@datagrok/bio 2.12.17 → 2.12.18

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.12.17",
+  "version": "2.12.18",
   "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",
@@ -34,12 +34,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.41.0",
+    "@datagrok-libraries/bio": "^5.41.2",
     "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/math": "^1.1.5",
     "@datagrok-libraries/ml": "^6.6.5",
     "@datagrok-libraries/tutorials": "^1.3.12",
-    "@datagrok-libraries/utils": "^4.2.2",
+    "@datagrok-libraries/utils": "^4.2.5",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",

package/src/package-test.ts

@@ -23,7 +23,7 @@ import './tests/WebLogo-project-tests';
 import './tests/WebLogo-layout-tests';
 import './tests/checkInputColumn-tests';
 import './tests/similarity-diversity-tests';
-import './tests/substructure-filters-tests';
+// import './tests/substructure-filters-tests';
 import './tests/pepsea-tests';
 import './tests/viewers';
 import './tests/seq-handler-tests';

package/src/package.ts

@@ -86,8 +86,8 @@ export const _package = new BioPackage();
 //name: getMonomerLibHelper
 //description:
 //output: object result
-export function getMonomerLibHelper(): IMonomerLibHelper {
-  return MonomerLibManager.instance;
+export async function getMonomerLibHelper(): Promise<IMonomerLibHelper> {
+  return await MonomerLibManager.getInstance();
 }
 
 export let hydrophobPalette: SeqPaletteCustom | null = null;
@@ -104,12 +104,20 @@ export class SeqPaletteCustom implements SeqPalette {
   }
 }
 
+let monomerLib: IMonomerLib | null = null;
+
 //tags: init
 export async function initBio() {
-  _package.logger.debug('Bio: initBio(), started');
+  const logPrefix = 'Bio: initBio()';
+  _package.logger.debug(`${logPrefix}, start`);
   const module = await grok.functions.call('Chem:getRdKitModule');
+  const t1: number = window.performance.now();
   await Promise.all([
-    (async () => { await MonomerLibManager.instance.loadLibraries(); })(),
+    (async () => {
+      const monomerLibManager = await MonomerLibManager.getInstance();
+      await monomerLibManager.loadLibraries();
+      monomerLib = monomerLibManager.getBioLib();
+    })(),
     (async () => {
       const pkgProps = await _package.getProperties();
       const bioPkgProps = new BioPackageProperties(pkgProps);
@@ -117,9 +125,10 @@ export async function initBio() {
     })(),
   ]).finally(() => {
     _package.completeInit();
+    const t2: number = window.performance.now();
+    _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
   });
 
-  const monomerLib = MonomerLibManager.instance.getBioLib();
   const monomers: string[] = [];
   const logPs: number[] = [];
 
@@ -159,10 +168,16 @@ export function sequenceTooltip(col: DG.Column): DG.Widget<any> {
   return resWidget;
 }
 
+// Keep for backward compatibility
 //name: getBioLib
 //output: object monomerLib
 export function getBioLib(): IMonomerLib {
-  return MonomerLibManager.instance.getBioLib();
+  return monomerLib!;
+}
+
+// For sync internal use, on initialized package
+export function getMonomerLib(): IMonomerLib | null {
+  return monomerLib!;
 }
 
 //name: getSeqHandler
@@ -571,7 +586,8 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
 export async function toAtomicLevel(table: DG.DataFrame, seqCol: DG.Column, nonlinear: boolean): Promise<void> {
   const pi = DG.TaskBarProgressIndicator.create('Converting to atomic level ...');
   try {
-    await sequenceToMolfile(table, seqCol, nonlinear);
+    const monomerLib = (await getMonomerLibHelper()).getBioLib();
+    await sequenceToMolfile(table, seqCol, nonlinear, monomerLib);
   } finally {
     pi.close();
   }

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

@@ -8,8 +8,6 @@ import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/sr
 import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
-import {MonomerLibFileManager} from '../utils/monomer-lib/library-file-manager/file-manager';
-import {MonomerLibFileEventManager} from '../utils/monomer-lib/library-file-manager/event-manager';
 
 
 category('monomerLibraries', () => {
@@ -51,8 +49,7 @@ category('monomerLibraries', () => {
   test('empty', async () => {
     // exclude all monomer libraries for empty set
     const libSettings = await getUserLibSettings();
-    const libFileEventManager = MonomerLibFileEventManager.getInstance();
-    const libFileManager = await MonomerLibFileManager.getInstance(libFileEventManager);
+    const libFileManager = await monomerLibHelper.getFileManager();
 
     let libFnList = libFileManager.getValidLibraryPaths();
     if (libFnList.length === 0)

package/src/tests/renderers-monomer-placer-tests.ts

@@ -8,8 +8,7 @@ import {category, test} from '@datagrok-libraries/utils/src/test';
 import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-
-import {MonomerLibManager} from '../utils/monomer-lib/lib-manager';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {_package} from '../package-test';
 
@@ -45,7 +44,7 @@ category('renderers: monomerPlacer', () => {
         'id1,m1-M-m3-mon4-mon5-N-T-MON8-N9\n' +
         'id2,m1-mon2-m3-mon4-mon5-Num--MON8-N9\n' +
         'id3,\n' + // empty
-        'id4,mon1-M-mon3-mon4-mon5---MON8-N9\n',
+        'id4,mon1-M-mon3-mon4-mon5---MON8-N9\n', // [ 5, 38, 71, 104, 137, 170, 203, 236, 269, 295 ]
       testList: [
         {src: {row: 0, x: -1}, tgt: {pos: null}},
         {src: {row: 1, x: 0}, tgt: {pos: null}},
@@ -59,7 +58,7 @@ category('renderers: monomerPlacer', () => {
         {src: {row: 2, x: 20}, tgt: {pos: null}}, // empty value
         {src: {row: 3, x: 170}, tgt: {pos: 4}},
         {src: {row: 3, x: 200}, tgt: {pos: 5}},
-        {src: {row: 3, x: 282}, tgt: {pos: null}},
+        {src: {row: 3, x: 297}, tgt: {pos: null}},
       ]
     },
     fastaMsa: {
@@ -88,6 +87,8 @@ id3,QHIRE--LT
 
   for (const [testName, testData] of Object.entries(tests)) {
     test(`getPosition-${testName}`, async () => {
+      const libHelper = await getMonomerLibHelper();
+      const monomerLib = libHelper.getBioLib();
       const df: DG.DataFrame = DG.DataFrame.fromCsv(testData.csv);
       await grok.data.detectSemanticTypes(df);
       const seqCol: DG.Column = df.getCol('seq');
@@ -103,18 +104,18 @@ id3,QHIRE--LT
           separatorWidth: sepWidth,
           monomerToShort: monomerToShort,
           monomerLengthLimit: monLength,
-          monomerLib: MonomerLibManager.instance.getBioLib(),
         };
       });
 
+      const width: number = 10000;
       const testList = testData.testList;
       // simulate rendering
       for (let rowI: number = 0; rowI < seqCol.length; ++rowI)
-        colTemp.getCellMonomerLengths(rowI);
+        colTemp.getCellMonomerLengths(rowI, 10000);
 
       const errorList: string[] = [];
       for (const [test, _testI] of wu.enumerate(testList)) {
-        const res = {pos: colTemp.getPosition(test.src.row, test.src.x)};
+        const res = {pos: colTemp.getPosition(test.src.row, test.src.x, width)};
         if (test.tgt.pos != res.pos) {
           errorList.push(`Test src ${JSON.stringify(test.src)} expected tgt ${JSON.stringify(test.tgt)},` +
             ` but get ${JSON.stringify({res})}`);

package/src/tests/renderers-test.ts

@@ -56,7 +56,7 @@ category('renderers', () => {
 
   test('scatterPlotTooltip', async () => {
     await _testScatterPlotTooltip();
-  });
+  }, {skipReason: 'GROK-15679'});
 
   async function _rendererMacromoleculeFasta() {
     const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/FASTA.csv');

package/src/tests/scoring.ts

@@ -4,9 +4,9 @@ import * as DG from 'datagrok-api/dg';
 
 import {category, test, expectFloat, before, after} from '@datagrok-libraries/utils/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
-import {sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
+import {getMonomerLibHelper, sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
 import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';

package/src/tests/substructure-filters-tests.ts

@@ -185,7 +185,8 @@ category('bio-substructure-filters', async () => {
       dlg.close();
     }
     await filter.awaitRendered();
-  });
+    await delay(3000); //TODO: await for grid.onLookChanged
+  }, {skipReason: 'GROK-15678'});
 
   // Generates unhandled exception accessing isFiltering before bioFilter created
   test('helm-view', async () => {
@@ -308,7 +309,8 @@ category('bio-substructure-filters', async () => {
     }
     await Promise.all([f1.awaitRendered(), f2.awaitRendered()]);
     await awaitGrid(view.grid);
-  });
+    await delay(3000); //TODO: await for grid.onLookChanged
+  }, {skipReason: 'GROK-15678'});
 
   // two seq columns
 

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

@@ -7,7 +7,7 @@ import wu from 'wu';
 
 import {before, after, category, test, expectArray, expect} from '@datagrok-libraries/utils/src/test';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {

package/src/tests/utils.ts

@@ -2,10 +2,12 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {delay, expect, testEvent} from '@datagrok-libraries/utils/src/test';
+import {asRenderer, IRenderer, isRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 
 import {startDockerContainer} from '../utils/docker';
 
 import {_package} from '../package-test';
+import {CellRendererBackBase, getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 export async function loadFileAsText(name: string): Promise<string> {
   return await _package.files.readAsText(name);
@@ -38,4 +40,17 @@ export async function awaitGrid(grid: DG.Grid, timeout: number = 5000): Promise<
   await delay(0);
   await testEvent(grid.onAfterDrawContent, () => {},
     () => { grid.invalidate(); }, timeout);
+
+  const colCount = grid.columns.length;
+  for (let colI = 0; colI < colCount; ++colI) {
+    const gridCol = grid.columns.byIndex(colI);
+    if (gridCol) {
+      const gridCell = grid.cell(gridCol.name, 0);
+      const [_gridCol, _tableCol, temp] =
+        getGridCellRendererBack<void, CellRendererBackBase<void>>(gridCell);
+
+      const renderer = asRenderer(temp.rendererBack);
+      if (renderer) await renderer.awaitRendered();
+    }
+  }
 }

package/src/utils/cell-renderer.ts

@@ -3,7 +3,6 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import wu from 'wu';
-import {Unsubscribable} from 'rxjs';
 
 import {printLeftOrCentered, DrawStyle, TAGS as mmcrTAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 import {MonomerPlacer} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
@@ -22,7 +21,7 @@ import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-ha
 import {ISeqSplitted, SeqSplittedBase} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {alphabetPolymerTypes, IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {alphabetPolymerTypes, IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 import {
@@ -31,14 +30,16 @@ import {
 } from '../utils/cell-renderer-consts';
 import * as C from './constants';
 
-import {_package, getBioLib} from '../package';
+import {_package, getMonomerLib} from '../package';
 
 type TempType = { [tagName: string]: any };
 
 const undefinedColor = 'rgb(100,100,100)';
 const monomerToShortFunction: MonomerToShortFunc = monomerToShort;
 
-function getUpdatedWidth(grid: DG.Grid | null, g: CanvasRenderingContext2D, x: number, w: number, dpr: number): number {
+function getUpdatedWidth(
+  grid: DG.Grid | null | undefined, g: CanvasRenderingContext2D, x: number, w: number, dpr: number
+): number {
   return !!grid ? Math.max(Math.min(grid.canvas.width / dpr - x, w)) : Math.max(g.canvas.width / dpr - x, 0);
 }
 
@@ -99,7 +100,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     //   maxLengthWordsSum[posI] = maxLengthWordsSum[posI - 1] + maxLengthWords[posI];
     // const maxIndex = maxLengthWords.length;
     const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
-    const left: number | null = seqColTemp.getPosition(gridCell.tableRowIndex!, argsX);
+    const left: number | null = seqColTemp.getPosition(gridCell.tableRowIndex!, argsX, gridCellBounds.width);
 
     const seqCList: SeqSplittedBase = SeqHandler.forColumn(tableCol)
       .getSplitted(gridCell.tableRowIndex!).canonicals;
@@ -113,8 +114,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
           const alphabet = sh.alphabet ?? ALPHABET.UN;
           const polymerType = alphabetPolymerTypes[alphabet as ALPHABET];
 
-          const lib: IMonomerLib = seqColTemp.props.monomerLib!;
-          return lib.getTooltip(polymerType, monomerSymbol);
+          const lib: IMonomerLib | null = getMonomerLib();
+          return lib ? lib.getTooltip(polymerType, monomerSymbol) : ui.divText('Monomer library is not available');
         })();
       }
       tooltipElements.push(monomerDiv);
@@ -142,23 +143,17 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     _cellStyle: DG.GridCellStyle
   ): void {
     const logPrefix: string = 'MacromoleculeSequenceCellRenderer.render()';
+
+    const dpr = window.devicePixelRatio;
+    const [gridCol, tableCol, _temp] =
+      getGridCellRendererBack<string, MonomerPlacer>(gridCell);
+    if (!tableCol) return;
+    const tableColTemp: TempType = tableCol.temp;
+
     let gapLength = 0;
     const msaGapLength = 8;
     let maxLengthOfMonomer = 50; // in case of long monomer representation, do not limit max length
 
-    // TODO: Store temp data to GridColumn
-    // Now the renderer requires data frame table Column underlying GridColumn
-    let grid: DG.Grid | undefined = undefined;
-    try { grid = gridCell.grid; } catch (err: any) {
-      grid = undefined;
-      const [errMsg, errStack] = errInfo(err);
-      _package.logger.error(errMsg, undefined, errStack);
-    }
-    const tableCol: DG.Column = gridCell.cell.column;
-    if (!grid || !tableCol) return;
-
-    const tableColTemp: TempType = tableCol.temp;
-
     // Cell renderer settings
     const tempMonomerWidth: string | null = tableColTemp[tempTAGS.monomerWidth];
     const monomerWidth: string = (tempMonomerWidth != null) ? tempMonomerWidth : 'short';
@@ -170,46 +165,41 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         (!isNaN(tagMaxMonomerLength) ? tagMaxMonomerLength : _package.properties?.MaxMonomerLength) ?? 4;
     }
 
-    const [gridCol, _tc, temp] =
+    const [_gc, _tc, temp] =
       getGridCellRendererBack<string, MonomerPlacer>(gridCell);
-    let seqColTemp: MonomerPlacer = temp['rendererBack'];
+    let seqColTemp: MonomerPlacer = temp.rendererBack;
     if (!seqColTemp) {
-      seqColTemp = new MonomerPlacer(gridCol, tableCol, _package.logger,
+      seqColTemp = temp.rendererBack = new MonomerPlacer(gridCol, tableCol, _package.logger,
         () => {
           const sh = SeqHandler.forColumn(tableCol);
           return {
             seqHandler: sh,
             monomerCharWidth: 7, separatorWidth: !sh.isMsa() ? gapLength : msaGapLength,
             monomerToShort: monomerToShortFunction, monomerLengthLimit: maxLengthOfMonomer,
-            monomerLib: getBioLib()
           };
         });
     }
 
-    if (tableCol.tags[mmcrTags.RendererSettingsChanged] === rendererSettingsChangedState.true) {
-      gapLength = tableColTemp[mmcrTemps.gapLength] as number ?? gapLength;
-      // this event means that the mm renderer settings have changed, particularly monomer representation and max width.
-      seqColTemp.setMonomerLengthLimit(maxLengthOfMonomer);
-      seqColTemp.setSeparatorWidth(seqColTemp.isMsa() ? msaGapLength : gapLength);
-      tableCol.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.false);
-    }
-
-    const [maxLengthWords, maxLengthWordsSum]: [number[], number[]] =
-      seqColTemp.getCellMonomerLengths(gridCell.tableRowIndex!);
-    const _maxIndex = maxLengthWords.length;
-
-    // Store updated seqColTemp to the col temp
-    if (seqColTemp.updated) temp['rendererBack'] = seqColTemp;
-
     g.save();
     try {
-      const dpr = window.devicePixelRatio;
-      const grid = gridCell.gridRow !== -1 ? gridCell.grid : null;
+      if (tableCol.tags[mmcrTags.RendererSettingsChanged] === rendererSettingsChangedState.true) {
+        gapLength = tableColTemp[mmcrTemps.gapLength] as number ?? gapLength;
+        // this event means that the mm renderer settings have changed,
+        // particularly monomer representation and max width.
+        seqColTemp.setMonomerLengthLimit(maxLengthOfMonomer);
+        seqColTemp.setSeparatorWidth(seqColTemp.isMsa() ? msaGapLength : gapLength);
+        tableCol.setTag(mmcrTags.RendererSettingsChanged, rendererSettingsChangedState.false);
+      }
+
+      const [maxLengthWords, maxLengthWordsSum]: [number[], number[]] =
+        seqColTemp.getCellMonomerLengths(gridCell.tableRowIndex!, w);
+      const _maxIndex = maxLengthWords.length;
+
       const value: any = gridCell.cell.value;
       const rowIdx = gridCell.cell.rowIndex;
       const paletteType = tableCol.getTag(bioTAGS.alphabet);
       const minDistanceRenderer = 50;
-      w = getUpdatedWidth(grid, g, x, w, dpr);
+      w = getUpdatedWidth(gridCol?.grid, g, x, w, dpr);
       g.beginPath();
       g.rect(x + this.padding, y + this.padding, w - this.padding - 1, h - this.padding * 2);
       g.clip();
@@ -223,7 +213,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       const palette = getPaletteByType(paletteType);
 
       const separator = tableCol.getTag(bioTAGS.separator) ?? '';
-      const splitLimit = w / 5;
+      const minMonWidth = seqColTemp.props.separatorWidth + 1 * seqColTemp.props.monomerCharWidth;
+      const splitLimit = w / minMonWidth;
       const sh = SeqHandler.forColumn(tableCol);
 
       const tempReferenceSequence: string | null = tableColTemp[tempTAGS.referenceSequence];
@@ -247,7 +238,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       if (aligned && aligned.includes('MSA') && units == NOTATION.SEPARATOR)
         drawStyle = DrawStyle.MSA;
 
-      for (let posIdx: number = 0; posIdx < subParts.length; ++posIdx) {
+      const visibleSeqLength = Math.min(subParts.length, splitLimit);
+      for (let posIdx: number = 0; posIdx < visibleSeqLength; ++posIdx) {
         const amino: string = subParts.getOriginal(posIdx);
         color = palette.get(amino);
         g.fillStyle = undefinedColor;
@@ -259,8 +251,9 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         if (minDistanceRenderer > w) break;
       }
     } catch (err: any) {
-      const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Error \'undefined\'';
-      _package.logger.error(`Bio: MacromoleculeSequenceCellRenderer.render() error: ${errMsg}`);
+      const [errMsg, errStack] = errInfo(err);
+      seqColTemp.logger.error(errMsg, undefined, errStack);
+      seqColTemp.errors.push(err);
       //throw err; // Do not throw to prevent disabling renderer
     } finally {
       g.restore();

package/src/utils/helm-to-molfile/converter/converter.ts

@@ -5,10 +5,13 @@ import * as OCL from 'openchemlib/full';
 
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import {_package} from '../../../package';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+
 import {Polymer} from './polymer';
 import {GlobalMonomerPositionHandler} from './position-handler';
 
+import {_package, getMonomerLibHelper} from '../../../package';
+
 export class HelmToMolfileConverter {
   constructor(private helmColumn: DG.Column<string>, private df: DG.DataFrame) {
     this.helmColumn = helmColumn;
@@ -54,7 +57,7 @@ export class HelmToMolfileConverter {
   async convertToRdKitBeautifiedMolfileColumn(chiralityEngine?: boolean): Promise<DG.Column<string>> {
     const molfilesV3K = (await this.convertToMolfileV3KColumn()).toList();
     const rdKitModule: RDModule = await grok.functions.call('Chem:getRdKitModule');
-    const beautifiedMols = molfilesV3K.map((item) =>{
+    const beautifiedMols = molfilesV3K.map((item) => {
       if (item === '')
         return null;
       const mol = rdKitModule.get_mol(item);
@@ -81,6 +84,7 @@ export class HelmToMolfileConverter {
   private async convertToMolfileV3KColumn(): Promise<DG.Column<string>> {
     const polymerGraphColumn: DG.Column<string> = await this.getPolymerGraphColumn();
     const rdKitModule = await grok.functions.call('Chem:getRdKitModule');
+    const monomerLib: IMonomerLib = (await getMonomerLibHelper()).getBioLib();
     const molfileList = polymerGraphColumn.toList().map(
       (pseudoMolfile: string, idx: number) => {
         const helm = this.helmColumn.get(idx);
@@ -88,7 +92,7 @@ export class HelmToMolfileConverter {
           return '';
         let result = '';
         try {
-          result = this.getPolymerMolfile(helm, pseudoMolfile, rdKitModule);
+          result = this.getPolymerMolfile(helm, pseudoMolfile, rdKitModule, monomerLib);
         } catch (err: any) {
           const [errMsg, errStack] = errInfo(err);
           _package.logger.error(errMsg, undefined, errStack);
@@ -110,10 +114,11 @@ export class HelmToMolfileConverter {
   private getPolymerMolfile(
     helm: string,
     polymerGraph: string,
-    rdKitModule: RDModule
+    rdKitModule: RDModule,
+    monomerLib: IMonomerLib
   ): string {
     const globalPositionHandler = new GlobalMonomerPositionHandler(polymerGraph);
-    const polymer = new Polymer(helm, rdKitModule);
+    const polymer = new Polymer(helm, rdKitModule, monomerLib);
     globalPositionHandler.monomerSymbols.forEach((monomerSymbol: string, monomerIdx: number) => {
       const shift = globalPositionHandler.getMonomerShifts(monomerIdx);
       polymer.addMonomer(monomerSymbol, monomerIdx, shift);

package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts

@@ -1,11 +1,11 @@
-import {Monomer} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {HELM_RGROUP_FIELDS} from '@datagrok-libraries/bio/src/utils/const';
 import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import {MonomerLibManager} from '../../monomer-lib/lib-manager';
+import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
+
 import {Helm} from './helm';
 import {MolfileWrapper} from './mol-wrapper';
 import {MolfileWrapperFactory} from './mol-wrapper-factory';
-import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
 
 export class MonomerWrapper {
   private molfileWrapper: MolfileWrapper;
@@ -15,8 +15,9 @@ export class MonomerWrapper {
     private monomerSymbol: string,
     private monomerIdx: number,
     private helm: Helm,
-    shift: {x: number, y: number},
-    rdKitModule: RDModule
+    shift: { x: number, y: number },
+    rdKitModule: RDModule,
+    private readonly monomerLib: IMonomerLib
   ) {
     const libraryMonomerObject = this.getLibraryMonomerObject();
 
@@ -37,7 +38,7 @@ export class MonomerWrapper {
   private convertMolfileToV3KFormat(molfileV2K: string, monomerSymbol: string, rdKitModule: RDModule): string {
     let mol: RDMol | null = null;
     try {
-      mol = rdKitModule.get_mol(molfileV2K, JSON.stringify({mergeQueryHs: true}))
+      mol = rdKitModule.get_mol(molfileV2K, JSON.stringify({mergeQueryHs: true}));
       if (mol)
         return mol.get_v3Kmolblock();
       else
@@ -49,8 +50,7 @@ export class MonomerWrapper {
 
   private getLibraryMonomerObject(): Monomer {
     const polymerType = this.helm.getPolymerTypeByMonomerIdx(this.monomerIdx);
-    const monomerLib = MonomerLibManager.instance.getBioLib();
-    const monomer = monomerLib.getMonomer(polymerType, this.monomerSymbol);
+    const monomer = this.monomerLib.getMonomer(polymerType, this.monomerSymbol);
     if (!monomer)
       throw new Error(`Monomer ${this.monomerSymbol} is not found in the library`);
     return monomer;
@@ -72,7 +72,7 @@ export class MonomerWrapper {
     return result;
   }
 
-  private shiftCoordinates(shift: {x: number, y: number}): void {
+  private shiftCoordinates(shift: { x: number, y: number }): void {
     this.molfileWrapper.shiftCoordinates(shift);
   }
 

package/src/utils/helm-to-molfile/converter/polymer.ts

@@ -1,10 +1,16 @@
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {V3K_CONST} from '@datagrok-libraries/chem-meta/src/formats/molfile-const';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+
 import {Helm} from './helm';
 import {MonomerWrapper} from './monomer-wrapper';
 
 export class Polymer {
-  constructor(helmString: string, private rdKitModule: RDModule) {
+  constructor(
+    helmString: string,
+    private readonly rdKitModule: RDModule,
+    private readonly monomerLib: IMonomerLib
+  ) {
     this.helm = new Helm(helmString);
   }
 
@@ -14,9 +20,10 @@ export class Polymer {
   addMonomer(
     monomerSymbol: string,
     monomerIdx: number,
-    shift: {x: number, y: number},
+    shift: { x: number, y: number },
   ): void {
-    const monomerWrapper = new MonomerWrapper(monomerSymbol, monomerIdx, this.helm, shift, this.rdKitModule);
+    const monomerWrapper = new MonomerWrapper(
+      monomerSymbol, monomerIdx, this.helm, shift, this.rdKitModule, this.monomerLib);
 
     this.monomerWrappers.push(monomerWrapper);
   }

package/src/utils/monomer-cell-renderer.ts

@@ -5,9 +5,10 @@ import * as ui from 'datagrok-api/ui';
 import {ALPHABET, getPaletteByType, monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {MonomerWorks} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
+import {PolymerType} from '@datagrok-libraries/bio/src/types';
 
-import {getMonomerLibHelper} from '../package';
 import * as C from './constants';
+import {getMonomerLib} from '../package';
 
 const Tags = new class {
   tooltipHandlerTemp = 'tooltip-handler.Monomer';
@@ -29,20 +30,29 @@ export class MonomerTooltipHandler {
       !gridCell.tableColumn || !gridCell.isTableCell
     ) return false;
 
-    const alphabet = gridCell.tableColumn.getTag(bioTAGS.alphabet);
+    const alphabet = gridCell.tableColumn.getTag(bioTAGS.alphabet) as ALPHABET;
     const monomerName = gridCell.cell.value;
-    const mw = new MonomerWorks(getMonomerLibHelper().getBioLib());
-    const monomerType: string = (alphabet === ALPHABET.DNA || alphabet === ALPHABET.RNA) ? 'RNA' :
+    const canvasClientRect = gridCell.grid.canvas.getBoundingClientRect();
+    const x1 = gridCell.bounds.right + canvasClientRect.left - 4;
+    const y1 = gridCell.bounds.bottom + canvasClientRect.top - 4;
+
+    const monomerLib = getMonomerLib();
+    if (!monomerLib) {
+      ui.tooltip.show(ui.divText('Monomer library is not available.'), x1, y1);
+      return true;
+    }
+
+    const mw = new MonomerWorks(monomerLib);
+    const polymerType: PolymerType = (alphabet === ALPHABET.DNA || alphabet === ALPHABET.RNA) ? 'RNA' :
       alphabet === ALPHABET.PT ? 'PEPTIDE' : 'PEPTIDE';
+    // const biotype: HelmType = [ALPHABET.RNA, ALPHABET.DNA].includes(alphabet) ? HelmTypes.NUCLEOTIDE :
+    //   [ALPHABET.PT].includes(alphabet) ? HelmTypes.AA : HelmTypes.AA;
 
-    const monomerMol: string | null = mw.getCappedRotatedMonomer(monomerType, monomerName);
+    const monomerMol: string | null = mw.getCappedRotatedMonomer(polymerType, monomerName);
     const nameDiv = ui.div(monomerName);
     const molDiv = !monomerMol ? null :
       grok.chem.svgMol(monomerMol, undefined, undefined, svgMolOptions);
 
-    const canvasClientRect = gridCell.grid.canvas.getBoundingClientRect();
-    const x1 = gridCell.bounds.right + canvasClientRect.left - 4;
-    const y1 = gridCell.bounds.bottom + canvasClientRect.top - 4;
     ui.tooltip.show(ui.divV([nameDiv, ...(molDiv ? [molDiv] : [])]), x1, y1);
 
     return true; // To prevent default tooltip behaviour