@datagrok-libraries/bio 5.44.4 → 5.45.0

package/CHANGELOG.md

@@ -1,5 +1,14 @@
 # bio changelog
 
+## 5.44.5 (2024-10-03)
+
+### Bug fixes
+
+* Fix MonomerPlacer to use IMonomerLibBase.getMonomerTextColor
+* Fix MonomerPlacer for changed column settings
+* Fix MonomerPlacer for original monomer symbol
+* Fix SeqHandler .isSeparator to account column tag
+
 ## 5.44.4 (2024-10-02)
 
 ### New features

package/package.json

@@ -8,13 +8,13 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.44.4",
+  "version": "5.45.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/gridext": "^1.3.71",
-    "@datagrok-libraries/ml": "^6.7.1",
-    "@datagrok-libraries/utils": "^4.3.4",
+    "@datagrok-libraries/gridext": "^1.3.73",
+    "@datagrok-libraries/ml": "^6.7.4",
+    "@datagrok-libraries/utils": "^4.3.6",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
     "datagrok-api": "^1.21.1",
@@ -28,8 +28,8 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.11",
-    "@datagrok-libraries/js-draw-lite": "^0.0.8",
+    "@datagrok-libraries/helm-web-editor": "^1.1.12",
+    "@datagrok-libraries/js-draw-lite": "^0.0.9",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",

package/src/helm/consts.d.ts

@@ -1,4 +1,4 @@
 import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
-import { MonomerNumberingTypes } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-export { HelmTypes, MonomerTypes, PolymerTypes, MonomerNumberingTypes };
+import { HelmTabKeys, MonomerNumberingTypes } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+export { HelmTypes, MonomerTypes, PolymerTypes, MonomerNumberingTypes, HelmTabKeys };
 //# sourceMappingURL=consts.d.ts.map

package/src/helm/consts.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,MAAM,gDAAgD,CAAC;AACrG,OAAO,EAAC,WAAW,EAAE,qBAAqB,EAAC,MAAM,wDAAwD,CAAC;AAE1G,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAE,qBAAqB,EAAE,WAAW,EAAC,CAAC"}

package/src/helm/consts.js.map

@@ -1 +1 @@
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+{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,SAAS,EAA6B,MAAM,gDAAgD,CAAC;AAGrG,OAAO,EAAC,SAAS,EAAiE,CAAC"}

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

@@ -1,9 +1,9 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
-import type { Point, App, HelmType } from './types';
-import { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor, HelmAtom, IHelmDrawOptions } from './types';
-import { IMonomerLib } from '../types/index';
+import type { Point, App, HelmType, IHelmEditorOptions } from './types';
+import { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor, HelmAtom } from './types';
+import { IMonomerLibBase } from '../types/index';
 export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol> & {
     editable: boolean;
 };
@@ -30,10 +30,10 @@ export declare class HelmNotSupportedError extends Error {
 }
 export interface IHelmHelper {
     createHelmInput(name: string, options?: IHelmInputInitOptions): HelmInputBase;
-    createHelmWebEditor(host?: HTMLElement, drawOptions?: Partial<IHelmDrawOptions>): IHelmWebEditor;
+    createHelmWebEditor(host?: HTMLElement, options?: Partial<IHelmEditorOptions>): IHelmWebEditor;
     createWebEditorApp(host: HTMLDivElement, helm?: string): App;
     get originalMonomersFuncs(): MonomersFuncs | null;
-    buildMonomersFuncsFromLib(monomerLib: IMonomerLib): MonomersFuncs;
+    buildMonomersFuncsFromLib(monomerLib: IMonomerLibBase): MonomersFuncs;
     overrideMonomersFuncs(monomersFuncs: MonomersFuncs): MonomersFuncs;
     revertOriginalMonomersFuncs(): MonomersFuncs;
     getHoveredAtom(x: number, y: number, mol: HelmMol, height: number): HelmAtom | null;

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,EAAE,UAAU,EAAE,cAAc,EAAE,QAAQ,EAC7E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,eAAe,EAAC,MAAM,gBAAgB,CAAC;AAE/C,MAAM,MAAM,qBAAqB,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,UAAU,GAAG,OAAO,CAAC,GAAG;IACrF,QAAQ,EAAE,OAAO,CAAC;CACnB,CAAC;AAEF,8BAAsB,aAAc,SAAQ,EAAE,CAAC,WAAW,CAAC,UAAU,CAAC;IACpE,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,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/helm/types.d.ts

@@ -1,11 +1,12 @@
-import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups, IMonomerColors, MonomerSetType } from '@datagrok-libraries/js-draw-lite/src/types/org';
+import type { HelmType, PolymerType, MonomerType, WebEditorRGroups, MonomerSetType } from '@datagrok-libraries/js-draw-lite/src/types/org';
 import type { Point } from '@datagrok-libraries/js-draw-lite/src/Point';
 import type { Atom } from '@datagrok-libraries/js-draw-lite/src/Atom';
 import type { IJsAtom } from '@datagrok-libraries/js-draw-lite/src/types/jsdraw2';
 import type { Bond } from '@datagrok-libraries/js-draw-lite/src/Bond';
 import type { Mol } from '@datagrok-libraries/js-draw-lite/src/Mol';
+import type { IMolHandler } from '@datagrok-libraries/js-draw-lite/src/types/mol-handler';
 import type { Editor } from '@datagrok-libraries/js-draw-lite/src/JSDraw.Editor';
-import type { HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs, IHelmDrawOptions } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+import type { HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs, IHelmEditorOptions, IHelmDrawOptions, IMonomerColors, IWebEditorMonomer } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 import type { HweWindow } from '@datagrok-libraries/helm-web-editor/src/types';
 import type { MonomerExplorer } from '@datagrok-libraries/helm-web-editor/helm/MonomerExplorer';
 import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
@@ -17,7 +18,7 @@ import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/t
 export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
 export { Point, Atom, IJsAtom, Bond, Mol, Editor, MonomerExplorer };
 export { HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString };
-export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, IHelmDrawOptions, App, Monomers, GetMonomerFunc, GetMonomerResType };
+export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, IMolHandler, IHelmEditorOptions, IHelmDrawOptions, GetMonomerFunc, GetMonomerResType, App, Monomers, };
 export { DojoType, DojoxType };
 export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
 export interface ISeqMonomer {

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

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

@@ -1,10 +1,11 @@
 import * as DG from 'datagrok-api/dg';
 import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import { IMonomerLib } from '../types/index';
+import { IMonomerLibBase } from '../types/index';
 import { ISeqMonomer } from '../helm/types';
 import { MonomerHoverLink } from './utils';
+import { ISeqHelper } from '../utils/seq-helper';
 export declare const MonomerHoverLinksTemp = "MonomerHoverLinks";
-export declare function buildMonomerHoverLink(seqCol: DG.Column<string>, molCol: DG.Column<string>, monomerLib: IMonomerLib, rdKitModule: RDModule): MonomerHoverLink;
+export declare function buildMonomerHoverLink(seqCol: DG.Column<string>, molCol: DG.Column<string>, monomerLib: IMonomerLibBase, seqHelper: ISeqHelper, rdKitModule: RDModule): MonomerHoverLink;
 export declare function execMonomerHoverLinks(seqGridCell: DG.GridCell, seqMonomer: ISeqMonomer | null): void;
 export declare function getMonomerHoverLinks(seqCol: DG.Column<string>): MonomerHoverLink[];
 //# sourceMappingURL=monomer-hover.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"monomer-hover.d.ts","sourceRoot":"","sources":["monomer-hover.ts"],"names":[],"mappings":"AACA,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,EAAkB,gBAAgB,EAAC,MAAM,SAAS,CAAC;AAG1D,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAE/C,eAAO,MAAM,qBAAqB,sBAAsB,CAAC;AAUzD,wBAAgB,qBAAqB,CACnC,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,GACxE,gBAAgB,CAkGlB;AAED,wBAAgB,qBAAqB,CACnC,WAAW,EAAE,EAAE,CAAC,QAAQ,EAAE,UAAU,EAAE,WAAW,GAAG,IAAI,GACvD,IAAI,CAcN;AAED,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,gBAAgB,EAAE,CAElF"}

package/src/monomer-works/monomer-hover.js

@@ -1,7 +1,6 @@
 import wu from 'wu';
 import { LRUCache } from 'lru-cache';
 import { addSubstructProvider, getMonomerHover, setMonomerHover } from '@datagrok-libraries/chem-meta/src/types';
-import { SeqHandler } from '../utils/seq-handler';
 import { ALPHABET } from '../utils/macromolecule';
 import { getMonomersDictFromLib } from './to-atomic-level';
 import { monomerSeqToMolfile } from './to-atomic-level-utils';
@@ -14,9 +13,9 @@ function addMonomerHoverLink(seqColTemp, resLink) {
     mhhList.push(resLink);
     seqColTemp[MonomerHoverLinksTemp] = mhhList;
 }
-export function buildMonomerHoverLink(seqCol, molCol, monomerLib, rdKitModule) {
+export function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelper, rdKitModule) {
     function buildMonomerMap(seqCol, tableRowIdx) {
-        const seqSH = SeqHandler.forColumn(seqCol);
+        const seqSH = seqHelper.getSeqHandler(seqCol);
         const seqSS = seqSH.getSplitted(tableRowIdx);
         const biotype = seqSH.defaultBiotype;
         const seqMList = wu.count(0).take(seqSS.length)
@@ -53,6 +52,7 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, rdKitModule) {
                 if (prev) {
                     setMonomerHover(null);
                     prev.gridCell.grid?.invalidate();
+                    // prev.gridCell.render();
                 }
                 if (!seqMonomer) {
                     setMonomerHover(null);
@@ -79,6 +79,7 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, rdKitModule) {
                 });
                 // TODO: Invalidate targetGridCell
                 grid.invalidate();
+                // targetGridCell.render();
             }
             return true;
         },

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

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

@@ -2,9 +2,10 @@ import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
 import { IMonomerLib, IMonomerSet } from '../types/index';
 import { ISeqSplitted } from '../utils/macromolecule/types';
-export declare function encodeMonomers(col: DG.Column): DG.Column | null;
-export declare function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): any[][] | null;
-export declare function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObject: any[]): any[][] | null;
+import { ISeqHelper } from '../utils/seq-helper';
+export declare function encodeMonomers(col: DG.Column, seqHelper: ISeqHelper): DG.Column | null;
+export declare function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[], seqHelper: ISeqHelper): any[][] | null;
+export declare function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObject: any[], seqHelper: ISeqHelper): any[][] | null;
 export declare function createMomomersMolDict(lib: any[]): {
     [key: string]: string | any;
 };
@@ -56,8 +57,8 @@ export declare function getMonomerLibHelper(): Promise<IMonomerLibHelper>;
  * @param {DG.Column<string>[]} positionColumns List of position columns containing monomers.
  * @param {string[]} referenceSequence Reference sequence.
  * @returns {Promise<DG.Column<number>>} Column with similarity values. */
-export declare function sequenceChemSimilarity(sequenceCol: DG.Column<string>, referenceSequence: ISeqSplitted): Promise<DG.Column<number>>;
-export declare function sequenceChemSimilarity(positionColumns: DG.Column<string>[], referenceSequence: ISeqSplitted): Promise<DG.Column<number>>;
+export declare function sequenceChemSimilarity(sequenceCol: DG.Column<string>, referenceSequence: ISeqSplitted, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
+export declare function sequenceChemSimilarity(positionColumns: DG.Column<string>[], referenceSequence: ISeqSplitted, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
 /** Calculates chemical similarity between each pair of monomers.
  * @param {string[]} monomerSet Set of unique monomers.
  * @returns {Promise<{scoringMatrix: number[][], alphabetIndexes: {[monomerId: string]: number}}>} Ojbect containing similarity scoring matrix and monomer to index mapping. */

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

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

@@ -3,19 +3,18 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
 import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, } from '../utils/const';
-import { SeqHandler } from '../utils/seq-handler';
 import { splitAlignedSequences } from '../utils/splitter';
 import { GAP_SYMBOL } from '../utils/macromolecule/consts';
-export function encodeMonomers(col) {
+export function encodeMonomers(col, seqHelper) {
     let encodeSymbol = MONOMER_ENCODE_MIN;
     const monomerSymbolDict = {};
-    const sh = SeqHandler.forColumn(col);
+    const sh = seqHelper.getSeqHandler(col);
     const encodedStringArray = [];
     const rowCount = col.length;
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         let encodedMonomerStr = '';
         const monomers = sh.getSplitted(rowIdx);
-        for (let posIdx = 0; posIdx < monomers.length; ++posIdx) {
+        for (let posIdx = 0; posIdx < rowCount; ++posIdx) {
             const cm = monomers.getCanonical(posIdx);
             if (!monomerSymbolDict[cm]) {
                 if (encodeSymbol > MONOMER_ENCODE_MAX) {
@@ -31,15 +30,15 @@ export function encodeMonomers(col) {
     }
     return DG.Column.fromStrings('encodedMolecules', encodedStringArray);
 }
-export function getMolfilesFromSeq(col, monomersLibObject) {
-    const sh = SeqHandler.forColumn(col);
+export function getMolfilesFromSeq(col, monomersLibObject, seqHelper) {
+    const sh = seqHelper.getSeqHandler(col);
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
     const rowCount = col.length;
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         const monomers = sh.getSplitted(rowIdx);
         const molFilesForSeq = [];
-        for (let j = 0; j < monomers.length; ++j) {
+        for (let j = 0; j < rowCount; ++j) {
             const cm = monomers.getCanonical(j);
             if (cm) {
                 if (!monomersDict[cm]) {
@@ -54,8 +53,8 @@ export function getMolfilesFromSeq(col, monomersLibObject) {
     }
     return molFiles;
 }
-export function getMolfilesFromSingleSeq(cell, monomersLibObject) {
-    const sh = SeqHandler.forColumn(cell.column);
+export function getMolfilesFromSingleSeq(cell, monomersLibObject, seqHelper) {
+    const sh = seqHelper.getSeqHandler(cell.column);
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
     const monomers = sh.getSplitted(cell.rowIndex);
@@ -132,10 +131,10 @@ export async function getMonomerLibHelper() {
     const res = (await funcList[0].prepare().call()).getOutputParamValue();
     return res;
 }
-export async function sequenceChemSimilarity(positionColumns, referenceSequence) {
+export async function sequenceChemSimilarity(positionColumns, referenceSequence, seqHelper) {
     /* eslint-enable max-len */
     if (positionColumns instanceof DG.Column)
-        positionColumns = splitAlignedSequences(positionColumns).columns.toList();
+        positionColumns = splitAlignedSequences(positionColumns, seqHelper).columns.toList();
     const libHelper = await getMonomerLibHelper();
     const monomerLib = libHelper.getMonomerLib();
     // const smilesCols: DG.Column<string>[] = new Array(monomerCols.length);

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

@@ -1 +1 @@
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package/src/monomer-works/seq-to-molfile.d.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import { ALPHABET } from '../utils/macromolecule';
 import { MonomerMap, MonomerMapValue, MonomerMolGraphMap } from './types';
-import { ToAtomicLevelRes } from '../utils/seq-helper';
+import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
 import { IMonomerLib, IMonomerLibBase } from '../types';
 import { PolymerType } from '../helm/types';
 import { ISubstruct } from '@datagrok-libraries/chem-meta/src/types';
@@ -13,6 +13,6 @@ export type SeqToMolfileResult = {
     }[];
     warnings: string[];
 };
-export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
+export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
 export declare function getMolHighlight(monomerMaps: Iterable<MonomerMapValue>, monomerLib: IMonomerLibBase): ISubstruct;
 //# sourceMappingURL=seq-to-molfile.d.ts.map

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,gBAAgB,EAAC,MAAM,qBAAqB,CAAC;AAGrD,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,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,GAC3F,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,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"}

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

@@ -1,9 +1,8 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { getMolColName, hexToPercentRgb } from './utils';
-import { SeqHandler } from '../utils/seq-handler';
 import { HelmTypes } from '../helm/consts';
-export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, rdKitModule) {
+export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule) {
     const srcColLength = seqCol.length;
     const df = seqCol.dataFrame;
     const threadCount = Math.max(navigator.hardwareConcurrency - 2, 1);
@@ -11,7 +10,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
         .map(() => new Worker(new URL('./seq-to-molfile-worker', import.meta.url)));
     const chunkSize = srcColLength / threadCount;
     const promises = new Array(threadCount);
-    const seqSH = SeqHandler.forColumn(seqCol);
+    const seqSH = seqHelper.getSeqHandler(seqCol);
     const biotype = polymerType == "RNA" /* PolymerTypes.RNA */ ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
     const seqList = wu.count(0).take(seqCol.length).map((rowIdx) => {
         const seqSS = seqSH.getSplitted(rowIdx);

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;AACvD,OAAO,EAAC,UAAU,EAAC,MAAM,sBAAsB,CAAC;AAGhD,OAAO,EAAC,SAAS,EAAe,MAAM,gBAAgB,CAAC;AAYvD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,MAAyB,EAAE,YAAgC,EAClG,QAAkB,EAAE,WAAwB,EAAE,UAAuB,EAAE,WAAqB;IAE5F,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,UAAU,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC;IAC3C,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,IAAI,OAAO,GAAqB,EAAE,CAAC;IACnC,IAAI,QAAQ,GAAa,EAAE,CAAC;IAC5B,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,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,IAAoB,EAAE,EAAE,CAAC,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,UAAU,CAAC,CAAC,CAAC;IAE7G,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,CAAC,OAAO,CAAC,CAAC;IAC7C,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"}
+{"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,IAAI,OAAO,GAAqB,EAAE,CAAC;IACnC,IAAI,QAAQ,GAAa,EAAE,CAAC;IAC5B,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,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,IAAoB,EAAE,EAAE,CAAC,eAAe,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,UAAU,CAAC,CAAC,CAAC;IAE7G,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,CAAC,OAAO,CAAC,CAAC;IAC7C,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"}

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

@@ -1,13 +1,13 @@
 import { MolfileWithMap, MonomerMolGraphMap } from './types';
 import { ALPHABET } from '../utils/macromolecule/consts';
-import { IMonomerLib } from '../types';
+import { IMonomerLibBase } from '../types';
 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
  * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
  * @param {ALPHABET} alphabet - Alphabet of the column
  * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/
-export declare function getFormattedMonomerLib(monomerLib: IMonomerLib, polymerType: PolymerType, alphabet: ALPHABET): Map<string, any>;
+export declare function getFormattedMonomerLib(monomerLib: IMonomerLibBase, polymerType: PolymerType, alphabet: ALPHABET): Map<string, any>;
 /** Translate a sequence of monomer symbols into Molfile V3000
  * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)
  * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects

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

@@ -1,20 +1,20 @@
 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, Monomer } from '../types';
+import { IMonomerLib, IMonomerLibBase, Monomer } from '../types';
 import { Bonds, MolGraph, MonomerMolGraphMap } from './types';
-import { ToAtomicLevelRes } from '../utils/seq-helper';
+import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
 import { ISeqMonomer, PolymerType } from '../helm/types';
 /** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
  */
-export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
+export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
 /** Get jagged array of monomer symbols for the dataframe
  * @param {DG.Column} macroMolCol - Column with macro-molecules
  * @return {string[]} - Jagged array of monomer symbols for the dataframe */
-export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>): ISeqMonomer[][];
+export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>, seqHelper: ISeqHelper): ISeqMonomer[][];
 /** Get a mapping of monomer symbols to MolGraph objects. Notice, the
  * transformation from molfile V2000 to V3000 takes place,
  * with the help of async function call from Chem (RdKit module)
@@ -23,7 +23,7 @@ export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>)
  * @param {PolymerType} polymerType - Polymer type
  * @param {ALPHABET} alphabet - Alphabet
  * @return {Map<string, MolGraph>} - Mapping of monomer symbols to MolGraph objects*/
-export declare function getMonomersDictFromLib(monomerSequencesArray: ISeqMonomer[][], polymerType: PolymerType, alphabet: ALPHABET, monomerLib: IMonomerLib, rdKitModule: RDModule): MonomerMolGraphMap;
+export declare function getMonomersDictFromLib(monomerSequencesArray: ISeqMonomer[][], polymerType: PolymerType, alphabet: ALPHABET, monomerLib: IMonomerLibBase, rdKitModule: RDModule): MonomerMolGraphMap;
 /** Parse element symbols for R-groups from the HELM monomer library R-group field
  * @param {any[]} rGroupObjList - R-group object list
  * @return {Map<number, number>} - Cap group index map*/