@datagrok/bio 2.19.0 → 2.20.1

package/src/utils/cell-renderer.ts

@@ -58,7 +58,6 @@ export function processSequence(subParts: string[]): [string[], boolean] {
 type RendererGridCellTemp = {
   [MmcrTemps.monomerPlacer]: MonomerPlacer
 }
-
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   private readonly seqHelper: ISeqHelper;
 
@@ -70,6 +69,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
   get defaultWidth(): number | null { return 230; }
 
+  hasMouseOver: boolean = false;
+
   constructor() {
     super();
     this.seqHelper = _package.seqHelper;
@@ -101,6 +102,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   override onMouseEnter(gridCell: DG.GridCell, e: MouseEvent) {
     const back = this.getRendererBack(gridCell);
     back?.onMouseEnter(gridCell, e);
+    this.hasMouseOver = true;
   }
 
   override onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
@@ -110,6 +112,14 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
   override onMouseLeave(gridCell: DG.GridCell, _e: MouseEvent) {
     execMonomerHoverLinks(gridCell, null);
+    if (gridCell?.grid) {
+      const sub = gridCell.grid.onEvent('d4-grid-show-tooltip').subscribe((e) => {
+        sub.unsubscribe();
+        if (this.hasMouseOver)
+          e.preventDefault();
+      });
+    }
+    this.hasMouseOver = false;
   }
 
   override onDoubleClick(gridCell: DG.GridCell, e: MouseEvent) {

package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts

@@ -10,7 +10,7 @@ import {MolfileWrapperFactory} from './mol-wrapper-factory';
 export class MonomerWrapper {
   private readonly molfileWrapper: MolfileWrapper;
   private capGroupElements: string[] = [];
-
+  private static molfileV2KToV3KCache: Map<string, string> = new Map();
   constructor(
     public readonly monomerSymbol: string,
     public readonly monomerIdx: number,
@@ -39,12 +39,16 @@ export class MonomerWrapper {
   public get bondCount() { return this.molfileWrapper.bondCount; }
 
   private convertMolfileToV3KFormat(molfileV2K: string, monomerSymbol: string, rdKitModule: RDModule): string {
+    if (MonomerWrapper.molfileV2KToV3KCache.has(molfileV2K))
+      return MonomerWrapper.molfileV2KToV3KCache.get(molfileV2K)!;
     let mol: RDMol | null = null;
     try {
       mol = rdKitModule.get_mol(molfileV2K, JSON.stringify({mergeQueryHs: true}));
-      if (mol)
-        return mol.get_v3Kmolblock();
-      else
+      if (mol) {
+        const res = mol.get_v3Kmolblock();
+        MonomerWrapper.molfileV2KToV3KCache.set(molfileV2K, res);
+        return res;
+      } else
         throw new Error(`Cannot convert ${monomerSymbol} to molV3000`);
     } finally {
       mol?.delete();

package/src/utils/pepsea.ts

@@ -7,7 +7,7 @@ import {Subject} from 'rxjs';
 
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {NOTATION, TAGS as bioTAGS, ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import { fetchWrapper } from '@datagrok-libraries/utils/src/fetch-utils';
+import {fetchWrapper} from '@datagrok-libraries/utils/src/fetch-utils';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 
 import {checkForSingleSeqClusters} from './multiple-sequence-alignment';
@@ -108,50 +108,33 @@ async function requestAlignedObjects(
     body: JSON.stringify(body),
   };
   const path = `/align?method=${method}&gap_open=${gapOpen}&gap_extend=${gapExtend}`;
-  let responseObj: any;
-  if ('fetchProxy' in grok.dapi.docker.dockerContainers) {
-    // new dockerContainers API
-    const t1: number = window.performance.now();
-    // @ts-ignore
-    const response: Response = await grok.dapi.docker.dockerContainers.fetchProxy(dockerfileId, path, params);
-    const t2: number = window.performance.now();
-    _package.logger.debug(`Bio: requestAlignedObjects() dockerContainers.fetchProxy(), ET: ${(t2 - t1)} ms`);
-    const responseContentType = response.headers.get('content-type');
-    const isJson: boolean = responseContentType === 'application/json';
-    if (!response.ok && isJson) {
-      const responseJson = await response.json();
-      const pepseaErrorMsg = responseJson['pepsea-error'];
-      if (!!pepseaErrorMsg)
-        throw new Error(`PepSeA error: ${pepseaErrorMsg}`);
-
-      const datagrokErrorMsg = responseJson['datagrok-error'];
-      if (!!datagrokErrorMsg)
-        throw new Error(`Datagrok error: ${datagrokErrorMsg}`);
-
-      throw new Error(response.statusText);
-    } else if (!response.ok && !isJson) {
-      const responseStr = await response.text();
-      throw new Error(`Error: ${responseStr}`);
-    } else if (!isJson) {
-      const responseStr = await response.text();
-      throw new Error(`Error: PepSeA expected JSON response, got '${responseStr}'.`);
-    }
-    responseObj = await response.json();
-  } else {
-    // @ts-ignore
-    const responseStr = await grok.dapi.docker.dockerContainers.request(dockerfileId, path, params)!;
-    if (!responseStr)
-      throw new Error('Empty response');
-    responseObj = JSON.parse(responseStr);
-
-    const pepseaErrorMsg = responseObj['pepsea-error'];
+  // new dockerContainers API
+  const t1: number = window.performance.now();
+  // @ts-ignore
+  const response: Response = await grok.dapi.docker.dockerContainers.fetchProxy(dockerfileId, path, params);
+  const t2: number = window.performance.now();
+  _package.logger.debug(`Bio: requestAlignedObjects() dockerContainers.fetchProxy(), ET: ${(t2 - t1)} ms`);
+  const responseContentType = response.headers.get('content-type');
+  const isJson: boolean = responseContentType === 'application/json';
+  if (!response.ok && isJson) {
+    const responseJson = await response.json();
+    const pepseaErrorMsg = responseJson['pepsea-error'];
     if (!!pepseaErrorMsg)
       throw new Error(`PepSeA error: ${pepseaErrorMsg}`);
 
-    const datagrokErrorMsg = responseObj['datagrok-error'];
+    const datagrokErrorMsg = responseJson['datagrok-error'];
     if (!!datagrokErrorMsg)
       throw new Error(`Datagrok error: ${datagrokErrorMsg}`);
+
+    throw new Error(response.statusText);
+  } else if (!response.ok && !isJson) {
+    const responseStr = await response.text();
+    throw new Error(`Error: ${responseStr}`);
+  } else if (!isJson) {
+    const responseStr = await response.text();
+    throw new Error(`Error: PepSeA expected JSON response, got '${responseStr}'.`);
   }
+  const responseObj = await response.json();
   // Check for pepsea stderr output
   if ('pepsea-stderr' in responseObj) {
     const pepseaStdErr: string = responseObj['pepsea-stderr'] as string;

package/src/utils/seq-helper/seq-helper.ts

@@ -86,43 +86,23 @@ export class SeqHelper implements ISeqHelper {
 
     const converter = await this.getHelmToMolfileConverter(monomerLib);
 
-    // //#region From HelmToMolfileConverter.convertToRdKitBeautifiedMolfileColumn
-
-    // const molfilesV3K = converter.convertToMolfileV3K(helmCol.toList());
-
-    // const beautifiedMolList: (RDMol | null)[] = molfilesV3K.map((item) => {
-    //   const molfile = item.molfile;
-    //   if (molfile === '')
-    //     return null;
-    //   const mol = this.rdKitModule.get_mol(molfile);
-    //   if (!mol)
-    //     return null;
-    //   mol.set_new_coords();
-    //   mol.normalize_depiction(1);
-    //   mol.straighten_depiction(true);
-    //   return mol;
-    // });
-
-    // let molList: string[];
-    // if (chiralityEngine)// also creates progress indicator
-    //   molList = converter.getMolV3000ViaOCL(beautifiedMolList, molColName).toList();
-    //   // TODO: Cleanup mol objects
-    // else {
-    //   molList = beautifiedMolList.map((mol) => {
-    //     if (mol === null)
-    //       return '';
-    //     const molBlock = mol.get_v3Kmolblock();
-    //     mol!.delete();
-    //     return molBlock;
-    //   });
-    // }
-
     //#endregion From HelmToMolfileConverter
     const helmList = helmCol.toList();
     const molList = new Array<string>(helmCol.length);
-    for (let i = 0; i < helmCol.length; i++)
-      molList[i] = (await this.helmToAtomicLevelSingle(helmList[i], converter, chiralityEngine)).molfile;
-
+    const beautifyMolsChemFunc = DG.Func.find({package: 'Chem', name: 'beautifyMols'})[0];
+    // both options set to false, ugly molfiles
+    for (let i = 0; i < helmCol.length; i++) {
+      molList[i] = (this.helmToAtomicLevelSingle(helmList[i], converter,
+        chiralityEngine, !beautifyMolsChemFunc)).molfile;
+    }
+    // need to beautify the molfiles
+    if (beautifyMolsChemFunc) {
+      const beautifiedMols = await beautifyMolsChemFunc.apply({mols: molList});
+      if (beautifiedMols && Array.isArray(beautifiedMols) && beautifiedMols.length === helmCol.length) {
+        for (let i = 0; i < helmCol.length; i++)
+          beautifiedMols[i] && (molList[i] = beautifiedMols[i]);
+      }
+    }
     //const molHlList = molfilesV3K.map((item: MolfileWithMap) => getMolHighlight(item.monomers.values(), monomerLib));
 
     const molCol = DG.Column.fromStrings(molColName, molList);

package/src/utils/ui-utils.ts

@@ -14,3 +14,26 @@ export function updateDivInnerHTML(div: HTMLElement, content: string | Node): vo
   div.innerHTML = '';
   div.append(content);
 }
+
+export function adjustGridcolAfterRender(
+  grid: DG.Grid, colName: string, width: number, rowHeight?: number, dontWait?: boolean
+) {
+  const update = () => {
+    const col = grid.col(colName);
+    if (col)
+      col.width = width;
+    if (rowHeight)
+      grid.props.rowHeight = rowHeight;
+  };
+  if (dontWait) {
+    update();
+    return;
+  }
+
+  const sub = grid.onAfterDrawOverlay.subscribe(() => {
+    sub.unsubscribe();
+    setTimeout(() => {
+      update();
+    });
+  });
+}