peptide - npm Package Compare versions

Comparing version 1.11.4 to 1.11.5

package.json

 {
   "name": "peptide",
-  "version": "1.11.4",
+  "version": "1.11.5",
   "description": "Peptide",
@@ -18,9 +18,11 @@ "keywords": [
   },
-  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/peptide#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/peptide#readme",
   "license": "MIT",
-  "main": "./src/index.js",
+  "main": "lib/index.js",
+  "module": "src/index.js",
   "files": [
-    "src"
+    "src",
+    "lib"
   ],
-  "gitHead": "78f6c10cea6825c99ba7fd6a103367dec9979564"
+  "gitHead": "bd2c06e05f2196c5f9c6ff011cf3ef41e1b6a0f9"
 }

README.md

@@ -144,3 +144,3 @@ # peptide
 [npm-url]: https://www.npmjs.com/package/peptide
-[travis-image]: https://img.shields.io/travis/cheminfo-js/peptide/master.svg?style=flat-square
+[travis-image]: https://img.shields.io/travis/cheminfo-js/peptide/main.svg?style=flat-square
 [travis-url]: https://travis-ci.org/cheminfo-js/peptide
@@ -147,0 +147,0 @@ [david-image]: https://img.shields.io/david/cheminfo-js/peptide.svg?style=flat-square

src/__tests__/allowNeutralLoss.test.js

@@ -1,10 +0,6 @@
-'use strict';
+import { allowNeutralLoss } from '../index.js';
 
-let PEP = require('..');
-
 describe('Checking allow neutral loss of peptides', () => {
   it('Check neutral loss of AASTAARKAA', () => {
-    let result = PEP.allowNeutralLoss(
-      'HAlaAlaSerThrAsp(H-1)GluArgLys(H+)AlaOH',
-    );
+    let result = allowNeutralLoss('HAlaAlaSerThrAsp(H-1)GluArgLys(H+)AlaOH');
     expect(result).toBe(
@@ -11,0 +7,0 @@ 'HAlaAlaSer(H-2O-1)0-1Thr(H-2O-1)0-1Asp(H-1)Glu(H-2O-1)0-1Arg(N-1H-3)0-1Lys(H+)AlaOH',

src/__tests__/chargePeptide.test.js

@@ -1,8 +0,6 @@
-'use strict';
+import { chargePeptide } from '..';
 
-let PEP = require('..');
-
 describe('Checking charge peptide', () => {
   it('Check charge with default option', () => {
-    let result = PEP.chargePeptide('HAlaGlyLysHisAspOH');
+    let result = chargePeptide('HAlaGlyLysHisAspOH');
     expect(result).toBe('H+HAlaGlyLys(H+)His(H+)AspOH');
@@ -12,3 +10,3 @@ });
   it('Check charge with pH = 1', () => {
-    let result = PEP.chargePeptide('HAlaGlyLysHisAspOH', { pH: 1 });
+    let result = chargePeptide('HAlaGlyLysHisAspOH', { pH: 1 });
     expect(result).toBe('H+HAlaGlyLys(H+)His(H+)AspOH');
@@ -18,3 +16,3 @@ });
   it('Check charge with pH = 7', () => {
-    let result = PEP.chargePeptide('HAlaGlyLysHisAspOH', { pH: 7 });
+    let result = chargePeptide('HAlaGlyLysHisAspOH', { pH: 7 });
     expect(result).toBe('H+HAlaGlyLys(H+)HisAsp(H-1-)O-');
@@ -24,3 +22,3 @@ });
   it('Check charge with pH = 13', () => {
-    let result = PEP.chargePeptide('HAlaGlyLysHisAspOH', { pH: 13 });
+    let result = chargePeptide('HAlaGlyLysHisAspOH', { pH: 13 });
     expect(result).toBe('HAlaGlyLysHisAsp(H-1-)O-');
@@ -30,3 +28,3 @@ });
   it('Charge an array of mfs', () => {
-    let result = PEP.chargePeptide(['HAlaGlyLysHisAspOH', 'HLysHisAspOH'], {
+    let result = chargePeptide(['HAlaGlyLysHisAspOH', 'HLysHisAspOH'], {
       pH: 13,
@@ -33,0 +31,0 @@ });

src/__tests__/convertAASequence.test.js

@@ -1,8 +0,6 @@
-'use strict';
+import { sequenceToMF } from '..';
 
-const convertAASequence = require('../convertAASequence');
-
 describe('Checking convert AA sequence', () => {
   it('AAAAAAA', () => {
-    const result = convertAASequence('AAAAAAA');
+    const result = sequenceToMF('AAAAAAA');
     expect(result).toBe('HAlaAlaAlaAlaAlaAlaAlaOH');
@@ -12,7 +10,7 @@ });
   it('HAlaAla(H-1OH)AlaOH', () => {
-    const result = convertAASequence('HAlaAla(H-1OH)AlaOH');
+    const result = sequenceToMF('HAlaAla(H-1OH)AlaOH');
     expect(result).toBe('HAlaAla(H-1OH)AlaOH');
   });
   it('(C33H37O6N3Si) GluTyrGluLys(C16H30O)GluTyrGluOH', () => {
-    const result = convertAASequence(
+    const result = sequenceToMF(
       '(C33H37O6N3Si) GluTyrGluLys(C16H30O)GluTyrGluOH',
@@ -24,3 +22,3 @@ );
   it('(Me)AAAAAAA(NH2)', () => {
-    const result = convertAASequence('(Me)AAAAAAA(NH2)');
+    const result = sequenceToMF('(Me)AAAAAAA(NH2)');
     expect(result).toBe('(Me)AlaAlaAlaAlaAlaAlaAla(NH2)');
@@ -30,3 +28,3 @@ });
   it('HAlaGlyProOH', () => {
-    const result = convertAASequence('HAlaGlyProOH');
+    const result = sequenceToMF('HAlaGlyProOH');
     expect(result).toBe('HAlaGlyProOH');
@@ -36,5 +34,5 @@ });
   it('ALA SER LYS GLY PRO', () => {
-    const result = convertAASequence('ALA SER LYS GLY PRO');
+    const result = sequenceToMF('ALA SER LYS GLY PRO');
     expect(result).toBe('HAlaSerLysGlyProOH');
   });
 });

src/__tests__/digestPeptide.test.js

@@ -1,8 +0,6 @@
-'use strict';
+import { digestPeptide } from '..';
 
-let PEP = require('..');
-
 describe('Checking digest sequence', () => {
   it('Normal sequence digest', () => {
-    let result = PEP.digestPeptide('HLysLysAlaAlaLysOH', {
+    let result = digestPeptide('HLysLysAlaAlaLysOH', {
       enzyme: 'trypsin',
@@ -20,3 +18,3 @@ minMissed: 0,
   it('Normal sequence digest, minMissed:0, maxMissed:1', () => {
-    let result = PEP.digestPeptide('HLysLysAlaAlaLysOH', {
+    let result = digestPeptide('HLysLysAlaAlaLysOH', {
       enzyme: 'trypsin',
@@ -36,3 +34,3 @@ minMissed: 0,
   it('Normal sequence digest, minMissed:1, maxMissed:1', () => {
-    let result = PEP.digestPeptide('HLysLysAlaAlaLysOH', {
+    let result = digestPeptide('HLysLysAlaAlaLysOH', {
       enzyme: 'trypsin',
@@ -46,3 +44,3 @@ minMissed: 1,
   it('Normal small sequence digest, default value', () => {
-    let result = PEP.digestPeptide('HLysAlaOH');
+    let result = digestPeptide('HLysAlaOH');
     expect(result).toStrictEqual(['HLysOH$D1>1', 'HAlaOH$D2>2']);
@@ -53,3 +51,3 @@ });
   it('HLysLeuValOH digest by thermolysin', () => {
-    let result = PEP.digestPeptide('HLysLeuProValOH', {
+    let result = digestPeptide('HLysLeuProValOH', {
       enzyme: 'thermolysin',
@@ -67,3 +65,3 @@ minMissed: 0,
   it('HLysLeu(H-1OH)ValOH digest at all amide bonds', () => {
-    let result = PEP.digestPeptide('HLysLeu(H-1OH)ValOH', {
+    let result = digestPeptide('HLysLeu(H-1OH)ValOH', {
       enzyme: 'any',
@@ -70,0 +68,0 @@ minMissed: 1,

src/__tests__/fragmentation.test.js

@@ -1,5 +0,8 @@
-'use strict';
+import {
+  generatePeptideFragments,
+  sequenceToMF,
+  chargePeptide,
+  allowNeutralLoss,
+} from '..';
 
-let PEP = require('..');
-
 // http://www.matrixscience.com/help/fragmentation_help.html
@@ -26,4 +29,4 @@
   it('Check KAA', () => {
-    let sequence = PEP.convertAASequence('KAA');
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('KAA');
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -42,4 +45,4 @@ b: true,
   it('Check AKLRCSTY', () => {
-    let sequence = PEP.convertAASequence('AKLRCSTY');
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKLRCSTY');
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -59,3 +62,3 @@ b: true,
   it('Check HLysAlaOH', () => {
-    let result = PEP.generatePeptideFragments('HLysAlaOH', {
+    let result = generatePeptideFragments('HLysAlaOH', {
       a: false,
@@ -75,3 +78,3 @@ b: true,
   it('Check HLys(COH)AlaOH side chain modified', () => {
-    let result = PEP.generatePeptideFragments('HLys(COH)AlaOH', {
+    let result = generatePeptideFragments('HLys(COH)AlaOH', {
       a: false,
@@ -91,5 +94,5 @@ b: true,
   it('Check AKLRCSTY ph=1', () => {
-    let sequence = PEP.convertAASequence('AKLRCSTY');
-    sequence = PEP.chargePeptide(sequence, { pH: 1 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKLRCSTY');
+    sequence = chargePeptide(sequence, { pH: 1 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -109,5 +112,5 @@ b: true,
   it('Check AKLRCSTY ph=13', () => {
-    let sequence = PEP.convertAASequence('AKLRCSTY');
-    sequence = PEP.chargePeptide(sequence, { pH: 13 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKLRCSTY');
+    sequence = chargePeptide(sequence, { pH: 13 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -127,6 +130,6 @@ b: true,
   it('Check AKLRCSTY neutral loss ph=1', () => {
-    let sequence = PEP.convertAASequence('AKLRCSTY');
-    sequence = PEP.allowNeutralLoss(sequence);
-    sequence = PEP.chargePeptide(sequence, { pH: 1 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKLRCSTY');
+    sequence = allowNeutralLoss(sequence);
+    sequence = chargePeptide(sequence, { pH: 1 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -146,6 +149,6 @@ b: true,
   it('Check AKLRCSTY neutral loss ph=13', () => {
-    let sequence = PEP.convertAASequence('AKLRCSTY');
-    sequence = PEP.allowNeutralLoss(sequence);
-    sequence = PEP.chargePeptide(sequence, { pH: 13 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKLRCSTY');
+    sequence = allowNeutralLoss(sequence);
+    sequence = chargePeptide(sequence, { pH: 13 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -165,5 +168,5 @@ b: true,
   it('Check AKLRCSTY neutral loss', () => {
-    let sequence = PEP.convertAASequence('AKLRCSTY');
-    sequence = PEP.allowNeutralLoss(sequence);
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKLRCSTY');
+    sequence = allowNeutralLoss(sequence);
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -183,10 +186,10 @@ b: true,
   it('ALP versus (H)ALP(OH) versus HAlaLeuProOH versus (H)AlaLeuPro(OH)', () => {
-    let sequence1 = PEP.convertAASequence('ALP');
-    let sequence2 = PEP.convertAASequence('(H)ALP(OH)');
-    let sequence3 = PEP.convertAASequence('HAlaLeuProOH');
-    let sequence4 = PEP.convertAASequence('(H)AlaLeuPro(OH)');
-    let result1 = PEP.generatePeptideFragments(sequence1);
-    let result2 = PEP.generatePeptideFragments(sequence2);
-    let result3 = PEP.generatePeptideFragments(sequence3);
-    let result4 = PEP.generatePeptideFragments(sequence4);
+    let sequence1 = sequenceToMF('ALP');
+    let sequence2 = sequenceToMF('(H)ALP(OH)');
+    let sequence3 = sequenceToMF('HAlaLeuProOH');
+    let sequence4 = sequenceToMF('(H)AlaLeuPro(OH)');
+    let result1 = generatePeptideFragments(sequence1);
+    let result2 = generatePeptideFragments(sequence2);
+    let result3 = generatePeptideFragments(sequence3);
+    let result4 = generatePeptideFragments(sequence4);
     expect(result1).toStrictEqual([
@@ -209,4 +212,4 @@ 'HAla(+1)$b1',
   it('AK(*1)T(H-1*2)Y', () => {
-    let sequence = PEP.convertAASequence('AK(*1)T(H-1*2)Y');
-    let result = PEP.generatePeptideFragments(sequence);
+    let sequence = sequenceToMF('AK(*1)T(H-1*2)Y');
+    let result = generatePeptideFragments(sequence);
     expect(result).toStrictEqual([
@@ -222,4 +225,4 @@ 'HAla(+1)$b1',
   it('HAlaLys(*1)Thr(H-1*2)TyrOH', () => {
-    let sequence = PEP.convertAASequence('HAlaLys(*1)Thr(H-1*2)TyrOH');
-    let result = PEP.generatePeptideFragments(sequence);
+    let sequence = sequenceToMF('HAlaLys(*1)Thr(H-1*2)TyrOH');
+    let result = generatePeptideFragments(sequence);
     expect(result).toStrictEqual([
@@ -226,0 +229,0 @@ 'HAla(+1)$b1',

src/__tests__/internal.test.js

@@ -1,5 +0,3 @@
-'use strict';
+import { generatePeptideFragments } from '..';
 
-let PEP = require('..');
-
 // http://www.matrixscience.com/help/fragmentation_help.html
@@ -9,3 +7,3 @@
   it('Check internal fragments for yb', () => {
-    let result = PEP.generatePeptideFragments('HAlaGlySerProPheOH', {
+    let result = generatePeptideFragments('HAlaGlySerProPheOH', {
       a: false,
@@ -32,3 +30,3 @@ b: false,
   it('Check internal fragments for ya', () => {
-    let result = PEP.generatePeptideFragments('HAlaGlySerProPheOH', {
+    let result = generatePeptideFragments('HAlaGlySerProPheOH', {
       a: false,
@@ -55,3 +53,3 @@ b: false,
   it('Check internal fragments for ya with maxInternal=2', () => {
-    let result = PEP.generatePeptideFragments('HAlaGlySerProPheOH', {
+    let result = generatePeptideFragments('HAlaGlySerProPheOH', {
       a: false,
@@ -78,3 +76,3 @@ b: false,
   it('Check internal fragments for ya with maxInternal=2 and minInternal=2', () => {
-    let result = PEP.generatePeptideFragments('HAlaGlySerProPheOH', {
+    let result = generatePeptideFragments('HAlaGlySerProPheOH', {
       a: false,
@@ -81,0 +79,0 @@ b: false,

src/__tests__/internalFragmentation.test.js

@@ -1,5 +0,8 @@
-'use strict';
+import {
+  generatePeptideFragments,
+  sequenceToMF,
+  chargePeptide,
+  allowNeutralLoss,
+} from '..';
 
-let PEP = require('..');
-
 // http://www.matrixscience.com/help/fragmentation_help.html
@@ -23,4 +26,4 @@
   it('Check AKDR', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -40,5 +43,5 @@ b: false,
   it('Check AKDR ph=1', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    sequence = PEP.chargePeptide(sequence, { pH: 1 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    sequence = chargePeptide(sequence, { pH: 1 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -58,5 +61,5 @@ b: false,
   it('Check AKLRCSTY ph=13', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    sequence = PEP.chargePeptide(sequence, { pH: 13 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    sequence = chargePeptide(sequence, { pH: 13 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -76,6 +79,6 @@ b: false,
   it('Check AKDR neutral loss ph=1', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    sequence = PEP.allowNeutralLoss(sequence);
-    sequence = PEP.chargePeptide(sequence, { pH: 1 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    sequence = allowNeutralLoss(sequence);
+    sequence = chargePeptide(sequence, { pH: 1 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -95,6 +98,6 @@ b: false,
   it('Check AKDR neutral loss ph=13', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    sequence = PEP.allowNeutralLoss(sequence);
-    sequence = PEP.chargePeptide(sequence, { pH: 13 });
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    sequence = allowNeutralLoss(sequence);
+    sequence = chargePeptide(sequence, { pH: 13 });
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -114,5 +117,5 @@ b: false,
   it('Check AKDR neutral loss  internal fragment yb', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    sequence = PEP.allowNeutralLoss(sequence);
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    sequence = allowNeutralLoss(sequence);
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -132,4 +135,4 @@ b: false,
   it('Check AKDR internal fragment yc', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -151,5 +154,5 @@ b: false,
   it('Check AKDR internal fragment zc', () => {
-    let sequence = PEP.convertAASequence('AKDR');
-    sequence = PEP.allowNeutralLoss(sequence);
-    let result = PEP.generatePeptideFragments(sequence, {
+    let sequence = sequenceToMF('AKDR');
+    sequence = allowNeutralLoss(sequence);
+    let result = generatePeptideFragments(sequence, {
       a: false,
@@ -156,0 +159,0 @@ b: false,

src/__tests__/peptide.test.js

@@ -1,5 +0,2 @@
-'use strict';
-
-let {
-  generatePeptideFragments,
+import {
   calculateIEP,
@@ -9,3 +6,4 @@ calculateIEPChart,
   calculateCharge,
-} = require('..');
+  generatePeptideFragments,
+} from '..';
 
@@ -12,0 +10,0 @@ describe('generatePeptideFragments', () => {

src/__tests__/splitPeptide.test.js

@@ -1,8 +0,6 @@
-'use strict';
+import { splitPeptide } from '..';
 
-let PEP = require('..');
-
 describe('Checking split peptide', () => {
   it('Normal sequence split', () => {
-    let result = PEP.splitPeptide('HAlaGlyLysHisAspOH');
+    let result = splitPeptide('HAlaGlyLysHisAspOH');
     expect(result).toStrictEqual(['Ala', 'Gly', 'Lys', 'His', 'Asp']);
@@ -12,3 +10,3 @@ });
   it('Sequence split : nothing on N-term', () => {
-    let result = PEP.splitPeptide('AlaGlyLysHisAspOH');
+    let result = splitPeptide('AlaGlyLysHisAspOH');
     expect(result).toStrictEqual(['Ala', 'Gly', 'Lys', 'His', 'Asp']);
@@ -18,5 +16,5 @@ });
   it('Sequence split : nothing on C-term', () => {
-    let result = PEP.splitPeptide('HAlaGlyLysHisAsp');
+    let result = splitPeptide('HAlaGlyLysHisAsp');
     expect(result).toStrictEqual(['Ala', 'Gly', 'Lys', 'His', 'Asp']);
   });
 });

src/allowNeutralLoss.js

@@ -1,11 +0,14 @@
-'use strict';
-
-function allowNeutralLoss(mf, options) {
+/**
+ * Add neutral loss on natural amino acids
+ * @param {*} mf
+ * @returns
+ */
+export function allowNeutralLoss(mf) {
   if (Array.isArray(mf)) {
     for (let i = 0; i < mf.length; i++) {
-      mf[i] = allowOneNeutralLoss(mf[i], options);
+      mf[i] = allowOneNeutralLoss(mf[i]);
     }
     return mf;
   } else {
-    return allowOneNeutralLoss(mf, options);
+    return allowOneNeutralLoss(mf);
   }
@@ -20,3 +23,1 @@ }
 }
-
-module.exports = allowNeutralLoss;

src/aminoAcids.js

@@ -1,6 +0,4 @@
-'use strict';
-
 // SOURCE: https://en.wikipedia.org/wiki/Amino_acid
 // Link for UTF8 code for modified: https://codepoints.net/search?sc=Grek
-module.exports = [
+export const aminoAcids = [
   // Standard amino acids
@@ -7,0 +5,0 @@ {

src/chargePeptide.js

@@ -1,8 +0,6 @@
-'use strict';
+import { getAA } from './getAA';
 
-let getAA = require('./getAA');
-
 // SOURCE: https://en.wikipedia.org/wiki/Amino_acid
 
-function chargePeptide(mf, options = {}) {
+export function chargePeptide(mf, options = {}) {
   if (options.pH === undefined) options.pH = 0;
@@ -52,3 +50,1 @@ if (Array.isArray(mf)) {
 }
-
-module.exports = chargePeptide;

src/digestPeptide.js

@@ -1,3 +0,1 @@
-'use strict';
-
 /*
@@ -12,3 +10,3 @@ Iotuibs:
 
-function digestSequence(sequence, options = {}) {
+export function digestPeptide(sequence, options = {}) {
   sequence = sequence.replace(/^H([^a-z])/, '$1').replace(/OH$/, '');
@@ -36,4 +34,4 @@
         sequence: fragments[i],
-        nbResidue: nbResidue,
-        from: from,
+        nbResidue,
+        from,
         to: from + nbResidue - 1,
@@ -96,3 +94,1 @@ };
 }
-
-module.exports = digestSequence;

src/generatePeptideFragments.js

@@ -1,4 +0,2 @@
-'use strict';
-
-module.exports = function generatePeptideFragments(mf, options) {
+export function generatePeptideFragments(mf, options) {
   if (options === undefined) {
@@ -75,3 +73,3 @@ options = {
   return mfs;
-};
+}
 
@@ -78,0 +76,0 @@ function addNTerm(mfs, nTerm, i, options) {

src/getAA.js

@@ -1,10 +0,8 @@
-'use strict';
+import { aminoAcids } from './aminoAcids';
 
-let aa = require('./aminoAcids');
-
-function getAA(code) {
+export function getAA(code) {
   if (code.length === 1) {
-    for (let i = 0; i < aa.length; i++) {
-      if (aa[i].aa1 === code) {
-        return aa[i];
+    for (let i = 0; i < aminoAcids.length; i++) {
+      if (aminoAcids[i].aa1 === code) {
+        return aminoAcids[i];
       }
@@ -14,5 +12,5 @@ }
   if (code.length === 3) {
-    for (let i = 0; i < aa.length; i++) {
-      if (aa[i].aa3 === code) {
-        return aa[i];
+    for (let i = 0; i < aminoAcids.length; i++) {
+      if (aminoAcids[i].aa3 === code) {
+        return aminoAcids[i];
       }
@@ -22,3 +20,1 @@ }
 }
-
-module.exports = getAA;

src/index.js

@@ -1,49 +0,37 @@
-'use strict';
+import { aminoAcids } from './aminoAcids';
+import * as IEP from './isoElectricPoint';
+import { splitPeptide } from './splitPeptide.js';
 
-const allowNeutralLoss = require('./allowNeutralLoss');
-const aa = require('./aminoAcids');
-const chargePeptide = require('./chargePeptide');
-const convertAASequence = require('./convertAASequence');
-const digestPeptide = require('./digestPeptide');
-const generatePeptideFragments = require('./generatePeptideFragments');
-const IEP = require('./isoElectricPoint');
-const splitPeptide = require('./splitPeptide');
+export * from './allowNeutralLoss';
+export * from './chargePeptide.js';
+export * from './sequenceToMF.js';
+export * from './generatePeptideFragments.js';
+export * from './digestPeptide.js';
+export * from './splitPeptide.js';
 
-exports.getInfo = () => {
-  return aa;
-};
+export function getInfo() {
+  return aminoAcids;
+}
 
 // sequence should be in the "right" format like HAlaGlyProOH
 
-exports.splitPeptide = splitPeptide;
-exports.digestPeptide = digestPeptide;
-
-exports.calculateIEP = function calculateIEP(sequence) {
+export function calculateIEP(sequence) {
   let aas = splitPeptide(sequence);
   let result = IEP.calculateIEP(aas);
   return result;
-};
+}
 
-exports.calculateIEPChart = function calculateIEPChart(sequence) {
+export function calculateIEPChart(sequence) {
   let aas = splitPeptide(sequence);
   let result = IEP.calculateChart(aas);
   return result;
-};
+}
 
-exports.getColorForIEP = function getColorForIEP(iep) {
+export function getColorForIEP(iep) {
   return IEP.getColor(iep);
-};
+}
 
-exports.calculateCharge = function calculateCharge(sequence, ph) {
+export function calculateCharge(sequence, ph) {
   let aas = splitPeptide(sequence);
   return IEP.calculateCharge(aas, ph);
-};
-
-exports.generatePeptideFragments = generatePeptideFragments;
-
-exports.chargePeptide = chargePeptide;
-exports.allowNeutralLoss = allowNeutralLoss;
-
-exports.convertAASequence = convertAASequence;
-
-exports.sequenceToMF = convertAASequence;
+}

src/isoElectricPoint.js

@@ -1,13 +0,10 @@
-'use strict';
+import { aminoAcids } from './aminoAcids';
 
-let aa = require('./aminoAcids');
-
 // we will convert the data to an object to be much faster
 let aaObject = {};
-for (let i = 0; i < aa.length; i++) {
-  aaObject[aa[i].aa3] = aa[i];
+for (let i = 0; i < aminoAcids.length; i++) {
+  aaObject[aminoAcids[i].aa3] = aminoAcids[i];
 }
 
-function calculateCharge(aas, pH) {
-  if (!pH) pH = 7.0;
+export function calculateCharge(aas, pH = 7.0) {
   let combined = combine(aas);
@@ -21,3 +18,3 @@ if (!combined) return;
 
-function calculateIEP(aas) {
+export function calculateIEP(aas) {
   let combined = combine(aas);
@@ -45,3 +42,3 @@ if (!combined) return;
 
-function calculateChart(aas) {
+export function calculateChart(aas) {
   let combined = combine(aas);
@@ -67,11 +64,9 @@ if (!combined) return;
   let total = 0;
-  total += 1 / (1 + Math.pow(10, pH - combined.first));
-  total += -1 / (1 + Math.pow(10, combined.last - pH));
+  total += 1 / (1 + 10 ** (pH - combined.first));
+  total += -1 / (1 + 10 ** (combined.last - pH));
   for (let key in combined.acid) {
-    total +=
-      -combined.acid[key] / (1 + Math.pow(10, aaObject[key].sc.pKa - pH));
+    total += -combined.acid[key] / (1 + 10 ** (aaObject[key].sc.pKa - pH));
   }
   for (let key in combined.basic) {
-    total +=
-      combined.basic[key] / (1 + Math.pow(10, pH - aaObject[key].sc.pKa));
+    total += combined.basic[key] / (1 + 10 ** (pH - aaObject[key].sc.pKa));
   }
@@ -121,3 +116,3 @@ return total;
  */
-function getColor(iep) {
+export function getColor(iep) {
   if (iep < 7) {
@@ -134,8 +129,1 @@ if (iep < 3) iep = 3;
 }
-
-module.exports = {
-  calculateIEP: calculateIEP,
-  calculateCharge: calculateCharge,
-  calculateChart: calculateChart,
-  getColor: getColor,
-};

src/splitPeptide.js

@@ -1,4 +0,2 @@
-'use strict';
-
-function splitSequence(sequence) {
+export function splitPeptide(sequence) {
   let aas = sequence.replace(/([A-Z])/g, ' $1').split(/ /);
@@ -16,3 +14,1 @@ let begin = 0;
 }
-
-module.exports = splitSequence;

No alert changes

Improved metrics

Total package byte prevSize

61534

increased by39.04%

Number of package files

23

increased by4.55%

Lines of code

2138

increased by49.2%

No dependency changes