mf-generator - npm Package Compare versions

Comparing version 0.4.3 to 0.5.0

package.json

 {
   "name": "mf-generator",
-  "version": "0.4.3",
+  "version": "0.5.0",
   "description": "",
@@ -21,4 +21,6 @@ "main": "src/index.js",
   "dependencies": {
-    "mf-parser": "^0.4.3"
+    "chemical-elements": "^0.5.0",
+    "mf-matcher": "^0.5.0",
+    "mf-parser": "^0.5.0"
   }
 }

src/index.js

 'use strict';
 
-const {ELECTRON_MASS} = require('chemical-elements/src/constants');
-
+const { ELECTRON_MASS } = require('chemical-elements/src/constants');
 const MF = require('mf-parser').MF;
+const matcher = require('mf-matcher');
+const sum = require('sum-object-keys');
 
@@ -13,10 +14,18 @@ /**
  * @param options
- * @param {number} [options.limit=1000000] - Maximum number of results
- * @param {number} [options.minMass=0] - Minimal monoisotopic mass
- * @param {number} [options.maxMass=+Infinity] - Maximal monoisotopic mass
- * @param {number} [options.minMSMass=0] - Minimal observed monoisotopic mass
- * @param {number} [options.maxMSMass=+Infinity] - Maximal observed monoisotopic mass
- * @param {number} [options.minCharge=-Infinity] - Minimal charge
- * @param {number} [options.maxCharge=+Infinity] - Maximal charge
+ * @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 {number} [options.filter.minMass=0] - Minimal monoisotopic mass
+ * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
+ * @param {number} [options.filter.minEM=0] - Minimal neutral 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.minCharge=-Infinity] - Minimal charge
+ * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
+ * @param {number} [options.filter.minUnsaturation=-Infinity] - Minimal unsaturation
+ * @param {number} [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
+ * @param {number} [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
+ * @param {number} [options.filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
+ * @param {object} [options.filter.atoms] - object of atom:{min, max}
  * @returns {Array}
@@ -28,4 +37,8 @@ */
     let {
-        limit = 1000000,
+        limit = 10000000,
+        uniqueMFs
     } = options;
+    if (uniqueMFs === undefined) uniqueMFs = true;
+    if (uniqueMFs === true) options.canonizeMF = true;
+    if (options.canonizeMF === undefined) options.canonizeMF = true;
 
@@ -82,6 +95,14 @@ if (!Array.isArray(keys)) throw new Error('You need to specify an array of strings or arrays');
         if (evolution > limit) {
-            throw new Error('You have reached the limit of ' + options.limit + '. You could still change this value using the limit option but it is likely to crash.');
+            throw new Error(`You have reached the limit of ${limit}. You could still change this value using the limit option but it is likely to crash.`);
         }
     }
     appendResult(results, currents, keys, options);
+    if (uniqueMFs) {
+        var uniqueMFsObject = {};
+        results.forEach((r) => {
+            uniqueMFsObject[r.mf] = r;
+        });
+        results = Object.keys(uniqueMFsObject).map((k) => uniqueMFsObject[k]);
+    }
+    results.sort((a, b) => (a.em - b.em));
     return results;
@@ -93,3 +114,3 @@ };
 
-// internal method to for cache
+// internal method used as a cache
 function getMonoisotopicMass(mfString) {
@@ -103,3 +124,5 @@ if (!ems[mfString]) {
             charge: info.charge,
-            mw: info.mass
+            mw: info.mass,
+            unsaturation: (info.unsaturation - 1) * 2,
+            atoms: info.atoms
         };
@@ -114,2 +137,5 @@ }
     var mw = 0;
+    var unsaturation = 0;
+    var validUnsaturation = true;
+    var atoms = {};
 
@@ -123,2 +149,6 @@ for (var i = 0; i < parts.length; i++) {
             mw += info.mw;
+            sum(atoms, info.atoms);
+            if (info.unsaturation && validUnsaturation) {
+                unsaturation += info.unsaturation;
+            }
         }
@@ -138,3 +168,5 @@ }
         msem,
-        mw
+        mw,
+        unsaturation: validUnsaturation ? unsaturation / 2 + 1 : undefined,
+        atoms
     };
@@ -145,11 +177,5 @@ }
     const {
-        minMass = 0,
-        maxMass = +Infinity,
-        minMSMass = 0,
-        maxMSMass = +Infinity,
-        minCharge = -Infinity,
-        maxCharge = +Infinity,
-        canonizeMF
+        canonizeMF,
+        filter
     } = options;
-
     // this script is designed to combine molecular formula
@@ -159,22 +185,8 @@ // that may contain comments after a "$" sign
 
-    var info = getEMFromParts(keys, currents);
+    var result = getEMFromParts(keys, currents);
+    if (!matcher(result, filter)) return;
 
-    var em = info.em;
-    var mw = info.mw;
-    var msem = info.msem;
-    var charge = info.charge;
+    result.parts = [];
+    result.mf = '';
 
-
-    if ((mw < minMass) || (mw > maxMass)) return;
-    if ((msem < minMSMass) || (msem > maxMSMass)) return;
-    if ((charge < minCharge) || (charge > maxCharge)) return;
-
-    var result = {
-        mf: '',
-        em,
-        mw,
-        msem,
-        charge,
-        parts: []
-    };
     var comments = [];
@@ -197,3 +209,3 @@ for (var i = 0; i < keys.length; i++) {
 
-    if (comments.length > 0) result.mf += '$' + comments.join(' ');
+    if (comments.length > 0) result.mf += `$${comments.join(' ')}`;
     results.push(result);
@@ -204,3 +216,3 @@ }
     var results = [];
-    var parts = string.split(/([0-9]+-[0-9]+)/).filter(v => v); // remove empty parts
+    var parts = string.split(/([0-9]+-[0-9]+)/).filter((v) => v); // remove empty parts
     let position = -1;
@@ -257,3 +269,3 @@ var mfs = [];
     }
-    if (comment) mf += '$' + comment;
+    if (comment) mf += `$${comment}`;
     return mf;
@@ -260,0 +272,0 @@ }

No alert changes

Improved metrics

Total package byte prevSize

16019

increased by14.95%

Lines of code

391

increased by12.36%

Worsened metrics

Dependency count

3

increased by200%

Dependency changes

• + Addedchemical-elements@^0.5.0

• + Addedmf-matcher@^0.5.0

• + Addedatom-sorter@0.5.12(transitive)

• + Addedchemical-elements@0.5.12(transitive)

• + Addedmf-matcher@0.5.12(transitive)

• + Addedmf-parser@0.5.12(transitive)

• + Addedmf-utilities@0.5.12(transitive)

• - Removedatom-sorter@0.4.3(transitive)

• - Removedchemical-elements@0.4.3(transitive)

• - Removedmf-parser@0.4.3(transitive)

• Updatedmf-parser@^0.5.0