feat!: rename keepIdCode to appendIDCode and add appendNoStereoIDCode…

…Hash and appendRacemateIDCodeHash

src/__tests__/acdPrediction/toc.json

@@ -3,25 +3,25 @@
     "id": "Oz9gTP3NhSQZlWBu4aT4cizhQzg=",
     "mf": "C4H8O2",
     "idCodeHash": "8dce89763ab899350b4a01be188c1555",
-    "idCode": "gGP`@df]j`@",
     "file": "./Bsp1/index.json",
     "title": "Bsp1",
+    "idCode": "gGP`@df]j`@",
     "selected": true
   },
   {
     "id": "Il6UfZ1v3NduB9nsPgFi5RA4Xbg=",
     "mf": "C4H8O2",
     "idCodeHash": "134d499936f8fedb1170e3f741f72b9e",
-    "idCode": "gGP`@dfUj`@",
     "file": "./Bsp2/index.json",
-    "title": "Bsp2"
+    "title": "Bsp2",
+    "idCode": "gGP`@dfUj`@"
   },
   {
     "id": "z3uJ3OLwf2z/bAlG9yYAuADV/gA=",
     "mf": "C4H8O",
     "idCodeHash": "21dcc0027d441801e362cec51f90e9b9",
-    "idCode": "gJQ@@eKS@@",
     "file": "./ethylvinylether/index.json",
-    "title": "ethylvinylether"
+    "title": "ethylvinylether",
+    "idCode": "gJQ@@eKS@@"
   }
 ]

src/__tests__/createExercisesTOC.test.js

@@ -8,22 +8,26 @@ import { createExercisesTOC } from '../commands/createExercisesTOC.js';
 
 test('createExercisesTOC', async () => {
   const dataDir = join(__dirname, 'exercises');
-  await createExercisesTOC(__dirname, { dataDir });
+  await createExercisesTOC(__dirname, {
+    dataDir,
+    appendNoStereoIDCodeHash: true,
+  });
 
   const files = (await readdir(dataDir)).sort();
   const sizes = files
     .filter((file) => file.match(/\.json$/))
     .map((file) => {
       return statSync(file).size;
     });
-  expect(sizes).toStrictEqual([257, 138, 258, 746, 412]);
+  expect(sizes).toStrictEqual([138, 257, 138, 258, 1053, 412]);
 });
 
 test('createExercisesTOC with predicted', async () => {
   const dataDir = join(__dirname, 'acdPrediction');
   await createExercisesTOC(__dirname, {
     dataDir,
-    keepIdCode: true,
+    appendIDCode: true,
+
     cleanJCAMP: true,
   });
 

src/__tests__/exercises/Chiral/index.json

@@ -0,0 +1,12 @@
+{
+  "spectra": [
+    {
+      "source": {
+        "jcampURL": "./1h.jdx"
+      },
+      "display": {
+        "name": ""
+      }
+    }
+  ]
+}

src/__tests__/exercises/Chiral/structure.mol

@@ -0,0 +1,18 @@
+
+Actelion Java MolfileCreator 1.0
+
+  7  6  0  0  1  0  0  0  0  0999 V2000
+    6.1251  -12.1252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.4241  -12.8752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.7231  -12.1252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.0222  -12.8752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.3211  -12.1252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.4241  -14.3752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    8.7231  -10.6252    0.0000 O   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  1  0  0  0  0
+  2  6  1  1  0  0  0
+  3  7  1  1  0  0  0
+M  END

src/__tests__/exercises/toc.json

@@ -1,11 +1,20 @@
 [
+  {
+    "id": "XjKWTz7MPgN2x3evAUQWsjpoXNE=",
+    "mf": "C5H12O2",
+    "idCodeHash": "3d95df75d24a4142629d4a1258458cfb",
+    "file": "./Chiral/index.json",
+    "title": "Chiral",
+    "noStereoIDCodeHash": "21244f700a4490ed7d963ae780723fd6",
+    "racemateIDCodeHash": "ad594ab988e3bfd5e52f0ab5ffe4e59c",
+    "selected": true
+  },
   {
     "id": "8x+bblgo31zA/Y8aAYQHBwjFaZg=",
     "mf": "C9H18",
     "idCodeHash": "7ec5fb4efcce0c89de85193a330e6679",
     "file": "./Exercises3/index.json",
-    "title": "Exercises3",
-    "selected": true
+    "title": "Exercises3"
   },
   {
     "groupName": "Series1",

src/commands/createExercisesTOC.js

@@ -6,7 +6,9 @@ import { processExerciseFolder } from './toc/processExerciseFolder.js';
  * @param {string} commandDir
  * @param {object} [options={}]
  * @param {string} [options.dataDir]
- * @param {boolean} [options.keepIdCode] - kepp idCode in the answer to be able to provide tips
+ * @param {boolean} [options.appendIDCode] - append idCode in the answer to be able to provide tips
+ * @param {boolean} [options.appendNoStereoIDCodeHash] - append noStrereo idCode hash to check the answer without stereochemistry
+ * @param {boolean} [options.appendRacemateIDCodeHash] - append racemate idCode hash to check the answer as a racemate
  * @param {boolean} [options.cleanJCAMP] - keep only the spectrum in the JCAMP-DX
  */
 export async function createExercisesTOC(commandDir, options = {}) {

src/commands/toc/createToc.js

@@ -14,7 +14,7 @@ const debug = debugFct('nmrium.toc');
  * @param {string} commandDir
  * @param {object} [options={}]
  * @param {string} [options.dataDir=commandDir]
- * @param {boolean} [options.keepIdCode=false] - Add the idCode to the toc
+ * @param {boolean} [options.appendIDCode=false] - Add the idCode to the toc
  */
 export async function createToc(commandDir, folderProcessor, options = {}) {
   const { dataDir = commandDir } = options;

src/commands/toc/processExerciseFolder.js

@@ -6,6 +6,7 @@ import { hashElement } from 'folder-hash';
 import { createTree } from 'jcampconverter';
 import md5 from 'md5';
 import OCL from 'openchemlib';
+import { makeRacemic } from 'openchemlib-utils';
 
 const { Molecule } = OCL;
 
@@ -21,7 +22,9 @@ let exercise = 0;
  * @param {object} toc
  * @param {object} [options={}]
  * @param {string} [options.spectraFilter] - comma separated list of experiments to process, if not defined all experiments are processed
- * @param {string} [options.keepIdCode=false] - Keep idCode in the toc
+ * @param {string} [options.appendIDCode=false] - Append idCode in the toc
+ * @param {string} [options.appendNoStereoIDCodeHash=false] - Append noStereo idCode hash to check
+ * @param {string} [options.appendRacemateIDCodeHash=true] - Append racemate idCode hash to check
  * @param {boolean} [options.cleanJCAMP] - keep only the spectrum in the JCAMP-DX
  */
 
@@ -31,13 +34,20 @@ export async function processExerciseFolder(
   toc,
   options = {},
 ) {
-  let { spectraFilter, keepIdCode = false, cleanJCAMP = false } = options;
+  let {
+    spectraFilter,
+    appendIDCode = false,
+    cleanJCAMP = false,
+    appendNoStereoIDCodeHash = false,
+    appendRacemateIDCodeHash = true,
+  } = options;
   if (spectraFilter) {
     spectraFilter = new RegExp(
       `^(${spectraFilter.split(',').join('|')}).`,
       'i',
     );
   }
+
   const currentFolder = join(basename, folder);
   const entries = readdirSync(currentFolder);
   const molfileName = readdirSync(currentFolder).filter((file) =>
@@ -51,6 +61,7 @@ export async function processExerciseFolder(
   const mf = molecule.getMolecularFormula().formula;
   const idCode = molecule.getIDCode();
   const idCodeHash = md5(idCode);
+
   const includedFiles = []; // we only hash the included files to find out if it is the same exercise
   for (let spectrumName of entries.filter(
     (file) =>
@@ -95,11 +106,29 @@ export async function processExerciseFolder(
     id,
     mf,
     idCodeHash,
-    idCode: keepIdCode ? idCode : undefined,
     file: `${URL_FOLDER}/${folder}/index.json`,
     title,
     selected: exercise === 1 || undefined,
   };
+  if (appendIDCode) {
+    tocEntry.idCode = idCode;
+  }
+
+  if (appendNoStereoIDCodeHash || appendRacemateIDCodeHash) {
+    const { noStereoIDCodeHash, racemateIDCodeHash } = getStereoHash(molecule);
+    if (
+      appendNoStereoIDCodeHash &&
+      tocEntry.idCodeHash !== noStereoIDCodeHash
+    ) {
+      tocEntry.noStereoIDCodeHash = noStereoIDCodeHash;
+    }
+    if (
+      appendRacemateIDCodeHash &&
+      tocEntry.idCodeHash !== racemateIDCodeHash
+    ) {
+      tocEntry.racemateIDCodeHash = racemateIDCodeHash;
+    }
+  }
   toc.push(tocEntry);
 }
 
@@ -143,3 +172,22 @@ function flattenTree(entries, flatten) {
     flatten.push(entry);
   }
 }
+
+/**
+ * get the hash without stereo information or racemate
+ *
+ * @param {import('openchemlib').Molecule} molecule
+ * @returns
+ */
+function getStereoHash(molecule) {
+  const moleculeNoStereo = molecule.getCompactCopy();
+  moleculeNoStereo.stripStereoInformation();
+  const noStereoIDCode = moleculeNoStereo.getIDCode();
+  const noStereoIDCodeHash = md5(noStereoIDCode);
+
+  const moleculeRacemate = molecule.getCompactCopy();
+  makeRacemic(moleculeRacemate);
+  const racemateIDCode = moleculeRacemate.getIDCode();
+  const racemateIDCodeHash = md5(racemateIDCode);
+  return { noStereoIDCodeHash, racemateIDCodeHash };
+}

src/index.js

@@ -18,11 +18,31 @@ yargs(hideBin(normalizeArgv(process.argv)))
   .scriptName('nmrium')
   .command('createExercisesTOC [options]', 'Build toc.json for exercises', {
     builder: (yargs) => {
-      return yargs.option('keepIdCode', {
-        alias: 'i',
-        type: 'boolean',
-        description: 'Add idCode in the exercise TOC',
-      });
+      return yargs
+        .option('appendIDCode', {
+          alias: 'i',
+          type: 'boolean',
+          default: false,
+          description: 'Add idCode in the exercise TOC',
+        })
+        .option('appendNoStereoIDCodeHash', {
+          alias: 's',
+          type: 'boolean',
+          default: false,
+          description:
+            'Add an idCode hash without stereo information in order to consider as correct the molecule with wrong stereo information',
+        })
+        .option('appendRacemateIDCodeHash', {
+          type: 'boolean',
+          default: true,
+          description:
+            'Allows to check the answer considering any enantiomer as correct',
+        })
+        .option('cleanJCAMP', {
+          type: 'boolean',
+          default: false,
+          description: 'Only keep the first spectrum in the JCAMP-DX file',
+        });
     },
     handler: (argv) => {
       createExercisesTOC(homeDir, { ...argv });