@datagrok/sequence-translator 1.10.13 → 1.10.15

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Files changed (36) hide show
  1. package/CHANGELOG.md +6 -0
  2. package/detectors.js +30 -2
  3. package/dist/455.js +1 -1
  4. package/dist/455.js.map +1 -1
  5. package/dist/package-test.js +1 -1
  6. package/dist/package-test.js.map +1 -1
  7. package/dist/package.js +1 -1
  8. package/dist/package.js.map +1 -1
  9. package/files/samples/sirna-demo.csv +38 -0
  10. package/files/tests/chem_enum_cores.csv +5 -0
  11. package/files/tests/chem_enum_rgroups.csv +5 -0
  12. package/package.json +2 -2
  13. package/src/apps/structure/view/ui.ts +1 -1
  14. package/src/apps/translator/view/ui.ts +1 -1
  15. package/src/oligo-renderer/canvas-renderer.ts +500 -0
  16. package/src/oligo-renderer/cell-renderer.ts +105 -0
  17. package/src/oligo-renderer/converters.ts +77 -0
  18. package/src/oligo-renderer/helm-parser.ts +154 -0
  19. package/src/oligo-renderer/legend-panel.ts +154 -0
  20. package/src/oligo-renderer/structures-panel.ts +96 -0
  21. package/src/oligo-renderer/tooltip.ts +223 -0
  22. package/src/oligo-renderer/types.ts +221 -0
  23. package/src/package-api.ts +43 -1
  24. package/src/package-test.ts +2 -0
  25. package/src/package.g.ts +56 -3
  26. package/src/package.ts +92 -5
  27. package/src/polytool/const.ts +1 -1
  28. package/src/polytool/pt-chem-enum-dialog.ts +940 -0
  29. package/src/polytool/pt-chem-enum.ts +553 -0
  30. package/src/polytool/pt-dialog.ts +4 -125
  31. package/src/polytool/pt-enumerate-seq-dialog.ts +3 -3
  32. package/src/tests/oligo-renderer-tests.ts +299 -0
  33. package/src/tests/polytool-enumerate-chem-tests.ts +408 -0
  34. package/test-console-output-1.log +303 -97
  35. package/test-record-1.mp4 +0 -0
  36. package/src/polytool/pt-enumeration-chem.ts +0 -100
package/test-record-1.mp4 CHANGED
Binary file
package/src/polytool/pt-enumeration-chem.ts DELETED
@@ -1,100 +0,0 @@
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- import * as ui from 'datagrok-api/ui';
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- import * as grok from 'datagrok-api/grok';
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- import * as DG from 'datagrok-api/dg';
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-
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- import {getAvailableMonomers, getAvailableMonomerMols} from './utils';
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- import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
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-
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- export const PT_CHEM_EXAMPLE = `
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-
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-
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- 22 24 0 0 0 0 0 0 0 0999 V2000
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- 0.3128 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 0.3128 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -0.4054 -1.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -1.1081 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -0.4054 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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- -1.1081 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -1.8175 -1.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 1.0222 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -1.8175 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -2.5292 -0.7509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 1.0222 1.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 1.7227 1.7263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -0.4054 -1.9896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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- -2.5292 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 2.4544 1.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 1.7406 0.0740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- 1.0222 -1.1623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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- 2.4544 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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- -1.8175 -1.9896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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- -3.2453 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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- 3.1670 1.7285 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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- 1.7149 2.5513 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
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- 2 1 2 0 0 0 0
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- 3 1 1 0 0 0 0
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- 4 3 1 0 0 0 0
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- 5 2 1 0 0 0 0
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- 6 5 1 0 0 0 0
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- 7 4 1 0 0 0 0
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- 8 2 1 0 0 0 0
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- 9 6 1 0 0 0 0
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- 10 7 2 0 0 0 0
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- 11 8 2 0 0 0 0
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- 12 11 1 0 0 0 0
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- 13 3 2 0 0 0 0
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- 14 9 2 0 0 0 0
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- 15 18 1 0 0 0 0
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- 16 8 1 0 0 0 0
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- 17 1 1 0 0 0 0
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- 18 16 2 0 0 0 0
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- 19 7 1 0 0 0 0
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- 20 14 1 0 0 0 0
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- 6 4 2 0 0 0 0
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- 15 12 2 0 0 0 0
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- 14 10 1 0 0 0 0
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- 15 21 1 0 0 0 0
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- 12 22 1 0 0 0 0
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- M RGP 1 22 1
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- M END`;
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-
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- export async function getEnumerationChem(molString: string, screenLibrary: string):
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- Promise<string[]> {
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- const variableMonomers = await getAvailableMonomers(screenLibrary);
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- const variableMols = await getAvailableMonomerMols(screenLibrary);
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- const enumerations = new Array<string>(variableMonomers.length);
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-
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- const rdkitModule: RDModule = await grok.functions.call('Chem:getRdKitModule');
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- const molScaffold: RDMol = rdkitModule.get_mol(molString);
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- const smiScaffold = molScaffold.get_smiles();
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- molScaffold.delete();
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-
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- const smilesSubsts = new Array<string>(variableMonomers.length);
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-
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- for (let i = 0; i < variableMonomers.length; i++) {
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- const name = variableMonomers[i];
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- const molBlock = variableMols[name];
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- const molSubst: RDMol = rdkitModule.get_mol(molBlock);
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- smilesSubsts[i] = molSubst.get_smiles();
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- molSubst.delete();
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- }
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-
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- for (let i = 0; i < variableMonomers.length; i++) {
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- let molRes: RDMol | null = null;
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- try {
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- //TODO: use RDKit linking function when exposed
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- const smiResRaw = `${smiScaffold}.${smilesSubsts[i]}`.replaceAll('[1*]C', 'C([1*])').replaceAll('[1*]c', 'c([1*])').replaceAll('[1*]O', 'O([1*])').replaceAll('[1*]N', 'N([1*])');
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- const smiRes = `${smiResRaw}`.replaceAll('([1*])', '9').replaceAll('[1*]', '9');
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- molRes = rdkitModule.get_mol(smiRes, JSON.stringify({mappedDummiesAreRGroups: true}));
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- const molV3 = molRes.get_v3Kmolblock();
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- enumerations[i] = molV3;
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- } catch (err:any) {
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- enumerations[i] = '';
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- } finally {
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- molRes?.delete();
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- }
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- }
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-
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-
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- return enumerations;
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- }