@datagrok/sequence-translator 1.9.15 → 1.10.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.9.15",
+  "version": "1.10.1",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -22,7 +22,7 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.54.8",
+    "@datagrok-libraries/bio": "^5.60.1",
     "@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/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';
@@ -20,8 +20,8 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
   const rdkit = await getRdKitModule();
   const argLib: { [symbol: string]: Monomer } = {};
 
-  let names: string [] = [];
-  let monomers: Monomer [] = [];
+  let names: (string | null) [] = [];
+  let monomers: (Monomer | null) [] = [];
 
   for (let i = 0; i < rules.reactionRules.length; i++) {
     try {
@@ -32,8 +32,11 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
       console.error(e);
       grok.shell.warning(e);
     } finally {
-      for (let j = 0; j < names.length; j ++)
-        argLib[names[j]] = monomers[j];
+      for (let j = 0; j < names.length; j ++) {
+        if (names[j] == null || monomers[j] == null)
+          continue;
+        argLib[names[j]!] = monomers[j]!;
+      }
     }
   }
 
@@ -44,16 +47,16 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
   return overriddenMonomerLib;
 }
 
-export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleReaction): [string[], Monomer[]] {
+export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleReaction): [(string | null)[], (Monomer | null)[]] {
   const reacSmarts = rule.reaction;
   const monomerName = rule.name;
   const totalLength = rule.firstMonomers.length + rule.secondMonomers.length + 1;
   const reactionMembers = rule.reaction.split('>>');
   const reactants = reactionMembers[0].split('.');
 
-  const monomerNames = new Array<string>(totalLength);
-  const resMonomers = new Array<Monomer>(totalLength);
-  const monomers = new Array<string>(totalLength);
+  const monomerNames = new Array<string | null>(totalLength);
+  const resMonomers = new Array<Monomer | null>(totalLength);
+  const monomers = new Array<string | null>(totalLength);
 
   const mainRxn = getReactionSmirks(rdkit, reacSmarts);
 
@@ -66,20 +69,21 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
   let counter = 0;
   for (let i = 0; i < rule.firstMonomers.length; i++) {
     const monomer = mLib.getMonomer('PEPTIDE', rule.firstMonomers[i]);
-    if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.firstMonomers[i]);
 
-    const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
-    monomers[counter] = sMolBlock;
-    monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    if (monomer) {
+      const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
+      monomers[counter] = sMolBlock;
+      monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    }
     counter++;
   }
   for (let i = 0; i < rule.secondMonomers.length; i++) {
     const monomer = mLib.getMonomer('PEPTIDE', rule.secondMonomers[i]);
-    if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.secondMonomers[i]);
-
-    const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
-    monomers[counter] = sMolBlock;
-    monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    if (monomer) {
+      const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
+      monomers[counter] = sMolBlock;
+      monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    }
     counter++;
   }
 
@@ -103,17 +107,21 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
 
   //after RDKit works - [X:N] is first atom which is exploited
   for (let i = 0; i < totalLength - 1; i ++) {
-    monomers[i] = monomers[i].replace('    0.0000    0.0000    0.0000 C   ', '    0.0000    0.0000    0.0000 R#  ')
-      .replace('M  RGP  2', 'M  RGP  3   2   3');
+    if (monomers[i]) {
+      monomers[i] = monomers[i]!.replace('    0.0000    0.0000    0.0000 C   ', '    0.0000    0.0000    0.0000 R#  ')
+        .replace('M  RGP  2', 'M  RGP  3   2   3');
+    }
   }
-  monomers[totalLength - 1] = modProduct(monomers[totalLength - 1]);
+  monomers[totalLength - 1] = modProduct(monomers[totalLength - 1]!);
 
   for (let i = 0; i < totalLength; i ++) {
     const isProduct = i == totalLength - 1 ? true : false;
+    if (!monomers[i] || !monomerNames[i])
+      continue;
     const resMonomer: Monomer = {
-      [REQ.SYMBOL]: monomerNames[i],
-      [REQ.NAME]: monomerNames[i],
-      [REQ.MOLFILE]: monomers[i],
+      [REQ.SYMBOL]: monomerNames[i]!,
+      [REQ.NAME]: monomerNames[i]!,
+      [REQ.MOLFILE]: monomers[i]!,
       [REQ.AUTHOR]: '',
       [REQ.ID]: 0,
       [REQ.RGROUPS]: getNewGroups(isProduct),

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'}
       ]
     }
   };

package/src/tests/polytool-enumerate-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

package/src/tests/toAtomicLevel-tests.ts

@@ -1,15 +1,16 @@
+/* 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, delay} from '@datagrok-libraries/utils/src/test';
-import {Monomer, MonomerLibData} from '@datagrok-libraries/bio/src/types/index';
+import {Monomer, MonomerLibData} from '@datagrok-libraries/bio/src/types/monomer-library';
 
 import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
 import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
@@ -79,9 +80,8 @@ category('toAtomicLevel', () => {
     const reactionRule = rules.reactionRules.find((r) => r.name == 'GGaz')!;
 
     const [newSymbols, newMonomers] = getNewMonomers(rdKitModule, systemMonomerLib, reactionRule);
-    expect(newSymbols[0], 'azG_GGaz');
-
-    const mol = rdKitModule.get_mol(newMonomers[0].molfile);
+    expect(newSymbols?.[0], 'azG_GGaz');
+    const mol = rdKitModule.get_mol(newMonomers[0]!.molfile);
     try {
       const molInchi = mol.get_inchi();
       const molInchiKey = rdKitModule.get_inchikey_for_inchi(molInchi);

package/src/tests/utils/detect-macromolecule-utils.ts

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