@datagrok/bio 1.5.7 → 1.5.8

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Files changed (36) hide show
  1. package/css/helm.css +3 -0
  2. package/detectors.js +9 -10
  3. package/dist/package-test.js +1095 -416
  4. package/dist/package.js +898 -250
  5. package/files/samples/sample_FASTA.csv +66 -66
  6. package/helm/JSDraw/Pistoia.HELM-uncompressed.js +9694 -0
  7. package/helm/JSDraw/Pistoia.HELM.js +27 -0
  8. package/helm/JSDraw/ReadMe.txt +8 -0
  9. package/helm/JSDraw/Scilligence.JSDraw2.Lite-uncompressed.js +31126 -0
  10. package/helm/JSDraw/Scilligence.JSDraw2.Lite.js +12 -0
  11. package/helm/JSDraw/Scilligence.JSDraw2.Resources.js +762 -0
  12. package/helm/JSDraw/dojo.js +250 -0
  13. package/helm/JSDraw/test.html +21 -0
  14. package/package.json +8 -1
  15. package/src/monomer-library.ts +199 -0
  16. package/src/package-test.ts +2 -0
  17. package/src/package.ts +41 -13
  18. package/src/tests/convert-test.ts +143 -22
  19. package/src/tests/detectors-test.ts +97 -156
  20. package/src/tests/renderer-test.ts +36 -0
  21. package/src/tests/splitter-test.ts +22 -0
  22. package/src/tests/types.ts +7 -0
  23. package/src/utils/atomic-works.ts +218 -97
  24. package/src/utils/cell-renderer.ts +214 -0
  25. package/src/utils/chem-palette.ts +280 -0
  26. package/src/utils/convert.ts +25 -16
  27. package/src/utils/misc.ts +29 -0
  28. package/src/utils/multiple-sequence-alignment.ts +1 -1
  29. package/src/utils/notation-converter.ts +120 -84
  30. package/src/utils/sequence-activity-cliffs.ts +2 -2
  31. package/src/utils/types.ts +13 -0
  32. package/src/utils/utils.ts +35 -30
  33. package/test-Bio-34f75e5127b8-c4c5a3dc.html +259 -0
  34. package/files/sample_FASTA.csv +0 -66
  35. package/files/sample_FASTA_with_activities.csv +0 -66
  36. package/files/sample_MSA.csv +0 -541
package/css/helm.css ADDED
@@ -0,0 +1,3 @@
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+ .d4-g-cell[semType="Macromolecule"] * {
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+ pointer-events: none !important;
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+ }
package/detectors.js CHANGED
@@ -13,16 +13,14 @@ class BioPackageDetectors extends DG.Package {
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  static mmSemType = 'Macromolecule';
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- static Units = {
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- FastaSeqPt: 'fasta:SEQ:PT', FastaSeqNt: 'fasta:SEQ:NT', FastaMsaPt: 'fasta:MSA:PT', FastaMsaNt: 'fasta:MSA:NT',
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- };
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-
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- static AminoacidsFastaAlphabet = new Set([
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+ static PeptideFastaAlphabet = new Set([
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  'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
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  'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',
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  ]);
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- static NucleotidesFastaAlphabet = new Set(['A', 'C', 'G', 'T']);
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+ static DnaFastaAlphabet = new Set(['A', 'C', 'G', 'T']);
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+
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+ static RnaFastaAlphabet = new Set(['A', 'C', 'G', 'U']);
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  /** @param s {String} - string to check
@@ -43,8 +41,9 @@ class BioPackageDetectors extends DG.Package {
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  }
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  const alphabetCandidates = [
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- ['NT', BioPackageDetectors.NucleotidesFastaAlphabet],
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- ['PT', BioPackageDetectors.AminoacidsFastaAlphabet],
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+ ['PT', BioPackageDetectors.PeptideFastaAlphabet],
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+ ['DNA', BioPackageDetectors.DnaFastaAlphabet],
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+ ['RNA', BioPackageDetectors.RnaFastaAlphabet],
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  ];
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  // TODO: Detect HELM sequence
@@ -103,8 +102,8 @@ class BioPackageDetectors extends DG.Package {
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  const cleanFreq = Object.assign({}, ...Object.entries(freq)
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  .filter(([m, f]) => m != ' ' &&
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  !noSeparatorChemRe.test(m) && !noSeparatorAlphaDigitRe.test(m) &&
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- !BioPackageDetectors.AminoacidsFastaAlphabet.has(m) &&
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- !BioPackageDetectors.NucleotidesFastaAlphabet.has(m))
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+ !BioPackageDetectors.PeptideFastaAlphabet.has(m) &&
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+ !BioPackageDetectors.DnaFastaAlphabet.has(m))
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  .map(([m, f]) => ({[m]: f})));
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  if (Object.keys(cleanFreq).length == 0) return null;
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