mf-generator - npm Package Compare versions

Comparing version 0.9.1 to 0.12.0

package.json

 {
   "name": "mf-generator",
-  "version": "0.9.1",
+  "version": "0.12.0",
   "description": "",
@@ -21,9 +21,10 @@ "main": "src/index.js",
   "dependencies": {
-    "chemical-elements": "^0.9.1",
-    "mf-finder": "^0.9.1",
-    "mf-matcher": "^0.9.1",
-    "mf-parser": "^0.9.1",
-    "mf-utilities": "^0.9.1",
+    "chemical-elements": "^0.12.0",
+    "mf-finder": "^0.12.0",
+    "mf-matcher": "^0.12.0",
+    "mf-parser": "^0.12.0",
+    "mf-utilities": "^0.12.0",
     "sum-object-keys": "^1.0.2"
-  }
+  },
+  "gitHead": "aa2e6571c5f7121dda616b7d6920b7a653a8f9c7"
 }

src/__tests__/generateMFs.test.js

@@ -6,4 +6,4 @@ 'use strict';
 test('generateMFs from array of array with comment', function () {
-  var mfsArray = [['C', 'H$YY'], [], [''], ['Cl', 'Br$XX']];
-  var result = generateMFs(mfsArray);
+  let mfsArray = [['C', 'H$YY'], [], [''], ['Cl', 'Br$XX']];
+  let result = generateMFs(mfsArray);
   expect(result[0].mf).toBe('HCl');
@@ -15,4 +15,4 @@ expect(result[0].comment).toBe('YY');
 test('generateMFs from array of string with empty', function () {
-  var mfsArray = ['C,H,', 'Cl,Br'];
-  var result = generateMFs(mfsArray).map((entry) => entry.mf);
+  let mfsArray = ['C,H,', 'Cl,Br'];
+  let result = generateMFs(mfsArray).map((entry) => entry.mf);
   expect(result).toStrictEqual(['Cl', 'HCl', 'CCl', 'Br', 'HBr', 'CBr']);
@@ -22,5 +22,5 @@ });
 test('generateMFs from array of string with comment', function () {
-  var mfsArray = ['C.H.O', '+,++', ['Cl', 'Br$XX']];
-  var result = generateMFs(mfsArray).sort((a, b) => a.em - b.em);
-  expect(result[0].mf).toBe('HCl(+1)');
+  let mfsArray = ['C.H.O', '+,++', ['Cl', 'Br$XX']];
+  let result = generateMFs(mfsArray).sort((a, b) => a.ms.em - b.ms.em);
+  expect(result[0].mf).toBe('HCl(+2)');
   expect(result).toHaveLength(12);
@@ -30,4 +30,4 @@ });
 test('generateMFs from  array of string with some range and non range', function () {
-  var mfsArray = ['CN0-2'];
-  var result = generateMFs(mfsArray);
+  let mfsArray = ['CN0-2'];
+  let result = generateMFs(mfsArray);
   expect(result[0].mf).toBe('C');
@@ -40,4 +40,4 @@ expect(result[1].mf).toBe('CN');
 test('From array of string with some range and non range CN0-2O00-1K', function () {
-  var mfsArray = ['CN0-2O00-1K'];
-  var result = generateMFs(mfsArray);
+  let mfsArray = ['CN0-2O00-1K'];
+  let result = generateMFs(mfsArray);
   expect(result[0].mf).toBe('CK');
@@ -53,4 +53,4 @@ expect(result[1].mf).toBe('CKN');
 test('From array of string with some range and non range NaK0-2', function () {
-  var mfsArray = ['NaK0-2'];
-  var result = generateMFs(mfsArray);
+  let mfsArray = ['NaK0-2'];
+  let result = generateMFs(mfsArray);
   expect(result[0].mf).toBe('Na');
@@ -63,4 +63,4 @@ expect(result[1].mf).toBe('KNa');
 test('From array of string with some range and non range C(Me(N2))0-2(CH3)0-1K', function () {
-  var mfsArray = ['C(Me(N2))0-2(CH3)0-1K'];
-  var result = generateMFs(mfsArray, { canonizeMF: false, uniqueMFs: false });
+  let mfsArray = ['C(Me(N2))0-2(CH3)0-1K'];
+  let result = generateMFs(mfsArray, { canonizeMF: false, uniqueMFs: false });
   expect(result[0].mf).toBe('CK');
@@ -76,4 +76,4 @@ expect(result[1].mf).toBe('C(CH3)K');
 test('From array of string with some range', function () {
-  var mfsArray = ['C1-3N0-2Cl0-0BrO1-1.C2-3H3-4', ['C', 'O']];
-  var result = generateMFs(mfsArray, { canonizeMF: true });
+  let mfsArray = ['C1-3N0-2Cl0-0BrO1-1.C2-3H3-4', ['C', 'O']];
+  let result = generateMFs(mfsArray, { canonizeMF: true });
   expect(result[0].mf).toBe('C3H3');
@@ -84,5 +84,5 @@ expect(result).toHaveLength(26);
 test('From array of string chem em and msem', function () {
-  var mfsArray = ['C0-2.O', ['+', '(-)', '++', '(--)']];
+  let mfsArray = ['C0-2.O', ['+', '(-)', '++', '(--)']];
 
-  var result = generateMFs(mfsArray);
+  let result = generateMFs(mfsArray);
   expect(result[0].mf).toMatch(/^(.*)$/);
@@ -94,4 +94,4 @@ expect(result[0].charge).not.toBe(0);
 test('From array of string to large array', function () {
-  var mfsArray = ['C0-100', 'O0-100'];
-  var result = generateMFs(mfsArray);
+  let mfsArray = ['C0-100', 'O0-100'];
+  let result = generateMFs(mfsArray);
   expect(result).toHaveLength(101 * 101);
@@ -101,4 +101,4 @@ });
 test('From array of string to large array and filter', function () {
-  var mfsArray = ['C0-100', 'O0-100'];
-  var result = generateMFs(mfsArray, { filter: { minEM: 0.1, maxEM: 13 } });
+  let mfsArray = ['C0-100', 'O0-100'];
+  let result = generateMFs(mfsArray, { filter: { minEM: 0.1, maxEM: 13 } });
   expect(result).toHaveLength(1);
@@ -108,5 +108,5 @@ });
 test('From array of string to large array and filter unsaturation', function () {
-  var mfsArray = ['C0-100', 'H0-100'];
-  var result = generateMFs(mfsArray, {
-    filter: { unsaturation: { min: 0, max: 1 } }
+  let mfsArray = ['C0-100', 'H0-100'];
+  let result = generateMFs(mfsArray, {
+    filter: { unsaturation: { min: 0, max: 1 } },
   });
@@ -117,5 +117,5 @@ expect(result).toHaveLength(151);
 test('From array of string to large array and filter unsaturation min/max and integer unsaturation', function () {
-  var mfsArray = ['C0-100', 'H0-100'];
-  var result = generateMFs(mfsArray, {
-    filter: { unsaturation: { min: 0, max: 1, onlyInteger: true } }
+  let mfsArray = ['C0-100', 'H0-100'];
+  let result = generateMFs(mfsArray, {
+    filter: { unsaturation: { min: 0, max: 1, onlyInteger: true } },
   });
@@ -126,3 +126,3 @@ expect(result).toHaveLength(101);
 test('Combine with ionizations', function () {
-  var result = generateMFs(['C1-2'], { ionizations: 'H+,Na+,H++' });
+  let result = generateMFs(['C1-2'], { ionizations: 'H+,Na+,H++' });
   expect(result.map((a) => a.ms.em).sort((a, b) => a - b)).toStrictEqual([
@@ -134,3 +134,3 @@ 6.50336393620593,
     34.989220702090925,
-    46.989220702090925
+    46.989220702090925,
   ]);
@@ -140,4 +140,4 @@ });
 test('Strange comments', function () {
-  var mfsArray = ['C$1>10', 'O$D2>20'];
-  var result = generateMFs(mfsArray);
+  let mfsArray = ['C$1>10', 'O$D2>20'];
+  let result = generateMFs(mfsArray);
   expect(result[0].mf).toBe('CO');
@@ -148,20 +148,12 @@ expect(result[0].comment).toBe('1>10 D2>20');
 test('Check info', function () {
-  var mfsArray = ['C', '', 'C5(C)2'];
-  var result = generateMFs(mfsArray, { canonizeMF: true })[0];
-  expect(result).toStrictEqual({
-    mf: 'C8',
-    em: 96,
-    ms: { em: 0, charge: 0, ionization: '' },
-    mw: 96.08588717388199,
-    charge: 0,
-    ionization: { mf: '', charge: 0, em: 0 },
-    parts: ['C', undefined, 'C5(C)2'],
-    atoms: { C: 8 },
-    unsaturation: 9
-  });
+  let mfsArray = ['C', '', 'C5(C)2'];
+  let result = generateMFs(mfsArray, { canonizeMF: true })[0];
+  expect(JSON.stringify(result)).toBe(
+    '{"charge":0,"em":96,"mw":96.08588717388199,"ionization":{"mf":"","em":0,"charge":0},"unsaturation":9,"atoms":{"C":8},"ms":{"ionization":"","em":0,"charge":0},"parts":["C",null,"C5(C)2"],"mf":"C8"}',
+  );
 });
 
 test('generateMFs from array of array with negative ionisation', function () {
-  var mfsArray = ['H2', ['Cl', 'Br']];
-  var result = generateMFs(mfsArray, { ionizations: '(H+)-2' });
+  let mfsArray = ['H2', ['Cl', 'Br']];
+  let result = generateMFs(mfsArray, { ionizations: '(H+)-2' });
   expect(result[0].ms.em).toBe(17.484974920909067);
@@ -173,4 +165,4 @@ expect(result[1].ms.em).toBe(39.45971737990907);
 test('generateMFs from array with charge and range', function () {
-  var mfsArray = ['(H+)2-3'];
-  var result = generateMFs(mfsArray, { ionizations: '(H+)-2,Na+' });
+  let mfsArray = ['(H+)2-3'];
+  let result = generateMFs(mfsArray, { ionizations: '(H+)-2,Na+' });
   expect(result.map((a) => a.ms.em).sort((a, b) => a - b)).toStrictEqual([
@@ -180,4 +172,29 @@ 0,
     6.50276251476343,
-    8.334591202244264
+    8.334591202244264,
   ]);
 });
+
+test('generateMFs from array with target masses', function () {
+  let mfsArray = ['C1-100'];
+  let result = generateMFs(mfsArray, {
+    ionizations: '+,++',
+    filter: {
+      targetMasses: [120, 240],
+      precision: 10,
+      targetIntensities: [1, 5],
+    },
+  });
+  expect(result).toHaveLength(4);
+
+  expect(result.sort((a, b) => a.em - b.em)).toMatchSnapshot();
+});
+
+test('generateMFs from array with charge and negative range', function () {
+  let mfsArray = ['(H+)-2--4'];
+  let result = generateMFs(mfsArray);
+  expect(result.map((a) => a.ms.em).sort((a, b) => a - b)).toStrictEqual([
+    -1.0072764523209299,
+    -1.0072764523209299,
+    -1.0072764523209299,
+  ]);
+});

src/index.js

@@ -7,3 +7,3 @@ 'use strict';
 const preprocessIonizations = require('mf-utilities/src/preprocessIonizations');
-
+const processRange = require('mf-utilities/src/processRange');
 /**
@@ -15,20 +15,22 @@ * Generate all the possible combinations of molecular formula and calculate
  * @param keys
- * @param {object} options
- * @param {number} [options.limit=10000000] - Maximum number of results
- * @param {boolean} [canonizeMF=true] - Canonize molecular formula
- * @param {boolean} [uniqueMFs=true] - Force canonization and make MF unique
- * @param {string} [ionizations=''] - Comma separated list of ionizations (to charge the molecule)
- * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
- * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
- * @param {number} [options.filter.minEM=0] - Minimal neutral monoisotopic mass
- * @param {number} [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
- * @param {number} [options.filter.targetMass] - Experimental observed mass
- * @param {number} [options.filter.precision=1000] - Precision
- * @param {number} [options.filter.minCharge=-Infinity] - Minimal charge
- * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
- * @param {number} [options.filter.minUnsaturation=-Infinity] - Minimal unsaturation
- * @param {number} [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
- * @param {number} [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
- * @param {number} [options.filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
- * @param {object} [options.filter.atoms] - object of atom:{min, max}
+ * @param {object}        [options={}]
+ * @param {number}        [options.limit=10000000] - Maximum number of results
+ * @param {boolean}       [canonizeMF=true] - Canonize molecular formula
+ * @param {boolean}       [uniqueMFs=true] - Force canonization and make MF unique
+ * @param {string}        [ionizations=''] - Comma separated list of ionizations (to charge the molecule)
+ * @param {number}        [options.filter.minMass=0] - Minimal monoisotopic mass
+ * @param {number}        [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
+ * @param {number}        [options.filter.minEM=0] - Minimal neutral monoisotopic mass
+ * @param {number}        [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
+ * @param {number}        [options.filter.precision=1000] - The precision on the experimental mass
+ * @param {number}        [options.filter.targetMass] - Target mass, allows to calculate error and filter results
+ * @param {Array<number>} [options.filter.targetMasses] - Target masses: SORTED array of numbers
+ * @param {number}        [options.filter.precision=1000] - Precision
+ * @param {number}        [options.filter.minCharge=-Infinity] - Minimal charge
+ * @param {number}        [options.filter.maxCharge=+Infinity] - Maximal charge
+ * @param {number}        [options.filter.minUnsaturation=-Infinity] - Minimal unsaturation
+ * @param {number}        [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
+ * @param {number}        [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
+ * @param {number}        [options.filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
+ * @param {object}        [options.filter.atoms] - object of atom:{min, max}
  * @returns {Array}
@@ -48,6 +50,6 @@ */
 
-  // we allow String delimited by ". , or ;" instead of an array
+  // we allow String delimited by ". or ;" instead of an array
   for (let i = 0; i < keys.length; i++) {
     if (!Array.isArray(keys[i])) {
-      keys[i] = keys[i].split(/[.,;]/);
+      keys[i] = keys[i].split(/[.,]/);
     }
@@ -57,3 +59,3 @@ }
   // we allow ranges in a string ...
-  // problem with ranges is that we need to now to what the range applies
+  // problem with ranges is that we need to know to what the range applies
   for (let i = 0; i < keys.length; i++) {
@@ -66,3 +68,4 @@ let parts = keys[i];
       part = part.replace(/\$.*/, '').replace(/\s/g, '');
-      if (~part.indexOf('-')) {
+      if (part.match(/[0-9]-[0-9-]/)) {
+        // deal with negative numbers
         // there are ranges ... we are in trouble !
@@ -86,3 +89,2 @@ newParts = newParts.concat(processRange(part, comment));
   let evolution = 0;
-
   while (position < currents.length) {
@@ -102,3 +104,3 @@ if (currents[position] < sizes[position]) {
       throw new Error(
-        `You have reached the limit of ${limit}. You could still change this value using the limit option but it is likely to crash.`
+        `You have reached the limit of ${limit}. You could still change this value using the limit option but it is likely to crash.`,
       );
@@ -108,5 +110,4 @@ }
   appendResult(results, currents, keys, options);
-
   if (uniqueMFs) {
-    var uniqueMFsObject = {};
+    let uniqueMFsObject = {};
     results.forEach((r) => {
@@ -121,3 +122,3 @@ uniqueMFsObject[r.mf + r.ionization.mf] = r;
 
-var ems = {};
+let ems = {};
 
@@ -135,3 +136,3 @@ // internal method used as a cache
       unsaturation: (info.unsaturation - 1) * 2,
-      atoms: info.atoms
+      atoms: info.atoms,
     };
@@ -143,8 +144,8 @@ }
 function getEMFromParts(parts, currents, ionization) {
-  var charge = 0;
-  var em = 0;
-  var mw = 0;
-  var unsaturation = 0;
-  var validUnsaturation = true;
-  var atoms = {};
+  let charge = 0;
+  let em = 0;
+  let mw = 0;
+  let unsaturation = 0;
+  let validUnsaturation = true;
+  let atoms = {};
 
@@ -171,3 +172,3 @@ for (let i = 0; i < parts.length; i++) {
     unsaturation: validUnsaturation ? unsaturation / 2 + 1 : undefined,
-    atoms
+    atoms,
   };
@@ -178,3 +179,2 @@ }
   const { canonizeMF, filter, ionizations } = options;
-
   // this script is designed to combine molecular formula
@@ -188,4 +188,3 @@ // that may contain comments after a "$" sign
     let match = matcher(result, filter);
-
-    if (!match) return;
+    if (!match) continue;
     result.ms = match.ms;
@@ -208,3 +207,2 @@ result.ionization = match.ionization;
     }
-
     if (canonizeMF) {
@@ -219,98 +217,1 @@ result.mf = new MF(result.mf).toMF();
 }
-
-function processRange(string, comment) {
-  var results = [];
-  var parts = string.split(/([0-9]+-[0-9]+)/).filter((v) => v); // remove empty parts
-  let position = -1;
-  var mfs = [];
-  for (let i = 0; i < parts.length; i++) {
-    let part = parts[i];
-    if (!~part.search(/[0-9]-[0-9]/)) {
-      position++;
-      mfs[position] = {
-        mf: part,
-        min: 1,
-        max: 1
-      };
-    } else {
-      mfs[position].min = part.replace(/^(-?[0-9]*)-(-?[0-9]*)/, '$1') >> 0;
-      mfs[position].max = part.replace(/^(-?[0-9]*)-(-?[0-9]*)/, '$2') >> 0;
-    }
-  }
-
-  let currents = new Array(mfs.length);
-  for (let i = 0; i < currents.length; i++) {
-    currents[i] = mfs[i].min;
-  }
-  position = 0;
-  while (position < currents.length) {
-    if (currents[position] < mfs[position].max) {
-      results.push(getMF(mfs, currents, comment));
-      currents[position]++;
-      for (let i = 0; i < position; i++) {
-        currents[i] = mfs[i].min;
-      }
-      position = 0;
-    } else {
-      position++;
-    }
-  }
-  results.push(getMF(mfs, currents, comment));
-  return results;
-}
-
-function getMF(mfs, currents, comment) {
-  let mf = '';
-  for (let i = 0; i < mfs.length; i++) {
-    if (currents[i] === 0) {
-      // TODO we need to remove from currents[i] till we reach another part of the MF
-      mf += removeMFLastPart(mfs[i].mf);
-    } else {
-      mf += mfs[i].mf;
-      if (currents[i] !== 1) {
-        mf += currents[i];
-      }
-    }
-  }
-  if (comment) mf += `$${comment}`;
-  return mf;
-}
-
-/*
- Allows to remove the last part of a MF. Useful when you have something with '0' times.
- C10H -> C10
- C10((Me)N) -> C10
- C10Ala -> C10
- C10Ala((Me)N) -> C10Ala
- */
-function removeMFLastPart(mf) {
-  let parenthesis = 0;
-  let start = true;
-  for (let i = mf.length - 1; i >= 0; i--) {
-    let ascii = mf.charCodeAt(i);
-
-    if (ascii > 96 && ascii < 123) {
-      // lowercase
-      if (!start && !parenthesis) {
-        return mf.substr(0, i + 1);
-      }
-    } else if (ascii > 64 && ascii < 91) {
-      // uppercase
-      if (!start && !parenthesis) {
-        return mf.substr(0, i + 1);
-      }
-      start = false;
-    } else if (ascii === 40) {
-      // (
-      parenthesis--;
-      if (!parenthesis) return mf.substr(0, i);
-    } else if (ascii === 41) {
-      // )
-      parenthesis++;
-    } else {
-      start = false;
-      if (!parenthesis) return mf.substr(0, i + 1);
-    }
-  }
-  return '';
-}

No alert changes

Improved metrics

Total package byte prevSize

17739

increased by6.3%

Number of package files

6

increased by20%

Worsened metrics

Lines of code

344

decreased by-17.7%

Dependency changes

• + Addedatom-sorter@0.12.0(transitive)

• + Addedchemical-elements@0.12.1(transitive)

• + Addedchemical-groups@0.12.1(transitive)

• + Addedis-any-array@0.0.3(transitive)

• + Addedmf-finder@0.12.1(transitive)

• + Addedmf-matcher@0.12.1(transitive)

• + Addedmf-parser@0.12.0(transitive)

• + Addedmf-utilities@0.12.1(transitive)

• + Addedml-spectra-processing@0.6.1(transitive)

• + Addedpapaparse@5.5.1(transitive)

• - Removedatom-sorter@0.9.1(transitive)

• - Removedchemical-elements@0.9.1(transitive)

• - Removedchemical-groups@0.9.1(transitive)

• - Removedmf-finder@0.9.1(transitive)

• - Removedmf-matcher@0.9.1(transitive)

• - Removedmf-parser@0.9.1(transitive)

• - Removedmf-utilities@0.9.1(transitive)

• - Removedpapaparse@4.6.3(transitive)

• Updatedchemical-elements@^0.12.0

• Updatedmf-finder@^0.12.0

• Updatedmf-matcher@^0.12.0

• Updatedmf-parser@^0.12.0

• Updatedmf-utilities@^0.12.0