mf-parser - npm Package Compare versions

Comparing version 0.1.0 to 0.4.2

package.json

 {
   "name": "mf-parser",
-  "version": "0.1.0",
-  "description": "Parse molecular formula",
-  "main": "./src/index.js",
+  "version": "0.4.2",
+  "description": "",
+  "main": "src/index.js",
   "files": [
     "src"
   ],
-  "scripts": {
-    "eslint": "eslint src test",
-    "eslint-fix": "npm run eslint -- --fix",
-    "test": "run-s testonly eslint",
-    "test-travis": "eslint src && jest --coverage && codecov",
-    "testonly": "jest",
-    "build": "cheminfo build --no-source-map"
-  },
   "repository": {
     "type": "git",
-    "url": "https://github.com/cheminfo-js/mf-parser.git"
+    "url": "git+https://github.com/cheminfo-js/mf-parser.git"
   },
   "keywords": [],
-  "author": "Luc Patiny <[e-mail]>",
+  "author": "Luc Patiny",
   "license": "MIT",
@@ -27,15 +19,7 @@ "bugs": {
   },
-  "homepage": "https://github.com/cheminfo-js/mf-parser#readme",
-  "jest": {
-    "testEnvironment": "node"
-  },
-  "devDependencies": {
-    "cheminfo-tools": "^1.20.1",
-    "codecov": "^3.0.0",
-    "eslint": "^4.12.0",
-    "eslint-config-cheminfo": "^1.8.0",
-    "eslint-plugin-no-only-tests": "^2.0.0",
-    "jest": "^21.2.1",
-    "npm-run-all": "^4.1.2"
+  "homepage": "https://github.com/cheminfo-js/mf-parser/tree/master/packages/mf-parser#readme",
+  "dependencies": {
+    "atom-sorter": "^0.4.2",
+    "molecular-formula-generator": "^0.0.0"
   }
 }

README.md

 # mf-parser
 
   [![NPM version][npm-image]][npm-url]
-  [![build status][travis-image]][travis-url]
-  [![Test coverage][codecov-image]][codecov-url]
-  [![David deps][david-image]][david-url]
   [![npm download][download-image]][download-url]
-  
-Parse molecular formula
 
+.
+
 ## Installation
 
-`$ npm install mf-parser`
+`$ npm install --save mf-parser`
 
-## [API Documentation](https://cheminfo-js.github.io/mf-parser/)
+## Usage
 
-## Example
-
 ```js
-const parseToHtml = require('mf-parser').parseToHtml;
-let html = parseToHtml('Et3N . 2HCl);
-```
+import library from 'mf-parser';
 
-You may also be interested to parse first the MF and then retrieve display representation
-```js
-const MFParser = require('mf-parser');
-let parsed = MFParser.parse('Et3N . 2HCl');
-let displayed = MFParser.toDisplay(parsed);
-// displayed could be used to ocreate a custom renderer
-console.log(displayed);
+const result = library(args);
+// result is ...
 ```
 
-
 ## License
 
-[MIT](./LICENSE)
+  [MIT](./LICENSE)
 
 [npm-image]: https://img.shields.io/npm/v/mf-parser.svg?style=flat-square
 [npm-url]: https://www.npmjs.com/package/mf-parser
-[travis-image]: https://img.shields.io/travis/cheminfo-js/mf-parser/master.svg?style=flat-square
-[travis-url]: https://travis-ci.org/cheminfo-js/mf-parser
-[codecov-image]: https://img.shields.io/codecov/c/github/cheminfo-js/mf-parser.svg?style=flat-square
-[codecov-url]: https://codecov.io/gh/cheminfo-js/mf-parser
-[david-image]: https://img.shields.io/david/cheminfo-js/mf-parser.svg?style=flat-square
-[david-url]: https://david-dm.org/cheminfo-js/mf-parser
 [download-image]: https://img.shields.io/npm/dm/mf-parser.svg?style=flat-square
 [download-url]: https://www.npmjs.com/package/mf-parser

src/__tests__/MF.js

@@ -5,15 +5,140 @@ 'use strict';
 
-test('MF', () => {
+test('MF of Et3N.HCl', () => {
     var mf = new MF('Et3N.HCl');
     var parts = mf.toParts();
+
     expect(parts).toEqual(
         [[
-            {kind: 'atom', value: 'Et', multiplier: 3},
+            {kind: 'atom', value: 'C', multiplier: 6},
+            {kind: 'atom', value: 'H', multiplier: 15},
             {kind: 'atom', value: 'N', multiplier: 1}
         ], [
-            {kind: 'atom', value: 'Cl', multiplier: 1},
+            {kind: 'atom', value: 'H', multiplier: 1},
+            {kind: 'atom', value: 'Cl', multiplier: 1}
+        ]]
+    );
+
+    var newMF = mf.toMF();
+    expect(newMF).toBe('C6H15N.HCl');
+
+    mf.canonize();
+    let html = mf.toHtml();
+
+    expect(html).toBe('C<sub>6</sub>H<sub>15</sub>N<sub>1</sub> • H<sub>1</sub>Cl<sub>1</sub>');
+
+    let info = mf.getInfo();
+    expect(info).toEqual({parts:
+        [{mass: 101.19022990269394,
+            monoisotopicMass: 101.12044948788001,
+            charge: 0,
+            mf: 'C6H15N'},
+        {mass: 36.460878336663775,
+            monoisotopicMass: 35.97667771423,
+            charge: 0,
+            mf: 'HCl'}],
+    monoisotopicMass: 137.09712720211002,
+    mass: 137.6511082393577,
+    charge: 0,
+    mf: 'C6H15N.HCl'}
+    );
+});
+
+test('MF of (Me2CH)3N no expand', () => {
+    var mf = new MF('(Me2CH)3N');
+    var parts = mf.toParts({expand: false});
+
+    expect(parts).toEqual(
+        [[
+            {kind: 'atom', value: 'C', multiplier: 3},
+            {kind: 'atom', value: 'H', multiplier: 3},
+            {kind: 'atom', value: 'Me', multiplier: 6},
+            {kind: 'atom', value: 'N', multiplier: 1}
+        ]]
+
+    );
+
+    var newMF = mf.toMF();
+    expect(newMF).toBe('C3H3Me6N');
+
+    let info = mf.getInfo();
+    expect(info).toEqual(
+        {mass: 143.27008211723435,
+            monoisotopicMass: 143.16739968126,
+            charge: 0,
+            mf: 'C3H3Me6N'
+        }
+    );
+});
+
+test('MF of (+)SO4(+)(-2)2', () => {
+    var mf = new MF('(+)SO4(+)(-2)2');
+    var parts = mf.toParts();
+
+    expect(parts).toEqual(
+        [[
+            {kind: 'atom', value: 'O', multiplier: 4},
+            {kind: 'atom', value: 'S', multiplier: 1},
+            {kind: 'charge', value: -2},
+        ]]
+    );
+
+    var newMF = mf.toMF();
+    expect(newMF).toBe('O4S(-2)');
+
+    let info = mf.getInfo();
+    expect(info).toEqual({
+        monoisotopicMass: 95.95172965268,
+        mass: 96.06240710340018,
+        charge: -2,
+        observedMonoisotopicMass: 47.97641340624907,
+        mf: 'O4S(-2)'}
+    );
+});
+
+test('MF of NC[13C][15N]2NN2', () => {
+    var mf = new MF('NC[13C][15N]2NN2');
+    var parts = mf.toParts();
+    expect(parts).toEqual(
+        [[
+            {kind: 'atom', value: 'C', 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}
+        ]]
+    );
+
+    let info = mf.getInfo();
+    expect(info).toEqual({
+        monoisotopicMass: 111.01586865055,
+        mass: 111.04112137534844,
+        charge: 0,
+        mf: 'C[13C]N4[15N]2'}
+    );
+
+    var newMF = mf.toMF();
+    expect(newMF).toBe('C[13C]N4[15N]2');
+});
+
+test('MF of CC{50,50}H', () => {
+    var mf = new MF('HC{50,50}C');
+    var parts = mf.toParts();
+    expect(parts).toEqual(
+        [[
+            {kind: 'atom', value: 'C', multiplier: 1},
+            {kind: 'isotopeRatio', value: {atom: 'C', ratio: [50, 50]}, multiplier: 1},
             {kind: 'atom', value: 'H', multiplier: 1}
+
         ]]
-    ); mf.canonize(); var toHtml = mf.toHtml();
-    expect(toHtml).toBe('Et<sub>3</sub>N<sub>1</sub> • Cl<sub>1</sub>H<sub>1</sub>');
+    );
+
+    var newMF = mf.toMF();
+    expect(newMF).toBe('CC{50,50}H');
+
+    let info = mf.getInfo();
+    expect(info).toEqual({
+        monoisotopicMass: 25.00782503223,
+        mass: 25.520354068326025,
+        charge: 0,
+        mf: 'CC{50,50}H'}
+    );
 });

src/__tests__/parse.js

@@ -20,2 +20,6 @@ 'use strict';
     'C(--)': [{kind: 'atom', value: 'C'}, {kind: 'charge', value: -2}],
+    '(H+)': [{kind: 'openingParenthesis', value: '('}, {kind: 'atom', value: 'H'}, {kind: 'charge', value: 1}, {kind: 'closingParenthesis', value: ')'}],
+    C$ABC: [{kind: 'atom', value: 'C'}, {kind: 'comment', value: 'ABC'}],
+    'C(-1)(-3)': [{kind: 'atom', value: 'C'}, {kind: 'charge', value: -1}, {kind: 'charge', value: -3}],
+    'C(-1)2(-3)3': [{kind: 'atom', value: 'C'}, {kind: 'charge', value: -1}, {kind: 'multiplier', value: 2}, {kind: 'charge', value: -3}, {kind: 'multiplier', value: 3}],
     'C(-2)': [{kind: 'atom', value: 'C'}, {kind: 'charge', value: -2}],
@@ -29,4 +33,3 @@ 'C(H-2)': [{kind: 'atom', value: 'C'}, {kind: 'openingParenthesis', value: '('}, {kind: 'atom', value: 'H'}, {kind: 'multiplier', value: -2}, {kind: 'closingParenthesis', value: ')'}],
 
-
-test('parse molecular formula', function () {
+test.only('parse molecular formula', function () {
     for (var key of Object.keys(tests)) {
@@ -43,2 +46,3 @@ check(key, tests[key]);
 
+
 function check(mf, result) {
@@ -45,0 +49,0 @@ var parsed = parse(mf);

src/Kind.js

@@ -18,3 +18,4 @@ 'use strict';
     MULTIPLIER: 'multiplier',
-    TEXT: 'text'
+    TEXT: 'text',
+    COMMENT: 'comment'
 };

src/MF.js

@@ -8,2 +8,4 @@ 'use strict';
 const toParts = require('./util/toParts');
+const getInfo = require('./util/getInfo');
+const partsToMF = require('./util/partsToMF');
 const partsToDisplay = require('./util/partsToDisplay');
@@ -30,5 +32,5 @@
 
-    toParts() {
+    toParts(options) {
         if (!this.cache.parts) {
-            this.cache.parts = toParts(this.parsed);
+            this.cache.parts = toParts(this.parsed, options);
         }
@@ -38,2 +40,25 @@ return this.cache.parts;
 
+    /**
+     * Returns an object with the global MF, global charge, monoisotopic mass and mass
+     * as well as the same informations for all the parts
+     */
+    getInfo() {
+        if (!this.cache.info) {
+            this.toParts();
+            this.cache.info = getInfo(this.cache.parts);
+        }
+        return this.cache.info;
+    }
+
+    /**
+     * Get a canonized MF
+     */
+    toMF() {
+        if (!this.cache.mf) {
+            this.toParts();
+            this.cache.mf = partsToMF(this.cache.parts);
+        }
+        return this.cache.mf;
+    }
+
     canonize() {
@@ -40,0 +65,0 @@ this.toParts();

src/parse.js

@@ -88,2 +88,5 @@ 'use strict';
                 this.result.push({kind: Kind.CHARGE, value: charge});
+            } else if (char === '$') { // it is a comment after
+                this.result.push({kind: Kind.COMMENT, value: this.mf.substring(this.i + 1)});
+                break;
             } else {
@@ -96,3 +99,2 @@ this.result.push({kind: Kind.TEXT, value: char});
         this.checkParenthesis();
-
         return this.result;
@@ -191,3 +193,4 @@ }
             ascii = this.mf.charCodeAt(this.i);
-        } while (ascii === 43 || ascii === 45 || (ascii > 47 && ascii < 58)); // closing parenthesis
+        } while (ascii === 43 || ascii === 45 || (ascii > 47 && ascii < 58));
+        this.i--;
         return parseCharge(substring);
@@ -194,0 +197,0 @@ }

src/util/__tests__/toParts.js

@@ -34,10 +34,11 @@ 'use strict';
     {
-        mf: 'Et3N.HCl',
+        mf: 'Et3N.ClH',
         result: [
             [
-                {kind: 'atom', value: 'Et', multiplier: 3},
+                {kind: 'atom', value: 'C', multiplier: 6},
+                {kind: 'atom', value: 'H', multiplier: 15},
                 {kind: 'atom', value: 'N', multiplier: 1}
             ], [
-                {kind: 'atom', value: 'Cl', multiplier: 1},
-                {kind: 'atom', value: 'H', multiplier: 1}
+                {kind: 'atom', value: 'H', multiplier: 1},
+                {kind: 'atom', value: 'Cl', multiplier: 1}
             ]
@@ -44,0 +45,0 @@ ]

src/util/toParts.js

 'use strict';
 
 const Kind = require('../Kind');
+const groups = require('chemical-elements/src/groupsObject.js');
+const atomSorter = require('atom-sorter');
 
-module.exports = function toParts(lines) {
+/**
+ *
+ * @param {*} lines
+ * @param {object} options
+ * @param {boolean} [true] options.expand - Should we expand the groups
+ */
+
+module.exports = function toParts(lines, options = {}) {
+    const {
+        expand: shouldExpandGroups = true
+    } = options;
     let parts = [];
@@ -11,3 +23,2 @@
     parts.push(currentPart);
-
     for (let line of lines) {
@@ -40,4 +51,6 @@ switch (line.kind) {
                 break;
+            case Kind.COMMENT: // we ignore comments to create the parts and canonized MF
+                break;
             default:
-                throw new Error('Can not process mf having ', line.kind);
+                throw new Error('Can not process mf having: ' + line.kind);
         }
@@ -47,4 +60,4 @@ previousKind = line.kind;
     globalPartMultiplier(currentPart);
-
-    return combineAtoms(parts);
+    if (shouldExpandGroups) expandGroups(parts);
+    return combineAtomsIsotopesCharges(parts);
 };
@@ -99,3 +112,27 @@
 
-function combineAtoms(parts) {
+function expandGroups(parts) {
+    for (let part of parts) {
+        let expanded = false;
+        for (let i = 0; i < part.lines.length; i++) {
+            let line = part.lines[i];
+            if (line.kind === Kind.ATOM) {
+                let group = groups[line.value];
+                if (group) {
+                    expanded = true;
+                    for (let element of group.elements) {
+                        part.lines.push({
+                            kind: 'atom',
+                            value: element.symbol,
+                            multiplier: line.multiplier * element.number
+                        });
+                    }
+                    part.lines[i] = undefined;
+                }
+            }
+        }
+        if (expanded) part.lines = part.lines.filter((a) => a);
+    }
+}
+
+function combineAtomsIsotopesCharges(parts) {
     let results = [];
@@ -107,8 +144,15 @@ for (let part of parts) {
 
-        // Kind.ATOM
-        {
-            let currentKey = '';
-            for (let key of part.keys) {
+        let currentKey = '';
+        for (let key of part.keys) {
+            if (key.key === Kind.CHARGE) {
                 if (currentKey !== key.key) {
-                    currentKey = key.key;
+                    result.push({
+                        kind: Kind.CHARGE,
+                        value: key.value.value * key.value.multiplier
+                    });
+                } else {
+                    result[result.length - 1].value += key.value.value * key.value.multiplier;
+                }
+            } else {
+                if (currentKey !== key.key) {
                     result.push(key.value);
@@ -119,3 +163,21 @@ } else {
             }
+            currentKey = key.key;
         }
+
+        result.sort((a, b) => {
+            if (a.kind === Kind.CHARGE) return 1;
+            if (b.kind === Kind.CHARGE) return -1;
+
+            let atomA = a.kind === Kind.ATOM ? a.value : a.value.atom;
+            let atomB = b.kind === Kind.ATOM ? b.value : b.value.atom;
+            if (atomA !== atomB) return atomSorter(atomA, atomB);
+            // same atome but some isotopes ...
+            if (a.kind === Kind.ATOM) return -1;
+            if (b.kind === Kind.ATOM) return 1;
+            if (a.kind === Kind.ISOTOPE) return -1;
+            if (b.kind === Kind.ISOTOPE) return 1;
+            if (a.kind === Kind.ISOTOPE_RATIO) return -1;
+            if (b.kind === Kind.ISOTOPE_RATIO) return 1;
+            return 0;
+        });
     }
@@ -138,8 +200,14 @@ return results;
     let key = [line.kind];
-    if (typeof line.value === 'string') {
-        key.push(line.value);
-    } else {
-        for (let prop of Object.keys(line.value).sort()) {
-            key.push(line.value[prop]);
-        }
+
+    switch (line.kind) {
+        case (Kind.CHARGE):
+            break;
+        default:
+            if (typeof line.value === 'string') {
+                key.push(line.value);
+            } else {
+                for (let prop of Object.keys(line.value).sort()) {
+                    key.push(line.value[prop]);
+                }
+            }
     }
@@ -146,0 +214,0 @@ return key.join('-');

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Improved metrics

Total package byte prevSize

43075

increased by34.48%

Dev dependency count

0

decreased by-100%

Number of package files

25

increased by8.7%

Lines of code

1125

increased by45.54%

Worsened metrics

Dependency count

2

increased byInfinity%

Number of lines in readme file

29

decreased by-39.58%

Dependency changes

• + Addedatom-sorter@^0.4.2

• + Addedmolecular-formula-generator@^0.0.0

• + Addedatom-sorter@0.4.3(transitive)