mass-fragmentation - npm Package Compare versions

Comparing version 0.4.0 to 0.5.0

lib/index.js

@@ -7,8 +7,3 @@ 'use strict';
 var openchemlibUtils = require('openchemlib-utils');
-var OCL = require('openchemlib');
 
-function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
-
-var OCL__default = /*#__PURE__*/_interopDefaultLegacy(OCL);
-
 /**
@@ -663,78 +658,43 @@ * The function performs the fragmentation of all single linear bonds
 
-function applyFragmentationReactions(
-  ionizedFragments,
-  reactions,
-  maxDepth,
-) {
-  const fragmentationReactions = reactions.filter(
-    (reaction) => reaction.Label !== 'Ionization',
-  );
-  for (let ionizedMolecule of ionizedFragments.products) {
-    if (ionizedMolecule.children?.length > 0) {
-      for (let child of ionizedMolecule.children) {
-        applyFragmentationReactions(child, fragmentationReactions, maxDepth);
-      }
-    } else {
-      let moleculeToFragment = OCL__default["default"].Molecule.fromIDCode(ionizedMolecule.idCode);
-      let fragmentation = openchemlibUtils.applyReactions(
-        [moleculeToFragment],
-        fragmentationReactions,
-        {
-          maxDepth,
-        },
-      );
-      ionizedMolecule.children = fragmentation;
-    }
+function getDatabase(databaseName) {
+  if (databaseName === 'cid') {
+    return cid;
   }
 }
 
-function applyIonizationReactions(molecule, reactions, ionizationLevel) {
-  const ionizationReaction = reactions.filter(
-    (reaction) => reaction.Label === 'Ionization',
-  );
-  let ionization = openchemlibUtils.applyReactions([molecule], ionizationReaction, {
-    maxDepth: 1,
-  });
-
-  function ionize(reactant, ionizationReactions, currentIonizationLevel) {
-    for (let product of reactant.products) {
-      if (currentIonizationLevel < ionizationLevel) {
-        let currentMolecule = OCL__default["default"].Molecule.fromIDCode(product.idCode);
-        let ionizedFragments = openchemlibUtils.applyReactions(
-          [currentMolecule],
-          ionizationReactions,
-          {
-            maxDepth: 1,
-          },
-        );
-        product.children = ionizedFragments;
-        currentIonizationLevel = currentIonizationLevel + 1;
-        if (product.children.length > 0) {
-          for (let child of product.children) {
-            ionize(child, ionizationReactions, currentIonizationLevel);
-          }
-        }
-      }
-    }
+/**
+ * @description Recursively insert monoisotopic mass information into the fragmentation trees, products and get array of monoisotopic masses
+ * @param {Array} trees Fragmentation trees
+ * @param {Array} products Fragmentation trees grouped by product idCode
+ * @returns {object} Object with the following properties:
+ * - masses: array of monoisotopic masses
+ * - trees: array of fragmentation trees with monoisotopic mass
+ * - products: array of trees grouped by product idCode with monoisotopic mass
+ */
+function insertMfInfoFragments(trees, products) {
+  let masses = {};
+  for (let tree of trees) {
+    mfInfoFragments(tree, masses);
   }
-
-  for (let ionizedFragment of ionization) {
-    ionize(ionizedFragment, ionizationReaction, 1);
+  for (let product of products) {
+    const productMF = new mfParser.MF(product.mf);
+    product.monoisotopicMass =
+      Math.round(
+        (productMF.getInfo().observedMonoisotopicMass ??
+          productMF.getInfo().monoisotopicMass) * 10000,
+      ) / 10000;
   }
-  return ionization;
-}
-
-const masses = {};
-
-function insertMfInfoFragments(fragmentation) {
-  for (let fragment of fragmentation) {
-    mfInfoFragments(fragment);
-  }
   return {
     masses: Object.keys(masses).map(Number),
-    tree: fragmentation,
+    trees,
+    products,
   };
 }
 
-function mfInfoFragments(reaction) {
+/**
+ * @description Recursively insert monoisotopic mass information into the fragmentation trees and get array of monoisotopic masses
+ * @param {*} reaction Fragmentation trees
+ * @param {*} masses Object with monoisotopic masses
+ */
+function mfInfoFragments(reaction, masses) {
   if (reaction?.reactant) {
@@ -752,7 +712,2 @@ const reactantMF = new mfParser.MF(reaction.reactant.mf);
     for (const product of reaction.products) {
-      if (product.children?.length > 0) {
-        for (const child of product.children) {
-          mfInfoFragments(child);
-        }
-      }
       const productMF = new mfParser.MF(product.mf);
@@ -765,2 +720,7 @@ product.monoisotopicMass =
       masses[product.monoisotopicMass] = true;
+      if (product.children?.length > 0) {
+        for (const child of product.children) {
+          mfInfoFragments(child, masses);
+        }
+      }
     }
@@ -770,31 +730,34 @@ }
 
-const databases = {
-  cid,
-};
-
-//ionizationLevel fix the maximum depth of the ionization reactions in the molecule
+/**
+ * @description Fragment a molecule by applying reactions from a custom database of reactions
+ * @param {import('openchemlib').Molecule} molecule - The OCL molecule to be fragmented
+ * @param {Object}  [options={}]
+ * @param {string}  [options.databaseName='cid'] - The database to be used
+ * @param {string}  [options.mode='positive'] - The mode to be used
+ * @param {number}  [options.maxDepth=5] - The maximum depth of the fragmentation tree
+ * @returns {object} In-Silico fragmentation results with the following properties:
+ * - masses: array of monoisotopic masses
+ * - trees: array of fragmentation trees
+ * - products: array of trees grouped by product idCode
+ */
 function reactionFragmentation(molecule, options = {}) {
-  let {
-    database = 'cid',
-    mode = 'positive',
-    maxDepth = 0,
-    ionizationLevel = 1,
-  } = options;
-  if (maxDepth === 0) {
-    let mass = molecule.getMolecularFormula().absoluteWeight;
-    maxDepth = Math.round(mass / 10);
+  let { databaseName = 'cid', mode = 'positive', maxDepth = 5 } = options;
+  let database = getDatabase(databaseName);
+  if (!database) {
+    throw new Error(`Database ${databaseName} not found`);
   }
-  const reactions = databases[database][mode];
-  let ionizedFragments = applyIonizationReactions(
-    molecule,
-    reactions,
-    ionizationLevel,
+
+  const reactions = database[mode];
+  let fragments = openchemlibUtils.applyReactions([molecule], reactions, {
+    maxDepth,
+  });
+
+  let { masses, trees, products } = insertMfInfoFragments(
+    fragments.trees,
+    fragments.products,
   );
-  for (let ionizedFragment of ionizedFragments) {
-    applyFragmentationReactions(ionizedFragment, reactions, maxDepth);
-  }
-  let { masses, tree } = insertMfInfoFragments(ionizedFragments);
   return {
     masses,
-    tree,
+    trees,
+    products,
   };
@@ -801,0 +764,0 @@ }

package.json

 {
   "name": "mass-fragmentation",
-  "version": "0.4.0",
+  "version": "0.5.0",
   "description": "Code to fragment molecules",
@@ -24,8 +24,9 @@ "main": "lib/index.js",
     "mf-parser": "^2.3.0",
-    "openchemlib-utils": "^2.4.0"
+    "openchemlib-utils": "^2.7.0"
   },
   "devDependencies": {
-    "openchemlib": "^8.2.0"
+    "openchemlib": "^8.3.0",
+    "react-tree-svg": "^0.1.0"
   },
-  "gitHead": "bc42b1937c4d78b61bf0548c5bf1397ab52d645a"
+  "gitHead": "c697f5fab6e34146c16194f54cead9ddd1c8465f"
 }

src/__tests__/reactionFragmentation.test.js

@@ -13,5 +13,19 @@ import OCL from 'openchemlib';
     };
-    const result = reactionFragmentation(molecule, options);
+    const { masses, trees, products } = reactionFragmentation(
+      molecule,
+      options,
+    );
 
-    expect(result).toMatchSnapshot();
+    expect(Object.keys(products[0])).toMatchInlineSnapshot(`
+      [
+        "idCode",
+        "mf",
+        "trees",
+        "reactions",
+        "minSteps",
+        "monoisotopicMass",
+      ]
+    `);
+    expect(masses).toHaveLength(17);
+    expect(trees).toMatchSnapshot();
   });
@@ -23,17 +37,155 @@ it('tropylium rearrangement: MDMA after Alpha cleavage', async () => {
     };
-    const result = reactionFragmentation(molecule, options);
-
-    expect(result).toMatchSnapshot();
+    const { masses, trees, products } = reactionFragmentation(
+      molecule,
+      options,
+    );
+    expect(Object.keys(products[0])).toMatchInlineSnapshot(`
+      [
+        "idCode",
+        "mf",
+        "trees",
+        "reactions",
+        "minSteps",
+        "monoisotopicMass",
+      ]
+    `);
+    expect(masses).toHaveLength(7);
+    expect(trees).toMatchSnapshot();
   });
 
   it('Full fragmentation: MDMA', async () => {
-    const molecule = Molecule.fromSmiles('CNC(Cc1ccc2c(c1)OCO2)C');
+    const molecule = Molecule.fromSmiles('CC(CC1=CC2=C(C=C1)OCO2)NC');
     const options = {
-      ionizationLevel: 1,
+      maxDepth: 5,
     };
+    let { masses, trees, products } = reactionFragmentation(molecule, options);
+    expect(masses).toMatchInlineSnapshot(`
+      [
+        193.1103,
+        194.1176,
+        31.0422,
+        32.0495,
+        163.0754,
+        135.0441,
+        68.0257,
+        45.6862,
+        30.047,
+        28.0313,
+        82.0413,
+        55.03,
+        97.5624,
+        65.3774,
+        65.0414,
+        68.5296,
+        97.0585,
+        58.0651,
+        136.0519,
+        193.1097,
+        135.0446,
+      ]
+    `);
+    expect(products[0]).toMatchInlineSnapshot(`
+      {
+        "idCode": "dg~DBMBmeJYW]gJxZB@jj@@",
+        "mf": "C11H16NO2(+)",
+        "minSteps": 1,
+        "monoisotopicMass": 194.1176,
+        "reactions": [
+          "eM\`BN\`~b@!eM\`\`fN\`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@",
+        ],
+        "trees": [
+          {
+            "products": [
+              {
+                "children": [],
+                "flag": true,
+                "idCode": "dg~DBMBmeJYW]gJxZB@jj@@",
+                "mf": "C11H16NO2(+)",
+                "molfile": "
+      Actelion Java MolfileCreator 1.0
 
-    const result = reactionFragmentation(molecule, options);
+       14 15  0  0  0  0  0  0  0  0999 V2000
+         18.7073   -7.2671   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         19.5677   -7.7768   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         19.5565   -8.7767   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         18.6849   -9.2670   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         18.6737  -10.2669   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         17.8021  -10.7572   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         16.9417  -10.2475   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         16.9529   -9.2475   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         17.8245   -8.7573   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         16.1911  -10.9082   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+         16.5876  -11.8263   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+         17.5832  -11.7329   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+         20.4444   -7.2836   -0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+         21.3075   -7.7768   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1  2  1  0  0  0  0
+        2  3  1  0  0  0  0
+        3  4  1  0  0  0  0
+        4  5  2  0  0  0  0
+        5  6  1  0  0  0  0
+        6  7  2  0  0  0  0
+        7  8  1  0  0  0  0
+        8  9  2  0  0  0  0
+        4  9  1  0  0  0  0
+        7 10  1  0  0  0  0
+       10 11  1  0  0  0  0
+       11 12  1  0  0  0  0
+        6 12  1  0  0  0  0
+       13  2  1  0  0  0  0
+       13 14  1  0  0  0  0
+      M  CHG  1  13   1
+      M  END
+      ",
+              },
+            ],
+            "reactant": {
+              "idCode": "dg~D@MBdie]v\\\\kahHBjh@@",
+              "mf": "C11H15NO2",
+              "molfile": "
+      Actelion Java MolfileCreator 1.0
 
-    expect(result).toMatchSnapshot();
+       14 15  0  0  0  0  0  0  0  0999 V2000
+          1.7321   -1.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          1.7321   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          2.5981   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          3.4641   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          4.3301   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          5.1962   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          5.1962   -1.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          4.3301   -2.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          3.4641   -1.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          6.1472   -1.8090   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+          6.7350   -1.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+          6.1472   -0.1910   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+          0.8660   -0.0000   -0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+          0.0000   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1  2  1  0  0  0  0
+        2  3  1  0  0  0  0
+        3  4  1  0  0  0  0
+        4  5  2  0  0  0  0
+        5  6  1  0  0  0  0
+        6  7  2  0  0  0  0
+        7  8  1  0  0  0  0
+        8  9  2  0  0  0  0
+        4  9  1  0  0  0  0
+        7 10  1  0  0  0  0
+       10 11  1  0  0  0  0
+       11 12  1  0  0  0  0
+        6 12  1  0  0  0  0
+        2 13  1  0  0  0  0
+       13 14  1  0  0  0  0
+      M  END
+      ",
+            },
+            "reaction": {
+              "Label": "Ionization",
+              "rxnCode": "eM\`BN\`~b@!eM\`\`fN\`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@",
+            },
+          },
+        ],
+      }
+    `);
+    expect(trees).toMatchSnapshot();
   });
 });

src/reactionFragmentation.js

@@ -1,36 +0,39 @@
-import { cid } from './database/collisionInducedDissociation';
-import { applyFragmentationReactions } from './utils/applyFragmentationReactions';
-import { applyIonizationReactions } from './utils/applyIonizationReactions';
+import { applyReactions } from 'openchemlib-utils';
+
+import getDatabase from './database/getDatabase';
 import { insertMfInfoFragments } from './utils/insertMfInfoFragments';
 
-const databases = {
-  cid,
-};
-
-//ionizationLevel fix the maximum depth of the ionization reactions in the molecule
+/**
+ * @description Fragment a molecule by applying reactions from a custom database of reactions
+ * @param {import('openchemlib').Molecule} molecule - The OCL molecule to be fragmented
+ * @param {Object}  [options={}]
+ * @param {string}  [options.databaseName='cid'] - The database to be used
+ * @param {string}  [options.mode='positive'] - The mode to be used
+ * @param {number}  [options.maxDepth=5] - The maximum depth of the fragmentation tree
+ * @returns {object} In-Silico fragmentation results with the following properties:
+ * - masses: array of monoisotopic masses
+ * - trees: array of fragmentation trees
+ * - products: array of trees grouped by product idCode
+ */
 export function reactionFragmentation(molecule, options = {}) {
-  let {
-    database = 'cid',
-    mode = 'positive',
-    maxDepth = 0,
-    ionizationLevel = 1,
-  } = options;
-  if (maxDepth === 0) {
-    let mass = molecule.getMolecularFormula().absoluteWeight;
-    maxDepth = Math.round(mass / 10);
+  let { databaseName = 'cid', mode = 'positive', maxDepth = 5 } = options;
+  let database = getDatabase(databaseName);
+  if (!database) {
+    throw new Error(`Database ${databaseName} not found`);
   }
-  const reactions = databases[database][mode];
-  let ionizedFragments = applyIonizationReactions(
-    molecule,
-    reactions,
-    ionizationLevel,
+
+  const reactions = database[mode];
+  let fragments = applyReactions([molecule], reactions, {
+    maxDepth,
+  });
+
+  let { masses, trees, products } = insertMfInfoFragments(
+    fragments.trees,
+    fragments.products,
   );
-  for (let ionizedFragment of ionizedFragments) {
-    applyFragmentationReactions(ionizedFragment, reactions, maxDepth);
-  }
-  let { masses, tree } = insertMfInfoFragments(ionizedFragments);
   return {
     masses,
-    tree,
+    trees,
+    products,
   };
 }

src/utils/insertMfInfoFragments.js

 import { MF } from 'mf-parser';
 
-const masses = {};
-
-export function insertMfInfoFragments(fragmentation) {
-  for (let fragment of fragmentation) {
-    mfInfoFragments(fragment);
+/**
+ * @description Recursively insert monoisotopic mass information into the fragmentation trees, products and get array of monoisotopic masses
+ * @param {Array} trees Fragmentation trees
+ * @param {Array} products Fragmentation trees grouped by product idCode
+ * @returns {object} Object with the following properties:
+ * - masses: array of monoisotopic masses
+ * - trees: array of fragmentation trees with monoisotopic mass
+ * - products: array of trees grouped by product idCode with monoisotopic mass
+ */
+export function insertMfInfoFragments(trees, products) {
+  let masses = {};
+  for (let tree of trees) {
+    mfInfoFragments(tree, masses);
   }
+  for (let product of products) {
+    const productMF = new MF(product.mf);
+    product.monoisotopicMass =
+      Math.round(
+        (productMF.getInfo().observedMonoisotopicMass ??
+          productMF.getInfo().monoisotopicMass) * 10000,
+      ) / 10000;
+  }
   return {
     masses: Object.keys(masses).map(Number),
-    tree: fragmentation,
+    trees,
+    products,
   };
 }
 
-function mfInfoFragments(reaction) {
+/**
+ * @description Recursively insert monoisotopic mass information into the fragmentation trees and get array of monoisotopic masses
+ * @param {*} reaction Fragmentation trees
+ * @param {*} masses Object with monoisotopic masses
+ */
+function mfInfoFragments(reaction, masses) {
   if (reaction?.reactant) {
@@ -28,7 +50,2 @@ const reactantMF = new MF(reaction.reactant.mf);
     for (const product of reaction.products) {
-      if (product.children?.length > 0) {
-        for (const child of product.children) {
-          mfInfoFragments(child);
-        }
-      }
       const productMF = new MF(product.mf);
@@ -41,4 +58,9 @@ product.monoisotopicMass =
       masses[product.monoisotopicMass] = true;
+      if (product.children?.length > 0) {
+        for (const child of product.children) {
+          mfInfoFragments(child, masses);
+        }
+      }
     }
   }
 }

No alert changes

Improved metrics

Total package byte prevSize

1314030

24.58%

Lines of code

3049

2.94%

Worsened metrics

Dev dependency count

2

100%

Number of package files

24

-7.69%

Dependency changes

• Updated

  openchemlib-utils@^2.7.0