fix: update database for auto labelling

Author: lpatiny

.ncurc.json

@@ -1,3 +1 @@
-{
-  "reject": ["openchemlib"]
-}
+{}

data/autoLabel/createJson.js

@@ -9,11 +9,14 @@ import { Canonizer, Molecule } from 'openchemlib';
 // this database will be ordered by molecule size
 
 async function createAutoLabelingJson() {
-  const allFiles = await readdir(join(import.meta.dirname, 'templates'));
+  const allFiles = await readdir(join(import.meta.dirname, 'templates'), {
+    recursive: true,
+  });
   const files = allFiles.filter((file) => file.endsWith('.mol'));
   const moleculeDatabase = [];
 
   for (const file of files) {
+    // console.log(file);
     const molfile = await readFile(
       join(import.meta.dirname, 'templates', file),
       'utf8',
@@ -24,8 +27,8 @@ async function createAutoLabelingJson() {
     molecule.setFragment(true);
 
     const canonizer = new Canonizer(molecule, { encodeAtomCustomLabels: true });
-
     const idCode = canonizer.getIDCode();
+
     const coordinates = canonizer.getEncodedCoordinates(false);
 
     moleculeDatabase.push({

package-lock.json

@@ -39,23 +39,23 @@
     "ml-floyd-warshall": "^3.0.1",
     "ml-matrix": "^6.12.1",
     "papaparse": "^5.5.3",
-    "sdf-parser": "^7.0.4"
+    "sdf-parser": "^8.0.0"
   },
   "peerDependencies": {
     "openchemlib": ">=9.12.0"
   },
   "devDependencies": {
-    "@types/node": "^25.2.3",
+    "@types/node": "^25.4.0",
     "@vitest/coverage-istanbul": "^4.0.18",
-    "@zakodium/tsconfig": "^1.0.2",
+    "@zakodium/tsconfig": "^1.0.3",
     "cheminfo-build": "^1.3.2",
     "cheminfo-types": "^1.10.0",
     "eslint": "^9.39.2",
     "eslint-config-cheminfo-typescript": "^21.1.0",
     "fifo-logger": "^2.0.1",
-    "globals": "^17.3.0",
-    "mf-parser": "^3.6.0",
-    "openchemlib": "^9.12.0",
+    "globals": "^17.4.0",
+    "mf-parser": "^3.7.1",
+    "openchemlib": "^9.20.0",
     "prettier": "^3.8.1",
     "rimraf": "^6.1.3",
     "typescript": "^5.9.3",