mf-generator - npm Package Compare versions

Comparing version 0.5.0 to 0.5.2

package.json

 {
   "name": "mf-generator",
-  "version": "0.5.0",
+  "version": "0.5.2",
   "description": "",
@@ -21,6 +21,9 @@ "main": "src/index.js",
   "dependencies": {
-    "chemical-elements": "^0.5.0",
-    "mf-matcher": "^0.5.0",
-    "mf-parser": "^0.5.0"
+    "chemical-elements": "^0.5.2",
+    "mf-finder": "^0.5.2",
+    "mf-matcher": "^0.5.2",
+    "mf-parser": "^0.5.2",
+    "mf-utilities": "^0.5.2",
+    "sum-object-keys": "^1.0.2"
   }
 }

src/index.js

 'use strict';
 
-const { ELECTRON_MASS } = require('chemical-elements/src/constants');
+
 const MF = require('mf-parser').MF;
-const matcher = require('mf-matcher');
+const matcher = require('mf-matcher').msem;
 const sum = require('sum-object-keys');
+const preprocessIonizations = require('mf-utilities/src/preprocessIonizations');
 
@@ -13,6 +14,7 @@ /**
  * @param keys
- * @param options
+ * @param {object} options
  * @param {number} [options.limit=10000000] - Maximum number of results
  * @param {boolean} [canonizeMF=true] - Canonize molecular formula
  * @param {boolean} [uniqueMFs=true] - Force canonization and make MF unique
+ * @param {string} [ionizations=''] - Comma separated list of ionizations (to charge the molecule)
  * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
@@ -22,4 +24,4 @@ * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
  * @param {number} [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
- * @param {number} [options.filter.minMSEM=0] - Minimal observed monoisotopic mass
- * @param {number} [options.filter.maxMSEM=+Infinity] - Maximal observed monoisotopic mass
+ * @param {number} [options.filter.targetMass] - Experimental observed mass
+ * @param {number} [options.filter.precision=1000] - Precision
  * @param {number} [options.filter.minCharge=-Infinity] - Minimal charge
@@ -36,6 +38,6 @@ * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
 
-module.exports = function combineMFs(keys, options = {}) {
+module.exports = function generateMFs(keys, options = {}) {
     let {
         limit = 10000000,
-        uniqueMFs
+        uniqueMFs,
     } = options;
@@ -45,3 +47,5 @@ if (uniqueMFs === undefined) uniqueMFs = true;
     if (options.canonizeMF === undefined) options.canonizeMF = true;
+    options.ionizations = preprocessIonizations(options.ionizations);
 
+
     if (!Array.isArray(keys)) throw new Error('You need to specify an array of strings or arrays');
@@ -101,6 +105,7 @@
     appendResult(results, currents, keys, options);
+
     if (uniqueMFs) {
         var uniqueMFsObject = {};
         results.forEach((r) => {
-            uniqueMFsObject[r.mf] = r;
+            uniqueMFsObject[r.mf + r.ionization.mf] = r;
         });
@@ -133,3 +138,3 @@ results = Object.keys(uniqueMFsObject).map((k) => uniqueMFsObject[k]);
 
-function getEMFromParts(parts, currents) {
+function getEMFromParts(parts, currents, ionization) {
     var charge = 0;
@@ -142,2 +147,3 @@ var em = 0;
 
+
     for (var i = 0; i < parts.length; i++) {
@@ -156,15 +162,8 @@ var part = parts[i][currents[i]];
     }
-    var msem = em;
-    if (charge > 0) {
-        msem = msem / charge - ELECTRON_MASS;
-    } else if (charge < 0) {
-        msem = msem / (charge * -1) + ELECTRON_MASS;
-    } else {
-        msem = 0;
-    }
+
     return {
         charge,
         em,
-        msem,
         mw,
+        ionization: ionization,
         unsaturation: validUnsaturation ? unsaturation / 2 + 1 : undefined,
@@ -178,4 +177,6 @@ atoms
         canonizeMF,
-        filter
+        filter,
+        ionizations
     } = options;
+
     // this script is designed to combine molecular formula
@@ -185,27 +186,33 @@ // that may contain comments after a "$" sign
 
-    var result = getEMFromParts(keys, currents);
-    if (!matcher(result, filter)) return;
+    for (var ionization of ionizations) {
 
-    result.parts = [];
-    result.mf = '';
+        var result = getEMFromParts(keys, currents, ionization);
 
-    var comments = [];
-    for (var i = 0; i < keys.length; i++) {
-        var key = keys[i][currents[i]];
-        if (key) {
-            result.parts[i] = key;
-            if (key.indexOf('$') > -1) {
-                comments.push(key.replace(/^[^$]*\$/, ''));
-                key = key.replace(/\$.*/, '');
+        var match = matcher(result, filter);
+        if (!match) return;
+        result.ms = match;
+        result.parts = [];
+        result.mf = '';
+
+        var comments = [];
+        for (var i = 0; i < keys.length; i++) {
+            var key = keys[i][currents[i]];
+            if (key) {
+                result.parts[i] = key;
+                if (key.indexOf('$') > -1) {
+                    comments.push(key.replace(/^[^$]*\$/, ''));
+                    key = key.replace(/\$.*/, '');
+                }
+                result.mf += key;
             }
-            result.mf += key;
         }
-    }
 
-    if (canonizeMF) {
-        result.mf = (new MF(result.mf)).toMF();
+        if (canonizeMF) {
+            result.mf = (new MF(result.mf)).toMF();
+        }
+
+        if (comments.length > 0) result.mf += `$${comments.join(' ')}`;
+        results.push(result);
     }
 
-    if (comments.length > 0) result.mf += `$${comments.join(' ')}`;
-    results.push(result);
 }
@@ -212,0 +219,0 @@

No alert changes

Improved metrics

Total package byte prevSize

16885

increased by5.41%

Lines of code

410

increased by4.86%

Worsened metrics

Dependency count

6

increased by100%

Dependency changes

• + Addedmf-finder@^0.5.2

• + Addedmf-utilities@^0.5.2

• + Addedsum-object-keys@^1.0.2

• + Addedisotope-abundances@2.0.4(transitive)

• + Addedmf-finder@0.5.12(transitive)

• + Addedmolecular-formula@1.1.5(transitive)

• + Addedsum-object-keys@1.0.2(transitive)

• Updatedchemical-elements@^0.5.2

• Updatedmf-matcher@^0.5.2

• Updatedmf-parser@^0.5.2