@datagrok/sequence-translator 1.10.18 → 1.10.20

package/files/enumeration/chem_enum_cores.csv

@@ -0,0 +1,5 @@
+Core
+n1nc([*:3])n([*:2])c1[*:1]
+C1C2CN([*:2])CC2CN1[*:1]
+OC1CN([*:2])CCC1N[*:1]
+CC1(N[*:1])CCN([*:2])C1

package/files/enumeration/chem_enum_rgroups.csv

@@ -0,0 +1,5 @@
+R1,R2,R3
+CC1CCN([*:1])C1C,O=C(C[*:2])NCC(F)(F)F,Cc1cccc([*:3])n1
+NCCC(=O)[*:1],O=C1NC(C(=O)[*:2])CO1,
+CC(=O)[*:1],O=C(CCCF)[*:2],
+O=C(c1cc[nH]n1)[*:1],c1ccc(C[*:2])nc1,

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.10.18",
+  "version": "1.10.20",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"

package/src/oligo-renderer/canvas-renderer.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-params */
 /**
  * Canvas drawing for the OligoNucleotide cell renderer.
  *
@@ -41,7 +42,7 @@ export interface RenderOpts {
   scheme?: string;
 }
 
-const DEFAULT_OPTS: RenderOpts = {showLetters: true, pairAlign: true};
+export const DEFAULT_OPTS: RenderOpts = {showLetters: true, pairAlign: true};
 
 /* Visual tuning. */
 const ASPECT_H_OVER_W = 1.25;
@@ -329,11 +330,11 @@ function fitsInBudget(widths: number[], leadW: number, chipGap: number, budget:
 export function drawDuplex(
   g: CanvasRenderingContext2D, cellX: number, cellY: number,
   cellW: number, cellH: number, model: ParsedDuplex,
-  opts: Partial<RenderOpts> = {},
+  opts: Partial<RenderOpts> = {}, skipDrawing = false,
 ): DuplexLayout {
   const o: RenderOpts = {...DEFAULT_OPTS, ...opts};
   const layout = computeLayout(cellW, cellH, model, o);
-
+  if (skipDrawing) return layout;
   g.save();
   g.beginPath();
   g.rect(cellX, cellY, cellW, cellH);

package/src/oligo-renderer/cell-renderer.ts

@@ -14,7 +14,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {drawDuplex, hitTest, DuplexLayout} from './canvas-renderer';
+import {drawDuplex, hitTest, DuplexLayout, RenderOpts, DEFAULT_OPTS} from './canvas-renderer';
 import {looksLikeHelm, parseHelmDuplex} from './helm-parser';
 import {ParsedDuplex} from './types';
 import {showMonomerTooltip} from './tooltip';
@@ -23,9 +23,9 @@ const CELL_TYPE = 'OligoNucleotide';
 
 export class OligoNucleotideCellRenderer extends DG.GridCellRenderer {
   /** WeakMap-by-value cache of parsed HELM. Avoids reparsing on redraw. */
-  private modelCache = new Map<string, ParsedDuplex>();
+  private modelCache = new DG.LruCache<string, ParsedDuplex>();
   /** Last-rendered layout per cell key, for hit-testing on subsequent moves. */
-  private layoutCache = new Map<string, DuplexLayout>();
+  private layoutCache = new DG.LruCache<string, DuplexLayout>();
 
   get name(): string { return CELL_TYPE; }
   get cellType(): string { return CELL_TYPE; }
@@ -54,11 +54,16 @@ export class OligoNucleotideCellRenderer extends DG.GridCellRenderer {
     }
 
     const model = this.getOrParse(value);
+    if (!gridCell.cell?.dart || !gridCell.cell.column) {
+      w = g.canvas.width;
+      h = g.canvas.height;
+      x = 0;
+      y = 0;
+      // this happens in forms....
+    }
     const layout = drawDuplex(g, x, y, w, h, model);
     // Cache for hit-test on subsequent mouse moves over the same cell.
-    this.layoutCache.set(this.cellKey(gridCell), layout);
-    // Avoid unbounded growth on big tables.
-    if (this.layoutCache.size > 5000) this.layoutCache.clear();
+    this.layoutCache.set(this.cellKey(value, w, h, DEFAULT_OPTS), layout);
   }
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
@@ -68,7 +73,11 @@ export class OligoNucleotideCellRenderer extends DG.GridCellRenderer {
       return;
     }
     const model = this.getOrParse(value);
-    const layout = this.layoutCache.get(this.cellKey(gridCell));
+    const layout = this.layoutCache.getOrCreate(
+      this.cellKey(value, gridCell.bounds.width, gridCell.bounds.height, DEFAULT_OPTS), (v) => drawDuplex(
+        null as unknown as CanvasRenderingContext2D, 0, 0, gridCell.bounds.width, gridCell.bounds.height,
+        model, DEFAULT_OPTS, true,
+      ));
     if (!layout) return;
 
     const bounds = gridCell.bounds;
@@ -88,24 +97,14 @@ export class OligoNucleotideCellRenderer extends DG.GridCellRenderer {
   }
 
   private getOrParse(helm: string): ParsedDuplex {
-    let m = this.modelCache.get(helm);
-    if (!m) {
-      m = parseHelmDuplex(helm);
-      // Cap cache to avoid unbounded growth on huge tables.
-      if (this.modelCache.size > 5000) this.modelCache.clear();
-      this.modelCache.set(helm, m);
-    }
-    return m;
+    return this.modelCache.getOrCreate(helm, (h) => parseHelmDuplex(h));
   }
 
   /** Cache key for a cell's layout. Includes the column's `version` so any
    * edit to the column (which bumps version) orphans previous cache entries
    * — preventing onMouseMove from hit-testing a stale layout that was cached
    * before the edit and not yet replaced by a fresh render(). */
-  private cellKey(gridCell: DG.GridCell): string {
-    const col = gridCell.tableColumn;
-    const colName = col?.name ?? gridCell.gridColumn?.name ?? '?';
-    const ver = col?.version ?? 0;
-    return `${colName}@${ver}::${gridCell.tableRowIndex ?? -1}`;
+  private cellKey(value: string, width: number, height: number, opts: RenderOpts): string {
+    return `${value}::${Math.floor(width)}x${Math.floor(height)}::${JSON.stringify(opts)}`;
   }
 }

package/src/package-api.ts

@@ -95,18 +95,11 @@ export namespace funcs {
     return await grok.functions.call('SequenceTranslator:PolyToolEnumerateHelmTopMenu', {});
   }
 
-  /**
-  Perform enumeration of a molecule using different fragments at specified positions
-  */
-  export async function polyToolEnumerateChemTopMenu(): Promise<void> {
-    return await grok.functions.call('SequenceTranslator:PolyToolEnumerateChemTopMenu', {});
-  }
-
   /**
   Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)
   */
-  export async function chemEnumerateReactionsTopMenu(): Promise<void> {
-    return await grok.functions.call('SequenceTranslator:ChemEnumerateReactionsTopMenu', {});
+  export async function chemEnumerateMarkushTopMenu(): Promise<void> {
+    return await grok.functions.call('SequenceTranslator:ChemEnumerateMarkushTopMenu', {});
   }
 
   export async function polyToolColumnChoice(df: DG.DataFrame , macroMolecule: DG.Column ): Promise<void> {

package/src/package.g.ts

@@ -141,18 +141,11 @@ export async function polyToolEnumerateHelmTopMenu() : Promise<void> {
   await PackageFunctions.polyToolEnumerateHelmTopMenu();
 }
 
-//name: polyToolEnumerateChem
-//description: Perform enumeration of a molecule using different fragments at specified positions
-//top-menu: Bio | PolyTool | Enumerate Chem...
-export async function polyToolEnumerateChemTopMenu() : Promise<void> {
-  await PackageFunctions.polyToolEnumerateChemTopMenu();
-}
-
-//name: chemEnumerateReactions
+//name: Markush Enumerator
 //description: Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)
-//top-menu: Chem | Transform | Reactions | Enumerate...
-export async function chemEnumerateReactionsTopMenu() : Promise<void> {
-  await PackageFunctions.chemEnumerateReactionsTopMenu();
+//top-menu: Chem | Transform | Markush Enumeration...
+export async function chemEnumerateMarkushTopMenu() : Promise<void> {
+  await PackageFunctions.chemEnumerateMarkushTopMenu();
 }
 
 //input: dataframe df { description: Input data table }
@@ -175,11 +168,11 @@ export async function ptEnumeratorHelmApp() : Promise<void> {
   await PackageFunctions.ptEnumeratorHelmApp();
 }
 
-//name: Chem Enumerator
+//name: Markush Enumerator
 //tags: app
 //output: view result
 //meta.icon: img/icons/structure.png
-//meta.browsePath: Chem | PolyTool
+//meta.browsePath: Chem
 //meta.role: app
 export async function ptEnumeratorChemApp() {
   return await PackageFunctions.ptEnumeratorChemApp();

package/src/package.ts

@@ -274,22 +274,15 @@ export class PackageFunctions {
 
 
   @grok.decorators.func({
-    'top-menu': 'Bio | PolyTool | Enumerate Chem...',
-    'name': 'polyToolEnumerateChem',
-    'description': 'Perform enumeration of a molecule using different fragments at specified positions'
-  })
-  static async polyToolEnumerateChemTopMenu(): Promise<void> {
-    polyToolEnumerateChemUI();
-  }
-
-
-  @grok.decorators.func({
-    'top-menu': 'Chem | Transform | Reactions | Enumerate...',
-    'name': 'chemEnumerateReactions',
+    'top-menu': 'Chem | Transform | Markush Enumeration...',
+    'name': 'Markush Enumerator',
     'description': 'Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)'
   })
-  static async chemEnumerateReactionsTopMenu(): Promise<void> {
-    polyToolEnumerateChemUI();
+  static async chemEnumerateMarkushTopMenu(): Promise<void> {
+    let cell: DG.Cell | undefined = undefined;
+    if (grok.shell.tv?.dataFrame && grok.shell.tv.dataFrame.currentCell && grok.shell.tv.dataFrame.currentCell.column.semType === DG.SEMTYPE.MOLECULE)
+      cell = grok.shell.tv.dataFrame.currentCell;
+    polyToolEnumerateChemUI(cell);
   }
 
 
@@ -331,10 +324,10 @@ export class PackageFunctions {
   @grok.decorators.func({
     meta: {
       icon: 'img/icons/structure.png',
-      browsePath: 'Chem | PolyTool',
+      browsePath: 'Chem',
       role: 'app'
     },
-    name: 'Chem Enumerator',
+    name: 'Markush Enumerator',
     tags: ['app'],
     outputs: [{type: 'view', name: 'result'}]
   })