@datagrok/helm 1.0.0 → 1.0.1

package/package.json

@@ -2,13 +2,16 @@
   "name": "@datagrok/helm",
   "beta": false,
   "friendlyName": "Helm",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "description": "",
   "dependencies": {
-    "datagrok-api": "^1.4.12",
-    "cash-dom": "latest",
-    "dayjs": "latest",
-    "@datagrok-libraries/utils": "latest <1.2.0"
+    "datagrok-api": "latest",
+		"cash-dom": "latest",
+		"dayjs": "latest",
+		"@datagrok-libraries/utils": "latest",
+		"@datagrok-libraries/bio": "^2.8.2",
+		"ts-loader": "^9.2.5",
+		"typescript": "^4.4.2"
   },
   "sources": [
     "css/helm.css",

package/src/package.ts

@@ -2,11 +2,16 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+//import {lru} from '../../Bio/src/utils/cell-renderer';
+import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
+//import {ConverterFunc, DfReaderFunc} from '../../Bio/src/tests/types';
 
 export const _package = new DG.Package();
 
 const lru = new DG.LruCache<any, any>(); 
 
+
+
 //tags: init
 export async function initChem(): Promise<void> {
   // apparently HELMWebEditor requires dojo to be initialized first
@@ -35,15 +40,30 @@ export function editMoleculeCell(cell: DG.GridCell): void {
   scil.apply(app.properties.parent.style, s);
   app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
   app.mex.resize(sizes.topheight - 80);
-  setTimeout(function() {
-    app.canvas.helm.setSequence(cell.cell.value , 'HELM');
-  }, 200);
-  //@ts-ignore
-  ui.dialog({ showHeader: false, showFooter: true })
-  .add(view)
-  .onOK(() => {
-    cell.cell.value = app.canvas.getHelm(true);
-  }).show({ modal: true, fullScreen: true});
+  if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === "HELM"){
+    setTimeout(function() {
+      app.canvas.helm.setSequence(cell.cell.value , 'HELM');
+    }, 200);
+    //@ts-ignore
+    ui.dialog({ showHeader: false, showFooter: true })
+    .add(view)
+    .onOK(() => {
+      cell.cell.value = app.canvas.getHelm(true);
+    }).show({ modal: true, fullScreen: true});
+  }
+  else if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === "fasta:SEQ:PT") {
+    const converter = new NotationConverter(cell.gridColumn.column);
+    const resStr = converter.convertFastaStringToHelm(null, null, cell.cell.value);
+    setTimeout(function() {
+      app.canvas.helm.setSequence(resStr , 'HELM');
+    }, 200);
+    //@ts-ignore
+    ui.dialog({ showHeader: false, showFooter: true })
+    .add(view)
+    .onOK(() => {
+      cell.cell.value;
+    }).show({ modal: true, fullScreen: true});
+  }
 }
 
 //name: Details
@@ -59,10 +79,10 @@ export function detailsPanel(helmString: string){
       'molecular weight': result[1],
       'extinction coefficient': result[2],
       'molfile': result[3],
-      /*'fasta': ui.wait(async () => ui.divText(await helmToFasta(helmString))),
+      'fasta': ui.wait(async () => ui.divText(await helmToFasta(helmString))),
       'rna analogue sequence': ui.wait(async () => ui.divText(await helmToRNA(helmString))),
       'smiles': ui.wait(async () => ui.divText(await helmToSmiles(helmString))),
-      'peptide analogue sequence': ui.wait(async () => ui.divText(await helmToPeptide(helmString))),*/
+      //'peptide analogue sequence': ui.wait(async () => ui.divText(await helmToPeptide(helmString))),
     })
   )
 }
@@ -75,9 +95,13 @@ async function loadDialog () {
   res = res.map((e) => e.path);
   //@ts-ignore
   let FilesList = await ui.choiceInput('Monomer Libraries', ' ', res);
+  let grid = grok.shell.tv.grid;
   ui.dialog('Load library from file')
   .add(FilesList)
-  .onOK(() => monomerManager(FilesList.value)).show();
+  .onOK(async () => {
+    await monomerManager(FilesList.value);
+    grid.invalidate()
+  }).show();
 };
 
 //name: Library

package/webpack.config.js

@@ -16,7 +16,16 @@ module.exports = {
   },
   module: {
     rules: [
-      { test: /\.tsx?$/, loader: 'ts-loader' }
+      {
+        test: /\.ts(x?)$/,
+        use: 'ts-loader',
+        exclude: /node_modules/,
+      },
+      {
+        test: /\.css$/,
+        use: ['style-loader', 'css-loader'],
+        exclude: /node_modules/,
+      },
     ],
   },
   devtool: 'inline-source-map',