icn3d 3.10.0 → 3.11.1

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Files changed (78) hide show
  1. package/CHANGELOG.md +6 -0
  2. package/README.md +4 -1
  3. package/build/icn3d.js +1463 -465
  4. package/build/icn3d.min.js +1 -1
  5. package/build/icn3d.module.js +1463 -465
  6. package/cpes5.sh +1 -1
  7. package/dist/CHANGELOG.md +6 -0
  8. package/dist/README.md +4 -1
  9. package/dist/full.html +4 -7
  10. package/dist/full2.html +7 -7
  11. package/dist/{full2_3.10.0.html → full2_3.11.1.html} +7 -7
  12. package/dist/{full_3.10.0.html → full_3.11.1.html} +4 -7
  13. package/dist/icn3d-3.11.1.zip +0 -0
  14. package/dist/icn3d.html +19 -2
  15. package/dist/icn3d.js +1463 -465
  16. package/dist/icn3d.min.js +1 -1
  17. package/dist/icn3d.module.js +1463 -465
  18. package/dist/{icn3d_3.10.0.css → icn3d_3.11.1.css} +0 -0
  19. package/dist/icn3d_3.11.1.min.js +2 -0
  20. package/dist/index.html +4 -7
  21. package/dist/module.html +7 -0
  22. package/es5/icn3d.min.js +1 -1
  23. package/es5/icn3d_all_full.min.js +1 -1
  24. package/es5/icn3d_all_full_3.10.0.min.js +1 -1
  25. package/es5/icn3d_all_full_3.10.1.min.js +14 -0
  26. package/es5/icn3d_all_full_3.11.0.min.js +14 -0
  27. package/es5/icn3d_all_full_3.11.1.min.js +14 -0
  28. package/full.html +1 -4
  29. package/full2.html +4 -4
  30. package/icn3d.html +19 -2
  31. package/index.html +1 -4
  32. package/jupyternotebook/setup.py +1 -1
  33. package/module.html +7 -0
  34. package/package.json +1 -1
  35. package/src/html/clickMenu.js +31 -8
  36. package/src/html/dialog.js +3 -0
  37. package/src/html/events.js +137 -36
  38. package/src/html/setDialog.js +48 -5
  39. package/src/html/setMenu.js +37 -20
  40. package/src/icn3d/analysis/scap.js +1 -1
  41. package/src/icn3d/analysis/symd.js +2 -2
  42. package/src/icn3d/annotations/addTrack.js +5 -3
  43. package/src/icn3d/annotations/annoCddSite.js +1 -1
  44. package/src/icn3d/annotations/annoDomain.js +11 -70
  45. package/src/icn3d/annotations/annoSnpClinVar.js +20 -7
  46. package/src/icn3d/annotations/domain3d.js +129 -19
  47. package/src/icn3d/annotations/showAnno.js +2 -2
  48. package/src/icn3d/annotations/showSeq.js +4 -4
  49. package/src/icn3d/display/alternate.js +4 -2
  50. package/src/icn3d/display/setColor.js +38 -3
  51. package/src/icn3d/display/setOption.js +13 -0
  52. package/src/icn3d/export/saveFile.js +6 -0
  53. package/src/icn3d/highlight/hlSeq.js +16 -2
  54. package/src/icn3d/icn3d.js +2 -0
  55. package/src/icn3d/interaction/contactMap.js +1 -1
  56. package/src/icn3d/interaction/lineGraph.js +29 -25
  57. package/src/icn3d/interaction/showInter.js +32 -19
  58. package/src/icn3d/interaction/viewInterPairs.js +1 -1
  59. package/src/icn3d/parsers/alignParser.js +2 -2
  60. package/src/icn3d/parsers/chainalignParser.js +555 -76
  61. package/src/icn3d/parsers/loadAtomData.js +41 -47
  62. package/src/icn3d/parsers/loadPDB.js +36 -41
  63. package/src/icn3d/parsers/mmcifParser.js +4 -4
  64. package/src/icn3d/parsers/mmdbParser.js +7 -7
  65. package/src/icn3d/parsers/opmParser.js +2 -2
  66. package/src/icn3d/parsers/parserUtils.js +8 -2
  67. package/src/icn3d/parsers/pdbParser.js +26 -11
  68. package/src/icn3d/parsers/realignParser.js +94 -23
  69. package/src/icn3d/parsers/sdfParser.js +1 -1
  70. package/src/icn3d/parsers/setSeqAlign.js +64 -28
  71. package/src/icn3d/selection/applyCommand.js +4 -2
  72. package/src/icn3d/selection/definedSets.js +1 -1
  73. package/src/icn3d/selection/loadScript.js +51 -0
  74. package/src/icn3d/selection/selection.js +1 -1
  75. package/src/icn3dui.js +18 -4
  76. package/src/utils/parasCls.js +4 -0
  77. package/dist/icn3d-3.10.0.zip +0 -0
  78. package/dist/icn3d_3.10.0.min.js +0 -2
package/CHANGELOG.md CHANGED
@@ -1,4 +1,10 @@
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  ## Change Log
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+ [icn3d-3.11.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.11.1.zip) was release on April 13, 2022. Users can input multiple PDB, MMDB, or AlphaFold IDs with the menu "File > Retrieve by ID > MMDB or AlphaFold IDs". Users can also load multiple PDB files at the same time with the menu "File > Open File > PDB Files (appendable)". The color legend became draggable.
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+ [icn3d-3.11.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.11.0.zip) was release on March 28, 2022. Users can align AlphaFold structures or PDB structures with the menu "File > Align > Multiple Chains" or "File > Align > Structure to Structure > Two AlphaFold Structures". Users can also load any structures as usual, then load your custom PDB file with the menu "File > Open File > PDB File (appendable)", then relaign these structures with the meu "File > Realign Selection > by Structure Alignment".
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+ [icn3d-3.10.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.10.1.zip) was release on March 9, 2022. Added the color option "Structure" and the style option "Hydrogens". Fixed some bugs on loading PDB files without headers.
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  [icn3d-3.10.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.10.0.zip) was release on March 7, 2022. Showed SNP and ClinVar annotations for AlphaFold structures.
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  [icn3d-3.9.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.9.0.zip) was release on February 28, 2022. Showed 3D domains for AlphaFold structures or any custom structures.
package/README.md CHANGED
@@ -31,7 +31,10 @@
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  You can download [npm "icn3d" package](https://www.npmjs.com/package/icn3d) to write Node.js scripts by calling iCn3D functions. These scripts can be used to process 3D structures (e.g., calculate interactions) in batch mode. The example scripts are at [icn3dnode](https://github.com/ncbi/icn3d/tree/master/icn3dnode).
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  * <b>Annotations for AlphaFold structures</b>:
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- For any custom structures such as AlphaFold structures, you can show annotations such as [conserved domains and 3D domains](https://structure.ncbi.nlm.nih.gov/icn3d/share.html?bPSkpeshtiH1TxbP8), etc.
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+ For any custom structures such as AlphaFold structures, you can show [conserved domain and 3D domain annotations](https://structure.ncbi.nlm.nih.gov/icn3d/share.html?bPSkpeshtiH1TxbP8). For AlphaFold structures, you can also show [SNP and ClinVar annotations](https://structure.ncbi.nlm.nih.gov/icn3d/share.html?XSQ5oqDCTfEQ3iAY7).
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+ * <b>Align AlphaFold structures</b>:
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+ You can align [AlphaFold structures or PDB structures](https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?chainalign=P69905_A,P01942_A,1HHO_A&showalignseq=1&bu=0) with the menu "File > Align > Multiple Chains" or "File > Align > Structure to Structure > Two AlphaFold Structures". You can also load any structures as usual, then load your custom PDB file with the menu "File > Open File > PDB File (appendable)", then relaign these structures with the meu "File > Realign Selection > by Structure Alignment".
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  * <b>Alternate SNPs in 3D</b>:
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  You can [alternate in 3D wild type and mutant of SNPs](https://structure.ncbi.nlm.nih.gov/icn3d/share.html?fNpzDuUE287SBFtz8) by clicking the menu "Analysis > Sequences & Annotations", the tab "Details", the checkbox "SNP", and mouseover on SNPs.