@datagrok/bio 2.27.0 → 2.27.1

package/src/analysis/sequence-activity-cliffs.ts

@@ -181,12 +181,14 @@ export function createDifferencesWithPositions(
 }
 
 export function createLinesGrid(df: DG.DataFrame, colNames: string[]): DG.Grid {
-  const seqDiffCol = DG.Column.string('seq_diff', df.rowCount)
-    .init((i) => `${df.get(colNames[0], i)}#${df.get(colNames[1], i)}`);
-  seqDiffCol.semType = 'MacromoleculeDifference';
-  seqDiffCol.meta.units = df.col(colNames[0])!.meta.units;
-  seqDiffCol.setTag(bioTAGS.separator, df.col(colNames[0])!.getTag(bioTAGS.separator));
-  df.columns.add(seqDiffCol);
+  if (!df.col('seq_diff')) {
+    const seqDiffCol = DG.Column.string('seq_diff', df.rowCount)
+      .init((i) => `${df.get(colNames[0], i)}#${df.get(colNames[1], i)}`);
+    seqDiffCol.semType = 'MacromoleculeDifference';
+    seqDiffCol.meta.units = df.col(colNames[0])!.meta.units;
+    seqDiffCol.setTag(bioTAGS.separator, df.col(colNames[0])!.getTag(bioTAGS.separator));
+    df.columns.add(seqDiffCol);
+  }
   const grid = df.plot.grid();
   grid.col(colNames[0])!.visible = false;
   grid.col(colNames[1])!.visible = false;

package/src/package-api.ts

@@ -15,8 +15,8 @@ export namespace scripts {
   /**
   Converts molecules to HELM notation based on monomer library
   */
-  export async function molToHelmConverterPy(moleculesDataframe: DG.DataFrame , moleculesColumn: DG.Column , libraryJSON: string ): Promise<DG.DataFrame> {
-    return await grok.functions.call('Bio:MolToHelmConverterPy', { moleculesDataframe, moleculesColumn, libraryJSON });
+  export async function molToHelmConverterPy(moleculesDataframe: DG.DataFrame , moleculesColumn: DG.Column , libraryFile: DG.FileInfo ): Promise<DG.DataFrame> {
+    return await grok.functions.call('Bio:MolToHelmConverterPy', { moleculesDataframe, moleculesColumn, libraryFile });
   }
 
   /**

package/src/package.ts

@@ -810,7 +810,8 @@ export class PackageFunctions {
     // collect current monomer library
     const monomerLib = _package.monomerLib;
     const libJSON = JSON.stringify(monomerLib.toJSON());
-    await api.scripts.molToHelmConverterPy(table, molecules, libJSON);
+    const fileInfo = DG.FileInfo.fromString('monomerLib.json', libJSON);
+    await api.scripts.molToHelmConverterPy(table, molecules, fileInfo);
 
     // semtype is not automatically set, so we set it manually
     const newCol = table.columns.toList().find((c) => c.name.toLowerCase().includes('regenerated sequence') && c.semType !== DG.SEMTYPE.MACROMOLECULE);

package/src/utils/annotations/annotation-manager-ui.ts

@@ -63,7 +63,7 @@ export function showAnnotationManagerDialog(): void {
         setColumnAnnotations(selectedCol, updated);
         df.fireValuesChanged();
         refreshList();
-      });
+      }, 'Delete');
       removeBtn.style.cursor = 'pointer';
       removeBtn.style.color = '#999';
       removeBtn.style.marginLeft = '8px';

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -198,7 +198,7 @@ class LibraryControlsManager {
       updateLibrarySelectionStatus(libInput.value, libFileName);
     }});
     ui.tooltip.bind(libInput.root, `Include monomers from ${libFileName}`);
-    const deleteIcon = ui.iconFA('trash-alt', () => this.promptForLibraryDeletion(libFileName));
+    const deleteIcon = ui.iconFA('trash-alt', () => this.promptForLibraryDeletion(libFileName), 'Delete');
     const editIcon = ui.icons.edit(async () => {
       grok.shell.v = await (await MonomerManager.getInstance()).getViewRoot(libFileName);
     }, 'Edit monomer library');

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

@@ -486,7 +486,7 @@ export class MonomerManager implements IMonomerManager {
       }
       const monomer = await monomerFromDfRow(this.tv!.dataFrame.rows.get(currentRowIdx));
       await this._newMonomerForm.removeMonomers([monomer], this.libInput.value!);
-    });
+    }, 'Delete');
 
     ui.tooltip.bind(deleteButton, () =>
       `${(this.tv?.dataFrame?.selection?.trueCount ?? 0) > 0 ? 'Delete selected monomers' : 'Delete monomer'}`);

package/src/utils/multiple-sequence-alignment-ui.ts

@@ -93,7 +93,7 @@ export async function multipleSequenceAlignmentUI(
         });
       }, 'Adjust alignment parameters such as penalties for opening and extending gaps');
       kalignParamsButton.classList.add('msa-params-button');
-      kalignParamsButton.prepend(ui.icons.settings(() => null));
+      kalignParamsButton.prepend(ui.icons.settings(() => null, 'Settings'));
 
       const kalignElements = [kalignParamsDiv, kalignParamsButton, kalignVersionDiv];
 
@@ -118,7 +118,7 @@ export async function multipleSequenceAlignmentUI(
         engineParamsDiv.hidden = !engineParamsDiv.hidden;
       }, 'Adjust engine-specific alignment parameters');
       engineParamsButton.classList.add('msa-params-button');
-      engineParamsButton.prepend(ui.icons.settings(() => null));
+      engineParamsButton.prepend(ui.icons.settings(() => null, 'Settings'));
 
       // "Include HELM" checkbox: shown when column has a notation provider with fromHelm
       const includeHelmInput = ui.input.bool('Include HELM', {value: true});