npm - @datagrok-libraries/bio - Versions diffs - 5.42.11 → 5.42.13 - Mend

@datagrok-libraries/bio 5.42.11 → 5.42.13

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/CHANGELOG.md +8 -0
package/package.json +3 -3
package/src/monomer-works/lib-settings.d.ts +2 -2
package/src/monomer-works/lib-settings.d.ts.map +1 -1
package/src/monomer-works/lib-settings.js +4 -2
package/src/monomer-works/lib-settings.js.map +1 -1
package/src/monomer-works/monomer-utils.d.ts +26 -1
package/src/monomer-works/monomer-utils.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.js.map +1 -1
package/src/monomer-works/types.d.ts +6 -0
package/src/monomer-works/types.d.ts.map +1 -1
package/src/types/index.d.ts +2 -0
package/src/types/index.d.ts.map +1 -1
package/src/types/index.js.map +1 -1
package/src/utils/const.d.ts +16 -11
package/src/utils/const.d.ts.map +1 -1
package/src/utils/const.js +10 -0
package/src/utils/const.js.map +1 -1
package/src/utils/macromolecule/monomers.d.ts +66 -0
package/src/utils/macromolecule/monomers.d.ts.map +1 -0
package/src/utils/macromolecule/monomers.js +230 -0
package/src/utils/macromolecule/monomers.js.map +1 -0
package/src/utils/macromolecule/types.d.ts +2 -0
package/src/utils/macromolecule/types.d.ts.map +1 -1
package/src/utils/macromolecule/types.js.map +1 -1
package/src/utils/seq-handler.d.ts +3 -1
package/src/utils/seq-handler.d.ts.map +1 -1
package/src/utils/seq-handler.js +11 -1
package/src/utils/seq-handler.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,13 @@
 # bio changelog
+## 5.42.13 (2024-09-02)
+* Add interfaces for monomer management
+## 5.42.12 (2024-08-30)
+Add getHelm to SeqHandler and INotationProvider
 ## 5.42.11 (2024-08-24)
 ### Bug fixes

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.11",
+  "version": "5.42.13",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.5",
@@ -27,8 +27,8 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.9",
-    "@datagrok-libraries/js-draw-lite": "^0.0.7",
+    "@datagrok-libraries/helm-web-editor": "^1.1.11",
+    "@datagrok-libraries/js-draw-lite": "^0.0.8",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",

package/src/monomer-works/lib-settings.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 import { UserLibSettings } from './types';
-export declare const LIB_STORAGE_NAME: string;
-export declare const LIB_PATH: string;
+export declare const LIB_STORAGE_NAME = "Libraries";
+export declare const LIB_PATH = "System:AppData/Bio/monomer-libraries/";
 export declare const SETS_STORAGE_NAME: string;
 export declare const SETS_PATH: string;
 export declare function getUserLibSettings(): Promise<UserLibSettings>;

package/src/monomer-works/lib-settings.d.ts.map CHANGED Viewed

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

@@ -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: [] };
+const LIB_SETTINGS_FOR_TESTS = { explicit: ['HELMCoreLibrary.json'], exclude: [], duplicateMonomerPreferences: {} };
 export const SETS_STORAGE_NAME = 'Monomer Sets';
 export const SETS_PATH = 'System:AppData/Bio/monomer-sets/';
 let userLibSettingsPromise = Promise.resolve();
@@ -10,10 +10,12 @@ export async function getUserLibSettings() {
     let res;
     userLibSettingsPromise = userLibSettingsPromise.then(async () => {
         const resStr = await grok.dapi.userDataStorage.getValue(LIB_STORAGE_NAME, 'Settings', true);
-        res = resStr ? JSON.parse(resStr) : { exclude: [], explicit: [] };
+        res = resStr ? JSON.parse(resStr) : { exclude: [], explicit: [], duplicateMonomerPreferences: {} };
         // Fix empty object returned in case there is no settings stored for user
         res.exclude = res.exclude instanceof Array ? res.exclude : [];
         res.explicit = res.explicit instanceof Array ? res.explicit : [];
+        res.duplicateMonomerPreferences = res.duplicateMonomerPreferences instanceof Object ?
+            res.duplicateMonomerPreferences : {};
         console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(res, undefined, 2)}`);
     });
     await userLibSettingsPromise;

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

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

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
 import { Observable } from 'rxjs';
-import { IMonomerLib, IMonomerSet } from '../types/index';
+import { IMonomerLib, Monomer, 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;
@@ -23,6 +24,30 @@ 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 */

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package/src/monomer-works/types.d.ts CHANGED Viewed

@@ -6,6 +6,12 @@ export interface ITypedArray {
 export type UserLibSettings = {
     exclude: string[];
     explicit: string[];
+    /** Libraries might contain different monomers for same symbol. Object for monomer symbol to library name of choice*/
+    duplicateMonomerPreferences: {
+        [polymerType: string]: {
+            [monomerSymbol: string]: string;
+        };
+    };
 };
 /** Stores necessary data about atoms of a monomer parsed from Molfile */
 export type Atoms = {

package/src/monomer-works/types.d.ts.map CHANGED Viewed

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

@@ -1,6 +1,7 @@
 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;
@@ -64,6 +65,7 @@ export interface IMonomerLib {
     getMonomerSymbolsByType(polymerType: PolymerType): string[];
     getPolymerTypes(): PolymerType[];
     update(lib: IMonomerLib): void;
+    toJSON(): Monomer[];
     get onChanged(): Observable<any>;
     /** Summary string with lib monomer count by type
      * @deprecated Keep for backward compatibility */

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

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

	@@ -1 +1 @@
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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"}

package/src/utils/const.d.ts CHANGED Viewed

@@ -1,9 +1,11 @@
+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 {
@@ -58,17 +60,20 @@ export declare const jsonSdfMonomerLibDict: {
     symbol: string;
 };
 export declare const DUMMY_MONOMER: {
-    monomerType: MonomerType;
-    smiles: string;
-    name: string;
-    author: string;
-    molfile: string;
-    naturalAnalog: string;
-    rgroups: RGroup[];
-    createDate: null;
-    id: number;
-    polymerType: PolymerType;
-    symbol: string;
+    readonly monomerType: MonomerType;
+    readonly smiles: "";
+    readonly name: "";
+    readonly author: "Datagrok";
+    readonly molfile: "";
+    readonly naturalAnalog: "";
+    readonly rgroups: RGroup[];
+    readonly createDate: null;
+    readonly id: 0;
+    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;

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

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

@@ -1,3 +1,4 @@
+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 */,
@@ -35,6 +36,15 @@ 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;

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package/src/utils/macromolecule/monomers.d.ts ADDED Viewed

@@ -0,0 +1,66 @@
+import BitArray from '@datagrok-libraries/utils/src/bit-array';
+export declare const naturalMonomers: {
+    RNA: {
+        A: string;
+        C: string;
+        G: string;
+        T: string;
+        U: string;
+    };
+    PEPTIDE: {
+        A: string;
+        C: string;
+        D: string;
+        E: string;
+        F: string;
+        G: string;
+        H: string;
+        I: string;
+        K: string;
+        L: string;
+        M: string;
+        N: string;
+        P: string;
+        Q: string;
+        R: string;
+        S: string;
+        T: string;
+        V: string;
+        W: string;
+        Y: string;
+    };
+};
+export declare const naturalMonomerFps: {
+    RNA: {
+        A: BitArray;
+        C: BitArray;
+        G: BitArray;
+        T: BitArray;
+        U: BitArray;
+    };
+    PEPTIDE: {
+        A: BitArray;
+        C: BitArray;
+        D: BitArray;
+        E: BitArray;
+        F: BitArray;
+        G: BitArray;
+        H: BitArray;
+        I: BitArray;
+        K: BitArray;
+        L: BitArray;
+        M: BitArray;
+        N: BitArray;
+        P: BitArray;
+        Q: BitArray;
+        R: BitArray;
+        S: BitArray;
+        T: BitArray;
+        V: BitArray;
+        W: BitArray;
+        Y: BitArray;
+    };
+};
+export declare function getMorganFingerprint(molString: string): Promise<BitArray | null | undefined>;
+export declare function mostSimilarNaturalAnalog(molString: string, monomerType: string, threshold?: number): Promise<string | null>;
+//# sourceMappingURL=monomers.d.ts.map

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

	@@ -0,0 +1 @@
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package/src/utils/macromolecule/monomers.js ADDED Viewed

@@ -0,0 +1,230 @@
+import * as DG from 'datagrok-api/dg';
+import BitArray from '@datagrok-libraries/utils/src/bit-array';
+import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
+const naturalAASmiles = {
+    A: 'C[C@H](N)C(=O)O',
+    C: 'N[C@@H](CS)C(=O)O',
+    D: 'N[C@@H](CC(=O)O)C(=O)O',
+    E: 'N[C@@H](CCC(=O)O)C(=O)O',
+    F: 'N[C@@H](Cc1ccccc1)C(=O)O',
+    G: 'NCC(=O)O',
+    H: 'N[C@@H](Cc1cnc[nH]1)C(=O)O',
+    I: 'CC[C@H](C)[C@H](N)C(=O)O',
+    K: 'NCCCC[C@H](N)C(=O)O',
+    L: 'CC(C)C[C@H](N)C(=O)O',
+    M: 'CSCC[C@H](N)C(=O)O',
+    N: 'NC(=O)C[C@H](N)C(=O)O',
+    P: 'O=C(O)[C@@H]1CCCN1',
+    Q: 'NC(=O)CC[C@H](N)C(=O)O',
+    R: 'N=C(N)NCCC[C@H](N)C(=O)O',
+    S: 'N[C@@H](CO)C(=O)O',
+    T: 'C[C@@H](O)[C@H](N)C(=O)O',
+    V: 'CC(C)[C@H](N)C(=O)O',
+    W: 'N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O',
+    Y: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O',
+}; // canonical smiles of canonical amino acids
+const naturalAAFps = {
+    A: new BitArray(new Uint32Array([
+        2, 0, 0, 0, 16, 0, 0, 0, 134217728, 0, 0, 0, 32, 0, 33554432, 0, 0, 0, 0,
+        0, 1024, 0, 0, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 524288, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1048576, 0,
+        536870912, 0, 0, 0, 0,
+    ]), 2048),
+    C: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 0, 0, 0, 32, 0, 0, 2, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
+        0, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 65536, 0, 0, 524288, 0, 0, 0, 0,
+        0, 0, 0, 524288, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 34603008, 0,
+        536870912, 64, 0, 0, 0,
+    ]), 2048),
+    D: new BitArray(new Uint32Array([
+        2, 0, 65600, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
+        0, 0, 262400, 128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2097152, 524288, 0, 0, 0,
+        1024, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 512, 0, 0, 34603008, 0,
+        536870912, 0, 0, 0, 0,
+    ]), 2048),
+    E: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
+        0, 8, 262144, 128, 0, 0, 16, 134217728, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0,
+        128, 0, 0, 0, 524288, 0, 0, 0, 268435456, 0, 0, 0, 0, 0, 512, 2147483648,
+        0, 34603008, 0, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    F: new BitArray(new Uint32Array([
+        2, 0, 98304, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
+        0, 0, 262144, 128, 33554432, 0, 0, 0, 0, 33554432, 0, 1024, 1, 0, 524288,
+        32768, 32, 0, 0, 0, 0, 16, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 71303168, 0,
+        0, 34603008, 131072, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    G: new BitArray(new Uint32Array([
+        134217728, 0, 65536, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0,
+        1024, 0, 0, 0, 0, 128, 0, 0, 0, 0, 2097216, 0, 0, 0, 0, 0, 524288, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 512, 0, 0, 0, 0, 536870912,
+        0, 0, 0, 0,
+    ]), 2048),
+    H: new BitArray(new Uint32Array([
+        2, 0, 1073840128, 0, 0, 0, 0, 0, 0, 0, 0, 67108864, 32, 0, 0, 0, 0, 0, 0,
+        0, 1024, 0, 512, 0, 262144, 192, 0, 268435456, 0, 0, 8200, 0, 0, 0,
+        67108864, 0, 524296, 0, 32, 0, 0, 0, 0, 16, 524288, 0, 0, 2147483648, 0,
+        0, 8, 0, 0, 0, 0, 0, 0, 34603008, 131072, 536870920, 4194304, 0, 0, 0,
+    ]), 2048),
+    I: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 0, 0, 0, 0, 150994944, 64, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0,
+        1024, 0, 8388608, 0, 327680, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 524288,
+        524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 256, 0, 0, 0, 0, 8388608, 0,
+        33554432, 0, 1048576, 0, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    K: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 0, 0, 0, 0, 0, 0, 0, 0, 268435488, 0, 0, 0, 0, 0, 0, 0,
+        1024, 0, 0, 8, 262144, 128, 0, 0, 0, 0, 2097152, 0, 0, 67108864, 0, 0,
+        524288, 0, 0, 0, 8, 0, 0, 0, 524288, 0, 0, 8192, 0, 0, 0, 0, 0, 0, 0,
+        2147483648, 0, 34668544, 0, 545259520, 0, 0, 0, 0,
+    ]), 2048),
+    L: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 0, 0, 0, 0, 134217728, 0, 0, 0, 32, 512, 0, 0, 0, 0, 0, 0,
+        1024, 256, 0, 8388608, 262400, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 524288,
+        0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 42991616,
+        0, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    M: new BitArray(new Uint32Array([
+        2050, 0, 65536, 1048576, 0, 0, 0, 0, 0, 0, 0, 0, 1056, 0, 0, 0, 0, 0, 0,
+        0, 1024, 0, 0, 8, 262144, 128, 0, 0, 0, 0, 0, 536870912, 0, 2, 0, 0,
+        1074266112, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 4194304, 0, 0, 0, 0, 0,
+        0, 2147483648, 0, 34603008, 0, 536870912, 4194304, 0, 0, 0,
+    ]), 2048),
+    N: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 4096, 0, 0, 0, 0, 0, 0, 16777216, 32, 0, 0, 0, 0, 0, 0, 0,
+        1024, 0, 0, 0, 262400, 128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0,
+        1024, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 34603008, 0,
+        536871936, 67108864, 0, 0, 0,
+    ]), 2048),
+    P: new BitArray(new Uint32Array([
+        0, 0, 1024, 0, 0, 0, 0, 0, 0, 131072, 0, 1024, 32, 0, 0, 0, 0, 512, 0, 0,
+        1024, 0, 0, 64, 0, 128, 0, 0, 1073741824, 0, 0, 138412032, 16, 0,
+        67108864, 0, 0, 0, 0, 0, 0, 8192, 0, 0, 8388608, 0, 0, 8, 0, 0, 0, 0, 0,
+        0, 256, 0, 0, 0, 0, 553648128, 0, 0, 0, 0,
+    ]), 2048),
+    Q: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 4096, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 2, 0, 0, 1024,
+        0, 0, 8, 262144, 128, 0, 0, 16, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 0,
+        0, 0, 0, 524288, 0, 0, 0, 268435456, 0, 0, 0, 0, 0, 16777216, 2147483648,
+        0, 34603008, 0, 536871936, 0, 0, 0, 0,
+    ]), 2048),
+    R: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 4096, 0, 32, 0, 0, 0, 0, 0, 268435488, 0, 0, 0, 0, 0, 0,
+        32768, 134218752, 0, 16, 8, 262144, 128, 0, 1073741824, 0, 0, 8388608, 0,
+        0, 0, 65536, 0, 524289, 0, 0, 0, 0, 0, 0, 0, 524288, 2048, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 2147483648, 0, 34603008, 1048576, 545259520, 0, 0, 0, 0,
+    ]), 2048),
+    S: new BitArray(new Uint32Array([
+        2, 0, 65536, 0, 0, 0, 1073741824, 0, 0, 0, 0, 0, 32, 0, 0, 4, 0, 0, 0, 0,
+        1024, 0, 0, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0,
+        1048576, 0, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8388608, 0, 0,
+        34603008, 0, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    T: new BitArray(new Uint32Array([
+        2, 0, 0, 0, 0, 0, 0, 8, 134217728, 0, 0, 67108864, 32, 0, 0, 0, 0, 0, 0,
+        0, 1024, 0, 8388608, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 524288,
+        524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 536870912, 0, 0, 0,
+        0, 1048576, 67108864, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    V: new BitArray(new Uint32Array([
+        2, 0, 0, 0, 0, 0, 0, 0, 134217728, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024,
+        0, 8388608, 0, 262144, 128, 0, 0, 0, 0, 0, 1073741824, 128, 2, 0, 524288,
+        524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8192, 0,
+        1048576, 0, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+    W: new BitArray(new Uint32Array([
+        2, 0, 98304, 8388608, 0, 0, 0, 0, 0, 0, 256, 4096, 32, 0, 0, 0, 0, 0, 0,
+        0, 1024, 0, 0, 0, 262144, 192, 0, 0, 0, 0, 0, 0, 0, 0, 67108865, 0,
+        524288, 32768, 32, 0, 0, 0, 8224, 16, 524288, 0, 0, 0, 0, 32, 128, 0,
+        2097152, 0, 4194304, 8388608, 0, 34603008, 8519680, 536870912, 131072,
+        262144, 0, 0,
+    ]), 2048),
+    Y: new BitArray(new Uint32Array([
+        2, 0, 98304, 0, 0, 0, 0, 0, 0, 4194304, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0,
+        1024, 0, 0, 512, 262144, 128, 33554432, 0, 0, 0, 0, 33554432, 0, 0, 0, 0,
+        524288, 0, 32, 0, 0, 2, 0, 16, 524288, 0, 0, 0, 0, 0, 4, 0, 0, 0,
+        71303168, 262144, 0, 34603008, 131072, 536870912, 0, 0, 0, 0,
+    ]), 2048),
+};
+const naturalRNASmiles = {
+    A: 'Nc1ncnc2[nH]cnc12',
+    C: 'Nc1cc[nH]c(=O)n1',
+    G: 'Nc1nc2[nH]cnc2c(=O)[nH]1',
+    T: 'Cc1c[nH]c(=O)[nH]c1=O',
+    U: 'O=c1cc[nH]c(=O)[nH]1',
+}; // canonical smiles of canonical NAs
+const naturalRNAFps = {
+    A: new BitArray(new Uint32Array([
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 1024, 0, 67108864, 0, 0, 0, 512, 0, 0, 0,
+        8388608, 0, 0, 512, 0, 0, 64, 4, 0, 0, 0, 4, 0, 0, 0, 67108864, 0, 524289,
+        0, 0, 0, 0, 0, 0, 16, 0, 659456, 0, 256, 0, 16, 0, 0, 0, 268435456, 0, 0,
+        262144, 0, 131072, 0, 0, 0, 8388608, 0,
+    ]), 2048),
+    C: new BitArray(new Uint32Array([
+        0, 1073741824, 0, 0, 0, 0, 0, 2147483648, 4, 67108864, 0, 67108864, 0, 256,
+        0, 0, 0, 0, 0, 0, 1024, 0, 128, 0, 0, 64, 0, 0, 0, 0, 0, 0, 0, 0, 67108864,
+        0, 524289, 0, 65536, 0, 0, 0, 0, 16, 0, 131072, 0, 4, 0, 0, 0, 0, 0, 0,
+        4194304, 0, 0, 2147483648, 131072, 0, 4096, 0, 0, 0,
+    ]), 2048),
+    G: new BitArray(new Uint32Array([
+        0, 0, 0, 0, 1024, 0, 0, 0, 0, 67109888, 16384, 67108864, 0, 0, 0, 0, 0, 0,
+        0, 33562624, 1024, 33554432, 512, 16384, 0, 64, 4, 0, 0, 33554432, 0, 0, 0,
+        0, 67108864, 0, 524289, 0, 0, 0, 0, 0, 0, 16, 0, 135168, 0, 268435456, 0, 0,
+        0, 0, 0, 268435456, 131072, 0, 0, 2147483648, 131072, 0, 0, 0, 8388608, 0,
+    ]), 2048),
+    T: new BitArray(new Uint32Array([
+        8388608, 0, 0, 0, 0, 0, 0, 0, 0, 67108864, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0,
+        1024, 0, 0, 16384, 0, 64, 0, 0, 0, 0, 0, 0, 0, 2, 67108864, 0, 0, 0, 0, 0,
+        0, 0, 0, 40976, 0, 0, 0, 0, 0, 0, 0, 0, 0, 67108864, 131072, 524288, 0, 0,
+        8519680, 0, 1, 33554432, 1048576, 0,
+    ]), 2048),
+    U: new BitArray(new Uint32Array([
+        0, 0, 131072, 1073741824, 0, 0, 0, 0, 0, 67108864, 0, 0, 0, 0, 0, 0, 0, 0,
+        0, 0, 1024, 0, 128, 0, 0, 64, 0, 0, 0, 0, 0, 0, 0, 32768, 67108864, 0, 0, 0,
+        0, 0, 0, 0, 0, 16, 0, 0, 0, 4, 0, 0, 2048, 0, 0, 0, 4341760, 0, 0, 0,
+        131072, 0, 0, 33554432, 1048576, 0,
+    ]), 2048),
+};
+export const naturalMonomers = {
+    RNA: naturalRNASmiles,
+    PEPTIDE: naturalAASmiles,
+};
+export const naturalMonomerFps = {
+    RNA: naturalRNAFps,
+    PEPTIDE: naturalAAFps,
+};
+export async function getMorganFingerprint(molString) {
+    const func = DG.Func.find({
+        package: 'Chem',
+        name: 'getMorganFingerprint',
+    })?.[0];
+    if (!func)
+        return null;
+    try {
+        const res = (await func.apply({ molString }))?.getBuffer().buffer;
+        if (res)
+            return new BitArray(new Uint32Array(res), 2048);
+    }
+    catch (_e) {
+        return null;
+    }
+}
+export async function mostSimilarNaturalAnalog(molString, monomerType, threshold = 0) {
+    if (!Object.keys(naturalMonomerFps).includes(monomerType))
+        return null;
+    const morganFp = await getMorganFingerprint(molString);
+    if (!morganFp)
+        return null;
+    const naturalFps = naturalMonomerFps[monomerType];
+    let maxSim = 0;
+    let mostSimilar = null;
+    for (const [name, fp] of Object.entries(naturalFps)) {
+        const sim = tanimotoSimilarity(morganFp, fp);
+        if (sim > maxSim && sim >= threshold) {
+            maxSim = sim;
+            mostSimilar = name;
+        }
+    }
+    return mostSimilar;
+}
+//# sourceMappingURL=monomers.js.map

package/src/utils/macromolecule/monomers.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/src/utils/macromolecule/types.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import * as DG from 'datagrok-api/dg';
 /** Canonical gap symbol */
 export declare const GAP_SYMBOL: string;
 export type SeqSplittedBase = ArrayLike<string> & Iterable<string>;
@@ -13,6 +14,7 @@ export interface ISeqSplitted {
 }
 export interface INotationProvider {
     get splitter(): SplitterFunc;
+    getHelm(seqCol: DG.Column<string>): Promise<DG.Column<string>>;
 }
 export type SeqColStats = {
     freq: MonomerFreqs;

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

	@@ -1 +1 @@
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package/src/utils/macromolecule/types.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { NOTATION } from './macromolecule';
-import { ISeqSplitted, SeqColStats, SplitterFunc, INotationProvider } from './macromolecule/types';
+import { INotationProvider, ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
 export declare const SeqTemps: {
@@ -45,6 +45,8 @@ export declare class SeqHandler {
     private _splitted;
     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>;
     private _stats;
     get stats(): SeqColStats;
     private _maxLength;

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package/src/utils/seq-handler.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { TAGS, ALPHABET, NOTATION, candidateAlphabets, positionSeparator, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, } from './macromolecule';
+import { ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS } from './macromolecule';
 import { GAP_SYMBOL, } from './macromolecule/types';
 import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
@@ -223,6 +223,16 @@ export class SeqHandler {
             return resSS;
         }
     }
+    /** Any Macromolecule can be represented on Helm format. The reverse is not always possible. */
+    async getHelm(rowIdx) {
+        const seq = this.column.get(rowIdx);
+        if (this.notationProvider) {
+            const helmCol = await this.notationProvider.getHelm(this.column);
+            return helmCol.get(rowIdx);
+        }
+        else
+            return this.convertToHelm(seq);
+    }
     get stats() {
         if (this._stats === null) {
             const freq = {};

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

	@@ -1 +1 @@
1	- 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