@datagrok/bio 2.4.25 → 2.4.26

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.25",
+  "version": "2.4.26",
   "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/scripts/sequence_generator.py

@@ -151,8 +151,8 @@ def generate_sequences(
         motif_length = mean_range(average_motif_length, dispersion)
 
         # sys.stderr.write(f"Cluster {n_cluster:2} motif template: {motif_notation(motif_template)}\n")
-        total_length = mean_range(average_random_length * 2, args.dispersion) + motif_length
-        prefix_length = mean_range(average_random_length, args.dispersion // 2)
+        total_length = mean_range(average_random_length * 2, dispersion) + motif_length
+        prefix_length = mean_range(average_random_length, dispersion // 2)
         suffix_length = total_length - motif_length - prefix_length
         sys.stderr.write(f"Generating sequences for cluster {n_cluster}\n")
         for n_seq, seq, activity, is_cliff in generate_cluster(

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

@@ -9,9 +9,10 @@ import {handleError} from './utils';
 import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {delay} from '@datagrok-libraries/utils/src/test';
 
-const dataFn: string = 'samples/sample_FASTA.csv';
-
 export async function demoBio03UI(): Promise<void> {
+  const dataFn: string = 'samples/sample_HELM.csv';
+  const seqColName = 'HELM';
+
   let df: DG.DataFrame;
   let view: DG.TableView;
   let dlg: DG.Dialog;
@@ -29,21 +30,21 @@ export async function demoBio03UI(): Promise<void> {
         view = grok.shell.addTableView(df);
         for (let colI: number = 0; colI < view.grid.columns.length; colI++) {
           const gCol: DG.GridColumn = view.grid.columns.byIndex(colI)!;
-          if (!(['Sequence', 'Activity'].includes(gCol.name))) gCol.visible = false;
+          if (!([seqColName, 'Activity'].includes(gCol.name))) gCol.visible = false;
         }
       }, {
         description: `Load dataset with macromolecules of 'fasta' notation, 'PT' alphabet (protein, aminoacids).`,
         delay: 2000,
       })
       .step('To atomic level', async () => {
-        const seqCol = df.getCol('Sequence');
+        const seqCol = df.getCol(seqColName);
         await toAtomicLevel(df, seqCol);
       }, {
         description: 'Get atomic level structures of Macromolecules.',
         delay: 2000,
       })
       .step('Sketcher', async () => {
-        const molColName: string = 'molfile(Sequence)';
+        const molColName: string = `molfile(${seqColName})`;
         df.currentCell = df.cell(1, molColName);
         const mol: string = df.currentCell.value;
 

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

@@ -61,6 +61,7 @@ export async function demoBio05UI(): Promise<void> {
       .step('Analyse sequence composition', async () => {
         wlViewer = await df.plot.fromType('WebLogo', {
           sequenceColumnName: msaHelmColName,
+          positionWidth: 40,
           maxHeight: 50,
         }) as DG.Viewer & IWebLogoViewer;
         view.dockManager.dock(wlViewer, DG.DOCK_TYPE.DOWN, null, 'Composition analysis', 0.2);

package/src/package.ts

@@ -506,16 +506,17 @@ export async function sdfToJsonLib(table: DG.DataFrame) {
   const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);
 }
 
-//name: Representations
-//tags: panel, widgets
-//input: cell macroMolecule {semType: Macromolecule}
-//output: widget result
-export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget> {
-  const monomersLibFile = await _package.files.readAsText(HELM_CORE_LIB_FILENAME);
-  const monomersLibObject: any[] = JSON.parse(monomersLibFile);
-
-  return representationsWidget(macroMolecule, monomersLibObject);
-}
+// 2023-05-17 Representations does not work at BioIT
+// //name: Representations
+// //tags: panel, widgets
+// //input: cell macroMolecule {semType: Macromolecule}
+// //output: widget result
+// export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget> {
+//   const monomersLibFile = await _package.files.readAsText(HELM_CORE_LIB_FILENAME);
+//   const monomersLibObject: any[] = JSON.parse(monomersLibFile);
+//
+//   return representationsWidget(macroMolecule, monomersLibObject);
+// }
 
 //name: importFasta
 //description: Opens FASTA file