mass-fragmentation - npm Package Compare versions

Comparing version 1.8.0 to 1.9.0

package.json

 {
   "name": "mass-fragmentation",
-  "version": "1.8.0",
+  "version": "1.9.0",
   "description": "Code to fragment molecules",
@@ -30,3 +30,3 @@ "main": "lib/index.js",
   },
-  "gitHead": "3300321a615311f64760cb500afac49f1f0f7d23"
+  "gitHead": "90cbc4b4397f04209190d40556c2d7e7752e6cbe"
 }

src/__tests__/reactionFragmentation.test.js

@@ -11,4 +11,4 @@ import OCL from 'openchemlib';
     const { trees, validNodes, masses } = reactionFragmentation(molecule);
-    expect(validNodes).toHaveLength(616);
-    expect(masses).toHaveLength(70);
+    expect(validNodes).toHaveLength(549);
+    expect(masses).toHaveLength(66);
     expect(trees).toMatchSnapshot();
@@ -24,3 +24,3 @@ });
     });
-    expect(validNodes).toHaveLength(243);
+    expect(validNodes).toHaveLength(249);
     expect(masses).toHaveLength(30);
@@ -35,3 +35,3 @@
     const { trees, validNodes, masses } = reactionFragmentation(molecule);
-    expect(validNodes).toHaveLength(973);
+    expect(validNodes).toHaveLength(997);
     expect(masses).toHaveLength(45);
@@ -38,0 +38,0 @@ expect(trees).toMatchSnapshot();

src/database/__tests__/getDatabase.test.js

@@ -6,3 +6,3 @@ import { getDatabase } from '../getDatabase.js';
     const db = getDatabase();
-    expect(db).toHaveLength(255);
+    expect(db).toHaveLength(187);
   });
@@ -12,3 +12,4 @@ it('kind:all and ionizationKind:esiPositive', () => {
       kind: ['ionization', 'resonance', 'reaction'],
-      ionizationKind: ['esiPositive'],
+      ionization: ['esi'],
+      mode: ['positive'],
     });
@@ -20,3 +21,4 @@ expect(db).toHaveLength(184);
       kind: ['ionization', 'resonance', 'reaction'],
-      ionizationKind: ['esiNegative'],
+      ionization: ['esi'],
+      mode: ['negative'],
     });
@@ -28,5 +30,5 @@ expect(db).toHaveLength(26);
       kind: ['ionization', 'resonance', 'reaction'],
-      ionizationKind: ['ei'],
+      ionization: ['ei'],
     });
-    expect(db).toHaveLength(45);
+    expect(db).toHaveLength(46);
   });
@@ -36,3 +38,4 @@ it('kind:ionization and ionizationKind:all', () => {
       kind: ['ionization'],
-      ionizationKind: ['esiPositive', 'esiNegative', 'ei'],
+      ionization: ['esi', 'ei'],
+      mode: ['positive', 'negative'],
     });
@@ -44,3 +47,4 @@ expect(db).toHaveLength(13);
       kind: ['ionization'],
-      ionizationKind: ['esiPositive'],
+      ionization: ['esi'],
+      mode: ['positive'],
     });
@@ -52,3 +56,4 @@ expect(db).toHaveLength(12);
       kind: ['ionization'],
-      ionizationKind: ['esiNegative'],
+      ionization: ['esi'],
+      mode: ['negative'],
     });
@@ -60,3 +65,3 @@ expect(db).toHaveLength(1);
       kind: ['ionization'],
-      ionizationKind: ['ei'],
+      ionization: ['ei'],
     });
@@ -68,3 +73,4 @@ expect(db).toHaveLength(0);
       kind: ['resonance'],
-      ionizationKind: ['esiPositive', 'esiNegative', 'ei'],
+      ionization: ['esi', 'ei'],
+      mode: ['positive', 'negative'],
     });
@@ -76,3 +82,4 @@ expect(db).toHaveLength(3);
       kind: ['resonance'],
-      ionizationKind: ['esiPositive'],
+      ionization: ['esi'],
+      mode: ['positive'],
     });
@@ -84,3 +91,4 @@ expect(db).toHaveLength(3);
       kind: ['resonance'],
-      ionizationKind: ['esiNegative'],
+      ionization: ['esi'],
+      mode: ['negative'],
     });
@@ -92,3 +100,3 @@ expect(db).toHaveLength(0);
       kind: ['resonance'],
-      ionizationKind: ['ei'],
+      ionization: ['ei'],
     });
@@ -100,5 +108,6 @@ expect(db).toHaveLength(0);
       kind: ['reaction'],
-      ionizationKind: ['esiPositive', 'esiNegative', 'ei'],
+      ionization: ['esi'],
+      mode: ['positive', 'negative'],
     });
-    expect(db).toHaveLength(239);
+    expect(db).toHaveLength(171);
   });
@@ -108,3 +117,4 @@ it('kind:reaction and ionizationKind:esiPositive', () => {
       kind: ['reaction'],
-      ionizationKind: ['esiPositive'],
+      ionization: ['esi'],
+      mode: ['positive'],
     });
@@ -116,3 +126,4 @@ expect(db).toHaveLength(169);
       kind: ['reaction'],
-      ionizationKind: ['esiNegative'],
+      ionization: ['esi'],
+      mode: ['negative'],
     });
@@ -124,6 +135,6 @@ expect(db).toHaveLength(25);
       kind: ['reaction'],
-      ionizationKind: ['ei'],
+      ionization: ['ei'],
     });
-    expect(db).toHaveLength(45);
+    expect(db).toHaveLength(46);
   });
 });

src/database/getDatabase.js

@@ -8,3 +8,4 @@ import { parseDwar } from 'openchemlib-utils';
  * @param {('ionization'|'resonance'|'reaction')[]} [options.kind=['ionization','resonance','reaction']] - The kind of database to be used
- * @param {('esiPositive'|'esiNegative'|'ei')[]} [options.ionizationKind=['esiPositive','esiNegative','ei']] - The ionization technique to be used
+ * @param {('esi'|'ei')[]} [options.ionization=['esi','ei']] - The ionization technique to be used
+ * @param {('positive'|'negative')[]} [options.mode=['positive','negative']] - The ionization mode to be used
  * @param {string} [options.dwar] - The dwar file to use. Default will use an included mass fragmentation database
@@ -16,3 +17,4 @@ * @returns
     kind = ['ionization', 'resonance', 'reaction'],
-    ionizationKind = ['esiPositive', 'esiNegative', 'ei'],
+    ionization = ['esi', 'ei'],
+    mode = ['positive', 'negative'],
     dwar,
@@ -24,5 +26,6 @@ } = options;
       kind.some((k) => entry.kind.includes(k)) &&
-      ionizationKind.some((ik) => entry.ionization.includes(ik)),
+      ionization.some((ik) => entry.ionization.split(',').includes(ik)) &&
+      mode.some((m) => entry.mode.split(',').includes(m)),
   );
   return database;
 }

src/reactionFragmentation.js

@@ -11,3 +11,4 @@ import { MF } from 'mf-parser';
  * @param {Object}  [options={}]
- * @param {('esiPositive'|'esiNegative'|'ei')[]}  [options.ionizationKind=['esiPositive']] - The ionization technique to be used
+ * @param {('esi'|'ei')[]}  [options.ionization=['esi']] - The ionization technique to be used
+ * @param {('positive'|'negative')[]}  [options.mode=['positive']] - The ionization mode to be used
  * @param {number}  [options.maxDepth=5] - The maximum depth of the overall fragmentation tree
@@ -27,3 +28,4 @@ * @param {number}  [options.limitReactions=200] - The maximum number of reactions to be applied to each branch
   const {
-    ionizationKind = ['esiPositive'],
+    ionization = ['esi'],
+    mode = ['positive'],
     dwar,
@@ -60,3 +62,4 @@ maxDepth = 5,
       kind: ['ionization'],
-      ionizationKind,
+      ionization,
+      mode,
       dwar,
@@ -69,3 +72,8 @@ }),
   );
-  const reactionDb = getDatabase({ kind: ['reaction'], ionizationKind, dwar });
+  const reactionDb = getDatabase({
+    kind: ['reaction'],
+    ionization,
+    mode,
+    dwar,
+  });
 
@@ -72,0 +80,0 @@ for (let i = 1; i <= maxReactions; i++) {

No alert changes

Worsened metrics

Total package byte prevSize

2432588

decreased by-4.51%

Lines of code

8189

decreased by-19.62%

No dependency changes