@datagrok/sequence-translator 1.0.17 → 1.1.4

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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/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)"
36
+ },
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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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+ },
92
+ "2'-OMe-U(o)": {
93
+ "fullName": "Nucleotide Uridine with 2'O-Methyl protection (overhang)",
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+ "symbols": ["mU"],
95
+ "color": "rgb(190, 237, 123)"
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+ }
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+ }
package/files/codes-to-symbols.json ADDED
@@ -0,0 +1,67 @@
1
+ {
2
+ "Axolabs": {
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+ "(GalNAc)": "(GalNAc)",
4
+ "Af": "2'-fluoro-A",
5
+ "Cf": "2'-fluoro-C",
6
+ "Gf": "2'-fluoro-G",
7
+ "Uf": "2'-fluoro-U",
8
+ "a": "2'OMe-rA",
9
+ "c": "2'OMe-rC",
10
+ "g": "2'OMe-rG",
11
+ "u": "2'OMe-rU",
12
+ "p": "p",
13
+ "s": "sp",
14
+ "Rpn": "Rpn linkage",
15
+ "Rps": "Rps linkage",
16
+ "Spn": "Spn linkage",
17
+ "Sps": "Sps linkage"
18
+ },
19
+ "BioSpring": {
20
+ "1": "2'-fluoro-U",
21
+ "2": "2'-fluoro-A",
22
+ "3": "2'-fluoro-C",
23
+ "4": "2'-fluoro-G",
24
+ "5": "2'OMe-rU",
25
+ "6": "2'OMe-rA",
26
+ "7": "2'OMe-rC",
27
+ "8": "2'OMe-rG",
28
+ "9": "5-Methyl-dC",
29
+ "A": "Deoxyadenosine",
30
+ "C": "Deoxycytidine",
31
+ "G": "Deoxyguanosine",
32
+ "T": "Deoxythymidine",
33
+ "p": "p",
34
+ "*": "sp",
35
+ "Rpn": "Rpn linkage",
36
+ "Rps": "Rps linkage",
37
+ "Spn": "Spn linkage",
38
+ "Sps": "Sps linkage"
39
+ },
40
+ "HELM": {},
41
+ "LCMS": {},
42
+ "Mermade12": {
43
+ "I": "2'-fluoro-A",
44
+ "i": "2'-fluoro-A-ps",
45
+ "J": "2'-fluoro-C",
46
+ "j": "2'-fluoro-C-ps",
47
+ "K": "2'-fluoro-G",
48
+ "k": "2'-fluoro-G-ps",
49
+ "L": "2'-fluoro-U",
50
+ "l": "2'-fluoro-U-ps",
51
+ "E": "2'OMe-rA",
52
+ "e": "2'OMe-rA-ps",
53
+ "F": "2'OMe-rC",
54
+ "f": "2'OMe-rC-ps",
55
+ "G": "2'OMe-rG",
56
+ "g": "2'OMe-rG-ps",
57
+ "H": "2'OMe-rU",
58
+ "h": "2'OMe-rU-ps"
59
+ },
60
+ "Nucleotides": {
61
+ "A": "Deoxyadenosine",
62
+ "C": "Deoxycytidine",
63
+ "G": "Guanosine",
64
+ "T": "Deoxythymidine",
65
+ "U": "Uridine"
66
+ }
67
+ }
package/files/formats-to-helm.json ADDED
@@ -0,0 +1,63 @@
1
+ {
2
+ "Axolabs": {
3
+ "nucleoside": {
4
+ "(GalNAc)": "[GalNAc]",
5
+ "Uf": "[fR](U)p",
6
+ "Af": "[fR](A)p",
7
+ "Cf": "[fR](C)p",
8
+ "Gf": "[fR](G)p",
9
+ "u": "[25r](U)p",
10
+ "a": "[25r](A)p",
11
+ "c": "[25r](C)p",
12
+ "g": "[25r](G)p"
13
+ },
14
+ "phosphateBackbone": {
15
+ "s": "[sp]"
16
+ }
17
+ },
18
+ "BioSpring": {
19
+ "nucleoside": {
20
+ "(GalNAc)": "[GalNAc]",
21
+ "A": "r(A)p",
22
+ "T": "r(T)p",
23
+ "G": "r(G)p",
24
+ "C": "r(C)p",
25
+ "1": "[fR](U)p",
26
+ "2": "[fR](A)p",
27
+ "3": "[fR](C)p",
28
+ "4": "[fR](G)p",
29
+ "5": "[25r](U)p",
30
+ "6": "[25r](A)p",
31
+ "7": "[25r](C)p",
32
+ "8": "[25r](G)p",
33
+ "9": "d([m5C])p"
34
+ },
35
+ "phosphateBackbone": {
36
+ "*": "[sp]"
37
+ }
38
+ },
39
+ "Mermade12": {
40
+ "nucleoside": {
41
+ "(GalNAc)": "[GalNAc]",
42
+ "h": "[25r](U)[sp]",
43
+ "e": "[25r](A)[sp]",
44
+ "f": "[25r](C)[sp]",
45
+ "g": "[25r](G)[sp]",
46
+ "l": "[fR](U)[sp]",
47
+ "i": "[fR](A)[sp]",
48
+ "j": "[fR](C)[sp]",
49
+ "k": "[fR](G)[sp]",
50
+ "L": "[fR](U)p",
51
+ "I": "[fR](A)p",
52
+ "J": "[fR](C)p",
53
+ "K": "[fR](G)p",
54
+ "H": "[25r](U)p",
55
+ "E": "[25r](A)p",
56
+ "F": "[25r](C)p",
57
+ "G": "[25r](G)p"
58
+ },
59
+ "phosphateBackbone": {
60
+ "<empty>": "[sp]"
61
+ }
62
+ }
63
+ }
package/files/linkers.json ADDED
@@ -0,0 +1,22 @@
1
+ {
2
+ "left": [
3
+ ],
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+ "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
+ }