mass-fragmentation - npm Package Compare versions

Comparing version 0.5.0 to 0.6.0

lib/index.js

@@ -7,3 +7,8 @@ '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);
+
 /**
@@ -492,48 +497,4 @@ * The function performs the fragmentation of all single linear bonds
     },
+
     {
-      Label: 'Ionization',
-      rxnCode: 'eF`BLGtX!eF``fLGt\\#Qd Qd#!R@FL]Rgp !R@FL]vgp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eM`BN`~b@!eM``fN`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'gCh@AGj@`!gChA@Icu@_PP#qTq qTq#!RbOvw?_x@GYK| !RbOvw?_x@GWk|',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode:
-        'gCa@@dmPFtwhHcMCAlp!eMH`eIhOhp#Qv@ Qv#!R@AL@[@@SGSH| !R@Fp@Dqwz``',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eMB@HchH!eMB`HIchOh`#Q[ Q[#!R@AM?Dqtbo@ !R@AM?Dquz@`',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eMHAIXMicLLG~r!eFH`fJGtP#QX QX#!R@AL@[AtbO@ !R@AL]nkp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eMHBN``!eMH`fN`~b@#Qg Qg#!R@FL?XqtJ_@ !R@FL?XqwZ_@',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eFHBLGtP!eFH`fLGtX#QX QX#!R@AL]Pmp !R@AL]^gp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eM`BN`~b@!eM``fN`~bOza@#Qg Qg#!R@Fq?[AuJ?@ !R@FM?Dqvz_@',
-    },
-    {
       Label: 'Oxonium Resonance',
@@ -658,6 +619,69 @@ rxnCode: 'eFH`fJGtP!eFHbfLGtP#QX QX#!R@Fp]rgp !R@FL]Nkp',
 };
-
+const ei = {
+  positive: [],
+  negative: [],
+};
+const esi = {
+  positive: [
+    {
+      Label: 'Ionization',
+      rxnCode: 'eF`BLGtX!eF``fLGt\\#Qd Qd#!R@FL]Rgp !R@FL]vgp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eM`BN`~b@!eM``fN`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'gCh@AGj@`!gChA@Icu@_PP#qTq qTq#!RbOvw?_x@GYK| !RbOvw?_x@GWk|',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode:
+        'gCa@@dmPFtwhHcMCAlp!eMH`eIhOhp#Qv@ Qv#!R@AL@[@@SGSH| !R@Fp@Dqwz``',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eMB@HchH!eMB`HIchOh`#Q[ Q[#!R@AM?Dqtbo@ !R@AM?Dquz@`',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eMHAIXMicLLG~r!eFH`fJGtP#QX QX#!R@AL@[AtbO@ !R@AL]nkp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eMHBN``!eMH`fN`~b@#Qg Qg#!R@FL?XqtJ_@ !R@FL?XqwZ_@',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eFHBLGtP!eFH`fLGtX#QX QX#!R@AL]Pmp !R@AL]^gp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eM`BN`~b@!eM``fN`~bOza@#Qg Qg#!R@Fq?[AuJ?@ !R@FM?Dqvz_@',
+    },
+  ],
+  negative: [],
+};
+/**
+ * @description get fragmentation databases based on the technique used
+ * @param {string} databaseName "cid", "ei" or "esi"
+ * @returns {object} object containing the fragmentation database
+ */
 function getDatabase(databaseName) {
-  if (databaseName === 'cid') {
-    return cid;
+  switch (databaseName) {
+    case 'cid':
+      return cid;
+    case 'ei':
+      return ei;
+    default:
+      return esi;
   }
@@ -667,3 +691,3 @@ }
 /**
- * @description Recursively insert monoisotopic mass information into the fragmentation trees, products and get array of monoisotopic masses
+ * @description get array of mz from fragmentation trees
  * @param {Array} trees Fragmentation trees
@@ -673,17 +697,11 @@ * @param {Array} products Fragmentation trees grouped by product idCode
  * - masses: array of monoisotopic masses
- * - trees: array of fragmentation trees with monoisotopic mass
- * - products: array of trees grouped by product idCode with monoisotopic mass
+ * - trees: array of fragmentation trees
+ * - products: array of trees grouped by product idCode
  */
-function insertMfInfoFragments(trees, products) {
+function getMasses(trees, products) {
   let masses = {};
-  for (let tree of trees) {
-    mfInfoFragments(tree, masses);
-  }
   for (let product of products) {
-    const productMF = new mfParser.MF(product.mf);
-    product.monoisotopicMass =
-      Math.round(
-        (productMF.getInfo().observedMonoisotopicMass ??
-          productMF.getInfo().monoisotopicMass) * 10000,
-      ) / 10000;
+    if (Math.abs(product.charge) > 0) {
+      masses[product.mz] = true;
+    }
   }
@@ -698,36 +716,2 @@ return {
 /**
- * @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) {
-    const reactantMF = new mfParser.MF(reaction.reactant.mf);
-    reaction.reactant.monoisotopicMass =
-      Math.round(
-        (reactantMF.getInfo().observedMonoisotopicMass ??
-          reactantMF.getInfo().monoisotopicMass) * 10000,
-      ) / 10000;
-    masses[reaction.reactant.monoisotopicMass] = true;
-  }
-
-  if (reaction?.products?.length > 0) {
-    for (const product of reaction.products) {
-      const productMF = new mfParser.MF(product.mf);
-      product.monoisotopicMass =
-        Math.round(
-          (productMF.getInfo().observedMonoisotopicMass ??
-            productMF.getInfo().monoisotopicMass) * 10000,
-        ) / 10000;
-      masses[product.monoisotopicMass] = true;
-      if (product.children?.length > 0) {
-        for (const child of product.children) {
-          mfInfoFragments(child, masses);
-        }
-      }
-    }
-  }
-}
-
-/**
  * @description Fragment a molecule by applying reactions from a custom database of reactions
@@ -739,2 +723,9 @@ * @param {import('openchemlib').Molecule} molecule - The OCL molecule to be fragmented
  * @param {number}  [options.maxDepth=5] - The maximum depth of the fragmentation tree
+ * @param {number}  [options.maxIonizationDepth=1] - The maximum depth of the ionization tree
+ * @param {Object}  [options.customDatabase={}] - A custom database of reactions
+ * @param {Array}  [options.customDatabase.positive] - A custom database of reactions for positive mode
+ * @param {Array}  [options.customDatabase.negative] - A custom database of reactions for negative mode
+ * @param {Object}  [options.customDatabase.ionization] - A custom database ionization reactions
+ * @param {Array}  [options.customDatabase.ionization.positive] - A custom database of ionization reactions for positive mode
+ * @param {Array}  [options.customDatabase.ionization.negative] - A custom database of ionization reactions for negative mode
  * @returns {object} In-Silico fragmentation results with the following properties:
@@ -746,17 +737,50 @@ * - masses: array of monoisotopic masses
 function reactionFragmentation(molecule, options = {}) {
-  let { databaseName = 'cid', mode = 'positive', maxDepth = 5 } = options;
-  let database = getDatabase(databaseName);
+  let {
+    databaseName = 'cid',
+    mode = 'positive',
+    maxDepth = 3,
+    maxIonizationDepth = 1,
+    customDatabase = {},
+  } = options;
+  let database;
+  let IonizationDb;
+  if (customDatabase[mode] && customDatabase[mode].length > 0) {
+    database = customDatabase;
+  } else {
+    database = getDatabase(databaseName);
+  }
   if (!database) {
     throw new Error(`Database ${databaseName} not found`);
   }
-
+  if (databaseName === 'cid') {
+    if (
+      customDatabase.ionization &&
+      customDatabase.ionization[mode].length > 0
+    ) {
+      IonizationDb = customDatabase.ionization[mode];
+    } else {
+      IonizationDb = getDatabase('')[mode];
+    }
+  }
+  let results = {};
   const reactions = database[mode];
-  let fragments = openchemlibUtils.applyReactions([molecule], reactions, {
-    maxDepth,
-  });
+  if (IonizationDb) {
+    let ionizationFragments = openchemlibUtils.applyReactions([molecule], IonizationDb, {
+      maxDepth: maxIonizationDepth,
+    });
 
-  let { masses, trees, products } = insertMfInfoFragments(
-    fragments.trees,
-    fragments.products,
-  );
+    for (let tree of ionizationFragments.trees) {
+      getMoleculesToFragment(tree, reactions, maxDepth);
+    }
+    ionizationFragments.products = openchemlibUtils.groupTreesByProducts(
+      ionizationFragments.trees,
+    );
+    results = ionizationFragments;
+  } else {
+    results = openchemlibUtils.applyReactions([molecule], reactions, {
+      maxDepth,
+    });
+  }
+
+  let { masses, trees, products } = getMasses(results.trees, results.products);
   return {
@@ -769,3 +793,24 @@ masses,
 
+function getMoleculesToFragment(tree, reactions, maxDepth) {
+  for (let product of tree.products) {
+    if (product.children.length === 0) {
+      if (product.charge !== 0) {
+        let molecule = OCL__default["default"].Molecule.fromIDCode(product.idCode);
+        let fragments = openchemlibUtils.applyReactions([molecule], reactions, {
+          maxDepth,
+        });
+        product.children = fragments.trees;
+      }
+    } else {
+      for (let child of product.children) {
+        getMoleculesToFragment(child, reactions, maxDepth);
+      }
+    }
+  }
+}
+
+exports.cid = cid;
+exports.ei = ei;
+exports.esi = esi;
 exports.fragment = fragment;
 exports.reactionFragmentation = reactionFragmentation;

package.json

 {
   "name": "mass-fragmentation",
-  "version": "0.5.0",
+  "version": "0.6.0",
   "description": "Code to fragment molecules",
@@ -24,9 +24,9 @@ "main": "lib/index.js",
     "mf-parser": "^2.3.0",
-    "openchemlib-utils": "^2.7.0"
+    "openchemlib-utils": "^5.0.2"
   },
   "devDependencies": {
-    "openchemlib": "^8.3.0",
-    "react-tree-svg": "^0.1.0"
+    "openchemlib": "^8.5.0",
+    "react-tree-svg": "^0.3.0"
   },
-  "gitHead": "c697f5fab6e34146c16194f54cead9ddd1c8465f"
+  "gitHead": "a288cfad35ed88e24f17546841389ef0b7fdcbc7"
 }

src/__tests__/reactionFragmentation.test.js

@@ -12,2 +12,3 @@ import OCL from 'openchemlib';
       maxDepth: 20,
+      maxIonizationDepth: 2,
     };
@@ -23,9 +24,11 @@ const { masses, trees, products } = reactionFragmentation(
         "mf",
+        "em",
+        "mz",
+        "charge",
         "trees",
         "reactions",
         "minSteps",
-        "monoisotopicMass",
       ]
     `);
-    expect(masses).toHaveLength(17);
+    expect(masses).toHaveLength(4);
     expect(trees).toMatchSnapshot();
@@ -36,3 +39,4 @@ });
     const options = {
-      maxDepth: 20,
+      maxDepth: 5,
+      maxIonizationDepth: 2,
     };
@@ -47,9 +51,11 @@ const { masses, trees, products } = reactionFragmentation(
         "mf",
+        "em",
+        "mz",
+        "charge",
         "trees",
         "reactions",
         "minSteps",
-        "monoisotopicMass",
       ]
     `);
-    expect(masses).toHaveLength(7);
+    expect(masses).toHaveLength(2);
     expect(trees).toMatchSnapshot();
@@ -66,23 +72,8 @@ });
       [
-        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,
+        194.11810400000002,
+        163.075905,
+        135.04460500000002,
+        105.03404,
+        193.11027900000002,
+        58.065674,
       ]
@@ -92,6 +83,8 @@ `);
       {
+        "charge": 1,
+        "em": 194.11810400000002,
         "idCode": "dg~DBMBmeJYW]gJxZB@jj@@",
         "mf": "C11H16NO2(+)",
         "minSteps": 1,
-        "monoisotopicMass": 194.1176,
+        "mz": 194.11810400000002,
         "reactions": [
@@ -104,3 +97,5 @@ "eM\`BN\`~b@!eM\`\`fN\`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@",
               {
+                "charge": 1,
                 "children": [],
+                "em": 194.11810400000002,
                 "flag": true,
@@ -145,5 +140,8 @@ "idCode": "dg~DBMBmeJYW]gJxZB@jj@@",
       ",
+                "mz": 194.11810400000002,
               },
             ],
             "reactant": {
+              "charge": 0,
+              "em": 193.11027900000002,
               "idCode": "dg~D@MBdie]v\\\\kahHBjh@@",
@@ -186,2 +184,3 @@ "mf": "C11H15NO2",
       ",
+              "mz": 193.11027900000002,
             },
@@ -198,2 +197,120 @@ "reaction": {
   });
+  it('Full fragmentation: MDMA with custom database', async () => {
+    const molecule = Molecule.fromSmiles('CC(CC1=CC2=C(C=C1)OCO2)NC');
+    const customDatabase = {
+      positive: [
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gCa@@duPGtF@!fI@Gu` eM@bXzB#qbq a` qQp#!RtEJHC^h@GPhB !RGUi| !R@FN?Dquz_@',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gJPI@DBTijhCzB@!gK`I@DJTcj`OhH@#qbqh qfUH#!Rmwwp_[]|_g|]lcp !R?`BE@[_|b@H]vgp',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gJPa@eJSKTA}E@!eMH`eIxH eFHBLGtP#qbqh qbH qu#!Rw`BH?J_|bMt]|hH !Rwpq?Dquz?@ !R?`@]vgp',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gJQIL@`ReMS@_PP!eMH`eIxH eFB@HcA}D@#qbqh qJh Ql#!Rm?wpwXE?y{p]lmp !Rwxq?Dquz?@ !R@NL]vgp',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gJXA@IRij`OhH@!gKhAAirPFhB#qbuH qfjH#!RM{upoPD@Mwp]lgp !R@BL?x~WAwrp]Vgp',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gJYADEJSKTA}E`!eMH`eIxH eF`BLGtX#qbqh qbH qu#!RO`BH?C_|bGt]|hH !Rwtq?Dquz_@ !R?`@]vgp',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gC`AAJTu@P!eF@bXpP eF@HpP#qTq qa Q\\#!R@AM?DpAlGTJB !R@DQCrip !R_sL}Nmp',
+        },
+        {
+          Label: 'Alpha cleavage',
+          rxnCode:
+            'gChA@IRfhCzC@!eF`BLD eF@bXpP#qbq Ql qQ#!R{|L@p~~lG[K| !R@DL]Vgp !R_xp]ngp',
+        },
+        {
+          Label: 'Aromatic Indicutive Cleavage',
+          rxnCode:
+            'gC`AAJTu@]SP!eF@bXpP eF@HhP#qrL QX qq#!Rgzp@kI}cG]K| !R@BL]vgp !R@BL]~kp',
+        },
+      ],
+      ionization: {
+        positive: [
+          {
+            Label: 'Ionization',
+            rxnCode: 'eF`BLGtX!eF``fLGt\\#Qd Qd#!R@FL]Rgp !R@FL]vgp',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eM`BN`~b@!eM``fN`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode:
+              'gCh@AGj@`!gChA@Icu@_PP#qTq qTq#!RbOvw?_x@GYK| !RbOvw?_x@GWk|',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode:
+              'gCa@@dmPFtwhHcMCAlp!eMH`eIhOhp#Qv@ Qv#!R@AL@[@@SGSH| !R@Fp@Dqwz``',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eMB@HchH!eMB`HIchOh`#Q[ Q[#!R@AM?Dqtbo@ !R@AM?Dquz@`',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eMHAIXMicLLG~r!eFH`fJGtP#QX QX#!R@AL@[AtbO@ !R@AL]nkp',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eMHBN``!eMH`fN`~b@#Qg Qg#!R@FL?XqtJ_@ !R@FL?XqwZ_@',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eFHBLGtP!eFH`fLGtX#QX QX#!R@AL]Pmp !R@AL]^gp',
+          },
+          {
+            Label: 'Ionization',
+            rxnCode: 'eM`BN`~b@!eM``fN`~bOza@#Qg Qg#!R@Fq?[AuJ?@ !R@FM?Dqvz_@',
+          },
+        ],
+      },
+    };
+
+    const options = {
+      maxDepth: 5,
+      customDatabase,
+    };
+    let { masses, trees, products } = reactionFragmentation(molecule, options);
+    expect(masses).toMatchInlineSnapshot(`
+      [
+        194.11810400000002,
+        163.075905,
+        135.04460500000002,
+        193.11027900000002,
+      ]
+    `);
+    expect(products[0].mf).toMatchInlineSnapshot('"C11H16NO2(+)"');
+    expect(trees).toMatchSnapshot();
+  });
 });

src/database/getDatabase.js

@@ -163,48 +163,4 @@ export const cid = {
     },
+
     {
-      Label: 'Ionization',
-      rxnCode: 'eF`BLGtX!eF``fLGt\\#Qd Qd#!R@FL]Rgp !R@FL]vgp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eM`BN`~b@!eM``fN`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'gCh@AGj@`!gChA@Icu@_PP#qTq qTq#!RbOvw?_x@GYK| !RbOvw?_x@GWk|',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode:
-        'gCa@@dmPFtwhHcMCAlp!eMH`eIhOhp#Qv@ Qv#!R@AL@[@@SGSH| !R@Fp@Dqwz``',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eMB@HchH!eMB`HIchOh`#Q[ Q[#!R@AM?Dqtbo@ !R@AM?Dquz@`',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eMHAIXMicLLG~r!eFH`fJGtP#QX QX#!R@AL@[AtbO@ !R@AL]nkp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eMHBN``!eMH`fN`~b@#Qg Qg#!R@FL?XqtJ_@ !R@FL?XqwZ_@',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eFHBLGtP!eFH`fLGtX#QX QX#!R@AL]Pmp !R@AL]^gp',
-    },
-    {
-      Label: 'Ionization',
-      rxnCode: 'eM`BN`~b@!eM``fN`~bOza@#Qg Qg#!R@Fq?[AuJ?@ !R@FM?Dqvz_@',
-    },
-    {
       Label: 'Oxonium Resonance',
@@ -329,7 +285,70 @@ rxnCode: 'eFH`fJGtP!eFHbfLGtP#QX QX#!R@Fp]rgp !R@FL]Nkp',
 };
-
+export const ei = {
+  positive: [],
+  negative: [],
+};
+export const esi = {
+  positive: [
+    {
+      Label: 'Ionization',
+      rxnCode: 'eF`BLGtX!eF``fLGt\\#Qd Qd#!R@FL]Rgp !R@FL]vgp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eM`BN`~b@!eM``fN`~c@#Q[ Q[#!R@AM?DquRo@ !R@AM?Dqtzo@',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'gCh@AGj@`!gChA@Icu@_PP#qTq qTq#!RbOvw?_x@GYK| !RbOvw?_x@GWk|',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode:
+        'gCa@@dmPFtwhHcMCAlp!eMH`eIhOhp#Qv@ Qv#!R@AL@[@@SGSH| !R@Fp@Dqwz``',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eMB@HchH!eMB`HIchOh`#Q[ Q[#!R@AM?Dqtbo@ !R@AM?Dquz@`',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eMHAIXMicLLG~r!eFH`fJGtP#QX QX#!R@AL@[AtbO@ !R@AL]nkp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eMHBN``!eMH`fN`~b@#Qg Qg#!R@FL?XqtJ_@ !R@FL?XqwZ_@',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eFB@HcA}D@!eFB`HIcA}F@#QX QX#!R_vp]bgp !R_vp]vgp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eFHBLGtP!eFH`fLGtX#QX QX#!R@AL]Pmp !R@AL]^gp',
+    },
+    {
+      Label: 'Ionization',
+      rxnCode: 'eM`BN`~b@!eM``fN`~bOza@#Qg Qg#!R@Fq?[AuJ?@ !R@FM?Dqvz_@',
+    },
+  ],
+  negative: [],
+};
+/**
+ * @description get fragmentation databases based on the technique used
+ * @param {string} databaseName "cid", "ei" or "esi"
+ * @returns {object} object containing the fragmentation database
+ */
 export default function getDatabase(databaseName) {
-  if (databaseName === 'cid') {
-    return cid;
+  switch (databaseName) {
+    case 'cid':
+      return cid;
+    case 'ei':
+      return ei;
+    default:
+      return esi;
   }
 }

src/index.js

 export * from './fragment.js';
 export * from './reactionFragmentation.js';
+export * from './database/getDatabase.js';

src/reactionFragmentation.js

@@ -1,6 +0,6 @@
-import { applyReactions } from 'openchemlib-utils';
+import OCL from 'openchemlib';
+import { applyReactions, groupTreesByProducts } from 'openchemlib-utils';
 
 import getDatabase from './database/getDatabase';
-import { insertMfInfoFragments } from './utils/insertMfInfoFragments';
-
+import { getMasses } from './utils/getMasses';
 /**
@@ -13,2 +13,9 @@ * @description Fragment a molecule by applying reactions from a custom database of reactions
  * @param {number}  [options.maxDepth=5] - The maximum depth of the fragmentation tree
+ * @param {number}  [options.maxIonizationDepth=1] - The maximum depth of the ionization tree
+ * @param {Object}  [options.customDatabase={}] - A custom database of reactions
+ * @param {Array}  [options.customDatabase.positive] - A custom database of reactions for positive mode
+ * @param {Array}  [options.customDatabase.negative] - A custom database of reactions for negative mode
+ * @param {Object}  [options.customDatabase.ionization] - A custom database ionization reactions
+ * @param {Array}  [options.customDatabase.ionization.positive] - A custom database of ionization reactions for positive mode
+ * @param {Array}  [options.customDatabase.ionization.negative] - A custom database of ionization reactions for negative mode
  * @returns {object} In-Silico fragmentation results with the following properties:
@@ -20,17 +27,50 @@ * - masses: array of monoisotopic masses
 export function reactionFragmentation(molecule, options = {}) {
-  let { databaseName = 'cid', mode = 'positive', maxDepth = 5 } = options;
-  let database = getDatabase(databaseName);
+  let {
+    databaseName = 'cid',
+    mode = 'positive',
+    maxDepth = 3,
+    maxIonizationDepth = 1,
+    customDatabase = {},
+  } = options;
+  let database;
+  let IonizationDb;
+  if (customDatabase[mode] && customDatabase[mode].length > 0) {
+    database = customDatabase;
+  } else {
+    database = getDatabase(databaseName);
+  }
   if (!database) {
     throw new Error(`Database ${databaseName} not found`);
   }
-
+  if (databaseName === 'cid') {
+    if (
+      customDatabase.ionization &&
+      customDatabase.ionization[mode].length > 0
+    ) {
+      IonizationDb = customDatabase.ionization[mode];
+    } else {
+      IonizationDb = getDatabase('')[mode];
+    }
+  }
+  let results = {};
   const reactions = database[mode];
-  let fragments = applyReactions([molecule], reactions, {
-    maxDepth,
-  });
+  if (IonizationDb) {
+    let ionizationFragments = applyReactions([molecule], IonizationDb, {
+      maxDepth: maxIonizationDepth,
+    });
 
-  let { masses, trees, products } = insertMfInfoFragments(
-    fragments.trees,
-    fragments.products,
-  );
+    for (let tree of ionizationFragments.trees) {
+      getMoleculesToFragment(tree, reactions, maxDepth);
+    }
+    ionizationFragments.products = groupTreesByProducts(
+      ionizationFragments.trees,
+    );
+    results = ionizationFragments;
+  } else {
+    results = applyReactions([molecule], reactions, {
+      maxDepth,
+    });
+  }
+
+  let { masses, trees, products } = getMasses(results.trees, results.products);
   return {
@@ -42,1 +82,19 @@ masses,
 }
+
+function getMoleculesToFragment(tree, reactions, maxDepth) {
+  for (let product of tree.products) {
+    if (product.children.length === 0) {
+      if (product.charge !== 0) {
+        let molecule = OCL.Molecule.fromIDCode(product.idCode);
+        let fragments = applyReactions([molecule], reactions, {
+          maxDepth,
+        });
+        product.children = fragments.trees;
+      }
+    } else {
+      for (let child of product.children) {
+        getMoleculesToFragment(child, reactions, maxDepth);
+      }
+    }
+  }
+}

No alert changes

Improved metrics

Lines of code

3248

increased by6.53%

Worsened metrics

Total package byte prevSize

779285

decreased by-40.7%

Dependency changes

• + Added@lukeed/csprng@1.1.0(transitive)

• + Added@lukeed/uuid@2.0.1(transitive)

• + Addedopenchemlib-utils@5.21.1(transitive)

• - Removedopenchemlib-utils@2.9.0(transitive)

• Updatedopenchemlib-utils@^5.0.2