@datagrok/bio 2.18.4 → 2.20.0

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Files changed (52) hide show
  1. package/CHANGELOG.md +5 -0
  2. package/README.md +2 -2
  3. package/dist/242.js +1 -1
  4. package/dist/242.js.map +1 -1
  5. package/dist/284.js +1 -1
  6. package/dist/284.js.map +1 -1
  7. package/dist/589.js +1 -1
  8. package/dist/589.js.map +1 -1
  9. package/dist/731.js +1 -1
  10. package/dist/731.js.map +1 -1
  11. package/dist/810.js +2 -0
  12. package/dist/810.js.map +1 -0
  13. package/dist/980.js +1 -1
  14. package/dist/980.js.map +1 -1
  15. package/dist/package-test.js +2 -2
  16. package/dist/package-test.js.map +1 -1
  17. package/dist/package.js +3 -3
  18. package/dist/package.js.map +1 -1
  19. package/dockerfiles/container.json +1 -1
  20. package/files/monomer-libraries/HELMCoreLibrary.json +18926 -18215
  21. package/files/samples/HELM_BI_CYCLIC.csv +7 -0
  22. package/files/samples/peptides-non-natural.csv +1001 -0
  23. package/files/tests/to-atomic-level-dna-fasta-output.csv +15077 -15077
  24. package/files/tests/to-atomic-level-msa-fasta-output.csv +1903 -1903
  25. package/files/tests/to-atomic-level-msa-separator-output.csv +3236 -3236
  26. package/files/tests/to-atomic-level-peptides-fasta-output.csv +32262 -32262
  27. package/files/tests/to-atomic-level-pt-fasta-2.mol +29 -29
  28. package/package.json +7 -7
  29. package/projects/seq_space_demo.zip +0 -0
  30. package/src/analysis/sequence-diversity-viewer.ts +22 -14
  31. package/src/analysis/sequence-search-base-viewer.ts +6 -72
  32. package/src/analysis/sequence-similarity-viewer.ts +42 -23
  33. package/src/demo/bio01-similarity-diversity.ts +21 -2
  34. package/src/demo/bio01a-hierarchical-clustering-and-sequence-space.ts +7 -0
  35. package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts +1 -1
  36. package/src/demo/bio03-atomic-level.ts +15 -0
  37. package/src/package.ts +29 -59
  38. package/src/tests/activity-cliffs-utils.ts +7 -6
  39. package/src/tests/scoring.ts +2 -2
  40. package/src/tests/similarity-diversity-tests.ts +2 -2
  41. package/src/utils/cell-renderer.ts +11 -1
  42. package/src/utils/helm-to-molfile/converter/converter.ts +21 -9
  43. package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts +8 -4
  44. package/src/utils/helm-to-molfile/converter/simple-polymer.ts +18 -9
  45. package/src/utils/monomer-lib/monomer-lib-base.ts +4 -4
  46. package/src/utils/pepsea.ts +22 -39
  47. package/src/utils/seq-helper/seq-handler.ts +2 -2
  48. package/src/utils/seq-helper/seq-helper.ts +50 -34
  49. package/src/utils/sequence-to-mol.ts +1 -1
  50. package/src/utils/ui-utils.ts +23 -0
  51. package/test-console-output-1.log +0 -7387
  52. package/test-record-1.mp4 +0 -0
package/files/samples/HELM_BI_CYCLIC.csv ADDED
@@ -0,0 +1,7 @@
1
+ HELM
2
+ "PEPTIDE1{C}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_3Cl].[Phe_34diCl].[meY].[dI].[Met_O].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu]}|PEPTIDE3{[meY].[Pro_4Me3OH].[Met_O].[NMe2Abz].[dI].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0"
3
+ "PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0"
4
+ "PEPTIDE1{[Asp_OMe]}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_3Cl].[Phe_34diCl].[meY].[dI].[Met_O].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu]}|PEPTIDE3{[meY].[Pro_4Me3OH].[Met_O].[NMe2Abz].[dI].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0"
5
+ "PEPTIDE1{E}|PEPTIDE2{[dI].S.[Asp_OMe].[dI].[meG].[Phe_3Cl].C.[meY].[dI].S.N.G.[meD].[xiIle].R.[Ala_tBu]}|PEPTIDE3{[meY].C.[Met_O].[meD].G.[3Pal].[xiIle].R.[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_34diCl].K}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0"
6
+ "PEPTIDE1{D}|PEPTIDE2{[dI].[Phg].[Asp_OMe].[dI].[meG].[Phe_3Cl].Q.C.[dI].[Ser_PO3H2].[NMe2Abz].[Tyr_Ph4OH].[3Pal].Q.D.[Ala_tBu]}|PEPTIDE3{[meY].[dN].[Met_O].[NMe2Abz].[D-Pen].[Pro_4Me3OH].[xiIle].[Pro_4Me3OH].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].K.[meG].[Phe_34diCl].[Ser_PO3H2]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0"
7
+ "PEPTIDE1{[meG]}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_3Cl].[Phe_34diCl].[meY].[dI].[Met_O].[NMe2Abz].[Tyr_Ph4OH].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu]}|PEPTIDE3{[meY].[Pro_4Me3OH].[Met_O].[NMe2Abz].[dI].[3Pal].[xiIle].[Tyr_35diI].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].[dI].[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0"