@datagrok-libraries/bio 5.42.12 → 5.42.13

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Files changed (22) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/package.json +1 -1
  3. package/src/monomer-works/lib-settings.d.ts +2 -2
  4. package/src/monomer-works/lib-settings.d.ts.map +1 -1
  5. package/src/monomer-works/lib-settings.js +4 -2
  6. package/src/monomer-works/lib-settings.js.map +1 -1
  7. package/src/monomer-works/monomer-utils.d.ts +26 -1
  8. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  9. package/src/monomer-works/monomer-utils.js.map +1 -1
  10. package/src/monomer-works/types.d.ts +6 -0
  11. package/src/monomer-works/types.d.ts.map +1 -1
  12. package/src/types/index.d.ts +2 -0
  13. package/src/types/index.d.ts.map +1 -1
  14. package/src/types/index.js.map +1 -1
  15. package/src/utils/const.d.ts +16 -11
  16. package/src/utils/const.d.ts.map +1 -1
  17. package/src/utils/const.js +10 -0
  18. package/src/utils/const.js.map +1 -1
  19. package/src/utils/macromolecule/monomers.d.ts +66 -0
  20. package/src/utils/macromolecule/monomers.d.ts.map +1 -0
  21. package/src/utils/macromolecule/monomers.js +230 -0
  22. package/src/utils/macromolecule/monomers.js.map +1 -0
package/CHANGELOG.md CHANGED
@@ -1,5 +1,9 @@
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  # bio changelog
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+ ## 5.42.13 (2024-09-02)
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+
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+ * Add interfaces for monomer management
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+
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  ## 5.42.12 (2024-08-30)
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  Add getHelm to SeqHandler and INotationProvider
package/package.json CHANGED
@@ -8,7 +8,7 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.42.12",
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+ "version": "5.42.13",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/chem-meta": "^1.2.5",
package/src/monomer-works/lib-settings.d.ts CHANGED
@@ -1,6 +1,6 @@
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1
  import { UserLibSettings } from './types';
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- export declare const LIB_STORAGE_NAME: string;
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- export declare const LIB_PATH: string;
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+ export declare const LIB_STORAGE_NAME = "Libraries";
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+ export declare const LIB_PATH = "System:AppData/Bio/monomer-libraries/";
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  export declare const SETS_STORAGE_NAME: string;
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  export declare const SETS_PATH: string;
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  export declare function getUserLibSettings(): Promise<UserLibSettings>;
package/src/monomer-works/lib-settings.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"lib-settings.d.ts","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,eAAe,EAAC,MAAM,SAAS,CAAC;AAGxC,eAAO,MAAM,gBAAgB,EAAE,MAAoB,CAAC;AACpD,eAAO,MAAM,QAAQ,EAAE,MAAgD,CAAC;AAGxE,eAAO,MAAM,iBAAiB,EAAE,MAAuB,CAAC;AACxD,eAAO,MAAM,SAAS,EAAE,MAA2C,CAAC;AAIpE,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,eAAe,CAAC,CAanE;AAED,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAM9E;AAED,oCAAoC;AACpC,wBAAsB,0BAA0B,IAAI,OAAO,CAAC,IAAI,CAAC,CAEhE"}
1
+ {"version":3,"file":"lib-settings.d.ts","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,eAAe,EAAC,MAAM,SAAS,CAAC;AAGxC,eAAO,MAAM,gBAAgB,cAAc,CAAC;AAC5C,eAAO,MAAM,QAAQ,0CAA0C,CAAC;AAIhE,eAAO,MAAM,iBAAiB,EAAE,MAAuB,CAAC;AACxD,eAAO,MAAM,SAAS,EAAE,MAA2C,CAAC;AAIpE,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,eAAe,CAAC,CAenE;AAED,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAM9E;AAED,oCAAoC;AACpC,wBAAsB,0BAA0B,IAAI,OAAO,CAAC,IAAI,CAAC,CAEhE"}
package/src/monomer-works/lib-settings.js CHANGED
@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
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  // -- Monomer libraries --
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  export const LIB_STORAGE_NAME = 'Libraries';
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  export const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
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- const LIB_SETTINGS_FOR_TESTS = { explicit: ['HELMCoreLibrary.json'], exclude: [] };
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+ const LIB_SETTINGS_FOR_TESTS = { explicit: ['HELMCoreLibrary.json'], exclude: [], duplicateMonomerPreferences: {} };
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  export const SETS_STORAGE_NAME = 'Monomer Sets';
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  export const SETS_PATH = 'System:AppData/Bio/monomer-sets/';
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  let userLibSettingsPromise = Promise.resolve();
@@ -10,10 +10,12 @@ export async function getUserLibSettings() {
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  let res;
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  userLibSettingsPromise = userLibSettingsPromise.then(async () => {
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12
  const resStr = await grok.dapi.userDataStorage.getValue(LIB_STORAGE_NAME, 'Settings', true);
13
- res = resStr ? JSON.parse(resStr) : { exclude: [], explicit: [] };
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+ res = resStr ? JSON.parse(resStr) : { exclude: [], explicit: [], duplicateMonomerPreferences: {} };
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  // Fix empty object returned in case there is no settings stored for user
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  res.exclude = res.exclude instanceof Array ? res.exclude : [];
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  res.explicit = res.explicit instanceof Array ? res.explicit : [];
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+ res.duplicateMonomerPreferences = res.duplicateMonomerPreferences instanceof Object ?
18
+ res.duplicateMonomerPreferences : {};
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  console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(res, undefined, 2)}`);
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  });
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  await userLibSettingsPromise;
package/src/monomer-works/lib-settings.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"lib-settings.js","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAG1C,0BAA0B;AAC1B,MAAM,CAAC,MAAM,gBAAgB,GAAW,WAAW,CAAC;AACpD,MAAM,CAAC,MAAM,QAAQ,GAAW,uCAAuC,CAAC;AACxE,MAAM,sBAAsB,GAAoB,EAAC,QAAQ,EAAE,CAAC,sBAAsB,CAAC,EAAE,OAAO,EAAE,EAAE,EAAC,CAAC;AAElG,MAAM,CAAC,MAAM,iBAAiB,GAAW,cAAc,CAAC;AACxD,MAAM,CAAC,MAAM,SAAS,GAAW,kCAAkC,CAAC;AAEpE,IAAI,sBAAsB,GAAkB,OAAO,CAAC,OAAO,EAAE,CAAC;AAE9D,MAAM,CAAC,KAAK,UAAU,kBAAkB;IACtC,IAAI,GAAoB,CAAC;IACzB,sBAAsB,GAAG,sBAAsB,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAC9D,MAAM,MAAM,GAAW,MAAM,IAAI,CAAC,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,gBAAgB,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC;QACpG,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAC,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAC,CAAC;QAEhE,yEAAyE;QACzE,GAAG,CAAC,OAAO,GAAG,GAAG,CAAC,OAAO,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9D,GAAG,CAAC,QAAQ,GAAG,GAAG,CAAC,QAAQ,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;QACjE,OAAO,CAAC,KAAK,CAAC,8BAA8B,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;IACnF,CAAC,CAAC,CAAC;IACH,MAAM,sBAAsB,CAAC;IAC7B,OAAO,GAAI,CAAC;AACd,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,KAAsB;IAC7D,sBAAsB,GAAG,sBAAsB,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAC9D,OAAO,CAAC,KAAK,CAAC,8BAA8B,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;QACnF,MAAM,IAAI,CAAC,IAAI,CAAC,eAAe,CAAC,SAAS,CAAC,gBAAgB,EAAE,UAAU,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC;IACvG,CAAC,CAAC,CAAC;IACH,MAAM,sBAAsB,CAAC;AAC/B,CAAC;AAED,oCAAoC;AACpC,MAAM,CAAC,KAAK,UAAU,0BAA0B;IAC9C,MAAM,kBAAkB,CAAC,sBAAsB,CAAC,CAAC;AACnD,CAAC"}
1
+ {"version":3,"file":"lib-settings.js","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAG1C,0BAA0B;AAC1B,MAAM,CAAC,MAAM,gBAAgB,GAAG,WAAW,CAAC;AAC5C,MAAM,CAAC,MAAM,QAAQ,GAAG,uCAAuC,CAAC;AAChE,MAAM,sBAAsB,GAC1B,EAAC,QAAQ,EAAE,CAAC,sBAAsB,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,2BAA2B,EAAE,EAAE,EAAC,CAAC;AAErF,MAAM,CAAC,MAAM,iBAAiB,GAAW,cAAc,CAAC;AACxD,MAAM,CAAC,MAAM,SAAS,GAAW,kCAAkC,CAAC;AAEpE,IAAI,sBAAsB,GAAkB,OAAO,CAAC,OAAO,EAAE,CAAC;AAE9D,MAAM,CAAC,KAAK,UAAU,kBAAkB;IACtC,IAAI,GAAoB,CAAC;IACzB,sBAAsB,GAAG,sBAAsB,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAC9D,MAAM,MAAM,GAAW,MAAM,IAAI,CAAC,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,gBAAgB,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC;QACpG,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAC,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,2BAA2B,EAAE,EAAE,EAAC,CAAC;QAEjG,yEAAyE;QACzE,GAAG,CAAC,OAAO,GAAG,GAAG,CAAC,OAAO,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9D,GAAG,CAAC,QAAQ,GAAG,GAAG,CAAC,QAAQ,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;QACjE,GAAG,CAAC,2BAA2B,GAAG,GAAG,CAAC,2BAA2B,YAAY,MAAM,CAAC,CAAC;YACnF,GAAG,CAAC,2BAA2B,CAAC,CAAC,CAAC,EAAE,CAAC;QACvC,OAAO,CAAC,KAAK,CAAC,8BAA8B,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;IACnF,CAAC,CAAC,CAAC;IACH,MAAM,sBAAsB,CAAC;IAC7B,OAAO,GAAI,CAAC;AACd,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,KAAsB;IAC7D,sBAAsB,GAAG,sBAAsB,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAC9D,OAAO,CAAC,KAAK,CAAC,8BAA8B,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;QACnF,MAAM,IAAI,CAAC,IAAI,CAAC,eAAe,CAAC,SAAS,CAAC,gBAAgB,EAAE,UAAU,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC;IACvG,CAAC,CAAC,CAAC;IACH,MAAM,sBAAsB,CAAC;AAC/B,CAAC;AAED,oCAAoC;AACpC,MAAM,CAAC,KAAK,UAAU,0BAA0B;IAC9C,MAAM,kBAAkB,CAAC,sBAAsB,CAAC,CAAC;AACnD,CAAC"}
package/src/monomer-works/monomer-utils.d.ts CHANGED
@@ -1,6 +1,7 @@
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  import * as DG from 'datagrok-api/dg';
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+ import * as grok from 'datagrok-api/grok';
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  import { Observable } from 'rxjs';
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- import { IMonomerLib, IMonomerSet } from '../types/index';
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+ import { IMonomerLib, Monomer, IMonomerSet } from '../types/index';
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  import { ISeqSplitted } from '../utils/macromolecule/types';
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  export declare function encodeMonomers(col: DG.Column): DG.Column | null;
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  export declare function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): any[][] | null;
@@ -23,6 +24,30 @@ export interface IMonomerLibFileManager {
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  deleteLibraryFile(fileName: string): Promise<void>;
24
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  loadLibraryFromFile(path: string, fileName: string): Promise<IMonomerLib>;
25
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  }
27
+ export interface INewMonomerForm {
28
+ get fieldInputs(): {
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+ [key: string]: DG.InputBase<any> | grok.chem.Sketcher;
30
+ };
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+ get form(): HTMLElement;
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+ get rgroupInputs(): {
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+ [key: string]: DG.InputBase<any>;
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+ }[];
35
+ get metaInputs(): {
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+ [key: string]: DG.InputBase<any>;
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+ }[];
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+ setMonomer(monomer: Monomer): void;
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+ }
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+ export interface IMonomerGallery {
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+ get monomerGallery(): HTMLElement;
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+ groupBy(by: string): void;
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+ filterBySearch(search: string): void;
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+ }
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+ export interface IMonomerManager {
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+ /** Creates new monomer library in correct folder and adds given monomers */
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+ createNewMonomerLib(libName: string, monomers: Monomer[]): Promise<void>;
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+ cloneMonomer(dfRow: DG.Row): Monomer;
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+ getNewMonomerForm(): INewMonomerForm;
50
+ }
26
51
  export interface IMonomerLibHelper {
27
52
  get eventManager(): IMonomerLibFileEventManager;
28
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  /** Ensures files are loaded and validated, throws error after timeout */
package/src/monomer-works/monomer-utils.d.ts.map CHANGED
@@ -1 +1 @@
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package/src/monomer-works/types.d.ts CHANGED
@@ -6,6 +6,12 @@ export interface ITypedArray {
6
6
  export type UserLibSettings = {
7
7
  exclude: string[];
8
8
  explicit: string[];
9
+ /** Libraries might contain different monomers for same symbol. Object for monomer symbol to library name of choice*/
10
+ duplicateMonomerPreferences: {
11
+ [polymerType: string]: {
12
+ [monomerSymbol: string]: string;
13
+ };
14
+ };
9
15
  };
10
16
  /** Stores necessary data about atoms of a monomer parsed from Molfile */
11
17
  export type Atoms = {
package/src/monomer-works/types.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AACA,MAAM,WAAW,WAAW;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC;CACtB;AAED,4DAA4D;AAC5D,MAAM,MAAM,eAAe,GAAG;IAC5B,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB,CAAA;AAED,yEAAyE;AACzE,MAAM,MAAM,KAAK,GAAG;IAChB,0CAA0C;IAC1C,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,+CAA+C;IAC/C,CAAC,EAAE,YAAY,CAAC;IAChB,CAAC,EAAE,YAAY,CAAC;IAChB,6CAA6C;IAC7C,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB,CAAA;AAEH,yEAAyE;AACzE,MAAM,MAAM,KAAK,GAAG;IAChB,qDAAqD;IACrD,SAAS,EAAE,WAAW,CAAC;IACvB,2DAA2D;IAC3D,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;IACtB;gEAC4D;IAC5D,iBAAiB,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvC,6CAA6C;IAC7C,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC/B,CAAA;AAED,sFAAsF;AACtF,MAAM,MAAM,eAAe,GAAG;IAC1B;oDACgD;IAChD,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,qFAAqF;IACrF,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,2EAA2E;IAC3E,aAAa,EAAE,MAAM,EAAE,GAAG,IAAI,CAAC;IAC/B,yEAAyE;IACzE,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;CAC/B,CAAA;AAED,MAAM,MAAM,QAAQ,GAAG;IACnB,KAAK,EAAE,KAAK,CAAC;IACb,KAAK,EAAE,KAAK,CAAC;IACb,IAAI,EAAE,eAAe,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAA;CACzB,CAAA;AAED,MAAM,MAAM,KAAK,GAAG;IAChB,CAAC,EAAE,MAAM,CAAC;IACV,CAAC,EAAE,MAAM,CAAA;CACZ,CAAA;AAED,sEAAsE;AACtE,MAAM,MAAM,aAAa,GAAG;IACxB,CAAC,EAAE,MAAM,CAAC;IACV,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,qBAAqB,EAAE,MAAM,EAAE,CAAC;IAChC,kBAAkB,EAAE,MAAM,CAAC;IAC3B,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,gBAAgB,EAAE,MAAM,CAAC;IACzB,UAAU,EAAE,MAAM,CAAC;CAEtB,CAAA;AAED,sEAAsE;AACtE,MAAM,MAAM,aAAa,GAAG;IACxB,KAAK,EAAE,QAAQ,GAAG,IAAI,CAAC;IACvB,SAAS,EAAE,QAAQ,GAAG,IAAI,CAAC;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACrB,CAAA;AAED,sDAAsD;AACtD,MAAM,MAAM,aAAa,GAAG;IACxB,KAAK,EAAE,MAAM,GAAG,IAAI,CAAA;CACvB,CAAA"}
1
+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AACA,MAAM,WAAW,WAAW;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC;CACtB;AAED,4DAA4D;AAC5D,MAAM,MAAM,eAAe,GAAG;IAC5B,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,qHAAqH;IACrH,2BAA2B,EAAE;QAAC,CAAC,WAAW,EAAE,MAAM,GAAG;YAAC,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;SAAC,CAAA;KAAC,CAAA;CACxF,CAAA;AAED,yEAAyE;AACzE,MAAM,MAAM,KAAK,GAAG;IAChB,0CAA0C;IAC1C,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,+CAA+C;IAC/C,CAAC,EAAE,YAAY,CAAC;IAChB,CAAC,EAAE,YAAY,CAAC;IAChB,6CAA6C;IAC7C,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB,CAAA;AAEH,yEAAyE;AACzE,MAAM,MAAM,KAAK,GAAG;IAChB,qDAAqD;IACrD,SAAS,EAAE,WAAW,CAAC;IACvB,2DAA2D;IAC3D,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;IACtB;gEAC4D;IAC5D,iBAAiB,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvC,6CAA6C;IAC7C,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC/B,CAAA;AAED,sFAAsF;AACtF,MAAM,MAAM,eAAe,GAAG;IAC1B;oDACgD;IAChD,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,qFAAqF;IACrF,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,2EAA2E;IAC3E,aAAa,EAAE,MAAM,EAAE,GAAG,IAAI,CAAC;IAC/B,yEAAyE;IACzE,WAAW,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;CAC/B,CAAA;AAED,MAAM,MAAM,QAAQ,GAAG;IACnB,KAAK,EAAE,KAAK,CAAC;IACb,KAAK,EAAE,KAAK,CAAC;IACb,IAAI,EAAE,eAAe,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAA;CACzB,CAAA;AAED,MAAM,MAAM,KAAK,GAAG;IAChB,CAAC,EAAE,MAAM,CAAC;IACV,CAAC,EAAE,MAAM,CAAA;CACZ,CAAA;AAED,sEAAsE;AACtE,MAAM,MAAM,aAAa,GAAG;IACxB,CAAC,EAAE,MAAM,CAAC;IACV,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,qBAAqB,EAAE,MAAM,EAAE,CAAC;IAChC,kBAAkB,EAAE,MAAM,CAAC;IAC3B,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,gBAAgB,EAAE,MAAM,CAAC;IACzB,UAAU,EAAE,MAAM,CAAC;CAEtB,CAAA;AAED,sEAAsE;AACtE,MAAM,MAAM,aAAa,GAAG;IACxB,KAAK,EAAE,QAAQ,GAAG,IAAI,CAAC;IACvB,SAAS,EAAE,QAAQ,GAAG,IAAI,CAAC;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACrB,CAAA;AAED,sDAAsD;AACtD,MAAM,MAAM,aAAa,GAAG;IACxB,KAAK,EAAE,MAAM,GAAG,IAAI,CAAA;CACvB,CAAA"}
package/src/types/index.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { Observable } from 'rxjs';
3
3
  import { HelmType, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
4
+ export { MonomerType, PolymerType };
4
5
  import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
5
6
  export type RGroup = {
6
7
  [RGP.CAP_GROUP_SMILES]: string;
@@ -64,6 +65,7 @@ export interface IMonomerLib {
64
65
  getMonomerSymbolsByType(polymerType: PolymerType): string[];
65
66
  getPolymerTypes(): PolymerType[];
66
67
  update(lib: IMonomerLib): void;
68
+ toJSON(): Monomer[];
67
69
  get onChanged(): Observable<any>;
68
70
  /** Summary string with lib monomer count by type
69
71
  * @deprecated Keep for backward compatibility */
package/src/types/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,EAAC,QAAQ,EAAE,iBAAiB,EAAE,cAAc,EAAE,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AACpG,OAAO,EACL,mBAAmB,IAAI,GAAG,EAC1B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EAAE,iBAAiB,EAC1E,MAAM,gBAAgB,CAAC;AAGxB,MAAM,MAAM,MAAM,GAAG;IACnB,CAAC,GAAG,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC/B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IAC7B,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACrB,CAAA;AAED,wFAAwF;AACxF,MAAM,MAAM,OAAO,GAAG;IACpB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IACnB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IACtB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,WAAW,CAAC;IAChC,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,WAAW,CAAC;IAChC,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC;IAC9B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAC;IAEzC,GAAG,CAAC,EAAE,WAAW,CAAC;IAClB,GAAG,CAAC,EAAE,iBAAiB,CAAC;CACzB,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,GAAG,IAAI,WAAW,CAAC;IACvB,IAAI,MAAM,IAAI,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,WAAW,IAAI,WAAW,CAAC;IAC/B,IAAI,WAAW,IAAI,WAAW,CAAC;IAC/B,IAAI,YAAY,IAAI,gBAAgB,EAAE,CAAC;IAEvC,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,MAAM,IAAI,MAAM,GAAG,SAAS,CAAC;IACjC,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAEhC,IAAI,WAAW,IAAI,MAAM,CAAC;IAC1B,IAAI,YAAY,IAAI,sBAAsB,EAAE,CAAC;CAC9C;AAED,MAAM,MAAM,qBAAqB,GAAG;IAAE,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEtE,MAAM,WAAW,WAAW;IAC1B,IAAI,MAAM,IAAI,MAAM,GAAG,SAAS,CAAC;IACjC,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAGhC,UAAU,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC;IACnF,iBAAiB,CAAC,WAAW,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,CAAC;IAC5E,2BAA2B,CAAC,WAAW,EAAE,WAAW,GAAG;QAAE,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAClG,yBAAyB,CAAC,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACtG,uBAAuB,CAAC,WAAW,EAAE,WAAW,GAAG,MAAM,EAAE,CAAC;IAC5D,eAAe,IAAI,WAAW,EAAE,CAAC;IACjC,MAAM,CAAC,GAAG,EAAE,WAAW,GAAG,IAAI,CAAC;IAC/B,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC;IAEjC;qDACiD;IACjD,UAAU,IAAI,MAAM,CAAC;IAErB,6CAA6C;IAC7C,aAAa,IAAI,qBAAqB,CAAC;IAEvC,0DAA0D;IAC1D,YAAY,IAAI,EAAE,CAAC,SAAS,CAAC;IAE7B,UAAU,CAAC,WAAW,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,GAAG,WAAW,CAAC;IAGzE,aAAa,CAAC,IAAI,EAAE,QAAQ,GAAG,cAAc,GAAG,IAAI,CAAC;CACtD;AAED,eAAO,MAAM,oBAAoB;;;;;CAKhC,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,EAAC,QAAQ,EAAE,iBAAiB,EAAE,cAAc,EAAE,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AACpG,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,CAAC;AAClC,OAAO,EACL,mBAAmB,IAAI,GAAG,EAC1B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EAAE,iBAAiB,EAC1E,MAAM,gBAAgB,CAAC;AAGxB,MAAM,MAAM,MAAM,GAAG;IACnB,CAAC,GAAG,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC/B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IAC7B,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACrB,CAAA;AAED,wFAAwF;AACxF,MAAM,MAAM,OAAO,GAAG;IACpB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IACnB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IACtB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,WAAW,CAAC;IAChC,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,WAAW,CAAC;IAChC,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC;IAC9B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAC;IAEzC,GAAG,CAAC,EAAE,WAAW,CAAC;IAClB,GAAG,CAAC,EAAE,iBAAiB,CAAC;CACzB,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,GAAG,IAAI,WAAW,CAAC;IACvB,IAAI,MAAM,IAAI,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,WAAW,IAAI,WAAW,CAAC;IAC/B,IAAI,WAAW,IAAI,WAAW,CAAC;IAC/B,IAAI,YAAY,IAAI,gBAAgB,EAAE,CAAC;IAEvC,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;CAC3B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,MAAM,IAAI,MAAM,GAAG,SAAS,CAAC;IACjC,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAEhC,IAAI,WAAW,IAAI,MAAM,CAAC;IAC1B,IAAI,YAAY,IAAI,sBAAsB,EAAE,CAAC;CAC9C;AAED,MAAM,MAAM,qBAAqB,GAAG;IAAE,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEtE,MAAM,WAAW,WAAW;IAC1B,IAAI,MAAM,IAAI,MAAM,GAAG,SAAS,CAAC;IACjC,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAGhC,UAAU,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC;IACnF,iBAAiB,CAAC,WAAW,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,CAAC;IAC5E,2BAA2B,CAAC,WAAW,EAAE,WAAW,GAAG;QAAE,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAClG,yBAAyB,CAAC,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACtG,uBAAuB,CAAC,WAAW,EAAE,WAAW,GAAG,MAAM,EAAE,CAAC;IAC5D,eAAe,IAAI,WAAW,EAAE,CAAC;IACjC,MAAM,CAAC,GAAG,EAAE,WAAW,GAAG,IAAI,CAAC;IAC/B,MAAM,IAAI,OAAO,EAAE,CAAC;IACpB,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC;IAEjC;qDACiD;IACjD,UAAU,IAAI,MAAM,CAAC;IAErB,6CAA6C;IAC7C,aAAa,IAAI,qBAAqB,CAAC;IAEvC,0DAA0D;IAC1D,YAAY,IAAI,EAAE,CAAC,SAAS,CAAC;IAE7B,UAAU,CAAC,WAAW,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,GAAG,WAAW,CAAC;IAGzE,aAAa,CAAC,IAAI,EAAE,QAAQ,GAAG,cAAc,GAAG,IAAI,CAAC;CACtD;AAED,eAAO,MAAM,oBAAoB;;;;;CAKhC,CAAC"}
package/src/types/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAWA,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAwFhD,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"}
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
@@ -1,9 +1,11 @@
1
+ import * as DG from 'datagrok-api/dg';
1
2
  import { MonomerType, PolymerType } from '../helm/types';
2
3
  import { MonomerTypes, PolymerTypes } from '../helm/consts';
3
4
  import HELM_POLYMER_TYPE = PolymerTypes;
4
5
  import HELM_MONOMER_TYPE = MonomerTypes;
5
6
  import { RGroup } from '../types';
6
7
  export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
8
+ export { PolymerTypes, MonomerTypes };
7
9
  /** Required HELM library monomer fields:
8
10
  * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
9
11
  export declare const enum HELM_REQUIRED_FIELD {
@@ -58,17 +60,20 @@ export declare const jsonSdfMonomerLibDict: {
58
60
  symbol: string;
59
61
  };
60
62
  export declare const DUMMY_MONOMER: {
61
- monomerType: MonomerType;
62
- smiles: string;
63
- name: string;
64
- author: string;
65
- molfile: string;
66
- naturalAnalog: string;
67
- rgroups: RGroup[];
68
- createDate: null;
69
- id: number;
70
- polymerType: PolymerType;
71
- symbol: string;
63
+ readonly monomerType: MonomerType;
64
+ readonly smiles: "";
65
+ readonly name: "";
66
+ readonly author: "Datagrok";
67
+ readonly molfile: "";
68
+ readonly naturalAnalog: "";
69
+ readonly rgroups: RGroup[];
70
+ readonly createDate: null;
71
+ readonly id: 0;
72
+ readonly polymerType: PolymerType;
73
+ readonly symbol: "";
74
+ };
75
+ export declare const MonomerInputProperties: {
76
+ [key: string]: DG.Property;
72
77
  };
73
78
  export declare const MONOMER_ENCODE_MIN = 256;
74
79
  export declare const MONOMER_ENCODE_MAX = 1034;
package/src/utils/const.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AACvD,OAAO,EAAC,YAAY,EAAE,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE1D,OAAO,iBAAiB,GAAG,YAAY,CAAC;AACxC,OAAO,iBAAiB,GAAG,YAAY,CAAC;AACxC,OAAO,EAAC,MAAM,EAAC,MAAM,UAAU,CAAC;AAEhC,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,CAAC;AAE9C,OAAO,EAAC,YAAY,EAAE,YAAY,EAAC,CAAC;AAGpC;uFACuF;AACvF,0BAAkB,mBAAmB;IACnC,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,EAAE,OAAO;IACT,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,YAAY,gBAAgB;IAC5B,YAAY,gBAAgB;IAC5B,WAAW,eAAe;CAC3B;AAGD,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IAEnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAGD,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAG9C,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAEF,eAAO,MAAM,aAAa;0BACK,WAAW;;;;;;sBAMvB,MAAM,EAAE;;;0BAGG,WAAW;;CAE/B,CAAC;AAEX,eAAO,MAAM,sBAAsB,EAAE;IAAC,CAAC,GAAG,EAAE,MAAM,GAAG,EAAE,CAAC,QAAQ,CAAA;CAQ/D,CAAC;AAGF,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC;AAExC,eAAO,MAAM,aAAa,MAAM,CAAC;AACjC,eAAO,MAAM,kBAAkB,MAAM,CAAC;AACtC,eAAO,MAAM,gBAAgB,MAAM,CAAC;AACpC,eAAO,MAAM,oBAAoB,QAGhC,CAAC"}
package/src/utils/const.js CHANGED
@@ -1,3 +1,4 @@
1
+ import * as DG from 'datagrok-api/dg';
1
2
  // core fields of HELM library object used in toAtomicLevel function
2
3
  export const HELM_CORE_FIELDS = [
3
4
  "symbol" /* HELM_FIELDS.SYMBOL */,
@@ -35,6 +36,15 @@ export const DUMMY_MONOMER = {
35
36
  'polymerType': 'PEPTIDE',
36
37
  'symbol': ''
37
38
  };
39
+ export const MonomerInputProperties = {
40
+ 'monomerType': DG.Property.js('monomerType', DG.TYPE.STRING, { choices: ["Backbone" /* MonomerTypes.BACKBONE */, "Branch" /* MonomerTypes.BRANCH */, "Terminal" /* MonomerTypes.TERMINAL */] }),
41
+ 'molecule': DG.Property.fromOptions({ name: 'molecule', type: DG.InputType.Molecule }),
42
+ 'name': DG.Property.js('name', DG.TYPE.STRING),
43
+ 'naturalAnalog': DG.Property.js('naturalAnalog', DG.TYPE.STRING),
44
+ 'id': DG.Property.js('id', DG.TYPE.INT),
45
+ 'polymerType': DG.Property.js('polymerType', DG.TYPE.STRING, { choices: ["RNA" /* PolymerTypes.RNA */, "PEPTIDE" /* PolymerTypes.PEPTIDE */, "CHEM" /* PolymerTypes.CHEM */, "BLOB" /* PolymerTypes.BLOB */, "G" /* PolymerTypes.G */] }),
46
+ 'symbol': DG.Property.js('symbol', DG.TYPE.STRING),
47
+ };
38
48
  // range of hex nubers used in PepSea library to endode monomers
39
49
  export const MONOMER_ENCODE_MIN = 0x100;
40
50
  export const MONOMER_ENCODE_MAX = 0x40A;
package/src/utils/const.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AA0DA,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG;;;;;IAK9B,2EAA2E;IAC3E,YAAY;CACb,CAAC;AAEF,MAAM,CAAC,MAAM,gBAAgB,GAAG,aAAa,CAAC;AAE9C,wDAAwD;AACxD,MAAM,CAAC,MAAM,qBAAqB,GAAG;IACnC,aAAa,EAAE,IAAI,EAAE,cAAc;IACnC,QAAQ,EAAE,IAAI;IACd,MAAM,EAAE,MAAM;IACd,QAAQ,EAAE,IAAI;IACd,SAAS,EAAE,UAAU;IACrB,eAAe,EAAE,0BAA0B;IAC3C,SAAS,EAAE,aAAa;IACxB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,IAAI;IACV,aAAa,EAAE,aAAa;IAC5B,QAAQ,EAAE,aAAa;CACxB,CAAC;AAEF,MAAM,CAAC,MAAM,aAAa,GAAG;IAC3B,aAAa,EAAE,UAAyB;IACxC,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,UAAU;IACpB,SAAS,EAAE,EAAE;IACb,eAAe,EAAE,EAAE;IACnB,SAAS,EAAE,EAAc;IACzB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,CAAC;IACP,aAAa,EAAE,SAAwB;IACvC,QAAQ,EAAE,EAAE;CACb,CAAC;AACF,gEAAgE;AAChE,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AAExC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAC;AACjC,MAAM,CAAC,MAAM,kBAAkB,GAAG,GAAG,CAAC;AACtC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAC;AACpC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,MAAM,CAC5C,IAAI,aAAa,GAAG,kBAAkB,eAAe,gBAAgB,GAAG,EACxE,GAAG,CACJ,CAAC"}
1
+ {"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AA2DtC,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG;;;;;IAK9B,2EAA2E;IAC3E,YAAY;CACb,CAAC;AAEF,MAAM,CAAC,MAAM,gBAAgB,GAAG,aAAa,CAAC;AAE9C,wDAAwD;AACxD,MAAM,CAAC,MAAM,qBAAqB,GAAG;IACnC,aAAa,EAAE,IAAI,EAAE,cAAc;IACnC,QAAQ,EAAE,IAAI;IACd,MAAM,EAAE,MAAM;IACd,QAAQ,EAAE,IAAI;IACd,SAAS,EAAE,UAAU;IACrB,eAAe,EAAE,0BAA0B;IAC3C,SAAS,EAAE,aAAa;IACxB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,IAAI;IACV,aAAa,EAAE,aAAa;IAC5B,QAAQ,EAAE,aAAa;CACxB,CAAC;AAEF,MAAM,CAAC,MAAM,aAAa,GAAG;IAC3B,aAAa,EAAE,UAAyB;IACxC,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,UAAU;IACpB,SAAS,EAAE,EAAE;IACb,eAAe,EAAE,EAAE;IACnB,SAAS,EAAE,EAAc;IACzB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,CAAC;IACP,aAAa,EAAE,SAAwB;IACvC,QAAQ,EAAE,EAAE;CACJ,CAAC;AAEX,MAAM,CAAC,MAAM,sBAAsB,GAAiC;IAClE,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;AAEF,gEAAgE;AAChE,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AAExC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAC;AACjC,MAAM,CAAC,MAAM,kBAAkB,GAAG,GAAG,CAAC;AACtC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAC;AACpC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,MAAM,CAC5C,IAAI,aAAa,GAAG,kBAAkB,eAAe,gBAAgB,GAAG,EACxE,GAAG,CACJ,CAAC"}
package/src/utils/macromolecule/monomers.d.ts ADDED
@@ -0,0 +1,66 @@
1
+ import BitArray from '@datagrok-libraries/utils/src/bit-array';
2
+ export declare const naturalMonomers: {
3
+ RNA: {
4
+ A: string;
5
+ C: string;
6
+ G: string;
7
+ T: string;
8
+ U: string;
9
+ };
10
+ PEPTIDE: {
11
+ A: string;
12
+ C: string;
13
+ D: string;
14
+ E: string;
15
+ F: string;
16
+ G: string;
17
+ H: string;
18
+ I: string;
19
+ K: string;
20
+ L: string;
21
+ M: string;
22
+ N: string;
23
+ P: string;
24
+ Q: string;
25
+ R: string;
26
+ S: string;
27
+ T: string;
28
+ V: string;
29
+ W: string;
30
+ Y: string;
31
+ };
32
+ };
33
+ export declare const naturalMonomerFps: {
34
+ RNA: {
35
+ A: BitArray;
36
+ C: BitArray;
37
+ G: BitArray;
38
+ T: BitArray;
39
+ U: BitArray;
40
+ };
41
+ PEPTIDE: {
42
+ A: BitArray;
43
+ C: BitArray;
44
+ D: BitArray;
45
+ E: BitArray;
46
+ F: BitArray;
47
+ G: BitArray;
48
+ H: BitArray;
49
+ I: BitArray;
50
+ K: BitArray;
51
+ L: BitArray;
52
+ M: BitArray;
53
+ N: BitArray;
54
+ P: BitArray;
55
+ Q: BitArray;
56
+ R: BitArray;
57
+ S: BitArray;
58
+ T: BitArray;
59
+ V: BitArray;
60
+ W: BitArray;
61
+ Y: BitArray;
62
+ };
63
+ };
64
+ export declare function getMorganFingerprint(molString: string): Promise<BitArray | null | undefined>;
65
+ export declare function mostSimilarNaturalAnalog(molString: string, monomerType: string, threshold?: number): Promise<string | null>;
66
+ //# sourceMappingURL=monomers.d.ts.map
package/src/utils/macromolecule/monomers.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"monomers.d.ts","sourceRoot":"","sources":["monomers.ts"],"names":[],"mappings":"AAGA,OAAO,QAAQ,MAAM,yCAAyC,CAAC;AA0Q/D,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAG3B,CAAC;AAEF,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAG7B,CAAC;AAEF,wBAAsB,oBAAoB,CAAC,SAAS,EAAE,MAAM,wCAc3D;AAED,wBAAsB,wBAAwB,CAAC,SAAS,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,SAAS,SAAI,0BAgBnG"}
package/src/utils/macromolecule/monomers.js ADDED
@@ -0,0 +1,230 @@
1
+ import * as DG from 'datagrok-api/dg';
2
+ import BitArray from '@datagrok-libraries/utils/src/bit-array';
3
+ import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
4
+ const naturalAASmiles = {
5
+ A: 'C[C@H](N)C(=O)O',
6
+ C: 'N[C@@H](CS)C(=O)O',
7
+ D: 'N[C@@H](CC(=O)O)C(=O)O',
8
+ E: 'N[C@@H](CCC(=O)O)C(=O)O',
9
+ F: 'N[C@@H](Cc1ccccc1)C(=O)O',
10
+ G: 'NCC(=O)O',
11
+ H: 'N[C@@H](Cc1cnc[nH]1)C(=O)O',
12
+ I: 'CC[C@H](C)[C@H](N)C(=O)O',
13
+ K: 'NCCCC[C@H](N)C(=O)O',
14
+ L: 'CC(C)C[C@H](N)C(=O)O',
15
+ M: 'CSCC[C@H](N)C(=O)O',
16
+ N: 'NC(=O)C[C@H](N)C(=O)O',
17
+ P: 'O=C(O)[C@@H]1CCCN1',
18
+ Q: 'NC(=O)CC[C@H](N)C(=O)O',
19
+ R: 'N=C(N)NCCC[C@H](N)C(=O)O',
20
+ S: 'N[C@@H](CO)C(=O)O',
21
+ T: 'C[C@@H](O)[C@H](N)C(=O)O',
22
+ V: 'CC(C)[C@H](N)C(=O)O',
23
+ W: 'N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O',
24
+ Y: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O',
25
+ }; // canonical smiles of canonical amino acids
26
+ const naturalAAFps = {
27
+ A: new BitArray(new Uint32Array([
28
+ 2, 0, 0, 0, 16, 0, 0, 0, 134217728, 0, 0, 0, 32, 0, 33554432, 0, 0, 0, 0,
29
+ 0, 1024, 0, 0, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 524288, 0, 0,
30
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1048576, 0,
31
+ 536870912, 0, 0, 0, 0,
32
+ ]), 2048),
33
+ C: new BitArray(new Uint32Array([
34
+ 2, 0, 65536, 0, 0, 0, 0, 32, 0, 0, 2, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
35
+ 0, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 65536, 0, 0, 524288, 0, 0, 0, 0,
36
+ 0, 0, 0, 524288, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 34603008, 0,
37
+ 536870912, 64, 0, 0, 0,
38
+ ]), 2048),
39
+ D: new BitArray(new Uint32Array([
40
+ 2, 0, 65600, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
41
+ 0, 0, 262400, 128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2097152, 524288, 0, 0, 0,
42
+ 1024, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 512, 0, 0, 34603008, 0,
43
+ 536870912, 0, 0, 0, 0,
44
+ ]), 2048),
45
+ E: new BitArray(new Uint32Array([
46
+ 2, 0, 65536, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
47
+ 0, 8, 262144, 128, 0, 0, 16, 134217728, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0,
48
+ 128, 0, 0, 0, 524288, 0, 0, 0, 268435456, 0, 0, 0, 0, 0, 512, 2147483648,
49
+ 0, 34603008, 0, 536870912, 0, 0, 0, 0,
50
+ ]), 2048),
51
+ F: new BitArray(new Uint32Array([
52
+ 2, 0, 98304, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024, 0,
53
+ 0, 0, 262144, 128, 33554432, 0, 0, 0, 0, 33554432, 0, 1024, 1, 0, 524288,
54
+ 32768, 32, 0, 0, 0, 0, 16, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 71303168, 0,
55
+ 0, 34603008, 131072, 536870912, 0, 0, 0, 0,
56
+ ]), 2048),
57
+ G: new BitArray(new Uint32Array([
58
+ 134217728, 0, 65536, 0, 0, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0,
59
+ 1024, 0, 0, 0, 0, 128, 0, 0, 0, 0, 2097216, 0, 0, 0, 0, 0, 524288, 0, 0,
60
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 512, 0, 0, 0, 0, 536870912,
61
+ 0, 0, 0, 0,
62
+ ]), 2048),
63
+ H: new BitArray(new Uint32Array([
64
+ 2, 0, 1073840128, 0, 0, 0, 0, 0, 0, 0, 0, 67108864, 32, 0, 0, 0, 0, 0, 0,
65
+ 0, 1024, 0, 512, 0, 262144, 192, 0, 268435456, 0, 0, 8200, 0, 0, 0,
66
+ 67108864, 0, 524296, 0, 32, 0, 0, 0, 0, 16, 524288, 0, 0, 2147483648, 0,
67
+ 0, 8, 0, 0, 0, 0, 0, 0, 34603008, 131072, 536870920, 4194304, 0, 0, 0,
68
+ ]), 2048),
69
+ I: new BitArray(new Uint32Array([
70
+ 2, 0, 65536, 0, 0, 0, 0, 0, 150994944, 64, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0,
71
+ 1024, 0, 8388608, 0, 327680, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 524288,
72
+ 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 256, 0, 0, 0, 0, 8388608, 0,
73
+ 33554432, 0, 1048576, 0, 536870912, 0, 0, 0, 0,
74
+ ]), 2048),
75
+ K: new BitArray(new Uint32Array([
76
+ 2, 0, 65536, 0, 0, 0, 0, 0, 0, 0, 0, 0, 268435488, 0, 0, 0, 0, 0, 0, 0,
77
+ 1024, 0, 0, 8, 262144, 128, 0, 0, 0, 0, 2097152, 0, 0, 67108864, 0, 0,
78
+ 524288, 0, 0, 0, 8, 0, 0, 0, 524288, 0, 0, 8192, 0, 0, 0, 0, 0, 0, 0,
79
+ 2147483648, 0, 34668544, 0, 545259520, 0, 0, 0, 0,
80
+ ]), 2048),
81
+ L: new BitArray(new Uint32Array([
82
+ 2, 0, 65536, 0, 0, 0, 0, 0, 134217728, 0, 0, 0, 32, 512, 0, 0, 0, 0, 0, 0,
83
+ 1024, 256, 0, 8388608, 262400, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 524288,
84
+ 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 42991616,
85
+ 0, 536870912, 0, 0, 0, 0,
86
+ ]), 2048),
87
+ M: new BitArray(new Uint32Array([
88
+ 2050, 0, 65536, 1048576, 0, 0, 0, 0, 0, 0, 0, 0, 1056, 0, 0, 0, 0, 0, 0,
89
+ 0, 1024, 0, 0, 8, 262144, 128, 0, 0, 0, 0, 0, 536870912, 0, 2, 0, 0,
90
+ 1074266112, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 4194304, 0, 0, 0, 0, 0,
91
+ 0, 2147483648, 0, 34603008, 0, 536870912, 4194304, 0, 0, 0,
92
+ ]), 2048),
93
+ N: new BitArray(new Uint32Array([
94
+ 2, 0, 65536, 0, 4096, 0, 0, 0, 0, 0, 0, 16777216, 32, 0, 0, 0, 0, 0, 0, 0,
95
+ 1024, 0, 0, 0, 262400, 128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0,
96
+ 1024, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 34603008, 0,
97
+ 536871936, 67108864, 0, 0, 0,
98
+ ]), 2048),
99
+ P: new BitArray(new Uint32Array([
100
+ 0, 0, 1024, 0, 0, 0, 0, 0, 0, 131072, 0, 1024, 32, 0, 0, 0, 0, 512, 0, 0,
101
+ 1024, 0, 0, 64, 0, 128, 0, 0, 1073741824, 0, 0, 138412032, 16, 0,
102
+ 67108864, 0, 0, 0, 0, 0, 0, 8192, 0, 0, 8388608, 0, 0, 8, 0, 0, 0, 0, 0,
103
+ 0, 256, 0, 0, 0, 0, 553648128, 0, 0, 0, 0,
104
+ ]), 2048),
105
+ Q: new BitArray(new Uint32Array([
106
+ 2, 0, 65536, 0, 4096, 0, 0, 0, 0, 0, 0, 0, 32, 0, 0, 0, 0, 2, 0, 0, 1024,
107
+ 0, 0, 8, 262144, 128, 0, 0, 16, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 0,
108
+ 0, 0, 0, 524288, 0, 0, 0, 268435456, 0, 0, 0, 0, 0, 16777216, 2147483648,
109
+ 0, 34603008, 0, 536871936, 0, 0, 0, 0,
110
+ ]), 2048),
111
+ R: new BitArray(new Uint32Array([
112
+ 2, 0, 65536, 0, 4096, 0, 32, 0, 0, 0, 0, 0, 268435488, 0, 0, 0, 0, 0, 0,
113
+ 32768, 134218752, 0, 16, 8, 262144, 128, 0, 1073741824, 0, 0, 8388608, 0,
114
+ 0, 0, 65536, 0, 524289, 0, 0, 0, 0, 0, 0, 0, 524288, 2048, 0, 0, 0, 0, 0,
115
+ 0, 0, 0, 0, 2147483648, 0, 34603008, 1048576, 545259520, 0, 0, 0, 0,
116
+ ]), 2048),
117
+ S: new BitArray(new Uint32Array([
118
+ 2, 0, 65536, 0, 0, 0, 1073741824, 0, 0, 0, 0, 0, 32, 0, 0, 4, 0, 0, 0, 0,
119
+ 1024, 0, 0, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0,
120
+ 1048576, 0, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8388608, 0, 0,
121
+ 34603008, 0, 536870912, 0, 0, 0, 0,
122
+ ]), 2048),
123
+ T: new BitArray(new Uint32Array([
124
+ 2, 0, 0, 0, 0, 0, 0, 8, 134217728, 0, 0, 67108864, 32, 0, 0, 0, 0, 0, 0,
125
+ 0, 1024, 0, 8388608, 0, 262144, 128, 0, 0, 0, 0, 0, 0, 0, 2, 0, 524288,
126
+ 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 536870912, 0, 0, 0,
127
+ 0, 1048576, 67108864, 536870912, 0, 0, 0, 0,
128
+ ]), 2048),
129
+ V: new BitArray(new Uint32Array([
130
+ 2, 0, 0, 0, 0, 0, 0, 0, 134217728, 0, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0, 1024,
131
+ 0, 8388608, 0, 262144, 128, 0, 0, 0, 0, 0, 1073741824, 128, 2, 0, 524288,
132
+ 524288, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8192, 0,
133
+ 1048576, 0, 536870912, 0, 0, 0, 0,
134
+ ]), 2048),
135
+ W: new BitArray(new Uint32Array([
136
+ 2, 0, 98304, 8388608, 0, 0, 0, 0, 0, 0, 256, 4096, 32, 0, 0, 0, 0, 0, 0,
137
+ 0, 1024, 0, 0, 0, 262144, 192, 0, 0, 0, 0, 0, 0, 0, 0, 67108865, 0,
138
+ 524288, 32768, 32, 0, 0, 0, 8224, 16, 524288, 0, 0, 0, 0, 32, 128, 0,
139
+ 2097152, 0, 4194304, 8388608, 0, 34603008, 8519680, 536870912, 131072,
140
+ 262144, 0, 0,
141
+ ]), 2048),
142
+ Y: new BitArray(new Uint32Array([
143
+ 2, 0, 98304, 0, 0, 0, 0, 0, 0, 4194304, 0, 0, 32, 0, 0, 0, 0, 0, 0, 0,
144
+ 1024, 0, 0, 512, 262144, 128, 33554432, 0, 0, 0, 0, 33554432, 0, 0, 0, 0,
145
+ 524288, 0, 32, 0, 0, 2, 0, 16, 524288, 0, 0, 0, 0, 0, 4, 0, 0, 0,
146
+ 71303168, 262144, 0, 34603008, 131072, 536870912, 0, 0, 0, 0,
147
+ ]), 2048),
148
+ };
149
+ const naturalRNASmiles = {
150
+ A: 'Nc1ncnc2[nH]cnc12',
151
+ C: 'Nc1cc[nH]c(=O)n1',
152
+ G: 'Nc1nc2[nH]cnc2c(=O)[nH]1',
153
+ T: 'Cc1c[nH]c(=O)[nH]c1=O',
154
+ U: 'O=c1cc[nH]c(=O)[nH]1',
155
+ }; // canonical smiles of canonical NAs
156
+ const naturalRNAFps = {
157
+ A: new BitArray(new Uint32Array([
158
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 1024, 0, 67108864, 0, 0, 0, 512, 0, 0, 0,
159
+ 8388608, 0, 0, 512, 0, 0, 64, 4, 0, 0, 0, 4, 0, 0, 0, 67108864, 0, 524289,
160
+ 0, 0, 0, 0, 0, 0, 16, 0, 659456, 0, 256, 0, 16, 0, 0, 0, 268435456, 0, 0,
161
+ 262144, 0, 131072, 0, 0, 0, 8388608, 0,
162
+ ]), 2048),
163
+ C: new BitArray(new Uint32Array([
164
+ 0, 1073741824, 0, 0, 0, 0, 0, 2147483648, 4, 67108864, 0, 67108864, 0, 256,
165
+ 0, 0, 0, 0, 0, 0, 1024, 0, 128, 0, 0, 64, 0, 0, 0, 0, 0, 0, 0, 0, 67108864,
166
+ 0, 524289, 0, 65536, 0, 0, 0, 0, 16, 0, 131072, 0, 4, 0, 0, 0, 0, 0, 0,
167
+ 4194304, 0, 0, 2147483648, 131072, 0, 4096, 0, 0, 0,
168
+ ]), 2048),
169
+ G: new BitArray(new Uint32Array([
170
+ 0, 0, 0, 0, 1024, 0, 0, 0, 0, 67109888, 16384, 67108864, 0, 0, 0, 0, 0, 0,
171
+ 0, 33562624, 1024, 33554432, 512, 16384, 0, 64, 4, 0, 0, 33554432, 0, 0, 0,
172
+ 0, 67108864, 0, 524289, 0, 0, 0, 0, 0, 0, 16, 0, 135168, 0, 268435456, 0, 0,
173
+ 0, 0, 0, 268435456, 131072, 0, 0, 2147483648, 131072, 0, 0, 0, 8388608, 0,
174
+ ]), 2048),
175
+ T: new BitArray(new Uint32Array([
176
+ 8388608, 0, 0, 0, 0, 0, 0, 0, 0, 67108864, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0,
177
+ 1024, 0, 0, 16384, 0, 64, 0, 0, 0, 0, 0, 0, 0, 2, 67108864, 0, 0, 0, 0, 0,
178
+ 0, 0, 0, 40976, 0, 0, 0, 0, 0, 0, 0, 0, 0, 67108864, 131072, 524288, 0, 0,
179
+ 8519680, 0, 1, 33554432, 1048576, 0,
180
+ ]), 2048),
181
+ U: new BitArray(new Uint32Array([
182
+ 0, 0, 131072, 1073741824, 0, 0, 0, 0, 0, 67108864, 0, 0, 0, 0, 0, 0, 0, 0,
183
+ 0, 0, 1024, 0, 128, 0, 0, 64, 0, 0, 0, 0, 0, 0, 0, 32768, 67108864, 0, 0, 0,
184
+ 0, 0, 0, 0, 0, 16, 0, 0, 0, 4, 0, 0, 2048, 0, 0, 0, 4341760, 0, 0, 0,
185
+ 131072, 0, 0, 33554432, 1048576, 0,
186
+ ]), 2048),
187
+ };
188
+ export const naturalMonomers = {
189
+ RNA: naturalRNASmiles,
190
+ PEPTIDE: naturalAASmiles,
191
+ };
192
+ export const naturalMonomerFps = {
193
+ RNA: naturalRNAFps,
194
+ PEPTIDE: naturalAAFps,
195
+ };
196
+ export async function getMorganFingerprint(molString) {
197
+ const func = DG.Func.find({
198
+ package: 'Chem',
199
+ name: 'getMorganFingerprint',
200
+ })?.[0];
201
+ if (!func)
202
+ return null;
203
+ try {
204
+ const res = (await func.apply({ molString }))?.getBuffer().buffer;
205
+ if (res)
206
+ return new BitArray(new Uint32Array(res), 2048);
207
+ }
208
+ catch (_e) {
209
+ return null;
210
+ }
211
+ }
212
+ export async function mostSimilarNaturalAnalog(molString, monomerType, threshold = 0) {
213
+ if (!Object.keys(naturalMonomerFps).includes(monomerType))
214
+ return null;
215
+ const morganFp = await getMorganFingerprint(molString);
216
+ if (!morganFp)
217
+ return null;
218
+ const naturalFps = naturalMonomerFps[monomerType];
219
+ let maxSim = 0;
220
+ let mostSimilar = null;
221
+ for (const [name, fp] of Object.entries(naturalFps)) {
222
+ const sim = tanimotoSimilarity(morganFp, fp);
223
+ if (sim > maxSim && sim >= threshold) {
224
+ maxSim = sim;
225
+ mostSimilar = name;
226
+ }
227
+ }
228
+ return mostSimilar;
229
+ }
230
+ //# sourceMappingURL=monomers.js.map
package/src/utils/macromolecule/monomers.js.map ADDED
@@ -0,0 +1 @@
1
+ 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