@datagrok/bio 2.23.2 → 2.25.0

package/files/samples/HELM_CHEMS.csv

@@ -0,0 +1,11 @@
+HELM,Activity
+"PEPTIDE1{[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@@H](C(=O)*)C |$_R1;;;;;_R2;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@@H](C(=O)*)Cc1ccccc1 |$_R1;;;;;_R2;;;;;;;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@H](C(=O)*)C |$_R1;;;;;_R2;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@@H](C(=O)*)Cc1ccccc1 |$_R1;;;;;_R2;;;;;;;$|]}$PEPTIDE1,PEPTIDE1,8:R2-1:R1$$$",5.3075109739681280
+"PEPTIDE1{[ac].D.A.D.E.[*N[C@H](C(=O)*)Cc1ccc(cc1)OC(C(=O)O)C(=O)O |$_R1;;;;;_R2;;;;;;;;;;;;;;;$|].L.[am]}$$$$	CHEMBL8284
+PEPTIDE1{[N[C@](C)(C(=O)O)Cc1ccc(c(c1)O)O]}$$$$",5.7238768534315438
+"PEPTIDE1{[meL].[*O[C@@H](C(=O)*)C |$_R1;;;;;_R2;$|].[meL].[*O[C@@H](C(=O)*)Cc1ccccc1 |$_R1;;;;;_R2;;;;;;;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@H](C(=O)*)C |$_R1;;;;;_R2;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@@H](C(=O)*)Cc1ccccc1 |$_R1;;;;;_R2;;;;;;;$|]}|PEPTIDE2{E.[*O[C@@H](C(=O)*)C |$_R1;;;;;_R2;$|].E.[*O[C@@H](C(=O)*)Cc1ccccc1 |$_R1;;;;;_R2;;;;;;;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@H](C(=O)*)C |$_R1;;;;;_R2;$|].[*N(C)[C@H](C(=O)*)CCC |$_R1;;;;;;_R2;;;$|].[*O[C@@H](C(=O)*)Cc1ccccc1 |$_R1;;;;;_R2;;;;;;;$|]}$PEPTIDE2,PEPTIDE2,8:R2-1:R1|PEPTIDE1,PEPTIDE2,1:R1-3:R3|PEPTIDE2,PEPTIDE1,1:R3-8:R2$$$V2.0",5.1858112460224372
+"PEPTIDE1{[[C@H](C(=O)*)CS* |$;;;_R2;;;_R3$|].F.I.Q.N.[dC].S.R.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$V2.0",6.2235023908043692
+"PEPTIDE1{A.[dP].D.[dW].F.[dF].N.[dY].Y.[dW].G.[dN].W.[dH].G.[*N[C@@H](C(=O)*)[C@@H](C)O |$_R1;;;;;_R2;;;$|]}$PEPTIDE1,PEPTIDE1,16:R2-1:R1$$$",3.8459123763832412
+PEPTIDE1{N.L.E.R.E.[*N[C@H](C(=O)*)CSCNC(=O)C |$_R1;;;;;_R2;;;;;;;$|].L.E.E.P.[*N[C@H](C(=O)*)CSCNC(=O)C |$_R1;;;;;_R2;;;;;;;$|].S.R.E.E.A.F}$$$$,3.2792043882465700
+"PEPTIDE1{[[C@H](C(=O)*)CS* |$;;;_R2;;;_R3$|].Y.[dF].G.[dN].[dC].[dP].R.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$",2.1058521529925680
+PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0,1.8036950016492720
+"CHEM1{[*N[C@H](C(=O)*)Cc1ccc(cc1)OP(=O)(O)O |$_R1;;;;;_R2;;;;;;;;;;;;$|]}|PEPTIDE1{[C[C@H](N[*])C(=O)C[*] |$;;;_R1;;;;_R2$|].G.G.G.C.C.K.K.K.K}$PEPTIDE1,CHEM1,10:R3-1:R1$$$V2.0",6.3880602836120888

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.23.2",
+  "version": "2.25.0",
   "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",
@@ -44,7 +44,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.55.1",
+    "@datagrok-libraries/bio": "^5.61.0",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.6",

package/src/analysis/sequence-space.ts

@@ -33,7 +33,7 @@ export async function getEncodedSeqSpaceCol(
   for (let rowIdx = 0; rowIdx < rowCount; rowIdx++) {
     const catI = seqColRawData[rowIdx];
     const seq = seqColCats[catI];
-    if (seq === null || seqCol.isNone(rowIdx)) {
+    if (seq == null || seqCol.isNone(rowIdx)) {
       //@ts-ignore
       encList[rowIdx] = null;
       continue;

package/src/demo/bio03-atomic-level.ts

@@ -18,7 +18,7 @@ export async function demoToAtomicLevel(): Promise<void> {
   adjustGridcolAfterRender(view.grid, 'molfile(HELM)', 500, 300, true);
   adjustGridcolAfterRender(view.grid, 'HELM', 500, undefined, true);
   grok.shell.info('Hover over monomers in HELM column to highlight them in molecular structure.', {timeout: 10});
-  grok.shell.windows.help.showHelp('/help/datagrok/solutions/domains/bio/bio.md#get-atomic-level-structure');
+  grok.shell.windows.help.showHelp('/help/datagrok/solutions/domains/bio/bio.md#convert-to-atomic-level');
 }
 
 export async function demoBio03UI(): Promise<void> {

package/src/package-types.ts

@@ -8,7 +8,7 @@ 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';
+import {IMonomerLib, IMonomerLibBase, IMonomerSet} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 /** Names of package properties/settings declared in properties section of {@link './package.json'} */
 export const enum BioPackagePropertiesNames {
@@ -41,7 +41,7 @@ export class BioPackageProperties extends Map<string, any> {
   }
 
   public set maxMonomerLength(value: number | null) {
-    const vs = value === null ? 'long' : value.toString();
+    const vs = value == null ? 'long' : value.toString();
     super.set(BioPackagePropertiesNames.MaxMonomerLength, vs);
     this._onPropertyChanged.next(BioPackagePropertiesNames.MaxMonomerLength);
   }

package/src/package.ts

@@ -13,11 +13,11 @@ import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cli
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetrics, KnownMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
 import {SCORE} from '@datagrok-libraries/bio/src/utils/macromolecule/scoring';
-import {createJsonMonomerLibFromSdf, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {createJsonMonomerLibFromSdf,} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {ActivityCliffsEditor} from '@datagrok-libraries/ml/src/functionEditors/activity-cliffs-function-editor';
 import BitArray from '@datagrok-libraries/utils/src/bit-array';
@@ -78,6 +78,7 @@ import {molecular3DStructureWidget, toAtomicLevelWidget} from './widgets/to-atom
 import {handleSequenceHeaderRendering} from './widgets/sequence-scrolling-widget';
 import {PolymerType} from '@datagrok-libraries/js-draw-lite/src/types/org';
 import {BilnNotationProvider} from './utils/biln';
+import {MonomerLibFromFilesProvider} from './utils/monomer-lib/library-file-manager/monomers-lib-provider';
 export const _package = new BioPackage(/*{debug: true}/**/);
 export * from './package.g';
 
@@ -122,7 +123,7 @@ export class PackageFunctions {
 
   @grok.decorators.init({})
   static async initBio(): Promise<void> {
-    if (initBioPromise === null)
+    if (initBioPromise == null)
       initBioPromise = initBioInt();
 
     await initBioPromise;
@@ -1056,9 +1057,14 @@ export class PackageFunctions {
     return await showManageLibrariesView(false);
   }
 
+  // @grok.decorators.func({tags: ['monomer-lib-provider'], result: {type: 'object', name: 'result'}})
+  // static async getMonomerLibFileProvider(): Promise<MonomerLibFromFilesProvider> {
+  //   return
+  // }
+
   @grok.decorators.func({name: 'Monomer Manager Tree Browser', meta: {role: 'appTreeBrowser'}})
   static async manageMonomerLibrariesViewTreeBrowser(treeNode: DG.TreeViewGroup) {
-    const libraries = (await (await MonomerLibManager.getInstance()).getFileManager()).getValidLibraryPaths();
+    const libraries = (await (await MonomerLibManager.getInstance()).getAvaliableLibraryNames());
     libraries.forEach((libName) => {
       const nodeName = libName.endsWith('.json') ? libName.substring(0, libName.length - 5) : libName;
       const libNode = treeNode.item(nodeName);

package/src/tests/activity-cliffs-tests.ts

@@ -8,7 +8,7 @@ import {_testActivityCliffsOpen} from './activity-cliffs-utils';
 
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
@@ -67,7 +67,7 @@ category('activityCliffs', async () => {
     if (helmPackInstalled) {
       const df = await _package.files.readCsv('samples/HELM_50.csv');
       const _view = grok.shell.addTableView(df);
-  
+
       await _testActivityCliffsOpen(df, DimReductionMethods.UMAP,
         'HELM', 'Activity', 65, 20, BitArrayMetricsNames.Tanimoto, helmEncodingFunc);
     }

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

@@ -3,13 +3,13 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {test, after, before, category, expect, expectObject} from '@datagrok-libraries/utils/src/test';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
 import {MonomerTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
-import {Monomer} from '@datagrok-libraries/bio/src/types/index';
+import {Monomer} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 import {monomerLibForTestsSummary} from '../utils/monomer-lib/consts';
 
@@ -50,11 +50,13 @@ category('monomerLibraries', () => {
   test('empty', async () => {
     // exclude all monomer libraries for empty set
     const libSettings = await getUserLibSettings();
-    const libFileManager = await monomerLibHelper.getFileManager();
 
-    let libFnList = libFileManager.getValidLibraryPaths();
-    if (libFnList.length === 0)
-      libFnList = await libFileManager.getValidLibraryPathsAsynchronously();
+
+    let libFnList = await monomerLibHelper.getAvaliableLibraryNames();
+    if (libFnList.length === 0) {
+      await monomerLibHelper.refreshValidLibraryLists();
+      libFnList = await monomerLibHelper.getAvaliableLibraryNames();
+    }
 
     libSettings.exclude = libFnList;
     libSettings.explicit = [];
@@ -81,7 +83,7 @@ category('monomerLibraries', () => {
     };
     const monomerLib = monomerLibHelper.getMonomerLib();
     const absentOverrideMonomer = monomerLib.getMonomer(overMon.polymerType, overMon.symbol);
-    expect(absentOverrideMonomer === null, true, `Unexpectedly found monomer '${overMon.symbol}' `);
+    expect(absentOverrideMonomer == null, true, `Unexpectedly found monomer '${overMon.symbol}' `);
 
     const overriddenMonomerLib = monomerLib.override({[overMon.polymerType]: {[overMon.symbol]: overMon}}, 'test');
     const resOverMon = overriddenMonomerLib.getMonomer(overMon.polymerType, overMon.symbol);

package/src/tests/renderers-monomer-placer-tests.ts

@@ -8,7 +8,7 @@ import wu from 'wu';
 import {after, before, category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
 import {MonomerPlacer, hitBounds} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';

package/src/tests/scoring.ts

@@ -6,7 +6,7 @@ import wu from 'wu';
 
 import {category, test, expectFloat, before, after, expect} from '@datagrok-libraries/utils/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {IMonomerLibHelper, getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {IMonomerLibHelper, getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 import {
   getUserLibSettings, setUserLibSettings

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

@@ -5,7 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 import {ISeqHelper, getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 

package/src/tests/splitters-test.ts

@@ -8,9 +8,9 @@ import {after, before, category, test, expect, expectArray} from '@datagrok-libr
 import {TAGS as bioTAGS, splitterAsFasta} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {splitterAsHelm} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {ISeqHelper, getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {splitToMonomersUI} from '../utils/split-to-monomers';

package/src/tests/substructure-filters-tests.ts

@@ -8,7 +8,7 @@ import $ from 'cash-dom';
 import wu from 'wu';
 
 import {after, before, category, test, expect, delay, testEvent, awaitCheck} from '@datagrok-libraries/utils/src/test';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
@@ -159,7 +159,7 @@ category('bio-substructure-filters', async () => {
       const view = grok.shell.addTableView(df);
       await grok.data.detectSemanticTypes(df);
       await df.meta.detectSemanticTypes();
-  
+
       _package.logger.debug(`${logPrefix}, filter attaching.`);
       const filter = new BioSubstructureFilter(seqHelper, _package.logger);
       filter.attach(df);
@@ -168,7 +168,7 @@ category('bio-substructure-filters', async () => {
       try {
         const bf = filter.bioFilter as HelmBioFilter;
         expect(filter.bioFilter !== null, true, 'bioFilter is not created');
-  
+
         // filter 1
         _package.logger.debug(`${logPrefix}, filter 1 change awaiting...`);
         await testEvent(df.onRowsFiltered, () => {}, () => {
@@ -177,7 +177,7 @@ category('bio-substructure-filters', async () => {
         _package.logger.debug(`${logPrefix}, filter 1 changed.`);
         expect(filter.dataFrame!.filter.trueCount, 1);
         expect(filter.dataFrame!.filter.toBinaryString(), '0001');
-  
+
         // filter 2
         _package.logger.debug(`${logPrefix}, filter 2 change awaiting...`);
         await testEvent(df.onRowsFiltered, () => {}, () => {
@@ -206,9 +206,9 @@ category('bio-substructure-filters', async () => {
       const col = df.getCol('HELM string');
       await grok.data.detectSemanticTypes(df);
       const view = grok.shell.addTableView(df);
-  
+
       const fg = view.getFiltersGroup();
-  
+
       // await awaitCheck(() => fg.filters.length == 1, 'await filters.length == 1', 1000);
       // const filter = fg.filters.filter((f) => f.columnName == col.name)[0] as BioSubstructureFilter;
       await awaitGrid(view.grid);
@@ -287,10 +287,10 @@ category('bio-substructure-filters', async () => {
       const df = await _package.files.readCsv('tests/filter_HELM.csv');
       await grok.data.detectSemanticTypes(df);
       const view = grok.shell.addTableView(df);
-  
+
       const fSubStr: string = 'PEPTIDE1{A.C}$$$$V2.0';
       const fTrueCount: number = 1;
-  
+
       const f1 = await createFilter('HELM string', df);
       const f2 = await createFilter('HELM string', df);
       const dlg = ui.dialog('Test filters').add(f1.root).add(f2.root).show(); // to waitForElementInDom
@@ -302,18 +302,18 @@ category('bio-substructure-filters', async () => {
         expect(f2.bioFilter!.type, 'HelmBioFilter');
         const bf1 = f1.bioFilter as HelmBioFilter;
         const bf2 = f2.bioFilter as HelmBioFilter;
-  
+
         await testEvent(df.onRowsFiltered, () => {}, () => {
           bf1.props = new BioFilterProps(fSubStr, undefined, _package.logger);
         }, 60000, 'await onRowsFiltered'); // wait to load monomers
         await awaitGrid(view.grid);
         //debugger;
-  
+
         _package.logger.debug('Bio tests: substructureFilters/sync-helm, before changed event');
         await delay(f1.debounceTime * 2);
         _package.logger.debug('Bio tests: substructureFilters/sync-helm, after changed event');
         expect(df.filter.trueCount, fTrueCount);
-  
+
         await f1.awaitRendered();
         expect(bf2.props.substructure, fSubStr);
       } finally {

package/src/tests/to-atomic-level-tests.ts

@@ -8,9 +8,9 @@ import wu from 'wu';
 import {before, after, category, test, expectArray, expect} from '@datagrok-libraries/utils/src/test';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';

package/src/tests/to-atomic-level-ui-tests.ts

@@ -2,9 +2,9 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {after, before, category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {sequenceToMolfile} from '../utils/sequence-to-mol';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
@@ -20,7 +20,6 @@ type TestDataType = {
 };
 
 category('toAtomicLevel-ui', () => {
-
   let monomerLibHelper: IMonomerLibHelper;
   let userLibSettings: UserLibSettings;
   let seqHelper: ISeqHelper;
@@ -64,16 +63,16 @@ category('toAtomicLevel-ui', () => {
     },
   };
 
-//   const fastaCsv = `seq
-// MDYKETLLMPKTDFPMRGGLPNKEPQIQEKW
-// MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL
-// MMELVLKTIIGPIVVGVVLRIVDKWLNKDK
-// `;
-//   const helmCsv = `seq
-// PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Aze.dV.E.N.dV.Phe_4Me}$$$$
-// PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.meM.D-Chg.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$
-// PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.D-Cit.N.D-Orn.D-aThr.Phe_4Me}$$$$
-// `;
+  //   const fastaCsv = `seq
+  // MDYKETLLMPKTDFPMRGGLPNKEPQIQEKW
+  // MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL
+  // MMELVLKTIIGPIVVGVVLRIVDKWLNKDK
+  // `;
+  //   const helmCsv = `seq
+  // PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Aze.dV.E.N.dV.Phe_4Me}$$$$
+  // PEPTIDE1{meI.hHis.Aca.N.T.dK.Thr_PO3H2.Aca.meM.D-Chg.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$$
+  // PEPTIDE1{meI.Aca.N.T.dK.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.D-Cit.N.D-Orn.D-aThr.Phe_4Me}$$$$
+  // `;
 
   const getSeqCol = async (testData: TestDataType): Promise<DG.Column<string>> => {
     const seq = testData.src.seq;
@@ -98,7 +97,7 @@ category('toAtomicLevel-ui', () => {
         await _testToAtomicLevelFunc(seqCol, true, testData.tgt);
       });
     }
-  } 
+  }
 
   async function _testToAtomicLevelFunc(
     seqCol: DG.Column<string>, nonlinear: boolean, tgt: TestDataTargetType,

package/src/utils/cell-renderer.ts

@@ -20,7 +20,7 @@ import {
 } from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
-import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {execMonomerHoverLinks} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
 import {CellRendererBackBase, getGridCellColTemp} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';

package/src/utils/get-region.ts

@@ -47,9 +47,9 @@ export function getRegionDo(
     if (sh.posList[posJ] == startPosName) startPosIdx = posJ;
     if (sh.posList[posJ] == endPosName) endPosIdx = posJ;
   }
-  if (startPosIdx === null && startPosName !== null)
+  if (startPosIdx == null && startPosName !== null)
     throw new Error(`Start position ${startPosName} not found.`);
-  if (endPosIdx === null && endPosName !== null)
+  if (endPosIdx == null && endPosName !== null)
     throw new Error(`End position ${endPosName} not found.`);
 
   if (sh.posList.length < endPosIdx!)

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

@@ -1,4 +1,3 @@
 export const HELM_ITEM_SEPARATOR = '|';
-export const HELM_SECTION_SEPARATOR = '$';
 
 export const HYDROGEN_SYMBOL = 'H';

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

@@ -4,7 +4,7 @@ import * as OCL from 'openchemlib/full';
 
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {MolfileWithMap, MonomerMap} from '@datagrok-libraries/bio/src/monomer-works/types';
 
@@ -29,7 +29,7 @@ export class HelmToMolfileConverter implements IHelmToMolfileConverter {
     const smilesColName = `smiles(${helmCol.name})`;
     const smilesColNameU = df ? df.columns.getUnusedName(smilesColName) : smilesColName;
     return DG.Column.fromStrings(smilesColNameU, smiles.map((molecule) => {
-      if (molecule === null)
+      if (molecule == null)
         return '';
       return molecule;
     }));
@@ -57,7 +57,7 @@ export class HelmToMolfileConverter implements IHelmToMolfileConverter {
 
   public getMolV3000ViaOCL(beautifiedMols: (RDMol | null)[], columnName: string): DG.Column<string> {
     const beautifiedMolV2000 = beautifiedMols.map((mol) => {
-      if (mol === null)
+      if (mol == null)
         return '';
       const molBlock = mol.get_v3Kmolblock();
       mol!.delete();
@@ -97,7 +97,7 @@ export class HelmToMolfileConverter implements IHelmToMolfileConverter {
     if (chiralityEngine)
       return this.getMolV3000ViaOCL(beautifiedMols, molColNameU);
     return DG.Column.fromStrings(molColNameU, beautifiedMols.map((mol) => {
-      if (mol === null)
+      if (mol == null)
         return '';
       const molBlock = mol.get_v3Kmolblock();
       mol!.delete();

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

@@ -1,16 +1,24 @@
 import {HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
 import {ConnectionList} from './connection-list';
-import {HELM_ITEM_SEPARATOR, HELM_SECTION_SEPARATOR} from './const';
+import {HELM_ITEM_SEPARATOR} from './const';
 import {SimplePolymer} from './simple-polymer';
 import {Bond} from './types';
 
 export class Helm {
   constructor(private helmString: string) {
-    const helmSections = this.helmString.split(HELM_SECTION_SEPARATOR);
-    const simplePolymers = helmSections[0].split(HELM_ITEM_SEPARATOR);
-    this.simplePolymers = simplePolymers
+    const indexOfSequenceEnd = helmString.indexOf('}$');
+    const sequencePart = helmString.substring(0, indexOfSequenceEnd + 1);
+    const connectionsEndPart = helmString.indexOf('$', indexOfSequenceEnd + 2);
+    const connectionsPart = helmString.substring(indexOfSequenceEnd + 2, connectionsEndPart);
+    // const helmParts = seq.split('$');
+    const spList = sequencePart.split('}|');
+    // since we removed }|, need to add } to last part
+    for (let i = 0; i < spList.length - 1; i++)
+      spList[i] = spList[i] + '}';
+
+    this.simplePolymers = spList
       .map((item) => new SimplePolymer(item));
-    this.connectionList = new ConnectionList(helmSections[1]);
+    this.connectionList = new ConnectionList(connectionsPart);
     this.bondData = this.getBondData();
 
     this.bondedRGroupsMap = this.getBondedRGroupsMap();
@@ -58,7 +66,7 @@ export class Helm {
     const lowerBound = shiftValues.sort((a, b) => b - a).find( // find the largest shift not exceeding monomerGlobalIdx
       (shift) => monomerGlobalIdx >= shift
     );
-    if (lowerBound === undefined)
+    if (lowerBound == undefined)
       throw new Error(`Cannot find simple polymer for monomer ${monomerGlobalIdx}`);
     const simplePolymerId = Object.keys(shifts).find((simplePolymerId) => shifts[simplePolymerId] === lowerBound)!;
     const simplePolymer = this.simplePolymers.find((simplePolymer) => simplePolymer.id === simplePolymerId)!;

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

@@ -4,7 +4,7 @@ export abstract class MolfileBonds {
   protected bondedAtomPairs: number[][] = [];
   protected rawBondLines: string[] = [];
 
-  public get count(): number { return this.bondedAtomPairs.length;}
+  public get count(): number { return this.bondedAtomPairs.length; }
 
   /** Get bond lines with new values for bonded atoms  */
   abstract getBondLines(): string[];
@@ -31,7 +31,7 @@ export abstract class MolfileBonds {
   }
 
   replacePositionsInBondsByDummy(positions: PositionInBonds[], dummy?: number): void {
-    if (dummy === undefined)
+    if (dummy == undefined)
       dummy = -1;
     positions.forEach((position) => {
       const {bondLineIdx, nodeIdx} = position;

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

@@ -15,7 +15,7 @@ export abstract class MolfileWrapper {
 
   protected shiftR1GroupToOrigin(): void {
     const r1Idx = this.rGroups.getAtomicIdx(1);
-    if (r1Idx === null)
+    if (r1Idx == null)
       return; // R1 group is not present, nothing to shift
     const {x, y} = this.atoms.atomCoordinates[r1Idx];
     this.atoms.shift({x: -x, y: -y});
@@ -23,7 +23,7 @@ export abstract class MolfileWrapper {
 
   protected alignR2AlongX(): void {
     const r2Idx = this.rGroups.getAtomicIdx(2);
-    if (r2Idx === null)
+    if (r2Idx == null)
       throw new Error(`Cannot find R2 group for monomer ${this.monomerSymbol}`);
     const r2Coordinates = this.atoms.atomCoordinates[r2Idx];
     const tan = r2Coordinates.y / r2Coordinates.x;

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

@@ -1,4 +1,4 @@
-import {IMonomerLib, IMonomerLibBase, Monomer} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, IMonomerLibBase, Monomer} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {HELM_RGROUP_FIELDS} from '@datagrok-libraries/bio/src/utils/const';
 import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';

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

@@ -3,7 +3,7 @@ import wu from 'wu';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {V3K_CONST} from '@datagrok-libraries/chem-meta/src/formats/molfile-const';
 import {HelmTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
-import {IMonomerLib, IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLib, IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {GapOriginals} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {MolfileWithMap, MonomerMap} from '@datagrok-libraries/bio/src/monomer-works/types';

package/src/utils/helm-to-molfile/converter/r-group-handler.ts

@@ -19,13 +19,13 @@ export class RGroupHandler {
 
   getAtomicIdx(rGroupId: number): number | null {
     const atomicIdx = this.rGroupIdToAtomicIndexMap.get(rGroupId);
-    return atomicIdx === undefined ? null : atomicIdx;
+    return atomicIdx == undefined ? null : atomicIdx;
   }
 
   private removeRGroupsFromAtomBlock(rGroupIds: number[]): void {
     rGroupIds.forEach((rgroupId) => {
       const atomicIdx = this.rGroupIdToAtomicIndexMap.get(rgroupId);
-      if (atomicIdx === undefined)
+      if (atomicIdx == undefined)
         throw new Error(`Cannot find atomic index for R group ${rgroupId}`);
     });
 

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

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 import {SeqHelper} from '../seq-helper';
 
@@ -14,7 +14,8 @@ export async function getMolColumnFromHelm(
 ): Promise<DG.Column<string>> {
   const seqHelper: SeqHelper = _package.seqHelper as SeqHelper;
   const converter = await seqHelper.getHelmToMolfileConverter(monomerLib);
-  const molCol = converter.convertToRdKitBeautifiedMolfileColumn(helmCol, chiralityEngine, _package.rdKitModule, monomerLib);
+  const molCol = converter
+    .convertToRdKitBeautifiedMolfileColumn(helmCol, chiralityEngine, _package.rdKitModule, monomerLib);
   molCol.semType = DG.SEMTYPE.MOLECULE;
   return molCol;
 }

package/src/utils/monomer-cell-renderer-base.ts

@@ -2,9 +2,8 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {CellRendererBackBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-back-base';
-import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLibBase, getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {ISeqHelper, getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {_package} from '../package';

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

@@ -3,12 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types/index';
-
-export const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
-export const SETS_PATH: string = 'System:AppData/Bio/monomer-sets/';
-
-export const HELM_JSON_SCHEMA_PATH = 'System:AppData/Bio/tests/libraries/HELMmonomerSchema.json';
+import {MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 export const LIB_SETTINGS_FOR_TESTS: UserLibSettings =
   {explicit: ['HELMCoreLibrary.json', 'polytool-lib.json'], exclude: [], duplicateMonomerPreferences: {}};