@datagrok-libraries/bio 5.43.1 → 5.44.1

package/CHANGELOG.md

@@ -1,12 +1,36 @@
 # bio changelog
 
-## 5.43.1
+## 5.44.1 (2024-09-25)
+
+### New features
+
+* Add IMonomerLibBase interface for overriding libraries
+* Add custom notation for sequences
+
+## 5.44.0 (2024-09-24)
+
+### New features
+
+* Add monomer hover link
+* Add getMolHighlight to build ISubstruct from monomer map
+* Add HelmHelper parse and removeGaps methods
+
+### Bug fixes
+
+* Fix toAtomicLevel for sequences with gaps
+* Fix toAtomicLevel for polymerType of sequence monomer
+* Fix ISeqMonomer for biotype and add position
+* Fix ISeqSplitted remove .canonicals and .originals
+* Fix IMonomerLib .getTooltip for biotype of HelmType
+* Fix toAtomicLevel linear for sequences with gaps
+
+## 5.43.1 (2024-09-22)
 
 Add monomer background coloring
 
-## 5.43.0
+## 5.43.0 (2024-09-18)
 
-Add coloring from monomer library to seaprator/fasta renderer
+Add coloring from monomer library to separator/fasta renderer
 
 ## 5.42.15 (2024-09-10)
 

package/package.json

@@ -8,19 +8,20 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.43.1",
+  "version": "5.44.1",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
-    "@datagrok-libraries/chem-meta": "^1.2.5",
+    "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/gridext": "^1.3.71",
     "@datagrok-libraries/ml": "^6.7.1",
-    "@datagrok-libraries/utils": "^4.3.0",
+    "@datagrok-libraries/utils": "^4.3.4",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
     "datagrok-api": "^1.21.1",
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",
+    "lru-cache": "^11.0.1",
     "mjolnir.js": "^2.7.0",
     "rxjs": "^6.5.5",
     "uuid": "^9.0.1",
@@ -52,4 +53,4 @@
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix"
   }
-}
+}

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 type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
+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 { Observable } from 'rxjs';
 export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol> & {
     editable: boolean;
 };
@@ -15,6 +15,17 @@ export declare abstract class HelmInputBase extends DG.JsInputBase<HelmString> {
     abstract redraw(): void;
     abstract showTooltip(content: HTMLElement | string, a: HelmAtom): void;
 }
+/**
+ * @property {Map<number, number>} monomerMap srcPosIdx -> resPosIdx
+ */
+export type HelmConvertRes = {
+    srcHelm: string;
+    resHelm: string;
+    monomerMap: Map<number, number> | null;
+};
+export declare class HelmNotSupportedError extends Error {
+    constructor(message?: string);
+}
 export interface IHelmHelper {
     createHelmInput(name: string, options?: IHelmInputInitOptions): HelmInputBase;
     createHelmWebEditor(host?: HTMLElement, drawOptions?: Partial<IHelmDrawOptions>): IHelmWebEditor;
@@ -26,6 +37,8 @@ export interface IHelmHelper {
     getHoveredAtom(x: number, y: number, mol: HelmMol, height: number): HelmAtom | null;
     /** Gets pseudo molfiles with monomers as atoms */
     getMolfiles(helmStrList: string[]): string[];
+    parse(helm: string, origin?: Point): HelmMol;
+    removeGaps(helm: string): HelmConvertRes;
 }
 export declare function getHelmHelper(): Promise<IHelmHelper>;
 declare module 'datagrok-api/ui' {
@@ -36,4 +49,6 @@ declare module 'datagrok-api/ui' {
         function helmAsync(name: string, options?: IHelmInputInitOptions): Promise<HelmInputBase>;
     }
 }
+/** Inputs logic */
+export declare function getMonomerHandleArgs(a: HelmAtom | HelmType, name?: string): [ /** biotype *//** biotype */ HelmType, /** elem */ string];
 //# sourceMappingURL=helm-helper.d.ts.map

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

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package/src/helm/helm-helper.js

@@ -2,6 +2,11 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 export class HelmInputBase extends DG.JsInputBase {
 }
+export class HelmNotSupportedError extends Error {
+    constructor(message) {
+        super(message);
+    }
+}
 export async function getHelmHelper() {
     const packageName = 'Helm';
     const funcList = DG.Func.find({ package: packageName, name: `getHelmHelper` });
@@ -13,4 +18,21 @@ export async function getHelmHelper() {
 ui.input.helmAsync = async function (name, options) {
     return (await getHelmHelper()).createHelmInput(name, options);
 };
+/** Inputs logic */
+export function getMonomerHandleArgs(a, name) {
+    if (!a)
+        throw new Error(`Argument 'a' of type Atom or HelmType is mandatory.`);
+    let biotype;
+    let elem;
+    const aa = a;
+    if (aa.T === 'ATOM') {
+        biotype = aa.biotype();
+        elem = aa.elem;
+    }
+    else {
+        biotype = a;
+        elem = name;
+    }
+    return [biotype, elem];
+}
 //# sourceMappingURL=helm-helper.js.map

package/src/helm/helm-helper.js.map

@@ -1 +1 @@
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package/src/helm/types.d.ts

@@ -1,4 +1,5 @@
 import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups, IMonomerColors, 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';
@@ -14,13 +15,14 @@ import type { OrgType } from '@datagrok-libraries/helm-web-editor/src/types/org-
 import type { Monomers } from '@datagrok-libraries/helm-web-editor/helm/Monomers';
 import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/types/dojo';
 export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
-export { Atom, IJsAtom, Bond, Mol, Editor, MonomerExplorer };
+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 { DojoType, DojoxType };
 export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
 export interface ISeqMonomer {
-    polymerType: PolymerType;
+    position: number;
+    biotype: HelmType;
     symbol: string;
 }
 export interface IHelmWebEditor {

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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,QAAQ,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,cAAc,EAAE,cAAc,EACxG,MAAM,gDAAgD,CAAC;AAExD,OAAO,KAAK,EAAC,KAAK,EAAC,MAAM,4CAA4C,CAAC;AACtE,OAAO,KAAK,EAAC,IAAI,EAAC,MAAM,2CAA2C,CAAC;AACpE,OAAO,KAAK,EAAC,OAAO,EAAC,MAAM,oDAAoD,CAAC;AAChF,OAAO,KAAK,EAAC,IAAI,EAAC,MAAM,2CAA2C,CAAC;AACpE,OAAO,KAAK,EAAC,GAAG,EAAC,MAAM,0CAA0C,CAAC;AAClE,OAAO,KAAK,EAAC,MAAM,EAAC,MAAM,oDAAoD,CAAC;AAE/E,OAAO,KAAK,EACV,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,UAAU,EAAE,UAAU,EACnD,iBAAiB,EAAE,gBAAgB,EAAE,cAAc,EAAE,iBAAiB,EAAE,aAAa,EACrF,gBAAgB,EACjB,MAAM,wDAAwD,CAAC;AAChE,OAAO,KAAK,EAAC,SAAS,EAAC,MAAM,+CAA+C,CAAC;AAC7E,OAAO,KAAK,EAAC,eAAe,EAAC,MAAM,0DAA0D,CAAC;AAC9F,OAAO,KAAK,EAAC,GAAG,EAAC,MAAM,8CAA8C,CAAC;AAGtE,OAAO,KAAK,EAAC,WAAW,EAAC,MAAM,2CAA2C,CAAC;AAC3E,OAAO,KAAK,EAAC,iBAAiB,EAAE,cAAc,EAAC,MAAM,4CAA4C,CAAC;AAClG,OAAO,KAAK,EAAC,OAAO,EAAC,MAAM,wDAAwD,CAAC;AACpF,OAAO,KAAK,EAAC,QAAQ,EAAC,MAAM,mDAAmD,CAAC;AAChF,OAAO,KAAK,EAAC,QAAQ,EAAE,SAAS,EAAC,MAAM,iDAAiD,CAAC;AAEzF,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAE,WAAW,EAAE,gBAAgB,EAAC,CAAC;AAC9D,OAAO,EAAC,KAAK,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,GAAG,EAAE,MAAM,EAAE,eAAe,EAAC,CAAC;AAElE,OAAO,EAAC,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,UAAU,EAAE,UAAU,EAAC,CAAC;AAE7D,OAAO,EACL,iBAAiB,EAAE,cAAc,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,gBAAgB,EACxF,GAAG,EAAE,QAAQ,EAAE,cAAc,EAAE,iBAAiB,EACjD,CAAC;AAEF,OAAO,EAAC,QAAQ,EAAE,SAAS,EAAC,CAAC;AAC7B,OAAO,EAAC,SAAS,EAAE,cAAc,EAAE,iBAAiB,EAAE,OAAO,EAAC,CAAC;AAG/D,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,QAAQ,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,MAAM,IAAI,UAAU,CAAC;IACzB,IAAI,IAAI,IAAI,cAAc,CAAC;IAE3B,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CACnD;AAED,OAAO,EAAC,cAAc,EAAE,aAAa,EAAE,WAAW,EAAC,CAAC"}

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

@@ -1,3 +1,4 @@
+import { PolymerTypes } from '../helm/consts';
 export declare const monomerWorksConsts: {
     readonly V2K_RGP_SHIFT: 8;
     readonly V2K_RGP_LINE: "M  RGP";
@@ -18,9 +19,18 @@ export declare const monomerWorksConsts: {
     readonly V3K_BEGIN_DATA_LINE: "M  V30 ";
     readonly V3K_END: "M  END";
     readonly PRECISION_FACTOR: 10000;
-    readonly DEOXYRIBOSE: "d";
-    readonly RIBOSE: "r";
-    readonly PHOSPHATE: "p";
+    readonly DEOXYRIBOSE: {
+        readonly polymerType: PolymerTypes.RNA;
+        readonly symbol: "d";
+    };
+    readonly RIBOSE: {
+        readonly polymerType: PolymerTypes.RNA;
+        readonly symbol: "r";
+    };
+    readonly PHOSPHATE: {
+        readonly polymerType: PolymerTypes.RNA;
+        readonly symbol: "p";
+    };
     readonly OXYGEN: "O";
     readonly HYDROGEN: "H";
 };

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

@@ -1 +1 @@
-{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;CA6BrB,CAAC"}
+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE5C,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA8BrB,CAAC"}

package/src/monomer-works/consts.js

@@ -21,9 +21,9 @@ export const monomerWorksConsts = {
     V3K_END: 'M  END',
     PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates
     // symbols for the corresponding monomers in HELM library
-    DEOXYRIBOSE: 'd',
-    RIBOSE: 'r',
-    PHOSPHATE: 'p',
+    DEOXYRIBOSE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'd' },
+    RIBOSE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'r' },
+    PHOSPHATE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'p' },
     OXYGEN: 'O',
     HYDROGEN: 'H',
 };

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

@@ -1 +1 @@
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+{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAClC,sCAAsC;IACpC,aAAa,EAAE,CAAC;IAChB,YAAY,EAAE,QAAQ;IACtB,UAAU,EAAE,KAAK;IACjB,wDAAwD;IACxD,gBAAgB,EAAE,EAAE;IACpB,aAAa,EAAE,CAAC;IAChB,qBAAqB,EAAE,sCAAsC;IAC7D,sBAAsB,EAAE,2CAA2C;IACnE,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,qBAAqB,EAAE,gBAAgB;IACvC,sBAAsB,EAAE,UAAU;IAClC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,eAAe,EAAE,OAAO;IACxB,mBAAmB,EAAE,SAAS;IAC9B,OAAO,EAAE,QAAQ;IACjB,gBAAgB,EAAE,KAAM,EAAE,mFAAmF;IAC7G,yDAAyD;IAEzD,WAAW,EAAE,EAAC,WAAW,8BAAkB,EAAE,MAAM,EAAE,GAAG,EAAC;IACzD,MAAM,EAAE,EAAC,WAAW,8BAAkB,EAAE,MAAM,EAAE,GAAG,EAAC;IACpD,SAAS,EAAE,EAAC,WAAW,8BAAkB,EAAE,MAAM,EAAE,GAAG,EAAC;IAEvD,MAAM,EAAE,GAAG;IACX,QAAQ,EAAE,GAAG;CACL,CAAC"}

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

@@ -0,0 +1,10 @@
+import * as DG from 'datagrok-api/dg';
+import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
+import { IMonomerLib } from '../types/index';
+import { ISeqMonomer } from '../helm/types';
+import { MonomerHoverLink } from './utils';
+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 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

@@ -0,0 +1 @@
+{"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,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAO1C,OAAO,EAAkB,gBAAgB,EAAC,MAAM,SAAS,CAAC;AAI1D,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,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,GACnG,gBAAgB,CAgGlB;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

@@ -0,0 +1,123 @@
+import wu from 'wu';
+import { LRUCache } from 'lru-cache';
+import { addSubstructProvider, getMonomerHover, setMonomerHover } from '@datagrok-libraries/chem-meta/src/types';
+import { HelmTypes } from '../helm/consts';
+import { SeqHandler } from '../utils/seq-handler';
+import { ALPHABET } from '../utils/macromolecule';
+import { getMonomersDictFromLib } from './to-atomic-level';
+import { monomerSeqToMolfile } from './to-atomic-level-utils';
+import { getMolHighlight } from './seq-to-molfile';
+export const MonomerHoverLinksTemp = 'MonomerHoverLinks';
+function addMonomerHoverLink(seqColTemp, resLink) {
+    let mhhList = seqColTemp[MonomerHoverLinksTemp];
+    if (!mhhList)
+        mhhList = seqColTemp[MonomerHoverLinksTemp] = [];
+    mhhList.push(resLink);
+    seqColTemp[MonomerHoverLinksTemp] = mhhList;
+}
+export function buildMonomerHoverLink(seqCol, molCol, monomerLib, rdKitModule) {
+    function buildMonomerMap(seqCol, tableRowIdx) {
+        const seqSH = SeqHandler.forColumn(seqCol);
+        const seqSS = seqSH.getSplitted(tableRowIdx);
+        const biotype = seqSH.alphabet == ALPHABET.RNA || seqSH.alphabet == ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+        const seqMList = wu.count(0).take(seqSS.length)
+            .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
+            .toArray();
+        const alphabet = seqSH.alphabet;
+        const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? "RNA" /* PolymerTypes.RNA */ : "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+        const monomersDict = getMonomersDictFromLib([seqMList], polymerType, alphabet, monomerLib, rdKitModule);
+        // Call seq-to-molfile worker core directly
+        const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
+        return molWM.monomers;
+    }
+    const monomerMapLruCache = new LRUCache({ max: 100 });
+    function getMonomerMap(seqCol, tableRowIdx) {
+        const seq = seqCol.get(tableRowIdx);
+        if (seq == null)
+            return null;
+        let resMonomerMap = monomerMapLruCache.get(seq);
+        if (!resMonomerMap) {
+            monomerMapLruCache.set(seq, resMonomerMap = buildMonomerMap(seqCol, tableRowIdx));
+        }
+        return resMonomerMap;
+    }
+    const resLink = {
+        targetCol: molCol,
+        handler: (seqGridCell, seqMonomer, targetGridCol) => {
+            const grid = targetGridCol.grid;
+            const tableRowIdx = seqGridCell.tableRowIndex;
+            const gridRowIdx = seqGridCell.gridRow;
+            const targetGridCell = grid.cell(targetGridCol.name, gridRowIdx);
+            const prev = getMonomerHover();
+            if (!prev || (prev && (prev.dataFrameId != seqCol.dataFrame.id || prev.gridRowIdx != gridRowIdx ||
+                prev.seqColName != seqCol.name || prev.seqPosition != seqMonomer?.position))) {
+                if (prev) {
+                    setMonomerHover(null);
+                    prev.gridCell.grid?.invalidate();
+                }
+                if (!seqMonomer) {
+                    setMonomerHover(null);
+                    return true;
+                }
+                setMonomerHover({
+                    gridCell: targetGridCell,
+                    dataFrameId: seqCol.dataFrame.id,
+                    gridRowIdx: gridRowIdx,
+                    seqColName: seqCol.name,
+                    seqPosition: seqMonomer ? seqMonomer.position : -1,
+                    getSubstruct: () => {
+                        if (!seqMonomer || seqMonomer.symbol === '*')
+                            return undefined;
+                        const molMonomerMap = getMonomerMap(seqCol, tableRowIdx);
+                        if (!molMonomerMap)
+                            return undefined;
+                        const monomerMap = molMonomerMap.get(seqMonomer.position); // single monomer
+                        if (!monomerMap)
+                            return { atoms: [], bonds: [], highlightAtomColors: [], highlightBondColors: [] };
+                        const res = getMolHighlight([monomerMap], monomerLib);
+                        return res;
+                    }
+                });
+                // TODO: Invalidate targetGridCell
+                grid.invalidate();
+            }
+            return true;
+        },
+        /* ISubstructProvider.*/ getSubstruct: (tableRowIdx) => {
+            if (molCol.getTag(".sequence-src-highlight-monomers" /* ChemTags.SEQUENCE_SRC_HL_MONOMERS */) != 'true')
+                return undefined;
+            if (tableRowIdx == null)
+                return undefined;
+            const seq = seqCol.get(tableRowIdx);
+            if (!seq)
+                return undefined;
+            const molMonomerMap = getMonomerMap(seqCol, tableRowIdx);
+            if (!molMonomerMap)
+                return undefined;
+            const res = getMolHighlight(molMonomerMap.values(), monomerLib);
+            return res;
+        }
+    };
+    addMonomerHoverLink(seqCol.temp, resLink);
+    addSubstructProvider(molCol.temp, resLink);
+    return resLink;
+}
+export function execMonomerHoverLinks(seqGridCell, seqMonomer) {
+    const seqCol = seqGridCell.tableColumn;
+    if (!seqCol)
+        return;
+    const mhlList = getMonomerHoverLinks(seqCol);
+    for (let mhlI = mhlList.length - 1; mhlI >= 0; --mhlI) {
+        const mhl = mhlList[mhlI];
+        const molGridCol = seqGridCell.grid.col(mhl.targetCol.name);
+        if (molGridCol) {
+            const handlerRes = mhl.handler(seqGridCell, seqMonomer, molGridCol);
+            if (!handlerRes)
+                break;
+        }
+    }
+}
+export function getMonomerHoverLinks(seqCol) {
+    return seqCol.temp[MonomerHoverLinksTemp] ?? [];
+}
+//# sourceMappingURL=monomer-hover.js.map

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

@@ -0,0 +1 @@
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package/src/monomer-works/monomer-utils.d.ts.map

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

@@ -3,9 +3,9 @@ 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 { GAP_SYMBOL } from '../utils/macromolecule/types';
 import { SeqHandler } from '../utils/seq-handler';
 import { splitAlignedSequences } from '../utils/splitter';
+import { GAP_SYMBOL } from '../utils/macromolecule/consts';
 export function encodeMonomers(col) {
     let encodeSymbol = MONOMER_ENCODE_MIN;
     const monomerSymbolDict = {};
@@ -15,7 +15,8 @@ export function encodeMonomers(col) {
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         let encodedMonomerStr = '';
         const monomers = sh.getSplitted(rowIdx);
-        for (const cm of monomers.canonicals) {
+        for (let posIdx = 0; posIdx < monomers.length; ++posIdx) {
+            const cm = monomers.getCanonical(posIdx);
             if (!monomerSymbolDict[cm]) {
                 if (encodeSymbol > MONOMER_ENCODE_MAX) {
                     grok.shell.error(`Not enough symbols to encode monomers`);

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

@@ -1 +1 @@
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package/src/monomer-works/seq-to-molfile-worker.js

@@ -1,12 +1,12 @@
 import { monomerSeqToMolfile } from './to-atomic-level-utils';
 onmessage = (event) => {
-    const { monomerSequencesArray, monomersDict, alphabet, polymerType, start, end } = event.data;
-    const molfileList = new Array(end - start);
+    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;
+    const resMolList = new Array(end - start);
     const molfileWarningList = new Array(0);
     for (let rowI = start; rowI < end; ++rowI) {
         try {
-            const monomerSeq = monomerSequencesArray[rowI];
-            molfileList[rowI - start] = monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType);
+            const seq = seqList[rowI];
+            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);
         }
         catch (err) {
             const errMsg = err instanceof Error ? err.message : err.toString();
@@ -14,6 +14,6 @@ onmessage = (event) => {
             molfileWarningList.push(msg);
         }
     }
-    postMessage({ molfileList, molfileWarningList });
+    postMessage({ molfiles: resMolList, warnings: molfileWarningList });
 };
 //# sourceMappingURL=seq-to-molfile-worker.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"seq-to-molfile-worker.js","sourceRoot":"","sources":["seq-to-molfile-worker.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAG5D,SAAS,GAAG,CAAC,KAAK,EAAE,EAAE;IACpB,MAAM,EAAC,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,GAA2B,KAAK,CAAC,IAAI,CAAC;IACtG,MAAM,UAAU,GAAqB,IAAI,KAAK,CAAiB,GAAG,GAAG,KAAK,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,IAAI,GAAG,KAAK,EAAE,IAAI,GAAG,GAAG,EAAE,EAAE,IAAI,EAAE,CAAC;QAC1C,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;YAC1B,UAAU,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,mBAAmB,CAAC,GAAG,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;QAC3F,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,MAAM,MAAM,GAAW,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC;YAC3E,MAAM,GAAG,GAAW,8BAA8B,IAAI,KAAK,MAAM,GAAG,CAAC;YACrE,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC/B,CAAC;IACH,CAAC;IACD,WAAW,CAAC,EAAC,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,kBAAkB,EAA0B,CAAC,CAAC;AAC7F,CAAC,CAAC"}

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

@@ -1,9 +1,18 @@
-import { HELM_POLYMER_TYPE } from '../utils/const';
+import * as DG from 'datagrok-api/dg';
+import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import { ALPHABET } from '../utils/macromolecule';
-import { MolGraph } from './types';
+import { MonomerMap, MonomerMapValue, MonomerMolGraphMap } from './types';
+import { ToAtomicLevelRes } from '../utils/seq-helper';
+import { IMonomerLib, IMonomerLibBase } from '../types';
+import { PolymerType } from '../helm/types';
+import { ISubstruct } from '@datagrok-libraries/chem-meta/src/types';
 export type SeqToMolfileResult = {
-    molfileWarningList: string[];
-    molfileList: string[];
+    mols: {
+        molfile: string;
+        monomers: MonomerMap;
+    }[];
+    warnings: string[];
 };
-export declare function seqToMolFileWorker(monomerSequencesArray: string[][], monomersDict: Map<string, MolGraph>, alphabet: ALPHABET, polymerType: HELM_POLYMER_TYPE, srcColLength: number): Promise<SeqToMolfileResult>;
+export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, 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":"AAAA,OAAO,EAAC,iBAAiB,EAAC,MAAM,gBAAgB,CAAC;AACjD,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EAAC,QAAQ,EAAC,MAAM,SAAS,CAAC;AAEjC,MAAM,MAAM,kBAAkB,GAAG;IAC7B,kBAAkB,EAAE,MAAM,EAAE,CAAA;IAC5B,WAAW,EAAE,MAAM,EAAE,CAAA;CACxB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,qBAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,EAC7G,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,GACvE,OAAO,CAAC,kBAAkB,CAAC,CA+B7B"}
+{"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"}