mf-parser - npm Package Compare versions

Comparing version 0.7.0 to 0.8.0

package.json

 {
   "name": "mf-parser",
-  "version": "0.7.0",
+  "version": "0.8.0",
   "description": "",
@@ -21,7 +21,7 @@ "main": "src/index.js",
   "dependencies": {
-    "atom-sorter": "^0.7.0",
+    "atom-sorter": "^0.8.0",
     "chemical-elements": "^0.7.0",
-    "chemical-groups": "^0.7.0",
-    "mf-utilities": "^0.7.0"
+    "chemical-groups": "^0.8.0",
+    "mf-utilities": "^0.8.0"
   }
 }

src/MF.js

 'use strict';
 
-
 const parse = require('./parse');
@@ -9,2 +8,3 @@ const toDisplay = require('./util/toDisplay');
 const getInfo = require('./util/getInfo');
+const getEA = require('./util/getEA');
 const getIsotopesInfo = require('./util/getIsotopesInfo');
@@ -15,68 +15,79 @@ const partsToMF = require('./util/partsToMF');
 class MF {
-    constructor(mf) {
-        this.parsed = parse(mf);
-        this.cache = {};
-    }
+  constructor(mf) {
+    this.parsed = parse(mf);
+    this.cache = {};
+  }
 
-    toDisplay() {
-        if (!this.cache.displayed) this.cache.displayed = toDisplay(this.parsed);
-        return this.cache.displayed;
+  toDisplay() {
+    if (!this.cache.displayed) this.cache.displayed = toDisplay(this.parsed);
+    return this.cache.displayed;
+  }
+
+  toHtml() {
+    if (!this.cache.html) {
+      this.toDisplay();
+      this.cache.html = toHtml(this.cache.displayed);
     }
+    return this.cache.html;
+  }
 
-    toHtml() {
-        if (!this.cache.html) {
-            this.toDisplay();
-            this.cache.html = toHtml(this.cache.displayed);
-        }
-        return this.cache.html;
+  toParts(options) {
+    if (!this.cache.parts) {
+      this.cache.parts = toParts(this.parsed, options);
     }
+    return this.cache.parts;
+  }
 
-    toParts(options) {
-        if (!this.cache.parts) {
-            this.cache.parts = toParts(this.parsed, options);
-        }
-        return this.cache.parts;
+  /**
+   * Returns an object with the global MF, global charge, monoisotopic mass and mass
+   * as well as the same informations for all the parts
+   */
+  getInfo(options = {}) {
+    if (!this.cache.info) {
+      this.toParts();
+      this.cache.info = getInfo(this.cache.parts, options);
     }
+    return this.cache.info;
+  }
 
-    /**
-     * Returns an object with the global MF, global charge, monoisotopic mass and mass
-     * as well as the same informations for all the parts
-     */
-    getInfo(options = {}) {
-        if (!this.cache.info) {
-            this.toParts();
-            this.cache.info = getInfo(this.cache.parts, options);
-        }
-        return this.cache.info;
+  /**
+   * Returns an object with the elemental analysis
+   */
+  getEA(options = {}) {
+    if (!this.cache.ea) {
+      this.toParts();
+      this.cache.ea = getEA(this.cache.parts, options);
     }
+    return this.cache.ea;
+  }
 
-    /**
-     * Returns an array with each atom and isotopic composition
-     */
-    getIsotopesInfo(options = {}) {
-        if (!this.cache.isotopesInfo) {
-            this.toParts();
-            this.cache.isotopesInfo = getIsotopesInfo(this.cache.parts, options);
-        }
-        return this.cache.isotopesInfo;
+  /**
+   * Returns an array with each atom and isotopic composition
+   */
+  getIsotopesInfo(options = {}) {
+    if (!this.cache.isotopesInfo) {
+      this.toParts();
+      this.cache.isotopesInfo = getIsotopesInfo(this.cache.parts, options);
     }
+    return this.cache.isotopesInfo;
+  }
 
-    /**
-     * Get a canonized MF
-     */
-    toMF() {
-        if (!this.cache.mf) {
-            this.toParts();
-            this.cache.mf = partsToMF(this.cache.parts);
-        }
-        return this.cache.mf;
+  /**
+   * Get a canonized MF
+   */
+  toMF() {
+    if (!this.cache.mf) {
+      this.toParts();
+      this.cache.mf = partsToMF(this.cache.parts);
     }
+    return this.cache.mf;
+  }
 
-    canonize() {
-        this.toParts();
-        this.cache.displayed = partsToDisplay(this.cache.parts);
-        this.cache.html = undefined;
-    }
+  canonize() {
+    this.toParts();
+    this.cache.displayed = partsToDisplay(this.cache.parts);
+    this.cache.html = undefined;
+  }
 }
 
 module.exports = MF;

src/util/getInfo.js

@@ -12,2 +12,3 @@ 'use strict';
 const isotopes = require('./getIsotopesObject');
+const getIsotopeRatioInfo = require('./getIsotopeRatioInfo');
 
@@ -129,28 +130,2 @@ /**
 
-function getIsotopeRatioInfo(value) {
-  let result = { mass: 0, monoisotopicMass: 0 };
-  let element = elements[value.atom];
-  if (!element) throw new Error(`Element not found: ${value.atom}`);
-  let isotopesArray = element.isotopes;
-  let ratios = normalize(value.ratio);
-  let max = Math.max(...ratios);
-  if (ratios.length > isotopesArray.length) {
-    throw new Error(
-      `the number of specified ratios is bigger that the number of stable isotopes: ${
-        value.atom
-      }`
-    );
-  }
-  for (let i = 0; i < ratios.length; i++) {
-    result.mass += ratios[i] * isotopesArray[i].mass;
-    if (max === ratios[i] && result.monoisotopicMass === 0) {
-      result.monoisotopicMass = isotopesArray[i].mass;
-    }
-  }
-  return result;
-}
 
-function normalize(array) {
-  let sum = array.reduce((prev, current) => prev + current, 0);
-  return array.map(a => a / sum);
-}

src/util/partToAtoms.js

@@ -7,3 +7,3 @@ 'use strict';
  * Convert a MF part to an array of atoms
- * This procedure will suppress the isotpes !
+ * This procedure will suppress the isotopes !
  * This is mainly used to make queries
@@ -13,24 +13,24 @@ */
 module.exports = function partToAtoms(part) {
-    var atoms = {};
-    for (let line of part) {
-        switch (line.kind) {
-            case Kind.ISOTOPE:
-                if (!atoms[line.value.atom]) atoms[line.value.atom] = 0;
-                atoms[line.value.atom] += line.multiplier;
-                break;
-            case Kind.ISOTOPE_RATIO:
-                if (!atoms[line.value.atom]) atoms[line.value.atom] = 0;
-                atoms[line.value.atom] += line.multiplier;
-                break;
-            case Kind.ATOM:
-                if (!atoms[line.value]) atoms[line.value] = 0;
-                atoms[line.value] += line.multiplier;
-                break;
-            case Kind.CHARGE:
-                break;
-            default:
-                throw new Error('partToMF unhandled Kind: ', line.kind);
-        }
+  var atoms = {};
+  for (let line of part) {
+    switch (line.kind) {
+      case Kind.ISOTOPE:
+        if (!atoms[line.value.atom]) atoms[line.value.atom] = 0;
+        atoms[line.value.atom] += line.multiplier;
+        break;
+      case Kind.ISOTOPE_RATIO:
+        if (!atoms[line.value.atom]) atoms[line.value.atom] = 0;
+        atoms[line.value.atom] += line.multiplier;
+        break;
+      case Kind.ATOM:
+        if (!atoms[line.value]) atoms[line.value] = 0;
+        atoms[line.value] += line.multiplier;
+        break;
+      case Kind.CHARGE:
+        break;
+      default:
+        throw new Error('partToMF unhandled Kind: ', line.kind);
     }
-    return atoms;
+  }
+  return atoms;
 };

No alert changes

Improved metrics

Total package byte prevSize

57600

increased by5.72%

Number of package files

32

increased by10.34%

Lines of code

1640

increased by7.68%

Dependency changes

• + Addedatom-sorter@0.8.0(transitive)

• + Addedchemical-groups@0.8.0(transitive)

• + Addedmf-utilities@0.8.0(transitive)

• - Removedatom-sorter@0.7.0(transitive)

• - Removedchemical-groups@0.7.0(transitive)

• - Removedmf-utilities@0.7.0(transitive)

• Updatedatom-sorter@^0.8.0

• Updatedchemical-groups@^0.8.0

• Updatedmf-utilities@^0.8.0