@datagrok/bio 2.12.23 → 2.13.3

package/files/monomer-libraries/sample-lib-Aca-colored.json

@@ -0,0 +1,37 @@
+[
+    {
+        "monomerType": "Backbone",
+        "smiles": "CCCCCCCC[C@H](N[H:1])C([OH:2])=O",
+        "name": "2-Aminocapric acid",
+        "author": "Pistoia Alliance HELM project",
+        "molfile": "HELM Core Monomer library\n     RDKit          2D\n\n 14 13  0  0  1  0  0  0  0  0999 V2000\n    0.6430   -4.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2375   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0301   -4.7725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.6246   -5.3445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.4172   -5.1157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.0117   -5.6877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.8044   -5.4589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.3988   -6.0310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.1915   -5.8021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.7859   -6.3742    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    7.5786   -6.1454    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    6.3896   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.7951   -4.4293    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    7.1823   -4.7725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  1  0\n  4  5  1  0\n  5  6  1  0\n  6  7  1  0\n  7  8  1  0\n  9  8  1  0\n  9 10  1  1\n 10 11  1  0\n  9 12  1  0\n 12 13  1  0\n 12 14  2  0\nM  RGP  2  11   1  13   2\nM  END\n",
+        "naturalAnalog": "X",
+        "rgroups": [
+            {
+                "capGroupSMILES": "[*:1][H]",
+                "alternateId": "R1-H",
+                "capGroupName": "H",
+                "label": "R1"
+            },
+            {
+                "capGroupSMILES": "O[*:2]",
+                "alternateId": "R2-OH",
+                "capGroupName": "OH",
+                "label": "R2"
+            }
+        ],
+        "meta": {
+            "colors": {
+                "default": {
+                    "line": "#202020",
+                    "text": "#202020",
+                    "background": "#60FF40"
+                }
+            }
+        },
+        "createDate": null,
+        "id": 0,
+        "polymerType": "PEPTIDE",
+        "symbol": "Aca"
+    }
+]

package/files/samples/FASTA_UN.csv

@@ -0,0 +1,4 @@
+seq
+[meI][hHis][Aca]NT[dE][Thr_PO3H2][Aca]D[meI][hHis][Aca]NT[dE][Thr_PO3H2][Aca]D[meI]
+[meI][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2][meI][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]
+[Lys_Boc][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2][Lys_Boc][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]

package/files/samples/FASTA_UN_MSA.csv

@@ -0,0 +1,4 @@
+seq
+[meI][hHis][Aca]NT[dE][Thr_PO3H2][Aca]D[meI][hHis][Aca]NT[dE][Thr_PO3H2][Aca]D
+[meI][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2][meI][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]
+[Lys_Boc][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2][Lys_Boc][hHis][Aca][Cys_SEt]T[dK][Thr_PO3H2][Aca][Tyr_PO3H2]

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.12.23",
+  "version": "2.13.3",
   "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",
@@ -15,18 +15,21 @@
   "properties": [
     {
       "name": "MaxMonomerLength",
-      "propertyType": "int",
-      "defaultValue": 4,
+      "description": "The max length of monomer symbol displayed without shortening, 'long' to no limit",
+      "propertyType": "string",
+      "defaultValue": "4",
       "nullable": false
     },
     {
       "name": "TooltipWebLogo",
+      "description": "Display WebLogo in a Macromolecule column header tooltip",
       "propertyType": "bool",
       "defaultValue": "true",
       "nullable": false
     },
     {
       "name": "DefaultSeparator",
+      "description": "Default separator using to convert sequences into separator notation",
       "propertyType": "string",
       "defaultValue": ".",
       "nullable": false
@@ -34,18 +37,18 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.41.8",
+    "@datagrok-libraries/bio": "^5.42.3",
     "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/math": "^1.1.5",
-    "@datagrok-libraries/ml": "^6.6.5",
+    "@datagrok-libraries/ml": "^6.6.12",
     "@datagrok-libraries/tutorials": "^1.3.12",
-    "@datagrok-libraries/utils": "^4.2.5",
+    "@datagrok-libraries/utils": "^4.2.11",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
-    "datagrok-api": "^1.17.4",
+    "datagrok-api": "^1.18.6",
     "dayjs": "^1.11.4",
     "fastest-levenshtein": "^1.0.16",
     "openchemlib": "^7.2.3",
@@ -55,6 +58,8 @@
     "wu": "latest"
   },
   "devDependencies": {
+    "@datagrok-libraries/helm-web-editor": "^1.1.5",
+    "@datagrok-libraries/js-draw-lite": "^0.0.3",
     "@datagrok/chem": "^1.9.2",
     "@datagrok/dendrogram": "^1.2.29",
     "@datagrok/helm": "^2.2.1",

package/src/package-types.ts

@@ -4,9 +4,11 @@ import * as ui from 'datagrok-api/ui';
 
 import {Observable, Subject} from 'rxjs';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {Group} from 'datagrok-api/dg';
 
 /** Names of package properties/settings declared in properties section of {@link './package.json'} */
 export const enum BioPackagePropertiesNames {
+  MonomerWidthMode = 'MonomerWidthMode',
   MaxMonomerLength = 'MaxMonomerLength',
   TooltipWebLogo = 'TooltipWebLogo',
   DefaultSeparator = 'DefaultSeparator',
@@ -17,13 +19,15 @@ export class BioPackageProperties extends Map<string, any> {
   private _onPropertyChanged: Subject<string> = new Subject<string>();
   public get onPropertyChanged(): Observable<string> { return this._onPropertyChanged; }
 
-  /** Monomer name maximum length displayed in short mode. */
-  public get MaxMonomerLength(): number {
-    return super.get(BioPackagePropertiesNames.MaxMonomerLength) as number;
+  /** Monomer symbol maximum length displayed, null for unlimited. */
+  public get MaxMonomerLength(): number | null {
+    const vs = super.get(BioPackagePropertiesNames.MaxMonomerLength);
+    return vs === 'long' ? null : parseInt(vs);
   }
 
-  public set MaxMonomerLength(value: number) {
-    super.set(BioPackagePropertiesNames.MaxMonomerLength, value);
+  public set MaxMonomerLength(value: number | null) {
+    const vs = value === null ? 'long' : value.toString();
+    super.set(BioPackagePropertiesNames.MaxMonomerLength, vs);
     this._onPropertyChanged.next(BioPackagePropertiesNames.MaxMonomerLength);
   }
 

package/src/package.ts

@@ -3,8 +3,6 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import '@datagrok-libraries/bio/src/types/helm';
-
 import {Options} from '@datagrok-libraries/utils/src/type-declarations';
 import {DimReductionBaseEditor, PreprocessFunctionReturnType}
   from '@datagrok-libraries/ml/src/functionEditors/dimensionality-reduction-editor';
@@ -78,6 +76,8 @@ import {generateLongSequence, generateLongSequence2} from '@datagrok-libraries/b
 
 import {CyclizedNotationProvider} from './utils/cyclized';
 import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
+import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 export const _package = new BioPackage();
 
@@ -109,13 +109,19 @@ let monomerLib: IMonomerLib | null = null;
 
 //tags: init
 export async function initBio() {
-  const logPrefix = 'Bio: initBio()';
+  const logPrefix = 'Bio: _package.initBio()';
   _package.logger.debug(`${logPrefix}, start`);
   const module = await grok.functions.call('Chem:getRdKitModule');
   const t1: number = window.performance.now();
   await Promise.all([
     (async () => {
       const monomerLibManager = await MonomerLibManager.getInstance();
+      // Fix user lib settings for explicit stuck from a terminated test
+      const libSettings = await getUserLibSettings();
+      if (libSettings.explicit) {
+        libSettings.explicit = [];
+        await setUserLibSettings(libSettings);
+      }
       await monomerLibManager.loadLibraries();
       monomerLib = monomerLibManager.getBioLib();
     })(),
@@ -152,7 +158,7 @@ export async function initBio() {
 
   hydrophobPalette = new SeqPaletteCustom(palette);
 
-  _package.logger.debug('Bio: initBio(), completed');
+  _package.logger.debug(`${logPrefix}, end`);
 }
 
 //name: sequenceTooltip

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

@@ -108,8 +108,6 @@ 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');
@@ -117,16 +115,16 @@ id3,QHIRE--LT
       const monLength: number = 3;
       const charWidth: number = 7;
       const sepWidth: number = 12;
-      const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, _package.logger, () => {
-        const sh = SeqHandler.forColumn(seqCol);
-        return {
-          seqHandler: sh,
-          monomerCharWidth: charWidth,
-          separatorWidth: sepWidth,
-          monomerToShort: monomerToShort,
-          monomerLengthLimit: monLength,
-        };
-      });
+      const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, _package.logger, monLength,
+        () => {
+          const sh = SeqHandler.forColumn(seqCol);
+          return {
+            seqHandler: sh,
+            monomerCharWidth: charWidth,
+            separatorWidth: sepWidth,
+            monomerToShort: monomerToShort,
+          };
+        });
 
       const width: number = 10000;
       const testList = testData.testList;

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

@@ -2,33 +2,25 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-export enum MonomerWidthMode {
-  long = 'long',
-  short = 'short',
-}
-
-export const enum Tags {
-  RendererSettingsChanged = '.mm.cellRenderer.settingsChanged',
-}
-
 export const rendererSettingsChangedState = {
   true: '1',
   false: '0',
 };
 
 export const enum Temps {
-  monomerWidth = '.mm.cellRenderer.monomerWidth',
+  maxMonomerLength = '.mm.cellRenderer.maxMonomerLength',
   colorCode = '.mm.cellRenderer.colorCode',
   compareWithCurrent = '.mm.cellRenderer.compareWithCurrent',
   highlightDifference = '.mm.cellRenderer.highlightDifference',
   gapLength = '.mm.cellRenderer.gapLength',
   monomerPlacer = '.mm.cellRenderer.monomerPlacer',
+
+  rendererSettingsChanged = '.mm.cellRenderer.settingsChanged',
 }
 
 export const enum tempTAGS {
   referenceSequence = 'reference-sequence',
   currentWord = 'current-word',
-  monomerWidth = 'monomer-width',
 }
 
 // export const MacromoleculeCellRendererDefaults = new class {

package/src/utils/cell-renderer.ts

@@ -25,8 +25,8 @@ import {alphabetPolymerTypes, IMonomerLib} from '@datagrok-libraries/bio/src/typ
 import {getGridCellRendererBack} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 
 import {
-  Temps as mmcrTemps, Tags as mmcrTags,
-  tempTAGS, rendererSettingsChangedState
+  Temps as mmcrTemps,
+  tempTAGS, rendererSettingsChangedState, Temps
 } from '../utils/cell-renderer-consts';
 import * as C from './constants';
 
@@ -152,43 +152,45 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     let gapLength = 0;
     const msaGapLength = 8;
-    let maxLengthOfMonomer = 50; // in case of long monomer representation, do not limit max length
 
     // Cell renderer settings
-    const tempMonomerWidth: string | null = tableColTemp[tempTAGS.monomerWidth];
-    const monomerWidth: string = (tempMonomerWidth != null) ? tempMonomerWidth : 'short';
-    if (monomerWidth === 'short') {
-      // Renderer can start to work before Bio package initialized, in that time _package.properties is null.
-      // TODO: Render function is available but package init method is not completed
-      const tagMaxMonomerLength: number = parseInt(tableCol.getTag(mmcrTAGS.maxMonomerLength));
-      maxLengthOfMonomer =
-        (!isNaN(tagMaxMonomerLength) ? tagMaxMonomerLength : _package.properties?.MaxMonomerLength) ?? 4;
+    let maxLengthOfMonomer: number = (_package.properties ? _package.properties.MaxMonomerLength : 4) ?? 50;
+    if (mmcrTAGS.maxMonomerLength in tableCol.tags) {
+      const v = parseInt(tableCol.getTag(mmcrTAGS.maxMonomerLength));
+      maxLengthOfMonomer = !isNaN(v) && v ? v : 50;
+    }
+    if (Temps.maxMonomerLength in tableColTemp) {
+      const v = tableColTemp[Temps.maxMonomerLength];
+      maxLengthOfMonomer = !isNaN(v) && v ? v : 50;
     }
 
     const [_gc, _tc, temp] =
       getGridCellRendererBack<string, MonomerPlacer>(gridCell);
     let seqColTemp: MonomerPlacer = temp.rendererBack;
     if (!seqColTemp) {
-      seqColTemp = temp.rendererBack = new MonomerPlacer(gridCol, tableCol, _package.logger,
+      seqColTemp = temp.rendererBack = new MonomerPlacer(gridCol, tableCol, _package.logger, maxLengthOfMonomer,
         () => {
           const sh = SeqHandler.forColumn(tableCol);
           return {
             seqHandler: sh,
             monomerCharWidth: 7, separatorWidth: !sh.isMsa() ? gapLength : msaGapLength,
-            monomerToShort: monomerToShortFunction, monomerLengthLimit: maxLengthOfMonomer,
+            monomerToShort: monomerToShortFunction,
           };
         });
     }
 
     g.save();
     try {
-      if (tableCol.tags[mmcrTags.RendererSettingsChanged] === rendererSettingsChangedState.true) {
+      if (
+        tableCol.temp[Temps.rendererSettingsChanged] === rendererSettingsChangedState.true ||
+        seqColTemp.monomerLengthLimit != maxLengthOfMonomer
+      ) {
         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);
+        tableCol.temp[Temps.rendererSettingsChanged] = rendererSettingsChangedState.false;
       }
 
       const [maxLengthWords, maxLengthWordsSum]: [number[], number[]] =
@@ -245,9 +247,13 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         g.fillStyle = undefinedColor;
         const last = posIdx === subParts.length - 1;
         /*x1 = */
-        printLeftOrCentered(x + this.padding, y, w, h,
-          g, amino, color, 0, true, 1.0, separator, last, drawStyle,
-          maxLengthWordsSum, posIdx, gridCell, referenceSequence, maxLengthOfMonomer, seqColTemp._monomerLengthMap);
+        const opts = {
+          color: color, pivot: 0, left: true, transparencyRate: 1.0, separator: separator, last: last,
+          drawStyle: drawStyle, maxWord: maxLengthWordsSum, wordIdx: posIdx, gridCell: gridCell,
+          referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
+          monomerTextSizeMap: seqColTemp._monomerLengthMap, logger: _package.logger
+        };
+        printLeftOrCentered(g, amino, x + this.padding, y, w, h, opts);
         if (minDistanceRenderer > w) break;
       }
     } catch (err: any) {
@@ -350,14 +356,17 @@ export function drawMoleculeDifferenceOnCanvas(
 
     if (amino1 != amino2) {
       const color2 = palette.get(amino2);
-      const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
-      const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
+      const subX0 = printLeftOrCentered(g, amino1, updatedX, updatedY - vShift, w, h,
+        {color: color1, pivot: 0, left: true});
+      const subX1 = printLeftOrCentered(g, amino2, updatedX, updatedY + vShift, w, h,
+        {color: color2, pivot: 0, left: true});
       updatedX = Math.max(subX1, subX0);
       if (molDifferences)
         molDifferences[i] = createDifferenceCanvas(amino1, amino2, color1, color2, updatedY, vShift, h);
     } else {
       //
-      updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
+      updatedX = printLeftOrCentered(g, amino1, updatedX, updatedY, w, h,
+        {color: color1, pivot: 0, left: true, transparencyRate: 0.5});
     }
     updatedX += 4;
   }
@@ -382,8 +391,8 @@ function createDifferenceCanvas(amino1: string, amino2: string, color1: string,
   canvas.width = width + 4;
   context.font = '12px monospace';
   context.textBaseline = 'top';
-  printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
-  printLeftOrCentered(0, y + shift, width, h, context, amino2, color2, 0, true);
+  printLeftOrCentered(context, amino1, 0, y - shift, width, h, {color: color1, pivot: 0, left: true});
+  printLeftOrCentered(context, amino2, 0, y + shift, width, h, {color: color2, pivot: 0, left: true});
   return canvas;
 }
 

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

@@ -2,10 +2,10 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
+import {PolymerType} from '@datagrok-libraries/bio/src/helm/types';
 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 * as C from './constants';
 import {getMonomerLib} from '../package';

package/src/utils/monomer-lib/library-file-manager/file-validator.ts

@@ -2,6 +2,12 @@ import {JSONSchemaType, ValidateFunction} from 'ajv';
 import Ajv2020 from 'ajv/dist/2020';
 import addErrors from 'ajv-errors';
 
+const NA_CODE: string = '#N/A';
+
+import {
+  HELM_REQUIRED_FIELD as REQ,
+} from '@datagrok-libraries/bio/src/utils/const';
+
 export class MonomerLibFileValidator {
   private validateMonomerSchema: ValidateFunction<any>;
 
@@ -14,25 +20,24 @@ export class MonomerLibFileValidator {
   }
 
   validateFile(fileContent: string, fileName: string): boolean {
-    const jsonContent = this.parseJson(fileContent);
+    const jsonContent = this.parseJson(fileContent, fileName);
     if (jsonContent === null)
       return false;
 
     if (!Array.isArray(jsonContent)) {
-      console.warn(
-        'Bio: Monomer Library File Validator: Invalid JSON format: The file must contain an array of monomers.'
-      );
+      console.warn(`Bio: Monomer Library File Validator file '${fileName}': Invalid JSON format: ` +
+        'The file must contain an array of monomers.');
       return false;
     }
 
     return this.validateJsonContent(jsonContent, fileName);
   }
 
-  private parseJson(fileContent: string): any[] | null {
+  private parseJson(fileContent: string, fileName: string): any[] | null {
     try {
       return JSON.parse(fileContent);
     } catch (e) {
-      console.error('Bio: Monomer Library File Validator: Invalid JSON format:', e);
+      console.error(`Bio: Monomer Library File Validator file '${fileName}': Invalid JSON format:`, e);
       return null;
     }
   }
@@ -40,10 +45,11 @@ export class MonomerLibFileValidator {
   private validateJsonContent(jsonContent: any[], fileName: string): boolean {
     let isValid = true;
     for (const monomer of jsonContent) {
+      const name = monomer[REQ.SYMBOL] ?? monomer[REQ.ID] ?? monomer[REQ.NAME] ?? NA_CODE;
       isValid = this.validateMonomerSchema(monomer);
       if (!isValid) {
         console.warn(
-          `Bio: Monomer Library File Validator:\nfile ${fileName}\n monomer violating JSON schema:`,
+          `Bio: Monomer Library File Validator file ${fileName}, monomer '${name}' violating JSON schema:`,
           monomer,
           '\nError reason: ',
           this.validateMonomerSchema.errors,

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -14,6 +14,7 @@ import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getMonomerLibHelper, IMonomerLibFileManager} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {MonomerLibFileEventManager} from './event-manager';
+import {_package} from '../../../package';
 
 export async function showManageLibrariesDialog(): Promise<void> {
   await DialogWrapper.showDialog();
@@ -89,7 +90,8 @@ class MonomerLibraryManagerWidget {
 
 class LibraryControlsManager {
   private constructor(
-    private fileManager: IMonomerLibFileManager
+    private fileManager: IMonomerLibFileManager,
+    private readonly userLibSettings: UserLibSettings,
   ) {
     this.fileManager.eventManager.updateUIControlsRequested$.subscribe(() => {
       this.updateControlsForm();
@@ -99,13 +101,18 @@ class LibraryControlsManager {
     });
   }
 
-  private userLibSettings: UserLibSettings;
+  private toLog(): string {
+    return `LibraryControlsManager<#>`;
+  }
 
   static async createControlsForm(): Promise<HTMLElement> {
-    const libHelper = await getMonomerLibHelper();
-    const fileManager = await libHelper.getFileManager();
-    const manager = new LibraryControlsManager(fileManager);
-    await manager.initialize();
+    const logPrefix = 'LibraryControlsForm.createControlsForm()';
+    _package.logger.debug(`${logPrefix}, start`);
+    const [fileManager, userLibSettings] = await Promise.all([
+      getMonomerLibHelper().then((libHelper) => libHelper.getFileManager()),
+      await getUserLibSettings(),
+    ]);
+    const manager = new LibraryControlsManager(fileManager, userLibSettings);
 
     return manager._createControlsForm();
   }
@@ -118,10 +125,6 @@ class LibraryControlsManager {
     return inputsForm;
   }
 
-  private async initialize(): Promise<void> {
-    this.userLibSettings = await getUserLibSettings();
-  };
-
   private updateControlsForm(): void {
     const updatedForm = this._createControlsForm();
     $('.monomer-lib-controls-form').replaceWith(updatedForm);
@@ -133,6 +136,8 @@ class LibraryControlsManager {
   }
 
   private createLibInput(libFileName: string): DG.InputBase<boolean | null> {
+    const logPrefix = `${this.toLog()}.createLibInput()`;
+    _package.logger.debug(`${logPrefix}, libFileName = '${libFileName}', start`);
     const isMonomerLibrarySelected = !this.userLibSettings.exclude.includes(libFileName);
     const libInput = ui.boolInput(
       libFileName,
@@ -144,6 +149,7 @@ class LibraryControlsManager {
     const deleteIcon = ui.iconFA('trash-alt', () => this.promptForLibraryDeletion(libFileName));
     ui.tooltip.bind(deleteIcon, `Delete ${libFileName}`);
     libInput.addOptions(deleteIcon);
+    _package.logger.debug(`${logPrefix}, libFileName = '${libFileName}', end`);
     return libInput;
   }
 

package/src/utils/monomer-lib/monomer-lib.ts

@@ -6,17 +6,18 @@ import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import {Observable, Subject} from 'rxjs';
 
-import {
-  IMonomerLib, Monomer, MonomerLibSummaryType, MonomerType, PolymerType, RGroup
-} from '@datagrok-libraries/bio/src/types';
-import {PolymerTypes} from '@datagrok-libraries/bio/src/utils/const';
+import {MonomerType, PolymerType} from '@datagrok-libraries/bio/src/helm/types';
+import {IMonomerLib, Monomer, MonomerLibSummaryType, RGroup} from '@datagrok-libraries/bio/src/types';
 import {HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP} from '@datagrok-libraries/bio/src/utils/const';
 import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
 
 import '../../../css/cell-renderer.css';
 
+import {_package} from '../../package';
+
 /** Wrapper for monomers obtained from different sources. For managing monomere
  * libraries, use MolfileHandler class instead */
 export class MonomerLib implements IMonomerLib {
@@ -75,7 +76,8 @@ export class MonomerLib implements IMonomerLib {
     return m;
   }
 
-  getMonomer(polymerType: PolymerType, argMonomerSymbol: string): Monomer | null {
+  getMonomer(polymerType: PolymerType | null, argMonomerSymbol: string): Monomer | null {
+    const logPrefix = `Bio: MonomerLib.getMonomer()`;
     // Adjust RNA's 'R' for ribose to 'r' and 'P' for phosphate to 'p' for case-sensitive monomer names.
     // There are uppercase 'R' and 'P' at RNA samples in test data 'helm2.csv' but lowercase in HELMCoreLibrary.json
     let monomerSymbol = argMonomerSymbol;
@@ -84,10 +86,20 @@ export class MonomerLib implements IMonomerLib {
     if (polymerType == 'RNA' && monomerSymbol == 'P')
       monomerSymbol = 'p';
 
-    if (polymerType in this._monomers! && monomerSymbol in this._monomers![polymerType])
-      return this._monomers![polymerType][monomerSymbol];
-    else
-      return null;
+    let res: Monomer | null = null;
+
+    if (!polymerType) {
+      _package.logger.warning(`${logPrefix} symbol '${argMonomerSymbol}', polymerType not specified.`);
+      // Assume any polymer type
+      for (const [polymerType, dict] of Object.entries(this._monomers)) {
+        res = dict[monomerSymbol];
+        if (res) break;
+      }
+    } else {
+      const dict = this._monomers[polymerType];
+      res = dict ? dict[monomerSymbol] : null;
+    }
+    return res;
   }
 
   getPolymerTypes(): PolymerType[] {
@@ -231,6 +243,7 @@ export class MonomerLib implements IMonomerLib {
       const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
       let structureEl: HTMLElement;
       if (monomer.molfile) {
+        //
         structureEl = grok.chem.svgMol(monomer.molfile, undefined, undefined, chemOptions);
       } else if (monomer.smiles) {
         structureEl = ui.divV([
@@ -245,7 +258,7 @@ export class MonomerLib implements IMonomerLib {
         {style: {display: 'flex', flexDirection: 'row', justifyContent: 'center', margin: '6px'}}));
 
       // Source
-      res.append(ui.divText(monomer.lib?.source ?? 'unknown'));
+      res.append(ui.divText(monomer.lib?.source ?? 'Missed in libraries'));
 
       // const label = (s: string) => {
       //   return ui.label(s /* span ? */, {classes: 'ui-input-label'});

package/src/utils/split-to-monomers.ts

@@ -31,7 +31,7 @@ export async function splitToMonomersUI(table: DG.DataFrame, seqCol: DG.Column<s
     colNameRe.lastIndex = 0;
     const ma = srcName.match(colNameRe);
     if (!ma) return srcName;
-    return `${ma[1]} (${parseInt(ma[2] ?? 0) + 1})`;
+    return `${ma[1]} (${parseInt(ma[2] ?? '0') + 1})`;
   };
 
   // if (tempDf.columns.length === 0) return;