feat: expose Reactor

README.md

@@ -60,6 +60,8 @@ It contains a structure viewer and a structure editor for browser applications.
 - [DrugScoreCalculator](https://cheminfo.github.io/openchemlib-js/modules/DrugScoreCalculator.html)
 - [ForceFieldMMFF94](https://cheminfo.github.io/openchemlib-js/classes/ForceFieldMMFF94.html)
 - [MoleculeProperties](https://cheminfo.github.io/openchemlib-js/classes/MoleculeProperties.html)
+- [ReactionEncoder](https://cheminfo.github.io/openchemlib-js/classes/ReactionEncoder.html)
+- [Reactor](https://cheminfo.github.io/openchemlib-js/classes/Reactor.html)
 - [ToxicityPredictor](https://cheminfo.github.io/openchemlib-js/classes/ToxicityPredictor.html)
 - [Transformer](https://cheminfo.github.io/openchemlib-js/classes/Transformer.html)
 

__tests__/Reactor.test.js

@@ -0,0 +1,144 @@
+'use strict';
+
+const { getMF } = require('openchemlib-utils');
+
+const { Reactor, Molecule, Reaction, ReactionEncoder } = require('../core');
+
+// the actelion reaction ID is encoded in the RXN file !!!
+// this code has priority so if it is there the rest of the RXN file is ignored
+// Currently we generate RXN files using ChemDraw
+
+describe('Reactor class', () => {
+  it('deshydratation', () => {
+    const reaction = ReactionEncoder.decode(
+      'eMHAIhH!eF@HhP#QF Qd#!R_vq?DqtJ_@ !R@Fp]Agp',
+    );
+
+    const reactor = new Reactor(reaction);
+
+    const match = reactor.setReactant(0, Molecule.fromSmiles('OC(C)CCCO'));
+    if (!match) return;
+
+    const products = reactor.getProducts();
+
+    const smiles = [];
+    for (let i = 0; i < products.length; i++) {
+      for (let j = 0; j < products[i].length; j++) {
+        smiles.push(products[i][j].toSmiles());
+      }
+    }
+
+    expect(smiles).toStrictEqual(['C(CCCO)=C', 'C(C)=CCCO', 'OC(C)CC=C']);
+  });
+
+  it('protonation, we add a H+ on the O', () => {
+    const rxn = `$RXN
+    
+    
+
+  1  1
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+    1.7321   -0.5000   -0.0000 O   0  0  0  0  0  0  0  0  0  1  0  0
+    0.8660   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
+    0.0000   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+M  END
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+    1.7321   -0.5000   -0.0000 O   0  3  0  0  0  0  0  0  0  1  0  0
+    0.8660   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
+    0.0000   -0.5000   -0.0000 C   0  0  0  0  0  0  0  0  0  3  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+M  END`;
+
+    const reaction = Reaction.fromRxn(rxn);
+
+    const reactor = new Reactor(reaction);
+
+    const match = reactor.setReactant(0, Molecule.fromSmiles('OC(C)CCCO'));
+    if (!match) return;
+
+    const products = reactor.getProducts();
+
+    const smiles = [];
+    for (let i = 0; i < products.length; i++) {
+      for (let j = 0; j < products[i].length; j++) {
+        smiles.push(products[i][j].toSmiles());
+      }
+    }
+    expect(smiles).toStrictEqual(['[OH2+]C(CCCO)C', 'OC(C)CCC[OH2+]']);
+  });
+
+  it('charge O and break bond', () => {
+    const rxn = `$RXN
+test.rxn
+  ChemDraw01042314002D
+
+  1  2
+$MOL
+
+
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+   -0.7145   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  2  0  0
+   -0.0000    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
+    0.7145   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  3  0  0
+  1  2  1  0        4
+  2  3  1  0        0
+M  END
+$MOL
+
+
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  4  0  0  0  0  0  0  0  2  0  0
+M  RAD  1   1   2
+M  END
+$MOL
+
+
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+   -0.3268    0.2643    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
+    0.3268   -0.2643    0.0000 O   0  3  0  0  0  0  0  0  0  3  0  0
+  1  2  1  0        0
+M  CHG  1   2   1
+M  END
+`;
+
+    const reaction = Reaction.fromRxn(rxn);
+
+    const reactor = new Reactor(reaction);
+
+    const match = reactor.setReactant(0, Molecule.fromSmiles('OC(C)CCCO'));
+    if (!match) return;
+
+    const products = reactor.getProducts();
+
+    const smiles = [];
+    const mfs = [];
+    for (let i = 0; i < products.length; i++) {
+      for (let j = 0; j < products[i].length; j++) {
+        smiles.push(products[i][j].toSmiles());
+        mfs.push(getMF(products[i][j]).mf);
+      }
+    }
+    expect(mfs).toStrictEqual([
+      'CH3',
+      'C4H11O2(+)',
+      'C3H7O',
+      'C2H7O(+)',
+      'C4H9O',
+      'CH5O(+)',
+    ]);
+  });
+});

__tests__/__snapshots__/library.js.snap

@@ -308,6 +308,13 @@ exports[`prototype properties of MoleculeProperties 1`] = `[]`;
 
 exports[`prototype properties of ReactionEncoder 1`] = `[]`;
 
+exports[`prototype properties of Reactor 1`] = `
+[
+  "getProducts",
+  "setReactant",
+]
+`;
+
 exports[`prototype properties of SDFileParser 1`] = `
 [
   "getField",
@@ -637,6 +644,8 @@ exports[`static properties of ReactionEncoder 1`] = `
 ]
 `;
 
+exports[`static properties of Reactor 1`] = `[]`;
+
 exports[`static properties of SDFileParser 1`] = `[]`;
 
 exports[`static properties of SSSearcher 1`] = `[]`;

__tests__/library.js

@@ -24,6 +24,7 @@ const coreAPI = [
   'ForceFieldMMFF94',
   'MoleculeProperties',
   'ReactionEncoder',
+  'Reactor',
   'ToxicityPredictor',
   'Transformer',
 ];

core.d.ts

@@ -9,6 +9,7 @@ export {
   IParameterizedString,
   MoleculeProperties,
   ReactionEncoder,
+  Reactor,
   Transformer,
   ToxicityPredictor,
 } from './types';