@datagrok/sequence-translator 1.0.16 → 1.1.0

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 (92) hide show
  1. package/.eslintrc.json +4 -3
  2. package/CHANGELOG.md +3 -0
  3. package/detectors.js +8 -28
  4. package/dist/package-test.js +2 -72987
  5. package/dist/package-test.js.map +1 -0
  6. package/dist/package.js +2 -72192
  7. package/dist/package.js.map +1 -0
  8. package/files/axolabs-style.json +97 -0
  9. package/files/codes-to-symbols.json +66 -0
  10. package/files/formats-to-helm.json +59 -0
  11. package/files/linkers.json +22 -0
  12. package/files/monomer-lib.json +1094 -0
  13. package/link-bio +7 -0
  14. package/package.json +30 -26
  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 → model/axolabs}/draw-svg.ts +1 -1
  21. package/src/{axolabs → model/axolabs}/helpers.ts +7 -5
  22. package/src/model/const.ts +19 -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 +48 -0
  28. package/src/model/format-translation/format-converter.ts +107 -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 +106 -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/{structures-works → model/sequence-to-structure-utils}/mol-transformations.ts +61 -87
  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 +94 -0
  38. package/src/model/sequence-to-structure-utils/sequence-to-molfile.ts +409 -0
  39. package/src/package.ts +106 -77
  40. package/src/tests/const.ts +17 -0
  41. package/src/tests/smiles-tests.ts +32 -457
  42. package/src/view/const/main-tab.ts +3 -0
  43. package/src/view/const/view.ts +10 -0
  44. package/src/view/css/axolabs-tab.css +1 -0
  45. package/src/view/css/colored-text-input.css +27 -0
  46. package/src/view/css/main-tab.css +46 -0
  47. package/src/view/css/sdf-tab.css +39 -0
  48. package/src/view/monomer-lib-viewer/viewer.ts +22 -0
  49. package/src/view/tabs/axolabs.ts +720 -0
  50. package/src/view/tabs/main.ts +174 -0
  51. package/src/view/tabs/sdf.ts +173 -0
  52. package/src/view/utils/app-info-dialog.ts +18 -0
  53. package/src/view/utils/colored-input/colored-text-input.ts +56 -0
  54. package/src/view/utils/colored-input/input-painters.ts +44 -0
  55. package/src/view/utils/draw-molecule.ts +86 -0
  56. package/src/view/utils/molecule-img.ts +106 -0
  57. package/src/view/view.ts +129 -0
  58. package/tsconfig.json +12 -18
  59. package/webpack.config.js +17 -4
  60. package/README.md +0 -84
  61. package/css/style.css +0 -18
  62. package/img/Sequence Translator Axolabs.png +0 -0
  63. package/jest.config.js +0 -33
  64. package/setup-unlink-clean.cmd +0 -14
  65. package/setup.cmd +0 -14
  66. package/setup.sh +0 -37
  67. package/src/__jest__/remote.test.ts +0 -77
  68. package/src/__jest__/test-node.ts +0 -97
  69. package/src/apps/oligo-sd-file-app.ts +0 -58
  70. package/src/autostart/ICDs.ts +0 -3
  71. package/src/autostart/IDPs.ts +0 -3
  72. package/src/autostart/calculations.ts +0 -40
  73. package/src/autostart/constants.ts +0 -37
  74. package/src/autostart/registration.ts +0 -241
  75. package/src/autostart/salts.ts +0 -2
  76. package/src/autostart/sources.ts +0 -3
  77. package/src/autostart/users.ts +0 -3
  78. package/src/axolabs/constants.ts +0 -101
  79. package/src/axolabs/define-pattern.ts +0 -873
  80. package/src/helpers.ts +0 -28
  81. package/src/main/main-view.ts +0 -262
  82. package/src/structures-works/const.ts +0 -5
  83. package/src/structures-works/converters.ts +0 -323
  84. package/src/structures-works/from-monomers.ts +0 -267
  85. package/src/structures-works/map.ts +0 -720
  86. package/src/structures-works/save-sense-antisense.ts +0 -91
  87. package/src/structures-works/sequence-codes-tools.ts +0 -344
  88. package/src/utils/parse.ts +0 -27
  89. package/src/utils/sdf-add-columns.ts +0 -118
  90. package/src/utils/sdf-save-table.ts +0 -56
  91. package/test-SequenceTranslator-6288c2fbe346-cce4ac1d.html +0 -259
  92. package/vendors/openchemlib-full.js +0 -293
package/files/axolabs-style.json ADDED
@@ -0,0 +1,97 @@
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+ {
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+ "RNA": {
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+ "fullName": "RNA nucleotides",
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+ "symbols": ["A", "C", "G", "U"],
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+ "color": "rgb(255,230,153)"
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+ },
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+ "DNA": {
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+ "fullName": "DNA nucleotides",
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+ "symbols": ["dA", "dC", "dG", "dT"],
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+ "color": "rgb(66, 120, 245)"
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+ },
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+ "2'-Fluoro": {
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+ "fullName": "2'-Fluoro nucleotides",
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+ "symbols": ["Af", "Cf", "Gf", "Uf"],
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+ "color": "rgb(95, 212, 245)"
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+ },
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+ "2'-O-Methyl": {
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+ "fullName": "2'-O-Methyl nucleotides",
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+ "symbols": ["a", "c", "g", "u"],
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+ "color": "rgb(150, 95, 245)"
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+ },
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+ "2'-O-MOE": {
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+ "fullName": "2'-O-MOE nucleotides (including 5-Methyl C)",
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+ "symbols": ["Am", "Cm", "Gm", "Tm"],
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+ "color": "rgb(129, 199, 130)"
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+ },
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+ "GNA": {
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+ "fullName": "Glycol nucleic acid",
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+ "symbols": ["(GNA-A)", "(GNA-C)", "(GNA-G)", "(GNA-T)"],
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+ "color": "rgb(199, 169, 129)"
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+ },
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+ "LNA": {
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+ "fullName": "Locked nucleic acid (including 5-Methyl C)",
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+ "symbols": ["Ab", "Cb", "Gb", "Tb"],
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+ "color": "rgb(250, 185, 182)"
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+ },
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+ "UNA": {
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+ "fullName": "Unlocked nucleotides",
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+ "symbols": ["Ao", "Co", "Go", "Uo"],
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+ "color": "rgb(237, 104, 184)"
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+ },
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+ "A": {
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+ "fullName": "Adenosine",
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+ "symbols": ["a"],
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+ "color": "rgb(255,230,153)"
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+ },
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+ "C": {
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+ "fullName": "Cytidine",
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+ "symbols": ["c"],
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+ "color": "rgb(255,230,153)"
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+ },
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+ "G": {
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+ "fullName": "Guanosine",
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+ "symbols": ["g"],
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+ "color": "rgb(255,230,153)"
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+ },
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+ "U": {
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+ "fullName": "Uridine",
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+ "symbols": ["u"],
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+ "color": "rgb(255,230,153)"
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+ },
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+ "X-New": {
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+ "fullName": "",
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+ "symbols": ["X"],
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+ "color": "rgb(196, 91, 252)"
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+ },
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+ "Y-New": {
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+ "fullName": "",
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+ "symbols": ["Y"],
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+ "color": "rgb(150, 177, 255)"
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+ },
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+ "Z-New": {
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+ "fullName": "",
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+ "symbols": ["Z"],
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+ "color": "rgb(11, 222, 71)"
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+ },
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+ "invAb": {
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+ "fullName": "Inverted abasic capped",
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+ "symbols": ["(invAb)"],
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+ "color": "rgb(243, 153, 247)"
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+ },
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+ "5'-vinylps": {
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+ "fullName": "5'-vinylphosphonate-2'-OMe-uridine",
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+ "symbols": ["(vinu)"],
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+ "color": "rgb(99, 3, 40)"
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+ },
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+ "invAb(o)": {
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+ "fullName": "Inverted abasic capped (overhang)",
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+ "symbols": ["(invAb)"],
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+ "color": "rgb(240, 224, 108)"
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+ },
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+ "2'-OMe-U(o)": {
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+ "fullName": "Nucleotide Uridine with 2'O-Methyl protection (overhang)",
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+ "symbols": ["mU"],
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+ "color": "rgb(190, 237, 123)"
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+ }
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+ }
package/files/codes-to-symbols.json ADDED
@@ -0,0 +1,66 @@
1
+ {
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+ "Axolabs": {
3
+ "Af": "2'-fluoro-A",
4
+ "Cf": "2'-fluoro-C",
5
+ "Gf": "2'-fluoro-G",
6
+ "Uf": "2'-fluoro-U",
7
+ "a": "2'OMe-rA",
8
+ "c": "2'OMe-rC",
9
+ "g": "2'OMe-rG",
10
+ "u": "2'OMe-rU",
11
+ "p": "p",
12
+ "s": "sp",
13
+ "Rpn": "Rpn linkage",
14
+ "Rps": "Rps linkage",
15
+ "Spn": "Spn linkage",
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+ "Sps": "Sps linkage"
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+ },
18
+ "BioSpring": {
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+ "1": "2'-fluoro-U",
20
+ "2": "2'-fluoro-A",
21
+ "3": "2'-fluoro-C",
22
+ "4": "2'-fluoro-G",
23
+ "5": "2'OMe-rU",
24
+ "6": "2'OMe-rA",
25
+ "7": "2'OMe-rC",
26
+ "8": "2'OMe-rG",
27
+ "9": "5-Methyl-dC",
28
+ "A": "Deoxyadenosine",
29
+ "C": "Deoxycytidine",
30
+ "G": "Deoxyguanosine",
31
+ "T": "Deoxythymidine",
32
+ "p": "p",
33
+ "*": "sp",
34
+ "Rpn": "Rpn linkage",
35
+ "Rps": "Rps linkage",
36
+ "Spn": "Spn linkage",
37
+ "Sps": "Sps linkage"
38
+ },
39
+ "HELM": {},
40
+ "LCMS": {},
41
+ "Mermade12": {
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+ "I": "2'-fluoro-A",
43
+ "i": "2'-fluoro-A-ps",
44
+ "J": "2'-fluoro-C",
45
+ "j": "2'-fluoro-C-ps",
46
+ "K": "2'-fluoro-G",
47
+ "k": "2'-fluoro-G-ps",
48
+ "L": "2'-fluoro-U",
49
+ "l": "2'-fluoro-U-ps",
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+ "E": "2'OMe-rA",
51
+ "e": "2'OMe-rA-ps",
52
+ "F": "2'OMe-rC",
53
+ "f": "2'OMe-rC-ps",
54
+ "G": "2'OMe-rG",
55
+ "g": "2'OMe-rG-ps",
56
+ "H": "2'OMe-rU",
57
+ "h": "2'OMe-rU-ps"
58
+ },
59
+ "Nucleotides": {
60
+ "A": "Deoxyadenosine",
61
+ "C": "Deoxycytidine",
62
+ "G": "Guanosine",
63
+ "T": "Deoxythymidine",
64
+ "U": "Uridine"
65
+ }
66
+ }
package/files/formats-to-helm.json ADDED
@@ -0,0 +1,59 @@
1
+ {
2
+ "Axolabs": {
3
+ "nucleoside": {
4
+ "Uf": "[fR](U)p",
5
+ "Af": "[fR](A)p",
6
+ "Cf": "[fR](C)p",
7
+ "Gf": "[fR](G)p",
8
+ "u": "[25r](U)p",
9
+ "a": "[25r](A)p",
10
+ "c": "[25r](C)p",
11
+ "g": "[25r](G)p"
12
+ },
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+ "phosphateBackbone": {
14
+ "s": "[sp]"
15
+ }
16
+ },
17
+ "BioSpring": {
18
+ "nucleoside": {
19
+ "A": "r(A)p",
20
+ "T": "r(T)p",
21
+ "G": "r(G)p",
22
+ "C": "r(C)p",
23
+ "1": "[fR](U)p",
24
+ "2": "[fR](A)p",
25
+ "3": "[fR](C)p",
26
+ "4": "[fR](G)p",
27
+ "5": "[25r](U)p",
28
+ "6": "[25r](A)p",
29
+ "7": "[25r](C)p",
30
+ "8": "[25r](G)p",
31
+ "9": "d([m5C])p"
32
+ },
33
+ "phosphateBackbone": {
34
+ "*": "[sp]"
35
+ }
36
+ },
37
+ "Mermade12": {
38
+ "nucleoside": {
39
+ "h": "[25r](U)[sp]",
40
+ "e": "[25r](A)[sp]",
41
+ "f": "[25r](C)[sp]",
42
+ "g": "[25r](G)[sp]",
43
+ "l": "[fR](U)[sp]",
44
+ "i": "[fR](A)[sp]",
45
+ "j": "[fR](C)[sp]",
46
+ "k": "[fR](G)[sp]",
47
+ "L": "[fR](U)p",
48
+ "I": "[fR](A)p",
49
+ "J": "[fR](C)p",
50
+ "K": "[fR](G)p",
51
+ "H": "[25r](U)p",
52
+ "E": "[25r](A)p",
53
+ "F": "[25r](C)p",
54
+ "G": "[25r](G)p"
55
+ },
56
+ "phosphateBackbone": {
57
+ }
58
+ }
59
+ }
package/files/linkers.json ADDED
@@ -0,0 +1,22 @@
1
+ {
2
+ "left": [
3
+ ],
4
+ "right": [
5
+ "2'-fluoro-A-ps",
6
+ "2'-fluoro-C-ps",
7
+ "2'-fluoro-G-ps",
8
+ "2'-fluoro-U-ps",
9
+ "2'OMe-rA-ps",
10
+ "2'OMe-rC-ps",
11
+ "2'OMe-rG-ps",
12
+ "2'OMe-rU-ps"
13
+ ],
14
+ "phosphate": [
15
+ "sp",
16
+ "p",
17
+ "Sps linkage",
18
+ "Spn linkage",
19
+ "Rpn linkage",
20
+ "Rps linkage"
21
+ ]
22
+ }