@datagrok/sequence-translator 1.9.14 → 1.10.0

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.9.14",
+  "version": "1.10.0",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -22,7 +22,7 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.54.8",
+    "@datagrok-libraries/bio": "^5.60.0",
     "@datagrok-libraries/chem-meta": "^1.2.8",
     "@datagrok-libraries/tutorials": "^1.6.1",
     "@datagrok-libraries/utils": "^4.6.5",
@@ -39,9 +39,9 @@
     "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.13",
+    "@datagrok-libraries/helm-web-editor": "^1.1.16",
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
-    "@datagrok/bio": "^2.18.0",
+    "@datagrok/bio": "^2.24.0",
     "@datagrok/chem": "^1.13.0",
     "@datagrok/helm": "^2.7.0",
     "@types/jquery": "^3.5.32",

package/src/apps/common/model/monomer-lib/lib-wrapper.ts

@@ -3,7 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import {_package} from '../../../../package';
 import {DEFAULT_FORMATS} from '../const';
 
-import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {HELM_REQUIRED_FIELD as REQ, HELM_OPTIONAL_FIELDS as OPT} from '@datagrok-libraries/bio/src/utils/const';
 
 import {META_FIELDS as MET} from './const';

package/src/apps/common/model/oligo-toolkit-package.ts

@@ -3,8 +3,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, Monomer, getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
@@ -21,7 +20,6 @@ import {FormatDetector} from './parsing-validation/format-detector';
 import {highlightInvalidSubsequence} from '../view/components/colored-input/input-painters';
 
 export class OligoToolkitPackage extends DG.Package implements ITranslationHelper {
-
   private _helmHelper: IHelmHelper;
   public get helmHelper(): IHelmHelper {
     if (!this._helmHelper)
@@ -119,7 +117,8 @@ async function loadMonomerLib(monomersPath: string): Promise<IMonomerLib> {
     `Initializing ${APP_NAME.COMBINED} monomer library ...`);
   try {
     const libHelper = await getMonomerLibHelper();
-    const res = await libHelper.readLibrary(monomersPath, DEFAULT_LIB_FILENAME);
+    const path = (monomersPath.endsWith('/') ? monomersPath : monomersPath + '/') + DEFAULT_LIB_FILENAME;
+    const res = await libHelper.readLibraryFromFilePath(path);
     return res;
   } finally { pi.close(); }
 }

package/src/apps/translator/view/ui.ts

@@ -22,8 +22,9 @@ import {convert, getSupportedTargetFormats, getTranslatedSequences} from '../mod
 import {ITranslationHelper} from '../../../types';
 
 import {NUCLEOTIDES_FORMAT, SEQUENCE_COPIED_MSG, SEQ_TOOLTIP_MSG} from './const';
-import './style.css';
 import {_package} from '../../../package';
+//@ts-ignore
+import './style.css';
 
 const enum REQUIRED_COLUMN_LABEL {
   SEQUENCE = 'Sequence',

package/src/package.ts

@@ -26,7 +26,7 @@ import {CyclizedNotationProvider} from './utils/cyclized';
 import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {PolyToolTags} from './consts';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import { getPTCombineDialog } from './polytool/pt-combine-dialog';
+import {getPTCombineDialog} from './polytool/pt-combine-dialog';
 
 export * from './package.g';
 
@@ -72,14 +72,13 @@ async function initSequenceTranslatorInt(): Promise<void> {
   _package.completeInit(helmHelper);
 }
 
-export class PackageFunctions{
+export class PackageFunctions {
   @grok.decorators.app({
     icon: 'img/icons/toolkit.png',
     browsePath: 'Peptides | Oligo Toolkit',
     name: 'Oligo Toolkit'
   })
   static async oligoToolkitApp(): Promise<DG.ViewBase> {
-  
     await _package.initLibData();
     const externalViewFactories = await getExternalAppViewFactories(_package);
     if (!externalViewFactories)
@@ -89,10 +88,9 @@ export class PackageFunctions{
     return view;
   }
 
-    
+
   @grok.decorators.init()
   static async init(): Promise<void> {
-  
     if (initSequenceTranslatorPromise === null)
       _package.startInit(initSequenceTranslatorPromise = initSequenceTranslatorInt());
 
@@ -105,7 +103,6 @@ export class PackageFunctions{
     name: 'Oligo Translator'
   })
   static async oligoTranslatorApp(): Promise<DG.ViewBase> {
-  
     const view = await getSpecifiedAppView(APP_NAME.TRANSLATOR);
     return view;
   }
@@ -117,7 +114,6 @@ export class PackageFunctions{
     name: 'Oligo Pattern'
   })
   static async oligoPatternApp(): Promise<DG.ViewBase> {
-  
     const view = await getSpecifiedAppView(APP_NAME.PATTERN);
     return view;
   }
@@ -129,7 +125,6 @@ export class PackageFunctions{
     name: 'Oligo Structure'
   })
   static async oligoStructureApp(): Promise<DG.ViewBase> {
-  
     const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
     return view;
   }
@@ -137,7 +132,6 @@ export class PackageFunctions{
 
   @grok.decorators.func({outputs: [{type: 'object', name: 'result'}]})
   static async getTranslationHelper(): Promise<ITranslationHelper> {
-  
     await _package.initLibData();
     return _package;
   }
@@ -145,7 +139,6 @@ export class PackageFunctions{
 
   @grok.decorators.func({outputs: [{type: 'object', name: 'result'}]})
   static getCodeToWeightsMap(): Record<string, number> {
-  
     const monomerLibWrapper = _package.monomerLibWrapper;
     const map = monomerLibWrapper.getCodesToWeightsMap();
     return Object.fromEntries(map);
@@ -155,7 +148,6 @@ export class PackageFunctions{
   @grok.decorators.func()
   static validateSequence(
     sequence: string): boolean {
-  
     const validator = _package.createSequenceValidator(sequence);
     const format = _package.createFormatDetector(sequence).getFormat();
     return (format === null) ? false : validator.isValidSequence(format!);
@@ -168,14 +160,13 @@ export class PackageFunctions{
   static getMolfileFromGcrsSequence(
     sequence: string,
     invert: boolean): string {
-  
     return (new SequenceToMolfileConverter(sequence, invert, 'GCRS')).convert();
   }
 
 
   @grok.decorators.func()
   static linkStrands(
-    @grok.decorators.param({type:'object'})  strands: { senseStrands: string[], antiStrands: string[] }): string {
+    @grok.decorators.param({type: 'object'}) strands: { senseStrands: string[], antiStrands: string[] }): string {
     return linkStrandsV3000(strands, true);
   }
 
@@ -202,7 +193,6 @@ export class PackageFunctions{
     description: 'Design a modification pattern for an oligonucleotide sequence'
   })
   static async demoOligoPattern(): Promise<void> {
-  
     await demoOligoPatternUI();
   }
 
@@ -215,7 +205,6 @@ export class PackageFunctions{
     description: 'Visualize duplex and save SDF'
   })
   static async demoOligoStructure(): Promise<void> {
-  
     await demoOligoStructureUI();
   }
 
@@ -224,65 +213,58 @@ export class PackageFunctions{
   static async translateOligonucleotideSequence(
     sequence: string, sourceFormat: string, targetFormat: string
   ): Promise<string> {
-  
     await _package.initLibData();
     return _package.createFormatConverter(sequence, sourceFormat).convertTo(targetFormat);
   }
 
   @grok.decorators.func({
     'top-menu': 'Bio | PolyTool | Convert...',
-    name: 'polyToolConvert',
-    description: 'Perform cyclization of polymers'
+    'name': 'polyToolConvert',
+    'description': 'Perform cyclization of polymers'
   })
   static async polyToolConvertTopMenu(): Promise<void> {
-  
     await polyToolConvertUI();
   }
 
   @grok.decorators.editor()
   static async getPolyToolConvertEditor(
     call: DG.FuncCall): Promise<DG.Column<string> | null> {
-  
     const funcEditor = await PolyToolConvertFuncEditor.create(call);
     return await funcEditor.showDialog();
   }
 
 
   @grok.decorators.func({
-    editor: 'SequenceTranslator:getPolyToolConvertEditor', 
+    editor: 'SequenceTranslator:getPolyToolConvertEditor',
   })
   static async polyToolConvert2(
     table: DG.DataFrame,
-    @grok.decorators.param({options: { caption: 'Sequence'}}) seqCol: DG.Column, 
-    @grok.decorators.param({options: { initialValue: 'true'}}) generateHelm: boolean, 
-    @grok.decorators.param({options: { initialValue: 'true'}}) chiralityEngine: boolean, 
+    @grok.decorators.param({options: {caption: 'Sequence'}}) seqCol: DG.Column,
+    @grok.decorators.param({options: {initialValue: 'true'}}) generateHelm: boolean,
+    @grok.decorators.param({options: {initialValue: 'true'}}) chiralityEngine: boolean,
     @grok.decorators.param({type: 'object'}) rules: string[]
   ): Promise<DG.Column<string>> {
-  
     const ptConvertRes = await polyToolConvert(seqCol, generateHelm, false, chiralityEngine, false, rules);
     return ptConvertRes[0];
   }
 
 
-
   @grok.decorators.func({
     'top-menu': 'Bio | PolyTool | Enumerate HELM...',
-    name: 'polyToolEnumerateHelm',
-    description: 'Perform cyclization of polymers'
+    'name': 'polyToolEnumerateHelm',
+    'description': 'Perform cyclization of polymers'
   })
   static async polyToolEnumerateHelmTopMenu(): Promise<void> {
-  
     await polyToolEnumerateHelmUI(grok.shell.tv?.dataFrame.currentCell);
   }
 
 
   @grok.decorators.func({
     'top-menu': 'Bio | PolyTool | Enumerate Chem...',
-    name: 'polyToolEnumerateChem',
-    description: 'Perform cyclization of polymers'
+    'name': 'polyToolEnumerateChem',
+    'description': 'Perform cyclization of polymers'
   })
   static async polyToolEnumerateChemTopMenu(): Promise<void> {
-  
     polyToolEnumerateChemUI();
   }
 
@@ -290,8 +272,7 @@ export class PackageFunctions{
   @grok.decorators.func()
   static async polyToolColumnChoice(
     @grok.decorators.param({options: {description: 'Input data table'}}) df: DG.DataFrame,
-    macroMolecule: DG.Column): Promise<void> {
-  
+      macroMolecule: DG.Column): Promise<void> {
     _setPeptideColumn(macroMolecule);
     await grok.data.detectSemanticTypes(df);
   }
@@ -300,7 +281,6 @@ export class PackageFunctions{
   @grok.decorators.func()
   static async createMonomerLibraryForPolyTool(
     file: DG.FileInfo) {
-  
     const fileContent = await file.readAsString();
     const libHandler = new PolyToolCsvLibHandler(file.fileName, fileContent);
     const libObject = await libHandler.getJson();
@@ -319,7 +299,6 @@ export class PackageFunctions{
     name: 'HELM Enumerator'
   })
   static async ptEnumeratorHelmApp(): Promise<void> {
-  
     await polyToolEnumerateHelmUI();
   }
 
@@ -333,18 +312,15 @@ export class PackageFunctions{
     name: 'Chem Enumerator'
   })
   static async ptEnumeratorChemApp(): Promise<void> {
-  
     polyToolEnumerateChemUI();
   }
 
 
-
   @grok.decorators.func({
     name: 'Polytool Helm Enumerator dialog'
   })
   static async getPtHelmEnumeratorDialog(
-    @grok.decorators.param({type:'object',options:{nullable:true}})  cell?: DG.Cell) {
-  
+    @grok.decorators.param({type: 'object', options: {nullable: true}}) cell?: DG.Cell) {
     return polyToolEnumerateHelmUI(cell);
   }
 
@@ -353,30 +329,26 @@ export class PackageFunctions{
     name: 'Polytool Chem Enumerator dialog'
   })
   static async getPtChemEnumeratorDialog(
-    @grok.decorators.param({type:'object',options:{nullable:true}})  cell?: DG.Cell) {
-  
+    @grok.decorators.param({type: 'object', options: {nullable: true}}) cell?: DG.Cell) {
     return polyToolEnumerateChemUI(cell);
   }
 
 
   @grok.decorators.func({
-    name: 'Combine Sequences',
+    'name': 'Combine Sequences',
     'top-menu': 'Bio | PolyTool | Combine Sequences...'
   })
   static async getPolyToolCombineDialog() {
-  
     getPTCombineDialog();
   }
 
 
-
   @grok.decorators.func({
     name: 'applyNotationProviderForHarmonizedSequence'
   })
   static applyNotationProviderForCyclized(
-    @grok.decorators.param({type:'column'}) col: DG.Column<string>,
-    separator: string) {
-  
+    @grok.decorators.param({type: 'column'}) col: DG.Column<string>,
+      separator: string) {
     col.setTag('aligned', 'SEQ');
     col.setTag('alphabet', 'UN');
     col.setTag('.alphabetIsMultichar', 'true');
@@ -392,4 +364,4 @@ async function getSpecifiedAppView(appName: string): Promise<DG.ViewBase> {
   const appUI = getSpecifiedAppUI(appName, _package);
   const view = await appUI.getAppView();
   return view;
-}
+}

package/src/polytool/conversion/pt-atomic.ts

@@ -1,11 +1,11 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {getSeqHelper, ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
 import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 
 export function dealGroups(col: DG.Column<string>): void {

package/src/polytool/conversion/pt-rule-cards.ts

@@ -2,9 +2,10 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+// @ts-ignore
 import './style.css';
 
-import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {Rules} from './pt-rules';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {doPolyToolConvert} from './pt-conversion';

package/src/polytool/conversion/pt-rules.ts

@@ -5,7 +5,7 @@ import * as ui from 'datagrok-api/ui';
 import {ActiveFiles} from '@datagrok-libraries/utils/src/settings/active-files-base';
 import {RulesManager} from './rule-manager';
 import {RuleCards} from './pt-rule-cards';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   _package,
   PackageFunctions} from '../../package';

package/src/polytool/conversion/pt-synthetic.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 import {Rules, RuleReaction, getMonomerPairs} from './pt-rules';
 import {InvalidReactionError, MonomerNotFoundError} from '../types';
@@ -7,8 +8,7 @@ import * as grok from 'datagrok-api/grok';
 
 import wu from 'wu';
 import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {IMonomerLib, IMonomerLibBase, Monomer, MonomerLibData, RGroup} from '@datagrok-libraries/bio/src/types';
+import {IMonomerLib, IMonomerLibBase, Monomer, MonomerLibData, RGroup, getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {RDModule, RDMol, RDReaction, MolList, RDReactionResult} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {HELM_REQUIRED_FIELD as REQ,
   HELM_OPTIONAL_FIELDS as OPT, HELM_RGROUP_FIELDS} from '@datagrok-libraries/bio/src/utils/const';

package/src/polytool/monomer-lib-handler.ts

@@ -7,7 +7,7 @@ import {HELM_FIELDS, DUMMY_MONOMER} from '@datagrok-libraries/bio/src/utils/cons
 import {
   helmFieldsToPolyToolInputFields, R_GROUP_BLOCK_DUMMY
 } from './const';
-import {Monomer, RGroup} from '@datagrok-libraries/bio/src/types/index';
+import {Monomer, RGroup} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 export class PolyToolMonomerLibHandler {
   constructor(private rawLib: any[]) { }

package/src/polytool/pt-dialog.ts

@@ -28,7 +28,7 @@ import {
 } from './const';
 
 import {_package} from '../package';
-import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {MonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/utils';
 import {MonomerMap} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {ISeqMonomer} from '@datagrok-libraries/bio/src/helm/types';
@@ -42,7 +42,6 @@ import {addSubstructProvider, getMonomerHover, ISubstruct, setMonomerHover}
 import {getMolHighlight} from '@datagrok-libraries/bio/src/monomer-works/seq-to-molfile';
 import {ChemTags} from '@datagrok-libraries/chem-meta/src/consts';
 import {mergeSubstructs} from '@datagrok-libraries/chem-meta/src/types';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {dealGroups, helmToMol} from './conversion/pt-atomic';
 
 type PolyToolConvertSerialized = {
@@ -94,13 +93,14 @@ export async function getPolyToolConvertDialog(srcCol?: DG.Column): Promise<DG.D
     if (!srcColVal) {
       if (srcColList.length < 1)
         throw new Error(PT_ERROR_DATAFRAME);
-      
+
       if (customSrcCols.length < 1) {
         const toAtomicLevelFunc = DG.Func.find({package: 'Bio', name: 'toAtomicLevel'})[0];
         if (toAtomicLevelFunc) {
           toAtomicLevelFunc.prepare().edit();
           return null;
         }
+        // eslint-disable-next-line max-len
         grok.shell.warning('Polytool requires a macromolecule column with custom notation. \n\nUse Top menu | Bio | Transform | To Atomic Level.');
         return null;
       }

package/src/polytool/pt-enumerate-seq-dialog.ts

@@ -10,7 +10,7 @@ import {Unsubscribable} from 'rxjs';
 
 import {GetMonomerResType, HelmAtom, MonomerNumberingTypes} from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 import {getHelmHelper, HelmInputBase, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {HelmType, PolymerType} from '@datagrok-libraries/bio/src/helm/types';
 import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
 import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
@@ -169,7 +169,7 @@ async function getPolyToolEnumerateDialog(
         const seqCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [PT_HELM_EXAMPLE]);
         seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
         const _tempDf = DG.DataFrame.fromColumns([seqCol]);
-        
+
         seqCol.meta.units = NOTATION.HELM;
         const sh = seqHelper.getSeqHandler(seqCol);
         resSeqValue = sh.getValue(0);
@@ -187,7 +187,7 @@ async function getPolyToolEnumerateDialog(
     const warningsTextDiv = ui.divText('', {style: {color: 'red'}});
     // #### Inputs
     inputs = {
-      macromolecule: helmHelper.createHelmInput(                                                     
+      macromolecule: helmHelper.createHelmInput(
         'Macromolecule', {
           editable: false,
           editorOptions: {
@@ -590,7 +590,11 @@ async function getPolyToolEnumerateDialog(
               return;
             }
             const monLibName = placeHoldersValue[0].monomers[0];
-            const monLib = await libHelper.readLibrary(LIB_PATH, monLibName);
+            const monLib = await libHelper.readSingleLibraryByName(monLibName);
+            if (!monLib) {
+              grok.shell.warning(`Monomer Library '${monLibName}' was not found`);
+              return;
+            }
             const peptideMonomers = monLib.getMonomerSymbolsByType(PolymerTypes.PEPTIDE);
             placeHoldersValue[0].monomers = peptideMonomers;
             enumerationType = PolyToolEnumeratorTypes.Single;

package/src/polytool/pt-enumeration-helm.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
@@ -10,7 +11,6 @@ import {
 
 
 import {PtBio} from './conversion/pt-tools-helmmol';
-import {getAvailableMonomers} from './utils';
 import {PolyToolEnumeratorParams, PolyToolEnumeratorTypes,
   PolyToolPlaceholder, PolyToolBreadthPlaceholder} from './types';
 

package/src/polytool/pt-unrule-dialog.ts

@@ -42,7 +42,7 @@ export async function getPolyToolUnruleDialog(srcCol?: DG.Column<string>): Promi
     });
     let ruleFileList: string[];
     const ruleInputs = new RuleInputs(RULES_PATH, RULES_STORAGE_NAME, '.json', {
-      onValueChanged: (value: string[]) => { ruleFileList = value;}
+      onValueChanged: (value: string[]) => { ruleFileList = value; }
     });
     const rulesHeader = ui.inlineText([PT_UI_RULES_USED]);
     const rulesForm = await ruleInputs.getForm();
@@ -95,7 +95,7 @@ export async function polyToolUnrule(
     const rules = await getRules(ruleFiles);
     const resHelmList = doPolyToolUnrule(srcCol.toList(), rules, helmHelper);
     const resHelmColName = `harmonized(srcCol.name)`;
-    const resHelmCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, resHelmColName, resHelmList,);
+    const resHelmCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, resHelmColName, resHelmList);
     resHelmCol.semType = DG.SEMTYPE.MACROMOLECULE;
     resHelmCol.meta.units = NOTATION.CUSTOM;
     if (table) {

package/src/polytool/utils.ts

@@ -8,8 +8,8 @@ import {ALPHABET, ALIGNMENT, NOTATION} from '@datagrok-libraries/bio/src/utils/m
 import {OrgType} from '@datagrok-libraries/bio/src/helm/types';
 
 import {
-  IMonomerLibFileManager, IMonomerLibHelper
-} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+  getMonomerLibHelper, IMonomerLibHelper
+} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 declare const org: OrgType;
 export const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
@@ -28,15 +28,23 @@ function addCommonTags(col: DG.Column<any>) {
 }
 
 export async function getAvailableMonomers(screenLibrary: string): Promise<string[]> {
-  const monomerLibHelper: IMonomerLibHelper = await grok.functions.call('Bio:getMonomerLibHelper', {});
-  const monomerLib = await monomerLibHelper.readLibrary(LIB_PATH, screenLibrary);
+  const monomerLibHelper: IMonomerLibHelper = await getMonomerLibHelper();
+  const monomerLib = await monomerLibHelper.readSingleLibraryByName(screenLibrary);
+  if (!monomerLib) {
+    _package.logger.error(`Monomer library '${screenLibrary}' not found.`);
+    return [];
+  }
   //NOTICE: works with Peptides only
   return monomerLib.getMonomerSymbolsByType('PEPTIDE');
 }
 
 export async function getAvailableMonomerMols(screenLibrary: string): Promise<{[monomerSymbol: string]: string}> {
-  const monomerLibHelper: IMonomerLibHelper = await grok.functions.call('Bio:getMonomerLibHelper', {});
-  const monomerLib = await monomerLibHelper.readLibrary(LIB_PATH, screenLibrary);
+  const monomerLibHelper: IMonomerLibHelper = await getMonomerLibHelper();
+  const monomerLib = await monomerLibHelper.readSingleLibraryByName(screenLibrary);
+  if (!monomerLib) {
+    _package.logger.error(`Monomer library '${screenLibrary}' not found.`);
+    return {};
+  }
   const monomers = monomerLib.getMonomerSymbolsByType('PEPTIDE');
   const mols = new Array<string>(monomers.length);
 
@@ -45,7 +53,6 @@ export async function getAvailableMonomerMols(screenLibrary: string): Promise<{[
 }
 
 export async function getLibrariesList(): Promise<string[]> {
-  const monomerLibHelper: IMonomerLibHelper = await grok.functions.call('Bio:getMonomerLibHelper', {});
-  const monomerFileManager: IMonomerLibFileManager = await monomerLibHelper.getFileManager();
-  return monomerFileManager.getValidLibraryPaths();
+  const monomerLibHelper: IMonomerLibHelper = await getMonomerLibHelper();
+  return monomerLibHelper.getAvaliableLibraryNames();
 }

package/src/tests/polytool-chain-from-notation-tests.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';

package/src/tests/polytool-chain-parse-notation-tests.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
@@ -81,7 +82,7 @@ category('PolyTool: Chain: parseNotation', () => {
     '3-in-1-1-6-3': {inIdx: 1, spIdx: 2, outIdx: 3, monomers: [['0'], ['1'], ['2', '3', '4', '5', '6', '7'], ['8', '9', '10']]},
     '7-in-1-1-6-3': {inIdx: 5, spIdx: 2, outIdx: 7, monomers: [['0'], ['1'], ['2', '3', '4', '5', '6', '7'], ['8', '9', '10']]},
     '8-in-1-1-6-3': {inIdx: 0, spIdx: 3, outIdx: 8, monomers: [['0'], ['1'], ['2', '3', '4', '5', '6', '7'], ['8', '9', '10']]},
-//    '11-in-1-1-6-3': {inIdx: 0, spIdx: 4}, src: {outIdx: 11, monomers: [['0'], ['1'], ['2', '3', '4', '5', '6', '7'], ['8', '9', '10']]}},
+    //    '11-in-1-1-6-3': {inIdx: 0, spIdx: 4}, src: {outIdx: 11, monomers: [['0'], ['1'], ['2', '3', '4', '5', '6', '7'], ['8', '9', '10']]}},
   };
 
   for (const [testName, {inIdx, spIdx, outIdx, monomers}] of Object.entries(innerIdxTests)) {

package/src/tests/polytool-convert-tests.ts

@@ -1,10 +1,11 @@
+/* eslint-disable max-len */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {before, after, category, expect, test, expectArray, testEvent, 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 {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
   getUserLibSettings, setUserLibSettings

package/src/tests/polytool-enumerate-breadth-tests.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
   getUserLibSettings, setUserLibSettings
@@ -94,15 +94,15 @@ category('PolyTool: Enumerate', () => {
         ],
       },
       tgt: [
-        {seq: "PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-W3K-K3Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-W3K-G4Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-W3K-P5Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-G4K-W3Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-G4K-K4Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-G4K-P5Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-P5K-W3Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-P5K-G4Y"},
-        {seq: "PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-P5K-K5Y"}
+        {seq: 'PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3K-K3Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3K-G4Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3K-P5Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4K-W3Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4K-K4Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4K-P5Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K-W3Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K-G4Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K-K5Y'}
       ]
     }
   };