molstar 2.3.3 → 2.3.5

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 (355) hide show
  1. package/CHANGELOG.md +18 -2
  2. package/build/viewer/index.html +7 -1
  3. package/build/viewer/molstar.js +1 -1
  4. package/lib/apps/viewer/index.d.ts +6 -4
  5. package/lib/apps/viewer/index.html +7 -1
  6. package/lib/apps/viewer/index.js +8 -4
  7. package/lib/apps/viewer/index.js.map +1 -1
  8. package/lib/cli/chem-comp-dict/util.d.ts +4 -4
  9. package/lib/commonjs/apps/viewer/index.d.ts +7 -5
  10. package/lib/commonjs/apps/viewer/index.js +8 -4
  11. package/lib/commonjs/apps/viewer/index.js.map +1 -1
  12. package/lib/commonjs/cli/chem-comp-dict/util.d.ts +4 -4
  13. package/lib/commonjs/extensions/cellpack/model.d.ts +1 -1
  14. package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts +1 -1
  15. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +4 -4
  16. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts +12 -12
  17. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +2 -2
  18. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +2 -2
  19. package/lib/commonjs/mol-canvas3d/camera/util.d.ts +4 -3
  20. package/lib/commonjs/mol-canvas3d/camera/util.js +15 -16
  21. package/lib/commonjs/mol-canvas3d/camera/util.js.map +1 -1
  22. package/lib/commonjs/mol-canvas3d/camera.d.ts +11 -3
  23. package/lib/commonjs/mol-canvas3d/camera.js +21 -1
  24. package/lib/commonjs/mol-canvas3d/camera.js.map +1 -1
  25. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +14 -4
  26. package/lib/commonjs/mol-canvas3d/canvas3d.js +8 -2
  27. package/lib/commonjs/mol-canvas3d/canvas3d.js.map +1 -1
  28. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +2 -2
  29. package/lib/commonjs/mol-canvas3d/helper/interaction-events.d.ts +13 -4
  30. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +43 -9
  31. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js.map +1 -1
  32. package/lib/commonjs/mol-canvas3d/passes/draw.js +1 -0
  33. package/lib/commonjs/mol-canvas3d/passes/draw.js.map +1 -1
  34. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +2 -2
  35. package/lib/commonjs/mol-canvas3d/passes/pick.d.ts +5 -2
  36. package/lib/commonjs/mol-canvas3d/passes/pick.js +17 -3
  37. package/lib/commonjs/mol-canvas3d/passes/pick.js.map +1 -1
  38. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +2 -2
  39. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +10 -1
  40. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js.map +1 -1
  41. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +2 -2
  42. package/lib/commonjs/mol-geo/geometry/image/image.js +4 -1
  43. package/lib/commonjs/mol-geo/geometry/image/image.js.map +1 -1
  44. package/lib/commonjs/mol-geo/geometry/lines/lines.js +1 -1
  45. package/lib/commonjs/mol-geo/geometry/lines/lines.js.map +1 -1
  46. package/lib/commonjs/mol-geo/geometry/points/points.js +1 -1
  47. package/lib/commonjs/mol-geo/geometry/points/points.js.map +1 -1
  48. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +6 -1
  49. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js.map +1 -1
  50. package/lib/commonjs/mol-gl/renderer.d.ts +3 -2
  51. package/lib/commonjs/mol-gl/renderer.js +3 -0
  52. package/lib/commonjs/mol-gl/renderer.js.map +1 -1
  53. package/lib/commonjs/mol-gl/shader/lines.vert.d.ts +1 -1
  54. package/lib/commonjs/mol-gl/shader/lines.vert.js +1 -1
  55. package/lib/commonjs/mol-gl/shader/lines.vert.js.map +1 -1
  56. package/lib/commonjs/mol-gl/shader/points.vert.d.ts +1 -1
  57. package/lib/commonjs/mol-gl/shader/points.vert.js +1 -1
  58. package/lib/commonjs/mol-gl/shader/points.vert.js.map +1 -1
  59. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  60. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +5 -5
  61. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +2 -2
  62. package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts +4 -4
  63. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +3 -3
  64. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +22 -22
  65. package/lib/commonjs/mol-io/reader/ply/schema.d.ts +1 -1
  66. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.d.ts +3 -1
  67. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js +11 -3
  68. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js.map +1 -1
  69. package/lib/commonjs/mol-math/misc.d.ts +3 -1
  70. package/lib/commonjs/mol-math/misc.js +24 -2
  71. package/lib/commonjs/mol-math/misc.js.map +1 -1
  72. package/lib/commonjs/mol-model/loci.d.ts +32 -32
  73. package/lib/commonjs/mol-model/loci.js +4 -3
  74. package/lib/commonjs/mol-model/loci.js.map +1 -1
  75. package/lib/commonjs/mol-model/shape/shape.d.ts +1 -1
  76. package/lib/commonjs/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
  77. package/lib/commonjs/mol-model/structure/structure/properties.d.ts +3 -3
  78. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  79. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js.map +1 -1
  80. package/lib/commonjs/mol-model/structure/structure/unit/bonds.d.ts +2 -1
  81. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +6 -1
  82. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js.map +1 -1
  83. package/lib/commonjs/mol-model/structure/structure/unit.d.ts +2 -2
  84. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +12 -12
  85. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +6 -6
  86. package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +8 -8
  87. package/lib/commonjs/mol-model-formats/structure/common/entity.d.ts +1 -1
  88. package/lib/commonjs/mol-model-formats/structure/pdb/entity.js +29 -3
  89. package/lib/commonjs/mol-model-formats/structure/pdb/entity.js.map +1 -1
  90. package/lib/commonjs/mol-model-props/sequence/themes/best-database-mapping.d.ts +12 -12
  91. package/lib/commonjs/mol-plugin/behavior/behavior.d.ts +1 -1
  92. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.d.ts +4 -2
  93. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +22 -8
  94. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js.map +1 -1
  95. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +10 -10
  96. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +7 -7
  97. package/lib/commonjs/mol-plugin/commands.d.ts +6 -2
  98. package/lib/commonjs/mol-plugin/config.d.ts +1 -0
  99. package/lib/commonjs/mol-plugin/config.js +1 -0
  100. package/lib/commonjs/mol-plugin/config.js.map +1 -1
  101. package/lib/commonjs/mol-plugin/context.js +6 -4
  102. package/lib/commonjs/mol-plugin/context.js.map +1 -1
  103. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +6 -6
  104. package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.d.ts +3 -3
  105. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +7 -7
  106. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts +7 -7
  107. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +10 -10
  108. package/lib/commonjs/mol-plugin-state/formats/volume.d.ts +16 -16
  109. package/lib/commonjs/mol-plugin-state/helpers/root-structure.d.ts +7 -7
  110. package/lib/commonjs/mol-plugin-state/helpers/structure-component.d.ts +1 -1
  111. package/lib/commonjs/mol-plugin-state/manager/interactivity.d.ts +2 -2
  112. package/lib/commonjs/mol-plugin-state/manager/interactivity.js +12 -11
  113. package/lib/commonjs/mol-plugin-state/manager/interactivity.js.map +1 -1
  114. package/lib/commonjs/mol-plugin-state/manager/structure/selection.d.ts +2 -2
  115. package/lib/commonjs/mol-plugin-state/transforms/data.d.ts +1 -1
  116. package/lib/commonjs/mol-plugin-state/transforms/model.d.ts +9 -9
  117. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +1 -1
  118. package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts +2 -2
  119. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +1 -1
  120. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +1 -1
  121. package/lib/commonjs/mol-repr/structure/params.d.ts +1 -1
  122. package/lib/commonjs/mol-repr/structure/registry.d.ts +23 -15
  123. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +9 -6
  124. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +9 -6
  125. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +6 -6
  126. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +3 -3
  127. package/lib/commonjs/mol-repr/structure/representation/line.d.ts +37 -19
  128. package/lib/commonjs/mol-repr/structure/representation/line.js +10 -4
  129. package/lib/commonjs/mol-repr/structure/representation/line.js.map +1 -1
  130. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +6 -6
  131. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +1 -1
  132. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +6 -4
  133. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +14 -9
  134. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js.map +1 -1
  135. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +3 -2
  136. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +12 -8
  137. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js.map +1 -1
  138. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +6 -4
  139. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +15 -7
  140. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js.map +1 -1
  141. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.d.ts +3 -2
  142. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +13 -6
  143. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js.map +1 -1
  144. package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts +26 -0
  145. package/lib/commonjs/mol-repr/structure/visual/element-cross.js +77 -0
  146. package/lib/commonjs/mol-repr/structure/visual/element-cross.js.map +1 -0
  147. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -2
  148. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +8 -8
  149. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +2 -2
  150. package/lib/commonjs/mol-repr/structure/visual/util/bond.d.ts +22 -16
  151. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +1 -0
  152. package/lib/commonjs/mol-repr/structure/visual/util/bond.js.map +1 -1
  153. package/lib/commonjs/mol-repr/structure/visual/util/color.d.ts +2 -2
  154. package/lib/commonjs/mol-repr/structure/visual/util/element.d.ts +4 -4
  155. package/lib/commonjs/mol-repr/structure/visual/util/link.d.ts +6 -4
  156. package/lib/commonjs/mol-repr/structure/visual/util/link.js +66 -23
  157. package/lib/commonjs/mol-repr/structure/visual/util/link.js.map +1 -1
  158. package/lib/commonjs/mol-repr/structure/visual/util/polymer.d.ts +2 -2
  159. package/lib/commonjs/mol-repr/volume/direct-volume.d.ts +5 -5
  160. package/lib/commonjs/mol-repr/volume/isosurface.d.ts +3 -3
  161. package/lib/commonjs/mol-repr/volume/registry.d.ts +4 -4
  162. package/lib/commonjs/mol-repr/volume/slice.d.ts +6 -6
  163. package/lib/commonjs/mol-theme/color/atom-id.d.ts +12 -12
  164. package/lib/commonjs/mol-theme/color/chain-id.d.ts +12 -12
  165. package/lib/commonjs/mol-theme/color/element-index.d.ts +12 -12
  166. package/lib/commonjs/mol-theme/color/element-symbol.d.ts +12 -12
  167. package/lib/commonjs/mol-theme/color/entity-id.d.ts +12 -12
  168. package/lib/commonjs/mol-theme/color/entity-source.d.ts +12 -12
  169. package/lib/commonjs/mol-theme/color/illustrative.d.ts +12 -12
  170. package/lib/commonjs/mol-theme/color/model-index.d.ts +12 -12
  171. package/lib/commonjs/mol-theme/color/operator-hkl.d.ts +12 -12
  172. package/lib/commonjs/mol-theme/color/operator-name.d.ts +12 -12
  173. package/lib/commonjs/mol-theme/color/polymer-id.d.ts +12 -12
  174. package/lib/commonjs/mol-theme/color/polymer-index.d.ts +12 -12
  175. package/lib/commonjs/mol-theme/color/unit-index.d.ts +12 -12
  176. package/lib/commonjs/mol-theme/color.d.ts +78 -78
  177. package/lib/commonjs/mol-util/color/palette.d.ts +12 -12
  178. package/lib/commonjs/servers/model/config.js +0 -1
  179. package/lib/commonjs/servers/model/config.js.map +1 -1
  180. package/lib/commonjs/servers/volume/config.js +0 -1
  181. package/lib/commonjs/servers/volume/config.js.map +1 -1
  182. package/lib/extensions/cellpack/model.d.ts +1 -1
  183. package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +4 -4
  184. package/lib/extensions/rcsb/assembly-symmetry/color.d.ts +12 -12
  185. package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts +2 -2
  186. package/lib/extensions/rcsb/validation-report/representation.js +2 -2
  187. package/lib/mol-canvas3d/camera/util.d.ts +4 -3
  188. package/lib/mol-canvas3d/camera/util.js +15 -16
  189. package/lib/mol-canvas3d/camera/util.js.map +1 -1
  190. package/lib/mol-canvas3d/camera.d.ts +11 -3
  191. package/lib/mol-canvas3d/camera.js +22 -2
  192. package/lib/mol-canvas3d/camera.js.map +1 -1
  193. package/lib/mol-canvas3d/canvas3d.d.ts +14 -4
  194. package/lib/mol-canvas3d/canvas3d.js +9 -3
  195. package/lib/mol-canvas3d/canvas3d.js.map +1 -1
  196. package/lib/mol-canvas3d/helper/camera-helper.d.ts +2 -2
  197. package/lib/mol-canvas3d/helper/interaction-events.d.ts +13 -4
  198. package/lib/mol-canvas3d/helper/interaction-events.js +43 -9
  199. package/lib/mol-canvas3d/helper/interaction-events.js.map +1 -1
  200. package/lib/mol-canvas3d/passes/draw.js +1 -0
  201. package/lib/mol-canvas3d/passes/draw.js.map +1 -1
  202. package/lib/mol-canvas3d/passes/image.d.ts +2 -2
  203. package/lib/mol-canvas3d/passes/pick.d.ts +5 -2
  204. package/lib/mol-canvas3d/passes/pick.js +17 -3
  205. package/lib/mol-canvas3d/passes/pick.js.map +1 -1
  206. package/lib/mol-data/int/impl/ordered-set.d.ts +3 -3
  207. package/lib/mol-geo/geometry/direct-volume/direct-volume.d.ts +2 -2
  208. package/lib/mol-geo/geometry/direct-volume/direct-volume.js +12 -3
  209. package/lib/mol-geo/geometry/direct-volume/direct-volume.js.map +1 -1
  210. package/lib/mol-geo/geometry/image/image.d.ts +2 -2
  211. package/lib/mol-geo/geometry/image/image.js +5 -2
  212. package/lib/mol-geo/geometry/image/image.js.map +1 -1
  213. package/lib/mol-geo/geometry/lines/lines.js +1 -1
  214. package/lib/mol-geo/geometry/lines/lines.js.map +1 -1
  215. package/lib/mol-geo/geometry/points/points.js +1 -1
  216. package/lib/mol-geo/geometry/points/points.js.map +1 -1
  217. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +6 -1
  218. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js.map +1 -1
  219. package/lib/mol-gl/renderer.d.ts +3 -2
  220. package/lib/mol-gl/renderer.js +3 -0
  221. package/lib/mol-gl/renderer.js.map +1 -1
  222. package/lib/mol-gl/shader/lines.vert.d.ts +1 -1
  223. package/lib/mol-gl/shader/lines.vert.js +1 -1
  224. package/lib/mol-gl/shader/lines.vert.js.map +1 -1
  225. package/lib/mol-gl/shader/points.vert.d.ts +1 -1
  226. package/lib/mol-gl/shader/points.vert.js +1 -1
  227. package/lib/mol-gl/shader/points.vert.js.map +1 -1
  228. package/lib/mol-gl/webgl/context.d.ts +1 -1
  229. package/lib/mol-io/reader/cif/schema/bird.d.ts +5 -5
  230. package/lib/mol-io/reader/cif/schema/ccd.d.ts +2 -2
  231. package/lib/mol-io/reader/cif/schema/density-server.d.ts +4 -4
  232. package/lib/mol-io/reader/cif/schema/mmcif-extras.d.ts +3 -3
  233. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +23 -23
  234. package/lib/mol-io/reader/ply/schema.d.ts +1 -1
  235. package/lib/mol-math/linear-algebra/3d/vec3.d.ts +3 -1
  236. package/lib/mol-math/linear-algebra/3d/vec3.js +11 -3
  237. package/lib/mol-math/linear-algebra/3d/vec3.js.map +1 -1
  238. package/lib/mol-math/misc.d.ts +3 -1
  239. package/lib/mol-math/misc.js +22 -1
  240. package/lib/mol-math/misc.js.map +1 -1
  241. package/lib/mol-model/loci.d.ts +32 -32
  242. package/lib/mol-model/loci.js +4 -3
  243. package/lib/mol-model/loci.js.map +1 -1
  244. package/lib/mol-model/shape/shape.d.ts +1 -1
  245. package/lib/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
  246. package/lib/mol-model/structure/structure/properties.d.ts +3 -3
  247. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  248. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js.map +1 -1
  249. package/lib/mol-model/structure/structure/unit/bonds.d.ts +2 -1
  250. package/lib/mol-model/structure/structure/unit/bonds.js +7 -2
  251. package/lib/mol-model/structure/structure/unit/bonds.js.map +1 -1
  252. package/lib/mol-model/structure/structure/unit.d.ts +2 -2
  253. package/lib/mol-model-formats/shape/ply.d.ts +12 -12
  254. package/lib/mol-model-formats/structure/basic/schema.d.ts +6 -6
  255. package/lib/mol-model-formats/structure/common/component.d.ts +8 -8
  256. package/lib/mol-model-formats/structure/common/entity.d.ts +1 -1
  257. package/lib/mol-model-formats/structure/pdb/entity.js +29 -3
  258. package/lib/mol-model-formats/structure/pdb/entity.js.map +1 -1
  259. package/lib/mol-model-props/sequence/themes/best-database-mapping.d.ts +12 -12
  260. package/lib/mol-plugin/behavior/behavior.d.ts +1 -1
  261. package/lib/mol-plugin/behavior/dynamic/representation.d.ts +4 -2
  262. package/lib/mol-plugin/behavior/dynamic/representation.js +23 -9
  263. package/lib/mol-plugin/behavior/dynamic/representation.js.map +1 -1
  264. package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +10 -10
  265. package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +7 -7
  266. package/lib/mol-plugin/commands.d.ts +6 -2
  267. package/lib/mol-plugin/config.d.ts +1 -0
  268. package/lib/mol-plugin/config.js +1 -0
  269. package/lib/mol-plugin/config.js.map +1 -1
  270. package/lib/mol-plugin/context.js +6 -4
  271. package/lib/mol-plugin/context.js.map +1 -1
  272. package/lib/mol-plugin/util/viewport-screenshot.d.ts +6 -6
  273. package/lib/mol-plugin/version.js +2 -2
  274. package/lib/mol-plugin-state/animation/built-in/model-index.d.ts +3 -3
  275. package/lib/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +7 -7
  276. package/lib/mol-plugin-state/builder/structure/hierarchy.d.ts +7 -7
  277. package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts +10 -10
  278. package/lib/mol-plugin-state/formats/volume.d.ts +16 -16
  279. package/lib/mol-plugin-state/helpers/root-structure.d.ts +7 -7
  280. package/lib/mol-plugin-state/helpers/structure-component.d.ts +1 -1
  281. package/lib/mol-plugin-state/manager/interactivity.d.ts +2 -2
  282. package/lib/mol-plugin-state/manager/interactivity.js +12 -11
  283. package/lib/mol-plugin-state/manager/interactivity.js.map +1 -1
  284. package/lib/mol-plugin-state/manager/structure/selection.d.ts +2 -2
  285. package/lib/mol-plugin-state/transforms/data.d.ts +1 -1
  286. package/lib/mol-plugin-state/transforms/model.d.ts +9 -9
  287. package/lib/mol-plugin-state/transforms/representation.d.ts +2 -2
  288. package/lib/mol-repr/shape/loci/orientation.d.ts +1 -1
  289. package/lib/mol-repr/shape/model/unitcell.d.ts +1 -1
  290. package/lib/mol-repr/structure/complex-visual.d.ts +1 -1
  291. package/lib/mol-repr/structure/params.d.ts +1 -1
  292. package/lib/mol-repr/structure/registry.d.ts +19 -11
  293. package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  294. package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  295. package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +6 -6
  296. package/lib/mol-repr/structure/representation/gaussian-volume.d.ts +3 -3
  297. package/lib/mol-repr/structure/representation/label.d.ts +3 -3
  298. package/lib/mol-repr/structure/representation/line.d.ts +34 -16
  299. package/lib/mol-repr/structure/representation/line.js +10 -4
  300. package/lib/mol-repr/structure/representation/line.js.map +1 -1
  301. package/lib/mol-repr/structure/representation/molecular-surface.d.ts +6 -6
  302. package/lib/mol-repr/structure/units-visual.d.ts +1 -1
  303. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  304. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +14 -9
  305. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js.map +1 -1
  306. package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -0
  307. package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +12 -8
  308. package/lib/mol-repr/structure/visual/bond-inter-unit-line.js.map +1 -1
  309. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  310. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +15 -7
  311. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js.map +1 -1
  312. package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts +1 -0
  313. package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +13 -6
  314. package/lib/mol-repr/structure/visual/bond-intra-unit-line.js.map +1 -1
  315. package/lib/mol-repr/structure/visual/element-cross.d.ts +26 -0
  316. package/lib/mol-repr/structure/visual/element-cross.js +72 -0
  317. package/lib/mol-repr/structure/visual/element-cross.js.map +1 -0
  318. package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -2
  319. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +8 -8
  320. package/lib/mol-repr/structure/visual/label-text.d.ts +1 -1
  321. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +2 -2
  322. package/lib/mol-repr/structure/visual/util/bond.d.ts +10 -4
  323. package/lib/mol-repr/structure/visual/util/bond.js +1 -0
  324. package/lib/mol-repr/structure/visual/util/bond.js.map +1 -1
  325. package/lib/mol-repr/structure/visual/util/color.d.ts +2 -2
  326. package/lib/mol-repr/structure/visual/util/element.d.ts +4 -4
  327. package/lib/mol-repr/structure/visual/util/link.d.ts +6 -4
  328. package/lib/mol-repr/structure/visual/util/link.js +66 -23
  329. package/lib/mol-repr/structure/visual/util/link.js.map +1 -1
  330. package/lib/mol-repr/structure/visual/util/polymer.d.ts +2 -2
  331. package/lib/mol-repr/volume/direct-volume.d.ts +5 -5
  332. package/lib/mol-repr/volume/isosurface.d.ts +3 -3
  333. package/lib/mol-repr/volume/registry.d.ts +4 -4
  334. package/lib/mol-repr/volume/slice.d.ts +6 -6
  335. package/lib/mol-theme/color/atom-id.d.ts +12 -12
  336. package/lib/mol-theme/color/chain-id.d.ts +12 -12
  337. package/lib/mol-theme/color/element-index.d.ts +12 -12
  338. package/lib/mol-theme/color/element-symbol.d.ts +12 -12
  339. package/lib/mol-theme/color/entity-id.d.ts +12 -12
  340. package/lib/mol-theme/color/entity-source.d.ts +12 -12
  341. package/lib/mol-theme/color/illustrative.d.ts +12 -12
  342. package/lib/mol-theme/color/model-index.d.ts +12 -12
  343. package/lib/mol-theme/color/operator-hkl.d.ts +12 -12
  344. package/lib/mol-theme/color/operator-name.d.ts +12 -12
  345. package/lib/mol-theme/color/polymer-id.d.ts +12 -12
  346. package/lib/mol-theme/color/polymer-index.d.ts +12 -12
  347. package/lib/mol-theme/color/unit-index.d.ts +12 -12
  348. package/lib/mol-theme/color.d.ts +78 -78
  349. package/lib/mol-util/color/palette.d.ts +12 -12
  350. package/lib/servers/model/config.js +0 -1
  351. package/lib/servers/model/config.js.map +1 -1
  352. package/lib/servers/volume/config.js +0 -1
  353. package/lib/servers/volume/config.js.map +1 -1
  354. package/lib/tsconfig.commonjs.tsbuildinfo +1 -1
  355. package/package.json +18 -18
package/lib/mol-repr/structure/visual/util/bond.d.ts CHANGED
@@ -16,12 +16,14 @@ export declare const BondParams: {
16
16
  excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
17
17
  ignoreHydrogens: PD.BooleanParam;
18
18
  aromaticBonds: PD.BooleanParam;
19
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
19
20
  };
20
21
  export declare const DefaultBondProps: PD.Values<{
21
22
  includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
22
23
  excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
23
24
  ignoreHydrogens: PD.BooleanParam;
24
25
  aromaticBonds: PD.BooleanParam;
26
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
25
27
  }>;
26
28
  export declare type BondProps = typeof DefaultBondProps;
27
29
  export declare const BondCylinderParams: {
@@ -30,6 +32,7 @@ export declare const BondCylinderParams: {
30
32
  excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
31
33
  ignoreHydrogens: PD.BooleanParam;
32
34
  aromaticBonds: PD.BooleanParam;
35
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
33
36
  linkScale: PD.Numeric;
34
37
  linkSpacing: PD.Numeric;
35
38
  linkCap: PD.BooleanParam;
@@ -45,6 +48,7 @@ export declare const DefaultBondCylinderProps: PD.Values<{
45
48
  excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
46
49
  ignoreHydrogens: PD.BooleanParam;
47
50
  aromaticBonds: PD.BooleanParam;
51
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
48
52
  linkScale: PD.Numeric;
49
53
  linkSpacing: PD.Numeric;
50
54
  linkCap: PD.BooleanParam;
@@ -60,6 +64,7 @@ export declare const BondLineParams: {
60
64
  excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
61
65
  ignoreHydrogens: PD.BooleanParam;
62
66
  aromaticBonds: PD.BooleanParam;
67
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
63
68
  linkScale: PD.Numeric;
64
69
  linkSpacing: PD.Numeric;
65
70
  dashCount: PD.Numeric;
@@ -69,6 +74,7 @@ export declare const DefaultBondLineProps: PD.Values<{
69
74
  excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
70
75
  ignoreHydrogens: PD.BooleanParam;
71
76
  aromaticBonds: PD.BooleanParam;
77
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
72
78
  linkScale: PD.Numeric;
73
79
  linkSpacing: PD.Numeric;
74
80
  dashCount: PD.Numeric;
@@ -81,11 +87,11 @@ export declare namespace BondIterator {
81
87
  function fromGroup(structureGroup: StructureGroup): LocationIterator;
82
88
  function fromStructure(structure: Structure): LocationIterator;
83
89
  }
84
- export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
90
+ export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
85
91
  kind: "empty-loci";
86
- } | Bond.Loci;
92
+ };
87
93
  export declare function eachIntraBond(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;
88
- export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): {
94
+ export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): Bond.Loci | {
89
95
  kind: "empty-loci";
90
- } | Bond.Loci;
96
+ };
91
97
  export declare function eachInterBond(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;
package/lib/mol-repr/structure/visual/util/bond.js CHANGED
@@ -18,6 +18,7 @@ export var BondParams = {
18
18
  excludeTypes: PD.MultiSelect([], PD.objectToOptions(BondType.Names)),
19
19
  ignoreHydrogens: PD.Boolean(false),
20
20
  aromaticBonds: PD.Boolean(false, { description: 'Display aromatic bonds with dashes' }),
21
+ multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'])),
21
22
  };
22
23
  export var DefaultBondProps = PD.getDefaultValues(BondParams);
23
24
  export var BondCylinderParams = __assign(__assign(__assign({}, LinkCylinderParams), BondParams), { adjustCylinderLength: PD.Boolean(true, { description: 'Shorten cylinders to reduce overlap with spheres.' }) });
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1
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package/lib/mol-repr/structure/visual/util/color.d.ts CHANGED
@@ -10,10 +10,10 @@ import { Texture } from '../../../../mol-gl/webgl/texture';
10
10
  import { Theme } from '../../../../mol-theme/theme';
11
11
  import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
12
12
  export declare const ColorSmoothingParams: {
13
- smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
13
+ smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
14
14
  resolutionFactor: number;
15
15
  sampleStride: number;
16
- }>, "on">>;
16
+ }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
17
17
  };
18
18
  export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
19
19
  export declare function getColorSmoothingProps(props: PD.Values<ColorSmoothingParams>, theme: Theme, resolution?: number): {
package/lib/mol-repr/structure/visual/util/element.d.ts CHANGED
@@ -29,13 +29,13 @@ export declare type ElementSphereImpostorProps = {
29
29
  } & ElementProps;
30
30
  export declare function createElementSphereImpostor(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereImpostorProps, spheres?: Spheres): Spheres;
31
31
  export declare function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;
32
- export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
32
+ export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): StructureElement.Loci | {
33
33
  kind: "empty-loci";
34
- } | StructureElement.Loci;
34
+ };
35
35
  export declare function eachSerialElement(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean;
36
- export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): {
36
+ export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): StructureElement.Loci | {
37
37
  kind: "empty-loci";
38
- } | StructureElement.Loci;
38
+ };
39
39
  export declare namespace ElementIterator {
40
40
  function fromGroup(structureGroup: StructureGroup): LocationIterator;
41
41
  function fromStructure(structure: Structure): LocationIterator;
package/lib/mol-repr/structure/visual/util/link.d.ts CHANGED
@@ -56,10 +56,12 @@ export declare const enum LinkStyle {
56
56
  Solid = 0,
57
57
  Dashed = 1,
58
58
  Double = 2,
59
- Triple = 3,
60
- Disk = 4,
61
- Aromatic = 5,
62
- MirroredAromatic = 6
59
+ OffsetDouble = 3,
60
+ Triple = 4,
61
+ OffsetTriple = 5,
62
+ Disk = 6,
63
+ Aromatic = 7,
64
+ MirroredAromatic = 8
63
65
  }
64
66
  /**
65
67
  * Each edge is included twice to allow for coloring/picking
package/lib/mol-repr/structure/visual/util/link.js CHANGED
@@ -91,12 +91,14 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
91
91
  continue;
92
92
  position(va, vb, edgeIndex);
93
93
  v3sub(tmpV12, vb, va);
94
+ var dirFlag = v3dot(tmpV12, up) > 0;
94
95
  var linkRadius = radius(edgeIndex);
95
96
  var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
96
97
  var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
97
- var _a = (v3dot(tmpV12, up) > 0) ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
98
+ var _a = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
98
99
  builderState.currentGroup = edgeIndex;
99
- var aromaticOffsetFactor = 4.5;
100
+ var aromaticOffsetFactor = 5.5;
101
+ var multipleOffsetFactor = 4;
100
102
  if (linkStyle === 0 /* Solid */) {
101
103
  cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
102
104
  cylinderProps.topCap = topCap;
@@ -108,15 +110,15 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
108
110
  cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
109
111
  addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
110
112
  }
111
- else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* Triple */ || linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
112
- var order = linkStyle === 2 /* Double */ ? 2 :
113
- linkStyle === 3 /* Triple */ ? 3 : 1.5;
113
+ else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
114
+ var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
115
+ linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
114
116
  var multiRadius = linkRadius * (linkScale / (0.5 * order));
115
117
  var absOffset = (linkRadius - multiRadius) * linkSpacing;
116
118
  calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
117
119
  cylinderProps.topCap = topCap;
118
120
  cylinderProps.bottomCap = bottomCap;
119
- if (linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
121
+ if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
120
122
  cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
121
123
  addCylinder(builderState, va, vb, 0.5, cylinderProps);
122
124
  cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * linkScale;
@@ -125,13 +127,34 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
125
127
  v3sub(va, va, vShift);
126
128
  v3sub(vb, vb, vShift);
127
129
  addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
128
- if (linkStyle === 6 /* MirroredAromatic */) {
130
+ if (linkStyle === 8 /* MirroredAromatic */) {
129
131
  v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
130
132
  v3add(va, va, vShift);
131
133
  v3add(vb, vb, vShift);
132
134
  addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
133
135
  }
134
136
  }
137
+ else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
138
+ v3setMagnitude(vShift, vShift, absOffset);
139
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
140
+ addCylinder(builderState, va, vb, 0.5, cylinderProps);
141
+ v3scale(tmpV12, tmpV12, linkSpacing * linkScale * 0.2);
142
+ v3add(va, va, tmpV12);
143
+ v3sub(vb, vb, tmpV12);
144
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
145
+ cylinderProps.topCap = dirFlag ? linkStub : dashCap;
146
+ cylinderProps.bottomCap = dirFlag ? dashCap : linkStub;
147
+ v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
148
+ v3sub(va, va, vShift);
149
+ v3sub(vb, vb, vShift);
150
+ addCylinder(builderState, va, vb, 0.5, cylinderProps);
151
+ if (order === 3) {
152
+ v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor * 2);
153
+ v3add(va, va, vShift);
154
+ v3add(vb, vb, vShift);
155
+ addCylinder(builderState, va, vb, 0.5, cylinderProps);
156
+ }
157
+ }
135
158
  else {
136
159
  v3setMagnitude(vShift, vShift, absOffset);
137
160
  cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
@@ -140,7 +163,7 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
140
163
  addDoubleCylinder(builderState, va, vb, 0.5, vShift, cylinderProps);
141
164
  }
142
165
  }
143
- else if (linkStyle === 4 /* Disk */) {
166
+ else if (linkStyle === 6 /* Disk */) {
144
167
  v3scale(tmpV12, tmpV12, 0.475);
145
168
  v3add(va, va, tmpV12);
146
169
  v3sub(vb, vb, tmpV12);
@@ -172,7 +195,8 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
172
195
  var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
173
196
  var aromaticSegmentCount = 3;
174
197
  var aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
175
- var aromaticOffsetFactor = 4.5;
198
+ var aromaticOffsetFactor = 5.5;
199
+ var multipleOffsetFactor = 4;
176
200
  for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
177
201
  if (ignore && ignore(edgeIndex))
178
202
  continue;
@@ -189,14 +213,14 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
189
213
  v3sub(vb, vb, tmpV12);
190
214
  builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
191
215
  }
192
- else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* Triple */ || linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
193
- var order = linkStyle === 2 /* Double */ ? 2 :
194
- linkStyle === 3 /* Triple */ ? 3 : 1.5;
216
+ else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
217
+ var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
218
+ linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
195
219
  var multiScale = linkScale / (0.5 * order);
196
220
  var absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
197
221
  v3scale(vm, v3add(vm, va, vb), 0.5);
198
222
  calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
199
- if (linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
223
+ if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
200
224
  builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
201
225
  v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
202
226
  v3sub(vb, vb, tmpV12);
@@ -204,22 +228,31 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
204
228
  v3sub(va, va, vShift);
205
229
  v3sub(vb, vb, vShift);
206
230
  builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
207
- if (linkStyle === 6 /* MirroredAromatic */) {
231
+ if (linkStyle === 8 /* MirroredAromatic */) {
208
232
  v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
209
233
  v3add(va, va, vShift);
210
234
  v3add(vb, vb, vShift);
211
235
  builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
212
236
  }
213
237
  }
238
+ else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
239
+ v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
240
+ builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
241
+ v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale * 0.2);
242
+ v3sub(va, va, tmpV12);
243
+ if (order === 3)
244
+ builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
245
+ builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, dashCap, linkStub, edgeIndex);
246
+ }
214
247
  else {
215
248
  v3setMagnitude(vShift, vShift, absOffset);
216
249
  if (order === 3)
217
- builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, false, edgeIndex);
250
+ builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, linkStub, edgeIndex);
218
251
  builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
219
252
  builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
220
253
  }
221
254
  }
222
- else if (linkStyle === 4 /* Disk */) {
255
+ else if (linkStyle === 6 /* Disk */) {
223
256
  v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
224
257
  v3add(va, va, tmpV12);
225
258
  v3sub(vb, vb, tmpV12);
@@ -249,6 +282,7 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
249
282
  var aromaticSegmentCount = 3;
250
283
  var aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
251
284
  var aromaticOffsetFactor = 4.5;
285
+ var multipleOffsetFactor = 3;
252
286
  for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
253
287
  if (ignore && ignore(edgeIndex))
254
288
  continue;
@@ -263,14 +297,14 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
263
297
  v3sub(vb, vb, tmpV12);
264
298
  builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
265
299
  }
266
- else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* Triple */ || linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
267
- var order = linkStyle === 2 /* Double */ ? 2 :
268
- linkStyle === 3 /* Triple */ ? 3 : 1.5;
300
+ else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
301
+ var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
302
+ linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
269
303
  var multiRadius = 1 * (linkScale / (0.5 * order));
270
304
  var absOffset = (1 - multiRadius) * linkSpacing;
271
305
  v3scale(vm, v3add(vm, va, vb), 0.5);
272
306
  calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
273
- if (linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
307
+ if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
274
308
  builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
275
309
  v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
276
310
  v3sub(vb, vb, tmpV12);
@@ -278,22 +312,31 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
278
312
  v3sub(va, va, vShift);
279
313
  v3sub(vb, vb, vShift);
280
314
  builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
281
- if (linkStyle === 6 /* MirroredAromatic */) {
315
+ if (linkStyle === 8 /* MirroredAromatic */) {
282
316
  v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
283
317
  v3add(va, va, vShift);
284
318
  v3add(vb, vb, vShift);
285
319
  builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
286
320
  }
287
321
  }
322
+ else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
323
+ v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
324
+ builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
325
+ v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale);
326
+ v3sub(va, va, tmpV12);
327
+ if (order === 3)
328
+ builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
329
+ builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
330
+ }
288
331
  else {
289
- v3setMagnitude(vShift, vShift, absOffset);
332
+ v3setMagnitude(vShift, vShift, absOffset * 1.5);
290
333
  if (order === 3)
291
334
  builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
292
335
  builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
293
336
  builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
294
337
  }
295
338
  }
296
- else if (linkStyle === 4 /* Disk */) {
339
+ else if (linkStyle === 6 /* Disk */) {
297
340
  v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
298
341
  v3add(va, va, tmpV12);
299
342
  v3sub(vb, vb, tmpV12);
package/lib/mol-repr/structure/visual/util/link.js.map CHANGED
@@ -1 +1 @@
1
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package/lib/mol-repr/structure/visual/util/polymer.d.ts CHANGED
@@ -34,7 +34,7 @@ export declare function eachAtomicUnitTracedElement(offset: number, groupSize: n
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  /** Mark a polymer element (e.g. part of a cartoon trace) */
35
35
  export declare function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;
36
36
  /** Return a Loci for both directions of the polymer gap element. */
37
- export declare function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
37
+ export declare function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
38
38
  kind: "empty-loci";
39
- } | Bond.Loci;
39
+ };
40
40
  export declare function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;
package/lib/mol-repr/volume/direct-volume.d.ts CHANGED
@@ -18,9 +18,9 @@ import { PickingId } from '../../mol-geo/geometry/picking';
18
18
  export declare function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume): DirectVolume;
19
19
  export declare function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume): DirectVolume;
20
20
  export declare function createDirectVolume(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<DirectVolumeParams>, directVolume?: DirectVolume): Promise<DirectVolume>;
21
- export declare function getDirectVolumeLoci(pickingId: PickingId, volume: Volume, props: DirectVolumeProps, id: number): Volume.Cell.Loci | {
21
+ export declare function getDirectVolumeLoci(pickingId: PickingId, volume: Volume, props: DirectVolumeProps, id: number): {
22
22
  kind: "empty-loci";
23
- };
23
+ } | Volume.Cell.Loci;
24
24
  export declare function eachDirectVolume(loci: Loci, volume: Volume, props: DirectVolumeProps, apply: (interval: Interval) => boolean): boolean;
25
25
  export declare const DirectVolumeParams: {
26
26
  quality: {
@@ -54,7 +54,7 @@ export declare const DirectVolumeParams: {
54
54
  renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
55
55
  controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
56
56
  list: {
57
- kind: "interpolate" | "set";
57
+ kind: "set" | "interpolate";
58
58
  colors: import("../../mol-util/color/color").ColorListEntry[];
59
59
  };
60
60
  }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -104,7 +104,7 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
104
104
  renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
105
105
  controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
106
106
  list: {
107
- kind: "interpolate" | "set";
107
+ kind: "set" | "interpolate";
108
108
  colors: import("../../mol-util/color/color").ColorListEntry[];
109
109
  };
110
110
  }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -156,7 +156,7 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
156
156
  renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
157
157
  controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
158
158
  list: {
159
- kind: "interpolate" | "set";
159
+ kind: "set" | "interpolate";
160
160
  colors: import("../../mol-util/color/color").ColorListEntry[];
161
161
  };
162
162
  }>, "volume"> | PD.NamedParams<PD.Normalize<{
package/lib/mol-repr/volume/isosurface.d.ts CHANGED
@@ -208,7 +208,7 @@ export declare const IsosurfaceWireframeParams: {
208
208
  export declare type IsosurfaceWireframeParams = typeof IsosurfaceWireframeParams;
209
209
  export declare function IsosurfaceWireframeVisual(materialId: number): VolumeVisual<IsosurfaceWireframeParams>;
210
210
  export declare const IsosurfaceParams: {
211
- visuals: PD.MultiSelect<"solid" | "wireframe">;
211
+ visuals: PD.MultiSelect<"wireframe" | "solid">;
212
212
  quality: {
213
213
  isEssential: boolean;
214
214
  type: "select";
@@ -266,7 +266,7 @@ export declare const IsosurfaceParams: {
266
266
  };
267
267
  export declare type IsosurfaceParams = typeof IsosurfaceParams;
268
268
  export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: Volume): {
269
- visuals: PD.MultiSelect<"solid" | "wireframe">;
269
+ visuals: PD.MultiSelect<"wireframe" | "solid">;
270
270
  quality: {
271
271
  isEssential: boolean;
272
272
  type: "select";
@@ -325,7 +325,7 @@ export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: V
325
325
  export declare type IsosurfaceRepresentation = VolumeRepresentation<IsosurfaceParams>;
326
326
  export declare function IsosurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, IsosurfaceParams>): IsosurfaceRepresentation;
327
327
  export declare const IsosurfaceRepresentationProvider: VolumeRepresentationProvider<{
328
- visuals: PD.MultiSelect<"solid" | "wireframe">;
328
+ visuals: PD.MultiSelect<"wireframe" | "solid">;
329
329
  quality: {
330
330
  isEssential: boolean;
331
331
  type: "select";
package/lib/mol-repr/volume/registry.d.ts CHANGED
@@ -11,7 +11,7 @@ export declare class VolumeRepresentationRegistry extends RepresentationRegistry
11
11
  export declare namespace VolumeRepresentationRegistry {
12
12
  export const BuiltIn: {
13
13
  isosurface: import("./representation").VolumeRepresentationProvider<{
14
- visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"solid" | "wireframe">;
14
+ visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"wireframe" | "solid">;
15
15
  quality: {
16
16
  isEssential: boolean;
17
17
  type: "select";
@@ -91,7 +91,7 @@ export declare namespace VolumeRepresentationRegistry {
91
91
  legend?: import("../../mol-util/legend").Legend | undefined;
92
92
  }) | undefined;
93
93
  };
94
- dimension: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<number, "x"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<number, "y"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<number, "z">>;
94
+ dimension: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<number, "y"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<number, "x"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<number, "z">>;
95
95
  isoValue: import("../../mol-util/param-definition").ParamDefinition.Conditioned<Readonly<{
96
96
  kind: "absolute";
97
97
  absoluteValue: number;
@@ -114,7 +114,7 @@ export declare namespace VolumeRepresentationRegistry {
114
114
  relativeValue: number;
115
115
  }>, number>;
116
116
  }>;
117
- interpolation: import("../../mol-util/param-definition").ParamDefinition.Select<"nearest" | "catmulrom" | "mitchell" | "bspline">;
117
+ interpolation: import("../../mol-util/param-definition").ParamDefinition.Select<"bspline" | "nearest" | "catmulrom" | "mitchell">;
118
118
  alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
119
119
  }, "slice">;
120
120
  'direct-volume': import("./representation").VolumeRepresentationProvider<{
@@ -149,7 +149,7 @@ export declare namespace VolumeRepresentationRegistry {
149
149
  renderMode: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
150
150
  controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
151
151
  list: {
152
- kind: "interpolate" | "set";
152
+ kind: "set" | "interpolate";
153
153
  colors: import("../../mol-util/color/color").ColorListEntry[];
154
154
  };
155
155
  }>, "volume"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{