mf-utilities - npm Package Compare versions

Comparing version 0.8.0 to 0.9.1

package.json

 {
   "name": "mf-utilities",
-  "version": "0.8.0",
+  "version": "0.9.1",
   "description": "Small utilities dealing with molecular formula",
@@ -21,5 +21,6 @@ "main": "src/index.js",
   "dependencies": {
-    "chemical-elements": "^0.7.0",
-    "mf-parser": "^0.8.0"
+    "chemical-elements": "^0.9.1",
+    "chemical-groups": "^0.9.1",
+    "mf-parser": "^0.9.1"
   }
 }

src/__tests__/getMsInfo.js

@@ -5,60 +5,61 @@ 'use strict';
 
-
 test('getMsInfo', () => {
+  let mf = {
+    mf: 'C10',
+    em: 120,
+    charge: 0
+  };
+  expect(getMsInfo(mf).ms).toMatchObject({
+    ionization: '',
+    em: 0,
+    charge: 0
+  });
 
-    let mf = {
-        mf: 'C10',
-        em: 120,
-        charge: 0
-    };
-    expect(getMsInfo(mf)).toMatchObject({
-        ionization: '',
-        em: 0,
-        charge: 0
-    });
+  expect(getMsInfo(mf, { allowNeutralMolecules: true }).ms).toMatchObject({
+    ionization: '',
+    em: 120,
+    charge: 0
+  });
 
-    expect(getMsInfo(mf, { allowNeutralMolecules: true })).toMatchObject({
-        ionization: '',
-        em: 120,
-        charge: 0
-    });
-
-    expect(getMsInfo(mf, { ionization: { mf: 'H+', charge: 1, em: 1 } })).toMatchObject({
-        ionization: 'H+',
-        em: 120.99945142009094,
-        charge: 1
-    });
-
+  expect(
+    getMsInfo(mf, { ionization: { mf: 'H+', charge: 1, em: 1 } }).ms
+  ).toMatchObject({
+    ionization: 'H+',
+    em: 120.99945142009094,
+    charge: 1
+  });
 });
 
 test('getMsInfo with targetMass', () => {
+  let mf = {
+    mf: 'C10',
+    em: 120,
+    charge: 0
+  };
 
-    let mf = {
-        mf: 'C10',
-        em: 120,
-        charge: 0,
-    };
+  expect(
+    getMsInfo(mf, {
+      allowNeutralMolecules: true,
+      targetMass: 120
+    }).ms
+  ).toMatchObject({
+    ionization: '',
+    em: 120,
+    charge: 0,
+    ppm: 0,
+    delta: 0
+  });
 
-    expect(getMsInfo(mf, {
-        allowNeutralMolecules: true,
-        targetMass: 120,
-    })).toMatchObject({
-        ionization: '',
-        em: 120,
-        charge: 0,
-        ppm: 0,
-        delta: 0
-    });
-
-    expect(getMsInfo(mf, {
-        ionization: { mf: 'H+', charge: 1, em: 1 }, // we use one as exact mass to test
-        targetMass: 121,
-    })).toMatchObject({
-        ionization: 'H+',
-        em: 120.99945142009094,
-        charge: 1,
-        ppm: 4.5337182567354,
-        delta: -0.0005485799090649834,
-    });
-
+  expect(
+    getMsInfo(mf, {
+      ionization: { mf: 'H+', charge: 1, em: 1 }, // we use one as exact mass to test
+      targetMass: 121
+    }).ms
+  ).toMatchObject({
+    ionization: 'H+',
+    em: 120.99945142009094,
+    charge: 1,
+    ppm: 4.5337182567354,
+    delta: -0.0005485799090649834
+  });
 });

src/__tests__/preprocessIonizations.js

@@ -6,8 +6,8 @@ 'use strict';
 describe('preprocessIonizations', () => {
-    it('check ionizations', () => {
-        let ionizations = preprocessIonizations('H+,Na+,(H+)2, K+');
-        expect(ionizations).toHaveLength(4);
-        expect(ionizations[0]).toMatchObject({ mf: 'H+', em: 1.00782503223, charge: 1 });
-        expect(ionizations[2]).toMatchObject({ mf: '(H+)2', em: 2.01565006446, charge: 2 });
-    });
+  it('check ionizations', () => {
+    let ionizations = preprocessIonizations('H+,Na+,(H+)2, K+');
+    expect(ionizations).toHaveLength(4);
+    expect(ionizations[0]).toMatchObject({ mf: 'H+', em: 1.00782503223, charge: 1 });
+    expect(ionizations[2]).toMatchObject({ mf: '(H+)2', em: 2.01565006446, charge: 2 });
+  });
 });

src/getMsem.js

@@ -6,9 +6,9 @@ 'use strict';
 module.exports = function getMsem(em, charge) {
-    if (charge > 0) {
-        return em / charge - ELECTRON_MASS;
-    } else if (charge < 0) {
-        return em / (charge * -1) + ELECTRON_MASS;
-    } else {
-        return 0;
-    }
+  if (charge > 0) {
+    return em / charge - ELECTRON_MASS;
+  } else if (charge < 0) {
+    return em / (charge * -1) + ELECTRON_MASS;
+  } else {
+    return 0;
+  }
 };

src/getMsInfo.js

@@ -6,34 +6,39 @@ 'use strict';
 /**
- * Adds a field 'ms' to an object containing em, charge and ioniwation
+ * Returns an object containing:
+ * {ms: {em, charge, ionization}, ionization: {}}
+ * We return the ionization in order to know which one has been selected
  */
 
 module.exports = function getMsInfo(entry, options = {}) {
-    const {
-        allowNeutralMolecules,
-        ionization = { mf: '', em: 0, charge: 0 },
-        forceIonization = false,
-        targetMass
-    } = options;
+  const {
+    allowNeutralMolecules,
+    ionization = { mf: '', em: 0, charge: 0 },
+    forceIonization = false,
+    targetMass
+  } = options;
 
-    let realIonization = ionization;
-    if (!forceIonization && entry.ionization) {
-        realIonization = entry.ionization;
-    }
+  let realIonization = ionization;
+  if (!forceIonization && entry.ionization && entry.ionization.mf !== '') {
+    realIonization = entry.ionization;
+  }
 
-    let result = {
-        ionization: realIonization.mf,
-        em: 0,
-        charge: entry.charge + realIonization.charge
-    };
+  let ms = {
+    ionization: realIonization.mf,
+    em: 0,
+    charge: entry.charge + realIonization.charge
+  };
 
-    if (result.charge !== 0) {
-        result.em = getMsem(entry.em + realIonization.em, result.charge);
-    } else if (allowNeutralMolecules) {
-        result.em = entry.em + realIonization.em;
-    }
-    if (targetMass) {
-        result.delta = result.em - targetMass;
-        result.ppm = Math.abs(((targetMass - result.em) / targetMass) * 1e6);
-    }
-    return result;
+  if (ms.charge !== 0) {
+    ms.em = getMsem(entry.em + realIonization.em, ms.charge);
+  } else if (allowNeutralMolecules) {
+    ms.em = entry.em + realIonization.em;
+  }
+  if (targetMass) {
+    ms.delta = ms.em - targetMass;
+    ms.ppm = Math.abs(((targetMass - ms.em) / targetMass) * 1e6);
+  }
+  return {
+    ms,
+    ionization: realIonization
+  };
 };

src/preprocessIonizations.js

@@ -6,10 +6,13 @@ 'use strict';
 module.exports = function preprocessIonizations(ionizationsString = '') {
-    let ionizations = ionizationsString.split(/ *[.,;\t\r\n]+ */).map((mf) => ({ mf }));
-    for (let ionization of ionizations) {
-        let info = new MF(ionization.mf).getInfo();
-        ionization.em = info.monoisotopicMass;
-        ionization.charge = info.charge;
-    }
+  if (Array.isArray(ionizationsString)) return ionizationsString;
+  let ionizations = ionizationsString
+    .split(/ *[.,;\t\r\n]+ */)
+    .map((mf) => ({ mf }));
+  for (let ionization of ionizations) {
+    let info = new MF(ionization.mf).getInfo();
+    ionization.em = info.monoisotopicMass;
+    ionization.charge = info.charge;
+  }
 
-    return ionizations;
+  return ionizations;
 };

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Fixed alerts

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Improved metrics

Total package byte prevSize

8991

increased by55.5%

Number of package files

12

increased by50%

Lines of code

250

increased by117.39%

Worsened metrics

Dependency count

3

increased by50%

Dependency changes

• + Addedchemical-groups@^0.9.1

• + Addedatom-sorter@0.9.1(transitive)

• + Addedchemical-elements@0.9.1(transitive)

• + Addedchemical-groups@0.9.1(transitive)

• + Addedmf-parser@0.9.1(transitive)

• - Removedatom-sorter@0.8.0(transitive)

• - Removedchemical-elements@0.7.0(transitive)

• - Removedchemical-groups@0.8.0(transitive)

• - Removedmf-parser@0.8.0(transitive)

• Updatedchemical-elements@^0.9.1

• Updatedmf-parser@^0.9.1