@datagrok/bio 2.22.6 → 2.22.7

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.22.6",
+  "version": "2.22.7",
   "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/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {_package, activityCliffs} from '../package';
+import {_package, PackageFunctions} from '../package';
 import $ from 'cash-dom';
 
 import {TEMPS as acTEMPS} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
@@ -51,7 +51,7 @@ export async function demoBio01bUI() {
       })
       .step('Find activity cliffs', async () => {
         const seqEncodingFunc = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
-        activityCliffsViewer = (await activityCliffs(
+        activityCliffsViewer = (await PackageFunctions.activityCliffs(
           df, df.getCol('Sequence'), df.getCol('Activity'),
           80, dimRedMethod, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc, {}, true)) as DG.ScatterPlotViewer;
         view.dockManager.dock(activityCliffsViewer, DG.DOCK_TYPE.RIGHT, null, 'Activity Cliffs', 0.35);
@@ -117,7 +117,7 @@ export async function demoActivityCliffsCyclic() {
   ui.setUpdateIndicator(tv.root, true);
   try {
     const seqEncodingFunc = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
-    const activityCliffsViewer = (await activityCliffs(
+    const activityCliffsViewer = (await PackageFunctions.activityCliffs(
       df, df.getCol('Sequence'), df.getCol('Activity'),
       96, DimReductionMethods.UMAP, MmDistanceFunctionsNames.MONOMER_CHEMICAL_DISTANCE,
       seqEncodingFunc, {}, true)) as DG.ScatterPlotViewer;

package/src/demo/bio03-atomic-level.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import {_package, toAtomicLevel} from '../package';
+import {_package, PackageFunctions} from '../package';
 import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {delay} from '@datagrok-libraries/utils/src/test';
@@ -14,7 +14,7 @@ export async function demoToAtomicLevel(): Promise<void> {
   await grok.data.detectSemanticTypes(data);
   const view = grok.shell.addTableView(data);
   const seqCol = data.col('HELM')!;
-  await toAtomicLevel(data, seqCol, true, false);
+  await PackageFunctions.toAtomicLevel(data, seqCol, true, false);
   adjustGridcolAfterRender(view.grid, 'molfile(HELM)', 500, 300, true);
   adjustGridcolAfterRender(view.grid, 'HELM', 500, undefined, true);
   grok.shell.info('Hover over monomers in HELM column to highlight them in molecular structure.', {timeout: 10});
@@ -47,7 +47,7 @@ export async function demoBio03UI(): Promise<void> {
       })
       .step('To atomic level', async () => {
         const seqCol = df.getCol(seqColName);
-        await toAtomicLevel(df, seqCol, false, false);
+        await PackageFunctions.toAtomicLevel(df, seqCol, false, false);
       }, {
         description: 'Get atomic level structures of Macromolecules.',
         delay: 2000,

package/src/demo/bio05-helm-msa-sequence-space.ts

@@ -8,7 +8,7 @@ import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
 import {Pepsea, pepseaMethods, runPepsea} from '../utils/pepsea';
-import {sequenceSpaceTopMenu} from '../package';
+import {PackageFunctions} from '../package';
 import {handleError} from './utils';
 
 import {_package} from '../package';
@@ -92,7 +92,7 @@ export async function demoBio05UI(): Promise<void> {
       })
       .step('Build sequence space', async () => {
         const preprocessingFunc = DG.Func.find({package: 'Bio', name: 'macromoleculePreprocessingFunction'})[0];
-        ssViewer = (await sequenceSpaceTopMenu(df, msaHelmCol,
+        ssViewer = (await PackageFunctions.sequenceSpaceTopMenu(df, msaHelmCol,
           dimRedMethod, MmDistanceFunctionsNames.LEVENSHTEIN, true, preprocessingFunc, undefined, undefined, true)) as DG.ScatterPlotViewer;
         view.dockManager.dock(ssViewer, DG.DOCK_TYPE.RIGHT, null, 'Sequence Space', 0.35);
       }, {

package/src/demo/utils.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {_package, sequenceSpaceTopMenu} from '../package';
+import {_package, PackageFunctions} from '../package';
 import {StringMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {getNormalizedEmbeddings} from
@@ -65,7 +65,7 @@ export async function demoSequenceSpace(
     })) as DG.ScatterPlotViewer;
   } else {
     const preprocessingFunc = DG.Func.find({package: 'Bio', name: 'macromoleculePreprocessingFunction'})[0];
-    resSpaceViewer = (await sequenceSpaceTopMenu(df, df.getCol(colName),
+    resSpaceViewer = (await PackageFunctions.sequenceSpaceTopMenu(df, df.getCol(colName),
       DimReductionMethods.UMAP, MmDistanceFunctionsNames.LEVENSHTEIN, true, preprocessingFunc)) as DG.ScatterPlotViewer;
   }
   view.dockManager.dock(resSpaceViewer!, DG.DOCK_TYPE.RIGHT, null, 'Sequence Space', 0.35);

package/src/package-api.ts

@@ -21,6 +21,10 @@ export namespace scripts {
 }
 
 export namespace funcs {
+  export async function test1(): Promise<any> {
+    return await grok.functions.call('Bio:Test1', {});
+  }
+
   /**
   Returns an instance of the monomer library helper
   */
@@ -51,9 +55,6 @@ export namespace funcs {
     return await grok.functions.call('Bio:GetRegionPanel', { seqCol });
   }
 
-  /**
-  //tags: panel, exclude-actions-panel
-  */
   export async function libraryPanel(seqColumn: DG.Column ): Promise<any> {
     return await grok.functions.call('Bio:LibraryPanel', { seqColumn });
   }
@@ -133,7 +134,7 @@ export namespace funcs {
   /**
   Detects pairs of molecules with similar structure and significant difference in any given property
   */
-  export async function activityCliffs(table: DG.DataFrame , molecules: DG.Column , activities: DG.Column , similarity: number , methodName: string , similarityMetric: string , preprocessingFunction: any , options?: any , demo?: boolean ): Promise<void> {
+  export async function activityCliffs(table: DG.DataFrame , molecules: string , activities: DG.Column , similarity: number , methodName: string , similarityMetric: string , preprocessingFunction: any , options?: any , demo?: boolean ): Promise<void> {
     return await grok.functions.call('Bio:ActivityCliffs', { table, molecules, activities, similarity, methodName, similarityMetric, preprocessingFunction, options, demo });
   }
 
@@ -410,8 +411,4 @@ export namespace funcs {
   export async function getMolFromHelm(df: DG.DataFrame , helmCol: DG.Column , chiralityEngine: boolean ): Promise<DG.Column> {
     return await grok.functions.call('Bio:GetMolFromHelm', { df, helmCol, chiralityEngine });
   }
-
-  export async function test1(): Promise<any> {
-    return await grok.functions.call('Bio:Test1', {});
-  }
 }