@datagrok-libraries/bio 5.42.6 → 5.42.8

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Files changed (74) hide show
  1. package/CHANGELOG.md +14 -0
  2. package/package.json +5 -5
  3. package/src/aminoacids.js +21 -21
  4. package/src/aminoacids.js.map +1 -1
  5. package/src/helm/consts.js +2 -1
  6. package/src/helm/consts.js.map +1 -1
  7. package/src/helm/helm-helper.d.ts +12 -16
  8. package/src/helm/helm-helper.d.ts.map +1 -1
  9. package/src/helm/helm-helper.js +2 -0
  10. package/src/helm/helm-helper.js.map +1 -1
  11. package/src/helm/types.d.ts +8 -8
  12. package/src/helm/types.d.ts.map +1 -1
  13. package/src/molecule/molecule-units-handler.js.map +1 -1
  14. package/src/molecule-3d/molecule-3d-units-handler.js.map +1 -1
  15. package/src/monomer-works/consts.js +1 -1
  16. package/src/monomer-works/consts.js.map +1 -1
  17. package/src/monomer-works/lib-settings.d.ts +4 -2
  18. package/src/monomer-works/lib-settings.d.ts.map +1 -1
  19. package/src/monomer-works/lib-settings.js +2 -0
  20. package/src/monomer-works/lib-settings.js.map +1 -1
  21. package/src/monomer-works/monomer-utils.d.ts +12 -2
  22. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  23. package/src/monomer-works/monomer-utils.js +12 -15
  24. package/src/monomer-works/monomer-utils.js.map +1 -1
  25. package/src/monomer-works/monomer-works.js +8 -7
  26. package/src/monomer-works/monomer-works.js.map +1 -1
  27. package/src/monomer-works/seq-to-molfile-worker.js.map +1 -1
  28. package/src/monomer-works/seq-to-molfile.js.map +1 -1
  29. package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
  30. package/src/monomer-works/to-atomic-level.js.map +1 -1
  31. package/src/nucleotides.js +1 -1
  32. package/src/nucleotides.js.map +1 -1
  33. package/src/pdb/format/types-base.js.map +1 -1
  34. package/src/sequence-encoder.js +6 -6
  35. package/src/sequence-encoder.js.map +1 -1
  36. package/src/tests/monomer-lib-tests.js.map +1 -1
  37. package/src/trees/phylocanvas.js.map +1 -1
  38. package/src/types/index.d.ts +24 -1
  39. package/src/types/index.d.ts.map +1 -1
  40. package/src/types/index.js.map +1 -1
  41. package/src/types/ngl.d.ts +0 -1
  42. package/src/types/ngl.d.ts.map +1 -1
  43. package/src/unknown.js.map +1 -1
  44. package/src/utils/cell-renderer-async-base.d.ts.map +1 -1
  45. package/src/utils/cell-renderer-async-base.js +10 -0
  46. package/src/utils/cell-renderer-async-base.js.map +1 -1
  47. package/src/utils/cell-renderer-back-base.d.ts +2 -1
  48. package/src/utils/cell-renderer-back-base.d.ts.map +1 -1
  49. package/src/utils/cell-renderer-back-base.js +5 -7
  50. package/src/utils/cell-renderer-back-base.js.map +1 -1
  51. package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
  52. package/src/utils/cell-renderer-monomer-placer.js +16 -5
  53. package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
  54. package/src/utils/cell-renderer.d.ts +1 -1
  55. package/src/utils/cell-renderer.d.ts.map +1 -1
  56. package/src/utils/cell-renderer.js.map +1 -1
  57. package/src/utils/const.d.ts +3 -2
  58. package/src/utils/const.d.ts.map +1 -1
  59. package/src/utils/const.js +1 -1
  60. package/src/utils/const.js.map +1 -1
  61. package/src/utils/docker.d.ts.map +1 -1
  62. package/src/utils/docker.js.map +1 -1
  63. package/src/utils/fasta-handler.js.map +1 -1
  64. package/src/utils/generator.js.map +1 -1
  65. package/src/utils/macromolecule/alignment.js.map +1 -1
  66. package/src/utils/macromolecule/scoring.js.map +1 -1
  67. package/src/utils/macromolecule/utils.js.map +1 -1
  68. package/src/utils/seq-handler.js +1 -1
  69. package/src/utils/seq-handler.js.map +1 -1
  70. package/src/utils/splitter.js.map +1 -1
  71. package/src/utils/units-handler-base.d.ts.map +1 -1
  72. package/src/utils/units-handler-base.js.map +1 -1
  73. package/src/utils.js.map +1 -1
  74. package/src/viewers/web-logo.d.ts.map +1 -1
package/CHANGELOG.md CHANGED
@@ -1,5 +1,19 @@
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  # bio changelog
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+ ## 5.42.8 (2024-08-14)
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+
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+ Fix monomer substitution matrix calculation
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+
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+ ## 5.42.7 (2024-08-12)
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+
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+ ### Features
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+
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+ * Monomer sets defined with .json files
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+
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+ ### Bug fixes
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+
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+ * Fix cell renderer base dirty flag and reset
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+
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  ## 5.42.6 (2024-07-29)
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  ### Features
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": "5.42.6",
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+ "version": "5.42.8",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.71",
@@ -26,8 +26,8 @@
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  "wu": "latest"
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  },
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  "devDependencies": {
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- "@datagrok-libraries/helm-web-editor": "^1.1.6",
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- "@datagrok-libraries/js-draw-lite": "^0.0.4",
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+ "@datagrok-libraries/helm-web-editor": "^1.1.7",
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+ "@datagrok-libraries/js-draw-lite": "^0.0.5",
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  "@types/signals": "1.0.1",
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  "@types/three": "^0.159.0",
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  "@types/uuid": "^9.0.1",
@@ -37,8 +37,8 @@
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  "datagrok-tools": "latest",
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  "eslint": "latest",
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  "eslint-config-google": "latest",
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- "ts-loader": "^9.2.6",
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- "typescript": "^4.9.5"
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+ "ts-loader": "^9.5.1",
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+ "typescript": "^5.5.3"
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  },
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  "scripts": {
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  "link": "npm link",
package/src/aminoacids.js CHANGED
@@ -29,26 +29,26 @@ export class AminoacidsPalettes extends SeqPaletteBase {
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  if (this.rasMol === void 0) {
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  this.rasMol = new AminoacidsPalettes({
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  // http://acces.ens-lyon.fr/biotic/rastop/help/colour.htm
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- 'D': '#E60A0A',
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- 'E': '#E60A0A',
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- 'C': '#E6E600',
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- 'M': '#E6E600',
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- 'K': '#145AFF',
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- 'R': '#145AFF',
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- 'S': '#FA9600',
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- 'T': '#FA9600',
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- 'F': '#3232AA',
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- 'Y': '#3232AA',
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- 'N': '#00DCDC',
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- 'Q': '#00DCDC',
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- 'G': '#EBEBEB',
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- 'L': '#0F820F',
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- 'V': '#0F820F',
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- 'I': '#0F820F',
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- 'A': '#C8C8C8',
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- 'W': '#B45AB4',
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- 'H': '#8282D2',
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- 'P': '#DC9682',
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+ 'D': '#E60A0A', // asp, aspartic acid, asp
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+ 'E': '#E60A0A', // glu, glutamic acid
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+ 'C': '#E6E600', // cys, cysteine
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+ 'M': '#E6E600', // met, methionine
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+ 'K': '#145AFF', // lys, lysine
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+ 'R': '#145AFF', // arg, arginine
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+ 'S': '#FA9600', // ser, serine
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+ 'T': '#FA9600', // thr, threonine
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+ 'F': '#3232AA', // phe, phenylalanine
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+ 'Y': '#3232AA', // tyr, tyrosine
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+ 'N': '#00DCDC', // asn, asparagine
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+ 'Q': '#00DCDC', // gln, glutamine
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+ 'G': '#EBEBEB', // gly, glycine
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+ 'L': '#0F820F', // leu, leucine
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+ 'V': '#0F820F', // val, valine
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+ 'I': '#0F820F', // ile, isoleucine
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+ 'A': '#C8C8C8', // ala, alanine
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+ 'W': '#B45AB4', // trp, tryptophan
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+ 'H': '#8282D2', // his, histidine
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+ 'P': '#DC9682', // pro, proline
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  'others': '#BEA06E',
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  });
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  }
@@ -62,7 +62,7 @@ export class AminoacidsPalettes extends SeqPaletteBase {
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  }
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  /** Only some of the synonyms. These were obtained from the clustered oligopeptide dataset. */
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  AminoacidsPalettes.aaSynonyms = {
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- 'MeNle': 'L',
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+ 'MeNle': 'L', // Nle - norleucine
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  'MeA': 'A',
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  'MeG': 'G',
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  'MeF': 'F',
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package/src/helm/consts.js CHANGED
@@ -1,2 +1,3 @@
1
- export {};
1
+ import { HelmTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
2
+ export { HelmTypes };
2
3
  //# sourceMappingURL=consts.js.map
package/src/helm/consts.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":""}
1
+ {"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,SAAS,EAA6B,MAAM,gDAAgD,CAAC;AAErG,OAAO,EAAC,SAAS,EAA6B,CAAC"}
package/src/helm/helm-helper.d.ts CHANGED
@@ -1,25 +1,21 @@
1
+ import * as ui from 'datagrok-api/ui';
1
2
  import * as DG from 'datagrok-api/dg';
2
3
  import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
3
- import { HelmMol, IHelmWebEditor } from './types';
4
+ import { MonomersFuncs, HelmMol, HelmString, IHelmWebEditor } from './types';
4
5
  import { IMonomerLib } from '../types/index';
5
- import { GetMonomerFunc } from '../helm/types';
6
- export interface IInputInitOptions<T = any> {
7
- value?: T;
8
- property?: DG.Property;
9
- nullable?: boolean;
10
- elementOptions?: DG.ElementOptions;
11
- tooltipText?: string;
12
- onCreated?: (input: DG.InputBase<T>) => void;
13
- onValueChanged?: (input: DG.InputBase<T>) => void;
6
+ export type IHelmInputInitOptions = ui.input.IInputInitOptions<HelmString | HelmMol>;
7
+ export declare abstract class HelmInputBase extends DG.JsInputBase<HelmString> {
8
+ abstract get molValue(): HelmMol;
9
+ abstract set molValue(value: HelmMol);
14
10
  }
15
11
  export interface IHelmHelper {
16
- createHelmInput(name: string, options?: IInputInitOptions<HelmMol>): DG.InputBase<HelmMol>;
12
+ createHelmInput(name: string, options?: IHelmInputInitOptions): HelmInputBase;
17
13
  createHelmWebEditor(host?: HTMLElement): IHelmWebEditor;
18
14
  createWebEditorApp(host: HTMLDivElement, helm?: string): App;
19
- get originalGetMonomer(): GetMonomerFunc | null;
20
- buildGetMonomerFromLib(monomerLib: IMonomerLib): GetMonomerFunc;
21
- overrideGetMonomer(getMonomerFunc: GetMonomerFunc): GetMonomerFunc;
22
- revertOriginalGetMonomer(): GetMonomerFunc;
15
+ get originalMonomersFuncs(): MonomersFuncs | null;
16
+ buildMonomersFuncsFromLib(monomerLib: IMonomerLib): MonomersFuncs;
17
+ overrideMonomersFuncs(monomersFuncs: MonomersFuncs): MonomersFuncs;
18
+ revertOriginalMonomersFuncs(): MonomersFuncs;
23
19
  }
24
20
  export declare function getHelmHelper(): Promise<IHelmHelper>;
25
21
  declare module 'datagrok-api/ui' {
@@ -27,7 +23,7 @@ declare module 'datagrok-api/ui' {
27
23
  /** To create HelmInput synchronously, get the {@link IHelmHelper} object
28
24
  * via {@link getHelmHelper} in advance, and call {@link IHelmHelper.createHelmInput}.
29
25
  */
30
- function helmAsync(name: string, options?: IInputInitOptions<HelmMol>): Promise<DG.InputBase<HelmMol>>;
26
+ function helmAsync(name: string, options?: IHelmInputInitOptions): Promise<HelmInputBase>;
31
27
  }
32
28
  }
33
29
  //# sourceMappingURL=helm-helper.d.ts.map
package/src/helm/helm-helper.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/src/helm/helm-helper.js CHANGED
@@ -1,5 +1,7 @@
1
1
  import * as ui from 'datagrok-api/ui';
2
2
  import * as DG from 'datagrok-api/dg';
3
+ export class HelmInputBase extends DG.JsInputBase {
4
+ }
3
5
  export async function getHelmHelper() {
4
6
  const packageName = 'Helm';
5
7
  const funcList = DG.Func.find({ package: packageName, name: `getHelmHelper` });
package/src/helm/helm-helper.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"helm-helper.js","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAiCtC,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,WAAW,GAAG,MAAM,CAAC;IAC3B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,qCAAqC,CAAC,CAAC;IAChF,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;IACtF,OAAO,GAAG,CAAC;AACb,CAAC;AAWD,EAAE,CAAC,KAAK,CAAC,SAAS,GAAG,KAAK,WACxB,IAAY,EAAE,OAAoC;IAClD,OAAO,CAAC,MAAM,aAAa,EAAE,CAAC,CAAC,eAAe,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;AAChE,CAAC,CAAC"}
1
+ {"version":3,"file":"helm-helper.js","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAStC,MAAM,OAAgB,aAAc,SAAQ,EAAE,CAAC,WAAuB;CAGrE;AAiBD,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,WAAW,GAAG,MAAM,CAAC;IAC3B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,qCAAqC,CAAC,CAAC;IAChF,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;IACtF,OAAO,GAAG,CAAC;AACb,CAAC;AAWD,EAAE,CAAC,KAAK,CAAC,SAAS,GAAG,KAAK,WACxB,IAAY,EAAE,OAA+B;IAC7C,OAAO,CAAC,MAAM,aAAa,EAAE,CAAC,CAAC,eAAe,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;AAChE,CAAC,CAAC"}
package/src/helm/types.d.ts CHANGED
@@ -1,22 +1,21 @@
1
- import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups, IMonomerColors } from '@datagrok-libraries/js-draw-lite/src/types/org';
1
+ import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups, IMonomerColors, MonomerSetType } from '@datagrok-libraries/js-draw-lite/src/types/org';
2
2
  import type { Atom } from '@datagrok-libraries/js-draw-lite/src/Atom';
3
3
  import type { IJsAtom } from '@datagrok-libraries/js-draw-lite/src/types/jsdraw2';
4
4
  import type { Bond } from '@datagrok-libraries/js-draw-lite/src/Bond';
5
5
  import type { Mol } from '@datagrok-libraries/js-draw-lite/src/Mol';
6
6
  import type { Editor } from '@datagrok-libraries/js-draw-lite/src/JSDraw.Editor';
7
- import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
8
- import type { IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
7
+ import type { HelmAtom, HelmBond, HelmMol, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
9
8
  import type { HweWindow } from '@datagrok-libraries/helm-web-editor/src/types';
9
+ import type { MonomerExplorer } from '@datagrok-libraries/helm-web-editor/helm/MonomerExplorer';
10
+ import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
11
+ import type { TabDescType } from '@datagrok-libraries/js-draw-lite/form/Tab';
10
12
  import type { JSDraw2ModuleType, ScilModuleType } from '@datagrok-libraries/js-draw-lite/src/types';
11
13
  import type { OrgType } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
12
14
  import type { Monomers } from '@datagrok-libraries/helm-web-editor/helm/Monomers';
13
15
  import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/types/dojo';
14
16
  export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
15
- export { Atom, IJsAtom, Bond, Mol, Editor };
16
- export type HelmString = string;
17
- export type HelmAtom = Atom<HelmType>;
18
- export type HelmBond = Bond<HelmType>;
19
- export type HelmMol = Mol<HelmType>;
17
+ export { Atom, IJsAtom, Bond, Mol, Editor, MonomerExplorer };
18
+ export { HelmAtom, HelmBond, HelmMol, HelmString };
20
19
  export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers, GetMonomerFunc, GetMonomerResType };
21
20
  export { DojoType, DojoxType };
22
21
  export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
@@ -29,4 +28,5 @@ export interface IHelmWebEditor {
29
28
  get host(): HTMLDivElement;
30
29
  resizeEditor(width: number, height: number): void;
31
30
  }
31
+ export { MonomerSetType, MonomersFuncs, TabDescType };
32
32
  //# sourceMappingURL=types.d.ts.map
package/src/helm/types.d.ts.map CHANGED
@@ -1 +1 @@
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package/src/molecule/molecule-units-handler.js.map CHANGED
@@ -1 +1 @@
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package/src/molecule-3d/molecule-3d-units-handler.js.map CHANGED
@@ -1 +1 @@
1
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package/src/monomer-works/consts.js CHANGED
@@ -19,7 +19,7 @@ export const monomerWorksConsts = {
19
19
  V3K_BOND_CONFIG: ' CFG=',
20
20
  V3K_BEGIN_DATA_LINE: 'M V30 ',
21
21
  V3K_END: 'M END',
22
- PRECISION_FACTOR: 10000,
22
+ PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates
23
23
  // symbols for the corresponding monomers in HELM library
24
24
  DEOXYRIBOSE: 'd',
25
25
  RIBOSE: 'r',
package/src/monomer-works/consts.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAClC,sCAAsC;IACpC,aAAa,EAAE,CAAC;IAChB,YAAY,EAAE,QAAQ;IACtB,UAAU,EAAE,KAAK;IACjB,wDAAwD;IACxD,gBAAgB,EAAE,EAAE;IACpB,aAAa,EAAE,CAAC;IAChB,qBAAqB,EAAE,sCAAsC;IAC7D,sBAAsB,EAAE,2CAA2C;IACnE,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,qBAAqB,EAAE,gBAAgB;IACvC,sBAAsB,EAAE,UAAU;IAClC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,eAAe,EAAE,OAAO;IACxB,mBAAmB,EAAE,SAAS;IAC9B,OAAO,EAAE,QAAQ;IACjB,gBAAgB,EAAE,KAAM,EAAE,mFAAmF;IAC7G,yDAAyD;IACzD,WAAW,EAAE,GAAG;IAChB,MAAM,EAAE,GAAG;IACX,SAAS,EAAE,GAAG;IAEd,MAAM,EAAE,GAAG;IACX,QAAQ,EAAE,GAAG;CACL,CAAC"}
package/src/monomer-works/lib-settings.d.ts CHANGED
@@ -1,6 +1,8 @@
1
1
  import { UserLibSettings } from './types';
2
- export declare const LIB_STORAGE_NAME = "Libraries";
3
- export declare const LIB_PATH = "System:AppData/Bio/monomer-libraries/";
2
+ export declare const LIB_STORAGE_NAME: string;
3
+ export declare const LIB_PATH: string;
4
+ export declare const SETS_STORAGE_NAME: string;
5
+ export declare const SETS_PATH: string;
4
6
  export declare function getUserLibSettings(): Promise<UserLibSettings>;
5
7
  export declare function setUserLibSettings(value: UserLibSettings): Promise<void>;
6
8
  /** Set only HELMCoreLibrary.json */
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,cAAc,CAAC;AAC5C,eAAO,MAAM,QAAQ,0CAA0C,CAAC;AAMhE,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,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"}
package/src/monomer-works/lib-settings.js CHANGED
@@ -3,6 +3,8 @@ import * as grok from 'datagrok-api/grok';
3
3
  export const LIB_STORAGE_NAME = 'Libraries';
4
4
  export const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
5
5
  const LIB_SETTINGS_FOR_TESTS = { explicit: ['HELMCoreLibrary.json'], exclude: [] };
6
+ export const SETS_STORAGE_NAME = 'Monomer Sets';
7
+ export const SETS_PATH = 'System:AppData/Bio/monomer-sets/';
6
8
  let userLibSettingsPromise = Promise.resolve();
7
9
  export async function getUserLibSettings() {
8
10
  let res;
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,GAAG,WAAW,CAAC;AAC5C,MAAM,CAAC,MAAM,QAAQ,GAAG,uCAAuC,CAAC;AAChE,MAAM,sBAAsB,GAAoB,EAAC,QAAQ,EAAE,CAAC,sBAAsB,CAAC,EAAE,OAAO,EAAE,EAAE,EAAC,CAAC;AAGlG,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,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"}
package/src/monomer-works/monomer-utils.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { Observable } from 'rxjs';
3
- import { IMonomerLib } from '../types/index';
3
+ import { IMonomerLib, IMonomerSet } from '../types/index';
4
4
  import { ISeqSplitted } from '../utils/macromolecule/types';
5
5
  export declare function encodeMonomers(col: DG.Column): DG.Column | null;
6
6
  export declare function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): any[][] | null;
@@ -27,13 +27,23 @@ export interface IMonomerLibHelper {
27
27
  get eventManager(): IMonomerLibFileEventManager;
28
28
  /** Ensures files are loaded and validated, throws error after timeout */
29
29
  awaitLoaded(timeout?: number): Promise<void>;
30
- /** Singleton monomer library */
30
+ /** Singleton monomer library collected from various sources */
31
+ getMonomerLib(): IMonomerLib;
32
+ /** @deprecated Use {@link getMonomerLib} */
31
33
  getBioLib(): IMonomerLib;
34
+ /** Singleton monomer set collected from various sources */
35
+ getMonomerSets(): IMonomerSet;
32
36
  getFileManager(): Promise<IMonomerLibFileManager>;
33
37
  /** (Re)Loads libraries based on settings in user storage {@link LIB_STORAGE_NAME} to singleton.
34
38
  * @param {boolean} reload Clean {@link monomerLib} before load libraries [false]
35
39
  */
40
+ loadMonomerLib(reload?: boolean): Promise<void>;
41
+ /** @deprecated Use {@link loadMonomerLib} */
36
42
  loadLibraries(reload?: boolean): Promise<void>;
43
+ /** (Re)loads monomer sets based on settings in user storage {@link SETS_STORAGE_NAME} to singleton.
44
+ * @param {boolean} reload Clean {@link monomerSets} before load sets [false]
45
+ */
46
+ loadMonomerSets(reload?: boolean): Promise<void>;
37
47
  /** Reads library from file shares, handles .json and .sdf */
38
48
  readLibrary(path: string, fileName: string): Promise<IMonomerLib>;
39
49
  }
package/src/monomer-works/monomer-utils.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAShC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAa,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAItE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CAoCpE;AAED,MAAM,WAAW,2BAA2B;IAC1C,IAAI,wBAAwB,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IACjD,IAAI,0BAA0B,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;IACvD,IAAI,0BAA0B,IAAI,UAAU,CAAC,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAEhE,4BAA4B,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,OAAO,GAAG,IAAI,CAAC;CAC9E;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,YAAY,IAAI,2BAA2B,CAAC;IAEhD,oBAAoB,IAAI,MAAM,EAAE,CAAC;IACjC,kCAAkC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAExD,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IACrE,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEnD,mBAAmB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CAC3E;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,YAAY,IAAI,2BAA2B,CAAC;IAEhD,yEAAyE;IACzE,WAAW,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE7C,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB,cAAc,IAAI,OAAO,CAAC,sBAAsB,CAAC,CAAC;IAElD;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAoEhJ;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAqB1F;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAoC1F"}
1
+ {"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAShC,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,gBAAgB,CAAC;AACxD,OAAO,EAAa,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAItE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CAoCpE;AAED,MAAM,WAAW,2BAA2B;IAC1C,IAAI,wBAAwB,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IACjD,IAAI,0BAA0B,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;IACvD,IAAI,0BAA0B,IAAI,UAAU,CAAC,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAEhE,4BAA4B,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,OAAO,GAAG,IAAI,CAAC;CAC9E;AAED,MAAM,WAAW,sBAAsB;IACrC,IAAI,YAAY,IAAI,2BAA2B,CAAC;IAEhD,oBAAoB,IAAI,MAAM,EAAE,CAAC;IACjC,kCAAkC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAExD,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IACrE,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEnD,mBAAmB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CAC3E;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,YAAY,IAAI,2BAA2B,CAAC;IAEhD,yEAAyE;IACzE,WAAW,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE7C,+DAA+D;IAC/D,aAAa,IAAI,WAAW,CAAC;IAE7B,6CAA6C;IAC7C,SAAS,IAAI,WAAW,CAAC;IAEzB,2DAA2D;IAC3D,cAAc,IAAI,WAAW,CAAC;IAE9B,cAAc,IAAI,OAAO,CAAC,sBAAsB,CAAC,CAAC;IAElD;;OAEG;IACH,cAAc,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEhD,6CAA6C;IAC7C,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C;;OAEG;IACH,eAAe,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEjD,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAgEhJ;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAqB1F;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAqC1F"}
package/src/monomer-works/monomer-utils.js CHANGED
@@ -136,7 +136,7 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
136
136
  if (positionColumns instanceof DG.Column)
137
137
  positionColumns = splitAlignedSequences(positionColumns).columns.toList();
138
138
  const libHelper = await getMonomerLibHelper();
139
- const monomerLib = libHelper.getBioLib();
139
+ const monomerLib = libHelper.getMonomerLib();
140
140
  // const smilesCols: DG.Column<string>[] = new Array(monomerCols.length);
141
141
  const rawCols = new Array(positionColumns.length);
142
142
  const rowCount = positionColumns[0].length;
@@ -146,8 +146,6 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
146
146
  const referenceMonomerCanonical = position < referenceSequence.length ?
147
147
  referenceSequence.getCanonical(position) : GAP_SYMBOL;
148
148
  const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomerCanonical)?.smiles ?? '';
149
- if (!referenceMol)
150
- grok.shell.warning(`Reference monomer ${referenceMonomerCanonical} not found in monomer library`);
151
149
  const monomerCol = positionColumns[position];
152
150
  const monomerColData = monomerCol.getRawData();
153
151
  const monomerColCategories = monomerCol.categories;
@@ -160,16 +158,14 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
160
158
  const _df = DG.DataFrame.fromColumns([molCol]); // getSimilarities expects that column is in dataframe
161
159
  const similarityCol = (await grok.chem.getSimilarities(molCol, referenceMol));
162
160
  const similarityColData = similarityCol ? similarityCol.getRawData() : null;
163
- if (similarityColData) {
164
- for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
165
- const monomerCategoryIdx = monomerColData[rowIdx];
166
- if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx) {
167
- totalSimilarity[rowIdx] += similarityColData[monomerCategoryIdx];
168
- }
169
- else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx) {
170
- totalSimilarity[rowIdx] += 1;
171
- } // Do not increase similarity on mismatch score/penalty equals 0;
161
+ for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
162
+ const monomerCategoryIdx = monomerColData[rowIdx];
163
+ if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx) {
164
+ totalSimilarity[rowIdx] += similarityColData[monomerCategoryIdx];
172
165
  }
166
+ else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx) {
167
+ totalSimilarity[rowIdx] += 1;
168
+ } // Do not increase similarity on mismatch score/penalty equals 0;
173
169
  }
174
170
  }
175
171
  for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {
@@ -194,7 +190,7 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
194
190
  export async function calculateMonomerSimilarity(monomerSet) {
195
191
  /* eslint-enable max-len */
196
192
  const libHelper = await getMonomerLibHelper();
197
- const monomerLib = libHelper.getBioLib();
193
+ const monomerLib = libHelper.getMonomerLib();
198
194
  const scoringMatrix = [];
199
195
  const alphabetIndexes = {};
200
196
  const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.smiles ?? '');
@@ -212,10 +208,11 @@ export async function calculateMonomerSimilarity(monomerSet) {
212
208
  }
213
209
  export async function getMonomerSubstitutionMatrix(monomerSet, fingerprintType = 'Morgan') {
214
210
  const libHelper = await getMonomerLibHelper();
215
- const monomerLib = libHelper.getBioLib();
211
+ const monomerLib = libHelper.getMonomerLib();
216
212
  const scoringMatrix = new Array(monomerSet.length).fill(0).map(() => new Array(monomerSet.length).fill(0));
217
213
  const alphabetIndexes = {};
218
- const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.smiles ?? '');
214
+ // note, below specifically boolean OR is used to get either molfile or smiles, because we want to skip '' molfiles
215
+ const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.molfile || monomerLib.getMonomer('PEPTIDE', monomer)?.smiles || '');
219
216
  const fingerprintsFunc = DG.Func.find({ package: 'Chem', name: 'getFingerprints' })[0];
220
217
  if (!fingerprintsFunc) {
221
218
  console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints');
package/src/monomer-works/monomer-utils.js.map CHANGED
@@ -1 +1 @@
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package/src/monomer-works/monomer-works.js CHANGED
@@ -1,3 +1,4 @@
1
+ import { HelmTypes } from '../helm/consts';
1
2
  export class MonomerWorks {
2
3
  //private molfileConverter: IMolfileConverter;
3
4
  constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {
@@ -16,21 +17,21 @@ export class MonomerWorks {
16
17
  export function helmTypeToPolymerType(helmType) {
17
18
  let polymerType = undefined;
18
19
  switch (helmType) {
19
- case "HELM_BASE" /* HelmTypes.BASE */:
20
- case "HELM_SUGAR" /* HelmTypes.SUGAR */: // r - ribose, d - deoxyribose
21
- case "HELM_LINKER" /* HelmTypes.LINKER */: // p - phosphate
22
- case "HELM_NUCLETIDE" /* HelmTypes.NUCLEOTIDE */:
20
+ case HelmTypes.BASE:
21
+ case HelmTypes.SUGAR: // r - ribose, d - deoxyribose
22
+ case HelmTypes.LINKER: // p - phosphate
23
+ case HelmTypes.NUCLEOTIDE:
23
24
  // @ts-ignore
24
25
  case 'nucleotide':
25
26
  polymerType = "RNA" /* PolymerTypes.RNA */;
26
27
  break;
27
- case "HELM_AA" /* HelmTypes.AA */:
28
+ case HelmTypes.AA:
28
29
  polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
29
30
  break;
30
- case "HELM_CHEM" /* HelmTypes.CHEM */:
31
+ case HelmTypes.CHEM:
31
32
  polymerType = "CHEM" /* PolymerTypes.CHEM */;
32
33
  break;
33
- case "HELM_BLOB" /* HelmTypes.BLOB */:
34
+ case HelmTypes.BLOB:
34
35
  polymerType = "BLOB" /* PolymerTypes.BLOB */;
35
36
  break;
36
37
  default:
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