mass-fragmentation - npm Package Compare versions

Comparing version 1.6.0 to 1.7.0

package.json

 {
   "name": "mass-fragmentation",
-  "version": "1.6.0",
+  "version": "1.7.0",
   "description": "Code to fragment molecules",
@@ -30,3 +30,3 @@ "main": "lib/index.js",
   },
-  "gitHead": "6603850b30bead58389d612027251b5a406e4d1d"
+  "gitHead": "5792f7e51124ce002a78753392b4e352e705a229"
 }

src/__tests__/getFragmentationSVG.test.js

@@ -13,3 +13,11 @@ import { writeFileSync } from 'fs';
     OCL,
-    masses: [97.5624, 105.0697, 58.065, 194.1173, 163.0752, 133.0647, 135.0439],
+    peaks: [
+      { mass: 97.5624, intensity: 100 },
+      { mass: 105.0697, intensity: 100 },
+      { mass: 58.065, intensity: 100 },
+      { mass: 194.1173, intensity: 100 },
+      { mass: 163.0752, intensity: 100 },
+      { mass: 133.0647, intensity: 100 },
+      { mass: 135.0439, intensity: 100 },
+    ],
     accuracy: 50,
@@ -16,0 +24,0 @@ });

src/__tests__/reactionFragmentation.test.js

@@ -11,4 +11,4 @@ import OCL from 'openchemlib';
     const { trees, validNodes, masses } = reactionFragmentation(molecule);
-    expect(validNodes).toHaveLength(159);
-    expect(masses).toHaveLength(18);
+    expect(validNodes).toHaveLength(624);
+    expect(masses).toHaveLength(70);
     expect(trees).toMatchSnapshot();
@@ -24,3 +24,3 @@ });
     });
-    expect(validNodes).toHaveLength(294);
+    expect(validNodes).toHaveLength(297);
     expect(masses).toHaveLength(35);
@@ -35,6 +35,6 @@
     const { trees, validNodes, masses } = reactionFragmentation(molecule);
-    expect(validNodes).toHaveLength(550);
-    expect(masses).toHaveLength(54);
+    expect(validNodes).toHaveLength(1266);
+    expect(masses).toHaveLength(50);
     expect(trees).toMatchSnapshot();
   });
 });

src/database/__tests__/getDatabase.test.js

@@ -6,3 +6,3 @@ import { getDatabase } from '../getDatabase.js';
     const db = getDatabase();
-    expect(db).toHaveLength(190);
+    expect(db).toHaveLength(251);
   });
@@ -14,3 +14,3 @@ it('kind:all and ionizationKind:esiPositive', () => {
     });
-    expect(db).toHaveLength(145);
+    expect(db).toHaveLength(181);
   });
@@ -22,3 +22,3 @@ it('kind:all and ionizationKind:esiNegative', () => {
     });
-    expect(db).toHaveLength(0);
+    expect(db).toHaveLength(25);
   });
@@ -37,3 +37,3 @@ it('kind:all and ionizationKind:ei', () => {
     });
-    expect(db).toHaveLength(7);
+    expect(db).toHaveLength(11);
   });
@@ -45,3 +45,3 @@ it('kind:ionization and ionizationKind:esiPositive', () => {
     });
-    expect(db).toHaveLength(7);
+    expect(db).toHaveLength(11);
   });
@@ -95,3 +95,3 @@ it('kind:ionization and ionizationKind:esiNegative', () => {
     });
-    expect(db).toHaveLength(183);
+    expect(db).toHaveLength(240);
   });
@@ -103,3 +103,3 @@ it('kind:reaction and ionizationKind:esiPositive', () => {
     });
-    expect(db).toHaveLength(138);
+    expect(db).toHaveLength(170);
   });
@@ -111,3 +111,3 @@ it('kind:reaction and ionizationKind:esiNegative', () => {
     });
-    expect(db).toHaveLength(0);
+    expect(db).toHaveLength(25);
   });
@@ -114,0 +114,0 @@ it('kind:reaction and ionizationKind:ei', () => {

src/getFragmentationSVG.js

 import { render, moleculeRenderer } from 'react-tree-svg';
 
+/**
+ * @typedef {object} MassPeak
+ * @property {number} mass
+ * @property {number} intensity
+ */
+
+/**
+ * @param {object[]} trees
+ * @param {object} [options={}]
+ * @param {object} [options.OCL]
+ * @param {number} [options.accuracy]
+ * @param {MassPeak[]} [options.peaks]
+ * @returns
+ */
 export function getFragmentationSVG(trees, options = {}) {
-  const { OCL, accuracy, masses = [] } = options;
+  const { OCL, accuracy, peaks = [] } = options;
 
+  const maxIntensity =
+    peaks?.length > 0
+      ? Math.log(Math.max(...peaks.map((peak) => peak.intensity)) + 1)
+      : 0;
+
   const rendererOptions = {
@@ -22,5 +41,8 @@ nodeRenderer: moleculeRenderer,
         for (const molecule of node.molecules) {
-          if (isInRange(masses, molecule?.info?.mz, accuracy)) {
+          const peak = getPeakInRange(peaks, molecule?.info?.mz, accuracy);
+          if (peak) {
             return {
-              fillOpacity: 0.2,
+              fillOpacity: maxIntensity
+                ? (0.2 * Math.log(peak.intensity + 1)) / maxIntensity
+                : 0.2,
               fill: 'red',
@@ -45,14 +67,14 @@ };
 
-function isInRange(masses, mass, accuracy) {
-  if (!mass || !masses) {
-    return false;
+function getPeakInRange(peaks, mass, accuracy) {
+  if (!mass || !Array.isArray(peaks)) {
+    return undefined;
   }
   const massAccuracy = (accuracy * mass) / 1e6;
 
-  for (const value of masses) {
-    if (Math.abs(value - mass) <= massAccuracy) {
-      return true;
+  for (const peak of peaks) {
+    if (Math.abs(peak.mass - mass) <= massAccuracy) {
+      return peak;
     }
   }
-  return false;
+  return undefined;
 }

No alert changes

Improved metrics

Total package byte prevSize

2852475

increased by89.13%

Lines of code

9568

increased by21.58%

No dependency changes