mf-parser - npm Package Compare versions

Comparing version 0.5.0 to 0.5.1

package.json

 {
   "name": "mf-parser",
-  "version": "0.5.0",
+  "version": "0.5.1",
   "description": "",
@@ -22,4 +22,4 @@ "main": "src/index.js",
     "atom-sorter": "^0.5.0",
-    "chemical-elements": "^0.5.0"
+    "chemical-elements": "^0.5.1"
   }
 }

README.md

@@ -31,4 +31,9 @@ # mf-parser
 
+## Unsaturation
 
+Unsaturation is based on Pretsch
 
+http://pubs.acs.org/doi/pdf/10.1021/ci000135o
+
+
 ## License
@@ -35,0 +40,0 @@

src/__tests__/MF.js

@@ -5,2 +5,34 @@ 'use strict';
 
+test('MF of C', () => {
+    var mf = new MF('C');
+    var parts = mf.toParts();
+
+    expect(parts).toEqual(
+        [[
+            { kind: 'atom', value: 'C', multiplier: 1 },
+        ]]
+    );
+
+    var newMF = mf.toMF();
+    expect(newMF).toBe('C');
+
+    mf.canonize();
+    let html = mf.toHtml();
+
+    expect(html).toBe('C');
+
+    let info = mf.getInfo();
+
+    expect(info).toEqual({
+        monoisotopicMass: 12,
+        mass: 12.010735896735248,
+        charge: 0,
+        unsaturation: 2,
+        mf: 'C',
+        atoms: {
+            C: 1
+        }
+    });
+});
+
 test('MF of Et3N.HCl', () => {
@@ -27,3 +59,3 @@ var mf = new MF('Et3N.HCl');
 
-    expect(html).toBe('C<sub>6</sub>H<sub>15</sub>N<sub>1</sub> • H<sub>1</sub>Cl<sub>1</sub>');
+    expect(html).toBe('C<sub>6</sub>H<sub>15</sub>N•HCl');
 
@@ -135,3 +167,3 @@ let info = mf.getInfo();
         mf: 'O4S(-2)',
-        unsaturation: 2,
+        unsaturation: 4,
         atoms: { O: 4, S: 1 } }
@@ -141,2 +173,13 @@ );
 
+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);
+});
+
 test('MF of NC[13C][15N]2NN2', () => {
@@ -143,0 +186,0 @@ var mf = new MF('NC[13C][15N]2NN2');

src/__tests__/parse.js

@@ -13,3 +13,8 @@ 'use strict';
     '[13C]': [{ kind: 'isotope', value: { atom: 'C', isotope: 13 } }],
+    '[2H]': [{ kind: 'isotope', value: { atom: 'H', isotope: 2 } }],
+    'C+': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: 1 }],
+    'C-': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: -1 }],
+    'C-H': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: -1 }, { kind: 'atom', value: 'H' }],
     'C++': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: 2 }],
+    'C--': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: -2 }],
     'C2+': [{ kind: 'atom', value: 'C' }, { kind: 'multiplier', value: 2 }, { kind: 'charge', value: 1 }],
@@ -20,2 +25,3 @@ 'C(2+)': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: 2 }],
     'C(2-)': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: -2 }],
+    'C(-2)': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: -2 }],
     'C(--)': [{ kind: 'atom', value: 'C' }, { kind: 'charge', value: -2 }],
@@ -26,3 +32,2 @@ '(H+)': [{ kind: 'openingParenthesis', value: '(' }, { kind: 'atom', value: 'H' }, { kind: 'charge', value: 1 }, { kind: 'closingParenthesis', value: ')' }],
     '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 }],
     'C(H-2)': [{ kind: 'atom', value: 'C' }, { kind: 'openingParenthesis', value: '(' }, { kind: 'atom', value: 'H' }, { kind: 'multiplier', value: -2 }, { kind: 'closingParenthesis', value: ')' }],
@@ -29,0 +34,0 @@ 'H.Cl': [{ kind: 'atom', value: 'H' }, { kind: 'salt', value: '.' }, { kind: 'atom', value: 'Cl' }],

src/MF.js

@@ -9,2 +9,3 @@ 'use strict';
 const getInfo = require('./util/getInfo');
+const getIsotopesInfo = require('./util/getIsotopesInfo');
 const partsToMF = require('./util/partsToMF');
@@ -52,2 +53,13 @@ const partsToDisplay = require('./util/partsToDisplay');
     /**
+     * Returns an array with each atom and isotopic composition
+     */
+    getIsotopesInfo(options = {}) {
+        if (!this.cache.isotopesInfo) {
+            this.toParts();
+            this.cache.isotopesInfo = getIsotopesInfo(this.cache.parts, options);
+        }
+        return this.cache.isotopesInfo;
+    }
+
+    /**
      * Get a canonized MF
@@ -54,0 +66,0 @@ */

src/parse.js

@@ -17,3 +17,3 @@ 'use strict';
 class MFParser {
-    parse(mf) {
+    parse(mf = '') {
         this.mf = mf;
@@ -89,2 +89,5 @@ this.i = 0;
                 this.result.push({ kind: Kind.CHARGE, value: charge });
+            } else if (char === '-') { // charge not in parenthesis
+                let charge = this.getNonParenthesisCharge(ascii);
+                this.result.push({ kind: Kind.CHARGE, value: charge });
             } else if (char === '$') { // it is a comment after
@@ -91,0 +94,0 @@ this.result.push({ kind: Kind.COMMENT, value: this.mf.substring(this.i + 1) });

src/util/getInfo.js

@@ -11,14 +11,4 @@ 'use strict';
 
-const isotopes = {};
-Object.keys(elements).forEach((key) => {
-    let e = elements[key];
+const isotopes = require('./getIsotopesObject');
 
-    e.monoisotopicMass = getMonoisotopicMass(e);
-    e.isotopes.forEach((i) => {
-        isotopes[i.nominal + key] = {
-            abundance: i.abundance,
-            mass: i.mass
-        };
-    });
-});
 
@@ -103,3 +93,5 @@ /**
                 currentPart.charge = line.value;
-                unsaturation += line.value;
+                if (validUnsaturation) {
+                    unsaturation -= line.value;
+                }
                 break;
@@ -158,12 +150,1 @@ default:
 
-function getMonoisotopicMass(element) {
-    var monoisotopicMass;
-    var maxAbundance = 0;
-    for (let isotope of element.isotopes) {
-        if (isotope.abundance > maxAbundance) {
-            maxAbundance = isotope.abundance;
-            monoisotopicMass = isotope.mass;
-        }
-    }
-    return monoisotopicMass;
-}

src/util/partToAtoms.js

@@ -11,3 +11,3 @@ 'use strict';
 
-module.exports = function partToMF(part) {
+module.exports = function partToAtoms(part) {
     var atoms = {};
@@ -14,0 +14,0 @@ for (let line of part) {

src/util/toDisplay.js

@@ -18,7 +18,9 @@ 'use strict';
             case Kind.MULTIPLIER:
-                result = {
-                    kind: Format.SUBSCRIPT,
-                    value: String(line.value)
-                };
-                results.push(result);
+                if (line.value !== 1) {
+                    result = {
+                        kind: Format.SUBSCRIPT,
+                        value: String(line.value)
+                    };
+                    results.push(result);
+                }
                 break;
@@ -25,0 +27,0 @@ case Kind.MULTIPLIER_RANGE:

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Improved metrics

Total package byte prevSize

53249

increased by12.42%

Number of package files

29

increased by11.54%

Lines of code

1386

increased by12.32%

Number of lines in readme file

46

increased by12.2%

Dependency changes

• Updatedchemical-elements@^0.5.1