@datagrok/bio 2.18.4 → 2.20.0

package/src/package.ts

@@ -47,11 +47,10 @@ import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
 import {WebLogoViewer} from './viewers/web-logo-viewer';
 import {MonomerLibManager} from './utils/monomer-lib/lib-manager';
 import {getMonomerLibraryManagerLink, showManageLibrariesDialog, showManageLibrariesView} from './utils/monomer-lib/library-file-manager/ui';
-import {demoBio01UI} from './demo/bio01-similarity-diversity';
-import {demoBio01aUI} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
+import {demoBioSimDiv} from './demo/bio01-similarity-diversity';
+import {demoSeqSpace} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
 import {demoBio01bUI} from './demo/bio01b-hierarchical-clustering-and-activity-cliffs';
-import {demoBio03UI} from './demo/bio03-atomic-level';
-import {demoBio05UI} from './demo/bio05-helm-msa-sequence-space';
+import {demoToAtomicLevel} from './demo/bio03-atomic-level';
 import {checkInputColumnUI} from './utils/check-input-column';
 import {MsaWarning} from './utils/multiple-sequence-alignment';
 import {multipleSequenceAlignmentUI} from './utils/multiple-sequence-alignment-ui';
@@ -422,7 +421,7 @@ export function getRegion(
     start ?? null, end ?? null, name ?? null);
 }
 
-//top-menu: Bio | Convert | Get Region...
+//top-menu: Bio | Calculate | Get Region...
 //name: Get Region Top Menu
 //description: Get sequences for a region specified from a Macromolecule
 //input: dataframe table                           [Input data table]
@@ -587,7 +586,7 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
   plotEmbeddings: boolean, preprocessingFunction?: DG.Func, options?: (IUMAPOptions | ITSNEOptions) & Options,
   clusterEmbeddings?: boolean, isDemo?: boolean
 ): Promise<DG.ScatterPlotViewer | undefined> {
-  const tableView = isDemo ? (grok.shell.view('Browse')! as DG.BrowseView)!.preview! as DG.TableView :
+  const tableView =
     grok.shell.tv.dataFrame == table ? grok.shell.tv : undefined;
   if (!checkInputColumnUI(molecules, 'Sequence Space'))
     return;
@@ -607,14 +606,13 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
   return res;
 }
 
-//top-menu: Bio | Convert | To Atomic Level...
+//top-menu: Bio | Transform | To Atomic Level...
 //name: To Atomic Level
 //description: Converts sequences to molblocks
 //input: dataframe table [Input data table]
 //input: column seqCol {caption: Sequence; semType: Macromolecule}
 //input: bool nonlinear =false {caption: Non-linear; description: Slower mode for cycling/branching HELM structures}
 //input: bool highlight =false {caption: Highlight monomers; description: Highlight monomers' substructures of the molecule }
-//output:
 export async function toAtomicLevel(
   table: DG.DataFrame, seqCol: DG.Column, nonlinear: boolean, highlight: boolean = false
 ): Promise<void> {
@@ -630,6 +628,17 @@ export async function toAtomicLevel(
   }
 }
 
+//name: To Atomic Level...
+//input: column seqCol {semType: Macromolecule}
+//meta.action: to atomic level
+export async function toAtomicLevelAction(seqCol: DG.Column) {
+  if (!seqCol?.dataFrame)
+    throw new Error('Sequence column is not found or its data frame is not empty');
+  const func = DG.Func.find({name: 'toAtomicLevel', package: 'Bio'})[0];
+  if (!func) throw new Error('To Atomic level Function not found');
+  func.prepare({table: seqCol.dataFrame, seqCol: seqCol}).edit();
+}
+
 //top-menu: Bio | Analyze | MSA...
 //name: MSA
 //description: Performs multiple sequence alignment
@@ -743,38 +752,20 @@ export function importBam(fileContent: string): DG.DataFrame [] {
   return [];
 }
 
-//top-menu: Bio | Convert | Notation...
+//top-menu: Bio | Transform | Convert Notation...
 //name: convertDialog
 export function convertDialog() {
   const col: DG.Column<string> | undefined = getMacromoleculeColumns()[0];
   convert(col, _package.seqHelper);
 }
 
-//top-menu: Bio | Convert | TestConvert
-//name: convertSeqNotation
-//description: RDKit-based conversion for SMILES, SMARTS, InChi, Molfile V2000 and Molfile V3000
-//input: string sequence {semType: Macromolecule}
-//input: string targetNotation
-//input: string separator
-//output: string result
-export async function convertSeqNotation(sequence: string, targetNotation: NOTATION, separator?: string): Promise<string | undefined | null> {
-  try {
-    const col = DG.Column.fromStrings('sequence', [sequence]);
-    const _df = DG.DataFrame.fromColumns([col]);
-    const semType = await grok.functions.call('Bio:detectMacromolecule', {col: col});
-    if (semType)
-      col.semType = semType;
-    const converterSh = _package.seqHelper.getSeqHandler(col);
-    const newColumn = converterSh.convert(targetNotation, separator);
-    return newColumn.get(0);
-  } catch (err: any) {
-    const [errMsg, errStack] = errInfo(err);
-    _package.logger.error(errMsg, undefined, errStack);
-    throw err;
-  }
+//name: Convert Notation...
+//input: column col {semType: Macromolecule}
+//meta.action: Convert Notation...
+export function convertColumnAction(col: DG.Column) {
+  convert(col, _package.seqHelper);
 }
 
-
 //name: monomerCellRenderer
 //tags: cellRenderer
 //meta.cellType: Monomer
@@ -835,7 +826,7 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
   return resDf;
 }
 
-//top-menu: Bio | Convert | Split to Monomers...
+//top-menu: Bio | Transform | Split to Monomers...
 //name: Split to Monomers
 //input: dataframe table
 //input: column sequence { semType: Macromolecule }
@@ -975,21 +966,14 @@ export async function manageLibrariesApp(): Promise<DG.View> {
 
 //name: Monomer Manager Tree Browser
 //input: dynamic treeNode
-//input: view browseView
-export async function manageLibrariesAppTreeBrowser(treeNode: DG.TreeViewGroup, browseView: DG.BrowseView) {
+//input: dynamic browsePanel
+export async function manageLibrariesAppTreeBrowser(treeNode: DG.TreeViewGroup, browsePanel: DG.BrowsePanel) {
   const libraries = (await (await MonomerLibManager.getInstance()).getFileManager()).getValidLibraryPaths();
   libraries.forEach((libName) => {
     const nodeName = libName.endsWith('.json') ? libName.substring(0, libName.length - 5) : libName;
     const libNode = treeNode.item(nodeName);
     // eslint-disable-next-line rxjs/no-ignored-subscription, rxjs/no-async-subscribe
     libNode.onSelected.subscribe(async () => {
-      const monomerManager = await MonomerManager.getNewInstance();
-      browseView.preview = await monomerManager.getViewRoot(libName, false);
-    });
-
-    libNode.root.addEventListener('dblclick', async (e) => {
-      e.preventDefault();
-      e.stopImmediatePropagation();
       const monomerManager = await MonomerManager.getInstance();
       await monomerManager.getViewRoot(libName, true);
       monomerManager.resetCurrentRowFollowing();
@@ -1111,10 +1095,9 @@ export function addCopyMenu(cell: DG.Cell, menu: DG.Menu): void {
 //meta.demoPath: Bioinformatics | Similarity, Diversity
 //description: Sequence similarity tracking and evaluation dataset diversity
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Similarity,%20Diversity
-//meta.isDemoScript: True
 //meta.demoSkip: GROK-14320
 export async function demoBioSimilarityDiversity(): Promise<void> {
-  await demoBio01UI();
+  await demoBioSimDiv();
 }
 
 // demoBio01a
@@ -1122,10 +1105,9 @@ export async function demoBioSimilarityDiversity(): Promise<void> {
 //meta.demoPath: Bioinformatics | Sequence Space
 //description: Exploring sequence space of Macromolecules, comparison with hierarchical clustering results
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Sequence%20Space
-//meta.isDemoScript: True
 //meta.demoSkip: GROK-14320
 export async function demoBioSequenceSpace(): Promise<void> {
-  await demoBio01aUI();
+  await demoSeqSpace();
 }
 
 // demoBio01b
@@ -1144,21 +1126,9 @@ export async function demoBioActivityCliffs(): Promise<void> {
 //meta.demoPath: Bioinformatics | Atomic Level
 //description: Atomic level structure of Macromolecules
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Atomic%20Level
-//meta.isDemoScript: True
 //meta.demoSkip: GROK-14320
 export async function demoBioAtomicLevel(): Promise<void> {
-  await demoBio03UI();
-}
-
-// demoBio05
-//name: demoBioHelmMsaSequenceSpace
-//meta.demoPath: Bioinformatics | Helm, MSA, Sequence Space
-//description: MSA and composition analysis on Helm data
-//meta.path: /apps/Tutorials/Demo/Bioinformatics/Helm,%20MSA,%20Sequence%20Space
-//meta.isDemoScript: True
-//meta.demoSkip: GROK-14320
-export async function demoBioHelmMsaSequenceSpace(): Promise<void> {
-  await demoBio05UI();
+  await demoToAtomicLevel();
 }
 
 //name: SDF to JSON Library

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

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {expect} from '@datagrok-libraries/utils/src/test';
+import {awaitCheck, 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';
@@ -25,9 +25,10 @@ export async function _testActivityCliffsOpen(df: DG.DataFrame, drMethod: DimRed
   })) 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(), `${tgtNumberCliffs} cliffs`);
+  await awaitCheck(() => {
+    const link = Array.from(scatterPlot!.root.getElementsByClassName('scatter_plot_link'));
+    if (link.length)
+      return (link[0] as HTMLElement).innerText.toLowerCase() === `${tgtNumberCliffs} cliffs`;
+    return true;
+  }, 'incorrect cliffs link', 3000);
 }

package/src/tests/scoring.ts

@@ -21,8 +21,8 @@ category('Scoring', () => {
   /* eslint-disable max-len */
   const table = DG.DataFrame.fromCsv(`${sequence},${expectedSimilarity},${expectedIdentity}
 PEPTIDE1{Aca.Orn.gGlu.Pqa.D-His_1Bn.dH.hHis.4Abz.D-Tic.D-Dap.Y.Iva.meS.F.P.F.D-1Nal}$$$$,1.0,1.0
-PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.68,0.53
-PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.34,0.0`
+PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.691,0.53
+PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.37,0.0`
   );
   const seqCol: DG.Column<string> = table.getCol(sequence);
   seqCol.meta.units = NOTATION.HELM;

package/src/tests/similarity-diversity-tests.ts

@@ -37,7 +37,7 @@ async function _testSimilaritySearchViewer() {
   await awaitCheck(() => getSearchViewer(moleculesView, 'Sequence Similarity Search') !== undefined,
     'Sequence Similarity Search viewer has not been created', 100);
   if (!viewer.initialized) throw new Error('The viewer is not initialized.');
-  if (!viewer.moleculeColumn) throw new Error('The viewer has not molecule column (onTableAttached).');
+  if (!viewer.targetColumn) throw new Error('The viewer has not molecule column (onTableAttached).');
   if (!viewer.beforeRender()) throw new Error('The viewer is not able to render.');
   if (!viewer.computeRequested) throw new Error('The viewer has not compute requested even.');
   if (!computeCompleted) throw new Error('The viewer has not compute completed.');
@@ -87,7 +87,7 @@ async function _testDiversitySearchViewer() {
   await awaitCheck(() => getSearchViewer(moleculesView, 'Sequence Diversity Search') !== undefined,
     'Sequence Diversity Search viewer has not been created', 100);
   if (!viewer.initialized) throw new Error('The viewer is not initialized.');
-  if (!viewer.moleculeColumn) throw new Error('The viewer has not molecule column (onTableAttached).');
+  if (!viewer.targetColumn) throw new Error('The viewer has not molecule column (onTableAttached).');
   if (!viewer.beforeRender()) throw new Error('The viewer is not able to render.');
   if (!viewer.computeRequested) throw new Error('The viewer has not compute requested even.');
   if (!computeCompleted) throw new Error('The viewer has not compute completed.');

package/src/utils/cell-renderer.ts

@@ -58,7 +58,6 @@ export function processSequence(subParts: string[]): [string[], boolean] {
 type RendererGridCellTemp = {
   [MmcrTemps.monomerPlacer]: MonomerPlacer
 }
-
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   private readonly seqHelper: ISeqHelper;
 
@@ -70,6 +69,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
   get defaultWidth(): number | null { return 230; }
 
+  hasMouseOver: boolean = false;
+
   constructor() {
     super();
     this.seqHelper = _package.seqHelper;
@@ -101,6 +102,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   override onMouseEnter(gridCell: DG.GridCell, e: MouseEvent) {
     const back = this.getRendererBack(gridCell);
     back?.onMouseEnter(gridCell, e);
+    this.hasMouseOver = true;
   }
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
@@ -110,6 +112,14 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
   override onMouseLeave(gridCell: DG.GridCell, _e: MouseEvent) {
     execMonomerHoverLinks(gridCell, null);
+    if (gridCell?.grid) {
+      const sub = gridCell.grid.onEvent('d4-grid-show-tooltip').subscribe((e) => {
+        sub.unsubscribe();
+        if (this.hasMouseOver)
+          e.preventDefault();
+      });
+    }
+    this.hasMouseOver = false;
   }
 
   override onDoubleClick(gridCell: DG.GridCell, e: MouseEvent) {

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

@@ -4,9 +4,8 @@ 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 {IMonomerLib, IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
-import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {MolfileWithMap, MonomerMap} from '@datagrok-libraries/bio/src/monomer-works/types';
 
 import {Polymer} from './polymer';
@@ -14,9 +13,10 @@ import {GlobalMonomerPositionHandler} from './position-handler';
 
 import {_package} from '../../../package';
 import {getUnusedColName} from '@datagrok-libraries/bio/src/monomer-works/utils';
+import {IHelmToMolfileConverter} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 
-export class HelmToMolfileConverter {
+export class HelmToMolfileConverter implements IHelmToMolfileConverter {
   constructor(
     private readonly helmHelper: IHelmHelper,
     private readonly rdKitModule: RDModule,
@@ -41,6 +41,20 @@ export class HelmToMolfileConverter {
     return smiles;
   }
 
+  public molV3KtoMolV3KOCL(molV3k: string): string {
+    try {
+      if (!molV3k)
+        return '';
+      const oclMolecule = OCL.Molecule.fromMolfile(molV3k);
+      const molV3000 = oclMolecule.toMolfileV3();
+      return molV3000.replace('STERAC1', 'STEABS');
+    } catch (err) {
+      const [errMsg, errStack] = errInfo(err);
+      _package.logger.error(errMsg, undefined, errStack);
+      return '';
+    }
+  }
+
   public getMolV3000ViaOCL(beautifiedMols: (RDMol | null)[], columnName: string): DG.Column<string> {
     const beautifiedMolV2000 = beautifiedMols.map((mol) => {
       if (mol === null)
@@ -52,9 +66,7 @@ export class HelmToMolfileConverter {
     const molv3000Arr = new Array<string>(beautifiedMolV2000.length);
     const chiralityPb = DG.TaskBarProgressIndicator.create(`Handling chirality...`);
     for (let i = 0; i < beautifiedMolV2000.length; i++) {
-      const oclMolecule = OCL.Molecule.fromMolfile(beautifiedMolV2000[i]);
-      const molV3000 = oclMolecule.toMolfileV3();
-      molv3000Arr[i] = molV3000.replace('STERAC1', 'STEABS');
+      molv3000Arr[i] = this.molV3KtoMolV3KOCL(beautifiedMolV2000[i]);
       const progress = i / beautifiedMolV2000.length * 100;
       chiralityPb.update(progress, `${progress?.toFixed(2)}% of molecules completed`);
     }
@@ -136,9 +148,9 @@ export class HelmToMolfileConverter {
     const woGapsRes = this.helmHelper.removeGaps(helm);
     const woGapsHelm = woGapsRes.resHelm;
     const woGapsReverseMap = new Map<number, number>();
-    for (const [orgPosIdx, woGapsPosIdx] of (woGapsRes.monomerMap?.entries() ?? [])) {
+    for (const [orgPosIdx, woGapsPosIdx] of (woGapsRes.monomerMap?.entries() ?? []))
       woGapsReverseMap.set(woGapsPosIdx, orgPosIdx);
-    }
+
     const pseudoMolfile = this.helmHelper.getMolfiles([woGapsHelm])[0];
     const globalPositionHandler = new GlobalMonomerPositionHandler(pseudoMolfile);
     const woGapsPolymer = new Polymer(woGapsHelm, this.rdKitModule, this.monomerLib);

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

@@ -10,7 +10,7 @@ import {MolfileWrapperFactory} from './mol-wrapper-factory';
 export class MonomerWrapper {
   private readonly molfileWrapper: MolfileWrapper;
   private capGroupElements: string[] = [];
-
+  private static molfileV2KToV3KCache: Map<string, string> = new Map();
   constructor(
     public readonly monomerSymbol: string,
     public readonly monomerIdx: number,
@@ -39,12 +39,16 @@ export class MonomerWrapper {
   public get bondCount() { return this.molfileWrapper.bondCount; }
 
   private convertMolfileToV3KFormat(molfileV2K: string, monomerSymbol: string, rdKitModule: RDModule): string {
+    if (MonomerWrapper.molfileV2KToV3KCache.has(molfileV2K))
+      return MonomerWrapper.molfileV2KToV3KCache.get(molfileV2K)!;
     let mol: RDMol | null = null;
     try {
       mol = rdKitModule.get_mol(molfileV2K, JSON.stringify({mergeQueryHs: true}));
-      if (mol)
-        return mol.get_v3Kmolblock();
-      else
+      if (mol) {
+        const res = mol.get_v3Kmolblock();
+        MonomerWrapper.molfileV2KToV3KCache.set(molfileV2K, res);
+        return res;
+      } else
         throw new Error(`Cannot convert ${monomerSymbol} to molV3000`);
     } finally {
       mol?.delete();

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

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import {HELM_MONOMER_TYPE, HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
 import {cleanupHelmSymbol} from '@datagrok-libraries/bio/src/helm/utils';
 
@@ -5,8 +6,10 @@ import {Bond} from './types';
 
 /** Wrapper over simple polymer substring of HELM, like RNA1{d(A)p}  */
 export class SimplePolymer {
+  private isNucleotideSequence = false;
   constructor(private simplePolymer: string) {
     this.polymerType = this.getPolymerType();
+    this.isNucleotideSequence = this.polymerType === HELM_POLYMER_TYPE.RNA;
     this.idx = this.getIdx();
     const {monomers, monomerTypes} = this.getMonomerSymbolsAndTypes();
     this.monomers = monomers;
@@ -49,17 +52,23 @@ export class SimplePolymer {
     const monomerList: string[] = [];
     const monomerTypeList: HELM_MONOMER_TYPE[] = [];
     monomerGroups.forEach((monomerGroup) => {
-      // const splitted = monomerGroup.split(/\(|\)/).map((el) => el.replace(/[\[\]]/g, ''));
-      // monomerList.push(...splitted);
-      // WARNING: only the groups of the form r(A)p, as in RNA, are supported
+      if (!this.isNucleotideSequence) {
+        // const splitted = monomerGroup.split(/\(|\)/).map((el) => el.replace(/[\[\]]/g, ''));
+        // monomerList.push(...splitted);
+        // WARNING: only the groups of the form r(A)p, as in RNA, are supported
 
-      monomerList.push(cleanupHelmSymbol(monomerGroup));
-      // const monomerTypes = splitted.map(
-      //   (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
-      // );
+        monomerList.push(cleanupHelmSymbol(monomerGroup));
+        // const monomerTypes = splitted.map(
+        //   (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
+        // );
 
-      // monomerTypeList.push(...monomerTypes);
-      monomerTypeList.push(HELM_MONOMER_TYPE.BACKBONE);
+        // monomerTypeList.push(...monomerTypes);
+        monomerTypeList.push(HELM_MONOMER_TYPE.BACKBONE);
+      } else {
+        const splitted = monomerGroup.split(/\(|\)/).filter((el) => !!el).map((el) => cleanupHelmSymbol(el));
+        monomerList.push(...splitted);
+        splitted.forEach((_, i) => monomerTypeList.push(i % 3 === 1 ? HELM_MONOMER_TYPE.BRANCH : HELM_MONOMER_TYPE.BACKBONE));
+      }
     });
     return {monomers: monomerList, monomerTypes: monomerTypeList};
   }

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

@@ -177,13 +177,13 @@ export class MonomerLibBase implements IMonomerLibBase {
       // Symbol & Name
       const symbol = monomer[REQ.SYMBOL];
       const _name = monomer[REQ.NAME];
-
-      const htmlColor = wem.backgroundcolor;
+      const [color, backgroundColor, lineColor] =
+        wem ? [wem.textcolor, wem.backgroundcolor, wem.linecolor] : ['#202020', '#A0A0A0', '#202020'];
       res.append(ui.divH([
         ui.div([symbol], {
           style: {
             /* fontWeight: 'bolder', */ textWrap: 'nowrap', marginLeft: '4px', marginRight: '4px',
-            color: wem.textcolor, backgroundColor: wem.backgroundcolor, borderColor: wem.linecolor,
+            color: color, backgroundColor: backgroundColor, borderColor: lineColor,
             borderWidth: '1px', borderStyle: 'solid', borderRadius: '2px', padding: '3px',
             minWidth: '24px', textAlign: 'center',
           }
@@ -192,7 +192,7 @@ export class MonomerLibBase implements IMonomerLibBase {
       ], {style: {display: 'flex', flexDirection: 'row', justifyContent: 'left'}}));
 
       // Structure
-      const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
+      //const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
       let structureEl: HTMLElement;
       if (monomer.molfile)
         structureEl = drawMoleculeCall(monomer.molfile);

package/src/utils/pepsea.ts

@@ -7,7 +7,7 @@ import {Subject} from 'rxjs';
 
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {NOTATION, TAGS as bioTAGS, ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import { fetchWrapper } from '@datagrok-libraries/utils/src/fetch-utils';
+import {fetchWrapper} from '@datagrok-libraries/utils/src/fetch-utils';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 
 import {checkForSingleSeqClusters} from './multiple-sequence-alignment';
@@ -108,50 +108,33 @@ async function requestAlignedObjects(
     body: JSON.stringify(body),
   };
   const path = `/align?method=${method}&gap_open=${gapOpen}&gap_extend=${gapExtend}`;
-  let responseObj: any;
-  if ('fetchProxy' in grok.dapi.docker.dockerContainers) {
-    // new dockerContainers API
-    const t1: number = window.performance.now();
-    // @ts-ignore
-    const response: Response = await grok.dapi.docker.dockerContainers.fetchProxy(dockerfileId, path, params);
-    const t2: number = window.performance.now();
-    _package.logger.debug(`Bio: requestAlignedObjects() dockerContainers.fetchProxy(), ET: ${(t2 - t1)} ms`);
-    const responseContentType = response.headers.get('content-type');
-    const isJson: boolean = responseContentType === 'application/json';
-    if (!response.ok && isJson) {
-      const responseJson = await response.json();
-      const pepseaErrorMsg = responseJson['pepsea-error'];
-      if (!!pepseaErrorMsg)
-        throw new Error(`PepSeA error: ${pepseaErrorMsg}`);
-
-      const datagrokErrorMsg = responseJson['datagrok-error'];
-      if (!!datagrokErrorMsg)
-        throw new Error(`Datagrok error: ${datagrokErrorMsg}`);
-
-      throw new Error(response.statusText);
-    } else if (!response.ok && !isJson) {
-      const responseStr = await response.text();
-      throw new Error(`Error: ${responseStr}`);
-    } else if (!isJson) {
-      const responseStr = await response.text();
-      throw new Error(`Error: PepSeA expected JSON response, got '${responseStr}'.`);
-    }
-    responseObj = await response.json();
-  } else {
-    // @ts-ignore
-    const responseStr = await grok.dapi.docker.dockerContainers.request(dockerfileId, path, params)!;
-    if (!responseStr)
-      throw new Error('Empty response');
-    responseObj = JSON.parse(responseStr);
-
-    const pepseaErrorMsg = responseObj['pepsea-error'];
+  // new dockerContainers API
+  const t1: number = window.performance.now();
+  // @ts-ignore
+  const response: Response = await grok.dapi.docker.dockerContainers.fetchProxy(dockerfileId, path, params);
+  const t2: number = window.performance.now();
+  _package.logger.debug(`Bio: requestAlignedObjects() dockerContainers.fetchProxy(), ET: ${(t2 - t1)} ms`);
+  const responseContentType = response.headers.get('content-type');
+  const isJson: boolean = responseContentType === 'application/json';
+  if (!response.ok && isJson) {
+    const responseJson = await response.json();
+    const pepseaErrorMsg = responseJson['pepsea-error'];
     if (!!pepseaErrorMsg)
       throw new Error(`PepSeA error: ${pepseaErrorMsg}`);
 
-    const datagrokErrorMsg = responseObj['datagrok-error'];
+    const datagrokErrorMsg = responseJson['datagrok-error'];
     if (!!datagrokErrorMsg)
       throw new Error(`Datagrok error: ${datagrokErrorMsg}`);
+
+    throw new Error(response.statusText);
+  } else if (!response.ok && !isJson) {
+    const responseStr = await response.text();
+    throw new Error(`Error: ${responseStr}`);
+  } else if (!isJson) {
+    const responseStr = await response.text();
+    throw new Error(`Error: PepSeA expected JSON response, got '${responseStr}'.`);
   }
+  const responseObj = await response.json();
   // Check for pepsea stderr output
   if ('pepsea-stderr' in responseObj) {
     const pepseaStdErr: string = responseObj['pepsea-stderr'] as string;

package/src/utils/seq-helper/seq-handler.ts

@@ -605,12 +605,12 @@ export class SeqHandler implements ISeqHandler {
 
     const isNucleotide = srcSeq.startsWith('RNA');
     // items can be monomers or helms
-    const helmItemsArray = this.splitter(srcSeq);
+    const helmItemsArray = splitterAsHelm(srcSeq);
     const tgtMonomersArray: string[] = [];
     for (let posIdx = 0; posIdx < helmItemsArray.length; ++posIdx) {
       let om: string = helmItemsArray.getOriginal(posIdx);
       if (isNucleotide)
-        om = om.replace(HELM_WRAPPERS_REGEXP, '');
+        om = om.replace(HELM_WRAPPERS_REGEXP, '$1');
       if (om === GapOriginals[NOTATION.HELM])
         tgtMonomersArray.push(tgtGapOriginal);
       else if (this.toFasta(tgtNotation as NOTATION) && om.length > 1) {