peptide - npm Package Compare versions

Comparing version 1.10.0 to 1.10.1

bower.json

 {
   "name": "peptide",
-  "version": "1.10.0",
+  "version": "1.10.1",
   "description": "Peptide",
@@ -5,0 +5,0 @@ "keywords": [

package.json

 {
   "name": "peptide",
-  "version": "1.10.0",
+  "version": "1.10.1",
   "description": "Peptide",
@@ -33,12 +33,12 @@ "keywords": [
     "cheminfo-tools": "^1.23.3",
-    "eslint": "^6.5.1",
-    "eslint-config-cheminfo": "^2.0.3",
+    "eslint": "^6.7.1",
+    "eslint-config-cheminfo": "^2.0.4",
     "eslint-plugin-import": "^2.18.2",
-    "eslint-plugin-jest": "^22.19.0",
+    "eslint-plugin-jest": "^23.0.4",
     "eslint-plugin-no-only-tests": "^2.3.1",
     "eslint-plugin-prettier": "^3.1.1",
     "jest": "^24.9.0",
-    "prettier": "^1.18.2"
+    "prettier": "^1.19.1"
   },
   "dependencies": {}
 }

src/__tests__/convertAASequence.test.js

@@ -9,6 +9,12 @@ const convertAASequence = require('../convertAASequence');
 
-test('HAlaAla(H-1OH)AlaOH', () => {
-  const result = convertAASequence('HAlaAla(H-1OH)AlaOH');
-  expect(result).toEqual('HAlaAla(H-1OH)AlaOH');
-})
+  test('HAlaAla(H-1OH)AlaOH', () => {
+    const result = convertAASequence('HAlaAla(H-1OH)AlaOH');
+    expect(result).toEqual('HAlaAla(H-1OH)AlaOH');
+  });
+  test('(C33H37O6N3Si) GluTyrGluLys(C16H30O)GluTyrGluOH', () => {
+    const result = convertAASequence(
+      '(C33H37O6N3Si) GluTyrGluLys(C16H30O)GluTyrGluOH'
+    );
+    expect(result).toEqual('(C33H37O6N3Si) GluTyrGluLys(C16H30O)GluTyrGluOH');
+  });
 
@@ -20,2 +26,7 @@ test('(Me)AAAAAAA(NH2)', () => {
 
+  test('HAlaGlyProOH', () => {
+    const result = convertAASequence('HAlaGlyProOH');
+    expect(result).toEqual('HAlaGlyProOH');
+  });
+
   test('ALA SER LYS GLY PRO', () => {
@@ -22,0 +33,0 @@ const result = convertAASequence('ALA SER LYS GLY PRO');

src/__tests__/fragmentation.test.js

@@ -21,3 +21,3 @@ 'use strict';
   'LeuArgCysSerThrTyr$y6',
-  'LysLeuArgCysSerThrTyr$y7',
+  'LysLeuArgCysSerThrTyr$y7'
 ];
@@ -36,3 +36,3 @@
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -52,3 +52,3 @@ expect(result).toHaveLength(4);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -68,3 +68,3 @@ expect(result).toHaveLength(14);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -84,3 +84,3 @@ expect(result).toHaveLength(2);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -102,3 +102,3 @@ expect(result).toHaveLength(2);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -120,3 +120,3 @@ expect(result).toHaveLength(14);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -139,3 +139,3 @@ expect(result).toHaveLength(14);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -158,3 +158,3 @@ expect(result).toHaveLength(14);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -176,3 +176,3 @@ expect(result).toHaveLength(14);
       yb: false,
-      ya: false,
+      ya: false
     });
@@ -182,2 +182,27 @@ expect(result).toHaveLength(14);
   });
+
+  it.only('ALP versus (H)ALP(OH) versus HAlaLeuProOH versus (H)AlaLeuPro(OH)', () => {
+    let sequence1 = PEP.convertAASequence('ALP');
+    let sequence2 = PEP.convertAASequence('(H)ALP(OH)');
+    let sequence3 = PEP.convertAASequence('HAlaLeuProOH');
+    let sequence4 = PEP.convertAASequence('(H)AlaLeuPro(OH)');
+    let result1 = PEP.generatePeptideFragments(sequence1);
+    let result2 = PEP.generatePeptideFragments(sequence2);
+    let result3 = PEP.generatePeptideFragments(sequence3);
+    let result4 = PEP.generatePeptideFragments(sequence4);
+    expect(result1).toStrictEqual([
+      'HAla(+1)$b1',
+      'H2(+1)ProOH$y1',
+      'HAlaLeu(+1)$b2',
+      'H2(+1)LeuProOH$y2'
+    ]);
+    expect(result2).toStrictEqual([
+      '(H)Ala(+1)$b1',
+      'H2(+1)Pro(OH)$y1',
+      '(H)AlaLeu(+1)$b2',
+      'H2(+1)LeuPro(OH)$y2'
+    ]);
+    expect(result1).toStrictEqual(result3);
+    expect(result2).toStrictEqual(result4);
+  });
 });
@@ -184,0 +209,0 @@

src/aminoAcids.js

@@ -12,6 +12,6 @@ 'use strict';
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.33,
-    pKaN: 9.71
+    pKaN: 9.71,
   },
@@ -24,6 +24,6 @@ {
       type: 'positive',
-      pKa: 12.1
+      pKa: 12.1,
     },
     pKaC: 2.03,
-    pKaN: 9.0
+    pKaN: 9.0,
   },
@@ -35,6 +35,6 @@ {
     sc: {
-      type: 'polar'
+      type: 'polar',
     },
     pKaC: 2.13,
-    pKaN: 9.05
+    pKaN: 9.05,
   },
@@ -47,6 +47,6 @@ {
       type: 'negative',
-      pKa: 3.71
+      pKa: 3.71,
     },
     pKaC: 1.95,
-    pKaN: 9.66
+    pKaN: 9.66,
   },
@@ -59,6 +59,6 @@ {
       type: 'special',
-      pKa: 8.14
+      pKa: 8.14,
     },
     pKaC: 1.91,
-    pKaN: 10.28
+    pKaN: 10.28,
   },
@@ -71,6 +71,6 @@ {
       type: 'negative',
-      pKa: 4.15
+      pKa: 4.15,
     },
     pKaC: 2.16,
-    pKaN: 9.58
+    pKaN: 9.58,
   },
@@ -82,6 +82,6 @@ {
     sc: {
-      type: 'polar'
+      type: 'polar',
     },
     pKaC: 2.18,
-    pKaN: 9.0
+    pKaN: 9.0,
   },
@@ -93,6 +93,6 @@ {
     sc: {
-      type: 'special'
+      type: 'special',
     },
     pKaC: 2.34,
-    pKaN: 9.58
+    pKaN: 9.58,
   },
@@ -105,6 +105,6 @@ {
       type: 'positive',
-      pKa: 6.04
+      pKa: 6.04,
     },
     pKaC: 1.7,
-    pKaN: 9.09
+    pKaN: 9.09,
   },
@@ -116,6 +116,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.26,
-    pKaN: 9.6
+    pKaN: 9.6,
   },
@@ -127,6 +127,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.32,
-    pKaN: 9.58
+    pKaN: 9.58,
   },
@@ -139,6 +139,6 @@ {
       type: 'positive',
-      pKa: 10.67
+      pKa: 10.67,
     },
     pKaC: 2.15,
-    pKaN: 9.16
+    pKaN: 9.16,
   },
@@ -150,6 +150,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.16,
-    pKaN: 9.08
+    pKaN: 9.08,
   },
@@ -161,6 +161,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.18,
-    pKaN: 9.09
+    pKaN: 9.09,
   },
@@ -172,6 +172,6 @@ {
     sc: {
-      type: 'special'
+      type: 'special',
     },
     pKaC: 1.95,
-    pKaN: 10.47
+    pKaN: 10.47,
   },
@@ -183,6 +183,6 @@ {
     sc: {
-      type: 'polar'
+      type: 'polar',
     },
     pKaC: 2.13,
-    pKaN: 9.05
+    pKaN: 9.05,
   },
@@ -194,6 +194,6 @@ {
     sc: {
-      type: 'polar'
+      type: 'polar',
     },
     pKaC: 2.2,
-    pKaN: 8.96
+    pKaN: 8.96,
   },
@@ -205,6 +205,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.38,
-    pKaN: 9.34
+    pKaN: 9.34,
   },
@@ -216,6 +216,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.24,
-    pKaN: 9.04
+    pKaN: 9.04,
   },
@@ -227,6 +227,6 @@ {
     sc: {
-      type: 'hydrophobic'
+      type: 'hydrophobic',
     },
     pKaC: 2.27,
-    pKaN: 9.52
+    pKaN: 9.52,
   },
@@ -237,3 +237,3 @@ // Additional
     aa3: 'Sec',
-    aa1: 'U'
+    aa1: 'U',
   },
@@ -243,3 +243,3 @@ {
     aa3: 'Pyl',
-    aa1: 'O'
+    aa1: 'O',
   },
@@ -250,3 +250,3 @@ // Ambiguous
     aa3: 'Asx',
-    aa1: 'B'
+    aa1: 'B',
   },
@@ -256,3 +256,3 @@ {
     aa3: 'Glx',
-    aa1: 'Z'
+    aa1: 'Z',
   },
@@ -262,3 +262,3 @@ {
     aa3: 'Xle',
-    aa1: 'J'
+    aa1: 'J',
   },
@@ -268,4 +268,4 @@ {
     aa3: 'Xaa',
-    aa1: 'X'
-  }
+    aa1: 'X',
+  },
 ];

src/generatePeptideFragments.js

@@ -31,2 +31,15 @@ 'use strict';
 
+  if (mfparts[0].startsWith('(')) {
+    nTerm += mfparts[0];
+    mfparts = mfparts.splice(1);
+  }
+
+  if (mfparts[mfparts.length - 1].includes('(')) {
+    cTerm += mfparts[mfparts.length - 1].replace(/^[^()]*/, '');
+    mfparts[mfparts.length - 1] = mfparts[mfparts.length - 1].replace(
+      /\(.*/,
+      '',
+    );
+  }
+
   for (let i = 1; i < mfparts.length; i++) {
@@ -33,0 +46,0 @@ nTerm += mfparts[i - 1];

No alert changes

Improved metrics

Total package byte prevSize

53305

increased by3.27%

Lines of code

1324

increased by3.52%

No dependency changes