@datagrok-libraries/bio 5.42.8 → 5.42.10

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # bio changelog
 
+## 5.42.10 (2024-08-23)
+
+### Features
+
+* Add SeqHandler
+
+## 5.42.9 (2024-08-16)
+
+### Features
+
+* HWE option for continuous monomer numbering
+* Add HelmInput mouse events redraw, showTooltip
+* Bump HWE dependencies versions
+
 ## 5.42.8 (2024-08-14)
 
 Fix monomer substitution matrix calculation

package/package.json

@@ -8,9 +8,10 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.8",
+  "version": "5.42.10",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
+    "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/gridext": "^1.3.71",
     "@datagrok-libraries/ml": "^6.6.11",
     "@datagrok-libraries/utils": "^4.2.11",
@@ -26,8 +27,8 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.7",
-    "@datagrok-libraries/js-draw-lite": "^0.0.5",
+    "@datagrok-libraries/helm-web-editor": "^1.1.9",
+    "@datagrok-libraries/js-draw-lite": "^0.0.7",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",
@@ -46,7 +47,7 @@
     "link-utils": "npm link @datagrok-libraries/utils",
     "link-all": "npm link datagrok-api @datagrok-libraries/gridext @datagrok-libraries/utils @datagrok-libraries/ml",
     "build-bio": "git clean -f -X -d ./src && tsc",
-    "build": "git clean -f -X -d ./src && tsc",
+    "build": "tsc",
     "build-all": "npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/gridext run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix"

package/src/chem/rdkit-module.d.ts

@@ -0,0 +1,3 @@
+import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
+export declare function getRdKitModule(): Promise<RDModule>;
+//# sourceMappingURL=rdkit-module.d.ts.map

package/src/chem/rdkit-module.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"rdkit-module.d.ts","sourceRoot":"","sources":["rdkit-module.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAErE,wBAAsB,cAAc,IAAI,OAAO,CAAC,QAAQ,CAAC,CAOxD"}

package/src/chem/rdkit-module.js

@@ -0,0 +1,9 @@
+import * as DG from 'datagrok-api/dg';
+export async function getRdKitModule() {
+    const funcList = DG.Func.find({ package: 'Chem', name: 'getRdKitModule' });
+    if (funcList.length === 0)
+        throw new Error('Package "Chem" must be installed for getRdKitModule.');
+    const res = (await funcList[0].prepare().call()).getOutputParamValue();
+    return res;
+}
+//# sourceMappingURL=rdkit-module.js.map

package/src/chem/rdkit-module.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"rdkit-module.js","sourceRoot":"","sources":["rdkit-module.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,MAAM,CAAC,KAAK,UAAU,cAAc;IAClC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACzE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAC;IAE1E,MAAM,GAAG,GAAa,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAc,CAAC;IAC7F,OAAO,GAAG,CAAC;AACb,CAAC"}

package/src/helm/consts.d.ts

@@ -1,3 +1,4 @@
 import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
-export { HelmTypes, MonomerTypes, PolymerTypes };
+import { MonomerNumberingTypes } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+export { HelmTypes, MonomerTypes, PolymerTypes, MonomerNumberingTypes };
 //# 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,qBAAqB,EAAC,MAAM,wDAAwD,CAAC;AAE7F,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAE,qBAAqB,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,EAAoD,CAAC"}

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

@@ -1,21 +1,31 @@
 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 { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor } from './types';
+import { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor, HelmAtom, IHelmDrawOptions } from './types';
 import { IMonomerLib } from '../types/index';
-export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol>;
+import { Observable } from 'rxjs';
+export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol> & {
+    editable: boolean;
+};
 export declare abstract class HelmInputBase extends DG.JsInputBase<HelmString> {
     abstract get molValue(): HelmMol;
     abstract set molValue(value: HelmMol);
+    abstract get onMouseMove(): Observable<MouseEvent>;
+    abstract get onClick(): Observable<MouseEvent>;
+    abstract redraw(): void;
+    abstract showTooltip(content: HTMLElement | string, a: HelmAtom): void;
 }
 export interface IHelmHelper {
     createHelmInput(name: string, options?: IHelmInputInitOptions): HelmInputBase;
-    createHelmWebEditor(host?: HTMLElement): IHelmWebEditor;
+    createHelmWebEditor(host?: HTMLElement, drawOptions?: Partial<IHelmDrawOptions>): IHelmWebEditor;
     createWebEditorApp(host: HTMLDivElement, helm?: string): App;
     get originalMonomersFuncs(): MonomersFuncs | null;
     buildMonomersFuncsFromLib(monomerLib: IMonomerLib): MonomersFuncs;
     overrideMonomersFuncs(monomersFuncs: MonomersFuncs): MonomersFuncs;
     revertOriginalMonomersFuncs(): MonomersFuncs;
+    getHoveredAtom(x: number, y: number, mol: HelmMol, height: number): HelmAtom | null;
+    /** Gets pseudo molfiles with monomers as atoms */
+    getMolfiles(helmStrList: string[]): string[];
 }
 export declare function getHelmHelper(): Promise<IHelmHelper>;
 declare module 'datagrok-api/ui' {

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,KAAK,EAAC,GAAG,EAAC,MAAM,8CAA8C,CAAC;AACtE,OAAO,EACW,aAAa,EAAE,OAAO,EAAE,UAAU,EAAE,cAAc,EAAE,QAAQ,EAAE,gBAAgB,EAC/F,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,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,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,WAAW,CAAC,EAAE,OAAO,CAAC,gBAAgB,CAAC,GAAG,cAAc,CAAC;IAEjG,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,WAAW,GAAG,aAAa,CAAC;IAElE,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;CAC9C;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"}

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

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

@@ -4,7 +4,7 @@ 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 { Editor } from '@datagrok-libraries/js-draw-lite/src/JSDraw.Editor';
-import type { HelmAtom, HelmBond, HelmMol, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+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 { 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';
@@ -15,8 +15,8 @@ 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 { HelmAtom, HelmBond, HelmMol, HelmString };
-export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers, GetMonomerFunc, GetMonomerResType };
+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 {
@@ -24,7 +24,7 @@ export interface ISeqMonomer {
     symbol: string;
 }
 export interface IHelmWebEditor {
-    get editor(): Editor<HelmType>;
+    get editor(): HelmEditor;
     get host(): HTMLDivElement;
     resizeEditor(width: number, height: number): void;
 }

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

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EACV,QAAQ,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,gBAAgB,EAAE,cAAc,EAAE,cAAc,EACxG,MAAM,gDAAgD,CAAC;AAExD,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,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,GAAG,EAAE,MAAM,EAAE,eAAe,EAAC,CAAC;AAE3D,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,WAAW,EAAE,WAAW,CAAC;IACzB,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/utils/logger.d.ts

@@ -7,7 +7,8 @@ export interface ILogger {
 export declare class LoggerWrapper implements ILogger {
     private readonly target;
     private debugEnabled;
-    constructor(target: ILogger, debugEnabled: boolean);
+    private prefix;
+    constructor(target: ILogger, debugEnabled: boolean, prefix?: string);
     error(message: any, params?: object | undefined, stackTrace?: string | undefined): void;
     warning(message: string, params?: object | undefined): void;
     info(message: string, params?: object | undefined): void;

package/src/utils/logger.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"logger.d.ts","sourceRoot":"","sources":["logger.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,OAAO;IACtB,KAAK,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACxF,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IAC5D,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACzD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;CAC3D;AAED,qBAAa,aAAc,YAAW,OAAO;IAEzC,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,YAAY;gBADH,MAAM,EAAE,OAAO,EACxB,YAAY,EAAE,OAAO;IAG/B,KAAK,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAIvF,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAI3D,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAIxD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;CAI1D"}
+{"version":3,"file":"logger.d.ts","sourceRoot":"","sources":["logger.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,OAAO;IACtB,KAAK,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACxF,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IAC5D,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACzD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;CAC3D;AAED,qBAAa,aAAc,YAAW,OAAO;IAEzC,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,YAAY;IACpB,OAAO,CAAC,MAAM;gBAFG,MAAM,EAAE,OAAO,EACxB,YAAY,EAAE,OAAO,EACrB,MAAM,GAAE,MAAW;IAG7B,KAAK,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAIvF,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAI3D,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;IAIxD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI;CAI1D"}

package/src/utils/logger.js

@@ -1,20 +1,21 @@
 export class LoggerWrapper {
-    constructor(target, debugEnabled) {
+    constructor(target, debugEnabled, prefix = '') {
         this.target = target;
         this.debugEnabled = debugEnabled;
+        this.prefix = prefix;
     }
     error(message, params, stackTrace) {
-        return this.target.error(message, params, stackTrace);
+        return this.target.error(this.prefix + message, params, stackTrace);
     }
     warning(message, params) {
-        return this.target.warning(message, params);
+        return this.target.warning(this.prefix + message, params);
     }
     info(message, params) {
-        return this.target.info(message, params);
+        return this.target.info(this.prefix + message, params);
     }
     debug(message, params) {
         if (this.debugEnabled)
-            return this.target.debug(message, params);
+            return this.target.debug(this.prefix + message, params);
     }
 }
 //# sourceMappingURL=logger.js.map

package/src/utils/logger.js.map

@@ -1 +1 @@
-{"version":3,"file":"logger.js","sourceRoot":"","sources":["logger.ts"],"names":[],"mappings":"AAWA,MAAM,OAAO,aAAa;IACxB,YACmB,MAAe,EACxB,YAAqB;QADZ,WAAM,GAAN,MAAM,CAAS;QACxB,iBAAY,GAAZ,YAAY,CAAS;IAC5B,CAAC;IAEJ,KAAK,CAAC,OAAY,EAAE,MAA2B,EAAE,UAA+B;QAC9E,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,CAAC,CAAC;IACxD,CAAC;IAED,OAAO,CAAC,OAAe,EAAE,MAA2B;QAClD,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;IAC9C,CAAC;IAED,IAAI,CAAC,OAAe,EAAE,MAA2B;QAC/C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;IAC3C,CAAC;IAED,KAAK,CAAC,OAAe,EAAE,MAA2B;QAChD,IAAI,IAAI,CAAC,YAAY;YACnB,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;IAC9C,CAAC;CACF"}
+{"version":3,"file":"logger.js","sourceRoot":"","sources":["logger.ts"],"names":[],"mappings":"AAWA,MAAM,OAAO,aAAa;IACxB,YACmB,MAAe,EACxB,YAAqB,EACrB,SAAiB,EAAE;QAFV,WAAM,GAAN,MAAM,CAAS;QACxB,iBAAY,GAAZ,YAAY,CAAS;QACrB,WAAM,GAAN,MAAM,CAAa;IAC1B,CAAC;IAEJ,KAAK,CAAC,OAAY,EAAE,MAA2B,EAAE,UAA+B;QAC9E,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,GAAG,OAAO,EAAE,MAAM,EAAE,UAAU,CAAC,CAAC;IACtE,CAAC;IAED,OAAO,CAAC,OAAe,EAAE,MAA2B;QAClD,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,GAAG,OAAO,EAAE,MAAM,CAAC,CAAC;IAC5D,CAAC;IAED,IAAI,CAAC,OAAe,EAAE,MAA2B;QAC/C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,OAAO,EAAE,MAAM,CAAC,CAAC;IACzD,CAAC;IAED,KAAK,CAAC,OAAe,EAAE,MAA2B;QAChD,IAAI,IAAI,CAAC,YAAY;YACnB,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,GAAG,OAAO,EAAE,MAAM,CAAC,CAAC;IAC5D,CAAC;CACF"}

package/src/utils/seq-helper.d.ts

@@ -0,0 +1,26 @@
+import * as DG from 'datagrok-api/dg';
+export declare const SUBSTRUCT_COL = "substruct-col";
+export interface ISubstruct {
+    atoms?: number[];
+    bonds?: number[];
+    highlightAtomColors?: {
+        [key: number]: number[] | null;
+    };
+    highlightBondColors?: {
+        [key: number]: number[] | null;
+    };
+}
+export type ToAtomicLevelResType = {
+    molCol: DG.Column<string>;
+    molHighlightCol: DG.Column<object>;
+};
+export interface ISeqHelper {
+    /**
+     * @param helmCol {DG.Column<string>} Macromolecules in Helm format
+     * @param chiralityEngine {boolean} [true] Use chirality engine for molecule visualization
+     * @param highlight {boolean} [true] Generates molHighlightCol of result
+     **/
+    helmToAtomicLevel(helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean): Promise<ToAtomicLevelResType>;
+}
+export declare function getSeqHelper(): Promise<ISeqHelper>;
+//# sourceMappingURL=seq-helper.d.ts.map

package/src/utils/seq-helper.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"seq-helper.d.ts","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,eAAO,MAAM,aAAa,kBAAkB,CAAC;AAE7C,MAAM,WAAW,UAAU;IACzB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,mBAAmB,CAAC,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;KAAE,CAAC;IACzD,mBAAmB,CAAC,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;KAAE,CAAA;CACzD;AAED,MAAM,MAAM,oBAAoB,GAAG;IACjC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAC1B,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;CACpC,CAAA;AAED,MAAM,WAAW,UAAU;IACzB;;;;QAII;IACJ,iBAAiB,CACf,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,EAAE,OAAO,EAAE,SAAS,CAAC,EAAE,OAAO,GACzE,OAAO,CAAC,oBAAoB,CAAC,CAAC;CAClC;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,UAAU,CAAC,CAOxD"}

package/src/utils/seq-helper.js

@@ -0,0 +1,11 @@
+import * as DG from 'datagrok-api/dg';
+export const SUBSTRUCT_COL = 'substruct-col';
+export async function getSeqHelper() {
+    const packageName = 'Bio';
+    const funcList = DG.Func.find({ package: packageName, name: `getSeqHelper` });
+    if (funcList.length === 0)
+        throw new Error(`Package '${packageName}' must be installed for SeqHelper.`);
+    const res = (await funcList[0].prepare().call()).getOutputParamValue();
+    return res;
+}
+//# sourceMappingURL=seq-helper.js.map

package/src/utils/seq-helper.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seq-helper.js","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,MAAM,CAAC,MAAM,aAAa,GAAG,eAAe,CAAC;AAyB7C,MAAM,CAAC,KAAK,UAAU,YAAY;IAChC,MAAM,WAAW,GAAG,KAAK,CAAC;IAC1B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,cAAc,EAAC,CAAC,CAAC;IAC5E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,oCAAoC,CAAC,CAAC;IAC/E,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAgB,CAAC;IACrF,OAAO,GAAG,CAAC;AACb,CAAC"}