feat(mf-parser): allow decimal isotopic composition

closes: #252
cheminfo · Dec 18, 2024 · dd51cc1 · dd51cc1
1 parent 4dddbfb
commit dd51cc1
Show file tree

Hide file tree

Showing 4 changed files with 41 additions and 4 deletions.
diff --git a/packages/mf-parser/src/__tests__/MF.test.ts b/packages/mf-parser/src/__tests__/MF.test.ts
@@ -416,7 +416,7 @@ describe('MF', () => {
     ]);
 
     expect(mf.toMF()).toBe('CC{50,50}H');
-    expect(mf.toText()).toBe('HC⁽⁵⁰˙⁵⁰⁾C');
+    expect(mf.toText()).toBe('HC⁽⁵⁰˒⁵⁰⁾C');
 
     const info = mf.getInfo();
     expect(info).toStrictEqual({
@@ -429,6 +429,36 @@ describe('MF', () => {
     });
   });
 
+  it('CC{0.5,0.5}H', () => {
+    const mf = new MF('HC{0.5,0.5}C');
+    const parts = mf.toParts();
+    expect(parts).toStrictEqual([
+      [
+        { kind: 'atom', value: 'C', multiplier: 1 },
+        {
+          kind: 'isotopeRatio',
+          value: { atom: 'C', ratio: [0.5, 0.5] },
+          multiplier: 1,
+        },
+        { kind: 'atom', value: 'H', multiplier: 1 },
+      ],
+    ]);
+
+    expect(mf.toMF()).toBe('CC{0.5,0.5}H');
+    expect(mf.toHtml()).toBe('HC<sup>{0.5,0.5}</sup>C');
+    expect(mf.toText()).toBe('HC⁽⁰˙⁵˒⁰˙⁵⁾C');
+
+    const info = mf.getInfo();
+    expect(info).toStrictEqual({
+      monoisotopicMass: 25.00782503223,
+      mass: 25.520354068326025,
+      charge: 0,
+      mf: 'CC{0.5,0.5}H',
+      unsaturation: 2.5,
+      atoms: { C: 2, H: 1 },
+    });
+  });
+
   it('H(+)(H+)-1H', () => {
     const mf = new MF('H(+)(H+)-1H');
 

diff --git a/packages/mf-parser/src/__tests__/parse.test.js b/packages/mf-parser/src/__tests__/parse.test.js
@@ -218,6 +218,13 @@ let tests = {
     { kind: 'anchor', value: 2 },
     { kind: 'atom', value: 'H' },
   ],
+  'C{50,50}': [{ kind: 'isotopeRatio', value: { atom: 'C', ratio: [50, 50] } }],
+  'C{0.50,0.50}': [
+    {
+      kind: 'isotopeRatio',
+      value: { atom: 'C', ratio: [0.5, 0.5] },
+    },
+  ],
 };
 
 test.each(Object.keys(tests))('parse molecular formula %s', (key) => {

diff --git a/packages/mf-parser/src/parse.js b/packages/mf-parser/src/parse.js
@@ -231,13 +231,13 @@ class MFParser {
       this.i++;
       ascii = this.mf.charCodeAt(this.i);
     } while (ascii !== 125 && this.i <= this.mf.length); // closing curly bracket
-    if (substring.match(/^[\d,]+$/)) {
+    if (substring.match(/^[0-9.,]+$/)) {
       return substring.split(',').map(Number);
     }
     throw new MFError(
       this.mf,
       this.i,
-      'Curly brackets should contain only number and comma',
+      'Curly brackets should contain only number, dot and comma',
     );
   }
 

diff --git a/packages/mf-parser/src/util/subSuperscript.js b/packages/mf-parser/src/util/subSuperscript.js
@@ -16,7 +16,7 @@ export const superscript = {
   '{': '⁽',
   '}': '⁾',
   '.': '˙',
-  ',': '˙',
+  ',': '˒',
 };
 
 export const subscript = {