isotopic-distribution - npm Package Compare versions

Comparing version 1.2.3 to 1.3.0

package.json

 {
   "name": "isotopic-distribution",
-  "version": "1.2.3",
+  "version": "1.3.0",
   "description": "Calculate the isotopic distribution of a molecular formula",
@@ -21,8 +21,11 @@ "main": "src/index.js",
   "dependencies": {
-    "chemical-elements": "^1.1.13",
-    "mf-parser": "^1.3.5",
-    "mf-utilities": "^1.2.12",
+    "chemical-elements": "^1.2.0",
+    "mf-parser": "^1.4.0",
+    "mf-utilities": "^1.2.13",
     "spectrum-generator": "^5.4.0"
   },
-  "gitHead": "3357658b99069e3a03c06471bc374c5effb919d8"
+  "devDependencies": {
+    "jest-matcher-deep-close-to": "^3.0.2"
+  },
+  "gitHead": "b044512a459c82c7bb816c52d0e90d48b8ffeae3"
 }

src/__tests__/append.test.js

@@ -8,7 +8,7 @@ 'use strict';
     let dist1 = new Distribution();
-    dist1.push(1, 2);
-    dist1.push(2, 3);
+    dist1.push({ x: 1, y: 2 });
+    dist1.push({ x: 2, y: 3 });
     let dist2 = new Distribution();
-    dist2.push(2, 4);
-    dist2.push(3, 5);
+    dist2.push({ x: 2, y: 4 });
+    dist2.push({ x: 3, y: 5 });
 
@@ -15,0 +15,0 @@ dist1.append(dist2);

src/__tests__/closestPointX.test.js

@@ -8,6 +8,6 @@ 'use strict';
     let dist = new Distribution();
-    dist.push(1, 2);
-    dist.push(2, 3);
-    dist.push(3, 3);
-    dist.push(4, 3);
+    dist.push({ x: 1, y: 2 });
+    dist.push({ x: 2, y: 3 });
+    dist.push({ x: 3, y: 3 });
+    dist.push({ x: 4, y: 3 });
 
@@ -14,0 +14,0 @@ expect(dist.closestPointX(2)).toStrictEqual({ x: 2, y: 3 });

src/__tests__/distribution.test.js

@@ -7,27 +7,27 @@ 'use strict';
   it('create array', () => {
-    let array = new Distribution();
-    array.push(1, 2);
-    array.push(2, 3);
-    expect(array).toHaveLength(2);
+    let dist = new Distribution();
+    dist.push({ x: 1, y: 2 });
+    dist.push({ x: 2, y: 3 });
+    expect(dist).toHaveLength(2);
   });
 
-  it('join array 0', () => {
-    let array = new Distribution();
-    array.join();
-    expect(array.array).toStrictEqual([]);
+  it('joinX array 0', () => {
+    let dist = new Distribution();
+    dist.joinX();
+    expect(dist.array).toStrictEqual([]);
   });
 
-  it('join array 1', () => {
-    let array = new Distribution();
-    array.push(1, 1);
-    array.join();
-    expect(array.array).toStrictEqual([{ x: 1, y: 1 }]);
+  it('joinX array 1', () => {
+    let dist = new Distribution();
+    dist.push({ x: 1, y: 1 });
+    dist.joinX();
+    expect(dist.array).toStrictEqual([{ x: 1, y: 1 }]);
   });
 
-  it('join array', () => {
-    let array = new Distribution();
-    array.push(0, 0);
-    array.push(1, 1);
-    array.join();
-    expect(array.array).toStrictEqual([
+  it('joinX array', () => {
+    let dist = new Distribution();
+    dist.push({ x: 0, y: 0 });
+    dist.push({ x: 1, y: 1 });
+    dist.joinX();
+    expect(dist.array).toStrictEqual([
       { x: 0, y: 0 },
@@ -38,43 +38,43 @@ { x: 1, y: 1 },
 
-  it('really join array', () => {
-    let array = new Distribution();
-    array.push(0, 0);
-    array.push(1, 1);
-    array.join(1);
-    expect(array.array).toStrictEqual([{ x: 1, y: 1 }]);
+  it('really joinX array', () => {
+    let dist = new Distribution();
+    dist.push({ x: 0, y: 0 });
+    dist.push({ x: 1, y: 1 });
+    dist.joinX(1);
+    expect(dist.array).toStrictEqual([{ x: 1, y: 1 }]);
   });
 
-  it('really join array shifted', () => {
-    let array = new Distribution();
-    array.push(1, 0);
-    array.push(2, 1);
-    array.join(1);
-    expect(array.array).toStrictEqual([{ x: 2, y: 1 }]);
+  it('really joinX array shifted', () => {
+    let dist = new Distribution();
+    dist.push({ x: 1, y: 0 });
+    dist.push({ x: 2, y: 1 });
+    dist.joinX(1);
+    expect(dist.array).toStrictEqual([{ x: 2, y: 1 }]);
   });
 
-  it('really join array shifted weighted', () => {
-    let array = new Distribution();
-    array.push(1, 1);
-    array.push(2, 3);
-    array.join(1);
-    expect(array.array).toStrictEqual([{ x: 1.75, y: 4 }]);
+  it('really joinX array shifted weighted', () => {
+    let dist = new Distribution();
+    dist.push({ x: 1, y: 1 });
+    dist.push({ x: 2, y: 3 });
+    dist.joinX(1);
+    expect(dist.array).toStrictEqual([{ x: 1.75, y: 4 }]);
   });
 
-  it('really join array shifted weighted 3', () => {
-    let array = new Distribution();
-    array.push(1, 1);
-    array.push(2, 3);
-    array.push(2.25, 1);
-    array.join(1);
-    expect(array.array).toStrictEqual([{ x: 1.85, y: 5 }]);
+  it('really joinX array shifted weighted 3', () => {
+    let dist = new Distribution();
+    dist.push({ x: 1, y: 1 });
+    dist.push({ x: 2, y: 3 });
+    dist.push({ x: 2.25, y: 1 });
+    dist.joinX(1);
+    expect(dist.array).toStrictEqual([{ x: 1.85, y: 5 }]);
   });
 
-  it('really join array shifted weighted 4', () => {
-    let array = new Distribution();
-    array.push(1, 1);
-    array.push(2, 3);
-    array.push(2.25, 1);
-    array.push(5, 1);
-    array.join(1);
-    expect(array.array).toStrictEqual([
+  it('really joinX array shifted weighted 4', () => {
+    let dist = new Distribution();
+    dist.push({ x: 1, y: 1 });
+    dist.push({ x: 2, y: 3 });
+    dist.push({ x: 2.25, y: 1 });
+    dist.push({ x: 5, y: 1 });
+    dist.joinX(1);
+    expect(dist.array).toStrictEqual([
       { x: 1.85, y: 5 },
@@ -81,0 +81,0 @@ { x: 5, y: 1 },

src/__tests__/multiply.test.js

@@ -8,7 +8,7 @@ 'use strict';
     let dist1 = new Distribution();
-    dist1.push(1, 2);
-    dist1.push(2, 3);
+    dist1.push({ x: 1, y: 2 });
+    dist1.push({ x: 2, y: 3 });
     let dist2 = new Distribution();
-    dist2.push(1, 2);
-    dist2.push(2, 3);
+    dist2.push({ x: 1, y: 2 });
+    dist2.push({ x: 2, y: 3 });
     let dist3 = dist1.multiply(dist2);
@@ -15,0 +15,0 @@

src/__tests__/normalize.test.js

@@ -8,4 +8,4 @@ 'use strict';
     let dist = new Distribution();
-    dist.push(1, 2);
-    dist.push(2, 3);
+    dist.push({ x: 1, y: 2 });
+    dist.push({ x: 2, y: 3 });
     dist.normalize();
@@ -12,0 +12,0 @@

src/__tests__/power.test.js

@@ -8,4 +8,4 @@ 'use strict';
     let dist = new Distribution();
-    dist.push(1, 2);
-    dist.push(2, 3);
+    dist.push({ x: 1, y: 2 });
+    dist.push({ x: 2, y: 3 });
     dist.power(2);
@@ -21,3 +21,3 @@ expect(dist.array).toStrictEqual([
     let dist = new Distribution();
-    dist.push(1, 1);
+    dist.push({ x: 1, y: 1 });
     dist.power(3);
@@ -29,4 +29,4 @@ expect(dist.array).toStrictEqual([{ x: 3, y: 1 }]);
     let dist = new Distribution();
-    dist.push(1, 1);
-    dist.push(2, 1);
+    dist.push({ x: 1, y: 1 });
+    dist.push({ x: 2, y: 1 });
     dist.power(3);
@@ -43,4 +43,4 @@ expect(dist.array).toStrictEqual([
     let dist = new Distribution();
-    dist.push(1, 1);
-    dist.push(2, 1);
+    dist.push({ x: 1, y: 1 });
+    dist.push({ x: 2, y: 1 });
     dist.power(1000);
@@ -53,4 +53,4 @@ expect(dist.array).toHaveLength(1001);
     let dist = new Distribution();
-    dist.push(1, 0.5);
-    dist.push(2, 0.5);
+    dist.push({ x: 1, y: 0.5 });
+    dist.push({ x: 2, y: 0.5 });
     dist.power(100000);
@@ -57,0 +57,0 @@ let sum = dist.array.reduce((s, a) => s + a.y, 0);

src/__tests__/square.test.js

@@ -8,4 +8,4 @@ 'use strict';
     let dist = new Distribution();
-    dist.push(1, 2);
-    dist.push(2, 3);
+    dist.push({ x: 1, y: 2 });
+    dist.push({ x: 2, y: 3 });
     dist.square();
@@ -12,0 +12,0 @@ expect(dist.array).toStrictEqual([

src/__tests__/topY.test.js

@@ -8,6 +8,6 @@ 'use strict';
     let dist = new Distribution();
-    dist.push(1, 2);
-    dist.push(2, 3);
-    dist.push(2, 1);
-    dist.push(2, 4);
+    dist.push({ x: 1, y: 2 });
+    dist.push({ x: 2, y: 3 });
+    dist.push({ x: 2, y: 1 });
+    dist.push({ x: 2, y: 4 });
     dist.topY(2);
@@ -14,0 +14,0 @@

src/Distribution.js

@@ -73,4 +73,5 @@ 'use strict';
 
-Distribution.prototype.push = function push(x, y) {
-  this.array.push({ x, y });
+Distribution.prototype.push = function push(point) {
+  this.array.push(point);
+
   this.xSorted = false;
@@ -94,3 +95,3 @@ this.ySorted = false;
 Distribution.prototype.sortY = require('./utils/sortY.js');
-Distribution.prototype.join = require('./utils/join.js');
+Distribution.prototype.joinX = require('./utils/joinX.js');
 Distribution.prototype.topY = require('./utils/topY.js');
@@ -97,0 +98,0 @@ Distribution.prototype.maxToOne = require('./utils/maxToOne.js');

src/IsotopicDistribution.js

@@ -10,3 +10,6 @@ 'use strict';
 const Distribution = require('./Distribution');
+const getDerivedCompositionInfo = require('./utils/getDerivedCompositionInfo');
 
+const MINIMAL_FWHM = 1e-8;
+
 /**
@@ -69,4 +72,4 @@ * An object containing two arrays
     // if fwhm is under 1e-8 there are some artifacts in the spectra
-    if (this.fwhm < 1e-8) this.fwhm = 1e-8;
-    this.minY = options.minY === undefined ? 1e-8 : options.minY;
+    if (this.fwhm < MINIMAL_FWHM) this.fwhm = MINIMAL_FWHM;
+    this.minY = options.minY === undefined ? MINIMAL_FWHM : options.minY;
     this.maxLines = options.maxLines || 5000;
@@ -100,2 +103,3 @@ this.allowNeutral =
           y: 1,
+          composition: this.fwhm === MINIMAL_FWHM ? {} : undefined,
         },
@@ -109,5 +113,14 @@ ]);
           if (isotope.number > 0) {
-            let isotopeDistribution = new Distribution(isotope.distribution);
-            isotopeDistribution.power(isotope.number, options);
-            totalDistribution.multiply(isotopeDistribution, options);
+            const newDistribution = JSON.parse(
+              JSON.stringify(isotope.distribution),
+            );
+            if (this.fwhm === MINIMAL_FWHM) {
+              // add composition
+              for (const entry of newDistribution) {
+                entry.composition = { [Math.round(entry.x) + isotope.atom]: 1 };
+              }
+            }
+            let distribution = new Distribution(newDistribution);
+            distribution.power(isotope.number, options);
+            totalDistribution.multiply(distribution, options);
           }
@@ -162,3 +175,9 @@ }
     }
-    if (finalDistribution) finalDistribution.join(this.fwhm);
+    if (finalDistribution) finalDistribution.joinX(this.fwhm);
+
+    for (let entry of finalDistribution.array) {
+      if (!entry.composition) continue;
+      Object.assign(entry, getDerivedCompositionInfo(entry.composition));
+    }
+
     this.confidence /= this.parts.length;
@@ -228,3 +247,3 @@ this.cachedDistribution = finalDistribution;
    * @param {number} [options.sumValue] // if sumValue is defined, maxValue is ignored
-   * @return {XY} an object containing 2 properties: x:[] and y:[]
+   * @return {XY} an object containing at least the 2 properties: x:[] and y:[]
    */
@@ -234,3 +253,3 @@ getXY(options = {}) {
     let points = this.getDistribution().array;
-    if (points.length === 0) return [];
+    if (points.length === 0) return { x: [], y: [] };
     let factor = 1;
@@ -245,6 +264,13 @@ if (sumValue) {
 
-    return {
+    const result = {
       x: points.map((a) => a.x),
       y: points.map((a) => a.y / factor),
     };
+    for (let key of Object.keys(points[0]).filter(
+      (k) => k !== 'x' && k !== 'y',
+    )) {
+      result[key] = points.map((a) => a[key]);
+    }
+
+    return result;
   }
@@ -251,0 +277,0 @@

src/utils/multiply.js

@@ -13,13 +13,35 @@ 'use strict';
       let y = entryA.y * entryB.y;
-      if (y > minY) result.push(entryA.x + entryB.x, y);
-      if (result.length > maxLines) {
-        result.join(deltaX);
-        result.topY(maxLines / 2);
+      if (y > minY) {
+        const composition = calculateComposition(entryA, entryB);
+        if (composition) {
+          result.push({ x: entryA.x + entryB.x, y, composition });
+        } else {
+          result.push({ x: entryA.x + entryB.x, y });
+        }
       }
+      if (result.length > maxLines * 2) {
+        result.joinX(deltaX);
+        result.topY(maxLines);
+      }
     }
   }
-  result.join(deltaX);
-  result.topY(maxLines / 2);
+  result.joinX(deltaX);
+  result.topY(maxLines);
   this.move(result);
   return this;
 };
+
+function calculateComposition(entryA, entryB) {
+  if (!entryA.composition || !entryB.composition) return;
+  let toReturn = {};
+  const keys = [
+    ...new Set(
+      Object.keys(entryA.composition).concat(Object.keys(entryB.composition)),
+    ),
+  ];
+  for (let key of keys) {
+    toReturn[key] =
+      (entryA.composition[key] || 0) + (entryB.composition[key] || 0);
+  }
+  return toReturn;
+}

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Improved metrics

Total package byte prevSize

48395

increased by24.07%

Number of package files

30

increased by11.11%

Lines of code

1322

increased by28.85%

Worsened metrics

Dev dependency count

1

increased byInfinity%

Dependency changes

• Updatedchemical-elements@^1.2.0

• Updatedmf-parser@^1.4.0

• Updatedmf-utilities@^1.2.13