@datagrok/bio 2.15.3 → 2.15.6

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 (69) hide show
  1. package/CHANGELOG.md +40 -0
  2. package/detectors.js +9 -2
  3. package/dist/284.js +1 -1
  4. package/dist/284.js.map +1 -1
  5. package/dist/455.js +2 -0
  6. package/dist/455.js.map +1 -0
  7. package/dist/980.js +1 -1
  8. package/dist/980.js.map +1 -1
  9. package/dist/package-test.js +3 -3
  10. package/dist/package-test.js.map +1 -1
  11. package/dist/package.js +2 -2
  12. package/dist/package.js.map +1 -1
  13. package/files/monomer-libraries/polytool-lib.json +52 -0
  14. package/files/tests/to-atomic-level-msa-fasta-output.csv +683 -683
  15. package/files/tests/to-atomic-level-msa-separator-output.csv +104 -104
  16. package/package.json +9 -9
  17. package/src/analysis/sequence-activity-cliffs.ts +3 -1
  18. package/src/calculations/monomerLevelMols.ts +2 -1
  19. package/src/demo/bio03-atomic-level.ts +1 -1
  20. package/src/package-test.ts +2 -1
  21. package/src/package.ts +151 -38
  22. package/src/tests/WebLogo-positions-test.ts +1 -1
  23. package/src/tests/activity-cliffs-tests.ts +2 -3
  24. package/src/tests/bio-tests.ts +1 -1
  25. package/src/tests/detectors-custom-notation-tests.ts +37 -0
  26. package/src/tests/detectors-tests.ts +20 -69
  27. package/src/tests/detectors-weak-and-likely-tests.ts +2 -2
  28. package/src/tests/monomer-libraries-tests.ts +31 -6
  29. package/src/tests/pepsea-tests.ts +1 -1
  30. package/src/tests/renderers-monomer-placer-tests.ts +2 -4
  31. package/src/tests/scoring.ts +2 -3
  32. package/src/tests/seq-handler-get-helm-tests.ts +2 -4
  33. package/src/tests/seq-handler-splitted-tests.ts +6 -2
  34. package/src/tests/splitters-test.ts +6 -6
  35. package/src/tests/substructure-filters-tests.ts +2 -3
  36. package/src/tests/to-atomic-level-tests.ts +22 -17
  37. package/src/tests/to-atomic-level-ui-tests.ts +76 -38
  38. package/src/tests/types.ts +0 -2
  39. package/src/tests/utils/detectors-utils.ts +63 -0
  40. package/src/tests/utils.ts +2 -2
  41. package/src/utils/cell-renderer-custom.ts +62 -0
  42. package/src/utils/cell-renderer.ts +58 -126
  43. package/src/utils/cyclized.ts +28 -14
  44. package/src/utils/dimerized.ts +0 -2
  45. package/src/utils/helm-to-molfile/converter/converter.ts +75 -54
  46. package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts +2 -2
  47. package/src/utils/helm-to-molfile/converter/polymer.ts +23 -16
  48. package/src/utils/helm-to-molfile/converter/types.ts +0 -10
  49. package/src/utils/helm-to-molfile/utils.ts +10 -7
  50. package/src/utils/monomer-lib/consts.ts +18 -0
  51. package/src/utils/monomer-lib/lib-manager.ts +13 -3
  52. package/src/utils/monomer-lib/library-file-manager/file-manager.ts +1 -2
  53. package/src/utils/monomer-lib/monomer-colors.ts +68 -0
  54. package/src/utils/monomer-lib/monomer-lib-base.ts +165 -0
  55. package/src/utils/monomer-lib/monomer-lib.ts +44 -72
  56. package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts +1 -1
  57. package/src/utils/monomer-lib/web-editor-monomer-dummy.ts +121 -0
  58. package/src/utils/monomer-lib/web-editor-monomer-of-library.ts +102 -0
  59. package/src/utils/pepsea.ts +1 -1
  60. package/src/utils/save-as-fasta.ts +1 -1
  61. package/src/utils/seq-helper/seq-helper.ts +20 -49
  62. package/src/utils/sequence-to-mol.ts +24 -28
  63. package/src/viewers/web-logo-viewer.ts +2 -1
  64. package/src/widgets/composition-analysis-widget.ts +4 -3
  65. package/src/widgets/representations.ts +8 -10
  66. package/dist/248.js +0 -2
  67. package/dist/248.js.map +0 -1
  68. package/src/utils/cell-renderer-consts.ts +0 -31
  69. package/src/utils/monomer-lib/library-file-manager/consts.ts +0 -1
package/files/monomer-libraries/polytool-lib.json CHANGED
@@ -44,5 +44,57 @@
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  "id": 0,
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  "polymerType": "PEPTIDE",
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  "symbol": "COOH"
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+ },
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+ {
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+ "monomerType": "Backbone",
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+ "smiles": "[H:1]NC(C#C)C([OH:2])=O",
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+ "name": "Acetylenil Glycine",
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+ "author": "Datagrok",
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+ "molfile": "\n MJ201900 \n\n 8 7 0 0 0 0 0 0 0 0999 V2000\n 3.7485 -4.0401 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 4.4629 -4.4526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.1773 -4.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.8917 -4.4526 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 5.1773 -3.2152 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 4.4630 -5.2776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.7485 -5.6901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0340 -4.4526 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 2 3 1 0 0 0 0\n 3 5 2 0 0 0 0\n 2 6 1 0 0 0 0\n 1 2 1 0 0 0 0\n 1 8 1 0 0 0 0\n 3 4 1 0 0 0 0\n 6 7 3 0 0 0 0\nM RGP 2 4 2 8 1\nM END",
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+ "naturalAnalog": "G",
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+ "rgroups": [
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+ {
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+ "capGroupSMILES": "[*:1][H]",
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+ "alternateId": "R1-H",
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+ "capGroupName": "H",
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+ "label": "R1"
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+ },
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+ {
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+ "capGroupSMILES": "O[*:2]",
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+ "alternateId": "R2-OH",
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+ "capGroupName": "OH",
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+ "label": "R2"
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+ }
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+ ],
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+ "createDate": null,
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+ "id": 0,
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+ "polymerType": "PEPTIDE",
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+ "symbol": "aG"
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+ },
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+ {
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+ "monomerType": "Backbone",
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+ "smiles": "[H:1]NC(CN=[N+]=[N-])C([OH:2])=O",
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+ "name": "Azido Glycine",
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+ "author": "Datagrok",
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+ "molfile": "\n MJ201900 \n\n 10 9 0 0 0 0 0 0 0 0999 V2000\n -0.7143 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7144 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.4288 0.0000 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7144 1.2374 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0001 -0.8249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4288 0.0000 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7142 -1.2375 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4511 -1.6510 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0\n -2.2101 -2.0717 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0\n 2 3 1 0 0 0 0\n 3 5 2 0 0 0 0\n 2 6 1 0 0 0 0\n 1 2 1 0 0 0 0\n 1 7 1 0 0 0 0\n 3 4 1 0 0 0 0\n 6 8 1 0 0 0 0\n 8 9 2 0 0 0 0\n 9 10 2 0 0 0 0\nM RGP 2 4 2 7 1\nM END",
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+ "naturalAnalog": "G",
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+ "rgroups": [
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+ {
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+ "capGroupSMILES": "[*:1][H]",
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+ "alternateId": "R1-H",
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+ "capGroupName": "H",
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+ "label": "R1"
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+ },
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+ {
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+ "capGroupSMILES": "O[*:2]",
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+ "alternateId": "R2-OH",
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+ "capGroupName": "OH",
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+ "label": "R2"
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+ }
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+ ],
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+ "createDate": null,
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+ "id": "0",
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+ "polymerType": "PEPTIDE",
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+ "symbol": "azG"
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  }
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  ]