@datagrok/bio 2.11.7 → 2.11.8

package/files/data/sample_HELM_50.csv

@@ -0,0 +1,51 @@
+HELM,Activity
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Aze.dV.E.N.dV.Phe_4Me}$$$$,2.1058521
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.meM.D-Chg.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,4.4416509
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.D-Cit.N.D-Orn.D-aThr.Phe_4Me}$$$$,5.0234375
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Dsu.N.D-Orn.D-aThr.Phe_4Me}$$$$,5.0660219
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Tyr_tBu.N.D-Orn.D-aThr.Phe_4Me}$$$$,5.6578050
+PEPTIDE1{aHyp.Hcy.N.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cys_SEt.N.D-Orn.D-aThr.Phe_4Me}$$$$,7.9036875
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.A.D-aThr.Phe_4Me}$$$$,3.8863654
+PEPTIDE1{meI.hHis.Aca.N.T.Tyr_Me.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.dV.Phe_4Me}$$$$,4.6697459
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.A.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,2.7280300
+"PEPTIDE1{meI.Pip.dK.Thr_PO3H2.[L-hArg(Et,Et)].D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$",4.4462886
+PEPTIDE1{meI.hHis.D-Hyp.N.T.dK.Thr_PO3H2.Trp_Ome.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,4.3900189
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.Phe_3Cl.meK.Phe_4Me}$$$$,3.6875632
+PEPTIDE1{Gly_allyl.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Thr_PO3H2.N.D-Orn.D-aThr.Phe_4Me}$$$$,6.1076937
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.Nle.D-aThr.Phe_4Me}$$$$,3.2512414
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.dF.Phe_4Me}$$$$,7.2294617
+PEPTIDE1{meI.hHis.Aca.N.T.D-Orn.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.pnG.Phe_4Me}$$$$,0.6217819
+PEPTIDE1{meI.Pip.dK.Thr_PO3H2.D-Thz.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.D-Thz.N.D-Orn.D-aThr.Phe_4Me}$$$$,4.4476070
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.Nle.aIle.Phe_4Me}$$$$,4.9557114
+PEPTIDE1{meY.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.pnG.Phe_4Me}$$$$,1.3188239
+PEPTIDE1{meI.Aca.N.T.W.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,7.6897125
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.hHis.D-aThr.Phe_4Me}$$$$,4.0970631
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.3Pal.D-aThr.Phe_4Me}$$$$,2.7782860
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.Thr_PO3H2.D-aThr.Phe_4Me}$$$$,4.9825664
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.D-Nle.Phe_4Me}$$$$,4.0829563
+PEPTIDE1{D-Nva.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Me}$$$$,2.7203233
+PEPTIDE1{meI.Thr_PO3H2.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Cys_SEt.N.Phe_3Cl.aIle.Phe_4Me}$$$$,0.7954721
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.seC.Tyr_ab-dehydroMe.meN.E.N.dV.Phe_4Me}$$$$,5.0775967
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.meN.E.N.3Pal.D-aThr.Phe_4Me}$$$$,4.1724143
+PEPTIDE1{D-Tic.Hcy.N.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cys_SEt.N.dV.Phe_4Me}$$$$,3.1429222
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.meN.E.N.dV.meF}$$$$,3.1327622
+PEPTIDE1{meI.Aca.N.T.Ser_PO3H2.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Me}$$$$,3.8640671
+PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.H.P.Phe_4Me}$$$$,4.1827374
+PEPTIDE1{Phe_4Sdihydroorotamido.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Me}$$$$,2.6165285
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.D-Thz.Phe_4Me}$$$$,3.2189791
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Met_O2.dV.E.N.H.D-aThr.Phe_4Me}$$$$,1.0362210
+PEPTIDE1{meI.Aca.N.T.D-1Nal.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.H.D-aThr.Phe_4Me}$$$$,3.8830254
+PEPTIDE1{meI.Aca.N.T.meV.Thr_PO3H2.Aca.D-Tyr_Et.Met_O2.D-Dap.Thr_PO3H2.N.H.D-aThr.Phe_4Me}$$$$,5.1701312
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Br.Phe_4Me}$$$$,3.1820068
+PEPTIDE1{meI.Aca.N.T.dK.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.dV.Phe_4Me}$$$$,4.4652672
+PEPTIDE1{meI.Aca.Q.T.W.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.dV.Phe_4Me}$$$$,2.8669512
+PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.aMePhe.Phe_4Me}$$$$,3.2571971
+PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.V.Phe_4Me}$$$$,4.4447875
+PEPTIDE1{meI.Aca.Aca.T.dK.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.Thr_PO3H2.Phe_4Me}$$$$,2.4899697
+PEPTIDE1{meI.hHis.Aca.Q.T.W.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cya.N.F.Phe_4Me}$$$$,0.3957288
+PEPTIDE1{meI.hHis.Aca.Q.T.W.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.F.aIle.Phe_4Me}$$$$,2.9058776
+PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.dV.Phe_4Me}$$$$,2.1254258
+PEPTIDE1{meI.Bux.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cys_SEt.N.Bmt.Phe_4Me}$$$$,1.7159123
+PEPTIDE1{D-Tyr_Et.hHis.Aca.Q.T.W.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.dV.Phe_4Me}$$$$,1.5285099
+PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.dP.Tyr_ab-dehydroMe.dV.E.N.Bmt.Phe_4Me}$$$$,3.9470999
+PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.Bmt.Phe_4Me}$$$$,3.7495575

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.7",
+  "version": "2.11.8",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -34,9 +34,9 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.2",
+    "@datagrok-libraries/bio": "^5.39.5",
     "@datagrok-libraries/chem-meta": "^1.0.1",
-    "@datagrok-libraries/ml": "^6.3.53",
+    "@datagrok-libraries/ml": "^6.3.55",
     "@datagrok-libraries/tutorials": "^1.3.6",
     "@datagrok-libraries/utils": "^4.0.17",
     "cash-dom": "^8.0.0",

package/src/analysis/sequence-space.ts

@@ -99,16 +99,23 @@ export async function getEncodedSeqSpaceCol(
     // sets distance function args in place.
     options = {scoringMatrix: monomerRes.scoringMatrix,
       alphabetIndexes: monomerHashToMatrixMap} satisfies mmDistanceFunctionArgs;
+  } else if (similarityMetric === MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH) {
+    const monomers = Array.from(charCodeMap.keys());
+    const monomerRes = await calculateMonomerSimilarity(monomers);
+    // the susbstitution matrix contains similarity, but we need distances
+    // monomerRes.scoringMatrix.forEach((row, i) => {
+    //   row.forEach((val, j) => {
+    //     monomerRes.scoringMatrix[i][j] = 1 - val;
+    //   });
+    // });
+    const monomerHashToMatrixMap: {[_: string]: number} = {};
+    Object.entries(monomerRes.alphabetIndexes).forEach(([key, value]) => {
+      monomerHashToMatrixMap[charCodeMap.get(key)!] = value;
+    });
+    // sets distance function args in place.
+    options = {scoringMatrix: monomerRes.scoringMatrix,
+      alphabetIndexes: monomerHashToMatrixMap} satisfies mmDistanceFunctionArgs;
   }
-  // else if (similarityMetric === MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH) {
-  //   const alphabetIndexes: any = {};
-  //   let i = 0;
-  //   charCodeMap.forEach((value) => {
-  //     alphabetIndexes[value] = i;
-  //     i++;
-  //   });
-  //   options = {alphabetIndexes};
-  // }
   return {seqList, options};
 }
 

package/src/package.ts

@@ -569,11 +569,15 @@ export async function sequenceSpaceTopMenu(
           pg.close();
         }
       });
-      const sequenceSpaceResPromise = new Promise<ISequenceSpaceResult | undefined>(async (resolve) => {
-        resolveF = resolve;
-        const res = await getSequenceSpace(chemSpaceParams,
-          options?.[BYPASS_LARGE_DATA_WARNING] ? undefined : progressFunc);
-        resolve(res);
+      const sequenceSpaceResPromise = new Promise<ISequenceSpaceResult | undefined>(async (resolve, reject) => {
+        try {
+          resolveF = resolve;
+          const res = await getSequenceSpace(chemSpaceParams,
+            options?.[BYPASS_LARGE_DATA_WARNING] ? undefined : progressFunc);
+          resolve(res);
+        } catch (e) {
+          reject(e);
+        }
       });
       const sequenceSpaceRes = await sequenceSpaceResPromise;
       pg.close();
@@ -585,7 +589,13 @@ export async function sequenceSpaceTopMenu(
       ui.dialog().add(ui.divText(`Sequence space analysis might take several minutes.
     Do you want to continue?`))
         .onOK(async () => {
-          await getSeqSpace();
+          await getSeqSpace().catch((err: any) => {
+            pg.close();
+            const [errMsg, errStack] = errInfo(err);
+            _package.logger.error(errMsg, undefined, errStack);
+            if (scatterPlot)
+              scatterPlot.close();
+          });
         })
         .onCancel(() => { pg.close(); })
         .show();
@@ -619,9 +629,11 @@ export async function sequenceSpaceTopMenu(
   } catch (e) {
     console.error(e);
     pg.close();
+    const [errMsg, errStack] = errInfo(e);
+    _package.logger.error(errMsg, undefined, errStack);
+    if (scatterPlot)
+      (scatterPlot as unknown as DG.Viewer).close();
   }
-
-
   /*   const encodedCol = encodeMonomers(macroMolecule);
   if (!encodedCol)
     return;
@@ -720,7 +732,7 @@ export async function compositionAnalysis(): Promise<void> {
       'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
     ui.dialog({
       title: 'Composition Analysis',
-      helpUrl: '/help/domains/bio/macromolecules.md#composition-analysis',
+      helpUrl: 'https://datagrok.ai/help/datagrok/solutions/domains/bio/#sequence-composition',
     })
       .add(ui.div([
         colInput,

package/src/tests/activity-cliffs-tests.ts

@@ -7,21 +7,30 @@ import {readDataframe} from './utils';
 import {_testActivityCliffsOpen} from './activity-cliffs-utils';
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 
-import {_package} from '../package-test';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {LIB_DEFAULT, LIB_STORAGE_NAME} from '../utils/monomer-lib';
 
+import {_package} from '../package-test';
 
 category('activityCliffs', async () => {
-  let actCliffsTableView: DG.TableView;
-  let actCliffsDf: DG.DataFrame;
-  let actCliffsTableViewWithEmptyRows: DG.TableView;
-  let actCliffsDfWithEmptyRows: DG.DataFrame;
-
   let viewList: DG.ViewBase[] = [];
   let dfList: DG.DataFrame[] = [];
 
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibrariesSettings: {};
+
+
   before(async () => {
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibrariesSettings = await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true);
+
+    // Test 'helm' requires default monomer library loaded
+    await grok.dapi.userDataStorage.post(LIB_STORAGE_NAME, LIB_DEFAULT, true);
+    await monomerLibHelper.loadLibraries(true); // load default libraries
+
     viewList = [];
     dfList = [];
   });
@@ -29,14 +38,18 @@ category('activityCliffs', async () => {
   after(async () => {
     // for (const df of dfList) grok.shell.closeTable(df);
     // for (const view of viewList) view.close();
+
+    // UserDataStorage.put() replaces existing data
+    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, userLibrariesSettings, true);
+    await monomerLibHelper.loadLibraries(true); // load user settings libraries
   });
 
   test('activityCliffsOpens', async () => {
-    actCliffsDf = await readDataframe(
+    const actCliffsDf = await readDataframe(
       DG.Test.isInBenchmark ? 'test/peptides_motif-with-random_10000.csv' : 'tests/100_3_clustests.csv',
     );
     dfList.push(actCliffsDf);
-    actCliffsTableView = grok.shell.addTableView(actCliffsDf);
+    const actCliffsTableView = grok.shell.addTableView(actCliffsDf);
     viewList.push(actCliffsTableView);
     const cliffsNum = DG.Test.isInBenchmark ? 6 : 3;
 
@@ -45,9 +58,9 @@ category('activityCliffs', async () => {
   });
 
   test('activityCliffsWithEmptyRows', async () => {
-    actCliffsDfWithEmptyRows = await readDataframe('tests/100_3_clustests_empty_vals.csv');
+    const actCliffsDfWithEmptyRows = await readDataframe('tests/100_3_clustests_empty_vals.csv');
     dfList.push(actCliffsDfWithEmptyRows);
-    actCliffsTableViewWithEmptyRows = grok.shell.addTableView(actCliffsDfWithEmptyRows);
+    const actCliffsTableViewWithEmptyRows = grok.shell.addTableView(actCliffsDfWithEmptyRows);
     viewList.push(actCliffsTableViewWithEmptyRows);
 
     await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, DimReductionMethods.UMAP,
@@ -55,10 +68,10 @@ category('activityCliffs', async () => {
   });
 
   test('Helm', async () => {
-    const df = await _package.files.readCsv('samples/sample_HELM.csv');
+    const df = await _package.files.readCsv('data/sample_HELM_50.csv');
     const view = grok.shell.addTableView(df);
 
     await _testActivityCliffsOpen(df, DimReductionMethods.UMAP,
-      'HELM', 'Activity', 90, 53, BitArrayMetricsNames.Tanimoto);
+      'HELM', 'Activity', 65, 4, BitArrayMetricsNames.Tanimoto);
   });
 });

package/src/tests/to-atomic-level-tests.ts

@@ -5,11 +5,11 @@ import * as DG from 'datagrok-api/dg';
 
 import {before, after, category, test, expectArray} from '@datagrok-libraries/utils/src/test';
 
-import {getMonomerLibHelper, toAtomicLevel} from '../package';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {toAtomicLevel} from '../package';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
-import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {LIB_STORAGE_NAME} from '../utils/monomer-lib';
+import {LIB_STORAGE_NAME, LIB_DEFAULT, getUserLibSettings} from '../utils/monomer-lib';
 
 const appPath = 'System:AppData/Bio';
 const fileSource = new DG.FileSource(appPath);
@@ -45,10 +45,10 @@ category('toAtomicLevel', async () => {
 
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
-    userLibrariesSettings = await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true);
-    // Clear settings to test default
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, {}, true);
-    await monomerLibHelper.loadLibraries(true);
+    userLibrariesSettings = {...await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true)};
+    const defaultLib = Object.values(LIB_DEFAULT)[0];
+    await monomerLibHelper.selectSpecifiedLibraries([defaultLib]);
+    monomerLibHelper.loadLibraries(true);
 
     for (const key in testNames) {
       sourceDf[key] = await fileSource.readCsv(inputPath[key]);

package/src/utils/monomer-lib.ts

@@ -307,6 +307,22 @@ export class MonomerLibHelper implements IMonomerLibHelper {
     return new MonomerLib(monomers);
   }
 
+  /** Reset user settings to the specified library. WARNING: clears user * settings */
+  public async selectSpecifiedLibraries(libFileNameList: string[]): Promise<void> {
+    const invalidNames = await this.getInvalidFileNames(libFileNameList);
+    if (invalidNames.length > 0)
+      throw new Error(`Cannot select libraries ${invalidNames}: no such library in the list`);
+    const settings = await getUserLibSettings();
+    settings.exclude = (await getLibFileNameList()).filter((fileName) => !libFileNameList.includes(fileName));
+    await setUserLibSetting(settings);
+  }
+
+  private async getInvalidFileNames(libFileNameList: string[]): Promise<string[]> {
+    const availableFileNames = await getLibFileNameList();
+    const invalidNames = libFileNameList.filter((fileName) => !availableFileNames.includes(fileName));
+    return invalidNames;
+  }
+
   // -- Instance singleton --
   private static _instance: MonomerLibHelper | null = null;