@datagrok/helm 2.6.0 → 2.7.1

package/files/samples/HELM_50.csv

@@ -0,0 +1,51 @@
+DBID,HELM,Activity,Cluster
+DBID55,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Aze.dV.E.N.dV.Phe_4Me}$$$$,2.1058521,1
+DBID83,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.meM.D-Chg.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,4.4416509,3
+DBID02,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.D-Cit.N.D-Orn.D-aThr.Phe_4Me}$$$$,5.0234375,1
+DBID05,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Dsu.N.D-Orn.D-aThr.Phe_4Me}$$$$,5.0660219,2
+DBID34,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Tyr_tBu.N.D-Orn.D-aThr.Phe_4Me}$$$$,5.6578050,4
+DBID02,PEPTIDE1{aHyp.Hcy.N.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cys_SEt.N.D-Orn.D-aThr.Phe_4Me}$$$$,7.9036875,3
+DBID64,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.A.D-aThr.Phe_4Me}$$$$,3.8863654,2
+DBID75,PEPTIDE1{meI.hHis.Aca.N.T.Tyr_Me.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.dV.Phe_4Me}$$$$,4.6697459,2
+DBID74,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.A.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,2.7280300,4
+DBID60,"PEPTIDE1{meI.Pip.dK.Thr_PO3H2.[L-hArg(Et,Et)].D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$",4.4462886,2
+DBID96,PEPTIDE1{meI.hHis.D-Hyp.N.T.dK.Thr_PO3H2.Trp_Ome.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,4.3900189,4
+DBID56,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.Phe_3Cl.meK.Phe_4Me}$$$$,3.6875632,4
+DBID65,PEPTIDE1{Gly_allyl.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Thr_PO3H2.N.D-Orn.D-aThr.Phe_4Me}$$$$,6.1076937,1
+DBID45,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.Nle.D-aThr.Phe_4Me}$$$$,3.2512414,0
+DBID13,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.dF.Phe_4Me}$$$$,7.2294617,0
+DBID94,PEPTIDE1{meI.hHis.Aca.N.T.D-Orn.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.pnG.Phe_4Me}$$$$,0.6217819,3
+DBID79,PEPTIDE1{meI.Pip.dK.Thr_PO3H2.D-Thz.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.D-Thz.N.D-Orn.D-aThr.Phe_4Me}$$$$,4.4476070,1
+DBID21,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.Nle.aIle.Phe_4Me}$$$$,4.9557114,1
+DBID10,PEPTIDE1{meY.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.pnG.Phe_4Me}$$$$,1.3188239,1
+DBID86,PEPTIDE1{meI.Aca.N.T.W.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$,7.6897125,2
+DBID52,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.hHis.D-aThr.Phe_4Me}$$$$,4.0970631,2
+DBID27,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.3Pal.D-aThr.Phe_4Me}$$$$,2.7782860,3
+DBID98,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.Thr_PO3H2.D-aThr.Phe_4Me}$$$$,4.9825664,2
+DBID94,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.D-Nle.Phe_4Me}$$$$,4.0829563,2
+DBID86,PEPTIDE1{D-Nva.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Me}$$$$,2.7203233,3
+DBID48,PEPTIDE1{meI.Thr_PO3H2.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Cys_SEt.N.Phe_3Cl.aIle.Phe_4Me}$$$$,0.7954721,1
+DBID22,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.seC.Tyr_ab-dehydroMe.meN.E.N.dV.Phe_4Me}$$$$,5.0775967,1
+DBID54,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.meN.E.N.3Pal.D-aThr.Phe_4Me}$$$$,4.1724143,3
+DBID17,PEPTIDE1{D-Tic.Hcy.N.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cys_SEt.N.dV.Phe_4Me}$$$$,3.1429222,3
+DBID76,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.meN.E.N.dV.meF}$$$$,3.1327622,0
+DBID20,PEPTIDE1{meI.Aca.N.T.Ser_PO3H2.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Me}$$$$,3.8640671,1
+DBID01,PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.H.P.Phe_4Me}$$$$,4.1827374,3
+DBID93,PEPTIDE1{Phe_4Sdihydroorotamido.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Me}$$$$,2.6165285,1
+DBID89,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.D-Thz.Phe_4Me}$$$$,3.2189791,0
+DBID30,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Met_O2.dV.E.N.H.D-aThr.Phe_4Me}$$$$,1.0362210,3
+DBID07,PEPTIDE1{meI.Aca.N.T.D-1Nal.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.H.D-aThr.Phe_4Me}$$$$,3.8830254,4
+DBID51,PEPTIDE1{meI.Aca.N.T.meV.Thr_PO3H2.Aca.D-Tyr_Et.Met_O2.D-Dap.Thr_PO3H2.N.H.D-aThr.Phe_4Me}$$$$,5.1701312,2
+DBID95,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.pnG.Phe_4Br.Phe_4Me}$$$$,3.1820068,1
+DBID47,PEPTIDE1{meI.Aca.N.T.dK.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.dV.Phe_4Me}$$$$,4.4652672,1
+DBID16,PEPTIDE1{meI.Aca.Q.T.W.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.dV.Phe_4Me}$$$$,2.8669512,4
+DBID52,PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.aMePhe.Phe_4Me}$$$$,3.2571971,1
+DBID41,PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.V.Phe_4Me}$$$$,4.4447875,0
+DBID78,PEPTIDE1{meI.Aca.Aca.T.dK.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.D-Dap.Thr_PO3H2.N.Thr_PO3H2.Phe_4Me}$$$$,2.4899697,4
+DBID95,PEPTIDE1{meI.hHis.Aca.Q.T.W.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cya.N.F.Phe_4Me}$$$$,0.3957288,4
+DBID92,PEPTIDE1{meI.hHis.Aca.Q.T.W.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.F.aIle.Phe_4Me}$$$$,2.9058776,3
+DBID88,PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.dV.Phe_4Me}$$$$,2.1254258,0
+DBID10,PEPTIDE1{meI.Bux.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.Cys_SEt.N.Bmt.Phe_4Me}$$$$,1.7159123,0
+DBID86,PEPTIDE1{D-Tyr_Et.hHis.Aca.Q.T.W.Q.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.dV.Phe_4Me}$$$$,1.5285099,0
+DBID43,PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.dP.Tyr_ab-dehydroMe.dV.E.N.Bmt.Phe_4Me}$$$$,3.9470999,3
+DBID26,PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.pnG.N.Bmt.Phe_4Me}$$$$,3.7495575,4

package/files/tests/filter_HELM.csv

@@ -0,0 +1,5 @@
+HELM string
+"PEPTIDE1{D.E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0"
+"PEPTIDE1{L.M.P.Q.R.S.T}$PEPTIDE1,PEPTIDE1,7:R2-1:R1$$$"
+"PEPTIDE1{N.P.F.V.L.P.[dV]}$PEPTIDE1,PEPTIDE1,7:R2-1:R1$$$"
+"PEPTIDE1{A.R.C.A.A.K.T.C.D.A}$PEPTIDE1,PEPTIDE1,8:R3-3:R3$$$"

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.6.0",
+  "version": "2.7.1",
   "author": {
-    "name": "Aleksandr Tanas",
-    "email": "atanas@datagrok.ai"
+    "name": "Maria Dolotova",
+    "email": "mdolotova@datagrok.ai"
   },
   "description": "Provides support for HELM notation (importing, detecting, rendering, conversion).",
   "sources-backup": [
@@ -18,9 +18,9 @@
   "dependencies": {
     "@datagrok-libraries/bio": "^5.45.11",
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/utils": "^4.3.7",
     "cash-dom": "^8.1.1",
-    "datagrok-api": "^1.21.1",
+    "@datagrok-libraries/utils": "^4.4.0",
+    "datagrok-api": "^1.23.0",
     "dayjs": "^1.10.6",
     "lru-cache": "^10.4.3",
     "rxjs": "^6.5.5",
@@ -29,8 +29,8 @@
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.13",
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
-    "@datagrok/bio": "^2.16.8",
-    "@datagrok/chem": "^1.12.3",
+    "@datagrok/bio": "^2.18.1",
+    "@datagrok/chem": "^1.13.0",
     "@types/node": "17.0.45",
     "@types/webpack-env": "^1.18.5",
     "@types/wu": "^2.1.44",
@@ -50,6 +50,7 @@
   },
   "scripts": {
     "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",
+    "link-bio": "npm link @datagrok-libraries/bio",
     "debug-helm": "webpack && grok publish",
     "release-helm": "webpack && grok publish --release",
     "build-helm": "webpack",

package/src/package-test.ts

@@ -19,6 +19,9 @@ import './tests/parse-helm-tests';
 import './tests/helm-web-editor-tests';
 import './tests/helm-input-tests';
 import './tests/helm-helper-tests';
+import './tests/helm-substructure-filter';
+import './tests/helm-activity-cliffs';
+import './tests/to-atomic-level-ui-non-linear';
 
 export const _package = new DG.Package();
 export {tests};

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

@@ -0,0 +1,77 @@
+import * as grok from 'datagrok-api/grok';
+import * as DG from 'datagrok-api/dg';
+
+import {after, before, category, test} from '@datagrok-libraries/utils/src/test';
+
+import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {
+  getUserLibSettings, setUserLibSettings
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
+import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {expect} from '@datagrok-libraries/utils/src/test';
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
+import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
+
+import {_package} from '../package-test';
+
+
+category('activityCliffs', async () => {
+  let helmHelper: IHelmHelper;
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+  const helmEncodingFunc = DG.Func.find({name: 'helmPreprocessingFunction', package: 'Bio'})[0];
+  before(async () => {
+    helmHelper = await getHelmHelper(); // init Helm package
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    // Test 'helm' requires default monomer library loaded
+    await monomerLibHelper.loadMonomerLibForTests();
+  });
+
+  after(async () => {
+    // UserDataStorage.put() replaces existing data
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
+  });
+
+
+  test('Helm', async () => {
+    const df = await _package.files.readCsv('samples/HELM_50.csv');
+    const _view = grok.shell.addTableView(df);
+
+    await _testActivityCliffsOpen(df, DimReductionMethods.UMAP,
+      'HELM', 'Activity', 65, 20, BitArrayMetricsNames.Tanimoto, helmEncodingFunc);
+  });
+});
+
+
+async function _testActivityCliffsOpen(df: DG.DataFrame, drMethod: DimReductionMethods,
+  seqColName: string, activityColName: string, similarityThr: number, tgtNumberCliffs: number,
+  similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics, preprocessingFunction: DG.Func,
+): Promise<void> {
+  await grok.data.detectSemanticTypes(df);
+  const scatterPlot = (await grok.functions.call('Bio:activityCliffs', {
+    table: df,
+    molecules: df.getCol(seqColName),
+    activities: df.getCol(activityColName),
+    similarity: similarityThr,
+    methodName: drMethod,
+    similarityMetric: similarityMetric,
+    preprocessingFunction: preprocessingFunction,
+    options: {[`${BYPASS_LARGE_DATA_WARNING}`]: true},
+    demo: false,
+  })) as DG.Viewer | undefined;
+  expect(scatterPlot != null, true);
+
+  const cliffsLink = Array.from(scatterPlot!.root.children).find((el) => {
+    const classList: string[] = el.className.split(' ');
+    return ['ui-btn', 'ui-btn-ok'].every((reqClassName) => classList.includes(reqClassName));
+  });
+  expect((cliffsLink as HTMLElement).innerText.toLowerCase(), `${tgtNumberCliffs} cliffs`);
+}

package/src/tests/helm-substructure-filter.ts

@@ -0,0 +1,163 @@
+/* eslint-disable max-lines */
+/* eslint-disable max-lines-per-function */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {after, before, category, test, expect, delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {
+  getUserLibSettings, setUserLibSettings
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {getSeqHelper, ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+
+import {awaitGrid, readDataframe} from './utils';
+
+import {BioFilterProps, IBioFilter}
+  from '@datagrok-libraries/bio/src/substructure-filter/bio-substructure-filter-types';
+
+import {_package} from '../package-test';
+
+category('bio-substructure-filters', async () => {
+  let seqHelper: ISeqHelper;
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+
+  before(async () => {
+    seqHelper = await getSeqHelper();
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    // Test 'helm' requires default monomer library loaded
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
+  });
+
+  after(async () => {
+    // UserDataStorage.put() replaces existing data
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
+  });
+
+
+  test('helm-dialog', async () => {
+    const logPrefix = 'Bio tests: substructureFilters/helm-dialog';
+    const df = await readDataframe('tests/filter_HELM.csv');
+    const view = grok.shell.addTableView(df);
+    await grok.data.detectSemanticTypes(df);
+    await df.meta.detectSemanticTypes();
+
+    _package.logger.debug(`${logPrefix}, filter attaching.`);
+    const filter = await grok.functions.call('Bio:bioSubstructureFilterTest');
+    filter.attach(df);
+    const dlg = ui.dialog('Test filters').add(filter.root).show(); // to waitForElementInDom
+    await filter.awaitRendered();
+    try {
+      const bf = filter.bioFilter as IBioFilter;
+      expect(filter.bioFilter !== null, true, 'bioFilter is not created');
+
+      // filter 1
+      _package.logger.debug(`${logPrefix}, filter 1 change awaiting...`);
+      await testEvent(df.onRowsFiltered, () => {}, () => {
+        bf.props = new BioFilterProps('PEPTIDE1{A.C}$$$$V2.0', undefined, _package.logger);
+      }, 20000);
+      _package.logger.debug(`${logPrefix}, filter 1 changed.`);
+      expect(filter.dataFrame!.filter.trueCount, 1);
+      expect(filter.dataFrame!.filter.toBinaryString(), '0001');
+
+      // filter 2
+      _package.logger.debug(`${logPrefix}, filter 2 change awaiting...`);
+      await testEvent(df.onRowsFiltered, () => {}, () => {
+        bf.props = new BioFilterProps('PEPTIDE1{C}$$$$V2.0', undefined, _package.logger);
+      }, 20000);
+      setTimeout(() => view.grid.invalidate(), 500);
+      await awaitGrid(view.grid);
+      await delay(1000);
+      _package.logger.debug(`${logPrefix}, filter 2 changed.`);
+      expect(filter.dataFrame!.filter.trueCount, 2);
+      expect(filter.dataFrame!.filter.toBinaryString(), '1001');
+    } finally {
+      dlg.close();
+    }
+    await filter.awaitRendered();
+    await delay(3000); //TODO: await for grid.onLookChanged
+  }, {});
+
+
+  // Generates unhandled exception accessing isFiltering before bioFilter created
+  test('helm-view', async () => {
+    const logPrefix = 'Bio tests: substructureFilters/helm-view';
+    const df = await readDataframe('tests/filter_HELM.csv');
+    const col = df.getCol('HELM string');
+    await grok.data.detectSemanticTypes(df);
+    const view = grok.shell.addTableView(df);
+
+    const fg = view.getFiltersGroup();
+
+    // await awaitCheck(() => fg.filters.length == 1, 'await filters.length == 1', 1000);
+    // const filter = fg.filters.filter((f) => f.columnName == col.name)[0] as BioSubstructureFilter;
+    await awaitGrid(view.grid);
+  });
+
+
+  test('sync-helm', async () => {
+    const df = await _package.files.readCsv('tests/filter_HELM.csv');
+    await grok.data.detectSemanticTypes(df);
+    const view = grok.shell.addTableView(df);
+
+    const fSubStr: string = 'PEPTIDE1{A.C}$$$$V2.0';
+    const fTrueCount: number = 1;
+
+    const f1 = await createFilter('HELM string', df);
+    const f2 = await createFilter('HELM string', df);
+    const dlg = ui.dialog('Test filters').add(f1.root).add(f2.root).show(); // to waitForElementInDom
+    await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
+    try {
+      expect(!!f1.bioFilter, true);
+      expect(!!f2.bioFilter, true);
+      expect(f1.bioFilter!.type, 'HelmBioFilter');
+      expect(f2.bioFilter!.type, 'HelmBioFilter');
+      const bf1 = f1.bioFilter as IBioFilter;
+      const bf2 = f2.bioFilter as IBioFilter;
+
+      await testEvent(df.onRowsFiltered, () => {}, () => {
+        bf1.props = new BioFilterProps(fSubStr, undefined, _package.logger);
+      }, 60000, 'await onRowsFiltered'); // wait to load monomers
+      await awaitGrid(view.grid);
+      //debugger;
+
+      _package.logger.debug('Bio tests: substructureFilters/sync-helm, before changed event');
+      await delay(f1.debounceTime * 2);
+      _package.logger.debug('Bio tests: substructureFilters/sync-helm, after changed event');
+      expect(df.filter.trueCount, fTrueCount);
+
+      await f1.awaitRendered();
+      expect((bf2.props as BioFilterProps).substructure, fSubStr);
+    } finally {
+      f1.detach();
+      f2.detach();
+      dlg.close();
+    }
+    await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
+    await awaitGrid(view.grid);
+    await delay(3000); //TODO: await for grid.onLookChanged
+  });
+
+
+  async function createFilter(colName: string, df: DG.DataFrame): Promise<any> {
+    if (!df.columns.names().includes(colName)) {
+      throw new Error(`The column '${colName}' not found. ` +
+        `Available in data frame are ${JSON.stringify(df.columns.names())}`);
+    }
+
+    const filter = await grok.functions.call('Bio:bioSubstructureFilterTest');
+    filter.attach(df);
+    filter.applyState({columnName: colName});
+    filter.column = df.col(colName);
+    filter.columnName = colName;
+    //filter.tableName = df.name;
+    return filter;
+  };
+} );
+

package/src/tests/renderers-tests.ts

@@ -55,6 +55,8 @@ category('renderers', () => {
       return $(tv.root).find('.d4-grid canvas').length > 0;
     }, 'Table view canvas not found', 100);
 
+    await grok.data.detectSemanticTypes(df);
+
     expect(helmCol.semType, DG.SEMTYPE.MACROMOLECULE);
     expect(helmCol.meta.units, NOTATION.HELM);
     expect(helmCol.getTag(DG.TAGS.CELL_RENDERER), 'helm');
@@ -78,6 +80,7 @@ RNA1{d(A)p.d(C)p.d(G)p.d(U)p}|PEPTIDE1{I.H.A.N.T.Thr_PO3H2}$$$$,0,1
     const df = DG.DataFrame.fromCsv(helmCoordsCsv);
     df.currentRowIdx = 0;
     const view = grok.shell.addTableView(df);
+    await grok.data.detectSemanticTypes(df);
     const sp: DG.ScatterPlotViewer = df.plot.scatter({x: 'x', y: 'y'});
     view.dockManager.dock(sp, DG.DOCK_TYPE.RIGHT, null);
     await Promise.all([

package/src/tests/to-atomic-level-ui-non-linear.ts

@@ -0,0 +1,96 @@
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
+import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
+import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+
+type TestDataTargetType = { atomCount: number, bondCount: number };
+type TestDataType = {
+  src: { seq: string, units: NOTATION },
+  tgt: TestDataTargetType,
+};
+
+category('toAtomicLevel-ui', () => {
+  let monomerLibHelper: IMonomerLibHelper;
+  let userLibSettings: UserLibSettings;
+  let monomerLib: IMonomerLib;
+  let rdKitModule: RDModule;
+
+  before(async () => {
+    rdKitModule = await getRdKitModule();
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    // Test 'helm' requires default monomer library loaded
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
+
+    monomerLib = monomerLibHelper.getMonomerLib();
+  });
+
+  after(async () => {
+    // UserDataStorage.put() replaces existing data
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
+  });
+
+  const tests: { [testName: string]: TestDataType } = {
+    'fasta': {
+      src: {seq: 'MDYKETLLMPK', units: NOTATION.FASTA},
+      tgt: {atomCount: 94, bondCount: 95},
+    },
+    'fasta-with-gap': {
+      src: {seq: 'MD-YKETLLMPK', units: NOTATION.FASTA},
+      tgt: {atomCount: 94, bondCount: 95},
+    },
+    'helm': {
+      src: {seq: 'PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2}$$$$', units: NOTATION.HELM},
+      tgt: {atomCount: 68, bondCount: 68},
+    },
+    'helm-with-gap': {
+      src: {seq: 'PEPTIDE1{meI.hHis.*.Aca.N.T.dK.Thr_PO3H2}$$$$', units: NOTATION.HELM},
+      tgt: {atomCount: 68, bondCount: 68},
+    },
+  };
+
+  const getDfAndSeqCol = async (testData: TestDataType): Promise<{df: DG.DataFrame, seqCol: DG.Column<string>}> => {
+    const seq = testData.src.seq;
+    const df = DG.DataFrame.fromColumns([DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [seq])]);
+    await grok.data.detectSemanticTypes(df);
+    return {df: df, seqCol: df.getCol('seq')};
+  };
+
+  for (const [testName, testData] of Object.entries(tests)) {
+    test(`${testName}-nonlinear`, async () => {
+      const res = await getDfAndSeqCol(testData);
+      await _testToAtomicLevelFunc(res.df, res.seqCol, true, testData.tgt);
+    });
+  }
+
+  async function _testToAtomicLevelFunc(
+    df: DG.DataFrame, seqCol: DG.Column<string>, nonlinear: boolean, tgt: TestDataTargetType,
+  ): Promise<void> {
+    await grok.functions.call('Bio:toAtomicLevel', {
+      table: df, seqCol: seqCol, nonlinear: true, highlight: false
+    });
+    const molCol = df.col('molfile(seq)');
+    expect(molCol?.semType, DG.SEMTYPE.MOLECULE);
+    const resMolStr = molCol?.get(0)!;
+    const resRdMol = rdKitModule.get_mol(resMolStr);
+    expect(resRdMol != null, true, 'No molecule generated');
+    try {
+      const resAtomCount = resRdMol.get_num_atoms();
+      const resBondCount = resRdMol.get_num_bonds();
+      expect(resAtomCount, tgt.atomCount);
+      expect(resBondCount, tgt.bondCount);
+    } finally {
+      resRdMol.delete();
+    }
+  }
+});

package/src/tests/utils.ts

@@ -4,6 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {_package} from '../package-test';
 
 
 export async function initHelmMainPackage(): Promise<void> {
@@ -15,3 +16,14 @@ export async function awaitGrid(grid: DG.Grid, timeout: number = 5000): Promise<
   await testEvent(grid.onAfterDrawContent, () => {},
     () => { grid.invalidate(); }, timeout);
 }
+
+export async function readDataframe(tableName: string): Promise<DG.DataFrame> {
+  const file = await loadFileAsText(tableName);
+  const df = DG.DataFrame.fromCsv(file);
+  df.name = tableName.replace('.csv', '');
+  return df;
+}
+
+export async function loadFileAsText(name: string): Promise<string> {
+  return await _package.files.readAsText(name);
+}

package/src/global.d.ts

@@ -1,13 +0,0 @@
-import * as grokNamespace from 'datagrok-api/grok';
-import * as uiNamespace from 'datagrok-api/ui';
-import * as DGNamespace from 'datagrok-api/dg';
-import * as rxjsNamespace from 'rxjs';
-import $Namespace from 'cash-dom';
-
-declare global {
-    const grok: typeof grokNamespace;
-    const ui: typeof uiNamespace;
-    const DG: typeof DGNamespace;
-    const rjxs: typeof rxjsNamespace;
-    const $: typeof $Namespace;
-}