@datagrok-libraries/bio 5.42.6 → 5.42.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (74) hide show
  1. package/CHANGELOG.md +10 -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 +10 -14
  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/src/monomer-works/to-atomic-level-utils.js.map CHANGED
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package/src/monomer-works/to-atomic-level.js.map CHANGED
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package/src/nucleotides.js CHANGED
@@ -5,7 +5,7 @@ export class NucleotidesPalettes extends SeqPaletteBase {
5
5
  this.chromatogram = new NucleotidesPalettes({
6
6
  'A': 'green',
7
7
  'C': 'blue',
8
- 'G': 'black',
8
+ 'G': 'black', // orange ?
9
9
  'T': 'red',
10
10
  'U': 'red',
11
11
  'others': 'gray',
package/src/nucleotides.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"nucleotides.js","sourceRoot":"","sources":["nucleotides.ts"],"names":[],"mappings":"AAKA,OAAO,EAAa,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAE1D,MAAM,OAAO,mBAAoB,SAAQ,cAAc;IAG9C,MAAM,KAAK,YAAY;QAC5B,IAAI,IAAI,CAAC,YAAY,KAAK,KAAK,CAAC,EAAE;YAChC,IAAI,CAAC,YAAY,GAAG,IAAI,mBAAmB,CAAC;gBAC1C,GAAG,EAAE,OAAO;gBACZ,GAAG,EAAE,MAAM;gBACX,GAAG,EAAE,OAAO;gBACZ,GAAG,EAAE,KAAK;gBACV,GAAG,EAAE,KAAK;gBACV,QAAQ,EAAE,MAAM;aACjB,CAAC,CAAC;SACJ;QACD,OAAO,IAAI,CAAC,YAAY,CAAC;IAC3B,CAAC;CACF;AAED,MAAM,OAAO,WAAW;;AACN,mBAAO,GAAW,aAAa,CAAC;AAEhC,oCAAwB,GAAW,8BAA8B,CAAC;AAEpE,iBAAK,GAAqB;IACtC,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,QAAQ;CACd,CAAC"}
1
+ {"version":3,"file":"nucleotides.js","sourceRoot":"","sources":["nucleotides.ts"],"names":[],"mappings":"AAKA,OAAO,EAAa,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAE1D,MAAM,OAAO,mBAAoB,SAAQ,cAAc;IAG9C,MAAM,KAAK,YAAY;QAC5B,IAAI,IAAI,CAAC,YAAY,KAAK,KAAK,CAAC,EAAE,CAAC;YACjC,IAAI,CAAC,YAAY,GAAG,IAAI,mBAAmB,CAAC;gBAC1C,GAAG,EAAE,OAAO;gBACZ,GAAG,EAAE,MAAM;gBACX,GAAG,EAAE,OAAO,EAAE,WAAW;gBACzB,GAAG,EAAE,KAAK;gBACV,GAAG,EAAE,KAAK;gBACV,QAAQ,EAAE,MAAM;aACjB,CAAC,CAAC;QACL,CAAC;QACD,OAAO,IAAI,CAAC,YAAY,CAAC;IAC3B,CAAC;CACF;AAED,MAAM,OAAO,WAAW;;AACN,mBAAO,GAAW,aAAa,CAAC;AAEhC,oCAAwB,GAAW,8BAA8B,CAAC;AAEpE,iBAAK,GAAqB;IACtC,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,QAAQ;CACd,CAAC"}
package/src/pdb/format/types-base.js.map CHANGED
@@ -1 +1 @@
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package/src/sequence-encoder.js CHANGED
@@ -14,19 +14,19 @@ SideChainScales.scales = {
14
14
  '-': 0,
15
15
  'A': 0.17,
16
16
  'C': -0.24,
17
- 'D': -0.07,
18
- 'E': -0.01,
19
- 'F': -1.13,
17
+ 'D': -0.07, // Asp-: 1.23
18
+ 'E': -0.01, // Glu-: 2.02
19
+ 'F': -1.13, //
20
20
  'G': 0.01,
21
- 'H': 0.17,
21
+ 'H': 0.17, // His+: 0.96
22
22
  'I': -0.31,
23
- 'K': 0.99,
23
+ 'K': 0.99, // Lys+
24
24
  'L': -0.56,
25
25
  'M': -0.23,
26
26
  'N': 0.42,
27
27
  'P': 0.45,
28
28
  'Q': 0.58,
29
- 'R': 0.81,
29
+ 'R': 0.81, // Arg+
30
30
  'S': 0.13,
31
31
  'T': 0.14,
32
32
  'V': 0.07,
package/src/sequence-encoder.js.map CHANGED
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package/src/types/index.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { Observable } from 'rxjs';
3
- import { IWebEditorMonomer, MonomerType, PolymerType } from '../helm/types';
3
+ import { HelmType, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
4
4
  import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
5
5
  export type RGroup = {
6
6
  [RGP.CAP_GROUP_SMILES]: string;
@@ -27,6 +27,28 @@ export type Monomer = {
27
27
  lib?: IMonomerLib;
28
28
  wem?: IWebEditorMonomer;
29
29
  };
30
+ export interface IMonomerLinkData {
31
+ source: string;
32
+ symbol: string;
33
+ notes: string;
34
+ }
35
+ export interface IMonomerLink {
36
+ get lib(): IMonomerLib;
37
+ get symbol(): string;
38
+ }
39
+ export interface IMonomerSetPlaceholder {
40
+ get symbol(): string;
41
+ get polymerType(): PolymerType;
42
+ get monomerType(): MonomerType;
43
+ get monomerLinks(): IMonomerLinkData[];
44
+ get monomers(): Monomer[];
45
+ }
46
+ export interface IMonomerSet {
47
+ get source(): string | undefined;
48
+ get error(): string | undefined;
49
+ get description(): string;
50
+ get placeholders(): IMonomerSetPlaceholder[];
51
+ }
30
52
  export type MonomerLibSummaryType = {
31
53
  [polymerType: string]: number;
32
54
  };
@@ -51,6 +73,7 @@ export interface IMonomerLib {
51
73
  /** Gets dataframe with columns 'polymerType', 'count'. */
52
74
  getSummaryDf(): DG.DataFrame;
53
75
  getTooltip(polymerType: PolymerType, monomerSymbol: string): HTMLElement;
76
+ getMonomerSet(type: HelmType): MonomerSetType | null;
54
77
  }
55
78
  export declare const alphabetPolymerTypes: {
56
79
  DNA: HELM_POLYMER_TYPE;
package/src/types/index.d.ts.map CHANGED
@@ -1 +1 @@
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package/src/types/index.js.map CHANGED
@@ -1 +1 @@
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package/src/types/ngl.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="signals" />
2
1
  declare module 'NGL' {
3
2
  import { Signal } from 'signals';
4
3
  import { Box3, Scene, WebGLRenderer } from 'three';
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package/src/utils/cell-renderer-async-base.js CHANGED
@@ -230,8 +230,18 @@ export class CellRendererBackAsyncBase extends CellRendererBackBase {
230
230
  // cellImageData.remove();
231
231
  }
232
232
  this.imageCache = new Map();
233
+ super.reset();
233
234
  }
234
235
  render(g, x, y, w, h, gridCell, cellStyle) {
236
+ if (this.dirty) {
237
+ try {
238
+ this.reset();
239
+ }
240
+ catch (err) {
241
+ const [errMsg, errStack] = errInfo(err);
242
+ this.logger.error(errMsg, undefined, errStack);
243
+ }
244
+ }
235
245
  const dpr = window.devicePixelRatio;
236
246
  const service = this.getRenderService();
237
247
  if (gridCell.tableRowIndex == null)