isotopic-distribution - npm Package Compare versions

Comparing version 0.5.6 to 0.5.8

package.json

 {
   "name": "isotopic-distribution",
-  "version": "0.5.6",
+  "version": "0.5.8",
   "description": "Calculate the isotopic distribution of a molecular formula",
@@ -21,7 +21,7 @@ "main": "src/index.js",
   "dependencies": {
-    "chemical-elements": "^0.5.2",
-    "mf-parser": "^0.5.2",
-    "mf-utilities": "^0.5.2",
-    "spectrum-generator": "^1.0.1"
+    "chemical-elements": "^0.5.8",
+    "mf-parser": "^0.5.8",
+    "mf-utilities": "^0.5.8",
+    "spectrum-generator": "^1.1.0"
   }
 }

src/__tests__/getGaussian.js

@@ -8,9 +8,8 @@ 'use strict';
     it('create distribution of C1 and getGaussian', () => {
-        let isotopicDistribution = new IsotopicDistribution('C');
+        let isotopicDistribution = new IsotopicDistribution('C', { fwhm: 0.1 });
         let gaussian = isotopicDistribution.getGaussian({
             from: 11.00,
             to: 13.00,
-            getWidth: () => 0.1,
-            pointsPerUnit: 10,
         });
+        expect(gaussian.x).toHaveLength(201);
         expect(Math.min(...gaussian.x)).toBe(11);
@@ -17,0 +16,0 @@ expect(Math.max(...gaussian.x)).toBe(13);

src/__tests__/isotopicDistribution.js

@@ -13,2 +13,64 @@ 'use strict';
 
+    it('create distribution for multiplepart, C.C2', () => {
+        let isotopicDistribution = new IsotopicDistribution('C.C2');
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array).toMatchObject([{ x: 12, y: 0.9893 },
+            { x: 13.00335483507, y: 0.0107 },
+            { x: 24, y: 0.9787144899999999 },
+            { x: 25.00335483507, y: 0.02117102 },
+            { x: 26.00670967014, y: 0.00011448999999999998 }]
+        );
+    });
+
+    it('create distribution for multiplepart, C.C2.C3', () => {
+        let isotopicDistribution = new IsotopicDistribution('C.C2.C3');
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array.reduce((e, p) => (e += p.y), 0)).toBeCloseTo(3, 5);
+    });
+
+    it('create distribution for charged multiplepart, C+.(C+)2', () => {
+        let isotopicDistribution = new IsotopicDistribution('C+.(C+)2');
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array).toMatchObject(
+            [
+                { x: 11.99945142009093, y: 1.9680144899999998 },
+                { x: 12.501128837625929, y: 0.02117102 },
+                { x: 13.00280625516093, y: 0.01081449 }
+            ]
+        );
+    });
+
+    it('getParts of isotopic distribution', () => {
+        let isotopicDistribution = new IsotopicDistribution('C', {
+            ionizations: 'H+'
+        });
+        let parts = isotopicDistribution.getParts();
+        expect(parts[0].ms.em).toBeCloseTo(13.00727645232093, 5);
+    });
+
+    it('create distribution for many ionizations, C + (+, ++)', () => {
+        let isotopicDistribution = new IsotopicDistribution('C', { ionizations: '+,++' });
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array).toMatchObject(
+            [
+                { x: 5.99945142009093, y: 0.9893 },
+                { x: 6.50112883762593, y: 0.0107 },
+                { x: 11.99945142009093, y: 0.9893 },
+                { x: 13.00280625516093, y: 0.0107 }
+            ]
+        );
+    });
+
+    it('create distribution for many ionizations, C + H+', () => {
+        let isotopicDistribution = new IsotopicDistribution('C', { ionizations: 'H+' });
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array).toMatchObject(
+            [
+                { x: 13.00727645232093, y: 0.9893 },
+                { x: 14.01063128739093, y: 0.0107 }
+            ]
+        );
+    });
+
+
     it('create distribution of C10 and getXY', () => {
@@ -78,3 +140,15 @@ let isotopicDistribution = new IsotopicDistribution('C10');
 
+    it('create distribution with no elements Ru0', () => {
+        let isotopicDistribution = new IsotopicDistribution('Ru0');
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array).toMatchObject([{ x: 0, y: 1 }]);
+    });
 
+
+    it('create distribution with null elements', () => {
+        let isotopicDistribution = new IsotopicDistribution('CRu0C');
+        let distribution = isotopicDistribution.getDistribution();
+        expect(distribution.array[0].x).toBe(24);
+    });
+
 });

src/Distribution.js

@@ -76,2 +76,14 @@ 'use strict';
 
+/**
+ * Appen another distribution to the current distribution
+ * @param {*} distribution
+ */
+Distribution.prototype.append = function append(distribution) {
+    for (let item of distribution.array) {
+        this.array.push(item);
+    }
+    this.xSorted = false;
+    this.ySorted = false;
+};
+
 Distribution.prototype.sortX = require('./utils/sortX.js');
@@ -78,0 +90,0 @@ Distribution.prototype.sortY = require('./utils/sortY.js');

src/IsotopicDistribution.js

@@ -10,5 +10,16 @@ 'use strict';
 const MF = require('mf-parser').MF;
+const preprocessIonizations = require('mf-utilities/src/preprocessIonizations');
+const getMsInfo = require('mf-utilities/src/getMsInfo');
 
+/**
+    * An object containing two arrays
+    * @typedef {object} XY
+    * @property {Array<number>} x - The x array
+    * @property {Array<number>} y - The y array
+*/
 
+
 class IsotopicDistribution {
+
+
     /**
@@ -18,17 +29,39 @@ * Class that manage isotopic distribution
      * @param {object} [options={}]
-     * @param {number} [fwhm=0.001] - Amount of Dalton under which 2 peaks are joined
+     * @param {string} [options.ionizations=''] - string containing a comma separated list of modifications
+     * @param {number} [options.fwhm=0.01] - Amount of Dalton under which 2 peaks are joined
+     * @param {number} [options.maxLines=5000] - Maximal number of lines during calculations
+     * @param {number} [options.minY=1e-8] - Minimal signal height during calculations
      */
+
     constructor(mf, options = {}) {
+        this.ionizations = preprocessIonizations(options.ionizations);
         this.mf = new MF(mf);
-        this.isotopesInfo = this.mf.getIsotopesInfo();
-        this.charge = this.isotopesInfo.charge;
-        this.absoluteCharge = Math.abs(this.isotopesInfo.charge);
-        this.cache = {};
+        this.mfInfo = this.mf.getInfo();
+        let parts = this.mfInfo.parts || [this.mfInfo];
+        this.parts = [];
+        for (let partOriginal of parts) { // we calculate informations for each part
+            for (const ionization of this.ionizations) {
+                let part = JSON.parse(JSON.stringify(partOriginal));
+                part.em = part.monoisotopicMass; // TODO: To remove !!! we change the name !?
+                part.isotopesInfo = (new MF(part.mf)).getIsotopesInfo();
+                part.confidence = 0;
+                part.ionization = ionization;
+                part.ms = getMsInfo(part, {
+                    ionization,
+                });
+                this.parts.push(part);
+            }
+        }
         this.options = options;
-        this.fwhm = options.fwhm || 0.001;
-        this.confidence = 0;
+        this.fwhm = options.fwhm || 0.01;
+        this.minY = options.minY || 1e-8;
+        this.maxLines = options.maxLines || 5000;
     }
 
+    getParts() {
+        return this.parts;
+    }
+
     /**
-     * @return {Distribution} returns the internal object that contains the isotopic distribution
+     * @return {Distribution} returns the total distribution (for all parts)
      */
@@ -38,34 +71,60 @@
         let options = {
-            threshold: this.fwhm
+            maxLines: this.maxLines,
+            minY: this.minY,
+            deltaX: this.fwhm,
         };
-        if (this.cache.distribution) return this.cache.distribution;
-        let totalDistribution = new Distribution([{ x: 0, y: 1 }]);
+        let finalDistribution;
+        this.confidence = 0;
+        for (let i = 0; i < this.parts.length; i++) {
+            let part = this.parts[i];
+            let totalDistribution = new Distribution([{ x: 0, y: 1 }]);
 
-        for (let isotope of this.isotopesInfo.isotopes) {
-            let isotopeDistribution = new Distribution(isotope.distribution);
-            isotopeDistribution.power(isotope.number, options);
-            totalDistribution.multiply(isotopeDistribution, options);
-        }
-        this.cache.distribution = totalDistribution;
-        this.confidence = this.cache.distribution.array.reduce((sum, value) => (sum + value.y), 0);
+            for (let isotope of part.isotopesInfo.isotopes) {
+                if (isotope.number) {
+                    let isotopeDistribution = new Distribution(isotope.distribution);
+                    isotopeDistribution.power(isotope.number, options);
+                    totalDistribution.multiply(isotopeDistribution, options);
+                }
+            }
+            this.confidence += totalDistribution.array.reduce((sum, value) => (sum + value.y), 0);
 
-        // we finally deal with the charge
-        if (this.isotopesInfo.charge) {
-            this.cache.distribution.array.forEach((e) => {
-                e.x = (e.x - ELECTRON_MASS * this.charge) / this.absoluteCharge;
-            });
+            // we finally deal with the charge
+            let charge = part.isotopesInfo.charge + part.ionization.charge;
+            let absoluteCharge = Math.abs(charge);
+            if (charge) {
+                totalDistribution.array.forEach((e) => {
+                    e.x = (e.x + part.ionization.em - ELECTRON_MASS * charge) / absoluteCharge;
+                });
+            }
+            if (i === 0) {
+                finalDistribution = totalDistribution;
+            } else {
+                finalDistribution.append(totalDistribution);
+            }
         }
+        finalDistribution.join(this.fwhm);
+        this.confidence /= this.parts.length;
+        return finalDistribution;
+    }
 
-        return this.cache.distribution;
+
+    getCSV() {
+        return this.getText(',');
     }
 
+    getTSV() {
+        return this.getText('\t');
+    }
 
-    /**
-    * An object containing two arrays
-    * @typedef {object} XY
-    * @property {Array<number>} x - The x array
-    * @property {Array<number>} y - The y array
-    */
+    getText(delimiter) {
+        let points = this.getDistribution().array;
+        let csv = [];
+        for (let point of points) {
+            csv.push(`${point.x.toFixed(5)}${delimiter}${(point.y * 100).toFixed(3)}`);
+        }
+        return csv.join('\n');
+    }
 
     /**
+     * Returns the isotopic distirubtion
      * @return {XY} an object containing 2 properties: x:[] and y:[]
@@ -88,5 +147,11 @@ */
 
+    /**
+     * Returns the isotopic distirubtion as the sum of gaussians
+     *  @return {XY} isotopic distribution as an object containing 2 properties: x:[] and y:[]
+     */
+
     getGaussian(options = {}) {
         let distribution = this.getDistribution();
         let points = distribution.array;
+        let pointsPerUnit = 10 / this.fwhm;
         if (points.length === 0) return [];
@@ -96,4 +161,5 @@ let gaussianOptions = {
             end: Math.ceil(options.to || distribution.maxX + 10),
-            pointsPerUnit: options.pointsPerUnit || 10,
-            getWidth: options.getWidth ? options.getWidth : () => 0.1,
+            pointsPerUnit,
+            getWidth: options.getWidth ? options.getWidth : () => this.fwhm,
+            maxSize: options.maxSize
         };
@@ -100,0 +166,0 @@

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Improved metrics

Total package byte prevSize

27029

increased by30.17%

Number of package files

24

increased by4.35%

Lines of code

680

increased by28.06%

Dependency changes

• Updatedchemical-elements@^0.5.8

• Updatedmf-parser@^0.5.8

• Updatedmf-utilities@^0.5.8

• Updatedspectrum-generator@^1.1.0