mf-finder - npm Package Compare versions

Comparing version 1.1.6 to 1.1.7

CHANGELOG.md

@@ -6,4 +6,16 @@ # Change Log
 
-## [1.1.6](https://github.com/cheminfo/molecular-formula/compare/mf-finder@1.1.5...mf-finder@1.1.6) (2020-08-19)
+## 1.1.7 (2021-03-12)
 
+
+
+## 0.59.2 (2021-03-12)
+
 **Note:** Version bump only for package mf-finder
+
+
+
+
+
+## [1.1.6](https://github.com/cheminfo/mass-tools/compare/mf-finder@1.1.5...mf-finder@1.1.6) (2020-08-19)
+
+**Note:** Version bump only for package mf-finder

package.json

 {
   "name": "mf-finder",
-  "version": "1.1.6",
+  "version": "1.1.7",
   "description": "Find a molecular formula from a monoisotopic mass",
@@ -11,3 +11,3 @@ "main": "src/index.js",
     "type": "git",
-    "url": "git+https://github.com/cheminfo/molecular-formula.git"
+    "url": "git+https://github.com/cheminfo/mass-tools.git"
   },
@@ -18,12 +18,12 @@ "keywords": [],
   "bugs": {
-    "url": "https://github.com/cheminfo/molecular-formula/issues"
+    "url": "https://github.com/cheminfo/mass-tools/issues"
   },
-  "homepage": "https://github.com/cheminfo/molecular-formula/tree/master/packages/mf-finder#readme",
+  "homepage": "https://github.com/cheminfo/mass-tools/tree/master/packages/mf-finder#readme",
   "dependencies": {
-    "atom-sorter": "^1.1.5",
-    "chemical-elements": "^1.1.5",
-    "mf-parser": "^1.1.6",
-    "mf-utilities": "^1.2.0"
-  },
-  "gitHead": "cfb4dd864b00757572700c8751b620d500682476"
+    "atom-sorter": "^1.1.6",
+    "chemical-elements": "^1.1.6",
+    "mf-matcher": "^1.1.7",
+    "mf-parser": "^1.1.7",
+    "mf-utilities": "^1.2.1"
+  }
 }

src/__tests__/mfFinder.test.js

@@ -46,2 +46,29 @@ 'use strict';
 
+  it('basic case with advanced filtering (callback)', () => {
+    let result = findMFs(12, {
+      ranges: [
+        { mf: 'C', min: 1, max: 10 },
+        { mf: 'H', min: 1, max: 10 },
+      ],
+      precision: 1e8,
+      ionizations: 'H+',
+      filter: {
+        callback: (entry) => entry.atoms.H === entry.atoms.C,
+      },
+    });
+    expect(result.mfs).toHaveLength(10);
+  });
+
+  it('basic case with limit', () => {
+    let result = findMFs(24, {
+      ranges: [{ mf: 'C', min: 1, max: 2 }],
+      precision: 1e6,
+      allowNeutral: true,
+      ionizations: ',H+',
+      limit: 1,
+    });
+    expect(result.mfs).toHaveLength(1);
+    expect(result.mfs[0].ms.ppm).toBe(0);
+  });
+
   it('basic case with double charge and extreme error', () => {
@@ -92,5 +119,7 @@ let result = findMFs(24, {
       allowNeutral: true,
-      unsaturation: {
-        min: 0,
-        max: 1,
+      filter: {
+        unsaturation: {
+          min: 0,
+          max: 1,
+        },
       },
@@ -110,6 +139,8 @@ });
       allowNeutral: true,
-      unsaturation: {
-        min: 0,
-        max: 1,
-        onlyInteger: true,
+      filter: {
+        unsaturation: {
+          min: 0,
+          max: 1,
+          onlyInteger: true,
+        },
       },
@@ -147,2 +178,13 @@ });
 
+  it('groups and atoms', () => {
+    let result = findMFs(92.99814, {
+      ranges: '(CH2)0-1C0-1',
+      precision: 1e10,
+      allowNeutral: true,
+    });
+    expect(result.mfs[0].atoms).toStrictEqual({ C: 2, H: 2 });
+    expect(result.mfs[0].groups).toStrictEqual({ '(CH2)': 1 });
+    expect(result.mfs[2].atoms).toStrictEqual({ C: 1 });
+    expect(result.mfs[2].groups).toStrictEqual({});
+  });
   it('simple combinations for polymers', () => {
@@ -285,4 +327,2 @@ let result = findMFs(92.99814, {
     expect(result.mfs).toHaveLength(2);
-
-    //      expect(result.mfs).toHaveLength(0);
   });
@@ -311,4 +351,6 @@
       precision: 1e5,
-      maxCharge: 1,
-      minCharge: 1,
+      filter: {
+        maxCharge: 1,
+        minCharge: 1,
+      },
     });
@@ -315,0 +357,0 @@ expect(result.mfs).toHaveLength(1);

src/index.js

 'use strict';
 
+const matcher = require('mf-matcher').msem;
 const atomSorter = require('atom-sorter');
@@ -10,18 +11,28 @@ const getMsInfo = require('mf-utilities/src/getMsInfo');
 
+let targetMassCache;
+
 /**
- * Returns possible combinations
- * {number} [targetMass]
- * {object} [options={}]
- * {string} [options.ionizations=''] - comma separated list of ionizations
- * @return {}
+ * @param {number} mass - Monoisotopic mass
+ * @param {object}        [options={}]
+ * @param {number}        [options.maxIterations=10000000] - Maximum number of iterations
+ * @param {number}        [options.limit=1000] - Maximum number of results
+ * @param {string}        [options.ionizations=''] - string containing a comma separated list of modifications
+ * @param {string}        [options.ranges='C0-100 H0-100 O0-100 N0-100'] - range of mfs to search
+ * @param {number}        [options.precision=100] - Allowed mass range based on precision
+ * @param {number}        [options.filter.minCharge=-Infinity] - Minimal charge
+ * @param {number}        [options.filter.maxCharge=+Infinity] - Maximal charge
+ * @param {number}        [options.filter.unsaturation={}]
+ * @param {number}        [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+ * @param {number}        [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
+ * @param {number}        [options.filter.unsaturation.onlyInteger=false] - Integer unsaturation
+ * @param {number}        [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
+ * @param {object}        [options.filter.atoms] - object of atom:{min, max}
+ * @param {function}      [options.filter.callback] - a function to filter the MF
  */
 
-let targetMassCache;
-
 module.exports = function (targetMass, options = {}) {
   const {
-    minCharge = Number.MIN_SAFE_INTEGER,
-    maxCharge = Number.MAX_SAFE_INTEGER,
-    unsaturation = {},
+    filter = {},
     maxIterations = 1e8,
+    limit = 1000,
     allowNeutral = true, // if there is no msem we use em !
@@ -36,2 +47,8 @@ ranges = [
 
+  const {
+    minCharge = Number.MIN_SAFE_INTEGER,
+    maxCharge = Number.MAX_SAFE_INTEGER,
+    unsaturation = {},
+  } = filter;
+
   let filterUnsaturation = unsaturation ? true : false;
@@ -52,2 +69,10 @@ // we calculate not the real unsaturation but the one before dividing by 2 + 1
 
+  let advancedFilter;
+  if (filter.atoms || filter.callback) {
+    advancedFilter = {
+      atoms: filter.atoms,
+      callback: filter.callback,
+    };
+  }
+
   let result = {
@@ -131,13 +156,22 @@ mfs: [],
       }
+
       if (isValid) {
-        result.mfs.push(
-          getResult(
-            possibilities,
-            targetMass,
-            allowNeutral,
-            ionization,
-            orderMapping,
-          ),
+        result.info.numberResults++;
+        let newResult = getResult(
+          possibilities,
+          targetMass,
+          allowNeutral,
+          ionization,
+          orderMapping,
         );
-        result.info.numberResults++;
+        if (advancedFilter) {
+          isValid = matcher(newResult, advancedFilter) !== false;
+        }
+        if (isValid) {
+          result.mfs.push(newResult);
+          if (result.mfs.length > 2 * limit) {
+            result.mfs.sort((a, b) => Math.abs(a.ms.ppm) - Math.abs(b.ms.ppm));
+            result.mfs.length = limit;
+          }
+        }
       }
@@ -177,2 +211,5 @@
   result.mfs.sort((a, b) => Math.abs(a.ms.ppm) - Math.abs(b.ms.ppm));
+  if (result.mfs.length > limit) {
+    result.mfs.length = limit;
+  }
   return result;
@@ -207,2 +244,4 @@ };
     ionization,
+    atoms: {},
+    groups: {},
   };
@@ -221,2 +260,7 @@
         }
+        if (result.groups[possibility.mf]) {
+          result.groups[possibility.mf] += possibility.currentCount;
+        } else {
+          result.groups[possibility.mf] = possibility.currentCount;
+        }
       } else {
@@ -228,2 +272,11 @@ result.mf += possibility.mf;
       }
+      for (let atom in possibility.atoms) {
+        if (result.atoms[atom]) {
+          result.atoms[atom] +=
+            possibility.atoms[atom] * possibility.currentCount;
+        } else {
+          result.atoms[atom] =
+            possibility.atoms[atom] * possibility.currentCount;
+        }
+      }
     }
@@ -230,0 +283,0 @@ }

src/preprocessRanges.js

@@ -114,3 +114,6 @@ 'use strict';
         : range.unsaturation;
-    if (possibility.mf !== info.mf) possibility.isGroup = true;
+    possibility.atoms = info.atoms;
+    if (possibility.mf !== info.mf) {
+      possibility.isGroup = true;
+    }
   }
@@ -117,0 +120,0 @@ possibilities = possibilities.filter(

No alert changes

Improved metrics

Total package byte prevSize

38455

increased by10.22%

Lines of code

1111

increased by9.24%

Worsened metrics

Dependency count

5

increased by25%

Dependency changes

• + Addedmf-matcher@^1.1.7

• + Addedbinary-search@1.3.6(transitive)

• + Addedcheminfo-types@1.8.1(transitive)

• + Addedd3-array@0.7.1(transitive)

• + Addedfft.js@4.0.4(transitive)

• + Addedis-any-array@2.0.1(transitive)

• + Addedmf-matcher@1.3.0(transitive)

• + Addedml-array-max@1.2.4(transitive)

• + Addedml-array-min@1.2.3(transitive)

• + Addedml-array-rescale@1.3.7(transitive)

• + Addedml-matrix@6.12.0(transitive)

• + Addedml-spectra-processing@11.17.0(transitive)

• + Addedml-xsadd@2.0.0(transitive)

• + Addedspline-interpolator@1.0.0(transitive)

• Updatedatom-sorter@^1.1.6

• Updatedchemical-elements@^1.1.6

• Updatedmf-parser@^1.1.7

• Updatedmf-utilities@^1.2.1