@datagrok-libraries/bio 5.39.13 → 5.39.15

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Files changed (26) hide show
  1. package/package.json +1 -1
  2. package/src/monomer-works/monomer-utils.d.ts +6 -0
  3. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  4. package/src/monomer-works/monomer-utils.js +35 -0
  5. package/src/monomer-works/monomer-utils.js.map +1 -1
  6. package/src/pdb/types.d.ts +2 -0
  7. package/src/pdb/types.d.ts.map +1 -1
  8. package/src/pdb/types.js.map +1 -1
  9. package/src/types/renderer.d.ts +1 -1
  10. package/src/types/renderer.d.ts.map +1 -1
  11. package/src/utils/data-provider.d.ts +4 -0
  12. package/src/utils/data-provider.d.ts.map +1 -0
  13. package/src/utils/data-provider.js +8 -0
  14. package/src/utils/data-provider.js.map +1 -0
  15. package/src/utils/docker.d.ts +1 -1
  16. package/src/utils/logger.d.ts +7 -0
  17. package/src/utils/logger.d.ts.map +1 -0
  18. package/src/utils/logger.js +2 -0
  19. package/src/utils/logger.js.map +1 -0
  20. package/src/utils/syncer.d.ts +1 -6
  21. package/src/utils/syncer.d.ts.map +1 -1
  22. package/src/utils/syncer.js.map +1 -1
  23. package/src/viewers/molstar-viewer.d.ts +5 -3
  24. package/src/viewers/molstar-viewer.d.ts.map +1 -1
  25. package/src/viewers/molstar-viewer.js +5 -2
  26. package/src/viewers/molstar-viewer.js.map +1 -1
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": "5.39.13",
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+ "version": "5.39.15",
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  "description": "",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.68",
package/src/monomer-works/monomer-utils.d.ts CHANGED
@@ -36,4 +36,10 @@ export declare function calculateMonomerSimilarity(monomerSet: string[]): Promis
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  [monomerId: string]: number;
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  };
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  }>;
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+ export declare function getMonomerSubstitutionMatrix(monomerSet: string[], fingerprintType?: string): Promise<{
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+ scoringMatrix: number[][];
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+ alphabetIndexes: {
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+ [monomerId: string]: number;
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+ };
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+ }>;
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  //# sourceMappingURL=monomer-utils.d.ts.map
package/src/monomer-works/monomer-utils.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"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;AAMxE,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;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;AA0DhJ;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAC,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAC,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC,CAAA;CAAC,CAAC,CAoBtF;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAC,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAC,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC,CAAA;CAAC,CAAC,CAmCtF"}
package/src/monomer-works/monomer-utils.js CHANGED
@@ -4,6 +4,7 @@ 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';
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  import { UnitsHandler } from '../utils/units-handler';
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  import { splitAlignedSequences } from '../utils/splitter';
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+ import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
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  export function encodeMonomers(col) {
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  let encodeSymbol = MONOMER_ENCODE_MIN;
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  const monomerSymbolDict = {};
@@ -192,4 +193,38 @@ export async function calculateMonomerSimilarity(monomerSet) {
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  }
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  return { scoringMatrix, alphabetIndexes };
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  }
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+ export async function getMonomerSubstitutionMatrix(monomerSet, fingerprintType = 'Morgan') {
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+ const libHelper = await getMonomerLibHelper();
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+ const monomerLib = libHelper.getBioLib();
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+ const scoringMatrix = new Array(monomerSet.length).fill(0).map(() => new Array(monomerSet.length).fill(0));
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+ const alphabetIndexes = {};
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+ const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.smiles ?? '');
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+ const fingerprintsFunc = DG.Func.find({ package: 'Chem', name: 'getFingerprints' })[0];
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+ if (!fingerprintsFunc) {
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+ console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints');
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+ return await calculateMonomerSimilarity(monomerSet);
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+ }
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+ const monomerMoleculesCol = DG.Column.fromStrings('smiles', monomerMolecules);
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+ // needed for function to work
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+ const _unusedMolDf = DG.DataFrame.fromColumns([monomerMoleculesCol]);
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+ const fingerPrints = (await fingerprintsFunc.apply({ col: monomerMoleculesCol, fingerprintType: fingerprintType }))?.entries;
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+ if (!fingerPrints) {
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+ console.warn(`${fingerprintType} Fingerprints could not be calculated for monomers from chem package.
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+ falling back to Morgan fingerprints`);
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+ return await calculateMonomerSimilarity(monomerSet);
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+ }
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+ for (let i = 0; i < fingerPrints.length; ++i) {
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+ scoringMatrix[i][i] = 1;
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+ alphabetIndexes[monomerSet[i]] = i;
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+ if (!fingerPrints[i])
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+ continue;
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+ for (let j = i + 1; j < fingerPrints.length; ++j) {
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+ if (!fingerPrints[j])
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+ continue;
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+ scoringMatrix[i][j] = scoringMatrix[j][i] = tanimotoSimilarity(fingerPrints[i], fingerPrints[j]);
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+ }
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+ }
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+ return { scoringMatrix, alphabetIndexes };
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+ }
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+ ;
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  //# sourceMappingURL=monomer-utils.js.map
package/src/monomer-works/monomer-utils.js.map CHANGED
@@ -1 +1 @@
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package/src/pdb/types.d.ts CHANGED
@@ -1,3 +1,4 @@
1
+ import { DataProviderFunc } from '../utils/data-provider';
1
2
  export type BiostructureData = {
2
3
  binary: boolean;
3
4
  ext: string;
@@ -7,6 +8,7 @@ export type BiostructureData = {
7
8
  dataLabel?: string;
8
9
  };
9
10
  };
11
+ export type BiostructureDataProviderFunc = DataProviderFunc<string, BiostructureData>;
10
12
  /**
11
13
  * Viewer does not support a property of type extending String event completely compatible
12
14
  */
package/src/pdb/types.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAMA,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,OAAO,CAAC;IAChB,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,GAAG,UAAU,CAAC;IAC1B,OAAO,CAAC,EAAE;QAAE,IAAI,CAAC,EAAE,MAAM,CAAC;QAAC,SAAS,CAAC,EAAE,MAAM,CAAC;KAAE,CAAC;CAClD,CAAA;AAED;;GAEG;AACH,qBAAa,oBAAqB,SAAQ,MAAM;IAC9C,SAAS,aAAa,KAAK,EAAE,MAAM;IAInC,MAAM,CAAC,IAAI,SAAU;IAErB,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,gBAAgB,GAAG,MAAM;IAK9C,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,MAAM,GAAG,gBAAgB;CAK7C"}
1
+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,gBAAgB,EAAC,MAAM,wBAAwB,CAAC;AAExD,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,OAAO,CAAC;IAChB,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,GAAG,UAAU,CAAC;IAC1B,OAAO,CAAC,EAAE;QAAE,IAAI,CAAC,EAAE,MAAM,CAAC;QAAC,SAAS,CAAC,EAAE,MAAM,CAAC;KAAE,CAAC;CAClD,CAAA;AAED,MAAM,MAAM,4BAA4B,GAAG,gBAAgB,CAAC,MAAM,EAAE,gBAAgB,CAAC,CAAC;AAEtF;;GAEG;AACH,qBAAa,oBAAqB,SAAQ,MAAM;IAC9C,SAAS,aAAa,KAAK,EAAE,MAAM;IAInC,MAAM,CAAC,IAAI,SAAU;IAErB,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,gBAAgB,GAAG,MAAM;IAK9C,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,MAAM,GAAG,gBAAgB;CAK7C"}
package/src/pdb/types.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,MAAM,EAAC,MAAM,WAAW,CAAC;AASjC;;GAEG;AACH,MAAM,OAAO,oBAAqB,SAAQ,MAAM;IAC9C,YAAsB,KAAa;QACjC,KAAK,CAAC,KAAK,CAAC,CAAC;IACf,CAAC;IAID,MAAM,CAAC,QAAQ,CAAC,GAAqB;QACnC,MAAM,OAAO,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,cAAc,CAAC,GAAG,CAAC,IAAkB,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAc,CAAC;QAChG,OAAO,IAAI,CAAC,SAAS,CAAC,EAAC,IAAI,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,GAAG,CAAC,OAAO,EAAC,CAAC,CAAC;IACjG,CAAC;IAED,MAAM,CAAC,MAAM,CAAC,GAAW;QACvB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAwB,CAAC,CAAC;QAClD,IAAI,IAAI;YAAE,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;QAC/E,OAAO,IAAI,CAAC;IACd,CAAC;;AAXM,yBAAI,GAAG,MAAM,CAAC"}
1
+ {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,MAAM,EAAC,MAAM,WAAW,CAAC;AAajC;;GAEG;AACH,MAAM,OAAO,oBAAqB,SAAQ,MAAM;IAC9C,YAAsB,KAAa;QACjC,KAAK,CAAC,KAAK,CAAC,CAAC;IACf,CAAC;IAID,MAAM,CAAC,QAAQ,CAAC,GAAqB;QACnC,MAAM,OAAO,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,cAAc,CAAC,GAAG,CAAC,IAAkB,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAc,CAAC;QAChG,OAAO,IAAI,CAAC,SAAS,CAAC,EAAC,IAAI,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,OAAO,EAAE,GAAG,CAAC,OAAO,EAAC,CAAC,CAAC;IACjG,CAAC;IAED,MAAM,CAAC,MAAM,CAAC,GAAW;QACvB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAwB,CAAC,CAAC;QAClD,IAAI,IAAI;YAAE,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;QAC/E,OAAO,IAAI,CAAC;IACd,CAAC;;AAXM,yBAAI,GAAG,MAAM,CAAC"}
package/src/types/renderer.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import { Observable } from 'rxjs';
2
2
  export interface IRenderer {
3
3
  get onRendered(): Observable<void>;
4
- invalidate(): void;
4
+ invalidate(caller?: string): void;
5
5
  /** @param timeout Default 5000 ms */
6
6
  awaitRendered(timeout?: number): Promise<void>;
7
7
  }
package/src/types/renderer.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"renderer.d.ts","sourceRoot":"","sources":["renderer.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,MAAM,WAAW,SAAS;IACxB,IAAI,UAAU,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IAEnC,UAAU,IAAI,IAAI,CAAC;IAEnB,sCAAsC;IACtC,aAAa,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;CAChD"}
1
+ {"version":3,"file":"renderer.d.ts","sourceRoot":"","sources":["renderer.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,MAAM,WAAW,SAAS;IACxB,IAAI,UAAU,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IAEnC,UAAU,CAAC,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAElC,sCAAsC;IACtC,aAAa,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;CAChD"}
package/src/utils/data-provider.d.ts ADDED
@@ -0,0 +1,4 @@
1
+ import * as DG from 'datagrok-api/dg';
2
+ export type DataProviderFunc<TId, TValue> = (id: TId) => Promise<TValue>;
3
+ export declare function getDataProviderList(semType: string): Promise<DG.Func[]>;
4
+ //# sourceMappingURL=data-provider.d.ts.map
package/src/utils/data-provider.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"data-provider.d.ts","sourceRoot":"","sources":["data-provider.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,MAAM,MAAM,gBAAgB,CAAC,GAAG,EAAE,MAAM,IAAI,CAAC,EAAE,EAAE,GAAG,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;AAEzE,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,EAAE,CAAC,IAAI,EAAE,CAAC,CAK7E"}
package/src/utils/data-provider.js ADDED
@@ -0,0 +1,8 @@
1
+ import * as grok from 'datagrok-api/grok';
2
+ export async function getDataProviderList(semType) {
3
+ return grok.dapi.functions
4
+ .include('params,entityTags')
5
+ .filter(`options.dataProvider="${semType}"`)
6
+ .list();
7
+ }
8
+ //# sourceMappingURL=data-provider.js.map
package/src/utils/data-provider.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"data-provider.js","sourceRoot":"","sources":["data-provider.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAK1C,MAAM,CAAC,KAAK,UAAU,mBAAmB,CAAC,OAAe;IACvD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS;SACvB,OAAO,CAAC,mBAAmB,CAAC;SAC5B,MAAM,CAAC,yBAAyB,OAAO,GAAG,CAAC;SAC3C,IAAI,EAAE,CAAC;AACZ,CAAC"}
package/src/utils/docker.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { ILogger } from './syncer';
1
+ import { ILogger } from './logger';
2
2
  export type DockerContainerStatus = 'stopped' | 'started' | 'pending change' | 'changing' | 'error' | 'checking';
3
3
  export declare function awaitStatus(dcId: string, targetStatus: DockerContainerStatus, timeout: number | undefined, logger: ILogger): Promise<void>;
4
4
  //# sourceMappingURL=docker.d.ts.map
package/src/utils/logger.d.ts ADDED
@@ -0,0 +1,7 @@
1
+ export interface ILogger {
2
+ error(message: any, params?: object | undefined, stackTrace?: string | undefined): void;
3
+ warning(message: string, params?: object | undefined): void;
4
+ info(message: string, params?: object | undefined): void;
5
+ debug(message: string, params?: object | undefined): void;
6
+ }
7
+ //# sourceMappingURL=logger.d.ts.map
package/src/utils/logger.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"logger.d.ts","sourceRoot":"","sources":["logger.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,OAAO;IACtB,KAAK,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACxF,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IAC5D,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACzD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;CAC3D"}
package/src/utils/logger.js ADDED
@@ -0,0 +1,2 @@
1
+ export {};
2
+ //# sourceMappingURL=logger.js.map
package/src/utils/logger.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"logger.js","sourceRoot":"","sources":["logger.ts"],"names":[],"mappings":""}
package/src/utils/syncer.d.ts CHANGED
@@ -1,15 +1,10 @@
1
+ import { ILogger } from './logger';
1
2
  export declare enum LogLevel {
2
3
  error = 0,
3
4
  warning = 1,
4
5
  info = 2,
5
6
  debug = 3
6
7
  }
7
- export interface ILogger {
8
- error(message: any, params?: object | undefined, stackTrace?: string | undefined): void;
9
- warning(message: string, params?: object | undefined): void;
10
- info(message: string, params?: object | undefined): void;
11
- debug(message: string, params?: object | undefined): void;
12
- }
13
8
  export declare class PromiseSyncer {
14
9
  private readonly logger;
15
10
  private promise;
package/src/utils/syncer.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"syncer.d.ts","sourceRoot":"","sources":["syncer.ts"],"names":[],"mappings":"AAQA,oBAAY,QAAQ;IAAG,KAAK,IAAI;IAAE,OAAO,IAAI;IAAE,IAAI,IAAI;IAAE,KAAK,IAAI;CAAC;AAEnE,MAAM,WAAW,OAAO;IACtB,KAAK,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACxF,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IAC5D,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;IACzD,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,IAAI,CAAC;CAC3D;AAED,qBAAa,aAAa;IAItB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAHzB,OAAO,CAAC,OAAO,CAAoC;gBAGhC,MAAM,EAAE,OAAO;IAGlC,OAAO,CAAC,WAAW,CAAa;IAEzB,IAAI,CAAC,SAAS,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI;CAahE"}
1
+ {"version":3,"file":"syncer.d.ts","sourceRoot":"","sources":["syncer.ts"],"names":[],"mappings":"AAOA,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAEjC,oBAAY,QAAQ;IAAG,KAAK,IAAI;IAAE,OAAO,IAAI;IAAE,IAAI,IAAI;IAAE,KAAK,IAAI;CAAC;AAEnE,qBAAa,aAAa;IAItB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAHzB,OAAO,CAAC,OAAO,CAAoC;gBAGhC,MAAM,EAAE,OAAO;IAGlC,OAAO,CAAC,WAAW,CAAa;IAEzB,IAAI,CAAC,SAAS,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI;CAahE"}
package/src/utils/syncer.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"syncer.js","sourceRoot":"","sources":["syncer.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,OAAO,EAAC,MAAM,YAAY,CAAC;AAEnC,MAAM,CAAN,IAAY,QAAuD;AAAnE,WAAY,QAAQ;IAAG,yCAAS,CAAA;IAAE,6CAAW,CAAA;IAAE,uCAAQ,CAAA;IAAE,yCAAS,CAAA;AAAA,CAAC,EAAvD,QAAQ,KAAR,QAAQ,QAA+C;AASnE,MAAM,OAAO,aAAa;IAGxB,YACmB,MAAe;QAAf,WAAM,GAAN,MAAM,CAAS;QAH1B,YAAO,GAAkB,OAAO,CAAC,OAAO,EAAE,CAAC;QAM3C,gBAAW,GAAW,CAAC,CAAC;IAF7B,CAAC;IAIG,IAAI,CAAC,SAAiB,EAAE,IAAyB;QACtD,MAAM,MAAM,GAAW,EAAE,IAAI,CAAC,WAAW,CAAC;QAC1C,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,OAAO,CAAC,CAAC;QAChE,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;YAC1C,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,UAAU,CAAC,CAAC;YACnE,MAAM,IAAI,EAAE,CAAC;YACb,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,QAAQ,CAAC,CAAC;QACnE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,GAAQ,EAAE,EAAE;YACpB,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC;YACxC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,aAAa,MAAM,EAAE,EAAE,SAAS,EAAE,QAAQ,CAAC,CAAC;QACrG,CAAC,CAAC,CAAC;QACH,mEAAmE;IACrE,CAAC;CACF"}
1
+ {"version":3,"file":"syncer.js","sourceRoot":"","sources":["syncer.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,OAAO,EAAC,MAAM,YAAY,CAAC;AAGnC,MAAM,CAAN,IAAY,QAAuD;AAAnE,WAAY,QAAQ;IAAG,yCAAS,CAAA;IAAE,6CAAW,CAAA;IAAE,uCAAQ,CAAA;IAAE,yCAAS,CAAA;AAAA,CAAC,EAAvD,QAAQ,KAAR,QAAQ,QAA+C;AAEnE,MAAM,OAAO,aAAa;IAGxB,YACmB,MAAe;QAAf,WAAM,GAAN,MAAM,CAAS;QAH1B,YAAO,GAAkB,OAAO,CAAC,OAAO,EAAE,CAAC;QAM3C,gBAAW,GAAW,CAAC,CAAC;IAF7B,CAAC;IAIG,IAAI,CAAC,SAAiB,EAAE,IAAyB;QACtD,MAAM,MAAM,GAAW,EAAE,IAAI,CAAC,WAAW,CAAC;QAC1C,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,OAAO,CAAC,CAAC;QAChE,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;YAC1C,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,UAAU,CAAC,CAAC;YACnE,MAAM,IAAI,EAAE,CAAC;YACb,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,QAAQ,CAAC,CAAC;QACnE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,GAAQ,EAAE,EAAE;YACpB,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC;YACxC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,SAAS,mBAAmB,MAAM,aAAa,MAAM,EAAE,EAAE,SAAS,EAAE,QAAQ,CAAC,CAAC;QACrG,CAAC,CAAC,CAAC;QACH,mEAAmE;IACrE,CAAC;CACF"}
package/src/viewers/molstar-viewer.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
- import { BiostructureDataJson } from '../pdb/types';
2
+ import { BiostructureData, BiostructureDataJson } from '../pdb/types';
3
3
  import { IViewer } from './viewer';
4
4
  import { PdbResDataFrameType } from '../pdb/pdb-helper';
5
5
  export declare enum RepresentationType {
@@ -29,9 +29,10 @@ export declare const BiostructurePropsDefault: {
29
29
  dataJson: BiostructureDataJson;
30
30
  pdb: string | null;
31
31
  pdbTag: string | null;
32
+ biostructureIdColumnName: string | null;
33
+ /** DG.Func nqName */
34
+ biostructureDataProvider: string | null;
32
35
  ligandColumnName: string | null;
33
- pdbProvider: string;
34
- emdbProvider: string;
35
36
  representation: RepresentationType;
36
37
  layoutIsExpanded: boolean;
37
38
  layoutShowControls: boolean;
@@ -68,6 +69,7 @@ export declare const BiostructurePropsDefault: {
68
69
  };
69
70
  export type BiostructureProps = typeof BiostructurePropsDefault;
70
71
  export interface IBiostructureViewer extends IViewer {
72
+ get dataEff(): BiostructureData | null;
71
73
  setOptions(options: Partial<BiostructureProps>): void;
72
74
  }
73
75
  export interface ISaguaroViewer extends IViewer {
package/src/viewers/molstar-viewer.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/viewers/molstar-viewer.js CHANGED
@@ -34,9 +34,12 @@ export const BiostructurePropsDefault = new class {
34
34
  this.dataJson = BiostructureDataJson.null;
35
35
  this.pdb = null;
36
36
  this.pdbTag = pdbTAGS.PDB;
37
+ this.biostructureIdColumnName = null;
38
+ /** DG.Func nqName */
39
+ this.biostructureDataProvider = null;
37
40
  this.ligandColumnName = null;
38
- this.pdbProvider = 'rcsb';
39
- this.emdbProvider = 'rcsb';
41
+ // pdbProvider: string = 'rcsb';
42
+ // emdbProvider: string = 'rcsb';
40
43
  // -- Style --
41
44
  this.representation = RepresentationType.Cartoon;
42
45
  // -- Layout --
package/src/viewers/molstar-viewer.js.map CHANGED
@@ -1 +1 @@
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