mf-parser - npm Package Compare versions

Comparing version 0.9.1 to 0.12.0

package.json

 {
   "name": "mf-parser",
-  "version": "0.9.1",
+  "version": "0.12.0",
   "description": "",
@@ -21,10 +21,10 @@ "main": "src/index.js",
   "dependencies": {
-    "atom-sorter": "^0.9.1",
-    "chemical-elements": "^0.9.1",
-    "chemical-groups": "^0.9.1",
-    "mf-utilities": "^0.9.1"
+    "atom-sorter": "^0.12.0",
+    "chemical-elements": "^0.12.0",
+    "chemical-groups": "^0.12.0"
   },
   "devDependencies": {
     "jest-matcher-deep-close-to": "^1.3.0"
-  }
+  },
+  "gitHead": "aa2e6571c5f7121dda616b7d6920b7a653a8f9c7"
 }

src/__tests__/getEA.test.js

@@ -7,3 +7,3 @@ 'use strict';
 
-var MF = require('../MF');
+let MF = require('../MF');
 
@@ -13,3 +13,3 @@ test('getEA', () => {
     [{ element: 'C', mass: 12.01, ratio: 1 }],
-    3
+    3,
   );
@@ -27,3 +27,3 @@
     [{ element: 'C', mass: 13.0033, ratio: 1 }],
-    3
+    3,
   );
@@ -33,3 +33,3 @@
     [{ element: 'C', mass: 125.016, ratio: 1 }],
-    3
+    3,
   );
@@ -40,6 +40,6 @@
       { element: 'C', mass: 24.02147, ratio: 0.7988 },
-      { element: 'H', mass: 6.0476, ratio: 0.20112 }
+      { element: 'H', mass: 6.0476, ratio: 0.20112 },
     ],
-    3
+    3,
   );
 });

src/__tests__/index.js

 'use strict';
 
-var MFParser = require('../index');
+let MFParser = require('../index');
 
 test('parseToHtml', () => {
-  var result = MFParser.parseToHtml('SO4(--)');
-  expect(result).toBe('SO<span style="flex-direction: column;display: inline-flex;justify-content: center;text-align: left;vertical-align: middle;"><sup style="line-height: 1; font-size: 70%">-2</sup><sub style="line-height: 1; font-size: 70%">4</sub></span>');
+  let result = MFParser.parseToHtml('SO4(--)');
+  expect(result).toBe(
+    'SO<span style="flex-direction: column;display: inline-flex;justify-content: center;text-align: left;vertical-align: middle;"><sup style="line-height: 1; font-size: 70%">-2</sup><sub style="line-height: 1; font-size: 70%">4</sub></span>',
+  );
 });

src/__tests__/MF.test.js

 'use strict';
 
-var MF = require('../MF');
+let MF = require('../MF');
 
 test('MF of C', () => {
-  var mf = new MF('C');
-  var parts = mf.toParts();
+  let mf = new MF('C');
+  let parts = mf.toParts();
 
   expect(parts).toStrictEqual([[{ kind: 'atom', value: 'C', multiplier: 1 }]]);
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('C');
@@ -27,3 +27,3 @@
     mf: 'C',
-    atoms: { C: 1 }
+    atoms: { C: 1 },
   });
@@ -33,6 +33,6 @@ });
 test('MF of D', () => {
-  var mfD = new MF('D');
-  var infoD = mfD.getInfo();
-  var mf2H = new MF('[2H]');
-  var info2H = mf2H.getInfo();
+  let mfD = new MF('D');
+  let infoD = mfD.getInfo();
+  let mf2H = new MF('[2H]');
+  let info2H = mf2H.getInfo();
   expect(infoD).toStrictEqual(info2H);
@@ -45,3 +45,3 @@ expect(infoD).toStrictEqual({
     monoisotopicMass: 2.01410177812,
-    unsaturation: 0.5
+    unsaturation: 0.5,
   });
@@ -51,4 +51,4 @@ });
 test('MF of Et3N.HCl', () => {
-  var mf = new MF('Et3N.HCl');
-  var parts = mf.toParts();
+  let mf = new MF('Et3N.HCl');
+  let parts = mf.toParts();
 
@@ -59,11 +59,11 @@ expect(parts).toStrictEqual([
       { kind: 'atom', value: 'H', multiplier: 15 },
-      { kind: 'atom', value: 'N', multiplier: 1 }
+      { kind: 'atom', value: 'N', multiplier: 1 },
     ],
     [
       { kind: 'atom', value: 'H', multiplier: 1 },
-      { kind: 'atom', value: 'Cl', multiplier: 1 }
-    ]
+      { kind: 'atom', value: 'Cl', multiplier: 1 },
+    ],
   ]);
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('C6H15N . HCl');
@@ -85,3 +85,3 @@
         unsaturation: 0,
-        atoms: { C: 6, H: 15, N: 1 }
+        atoms: { C: 6, H: 15, N: 1 },
       },
@@ -94,4 +94,4 @@ {
         unsaturation: 0,
-        atoms: { H: 1, Cl: 1 }
-      }
+        atoms: { H: 1, Cl: 1 },
+      },
     ],
@@ -101,9 +101,14 @@ monoisotopicMass: 137.09712720211002,
     charge: 0,
-    mf: 'C6H15N.HCl'
+    mf: 'C6H15N.HCl',
   });
 });
 
+test('MF of (ch3ch2)3n', () => {
+  let mf = new MF('(ch3ch2)3n', { ensureCase: true });
+  expect(mf.toMF()).toBe('C6H15N');
+});
+
 test('MF of (Me2CH)3N no expand', () => {
-  var mf = new MF('(Me2CH)3N');
-  var parts = mf.toParts({ expand: false });
+  let mf = new MF('(Me2CH)3N');
+  let parts = mf.toParts({ expand: false });
 
@@ -115,7 +120,7 @@ expect(parts).toStrictEqual([
       { kind: 'atom', value: 'Me', multiplier: 6 },
-      { kind: 'atom', value: 'N', multiplier: 1 }
-    ]
+      { kind: 'atom', value: 'N', multiplier: 1 },
+    ],
   ]);
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('C3H3Me6N');
@@ -130,3 +135,3 @@
     unsaturation: 0,
-    atoms: { C: 3, H: 3, Me: 6, N: 1 }
+    atoms: { C: 3, H: 3, Me: 6, N: 1 },
   });
@@ -136,4 +141,4 @@ });
 test('MF of (Me2CH)3N with expand', () => {
-  var mf = new MF('(Me2CH)3N');
-  var parts = mf.toParts({ expand: true });
+  let mf = new MF('(Me2CH)3N');
+  let parts = mf.toParts({ expand: true });
 
@@ -144,7 +149,7 @@ expect(parts).toStrictEqual([
       { kind: 'atom', value: 'H', multiplier: 21 },
-      { kind: 'atom', value: 'N', multiplier: 1 }
-    ]
+      { kind: 'atom', value: 'N', multiplier: 1 },
+    ],
   ]);
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('C9H21N');
@@ -159,3 +164,3 @@
     unsaturation: 0,
-    atoms: { C: 9, H: 21, N: 1 }
+    atoms: { C: 9, H: 21, N: 1 },
   });
@@ -165,4 +170,4 @@ });
 test('MF of (+)SO4(+)(-2)2', () => {
-  var mf = new MF('(+)SO4(+)(-2)2');
-  var parts = mf.toParts();
+  let mf = new MF('(+)SO4(+)(-2)2');
+  let parts = mf.toParts();
 
@@ -173,9 +178,12 @@ expect(parts).toStrictEqual([
       { kind: 'atom', value: 'S', multiplier: 1 },
-      { kind: 'charge', value: -2 }
-    ]
+      { kind: 'charge', value: -2 },
+    ],
   ]);
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('O4S(-2)');
 
+  let neutralMF = mf.toNeutralMF();
+  expect(neutralMF).toBe('O4S');
+
   let info = mf.getInfo({ customUnsaturations: { S: 4 } });
@@ -189,3 +197,3 @@ expect(info).toStrictEqual({
     unsaturation: 4,
-    atoms: { O: 4, S: 1 }
+    atoms: { O: 4, S: 1 },
   });
@@ -208,4 +216,4 @@ });
 test('MF of NC[13C][15N]2NN2', () => {
-  var mf = new MF('NC[13C][15N]2NN2');
-  var parts = mf.toParts();
+  let mf = new MF('NC[13C][15N]2NN2');
+  let parts = mf.toParts();
   expect(parts).toStrictEqual([
@@ -216,4 +224,4 @@ [
       { kind: 'atom', value: 'N', multiplier: 4 },
-      { kind: 'isotope', value: { atom: 'N', isotope: 15 }, multiplier: 2 }
-    ]
+      { kind: 'isotope', value: { atom: 'N', isotope: 15 }, multiplier: 2 },
+    ],
   ]);
@@ -228,6 +236,6 @@
     unsaturation: 6,
-    atoms: { C: 2, N: 6 }
+    atoms: { C: 2, N: 6 },
   });
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('C[13C]N4[15N]2');
@@ -237,4 +245,4 @@ });
 test('MF of DNA HODampDtmpDcmpDgmpH  ', () => {
-  var mf = new MF('HODampDtmpDgmpDcmpH');
-  var info = mf.getInfo();
+  let mf = new MF('HODampDtmpDgmpDcmpH');
+  let info = mf.getInfo();
   expect(info).toStrictEqual({
@@ -246,3 +254,3 @@ mass: 1253.8043977028433,
     atoms: { C: 39, H: 51, N: 15, O: 25, P: 4 },
-    unsaturation: 24
+    unsaturation: 24,
   });
@@ -252,4 +260,4 @@ });
 test('MF of RNA HOAmpUmpH  ', () => {
-  var mf = new MF('HOAmpUmpH');
-  var info = mf.getInfo();
+  let mf = new MF('HOAmpUmpH');
+  let info = mf.getInfo();
   expect(info).toStrictEqual({
@@ -261,3 +269,3 @@ mass: 653.388021231099,
     atoms: { C: 19, H: 25, N: 7, O: 15, P: 2 },
-    unsaturation: 12
+    unsaturation: 12,
   });
@@ -267,4 +275,4 @@ });
 test('MF of CC{50,50}H', () => {
-  var mf = new MF('HC{50,50}C');
-  var parts = mf.toParts();
+  let mf = new MF('HC{50,50}C');
+  let parts = mf.toParts();
   expect(parts).toStrictEqual([
@@ -276,9 +284,9 @@ [
         value: { atom: 'C', ratio: [50, 50] },
-        multiplier: 1
+        multiplier: 1,
       },
-      { kind: 'atom', value: 'H', multiplier: 1 }
-    ]
+      { kind: 'atom', value: 'H', multiplier: 1 },
+    ],
   ]);
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('CC{50,50}H');
@@ -293,3 +301,3 @@
     unsaturation: 2.5,
-    atoms: { C: 2, H: 1 }
+    atoms: { C: 2, H: 1 },
   });
@@ -299,5 +307,5 @@ });
 test('MF of H(+)(H+)-1H', () => {
-  var mf = new MF('H(+)(H+)-1H');
+  let mf = new MF('H(+)(H+)-1H');
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('H');
@@ -312,3 +320,3 @@
     monoisotopicMass: 1.00782503223,
-    unsaturation: 0.5
+    unsaturation: 0.5,
   });
@@ -318,6 +326,6 @@ });
 test('MF of 2NH3 . 2HCl', () => {
-  var mf = new MF('2NH3 . 2HCl');
+  let mf = new MF('2NH3 . 2HCl');
 
-  var newMF = mf.toMF();
+  let newMF = mf.toMF();
   expect(newMF).toBe('H6N2 . H2Cl2');
 });

src/__tests__/parse.test.js

@@ -5,3 +5,3 @@ 'use strict';
 
-var tests = {
+let tests = {
   C10: [{ kind: 'atom', value: 'C' }, { kind: 'multiplier', value: 10 }],
@@ -11,3 +11,3 @@ 'C-1': [{ kind: 'atom', value: 'C' }, { kind: 'multiplier', value: -1 }],
     { kind: 'atom', value: 'C' },
-    { kind: 'multiplierRange', value: { from: 1, to: 10 } }
+    { kind: 'multiplierRange', value: { from: 1, to: 10 } },
   ],
@@ -22,3 +22,3 @@ '2H': [{ kind: 'preMultiplier', value: 2 }, { kind: 'atom', value: 'H' }],
     { kind: 'charge', value: -1 },
-    { kind: 'atom', value: 'H' }
+    { kind: 'atom', value: 'H' },
   ],
@@ -30,3 +30,3 @@ 'C++': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: 2 }],
     { kind: 'multiplier', value: 2 },
-    { kind: 'charge', value: 1 }
+    { kind: 'charge', value: 1 },
   ],
@@ -43,3 +43,3 @@ 'C(2+)': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: 2 }],
     { kind: 'charge', value: 1 },
-    { kind: 'closingParenthesis', value: ')' }
+    { kind: 'closingParenthesis', value: ')' },
   ],
@@ -50,3 +50,3 @@ C$ABC: [{ kind: 'atom', value: 'C' }, { kind: 'comment', value: 'ABC' }],
     { kind: 'charge', value: -1 },
-    { kind: 'charge', value: -3 }
+    { kind: 'charge', value: -3 },
   ],
@@ -58,3 +58,3 @@ 'C(-1)2(-3)3': [
     { kind: 'charge', value: -3 },
-    { kind: 'multiplier', value: 3 }
+    { kind: 'multiplier', value: 3 },
   ],
@@ -66,3 +66,3 @@ 'C(H-2)': [
     { kind: 'multiplier', value: -2 },
-    { kind: 'closingParenthesis', value: ')' }
+    { kind: 'closingParenthesis', value: ')' },
   ],
@@ -72,3 +72,3 @@ 'H.Cl': [
     { kind: 'salt', value: '.' },
-    { kind: 'atom', value: 'Cl' }
+    { kind: 'atom', value: 'Cl' },
   ],
@@ -83,3 +83,3 @@ 'H{1,1}': [{ kind: 'isotopeRatio', value: { atom: 'H', ratio: [1, 1] } }],
     { kind: 'atom', value: 'H' },
-    { kind: 'multiplier', value: 20 }
+    { kind: 'multiplier', value: 20 },
   ],
@@ -102,3 +102,3 @@ '(CH(CH3)2)3N.2HCl': [
     { kind: 'atom', value: 'H' },
-    { kind: 'atom', value: 'Cl' }
+    { kind: 'atom', value: 'Cl' },
   ],
@@ -112,3 +112,3 @@ 'C.C2.C3': [
     { kind: 'atom', value: 'C' },
-    { kind: 'multiplier', value: 3 }
+    { kind: 'multiplier', value: 3 },
   ],
@@ -123,3 +123,3 @@ 'C10.C20.C30': [
     { kind: 'atom', value: 'C' },
-    { kind: 'multiplier', value: 30 }
+    { kind: 'multiplier', value: 30 },
   ],
@@ -136,3 +136,3 @@ 'C.0.5H2O.0.6HCl': [
     { kind: 'atom', value: 'H' },
-    { kind: 'atom', value: 'Cl' }
+    { kind: 'atom', value: 'Cl' },
   ],
@@ -148,3 +148,3 @@ 'NH3 . 2HCl': [
     { kind: 'atom', value: 'H' },
-    { kind: 'atom', value: 'Cl' }
+    { kind: 'atom', value: 'Cl' },
   ],
@@ -161,5 +161,17 @@ '2NH3 . 2HCl': [
     { kind: 'atom', value: 'H' },
-    { kind: 'atom', value: 'Cl' }
+    { kind: 'atom', value: 'Cl' },
   ],
-  D: [{ kind: 'atom', value: 'D' }]
+  D: [{ kind: 'atom', value: 'D' }],
+  'C1-2': [
+    { kind: 'atom', value: 'C' },
+    { kind: 'multiplierRange', value: { from: 1, to: 2 } },
+  ],
+  'C2-1': [
+    { kind: 'atom', value: 'C' },
+    { kind: 'multiplierRange', value: { from: 1, to: 2 } },
+  ],
+  'C-1--2': [
+    { kind: 'atom', value: 'C' },
+    { kind: 'multiplierRange', value: { from: -2, to: -1 } },
+  ],
 };
@@ -166,0 +178,0 @@

src/Format.js

@@ -11,3 +11,3 @@ 'use strict';
   SUPERIMPOSE: 'superimpose',
-  TEXT: 'text'
+  TEXT: 'text',
 };

src/index.js

@@ -12,4 +12,4 @@ 'use strict';
 function parseToHtml(mf) {
-  var parsed = parse(mf);
-  var display = toDisplay(parsed);
+  let parsed = parse(mf);
+  let display = toDisplay(parsed);
   return toHtml(display);
@@ -23,2 +23,3 @@ }
   parse: require('./parse'),
+  ensureCase: require('./ensureCase'),
   toDisplay,
@@ -25,0 +26,0 @@ toHtml,

src/Kind.js

@@ -19,3 +19,3 @@ 'use strict';
   TEXT: 'text',
-  COMMENT: 'comment'
+  COMMENT: 'comment',
 };

src/MF.js

@@ -8,2 +8,3 @@ 'use strict';
 const getInfo = require('./util/getInfo');
+const ensureCase = require('./ensureCase');
 const getEA = require('./util/getEA');
@@ -15,3 +16,6 @@ const getIsotopesInfo = require('./util/getIsotopesInfo');
 class MF {
-  constructor(mf) {
+  constructor(mf, options = {}) {
+    if (options.ensureCase) {
+      mf = ensureCase(mf);
+    }
     this.parsed = parse(mf);
@@ -44,2 +48,3 @@ this.cache = {};
    * as well as the same informations for all the parts
+   * @param {object} [options={}] options
    */
@@ -87,2 +92,13 @@ getInfo(options = {}) {
 
+  /**
+   * Get a canonized MF
+   */
+  toNeutralMF() {
+    if (!this.cache.neutralMF) {
+      this.toParts();
+      this.cache.neutralMF = partsToMF(this.cache.parts, { neutral: true });
+    }
+    return this.cache.neutralMF;
+  }
+
   canonize() {
@@ -89,0 +105,0 @@ this.toParts();

src/parse.js

 'use strict';
 
-
 const Kind = require('./Kind');
@@ -24,3 +23,6 @@ const parseCharge = require('./util/parseCharge');
     while (this.i < mf.length) {
-      if (this.result.length > 0 && this.result[this.result.length - 1].kind !== Kind.TEXT) {
+      if (
+        this.result.length > 0 &&
+        this.result[this.result.length - 1].kind !== Kind.TEXT
+      ) {
         lastKind = this.result[this.result.length - 1].kind;
@@ -33,10 +35,30 @@ }
 
-      if ((ascii > 47 && ascii < 58) || (char === '-' && nextAscii > 47 && nextAscii < 58)) { // a number
+      if (
+        (ascii > 47 && ascii < 58) ||
+        (char === '-' && nextAscii > 47 && nextAscii < 58)
+      ) {
+        // a number
         let value = this.getNumber(ascii);
-        if (lastKind === Kind.SALT || lastKind === Kind.BEGIN || lastKind === Kind.OPENING_PARENTHESIS) {
-          if (value.to) throw new MFError(this.mf, this.i, 'Premultiplier may not contain a -');
+        if (
+          lastKind === Kind.SALT ||
+          lastKind === Kind.BEGIN ||
+          lastKind === Kind.OPENING_PARENTHESIS
+        ) {
+          if (value.to) {
+            throw new MFError(
+              this.mf,
+              this.i,
+              'Premultiplier may not contain a -',
+            );
+          }
           this.result.push({ kind: Kind.PRE_MULTIPLIER, value: value.from });
         } else {
           if (value.to) {
-            this.result.push({ kind: Kind.MULTIPLIER_RANGE, value });
+            this.result.push({
+              kind: Kind.MULTIPLIER_RANGE,
+              value: {
+                from: Math.min(value.from, value.to),
+                to: Math.max(value.from, value.to),
+              },
+            });
           } else {
@@ -48,12 +70,19 @@ this.result.push({ kind: Kind.MULTIPLIER, value: value.from });
         continue;
-      } else if (char === '.') { // a point
+      } else if (char === '.') {
+        // a point
         this.result.push({ kind: Kind.SALT, value: char });
         // it is not in a number otherwise it would have been taken before
         // it must be in a salt
-      } else if (ascii > 64 && ascii < 91) { // an uppercase = new atom
+      } else if (ascii > 64 && ascii < 91) {
+        // an uppercase = new atom
         let value = this.getAtom(ascii);
         this.result.push({ kind: Kind.ATOM, value });
         continue;
-      } else if (ascii > 96 && ascii < 123) { // a lowercase
-        throw new MFError(this.mf, this.i, 'found a lowercase not following an uppercase');
+      } else if (ascii > 96 && ascii < 123) {
+        // a lowercase
+        throw new MFError(
+          this.mf,
+          this.i,
+          'found a lowercase not following an uppercase',
+        );
       } else if (char === '(') {
@@ -68,8 +97,14 @@ let charge = this.getParenthesisCharge(ascii);
         this.result.push({ kind: Kind.CLOSING_PARENTHESIS, value: ')' });
-      } else if (char === '[') { // defines an isotope
+      } else if (char === '[') {
+        // defines an isotope
         let isotope = this.getIsotope(ascii);
         this.result.push({ kind: Kind.ISOTOPE, value: isotope });
       } else if (char === ']') {
-        throw new MFError(this.mf, this.i, 'should never meet an closing bracket not in isotopes');
-      } else if (char === '{') { // can define an exotic isotopic ratio or mixtures of groups
+        throw new MFError(
+          this.mf,
+          this.i,
+          'should never meet an closing bracket not in isotopes',
+        );
+      } else if (char === '{') {
+        // can define an exotic isotopic ratio or mixtures of groups
         let isotopeRatio = this.getCurlyBracketIsotopeRatio(ascii);
@@ -81,17 +116,31 @@ if (lastKind === Kind.ATOM) {
             atom: lastResult.value,
-            ratio: isotopeRatio
+            ratio: isotopeRatio,
           };
         } else {
-          throw new MFError(this.mf, this.i, 'isotopic composition has to follow an atom');
+          throw new MFError(
+            this.mf,
+            this.i,
+            'isotopic composition has to follow an atom',
+          );
         }
       } else if (char === '}') {
-        throw new MFError(this.mf, this.i, 'found a unexpected closing curly bracket');
-      } else if (char === '+') { // charge not in parenthesis
+        throw new MFError(
+          this.mf,
+          this.i,
+          'found a unexpected closing curly bracket',
+        );
+      } else if (char === '+') {
+        // charge not in parenthesis
         let charge = this.getNonParenthesisCharge(ascii);
         this.result.push({ kind: Kind.CHARGE, value: charge });
-      } else if (char === '-') { // charge not in parenthesis
+      } else if (char === '-') {
+        // charge not in parenthesis
         let charge = this.getNonParenthesisCharge(ascii);
         this.result.push({ kind: Kind.CHARGE, value: charge });
-      } else if (char === '$') { // it is a comment after
-        this.result.push({ kind: Kind.COMMENT, value: this.mf.substring(this.i + 1) });
+      } else if (char === '$') {
+        // it is a comment after
+        this.result.push({
+          kind: Kind.COMMENT,
+          value: this.mf.substring(this.i + 1),
+        });
         break;
@@ -115,3 +164,7 @@ } else {
     if (counter !== 0) {
-      throw new MFError(this.mf, this.i, 'number of opening and closing parenthesis not equal');
+      throw new MFError(
+        this.mf,
+        this.i,
+        'number of opening and closing parenthesis not equal',
+      );
     }
@@ -128,3 +181,3 @@ }
       ascii = this.mf.charCodeAt(this.i);
-    } while (ascii > 47 && ascii < 58 || ascii === 46 || ascii === 45); // number, . or -
+    } while ((ascii > 47 && ascii < 58) || ascii === 46 || ascii === 45); // number, . or -
     // we need to deal with the case there is a from / to
@@ -135,3 +188,6 @@ if (previous === 46) this.i--;
     if (indexOfDash > -1) {
-      return { from: Number(number.substr(0, indexOfDash)), to: Number(number.substr(indexOfDash + 1)) };
+      return {
+        from: Number(number.substr(0, indexOfDash)),
+        to: Number(number.substr(indexOfDash + 1)),
+      };
     }
@@ -151,3 +207,4 @@ return { from: Number(number) };
 
-  getIsotope(ascii) { // [13C]
+  getIsotope(ascii) {
+    // [13C]
     let substring = '';
@@ -165,3 +222,2 @@ do {
 
-
   getCurlyBracketIsotopeRatio(ascii) {
@@ -182,3 +238,7 @@ let substring = '';
     }
-    throw new MFError(this.mf, this.i, 'Curly brackets should contain only number and comma');
+    throw new MFError(
+      this.mf,
+      this.i,
+      'Curly brackets should contain only number and comma',
+    );
   }
@@ -185,0 +245,0 @@

src/Style.js

 'use strict';
 
 module.exports = {
-  SUPERIMPOSE: 'flex-direction: column;display: inline-flex;justify-content: center;text-align: left;vertical-align: middle;',
-  SUPERIMPOSE_SUP_SUB: 'line-height: 1; font-size: 70%'
+  SUPERIMPOSE:
+    'flex-direction: column;display: inline-flex;justify-content: center;text-align: left;vertical-align: middle;',
+  SUPERIMPOSE_SUP_SUB: 'line-height: 1; font-size: 70%',
 };
-

src/util/__tests__/toDisplay.test.js

 'use strict';
 
-var tests = [
+let tests = [
   {
     mf: 'C10',
     parsed: [{ kind: 'atom', value: 'C' }, { kind: 'multiplier', value: 10 }],
-    result: [{ kind: 'text', value: 'C' }, { kind: 'subscript', value: '10' }]
+    result: [{ kind: 'text', value: 'C' }, { kind: 'subscript', value: '10' }],
   },
@@ -12,3 +12,3 @@ {
     parsed: [{ kind: 'atom', value: 'C' }, { kind: 'multiplier', value: -1 }],
-    result: [{ kind: 'text', value: 'C' }, { kind: 'subscript', value: '-1' }]
+    result: [{ kind: 'text', value: 'C' }, { kind: 'subscript', value: '-1' }],
   },
@@ -19,5 +19,8 @@ {
       { kind: 'atom', value: 'C' },
-      { kind: 'multiplierRange', value: { from: 1, to: 10 } }
+      { kind: 'multiplierRange', value: { from: 1, to: 10 } },
     ],
-    result: [{ kind: 'text', value: 'C' }, { kind: 'subscript', value: '1-10' }]
+    result: [
+      { kind: 'text', value: 'C' },
+      { kind: 'subscript', value: '1-10' },
+    ],
   },
@@ -27,3 +30,3 @@ {
     parsed: [{ kind: 'preMultiplier', value: 2 }, { kind: 'atom', value: 'H' }],
-    result: [{ kind: 'text', value: '2H' }]
+    result: [{ kind: 'text', value: '2H' }],
   },
@@ -33,3 +36,3 @@ {
     parsed: [{ kind: 'isotope', value: { atom: 'C', isotope: 13 } }],
-    result: [{ kind: 'superscript', value: 13 }, { kind: 'text', value: 'C' }]
+    result: [{ kind: 'superscript', value: 13 }, { kind: 'text', value: 'C' }],
   },
@@ -39,3 +42,6 @@ {
     parsed: [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: 2 }],
-    result: [{ kind: 'text', value: 'C' }, { kind: 'superscript', value: '+2' }]
+    result: [
+      { kind: 'text', value: 'C' },
+      { kind: 'superscript', value: '+2' },
+    ],
   },
@@ -47,8 +53,8 @@ {
       { kind: 'multiplier', value: 2 },
-      { kind: 'charge', value: 1 }
+      { kind: 'charge', value: 1 },
     ],
     result: [
       { kind: 'text', value: 'C' },
-      { kind: 'superimpose', over: '+', under: '2' }
-    ]
+      { kind: 'superimpose', over: '+', under: '2' },
+    ],
   },
@@ -62,3 +68,3 @@ {
       { kind: 'multiplier', value: -2 },
-      { kind: 'closingParenthesis', value: ')' }
+      { kind: 'closingParenthesis', value: ')' },
     ],
@@ -68,4 +74,4 @@ result: [
       { kind: 'subscript', value: '-2' },
-      { kind: 'text', value: ')' }
-    ]
+      { kind: 'text', value: ')' },
+    ],
   },
@@ -77,5 +83,5 @@ {
       { kind: 'salt', value: '.' },
-      { kind: 'atom', value: 'Cl' }
+      { kind: 'atom', value: 'Cl' },
     ],
-    result: [{ kind: 'text', value: 'H•Cl' }]
+    result: [{ kind: 'text', value: 'H•Cl' }],
   },
@@ -87,5 +93,5 @@ {
       { kind: 'text', value: 'H' },
-      { kind: 'superscript', value: '{1,1}' }
-    ]
-  }
+      { kind: 'superscript', value: '{1,1}' },
+    ],
+  },
 ];
@@ -96,4 +102,4 @@
 test.each(tests)('toDisplay', function (aTest) {
-  var display = toDisplay(aTest.parsed);
+  let display = toDisplay(aTest.parsed);
   expect(display).toMatchObject(aTest.result);
 });

src/util/__tests__/toParts.test.js

@@ -5,3 +5,3 @@ 'use strict';
 
-var tests = [
+let tests = [
   { mf: 'C', result: [[{ kind: 'atom', value: 'C', multiplier: 1 }]] },
@@ -55,5 +55,5 @@ { mf: 'C2', result: [[{ kind: 'atom', value: 'C', multiplier: 2 }]] },
 test.each(tests)('toParts %p', function (aTest) {
-  var parsed = parse(aTest.mf);
-  var parts = toParts(parsed);
+  let parsed = parse(aTest.mf);
+  let parts = toParts(parsed);
   expect(parts).toMatchObject(aTest.result);
 });

src/util/getEA.js

@@ -16,4 +16,4 @@ 'use strict';
  */
-module.exports = function getInfo(parts) {
-  var results = {};
+module.exports = function getEA(parts) {
+  let results = {};
   for (let part of parts) {
@@ -26,3 +26,3 @@ for (let line of part) {
             throw new Error(
-              `Unknown isotope: ${line.value.isotope}${line.value.atom}`
+              `Unknown isotope: ${line.value.isotope}${line.value.atom}`,
             );
@@ -39,3 +39,3 @@ }
             line.value.atom,
-            isotopeRatioInfo.mass * line.multiplier
+            isotopeRatioInfo.mass * line.multiplier,
           );
@@ -70,3 +70,3 @@ break;
       element: key,
-      mass: results[key]
+      mass: results[key],
     });
@@ -78,3 +78,2 @@ }
   });
-
   return eas;
@@ -81,0 +80,0 @@ };

src/util/getInfo.js

@@ -6,7 +6,6 @@ 'use strict';
 const unsaturations = require('chemical-elements/src/unsaturationsObject.js');
+const { ELECTRON_MASS } = require('chemical-elements/src/constants');
 
 const Kind = require('../Kind');
 
-const { ELECTRON_MASS } = require('chemical-elements/src/constants');
-
 const partToMF = require('./partToMF');
@@ -29,3 +28,3 @@ const partToAtoms = require('./partToAtoms');
 
-  var result = { parts: [] };
+  let result = { parts: [] };
   for (let part of parts) {
@@ -53,3 +52,3 @@ result.parts.push(getProcessedPart(part, customUnsaturations));
     mf: '',
-    atoms: partToAtoms(part)
+    atoms: partToAtoms(part),
   };
@@ -87,3 +86,3 @@ let unsaturation = 0;
           throw new Error(
-            `Unknown isotope: ${line.value.isotope}${line.value.atom}`
+            `Unknown isotope: ${line.value.isotope}${line.value.atom}`,
           );
@@ -134,2 +133,1 @@ }
 }
-

src/util/getIsotopeRatioInfo.js

@@ -14,5 +14,3 @@ 'use strict';
     throw new Error(
-      `the number of specified ratios is bigger that the number of stable isotopes: ${
-        value.atom
-      }`
+      `the number of specified ratios is bigger that the number of stable isotopes: ${value.atom}`,
     );
@@ -19,0 +17,0 @@ }

src/util/getIsotopesInfo.js

@@ -16,3 +16,5 @@ 'use strict';
   if (parts.length === 0) return [];
-  if (parts.length > 1) throw new Error('getIsotopesInfo can not be applied on multipart MF');
+  if (parts.length > 1) {
+    throw new Error('getIsotopesInfo can not be applied on multipart MF');
+  }
 
@@ -25,3 +27,3 @@ return getProcessedPart(parts[0]);
     charge: 0,
-    isotopes: []
+    isotopes: [],
   };
@@ -32,21 +34,27 @@ for (let line of part) {
         let isotope = isotopes[line.value.isotope + line.value.atom];
-        if (!isotope) throw Error('unknown isotope:', line.value.atom, line.value.isotope);
+        if (!isotope) {
+          throw Error('unknown isotope:', line.value.atom, line.value.isotope);
+        }
         result.isotopes.push({
           atom: `[${line.value.isotope}${line.value.atom}]`,
           number: line.multiplier,
-          distribution: [{ x: isotope.mass, y: 1 }]
+          distribution: [{ x: isotope.mass, y: 1 }],
         });
         break;
       }
-      case Kind.ISOTOPE_RATIO: {
-        let element = elements[line.value.atom];
-        if (!element) throw new Error('unknown element:', line.value);
+      case Kind.ISOTOPE_RATIO:
+        {
+          let element = elements[line.value.atom];
+          if (!element) throw new Error('unknown element:', line.value);
 
-        let distribution = getDistribution(element.isotopes, line.value.ratio);
-        result.isotopes.push({
-          atom: `${line.value.atom}{${line.value.ratio.join(',')}}`,
-          number: line.multiplier,
-          distribution
-        });
-      }
+          let distribution = getDistribution(
+            element.isotopes,
+            line.value.ratio,
+          );
+          result.isotopes.push({
+            atom: `${line.value.atom}{${line.value.ratio.join(',')}}`,
+            number: line.multiplier,
+            distribution,
+          });
+        }
         break;
@@ -59,3 +67,6 @@ case Kind.ATOM: {
           number: line.multiplier,
-          distribution: element.isotopes.map((e) => ({ x: e.mass, y: e.abundance }))
+          distribution: element.isotopes.map((e) => ({
+            x: e.mass,
+            y: e.abundance,
+          })),
         });
@@ -74,3 +85,2 @@ break;
 
-
 function getDistribution(isotopesArray, ratio) {
@@ -80,3 +90,5 @@ let ratios = normalize(ratio);
   if (ratios.length > isotopesArray.length) {
-    throw new Error(`the number of specified ratios is bigger that the number of stable isotopes: ${isotopes}`);
+    throw new Error(
+      `the number of specified ratios is bigger that the number of stable isotopes: ${isotopes}`,
+    );
   }
@@ -86,3 +98,3 @@ for (let i = 0; i < ratios.length; i++) {
       x: isotopesArray[i].mass,
-      y: ratios[i]
+      y: ratios[i],
     });
@@ -89,0 +101,0 @@ }

src/util/getIsotopesObject.js

@@ -11,3 +11,3 @@ 'use strict';
       abundance: i.abundance,
-      mass: i.mass
+      mass: i.mass,
     };
@@ -18,2 +18,1 @@ });
 module.exports = isotopes;
-

src/util/parseCharge.js

 'use strict';
 
-
 /**
@@ -12,5 +11,5 @@ * Parse a string to extract the charge
   charge = charge.replace(/[()]/g, '');
-  var chargeNumber = 0;
+  let chargeNumber = 0;
   if (charge.match(/^[+-]+$/)) {
-    for (var i = 0; i < charge.length; i++) {
+    for (let i = 0; i < charge.length; i++) {
       if (charge.charAt(i) === '+') chargeNumber++;
@@ -20,3 +19,5 @@ else chargeNumber--;
   } else if (charge.match(/^[0-9]+[+-]$/)) {
-    chargeNumber = Number(charge.charAt(charge.length - 1) + charge.substring(0, charge.length - 1));
+    chargeNumber = Number(
+      charge.charAt(charge.length - 1) + charge.substring(0, charge.length - 1),
+    );
   } else {
@@ -23,0 +24,0 @@ chargeNumber = Number(charge);

src/util/partsToDisplay.js

@@ -12,3 +12,3 @@ 'use strict';
 module.exports = function partsToDisplay(parts) {
-  var lines = [];
+  let lines = [];
   for (let part of parts) {
@@ -21,3 +21,3 @@ if (lines.length > 0) lines.push({ kind: Kind.SALT, value: '•' });
           kind: Kind.MULTIPLIER,
-          value: partLine.multiplier
+          value: partLine.multiplier,
         });
@@ -24,0 +24,0 @@ }

src/util/partsToMF.js

@@ -5,8 +5,8 @@ 'use strict';
 
-module.exports = function partsToMF(parts) {
-  var mf = [];
+module.exports = function partsToMF(parts, options) {
+  let mf = [];
   for (let part of parts) {
-    mf.push(partToMF(part));
+    mf.push(partToMF(part, options));
   }
   return mf.join(' . ');
 };

src/util/partToAtoms.js

@@ -12,3 +12,3 @@ 'use strict';
 module.exports = function partToAtoms(part) {
-  var atoms = {};
+  let atoms = {};
   for (let line of part) {
@@ -15,0 +15,0 @@ switch (line.kind) {

src/util/partToMF.js

@@ -5,4 +5,4 @@ 'use strict';
 
-module.exports = function partToMF(part) {
-  var mf = [];
+module.exports = function partToMF(part, options = {}) {
+  let mf = [];
   for (let line of part) {
@@ -15,3 +15,3 @@ switch (line.kind) {
               line.multiplier !== 1 ? line.multiplier : ''
-            }`
+            }`,
           );
@@ -25,3 +25,3 @@ }
               line.multiplier !== 1 ? line.multiplier : ''
-            }`
+            }`,
           );
@@ -36,3 +36,3 @@ }
       case Kind.CHARGE:
-        if (line.value === 0) break;
+        if (line.value === 0 || options.neutral) break;
         mf.push(`(${line.value > 0 ? `+${line.value}` : line.value})`);
@@ -39,0 +39,0 @@ break;

src/util/toDisplay.js

@@ -22,3 +22,3 @@ 'use strict';
             kind: Format.SUBSCRIPT,
-            value: String(line.value)
+            value: String(line.value),
           };
@@ -31,3 +31,3 @@ results.push(result);
           kind: Format.SUBSCRIPT,
-          value: `${String(line.value.from)}-${line.value.to}`
+          value: `${String(line.value.from)}-${line.value.to}`,
         };
@@ -45,3 +45,3 @@ results.push(result);
             kind: Format.SUPERSCRIPT,
-            value: formatCharge(line.value)
+            value: formatCharge(line.value),
           };
@@ -56,3 +56,3 @@ results.push(result);
           kind: Format.SUPERSCRIPT,
-          value: line.value.isotope
+          value: line.value.isotope,
         };
@@ -62,3 +62,3 @@ results.push(result);
           kind: Format.TEXT,
-          value: line.value.atom
+          value: line.value.atom,
         };
@@ -74,3 +74,3 @@ results.push(result);
             kind: Format.TEXT,
-            value: line.value.atom
+            value: line.value.atom,
           };
@@ -81,3 +81,3 @@ results.push(result);
           kind: Format.SUPERSCRIPT,
-          value: `{${line.value.ratio.join(',')}}`
+          value: `{${line.value.ratio.join(',')}}`,
         };
@@ -92,3 +92,3 @@ results.push(result);
             kind: Format.TEXT,
-            value: ' • '
+            value: ' • ',
           };
@@ -104,3 +104,3 @@ results.push(result);
             kind: Format.TEXT,
-            value: line.value
+            value: line.value,
           };
@@ -107,0 +107,0 @@ results.push(result);

src/util/toHtml.js

@@ -7,3 +7,3 @@ 'use strict';
 module.exports = function getHtml(lines) {
-  var html = [];
+  let html = [];
   for (let line of lines) {
@@ -19,4 +19,8 @@ switch (line.kind) {
         html.push(`<span style="${Style.SUPERIMPOSE}">`);
-        html.push(`<sup style="${Style.SUPERIMPOSE_SUP_SUB}">${line.over}</sup>`);
-        html.push(`<sub style="${Style.SUPERIMPOSE_SUP_SUB}">${line.under}</sub>`);
+        html.push(
+          `<sup style="${Style.SUPERIMPOSE_SUP_SUB}">${line.over}</sup>`,
+        );
+        html.push(
+          `<sub style="${Style.SUPERIMPOSE_SUP_SUB}">${line.under}</sub>`,
+        );
         html.push('</span>');
@@ -23,0 +27,0 @@ break;

src/util/toParts.js

@@ -11,4 +11,4 @@ 'use strict';
  * @param {*} lines
- * @param {object} options
- * @param {boolean} [true] options.expand - Should we expand the groups
+ * @param {object} [options={}]
+ * @param {boolean} [options.expand=true] - Should we expand the groups
  */
@@ -69,3 +69,3 @@
     value: 1,
-    fromIndex: currentPart.lines.length
+    fromIndex: currentPart.lines.length,
   };
@@ -133,3 +133,3 @@ currentPart.multipliers.push(currentPart.currentMultiplier);
                 value: { atom: element.symbol, isotope: element.isotope },
-                multiplier: line.multiplier * element.number
+                multiplier: line.multiplier * element.number,
               });
@@ -140,3 +140,3 @@ } else {
                 value: element.symbol,
-                multiplier: line.multiplier * element.number
+                multiplier: line.multiplier * element.number,
               });
@@ -166,3 +166,3 @@ }
             kind: Kind.CHARGE,
-            value: key.value.value * key.value.multiplier
+            value: key.value.value * key.value.multiplier,
           });
@@ -205,3 +205,3 @@ } else {
   part.keys = [];
-  for (var line of part.lines) {
+  for (let line of part.lines) {
     part.keys.push({ key: getKey(line), value: line });
@@ -208,0 +208,0 @@ }

New alerts

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License

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Found 1 instance in 1 package

Fixed alerts

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Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

59961

increased by7.41%

Dependency count

3

decreased by-25%

Number of package files

34

increased by6.25%

Lines of code

1908

increased by11.19%

Dependency changes

• + Addedatom-sorter@0.12.0(transitive)

• + Addedchemical-elements@0.12.1(transitive)

• + Addedchemical-groups@0.12.1(transitive)

• + Addedpapaparse@5.4.1(transitive)

• - Removedmf-utilities@^0.9.1

• - Removedatom-sorter@0.9.1(transitive)

• - Removedchemical-elements@0.9.1(transitive)

• - Removedchemical-groups@0.9.1(transitive)

• - Removedmf-utilities@0.9.1(transitive)

• - Removedpapaparse@4.6.3(transitive)

• Updatedatom-sorter@^0.12.0

• Updatedchemical-elements@^0.12.0

• Updatedchemical-groups@^0.12.0