@datagrok-libraries/bio - npm Package Compare versions

Comparing version 5.42.12 to 5.42.13

CHANGELOG.md

 # bio changelog
 
+## 5.42.13 (2024-09-02)
+
+* Add interfaces for monomer management
+
 ## 5.42.12 (2024-08-30)
@@ -4,0 +8,0 @@

package.json

@@ -11,3 +11,3 @@ {
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.12",
+  "version": "5.42.13",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
@@ -14,0 +14,0 @@ "dependencies": {

src/monomer-works/lib-settings.d.ts

 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;
@@ -5,0 +5,0 @@ export declare const SETS_PATH: string;

src/monomer-works/lib-settings.js

@@ -5,3 +5,3 @@ import * as grok from 'datagrok-api/grok';
 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';
@@ -14,6 +14,8 @@ export const SETS_PATH = 'System:AppData/Bio/monomer-sets/';
         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)}`);
@@ -20,0 +22,0 @@ });

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

 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';
@@ -26,2 +27,26 @@ export declare function encodeMonomers(col: DG.Column): DG.Column | null;
 }
+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 {
@@ -28,0 +53,0 @@ get eventManager(): IMonomerLibFileEventManager;

src/monomer-works/types.d.ts

@@ -9,2 +9,8 @@ export interface ITypedArray {
     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;
+        };
+    };
 };
@@ -11,0 +17,0 @@ /** Stores necessary data about atoms of a monomer parsed from Molfile */

src/types/index.d.ts

 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';
@@ -67,2 +68,3 @@ export type RGroup = {
     update(lib: IMonomerLib): void;
+    toJSON(): Monomer[];
     get onChanged(): Observable<any>;
@@ -69,0 +71,0 @@ /** Summary string with lib monomer count by type

src/utils/const.d.ts

@@ -0,1 +1,2 @@
+import * as DG from 'datagrok-api/dg';
 import { MonomerType, PolymerType } from '../helm/types';
@@ -7,2 +8,3 @@ import { MonomerTypes, PolymerTypes } from '../helm/consts';
 export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
+export { PolymerTypes, MonomerTypes };
 /** Required HELM library monomer fields:
@@ -62,14 +64,17 @@ * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
 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;
@@ -76,0 +81,0 @@ export declare const MONOMER_ENCODE_MAX = 1034;

src/utils/const.js

@@ -0,1 +1,2 @@
+import * as DG from 'datagrok-api/dg';
 // core fields of HELM library object used in toAtomicLevel function
@@ -38,2 +39,11 @@ export const HELM_CORE_FIELDS = [
 };
+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
@@ -40,0 +50,0 @@ export const MONOMER_ENCODE_MIN = 0x100;

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Improved metrics

Total package byte prevSize

759146

increased by5.25%

Number of package files

335

increased by1.21%

Lines of code

9425

increased by3.79%

No dependency changes