molstar 4.5.0 → 4.6.0

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 (241) hide show
  1. package/build/viewer/molstar.js +1 -1
  2. package/lib/apps/mesoscale-explorer/embedded.html +79 -0
  3. package/lib/apps/mesoscale-explorer/index.html +2 -1
  4. package/lib/apps/mesoscale-explorer/ui/states.js +12 -0
  5. package/lib/apps/viewer/app.js +4 -1
  6. package/lib/commonjs/apps/mesoscale-explorer/ui/states.js +12 -0
  7. package/lib/commonjs/apps/viewer/app.js +4 -1
  8. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +1 -1
  9. package/lib/commonjs/extensions/mp4-export/encoder.d.ts +1 -1
  10. package/lib/commonjs/extensions/mp4-export/encoder.js +2 -2
  11. package/lib/commonjs/mol-canvas3d/camera.js +4 -9
  12. package/lib/commonjs/mol-canvas3d/passes/background.d.ts +3 -1
  13. package/lib/commonjs/mol-canvas3d/passes/background.js +22 -2
  14. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +4 -3
  15. package/lib/commonjs/mol-canvas3d/passes/image.js +18 -4
  16. package/lib/commonjs/mol-canvas3d/passes/outline.d.ts +7 -6
  17. package/lib/commonjs/mol-canvas3d/passes/outline.js +35 -27
  18. package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +0 -1
  19. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +9 -30
  20. package/lib/commonjs/mol-canvas3d/passes/shadow.d.ts +4 -5
  21. package/lib/commonjs/mol-canvas3d/passes/shadow.js +29 -31
  22. package/lib/commonjs/mol-canvas3d/passes/ssao.d.ts +10 -10
  23. package/lib/commonjs/mol-canvas3d/passes/ssao.js +84 -83
  24. package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.d.ts +3 -2
  25. package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +23 -8
  26. package/lib/commonjs/mol-geo/util/location-iterator.d.ts +1 -0
  27. package/lib/commonjs/mol-geo/util/location-iterator.js +24 -0
  28. package/lib/commonjs/mol-gl/webgl/timer.js +1 -1
  29. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +1 -1
  30. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +1 -1
  31. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  32. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +1 -1
  33. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +5 -1
  34. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +5 -1
  35. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +1 -1
  36. package/lib/commonjs/mol-io/reader/prmtop/parser.js +7 -4
  37. package/lib/commonjs/mol-model/structure/model/model.d.ts +8 -3
  38. package/lib/commonjs/mol-model/structure/model/model.js +56 -8
  39. package/lib/commonjs/mol-model/structure/model/types.d.ts +1 -1
  40. package/lib/commonjs/mol-model/structure/model/types.js +3 -3
  41. package/lib/commonjs/mol-model/structure/structure/structure.d.ts +1 -1
  42. package/lib/commonjs/mol-model/structure/structure/structure.js +14 -83
  43. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +23 -5
  44. package/lib/commonjs/mol-model/structure/structure/unit.d.ts +2 -1
  45. package/lib/commonjs/mol-model/structure/structure/unit.js +1 -0
  46. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +1 -0
  47. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.d.ts +5 -1
  48. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +3 -2
  49. package/lib/commonjs/mol-model-props/computed/secondary-structure/zhang-skolnik.d.ts +14 -0
  50. package/lib/commonjs/mol-model-props/computed/secondary-structure/zhang-skolnik.js +107 -1
  51. package/lib/commonjs/mol-model-props/computed/secondary-structure.d.ts +3 -3
  52. package/lib/commonjs/mol-model-props/computed/secondary-structure.js +43 -21
  53. package/lib/commonjs/mol-plugin/headless-plugin-context.d.ts +1 -1
  54. package/lib/commonjs/mol-plugin/headless-plugin-context.js +22 -9
  55. package/lib/commonjs/mol-plugin/util/headless-screenshot.d.ts +5 -4
  56. package/lib/commonjs/mol-plugin/util/headless-screenshot.js +11 -11
  57. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +3 -2
  58. package/lib/commonjs/mol-plugin/util/viewport-screenshot.js +16 -12
  59. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +3 -3
  60. package/lib/commonjs/mol-plugin-state/actions/structure.js +22 -10
  61. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +5 -5
  62. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +5 -17
  63. package/lib/commonjs/mol-plugin-state/manager/snapshots.d.ts +1 -1
  64. package/lib/commonjs/mol-plugin-state/manager/snapshots.js +15 -11
  65. package/lib/commonjs/mol-plugin-ui/controls/screenshot.d.ts +1 -1
  66. package/lib/commonjs/mol-plugin-ui/controls/screenshot.js +46 -39
  67. package/lib/commonjs/mol-plugin-ui/sequence.js +1 -1
  68. package/lib/commonjs/mol-repr/representation.d.ts +1 -1
  69. package/lib/commonjs/mol-repr/structure/registry.d.ts +1 -0
  70. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +3 -0
  71. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +1 -0
  72. package/lib/commonjs/mol-repr/structure/units-visual.js +2 -1
  73. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +17 -4
  74. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +9 -2
  75. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +4 -0
  76. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +2 -0
  77. package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts +1 -1
  78. package/lib/commonjs/mol-repr/structure/visual/element-cross.js +21 -4
  79. package/lib/commonjs/mol-repr/structure/visual/element-point.js +1 -1
  80. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -1
  81. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.js +2 -2
  82. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +5 -1
  83. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +35 -25
  84. package/lib/commonjs/mol-repr/structure/visual/util/bond.d.ts +7 -1
  85. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +13 -1
  86. package/lib/commonjs/mol-repr/structure/visual/util/element.js +4 -4
  87. package/lib/commonjs/mol-repr/structure/visual/util/link.js +3 -3
  88. package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.d.ts +1 -2
  89. package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +14 -8
  90. package/lib/commonjs/mol-repr/structure/visual/util/polymer.d.ts +4 -2
  91. package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +7 -3
  92. package/lib/commonjs/mol-theme/color/cartoon.d.ts +60 -2
  93. package/lib/commonjs/mol-theme/color/cartoon.js +17 -2
  94. package/lib/commonjs/mol-theme/color/entity-id.d.ts +1 -1
  95. package/lib/commonjs/mol-theme/color/entity-id.js +26 -12
  96. package/lib/commonjs/mol-theme/color/formal-charge.d.ts +19 -0
  97. package/lib/commonjs/mol-theme/color/formal-charge.js +67 -0
  98. package/lib/commonjs/mol-theme/color.d.ts +35 -2
  99. package/lib/commonjs/mol-theme/color.js +3 -1
  100. package/lib/commonjs/mol-util/object.d.ts +2 -4
  101. package/lib/commonjs/mol-util/object.js +1 -1
  102. package/lib/commonjs/mol-util/zip/deflate.d.ts +1 -1
  103. package/lib/commonjs/mol-util/zip/deflate.js +21 -1
  104. package/lib/commonjs/mol-util/zip/inflate.d.ts +1 -1
  105. package/lib/commonjs/mol-util/zip/inflate.js +47 -1
  106. package/lib/commonjs/mol-util/zip/util.d.ts +4 -1
  107. package/lib/commonjs/mol-util/zip/util.js +19 -1
  108. package/lib/commonjs/mol-util/zip/zip.d.ts +1 -1
  109. package/lib/commonjs/mol-util/zip/zip.js +13 -11
  110. package/lib/commonjs/servers/common/util.d.ts +9 -1
  111. package/lib/commonjs/servers/common/util.js +36 -1
  112. package/lib/commonjs/servers/model/config.d.ts +10 -1
  113. package/lib/commonjs/servers/model/config.js +13 -2
  114. package/lib/commonjs/servers/model/server/api-web.d.ts +1 -1
  115. package/lib/commonjs/servers/model/server/api-web.js +4 -1
  116. package/lib/commonjs/servers/model/version.d.ts +2 -2
  117. package/lib/commonjs/servers/model/version.js +2 -2
  118. package/lib/commonjs/servers/volume/config.d.ts +4 -1
  119. package/lib/commonjs/servers/volume/config.js +10 -2
  120. package/lib/commonjs/servers/volume/server/version.d.ts +2 -2
  121. package/lib/commonjs/servers/volume/server/version.js +2 -2
  122. package/lib/commonjs/servers/volume/server/web-api.d.ts +1 -1
  123. package/lib/commonjs/servers/volume/server/web-api.js +4 -1
  124. package/lib/extensions/model-archive/quality-assessment/color/plddt.js +2 -2
  125. package/lib/extensions/mp4-export/encoder.d.ts +1 -1
  126. package/lib/extensions/mp4-export/encoder.js +2 -2
  127. package/lib/mol-canvas3d/camera.js +4 -9
  128. package/lib/mol-canvas3d/passes/background.d.ts +3 -1
  129. package/lib/mol-canvas3d/passes/background.js +22 -2
  130. package/lib/mol-canvas3d/passes/image.d.ts +4 -3
  131. package/lib/mol-canvas3d/passes/image.js +18 -4
  132. package/lib/mol-canvas3d/passes/outline.d.ts +7 -6
  133. package/lib/mol-canvas3d/passes/outline.js +35 -27
  134. package/lib/mol-canvas3d/passes/postprocessing.d.ts +0 -1
  135. package/lib/mol-canvas3d/passes/postprocessing.js +10 -31
  136. package/lib/mol-canvas3d/passes/shadow.d.ts +4 -5
  137. package/lib/mol-canvas3d/passes/shadow.js +29 -31
  138. package/lib/mol-canvas3d/passes/ssao.d.ts +10 -10
  139. package/lib/mol-canvas3d/passes/ssao.js +84 -83
  140. package/lib/mol-geo/geometry/mesh/builder/tube.d.ts +3 -2
  141. package/lib/mol-geo/geometry/mesh/builder/tube.js +23 -8
  142. package/lib/mol-geo/util/location-iterator.d.ts +1 -0
  143. package/lib/mol-geo/util/location-iterator.js +23 -0
  144. package/lib/mol-gl/webgl/timer.js +1 -1
  145. package/lib/mol-io/reader/cif/schema/bird.d.ts +1 -1
  146. package/lib/mol-io/reader/cif/schema/bird.js +1 -1
  147. package/lib/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  148. package/lib/mol-io/reader/cif/schema/ccd.js +1 -1
  149. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +5 -1
  150. package/lib/mol-io/reader/cif/schema/mmcif.js +5 -1
  151. package/lib/mol-io/reader/prmtop/parser.d.ts +1 -1
  152. package/lib/mol-io/reader/prmtop/parser.js +7 -4
  153. package/lib/mol-model/structure/model/model.d.ts +8 -3
  154. package/lib/mol-model/structure/model/model.js +56 -8
  155. package/lib/mol-model/structure/model/types.d.ts +1 -1
  156. package/lib/mol-model/structure/model/types.js +3 -3
  157. package/lib/mol-model/structure/structure/structure.d.ts +1 -1
  158. package/lib/mol-model/structure/structure/structure.js +12 -81
  159. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +23 -5
  160. package/lib/mol-model/structure/structure/unit.d.ts +2 -1
  161. package/lib/mol-model/structure/structure/unit.js +1 -0
  162. package/lib/mol-model-formats/structure/basic/schema.d.ts +1 -0
  163. package/lib/mol-model-props/computed/secondary-structure/dssp.d.ts +5 -1
  164. package/lib/mol-model-props/computed/secondary-structure/dssp.js +2 -1
  165. package/lib/mol-model-props/computed/secondary-structure/zhang-skolnik.d.ts +14 -0
  166. package/lib/mol-model-props/computed/secondary-structure/zhang-skolnik.js +105 -2
  167. package/lib/mol-model-props/computed/secondary-structure.d.ts +3 -3
  168. package/lib/mol-model-props/computed/secondary-structure.js +44 -22
  169. package/lib/mol-plugin/headless-plugin-context.d.ts +1 -1
  170. package/lib/mol-plugin/headless-plugin-context.js +22 -9
  171. package/lib/mol-plugin/util/headless-screenshot.d.ts +5 -4
  172. package/lib/mol-plugin/util/headless-screenshot.js +11 -11
  173. package/lib/mol-plugin/util/viewport-screenshot.d.ts +3 -2
  174. package/lib/mol-plugin/util/viewport-screenshot.js +16 -12
  175. package/lib/mol-plugin/version.js +2 -2
  176. package/lib/mol-plugin-state/actions/structure.d.ts +3 -3
  177. package/lib/mol-plugin-state/actions/structure.js +22 -10
  178. package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts +5 -5
  179. package/lib/mol-plugin-state/builder/structure/representation-preset.js +5 -17
  180. package/lib/mol-plugin-state/manager/snapshots.d.ts +1 -1
  181. package/lib/mol-plugin-state/manager/snapshots.js +15 -11
  182. package/lib/mol-plugin-ui/controls/screenshot.d.ts +1 -1
  183. package/lib/mol-plugin-ui/controls/screenshot.js +46 -39
  184. package/lib/mol-plugin-ui/sequence.js +1 -1
  185. package/lib/mol-repr/representation.d.ts +1 -1
  186. package/lib/mol-repr/structure/registry.d.ts +1 -0
  187. package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
  188. package/lib/mol-repr/structure/units-visual.d.ts +1 -0
  189. package/lib/mol-repr/structure/units-visual.js +2 -1
  190. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +18 -5
  191. package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -3
  192. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +5 -1
  193. package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +3 -1
  194. package/lib/mol-repr/structure/visual/element-cross.d.ts +1 -1
  195. package/lib/mol-repr/structure/visual/element-cross.js +21 -4
  196. package/lib/mol-repr/structure/visual/element-point.js +1 -1
  197. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -1
  198. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.js +2 -2
  199. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +5 -1
  200. package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +35 -25
  201. package/lib/mol-repr/structure/visual/util/bond.d.ts +7 -1
  202. package/lib/mol-repr/structure/visual/util/bond.js +11 -1
  203. package/lib/mol-repr/structure/visual/util/element.js +4 -4
  204. package/lib/mol-repr/structure/visual/util/link.js +3 -3
  205. package/lib/mol-repr/structure/visual/util/polymer/trace-iterator.d.ts +1 -2
  206. package/lib/mol-repr/structure/visual/util/polymer/trace-iterator.js +14 -8
  207. package/lib/mol-repr/structure/visual/util/polymer.d.ts +4 -2
  208. package/lib/mol-repr/structure/visual/util/polymer.js +7 -3
  209. package/lib/mol-theme/color/cartoon.d.ts +60 -2
  210. package/lib/mol-theme/color/cartoon.js +17 -2
  211. package/lib/mol-theme/color/entity-id.d.ts +1 -1
  212. package/lib/mol-theme/color/entity-id.js +26 -12
  213. package/lib/mol-theme/color/formal-charge.d.ts +19 -0
  214. package/lib/mol-theme/color/formal-charge.js +62 -0
  215. package/lib/mol-theme/color.d.ts +35 -2
  216. package/lib/mol-theme/color.js +3 -1
  217. package/lib/mol-util/object.d.ts +2 -4
  218. package/lib/mol-util/object.js +1 -1
  219. package/lib/mol-util/zip/deflate.d.ts +1 -1
  220. package/lib/mol-util/zip/deflate.js +22 -2
  221. package/lib/mol-util/zip/inflate.d.ts +1 -1
  222. package/lib/mol-util/zip/inflate.js +48 -2
  223. package/lib/mol-util/zip/util.d.ts +4 -1
  224. package/lib/mol-util/zip/util.js +18 -1
  225. package/lib/mol-util/zip/zip.d.ts +1 -1
  226. package/lib/mol-util/zip/zip.js +13 -11
  227. package/lib/servers/common/util.d.ts +9 -1
  228. package/lib/servers/common/util.js +35 -1
  229. package/lib/servers/model/config.d.ts +10 -1
  230. package/lib/servers/model/config.js +13 -2
  231. package/lib/servers/model/server/api-web.d.ts +1 -1
  232. package/lib/servers/model/server/api-web.js +4 -1
  233. package/lib/servers/model/version.d.ts +2 -2
  234. package/lib/servers/model/version.js +2 -2
  235. package/lib/servers/volume/config.d.ts +4 -1
  236. package/lib/servers/volume/config.js +10 -2
  237. package/lib/servers/volume/server/version.d.ts +2 -2
  238. package/lib/servers/volume/server/version.js +2 -2
  239. package/lib/servers/volume/server/web-api.d.ts +1 -1
  240. package/lib/servers/volume/server/web-api.js +4 -1
  241. package/package.json +11 -11

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