mf-parser - npm Package Compare versions

Comparing version 0.5.11 to 0.5.12

package.json

 {
   "name": "mf-parser",
-  "version": "0.5.11",
+  "version": "0.5.12",
   "description": "",
@@ -21,6 +21,6 @@ "main": "src/index.js",
   "dependencies": {
-    "atom-sorter": "^0.5.11",
-    "chemical-elements": "^0.5.11",
-    "mf-utilities": "^0.5.11"
+    "atom-sorter": "^0.5.12",
+    "chemical-elements": "^0.5.12",
+    "mf-utilities": "^0.5.12"
   }
 }

src/__tests__/MF.js

@@ -9,7 +9,3 @@ 'use strict';
 
-    expect(parts).toEqual(
-        [[
-            { kind: 'atom', value: 'C', multiplier: 1 },
-        ]]
-    );
+    expect(parts).toEqual([[{ kind: 'atom', value: 'C', multiplier: 1 }]]);
 
@@ -42,12 +38,13 @@ var newMF = mf.toMF();
 
-    expect(parts).toEqual(
-        [[
+    expect(parts).toEqual([
+        [
             { kind: 'atom', value: 'C', multiplier: 6 },
             { kind: 'atom', value: 'H', multiplier: 15 },
             { kind: 'atom', value: 'N', multiplier: 1 }
-        ], [
+        ],
+        [
             { kind: 'atom', value: 'H', multiplier: 1 },
             { kind: 'atom', value: 'Cl', multiplier: 1 }
-        ]]
-    );
+        ]
+    ]);
 
@@ -63,20 +60,26 @@ var newMF = mf.toMF();
     let info = mf.getInfo();
-    expect(info).toEqual({ parts:
-        [{ mass: 101.19022990269394,
-            monoisotopicMass: 101.12044948788001,
-            charge: 0,
-            mf: 'C6H15N',
-            unsaturation: 0,
-            atoms: { C: 6, H: 15, N: 1 } },
-        { mass: 36.460878336663775,
-            monoisotopicMass: 35.97667771423,
-            charge: 0,
-            mf: 'HCl',
-            unsaturation: 0,
-            atoms: { H: 1, Cl: 1 } }],
-    monoisotopicMass: 137.09712720211002,
-    mass: 137.6511082393577,
-    charge: 0,
-    mf: 'C6H15N.HCl' }
-    );
+    expect(info).toEqual({
+        parts: [
+            {
+                mass: 101.19022990269394,
+                monoisotopicMass: 101.12044948788001,
+                charge: 0,
+                mf: 'C6H15N',
+                unsaturation: 0,
+                atoms: { C: 6, H: 15, N: 1 }
+            },
+            {
+                mass: 36.460878336663775,
+                monoisotopicMass: 35.97667771423,
+                charge: 0,
+                mf: 'HCl',
+                unsaturation: 0,
+                atoms: { H: 1, Cl: 1 }
+            }
+        ],
+        monoisotopicMass: 137.09712720211002,
+        mass: 137.6511082393577,
+        charge: 0,
+        mf: 'C6H15N.HCl'
+    });
 });
@@ -88,4 +91,4 @@
 
-    expect(parts).toEqual(
-        [[
+    expect(parts).toEqual([
+        [
             { kind: 'atom', value: 'C', multiplier: 3 },
@@ -95,6 +98,5 @@ { kind: 'atom', value: 'H', multiplier: 3 },
             { kind: 'atom', value: 'N', multiplier: 1 }
-        ]]
+        ]
+    ]);
 
-    );
-
     var newMF = mf.toMF();
@@ -104,12 +106,10 @@ expect(newMF).toBe('C3H3Me6N');
     let info = mf.getInfo();
-    expect(info).toEqual(
-        {
-            mass: 143.27008211723435,
-            monoisotopicMass: 143.16739968126,
-            charge: 0,
-            mf: 'C3H3Me6N',
-            unsaturation: 0,
-            atoms: { C: 3, H: 3, Me: 6, N: 1 }
-        }
-    );
+    expect(info).toEqual({
+        mass: 143.27008211723435,
+        monoisotopicMass: 143.16739968126,
+        charge: 0,
+        mf: 'C3H3Me6N',
+        unsaturation: 0,
+        atoms: { C: 3, H: 3, Me: 6, N: 1 }
+    });
 });
@@ -121,9 +121,9 @@
 
-    expect(parts).toEqual(
-        [[
+    expect(parts).toEqual([
+        [
             { kind: 'atom', value: 'C', multiplier: 9 },
             { kind: 'atom', value: 'H', multiplier: 21 },
             { kind: 'atom', value: 'N', multiplier: 1 }
-        ]]
-    );
+        ]
+    ]);
 
@@ -134,12 +134,10 @@ var newMF = mf.toMF();
     let info = mf.getInfo();
-    expect(info).toEqual(
-        {
-            mass: 143.27008211723435,
-            monoisotopicMass: 143.16739968126,
-            charge: 0,
-            mf: 'C9H21N',
-            unsaturation: 0,
-            atoms: { C: 9, H: 21, N: 1 }
-        }
-    );
+    expect(info).toEqual({
+        mass: 143.27008211723435,
+        monoisotopicMass: 143.16739968126,
+        charge: 0,
+        mf: 'C9H21N',
+        unsaturation: 0,
+        atoms: { C: 9, H: 21, N: 1 }
+    });
 });
@@ -151,9 +149,9 @@
 
-    expect(parts).toEqual(
-        [[
+    expect(parts).toEqual([
+        [
             { kind: 'atom', value: 'O', multiplier: 4 },
             { kind: 'atom', value: 'S', multiplier: 1 },
-            { kind: 'charge', value: -2 },
-        ]]
-    );
+            { kind: 'charge', value: -2 }
+        ]
+    ]);
 
@@ -175,15 +173,15 @@ var newMF = mf.toMF();
         unsaturation: 4,
-        atoms: { O: 4, S: 1 } }
-    );
+        atoms: { O: 4, S: 1 }
+    });
 });
 
 test('test unsaturation with charges', () => {
-    expect((new MF('CH4')).getInfo().unsaturation).toBe(0);
-    expect((new MF('C10H22O')).getInfo().unsaturation).toBe(0);
-    expect((new MF('H+')).getInfo().unsaturation).toBe(0);
-    expect((new MF('CO3(--)')).getInfo().unsaturation).toBe(3);
-    expect((new MF('HO(-)')).getInfo().unsaturation).toBe(1);
-    expect((new MF('F(-)')).getInfo().unsaturation).toBe(1);
-    expect((new MF('Na+')).getInfo().unsaturation).toBe(0);
-    expect((new MF('NH4+')).getInfo().unsaturation).toBe(-1);
+    expect(new MF('CH4').getInfo().unsaturation).toBe(0);
+    expect(new MF('C10H22O').getInfo().unsaturation).toBe(0);
+    expect(new MF('H+').getInfo().unsaturation).toBe(0);
+    expect(new MF('CO3(--)').getInfo().unsaturation).toBe(3);
+    expect(new MF('HO(-)').getInfo().unsaturation).toBe(1);
+    expect(new MF('F(-)').getInfo().unsaturation).toBe(1);
+    expect(new MF('Na+').getInfo().unsaturation).toBe(0);
+    expect(new MF('NH4+').getInfo().unsaturation).toBe(-1);
 });
@@ -194,10 +192,18 @@
     var parts = mf.toParts();
-    expect(parts).toEqual(
-        [[
+    expect(parts).toEqual([
+        [
             { kind: 'atom', value: 'C', multiplier: 1 },
-            { kind: 'isotope', value: { atom: 'C', isotope: 13 }, multiplier: 1 },
+            {
+                kind: 'isotope',
+                value: { atom: 'C', isotope: 13 },
+                multiplier: 1
+            },
             { kind: 'atom', value: 'N', multiplier: 4 },
-            { kind: 'isotope', value: { atom: 'N', isotope: 15 }, multiplier: 2 },
-        ]]
-    );
+            {
+                kind: 'isotope',
+                value: { atom: 'N', isotope: 15 },
+                multiplier: 2
+            }
+        ]
+    ]);
 
@@ -211,3 +217,3 @@ let info = mf.getInfo();
         unsaturation: 6,
-        atoms: { C: 2, N: 6 },
+        atoms: { C: 2, N: 6 }
     });
@@ -219,12 +225,38 @@
 
+test('MF of DNA HODampDtmpDcmpDgmpH  ', () => {
+    var mf = new MF('HODampDtmpDgmpDcmpH');
+    var info = mf.getInfo();
+    expect(info).toEqual({ mass: 1253.8043977028433,
+        monoisotopicMass: 1253.21310019311,
+        charge: 0,
+        mf: 'C39H51N15O25P4',
+        atoms: { C: 39, H: 51, N: 15, O: 25, P: 4 },
+        unsaturation: 24 });
+});
+
+test('MF of RNA HOAmpUmpH  ', () => {
+    var mf = new MF('HOAmpUmpH');
+    var info = mf.getInfo();
+    expect(info).toEqual({ mass: 653.388021231099,
+        monoisotopicMass: 653.08838712715,
+        charge: 0,
+        mf: 'C19H25N7O15P2',
+        atoms: { C: 19, H: 25, N: 7, O: 15, P: 2 },
+        unsaturation: 12 });
+});
+
 test('MF of CC{50,50}H', () => {
     var mf = new MF('HC{50,50}C');
     var parts = mf.toParts();
-    expect(parts).toEqual(
-        [[
+    expect(parts).toEqual([
+        [
             { kind: 'atom', value: 'C', multiplier: 1 },
-            { kind: 'isotopeRatio', value: { atom: 'C', ratio: [50, 50] }, multiplier: 1 },
+            {
+                kind: 'isotopeRatio',
+                value: { atom: 'C', ratio: [50, 50] },
+                multiplier: 1
+            },
             { kind: 'atom', value: 'H', multiplier: 1 }
-        ]]
-    );
+        ]
+    ]);
 
@@ -235,12 +267,10 @@ var newMF = mf.toMF();
     let info = mf.getInfo();
-    expect(info).toEqual(
-        {
-            monoisotopicMass: 25.00782503223,
-            mass: 25.520354068326025,
-            charge: 0,
-            mf: 'CC{50,50}H',
-            unsaturation: 2.5,
-            atoms: { C: 2, H: 1 }
-        }
-    );
+    expect(info).toEqual({
+        monoisotopicMass: 25.00782503223,
+        mass: 25.520354068326025,
+        charge: 0,
+        mf: 'CC{50,50}H',
+        unsaturation: 2.5,
+        atoms: { C: 2, H: 1 }
+    });
 });

src/util/getInfo.js

@@ -13,3 +13,2 @@ 'use strict';
 
-
 /**
@@ -21,7 +20,7 @@ *
 module.exports = function getInfo(parts, options = {}) {
-    let {
-        customUnsaturations = {}
-    } = options;
+    let { customUnsaturations = {} } = options;
     if (parts.length === 0) return {};
-    if (parts.length === 1) return getProcessedPart(parts[0], customUnsaturations);
+    if (parts.length === 1) {
+        return getProcessedPart(parts[0], customUnsaturations);
+    }
 
@@ -67,2 +66,3 @@ var result = {
                     element = groups[line.value];
+                    if (!element) throw Error(`Unknown element: ${line.value}`);
                     if (!customUnsaturations[line.value]) {
@@ -74,3 +74,4 @@ customUnsaturations[line.value] = element.unsaturation;
                 if (!element) throw new Error(`Unknown element: ${line.value}`);
-                currentPart.monoisotopicMass += element.monoisotopicMass * line.multiplier;
+                currentPart.monoisotopicMass +=
+                    element.monoisotopicMass * line.multiplier;
                 currentPart.mass += element.mass * line.multiplier;
@@ -82,3 +83,9 @@ break;
                 let isotope = isotopes[line.value.isotope + line.value.atom];
-                if (!isotope) throw new Error(`Unknown isotope: ${line.value.isotope}${line.value.atom}`);
+                if (!isotope) {
+                    throw new Error(
+                        `Unknown isotope: ${line.value.isotope}${
+                            line.value.atom
+                        }`
+                    );
+                }
                 currentPart.monoisotopicMass += isotope.mass * line.multiplier;
@@ -91,3 +98,4 @@ currentPart.mass += isotope.mass * line.multiplier;
                 let isotopeRatioInfo = getIsotopeRatioInfo(line.value);
-                currentPart.monoisotopicMass += isotopeRatioInfo.monoisotopicMass * line.multiplier;
+                currentPart.monoisotopicMass +=
+                    isotopeRatioInfo.monoisotopicMass * line.multiplier;
                 currentPart.mass += isotopeRatioInfo.mass * line.multiplier;
@@ -107,3 +115,4 @@ break;
             if (customUnsaturations[currentElement] !== undefined) {
-                unsaturation += customUnsaturations[currentElement] * line.multiplier;
+                unsaturation +=
+                    customUnsaturations[currentElement] * line.multiplier;
             } else if (unsaturations[currentElement] !== undefined) {
@@ -119,3 +128,6 @@ unsaturation += unsaturations[currentElement] * line.multiplier;
     if (currentPart.charge) {
-        currentPart.observedMonoisotopicMass = (currentPart.monoisotopicMass - currentPart.charge * ELECTRON_MASS) / Math.abs(currentPart.charge);
+        currentPart.observedMonoisotopicMass =
+            (currentPart.monoisotopicMass -
+                currentPart.charge * ELECTRON_MASS) /
+            Math.abs(currentPart.charge);
     }
@@ -128,3 +140,2 @@ if (validUnsaturation) {
 
-
 function getIsotopeRatioInfo(value) {
@@ -141,3 +152,7 @@ let result = {
     if (ratios.length > isotopesArray.length) {
-        throw new Error(`the number of specified ratios is bigger that the number of stable isotopes: ${value.atom}`);
+        throw new Error(
+            `the number of specified ratios is bigger that the number of stable isotopes: ${
+                value.atom
+            }`
+        );
     }
@@ -157,2 +172,1 @@ for (let i = 0; i < ratios.length; i++) {
 }
-

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Improved metrics

Total package byte prevSize

55479

increased by2.21%

Lines of code

1439

increased by3.3%

Dependency changes

• - Removedmf-parser@0.5.12(transitive)

• Updatedatom-sorter@^0.5.12

• Updatedchemical-elements@^0.5.12

• Updatedmf-utilities@^0.5.12