@datagrok/bio 2.16.4 → 2.16.6

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.16.4",
+  "version": "2.16.6",
   "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",
@@ -37,7 +37,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.45.3",
+    "@datagrok-libraries/bio": "^5.45.4",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.2",
     "@datagrok-libraries/ml": "^6.7.4",

package/src/package.ts

@@ -27,6 +27,7 @@ import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {MmcrTemps} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
 
 import {getMacromoleculeColumns} from './utils/ui-utils';
 import {MacromoleculeDifferenceCellRenderer, MacromoleculeSequenceCellRenderer,} from './utils/cell-renderer';
@@ -630,7 +631,7 @@ export async function toAtomicLevel(
   const pi = DG.TaskBarProgressIndicator.create('Converting to atomic level ...');
   try {
     await initBioPromise;
-    const monomerLib = _package.monomerLib;
+    const monomerLib = seqCol.temp[MmcrTemps.overriddenLibrary] ?? _package.monomerLib;
     const seqHelper = _package.seqHelper;
     const rdKitModule = _package.rdKitModule;
     await sequenceToMolfile(table, seqCol, nonlinear, highlight, monomerLib, seqHelper, rdKitModule);

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

@@ -85,6 +85,7 @@ category('monomerLibraries', () => {
 
     const overriddenMonomerLib = monomerLib.override({[overMon.polymerType]: {[overMon.symbol]: overMon}}, 'test');
     const resOverMon = overriddenMonomerLib.getMonomer(overMon.polymerType, overMon.symbol);
+    if (resOverMon) resOverMon.lib = undefined; // cleanup to prevent infinite recursive comparison
     expectObject(resOverMon as any, overMon);
   });
 });

package/src/tests/seq-handler-get-helm-tests.ts

@@ -81,8 +81,8 @@ category('SeqHandler: getHelm', () => {
     await grok.data.detectSemanticTypes(df);
 
     const sh = seqHelper.getSeqHandler(seqCol);
-    const resSemValue = await sh.getHelm(0);
-    const resHelm = resSemValue.value;
+    const resMValue = await sh.getValue(0);
+    const resHelm = resMValue.helm;
     expect(resHelm, tgtHelm);
   }
 });

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

@@ -94,53 +94,33 @@ export class HelmToMolfileConverter {
   }
 
 
-  public convertToMolfileV3KColumn(
-    helmCol: DG.Column<string>
-  ): DG.Column<string> {
+  public convertToMolfileV3KColumn(helmCol: DG.Column<string>): DG.Column<string> {
     const df = helmCol.dataFrame;
-    const polymerGraphColumn: DG.Column<string> = this.getPolymerGraphColumn(helmCol);
-    const molfileList = polymerGraphColumn.toList().map(
-      (pseudoMolfile: string, idx: number) => {
-        const helm = helmCol.get(idx);
-        if (!helm) return '';
-
-        let resMolfileWithMap: MolfileWithMap;
-        try {
-          resMolfileWithMap = this.getPolymerMolfile(helm, pseudoMolfile);
-        } catch (err: any) {
-          const [errMsg, errStack] = errInfo(err);
-          _package.logger.error(errMsg, undefined, errStack);
-          resMolfileWithMap = MolfileWithMap.createEmpty();
-        }
-        return resMolfileWithMap.molfile;
-      });
+    const molfileList = this.convertToMolfileV3K(helmCol.toList()).map((mwm) => mwm.molfile);
     const molColName = getUnusedColName(df, `molfileV2K(${helmCol.name})`);
     const molfileColumn = DG.Column.fromList('string', molColName, molfileList);
     return molfileColumn;
   }
 
   /** Gets list of monomer molfiles */
-  public convertToMolfileV3K(helmCol: DG.Column<string>, rdKitModule: RDModule, monomerLib: IMonomerLibBase): MolfileWithMap[] {
-    const polymerGraphColumn: DG.Column<string> = this.getPolymerGraphColumn(helmCol);
-    const rowCount = helmCol.length;
-    const resList: MolfileWithMap[] = new Array<MolfileWithMap>(rowCount);
-    for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
-      const helm = helmCol.get(rowIdx);
+  public convertToMolfileV3K(helmList: string[]): MolfileWithMap[] {
+    const resList: MolfileWithMap[] = new Array<MolfileWithMap>(helmList.length);
+    for (let i = 0; i < helmList.length; ++i) {
+      const helm = helmList[i];
       if (!helm) {
-        resList[rowIdx] = MolfileWithMap.createEmpty();
+        resList[i] = MolfileWithMap.createEmpty();
         continue;
       }
 
-      const pseudoMolfile = polymerGraphColumn.get(rowIdx)!;
       let resMolfile: MolfileWithMap;
       try {
-        resMolfile = this.getPolymerMolfile(helm, pseudoMolfile);
+        resMolfile = this.getPolymerMolfile(helm);
       } catch (err: any) {
         const [errMsg, errStack] = errInfo(err);
         _package.logger.error(errMsg, undefined, errStack);
         resMolfile = MolfileWithMap.createEmpty();
       }
-      resList[rowIdx] = resMolfile;
+      resList[i] = resMolfile;
     }
     return resList;
   }
@@ -152,16 +132,15 @@ export class HelmToMolfileConverter {
     return molfileCol;
   }
 
-  private getPolymerMolfile(
-    helm: string, polymerGraph: string
-  ): MolfileWithMap {
+  private getPolymerMolfile(helm: string): MolfileWithMap {
     const woGapsRes = this.helmHelper.removeGaps(helm);
     const woGapsHelm = woGapsRes.resHelm;
     const woGapsReverseMap = new Map<number, number>();
     for (const [orgPosIdx, woGapsPosIdx] of (woGapsRes.monomerMap?.entries() ?? [])) {
       woGapsReverseMap.set(woGapsPosIdx, orgPosIdx);
     }
-    const globalPositionHandler = new GlobalMonomerPositionHandler(polymerGraph);
+    const pseudoMolfile = this.helmHelper.getMolfiles([woGapsHelm])[0];
+    const globalPositionHandler = new GlobalMonomerPositionHandler(pseudoMolfile);
     const woGapsPolymer = new Polymer(woGapsHelm, this.rdKitModule, this.monomerLib);
     globalPositionHandler.monomerSymbols.forEach((monomerSymbol: string, monomerIdx: number) => {
       const shift = globalPositionHandler.getMonomerShifts(monomerIdx);

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

@@ -1,4 +1,6 @@
 import {HELM_MONOMER_TYPE, HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
+import {cleanupHelmSymbol} from '@datagrok-libraries/bio/src/helm/utils';
+
 import {Bond} from './types';
 
 /** Wrapper over simple polymer substring of HELM, like RNA1{d(A)p}  */
@@ -41,7 +43,7 @@ export class SimplePolymer {
     return id;
   }
 
-  private getMonomerSymbolsAndTypes(): {monomers: string[], monomerTypes: HELM_MONOMER_TYPE[]} {
+  private getMonomerSymbolsAndTypes(): { monomers: string[], monomerTypes: HELM_MONOMER_TYPE[] } {
     const helmWrapperRegex = new RegExp(`${this.polymerType}${this.idx}{|}`, 'g');
     const monomerGroups = this.simplePolymer.replace(helmWrapperRegex, '').split('.');
     const monomerList: string[] = [];
@@ -51,7 +53,7 @@ export class SimplePolymer {
       // monomerList.push(...splitted);
       // WARNING: only the groups of the form r(A)p, as in RNA, are supported
 
-      monomerList.push(monomerGroup);
+      monomerList.push(cleanupHelmSymbol(monomerGroup));
       // const monomerTypes = splitted.map(
       //   (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
       // );

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

@@ -46,6 +46,10 @@ export class MonomerLibBase implements IMonomerLibBase {
   ) {
     this._isEmpty = !this._monomers || Object.keys(this._monomers).length === 0 ||
       Object.entries(this._monomers).every(([_, ptMonomers]) => Object.keys(ptMonomers).length === 0);
+    for (const [_monomerType, monomersOfType] of Object.entries(this._monomers)) {
+      for (const [_monomerSymbol, monomer] of Object.entries(monomersOfType))
+        monomer.lib = this;
+    }
   }
 
   getMonomerSymbolsByType(polymerType: PolymerType): string[] {

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

@@ -43,10 +43,6 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     public readonly error: string | undefined = undefined,
   ) {
     super(monomers, source);
-    for (const [_monomerType, monomersOfType] of Object.entries(this._monomers)) {
-      for (const [_monomerSymbol, monomer] of Object.entries(monomersOfType))
-        monomer.lib = this;
-    }
   }
 
   toJSON(): Monomer[] {
@@ -237,8 +233,10 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     return resStr;
   }
 
+  static overrideCounter: number = 0;
+
   override(data: MonomerLibData, source: string): IMonomerLibBase {
-    return new OverriddenMonomerLib(data, source, this);
+    return new OverriddenMonomerLib(data, `override: ${++MonomerLib.overrideCounter}, ${source}`, this);
   }
 }
 

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

@@ -16,7 +16,7 @@ import {MonomerLibManager} from '../lib-manager';
 import {LIB_PATH} from '../consts';
 
 import '../../../../css/monomer-manager.css';
-import { MONOMER_RENDERER_TAGS } from '@datagrok-libraries/bio/src/utils/cell-renderer';
+import {MONOMER_RENDERER_TAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
 // columns of monomers dataframe, note that rgroups is hidden and will be displayed as separate columns
 export enum MONOMER_DF_COLUMN_NAMES {
@@ -51,7 +51,6 @@ export const MONOMER_DF_COLUMNS = {
 
 
 export class MonomerManager implements IMonomerManager {
-
   private adjustColWidths() {
     setTimeout(() => {
       if (this.tv?.grid) {
@@ -87,7 +86,6 @@ export class MonomerManager implements IMonomerManager {
           }, 500);
         }
       }
-      
     }, () => this.tv?.dataFrame);
   }
 
@@ -203,6 +201,7 @@ export class MonomerManager implements IMonomerManager {
         }
       })
     );
+    this.tv.grid && (this.tv.grid.props.allowEdit = false); // disable editing
     return this.tv;
   }
 
@@ -239,6 +238,10 @@ export class MonomerManager implements IMonomerManager {
     });
     ribbons = ribbons.filter((r) => r.length > 0);
 
+    const newMonomerButton = ui.icons.add(() => {
+      this._newMonomerForm.setEmptyMonomer();
+    }, 'Add New Monomer');
+
     const editButton = ui.icons.edit(() => {
       if ((this.tv?.dataFrame?.currentRowIdx ?? -1) < 0) return;
       this.cloneMonomer(this.tv!.dataFrame.rows.get(this.tv!.dataFrame.currentRowIdx));
@@ -277,19 +280,19 @@ export class MonomerManager implements IMonomerManager {
       DG.Utils.download(libName!, lib!, 'text/plain');
     }, 'Download Monomer Library');
 
-    ribbons.push([editButton, deleteButton, downloadButton]);
+    ribbons.push([newMonomerButton, editButton, deleteButton, downloadButton]);
     this.tv.setRibbonPanels(ribbons);
 
 
     this.tv.name = MonomerManager.VIEW_NAME;
     this.libInput = ui.input.choice('Monomer Library', {value: libName, items: availableMonLibs, nullable: false, onValueChanged: async () => {
-        try {
-          const df = await this.getMonomersDf(this.libInput.value!);
+      try {
+        const df = await this.getMonomersDf(this.libInput.value!);
           this.tv!.dataFrame = df;
           this.adjustColWidths();
-        } catch (e) {
-          console.error(e);
-        }
+      } catch (e) {
+        console.error(e);
+      }
     }});
     this.libInput.addOptions(ui.icons.add(() => { this.createNewLibDialog(); }, 'Create new monomer library...'));
     const monForm = this._newMonomerForm.form;
@@ -370,6 +373,7 @@ export class MonomerManager implements IMonomerManager {
         df.col(rgName)!.semType = DG.SEMTYPE.MOLECULE;
       });
       df.currentRowIdx = -1;
+      // eslint-disable-next-line rxjs/no-ignored-subscription
       df.onCurrentRowChanged.subscribe((_) => {
         try {
           if (df.currentRowIdx === -1 || this._newMonomerForm.molChanged)
@@ -541,6 +545,7 @@ class MonomerForm implements INewMonomerForm {
       await this.saveMonomer();
     });
     // this.saveButton.style.pointerEvents = 'revert';
+    // eslint-disable-next-line rxjs/no-async-subscribe
     this.molSketcher.subs.push(this.molSketcher.onChanged.subscribe(async () => {
       if (!this.triggerMolChange) {
         this.triggerMolChange = true;
@@ -551,6 +556,9 @@ class MonomerForm implements INewMonomerForm {
         let smiles = this.molSketcher.getSmiles();
         if (!smiles) {
           this.rgroupsGrid.items = [];
+          this.rgroupsGrid.render();
+          this.saveValidationResult = 'Monomer molecule is required';
+          this.invalidateSaveButton();
           return;
         }
         smiles = getCorrectedSmiles([], smiles);
@@ -559,6 +567,8 @@ class MonomerForm implements INewMonomerForm {
         if (rGroupMatches.length === 0) {
           this.rgroupsGrid.items = [];
           this.rgroupsGrid.render();
+          this.saveValidationResult = 'At least one R-group is required';
+          this.invalidateSaveButton();
           return;
         }
         const rGroupNums = rGroupMatches.map((match) => Number.parseInt(match[0].match(/[1-9]/g)![0]));
@@ -606,6 +616,7 @@ class MonomerForm implements INewMonomerForm {
         [HELM_RGROUP_FIELDS.LABEL]: 'Label',
       },
     });
+    // eslint-disable-next-line rxjs/no-ignored-subscription
     this.rgroupsGrid.onItemChanged.subscribe(() => this.onMonomerInputChanged());
 
     this.rgroupsGridRoot = ui.divV([this.rgroupsGrid.root]);
@@ -633,17 +644,19 @@ class MonomerForm implements INewMonomerForm {
       'Meta': ui.divV([this.metaGrid.root]),
       'Colors': this.colorsEditor.form,
     }, false);
+  }
 
+  invalidateSaveButton() {
+    if (this.saveValidationResult)
+      this.saveButton.classList.add('d4-disabled');
+    else
+      this.saveButton.classList.remove('d4-disabled');
   }
 
   onMonomerInputChanged() {
     setTimeout(() => {
       this.saveValidationResult = this.validateInputs();
-      if (this.saveValidationResult)
-        this.saveButton.classList.add('d4-disabled');
-      else
-        this.saveButton.classList.remove('d4-disabled');
-
+      this.invalidateSaveButton();
       const monomerExists = this.polymerTypeInput.value && this.polymerTypeInput.value &&
         !!this.getMonomerLib()?.getMonomer(this.polymerTypeInput.value as PolymerType, this.monomerSymbolInput.value);
 
@@ -651,6 +664,27 @@ class MonomerForm implements INewMonomerForm {
     }, 200);
   }
 
+  setEmptyMonomer() {
+    this.triggerMolChange = false;
+    this.molSketcher.setSmiles('');
+    // leave polymer and monomer type as is
+    this.monomerSymbolInput.value = '';
+    this.monomerNameInput.value = '';
+    this.monomerIdInput.value = null;
+    this.monomerNaturalAnalogInput.value = null;
+    this.rgroupsGrid.items = [];
+    this.metaGrid.items = [];
+    this.rgroupsGrid.render();
+    this.metaGrid.render();
+    this.rgroupsGridRoot.style.display = 'none';
+    this.onMonomerInputChanged();
+    this.colorsEditor.colors = {
+      line: '#000000',
+      background: '#000000',
+      text: '#000000',
+    };
+  }
+
   setMonomer(monomer: Monomer) {
     this.triggerMolChange = false;
     this.molSketcher.setSmiles(monomer.smiles);
@@ -661,7 +695,7 @@ class MonomerForm implements INewMonomerForm {
     this.monomerIdInput.value = monomer.id;
     this.monomerNaturalAnalogInput.value = monomer.naturalAnalog ?? null;
     this.rgroupsGrid.items = resolveRGroupInfo(monomer.rgroups);
-    this.metaGrid.items = Object.entries(monomer.meta ?? {}).filter(([k, v]) => k?.toLowerCase() !== 'colors').map(([k, v]) => {
+    this.metaGrid.items = Object.entries(monomer.meta ?? {}).filter(([k, _v]) => k?.toLowerCase() !== 'colors').map(([k, v]) => {
       return {Property: k, Value: v};
     });
     this.rgroupsGrid.render();
@@ -681,7 +715,7 @@ class MonomerForm implements INewMonomerForm {
     } catch (e) {
       console.error(e);
     }
-    
+
     this.colorsEditor.colors = {
       line: colorsObj.line ?? '#000000',
       background: colorsObj.background ?? '#000000',
@@ -693,7 +727,7 @@ class MonomerForm implements INewMonomerForm {
     const rGroupsPane = this.inputsTabControl.panes.find((p) => p.name?.toLowerCase() === 'r-groups');
     rGroupsPane && (rGroupsPane.header.style.removeProperty('background-color'));
     if (!this.molSketcher.getSmiles()) return 'Monomer Molecule field is required';
-    for (const i of [this.polymerTypeInput, this.monomerTypeInput, this.monomerSymbolInput, this.monomerNameInput, this.monomerIdInput]) {
+    for (const i of [this.polymerTypeInput, this.monomerTypeInput, this.monomerSymbolInput, this.monomerNameInput]) {
       if (i.value == null || i.value === '')
         return `${i.caption} field is required`;
     }
@@ -703,17 +737,18 @@ class MonomerForm implements INewMonomerForm {
     if (!rgroupError) {
       outerFor:
       for (const item of this.rgroupsGrid.items) {
-        for (const [k, v] of Object.entries(item))
-          if (!v){
+        for (const [k, v] of Object.entries(item)) {
+          if (!v) {
             rgroupError = `R-group ${k} field is required for ${item[HELM_RGROUP_FIELDS.LABEL]}`;
             break outerFor;
-          } 
+          }
+        }
       }
     }
 
-    if (!rgroupError && this.rgroupsGrid.hasErrors()){ 
+    if (!rgroupError && this.rgroupsGrid.hasErrors())
       rgroupError = 'R-group fields contain errors';
-    }
+
     if (rgroupError) {
       rGroupsPane && (rGroupsPane.header.style.setProperty('background-color', '#ff000030'));
       return rgroupError;
@@ -730,7 +765,6 @@ class MonomerForm implements INewMonomerForm {
   }
 
   get form() {
-    
     this.inputsTabControl.root.classList.add('monomer-manager-form-tab-control');
     this.inputsTabControl.header.style.marginBottom = '10px';
     const saveB = ui.buttonsInput([this.saveButton]);
@@ -826,11 +860,11 @@ class MonomerForm implements INewMonomerForm {
       try {
         // first remove the existing monomer with that symbol
         const monomerIdx = libJSON.findIndex((m) => m.symbol === monomer.symbol && m.polymerType === monomer.polymerType);
-        if (monomerIdx >= 0) {
+        if (monomerIdx >= 0)
           libJSON[monomerIdx] = {...monomer, lib: undefined, wem: undefined};
-        } else {
+        else
           libJSON.push({...monomer, lib: undefined, wem: undefined});
-        }
+
         await grok.dapi.files.writeAsText(LIB_PATH + libName, JSON.stringify(libJSON));
         await (await MonomerLibManager.getInstance()).loadLibraries(true);
         await this.refreshTable(monomer.symbol);
@@ -839,6 +873,7 @@ class MonomerForm implements INewMonomerForm {
         grok.shell.error('Error saving monomer');
         console.error(e);
       }
+      this.onMonomerInputChanged();
     };
     let infoTable: HTMLDivElement | null = null;
     let promptMessage = '';
@@ -882,9 +917,9 @@ class MonomerForm implements INewMonomerForm {
       meta[item['Property']] = item['Value'];
     });
     const addingItem = this.metaGrid.addingItem;
-    if (addingItem && addingItem['Property'] && addingItem['Value']) {
+    if (addingItem && addingItem['Property'] && addingItem['Value'])
       meta[addingItem['Property']] = addingItem['Value'];
-    }
+
     //console.log(this.metaGrid.addingItem);
     if (this.colorsEditor.colors.line !== '#000000' || this.colorsEditor.colors.background !== '#000000' || this.colorsEditor.colors.text !== '#000000')
       meta.colors = {default: this.colorsEditor.colors};
@@ -975,7 +1010,7 @@ function getCorrectedMolBlock(molBlock: string) {
 
   if (rgpLineIdx === -1) {
     // number of r groups has 3 empty slots before it, atom numbers have 4 empty slots before them
-    let rgpLine = `M  RGP${rgroupLineNums.length.toString().padStart(3,' ')}${Object.entries(rgroupLineNumbers).map(([atomLine, rGroupNum]) => `${atomLine.toString().padStart(4, ' ')}${rGroupNum.toString().padStart(4, ' ')}`).join('')}`;
+    const rgpLine = `M  RGP${rgroupLineNums.length.toString().padStart(3, ' ')}${Object.entries(rgroupLineNumbers).map(([atomLine, rGroupNum]) => `${atomLine.toString().padStart(4, ' ')}${rGroupNum.toString().padStart(4, ' ')}`).join('')}`;
     const mEndIdx = lines.findIndex((line) => line.startsWith('M') && line.includes('END'));
     lines.splice(mEndIdx, 0, rgpLine);
   }
@@ -1042,9 +1077,8 @@ class ColorsEditor {
     };
 
     this._colors = colsHex;
-    for (const key in this._colorInputs) {
+    for (const key in this._colorInputs)
       this._colorInputs[key as keyof ColorsEditor['_colors']].value = colsHex[key as keyof ColorsEditor['_colors']];
-    }
   }
 
   get colorsMetaFormat() {
@@ -1054,4 +1088,4 @@ class ColorsEditor {
   get form() {
     return ui.form(Object.values(this._colorInputs));
   }
-}
+}

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

@@ -14,7 +14,7 @@ import {GAP_SYMBOL, GapOriginals} from '@datagrok-libraries/bio/src/utils/macrom
 import {CellRendererBackBase, GridCellRendererTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
-import {ISeqHandler, ConvertFunc, JoinerFunc, SeqTemps} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {ISeqHandler, ConvertFunc, JoinerFunc, SeqTemps, MacromoleculeValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 import {SeqHelper} from './seq-helper';
 
@@ -241,18 +241,16 @@ export class SeqHandler implements ISeqHandler {
   }
 
   /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
-  public async getHelm(rowIdx: number, options?: any): Promise<DG.SemanticValue<string>> {
+  public async getValue(rowIdx: number, options?: any): Promise<MacromoleculeValueBase> {
     const seq: string = this.column.get(rowIdx);
-    let resHelmSV: DG.SemanticValue<string>;
+    let resHelm: string;
     if (this.notationProvider)
-      resHelmSV = await this.notationProvider.getHelm(seq, options);
+      resHelm = await this.notationProvider.getHelm(seq, options);
     else {
-      const resHelm = this.convertToHelm(seq);
-      resHelmSV = DG.SemanticValue.fromValueType(resHelm, DG.SEMTYPE.MACROMOLECULE, NOTATION.HELM);
-      // TODO: set tags from column
+      resHelm = this.convertToHelm(seq);
     }
-
-    return resHelmSV;
+    const resMValue = new MacromoleculeValueBase(resHelm, this, rowIdx);
+    return resMValue;
   }
 
   private _stats: SeqColStats | null = null;

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

@@ -56,7 +56,7 @@ export class SeqHelper implements ISeqHelper {
 
     //#region From HelmToMolfileConverter.convertToRdKitBeautifiedMolfileColumn
 
-    const molfilesV3K = converter.convertToMolfileV3K(helmCol, this.rdKitModule, monomerLib);
+    const molfilesV3K = converter.convertToMolfileV3K(helmCol.toList());
 
     const beautifiedMolList: (RDMol | null)[] = molfilesV3K.map((item) => {
       const molfile = item.molfile;

package/src/viewers/web-logo-viewer.ts

@@ -395,14 +395,14 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
 
     // -- Data --
     this.sequenceColumnName = this.string(PROPS.sequenceColumnName, defaults.sequenceColumnName,
-      {category: PROPS_CATS.DATA});
+      {category: PROPS_CATS.DATA, semType: DG.SEMTYPE.MACROMOLECULE});
     const aggExcludeList = [DG.AGG.KEY, DG.AGG.PIVOT, DG.AGG.MISSING_VALUE_COUNT, DG.AGG.SKEW, DG.AGG.KURT,
       DG.AGG.SELECTED_ROWS_COUNT];
     const aggChoices = Object.values(DG.AGG).filter((agg) => !aggExcludeList.includes(agg));
     this.valueAggrType = this.string(PROPS.valueAggrType, defaults.valueAggrType,
       {category: PROPS_CATS.DATA, choices: aggChoices}) as DG.AggregationType;
     this.valueColumnName = this.string(PROPS.valueColumnName, defaults.valueColumnName,
-      {category: PROPS_CATS.DATA});
+      {category: PROPS_CATS.DATA, columnTypeFilter: 'numerical'});
     this.startPositionName = this.string(PROPS.startPositionName, defaults.startPositionName,
       {category: PROPS_CATS.DATA});
     this.endPositionName = this.string(PROPS.endPositionName, defaults.endPositionName,
@@ -1022,20 +1022,18 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
 
       // 2022-05-05 askalkin instructed to show WebLogo based on filter (not selection)
       const dfRowCount = this.dataFrame.rowCount;
-
+      const filterIndexes = dfFilter.getSelectedIndexes();
       for (let jPos = 0; jPos < length; ++jPos) {
         // Here we want to build lists of values for every monomer in position jPos
-        for (let rowI = 0; rowI < dfRowCount; ++rowI) {
-          if (dfFilter.get(rowI)) {
-            const seqS: ISeqSplitted = this.seqHandler.getSplitted(rowI);
-            const om: string = jPos < seqS.length ? seqS.getCanonical(this.startPosition + jPos) :
-              this.seqHandler.defaultGapOriginal;
-            const cm: string = this.seqHandler.defaultGapOriginal === om ? GAP_SYMBOL : om;
-            const pi = this.positions[jPos];
-            const pmi = pi.getFreq(cm);
-            ++pi.sumRowCount;
-            pmi.value = ++pmi.rowCount;
-          }
+        for (const rowI of filterIndexes) {
+          const seqS: ISeqSplitted = this.seqHandler.getSplitted(rowI);
+          const om: string = jPos + this.startPosition < seqS.length ? seqS.getCanonical(this.startPosition + jPos) :
+            this.seqHandler.defaultGapOriginal;
+          const cm: string = this.seqHandler.defaultGapOriginal === om ? GAP_SYMBOL : om;
+          const pi = this.positions[jPos];
+          const pmi = pi.getFreq(cm);
+          ++pi.sumRowCount;
+          pmi.value = ++pmi.rowCount;
         }
         if (this.valueAggrType === DG.AGG.TOTAL_COUNT) continue;
 
@@ -1048,13 +1046,13 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
         } catch { valueCol = null; }
         if (!valueCol) continue; // fallback to TOTAL_COUNT
 
-        for (let rowI = 0; rowI < dfRowCount; ++rowI) {
-          if (dfFilter.get(rowI)) { // respect the filter
-            const seqMList: ISeqSplitted = this.seqHandler.getSplitted(rowI);
-            const cm: string = seqMList.getCanonical(this.startPosition + jPos);
-            const value: number | null = valueCol.get(rowI);
-            this.positions[jPos].getFreq(cm).push(value);
-          }
+        for (const rowI of filterIndexes) {
+          const seqS: ISeqSplitted = this.seqHandler.getSplitted(rowI);
+          const om: string = jPos + this.startPosition < seqS.length ? seqS.getCanonical(this.startPosition + jPos) :
+            this.seqHandler.defaultGapOriginal;
+          const cm: string = this.seqHandler.defaultGapOriginal === om ? GAP_SYMBOL : om;
+          const value: number | null = valueCol.get(rowI);
+          this.positions[jPos].getFreq(cm).push(value);
         }
         this.positions[jPos].aggregate(this.valueAggrType);
       }