@datagrok/sequence-translator 1.0.17 → 1.1.4

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 (100) hide show
  1. package/.eslintrc.json +4 -3
  2. package/CHANGELOG.md +36 -0
  3. package/detectors.js +8 -0
  4. package/dist/package-test.js +2 -73079
  5. package/dist/package-test.js.map +1 -0
  6. package/dist/package.js +2 -72284
  7. package/dist/package.js.map +1 -0
  8. package/files/axolabs-style.json +97 -0
  9. package/files/codes-to-symbols.json +67 -0
  10. package/files/formats-to-helm.json +63 -0
  11. package/files/linkers.json +22 -0
  12. package/files/monomer-lib.json +1142 -0
  13. package/link-bio +7 -0
  14. package/package.json +30 -31
  15. package/scripts/build-monomer-lib.py +391 -122
  16. package/src/demo/demo-st-ui.ts +71 -0
  17. package/src/demo/handle-error.ts +12 -0
  18. package/src/model/axolabs/axolabs-tab.ts +111 -0
  19. package/src/model/axolabs/const.ts +33 -0
  20. package/src/{axolabs-tab → model/axolabs}/draw-svg.ts +1 -1
  21. package/src/{axolabs-tab → model/axolabs}/helpers.ts +7 -5
  22. package/src/model/const.ts +18 -0
  23. package/src/model/data-loading-utils/const.ts +8 -0
  24. package/src/model/data-loading-utils/json-loader.ts +38 -0
  25. package/src/model/data-loading-utils/types.ts +30 -0
  26. package/src/model/format-translation/const.ts +8 -0
  27. package/src/model/format-translation/conversion-utils.ts +49 -0
  28. package/src/model/format-translation/format-converter.ts +109 -0
  29. package/src/model/helpers.ts +12 -0
  30. package/src/model/monomer-lib/const.ts +3 -0
  31. package/src/model/monomer-lib/lib-wrapper.ts +119 -0
  32. package/src/model/parsing-validation/format-detector.ts +57 -0
  33. package/src/model/parsing-validation/sequence-validator.ts +52 -0
  34. package/src/model/sequence-to-structure-utils/const.ts +1 -0
  35. package/src/{utils/structures-works → model/sequence-to-structure-utils}/mol-transformations.ts +33 -41
  36. package/src/model/sequence-to-structure-utils/monomer-code-parser.ts +92 -0
  37. package/src/model/sequence-to-structure-utils/sdf-tab.ts +97 -0
  38. package/src/model/sequence-to-structure-utils/sequence-to-molfile.ts +409 -0
  39. package/src/package-test.ts +3 -1
  40. package/src/package.ts +113 -91
  41. package/src/tests/const.ts +24 -0
  42. package/src/tests/formats-support.ts +40 -0
  43. package/src/tests/formats-to-helm.ts +53 -0
  44. package/src/tests/helm-to-nucleotides.ts +28 -0
  45. package/src/view/const/main-tab.ts +3 -0
  46. package/src/view/const/view.ts +10 -0
  47. package/src/view/css/axolabs-tab.css +1 -0
  48. package/src/view/css/colored-text-input.css +27 -0
  49. package/src/view/css/main-tab.css +46 -0
  50. package/src/view/css/sdf-tab.css +39 -0
  51. package/src/view/monomer-lib-viewer/viewer.ts +22 -0
  52. package/src/view/tabs/axolabs.ts +719 -0
  53. package/src/view/tabs/main.ts +174 -0
  54. package/src/view/tabs/sdf.ts +193 -0
  55. package/src/view/utils/app-info-dialog.ts +18 -0
  56. package/src/view/utils/colored-input/colored-text-input.ts +56 -0
  57. package/src/view/utils/colored-input/input-painters.ts +44 -0
  58. package/src/view/utils/draw-molecule.ts +86 -0
  59. package/src/view/utils/molecule-img.ts +106 -0
  60. package/src/view/view.ts +127 -0
  61. package/tsconfig.json +12 -18
  62. package/webpack.config.js +17 -4
  63. package/README.md +0 -84
  64. package/css/style.css +0 -18
  65. package/img/Sequence Translator Axolabs.png +0 -0
  66. package/jest.config.js +0 -33
  67. package/setup-unlink-clean.cmd +0 -14
  68. package/setup-unlink-clean.sh +0 -21
  69. package/setup.cmd +0 -14
  70. package/setup.sh +0 -37
  71. package/src/__jest__/remote.test.ts +0 -77
  72. package/src/__jest__/test-node.ts +0 -97
  73. package/src/apps/oligo-sd-file-app.ts +0 -58
  74. package/src/autostart/calculations.ts +0 -40
  75. package/src/autostart/constants.ts +0 -37
  76. package/src/autostart/registration.ts +0 -306
  77. package/src/axolabs-tab/axolabs-tab.ts +0 -873
  78. package/src/axolabs-tab/define-pattern.ts +0 -874
  79. package/src/hardcode-to-be-eliminated/ICDs.ts +0 -3
  80. package/src/hardcode-to-be-eliminated/IDPs.ts +0 -3
  81. package/src/hardcode-to-be-eliminated/const.ts +0 -5
  82. package/src/hardcode-to-be-eliminated/constants.ts +0 -101
  83. package/src/hardcode-to-be-eliminated/converters.ts +0 -323
  84. package/src/hardcode-to-be-eliminated/map.ts +0 -720
  85. package/src/hardcode-to-be-eliminated/salts.ts +0 -2
  86. package/src/hardcode-to-be-eliminated/sources.ts +0 -3
  87. package/src/hardcode-to-be-eliminated/users.ts +0 -3
  88. package/src/main-tab/main-tab.ts +0 -210
  89. package/src/sdf-tab/sdf-tab.ts +0 -163
  90. package/src/sdf-tab/sequence-codes-tools.ts +0 -347
  91. package/src/tests/smiles-tests.ts +0 -458
  92. package/src/utils/const.ts +0 -0
  93. package/src/utils/helpers.ts +0 -28
  94. package/src/utils/parse.ts +0 -27
  95. package/src/utils/sdf-add-columns.ts +0 -118
  96. package/src/utils/sdf-save-table.ts +0 -56
  97. package/src/utils/structures-works/draw-molecule.ts +0 -84
  98. package/src/utils/structures-works/from-monomers.ts +0 -266
  99. package/test-SequenceTranslator-6288c2fbe346-695b7b55.html +0 -259
  100. package/vendors/openchemlib-full.js +0 -293
package/.eslintrc.json CHANGED
@@ -1,7 +1,7 @@
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  {
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  "env": {
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  "browser": true,
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- "es2021": true
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+ "es2022": true
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  },
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  "extends": [
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  "google"
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  "error",
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  120
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  ],
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- "no-unused-vars": "warn",
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+ "no-unused-vars": "off",
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+ "@typescript-eslint/no-unused-vars": "warn",
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  "require-jsdoc": "off",
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  "valid-jsdoc": "off",
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  "spaced-comment": "off",
@@ -49,4 +50,4 @@
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  }],
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  "guard-for-in": "off"
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  }
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- }
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+ }
package/CHANGELOG.md ADDED
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+ # Sequence Translator changelog
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+
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+ ## 1.1.4 (2023-09-07)
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+
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+ ### Bug fixes
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+
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+ * Fixed molfile direction for AS and AS2 on SDF tab
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+
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+ ## 1.1.3 (2023-09-07)
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+
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+ ### Bug fixes
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+
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+ * Fixed Direction of AS and AS2 for SDF tab
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+
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+ ## 1.1.2 (2023-08-16)
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+
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+ ### Bug fixes
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+
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+ * Fixed HELM generation for modifications
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+
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+ ## 1.1.1 (2023-08-10)
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+
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+ ### Features
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+
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+ * Updated dependencies
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+
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+ ## 1.1.0 (2023-07-26)
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+
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+ * Dependency: datgarok-api >= 1.15.2
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+
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+ ### Features
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+
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+ * Option to add extra formats for translation in addition to `Axolabs`, `BioSpring` and `MerMade12`
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+ * Generation of HELM strings
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+ * Improved SMILES generation
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+ * UI/UX adjustments
package/detectors.js CHANGED
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+ /**
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+ * The class contains semantic type detectors.
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+ * Detectors are functions tagged with `DG.FUNC_TYPES.SEM_TYPE_DETECTOR`.
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+ * See also: https://datagrok.ai/help/develop/how-to/define-semantic-type-detectors
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+ * The class name is comprised of <PackageName> and the `PackageDetectors` suffix.
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+ * Follow this naming convention to ensure that your detectors are properly loaded.
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+ */
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+