peptide - npm Package Compare versions

Comparing version 1.6.2 to 1.7.0

__tests__/digestPeptide.js

@@ -53,2 +53,12 @@ 'use strict';
   });
+
+  test('HLysLeu(H-1OH)ValOH digest at all amide bonds', () => {
+    var result = PEP.digestPeptide('HLysLeu(H-1OH)ValOH', {
+      enzyme: 'any',
+      minMissed: 1,
+      maxMissed: 1
+    });
+
+    expect(result).toEqual(['HLysLeu(H-1OH)OH$D1>2', 'HLeu(H-1OH)ValOH$D2>3']);
+  });
 });

__tests__/fragmentation.js

@@ -7,109 +7,183 @@ 'use strict';
 
-
-var allowed=[
-    "Ala$b1",
-    "AlaLys$b2",
-    "AlaLysLeu$b3",
-    "AlaLysLeuArg$b4",
-    "AlaLysLeuArgCys$b5",
-    "AlaLysLeuArgCysSer$b6",
-    "AlaLysLeuArgCysSerThr$b7",
-    "Tyr$y1",
-    "ThrTyr$y2",
-    "SerThrTyr$y3",
-    "CysSerThrTyr$y4",
-    "ArgCysSerThrTyr$y5",
-    "LeuArgCysSerThrTyr$y6",
-    "LysLeuArgCysSerThrTyr$y7"
+var allowed = [
+  'Ala$b1',
+  'AlaLys$b2',
+  'AlaLysLeu$b3',
+  'AlaLysLeuArg$b4',
+  'AlaLysLeuArgCys$b5',
+  'AlaLysLeuArgCysSer$b6',
+  'AlaLysLeuArgCysSerThr$b7',
+  'Tyr$y1',
+  'ThrTyr$y2',
+  'SerThrTyr$y3',
+  'CysSerThrTyr$y4',
+  'ArgCysSerThrTyr$y5',
+  'LeuArgCysSerThrTyr$y6',
+  'LysLeuArgCysSerThrTyr$y7'
 ];
 
-
 describe('Check fragmentation', () => {
-    
-    test('Check KA', () => {
-        var sequence=PEP.convertAASequence('KAA');
-        console.log(sequence);
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(4);
+  test('Check KA', () => {
+    var sequence = PEP.convertAASequence('KAA');
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(4);
+  });
 
-    test('Check AKLRCSTY', () => {
-        var sequence=PEP.convertAASequence('AKLRCSTY');
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(14);
-        checkAllowed(result);
+  test('Check AKLRCSTY', () => {
+    var sequence = PEP.convertAASequence('AKLRCSTY');
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(14);
+    checkAllowed(result);
+  });
 
-
-
-    test('Check HLysAlaOH', () => {
-        var result=PEP.generatePeptideFragments('HLysAlaOH',{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(2);
-        expect(result).toEqual( [ 'HLys(+1)$b1', 'H2(+1)AlaOH$y1' ]);
+  test('Check HLysAlaOH', () => {
+    var result = PEP.generatePeptideFragments('HLysAlaOH', {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(2);
+    expect(result).toEqual(['HLys(+1)$b1', 'H2(+1)AlaOH$y1']);
+  });
 
-    
-    test('Check HLys(COH)AlaOH side chain modified', () => {
-        var result=PEP.generatePeptideFragments('HLys(COH)AlaOH',{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(2);
-        expect(result).toEqual( ["HLys(COH)(+1)$b1", "H2(+1)AlaOH$y1"]);
+  test('Check HLys(COH)AlaOH side chain modified', () => {
+    var result = PEP.generatePeptideFragments('HLys(COH)AlaOH', {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(2);
+    expect(result).toEqual(['HLys(COH)(+1)$b1', 'H2(+1)AlaOH$y1']);
+  });
 
-    test('Check AKLRCSTY ph=1', () => {
-        var sequence=PEP.convertAASequence('AKLRCSTY');
-        sequence=PEP.chargePeptide(sequence, {pH: 1});
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(14);
-        checkAllowed(result);
+  test('Check AKLRCSTY ph=1', () => {
+    var sequence = PEP.convertAASequence('AKLRCSTY');
+    sequence = PEP.chargePeptide(sequence, { pH: 1 });
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(14);
+    checkAllowed(result);
+  });
 
-    test('Check AKLRCSTY ph=13', () => {
-        var sequence=PEP.convertAASequence('AKLRCSTY');
-        sequence=PEP.chargePeptide(sequence, {pH: 13});
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(14);
-        checkAllowed(result);
+  test('Check AKLRCSTY ph=13', () => {
+    var sequence = PEP.convertAASequence('AKLRCSTY');
+    sequence = PEP.chargePeptide(sequence, { pH: 13 });
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(14);
+    checkAllowed(result);
+  });
 
-    test('Check AKLRCSTY neutral loss ph=1', () => {
-        var sequence=PEP.convertAASequence('AKLRCSTY');
-        sequence=PEP.allowNeutralLoss(sequence);
-        sequence=PEP.chargePeptide(sequence, {pH: 1});
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(14);
-        checkAllowed(result);
+  test('Check AKLRCSTY neutral loss ph=1', () => {
+    var sequence = PEP.convertAASequence('AKLRCSTY');
+    sequence = PEP.allowNeutralLoss(sequence);
+    sequence = PEP.chargePeptide(sequence, { pH: 1 });
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(14);
+    checkAllowed(result);
+  });
 
-    test('Check AKLRCSTY neutral loss ph=13', () => {
-        var sequence=PEP.convertAASequence('AKLRCSTY');
-        sequence=PEP.allowNeutralLoss(sequence);
-        sequence=PEP.chargePeptide(sequence, {pH: 13});
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(14);
-        checkAllowed(result);
+  test('Check AKLRCSTY neutral loss ph=13', () => {
+    var sequence = PEP.convertAASequence('AKLRCSTY');
+    sequence = PEP.allowNeutralLoss(sequence);
+    sequence = PEP.chargePeptide(sequence, { pH: 13 });
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(14);
+    checkAllowed(result);
+  });
 
-    test('Check AKLRCSTY neutral loss', () => {
-        var sequence=PEP.convertAASequence('AKLRCSTY');
-        sequence=PEP.allowNeutralLoss(sequence);
-        var result=PEP.generatePeptideFragments(sequence,{a:false, b:true, c:false, x:false, y:true, z:false, yb:false, ya:false});
-        expect(result).toHaveLength(14);
-        checkAllowed(result);
+  test('Check AKLRCSTY neutral loss', () => {
+    var sequence = PEP.convertAASequence('AKLRCSTY');
+    sequence = PEP.allowNeutralLoss(sequence);
+    var result = PEP.generatePeptideFragments(sequence, {
+      a: false,
+      b: true,
+      c: false,
+      x: false,
+      y: true,
+      z: false,
+      yb: false,
+      ya: false
     });
+    expect(result).toHaveLength(14);
+    checkAllowed(result);
+  });
 });
 
 function clean(mfs) {
-    for (var i=0; i<mfs.length; i++) {
-        var mf=mfs[i]
-        mfs[i]=mfs[i].replace(/\([^\(]*\)[0-9-]*/g,'');
-        mfs[i]=mfs[i].replace(/^[H\d+]*(?=[A-Z])/,'');
-        mfs[i]=mfs[i].replace(/O[H-]\$/,'$');
-    }
+  for (var i = 0; i < mfs.length; i++) {
+    var mf = mfs[i];
+    mfs[i] = mfs[i].replace(/\([^\(]*\)[0-9-]*/g, '');
+    mfs[i] = mfs[i].replace(/^[H\d+]*(?=[A-Z])/, '');
+    mfs[i] = mfs[i].replace(/O[H-]\$/, '$');
+  }
 }
 
 function checkAllowed(mfs) {
-    clean(mfs);
-    for (var mf of mfs) {
-        expect(allowed).toContain(mf);
-    }
-}
+  clean(mfs);
+  for (var mf of mfs) {
+    expect(allowed).toContain(mf);
+  }
+}

__tests__/splitPeptide.js

@@ -5,22 +5,17 @@ 'use strict';
 
-
 describe('Checking split peptide', () => {
-    test('Normal sequence split', () => {
-        var result=PEP.splitPeptide("HAlaGlyLysHisAspOH");
-        expect(result).toEqual(["Ala","Gly","Lys","His","Asp"]);
-    });
+  test('Normal sequence split', () => {
+    var result = PEP.splitPeptide('HAlaGlyLysHisAspOH');
+    expect(result).toEqual(['Ala', 'Gly', 'Lys', 'His', 'Asp']);
+  });
 
-    test('Sequence split : nothing on N-term', () => {
-        var result=PEP.splitPeptide("AlaGlyLysHisAspOH");
-        expect(result).toEqual(["Ala","Gly","Lys","His","Asp"]);
-    });
+  test('Sequence split : nothing on N-term', () => {
+    var result = PEP.splitPeptide('AlaGlyLysHisAspOH');
+    expect(result).toEqual(['Ala', 'Gly', 'Lys', 'His', 'Asp']);
+  });
 
-    test('Sequence split : nothing on C-term', () => {
-        var result=PEP.splitPeptide("HAlaGlyLysHisAsp");
-        expect(result).toEqual(["Ala","Gly","Lys","His","Asp"]);
-    });
-
-    
+  test('Sequence split : nothing on C-term', () => {
+    var result = PEP.splitPeptide('HAlaGlyLysHisAsp');
+    expect(result).toEqual(['Ala', 'Gly', 'Lys', 'His', 'Asp']);
+  });
 });
-
-

bower.json

 {
   "name": "peptide",
-  "version": "1.6.2",
+  "version": "1.7.0",
   "description": "Peptide",
@@ -5,0 +5,0 @@ "keywords": [

package.json

 {
   "name": "peptide",
-  "version": "1.6.2",
+  "version": "1.7.0",
   "description": "Peptide",
@@ -33,3 +33,3 @@ "keywords": [
     "cheminfo-tools": "^1.20.2",
-    "eslint": "^5.14.1",
+    "eslint": "^5.15.1",
     "eslint-config-cheminfo": "^1.18.0",
@@ -36,0 +36,0 @@ "eslint-plugin-jest": "^22.3.0",

src/digestPeptide.js

@@ -25,14 +25,18 @@ 'use strict';
   var regexp = getRegexp(options.enzyme);
-  var fragments = sequence.replace(regexp, '$1 ').split(/ /);
-  if (!fragments[fragments.length - 1])
-    fragments = fragments.slice(0, fragments.length - 1);
+  var fragments = sequence
+    .replace(regexp, '$1 ')
+    .split(/ /)
+    .filter(entry => entry);
 
   var from = 0;
   for (var i = 0; i < fragments.length; i++) {
-    var nbResidue = splitSequence(fragments[i]).length;
+    var nbResidue = fragments[i]
+      .replace(/([A-Z][a-z][a-z])/g, ' $1')
+      .split(/ /)
+      .filter(entry => entry).length;
     fragments[i] = {
       sequence: fragments[i],
       nbResidue: nbResidue,
-      from: from + 1,
-      to: from + nbResidue
+      from: from,
+      to: from + nbResidue - 1
     };
@@ -56,4 +60,4 @@ from += nbResidue;
       }
-      var from = fragments[i].from;
-      var to = fragments[i + j].to;
+      var from = fragments[i].from + 1;
+      var to = fragments[i + j].to + 1;
       if (
@@ -88,2 +92,4 @@ fragment &&
       return /(Met)/g;
+    case 'any':
+      return /()(?=[A-Z][a-z][a-z])/g;
   }
@@ -90,0 +96,0 @@ throw new Error('Digestion enzyme: ' + enzyme + ' is unknown');

src/splitPeptide.js

 'use strict';
 
 function splitSequence(sequence) {
-    var aas=sequence.replace(/([A-Z])/g," $1").split(/ /);
-    var begin=0;
-    while (aas[begin]==='' || aas[begin]==='H') {
-        begin++;
-    }
-    var end=aas.length-1;
-    while (aas[end]==='O' || aas[end]==='H') {
-        end--;
-    }
-    aas=aas.slice(begin,end+1);
-    return aas;
+  var aas = sequence.replace(/([A-Z])/g, ' $1').split(/ /);
+  var begin = 0;
+  while (aas[begin] === '' || aas[begin] === 'H') {
+    begin++;
+  }
+  var end = aas.length - 1;
+  while (aas[end] === 'O' || aas[end] === 'H') {
+    end--;
+  }
+  aas = aas.slice(begin, end + 1);
+  return aas;
 }
 
-
 module.exports = splitSequence;
-

No alert changes

Improved metrics

Total package byte prevSize

43045

increased by1.57%

Lines of code

1222

increased by8.43%

No dependency changes