@datagrok/bio 2.20.0 → 2.20.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.20.0",
+  "version": "2.20.2",
   "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/analysis/sequence-search-base-viewer.ts

@@ -13,7 +13,7 @@ export class SequenceSearchBaseViewer extends SearchBaseViewer {
   fingerprint: string;
   metricsProperties = ['distanceMetric', 'fingerprint'];
   fingerprintChoices = ['Morgan', 'Pattern'];
-  tags = [DG.TAGS.UNITS, bioTAGS.aligned, bioTAGS.separator, bioTAGS.alphabet];
+  tags = [DG.TAGS.UNITS, bioTAGS.aligned, bioTAGS.separator, bioTAGS.alphabet, 'cell.renderer'];
   preComputeDistanceMatrix: boolean = false;
 
   constructor(name: string, semType: string) {

package/src/analysis/sequence-similarity-viewer.ts

@@ -3,7 +3,6 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {SequenceSearchBaseViewer} from './sequence-search-base-viewer';
-import {getMonomericMols} from '../calculations/monomerLevelMols';
 import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
 import {adjustGridcolAfterRender, updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
@@ -57,8 +56,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     if (this.targetColumn) {
       this.curIdx = this.dataFrame!.currentRowIdx == -1 ? 0 : this.dataFrame!.currentRowIdx;
       if (computeData && !this.gridSelect) {
-        this.targetMoleculeIdx = this.dataFrame!.currentRowIdx == -1 ? 0 : this.dataFrame!.currentRowIdx;
-        const sh = this.seqHelper.getSeqHandler(this.targetColumn!);
+        this.targetMoleculeIdx = (this.dataFrame!.currentRowIdx ?? -1) < 0 ? 0 : this.dataFrame!.currentRowIdx;
 
         await this.computeByMM();
         const similarColumnName: string = this.similarColumnLabel != null ? this.similarColumnLabel :
@@ -103,23 +101,6 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     }
   }
 
-  private async computeByChem() {
-    const monomericMols = await getMonomericMols(this.targetColumn!, this.seqHelper);
-    //need to create df to calculate fingerprints
-    const _monomericMolsDf = DG.DataFrame.fromColumns([monomericMols]);
-    const df = await grok.functions.call('Chem:callChemSimilaritySearch', {
-      df: this.dataFrame,
-      col: monomericMols,
-      molecule: monomericMols.get(this.targetMoleculeIdx),
-      metricName: this.distanceMetric,
-      limit: this.limit,
-      minScore: this.cutoff,
-      fingerprint: this.fingerprint,
-    });
-    this.idxs = df.getCol('indexes');
-    this.scores = df.getCol('score');
-  }
-
   private async computeByMM() {
     const len = this.targetColumn!.length;
     const actualLimit = Math.min(this.limit, len - 1);

package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts

@@ -107,3 +107,40 @@ export async function demoBio01bUI() {
     handleError(err);
   }
 }
+
+export async function demoActivityCliffsCyclic() {
+  const df = await _package.files.readCsv('tests/helm_cyclic_cliffs.csv');
+  df.name = 'Activity Cliffs Demo';
+  await grok.data.detectSemanticTypes(df);
+  await df.meta.detectSemanticTypes();
+  const tv = grok.shell.addTableView(df);
+  ui.setUpdateIndicator(tv.root, true);
+  try {
+    const seqEncodingFunc = DG.Func.find({name: 'macromoleculePreprocessingFunction', package: 'Bio'})[0];
+    const activityCliffsViewer = (await activityCliffs(
+      df, df.getCol('Sequence'), df.getCol('Activity'),
+      96, DimReductionMethods.UMAP, MmDistanceFunctionsNames.MONOMER_CHEMICAL_DISTANCE,
+      seqEncodingFunc, {}, true)) as DG.ScatterPlotViewer;
+    tv.dockManager.dock(activityCliffsViewer, DG.DOCK_TYPE.RIGHT, null, 'Activity Cliffs', 0.65);
+    await DG.delay(100);
+    const cliffsLink: HTMLButtonElement = $(activityCliffsViewer.root)
+      .find('button.scatter_plot_link,cliffs_grid').get()[0] as HTMLButtonElement;
+    cliffsLink.click();
+    await DG.delay(100);
+    tv.grid.props.rowHeight = 180;
+    tv.grid.col('sequence') && (tv.grid.col('sequence')!.width = 300);
+    tv.grid.col('structure') && (tv.grid.col('structure')!.width = 300);
+    const cliffsGrid = Array.from(tv.viewers).find((v) => v !== tv.grid && v.type === DG.VIEWER.GRID) as DG.Grid;
+    if (cliffsGrid) {
+      cliffsGrid.props.rowHeight = 40;
+      cliffsGrid.col('seq_diff')!.width = 600;
+      tv.dockManager.dock(cliffsGrid, DG.DOCK_TYPE.DOWN, null, 'Cliffs', 0.35);
+      tv.dockManager.dock(activityCliffsViewer, DG.DOCK_TYPE.RIGHT, null, 'Activity Cliffs', 0.55);
+    }
+  } catch (err: any) {
+    handleError(err);
+  } finally {
+    ui.setUpdateIndicator(tv.root, false);
+  }
+  grok.shell.windows.help.showHelp('/help/datagrok/solutions/domains/bio/bio.md#activity-cliffs');
+}

package/src/package.ts

@@ -49,7 +49,7 @@ import {MonomerLibManager} from './utils/monomer-lib/lib-manager';
 import {getMonomerLibraryManagerLink, showManageLibrariesDialog, showManageLibrariesView} from './utils/monomer-lib/library-file-manager/ui';
 import {demoBioSimDiv} from './demo/bio01-similarity-diversity';
 import {demoSeqSpace} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
-import {demoBio01bUI} from './demo/bio01b-hierarchical-clustering-and-activity-cliffs';
+import {demoActivityCliffsCyclic} from './demo/bio01b-hierarchical-clustering-and-activity-cliffs';
 import {demoToAtomicLevel} from './demo/bio03-atomic-level';
 import {checkInputColumnUI} from './utils/check-input-column';
 import {MsaWarning} from './utils/multiple-sequence-alignment';
@@ -71,6 +71,8 @@ import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
 import {MonomerManager} from './utils/monomer-lib/monomer-manager/monomer-manager';
 import {calculateScoresWithEmptyValues} from './utils/calculate-scores';
 import {SeqHelper} from './utils/seq-helper/seq-helper';
+import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
+import {toAtomicLevelWidget} from './widgets/to-atomic-level-widget';
 
 export const _package = new BioPackage(/*{debug: true}/**/);
 
@@ -639,6 +641,14 @@ export async function toAtomicLevelAction(seqCol: DG.Column) {
   func.prepare({table: seqCol.dataFrame, seqCol: seqCol}).edit();
 }
 
+//name: Molecular Structure
+//tags: panel, bio, widgets
+//input: semantic_value sequence { semType: Macromolecule }
+//output: widget result
+export async function toAtomicLevelPanel(sequence: DG.SemanticValue): Promise<DG.Widget> {
+  return toAtomicLevelWidget(sequence);
+}
+
 //top-menu: Bio | Analyze | MSA...
 //name: MSA
 //description: Performs multiple sequence alignment
@@ -1115,10 +1125,9 @@ export async function demoBioSequenceSpace(): Promise<void> {
 //meta.demoPath: Bioinformatics | Activity Cliffs
 //description: Activity Cliffs analysis on Macromolecules data
 //meta.path: /apps/Tutorials/Demo/Bioinformatics/Activity%20Cliffs
-//meta.isDemoScript: True
 //meta.demoSkip: GROK-14320
 export async function demoBioActivityCliffs(): Promise<void> {
-  await demoBio01bUI();
+  await demoActivityCliffsCyclic();
 }
 
 // demoBio03

package/src/widgets/to-atomic-level-widget.ts

@@ -0,0 +1,79 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {_package, getSeqHelper, toAtomicLevel} from '../package';
+
+
+export async function toAtomicLevelWidget(sequence: DG.SemanticValue): Promise<DG.Widget> {
+  const errorDiv = ui.divText('');
+  const errorWidget = DG.Widget.fromRoot(errorDiv);
+  try {
+    if (!sequence || !sequence.value) {
+      errorDiv.innerText = 'No sequence provided';
+      return errorWidget;
+    }
+    if (!sequence.cell || !sequence.cell.dart || !sequence.cell.dataFrame || !sequence.cell.column) {
+      errorDiv.innerText = 'Atomic level conversion requeires a sequence column';
+      return errorWidget;
+    }
+    const supportedUnits: string[] = [NOTATION.FASTA, NOTATION.SEPARATOR, NOTATION.HELM];
+    //todo: add support for custom notations
+    if (!supportedUnits.includes(sequence.cell.column.meta.units?.toLowerCase() ?? '')) {
+      errorDiv.innerText = 'Unsupported sequence notation. please use Bio | Polytool | Convert';
+      return errorWidget;
+    }
+    const seqHelper = await getSeqHelper();
+    const seqSh = seqHelper.getSeqHandler(sequence.cell.column);
+    if (!seqSh) {
+      errorDiv.innerText = 'No sequence handler found';
+      return errorWidget;
+    }
+    if ((seqSh.getSplitted(sequence.cell.rowIndex, 50)?.length ?? 100) > 40) {
+      errorDiv.innerText = 'Maximum number of monomers is 40';
+      return errorWidget;
+    }
+    const singleValCol = DG.Column.fromStrings('singleVal', [sequence.value]);
+    const sDf = DG.DataFrame.fromColumns([singleValCol]);
+    // copy over all the tags
+    Object.entries(sequence.cell.column.tags).forEach(([key, value]) => {
+      singleValCol.setTag(key, value as string);
+    });
+    await toAtomicLevel(sDf, singleValCol, sequence.cell.column.meta.units === NOTATION.HELM, false);
+    if (sDf.columns.length < 2) {
+      errorDiv.innerText = 'No structure generated';
+      return errorWidget;
+    }
+    const molCol = sDf.columns.byIndex(1);
+    const molfile = molCol.get(0);
+    if (!molfile) {
+      errorDiv.innerText = 'No structure generated';
+      return errorWidget;
+    }
+    molCol.semType = DG.SEMTYPE.MOLECULE;
+    const molSemanticValue = DG.SemanticValue.fromTableCell(sDf.cell(0, molCol.name));
+    const panel = ui.panels.infoPanel(molSemanticValue);
+    let molPanel: DG.Widget | null = null;
+    if (panel)
+      molPanel = DG.Widget.fromRoot(panel.root);
+
+
+    const root = grok.chem.drawMolecule(molfile, 300, 300, false);
+    root.style.cursor = 'pointer';
+    ui.tooltip.bind(root, 'Click to expand');
+    root.onclick = () => {
+      const width = window.innerWidth - 200;
+      const height = window.innerHeight - 200;
+      const bigMol = grok.chem.drawMolecule(molfile, width, height, false);
+      ui.dialog({title: 'Molecule'}).add(bigMol).showModal(true);
+    };
+    if (molPanel)
+      molPanel.root.prepend(root);
+    return molPanel ?? DG.Widget.fromRoot(root);
+  } catch (e) {
+    _package.logger.error(e);
+  }
+
+  errorDiv.innerText = 'No Structure generated';
+  return errorWidget;
+}