molstar 3.0.0 → 3.2.0

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 (256) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +194 -194
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +106 -106
  5. package/build/viewer/molstar.js +1 -1
  6. package/lib/apps/docking-viewer/index.html +36 -36
  7. package/lib/apps/docking-viewer/viewport.d.ts +2 -0
  8. package/lib/apps/viewer/app.d.ts +1 -0
  9. package/lib/apps/viewer/app.js +6 -3
  10. package/lib/apps/viewer/embedded.html +43 -43
  11. package/lib/apps/viewer/index.html +106 -106
  12. package/lib/commonjs/apps/docking-viewer/viewport.d.ts +2 -0
  13. package/lib/commonjs/apps/viewer/app.d.ts +1 -0
  14. package/lib/commonjs/apps/viewer/app.js +8 -5
  15. package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
  16. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts +1 -0
  17. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +2 -0
  18. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +4 -2
  19. package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +11 -11
  20. package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts +3 -0
  21. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +1 -1
  22. package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +1 -1
  23. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  24. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
  25. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  26. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  27. package/lib/commonjs/mol-gl/renderer.d.ts +2 -2
  28. package/lib/commonjs/mol-gl/renderer.js +3 -3
  29. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +2 -2
  30. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +2 -2
  31. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +2 -2
  32. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +2 -2
  33. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +2 -2
  34. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +2 -2
  35. package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +2 -2
  36. package/lib/commonjs/mol-gl/shader/mesh.frag.js +2 -2
  37. package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +2 -2
  38. package/lib/commonjs/mol-gl/shader/spheres.frag.js +2 -2
  39. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +1 -1
  40. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +1 -1
  41. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  42. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +1 -1
  43. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +24 -2
  44. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +23 -1
  45. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.d.ts +1 -1
  46. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +17 -4
  47. package/lib/commonjs/mol-model/structure/export/categories/atom_site.js +68 -1
  48. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +8 -8
  49. package/lib/commonjs/mol-model/structure/model/properties/coarse/hierarchy.d.ts +1 -1
  50. package/lib/commonjs/mol-model/structure/model/properties/coarse/hierarchy.js +24 -2
  51. package/lib/commonjs/mol-model/structure/structure/element/loci.d.ts +1 -1
  52. package/lib/commonjs/mol-model/structure/structure/element/loci.js +4 -2
  53. package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.d.ts +21 -0
  54. package/lib/commonjs/mol-model/structure/structure/util/{superposition-db-mapping.js → superposition-sifts-mapping.js} +40 -20
  55. package/lib/commonjs/mol-model/volume/volume.d.ts +7 -0
  56. package/lib/commonjs/mol-model/volume/volume.js +18 -0
  57. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +5 -0
  58. package/lib/commonjs/mol-model-formats/structure/common/property.d.ts +5 -2
  59. package/lib/commonjs/mol-model-formats/structure/common/property.js +20 -8
  60. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts +1 -0
  61. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +2 -1
  62. package/lib/commonjs/mol-model-props/computed/interactions/common.d.ts +1 -1
  63. package/lib/commonjs/mol-model-props/computed/interactions/common.js +16 -24
  64. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -1
  65. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +44 -18
  66. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +14 -4
  67. package/lib/commonjs/mol-model-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +7 -5
  68. package/lib/commonjs/mol-model-props/sequence/{best-database-mapping.js → sifts-mapping.js} +29 -26
  69. package/lib/{mol-model-props/sequence/themes/best-database-mapping.d.ts → commonjs/mol-model-props/sequence/themes/sifts-mapping.d.ts} +5 -5
  70. package/lib/commonjs/mol-model-props/sequence/themes/{best-database-mapping.js → sifts-mapping.js} +22 -22
  71. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +1 -1
  72. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.js → sifts-mapping.js} +11 -11
  73. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.d.ts +1 -1
  74. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.js +2 -2
  75. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.d.ts +1 -1
  76. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +11 -6
  77. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +2 -1
  78. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +16 -7
  79. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  80. package/lib/commonjs/mol-plugin/behavior/static/representation.js +1 -1
  81. package/lib/commonjs/mol-plugin-state/actions/volume.d.ts +1 -1
  82. package/lib/commonjs/mol-plugin-state/actions/volume.js +3 -3
  83. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +2 -0
  84. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -0
  85. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +155 -125
  86. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +5 -31
  87. package/lib/commonjs/mol-plugin-state/builder/structure/representation.d.ts +2 -1
  88. package/lib/commonjs/mol-plugin-state/formats/volume.js +1 -11
  89. package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +2 -1
  90. package/lib/commonjs/mol-plugin-state/manager/structure/component.js +11 -8
  91. package/lib/commonjs/mol-plugin-ui/controls/icons.d.ts +2 -1
  92. package/lib/commonjs/mol-plugin-ui/controls/icons.js +8 -5
  93. package/lib/commonjs/mol-plugin-ui/controls.d.ts +1 -1
  94. package/lib/commonjs/mol-plugin-ui/controls.js +2 -1
  95. package/lib/commonjs/mol-plugin-ui/structure/quick-styles.d.ts +25 -0
  96. package/lib/commonjs/mol-plugin-ui/structure/quick-styles.js +131 -0
  97. package/lib/commonjs/mol-plugin-ui/structure/superposition.d.ts +4 -1
  98. package/lib/commonjs/mol-plugin-ui/structure/superposition.js +66 -30
  99. package/lib/commonjs/mol-plugin-ui/structure/volume.js +4 -4
  100. package/lib/commonjs/mol-repr/shape/loci/common.d.ts +1 -1
  101. package/lib/commonjs/mol-repr/shape/loci/common.js +3 -3
  102. package/lib/commonjs/mol-repr/structure/registry.d.ts +1 -1
  103. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +4 -4
  104. package/lib/commonjs/mol-repr/structure/representation/cartoon.js +3 -3
  105. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -1
  106. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +2 -2
  107. package/lib/commonjs/mol-repr/structure/visual/util/bond.d.ts +1 -1
  108. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +5 -4
  109. package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
  110. package/lib/commonjs/mol-state/transform.js +12 -2
  111. package/lib/commonjs/mol-theme/color/element-symbol.d.ts +46 -2
  112. package/lib/commonjs/mol-theme/color/element-symbol.js +15 -10
  113. package/lib/commonjs/mol-theme/color/entity-id.js +14 -11
  114. package/lib/commonjs/mol-theme/color/illustrative.d.ts +32 -32
  115. package/lib/commonjs/mol-theme/color.d.ts +39 -17
  116. package/lib/commonjs/servers/volume/config.js +3 -3
  117. package/lib/commonjs/servers/volume/query.js +1 -1
  118. package/lib/examples/alpha-orbitals/index.html +61 -61
  119. package/lib/examples/basic-wrapper/index.html +137 -137
  120. package/lib/examples/lighting/index.html +88 -88
  121. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  122. package/lib/extensions/anvil/behavior.d.ts +1 -0
  123. package/lib/extensions/dnatco/confal-pyramids/behavior.d.ts +1 -0
  124. package/lib/extensions/model-archive/quality-assessment/behavior.d.ts +2 -0
  125. package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +4 -2
  126. package/lib/extensions/rcsb/graphql/types.d.ts +11 -11
  127. package/lib/extensions/rcsb/validation-report/behavior.d.ts +3 -0
  128. package/lib/mol-canvas3d/helper/interaction-events.js +1 -1
  129. package/lib/mol-canvas3d/passes/draw.d.ts +1 -1
  130. package/lib/mol-canvas3d/passes/draw.js +3 -3
  131. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
  132. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  133. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  134. package/lib/mol-gl/renderer.d.ts +2 -2
  135. package/lib/mol-gl/renderer.js +3 -3
  136. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +2 -2
  137. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js +2 -2
  138. package/lib/mol-gl/shader/cylinders.frag.d.ts +2 -2
  139. package/lib/mol-gl/shader/cylinders.frag.js +2 -2
  140. package/lib/mol-gl/shader/direct-volume.frag.d.ts +2 -2
  141. package/lib/mol-gl/shader/direct-volume.frag.js +2 -2
  142. package/lib/mol-gl/shader/mesh.frag.d.ts +2 -2
  143. package/lib/mol-gl/shader/mesh.frag.js +2 -2
  144. package/lib/mol-gl/shader/spheres.frag.d.ts +2 -2
  145. package/lib/mol-gl/shader/spheres.frag.js +2 -2
  146. package/lib/mol-io/reader/cif/schema/bird.d.ts +1 -1
  147. package/lib/mol-io/reader/cif/schema/bird.js +1 -1
  148. package/lib/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  149. package/lib/mol-io/reader/cif/schema/ccd.js +1 -1
  150. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +24 -2
  151. package/lib/mol-io/reader/cif/schema/mmcif.js +23 -1
  152. package/lib/mol-math/geometry/primitives/sphere3d.d.ts +1 -1
  153. package/lib/mol-math/geometry/primitives/sphere3d.js +17 -4
  154. package/lib/mol-model/structure/export/categories/atom_site.js +68 -1
  155. package/lib/mol-model/structure/export/categories/secondary-structure.js +8 -8
  156. package/lib/mol-model/structure/model/properties/coarse/hierarchy.d.ts +1 -1
  157. package/lib/mol-model/structure/model/properties/coarse/hierarchy.js +24 -2
  158. package/lib/mol-model/structure/structure/element/loci.d.ts +1 -1
  159. package/lib/mol-model/structure/structure/element/loci.js +4 -2
  160. package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.d.ts +21 -0
  161. package/lib/mol-model/structure/structure/util/{superposition-db-mapping.js → superposition-sifts-mapping.js} +38 -18
  162. package/lib/mol-model/volume/volume.d.ts +7 -0
  163. package/lib/mol-model/volume/volume.js +18 -0
  164. package/lib/mol-model-formats/structure/basic/schema.d.ts +5 -0
  165. package/lib/mol-model-formats/structure/common/property.d.ts +5 -2
  166. package/lib/mol-model-formats/structure/common/property.js +20 -8
  167. package/lib/mol-model-formats/structure/property/bonds/index-pair.d.ts +1 -0
  168. package/lib/mol-model-formats/structure/property/bonds/index-pair.js +2 -1
  169. package/lib/mol-model-props/computed/interactions/common.d.ts +1 -1
  170. package/lib/mol-model-props/computed/interactions/common.js +16 -24
  171. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -1
  172. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +44 -18
  173. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +14 -4
  174. package/lib/mol-model-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +7 -5
  175. package/lib/mol-model-props/sequence/{best-database-mapping.js → sifts-mapping.js} +28 -25
  176. package/lib/{commonjs/mol-model-props/sequence/themes/best-database-mapping.d.ts → mol-model-props/sequence/themes/sifts-mapping.d.ts} +5 -5
  177. package/lib/mol-model-props/sequence/themes/{best-database-mapping.js → sifts-mapping.js} +19 -19
  178. package/lib/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +1 -1
  179. package/lib/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.js → sifts-mapping.js} +8 -8
  180. package/lib/mol-plugin/behavior/dynamic/custom-props.d.ts +1 -1
  181. package/lib/mol-plugin/behavior/dynamic/custom-props.js +1 -1
  182. package/lib/mol-plugin/behavior/dynamic/representation.d.ts +1 -1
  183. package/lib/mol-plugin/behavior/dynamic/representation.js +11 -6
  184. package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +2 -1
  185. package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +16 -7
  186. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  187. package/lib/mol-plugin/behavior/static/representation.js +1 -1
  188. package/lib/mol-plugin/version.js +2 -2
  189. package/lib/mol-plugin-state/actions/volume.d.ts +1 -1
  190. package/lib/mol-plugin-state/actions/volume.js +3 -3
  191. package/lib/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +2 -0
  192. package/lib/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -0
  193. package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts +155 -125
  194. package/lib/mol-plugin-state/builder/structure/representation-preset.js +5 -31
  195. package/lib/mol-plugin-state/builder/structure/representation.d.ts +2 -1
  196. package/lib/mol-plugin-state/formats/volume.js +1 -11
  197. package/lib/mol-plugin-state/manager/structure/component.d.ts +2 -1
  198. package/lib/mol-plugin-state/manager/structure/component.js +11 -8
  199. package/lib/mol-plugin-ui/controls/icons.d.ts +2 -1
  200. package/lib/mol-plugin-ui/controls/icons.js +5 -3
  201. package/lib/mol-plugin-ui/controls.d.ts +1 -1
  202. package/lib/mol-plugin-ui/controls.js +2 -1
  203. package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
  204. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  205. package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
  206. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  207. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  208. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  209. package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
  210. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  211. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  212. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  213. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  214. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  215. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +127 -127
  216. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  217. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  218. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  219. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  220. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  221. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  222. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  223. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  224. package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
  225. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  226. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  227. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  228. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  229. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  230. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  231. package/lib/mol-plugin-ui/structure/quick-styles.d.ts +25 -0
  232. package/lib/mol-plugin-ui/structure/quick-styles.js +128 -0
  233. package/lib/mol-plugin-ui/structure/superposition.d.ts +4 -1
  234. package/lib/mol-plugin-ui/structure/superposition.js +66 -30
  235. package/lib/mol-plugin-ui/structure/volume.js +4 -4
  236. package/lib/mol-repr/shape/loci/common.d.ts +1 -1
  237. package/lib/mol-repr/shape/loci/common.js +3 -3
  238. package/lib/mol-repr/structure/registry.d.ts +1 -1
  239. package/lib/mol-repr/structure/representation/cartoon.d.ts +4 -4
  240. package/lib/mol-repr/structure/representation/cartoon.js +3 -3
  241. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -1
  242. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +2 -2
  243. package/lib/mol-repr/structure/visual/util/bond.d.ts +1 -1
  244. package/lib/mol-repr/structure/visual/util/bond.js +5 -4
  245. package/lib/mol-script/language/builder.d.ts +1 -0
  246. package/lib/mol-state/transform.js +12 -2
  247. package/lib/mol-theme/color/element-symbol.d.ts +46 -2
  248. package/lib/mol-theme/color/element-symbol.js +15 -10
  249. package/lib/mol-theme/color/entity-id.js +14 -11
  250. package/lib/mol-theme/color/illustrative.d.ts +32 -32
  251. package/lib/mol-theme/color.d.ts +39 -17
  252. package/lib/servers/volume/config.js +3 -3
  253. package/lib/servers/volume/query.js +1 -1
  254. package/package.json +160 -163
  255. package/lib/commonjs/mol-model/structure/structure/util/superposition-db-mapping.d.ts +0 -13
  256. package/lib/mol-model/structure/structure/util/superposition-db-mapping.d.ts +0 -13

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