@datagrok/bio 2.20.1 → 2.20.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.20.1",
+  "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/package.ts

@@ -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

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;
+}