@datagrok/bio 2.17.2 → 2.17.3

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.17.2",
+  "version": "2.17.3",
   "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/package.ts

@@ -419,14 +419,6 @@ export function getRegion(
     start ?? null, end ?? null, name ?? null);
 }
 
-//top-menu: Bio | Manage | Monomers
-//name: manageMonomersView
-//description: Edit and create monomers
-export async function manageMonomersView() {
-  const monomerManager = await MonomerManager.getInstance();
-  await monomerManager.getViewRoot();
-}
-
 //top-menu: Bio | Convert | Get Region...
 //name: Get Region Top Menu
 //description: Get sequences for a region specified from a Macromolecule
@@ -961,6 +953,29 @@ export async function manageLibrariesView(): Promise<void> {
   await showManageLibrariesView();
 }
 
+//top-menu: Bio | Manage | Monomers
+//name: manageMonomersView
+//description: Edit and create monomers
+export async function manageMonomersView() {
+  const monomerManager = await MonomerManager.getInstance();
+  await monomerManager.getViewRoot();
+}
+
+//name: Manage Monomers
+//tags: app
+//meta.browsePath: Peptides | Monomers
+export async function manageMonomersApp() {
+  const monomerManager = await MonomerManager.getInstance();
+  await monomerManager.getViewRoot();
+}
+
+//name: Manage Libraries
+//tags: app
+//meta.browsePath: Peptides | Monomers
+export async function manageLibrariesApp(): Promise<void> {
+  await showManageLibrariesView();
+}
+
 //name: saveAsFasta
 //description: As FASTA...
 //tags: fileExporter

package/src/utils/convert.ts

@@ -41,11 +41,6 @@ export function convert(col: DG.Column<string> | undefined, seqHelper: ISeqHelpe
     NOTATION.HELM,
   ];
   const toggleColumn = (newCol: DG.Column) => {
-    if (newCol.semType !== DG.SEMTYPE.MACROMOLECULE) {
-      targetColumnInput.value = srcCol;
-      return;
-    }
-
     srcCol = newCol;
     converterSh = seqHelper.getSeqHandler(srcCol);
     currentNotation = converterSh.notation;
@@ -69,6 +64,8 @@ export function convert(col: DG.Column<string> | undefined, seqHelper: ISeqHelpe
 
   const targetColumnInput = ui.input.column('Column', {
     table: grok.shell.t, value: srcCol,
+    filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE,
+    nullable: false,
     onValueChanged: (value) => toggleColumn(value)
   });
 

package/src/utils/sequence-to-mol.ts

@@ -34,7 +34,7 @@ export async function sequenceToMolfile(
       df.columns.add(helmCol, false);
     }
     try {
-      res = await seqHelper.helmToAtomicLevel(helmCol, true, true);
+      res = await seqHelper.helmToAtomicLevel(helmCol, true, true, monomerLib);
     } finally {
       if (helmCol !== macroMolecule) {
         df.columns.remove(helmCol.name);

package/src/global.d.ts

@@ -1,13 +0,0 @@
-import * as grokNamespace from 'datagrok-api/grok';
-import * as uiNamespace from 'datagrok-api/ui';
-import * as DGNamespace from 'datagrok-api/dg';
-import * as rxjsNamespace from 'rxjs';
-import $Namespace from 'cash-dom';
-
-declare global {
-    const grok: typeof grokNamespace;
-    const ui: typeof uiNamespace;
-    const DG: typeof DGNamespace;
-    const rjxs: typeof rxjsNamespace;
-    const $: typeof $Namespace;
-}