@datagrok-libraries/bio 5.42.13 → 5.42.14

package/CHANGELOG.md

@@ -1,5 +1,14 @@
 # bio changelog
 
+## 5.42.14 (2024-09-04)
+
+### Bug fixes
+
+* Fix toAtomicLevel workers error DG is not defined
+* Fix SeqHandler.getHelm lost cycles, add tests`
+* Add options for SeqHandler.getHelm
+* Fix default monomer libs for PolyTool rules
+
 ## 5.42.13 (2024-09-02)
 
 * Add interfaces for monomer management

package/package.json

@@ -8,16 +8,16 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.13",
+  "version": "5.42.14",
   "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": "^4.2.29",
+    "@datagrok-libraries/ml": "^6.7.0",
+    "@datagrok-libraries/utils": "^4.3.0",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
-    "datagrok-api": "^1.20.0",
+    "datagrok-api": "^1.21.1",
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",

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

@@ -1 +1 @@
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package/src/monomer-works/lib-settings.js

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 // -- Monomer libraries --
 export const LIB_STORAGE_NAME = 'Libraries';
 export const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
-const LIB_SETTINGS_FOR_TESTS = { explicit: ['HELMCoreLibrary.json'], exclude: [], duplicateMonomerPreferences: {} };
+const LIB_SETTINGS_FOR_TESTS = { explicit: ['HELMCoreLibrary.json', 'polytool-lib.json'], exclude: [], duplicateMonomerPreferences: {} };
 export const SETS_STORAGE_NAME = 'Monomer Sets';
 export const SETS_PATH = 'System:AppData/Bio/monomer-sets/';
 let userLibSettingsPromise = Promise.resolve();

package/src/monomer-works/lib-settings.js.map

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

@@ -1,7 +1,6 @@
 import * as DG from 'datagrok-api/dg';
-import * as grok from 'datagrok-api/grok';
 import { Observable } from 'rxjs';
-import { IMonomerLib, Monomer, IMonomerSet } from '../types/index';
+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;
@@ -24,30 +23,6 @@ export interface IMonomerLibFileManager {
     deleteLibraryFile(fileName: string): Promise<void>;
     loadLibraryFromFile(path: string, fileName: string): Promise<IMonomerLib>;
 }
-export interface INewMonomerForm {
-    get fieldInputs(): {
-        [key: string]: DG.InputBase<any> | grok.chem.Sketcher;
-    };
-    get form(): HTMLElement;
-    get rgroupInputs(): {
-        [key: string]: DG.InputBase<any>;
-    }[];
-    get metaInputs(): {
-        [key: string]: DG.InputBase<any>;
-    }[];
-    setMonomer(monomer: Monomer): void;
-}
-export interface IMonomerGallery {
-    get monomerGallery(): HTMLElement;
-    groupBy(by: string): void;
-    filterBySearch(search: string): void;
-}
-export interface IMonomerManager {
-    /** Creates new monomer library in correct folder and adds given monomers */
-    createNewMonomerLib(libName: string, monomers: Monomer[]): Promise<void>;
-    cloneMonomer(dfRow: DG.Row): Monomer;
-    getNewMonomerForm(): INewMonomerForm;
-}
 export interface IMonomerLibHelper {
     get eventManager(): IMonomerLibFileEventManager;
     /** Ensures files are loaded and validated, throws error after timeout */

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

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

@@ -1,7 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
 import { HelmType, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
-export { MonomerType, PolymerType };
 import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
 export type RGroup = {
     [RGP.CAP_GROUP_SMILES]: string;

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

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

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAYA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAyFhD,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;IACxC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;CACzC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAyFhD,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,GAAG,CAAC,mCAAuB;IACrC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;IACxC,CAAC,QAAQ,CAAC,EAAE,CAAC,2CAA2B;CACzC,CAAC"}

package/src/types/input.d.ts

@@ -0,0 +1,13 @@
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+export declare class InputColumnBase extends DG.InputBase<DG.Column | null> {
+    private readonly options?;
+    constructor(name: string, options?: ui.input.IColumnInputInitOptions<DG.Column>);
+    setColumnInputTable(table?: DG.DataFrame): void;
+}
+declare module 'datagrok-api/ui' {
+    namespace input {
+        function column2(name: string, options?: ui.input.IColumnInputInitOptions<DG.Column>): InputColumnBase;
+    }
+}
+//# sourceMappingURL=input.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"input.d.ts","sourceRoot":"","sources":["input.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,qBAAa,eAAgB,SAAQ,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC;IAEjE,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAC,CAA8C;gBAE3D,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,uBAAuB,CAAC,EAAE,CAAC,MAAM,CAAC;IAM/E,mBAAmB,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,SAAS,GAAG,IAAI;CAGhD;AAED,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAU,KAAK,CAAC;QACd,SAAS,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,uBAAuB,CAAC,EAAE,CAAC,MAAM,CAAC,GAAG,eAAe,CAAC;KACxG;CACF"}

package/src/types/input.js

@@ -0,0 +1,17 @@
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+export class InputColumnBase extends DG.InputBase {
+    constructor(name, options) {
+        const base = ui.input.column(name, options);
+        super(base.dart, options?.onValueChanged);
+        this.options = options;
+    }
+    setColumnInputTable(table) {
+        ui.input.setColumnInputTable(this, table, this.options?.filter);
+    }
+}
+ui.input.column2 = function (name, options) {
+    const res = new InputColumnBase(name, options);
+    return res;
+};
+//# sourceMappingURL=input.js.map

package/src/types/input.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"input.js","sourceRoot":"","sources":["input.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,MAAM,OAAO,eAAgB,SAAQ,EAAE,CAAC,SAA2B;IAIjE,YAAY,IAAY,EAAE,OAAqD;QAC7E,MAAM,IAAI,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;QAC5C,KAAK,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,EAAE,cAAc,CAAC,CAAC;QAC1C,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;IACzB,CAAC;IAED,mBAAmB,CAAC,KAAoB;QACtC,EAAE,CAAC,KAAK,CAAC,mBAAmB,CAAC,IAAI,EAAE,KAAM,EAAE,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;IACnE,CAAC;CACF;AAQD,EAAE,CAAC,KAAK,CAAC,OAAO,GAAG,UAAS,IAAY,EAAE,OAAqD;IAC7F,MAAM,GAAG,GAAG,IAAI,eAAe,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IAC/C,OAAO,GAAG,CAAC;AACb,CAAC,CAAC"}

package/src/utils/const.d.ts

@@ -1,11 +1,9 @@
-import * as DG from 'datagrok-api/dg';
 import { MonomerType, PolymerType } from '../helm/types';
 import { MonomerTypes, PolymerTypes } from '../helm/consts';
 import HELM_POLYMER_TYPE = PolymerTypes;
 import HELM_MONOMER_TYPE = MonomerTypes;
 import { RGroup } from '../types';
 export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
-export { PolymerTypes, MonomerTypes };
 /** Required HELM library monomer fields:
  * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
 export declare const enum HELM_REQUIRED_FIELD {
@@ -72,9 +70,6 @@ export declare const DUMMY_MONOMER: {
     readonly polymerType: PolymerType;
     readonly symbol: "";
 };
-export declare const MonomerInputProperties: {
-    [key: string]: DG.Property;
-};
 export declare const MONOMER_ENCODE_MIN = 256;
 export declare const MONOMER_ENCODE_MAX = 1034;
 export declare const RIBOSE_SYMBOL = "r";

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

@@ -1 +1 @@
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package/src/utils/const.js

@@ -1,4 +1,3 @@
-import * as DG from 'datagrok-api/dg';
 // core fields of HELM library object used in toAtomicLevel function
 export const HELM_CORE_FIELDS = [
     "symbol" /* HELM_FIELDS.SYMBOL */,
@@ -36,15 +35,6 @@ export const DUMMY_MONOMER = {
     'polymerType': 'PEPTIDE',
     'symbol': ''
 };
-export const MonomerInputProperties = {
-    'monomerType': DG.Property.js('monomerType', DG.TYPE.STRING, { choices: ["Backbone" /* MonomerTypes.BACKBONE */, "Branch" /* MonomerTypes.BRANCH */, "Terminal" /* MonomerTypes.TERMINAL */] }),
-    'molecule': DG.Property.fromOptions({ name: 'molecule', type: DG.InputType.Molecule }),
-    'name': DG.Property.js('name', DG.TYPE.STRING),
-    'naturalAnalog': DG.Property.js('naturalAnalog', DG.TYPE.STRING),
-    'id': DG.Property.js('id', DG.TYPE.INT),
-    'polymerType': DG.Property.js('polymerType', DG.TYPE.STRING, { choices: ["RNA" /* PolymerTypes.RNA */, "PEPTIDE" /* PolymerTypes.PEPTIDE */, "CHEM" /* PolymerTypes.CHEM */, "BLOB" /* PolymerTypes.BLOB */, "G" /* PolymerTypes.G */] }),
-    'symbol': DG.Property.js('symbol', DG.TYPE.STRING),
-};
 // range of hex nubers used in PepSea library to endode monomers
 export const MONOMER_ENCODE_MIN = 0x100;
 export const MONOMER_ENCODE_MAX = 0x40A;

package/src/utils/const.js.map

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package/src/utils/macromolecule/monomers.d.ts.map

@@ -1 +1 @@
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package/src/utils/macromolecule/monomers.js.map

@@ -1 +1 @@
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package/src/utils/macromolecule/types.d.ts

@@ -14,7 +14,7 @@ export interface ISeqSplitted {
 }
 export interface INotationProvider {
     get splitter(): SplitterFunc;
-    getHelm(seqCol: DG.Column<string>): Promise<DG.Column<string>>;
+    getHelm(seqCol: DG.Column<string>, options?: any): Promise<DG.Column<string>>;
 }
 export type SeqColStats = {
     freq: MonomerFreqs;

package/src/utils/macromolecule/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,IAAI,UAAU,IAAI,eAAe,CAAC;IAClC,IAAI,SAAS,IAAI,eAAe,CAAC;IAEjC,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEpC,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;CAChE;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,IAAI,UAAU,IAAI,eAAe,CAAC;IAClC,IAAI,SAAS,IAAI,eAAe,CAAC;IAEjC,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEpC,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;CAC/E;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}

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

@@ -0,0 +1,31 @@
+import * as grok from 'datagrok-api/grok';
+import * as DG from 'datagrok-api/dg';
+import { Monomer } from '../types/index';
+export interface INewMonomerForm {
+    get fieldInputs(): {
+        [key: string]: DG.InputBase<any> | grok.chem.Sketcher;
+    };
+    get form(): HTMLElement;
+    get rgroupInputs(): {
+        [key: string]: DG.InputBase<any>;
+    }[];
+    get metaInputs(): {
+        [key: string]: DG.InputBase<any>;
+    }[];
+    setMonomer(monomer: Monomer): void;
+}
+export interface IMonomerGallery {
+    get monomerGallery(): HTMLElement;
+    groupBy(by: string): void;
+    filterBySearch(search: string): void;
+}
+export interface IMonomerManager {
+    /** Creates new monomer library in correct folder and adds given monomers */
+    createNewMonomerLib(libName: string, monomers: Monomer[]): Promise<void>;
+    cloneMonomer(dfRow: DG.Row): Monomer;
+    getNewMonomerForm(): INewMonomerForm;
+}
+export declare const MonomerInputProperties: {
+    [key: string]: DG.Property;
+};
+//# sourceMappingURL=monomer-ui.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-ui.d.ts","sourceRoot":"","sources":["monomer-ui.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAC1C,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,OAAO,EAAC,MAAM,gBAAgB,CAAC;AAGvC,MAAM,WAAW,eAAe;IAC9B,IAAI,WAAW,IAAI;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAA;KAAE,CAAC;IAC7E,IAAI,IAAI,IAAI,WAAW,CAAC;IACxB,IAAI,YAAY,IAAI;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;KAAE,EAAE,CAAC;IAC3D,IAAI,UAAU,IAAI;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;KAAE,EAAE,CAAC;IACzD,UAAU,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAAC;CACpC;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,cAAc,IAAI,WAAW,CAAC;IAClC,OAAO,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CACtC;AAED,MAAM,WAAW,eAAe;IAE9B,4EAA4E;IAC5E,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEzE,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,GAAG,GAAG,OAAO,CAAC;IAErC,iBAAiB,IAAI,eAAe,CAAC;CAGtC;AAED,eAAO,MAAM,sBAAsB,EAAE;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,EAAE,CAAC,QAAQ,CAAA;CAQhE,CAAC"}

package/src/utils/monomer-ui.js

@@ -0,0 +1,11 @@
+import * as DG from 'datagrok-api/dg';
+export const MonomerInputProperties = {
+    'monomerType': DG.Property.js('monomerType', DG.TYPE.STRING, { choices: ["Backbone" /* MonomerTypes.BACKBONE */, "Branch" /* MonomerTypes.BRANCH */, "Terminal" /* MonomerTypes.TERMINAL */] }),
+    'molecule': DG.Property.fromOptions({ name: 'molecule', type: DG.InputType.Molecule }),
+    'name': DG.Property.js('name', DG.TYPE.STRING),
+    'naturalAnalog': DG.Property.js('naturalAnalog', DG.TYPE.STRING),
+    'id': DG.Property.js('id', DG.TYPE.INT),
+    'polymerType': DG.Property.js('polymerType', DG.TYPE.STRING, { choices: ["RNA" /* PolymerTypes.RNA */, "PEPTIDE" /* PolymerTypes.PEPTIDE */, "CHEM" /* PolymerTypes.CHEM */, "BLOB" /* PolymerTypes.BLOB */, "G" /* PolymerTypes.G */] }),
+    'symbol': DG.Property.js('symbol', DG.TYPE.STRING),
+};
+//# sourceMappingURL=monomer-ui.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-ui.js","sourceRoot":"","sources":["monomer-ui.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AA+BtC,MAAM,CAAC,MAAM,sBAAsB,GAAmC;IACpE,aAAa,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,aAAa,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,EAAE,EAAC,OAAO,EAAE,oHAAmE,EAAC,CAAC;IAC5I,UAAU,EAAE,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAC,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,EAAE,CAAC,SAAS,CAAC,QAAQ,EAAC,CAAC;IACpF,MAAM,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC;IAC9C,eAAe,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,eAAe,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC;IAChE,IAAI,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC;IACvC,aAAa,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,aAAa,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,EAAE,EAAC,OAAO,EAAE,8JAA8F,EAAC,CAAC;IACvK,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,QAAQ,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC;CACnD,CAAC"}

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

@@ -46,7 +46,7 @@ export declare class SeqHandler {
     private columnVersion;
     getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
     /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
-    getHelm(rowIdx: number): Promise<string>;
+    getHelm(rowIdx: number, options?: any): Promise<string>;
     private _stats;
     get stats(): SeqColStats;
     private _maxLength;

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

@@ -1 +1 @@
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package/src/utils/seq-handler.js

@@ -224,10 +224,10 @@ export class SeqHandler {
         }
     }
     /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
-    async getHelm(rowIdx) {
+    async getHelm(rowIdx, options) {
         const seq = this.column.get(rowIdx);
         if (this.notationProvider) {
-            const helmCol = await this.notationProvider.getHelm(this.column);
+            const helmCol = await this.notationProvider.getHelm(this.column, options);
             return helmCol.get(rowIdx);
         }
         else
@@ -671,6 +671,8 @@ export class SeqHandler {
         return joinToSeparator(srcSS, tgtSeparator, this.isHelm());
     }
     convertToHelm(src) {
+        if (this.notation == NOTATION.HELM)
+            return src;
         const wrappers = this.getHelmWrappers();
         const isDnaOrRna = src.startsWith('DNA') || src.startsWith('RNA');
         const srcSS = this.splitter(src);

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

@@ -1 +1 @@
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