n\n### Peptides\n\n#### convertAASequence(sequence)\n\nReturns a peptidic sequence from a PDB or one letter code to the internal molecular formula format\n\n__Arguments__\n\n* `sequence` - string with the amino acids sequence\n\n#### chargePeptide(mf, options)\n\nCharge the peptide at a specific pH. 'mf' is either a 3 letter peptide sequence or an array of peptide sequences.\n\n__Arguments__\n\n* `mf` - string with a molecular formula to charge\n* options:\n * pH : you may specify the pH to calculate the protonation state. By default: 0,\n   it has the consequence to add a positive charge on Arg, His and Lys.\n\n#### allowNeutralLoss(mf, options)\n\nAllow neutral loss for the follow residues:\n- H2O for S, T, E, D\n- NH3 for R, K, Q, N\n\nThe residues may not be side-chain modified.\n\n#### generatePeptideFragments(mf, [options])\n\nGenerate [peptide fragmentation](http://en.wikipedia.org/wiki/Peptide_sequence_tag).\nReturns an array of molecular formulas with the different fragments.\n\n__Arguments__\n\n* `mf` - string with the molecular formula\n* `options` - object with requested fragments. Default: `{a:false, b:true, c:false, x:false, y:true, z:false, i:false}`\n\n\n#### splitPeptide(sequence)\n\nSplit a 3 letter code sequence respecting uppercase, lowercase in an array of residu.\n\n__Arguments__\n\n* `sequence` - string with the amino acids sequence\n\n\n#### digestPeptide(sequence, options)\n\nAllows to digest virtually a peptide\n\n__Arguments__\n\n* `sequence` - string with the amino acids sequence\n* `options`\n  * `minMissed` - minimal missed cleavage (default: 0)\n  * `maxMissed` - maximal missed cleavage (default: 0)\n  * `minResidue` - minimal number of residues (default: 0)\n  * `maxResidue` - maximal number of residues (default: infinity)\n  * `enzyme` - enzyme used for digestion\n    * chymotrypsin : (Phe|Tyr|Trp)(?!Pro)\n    * trypsin : (Lys|Arg)(?!Pro)\n    * lysc : (Lys)(?!Pro)\n    * glucph4 : (Glu)(?!Pro|Glu)\n    * glucph8 : (Asp|Glu)(?!Pro|Glu)\n    * thermolysin : (Leu|Ile|Met|Phe|Trp)\n    * cyanogenbromide : (Met)\n\n## Development\n\n### Install dev dependencies\n\n`npm install`\n\n### Execute test suite\n\n`npm test`\n\n## License\n\n  [MIT](./LICENSE)\n\n[npm-image]: https://img.shields.io/npm/v/chemcalc-extended.svg?style=flat-square\n[npm-url]: https://www.npmjs.com/package/chemcalc-extended\n[travis-image]: https://img.shields.io/travis/cheminfo-js/chemcalc-extended/master.svg?style=flat-square\n[travis-url]: https://travis-ci.org/cheminfo-js/chemcalc-extended\n[coveralls-image]: https://img.shields.io/coveralls/cheminfo-js/chemcalc-extended.svg?style=flat-square\n[coveralls-url]: https://coveralls.io/github/cheminfo-js/chemcalc-extended\n[david-image]: https://img.shields.io/david/cheminfo-js/chemcalc-extended.svg?style=flat-square\n[david-url]: https://david-dm.org/cheminfo-js/chemcalc-extended\n[download-image]: https://img.shields.io/npm/dm/chemcalc-extended.svg?style=flat-square\n[download-url]: https://www.npmjs.com/package/chemcalc-extended\n","maintainers":[{"name":"lpatiny","email":"lpatiny@gmail.com"},{"name":"cheminfo-bot","email":"admin@cheminfo.org"}],"time":{"modified":"2022-06-13T05:56:42.824Z","created":"2015-03-16T15:56:16.770Z","1.1.0":"2015-03-16T15:56:16.770Z","1.1.1":"2015-03-16T16:06:28.284Z","1.2.2":"2015-03-17T12:48:37.960Z","1.4.0":"2015-04-27T11:52:01.500Z","1.4.2":"2015-04-30T13:04:32.739Z","1.5.0":"2015-05-20T15:21:39.031Z","1.5.1":"2015-05-29T13:05:50.971Z","1.8.2":"2015-09-02T14:40:20.948Z","1.8.4":"2015-09-03T07:13:50.404Z","1.8.5":"2015-09-03T07:22:43.087Z","1.17.0":"2015-12-15T15:57:49.631Z","1.19.1":"2016-04-20T09:22:21.047Z","1.22.1":"2016-05-02T06:45:18.119Z","1.25.0":"2016-06-16T11:26:45.060Z","1.27.0":"2016-12-23T18:56:21.879Z","1.27.4":"2017-01-09T13:21:40.587Z","1.27.5":"2017-08-18T06:20:39.071Z","1.28.0":"2017-08-18T06:23:41.021Z","1.29.0":"2017-08-18T13:37:12.694Z","2.0.0":"2017-09-27T08:48:21.786Z","2.1.0":"2017-09-28T12:14:27.841Z"},"homepage":"https://github.com/cheminfo-js/chemcalc-extended","keywords":["chemcalc-extended","mass similarity","mass spectrometry","chemcalc","molecular formula","monoisotopic mass","eutrophication potential"],"repository":{"type":"git","url":"git+https://github.com/cheminfo-js/chemcalc-extended.git"},"author":{"name":"Luc Patiny"},"bugs":{"url":"https://github.com/cheminfo-js/chemcalc-extended/issues"},"license":"MIT","readmeFilename":"README.md","users":{"slowbrain":true}}