@datagrok/bio 2.15.11 → 2.15.13

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.15.11",
+  "version": "2.15.13",
   "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",

package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts

@@ -72,11 +72,20 @@ export class MonomerManager implements IMonomerManager {
 
   protected constructor(public monomerLibManamger: MonomerLibManager) {
     this.monomerLib = monomerLibManamger.getBioLib();
-    this._newMonomerForm = new MonomerForm(monomerLibManamger, () => this.activeMonomerLib, async () => {
+    this._newMonomerForm = new MonomerForm(monomerLibManamger, () => this.activeMonomerLib, async (scrollToRowSymbol?: string) => {
       const df = await this.getMonomersDf(this.libInput.value!);
       if (this.tv?.dataFrame) {
         this.tv.dataFrame = df;
         this.adjustColWidths();
+        if (scrollToRowSymbol != undefined) {
+          setTimeout(() => {
+            const col = df.col(MONOMER_DF_COLUMN_NAMES.SYMBOL)!;
+            const scrollToRow = col.toList().indexOf(scrollToRowSymbol);
+            if (scrollToRow === -1) return;
+            this.tv?.grid.scrollToCell(df.columns.byIndex(0), scrollToRow);
+            df.currentRow = df.rows.get(scrollToRow);
+          }, 500);
+        }
       }
       
     }, () => this.tv?.dataFrame);
@@ -502,7 +511,7 @@ class MonomerForm implements INewMonomerForm {
   private triggerMolChange: boolean = true; // makes sure that change is not triggered by copying the molecule from grid
   inputsTabControl: DG.TabControl;
   constructor(public monomerLibManager: MonomerLibManager,
-    private getMonomerLib: () => IMonomerLib | null, private refreshTable: () => Promise<void>,
+    private getMonomerLib: () => IMonomerLib | null, private refreshTable: (scrollToRowSymbol?: string) => Promise<void | undefined>,
     private getMonomersDataFrame: () => DG.DataFrame | undefined) {
     const monomerTypes = ['PEPTIDE', 'RNA', 'CHEM', 'BLOB', 'G'];
     this.colors = {
@@ -824,7 +833,7 @@ class MonomerForm implements INewMonomerForm {
         }
         await grok.dapi.files.writeAsText(LIB_PATH + libName, JSON.stringify(libJSON));
         await (await MonomerLibManager.getInstance()).loadLibraries(true);
-        await this.refreshTable();
+        await this.refreshTable(monomer.symbol);
         grok.shell.info(`Monomer ${monomer.symbol} was successfully saved in library ${libName}`);
       } catch (e) {
         grok.shell.error('Error saving monomer');
@@ -965,7 +974,8 @@ function getCorrectedMolBlock(molBlock: string) {
   const rgpLineIdx = lines.findIndex((line) => line.startsWith('M') && line.includes('RGP'));
 
   if (rgpLineIdx === -1) {
-    const rgpLine = `M  RGP ${rgroupLineNums.length} ${Object.entries(rgroupLineNumbers).map(([atomLine, rGroupNum]) => `${atomLine} ${rGroupNum}`).join(' ')}`;
+    // number of r groups has 3 empty slots before it, atom numbers have 4 empty slots before them
+    let rgpLine = `M  RGP${rgroupLineNums.length.toString().padStart(3,' ')}${Object.entries(rgroupLineNumbers).map(([atomLine, rGroupNum]) => `${atomLine.toString().padStart(4, ' ')}${rGroupNum.toString().padStart(4, ' ')}`).join('')}`;
     const mEndIdx = lines.findIndex((line) => line.startsWith('M') && line.includes('END'));
     lines.splice(mEndIdx, 0, rgpLine);
   }

package/src/viewers/web-logo-viewer.ts

@@ -211,10 +211,8 @@ export class PositionInfo {
         const left = b.left;
 
         let color: string = undefinedColor;
-        if (monomerLib) {
-          const wem = monomerLib.getWebEditorMonomer(biotype, monomer)!;
-          color = wem.backgroundcolor!;
-        }
+        if (monomerLib)
+          color = monomerLib.getMonomerTextColor(biotype, monomer)!;
 
         g.resetTransform();
         g.strokeStyle = 'lightgray';