@datagrok/helm 2.5.7 → 2.5.9

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.5.7",
+  "version": "2.5.9",
   "author": {
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
@@ -16,9 +16,9 @@
     "css/helm.css"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.45.5",
+    "@datagrok-libraries/bio": "^5.45.7",
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/utils": "^4.3.6",
+    "@datagrok-libraries/utils": "^4.3.7",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.21.1",
     "dayjs": "^1.10.6",
@@ -27,9 +27,9 @@
     "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.12",
-    "@datagrok-libraries/js-draw-lite": "^0.0.9",
-    "@datagrok/bio": "^2.16.6",
+    "@datagrok-libraries/helm-web-editor": "^1.1.13",
+    "@datagrok-libraries/js-draw-lite": "^0.0.10",
+    "@datagrok/bio": "^2.16.8",
     "@datagrok/chem": "^1.12.3",
     "@types/node": "17.0.45",
     "@types/webpack-env": "^1.18.5",

package/src/helm-helper.ts

@@ -6,9 +6,9 @@ import $ from 'cash-dom';
 
 /* eslint-disable max-len */
 import {
-  App, Point, HelmAtom, HelmBond, HelmMol, HelmType, GetMonomerFunc, GetMonomerResType,
+  App, Point, HelmType, IHelmBio, HelmAtom, HelmBond, HelmMol, GetMonomerFunc, GetMonomerResType,
   MonomerExplorer, TabDescType, MonomersFuncs, MonomerSetType, ISeqMonomer, PolymerType, MonomerType,
-  DojoType, JSDraw2ModuleType, IHelmEditorOptions, IHelmDrawOptions
+  DojoType, JSDraw2ModuleType, IHelmEditorOptions, IHelmDrawOptions,
 } from '@datagrok-libraries/bio/src/helm/types';
 import {HelmTabKeys, HelmTypes, MonomerTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
@@ -344,7 +344,7 @@ export class HelmHelper implements IHelmHelper {
   }
 
   public parse(helm: string, origin?: Point): HelmMol {
-    const molHandler = new JSDraw2.MolHandler<HelmType, IHelmEditorOptions>();
+    const molHandler = new JSDraw2.MolHandler<HelmType, IHelmBio, IHelmEditorOptions>();
     const plugin = new org.helm.webeditor.Plugin(molHandler);
     org.helm.webeditor.IO.parseHelm(plugin, helm, origin ?? new JSDraw2.Point(0, 0));
     return plugin.jsd.m;
@@ -401,7 +401,7 @@ export class HelmHelper implements IHelmHelper {
 
     for (let aI: number = 0; aI < mol.atoms.length; ++aI) {
       const a: HelmAtom = mol.atoms[aI];
-      monomerMap.set(parseInt(a.bio!.continuousId as string) - 1, aI);
+      monomerMap.set(a.bio!.continuousId - 1, aI);
     }
 
     const resHelm = org.helm.webeditor.IO.getHelm(mol)!;

package/src/package-utils.ts

@@ -207,7 +207,7 @@ export const helmJsonReplacer = (key: string, value: any): any => {
 export class HelmPackage extends DG.Package {
   public alertOriginal: ((s: string) => void) | null = null;
 
-  private _helmHelper: IHelmHelper;
+  private _helmHelper?: IHelmHelper;
   public get helmHelper(): IHelmHelper {
     if (!this._helmHelper)
       throw new Error('Package Helm .helmHelper is not initialized');
@@ -215,7 +215,7 @@ export class HelmPackage extends DG.Package {
   };
 
   public get seqHelper(): ISeqHelper {
-    return this._helmHelper.seqHelper;
+    return this.helmHelper!.seqHelper;
   }
 
   public _libHelper!: IMonomerLibHelper;

package/src/package.ts

@@ -18,6 +18,7 @@ import {getPropertiesWidget} from './widgets/properties-widget';
 import {HelmGridCellRenderer, HelmGridCellRendererBack} from './utils/helm-grid-cell-renderer';
 import {_getHelmService, HelmPackage} from './package-utils';
 import {HelmHelper} from './helm-helper';
+import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 
 // Do not import anything than types from @datagrok/helm-web-editor/src/types
 import type {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
@@ -51,11 +52,11 @@ async function initHelmInt(): Promise<void> {
   _package.logger.debug(`${logPrefix}, start`);
 
   try {
-    const [_, seqHelper, libHelper] = await Promise.all([
-      _package.initHELMWebEditor(),
-      getSeqHelper(),
-      getMonomerLibHelper(),
-    ]);
+    // order of things is very important
+    await getRdKitModule();
+    const seqHelper = await getSeqHelper();
+    const libHelper = await getMonomerLibHelper();
+    await _package.initHELMWebEditor();
     const helmHelper: IHelmHelper = new HelmHelper(seqHelper, _package.logger);
     _package.completeInit(helmHelper, libHelper);
   } catch (err: any) {

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

@@ -9,7 +9,7 @@ import {
 } from '@datagrok-libraries/utils/src/test';
 import {getHelmHelper, getMonomerHandleArgs} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {Atom, HelmType, IJsAtom, GetMonomerFunc} from '@datagrok-libraries/bio/src/helm/types';
+import {Atom, HelmType, IJsAtom, GetMonomerFunc, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';
 import {MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
@@ -138,7 +138,7 @@ category('getMonomer', ()=>{
     }
 
     for (const [[testName, testData], testI] of wu.enumerate(Object.entries(tests))) {
-      const a: Atom<HelmType> | HelmType = getAtomFromJson(testData.args.a);
+      const a: HelmAtom | HelmType = getAtomFromJson(testData.args.a);
       const [biotype, elem] = getMonomerHandleArgs(a, testData.args.name);
       const tgt = testData.tgt;
 
@@ -173,8 +173,8 @@ category('getMonomer', ()=>{
   });
 });
 
-function getAtomFromJson(argA: IJsAtom<HelmType> | HelmType): Atom<HelmType> | HelmType {
-  let res: Atom<HelmType> | HelmType;
+function getAtomFromJson(argA: IJsAtom<HelmType> | HelmType): HelmAtom | HelmType {
+  let res: HelmAtom | HelmType;
   const a = argA as IJsAtom<HelmType>;
   if (a.T === 'ATOM')
     res = new JSDraw2.Atom(a.p, a.elem, a.bio);

package/src/tests/parse-helm-tests.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 
 import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/utils/src/test';
-import {HelmType, IHelmEditorOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmMol, HelmType, IHelmBio, IHelmEditorOptions, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
@@ -104,13 +104,13 @@ function _testParseHelmWithEditor(src: string, tgt: TestTgtType): void {
   const io = org.helm.webeditor.IO;
 
   const editorHost = ui.div();
-  const editor = new JSDraw2.Editor<HelmType, IHelmEditorOptions>(editorHost, {viewonly: true});
+  const editor = new JSDraw2.Editor<HelmType, IHelmBio, IHelmEditorOptions>(editorHost, {viewonly: true});
 
   const plugin = new org.helm.webeditor.Plugin(editor);
   const origin = new JSDraw2.Point(0, 0);
   io.parseHelm(plugin, src, origin, undefined);
 
-  const m: Mol<HelmType> = plugin.jsd.m;
+  const m: HelmMol = plugin.jsd.m;
   expect(m.atoms.length, tgt.atomCount);
   expect(m.bonds.length, tgt.bondCount);
 }
@@ -132,13 +132,13 @@ function _testParseHelmWithHelmHelper(src: string, tgt: TestTgtType, helmHelper:
 function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
   const io = org.helm.webeditor.IO;
 
-  const molHandler = new JSDraw2.MolHandler<HelmType, IHelmEditorOptions>();
+  const molHandler = new JSDraw2.MolHandler<HelmType, IHelmBio, IHelmEditorOptions>();
 
   const plugin = new org.helm.webeditor.Plugin(molHandler);
   const origin = new JSDraw2.Point(0, 0);
   io.parseHelm(plugin, src, origin, undefined);
 
-  const m: Mol<HelmType> = plugin.jsd.m;
+  const m: HelmMol = plugin.jsd.m;
   const resHelm = io.getHelm(m);
   expect(m.atoms.length, tgt.atomCount);
   expect(m.bonds.length, tgt.bondCount);

package/src/utils/get-hovered.ts

@@ -8,6 +8,7 @@ import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/m
 
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {GAP_SYMBOL, GapOriginals, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {SeqValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 export function getHoveredMonomerFromEditorMol(
   argsX: number, argsY: number, mol: HelmMol, cellHeight?: number
@@ -47,9 +48,11 @@ export function getHoveredMonomerFromEditorMol(
   return resAtom;
 }
 
-export function getSeqMonomerFromHelmAtom(atom: HelmAtom): ISeqMonomer {
-  const canonicalSymbol = atom.elem === GapOriginals[NOTATION.HELM] ? GAP_SYMBOL : atom.elem;
-  return {position: parseInt(atom.bio!.continuousId as string) - 1, symbol: canonicalSymbol, biotype: atom.bio!.type};
+export function getSeqMonomerFromHelmAtom(seqValue: SeqValueBase, atom: HelmAtom): ISeqMonomer {
+  const pos: number = atom.bio!.continuousId - 1;
+  const canonicalSymbol = seqValue.getSplitted().getCanonical(pos);
+  // const canonicalSymbol = atom.elem === GapOriginals[NOTATION.HELM] ? GAP_SYMBOL : atom.elem;
+  return {position: atom.bio!.continuousId - 1, symbol: canonicalSymbol, biotype: atom.bio!.type};
 }
 
 /** Linear

package/src/utils/get-monomer.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
-import {Atom, HelmType, IWebEditorMonomer, GetMonomerResType} from '@datagrok-libraries/bio/src/helm/types';
+import {Atom, HelmType, IWebEditorMonomer, GetMonomerResType, IHelmBio, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';
 
 import {OrgHelmModule, ScilModule} from '../types';
 import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
@@ -15,8 +15,8 @@ declare const org: OrgHelmModule;
 declare const scil: ScilModule;
 
 type GetMonomerOverridingFunc = (
-  a: Atom<HelmType> | HelmType, name: string | undefined, monomerLib: IMonomerLib,
-  originalGetMonomer: (a: Atom<HelmType> | HelmType, name: string) => GetMonomerResType) => GetMonomerResType;
+  a: HelmAtom | HelmType, name: string | undefined, monomerLib: IMonomerLib,
+  originalGetMonomer: (a: HelmAtom | HelmType, name: string) => GetMonomerResType) => GetMonomerResType;
 
 export function getMonomerOverrideAndLogAlert(
   monomerLib: IMonomerLib, getMonomerOverriding: GetMonomerOverridingFunc, trigger: () => void, logger: ILogger,
@@ -27,7 +27,7 @@ export function getMonomerOverrideAndLogAlert(
   const alertOriginal = scil.Utils.alert;
   try {
     org.helm.webeditor.Monomers.getMonomer =
-      (a: Atom<HelmType> | HelmType, name?: string): GetMonomerResType => {
+      (a: HelmAtom | HelmType, name?: string): GetMonomerResType => {
         return getMonomerOverriding(a, name, monomerLib, getMonomerOriginal);
       };
     // Preventing alert message box for missing monomers with compressed Scilligence.JSDraw2.Lite.js

package/src/utils/helm-grid-cell-renderer.ts

@@ -4,7 +4,7 @@ import * as ui from 'datagrok-api/ui';
 
 import wu from 'wu';
 
-import {HelmType, ISeqMonomer, Mol} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmType, IHelmBio, ISeqMonomer, Mol} from '@datagrok-libraries/bio/src/helm/types';
 import {
   CellRendererBackAsyncBase, RenderServiceBase
 } from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
@@ -16,6 +16,7 @@ import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/mon
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
 import {execMonomerHoverLinks} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
 import {MmcrTemps} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
+import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
 import {getHoveredMonomerFromEditorMol, getSeqMonomerFromHelmAtom} from './get-hovered';
 
@@ -25,6 +26,7 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
   private _auxList: (HelmAux | null)[];
 
   private sysMonomerLib: IMonomerLibBase | null = null;
+  private helmHelper: IHelmHelper | null = null;
   private helmRenderService: HelmServiceBase | null = null;
 
   // eslint-disable-next-line max-len
@@ -43,6 +45,9 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
         const libHelper = await getMonomerLibHelper();
         this.sysMonomerLib = libHelper.getMonomerLib();
       })(),
+      (async () => {
+        this.helmHelper = await getHelmHelper();
+      })(),
       (async () => {
         this.helmRenderService = await getHelmService();
       })(),
@@ -167,7 +172,7 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
     const bX = aux.bBox.x + (cX - aux.dBox.x) * aux.bBox.width / aux.dBox.width;
     const bY = aux.bBox.y + (cY - aux.dBox.y) * aux.bBox.height / aux.dBox.height;
 
-    const editorMol: Mol<HelmType> | null = aux.mol; // in bBox world
+    const editorMol: Mol<HelmType, IHelmBio> | null = aux.mol; // in bBox world
     if (!editorMol) {
       this.logger.warning(`${logPrefix}, editorMol of the cell not found.`);
       return; // The gridCell is not rendered yet
@@ -175,8 +180,10 @@ export class HelmGridCellRendererBack extends CellRendererBackAsyncBase<HelmProp
     const hoveredAtom = getHoveredMonomerFromEditorMol(bX, bY, editorMol, gridCell.bounds.height);
 
     let seqMonomer: ISeqMonomer | null = null;
-    if (hoveredAtom) {
-      seqMonomer = getSeqMonomerFromHelmAtom(hoveredAtom);
+    if (hoveredAtom && this.helmHelper && gridCell.tableRowIndex != null) {
+      const seqHandler = this.helmHelper.seqHelper.getSeqHandler(this.tableCol);
+      const seqValue = seqHandler.getValue(gridCell.tableRowIndex);
+      seqMonomer = getSeqMonomerFromHelmAtom(seqValue, hoveredAtom);
       const monomerLib = this.tableCol.temp[MmcrTemps.overriddenLibrary] ?? _package.monomerLib;
       const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
         ui.divText('Monomer library is not available');

package/src/utils/helm-service.ts

@@ -5,7 +5,7 @@ import $ from 'cash-dom';
 import {Subject, Unsubscribable} from 'rxjs';
 import {LRUCache} from 'lru-cache';
 
-import {HelmEditor, HelmType, IHelmEditorOptions} from '@datagrok-libraries/bio/src/helm/types';
+import {HelmEditor, HelmType, IHelmBio, IHelmEditorOptions} from '@datagrok-libraries/bio/src/helm/types';
 import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
 import {HelmAux, HelmProps, HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {svgToImage} from '@datagrok-libraries/utils/src/svg';
@@ -49,8 +49,8 @@ export class HelmService extends HelmServiceBase {
 
     let resEditor: HelmEditor | undefined = this.editorLruCache.get(editorKey);
     if (!resEditor) {
-      const getMonomerFuncs = _package.helmHelper.buildMonomersFuncsFromLib(props.monomerLib);
-      resEditor = new JSDraw2.Editor<HelmType, IHelmEditorOptions>(this.hostDiv, {
+      const getMonomerFuncs = _package.helmHelper.buildMonomersFuncsFromLib(props.monomerLib, );
+      resEditor = new JSDraw2.Editor<HelmType, IHelmBio, IHelmEditorOptions>(this.hostDiv, {
         width: props.width, height: props.height, skin: 'w8', viewonly: true,
         drawOptions: {getMonomer: getMonomerFuncs.getMonomer},
       });

package/src/widgets/helm-input.ts

@@ -8,11 +8,13 @@ import {fromEvent, Observable, Unsubscribable} from 'rxjs';
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
 import {HelmInputBase, IHelmHelper, IHelmInputInitOptions} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmAtom, HelmMol, HelmString, IHelmEditorOptions, IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
+import {SeqValueBase} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
+import {MonomerNumberingTypes} from '@datagrok-libraries/bio/src/helm/consts';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 import {defaultErrorHandler} from '../utils/err-info';
 import {getHoveredMonomerFromEditorMol, getSeqMonomerFromHelmAtom} from '../utils/get-hovered';
 
-import {MonomerNumberingTypes} from '@datagrok-libraries/bio/src/helm/consts';
 
 import {_package} from '../package';
 
@@ -31,20 +33,27 @@ export class HelmInput extends HelmInputBase {
     return this.viewerHost;
   }
 
-  getValue(): HelmString {
-    return this.viewer.editor.getHelm();
-  }
+  private _seqValue: SeqValueBase;
 
-  setValue(value: HelmString): void {
-    this.viewer.editor.setHelm(value);
-  }
+  getValue(): SeqValueBase { return this._seqValue; }
 
-  getStringValue(): string {
-    return this.viewer.editor.getHelm();
+  setValue(value: SeqValueBase): void {
+    this._seqValue = value;
+    this.viewer.editor.setHelm(this._seqValue.helm);
   }
 
+  getStringValue(): string { return this._seqValue?.helm ?? ''; }
+
   setStringValue(value: string): void {
-    this.viewer.editor.setHelm(value);
+    if (!this._seqValue) {
+      let seqCol: DG.Column;
+      DG.DataFrame.fromColumns([seqCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [value])]);
+      seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+      seqCol.meta.units = NOTATION.HELM;
+      const sh = this.helmHelper.seqHelper.getSeqHandler(seqCol);
+      this._seqValue = sh.getValue(0);
+    }
+    this.viewer.editor.setHelm(this._seqValue.value = value);
   }
 
   // -- IHelmInput --
@@ -55,6 +64,7 @@ export class HelmInput extends HelmInputBase {
 
   set molValue(value: HelmMol) {
     this.viewer.editor.setMol(value);
+    this._seqValue.value = this.viewer.editor.getHelm();
   }
 
   get onMouseMove(): Observable<MouseEvent> { return fromEvent<MouseEvent>(this.viewer.host, 'mousemove'); }
@@ -85,9 +95,7 @@ export class HelmInput extends HelmInputBase {
       classes: 'ui-input-editor',
       style: {width: '100%', height: '100%', overflow: 'hidden'},
     });
-    this.viewer = this.helmHelper.createHelmWebEditor(this.viewerHost, {
-      drawOptions: {monomerNumbering: MonomerNumberingTypes.continuous},
-    });
+    this.viewer = this.helmHelper.createHelmWebEditor(this.viewerHost, options?.editorOptions);
 
     this.editHintDiv = ui.divH([
       ui.link('Click to edit', () => { this.viewer.host.click(); }, undefined, {}),
@@ -140,16 +148,8 @@ export class HelmInput extends HelmInputBase {
   ): HelmInput {
     const input = new HelmInput(helmHelper, monomerLib, name, options);
     // TODO: Apply options
-    const value: HelmMol | string | undefined = options?.value;
-    if (value !== undefined) {
-      if (value instanceof String || typeof value === 'string')
-        input.stringValue = value as any as string;
-      else if (typeof value === 'object' /* && value.T === 'MOL'*/)
-        input.molValue = value;
-      else
-        throw new Error(`Unsupported value of type '${typeof value}'.`);
-    }
-
+    if (options?.value != null)
+      input.value = options.value;
     return input;
   }
 
@@ -181,7 +181,7 @@ export class HelmInput extends HelmInputBase {
     const mol = this.viewer.editor.m;
     const hoveredAtom = getHoveredMonomerFromEditorMol(argsX, argsY, mol, this.viewer.editor.div.clientHeight);
     if (hoveredAtom) {
-      const seqMonomer = getSeqMonomerFromHelmAtom(hoveredAtom);
+      const seqMonomer = getSeqMonomerFromHelmAtom(this.value, hoveredAtom);
       const monomerLib = _package.monomerLib;
       const tooltipEl = monomerLib ? monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
         ui.divText('Monomer library is not available');