@datagrok/helm 2.13.7 → 3.0.0

package/helm/dojo/package.ts

@@ -1,41 +0,0 @@
-import type {DojoWindowType} from './types';
-
-declare const window: Window & DojoWindowType;
-
-export async function initDojo(): Promise<void> {
-  window.dojo$ = window.dojo$ || {};
-  if (!window.dojo$.initPromise) {
-    window.dojo$.initPromise = (async () => {
-      const logPrefix: string = `dojo: _package.initDojo()`;
-      console.debug(`${logPrefix}, start`);
-
-      console.debug(`${logPrefix}, loadModules(), before`);
-      const t1 = window.performance.now();
-      await loadModules();
-      const t2 = window.performance.now();
-      console.debug(`${logPrefix}, loadModules(), after, ET: ${t2 - t1} ms`);
-
-      console.debug(`${logPrefix}, end`);
-    })();
-  }
-  return window.dojo$.initPromise;
-}
-
-const dojoPath = '../../vendor/dojo-1.10.10';
-
-async function loadModules(): Promise<void> {
-  const logPrefix: string = `dojo: _package.loadModules()`;
-
-  const unc = '';
-  window.dojo$.ctx = require.context('../../vendor/dojo-1.10.10', true, /\.js$/);
-  // const unc = '.uncompressed.js'; // '';
-  // window.dojo$.ctx = require.context('../../vendor/dojo-1.10.10', true, /\.js\.uncompressed\.js$/);
-
-  window.dojo$.uncompressed = unc;
-  await window.dojo$.ctx(`./dojo/dojo.js${unc}`);
-}
-
-
-(async () => {
-  await initDojo();
-})();

package/helm/dojo/types.ts

@@ -1,12 +0,0 @@
-import type {DojoType, DojoxType} from '@datagrok-libraries/js-draw-lite/src/types/dojo';
-
-export type DojoWindowType = {
-  dojo$: {
-    /** dojo source file postfix: '' for compressed, '.uncompressed.js' for uncompressed */
-    uncompressed: string;
-    ctx: { <T>(id: string): T };
-    initPromise: Promise<void>;
-  },
-  dojo: DojoType;
-  dojox: DojoxType;
-}

package/src/helm-web-editor.ts

@@ -1,68 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {Unsubscribable} from 'rxjs';
-
-import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
-import {
-  App, Editor, HelmType, IHelmWebEditor, HelmEditor, IHelmEditorOptions
-} from '@datagrok-libraries/bio/src/helm/types';
-
-import {JSDraw2Module, OrgHelmModule, ScilModule} from './types';
-
-import {_package} from './package';
-
-declare const scil: ScilModule;
-declare const JSDraw2: JSDraw2Module;
-declare const org: OrgHelmModule;
-
-export class HelmWebEditor implements IHelmWebEditor {
-  editor: HelmEditor;
-  host: HTMLDivElement;
-
-  w = 200;
-  h = 100;
-  private subs: Unsubscribable[];
-
-  constructor(
-    host?: HTMLDivElement,
-    options?: Partial<IHelmEditorOptions>,
-    private logger: ILogger = _package.logger
-  ) {
-    this.host = host ?? ui.div([], {style: {width: `${this.w}px`, height: `${this.h}px`}});
-
-    const styleBackup = {
-      width: this.host.style.width, height: this.host.style.height,
-      overflow: this.host.style.overflow
-    };
-    this.editor = new JSDraw2.Editor(this.host,
-      Object.assign({width: this.w, height: this.h, viewonly: true}, options));
-    this.host.style.width = styleBackup.width;
-    this.host.style.height = styleBackup.height;
-    this.host.style.overflow = styleBackup.overflow;
-
-    this.subs = [];
-    this.subs.push(ui.onSizeChanged(this.host).subscribe(this.hostOnSizeChanged.bind(this)));
-  }
-
-  protected toLog(): string {
-    return `Helm: HelmWebEditor<#>`;
-  }
-
-  private lastSize: { width: number, height: number } = {width: -1, height: -1};
-
-  private hostOnSizeChanged(value: any): void {
-    const size = {width: value.target.clientWidth, height: value.target.clientHeight};
-    if (this.lastSize.width != size.width || this.lastSize.height != size.height) {
-      const logPrefix = `${this.toLog()}.hostOnSizeChanged()`;
-      this.logger.debug(`${logPrefix}`);
-      this.editor.setSize(this.host.clientWidth, this.host.clientHeight);
-    }
-    this.lastSize = size;
-  }
-
-  resizeEditor(w: number, h: number) {
-    this.editor.setSize(w, h);
-  }
-}

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

@@ -1,214 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import wu from 'wu';
-
-import {
-  after, before, category, delay, expect, test, expectArray, testEvent, expectFloat, timeout
-} from '@datagrok-libraries/test/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, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';
-import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
-import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {
-  getUserLibSettings, setUserLibSettings,
-} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
-import {expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
-
-import {rewriteLibraries} from '../utils/get-monomer';
-import {JSDraw2Module, OrgHelmModule} from '../types';
-
-import {initHelmMainPackage} from './utils';
-
-import {_package} from '../package-test';
-import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
-
-declare const org: OrgHelmModule;
-declare const JSDraw2: JSDraw2Module;
-
-type TestDataType = { args: { a: any, name?: string }, tgt: any };
-
-const getResultDf = false;
-
-const tests: { [testName: string]: TestDataType } =
-  /* eslint-disable */
-  //@formatter:off
-  {
-    t0:{"args":{"a":"HELM_BASE","name":"A"},"tgt":{"id":"A","m":"\n     RDKit          2D\n\n 11 12  0  0  0  0  0  0  0  0999 V2000\n   -3.1265    0.5194    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8274   -0.2306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8274   -1.7306    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5284   -2.4806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7707   -1.7306    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7707   -0.2306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5284    0.5194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.2165    1.9866    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2753    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8854    0.7731    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    3.3526    0.4612    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  2  0\n  3  4  1  0\n  4  5  2  0\n  5  6  1  0\n  6  7  2  0\n  7  8  1  0\n  8  9  2  0\n  9 10  1  0\n 10 11  1  0\n  7  2  1  0\n 10  6  1  0\nM  RGP  1  11   1\nM  END\n","n":"Adenine","na":"A","rs":1,"at":{"R1":"H"}}},
-t1:{"args":{"a":"HELM_BASE","name":"C"},"tgt":{"id":"C","m":"\n     RDKit          2D\n\n  9  9  0  0  0  0  0  0  0  0999 V2000\n    2.8868    1.3333    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.5877    0.5833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.5877   -0.9167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.2887   -1.6667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0104   -0.9167    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3094   -1.6667    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0104    0.5833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3094    1.3333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.2887    1.3333    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  2  0\n  4  5  1  0\n  5  6  1  0\n  5  7  1  0\n  7  8  2  0\n  7  9  1  0\n  9  2  2  0\nM  RGP  1   6   1\nM  END\n","n":"Cytosine","na":"C","rs":1,"at":{"R1":"H"}}},
-t2:{"args":{"a":"HELM_BASE","name":"G"},"tgt":{"id":"G","m":"\n     RDKit          2D\n\n 12 13  0  0  0  0  0  0  0  0999 V2000\n    3.4022   -1.4050    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1032   -0.6550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8041   -1.4050    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4949   -0.6550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4949    0.8450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9215    1.3085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.8032    0.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9215   -1.1185    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3850   -2.5451    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.8041    1.5950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8041    3.0950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1032    0.8450    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  2  0\n  3  4  1  0\n  4  5  2  0\n  5  6  1  0\n  6  7  2  0\n  7  8  1  0\n  8  9  1  0\n  5 10  1  0\n 10 11  2  0\n 10 12  1  0\n 12  2  1  0\n  8  4  1  0\nM  RGP  1   9   1\nM  END\n","n":"Guanine","na":"G","rs":1,"at":{"R1":"H"}}},
-t3:{"args":{"a":"HELM_LINKER","name":"p"},"tgt":{"id":"p","m":"\n     RDKit          2D\n\n  5  4  0  0  0  0  0  0  0  0999 V2000\n   -1.2990    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2990   -0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7500   -1.2990    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.7500    1.2990    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0\n  2  3  1  0\n  2  4  1  0\n  2  5  1  0\nM  RGP  2   4   1   5   2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
-t4:{"args":{"a":"HELM_SUGAR","name":"p"},"tgt":null},
-t5:{"args":{"a":"HELM_SUGAR","name":"r"},"tgt":{"id":"r","m":"\n     RDKit          2D\n\n 12 12  0  0  0  0  0  0  0  0999 V2000\n    3.0807    1.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672    0.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406    0.9640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0229    2.3906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4901    2.7025    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6910   -1.5485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.1910   -1.5485    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406   -1.4630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672   -0.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0807   -1.8812    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  1  1  6\n  2  3  1  0\n  3  4  1  1\n  4  5  1  0\n  3  6  1  0\n  6  7  1  6\n  7  8  1  0\n  8  9  1  0\n  6 10  1  0\n 10 11  1  0\n 11 12  1  6\n 11  2  1  0\nM  RGP  3   5   2   9   1  12   3\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
-t6:{"args":{"a":{"T":"ATOM","p":{"x":144,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_SUGAR","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"r","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"_parent":"[object Object]","_aaid":4}},"tgt":{"id":"r","m":"\n     RDKit          2D\n\n 12 12  0  0  0  0  0  0  0  0999 V2000\n    3.0807    1.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672    0.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406    0.9640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0229    2.3906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4901    2.7025    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6910   -1.5485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.1910   -1.5485    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406   -1.4630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672   -0.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0807   -1.8812    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  1  1  6\n  2  3  1  0\n  3  4  1  1\n  4  5  1  0\n  3  6  1  0\n  6  7  1  6\n  7  8  1  0\n  8  9  1  0\n  6 10  1  0\n 10 11  1  0\n 11 12  1  6\n 11  2  1  0\nM  RGP  3   5   2   9   1  12   3\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
-t7:{"args":{"a":{"T":"ATOM","p":{"x":144,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_SUGAR","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"r","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":4}},"tgt":{"id":"r","m":"\n     RDKit          2D\n\n 12 12  0  0  0  0  0  0  0  0999 V2000\n    3.0807    1.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672    0.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406    0.9640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0229    2.3906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4901    2.7025    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6910   -1.5485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.1910   -1.5485    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406   -1.4630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672   -0.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0807   -1.8812    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  1  1  6\n  2  3  1  0\n  3  4  1  1\n  4  5  1  0\n  3  6  1  0\n  6  7  1  6\n  7  8  1  0\n  8  9  1  0\n  6 10  1  0\n 10 11  1  0\n 11 12  1  6\n 11  2  1  0\nM  RGP  3   5   2   9   1  12   3\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
-t8:{"args":{"a":{"T":"ATOM","p":{"x":144,"y":48},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_BASE","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"G","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":5}},"tgt":{"id":"G","m":"\n     RDKit          2D\n\n 12 13  0  0  0  0  0  0  0  0999 V2000\n    3.4022   -1.4050    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1032   -0.6550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8041   -1.4050    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4949   -0.6550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4949    0.8450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9215    1.3085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.8032    0.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9215   -1.1185    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.3850   -2.5451    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.8041    1.5950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8041    3.0950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1032    0.8450    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  2  0\n  3  4  1  0\n  4  5  2  0\n  5  6  1  0\n  6  7  2  0\n  7  8  1  0\n  8  9  1  0\n  5 10  1  0\n 10 11  2  0\n 10 12  1  0\n 12  2  1  0\n  8  4  1  0\nM  RGP  1   9   1\nM  END\n","n":"Guanine","na":"G","rs":1,"at":{"R1":"H"}}},
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-t25:{"args":{"a":{"T":"ATOM","p":{"x":48,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_SUGAR","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"r","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":1}},"tgt":{"id":"r","m":"\n     RDKit          2D\n\n 12 12  0  0  0  0  0  0  0  0999 V2000\n    3.0807    1.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672    0.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406    0.9640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0229    2.3906    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4901    2.7025    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.4410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.9410   -0.2495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.6910   -1.5485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -4.1910   -1.5485    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.4406   -1.4630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8672   -0.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0807   -1.8812    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  1  1  6\n  2  3  1  0\n  3  4  1  1\n  4  5  1  0\n  3  6  1  0\n  6  7  1  6\n  7  8  1  0\n  8  9  1  0\n  6 10  1  0\n 10 11  1  0\n 11 12  1  6\n 11  2  1  0\nM  RGP  3   5   2   9   1  12   3\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
-t26:{"args":{"a":{"T":"ATOM","p":{"x":48,"y":48},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_BASE","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"A","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":2}},"tgt":{"id":"A","m":"\n     RDKit          2D\n\n 11 12  0  0  0  0  0  0  0  0999 V2000\n   -3.1265    0.5194    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8274   -0.2306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.8274   -1.7306    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5284   -2.4806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7707   -1.7306    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7707   -0.2306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.5284    0.5194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.2165    1.9866    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2753    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8854    0.7731    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    3.3526    0.4612    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  2  0\n  3  4  1  0\n  4  5  2  0\n  5  6  1  0\n  6  7  2  0\n  7  8  1  0\n  8  9  2  0\n  9 10  1  0\n 10 11  1  0\n  7  2  1  0\n 10  6  1  0\nM  RGP  1  11   1\nM  END\n","n":"Adenine","na":"A","rs":1,"at":{"R1":"H"}}},
-t27:{"args":{"a":{"T":"ATOM","p":{"x":96,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_LINKER","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"p","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"_parent":"[object Object]","_aaid":3}},"tgt":{"id":"p","m":"\n     RDKit          2D\n\n  5  4  0  0  0  0  0  0  0  0999 V2000\n   -1.2990    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2990   -0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7500   -1.2990    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.7500    1.2990    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0\n  2  3  1  0\n  2  4  1  0\n  2  5  1  0\nM  RGP  2   4   1   5   2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
-t28:{"args":{"a":{"T":"ATOM","p":{"x":96,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_LINKER","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"p","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":3}},"tgt":{"id":"p","m":"\n     RDKit          2D\n\n  5  4  0  0  0  0  0  0  0  0999 V2000\n   -1.2990    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2990   -0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7500   -1.2990    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.7500    1.2990    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0\n  2  3  1  0\n  2  4  1  0\n  2  5  1  0\nM  RGP  2   4   1   5   2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}}
-    //@formatter:off
-  /* eslint-enable */
-  };
-
-category('getMonomer', ()=> {
-  let helmHelper: IHelmHelper;
-  let monomerLibHelper: IMonomerLibHelper;
-  /** Backup actual user's monomer libraries settings */
-  let userLibSettings: UserLibSettings;
-
-  before(async ()=>{
-    await initHelmMainPackage();
-
-    [monomerLibHelper, helmHelper, userLibSettings] = await Promise.all(
-      [getMonomerLibHelper(), getHelmHelper(), getUserLibSettings()]);
-
-    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries for tests
-  });
-
-  after(async ()=>{
-    await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadMonomerLib(true);
-  });
-
-  test('original', async () =>{
-    const monomerLib = monomerLibHelper.getMonomerLib();
-    rewriteLibraries(monomerLib);
-
-    const helmHelper: IHelmHelper = await getHelmHelper();
-    expect(helmHelper != null, true);
-    const getMonomerFunc: GetMonomerFunc = helmHelper.originalMonomersFuncs!.getMonomer!;
-    const res = _testAll('original', getMonomerFunc);
-    return getResultDf ? (res ?? DG.DataFrame.create(0)) : null;
-  }, {isAggregated: getResultDf});
-
-  test('monomerLib', async () =>{
-    const getMonomerFunc = org.helm.webeditor.Monomers.getMonomer;
-    const res = _testAll('monomerLib', getMonomerFunc);
-    return getResultDf ? (res ?? DG.DataFrame.create(0)) : null;
-  }, {isAggregated: getResultDf});
-
-  function _testAll(prefix: string, getMonomerFunc: GetMonomerFunc): DG.DataFrame {
-    const resDf = DG.DataFrame.fromColumns([
-      DG.Column.fromStrings('subTest', []),
-      DG.Column.fromList(DG.COLUMN_TYPE.BOOL, 'success', []),
-      DG.Column.fromStrings('res', []),
-      DG.Column.fromStrings('tgt', []),
-      DG.Column.fromStrings('error', []),
-      DG.Column.fromStrings('stack', []),
-    ]);
-
-    // const testCount: number = Object.keys(tests).length + 1;
-    // //* eslint-disable no-array-constructor */
-    // const subTestList: string[] = new Array<string>(testCount);
-    // const successList: boolean[] = new Array<boolean>(testCount);
-    // const resList: string[] = new Array<string>(testCount);
-    // const tgtList:string[] = new Array<string>(testCount);
-    // const errorList: string[] = new Array<string>(testCount);
-    // const stackList: string[] = new Array<string>(testCount);
-    // /* eslint-enable no-array-constructor */
-
-    const resI = resDf.rows.addNew().idx;
-    resDf.set('subTest', resI, 'Monomer lib');
-    resDf.set('res', resI, '');
-    resDf.set('tgt', resI, '');
-    try {
-      resDf.set('success', resI, true);
-    } catch (err) {
-      const [errMsg, errStack] = errInfo(err);
-      resDf.set('error', resI, errMsg);
-      resDf.set('stack', resI, errStack);
-      resDf.set('success', resI, false);
-      throw err;
-    }
-
-    for (const [[testName, testData], testI] of wu.enumerate(Object.entries(tests))) {
-      const a: HelmAtom | HelmType = getAtomFromJson(testData.args.a);
-      const [biotype, elem] = getMonomerHandleArgs(a, testData.args.name);
-      const tgt = testData.tgt;
-
-      const resI = resDf.rows.addNew().idx;
-      resDf.set('subTest', resI, `${prefix}-${testName}-${biotype}-${elem}`);
-      resDf.set('tgt', resI, JSON.stringify(tgt ? {id: tgt.id, n: tgt.n, rs: tgt.rs} : null));
-      try {
-        const res: any = getMonomerFunc(a, testData.args.name);
-        resDf.set('res', resI, JSON.stringify(res ? {id: res.id, n: res.n, rs: res.rs} : null));
-        expectObjectWithNull(res, tgt);
-        resDf.set('success', resI, true);
-      } catch (err) {
-        const [errMsg, errStack] = errInfo(err);
-        resDf.set('error', resI, errMsg);
-        resDf.set('stack', resI, errStack);
-        resDf.set('success', resI, false);
-        throw err;
-      }
-    }
-    return resDf;
-  }
-
-  test('missing', async ()=> {
-    const monomerLib = monomerLibHelper.getMonomerLib();
-    /* Tests getMonomer function adding missing monomers. */
-    const helmStr = 'PEPTIDE1{[mis1].R.[mis2].T.C.F}$$$$;';
-
-    const libSummary = monomerLib.getSummaryObj();
-    const editor = new JSDraw2.Editor(ui.div(), {viewonly: true});
-    editor.setHelm(helmStr);
-    libSummary[PolymerTypes.PEPTIDE] += 2;
-    expectMonomerLib(monomerLib, libSummary);
-  });
-});
-
-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);
-  else
-    res = argA as HelmType;
-  return res;
-}
-
-export function expectObjectWithNull(actual: { [key: string]: any }, expected: { [key: string]: any }) {
-  if (actual == null && expected == null)
-    return;
-  else if (actual == null && expected != null)
-    throw new Error('actual is null, but expected is not null');
-  else if (actual!= null && expected == null)
-    throw new Error('actual is not null, but expected is null');
-  else {
-    for (const [expectedKey, expectedValue] of Object.entries(expected)) {
-      if (!(expectedKey in actual || actual.hasOwnProperty(expectedKey)))
-        throw new Error(`Expected property "${expectedKey}" not found`);
-
-      const actualValue = actual[expectedKey];
-      if (actualValue instanceof Array && expectedValue instanceof Array)
-        expectArray(actualValue, expectedValue);
-      else if (actualValue instanceof Object && expectedValue instanceof Object)
-        expectObjectWithNull(actualValue, expectedValue);
-      else if (Number.isFinite(actualValue) && Number.isFinite(expectedValue))
-        expectFloat(actualValue, expectedValue);
-      else if (actualValue != expectedValue)
-        throw new Error(`Expected (${expectedValue}) for key '${expectedKey}', got (${actualValue})`);
-    }
-  }
-}

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

@@ -1,98 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {Subject} from 'rxjs';
-
-import {
-  category, expect, test, awaitCheck, delay, testEvent, before, after
-} from '@datagrok-libraries/test/src/test';
-import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {
-  getHelmService, HelmServiceBase, HelmAux, HelmProps
-} from '@datagrok-libraries/bio/src/viewers/helm-service';
-import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
-
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
-import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {
-  getUserLibSettings, setUserLibSettings,
-} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
-
-import {initHelmMainPackage} from './utils';
-
-import {_package} from '../package-test';
-
-category('HelmService', () => {
-  let monomerLibHelper: IMonomerLibHelper;
-  /** Backup actual user's monomer libraries settings */
-  let userLibSettings: UserLibSettings;
-
-  let helmSvc: HelmServiceBase;
-
-  before(async () => {
-    const logPrefix = `Helm: tests: HelmService: before`;
-    _package.logger.debug(`${logPrefix}, start`);
-    await initHelmMainPackage();
-    try {
-      monomerLibHelper = await getMonomerLibHelper();
-      userLibSettings = await getUserLibSettings();
-
-      await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
-
-      helmSvc = await getHelmService();
-      await helmSvc.reset();
-
-      _package.logger.debug(`${logPrefix}, end`);
-    } finally {
-      _package.logger.debug(`${logPrefix}, fina`);
-    }
-  });
-
-  after(async () => {
-    const logPrefix = `Helm: tests: HelmService: after`;
-    _package.logger.debug(`${logPrefix}, start`);
-
-    await helmSvc.reset();
-
-    await setUserLibSettings(userLibSettings);
-    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
-    _package.logger.debug(`${logPrefix}, end`);
-  });
-
-  test('helm', async () => {
-    const logPrefix: string = `Helm: tests: HelmService: helm`;
-    _package.logger.debug(`${logPrefix}, start`);
-    const helmStr: string = 'PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$';
-    const monomerLib = monomerLibHelper.getMonomerLib();
-    let consumerId: number | null = null;
-    let taskAux: HelmAux | null = null;
-    const event = new Subject<void>();
-    await testEvent(event,
-      () => {
-      },
-      () => {
-        const task: RenderTask<HelmProps, HelmAux> = {
-          name: 'test1',
-          props: {
-            helm: helmStr, monomerLib: monomerLib,
-            backColor: DG.Color.fromHtml('#FFFFFF'),
-            width: 300, height: 100,
-          },
-          onAfterRender: (canvas: HTMLCanvasElement, aux: HelmAux) => {
-            taskAux = aux;
-            event.next();
-          }
-        };
-        helmSvc.reset();
-        consumerId = helmSvc.render(consumerId, task, 0);
-      }, 7000);
-    expect(taskAux !== null, true, 'Helm task aux is null');
-    expect(taskAux!.mol.atoms.length > 0, true, 'Polymer mol atoms empty');
-    expect(taskAux!.mol.atoms.length, 8);
-    expect(taskAux!.mol.bonds.length, 7);
-    expect(helmSvc.errorCount, 0, 'There was errors in NglGlService.');
-    expect(consumerId !== null, true, 'consumerId not assigned');
-    _package.logger.debug(`${logPrefix}, end`);
-  }, {timeout: 10000});
-});

package/src/types/dojo.ts

@@ -1,3 +0,0 @@
-declare module 'dojo' {
-  export function ready(callback: () => void): void;
-}

package/src/types/index.ts

@@ -1,5 +0,0 @@
-import {HelmType, JSDraw2ModuleType, OrgType, ScilModuleType} from '@datagrok-libraries/bio/src/helm/types';
-
-export type ScilModule = ScilModuleType;
-export type JSDraw2Module = JSDraw2ModuleType;
-export type OrgHelmModule = OrgType;

package/src/utils/get-monomer.ts

@@ -1,90 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-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/monomer-library';
-import {Atom, HelmType, IWebEditorMonomer, GetMonomerResType, HelmAtom} from '@datagrok-libraries/bio/src/helm/types';
-
-import {OrgHelmModule, ScilModule} from '../types';
-import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
-
-import {_package} from '../package';
-
-declare const org: OrgHelmModule;
-declare const scil: ScilModule;
-
-type GetMonomerOverridingFunc = (
-  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,
-): void {
-  const logPrefix = 'Helm: overrideGetMonomerAndAlert()';
-  const monomers = org.helm.webeditor.Monomers;
-  const getMonomerOriginal = monomers.getMonomer.bind(monomers);
-  const alertOriginal = scil.Utils.alert;
-  try {
-    org.helm.webeditor.Monomers.getMonomer =
-      (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
-    scil.Utils.alert = (s: string): void => {
-      logger.warning(`${logPrefix}, scil.Utils.alert() s = 's'.`);
-    };
-    trigger();
-  } finally {
-    monomers.getMonomer = getMonomerOriginal;
-    scil.Utils.alert = alertOriginal;
-  }
-}
-
-/** Fills org.helm.webeditor.Monomers dictionary for WebEditor */
-export function rewriteLibraries(monomerLib: IMonomerLib): void {
-  org.helm.webeditor.Monomers.clear();
-  monomerLib!.getPolymerTypes().forEach((polymerType) => {
-    const monomerSymbols = monomerLib!.getMonomerSymbolsByType(polymerType);
-    monomerSymbols.forEach((monomerSymbol) => {
-      let isBroken = false;
-      const monomer: Monomer = monomerLib!.getMonomer(polymerType, monomerSymbol)!;
-      const webEditorMonomer: IWebEditorMonomer = {
-        id: monomerSymbol,
-        m: monomer.molfile,
-        n: monomer.name,
-        na: monomer.naturalAnalog,
-        rs: monomer.rgroups.length,
-        type: monomer.polymerType,
-        mt: monomer.monomerType,
-        at: {},
-      };
-
-      if (monomer.rgroups.length > 0) {
-        // @ts-ignore
-        webEditorMonomer.rs = monomer.rgroups.length;
-        const at: { [prop: string]: any } = {};
-        monomer.rgroups.forEach((it) => {
-          at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
-        });
-        webEditorMonomer.at = at;
-      } else if (monomer[SMILES] != null) {
-        const rs = monomerLib.getRS(monomer[SMILES].toString());
-        if (rs == null || Object.keys(rs).length === 0)
-          isBroken = true;
-        else {
-          webEditorMonomer.rs = Object.keys(rs).length;
-          webEditorMonomer.at = rs;
-        }
-      } else
-        isBroken = true;
-
-      if (!isBroken)
-        org.helm.webeditor.Monomers.addOneMonomer(webEditorMonomer);
-    });
-  });
-
-  // Obsolete
-  const grid: DG.Grid = grok.shell.tv?.grid;
-  if (grid) grid.invalidate();
-}