@datagrok/helm 2.4.4 → 2.4.6

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.4.4",
+  "version": "2.4.6",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
@@ -26,7 +26,7 @@
     "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": "^2.14.1",
     "@datagrok/chem": "^1.9.2",

package/src/package.ts

@@ -86,7 +86,7 @@ export function helmCellRenderer(): HelmCellRenderer {
   return new HelmGridCellRenderer(); // new
 }
 
-function checkMonomersAndOpenWebEditor(cell: DG.Cell, value?: string, units?: string) {
+function checkMonomersAndOpenWebEditor(cell: DG.GridCell, value?: string, units?: string) {
   openWebEditor(cell, value, units);
 }
 
@@ -95,7 +95,7 @@ function checkMonomersAndOpenWebEditor(cell: DG.Cell, value?: string, units?: st
 //input: grid_cell cell
 //meta.columnTags: quality=Macromolecule, units=helm
 export function editMoleculeCell(cell: DG.GridCell): void {
-  checkMonomersAndOpenWebEditor(cell.cell, undefined, undefined);
+  checkMonomersAndOpenWebEditor(cell, undefined, undefined);
 }
 
 //name: Open Helm Web Editor
@@ -107,11 +107,14 @@ export function openEditor(mol: string): void {
   const col = df.columns.bySemType('Macromolecule')! as DG.Column<string>;
   const colSh = SeqHandler.forColumn(col);
   const colUnits = col.meta.units;
+  if (df.currentRowIdx === -1)
+    return;
+  const gCell = DG.GridCell.fromColumnRow(grok.shell.tv.grid, col.name, df.currentRowIdx);
   if (colUnits === NOTATION.HELM)
-    checkMonomersAndOpenWebEditor(df.currentCell, undefined, undefined);
+    checkMonomersAndOpenWebEditor(gCell, undefined, undefined);
   const convert = colSh.getConverter(NOTATION.HELM);
   const helmMol = convert(mol);
-  checkMonomersAndOpenWebEditor(df.currentCell, helmMol, col.meta.units!);
+  checkMonomersAndOpenWebEditor(gCell, helmMol, col.meta.units!);
 }
 
 //name: Properties
@@ -122,14 +125,14 @@ export function propertiesWidget(sequence: DG.SemanticValue): DG.Widget {
   return getPropertiesWidget(sequence);
 }
 
-function openWebEditor(cell: DG.Cell, value?: string, units?: string) {
+function openWebEditor(cell: DG.GridCell, value?: string, units?: string) {
   const view = ui.div();
   // const df = grok.shell.tv.grid.dataFrame;
-  // const col = df.columns.bySemType('Macromolecule')!;
-  const col = cell.column as DG.Column<string>;
+  // const col = df.columns.bySemType('Macromolecule')!
+  const col = cell.cell.column as DG.Column<string>;
   const sh = SeqHandler.forColumn(col);
-  const rowIdx = cell.rowIndex;
-  const app: App = _package.helmHelper.createWebEditorApp(view, !!cell && units === undefined ? cell.value : value!);
+  const app: App =
+    _package.helmHelper.createWebEditorApp(view, !!cell && units === undefined ? cell.cell.value : value!);
   const dlg = ui.dialog({showHeader: false, showFooter: true});
   dlg.add(view)
     .onOK(() => {
@@ -137,10 +140,10 @@ function openWebEditor(cell: DG.Cell, value?: string, units?: string) {
         .replace(/<span style='background:#bbf;'>/g, '');
       if (!!cell) {
         if (units === undefined)
-          cell.value = helmValue;
+          cell.setValue(helmValue);
         else {
           const convertedRes = sh.convertHelmToFastaSeparator(helmValue, units!, sh.separator);
-          cell.value = convertedRes;
+          cell.setValue(convertedRes);
         }
       }
     }).show({modal: true, fullScreen: true});

package/src/tests/parse-helm-tests.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 
 import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/utils/src/test';
-import {HelmType, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmType, IHelmDrawOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
@@ -13,22 +13,31 @@ import {
 
 import {JSDraw2Module} from '../types';
 import {initHelmMainPackage} from './utils';
-import {IHelmDrawOptions} from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 
 declare const org: OrgType;
 declare const JSDraw2: JSDraw2Module;
 
-type TestTgtType = { atomCount: number, bondCount: number };
+type TestTgtType = { atomCount: number, bondCount: number, helm: string };
 
 category('parseHelm', () => {
   const testData: { [testName: string]: { src: string, tgt: TestTgtType } } = {
     'PT': {
       src: 'PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0',
-      tgt: {atomCount: 6, bondCount: 5}
+      tgt: {
+        atomCount: 6, bondCount: 5,
+        helm: 'PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0'
+      }
+    },
+    'PT-cycic': {
+      src: 'PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0',
+      tgt: {
+        atomCount: 8, bondCount: 8,
+        helm: 'PEPTIDE1{[meI].C.[Aca].[Cys_SEt].T.C.[Thr_PO3H2].[Aca]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$V2.0'
+      },
     },
     'RNA': {
       src: 'RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0',
-      tgt: {atomCount: 12, bondCount: 11}
+      tgt: {atomCount: 12, bondCount: 11, helm: 'RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0',}
     }
   };
 
@@ -94,6 +103,9 @@ function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
   io.parseHelm(plugin, src, origin, undefined);
 
   const m: Mol<HelmType> = plugin.jsd.m;
+  debugger;
+  const resHelm = io.getHelm(m);
   expect(m.atoms.length, tgt.atomCount);
   expect(m.bonds.length, tgt.bondCount);
+  expect(resHelm, tgt.helm);
 }

package/src/utils/helm-grid-cell-renderer.ts

@@ -146,9 +146,8 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
     gridCell: DG.GridCell, cellStyle: DG.GridCellStyle) {
     if (!this.monomerLib) {
       this.monomerLib = _package.monomerLib;
-      if (this.monomerLib) {
+      if (this.monomerLib)
         this.subs.push(this.monomerLib.onChanged.subscribe(this.monomerLibOnChanged.bind(this)));
-      }
     }
     super.render(g, x, y, w, h, gridCell, cellStyle);
   }