@datagrok/bio 2.18.4 → 2.20.0

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

@@ -9,9 +9,8 @@ import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {MolfileWithMap} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {getMolColName, hexToPercentRgb} from '@datagrok-libraries/bio/src/monomer-works/utils';
+import {getMolColName} from '@datagrok-libraries/bio/src/monomer-works/utils';
 import {ChemTags} from '@datagrok-libraries/chem-meta/src/consts';
-import {getMolHighlight} from '@datagrok-libraries/bio/src/monomer-works/seq-to-molfile';
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
 
 import {HelmToMolfileConverter} from '../helm-to-molfile/converter';
@@ -19,6 +18,8 @@ import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-h
 import {SeqHandler} from './seq-handler';
 import {Column} from 'datagrok-api/dg';
 import {NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {_package} from '../../package';
 
 type SeqHelperWindowType = Window & { $seqHelperPromise?: Promise<SeqHelper> };
 declare const window: SeqHelperWindowType;
@@ -44,6 +45,37 @@ export class SeqHelper implements ISeqHelper {
     return new HelmToMolfileConverter(helmHelper, this.rdKitModule, monomerLib);
   }
 
+  helmToAtomicLevelSingle(
+    helm: string, converter: HelmToMolfileConverter, chiralityEngine?: boolean, beautifyMol: boolean = true) {
+    if (!helm)
+      return MolfileWithMap.createEmpty();
+    const molfileV3k = converter.convertToMolfileV3K([helm])[0];
+    if (!molfileV3k || !molfileV3k.molfile)
+      return MolfileWithMap.createEmpty();
+    let mol: RDMol | null = null;
+    try {
+      let v3k = molfileV3k.molfile;
+      if (beautifyMol) {
+        mol = this.rdKitModule.get_mol(v3k);
+        if (!mol)
+          return MolfileWithMap.createEmpty();
+        mol.set_new_coords();
+        mol.normalize_depiction(1);
+        mol.straighten_depiction(true);
+        v3k = mol.get_v3Kmolblock();
+      }
+      if (chiralityEngine)
+        v3k = converter.molV3KtoMolV3KOCL(v3k);
+      return new MolfileWithMap(v3k, molfileV3k.monomers);
+    } catch (err) {
+      const [errMsg, errStack] = errInfo(err);
+      _package.logger.error(errMsg, undefined, errStack);
+      return MolfileWithMap.createEmpty();
+    } finally {
+      mol?.delete();
+    }
+  }
+
   async helmToAtomicLevel(
     helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean, overrideMonomerLib?: IMonomerLibBase
   ): Promise<ToAtomicLevelRes> {
@@ -54,39 +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) {
-      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);
+    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/sequence-to-mol.ts

@@ -53,7 +53,7 @@ export async function sequenceToMolfile(
     res.molCol.name = molColName;
     df.columns.add(res.molCol, true);
 
-    buildMonomerHoverLink(macroMolecule, res.molCol, monomerLib, seqHelper, rdKitModule);
+    await buildMonomerHoverLink(macroMolecule, res.molCol, monomerLib, seqHelper, rdKitModule, nonlinear);
     res.molCol.setTag(ChemTags.SEQUENCE_SRC_HL_MONOMERS, String(highlight));
     await grok.data.detectSemanticTypes(df);
   }

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();
+    });
+  });
+}