@datagrok/bio 2.15.13 → 2.16.2

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.15.13",
+  "version": "2.16.2",
   "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",
@@ -37,10 +37,10 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.44.5",
+    "@datagrok-libraries/bio": "^5.45.2",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.7.3",
+    "@datagrok-libraries/ml": "^6.7.4",
     "@datagrok-libraries/tutorials": "^1.4.3",
     "@datagrok-libraries/utils": "^4.3.6",
     "@webgpu/types": "^0.1.40",
@@ -55,27 +55,27 @@
     "rxjs": "^6.5.5",
     "style-loader": "^3.3.1",
     "umap-js": "^1.3.3",
-    "wu": "latest"
+    "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.11",
-    "@datagrok-libraries/js-draw-lite": "^0.0.8",
+    "@datagrok-libraries/helm-web-editor": "^1.1.12",
+    "@datagrok-libraries/js-draw-lite": "^0.0.9",
     "@datagrok/chem": "^1.12.3",
     "@datagrok/dendrogram": "^1.2.33",
     "@datagrok/helm": "^2.5.3",
     "@types/node": "^17.0.24",
-    "@types/wu": "latest",
-    "@typescript-eslint/eslint-plugin": "latest",
-    "@typescript-eslint/parser": "latest",
+    "@types/wu": "^2.1.44",
+    "@typescript-eslint/eslint-plugin": "^8.8.1",
+    "@typescript-eslint/parser": "^8.8.1",
     "datagrok-tools": "latest",
-    "eslint": "latest",
-    "eslint-config-google": "latest",
-    "eslint-plugin-rxjs": "latest",
-    "source-map-loader": "latest",
+    "eslint": "^9.12.0",
+    "eslint-config-google": "^0.14.0",
+    "eslint-plugin-rxjs": "^5.0.3",
+    "source-map-loader": "^5.0.0",
     "ts-loader": "^9.5.1",
     "typescript": "^5.5.3",
     "webpack": "^5.92.1",
-    "webpack-bundle-analyzer": "latest",
+    "webpack-bundle-analyzer": "^4.10.2",
     "webpack-cli": "^5.1.4"
   },
   "scripts": {

package/src/analysis/sequence-activity-cliffs.ts

@@ -6,15 +6,16 @@ import wu from 'wu';
 
 import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {getSimilarityFromDistance} from '@datagrok-libraries/ml/src/distance-metrics-methods';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {AvailableMetrics, DistanceMetricsSubjects, StringMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
-import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
-import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
 import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 
-import {getMonomerLib} from '../package';
+import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
+import {invalidateMols, MONOMERIC_COL_TAGS} from '../substructure-search/substructure-search';
+
+import {_package} from '../package';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
   const stringArray = col.toList();
@@ -47,11 +48,11 @@ export async function getSimilaritiesMatrix(
   return simArr;
 }
 
-export async function getChemSimilaritiesMatrix(dim: number, seqCol: DG.Column,
+export async function getChemSimilaritiesMatrix(dim: number, seqCol: DG.Column, seqHelper: ISeqHelper,
   df: DG.DataFrame, colName: string, simArr: (DG.Column | null)[])
   : Promise<(DG.Column | null)[]> {
   if (seqCol.version !== seqCol.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
-    await invalidateMols(seqCol, false);
+    await invalidateMols(seqCol, seqHelper, false);
   const fpDf = DG.DataFrame.create(seqCol.length);
   fpDf.columns.addNewString(colName).init((i) => seqCol.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS].get(i));
   const res = await grok.functions.call('Chem:getChemSimilaritiesMatrix', {
@@ -108,7 +109,7 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
   });
 
   const molDifferences: { [key: number]: HTMLCanvasElement } = {};
-  const sh = SeqHandler.forColumn(params.seqCol);
+  const sh = _package.seqHelper.getSeqHandler(params.seqCol);
   const biotype = sh.defaultBiotype;
   const subParts1 = sh.getSplitted(params.points[0]);
   const subParts2 = sh.getSplitted(params.points[1]);
@@ -138,7 +139,7 @@ export function createDifferenceCanvas(
   const canvas = document.createElement('canvas');
   const context = canvas.getContext('2d');
   canvas.height = 30;
-  const monomerLib = getMonomerLib();
+  const monomerLib = _package.monomerLib;
   drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30,
     wu.count(0).take(subParts1.length).map((posIdx) => subParts1.getCanonical(posIdx)).toArray(),
     wu.count(0).take(subParts2.length).map((posIdx) => subParts2.getCanonical(posIdx)).toArray(),

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

@@ -7,7 +7,7 @@ import {SequenceSearchBaseViewer} from './sequence-search-base-viewer';
 import {getMonomericMols} from '../calculations/monomerLevelMols';
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {getEncodedSeqSpaceCol} from './sequence-space';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {DistanceMatrixService, dmLinearIndex} from '@datagrok-libraries/ml/src/distance-matrix';
@@ -19,7 +19,9 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   columnNames = [];
   computeCompleted = new Subject<boolean>();
 
-  constructor() {
+  constructor(
+    private readonly seqHelper: ISeqHelper,
+  ) {
     super('diversity');
     this.diverseColumnLabel = this.string('diverseColumnLabel', null);
   }
@@ -29,7 +31,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
       return;
     if (this.dataFrame) {
       if (computeData && this.moleculeColumn) {
-        const sh = SeqHandler.forColumn(this.moleculeColumn);
+        const sh = this.seqHelper.getSeqHandler(this.moleculeColumn);
         await (sh.isFasta() ? this.computeByMM() : this.computeByChem());
 
         const diverseColumnName: string = this.diverseColumnLabel != null ? this.diverseColumnLabel :
@@ -48,7 +50,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   }
 
   private async computeByChem() {
-    const monomericMols = await getMonomericMols(this.moleculeColumn!);
+    const monomericMols = await getMonomericMols(this.moleculeColumn!, this.seqHelper);
     //need to create df to calculate fingerprints
     const _monomericMolsDf = DG.DataFrame.fromColumns([monomericMols]);
     this.renderMolIds = await grok.functions.call('Chem:callChemDiversitySearch', {

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

@@ -7,7 +7,7 @@ import {getMonomericMols} from '../calculations/monomerLevelMols';
 import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
 import {updateDivInnerHTML} from '../utils/ui-utils';
 import {Subject} from 'rxjs';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {alignSequencePair} from '@datagrok-libraries/bio/src/utils/macromolecule/alignment';
 import {KnnResult, SparseMatrixService} from '@datagrok-libraries/ml/src/distance-matrix/sparse-matrix-service';
 import {getEncodedSeqSpaceCol} from './sequence-space';
@@ -32,7 +32,10 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   kPrevNeighbors: number = 0;
   demo?: boolean;
 
-  constructor(demo?: boolean) {
+  constructor(
+    private readonly seqHelper: ISeqHelper,
+    demo?: boolean,
+  ) {
     super('similarity');
     this.cutoff = this.float('cutoff', 0.01, {min: 0, max: 1});
     this.hotSearch = this.bool('hotSearch', true);
@@ -52,7 +55,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
       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 = SeqHandler.forColumn(this.moleculeColumn!);
+        const sh = this.seqHelper.getSeqHandler(this.moleculeColumn!);
 
         await (!sh.isHelm() ? this.computeByMM() : this.computeByChem());
         const similarColumnName: string = this.similarColumnLabel != null ? this.similarColumnLabel :
@@ -83,7 +86,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   }
 
   private async computeByChem() {
-    const monomericMols = await getMonomericMols(this.moleculeColumn!);
+    const monomericMols = await getMonomericMols(this.moleculeColumn!, this.seqHelper);
     //need to create df to calculate fingerprints
     const _monomericMolsDf = DG.DataFrame.fromColumns([monomericMols]);
     const df = await grok.functions.call('Chem:callChemSimilaritySearch', {
@@ -125,8 +128,8 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     const molDifferences: { [key: number]: HTMLCanvasElement } = {};
     const molColName = this.molCol?.name!;
     const resCol: DG.Column<string> = resDf.col(molColName)!;
-    const molColSh = SeqHandler.forColumn(this.moleculeColumn!);
-    const resSh = SeqHandler.forColumn(resCol);
+    const molColSh = this.seqHelper.getSeqHandler(this.moleculeColumn!);
+    const resSh = this.seqHelper.getSeqHandler(resCol);
     const subParts1 = molColSh.getSplitted(this.targetMoleculeIdx);
     const subParts2 = resSh.getSplitted(resDf.currentRowIdx);
     const alignment = alignSequencePair(subParts1, subParts2);

package/src/analysis/sequence-space.ts

@@ -4,10 +4,11 @@ import * as grok from 'datagrok-api/grok';
 
 import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {mmDistanceFunctionArgs} from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {getMonomerSubstitutionMatrix} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
+import {_package} from '../package';
+
 export interface ISequenceSpaceResult {
   distance?: Float32Array;
   coordinates: DG.ColumnList;
@@ -18,7 +19,7 @@ export async function getEncodedSeqSpaceCol(
 ): Promise<{ seqList: string[], options: { [_: string]: any } }> {
 // encodes sequences using utf characters to also support multichar and non fasta sequences
   const rowCount = seqCol.length;
-  const sh = SeqHandler.forColumn(seqCol);
+  const sh = _package.seqHelper.getSeqHandler(seqCol);
   const encList = Array<string>(rowCount);
   let charCodeCounter = 1; // start at 1, 0 is reserved for null.
   const charCodeMap = new Map<string, string>();

package/src/calculations/monomerLevelMols.ts

@@ -4,21 +4,20 @@ import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
 
-import {getHelmMonomers} from '../package';
-import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 const V2000_ATOM_NAME_POS = 31;
 
 export async function getMonomericMols(
-  mcol: DG.Column<string>, pattern: boolean = false, monomersDict?: Map<string, string>
+  mcol: DG.Column<string>, seqHelper: ISeqHelper, pattern: boolean = false, monomersDict?: Map<string, string>
 ): Promise<DG.Column> {
-  const sh = SeqHandler.forColumn(mcol);
+  const sh = seqHelper.getSeqHandler(mcol);
   let molV3000Array;
   monomersDict ??= new Map();
   const monomers = sh.isHelm() ?
-    getHelmMonomers(mcol) : Object.keys(sh.stats.freq).filter((it) => it !== '');
+    seqHelper.getSeqMonomers(mcol) : Object.keys(sh.stats.freq).filter((it) => it !== '');
 
   for (let i = 0; i < monomers.length; i++) {
     if (!monomersDict.has(monomers[i]))

package/src/demo/bio01-similarity-diversity.ts

@@ -7,10 +7,13 @@ import {DemoScript} from '@datagrok-libraries/tutorials/src/demo-script';
 import {handleError} from './utils';
 import {SequenceDiversityViewer} from '../analysis/sequence-diversity-viewer';
 import {SequenceSimilarityViewer} from '../analysis/sequence-similarity-viewer';
+import {getSeqHelper, ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 const dataFn: string = 'samples/FASTA_PT_activity.csv';
 
 export async function demoBio01UI() {
+  let seqHelper: ISeqHelper = await getSeqHelper();
+
   let view: DG.TableView;
   let df: DG.DataFrame;
 
@@ -37,7 +40,7 @@ export async function demoBio01UI() {
         delay: 2000,
       })
       .step('Find the most similar sequences to the current one', async () => {
-        const simViewer = new SequenceSimilarityViewer(true);
+        const simViewer = new SequenceSimilarityViewer(seqHelper, true);
         view.addViewer(simViewer, {
           moleculeColumnName: 'sequence',
           similarColumnLabel: 'Similar to current',

package/src/package-test.ts

@@ -8,7 +8,6 @@ import './tests/_first-tests';
 import './tests/Palettes-test';
 import './tests/detectors-tests';
 import './tests/detectors-weak-and-likely-tests';
-import './tests/detectors-custom-notation-tests';
 import './tests/detectors-benchmark-tests';
 import './tests/msa-tests';
 import './tests/splitters-test';
@@ -31,6 +30,7 @@ import './tests/seq-handler-tests';
 import './tests/seq-handler-splitted-tests';
 import './tests/seq-handler-get-region-tests';
 import './tests/seq-handler-get-helm-tests';
+import './tests/helm-tests';
 import './tests/to-atomic-level-tests';
 import './tests/to-atomic-level-ui-tests';
 import './tests/mm-distance-tests';

package/src/package-types.ts

@@ -7,6 +7,8 @@ import {Observable, Subject} from 'rxjs';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {IMonomerLib, IMonomerLibBase, IMonomerSet} from '@datagrok-libraries/bio/src/types';
 
 /** Names of package properties/settings declared in properties section of {@link './package.json'} */
 export const enum BioPackagePropertiesNames {
@@ -60,8 +62,33 @@ export class BioPackageProperties extends Map<string, any> {
 export class BioPackage extends DG.Package {
   private _properties: BioPackageProperties;
 
+  private _seqHelper: ISeqHelper;
+  public get seqHelper(): ISeqHelper {
+    if (!this._seqHelper)
+      throw new Error('Package Bio .seqHelper is not initialized.');
+    return this._seqHelper;
+  };
+
+  private _monomerLib: IMonomerLib;
+  public get monomerLib(): IMonomerLib {
+    if (!this._monomerLib)
+      throw new Error('Package Bio .monomerLib is not initialized.');
+    return this._monomerLib;
+  };
+
+  private _monomerSets: IMonomerSet;
+  public get monomerSets(): IMonomerSet {
+    if (!this._monomerSets)
+      throw new Error('Package Bio .monomerSets is not initialized.');
+    return this._monomerSets;
+  };
+
   private _rdKitModule: RDModule;
-  public get rdKitModule(): RDModule { return this._rdKitModule;};
+  public get rdKitModule(): RDModule {
+    if (!this._rdKitModule)
+      throw new Error('Package Bio .rdKitModule is not initialized.');
+    return this._rdKitModule;
+  };
 
   /** Package properties/settings declared in properties section of {@link './package.json'} */
   public get properties(): BioPackageProperties { return this._properties; };
@@ -78,7 +105,12 @@ export class BioPackage extends DG.Package {
     super._logger = new LoggerWrapper(super.logger, opts.debug);
   }
 
-  public completeInit(rdKitModule: RDModule): void {
+  public completeInit(
+    seqHelper: ISeqHelper, monomerLib: IMonomerLib, monomerSets: IMonomerSet, rdKitModule: RDModule
+  ): void {
+    this._seqHelper = seqHelper;
+    this._monomerLib = monomerLib;
+    this._monomerSets = monomerSets;
     this._rdKitModule = rdKitModule;
     this._initialized = true;
   }