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/commonjs/mol-repr/structure/representation/molecular-surface.d.ts CHANGED
@@ -21,10 +21,10 @@ export declare const MolecularSurfaceParams: {
21
21
  lineSizeAttenuation: PD.BooleanParam;
22
22
  alpha: PD.Numeric;
23
23
  quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
24
- smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
24
+ smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
25
25
  resolutionFactor: number;
26
26
  sampleStride: number;
27
- }>, "on">>;
27
+ }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
28
28
  doubleSided: PD.BooleanParam;
29
29
  flipSided: PD.BooleanParam;
30
30
  flatShaded: PD.BooleanParam;
@@ -45,10 +45,10 @@ export declare function getMolecularSurfaceParams(ctx: ThemeRegistryContext, str
45
45
  lineSizeAttenuation: PD.BooleanParam;
46
46
  alpha: PD.Numeric;
47
47
  quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
48
- smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
48
+ smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
49
49
  resolutionFactor: number;
50
50
  sampleStride: number;
51
- }>, "on">>;
51
+ }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
52
52
  doubleSided: PD.BooleanParam;
53
53
  flipSided: PD.BooleanParam;
54
54
  flatShaded: PD.BooleanParam;
@@ -70,10 +70,10 @@ export declare const MolecularSurfaceRepresentationProvider: StructureRepresenta
70
70
  lineSizeAttenuation: PD.BooleanParam;
71
71
  alpha: PD.Numeric;
72
72
  quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
73
- smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
73
+ smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
74
74
  resolutionFactor: number;
75
75
  sampleStride: number;
76
- }>, "on">>;
76
+ }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
77
77
  doubleSided: PD.BooleanParam;
78
78
  flipSided: PD.BooleanParam;
79
79
  flatShaded: PD.BooleanParam;
package/lib/commonjs/mol-repr/structure/units-visual.d.ts CHANGED
@@ -152,7 +152,7 @@ export declare const UnitsDirectVolumeParams: {
152
152
  renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
153
153
  controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
154
154
  list: {
155
- kind: "interpolate" | "set";
155
+ kind: "set" | "interpolate";
156
156
  colors: import("../../mol-util/color/color").ColorListEntry[];
157
157
  };
158
158
  }>, "volume"> | PD.NamedParams<PD.Normalize<{
package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts CHANGED
@@ -13,10 +13,11 @@ export declare const InterUnitBondCylinderParams: {
13
13
  tryUseImpostor: PD.BooleanParam;
14
14
  includeParent: PD.BooleanParam;
15
15
  adjustCylinderLength: PD.BooleanParam;
16
- includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
17
- excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
16
+ includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
17
+ excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
18
18
  ignoreHydrogens: PD.BooleanParam;
19
19
  aromaticBonds: PD.BooleanParam;
20
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
20
21
  linkScale: PD.Numeric;
21
22
  linkSpacing: PD.Numeric;
22
23
  linkCap: PD.BooleanParam;
@@ -41,10 +42,11 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
41
42
  tryUseImpostor: PD.BooleanParam;
42
43
  includeParent: PD.BooleanParam;
43
44
  adjustCylinderLength: PD.BooleanParam;
44
- includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
45
- excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
45
+ includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
46
+ excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
46
47
  ignoreHydrogens: PD.BooleanParam;
47
48
  aromaticBonds: PD.BooleanParam;
49
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
48
50
  linkScale: PD.Numeric;
49
51
  linkSpacing: PD.Numeric;
50
52
  linkCap: PD.BooleanParam;
package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js CHANGED
@@ -35,7 +35,9 @@ function getInterUnitBondCylinderBuilderProps(structure, theme, props) {
35
35
  var locB = structure_1.Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
36
36
  var bonds = structure.interUnitBonds;
37
37
  var edgeCount = bonds.edgeCount, edges = bonds.edges;
38
- var sizeFactor = props.sizeFactor, sizeAspectRatio = props.sizeAspectRatio, adjustCylinderLength = props.adjustCylinderLength, aromaticBonds = props.aromaticBonds;
38
+ var sizeFactor = props.sizeFactor, sizeAspectRatio = props.sizeAspectRatio, adjustCylinderLength = props.adjustCylinderLength, aromaticBonds = props.aromaticBonds, multipleBonds = props.multipleBonds;
39
+ var mbOff = multipleBonds === 'off';
40
+ var mbSymmetric = multipleBonds === 'symmetric';
39
41
  var delta = (0, linear_algebra_1.Vec3)();
40
42
  var stub;
41
43
  var child = structure.child;
@@ -121,15 +123,16 @@ function getInterUnitBondCylinderBuilderProps(structure, theme, props) {
121
123
  return 1 /* Dashed */;
122
124
  }
123
125
  else if (o === 3) {
124
- return 3 /* Triple */;
126
+ return mbOff ? 0 /* Solid */ :
127
+ mbSymmetric ? 4 /* Triple */ :
128
+ 5 /* OffsetTriple */;
125
129
  }
126
130
  else if (aromaticBonds && types_1.BondType.is(f, 16 /* Aromatic */)) {
127
- return 5 /* Aromatic */;
131
+ return 7 /* Aromatic */;
128
132
  }
129
- else if (o === 2) {
130
- return 2 /* Double */;
131
- }
132
- return 0 /* Solid */;
133
+ return (o !== 2 || mbOff) ? 0 /* Solid */ :
134
+ mbSymmetric ? 2 /* Double */ :
135
+ 3 /* OffsetDouble */;
133
136
  },
134
137
  radius: function (edgeIndex) {
135
138
  return radius(edgeIndex) * sizeAspectRatio;
@@ -184,7 +187,8 @@ function InterUnitBondCylinderImpostorVisual(materialId) {
184
187
  newProps.stubCap !== currentProps.stubCap ||
185
188
  !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
186
189
  !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
187
- newProps.adjustCylinderLength !== currentProps.adjustCylinderLength);
190
+ newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
191
+ newProps.multipleBonds !== currentProps.multipleBonds);
188
192
  if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
189
193
  state.createGeometry = true;
190
194
  state.updateTransform = true;
@@ -219,7 +223,8 @@ function InterUnitBondCylinderMeshVisual(materialId) {
219
223
  newProps.stubCap !== currentProps.stubCap ||
220
224
  !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
221
225
  !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
222
- newProps.adjustCylinderLength !== currentProps.adjustCylinderLength);
226
+ newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
227
+ newProps.multipleBonds !== currentProps.multipleBonds);
223
228
  if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
224
229
  state.createGeometry = true;
225
230
  state.updateTransform = true;
package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts CHANGED
@@ -7,10 +7,11 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
7
7
  import { ComplexVisual } from '../complex-visual';
8
8
  export declare const InterUnitBondLineParams: {
9
9
  includeParent: PD.BooleanParam;
10
- includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
11
- excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
10
+ includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
11
+ excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
12
12
  ignoreHydrogens: PD.BooleanParam;
13
13
  aromaticBonds: PD.BooleanParam;
14
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
14
15
  linkScale: PD.Numeric;
15
16
  linkSpacing: PD.Numeric;
16
17
  dashCount: PD.Numeric;
package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js CHANGED
@@ -30,9 +30,11 @@ function setRefPosition(pos, structure, unit, index) {
30
30
  function createInterUnitBondLines(ctx, structure, theme, props, lines) {
31
31
  var bonds = structure.interUnitBonds;
32
32
  var edgeCount = bonds.edgeCount, edges = bonds.edges;
33
- var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds;
34
33
  if (!edgeCount)
35
34
  return lines_1.Lines.createEmpty(lines);
35
+ var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds, multipleBonds = props.multipleBonds;
36
+ var mbOff = multipleBonds === 'off';
37
+ var mbSymmetric = multipleBonds === 'symmetric';
36
38
  var ref = (0, linear_algebra_1.Vec3)();
37
39
  var loc = structure_1.StructureElement.Location.create();
38
40
  var builderProps = {
@@ -73,15 +75,16 @@ function createInterUnitBondLines(ctx, structure, theme, props, lines) {
73
75
  return 1 /* Dashed */;
74
76
  }
75
77
  else if (o === 3) {
76
- return 3 /* Triple */;
78
+ return mbOff ? 0 /* Solid */ :
79
+ mbSymmetric ? 4 /* Triple */ :
80
+ 5 /* OffsetTriple */;
77
81
  }
78
82
  else if (aromaticBonds && types_1.BondType.is(f, 16 /* Aromatic */)) {
79
- return 5 /* Aromatic */;
83
+ return 7 /* Aromatic */;
80
84
  }
81
- else if (o === 2) {
82
- return 2 /* Double */;
83
- }
84
- return 0 /* Solid */;
85
+ return (o !== 2 || mbOff) ? 0 /* Solid */ :
86
+ mbSymmetric ? 2 /* Double */ :
87
+ 3 /* OffsetDouble */;
85
88
  },
86
89
  radius: function (edgeIndex) {
87
90
  var b = edges[edgeIndex];
@@ -117,7 +120,8 @@ function InterUnitBondLineVisual(materialId) {
117
120
  newProps.dashCount !== currentProps.dashCount ||
118
121
  newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
119
122
  !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
120
- !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes));
123
+ !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
124
+ newProps.multipleBonds !== currentProps.multipleBonds);
121
125
  if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
122
126
  state.createGeometry = true;
123
127
  state.updateTransform = true;
package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts CHANGED
@@ -14,10 +14,11 @@ export declare const IntraUnitBondCylinderParams: {
14
14
  tryUseImpostor: PD.BooleanParam;
15
15
  includeParent: PD.BooleanParam;
16
16
  adjustCylinderLength: PD.BooleanParam;
17
- includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
18
- excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
17
+ includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
18
+ excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
19
19
  ignoreHydrogens: PD.BooleanParam;
20
20
  aromaticBonds: PD.BooleanParam;
21
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
21
22
  linkScale: PD.Numeric;
22
23
  linkSpacing: PD.Numeric;
23
24
  linkCap: PD.BooleanParam;
@@ -42,10 +43,11 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
42
43
  tryUseImpostor: PD.BooleanParam;
43
44
  includeParent: PD.BooleanParam;
44
45
  adjustCylinderLength: PD.BooleanParam;
45
- includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
46
- excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
46
+ includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
47
+ excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
47
48
  ignoreHydrogens: PD.BooleanParam;
48
49
  aromaticBonds: PD.BooleanParam;
50
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
49
51
  linkScale: PD.Numeric;
50
52
  linkSpacing: PD.Numeric;
51
53
  linkCap: PD.BooleanParam;
package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js CHANGED
@@ -29,7 +29,9 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
29
29
  var bonds = unit.bonds;
30
30
  var edgeCount = bonds.edgeCount, a = bonds.a, b = bonds.b, edgeProps = bonds.edgeProps, offset = bonds.offset;
31
31
  var _order = edgeProps.order, _flags = edgeProps.flags;
32
- var sizeFactor = props.sizeFactor, sizeAspectRatio = props.sizeAspectRatio, adjustCylinderLength = props.adjustCylinderLength, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
32
+ var sizeFactor = props.sizeFactor, sizeAspectRatio = props.sizeAspectRatio, adjustCylinderLength = props.adjustCylinderLength, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes, multipleBonds = props.multipleBonds;
33
+ var mbOff = multipleBonds === 'off';
34
+ var mbSymmetric = multipleBonds === 'symmetric';
33
35
  var include = types_1.BondType.fromNames(includeTypes);
34
36
  var exclude = types_1.BondType.fromNames(excludeTypes);
35
37
  var ignoreComputedAromatic = (0, bond_1.ignoreBondType)(include, exclude, 32 /* Computed */);
@@ -117,7 +119,9 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
117
119
  return 1 /* Dashed */;
118
120
  }
119
121
  else if (o === 3) {
120
- return 3 /* Triple */;
122
+ return mbOff ? 0 /* Solid */ :
123
+ mbSymmetric ? 4 /* Triple */ :
124
+ 5 /* OffsetTriple */;
121
125
  }
122
126
  else if (aromaticBonds) {
123
127
  var aI = a[edgeIndex], bI = b[edgeIndex];
@@ -126,14 +130,16 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
126
130
  var arCount = (aR && bR) ? (0, array_1.arrayIntersectionSize)(aR, bR) : 0;
127
131
  if (isBondType(f, 16 /* Aromatic */) || (arCount && !ignoreComputedAromatic)) {
128
132
  if (arCount === 2) {
129
- return 6 /* MirroredAromatic */;
133
+ return 8 /* MirroredAromatic */;
130
134
  }
131
135
  else {
132
- return 5 /* Aromatic */;
136
+ return 7 /* Aromatic */;
133
137
  }
134
138
  }
135
139
  }
136
- return o === 2 ? 2 /* Double */ : 0 /* Solid */;
140
+ return (o !== 2 || mbOff) ? 0 /* Solid */ :
141
+ mbSymmetric ? 2 /* Double */ :
142
+ 3 /* OffsetDouble */;
137
143
  },
138
144
  radius: function (edgeIndex) {
139
145
  return radius(edgeIndex) * sizeAspectRatio;
@@ -199,7 +205,8 @@ function IntraUnitBondCylinderImpostorVisual(materialId) {
199
205
  !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
200
206
  !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
201
207
  newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
202
- newProps.aromaticBonds !== currentProps.aromaticBonds);
208
+ newProps.aromaticBonds !== currentProps.aromaticBonds ||
209
+ newProps.multipleBonds !== currentProps.multipleBonds);
203
210
  var newUnit = newStructureGroup.group.units[0];
204
211
  var currentUnit = currentStructureGroup.group.units[0];
205
212
  if (structure_1.Unit.isAtomic(newUnit) && structure_1.Unit.isAtomic(currentUnit)) {
@@ -239,7 +246,8 @@ function IntraUnitBondCylinderMeshVisual(materialId) {
239
246
  !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
240
247
  !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
241
248
  newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
242
- newProps.aromaticBonds !== currentProps.aromaticBonds);
249
+ newProps.aromaticBonds !== currentProps.aromaticBonds ||
250
+ newProps.multipleBonds !== currentProps.multipleBonds);
243
251
  var newUnit = newStructureGroup.group.units[0];
244
252
  var currentUnit = currentStructureGroup.group.units[0];
245
253
  if (structure_1.Unit.isAtomic(newUnit) && structure_1.Unit.isAtomic(currentUnit)) {
package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.d.ts CHANGED
@@ -7,10 +7,11 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
7
7
  import { UnitsVisual } from '../units-visual';
8
8
  export declare const IntraUnitBondLineParams: {
9
9
  includeParent: PD.BooleanParam;
10
- includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
11
- excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
10
+ includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
11
+ excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
12
12
  ignoreHydrogens: PD.BooleanParam;
13
13
  aromaticBonds: PD.BooleanParam;
14
+ multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
14
15
  linkScale: PD.Numeric;
15
16
  linkSpacing: PD.Numeric;
16
17
  dashCount: PD.Numeric;
package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js CHANGED
@@ -35,7 +35,9 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
35
35
  if (!edgeCount)
36
36
  return lines_1.Lines.createEmpty(lines);
37
37
  var _order = edgeProps.order, _flags = edgeProps.flags;
38
- var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
38
+ var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes, multipleBonds = props.multipleBonds;
39
+ var mbOff = multipleBonds === 'off';
40
+ var mbSymmetric = multipleBonds === 'symmetric';
39
41
  var include = types_1.BondType.fromNames(includeTypes);
40
42
  var exclude = types_1.BondType.fromNames(excludeTypes);
41
43
  var ignoreComputedAromatic = (0, bond_1.ignoreBondType)(include, exclude, 32 /* Computed */);
@@ -85,7 +87,9 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
85
87
  return 1 /* Dashed */;
86
88
  }
87
89
  else if (o === 3) {
88
- return 3 /* Triple */;
90
+ return mbOff ? 0 /* Solid */ :
91
+ mbSymmetric ? 4 /* Triple */ :
92
+ 5 /* OffsetTriple */;
89
93
  }
90
94
  else if (aromaticBonds) {
91
95
  var aI = a[edgeIndex], bI = b[edgeIndex];
@@ -94,14 +98,16 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
94
98
  var arCount = (aR && bR) ? (0, array_1.arrayIntersectionSize)(aR, bR) : 0;
95
99
  if (isBondType(f, 16 /* Aromatic */) || (arCount && !ignoreComputedAromatic)) {
96
100
  if (arCount === 2) {
97
- return 6 /* MirroredAromatic */;
101
+ return 8 /* MirroredAromatic */;
98
102
  }
99
103
  else {
100
- return 5 /* Aromatic */;
104
+ return 7 /* Aromatic */;
101
105
  }
102
106
  }
103
107
  }
104
- return o === 2 ? 2 /* Double */ : 0 /* Solid */;
108
+ return (o !== 2 || mbOff) ? 0 /* Solid */ :
109
+ mbSymmetric ? 2 /* Double */ :
110
+ 3 /* OffsetDouble */;
105
111
  },
106
112
  radius: function (edgeIndex) {
107
113
  location.element = elements[a[edgeIndex]];
@@ -133,7 +139,8 @@ function IntraUnitBondLineVisual(materialId) {
133
139
  newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
134
140
  !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
135
141
  !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
136
- newProps.aromaticBonds !== currentProps.aromaticBonds);
142
+ newProps.aromaticBonds !== currentProps.aromaticBonds ||
143
+ newProps.multipleBonds !== currentProps.multipleBonds);
137
144
  var newUnit = newStructureGroup.group.units[0];
138
145
  var currentUnit = currentStructureGroup.group.units[0];
139
146
  if (structure_1.Unit.isAtomic(newUnit) && structure_1.Unit.isAtomic(currentUnit)) {
package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts ADDED
@@ -0,0 +1,26 @@
1
+ /**
2
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ *
4
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
+ */
6
+ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
7
+ import { UnitsVisual } from '../units-visual';
8
+ import { VisualContext } from '../../visual';
9
+ import { Unit, Structure } from '../../../mol-model/structure';
10
+ import { Theme } from '../../../mol-theme/theme';
11
+ import { Lines } from '../../../mol-geo/geometry/lines/lines';
12
+ export declare const ElementCrossParams: {
13
+ lineSizeAttenuation: PD.BooleanParam;
14
+ ignoreHydrogens: PD.BooleanParam;
15
+ traceOnly: PD.BooleanParam;
16
+ crosses: PD.Select<"all" | "lone">;
17
+ crossSize: PD.Numeric;
18
+ unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
19
+ includeParent: PD.BooleanParam;
20
+ sizeFactor: PD.Numeric;
21
+ alpha: PD.Numeric;
22
+ quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
23
+ };
24
+ export declare type ElementCrossParams = typeof ElementCrossParams;
25
+ export declare function createElementCross(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementCrossParams>, lines: Lines): Lines;
26
+ export declare function ElementCrossVisual(materialId: number): UnitsVisual<ElementCrossParams>;