@datagrok/sequence-translator 1.3.13 → 1.3.15

package/files/polytool-rules/rules_example.json

@@ -1,34 +1,34 @@
-[ 
-	{
-		"type": "link",
-		"code": "1",
-		"monomericSubstitution": {
-		    "firstMonomer": "C",
-		    "secondMonomer": "C",
-		    "firstLinkingGroup":"3",
-		    "secondLinkingGroup":"3",
-		    "firstSubstitution": "C",
-		    "secondSubstitution": "C"
-		}
-	},
-	{
-		"type": "link",
-		"code": "2",
-		"monomericSubstitution": {
-		    "firstMonomer": "NH2",
-		    "secondMonomer": "L",
-		    "firstLinkingGroup":"2",
-		    "secondLinkingGroup":"3",
-		    "firstSubstitution": "NH2",
-		    "secondSubstitution": "L"
-		}
-	},
-	{
-		"type": "fragmentDuplication",
-		"code": "#3"
-	},
-	{
-		"type": "differentFragments",
-		"code": "$4"
-	}
-]
+[
+  {
+    "type": "link",
+    "code": "1",
+    "monomericSubstitution": {
+      "firstMonomer": "C",
+      "secondMonomer": "C",
+      "firstLinkingGroup": "3",
+      "secondLinkingGroup": "3",
+      "firstSubstitution": "C",
+      "secondSubstitution": "C"
+    }
+  },
+  {
+    "type": "link",
+    "code": "2",
+    "monomericSubstitution": {
+      "firstMonomer": "NH2",
+      "secondMonomer": "D",
+      "firstLinkingGroup": "2",
+      "secondLinkingGroup": "3",
+      "firstSubstitution": "NH2",
+      "secondSubstitution": "D"
+    }
+  },
+  {
+    "type": "fragmentDuplication",
+    "code": "#3"
+  },
+  {
+    "type": "differentFragments",
+    "code": "$4"
+  }
+]

package/files/samples/cyclized.csv

@@ -0,0 +1,6 @@
+n,seqs
+1,R-F-C(1)-T-G-H-F-Y-P-C(1)-meI
+2,C(1)-T-G-H-F-Y-P-C(1)-meI
+3,R-F-C(1)-T-G-H-F-Y-P-C(1)
+4,C(1)-T-G-H-F-H-P-C(1)
+5,R-F-D(2)-T-G-H-F-Y-P-NH2(2)

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.3.13",
+  "version": "1.3.15",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
@@ -22,13 +22,13 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.42.11",
+    "@datagrok-libraries/bio": "^5.42.14",
     "@datagrok-libraries/chem-meta": "^1.2.5",
-    "@datagrok-libraries/tutorials": "^1.3.13",
-    "@datagrok-libraries/utils": "^4.2.29",
+    "@datagrok-libraries/tutorials": "^1.4.0",
+    "@datagrok-libraries/utils": "^4.3.0",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
-    "datagrok-api": "^1.20.0",
+    "datagrok-api": "^1.21.1",
     "lodash": "^4.17.21",
     "object-hash": "^3.0.0",
     "openchemlib": "6.0.1",
@@ -39,11 +39,11 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.10",
+    "@datagrok-libraries/helm-web-editor": "^1.1.11",
     "@datagrok-libraries/js-draw-lite": "^0.0.8",
-    "@datagrok/bio": "^2.14.2",
-    "@datagrok/helm": "^2.4.4",
-    "@datagrok/chem": "^1.11.3",
+    "@datagrok/bio": "^2.15.0",
+    "@datagrok/helm": "^2.5.0",
+    "@datagrok/chem": "^1.12.0",
     "@types/jquery": "^3.5.14",
     "@types/js-yaml": "^4.0.5",
     "@types/lodash": "^4.14.202",
@@ -54,7 +54,6 @@
     "@typescript-eslint/eslint-plugin": "^7.2.0",
     "@typescript-eslint/parser": "^7.2.0",
     "css-loader": "^6.7.3",
-    "datagrok-tools": "latest",
     "eslint": "^8.57.0",
     "eslint-config-google": "latest",
     "style-loader": "^3.3.1",

package/src/apps/common/view/components/colored-input/colored-text-input.ts

@@ -22,7 +22,7 @@ export class ColoredTextInput {
     $(this.root).addClass('colored-text-input');
     if (resizeable) {
       // make input field automatically resizeable
-      this.textInputBase.onChanged(
+      this.textInputBase.onChanged.subscribe(
         () => {
           // necessary for the field to be squeezable, not only expandable
           $(this.textArea).css('height', 0);
@@ -34,7 +34,7 @@ export class ColoredTextInput {
     this.root.appendChild(this.highlights);
     this.colorize();
 
-    this.textInputBase.onChanged(() => this.colorize());
+    this.textInputBase.onChanged.subscribe(() => this.colorize());
   }
 
   private highlights: HTMLDivElement;

package/src/apps/pattern/view/components/bulk-convert/column-input.ts

@@ -54,7 +54,7 @@ export class ColumnInputManager {
       [];
     const strandColumnInput = Object.fromEntries(STRANDS.map((strand) => {
       const input = ui.input.choice(`${STRAND_LABEL[strand]} column`, {value: columns[0], items: columns,
-        onValueChanged: (input) => this.eventBus.selectStrandColumn(strand, input.value)}
+        onValueChanged: (value) => this.eventBus.selectStrandColumn(strand, value)}
       );
       this.eventBus.selectStrandColumn(strand, columns[0]);
       return [strand, input.root];
@@ -65,7 +65,7 @@ export class ColumnInputManager {
   private createIdColumnInput(): HTMLElement {
     const columns = this.selectedTable ? this.selectedTable.columns.names() : [];
     const idColumnInput = ui.input.choice('ID column', {value: columns[0], items: columns,
-      onValueChanged: (input) => this.eventBus.selectIdColumn(input.value)}
+      onValueChanged: (value) => this.eventBus.selectIdColumn(value)}
     );
     this.eventBus.selectIdColumn(columns[0]);
     return idColumnInput.root;

package/src/apps/pattern/view/components/bulk-convert/table-input.ts

@@ -28,7 +28,7 @@ export class TableInputManager {
   }
 
   private getTableFromEventData(eventData: any): DG.DataFrame {
-    if (! eventData && eventData.args && eventData.args.dataFrame instanceof DG.DataFrame)
+    if (!eventData && eventData.args && eventData.args.dataFrame instanceof DG.DataFrame)
       throw new Error(`EventData does not contain a dataframe`, eventData);
 
     return eventData.args.dataFrame as DG.DataFrame;
@@ -63,13 +63,15 @@ export class TableInputManager {
   private createTableInput(): DG.InputBase<DG.DataFrame | null> {
     const currentlySelectedTable = this.eventBus.getTableSelection();
 
-    const tableInput = ui.input.table('Tables', {value: currentlySelectedTable!, items: this.availableTables,
-      onValueChanged: (input) => {
+    const tableInput = ui.input.table('Tables', {
+      value: currentlySelectedTable!, items: this.availableTables,
+      onValueChanged: (value) => {
         // WARNING: non-null check necessary to prevent resetting columns to
         // null upon handling onTableAdded
-        if (input.value !== null)
-          this.eventBus.selectTable(input.value);
-      }});
+        if (value !== null)
+          this.eventBus.selectTable(value);
+      }
+    });
     return tableInput;
   }
 

package/src/apps/pattern/view/components/edit-block-controls.ts

@@ -79,7 +79,7 @@ export class PatternEditControlsManager {
       {value: this.eventBus.isAntisenseStrandActive()}
     );
 
-    toggleAntisenseStrand.onInput(
+    toggleAntisenseStrand.onInput.subscribe(
       () => this.eventBus.toggleAntisenseStrand(toggleAntisenseStrand.value)
     );
 
@@ -97,7 +97,7 @@ export class PatternEditControlsManager {
       const sequenceLength = this.eventBus.getNucleotideSequences()[strand].length;
 
       const input = ui.input.int(`${STRAND_LABEL[strand]} length`, {value: sequenceLength});
-      input.onInput(() => updateStrandLengthInputs(strand, input));
+      input.onInput.subscribe(() => updateStrandLengthInputs(strand, input));
 
       this.eventBus.nucleotideSequencesChanged$.subscribe(() => {
         input.value = this.eventBus.getNucleotideSequences()[strand].length;
@@ -141,7 +141,7 @@ export class PatternEditControlsManager {
 
     const sequenceBaseInput = ui.input.choice('Sequence basis', {value: defaultNucleotideBase, items: availableNucleoBases});
 
-    sequenceBaseInput.onInput(() => this.eventBus.replaceSequenceBase(sequenceBaseInput.value!));
+    sequenceBaseInput.onInput.subscribe(() => this.eventBus.replaceSequenceBase(sequenceBaseInput.value!));
 
     this.eventBus.nucleotideSequencesChanged$.subscribe(() => {
       sequenceBaseInput.value = this.eventBus.getSequenceBase();
@@ -156,7 +156,7 @@ export class PatternEditControlsManager {
 
     $(patternCommentInput.root).addClass('st-pattern-text-input');
 
-    patternCommentInput.onInput(
+    patternCommentInput.onInput.subscribe(
       () => this.eventBus.updateComment(patternCommentInput.value!)
     );
 
@@ -172,7 +172,7 @@ export class PatternEditControlsManager {
 
     $(patternNameInput.root).addClass('st-pattern-text-input');
 
-    patternNameInput.onInput(
+    patternNameInput.onInput.subscribe(
       () => this.eventBus.updatePatternName(patternNameInput.value)
     );
     this.eventBus.patternLoaded$.subscribe(() => {

package/src/apps/pattern/view/components/load-block-controls.ts

@@ -96,7 +96,7 @@ export class PatternLoadControlsManager {
     const authorChoiceInput = ui.input.choice(
       'Author', {value: this.eventBus.getSelectedAuthor(), items: possibleValues});
 
-    authorChoiceInput.onInput(() => {
+    authorChoiceInput.onInput.subscribe(() => {
       this.authorSelectedByUser = true;
       if (authorChoiceInput.value === null)
         throw new Error('author choice must be non-null');
@@ -142,7 +142,7 @@ export class PatternLoadControlsManager {
     });
 
     this.subscriptions.add(
-      choiceInput.onInput(
+      choiceInput.onInput.subscribe(
         () => {
           const patternHash = this.dataManager.getPatternHash(choiceInput.value!, this.isCurrentUserSelected());
           this.eventBus.requestPatternLoad(patternHash);
@@ -164,7 +164,11 @@ export class PatternLoadControlsManager {
 
   private getPatternName(patternList: string[]): string {
     return patternList.find(
-      (patternName) => patternName === this.eventBus.getPatternName()
+      (longPatternName) => {
+        // The pattern name can be followed by the author name in parenths
+        const shortPatternName = longPatternName.split(' (')[0];
+        return shortPatternName === this.eventBus.getPatternName();
+      }
     ) ?? patternList[0];
   }
 

package/src/apps/pattern/view/components/numeric-label-visibility-controls.ts

@@ -46,7 +46,7 @@ export class NumericLabelVisibilityControls {
     const initialValue = this.eventBus.getModificationsWithNumericLabels().includes(nucleotide);
     const input = ui.input.bool(nucleotide, {
       value: initialValue,
-      onValueChanged: (input) => this.handleNumericLabelToggle(nucleotide, input.value)
+      onValueChanged: (value) => this.handleNumericLabelToggle(nucleotide, value)
     });
     $(input.root).css('padding-right', '20px');
 

package/src/apps/pattern/view/components/strand-editor/header-controls.ts

@@ -45,7 +45,7 @@ export class HeaderControls {
     const initialValue = this.areAllPtoLinkagesSet(flags);
     const allPtoActivationInput = ui.input.bool('All PTO', {value: initialValue});
 
-    allPtoActivationInput.onInput(() => {
+    allPtoActivationInput.onInput.subscribe(() => {
       const value = allPtoActivationInput.value!;
       this.eventBus.setAllPTOLinkages(value);
     });
@@ -81,7 +81,7 @@ export class HeaderControls {
       const initialValue = this.isFirstPtoActive(strand);
       const firstPtoInput = ui.input.bool(`First ${strand} PTO`, {value: initialValue});
 
-      firstPtoInput.onInput(() => {
+      firstPtoInput.onInput.subscribe(() => {
         const value = firstPtoInput.value!;
         this.eventBus.setPhosphorothioateLinkageFlag(strand, 0, value);
       });

package/src/apps/pattern/view/components/strand-editor/strand-controls.ts

@@ -79,7 +79,7 @@ export class StrandControls {
     const nucleotides = this.eventBus.getNucleotideSequences()[strand];
     const choiceInputs = nucleotides.map((nucleotide, index) => {
       const input = ui.input.choice<string>('', {value: nucleotide, items: nucleotideBaseChoices});
-      input.onInput(() => {
+      input.onInput.subscribe(() => {
         const newValue = input.value!;
         this.eventBus.setNucleotide(strand, index, newValue);
       });
@@ -93,7 +93,7 @@ export class StrandControls {
     const ptoLinkageFlags = this.eventBus.getPhosphorothioateLinkageFlags()[strand].slice(1);
     const ptoLinkageInputs = ptoLinkageFlags.map((flag, index) => {
       const input = ui.input.bool('', {value: flag});
-      input.onInput(() => {
+      input.onInput.subscribe(() => {
         const newValue = input.value!;
         this.eventBus.setPhosphorothioateLinkageFlag(strand, index + 1, newValue);
       });

package/src/apps/pattern/view/components/terminal-modification-editor.ts

@@ -109,7 +109,7 @@ class StrandTerminalModificationControls {
     const input = ui.input.textArea(terminus, {value: initialValue});
     this.applyStylingToInput(input);
 
-    input.onInput(() => {
+    input.onInput.subscribe(() => {
       const newValue = input.value;
       if (newValue === null)
         return;

package/src/apps/structure/view/ui.ts

@@ -110,12 +110,12 @@ class StructureAppLayout {
     );
 
     STRANDS.forEach((strand, idx) => {
-      directionChoiceInput[strand].onChanged(() => {
-        let value = directionChoiceInput[strand].value === DIRECTION.INVERSE;
+      directionChoiceInput[strand].onChanged.subscribe((value) => {
+        let inputValue = value === DIRECTION.INVERSE;
         // warning: the next line is necessary
         // until the legacy notion of direction used in the molfile generation gets fixed
-        if (idx > 0) value = !value;
-        this.directionInversion[strand] = value;
+        if (idx > 0) inputValue = !inputValue;
+        this.directionInversion[strand] = inputValue;
         this.onInput.next();
       });
     });
@@ -142,7 +142,7 @@ class StructureAppLayout {
 
     const sequenseInputs = ui.form([], 'st-structure-inputs');
     const clearButtons = ui.divV([], 'st-structure-clear-buttons');
-    const directionInputs = ui.form([], 'st-direction-inputs'); 
+    const directionInputs = ui.form([], 'st-direction-inputs');
 
     for (const strand of STRANDS) {
       sequenseInputs.append(this.inputBase[strand].root);

package/src/apps/translator/view/ui.ts

@@ -47,11 +47,14 @@ class TranslatorAppLayout {
     this.moleculeImgDiv.style.marginTop = '12px';
 
     this.outputTableDiv = ui.div([]);
-    this.formatChoiceInput = ui.input.choice('', {value: DEFAULT_FORMATS.HELM, items: this.inputFormats, onValueChanged: async () => {
-      this.format = this.formatChoiceInput.value;
-      this.updateTable();
-      await this.updateMolImg();
-    }});
+    this.formatChoiceInput = ui.input.choice('', {
+      value: DEFAULT_FORMATS.HELM, items: this.inputFormats,
+      onValueChanged: async (value, input) => {
+        this.format = value;
+        this.updateTable();
+        await this.updateMolImg();
+      }
+    });
     this.sequenceInputBase = ui.input.textArea('', {value: DEFAULT_AXOLABS_INPUT, onValueChanged: () => { this.onInput.next(); }});
 
     this.init();
@@ -99,13 +102,15 @@ class TranslatorAppLayout {
 
     const tableControlsManager = new TableControlsManager(this.eventBus);
     const tableControls = tableControlsManager.createUIComponents();
-    const inputFormats = ui.input.choice('Input format', {value: DEFAULT_FORMATS.AXOLABS,
-      items: this.inputFormats, onValueChanged: (input) => this.eventBus.selectInputFormat(input.value)}
-    );
+    const inputFormats = ui.input.choice('Input format', {
+      value: DEFAULT_FORMATS.AXOLABS,
+      items: this.inputFormats, onValueChanged: (value) => this.eventBus.selectInputFormat(value)
+    });
 
-    const outputFormats = ui.input.choice('Output format', {value: NUCLEOTIDES_FORMAT,
-      items: getSupportedTargetFormats(this.th), onValueChanged: (input) => this.eventBus.selectOutputFormat(input.value)}
-    );
+    const outputFormats = ui.input.choice('Output format', {
+      value: NUCLEOTIDES_FORMAT,
+      items: getSupportedTargetFormats(this.th), onValueChanged: (value) => this.eventBus.selectOutputFormat(value)
+    });
     const convertBulkButton = this.createConvertBulkButton();
 
     const tableControlsContainer = ui.div([
@@ -374,13 +379,15 @@ class TableInputManager {
   private createTableInput(): DG.InputBase<DG.DataFrame | null> {
     const currentlySelectedTable = this.eventBus.getSelectedTable();
 
-    const tableInput = ui.input.table('Table', {value: currentlySelectedTable!, items: this.availableTables,
-      onValueChanged: (input) => {
+    const tableInput = ui.input.table('Table', {
+      value: currentlySelectedTable!, items: this.availableTables,
+      onValueChanged: (value) => {
         // WARNING: non-null check necessary to prevent resetting columns to
         // null upon handling onTableAdded
-        if (input.value !== null)
-          this.eventBus.selectTable(input.value);
-      }});
+        if (value !== null)
+          this.eventBus.selectTable(value);
+      }
+    });
     return tableInput;
   }
 
@@ -449,8 +456,10 @@ class ColumnInputsManager {
     const selectedColumnName = matchingColumnName ? matchingColumnName : columnNames[0];
     this.selectColumnIfTableNotNull(selectedTable, selectedColumnName, columnLabel);
 
-    const input = ui.input.choice(`${columnLabel}`, {value: selectedColumnName, items: columnNames,
-      onValueChanged: (input) => this.selectColumnIfTableNotNull(selectedTable, input.value, columnLabel)}
+    const input = ui.input.choice(`${columnLabel}`, {
+        value: selectedColumnName, items: columnNames,
+        onValueChanged: (value) => this.selectColumnIfTableNotNull(selectedTable, value, columnLabel)
+      }
     );
 
     return input;

package/src/package-test.ts

@@ -8,6 +8,7 @@ import './tests/formats-to-helm';
 import './tests/helm-to-nucleotides';
 import './tests/formats-support';
 import './tests/files-tests';
+import './tests/polytool-convert-tests';
 import './tests/polytool-enumerate-tests';
 
 import {OligoToolkitTestPackage} from './tests/utils';

package/src/package.ts

@@ -14,16 +14,19 @@ import {SequenceToMolfileConverter} from './apps/structure/model/sequence-to-mol
 import {FormatConverter} from './apps/translator/model/format-converter';
 import {demoOligoPatternUI, demoOligoStructureUI, demoOligoTranslatorUI} from './demo/demo-st-ui';
 import {getExternalAppViewFactories} from './plugins/mermade';
+import {defaultErrorHandler} from './utils/err-info';
 
 //polytool specific
-import {getPolyToolConversionDialog, polyToolEnumerateChemUI} from './polytool/pt-dialog';
+import {polyToolConvert, polyToolConvertUI} from './polytool/pt-dialog';
+import {polyToolEnumerateChemUI} from './polytool/pt-dialog';
 import {polyToolEnumerateHelmUI} from './polytool/pt-enumeration-helm-dialog';
 import {_setPeptideColumn} from './polytool/utils';
 import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converter';
 import {ITranslationHelper} from './types';
 import {addContextMenuUI} from './utils/context-menu';
+import {PolyToolConvertFuncEditor} from './polytool/pt-convert-editor';
 
-export const _package: OligoToolkitPackage = new OligoToolkitPackage(/*{debug: true}/**/);
+export const _package: OligoToolkitPackage = new OligoToolkitPackage({debug: true}/**/);
 
 //name: Oligo Toolkit
 //meta.icon: img/icons/toolkit.png
@@ -155,27 +158,46 @@ async function getSpecifiedAppView(appName: string): Promise<DG.ViewBase> {
 //top-menu: Bio | PolyTool | Convert...
 //name: polyToolConvert
 //description: Perform cyclization of polymers
-export async function polyToolConvert(): Promise<void> {
-  let dialog: DG.Dialog;
-  try {
-    dialog = await getPolyToolConversionDialog();
-    dialog.show();
-  } catch (err: any) {
-    grok.shell.warning('To run PolyTool Conversion, open a dataframe with macromolecules');
-  }
+export async function polyToolConvertTopMenu(): Promise<void> {
+  await polyToolConvertUI();
 }
 
+//name: getPolyToolConvertEditor
+//tags: editor
+//input: funccall call
+//output: column resCol
+export async function getPolyToolConvertEditor(call: DG.FuncCall): Promise<DG.Column<string> | null> {
+  const funcEditor = await PolyToolConvertFuncEditor.create(call);
+  return await funcEditor.showDialog();
+}
+
+//name: polyToolConvert2
+//input: dataframe table
+//input: column seqCol { caption: Sequence }
+//input: bool generateHelm = true
+//input: bool chiralityEngine = true
+//input: object rules
+//output: column resCol
+//editor: SequenceTranslator:getPolyToolConvertEditor
+export async function polyToolConvert2(table: DG.DataFrame,
+  seqCol: DG.Column, generateHelm: boolean, chiralityEngine: boolean, rules: string[]
+): Promise<DG.Column<string>> {
+  const ptConvertRes = await polyToolConvert(seqCol, generateHelm, chiralityEngine, rules);
+  return ptConvertRes[0];
+}
+
+
 //top-menu: Bio | PolyTool | Enumerate HELM...
 //name: polyToolEnumerateHelm
 //description: Perform cyclization of polymers
-export async function polyToolEnumerateHelm(): Promise<void> {
+export async function polyToolEnumerateHelmTopMenu(): Promise<void> {
   await polyToolEnumerateHelmUI(grok.shell.tv?.dataFrame.currentCell);
 }
 
 //top-menu: Bio | PolyTool | Enumerate Chem...
 //name: polyToolEnumerateChem
 //description: Perform cyclization of polymers
-export async function polyToolEnumerateChem(): Promise<void> {
+export async function polyToolEnumerateChemTopMenu(): Promise<void> {
   polyToolEnumerateChemUI();
 }
 

package/src/polytool/pt-conversion.ts

@@ -265,7 +265,8 @@ export class Chain {
   }
 }
 
-function getHelms(sequences: string[], rules: Rules): string[] {
+/** The main PolyTool convert engine. Returns list of Helms. Covered with tests. */
+export function doPolyToolConvert(sequences: string[], rules: Rules): string[] {
   const helms = new Array<string>(sequences.length);
   for (let i = 0; i < sequences.length; i++) {
     if (sequences[i] === undefined)
@@ -278,35 +279,3 @@ function getHelms(sequences: string[], rules: Rules): string[] {
 
   return helms;
 }
-
-export async function addTransformedColumn(
-  sequencesCol: DG.Column<string>, addHelm: boolean, ruleFiles: string[], chiralityEngine?: boolean
-): Promise<void> {
-  const df = sequencesCol.dataFrame;
-
-  const rules = await getRules(ruleFiles);
-  const targetList = getHelms(sequencesCol.toList(), rules);
-  const helmColName = df.columns.getUnusedName('transformed(' + sequencesCol.name + ')');
-  const targetHelmCol = DG.Column.fromList('string', helmColName, targetList);
-
-  addCommonTags(targetHelmCol);
-  targetHelmCol.meta.units = NOTATION.HELM;
-
-  if (addHelm) {
-    targetHelmCol.setTag('cell.renderer', 'helm');
-    df.columns.add(targetHelmCol);
-  }
-
-  // toAtomicLevel
-  const molCol = await grok.functions.call('Bio:getMolFromHelm', {
-    'df': df,
-    'helmCol': targetHelmCol,
-    'chiralityEngine': chiralityEngine
-  });
-
-  molCol.name = df.columns.getUnusedName('molfile(' + sequencesCol.name + ')');
-  molCol.semType = DG.SEMTYPE.MOLECULE;
-
-  df.columns.add(molCol, true);
-  await grok.data.detectSemanticTypes(df);
-}