mf-finder - npm Package Compare versions

Comparing version 0.5.8 to 0.5.9

package.json

 {
   "name": "mf-finder",
-  "version": "0.5.8",
+  "version": "0.5.9",
   "description": "Find a molecular formula from a monoisotopic mass",
@@ -21,7 +21,8 @@ "main": "src/index.js",
   "dependencies": {
-    "chemical-elements": "^0.5.8",
-    "mf-parser": "^0.5.8",
-    "mf-utilities": "^0.5.8",
+    "atom-sorter": "^0.5.9",
+    "chemical-elements": "^0.5.9",
+    "mf-parser": "^0.5.9",
+    "mf-utilities": "^0.5.9",
     "molecular-formula": "^1.1.0"
   }
 }

src/__tests__/mfFinder.js

@@ -96,4 +96,6 @@ 'use strict';
             allowNeutral: true,
-            minUnsaturation: 0,
-            maxUnsaturation: 1
+            unsaturation: {
+                min: 0,
+                max: 1
+            }
         });
@@ -112,5 +114,7 @@ expect(result.mfs).toHaveLength(2);
             allowNeutral: true,
-            minUnsaturation: 0,
-            maxUnsaturation: 1,
-            onlyIntegerUnsaturation: true,
+            unsaturation: {
+                min: 0,
+                max: 1,
+                onlyInteger: true
+            }
         });
@@ -239,2 +243,17 @@ expect(result.mfs).toHaveLength(1);
 
+    it('check order in molecular formula', () => {
+        let result = findMFs(1199, {
+            ranges: [
+                { mf: 'C', min: 0, max: 100 },
+                { mf: 'H', min: 0, max: 100 },
+                { mf: 'S', min: 0, max: 10 },
+                { mf: 'N', min: 0, max: 10 },
+                { mf: 'O', min: 0, max: 10 },
+            ],
+            precision: 1,
+            allowNeutral: true
+        });
+        expect(result.mfs[0].mf).toBe('C88H5N3O4S');
+    });
+
     it('check impossible charge', () => {
@@ -241,0 +260,0 @@

src/index.js

 'use strict';
 
+const atomSorter = require('atom-sorter');
 const preprocessRanges = require('./preprocessRanges');
@@ -23,6 +24,3 @@ const preprocessIonizations = require('mf-utilities/src/preprocessIonizations');
         maxCharge = Number.MAX_SAFE_INTEGER,
-        minUnsaturation = Number.MIN_SAFE_INTEGER,
-        maxUnsaturation = Number.MAX_SAFE_INTEGER,
-        onlyIntegerUnsaturation = false,
-        onlyNonIntegerUnsaturation = false,
+        unsaturation = {},
         maxIterations = 1e8,
@@ -38,6 +36,6 @@ allowNeutral = true, // if there is no msem we use em !
 
-    let filterUnsaturation = (minUnsaturation !== Number.MIN_SAFE_INTEGER || maxUnsaturation !== Number.MAX_SAFE_INTEGER || onlyIntegerUnsaturation || onlyNonIntegerUnsaturation);
+    let filterUnsaturation = unsaturation ? true : false;
     // we calculate not the real unsaturation but the one before dividing by 2 + 1
-    let fakeMinUnsaturation = (minUnsaturation === Number.MIN_SAFE_INTEGER) ? Number.MIN_SAFE_INTEGER : (minUnsaturation - 1) * 2;
-    let fakeMaxUnsaturation = (maxUnsaturation === Number.MAX_SAFE_INTEGER) ? Number.MAX_SAFE_INTEGER : (maxUnsaturation - 1) * 2;
+    let fakeMinUnsaturation = (unsaturation.min === undefined) ? Number.MIN_SAFE_INTEGER : (unsaturation.min - 1) * 2;
+    let fakeMaxUnsaturation = (unsaturation.max === undefined) ? Number.MAX_SAFE_INTEGER : (unsaturation.max - 1) * 2;
 
@@ -49,2 +47,3 @@ let filterCharge = (minCharge !== Number.MIN_SAFE_INTEGER || maxCharge !== Number.MAX_SAFE_INTEGER);
     };
+    let orderMapping = []; // used to sort the atoms
 
@@ -63,2 +62,4 @@ // we need to make the processing for all the ionizations
         let possibilities = preprocessRanges(ranges);
+        orderMapping = getOrderMapping(possibilities);
+
         if (possibilities.length === 0) return { mfs: [] };
@@ -90,9 +91,9 @@ targetMassCache = new TargetMassCache(targetMass, possibilities, Object.assign({}, options, { charge: ionization.charge }));
             if (filterUnsaturation) {
-                let unsaturation = lastPossibility.currentUnsaturation;
-                let isOdd = Math.abs(unsaturation % 2);
+                let unsaturationValue = lastPossibility.currentUnsaturation;
+                let isOdd = Math.abs(unsaturationValue % 2);
                 if (
-                    (onlyIntegerUnsaturation && isOdd === 1) ||
-                    (onlyNonIntegerUnsaturation && isOdd === 0) ||
-                    (fakeMinUnsaturation > unsaturation) ||
-                    (fakeMaxUnsaturation < unsaturation)
+                    (unsaturation.onlyInteger && isOdd === 1) ||
+                    (unsaturation.onlyNonInteger && isOdd === 0) ||
+                    (fakeMinUnsaturation > unsaturationValue) ||
+                    (fakeMaxUnsaturation < unsaturationValue)
                 ) isValid = false;
@@ -112,3 +113,3 @@ }
             if (isValid) {
-                result.mfs.push(getResult(possibilities, targetMass, allowNeutral, ionization));
+                result.mfs.push(getResult(possibilities, targetMass, allowNeutral, ionization, orderMapping));
                 result.info.numberResults++;
@@ -152,3 +153,3 @@ }
 
-function getResult(possibilities, targetMass, allowNeutralMolecules, ionization) {
+function getResult(possibilities, targetMass, allowNeutralMolecules, ionization, orderMapping) {
     let lastPossibility = possibilities[possibilities.length - 1];
@@ -167,3 +168,5 @@
     // in the final result
-    for (let possibility of possibilities) {
+
+    for (let i = 0; i < possibilities.length; i++) {
+        let possibility = possibilities[orderMapping[i]];
         if (possibility.currentCount !== 0) {
@@ -215,1 +218,9 @@ if (possibility.isGroup) {
 }
+
+function getOrderMapping(possibilities) {
+    let mapping = possibilities.map((p, i) => ({ atom: p.mf, index: i }));
+    mapping.sort((a, b) => {
+        return atomSorter(a.atom, b.atom);
+    });
+    return mapping.map((a) => a.index);
+}

No alert changes

Improved metrics

Total package byte prevSize

34928

increased by2.23%

Lines of code

823

increased by3.26%

Worsened metrics

Dependency count

5

increased by25%

Dependency changes

• + Addedatom-sorter@^0.5.9

• Updatedchemical-elements@^0.5.9

• Updatedmf-parser@^0.5.9

• Updatedmf-utilities@^0.5.9