@datagrok/bio 2.23.1 → 2.23.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.23.1",
+  "version": "2.23.2",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -65,7 +65,7 @@
     "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.14",
+    "@datagrok-libraries/helm-web-editor": "^1.1.16",
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/chem": "^1.15.0",
     "@datagrok/dendrogram": "^1.2.33",

package/src/package-api.ts

@@ -98,6 +98,14 @@ export namespace funcs {
     return await grok.functions.call('Bio:SeparatorSequenceCellRenderer', {});
   }
 
+  export async function bilnSequenceCellRenderer(): Promise<any> {
+    return await grok.functions.call('Bio:BilnSequenceCellRenderer', {});
+  }
+
+  export async function refineNotationProviderForBiln(col: DG.Column , stats: any , separator?: string | null): Promise<boolean> {
+    return await grok.functions.call('Bio:RefineNotationProviderForBiln', { col, stats, separator });
+  }
+
   export async function macroMolColumnPropertyPanel(molColumn: DG.Column ): Promise<any> {
     return await grok.functions.call('Bio:MacroMolColumnPropertyPanel', { molColumn });
   }

package/src/utils/convert.ts

@@ -48,7 +48,7 @@ export function convert(col: DG.Column<string> | undefined, seqHelper: ISeqHelpe
     if (currentNotation === NOTATION.HELM)
       separatorInput.value = '/'; // helm monomers can have - in the name like D-aThr;
     dialogHeader.textContent = 'Current notation: ' + currentNotation;
-    filteredNotations = notations;//.filter((e) => e !== currentNotation); TEMPORARY DO NOT FORGET TO UNCOMMENT
+    filteredNotations = notations.filter((e) => e !== currentNotation);
     targetNotationInput = ui.input.choice('Convert to', {
       value: filteredNotations[0], items: filteredNotations,
       onValueChanged: toggleSeparator
@@ -71,7 +71,7 @@ export function convert(col: DG.Column<string> | undefined, seqHelper: ISeqHelpe
   });
 
   const separatorArray = ['-', '.', '/'];
-  let filteredNotations = notations;//.filter((e) => e !== currentNotation); // TEMPORARY DO NOT FORGET TO UNCOMMENT
+  let filteredNotations = notations.filter((e) => e !== currentNotation);
 
   const separatorInput = ui.input.choice('Separator', {value: separatorArray[0], items: separatorArray});
 

package/src/utils/helm-to-molfile/converter/connection-list.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import {HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
 import {HELM_ITEM_SEPARATOR} from './const';
 import {Bond} from './types';
@@ -12,7 +13,7 @@ export class ConnectionList {
   public connectionItems: string[];
 
   private validateConnectionItem(connectionItem: string): void {
-    const allowedType = `(${HELM_POLYMER_TYPE.PEPTIDE}|${HELM_POLYMER_TYPE.RNA})`;
+    const allowedType = `(${HELM_POLYMER_TYPE.PEPTIDE}|${HELM_POLYMER_TYPE.RNA}|${HELM_POLYMER_TYPE.CHEM}|${HELM_POLYMER_TYPE.BLOB})`;
     const regex = new RegExp(`${allowedType}[0-9]+,${allowedType}[0-9]+,[0-9]+:R[0-9]+-[0-9]+:R[0-9]+`, 'g');
     if (!connectionItem.match(regex))
       throw new Error(`Cannot parse connection item from ${connectionItem}`);

package/src/utils/helm-to-molfile/converter/simple-polymer.ts

@@ -28,7 +28,7 @@ export class SimplePolymer {
 
   private getPolymerType(): string {
     const regex = new RegExp(
-      `(${HELM_POLYMER_TYPE.PEPTIDE}|${HELM_POLYMER_TYPE.RNA})[0-9]+{`
+      `(${HELM_POLYMER_TYPE.PEPTIDE}|${HELM_POLYMER_TYPE.RNA}|${HELM_POLYMER_TYPE.CHEM}|${HELM_POLYMER_TYPE.BLOB})[0-9]+{`
     );
     const match = this.simplePolymer.match(regex);
     if (!match)