@datagrok-libraries/bio 5.55.1 → 5.60.0

package/CHANGELOG.md

@@ -1,5 +1,10 @@
 # bio changelog
 
+## 5.60.0 (2025-10-28)
+
+* Monomer library management rework: Transition to library providers, instead of single file based monomer libraries. Support multiple library providers.
+* NB! BREAKING CHANGE to the monomer library management API. Update your code accordingly.
+
 ## 5.55.0 (2025-10-03)
 
 * Full BILN support: conversion to/from HELM/separator/fasta/molecular form, parsing, rendering, monomer library handling.

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.55.1",
+  "version": "5.60.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",
@@ -28,7 +28,7 @@
     "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",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",

package/src/helm/helm-helper.d.ts

@@ -3,7 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
 import type { Point, App, HelmType, IHelmEditorOptions } from './types';
 import { MonomersFuncs, HelmMol, IHelmWebEditor, HelmAtom } from './types';
-import { IMonomerLibBase } from '../types/index';
+import { IMonomerLibBase } from '../types/monomer-library';
 import { ISeqHelper } from '../utils/seq-helper';
 import { SeqValueBase } from '../utils/macromolecule/seq-handler';
 export type IHelmInputInitOptions = ui.input.IInputInitOptions<SeqValueBase> & {

package/src/helm/helm-helper.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"helm-helper.d.ts","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,KAAK,EAAC,KAAK,EAAE,GAAG,EAAE,QAAQ,EAAE,kBAAkB,EAAC,MAAM,SAAS,CAAC;AACtE,OAAO,EACW,aAAa,EAAE,OAAO,EAAc,cAAc,EAAE,QAAQ,EAC7E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAC,YAAY,EAAC,MAAM,oCAAoC,CAAC;AAEhE,MAAM,MAAM,qBAAqB,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,YAAY,CAAC,GAAG;IAC7E,aAAa,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC3C,QAAQ,EAAE,OAAO,CAAC;CACnB,CAAC;AAEF,8BAAsB,aAAc,SAAQ,EAAE,CAAC,WAAW,CAAC,YAAY,CAAC;IACtE,QAAQ,KAAK,QAAQ,IAAI,OAAO,CAAC;IACjC,QAAQ,KAAK,QAAQ,CAAC,KAAK,EAAE,OAAO,EAAE;IAEtC,QAAQ,KAAK,WAAW,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAEnD,QAAQ,KAAK,OAAO,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAE/C,QAAQ,CAAC,MAAM,IAAI,IAAI;IAEvB,QAAQ,CAAC,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,IAAI;CACvE;AAED;;GAEG;AACH,MAAM,MAAM,cAAc,GAAG;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC;CACxC,CAAA;AAED,eAAO,MAAM,yBAAyB,0BAA0B,CAAC;AAEjE,qBAAa,qBAAsB,SAAQ,KAAK;IAC9C,SAAgB,IAAI,2BAA6B;gBAErC,OAAO,CAAC,EAAE,MAAM;CAG7B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,SAAS,IAAI,UAAU,CAAC;IAE5B,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,aAAa,CAAC;IAE9E,mBAAmB,CAAC,IAAI,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE,OAAO,CAAC,kBAAkB,CAAC,GAAG,cAAc,CAAC;IAE/F,kBAAkB,CAAC,IAAI,EAAE,cAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC;IAE7D,IAAI,qBAAqB,IAAI,aAAa,GAAG,IAAI,CAAC;IAElD,yBAAyB,CAAC,UAAU,EAAE,eAAe,GAAG,aAAa,CAAC;IAEtE,qBAAqB,CAAC,aAAa,EAAE,aAAa,GAAG,aAAa,CAAC;IACnE,2BAA2B,IAAI,aAAa,CAAC;IAE7C,cAAc,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IAEpF,kDAAkD;IAClD,WAAW,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAAC;IAE7C,KAAK,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,KAAK,GAAG,OAAO,CAAC;IAC7C,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;CAC1C;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D;AAED,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAiB,KAAK,CAAC;QACrB;;WAEG;QACH,SAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;KAClG;CACF;AAOD,mBAAmB;AACnB,wBAAgB,oBAAoB,CAClC,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,IAAI,CAAC,EAAE,MAAM,GACpC,EAAC,cAAc,AAAd,cAAc,CAAC,QAAQ,EAAE,WAAW,CAAC,MAAM,CAAC,CAc/C"}

package/src/monomer-works/monomer-hover.d.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import { IMonomerLibBase } from '../types/index';
+import { IMonomerLibBase } from '../types/monomer-library';
 import { ISeqMonomer } from '../helm/types';
 import { MonomerHoverLink } from './utils';
 import { ISeqHelper } from '../utils/seq-helper';

package/src/monomer-works/monomer-hover.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-hover.d.ts","sourceRoot":"","sources":["monomer-hover.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAIrE,OAAO,EAAC,eAAe,EAAC,MAAM,gBAAgB,CAAC;AAC/C,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAK1C,OAAO,EAAC,gBAAgB,EAAC,MAAM,SAAS,CAAC;AAGzC,OAAO,EAA0B,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAExE,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AAEzD,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,GAAG,EAAE,OAAO,EAAE,gBAAgB,QAM7E;AAED;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EACpD,UAAU,EAAE,eAAe,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,EAAE,UAAU,GAAE,OAAe,GACrG,OAAO,CAAC,gBAAgB,CAAC,CAyH3B;AAED,wBAAgB,qBAAqB,CACnC,WAAW,EAAE,EAAE,CAAC,QAAQ,EAAE,UAAU,EAAE,WAAW,GAAG,IAAI,GACvD,IAAI,CAkBN;AAED,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,gBAAgB,EAAE,CAElF"}
+{"version":3,"file":"monomer-hover.d.ts","sourceRoot":"","sources":["monomer-hover.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAIrE,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAK1C,OAAO,EAAC,gBAAgB,EAAC,MAAM,SAAS,CAAC;AAGzC,OAAO,EAA0B,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAExE,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AAEzD,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,GAAG,EAAE,OAAO,EAAE,gBAAgB,QAM7E;AAED;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EACpD,UAAU,EAAE,eAAe,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,EAAE,UAAU,GAAE,OAAe,GACrG,OAAO,CAAC,gBAAgB,CAAC,CAyH3B;AAED,wBAAgB,qBAAqB,CACnC,WAAW,EAAE,EAAE,CAAC,QAAQ,EAAE,UAAU,EAAE,WAAW,GAAG,IAAI,GACvD,IAAI,CAkBN;AAED,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,gBAAgB,EAAE,CAElF"}

package/src/monomer-works/monomer-utils.d.ts

@@ -1,6 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import { Observable } from 'rxjs';
-import { IMonomerLib, IMonomerSet } from '../types/index';
 import { ISeqSplitted } from '../utils/macromolecule/types';
 import { ISeqHelper } from '../utils/seq-helper';
 export declare function encodeMonomers(col: DG.Column, seqHelper: ISeqHelper): DG.Column | null;
@@ -10,47 +8,6 @@ export declare function createMomomersMolDict(lib: any[]): {
     [key: string]: string | any;
 };
 export declare function createJsonMonomerLibFromSdf(table: DG.DataFrame): any;
-export interface IMonomerLibFileEventManager {
-    get addLibraryFileRequested$(): Observable<void>;
-    get updateUIControlsRequested$(): Observable<string[]>;
-    get librarySelectionRequested$(): Observable<[string, boolean]>;
-    updateLibrarySelectionStatus(libFileName: string, isSelected: boolean): void;
-}
-export interface IMonomerLibFileManager {
-    get eventManager(): IMonomerLibFileEventManager;
-    getValidLibraryPaths(): string[];
-    getValidLibraryPathsAsynchronously(): Promise<string[]>;
-    addLibraryFile(fileContent: string, fileName: string): Promise<void>;
-    deleteLibraryFile(fileName: string): Promise<void>;
-    loadLibraryFromFile(path: string, fileName: string): Promise<IMonomerLib>;
-}
-export interface IMonomerLibHelper {
-    get eventManager(): IMonomerLibFileEventManager;
-    /** Ensures files are loaded and validated, throws error after timeout */
-    awaitLoaded(timeout?: number): Promise<void>;
-    /** Singleton monomer library collected from various sources */
-    getMonomerLib(): IMonomerLib;
-    /**  @deprecated Use {@link getMonomerLib} */
-    getBioLib(): IMonomerLib;
-    /** Singleton monomer set collected from various sources */
-    getMonomerSets(): IMonomerSet;
-    getFileManager(): Promise<IMonomerLibFileManager>;
-    /** (Re)Loads libraries based on settings in user storage {@link LIB_STORAGE_NAME} to singleton.
-     * @param {boolean} reload Clean {@link monomerLib} before load libraries [false]
-     */
-    loadMonomerLib(reload?: boolean): Promise<void>;
-    /** @deprecated Use {@link loadMonomerLib} */
-    loadLibraries(reload?: boolean): Promise<void>;
-    /** (Re)loads monomer sets based on settings in user storage {@link SETS_STORAGE_NAME} to singleton.
-     * @param {boolean} reload Clean {@link monomerSets} before load sets [false]
-     */
-    loadMonomerSets(reload?: boolean): Promise<void>;
-    /** Reads library from file shares, handles .json and .sdf */
-    readLibrary(path: string, fileName: string): Promise<IMonomerLib>;
-    /** Changes user lib settings. */
-    loadMonomerLibForTests(): Promise<void>;
-}
-export declare function getMonomerLibHelper(): Promise<IMonomerLibHelper>;
 /** Calculates chemical similarity between reference sequence and list of sequences.
  * Similarity is computed as a sum of monomer similarities on corresponding positions. Monomer similarity is calculated
  * based on Morgan fingerprints.

package/src/monomer-works/monomer-utils.d.ts.map

@@ -1 +1 @@
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package/src/monomer-works/monomer-utils.js

@@ -5,6 +5,7 @@ import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-
 import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, } from '../utils/const';
 import { splitAlignedSequences } from '../utils/splitter';
 import { GAP_SYMBOL } from '../utils/macromolecule/consts';
+import { getMonomerLibHelper } from '../types/monomer-library';
 export function encodeMonomers(col, seqHelper) {
     let encodeSymbol = MONOMER_ENCODE_MIN;
     const monomerSymbolDict = {};
@@ -124,13 +125,6 @@ export function createJsonMonomerLibFromSdf(table) {
     }
     return resultLib;
 }
-export async function getMonomerLibHelper() {
-    const funcList = DG.Func.find({ package: 'Bio', name: 'getMonomerLibHelper' });
-    if (funcList.length === 0)
-        throw new Error('Package "Bio" must be installed for MonomerLibHelper.');
-    const res = (await funcList[0].prepare().call()).getOutputParamValue();
-    return res;
-}
 export async function sequenceChemSimilarity(positionColumns, referenceSequence, seqHelper) {
     /* eslint-enable max-len */
     if (positionColumns instanceof DG.Column)
@@ -160,12 +154,11 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence,
         const similarityColData = similarityCol ? similarityCol.getRawData() : null;
         for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
             const monomerCategoryIdx = monomerColData[rowIdx];
-            if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx) {
+            if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx)
                 totalSimilarity[rowIdx] += similarityColData[monomerCategoryIdx];
-            }
-            else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx) {
+            else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx)
                 totalSimilarity[rowIdx] += 1;
-            } // Do not increase similarity on mismatch score/penalty equals 0;
+            // Do not increase similarity on mismatch score/penalty equals 0;
         }
     }
     for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {
@@ -212,7 +205,9 @@ export async function getMonomerSubstitutionMatrix(monomerSet, fingerprintType =
     const scoringMatrix = new Array(monomerSet.length).fill(0).map(() => new Array(monomerSet.length).fill(0));
     const alphabetIndexes = {};
     // note, below specifically boolean OR is used to get either molfile or smiles, because we want to skip '' molfiles
-    const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.molfile || monomerLib.getMonomer('PEPTIDE', monomer)?.smiles || '');
+    const monomerMolecules = monomerSet
+        .map((monomer) => monomerLib
+        .getMonomer('PEPTIDE', monomer)?.molfile || monomerLib.getMonomer('PEPTIDE', monomer)?.smiles || '');
     const fingerprintsFunc = DG.Func.find({ package: 'Chem', name: 'getFingerprints' })[0];
     if (!fingerprintsFunc) {
         console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints');

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package/src/monomer-works/monomer-works.d.ts

@@ -1,4 +1,4 @@
-import { IMonomerLibBase } from '../types';
+import { IMonomerLibBase } from '../types/monomer-library';
 import { HelmType, PolymerType } from '../helm/types';
 /** Hypothetical interface to convert mol block notation.
  * It should be placed in the chem-meta package, and have an implementation in the Chem package.

package/src/monomer-works/monomer-works.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-works.d.ts","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,eAAe,EAAC,MAAM,UAAU,CAAC;AACzC,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAGpD;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;IAEzC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;CAC1C;AAED,qBAAa,YAAY;IACvB,OAAO,CAAC,UAAU,CAAkB;gBAIxB,UAAU,EAAE,eAAe;IAMhC,uBAAuB,CAAC,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;CAQ7F;AAED,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,GAAG,WAAW,CAyBrE"}
+{"version":3,"file":"monomer-works.d.ts","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAGpD;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;IAEzC,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;CAC1C;AAED,qBAAa,YAAY;IACvB,OAAO,CAAC,UAAU,CAAkB;gBAIxB,UAAU,EAAE,eAAe;IAMhC,uBAAuB,CAAC,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;CAQ7F;AAED,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,GAAG,WAAW,CAyBrE"}

package/src/monomer-works/seq-to-molfile.d.ts

@@ -3,7 +3,7 @@ import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import { ALPHABET } from '../utils/macromolecule';
 import { MonomerMap, MonomerMapValue, MonomerMolGraphMap } from './types';
 import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
-import { IMonomerLib, IMonomerLibBase } from '../types';
+import { IMonomerLib, IMonomerLibBase } from '../types/monomer-library';
 import { PolymerType } from '../helm/types';
 import { ISubstruct } from '@datagrok-libraries/chem-meta/src/types';
 export type SeqToMolfileResult = {

package/src/monomer-works/seq-to-molfile.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"seq-to-molfile.d.ts","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAGrE,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EACqB,UAAU,EAAE,eAAe,EAAE,kBAAkB,EAC1E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,UAAU,EAAE,gBAAgB,EAAC,MAAM,qBAAqB,CAAC;AAEjE,OAAO,EAAC,WAAW,EAAE,eAAe,EAAC,MAAM,UAAU,CAAC;AACtD,OAAO,EAAc,WAAW,EAAC,MAAM,eAAe,CAAC;AAEvD,OAAO,EAAC,UAAU,EAAC,MAAM,yCAAyC,CAAC;AAGnE,MAAM,MAAM,kBAAkB,GAAG;IAC/B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM,CAAC;QAChB,QAAQ,EAAE,UAAU,CAAA;KACrB,EAAE,CAAC;IACJ,QAAQ,EAAE,MAAM,EAAE,CAAA;CACnB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,kBAAkB,EAClG,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,UAAU,EAAE,WAAW,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,GACpE,OAAO,CAAC,gBAAgB,CAAC,CAoD3B;AAED,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,EAAE,UAAU,EAAE,eAAe,GAAG,UAAU,CAsB/G"}
+{"version":3,"file":"seq-to-molfile.d.ts","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAGrE,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EACqB,UAAU,EAAE,eAAe,EAAE,kBAAkB,EAE1E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,UAAU,EAAE,gBAAgB,EAAC,MAAM,qBAAqB,CAAC;AAEjE,OAAO,EAAC,WAAW,EAAE,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACtE,OAAO,EAAc,WAAW,EAAC,MAAM,eAAe,CAAC;AAEvD,OAAO,EAAC,UAAU,EAAC,MAAM,yCAAyC,CAAC;AAGnE,MAAM,MAAM,kBAAkB,GAAG;IAC/B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM,CAAC;QAChB,QAAQ,EAAE,UAAU,CAAA;KACrB,EAAE,CAAC;IACJ,QAAQ,EAAE,MAAM,EAAE,CAAA;CACnB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,kBAAkB,EAClG,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,UAAU,EAAE,WAAW,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,GACpE,OAAO,CAAC,gBAAgB,CAAC,CAsD3B;AAED,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,EAAE,UAAU,EAAE,eAAe,GAAG,UAAU,CAuB/G"}

package/src/monomer-works/seq-to-molfile.js

@@ -15,7 +15,9 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
     const seqList = wu.count(0).take(seqCol.length).map((rowIdx) => {
         const seqSS = seqSH.getSplitted(rowIdx);
         return wu.count(0).take(seqSS.length)
-            .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
+            .map((posIdx) => {
+            return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype };
+        })
             .toArray();
     }).toArray();
     for (let i = 0; i < threadCount; i++) {
@@ -57,13 +59,14 @@ export function getMolHighlight(monomerMaps, monomerLib) {
     for (const monomerMapValue of monomerMaps) {
         const wem = monomerLib.getWebEditorMonomer(monomerMapValue.biotype, monomerMapValue.symbol);
         const mColorStr = wem.backgroundcolor;
+        // eslint-disable-next-line deprecation/deprecation
         const mColorA = hexToPercentRgb(mColorStr ?? DG.Color.toRgb(DG.Color.mouseOverRows)) ?? [1.0, 0.0, 0.0, 0.7];
         for (const mAtom of monomerMapValue.atoms)
             hlAtoms[mAtom] = mColorA;
         for (const mBond of monomerMapValue.bonds)
             hlBonds[mBond] = mColorA;
     }
-    let resSubstruct = {
+    const resSubstruct = {
         atoms: Object.keys(hlAtoms).map((k) => parseInt(k)),
         bonds: Object.keys(hlBonds).map((k) => parseInt(k)),
         highlightAtomColors: hlAtoms,

package/src/monomer-works/seq-to-molfile.js.map

@@ -1 +1 @@
-{"version":3,"file":"seq-to-molfile.js","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAUpB,OAAO,EAAC,aAAa,EAAE,eAAe,EAAC,MAAM,SAAS,CAAC;AAGvD,OAAO,EAAC,SAAS,EAAe,MAAM,gBAAgB,CAAC;AAYvD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,MAAyB,EAAE,YAAgC,EAClG,QAAkB,EAAE,WAAwB,EAC5C,UAAuB,EAAE,SAAqB,EAAE,WAAqB;IAErE,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC;IACnC,MAAM,EAAE,GAA6B,MAAM,CAAC,SAAS,CAAC;IACtD,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,mBAAmB,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;IACnE,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;SAC9C,GAAG,CAAC,GAAG,EAAE,CAAC,IAAI,MAAM,CAAC,IAAI,GAAG,CAAC,yBAAyB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAC9E,MAAM,SAAS,GAAG,YAAY,GAAG,WAAW,CAAC;IAC7C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAiC,WAAW,CAAC,CAAC;IACxE,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,OAAO,GAAG,WAAW,gCAAoB,CAAC,CAAC,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;IACtF,MAAM,OAAO,GAAoB,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;QAC9E,MAAM,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QACxC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC;aAClC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,GAAG,OAAO,EAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,OAAO,EAAgB,CAAC,CAAC,CAAC,CAAC;aACpH,OAAO,EAAE,CAAC;IACf,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC;QACxC,MAAM,GAAG,GAAG,CAAC,CAAC,KAAK,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC;QACrF,QAAQ,CAAC,CAAC,CAAC,GAAG,IAAI,OAAO,CAAwB,CAAC,OAAO,EAAE,EAAE;YAC3D,MAAM,CAAC,SAAS,GAAG,CAAC,GAAoC,EAAQ,EAAE;gBAChE,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;YACpB,CAAC,CAAC;QACJ,CAAC,CAAC,CAAC;QACH,MAAM,CAAC,WAAW,CAAC,EAAC,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAA2B,CAAC,CAAC;IAC3G,CAAC;IAED,MAAM,OAAO,GAAqB,EAAE,CAAC;IACrC,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,MAAM,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,QAAiC,EAAE,EAAE;QACrE,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;YAC/B,OAAO,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAClC,QAAQ,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QACrC,CAAC;IACH,CAAC,CAAC,CAAC;IAEH,+GAA+G;IAE/G,UAAU,CAAC,GAAG,EAAE;QACd,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,EAAE;YACzB,MAAM,CAAC,SAAS,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC,EAAE,CAAC,CAAC,CAAC;IACN,MAAM,UAAU,GAAG,aAAa,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC;IAClD,MAAM,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC;SAChF,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,CAAC;IAC9C,MAAM,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC;IACrC,MAAM,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC;IAC/C,MAAM,CAAC,MAAM,sDAA4B,MAAM,CAAC,IAAI,CAAC,CAAC;IAEtD,OAAO,EAAC,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAC,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,WAAsC,EAAE,UAA2B;IACjG,MAAM,OAAO,GAAgC,EAAE,CAAC;IAChD,MAAM,OAAO,GAAgC,EAAE,CAAC;IAEhD,KAAK,MAAM,eAAe,IAAI,WAAW,EAAE,CAAC;QAC1C,MAAM,GAAG,GAAG,UAAU,CAAC,mBAAmB,CAAC,eAAe,CAAC,OAAO,EAAE,eAAe,CAAC,MAAM,CAAE,CAAC;QAC7F,MAAM,SAAS,GAAG,GAAG,CAAC,eAAe,CAAC;QACtC,MAAM,OAAO,GAAG,eAAe,CAAC,SAAS,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;QAC7G,KAAK,MAAM,KAAK,IAAI,eAAe,CAAC,KAAK;YACvC,OAAO,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;QAC3B,KAAK,MAAM,KAAK,IAAI,eAAe,CAAC,KAAK;YACvC,OAAO,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;IAC7B,CAAC;IAED,IAAI,YAAY,GAAe;QAC7B,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnD,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnD,mBAAmB,EAAE,OAAO;QAC5B,mBAAmB,EAAE,OAAO;KAC7B,CAAC;IAEF,OAAO,YAAY,CAAC;AACtB,CAAC"}
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package/src/monomer-works/to-atomic-level-utils.d.ts

@@ -1,6 +1,6 @@
 import { MolfileWithMap, MonomerMolGraphMap } from './types';
 import { ALPHABET } from '../utils/macromolecule/consts';
-import { IMonomerLibBase } from '../types';
+import { IMonomerLibBase } from '../types/monomer-library';
 import { ISeqMonomer, PolymerType } from '../helm/types';
 /** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.
  * @param {IMonomerLib} monomerLib - Monomer library

package/src/monomer-works/to-atomic-level-utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAEA,OAAO,EAA4C,cAAc,EAAwB,kBAAkB,EAAC,MAAM,SAAS,CAAC;AAE5H,OAAO,EAAC,QAAQ,EAAa,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAC,eAAe,EAAU,MAAM,UAAU,CAAC;AAClD,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAIvD;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,GACxE,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAsBlB;AAED;;;;;qCAKqC;AACrC,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,WAAW,EAAE,EAAE,YAAY,EAAE,kBAAkB,EAC3D,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAC3C,cAAc,CAyGhB;AAqQD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}
+{"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAEA,OAAO,EAA4C,cAAc,EAAwB,kBAAkB,EAAC,MAAM,SAAS,CAAC;AAE5H,OAAO,EAAC,QAAQ,EAAa,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAC,eAAe,EAAU,MAAM,0BAA0B,CAAC;AAClE,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAIvD;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,GACxE,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAsBlB;AAED;;;;;qCAKqC;AACrC,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,WAAW,EAAE,EAAE,YAAY,EAAE,kBAAkB,EAC3D,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,GAC3C,cAAc,CAyGhB;AAqQD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}

package/src/monomer-works/to-atomic-level.d.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import { ALPHABET } from '../utils/macromolecule/consts';
-import { IMonomerLib, IMonomerLibBase, Monomer } from '../types';
+import { IMonomerLib, IMonomerLibBase, Monomer } from '../types/monomer-library';
 import { Bonds, MolGraph, MonomerMolGraphMap } from './types';
 import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
 import { ISeqMonomer, PolymerType } from '../helm/types';

package/src/monomer-works/to-atomic-level.d.ts.map

@@ -1 +1 @@
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package/src/monomer-works/utils.js

@@ -15,9 +15,8 @@ export function alphabetToPolymerType(alphabet) {
         resPolymerType = "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */;
     else if (alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA)
         resPolymerType = "RNA" /* HELM_POLYMER_TYPE.RNA */;
-    else {
+    else
         throw new Error(`Unexpected alphabet '${alphabet}'.`);
-    }
     return resPolymerType;
 }
 /** @deprecated Use DG.Color.hexToPercentRgb */

package/src/monomer-works/utils.js.map

@@ -1 +1 @@
-{"version":3,"file":"utils.js","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAYA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAShD,MAAM,UAAU,gBAAgB,CAAC,EAA4B,EAAE,OAAe;IAC5E,IAAI,CAAC,EAAE;QAAE,OAAO,OAAO,CAAC;IACxB,OAAO,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;AAC3C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,EAA4B,EAAE,UAAkB;IAC5E,OAAO,gBAAgB,CAAC,EAAE,EAAE,WAAW,UAAU,GAAG,CAAC,CAAC;AACxD,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,8DAA8D;IAC9D,IAAI,cAAiC,CAAC;IACtC,6EAA6E;IAC7E,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE;QACtD,cAAc,4CAA4B,CAAC;SACxC,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG;QAC7D,cAAc,oCAAwB,CAAC;SACpC,CAAC;QACJ,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,IAAI,CAAC,CAAC;IACxD,CAAC;IACD,OAAO,cAAc,CAAC;AACxB,CAAC;AAED,+CAA+C;AAC/C,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QACvF,uDAAuD,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACpE,OAAO,MAAM,CAAC,CAAC,CAAC;QACd,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG;KACxD,CAAC,CAAC,CAAC,IAAI,CAAC;AACX,CAAC"}
+{"version":3,"file":"utils.js","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAYA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAShD,MAAM,UAAU,gBAAgB,CAAC,EAA4B,EAAE,OAAe;IAC5E,IAAI,CAAC,EAAE;QAAE,OAAO,OAAO,CAAC;IACxB,OAAO,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;AAC3C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,EAA4B,EAAE,UAAkB;IAC5E,OAAO,gBAAgB,CAAC,EAAE,EAAE,WAAW,UAAU,GAAG,CAAC,CAAC;AACxD,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,8DAA8D;IAC9D,IAAI,cAAiC,CAAC;IACtC,6EAA6E;IAC7E,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE;QACtD,cAAc,4CAA4B,CAAC;SACxC,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG;QAC7D,cAAc,oCAAwB,CAAC;;QAEvC,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,IAAI,CAAC,CAAC;IAExD,OAAO,cAAc,CAAC;AACxB,CAAC;AAED,+CAA+C;AAC/C,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QACvF,uDAAuD,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACpE,OAAO,MAAM,CAAC,CAAC,CAAC;QACd,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG;KACxD,CAAC,CAAC,CAAC,IAAI,CAAC;AACX,CAAC"}

package/src/tests/monomer-lib-tests.d.ts

@@ -1,4 +1,4 @@
-import { IMonomerLib } from '../types/index';
+import { IMonomerLib } from '../types/monomer-library';
 export declare function expectMonomerLib(lib: IMonomerLib, summary: {
     [polymerType: string]: number;
 }): void;

package/src/tests/monomer-lib-tests.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-lib-tests.d.ts","sourceRoot":"","sources":["monomer-lib-tests.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,WAAW,EAAwB,MAAM,gBAAgB,CAAC;AAElE,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,EAAE;IAAE,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,GAAG,IAAI,CAqBnG"}
+{"version":3,"file":"monomer-lib-tests.d.ts","sourceRoot":"","sources":["monomer-lib-tests.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,WAAW,EAAwB,MAAM,0BAA0B,CAAC;AAE5E,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,EAAE;IAAE,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,GAAG,IAAI,CAqBnG"}

package/src/types/index.d.ts

@@ -1,95 +1,2 @@
-import * as DG from 'datagrok-api/dg';
-import { Observable } from 'rxjs';
-import { HelmAtom } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-import { HelmType, IMonomerColors, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
-import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT } from '../utils/const';
-export type RGroup = {
-    [RGP.CAP_GROUP_SMILES]: string;
-    [RGP.ALTERNATE_ID]: string;
-    [RGP.CAP_GROUP_NAME]: string;
-    [RGP.LABEL]: string;
-};
-/** https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
-export type Monomer = {
-    [REQ.SYMBOL]: string;
-    [REQ.NAME]: string;
-    [REQ.MOLFILE]: string;
-    [REQ.AUTHOR]: string;
-    [REQ.ID]: number;
-    [REQ.RGROUPS]: RGroup[];
-    [REQ.SMILES]: string;
-    [REQ.POLYMER_TYPE]: PolymerType;
-    [REQ.MONOMER_TYPE]: MonomerType;
-    [REQ.CREATE_DATE]: string | null;
-    [OPT.NATURAL_ANALOG]?: string;
-    [OPT.META]?: {
-        [property: string]: any;
-    };
-    lib?: IMonomerLibBase;
-    wem?: IWebEditorMonomer;
-};
-export interface IMonomerLinkData {
-    source: string;
-    symbol: string;
-    notes: string;
-}
-export interface IMonomerLink {
-    get lib(): IMonomerLib;
-    get symbol(): string;
-}
-export interface IMonomerSetPlaceholder {
-    get symbol(): string;
-    get polymerType(): PolymerType;
-    get monomerType(): MonomerType;
-    get monomerLinks(): IMonomerLinkData[];
-    get monomers(): Monomer[];
-}
-export interface IMonomerSet {
-    get source(): string | undefined;
-    get error(): string | undefined;
-    get description(): string;
-    get placeholders(): IMonomerSetPlaceholder[];
-}
-export type MonomerLibSummaryType = {
-    [polymerType: string]: number;
-};
-export type MonomerLibData = {
-    [polymerType: string]: {
-        [symbol: string]: Monomer;
-    };
-};
-export interface IMonomerLibBase {
-    get source(): string;
-    get isEmpty(): boolean;
-    get onChanged(): Observable<any>;
-    getMonomerSymbolsByType(polymerType: PolymerType): string[];
-    addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
-    getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
-    /** HELMWebEditor expects null for HelmTypes.LINKER and R-Group count != 2 */
-    getWebEditorMonomer(a: HelmAtom | HelmType, symbol?: string): IWebEditorMonomer | null;
-    getRS(smiles: string): {
-        [r: string]: string;
-    };
-    getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
-    getMonomerColors(biotype: HelmType, symbol: string): IMonomerColors;
-    getMonomerTextColor(biotype: HelmType, symbol: string): string;
-}
-export interface IMonomerLib extends IMonomerLibBase {
-    get error(): string | undefined;
-    getMonomerMolsByPolymerType(polymerType: PolymerType): {
-        [monomerSymbol: string]: string;
-    } | null;
-    getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: PolymerType, element?: string): string[];
-    getPolymerTypes(): PolymerType[];
-    toJSON(): Monomer[];
-    /** Summary string with lib monomer count by type
-     * @deprecated Keep for backward compatibility */
-    getSummary(): string;
-    /** Summary with lib monomer count by type */
-    getSummaryObj(): MonomerLibSummaryType;
-    /** Gets dataframe with columns 'polymerType', 'count'. */
-    getSummaryDf(): DG.DataFrame;
-    getMonomerSet(biotype: HelmType): MonomerSetType | null;
-    override(overrideData: MonomerLibData, source: string): IMonomerLibBase;
-}
+export * from './monomer-library';
 //# sourceMappingURL=index.d.ts.map

package/src/types/index.d.ts.map

@@ -1 +1 @@
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package/src/types/index.js

@@ -1,2 +1,2 @@
-export {};
+export * from './monomer-library';
 //# sourceMappingURL=index.js.map

package/src/types/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAAA,cAAc,mBAAmB,CAAC"}

package/src/types/input.d.ts.map

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package/src/types/input.js.map

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