@datagrok/helm 2.3.4 → 2.4.1

package/src/package.ts

@@ -4,6 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
+import {Unsubscribable} from 'rxjs';
 
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
@@ -11,8 +12,8 @@ import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
-import {App, HelmMol, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
-import {IHelmHelper, IInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {App, Editor, HelmMol, HelmType, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmInputBase, IHelmHelper, IHelmInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
@@ -25,12 +26,9 @@ import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
 import {getRS} from './utils/get-monomer-dummy';
 
 // Do not import anything than types from @datagrok/helm-web-editor/src/types
-import {buildWebEditorApp} from './helm-web-editor';
-import {JSDraw2HelmModule, OrgHelmModule, ScilModule} from './types';
+import type {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
 
-export const _package = new HelmPackage(/*{debug: true}/**/);
-
-let monomerLib: IMonomerLib | null = null;
+export const _package = new HelmPackage({debug: true});
 
 /*
   Loading modules:
@@ -42,7 +40,7 @@ let monomerLib: IMonomerLib | null = null;
 
 declare const window: Window & HweWindow;
 declare const scil: ScilModule;
-declare const JSDraw2: JSDraw2HelmModule;
+declare const JSDraw2: JSDraw2Module;
 declare const org: OrgHelmModule;
 
 //tags: init
@@ -51,14 +49,13 @@ export async function initHelm(): Promise<void> {
   _package.logger.debug(`${logPrefix}, start`);
 
   try {
-    await Promise.all([
+    const [_, libHelper] = await Promise.all([
       _package.initHELMWebEditor(),
-      _package.initMonomerLibHelper(),
-    ]).then(() => {
-      _package.initMonomerLib();
-    });
+      getMonomerLibHelper(),
+    ]);
 
-    _package.logger.debug(`${logPrefix}, then(), lib loaded`);
+    _package.logger.debug(`${logPrefix}, lib loaded`);
+    _package.initMonomerLib(libHelper);
   } catch (err: any) {
     const [errMsg, errStack] = errInfo(err);
     // const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Exception \'undefined\'';
@@ -133,14 +130,7 @@ function openWebEditor(cell: DG.Cell, value?: string, units?: string) {
   const col = cell.column as DG.Column<string>;
   const sh = SeqHandler.forColumn(col);
   const rowIdx = cell.rowIndex;
-  let app: App;
-  setTimeout(async () => {
-    app = await buildWebEditorApp(view);
-    if (!!cell && units === undefined)
-      app.canvas!.helm!.setSequence(cell.value, 'HELM');
-    else
-      app.canvas!.helm!.setSequence(value!, 'HELM');
-  }, 20);
+  const app: App = _package.helmHelper.createWebEditorApp(view, !!cell && units === undefined ? cell.value : value!);
   const dlg = ui.dialog({showHeader: false, showFooter: true});
   dlg.add(view)
     .onOK(() => {
@@ -192,7 +182,7 @@ export function getMolfiles(col: DG.Column): DG.Column {
 //input: string name =undefined {optional: true}
 //input: object options =undefined {optional: true}
 //output: object result
-export function helmInput(name: string, options: IInputInitOptions<HelmMol>): DG.InputBase<HelmMol> {
+export function helmInput(name: string, options: IHelmInputInitOptions): HelmInputBase {
   // TODO: Annotate for semType = 'Macromolecule' AND units = 'helm'
   return _package.helmHelper.createHelmInput(name, options);
 }

package/src/tests/findMonomers-tests.ts

@@ -26,12 +26,12 @@ category('findMonomers', () => {
 
     // Tests 'findMonomers' requires default monomer library loaded
     await setUserLibSettingsForTests();
-    await monomerLibHelper.loadLibraries(true); // load default libraries for tests
+    await monomerLibHelper.loadMonomerLib(true); // load default libraries for tests
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   const tests: { [testName: string]: { test: string, tgt: Set<string> } } = {
@@ -53,7 +53,7 @@ category('findMonomers', () => {
   }
 
   function _testFindMonomers(testHelmValue: string, tgtMissedSet: Set<string>): void {
-    const monomerLib = monomerLibHelper.getBioLib();
+    const monomerLib = monomerLibHelper.getMonomerLib();
     const monomerSymbolList: string[] = parseHelm(testHelmValue);
     const resMissedSet: Set<string> = findMonomers(monomerSymbolList, monomerLib);
     expectObject(resMissedSet, tgtMissedSet);

package/src/tests/get-molfiles-tests.ts

@@ -25,12 +25,12 @@ category('getMolfiles', () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
     await setUserLibSettingsForTests();
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   const csv = `Helm, atoms, bonds

package/src/tests/get-monomer-tests.ts

@@ -20,13 +20,17 @@ import {
 import {defaultMonomerLibSummary, expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
 
 import {getMonomerHandleArgs, rewriteLibraries} from '../utils/get-monomer';
-import {JSDraw2HelmModule, OrgHelmModule} from '../types';
+import {JSDraw2Module, OrgHelmModule} from '../types';
+
+import {HelmHelper} from '../helm-helper';
+import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
+import {getRS} from '../utils/get-monomer-dummy';
 import {initHelmMainPackage} from './utils';
 
 import {_package} from '../package-test';
 
 declare const org: OrgHelmModule;
-declare const JSDraw2: JSDraw2HelmModule;
+declare const JSDraw2: JSDraw2Module;
 
 type TestDataType = { args: { a: any, name?: string }, tgt: any };
 
@@ -89,34 +93,33 @@ category('getMonomer', ()=>{
       'set user lib settings for tests');
     await timeout(async ()=> { await monomerLibHelper.awaitLoaded(); }, 5000,
       'await monomerLib to be loaded');
-    await timeout(async () => { await monomerLibHelper.loadLibraries(true); }, 5000,
+    await timeout(async () => { await monomerLibHelper.loadMonomerLib(true); }, 5000,
       'reload monomerLib with settings for tests'); // load default libraries for tests
   });
 
   after(async ()=>{
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   test('original', async () =>{
-    const monomerLib = libHelper.getBioLib();
+    const monomerLib = libHelper.getMonomerLib();
     rewriteLibraries(monomerLib);
 
-    // const overriddenGetMonomer = helmHelper.revertOriginalGetMonomer();
+    // const overriddenMonomersFuncs = helmHelper.revertOriginalMonomersFuncs();
     // try {
-    const helmHelper: IHelmHelper = await getHelmHelper();
-    expect(helmHelper != null, true);
-    // @ts-ignore
-    const getMonomerFunc = helmHelper.originalGetMonomer!;
+      const helmHelper: IHelmHelper = await getHelmHelper();
+      expect(helmHelper != null, true);
+      const getMonomerFunc: GetMonomerFunc = helmHelper.originalMonomersFuncs!.getMonomer!;
 
-    return _testAll('original', getMonomerFunc);
+      return _testAll('original', getMonomerFunc);
     // } finally {
-    //   helmHelper.overrideGetMonomer(overriddenGetMonomer);
+    //   helmHelper.overrideMonomersFuncs(overriddenMonomersFuncs);
     // }
   }, {isAggregated: true});
 
   test('monomerLib', async () =>{
-    const monomerLib = monomerLibHelper.getBioLib();
+    const monomerLib = monomerLibHelper.getMonomerLib();
     expectMonomerLib(monomerLib);
 
     const getMonomerFunc = org.helm.webeditor.Monomers.getMonomer;
@@ -148,7 +151,7 @@ category('getMonomer', ()=>{
     resDf.set('res', resI, '');
     resDf.set('tgt', resI, '');
     try {
-      const monomerLib = monomerLibHelper.getBioLib();
+      const monomerLib = monomerLibHelper.getMonomerLib();
       expectMonomerLib(monomerLib);
       resDf.set('success', resI, true);
     } catch (err) {
@@ -185,13 +188,13 @@ category('getMonomer', ()=>{
     /* Tests getMonomer function adding missing monomers. */
     const helmStr = 'PEPTIDE1{[mis1].R.[mis2].T.C.F}$$$$;';
 
-    expectMonomerLib(monomerLibHelper.getBioLib());
+    expectMonomerLib(monomerLibHelper.getMonomerLib());
     const editor = new JSDraw2.Editor(ui.div(), {viewonly: true});
     editor.setHelm(helmStr);
     const withMissing = JSON.parse(JSON.stringify(
       defaultMonomerLibSummary)) as MonomerLibSummaryType;
     withMissing['PEPTIDE'] += 2;
-    expectMonomerLib(monomerLibHelper.getBioLib(), withMissing);
+    expectMonomerLib(monomerLibHelper.getMonomerLib(), withMissing);
   });
 });
 

package/src/tests/helm-input-tests.ts

@@ -30,12 +30,12 @@ category('HelmInput', () => {
     // Test 'helm' requires default monomer library loaded
     await setUserLibSettingsForTests();
     await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadLibraries(true); // load default libraries
+    await monomerLibHelper.loadMonomerLib(true); // load default libraries
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
   });
 
   test('inDialog', async () => {
@@ -47,7 +47,7 @@ category('HelmInput', () => {
       .show();
     await delay(500);
 
-    const mol = helmInput.value;
+    const mol = helmInput.molValue;
     expect(mol.atoms.length, 4);
     expect(mol.bonds.length, 3);
   });
@@ -73,7 +73,7 @@ async function _testTooltipOnHelmInput(): Promise<void> {
     expect(helmInput.getInput(), dialogInputEl);
 
     const mon = {i: 0, elem: 'meY'};
-    const a = helmInput.value.atoms[mon.i];
+    const a = helmInput.molValue.atoms[mon.i];
     const iEl = helmInput.getInput();
     const iBcr = iEl.getBoundingClientRect();
     const ev = new MouseEvent('mousemove', {

package/src/tests/helm-service-tests.ts

@@ -41,8 +41,8 @@ category('HelmService', () => {
       await delay(1000); // for loading monomer libraries files
       // Test 'helm' requires default monomer library loaded
       await setUserLibSettingsForTests();
-      await monomerLibHelper.loadLibraries(true); // load default libraries
-      const libSummary = monomerLibHelper.getBioLib().getSummary();
+      await monomerLibHelper.loadMonomerLib(true); // load default libraries
+      const libSummary = monomerLibHelper.getMonomerLib().getSummaryObj();
 
       helmSvc = await getHelmService();
       await helmSvc.reset();
@@ -60,7 +60,7 @@ category('HelmService', () => {
     await helmSvc.reset();
 
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
     _package.logger.debug(`${logPrefix}, end`);
   });
 

package/src/tests/helm-tests.ts

@@ -4,7 +4,6 @@ import * as DG from 'datagrok-api/dg';
 
 import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
 
-//import {findMonomers, helmToFasta, helmToPeptide, helmToRNA, initHelm} from '../package';
 import {parseHelm} from '../utils';
 import {initHelmMainPackage} from './utils';
 
@@ -74,7 +73,7 @@ category('Helm', () => {
   ];
 
   const complexTestNames = [
-    'comples-monomer', 'complex-monomer+side-chain', 'complex-monomer+side-chain-RNA',
+    'complex-monomer', 'complex-monomer+side-chain', 'complex-monomer+side-chain-RNA',
     'complex-side-chain', 'complex+side-chain+linker'
   ];
 

package/src/tests/helm-web-editor-tests.ts

@@ -24,14 +24,14 @@ category('helm-web-editor', async () => {
     userLibSettings = await getUserLibSettings();
     await setUserLibSettingsForTests();
     await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
 
     hh = await getHelmHelper();
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true);
+    await monomerLibHelper.loadMonomerLib(true);
   });
 
   test('helm-web-editor', async () => {

package/src/tests/parse-helm-tests.ts

@@ -11,11 +11,12 @@ import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
-import {JSDraw2HelmModule} from '../types';
+import {JSDraw2Module} from '../types';
 import {initHelmMainPackage} from './utils';
+import {IHelmDrawOptions} from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 
 declare const org: OrgType;
-declare const JSDraw2: JSDraw2HelmModule;
+declare const JSDraw2: JSDraw2Module;
 
 type TestTgtType = { atomCount: number, bondCount: number };
 
@@ -47,12 +48,12 @@ category('parseHelm', () => {
     await setUserLibSettingsForTests();
     await timeout(async () => { await libHelper.awaitLoaded(); }, 5000,
       'await monomerLib to be loaded');
-    await libHelper.loadLibraries(true);
+    await libHelper.loadMonomerLib(true);
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await libHelper.loadLibraries(true);
+    await libHelper.loadMonomerLib(true);
   });
 
   for (const [testName, {src, tgt}] of Object.entries(testData)) {
@@ -72,11 +73,11 @@ function _testParseHelmWithEditor(src: string, tgt: TestTgtType): void {
   const io = org.helm.webeditor.IO;
 
   const editorHost = ui.div();
-  const editor = new JSDraw2.Editor(editorHost, {viewonly: true});
+  const editor = new JSDraw2.Editor<HelmType, IHelmDrawOptions>(editorHost, {viewonly: true});
 
   const plugin = new org.helm.webeditor.Plugin(editor);
   const origin = new JSDraw2.Point(0, 0);
-  io.parseHelm(plugin, src, origin, null);
+  io.parseHelm(plugin, src, origin, undefined);
 
   const m: Mol<HelmType> = plugin.jsd.m;
   expect(m.atoms.length, tgt.atomCount);
@@ -86,11 +87,11 @@ function _testParseHelmWithEditor(src: string, tgt: TestTgtType): void {
 function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
   const io = org.helm.webeditor.IO;
 
-  const molHandler = new JSDraw2.MolHandler();
+  const molHandler = new JSDraw2.MolHandler<HelmType>();
 
   const plugin = new org.helm.webeditor.Plugin(molHandler);
   const origin = new JSDraw2.Point(0, 0);
-  io.parseHelm(plugin, src, origin, null);
+  io.parseHelm(plugin, src, origin, undefined);
 
   const m: Mol<HelmType> = plugin.jsd.m;
   expect(m.atoms.length, tgt.atomCount);

package/src/tests/properties-widget-tests.ts

@@ -85,12 +85,12 @@ category('properties-widget', () => {
     await setUserLibSettingsForTests();
     await timeout(async () => { await monomerLibHelper.awaitLoaded(); },
       5000, 'MonomerLibHelper.awaitLoaded() timeout');
-    await monomerLibHelper.loadLibraries(true); // load default libraries
+    await monomerLibHelper.loadMonomerLib(true); // load default libraries
   });
 
   after(async () => {
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
   });
 
   for (const [testName, testData] of Object.entries(TestsData)) {

package/src/tests/renderers-tests.ts

@@ -33,13 +33,13 @@ category('renderers', () => {
 
     // Test 'helm' requires default monomer library loaded
     await setUserLibSettingsForTests();
-    await monomerLibHelper.loadLibraries(true); // load default libraries
+    await monomerLibHelper.loadMonomerLib(true); // load default libraries
   });
 
   after(async () => {
     // UserDataStorage.put() replaces existing data
     await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
   });
 
 

package/src/types/index.ts

@@ -1,5 +1,5 @@
 import {HelmType, JSDraw2ModuleType, OrgType, ScilModuleType} from '@datagrok-libraries/bio/src/helm/types';
 
 export type ScilModule = ScilModuleType;
-export type JSDraw2HelmModule = JSDraw2ModuleType<HelmType>;
+export type JSDraw2Module = JSDraw2ModuleType;
 export type OrgHelmModule = OrgType;

package/src/utils/get-hovered.ts

@@ -2,17 +2,15 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {HelmType, PolymerType, Atom, Mol, ISeqMonomer} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmType, PolymerType, Atom, Mol, ISeqMonomer, HelmMol, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';
 
 import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
 
 import {HelmMonomerPlacer} from '../helm-monomer-placer';
 
 export function getHoveredMonomerFromEditorMol(
-  argsX: number, argsY: number, mol: Mol<HelmType>, cellHeight? : number
-): ISeqMonomer | null {
-  let hoveredSeqMonomer: ISeqMonomer | null = null;
-
+  argsX: number, argsY: number, mol: HelmMol, cellHeight?: number
+): HelmAtom | null {
   /** @return {[number, number]} [atom, distance] */
   function getNearest(excluded: (number | undefined)[]): [number | undefined, number | undefined] {
     let atom: number | undefined = undefined;
@@ -34,18 +32,18 @@ export function getHoveredMonomerFromEditorMol(
   const [firstAtomI, firstDistance] = getNearest([]);
   const [secondAtomI, secondDistance] = getNearest([firstAtomI]);
 
+  let resAtom: HelmAtom | null = null;
   if (firstAtomI !== undefined && firstDistance !== undefined) {
     const firstAtom = mol.atoms[firstAtomI];
-    const firstSeqMonomer = getSeqMonomerFromHelmAtom(firstAtom);
     if (secondAtomI !== undefined && secondDistance !== undefined) {
       if (firstDistance < secondDistance * 0.45)
-        hoveredSeqMonomer = firstSeqMonomer;
+        resAtom = firstAtom;
     } else {
       if (cellHeight && firstDistance < 0.35 * cellHeight)
-        hoveredSeqMonomer = firstSeqMonomer;
+        resAtom = firstAtom;
     }
   }
-  return hoveredSeqMonomer;
+  return resAtom;
 }
 
 export function getHoveredMonomerFallback(
@@ -83,7 +81,7 @@ export function getHoveredMonomerFallback(
   return hoveredSeqMonomer;
 }
 
-function getSeqMonomerFromHelmAtom(atom: Atom<HelmType>): ISeqMonomer {
+export function getSeqMonomerFromHelmAtom(atom: HelmAtom): ISeqMonomer {
   const polymerType = helmTypeToPolymerType(atom.bio!.type);
   return {symbol: atom.elem, polymerType: polymerType};
 }

package/src/utils/get-monomer.ts

@@ -11,10 +11,7 @@ import {
 } from '@datagrok-libraries/bio/src/utils/const';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 
-
-import {
-  AmbiguousWebEditorMonomer, GapWebEditorMonomer, getRS, MissingWebEditorMonomer
-} from './get-monomer-dummy';
+import {AmbiguousWebEditorMonomer, GapWebEditorMonomer, getRS, MissingWebEditorMonomer} from './get-monomer-dummy';
 import {LibraryWebEditorMonomer} from './get-monomer-of-library';
 import {OrgHelmModule, ScilModule} from '../types';
 import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
@@ -59,6 +56,8 @@ export function getMonomerOverrideAndLogAlert(
 export function getMonomerHandleArgs(
   a: Atom<HelmType> | HelmType, name?: string
 ): [/** biotype */ HelmType, /** elem */ string] {
+  if (!a)
+    throw new Error(`Argument 'a' of type Atom or HelmType is mandatory.`);
   let biotype: HelmType;
   let elem: string;
   if ((a as Atom<HelmType>).T === 'ATOM') {

package/src/utils/helm-grid-cell-renderer.ts

@@ -9,54 +9,38 @@ import {
   CellRendererBackAsyncBase, RenderServiceBase
 } from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
 import {HelmAux, HelmProps} from '@datagrok-libraries/bio/src/viewers/helm-service';
+import {_getHelmService} from '../package-utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
 
-import {getHoveredMonomerFromEditorMol} from './get-hovered';
-import {_getHelmService} from '../package-utils';
+import {getHoveredMonomerFromEditorMol, getSeqMonomerFromHelmAtom} from './get-hovered';
 
 import {_package} from '../package';
 
-class WrapLogger implements ILogger {
-  constructor(
-    private readonly base: ILogger
-  ) {}
-
-  error(message: any, params?: object | undefined, stackTrace?: string | undefined): void {
-    this.base.error(message, params, stackTrace);
-  }
-
-  warning(message: string, params?: object | undefined): void {
-    this.base.warning(message, params);
-  }
-
-  info(message: string, params?: object | undefined): void {
-    // this.base.info(message, params);
-  }
-
-  debug(message: string, params?: object | undefined): void {
-    // this.base.debug(message, params);
-  }
-}
-
 export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProps, HelmAux> {
   private _auxList: (HelmAux | null)[];
 
   private monomerLib: IMonomerLib | null = null;
 
+  // eslint-disable-next-line max-len
+  private readonly uuid: string = wu.repeat(1).map(() => Math.floor((Math.random() * 36)).toString(36)).take(4).toArray().join('');
+
   constructor(
     gridCol: DG.GridColumn | null,
     tableCol: DG.Column<string>,
   ) {
-    super(gridCol, tableCol, new WrapLogger(_package.logger) /* _package.logger */, true);
+    super(gridCol, tableCol, _package.logger, true);
   }
 
   protected override reset(): void {
+    const logPrefix = `${this.toLog()}.reset()`;
+    this.logger.debug(`${logPrefix}, start`);
     super.reset();
     this._auxList = new Array<HelmAux | null>(this.tableCol.length).fill(null);
     if (this.gridCol && this.gridCol.dart) this.gridCol.grid?.invalidate();
+    this.logger.debug(`${logPrefix}, end`);
   }
 
   protected override getRenderService(): RenderServiceBase<HelmProps, HelmAux> {
@@ -70,6 +54,8 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
   }
 
   protected override storeAux(gridCell: DG.GridCell, aux: HelmAux): void {
+    const logPrefix = `${this.toLog()}.storeAux()`;
+    this.logger.debug(`${logPrefix}, start`);
     if (gridCell.tableRowIndex !== null)
       this._auxList[gridCell.tableRowIndex] = aux;
   }
@@ -141,10 +127,10 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
       this.logger.warning(`${logPrefix}, editorMol of the cell not found.`);
       return; // The gridCell is not rendered yet
     }
-    const seqMonomer: ISeqMonomer | null =
-      getHoveredMonomerFromEditorMol(argsX, argsY, editorMol, gridCell.bounds.height);
+    const hoveredAtom = getHoveredMonomerFromEditorMol(argsX, argsY, editorMol, gridCell.bounds.height);
 
-    if (seqMonomer) {
+    if (hoveredAtom) {
+      const seqMonomer = getSeqMonomerFromHelmAtom(hoveredAtom);
       const monomerLib = _package.monomerLib;
       const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.polymerType, seqMonomer.symbol) :
         ui.divText('Monomer library is not available');
@@ -170,7 +156,8 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
   // -- Handle events --
 
   private monomerLibOnChanged(_value: any): void {
-    this.reset();
+    this.dirty = true;
+    this.invalidateGrid();
   }
 
   static getOrCreate(gridCell: DG.GridCell): HelmGridCellRendererBack {

package/src/utils/helm-service.ts

@@ -5,23 +5,21 @@ import * as DG from 'datagrok-api/dg';
 import $ from 'cash-dom';
 import {Subject, Unsubscribable} from 'rxjs';
 
-import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
-import {Editor, HelmType} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmEditor} from '@datagrok-libraries/bio/src/helm/types';
 import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
 import {HelmAux, HelmProps, HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {svgToImage} from '@datagrok-libraries/utils/src/svg';
 
-import {JSDraw2HelmModule} from '../types';
+import {JSDraw2Module} from '../types';
 
 import {_package} from '../package';
 
-declare const JSDraw2: JSDraw2HelmModule;
+declare const JSDraw2: JSDraw2Module;
 
 export class HelmService extends HelmServiceBase {
   private readonly hostDiv: HTMLDivElement;
 
-  private editor!: Editor<HelmType>;
+  private editor!: HelmEditor;
   private image: HTMLImageElement | null = null;
 
   constructor() {