@datagrok-libraries/bio 5.38.2 → 5.38.4

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Files changed (31) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/cleanup +0 -0
  3. package/package.json +3 -3
  4. package/src/monomer-works/monomer-utils.d.ts +3 -0
  5. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  6. package/src/monomer-works/monomer-utils.js +52 -1
  7. package/src/monomer-works/monomer-utils.js.map +1 -1
  8. package/src/types/index.d.ts +1 -0
  9. package/src/types/index.d.ts.map +1 -1
  10. package/src/utils/cell-renderer.d.ts +3 -0
  11. package/src/utils/cell-renderer.d.ts.map +1 -1
  12. package/src/utils/cell-renderer.js +4 -0
  13. package/src/utils/cell-renderer.js.map +1 -1
  14. package/src/utils/const.d.ts +26 -0
  15. package/src/utils/const.d.ts.map +1 -1
  16. package/src/utils/const.js +34 -0
  17. package/src/utils/const.js.map +1 -1
  18. package/src/utils/types.d.ts +7 -0
  19. package/src/utils/types.d.ts.map +1 -0
  20. package/src/utils/types.js +2 -0
  21. package/src/utils/types.js.map +1 -0
  22. package/src/utils/units-handler.d.ts.map +1 -1
  23. package/src/utils/units-handler.js +10 -4
  24. package/src/utils/units-handler.js.map +1 -1
  25. package/src/viewers/vd-regions.d.ts +1 -0
  26. package/src/viewers/vd-regions.d.ts.map +1 -1
  27. package/src/viewers/vd-regions.js +1 -0
  28. package/src/viewers/vd-regions.js.map +1 -1
  29. package/src/viewers/web-logo.d.ts +1 -0
  30. package/src/viewers/web-logo.d.ts.map +1 -1
  31. package/src/viewers/web-logo.js.map +1 -1
package/CHANGELOG.md CHANGED
@@ -6,6 +6,10 @@
6
6
 
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  * Fix getSplitterWithSeparator for empty seq.
8
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  * Fix MonomerPlacer getPosition for empty seq.
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+ * Move maxMonomerLength from column's temp to tags
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+ * Add property fitWidth for VdRegionsViewer
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+ * Fix UnitsHandler to not replace existing tags
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+ * Fix VdRegionsViewer fit width accounting position margin of WebLogo
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13
 
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  ## 5.38.0 (2023-09-06)
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15
 
package/cleanup CHANGED
File without changes
package/package.json CHANGED
@@ -8,15 +8,15 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.38.2",
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+ "version": "5.38.4",
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  "description": "",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.64",
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- "@datagrok-libraries/utils": "^2.5.0",
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+ "@datagrok-libraries/utils": "^4.1.0",
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  "@datagrok-libraries/ml": "^6.3.28",
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  "@deck.gl/core": "8.8.12",
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  "cash-dom": "latest",
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- "datagrok-api": "^1.10.2",
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+ "datagrok-api": "^1.13.3",
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  "dayjs": "latest",
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  "fastest-levenshtein": "^1.0.16",
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  "mjolnir.js": "^2.7.0",
package/src/monomer-works/monomer-utils.d.ts CHANGED
@@ -7,6 +7,9 @@ export declare function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObjec
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  export declare function createMomomersMolDict(lib: any[]): {
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  [key: string]: string | any;
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  };
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+ export declare function isValidEnumeratorLib(json: any[]): boolean;
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+ /** Specific to Enumerator for peptides */
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+ export declare function getJsonMonomerLibForEnumerator(rawLib: any[]): any;
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  export declare function createJsonMonomerLibFromSdf(table: DG.DataFrame): any;
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  export interface IMonomerLibHelper {
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  /** Singleton monomer library */
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;AAOtC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAC,YAAY,EAAe,MAAM,8BAA8B,CAAC;AAIxE,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,CAmBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAED,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CA8BpE;AAED,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;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;AAC1E,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"}
1
+ {"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAQtC,OAAO,EAAC,WAAW,EAAU,MAAM,gBAAgB,CAAC;AACpD,OAAO,EAAC,YAAY,EAAe,MAAM,8BAA8B,CAAC;AAIxE,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,CAmBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAED,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,OAAO,CAQzD;AAED,0CAA0C;AAC1C,wBAAgB,8BAA8B,CAAC,MAAM,EAAE,GAAG,EAAE,GAAG,GAAG,CAkDjE;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CA8BpE;AAED,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;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;AAC1E,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"}
package/src/monomer-works/monomer-utils.js CHANGED
@@ -1,7 +1,7 @@
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  // import * as ui from 'datagrok-api/ui';
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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 { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME } from '../utils/const';
4
+ import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, helmFieldsToEnumeratorInputFields, rGroupsDummy, dummyMonomer } from '../utils/const';
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  import { UnitsHandler } from '../utils/units-handler';
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  import { splitAlignedSequences } from '../utils/splitter';
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  export function encodeMonomers(col) {
@@ -84,6 +84,57 @@ export function createMomomersMolDict(lib) {
84
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  });
85
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  return dict;
86
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  }
87
+ export function isValidEnumeratorLib(json) {
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+ return json.every((entry) => {
89
+ return typeof entry === 'object' &&
90
+ Object.values(helmFieldsToEnumeratorInputFields).every((field) => {
91
+ return field in entry &&
92
+ typeof entry[field] === 'string';
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+ });
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+ });
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+ }
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+ /** Specific to Enumerator for peptides */
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+ export function getJsonMonomerLibForEnumerator(rawLib) {
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+ // todo
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+ function validateMonomerLibWithSmiles() {
100
+ }
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+ function restoreRgroupsInSmiles(rawSmiles) {
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+ const regex = new RegExp('\\[r\\]', 'g');
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+ let i = 0;
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+ return rawSmiles.replace(regex, (match) => { ++i; return `[${i}*]`; });
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+ }
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+ function prepareOutputSmilesColValue(smilesWithRestoredRgroups) {
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+ const result = smilesWithRestoredRgroups.replace('[1*]', '[H:1]');
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+ return result.replace('[2*]', '[OH:2]');
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+ }
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+ function prepareMolblock(rawMolblock) {
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+ return rawMolblock.replace('M ISO', 'M RGP');
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+ }
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+ const resultLib = [];
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+ validateMonomerLibWithSmiles();
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+ rawLib.forEach((rawMonomer) => {
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+ const monomer = { ...dummyMonomer };
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+ Object.entries(helmFieldsToEnumeratorInputFields).forEach(([key, value]) => {
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+ const monomerSymbol = rawMonomer[value];
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+ //@ts-ignore
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+ monomer[key] = monomerSymbol;
121
+ });
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+ let key = "smiles" /* HELM_FIELDS.SMILES */;
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+ const rawSmiles = rawMonomer[helmFieldsToEnumeratorInputFields[key]];
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+ const smilesWithRestoredRgroups = restoreRgroupsInSmiles(rawSmiles);
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+ const smiles = prepareOutputSmilesColValue(smilesWithRestoredRgroups);
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+ monomer[key] = smiles;
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+ key = "rgroups" /* HELM_FIELDS.RGROUPS */;
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+ monomer[key] = rGroupsDummy;
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+ key = "molfile" /* HELM_FIELDS.MOLFILE */;
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+ const smilesWithRgroups = restoreRgroupsInSmiles(rawSmiles);
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+ const rawMolfile = DG.chem.convert(smilesWithRgroups, DG.chem.Notation.Smiles, DG.chem.Notation.MolBlock);
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+ monomer[key] = prepareMolblock(rawMolfile);
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+ resultLib.push(monomer);
134
+ });
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+ console.log('resultLib:', resultLib);
136
+ return resultLib;
137
+ }
87
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  export function createJsonMonomerLibFromSdf(table) {
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  const resultLib = [];
89
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  for (let i = 0; i < table.rowCount; i++) {
package/src/monomer-works/monomer-utils.js.map CHANGED
@@ -1 +1 @@
1
- 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package/src/types/index.d.ts CHANGED
@@ -28,6 +28,7 @@ export interface IMonomerLib {
28
28
  getMonomerMolsByPolymerType(polymerType: string): {
29
29
  [monomerSymbol: string]: string;
30
30
  } | null;
31
+ getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: string, element?: string): string[];
31
32
  getMonomerSymbolsByType(polymerType: string): string[];
32
33
  getPolymerTypes(): string[];
33
34
  update(lib: IMonomerLib): void;
package/src/types/index.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/utils/cell-renderer.d.ts CHANGED
@@ -1,5 +1,8 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { ISeqSplitted } from './macromolecule/types';
3
+ export declare enum TAGS {
4
+ maxMonomerLength = ".mm.cellRenderer.maxMonomerLength"
5
+ }
3
6
  export declare enum DrawStyle {
4
7
  MSA = "MSA",
5
8
  classic = "classic"
package/src/utils/cell-renderer.d.ts.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"cell-renderer.d.ts","sourceRoot":"","sources":["cell-renderer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,YAAY,EAAC,MAAM,uBAAuB,CAAC;AAOnD,oBAAY,IAAI;IACd,gBAAgB,sCAAsC;CACvD;AAED,oBAAY,SAAS;IACnB,GAAG,QAAQ;IACX,OAAO,YAAY;CACpB;AAED;;;;;;;;;;;;;;;;;;;;wDAoBwD;AACxD,wBAAgB,mBAAmB,CACjC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAC1C,CAAC,EAAE,wBAAwB,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,GAAE,MAAuB,EACtE,KAAK,GAAE,MAAU,EAAE,IAAI,GAAE,OAAe,EAAE,gBAAgB,GAAE,MAAY,EACxE,SAAS,GAAE,MAAW,EAAE,IAAI,GAAE,OAAe,EAAE,SAAS,GAAE,SAA6B,EACvF,OAAO,GAAE,MAAM,EAAO,EAAE,OAAO,GAAE,MAAU,EAAE,QAAQ,GAAE,EAAE,CAAC,QAAQ,GAAG,IAAW,EAChF,iBAAiB,GAAE,YAAiB,EAAE,kBAAkB,GAAE,MAAM,GAAG,IAAW,EAC9E,kBAAkB,GAAE;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;CAAO,GAAG,MAAM,CA4DjE"}
package/src/utils/cell-renderer.js CHANGED
@@ -3,6 +3,10 @@ const undefinedColor = 'rgb(100,100,100)';
3
3
  const grayColor = '#808080';
4
4
  const blackColor = 'rgb(0,0,0)';
5
5
  const monomerToShortFunction = monomerToShort;
6
+ export var TAGS;
7
+ (function (TAGS) {
8
+ TAGS["maxMonomerLength"] = ".mm.cellRenderer.maxMonomerLength";
9
+ })(TAGS || (TAGS = {}));
6
10
  export var DrawStyle;
7
11
  (function (DrawStyle) {
8
12
  DrawStyle["MSA"] = "MSA";
package/src/utils/cell-renderer.js.map CHANGED
@@ -1 +1 @@
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1
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package/src/utils/const.d.ts CHANGED
@@ -48,6 +48,19 @@ export declare const enum HELM_MONOMER_TYPE {
48
48
  }
49
49
  export declare const HELM_CORE_FIELDS: HELM_FIELDS[];
50
50
  export declare const SDF_MONOMER_NAME = "MonomerName";
51
+ /** For Enumerator */
52
+ export declare const helmFieldsToEnumeratorInputFields: {
53
+ symbol: string;
54
+ name: string;
55
+ smiles: string;
56
+ };
57
+ /** For Enumerator */
58
+ export declare const rGroupsDummy: {
59
+ capGroupSmiles: string;
60
+ alternateId: string;
61
+ capGroupName: string;
62
+ label: string;
63
+ }[];
51
64
  export declare const jsonSdfMonomerLibDict: {
52
65
  monomerType: null;
53
66
  smiles: null;
@@ -61,6 +74,19 @@ export declare const jsonSdfMonomerLibDict: {
61
74
  polymerType: string;
62
75
  symbol: string;
63
76
  };
77
+ export declare const dummyMonomer: {
78
+ monomerType: string;
79
+ smiles: string;
80
+ name: string;
81
+ author: string;
82
+ molfile: string;
83
+ naturalAnalog: string;
84
+ rgroups: never[];
85
+ createDate: null;
86
+ id: number;
87
+ polymerType: string;
88
+ symbol: string;
89
+ };
64
90
  export declare const MONOMER_ENCODE_MIN = 256;
65
91
  export declare const MONOMER_ENCODE_MAX = 1034;
66
92
  //# sourceMappingURL=const.d.ts.map
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":"AAIA,eAAO,MAAM,sBAAsB,+BAA+B,CAAC;AAEnE;uFACuF;AACvF,0BAAkB,oBAAoB;IACpC,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;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAED,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,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IACnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAGD,0BAAkB,iBAAiB;IACjC,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,iBAAiB;IACjC,QAAQ,aAAa;IACrB,QAAQ,aAAa;IACrB,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAE9C,sBAAsB;AACtB,eAAO,MAAM,iCAAiC;;;;CAI7C,CAAC;AAEF,sBAAsB;AACtB,eAAO,MAAM,YAAY;;;;;GAaxB,CAAC;AAGF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAEF,eAAO,MAAM,YAAY;;;;;;;;;;;;CAYxB,CAAC;AAEF,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC"}
package/src/utils/const.js CHANGED
@@ -9,6 +9,27 @@ export const HELM_CORE_FIELDS = [
9
9
  // supported
10
10
  ];
11
11
  export const SDF_MONOMER_NAME = 'MonomerName';
12
+ /** For Enumerator */
13
+ export const helmFieldsToEnumeratorInputFields = {
14
+ ["symbol" /* HELM_REQUIRED_FIELDS.SYMBOL */]: 'Short Name',
15
+ ["name" /* HELM_REQUIRED_FIELDS.NAME */]: 'Medium Name',
16
+ ["smiles" /* HELM_REQUIRED_FIELDS.SMILES */]: 'SMILES',
17
+ };
18
+ /** For Enumerator */
19
+ export const rGroupsDummy = [
20
+ {
21
+ 'capGroupSmiles': '[*:1][H]',
22
+ 'alternateId': 'R1-H',
23
+ 'capGroupName': 'H',
24
+ 'label': 'R1'
25
+ },
26
+ {
27
+ 'capGroupSmiles': 'O[*:2]',
28
+ 'alternateId': 'R2-OH',
29
+ 'capGroupName': 'OH',
30
+ 'label': 'R2'
31
+ }
32
+ ];
12
33
  // todo: ideally, keys should be expressed via constants
13
34
  export const jsonSdfMonomerLibDict = {
14
35
  'monomerType': null,
@@ -23,6 +44,19 @@ export const jsonSdfMonomerLibDict = {
23
44
  'polymerType': 'MonomerType',
24
45
  'symbol': 'MonomerCode'
25
46
  };
47
+ export const dummyMonomer = {
48
+ 'monomerType': 'Backbone',
49
+ 'smiles': '',
50
+ 'name': '',
51
+ 'author': 'Datagrok',
52
+ 'molfile': '',
53
+ 'naturalAnalog': '',
54
+ 'rgroups': [],
55
+ 'createDate': null,
56
+ 'id': 0,
57
+ 'polymerType': 'PEPTIDE',
58
+ 'symbol': ''
59
+ };
26
60
  // range of hex nubers used in PepSea library to endode monomers
27
61
  export const MONOMER_ENCODE_MIN = 0x100;
28
62
  export const MONOMER_ENCODE_MAX = 0x40A;
package/src/utils/const.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,MAAM,CAAC,MAAM,sBAAsB,GAAG,4BAA4B,CAAC;AAyDnE,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG;;;;;IAK9B,2EAA2E;IAC3E,YAAY;CACb,CAAC;AAEF,MAAM,CAAC,MAAM,gBAAgB,GAAG,aAAa,CAAC;AAE9C,sBAAsB;AACtB,MAAM,CAAC,MAAM,iCAAiC,GAAG;IAC/C,4CAA6B,EAAE,YAAY;IAC3C,wCAA2B,EAAE,aAAa;IAC1C,4CAA6B,EAAE,QAAQ;CACxC,CAAC;AAEF,sBAAsB;AACtB,MAAM,CAAC,MAAM,YAAY,GAAG;IAC1B;QACE,gBAAgB,EAAE,UAAU;QAC5B,aAAa,EAAE,MAAM;QACrB,cAAc,EAAE,GAAG;QACnB,OAAO,EAAE,IAAI;KACd;IACD;QACE,gBAAgB,EAAE,QAAQ;QAC1B,aAAa,EAAE,OAAO;QACtB,cAAc,EAAE,IAAI;QACpB,OAAO,EAAE,IAAI;KACd;CACF,CAAC;AAEF,wDAAwD;AACxD,MAAM,CAAC,MAAM,qBAAqB,GAAG;IACnC,aAAa,EAAE,IAAI;IACnB,QAAQ,EAAE,IAAI;IACd,MAAM,EAAE,aAAa;IACrB,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,YAAY,GAAG;IAC1B,aAAa,EAAE,UAAU;IACzB,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,UAAU;IACpB,SAAS,EAAE,EAAE;IACb,eAAe,EAAE,EAAE;IACnB,SAAS,EAAE,EAAE;IACb,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,CAAC;IACP,aAAa,EAAE,SAAS;IACxB,QAAQ,EAAE,EAAE;CACb,CAAC;AACF,gEAAgE;AAChE,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC"}
package/src/utils/types.d.ts ADDED
@@ -0,0 +1,7 @@
1
+ export type EnumeratorLib = {
2
+ 'Short Name': string;
3
+ 'Medium Name': string;
4
+ 'SMILES': string;
5
+ 'Synonyms': string;
6
+ };
7
+ //# sourceMappingURL=types.d.ts.map
package/src/utils/types.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,aAAa,GAAG;IAC1B,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,MAAM,CAAA;CACnB,CAAA"}
package/src/utils/types.js ADDED
@@ -0,0 +1,2 @@
1
+ export {};
2
+ //# sourceMappingURL=types.js.map
package/src/utils/types.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}
package/src/utils/units-handler.d.ts.map CHANGED
@@ -1 +1 @@
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package/src/utils/units-handler.js CHANGED
@@ -49,10 +49,16 @@ export class UnitsHandler {
49
49
  // Empty monomer alphabet is not allowed
50
50
  if (Object.keys(stats.freq).length === 0)
51
51
  throw new Error('Alphabet is empty');
52
- const aligned = stats.sameLength ? "SEQ.MSA" /* ALIGNMENT.SEQ_MSA */ : "SEQ" /* ALIGNMENT.SEQ */;
53
- uh.column.setTag("aligned" /* TAGS.aligned */, aligned);
54
- const alphabet = detectAlphabet(stats.freq, candidateAlphabets);
55
- uh.column.setTag("alphabet" /* TAGS.alphabet */, alphabet);
52
+ let aligned = uh.column.getTag("aligned" /* TAGS.aligned */);
53
+ if (aligned === null) {
54
+ aligned = stats.sameLength ? "SEQ.MSA" /* ALIGNMENT.SEQ_MSA */ : "SEQ" /* ALIGNMENT.SEQ */;
55
+ uh.column.setTag("aligned" /* TAGS.aligned */, aligned);
56
+ }
57
+ let alphabet = uh.column.getTag("alphabet" /* TAGS.alphabet */);
58
+ if (alphabet === null) {
59
+ alphabet = detectAlphabet(stats.freq, candidateAlphabets);
60
+ uh.column.setTag("alphabet" /* TAGS.alphabet */, alphabet);
61
+ }
56
62
  if (alphabet === "UN" /* ALPHABET.UN */) {
57
63
  const alphabetSize = Object.keys(stats.freq).length;
58
64
  const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
package/src/utils/units-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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package/src/viewers/vd-regions.d.ts CHANGED
@@ -27,6 +27,7 @@ export declare const VdRegionsPropsDefault: {
27
27
  regionTypes: VdRegionType[];
28
28
  chains: string[];
29
29
  skipEmptyPositions: boolean;
30
+ fitWidth: boolean;
30
31
  positionWidth: number;
31
32
  positionHeight: PositionHeight;
32
33
  };
package/src/viewers/vd-regions.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/viewers/vd-regions.js CHANGED
@@ -12,6 +12,7 @@ export const VdRegionsPropsDefault = new class {
12
12
  this.chains = ['Heavy', 'Light'];
13
13
  //sequenceColumnNamePostfix: string = 'chain sequence';
14
14
  this.skipEmptyPositions = false;
15
+ this.fitWidth = false;
15
16
  this.positionWidth = 16;
16
17
  this.positionHeight = PositionHeight.Entropy;
17
18
  }
package/src/viewers/vd-regions.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"vd-regions.js","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,cAAc,EAAC,MAAM,YAAY,CAAC;AAE1C,qDAAqD;AAErD,MAAM,CAAN,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,mCAAmB,CAAA;IACnB,gCAAgB,CAAA;IAChB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,KAAZ,YAAY,QAIvB;AAwBD,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI;IAAA;QACvC,gBAAW,GAAmB,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC;QACjD,WAAM,GAAa,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACtC,uDAAuD;QAEvD,uBAAkB,GAAY,KAAK,CAAC;QACpC,aAAQ,GAAY,KAAK,CAAC;QAC1B,kBAAa,GAAW,EAAE,CAAC;QAC3B,mBAAc,GAAmB,cAAc,CAAC,OAAO,CAAC;IAC1D,CAAC;CAAA,EAAE,CAAC"}
package/src/viewers/web-logo.d.ts CHANGED
@@ -57,6 +57,7 @@ export declare const WebLogoPropsDefault: {
57
57
  export type WebLogoProps = Required<typeof WebLogoPropsDefault>;
58
58
  export interface IWebLogoViewer extends WebLogoProps, IViewer {
59
59
  get onSizeChanged(): Observable<void>;
60
+ get positionMarginValue(): number;
60
61
  setOptions(options: Partial<WebLogoProps>): void;
61
62
  }
62
63
  export declare const positionRe: RegExp;
package/src/viewers/web-logo.d.ts.map CHANGED
@@ -1 +1 @@
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package/src/viewers/web-logo.js.map CHANGED
@@ -1 +1 @@
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