@datagrok/bio 2.16.5 → 2.16.7

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.16.5",
+  "version": "2.16.7",
   "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",
@@ -37,7 +37,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.45.3",
+    "@datagrok-libraries/bio": "^5.45.5",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.2",
     "@datagrok-libraries/ml": "^6.7.4",

package/src/package.ts

@@ -27,6 +27,7 @@ import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {MmcrTemps} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
 
 import {getMacromoleculeColumns} from './utils/ui-utils';
 import {MacromoleculeDifferenceCellRenderer, MacromoleculeSequenceCellRenderer,} from './utils/cell-renderer';
@@ -630,7 +631,7 @@ export async function toAtomicLevel(
   const pi = DG.TaskBarProgressIndicator.create('Converting to atomic level ...');
   try {
     await initBioPromise;
-    const monomerLib = _package.monomerLib;
+    const monomerLib = seqCol.temp[MmcrTemps.overriddenLibrary] ?? _package.monomerLib;
     const seqHelper = _package.seqHelper;
     const rdKitModule = _package.rdKitModule;
     await sequenceToMolfile(table, seqCol, nonlinear, highlight, monomerLib, seqHelper, rdKitModule);
@@ -1138,7 +1139,6 @@ export async function sdfToJsonLib(table: DG.DataFrame) {
 //input: string seq { semType: Macromolecule }
 //input: bool nonlinear
 //output: string molfile { semType: Molecule }
-//meta.role: converter
 export async function seq2atomic(seq: string, nonlinear: boolean): Promise<string | undefined> {
   if (!(seq.trim())) return '';
   try {

package/src/tests/monomer-libraries-tests.ts

@@ -85,6 +85,7 @@ category('monomerLibraries', () => {
 
     const overriddenMonomerLib = monomerLib.override({[overMon.polymerType]: {[overMon.symbol]: overMon}}, 'test');
     const resOverMon = overriddenMonomerLib.getMonomer(overMon.polymerType, overMon.symbol);
+    if (resOverMon) resOverMon.lib = undefined; // cleanup to prevent infinite recursive comparison
     expectObject(resOverMon as any, overMon);
   });
 });

package/src/tests/seq-handler-get-helm-tests.ts

@@ -81,8 +81,8 @@ category('SeqHandler: getHelm', () => {
     await grok.data.detectSemanticTypes(df);
 
     const sh = seqHelper.getSeqHandler(seqCol);
-    const resSemValue = await sh.getHelm(0);
-    const resHelm = resSemValue.value;
+    const resMValue = await sh.getValue(0);
+    const resHelm = resMValue.helm;
     expect(resHelm, tgtHelm);
   }
 });

package/src/tests/seq-handler-splitted-tests.ts

@@ -114,7 +114,8 @@ rut2-rty-her2---wert-rut12-rty-her2---wert
 PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Thr_PO3H2.Aca.D-Tyr_Et}$$$$
 PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.dK.Thr_PO3H2.Aca}$$$$
 PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.dK.Thr_PO3H2.Aca}$$$$
-PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.T.dK.Thr_PO3H2}$$$$`
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.T.dK.Thr_PO3H2}$$$$,
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.T.dK}|PEPTIDE2{Thr_PO3H2}$$$$`,
       },
       tgt: {
         notation: NOTATION.HELM,
@@ -123,6 +124,7 @@ PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.T.dK.Thr_PO3H2}$$$$`
           ['meI', 'hHis', 'Aca', 'Cys_SEt', 'T', 'dK', 'Thr_PO3H2', 'Aca', 'dK', 'Thr_PO3H2', 'Aca'],
           ['Lys_Boc', 'hHis', 'Aca', 'Cys_SEt', 'T', 'dK', 'Thr_PO3H2', 'Aca', 'dK', 'Thr_PO3H2', 'Aca'],
           ['meI', 'hHis', 'Aca', 'Cys_SEt', 'T', 'dK', 'Thr_PO3H2', 'T', 'dK', 'Thr_PO3H2'],
+          ['meI', 'hHis', 'Aca', 'Cys_SEt', 'T', 'dK', 'Thr_PO3H2', 'T', 'dK', 'Thr_PO3H2'],
         ]
       }
     }

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

@@ -94,53 +94,33 @@ export class HelmToMolfileConverter {
   }
 
 
-  public convertToMolfileV3KColumn(
-    helmCol: DG.Column<string>
-  ): DG.Column<string> {
+  public convertToMolfileV3KColumn(helmCol: DG.Column<string>): DG.Column<string> {
     const df = helmCol.dataFrame;
-    const polymerGraphColumn: DG.Column<string> = this.getPolymerGraphColumn(helmCol);
-    const molfileList = polymerGraphColumn.toList().map(
-      (pseudoMolfile: string, idx: number) => {
-        const helm = helmCol.get(idx);
-        if (!helm) return '';
-
-        let resMolfileWithMap: MolfileWithMap;
-        try {
-          resMolfileWithMap = this.getPolymerMolfile(helm, pseudoMolfile);
-        } catch (err: any) {
-          const [errMsg, errStack] = errInfo(err);
-          _package.logger.error(errMsg, undefined, errStack);
-          resMolfileWithMap = MolfileWithMap.createEmpty();
-        }
-        return resMolfileWithMap.molfile;
-      });
+    const molfileList = this.convertToMolfileV3K(helmCol.toList()).map((mwm) => mwm.molfile);
     const molColName = getUnusedColName(df, `molfileV2K(${helmCol.name})`);
     const molfileColumn = DG.Column.fromList('string', molColName, molfileList);
     return molfileColumn;
   }
 
   /** Gets list of monomer molfiles */
-  public convertToMolfileV3K(helmCol: DG.Column<string>, rdKitModule: RDModule, monomerLib: IMonomerLibBase): MolfileWithMap[] {
-    const polymerGraphColumn: DG.Column<string> = this.getPolymerGraphColumn(helmCol);
-    const rowCount = helmCol.length;
-    const resList: MolfileWithMap[] = new Array<MolfileWithMap>(rowCount);
-    for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
-      const helm = helmCol.get(rowIdx);
+  public convertToMolfileV3K(helmList: string[]): MolfileWithMap[] {
+    const resList: MolfileWithMap[] = new Array<MolfileWithMap>(helmList.length);
+    for (let i = 0; i < helmList.length; ++i) {
+      const helm = helmList[i];
       if (!helm) {
-        resList[rowIdx] = MolfileWithMap.createEmpty();
+        resList[i] = MolfileWithMap.createEmpty();
         continue;
       }
 
-      const pseudoMolfile = polymerGraphColumn.get(rowIdx)!;
       let resMolfile: MolfileWithMap;
       try {
-        resMolfile = this.getPolymerMolfile(helm, pseudoMolfile);
+        resMolfile = this.getPolymerMolfile(helm);
       } catch (err: any) {
         const [errMsg, errStack] = errInfo(err);
         _package.logger.error(errMsg, undefined, errStack);
         resMolfile = MolfileWithMap.createEmpty();
       }
-      resList[rowIdx] = resMolfile;
+      resList[i] = resMolfile;
     }
     return resList;
   }
@@ -152,16 +132,15 @@ export class HelmToMolfileConverter {
     return molfileCol;
   }
 
-  private getPolymerMolfile(
-    helm: string, polymerGraph: string
-  ): MolfileWithMap {
+  private getPolymerMolfile(helm: string): MolfileWithMap {
     const woGapsRes = this.helmHelper.removeGaps(helm);
     const woGapsHelm = woGapsRes.resHelm;
     const woGapsReverseMap = new Map<number, number>();
     for (const [orgPosIdx, woGapsPosIdx] of (woGapsRes.monomerMap?.entries() ?? [])) {
       woGapsReverseMap.set(woGapsPosIdx, orgPosIdx);
     }
-    const globalPositionHandler = new GlobalMonomerPositionHandler(polymerGraph);
+    const pseudoMolfile = this.helmHelper.getMolfiles([woGapsHelm])[0];
+    const globalPositionHandler = new GlobalMonomerPositionHandler(pseudoMolfile);
     const woGapsPolymer = new Polymer(woGapsHelm, this.rdKitModule, this.monomerLib);
     globalPositionHandler.monomerSymbols.forEach((monomerSymbol: string, monomerIdx: number) => {
       const shift = globalPositionHandler.getMonomerShifts(monomerIdx);

package/src/utils/helm-to-molfile/converter/simple-polymer.ts

@@ -1,4 +1,6 @@
 import {HELM_MONOMER_TYPE, HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
+import {cleanupHelmSymbol} from '@datagrok-libraries/bio/src/helm/utils';
+
 import {Bond} from './types';
 
 /** Wrapper over simple polymer substring of HELM, like RNA1{d(A)p}  */
@@ -41,7 +43,7 @@ export class SimplePolymer {
     return id;
   }
 
-  private getMonomerSymbolsAndTypes(): {monomers: string[], monomerTypes: HELM_MONOMER_TYPE[]} {
+  private getMonomerSymbolsAndTypes(): { monomers: string[], monomerTypes: HELM_MONOMER_TYPE[] } {
     const helmWrapperRegex = new RegExp(`${this.polymerType}${this.idx}{|}`, 'g');
     const monomerGroups = this.simplePolymer.replace(helmWrapperRegex, '').split('.');
     const monomerList: string[] = [];
@@ -51,7 +53,7 @@ export class SimplePolymer {
       // monomerList.push(...splitted);
       // WARNING: only the groups of the form r(A)p, as in RNA, are supported
 
-      monomerList.push(monomerGroup);
+      monomerList.push(cleanupHelmSymbol(monomerGroup));
       // const monomerTypes = splitted.map(
       //   (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
       // );

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -132,7 +132,7 @@ class LibraryControlsManager {
 
   private _createControlsForm(): HTMLElement {
     const libraryControls = this.createLibraryControls();
-    const inputsForm = ui.form(libraryControls);
+    const inputsForm = ui.form(libraryControls, undefined, false);
     $(inputsForm).addClass('monomer-lib-controls-form');
 
     return inputsForm;

package/src/utils/monomer-lib/monomer-lib-base.ts

@@ -46,6 +46,10 @@ export class MonomerLibBase implements IMonomerLibBase {
   ) {
     this._isEmpty = !this._monomers || Object.keys(this._monomers).length === 0 ||
       Object.entries(this._monomers).every(([_, ptMonomers]) => Object.keys(ptMonomers).length === 0);
+    for (const [_monomerType, monomersOfType] of Object.entries(this._monomers)) {
+      for (const [_monomerSymbol, monomer] of Object.entries(monomersOfType))
+        monomer.lib = this;
+    }
   }
 
   getMonomerSymbolsByType(polymerType: PolymerType): string[] {

package/src/utils/monomer-lib/monomer-lib.ts

@@ -43,10 +43,6 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     public readonly error: string | undefined = undefined,
   ) {
     super(monomers, source);
-    for (const [_monomerType, monomersOfType] of Object.entries(this._monomers)) {
-      for (const [_monomerSymbol, monomer] of Object.entries(monomersOfType))
-        monomer.lib = this;
-    }
   }
 
   toJSON(): Monomer[] {
@@ -237,8 +233,10 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     return resStr;
   }
 
+  static overrideCounter: number = 0;
+
   override(data: MonomerLibData, source: string): IMonomerLibBase {
-    return new OverriddenMonomerLib(data, source, this);
+    return new OverriddenMonomerLib(data, `override: ${++MonomerLib.overrideCounter}, ${source}`, this);
   }
 }
 

package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts

@@ -868,6 +868,7 @@ class MonomerForm implements INewMonomerForm {
         await grok.dapi.files.writeAsText(LIB_PATH + libName, JSON.stringify(libJSON));
         await (await MonomerLibManager.getInstance()).loadLibraries(true);
         await this.refreshTable(monomer.symbol);
+        this._molChanged = false; // reset the flag
         grok.shell.info(`Monomer ${monomer.symbol} was successfully saved in library ${libName}`);
       } catch (e) {
         grok.shell.error('Error saving monomer');

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

@@ -14,7 +14,7 @@ import {GAP_SYMBOL, GapOriginals} from '@datagrok-libraries/bio/src/utils/macrom
 import {CellRendererBackBase, GridCellRendererTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
-import {ISeqHandler, ConvertFunc, JoinerFunc, SeqTemps} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {ISeqHandler, ConvertFunc, JoinerFunc, SeqTemps, MacromoleculeValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 import {SeqHelper} from './seq-helper';
 
@@ -241,18 +241,16 @@ export class SeqHandler implements ISeqHandler {
   }
 
   /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
-  public async getHelm(rowIdx: number, options?: any): Promise<DG.SemanticValue<string>> {
+  public async getValue(rowIdx: number, options?: any): Promise<MacromoleculeValueBase> {
     const seq: string = this.column.get(rowIdx);
-    let resHelmSV: DG.SemanticValue<string>;
+    let resHelm: string;
     if (this.notationProvider)
-      resHelmSV = await this.notationProvider.getHelm(seq, options);
+      resHelm = await this.notationProvider.getHelm(seq, options);
     else {
-      const resHelm = this.convertToHelm(seq);
-      resHelmSV = DG.SemanticValue.fromValueType(resHelm, DG.SEMTYPE.MACROMOLECULE, NOTATION.HELM);
-      // TODO: set tags from column
+      resHelm = this.convertToHelm(seq);
     }
-
-    return resHelmSV;
+    const resMValue = new MacromoleculeValueBase(resHelm, this, rowIdx);
+    return resMValue;
   }
 
   private _stats: SeqColStats | null = null;

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

@@ -56,7 +56,7 @@ export class SeqHelper implements ISeqHelper {
 
     //#region From HelmToMolfileConverter.convertToRdKitBeautifiedMolfileColumn
 
-    const molfilesV3K = converter.convertToMolfileV3K(helmCol, this.rdKitModule, monomerLib);
+    const molfilesV3K = converter.convertToMolfileV3K(helmCol.toList());
 
     const beautifiedMolList: (RDMol | null)[] = molfilesV3K.map((item) => {
       const molfile = item.molfile;