@datagrok/sequence-translator 1.10.13 → 1.10.15

package/src/package.ts

@@ -16,8 +16,13 @@ import {demoOligoPatternUI, demoOligoStructureUI, demoOligoTranslatorUI} from '.
 import {getExternalAppViewFactories} from './plugins/mermade';
 import {defaultErrorHandler} from './utils/err-info';
 
+import {OligoNucleotideCellRenderer} from './oligo-renderer/cell-renderer';
+import {buildOligoPanel} from './oligo-renderer/legend-panel';
+import {buildOligoStructuresPanel} from './oligo-renderer/structures-panel';
+import {combineSenseAntisenseToOligo, convertHelmColumnToOligo} from './oligo-renderer/converters';
+
 import {polyToolConvert, polyToolConvertUI} from './polytool/pt-dialog';
-import {polyToolEnumerateChemUI} from './polytool/pt-dialog';
+import {polyToolEnumerateChemApp, polyToolEnumerateChemUI} from './polytool/pt-chem-enum-dialog';
 import {polyToolEnumerateHelmUI, polyToolEnumerateSeq} from './polytool/pt-enumerate-seq-dialog';
 import {_setPeptideColumn} from './polytool/utils';
 import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converter';
@@ -276,6 +281,16 @@ export class PackageFunctions {
   }
 
 
+  @grok.decorators.func({
+    'top-menu': 'Chem | Transform | Reactions | Enumerate...',
+    'name': 'chemEnumerateReactions',
+    'description': 'Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)'
+  })
+  static async chemEnumerateReactionsTopMenu(): Promise<void> {
+    polyToolEnumerateChemUI();
+  }
+
+
   @grok.decorators.func()
   static async polyToolColumnChoice(
     @grok.decorators.param({options: {description: 'Input data table'}}) df: DG.DataFrame,
@@ -314,14 +329,15 @@ export class PackageFunctions {
   @grok.decorators.func({
     meta: {
       icon: 'img/icons/structure.png',
-      browsePath: 'Peptides | PolyTool',
+      browsePath: 'Chem | PolyTool',
       role: 'app'
     },
     name: 'Chem Enumerator',
-    tags: ['app']
+    tags: ['app'],
+    outputs: [{type: 'view', name: 'result'}]
   })
-  static async ptEnumeratorChemApp(): Promise<void> {
-    polyToolEnumerateChemUI();
+  static async ptEnumeratorChemApp() {
+    return await polyToolEnumerateChemApp();
   }
 
 
@@ -387,6 +403,77 @@ export class PackageFunctions {
   }
 
 
+  // ---- OligoNucleotide cell renderer + panel + converters ----
+
+  @grok.decorators.func({
+    name: 'oligoNucleotideCellRenderer',
+    description: 'Renders OligoNucleotide (siRNA / ASO) duplex view in grid cells',
+    tags: ['cellRenderer'],
+    meta: {
+      cellType: 'OligoNucleotide',
+      columnTags: 'quality=OligoNucleotide',
+      role: 'cellRenderer',
+    },
+    outputs: [{type: 'grid_cell_renderer', name: 'result'}],
+  })
+  static oligoNucleotideCellRenderer(): DG.GridCellRenderer {
+    return new OligoNucleotideCellRenderer();
+  }
+
+  @grok.decorators.func({
+    name: 'Oligo-Nucleotide',
+    description: 'Modifications, lengths, conjugates and color legend for an OligoNucleotide cell',
+    tags: ['panel', 'widgets'],
+    outputs: [{type: 'widget', name: 'result'}],
+  })
+  static oligoNucleotidePanel(
+    @grok.decorators.param({type: 'semantic_value', options: {semType: 'OligoNucleotide'}}) value: DG.SemanticValue,
+  ): DG.Widget {
+    return buildOligoPanel(value);
+  }
+
+  @grok.decorators.func({
+    name: 'Oligo Structures',
+    description: 'Sense and antisense full molecular structures rendered separately',
+    tags: ['panel', 'widgets'],
+    outputs: [{type: 'widget', name: 'result'}],
+  })
+  static oligoNucleotideStructuresPanel(
+    @grok.decorators.param({type: 'semantic_value', options: {semType: 'OligoNucleotide'}}) value: DG.SemanticValue,
+  ): DG.Widget {
+    return buildOligoStructuresPanel(value);
+  }
+
+  // Invoked from the column / cell context menu via detectors.js (no top-menu).
+  @grok.decorators.func({
+    name: 'convertHelmToOligoNucleotide',
+    description: 'Create a new column tagged as OligoNucleotide so HELM duplex cells render with the oligo view',
+  })
+  static async convertHelmToOligoNucleotide(
+    table: DG.DataFrame,
+    @grok.decorators.param({options: {caption: 'HELM column', semType: 'Macromolecule'}}) helmCol: DG.Column,
+  ): Promise<DG.Column> {
+    const out = convertHelmColumnToOligo(table, helmCol);
+    await grok.data.detectSemanticTypes(table);
+    return out;
+  }
+
+  // Invoked from the column / cell context menu via detectors.js — opens the
+  // function editor (`.prepare().edit()`) so the user can pick antisense column.
+  @grok.decorators.func({
+    name: 'combineSenseAntisenseToOligoNucleotide',
+    description: 'Combine separate sense + antisense HELM columns into one OligoNucleotide column',
+  })
+  static async combineSenseAntisenseToOligoNucleotide(
+    table: DG.DataFrame,
+    @grok.decorators.param({options: {caption: 'Sense', semType: 'Macromolecule'}}) senseCol: DG.Column,
+    @grok.decorators.param({options: {caption: 'Antisense', semType: 'Macromolecule'}}) antiCol: DG.Column,
+  ): Promise<DG.Column> {
+    const out = combineSenseAntisenseToOligo(table, senseCol, antiCol);
+    await grok.data.detectSemanticTypes(table);
+    return out;
+  }
+
   @grok.decorators.func({
     name: 'applyNotationProviderForHarmonizedSequence'
   })

package/src/polytool/const.ts

@@ -38,7 +38,7 @@ export const PT_UI_USE_CHIRALITY = 'Chirality engine';
 export const PT_UI_HIGHLIGHT_MONOMERS = 'Highlight monomers';
 export const PT_UI_DIALOG_CONVERSION = 'PolyTool Conversion';
 export const PT_UI_DIALOG_UNRULE = 'PolyTool Unrule';
-export const PT_UI_DIALOG_ENUMERATION = 'PolyTool Enumeration';
+export const PT_HELM_UI_DIALOG_ENUMERATION = 'PolyTool Helm Enumeration';
 export const PT_UI_RULES_USED = 'Rules used';
 
 export const PT_ENUM_TYPE_TOOLTIPS: Record<string, string> = {