molstar 4.2.0 → 4.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1216) hide show
  1. package/build/viewer/molstar.css +1 -1
  2. package/build/viewer/molstar.js +1 -1
  3. package/lib/apps/docking-viewer/viewport.d.ts +1 -1
  4. package/lib/apps/docking-viewer/viewport.js +2 -1
  5. package/lib/apps/mesoscale-explorer/app.d.ts +3 -1
  6. package/lib/apps/mesoscale-explorer/app.js +12 -1
  7. package/lib/apps/mesoscale-explorer/behavior/camera.d.ts +12 -0
  8. package/lib/apps/mesoscale-explorer/behavior/camera.js +32 -6
  9. package/lib/apps/mesoscale-explorer/behavior/select.d.ts +1 -0
  10. package/lib/apps/mesoscale-explorer/behavior/select.js +58 -9
  11. package/lib/apps/mesoscale-explorer/data/cellpack/model.js +4 -6
  12. package/lib/apps/mesoscale-explorer/data/cellpack/preset.js +8 -5
  13. package/lib/apps/mesoscale-explorer/data/generic/model.d.ts +1 -0
  14. package/lib/apps/mesoscale-explorer/data/generic/model.js +2 -1
  15. package/lib/apps/mesoscale-explorer/data/generic/preset.js +7 -6
  16. package/lib/apps/mesoscale-explorer/data/mmcif/model.js +3 -1
  17. package/lib/apps/mesoscale-explorer/data/mmcif/preset.js +6 -3
  18. package/lib/apps/mesoscale-explorer/data/petworld/model.js +3 -1
  19. package/lib/apps/mesoscale-explorer/data/petworld/preset.js +6 -3
  20. package/lib/apps/mesoscale-explorer/data/state.d.ts +48 -10
  21. package/lib/apps/mesoscale-explorer/data/state.js +83 -8
  22. package/lib/apps/mesoscale-explorer/index.html +6 -1
  23. package/lib/apps/mesoscale-explorer/style.scss +33 -0
  24. package/lib/apps/mesoscale-explorer/ui/entities.d.ts +23 -1
  25. package/lib/apps/mesoscale-explorer/ui/entities.js +301 -32
  26. package/lib/apps/mesoscale-explorer/ui/panels.d.ts +1 -0
  27. package/lib/apps/mesoscale-explorer/ui/panels.js +42 -5
  28. package/lib/apps/mesoscale-explorer/ui/states.d.ts +60 -2
  29. package/lib/apps/mesoscale-explorer/ui/states.js +471 -11
  30. package/lib/apps/viewer/app.d.ts +12 -5
  31. package/lib/apps/viewer/app.js +30 -1
  32. package/lib/commonjs/apps/docking-viewer/viewport.d.ts +1 -1
  33. package/lib/commonjs/apps/docking-viewer/viewport.js +2 -1
  34. package/lib/commonjs/apps/mesoscale-explorer/app.d.ts +3 -1
  35. package/lib/commonjs/apps/mesoscale-explorer/app.js +12 -1
  36. package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.d.ts +12 -0
  37. package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.js +34 -8
  38. package/lib/commonjs/apps/mesoscale-explorer/behavior/select.d.ts +1 -0
  39. package/lib/commonjs/apps/mesoscale-explorer/behavior/select.js +58 -9
  40. package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/model.js +4 -6
  41. package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.js +8 -6
  42. package/lib/commonjs/apps/mesoscale-explorer/data/generic/model.d.ts +1 -0
  43. package/lib/commonjs/apps/mesoscale-explorer/data/generic/model.js +2 -1
  44. package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.js +9 -9
  45. package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/model.js +3 -1
  46. package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.js +6 -4
  47. package/lib/commonjs/apps/mesoscale-explorer/data/petworld/model.js +3 -1
  48. package/lib/commonjs/apps/mesoscale-explorer/data/petworld/preset.js +6 -4
  49. package/lib/commonjs/apps/mesoscale-explorer/data/state.d.ts +48 -10
  50. package/lib/commonjs/apps/mesoscale-explorer/data/state.js +107 -28
  51. package/lib/commonjs/apps/mesoscale-explorer/data/util.js +2 -3
  52. package/lib/commonjs/apps/mesoscale-explorer/ui/entities.d.ts +23 -1
  53. package/lib/commonjs/apps/mesoscale-explorer/ui/entities.js +302 -30
  54. package/lib/commonjs/apps/mesoscale-explorer/ui/panels.d.ts +1 -0
  55. package/lib/commonjs/apps/mesoscale-explorer/ui/panels.js +39 -2
  56. package/lib/commonjs/apps/mesoscale-explorer/ui/states.d.ts +60 -2
  57. package/lib/commonjs/apps/mesoscale-explorer/ui/states.js +477 -13
  58. package/lib/commonjs/apps/viewer/app.d.ts +12 -5
  59. package/lib/commonjs/apps/viewer/app.js +29 -0
  60. package/lib/commonjs/cli/chem-comp-dict/util.js +7 -7
  61. package/lib/commonjs/cli/cif2bcif/converter.js +1 -2
  62. package/lib/commonjs/cli/cifschema/util/cif-dic.js +2 -3
  63. package/lib/commonjs/cli/cifschema/util/generate.js +1 -2
  64. package/lib/commonjs/cli/cifschema/util/helper.js +1 -2
  65. package/lib/commonjs/cli/cifschema/util/schema.js +9 -10
  66. package/lib/commonjs/cli/state-docs/pd-to-md.js +1 -2
  67. package/lib/commonjs/cli/structure-info/helpers.js +2 -3
  68. package/lib/commonjs/cli/structure-info/model.js +11 -12
  69. package/lib/commonjs/examples/alpha-orbitals/controls.js +1 -2
  70. package/lib/commonjs/examples/basic-wrapper/custom-theme.js +2 -2
  71. package/lib/commonjs/examples/basic-wrapper/superposition.js +3 -3
  72. package/lib/commonjs/examples/domain-annotation-server/mapping.js +1 -2
  73. package/lib/commonjs/examples/lighting/index.d.ts +1 -1
  74. package/lib/commonjs/examples/lighting/index.js +2 -1
  75. package/lib/commonjs/examples/proteopedia-wrapper/coloring.d.ts +5 -20
  76. package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +1 -2
  77. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +1 -2
  78. package/lib/commonjs/examples/task.js +6 -6
  79. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +1 -2
  80. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +4 -5
  81. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -3
  82. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -3
  83. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -3
  84. package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.js +2 -2
  85. package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts +3 -3
  86. package/lib/commonjs/extensions/anvil/algorithm.js +5 -5
  87. package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
  88. package/lib/commonjs/extensions/anvil/behavior.js +2 -2
  89. package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
  90. package/lib/commonjs/extensions/anvil/representation.js +3 -3
  91. package/lib/commonjs/extensions/assembly-symmetry/behavior.d.ts +1 -0
  92. package/lib/commonjs/extensions/assembly-symmetry/behavior.js +3 -3
  93. package/lib/commonjs/extensions/assembly-symmetry/color.d.ts +2 -2
  94. package/lib/commonjs/extensions/assembly-symmetry/color.js +3 -3
  95. package/lib/commonjs/extensions/assembly-symmetry/prop.js +3 -3
  96. package/lib/commonjs/extensions/assembly-symmetry/representation.d.ts +1 -0
  97. package/lib/commonjs/extensions/assembly-symmetry/representation.js +2 -2
  98. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +2 -2
  99. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +3 -3
  100. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  101. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +3 -3
  102. package/lib/commonjs/extensions/dnatco/ntc-tube/behavior.js +2 -2
  103. package/lib/commonjs/extensions/dnatco/ntc-tube/color.js +3 -3
  104. package/lib/commonjs/extensions/dnatco/ntc-tube/representation.d.ts +3 -0
  105. package/lib/commonjs/extensions/dnatco/ntc-tube/representation.js +3 -3
  106. package/lib/commonjs/extensions/g3d/data.js +2 -3
  107. package/lib/commonjs/extensions/g3d/format.d.ts +3 -3
  108. package/lib/commonjs/extensions/g3d/model.js +5 -5
  109. package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts +2 -2
  110. package/lib/commonjs/extensions/geo-export/ui.d.ts +0 -1
  111. package/lib/commonjs/extensions/meshes/examples.js +9 -9
  112. package/lib/commonjs/extensions/meshes/mesh-extension.d.ts +3 -5
  113. package/lib/commonjs/extensions/meshes/mesh-extension.js +2 -2
  114. package/lib/commonjs/extensions/meshes/mesh-streaming/behavior.d.ts +3 -3
  115. package/lib/commonjs/extensions/meshes/mesh-streaming/server-info.d.ts +3 -3
  116. package/lib/commonjs/extensions/meshes/mesh-utils.js +9 -9
  117. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.d.ts +1 -1
  118. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +11 -8
  119. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +3 -3
  120. package/lib/commonjs/extensions/model-export/export.js +2 -2
  121. package/lib/commonjs/extensions/model-export/ui.d.ts +0 -1
  122. package/lib/commonjs/extensions/mp4-export/controls.d.ts +1 -1
  123. package/lib/commonjs/extensions/mp4-export/encoder.js +2 -3
  124. package/lib/commonjs/extensions/mp4-export/ui.d.ts +0 -1
  125. package/lib/commonjs/extensions/mvs/camera.js +4 -5
  126. package/lib/commonjs/extensions/mvs/components/annotation-color-theme.js +2 -2
  127. package/lib/commonjs/extensions/mvs/components/annotation-label/representation.d.ts +32 -34
  128. package/lib/commonjs/extensions/mvs/components/annotation-label/representation.js +2 -2
  129. package/lib/commonjs/extensions/mvs/components/annotation-label/visual.d.ts +16 -16
  130. package/lib/commonjs/extensions/mvs/components/annotation-label/visual.js +2 -2
  131. package/lib/commonjs/extensions/mvs/components/annotation-prop.js +2 -2
  132. package/lib/commonjs/extensions/mvs/components/annotation-structure-component.js +4 -4
  133. package/lib/commonjs/extensions/mvs/components/custom-label/representation.d.ts +32 -32
  134. package/lib/commonjs/extensions/mvs/components/custom-label/representation.js +2 -2
  135. package/lib/commonjs/extensions/mvs/components/custom-label/visual.d.ts +16 -16
  136. package/lib/commonjs/extensions/mvs/components/custom-label/visual.js +2 -2
  137. package/lib/commonjs/extensions/mvs/components/formats.d.ts +6 -6
  138. package/lib/commonjs/extensions/mvs/components/formats.js +2 -2
  139. package/lib/commonjs/extensions/mvs/components/is-mvs-model-prop.js +3 -3
  140. package/lib/commonjs/extensions/mvs/components/multilayer-color-theme.js +3 -3
  141. package/lib/commonjs/extensions/mvs/components/selector.js +3 -3
  142. package/lib/commonjs/extensions/mvs/helpers/indexing.d.ts +2 -2
  143. package/lib/commonjs/extensions/mvs/helpers/label-text.js +1 -2
  144. package/lib/commonjs/extensions/mvs/helpers/param-definition.js +2 -3
  145. package/lib/commonjs/extensions/mvs/helpers/schemas.d.ts +1 -1
  146. package/lib/commonjs/extensions/mvs/helpers/schemas.js +2 -2
  147. package/lib/commonjs/extensions/mvs/helpers/selections.js +6 -7
  148. package/lib/commonjs/extensions/mvs/helpers/utils.d.ts +1 -1
  149. package/lib/commonjs/extensions/mvs/helpers/utils.js +7 -7
  150. package/lib/commonjs/extensions/mvs/load-helpers.d.ts +1 -1
  151. package/lib/commonjs/extensions/mvs/load-helpers.js +17 -17
  152. package/lib/commonjs/extensions/mvs/load.js +1 -2
  153. package/lib/commonjs/extensions/mvs/tree/generic/params-schema.js +8 -8
  154. package/lib/commonjs/extensions/mvs/tree/generic/tree-schema.js +8 -9
  155. package/lib/commonjs/extensions/mvs/tree/generic/tree-utils.js +10 -11
  156. package/lib/commonjs/extensions/mvs/tree/molstar/conversion.js +4 -4
  157. package/lib/commonjs/extensions/mvs/tree/mvs/mvs-builder.d.ts +0 -2
  158. package/lib/commonjs/extensions/mvs/tree/mvs/mvs-builder.js +3 -3
  159. package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +2 -2
  160. package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +2 -2
  161. package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +3 -3
  162. package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +2 -2
  163. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
  164. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +5 -5
  165. package/lib/commonjs/extensions/sb-ncbr/index.d.ts +8 -0
  166. package/lib/commonjs/extensions/sb-ncbr/index.js +14 -1
  167. package/lib/commonjs/extensions/sb-ncbr/partial-charges/color.js +3 -3
  168. package/lib/commonjs/extensions/sb-ncbr/partial-charges/labels.js +1 -2
  169. package/lib/commonjs/extensions/sb-ncbr/partial-charges/property.js +2 -2
  170. package/lib/commonjs/extensions/sb-ncbr/tunnels/actions.d.ts +20 -0
  171. package/lib/commonjs/extensions/sb-ncbr/tunnels/actions.js +89 -0
  172. package/lib/commonjs/extensions/sb-ncbr/tunnels/algorithm.d.ts +26 -0
  173. package/lib/commonjs/extensions/sb-ncbr/tunnels/algorithm.js +473 -0
  174. package/lib/commonjs/extensions/sb-ncbr/tunnels/behavior.d.ts +40 -0
  175. package/lib/commonjs/extensions/sb-ncbr/tunnels/behavior.js +96 -0
  176. package/lib/commonjs/extensions/sb-ncbr/tunnels/data-model.d.ts +146 -0
  177. package/lib/commonjs/extensions/sb-ncbr/tunnels/data-model.js +28 -0
  178. package/lib/commonjs/extensions/sb-ncbr/tunnels/examples.d.ts +12 -0
  179. package/lib/commonjs/extensions/sb-ncbr/tunnels/examples.js +54 -0
  180. package/lib/commonjs/extensions/sb-ncbr/tunnels/props.d.ts +19 -0
  181. package/lib/commonjs/extensions/sb-ncbr/tunnels/props.js +26 -0
  182. package/lib/commonjs/extensions/sb-ncbr/tunnels/representation.d.ts +29 -0
  183. package/lib/commonjs/extensions/sb-ncbr/tunnels/representation.js +99 -0
  184. package/lib/commonjs/extensions/volumes-and-segmentations/entry-root.d.ts +3 -3
  185. package/lib/commonjs/extensions/volumes-and-segmentations/entry-root.js +3 -3
  186. package/lib/commonjs/extensions/volumes-and-segmentations/entry-state.d.ts +3 -3
  187. package/lib/commonjs/extensions/volumes-and-segmentations/external-api.js +2 -3
  188. package/lib/commonjs/extensions/volumes-and-segmentations/global-state.d.ts +3 -3
  189. package/lib/commonjs/extensions/volumes-and-segmentations/helpers.js +6 -6
  190. package/lib/commonjs/extensions/volumes-and-segmentations/ui.d.ts +0 -1
  191. package/lib/commonjs/extensions/zenodo/ui.d.ts +0 -1
  192. package/lib/commonjs/mol-canvas3d/camera/transition.d.ts +1 -1
  193. package/lib/commonjs/mol-canvas3d/camera/transition.js +23 -6
  194. package/lib/commonjs/mol-canvas3d/camera/util.js +3 -4
  195. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +26 -1
  196. package/lib/commonjs/mol-canvas3d/canvas3d.js +4 -0
  197. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.d.ts +1 -6
  198. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +2 -2
  199. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  200. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +2 -2
  201. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  202. package/lib/commonjs/mol-canvas3d/passes/dof.d.ts +34 -0
  203. package/lib/commonjs/mol-canvas3d/passes/dof.js +167 -0
  204. package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +2 -0
  205. package/lib/commonjs/mol-canvas3d/passes/draw.js +31 -8
  206. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +10 -0
  207. package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +2 -1
  208. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +4 -3
  209. package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +9 -0
  210. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -2
  211. package/lib/commonjs/mol-canvas3d/util.js +3 -4
  212. package/lib/commonjs/mol-data/db/column-helpers.js +6 -7
  213. package/lib/commonjs/mol-data/db/column.d.ts +1 -1
  214. package/lib/commonjs/mol-data/generic/hash-set.js +1 -2
  215. package/lib/commonjs/mol-data/generic/linked-list.js +1 -2
  216. package/lib/commonjs/mol-data/int/impl/interval.js +15 -15
  217. package/lib/commonjs/mol-data/int/impl/ordered-set.js +25 -25
  218. package/lib/commonjs/mol-data/int/impl/segmentation.js +7 -7
  219. package/lib/commonjs/mol-data/int/impl/sorted-array.js +31 -31
  220. package/lib/commonjs/mol-data/int/linked-index.js +1 -2
  221. package/lib/commonjs/mol-data/util/array.js +5 -6
  222. package/lib/commonjs/mol-data/util/buckets.js +1 -2
  223. package/lib/commonjs/mol-data/util/combination.js +2 -2
  224. package/lib/commonjs/mol-data/util/equivalence-classes.js +2 -2
  225. package/lib/commonjs/mol-data/util/grouping.js +2 -3
  226. package/lib/commonjs/mol-data/util/hash-functions.js +9 -10
  227. package/lib/commonjs/mol-data/util/sort.js +5 -6
  228. package/lib/commonjs/mol-geo/geometry/base.d.ts +1 -1
  229. package/lib/commonjs/mol-geo/geometry/base.js +3 -3
  230. package/lib/commonjs/mol-geo/geometry/clipping-data.js +4 -5
  231. package/lib/commonjs/mol-geo/geometry/color-data.js +4 -5
  232. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +1 -0
  233. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -0
  234. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +1 -0
  235. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -0
  236. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +3 -4
  237. package/lib/commonjs/mol-geo/geometry/emissive-data.js +5 -6
  238. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +1 -1
  239. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  240. package/lib/commonjs/mol-geo/geometry/marker-data.js +3 -4
  241. package/lib/commonjs/mol-geo/geometry/mesh/builder/axes.js +1 -2
  242. package/lib/commonjs/mol-geo/geometry/mesh/builder/box.js +2 -3
  243. package/lib/commonjs/mol-geo/geometry/mesh/builder/cylinder.js +4 -5
  244. package/lib/commonjs/mol-geo/geometry/mesh/builder/ellipsoid.js +1 -2
  245. package/lib/commonjs/mol-geo/geometry/mesh/builder/ribbon.js +1 -2
  246. package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +1 -2
  247. package/lib/commonjs/mol-geo/geometry/mesh/builder/sphere.js +2 -3
  248. package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +1 -2
  249. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +7 -8
  250. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +1 -0
  251. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -0
  252. package/lib/commonjs/mol-geo/geometry/overpaint-data.js +4 -5
  253. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  254. package/lib/commonjs/mol-geo/geometry/size-data.js +9 -9
  255. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +1 -0
  256. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -0
  257. package/lib/commonjs/mol-geo/geometry/substance-data.js +4 -5
  258. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +3 -3
  259. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +7 -7
  260. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +1 -0
  261. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -0
  262. package/lib/commonjs/mol-geo/geometry/transform-data.js +4 -5
  263. package/lib/commonjs/mol-geo/geometry/transparency-data.js +5 -6
  264. package/lib/commonjs/mol-geo/primitive/box.js +3 -4
  265. package/lib/commonjs/mol-geo/primitive/cage.js +3 -4
  266. package/lib/commonjs/mol-geo/primitive/circle.js +2 -2
  267. package/lib/commonjs/mol-geo/primitive/cylinder.js +2 -2
  268. package/lib/commonjs/mol-geo/primitive/dodecahedron.js +3 -3
  269. package/lib/commonjs/mol-geo/primitive/icosahedron.js +2 -3
  270. package/lib/commonjs/mol-geo/primitive/octahedron.js +4 -4
  271. package/lib/commonjs/mol-geo/primitive/plane.js +2 -3
  272. package/lib/commonjs/mol-geo/primitive/polygon.js +1 -2
  273. package/lib/commonjs/mol-geo/primitive/polyhedron.js +2 -2
  274. package/lib/commonjs/mol-geo/primitive/primitive.js +4 -5
  275. package/lib/commonjs/mol-geo/primitive/prism.js +11 -11
  276. package/lib/commonjs/mol-geo/primitive/pyramid.js +6 -7
  277. package/lib/commonjs/mol-geo/primitive/sphere.js +2 -3
  278. package/lib/commonjs/mol-geo/primitive/spiked-ball.js +1 -2
  279. package/lib/commonjs/mol-geo/primitive/star.js +2 -2
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  1115. package/lib/mol-plugin-state/objects.d.ts +97 -97
  1116. package/lib/mol-plugin-state/transforms/data.d.ts +10 -1
  1117. package/lib/mol-plugin-state/transforms/data.js +30 -1
  1118. package/lib/mol-plugin-state/transforms/representation.d.ts +6 -0
  1119. package/lib/mol-plugin-ui/base.js +2 -1
  1120. package/lib/mol-plugin-ui/controls/icons.d.ts +5 -0
  1121. package/lib/mol-plugin-ui/controls/icons.js +10 -0
  1122. package/lib/mol-plugin-ui/controls/parameters.d.ts +3 -3
  1123. package/lib/mol-plugin-ui/controls.js +1 -1
  1124. package/lib/mol-plugin-ui/left-panel.d.ts +0 -1
  1125. package/lib/mol-plugin-ui/plugin.js +3 -2
  1126. package/lib/mol-plugin-ui/skin/base/components/controls.scss +6 -0
  1127. package/lib/mol-plugin-ui/spec.d.ts +10 -10
  1128. package/lib/mol-plugin-ui/spec.js +1 -1
  1129. package/lib/mol-plugin-ui/state/apply-action.d.ts +1 -1
  1130. package/lib/mol-plugin-ui/state/update-transform.d.ts +1 -1
  1131. package/lib/mol-plugin-ui/structure/quick-styles.d.ts +2 -1
  1132. package/lib/mol-plugin-ui/structure/quick-styles.js +5 -2
  1133. package/lib/mol-plugin-ui/structure/selection.d.ts +2 -2
  1134. package/lib/mol-plugin-ui/viewport/simple-settings.js +3 -0
  1135. package/lib/mol-repr/representation.d.ts +3 -3
  1136. package/lib/mol-repr/shape/loci/angle.d.ts +1 -0
  1137. package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
  1138. package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
  1139. package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
  1140. package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
  1141. package/lib/mol-repr/structure/complex-visual.d.ts +5 -0
  1142. package/lib/mol-repr/structure/params.d.ts +5 -0
  1143. package/lib/mol-repr/structure/registry.d.ts +11 -0
  1144. package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
  1145. package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  1146. package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  1147. package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
  1148. package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  1149. package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  1150. package/lib/mol-repr/structure/representation/gaussian-volume.d.ts +3 -0
  1151. package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  1152. package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
  1153. package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
  1154. package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
  1155. package/lib/mol-repr/structure/units-visual.d.ts +5 -0
  1156. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  1157. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  1158. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  1159. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  1160. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  1161. package/lib/mol-repr/structure/visual/element-sphere.d.ts +4 -0
  1162. package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  1163. package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -0
  1164. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +4 -0
  1165. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  1166. package/lib/mol-repr/structure/visual/nucleotide-atomic-bond.d.ts +2 -0
  1167. package/lib/mol-repr/structure/visual/nucleotide-atomic-element.d.ts +2 -0
  1168. package/lib/mol-repr/structure/visual/nucleotide-atomic-ring-fill.d.ts +1 -0
  1169. package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  1170. package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  1171. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  1172. package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  1173. package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  1174. package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  1175. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  1176. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  1177. package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  1178. package/lib/mol-repr/structure/visual/util/nucleotide.d.ts +60 -60
  1179. package/lib/mol-repr/volume/direct-volume.d.ts +48 -45
  1180. package/lib/mol-repr/volume/isosurface.d.ts +95 -90
  1181. package/lib/mol-repr/volume/registry.d.ts +63 -60
  1182. package/lib/mol-repr/volume/segment.d.ts +80 -75
  1183. package/lib/mol-repr/volume/slice.d.ts +45 -45
  1184. package/lib/mol-script/language/symbol-table/core.d.ts +1 -1
  1185. package/lib/mol-state/object.d.ts +4 -4
  1186. package/lib/mol-state/state.d.ts +4 -4
  1187. package/lib/mol-state/transform.d.ts +1 -1
  1188. package/lib/mol-state/transformer.d.ts +1 -1
  1189. package/lib/mol-task/util/scheduler.d.ts +0 -1
  1190. package/lib/mol-theme/color/atom-id.d.ts +2 -2
  1191. package/lib/mol-theme/color/chain-id.d.ts +2 -2
  1192. package/lib/mol-theme/color/element-index.d.ts +2 -2
  1193. package/lib/mol-theme/color/entity-id.d.ts +2 -2
  1194. package/lib/mol-theme/color/entity-source.d.ts +2 -2
  1195. package/lib/mol-theme/color/external-volume.d.ts +2 -2
  1196. package/lib/mol-theme/color/model-index.d.ts +2 -2
  1197. package/lib/mol-theme/color/operator-hkl.d.ts +2 -2
  1198. package/lib/mol-theme/color/operator-name.d.ts +2 -2
  1199. package/lib/mol-theme/color/polymer-id.d.ts +2 -2
  1200. package/lib/mol-theme/color/polymer-index.d.ts +2 -2
  1201. package/lib/mol-theme/color/structure-index.d.ts +2 -2
  1202. package/lib/mol-theme/color/trajectory-index.d.ts +2 -2
  1203. package/lib/mol-theme/color/unit-index.d.ts +2 -2
  1204. package/lib/mol-theme/color/volume-segment.d.ts +2 -2
  1205. package/lib/mol-theme/color.d.ts +16 -16
  1206. package/lib/mol-theme/theme.d.ts +3 -3
  1207. package/lib/mol-util/color/palette.d.ts +4 -3
  1208. package/lib/mol-util/color/scale.d.ts +2 -1
  1209. package/lib/mol-util/data-source.d.ts +0 -1
  1210. package/lib/mol-util/nodejs-shims.d.ts +1 -1
  1211. package/lib/servers/model/config.d.ts +4 -4
  1212. package/lib/servers/model/utils/tar.d.ts +0 -1
  1213. package/lib/servers/volume/common/binary-schema.d.ts +0 -1
  1214. package/lib/servers/volume/common/data-format.d.ts +0 -1
  1215. package/lib/servers/volume/config.d.ts +1 -5
  1216. package/package.json +18 -16
@@ -23,24 +23,24 @@ export declare function SegmentVisual(materialId: number, volume: Volume, key: n
23
23
  isEssential: boolean;
24
24
  type: "select";
25
25
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
26
- cycle?: boolean | undefined;
27
- isOptional?: boolean | undefined;
26
+ cycle?: boolean;
27
+ isOptional?: boolean;
28
28
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
29
- label?: string | undefined;
30
- description?: string | undefined;
31
- legend?: import("../../mol-util/legend").Legend | undefined;
29
+ label?: string;
30
+ description?: string;
31
+ legend?: import("../../mol-util/legend").Legend;
32
32
  fieldLabels?: {
33
33
  [name: string]: string;
34
- } | undefined;
35
- isHidden?: boolean | undefined;
36
- shortLabel?: boolean | undefined;
37
- twoColumns?: boolean | undefined;
38
- category?: string | undefined;
39
- hideIf?: ((currentGroup: any) => boolean) | undefined;
40
- help?: ((value: any) => {
41
- description?: string | undefined;
42
- legend?: import("../../mol-util/legend").Legend | undefined;
43
- }) | undefined;
34
+ };
35
+ isHidden?: boolean;
36
+ shortLabel?: boolean;
37
+ twoColumns?: boolean;
38
+ category?: string;
39
+ hideIf?: (currentGroup: any) => boolean;
40
+ help?: (value: any) => {
41
+ description?: string;
42
+ legend?: import("../../mol-util/legend").Legend;
43
+ };
44
44
  };
45
45
  tryUseGpu: PD.BooleanParam;
46
46
  segments: PD.Converted<number[], string[]>;
@@ -48,6 +48,7 @@ export declare function SegmentVisual(materialId: number, volume: Volume, key: n
48
48
  flipSided: PD.BooleanParam;
49
49
  flatShaded: PD.BooleanParam;
50
50
  ignoreLight: PD.BooleanParam;
51
+ celShaded: PD.BooleanParam;
51
52
  xrayShaded: PD.Select<boolean | "inverted">;
52
53
  transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
53
54
  bumpFrequency: PD.Numeric;
@@ -81,24 +82,24 @@ export declare const SegmentMeshParams: {
81
82
  isEssential: boolean;
82
83
  type: "select";
83
84
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
84
- cycle?: boolean | undefined;
85
- isOptional?: boolean | undefined;
85
+ cycle?: boolean;
86
+ isOptional?: boolean;
86
87
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
87
- label?: string | undefined;
88
- description?: string | undefined;
89
- legend?: import("../../mol-util/legend").Legend | undefined;
88
+ label?: string;
89
+ description?: string;
90
+ legend?: import("../../mol-util/legend").Legend;
90
91
  fieldLabels?: {
91
92
  [name: string]: string;
92
- } | undefined;
93
- isHidden?: boolean | undefined;
94
- shortLabel?: boolean | undefined;
95
- twoColumns?: boolean | undefined;
96
- category?: string | undefined;
97
- hideIf?: ((currentGroup: any) => boolean) | undefined;
98
- help?: ((value: any) => {
99
- description?: string | undefined;
100
- legend?: import("../../mol-util/legend").Legend | undefined;
101
- }) | undefined;
93
+ };
94
+ isHidden?: boolean;
95
+ shortLabel?: boolean;
96
+ twoColumns?: boolean;
97
+ category?: string;
98
+ hideIf?: (currentGroup: any) => boolean;
99
+ help?: (value: any) => {
100
+ description?: string;
101
+ legend?: import("../../mol-util/legend").Legend;
102
+ };
102
103
  };
103
104
  tryUseGpu: PD.BooleanParam;
104
105
  segments: PD.Converted<number[], string[]>;
@@ -106,6 +107,7 @@ export declare const SegmentMeshParams: {
106
107
  flipSided: PD.BooleanParam;
107
108
  flatShaded: PD.BooleanParam;
108
109
  ignoreLight: PD.BooleanParam;
110
+ celShaded: PD.BooleanParam;
109
111
  xrayShaded: PD.Select<boolean | "inverted">;
110
112
  transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
111
113
  bumpFrequency: PD.Numeric;
@@ -142,24 +144,24 @@ export declare const SegmentParams: {
142
144
  isEssential: boolean;
143
145
  type: "select";
144
146
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
145
- cycle?: boolean | undefined;
146
- isOptional?: boolean | undefined;
147
+ cycle?: boolean;
148
+ isOptional?: boolean;
147
149
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
148
- label?: string | undefined;
149
- description?: string | undefined;
150
- legend?: import("../../mol-util/legend").Legend | undefined;
150
+ label?: string;
151
+ description?: string;
152
+ legend?: import("../../mol-util/legend").Legend;
151
153
  fieldLabels?: {
152
154
  [name: string]: string;
153
- } | undefined;
154
- isHidden?: boolean | undefined;
155
- shortLabel?: boolean | undefined;
156
- twoColumns?: boolean | undefined;
157
- category?: string | undefined;
158
- hideIf?: ((currentGroup: any) => boolean) | undefined;
159
- help?: ((value: any) => {
160
- description?: string | undefined;
161
- legend?: import("../../mol-util/legend").Legend | undefined;
162
- }) | undefined;
155
+ };
156
+ isHidden?: boolean;
157
+ shortLabel?: boolean;
158
+ twoColumns?: boolean;
159
+ category?: string;
160
+ hideIf?: (currentGroup: any) => boolean;
161
+ help?: (value: any) => {
162
+ description?: string;
163
+ legend?: import("../../mol-util/legend").Legend;
164
+ };
163
165
  };
164
166
  tryUseGpu: PD.BooleanParam;
165
167
  segments: PD.Converted<number[], string[]>;
@@ -167,6 +169,7 @@ export declare const SegmentParams: {
167
169
  flipSided: PD.BooleanParam;
168
170
  flatShaded: PD.BooleanParam;
169
171
  ignoreLight: PD.BooleanParam;
172
+ celShaded: PD.BooleanParam;
170
173
  xrayShaded: PD.Select<boolean | "inverted">;
171
174
  transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
172
175
  bumpAmplitude: PD.Numeric;
@@ -200,24 +203,24 @@ export declare function getSegmentParams(ctx: ThemeRegistryContext, volume: Volu
200
203
  isEssential: boolean;
201
204
  type: "select";
202
205
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
203
- cycle?: boolean | undefined;
204
- isOptional?: boolean | undefined;
206
+ cycle?: boolean;
207
+ isOptional?: boolean;
205
208
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
206
- label?: string | undefined;
207
- description?: string | undefined;
208
- legend?: import("../../mol-util/legend").Legend | undefined;
209
+ label?: string;
210
+ description?: string;
211
+ legend?: import("../../mol-util/legend").Legend;
209
212
  fieldLabels?: {
210
213
  [name: string]: string;
211
- } | undefined;
212
- isHidden?: boolean | undefined;
213
- shortLabel?: boolean | undefined;
214
- twoColumns?: boolean | undefined;
215
- category?: string | undefined;
216
- hideIf?: ((currentGroup: any) => boolean) | undefined;
217
- help?: ((value: any) => {
218
- description?: string | undefined;
219
- legend?: import("../../mol-util/legend").Legend | undefined;
220
- }) | undefined;
214
+ };
215
+ isHidden?: boolean;
216
+ shortLabel?: boolean;
217
+ twoColumns?: boolean;
218
+ category?: string;
219
+ hideIf?: (currentGroup: any) => boolean;
220
+ help?: (value: any) => {
221
+ description?: string;
222
+ legend?: import("../../mol-util/legend").Legend;
223
+ };
221
224
  };
222
225
  tryUseGpu: PD.BooleanParam;
223
226
  segments: PD.Converted<number[], string[]>;
@@ -225,6 +228,7 @@ export declare function getSegmentParams(ctx: ThemeRegistryContext, volume: Volu
225
228
  flipSided: PD.BooleanParam;
226
229
  flatShaded: PD.BooleanParam;
227
230
  ignoreLight: PD.BooleanParam;
231
+ celShaded: PD.BooleanParam;
228
232
  xrayShaded: PD.Select<boolean | "inverted">;
229
233
  transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
230
234
  bumpAmplitude: PD.Numeric;
@@ -259,24 +263,24 @@ export declare const SegmentRepresentationProvider: VolumeRepresentationProvider
259
263
  isEssential: boolean;
260
264
  type: "select";
261
265
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
262
- cycle?: boolean | undefined;
263
- isOptional?: boolean | undefined;
266
+ cycle?: boolean;
267
+ isOptional?: boolean;
264
268
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
265
- label?: string | undefined;
266
- description?: string | undefined;
267
- legend?: import("../../mol-util/legend").Legend | undefined;
269
+ label?: string;
270
+ description?: string;
271
+ legend?: import("../../mol-util/legend").Legend;
268
272
  fieldLabels?: {
269
273
  [name: string]: string;
270
- } | undefined;
271
- isHidden?: boolean | undefined;
272
- shortLabel?: boolean | undefined;
273
- twoColumns?: boolean | undefined;
274
- category?: string | undefined;
275
- hideIf?: ((currentGroup: any) => boolean) | undefined;
276
- help?: ((value: any) => {
277
- description?: string | undefined;
278
- legend?: import("../../mol-util/legend").Legend | undefined;
279
- }) | undefined;
274
+ };
275
+ isHidden?: boolean;
276
+ shortLabel?: boolean;
277
+ twoColumns?: boolean;
278
+ category?: string;
279
+ hideIf?: (currentGroup: any) => boolean;
280
+ help?: (value: any) => {
281
+ description?: string;
282
+ legend?: import("../../mol-util/legend").Legend;
283
+ };
280
284
  };
281
285
  tryUseGpu: PD.BooleanParam;
282
286
  segments: PD.Converted<number[], string[]>;
@@ -284,6 +288,7 @@ export declare const SegmentRepresentationProvider: VolumeRepresentationProvider
284
288
  flipSided: PD.BooleanParam;
285
289
  flatShaded: PD.BooleanParam;
286
290
  ignoreLight: PD.BooleanParam;
291
+ celShaded: PD.BooleanParam;
287
292
  xrayShaded: PD.Select<boolean | "inverted">;
288
293
  transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
289
294
  bumpAmplitude: PD.Numeric;
@@ -5,7 +5,14 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.SegmentRepresentationProvider = exports.SegmentRepresentation = exports.getSegmentParams = exports.SegmentParams = exports.SegmentTextureMeshVisual = exports.SegmentMeshVisual = exports.SegmentMeshParams = exports.createVolumeSegmentMesh = exports.eachSegment = exports.SegmentVisual = exports.VolumeSegmentParams = void 0;
8
+ exports.SegmentRepresentationProvider = exports.SegmentParams = exports.SegmentMeshParams = exports.VolumeSegmentParams = void 0;
9
+ exports.SegmentVisual = SegmentVisual;
10
+ exports.eachSegment = eachSegment;
11
+ exports.createVolumeSegmentMesh = createVolumeSegmentMesh;
12
+ exports.SegmentMeshVisual = SegmentMeshVisual;
13
+ exports.SegmentTextureMeshVisual = SegmentTextureMeshVisual;
14
+ exports.getSegmentParams = getSegmentParams;
15
+ exports.SegmentRepresentation = SegmentRepresentation;
9
16
  const param_definition_1 = require("../../mol-util/param-definition");
10
17
  const volume_1 = require("../../mol-model/volume");
11
18
  const mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
@@ -54,7 +61,6 @@ function SegmentVisual(materialId, volume, key, props, webgl) {
54
61
  }
55
62
  return SegmentMeshVisual(materialId);
56
63
  }
57
- exports.SegmentVisual = SegmentVisual;
58
64
  function getLoci(volume, props) {
59
65
  return volume_1.Volume.Segment.Loci(volume, props.segments);
60
66
  }
@@ -78,7 +84,6 @@ function eachSegment(loci, volume, key, props, apply) {
78
84
  const segments = int_1.SortedArray.ofSingleton(key);
79
85
  return (0, util_1.eachVolumeLoci)(loci, volume, { segments }, apply);
80
86
  }
81
- exports.eachSegment = eachSegment;
82
87
  //
83
88
  function getSegmentCells(set, bbox, cells) {
84
89
  const data = cells.data;
@@ -140,7 +145,6 @@ async function createVolumeSegmentMesh(ctx, volume, key, theme, props, mesh) {
140
145
  surface.setBoundingSphere(volume_1.Volume.Segment.getBoundingSphere(volume, [key]));
141
146
  return surface;
142
147
  }
143
- exports.createVolumeSegmentMesh = createVolumeSegmentMesh;
144
148
  exports.SegmentMeshParams = {
145
149
  ...mesh_1.Mesh.Params,
146
150
  ...texture_mesh_1.TextureMesh.Params,
@@ -166,7 +170,6 @@ function SegmentMeshVisual(materialId) {
166
170
  }
167
171
  }, materialId);
168
172
  }
169
- exports.SegmentMeshVisual = SegmentMeshVisual;
170
173
  //
171
174
  const SegmentTextureName = 'segment-texture';
172
175
  function getSegmentTexture(volume, segment, webgl) {
@@ -241,7 +244,6 @@ function SegmentTextureMeshVisual(materialId) {
241
244
  }
242
245
  }, materialId);
243
246
  }
244
- exports.SegmentTextureMeshVisual = SegmentTextureMeshVisual;
245
247
  //
246
248
  function getSegments(props) {
247
249
  return int_1.SortedArray.ofUnsortedArray(props.segments);
@@ -265,11 +267,9 @@ function getSegmentParams(ctx, volume) {
265
267
  }
266
268
  return p;
267
269
  }
268
- exports.getSegmentParams = getSegmentParams;
269
270
  function SegmentRepresentation(ctx, getParams) {
270
271
  return representation_2.Representation.createMulti('Segment', ctx, getParams, representation_2.Representation.StateBuilder, SegmentVisuals);
271
272
  }
272
- exports.SegmentRepresentation = SegmentRepresentation;
273
273
  exports.SegmentRepresentationProvider = (0, representation_1.VolumeRepresentationProvider)({
274
274
  name: 'segment',
275
275
  label: 'Segment',
@@ -16,24 +16,24 @@ export declare const SliceParams: {
16
16
  isEssential: boolean;
17
17
  type: "select";
18
18
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
19
- cycle?: boolean | undefined;
20
- isOptional?: boolean | undefined;
19
+ cycle?: boolean;
20
+ isOptional?: boolean;
21
21
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
22
- label?: string | undefined;
23
- description?: string | undefined;
24
- legend?: import("../../mol-util/legend").Legend | undefined;
22
+ label?: string;
23
+ description?: string;
24
+ legend?: import("../../mol-util/legend").Legend;
25
25
  fieldLabels?: {
26
26
  [name: string]: string;
27
- } | undefined;
28
- isHidden?: boolean | undefined;
29
- shortLabel?: boolean | undefined;
30
- twoColumns?: boolean | undefined;
31
- category?: string | undefined;
32
- hideIf?: ((currentGroup: any) => boolean) | undefined;
33
- help?: ((value: any) => {
34
- description?: string | undefined;
35
- legend?: import("../../mol-util/legend").Legend | undefined;
36
- }) | undefined;
27
+ };
28
+ isHidden?: boolean;
29
+ shortLabel?: boolean;
30
+ twoColumns?: boolean;
31
+ category?: string;
32
+ hideIf?: (currentGroup: any) => boolean;
33
+ help?: (value: any) => {
34
+ description?: string;
35
+ legend?: import("../../mol-util/legend").Legend;
36
+ };
37
37
  };
38
38
  dimension: PD.Mapped<PD.NamedParams<number, "x"> | PD.NamedParams<number, "y"> | PD.NamedParams<number, "z">>;
39
39
  isoValue: PD.Conditioned<Readonly<{
@@ -87,24 +87,24 @@ export declare function getSliceParams(ctx: ThemeRegistryContext, volume: Volume
87
87
  isEssential: boolean;
88
88
  type: "select";
89
89
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
90
- cycle?: boolean | undefined;
91
- isOptional?: boolean | undefined;
90
+ cycle?: boolean;
91
+ isOptional?: boolean;
92
92
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
93
- label?: string | undefined;
94
- description?: string | undefined;
95
- legend?: import("../../mol-util/legend").Legend | undefined;
93
+ label?: string;
94
+ description?: string;
95
+ legend?: import("../../mol-util/legend").Legend;
96
96
  fieldLabels?: {
97
97
  [name: string]: string;
98
- } | undefined;
99
- isHidden?: boolean | undefined;
100
- shortLabel?: boolean | undefined;
101
- twoColumns?: boolean | undefined;
102
- category?: string | undefined;
103
- hideIf?: ((currentGroup: any) => boolean) | undefined;
104
- help?: ((value: any) => {
105
- description?: string | undefined;
106
- legend?: import("../../mol-util/legend").Legend | undefined;
107
- }) | undefined;
98
+ };
99
+ isHidden?: boolean;
100
+ shortLabel?: boolean;
101
+ twoColumns?: boolean;
102
+ category?: string;
103
+ hideIf?: (currentGroup: any) => boolean;
104
+ help?: (value: any) => {
105
+ description?: string;
106
+ legend?: import("../../mol-util/legend").Legend;
107
+ };
108
108
  };
109
109
  dimension: PD.Mapped<PD.NamedParams<number, "x"> | PD.NamedParams<number, "y"> | PD.NamedParams<number, "z">>;
110
110
  isoValue: PD.Conditioned<Readonly<{
@@ -159,24 +159,24 @@ export declare const SliceRepresentationProvider: VolumeRepresentationProvider<{
159
159
  isEssential: boolean;
160
160
  type: "select";
161
161
  options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
162
- cycle?: boolean | undefined;
163
- isOptional?: boolean | undefined;
162
+ cycle?: boolean;
163
+ isOptional?: boolean;
164
164
  defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
165
- label?: string | undefined;
166
- description?: string | undefined;
167
- legend?: import("../../mol-util/legend").Legend | undefined;
165
+ label?: string;
166
+ description?: string;
167
+ legend?: import("../../mol-util/legend").Legend;
168
168
  fieldLabels?: {
169
169
  [name: string]: string;
170
- } | undefined;
171
- isHidden?: boolean | undefined;
172
- shortLabel?: boolean | undefined;
173
- twoColumns?: boolean | undefined;
174
- category?: string | undefined;
175
- hideIf?: ((currentGroup: any) => boolean) | undefined;
176
- help?: ((value: any) => {
177
- description?: string | undefined;
178
- legend?: import("../../mol-util/legend").Legend | undefined;
179
- }) | undefined;
170
+ };
171
+ isHidden?: boolean;
172
+ shortLabel?: boolean;
173
+ twoColumns?: boolean;
174
+ category?: string;
175
+ hideIf?: (currentGroup: any) => boolean;
176
+ help?: (value: any) => {
177
+ description?: string;
178
+ legend?: import("../../mol-util/legend").Legend;
179
+ };
180
180
  };
181
181
  dimension: PD.Mapped<PD.NamedParams<number, "x"> | PD.NamedParams<number, "y"> | PD.NamedParams<number, "z">>;
182
182
  isoValue: PD.Conditioned<Readonly<{
@@ -5,7 +5,11 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.SliceRepresentationProvider = exports.SliceRepresentation = exports.SliceVisual = exports.getSliceParams = exports.SliceParams = exports.createImage = void 0;
8
+ exports.SliceRepresentationProvider = exports.SliceParams = void 0;
9
+ exports.createImage = createImage;
10
+ exports.getSliceParams = getSliceParams;
11
+ exports.SliceVisual = SliceVisual;
12
+ exports.SliceRepresentation = SliceRepresentation;
9
13
  const param_definition_1 = require("../../mol-util/param-definition");
10
14
  const image_1 = require("../../mol-geo/geometry/image/image");
11
15
  const volume_1 = require("../../mol-model/volume");
@@ -53,7 +57,6 @@ async function createImage(ctx, volume, key, theme, props, image) {
53
57
  (0, util_1.transformPositionArray)(transform, corners, 0, 4);
54
58
  return image_1.Image.create(imageTexture, corners, groupTexture, image);
55
59
  }
56
- exports.createImage = createImage;
57
60
  function getSliceInfo(grid, props) {
58
61
  const { dimension: { name: dim, params: index } } = props;
59
62
  const { space } = grid.cells;
@@ -159,7 +162,6 @@ function getSliceParams(ctx, volume) {
159
162
  p.isoValue = volume_1.Volume.createIsoValueParam(volume_1.Volume.IsoValue.absolute(volume.grid.stats.min), volume.grid.stats);
160
163
  return p;
161
164
  }
162
- exports.getSliceParams = getSliceParams;
163
165
  function SliceVisual(materialId) {
164
166
  return (0, representation_1.VolumeVisual)({
165
167
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.SliceParams),
@@ -184,7 +186,6 @@ function SliceVisual(materialId) {
184
186
  }
185
187
  }, materialId);
186
188
  }
187
- exports.SliceVisual = SliceVisual;
188
189
  function updateRenderableState(state, props) {
189
190
  image_1.Image.Utils.updateRenderableState(state, props);
190
191
  state.opaque = false;
@@ -193,7 +194,6 @@ function updateRenderableState(state, props) {
193
194
  function SliceRepresentation(ctx, getParams) {
194
195
  return (0, representation_1.VolumeRepresentation)('Slice', ctx, getParams, SliceVisual, getLoci);
195
196
  }
196
- exports.SliceRepresentation = SliceRepresentation;
197
197
  exports.SliceRepresentationProvider = (0, representation_1.VolumeRepresentationProvider)({
198
198
  name: 'slice',
199
199
  label: 'Slice',
@@ -5,7 +5,11 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.createSegmentTexture2d = exports.createVolumeTexture3d = exports.createVolumeTexture2d = exports.getVolumeTexture2dLayout = exports.eachVolumeLoci = void 0;
8
+ exports.eachVolumeLoci = eachVolumeLoci;
9
+ exports.getVolumeTexture2dLayout = getVolumeTexture2dLayout;
10
+ exports.createVolumeTexture2d = createVolumeTexture2d;
11
+ exports.createVolumeTexture3d = createVolumeTexture3d;
12
+ exports.createSegmentTexture2d = createSegmentTexture2d;
9
13
  const volume_1 = require("../../mol-model/volume");
10
14
  const int_1 = require("../../mol-data/int");
11
15
  const common_1 = require("../../mol-math/linear-algebra/3d/common");
@@ -92,7 +96,6 @@ function eachVolumeLoci(loci, volume, props, apply) {
92
96
  }
93
97
  return changed;
94
98
  }
95
- exports.eachVolumeLoci = eachVolumeLoci;
96
99
  //
97
100
  function getVolumeTexture2dLayout(dim, padding = 0) {
98
101
  const area = dim[0] * dim[1] * dim[2];
@@ -113,7 +116,6 @@ function getVolumeTexture2dLayout(dim, padding = 0) {
113
116
  }
114
117
  return { width, height, columns, rows, powerOfTwoSize: height < powerOfTwoSize ? powerOfTwoSize : powerOfTwoSize * 2 };
115
118
  }
116
- exports.getVolumeTexture2dLayout = getVolumeTexture2dLayout;
117
119
  function createVolumeTexture2d(volume, variant, padding = 0) {
118
120
  const { cells: { space, data }, stats: { max, min } } = volume.grid;
119
121
  const dim = space.dimensions;
@@ -160,7 +162,6 @@ function createVolumeTexture2d(volume, variant, padding = 0) {
160
162
  }
161
163
  return textureImage;
162
164
  }
163
- exports.createVolumeTexture2d = createVolumeTexture2d;
164
165
  function createVolumeTexture3d(volume) {
165
166
  const { cells: { space, data }, stats: { max, min } } = volume.grid;
166
167
  const [width, height, depth] = space.dimensions;
@@ -190,7 +191,6 @@ function createVolumeTexture3d(volume) {
190
191
  }
191
192
  return textureVolume;
192
193
  }
193
- exports.createVolumeTexture3d = createVolumeTexture3d;
194
194
  function createSegmentTexture2d(volume, set, bbox, padding = 0) {
195
195
  const data = volume.grid.cells.data;
196
196
  const dim = geometry_1.Box3D.size((0, vec3_1.Vec3)(), bbox);
@@ -227,4 +227,3 @@ function createSegmentTexture2d(volume, set, bbox, padding = 0) {
227
227
  }
228
228
  return textureImage;
229
229
  }
230
- exports.createSegmentTexture2d = createSegmentTexture2d;
@@ -5,7 +5,7 @@
5
5
  * @author David Sehnal <david.sehnal@gmail.com>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.formatMolScript = void 0;
8
+ exports.formatMolScript = formatMolScript;
9
9
  const expression_1 = require("./expression");
10
10
  const { isLiteral, isSymbol, isArgumentsArray } = expression_1.Expression;
11
11
  class Writer {
@@ -123,4 +123,3 @@ function formatMolScript(e) {
123
123
  _format(e, writer);
124
124
  return writer.getStr();
125
125
  }
126
- exports.formatMolScript = formatMolScript;
@@ -5,22 +5,21 @@
5
5
  * @author David Sehnal <david.sehnal@gmail.com>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.symbolList = exports.normalizeTable = exports.symbol = void 0;
8
+ exports.symbol = symbol;
9
+ exports.normalizeTable = normalizeTable;
10
+ exports.symbolList = symbolList;
9
11
  const symbol_1 = require("./symbol");
10
12
  function symbol(args, type, description) {
11
13
  return (0, symbol_1.MSymbol)('', args, type, description);
12
14
  }
13
- exports.symbol = symbol;
14
15
  function normalizeTable(table) {
15
16
  _normalizeTable('', '', table);
16
17
  }
17
- exports.normalizeTable = normalizeTable;
18
18
  function symbolList(table) {
19
19
  const list = [];
20
20
  _symbolList(table, list);
21
21
  return list;
22
22
  }
23
- exports.symbolList = symbolList;
24
23
  function formatKey(key) {
25
24
  const regex = /([a-z])([A-Z])([a-z]|$)/g;
26
25
  // do this twice because 'xXxX'
@@ -5,7 +5,7 @@
5
5
  * @author David Sehnal <david.sehnal@gmail.com>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.parseMolScript = void 0;
8
+ exports.parseMolScript = parseMolScript;
9
9
  const monadic_parser_1 = require("../../mol-util/monadic-parser");
10
10
  const expression_1 = require("./expression");
11
11
  const builder_1 = require("./builder");
@@ -13,7 +13,6 @@ const type_helpers_1 = require("../../mol-util/type-helpers");
13
13
  function parseMolScript(input) {
14
14
  return Language.parse(input);
15
15
  }
16
- exports.parseMolScript = parseMolScript;
17
16
  var Language;
18
17
  (function (Language) {
19
18
  let ASTNode;
@@ -16,7 +16,7 @@ export declare namespace Types {
16
16
  const Regex: Type.Value<RegExp>;
17
17
  const Set: <T extends Type>(t?: T) => Type.Container<Set<T["@type"]>>;
18
18
  const List: <T extends Type>(t?: T) => Type.Container<List<T["@type"]>>;
19
- const Fn: <T extends Type>(t?: T, alias?: string) => Type.Container<(env: any) => T['@type']>;
19
+ const Fn: <T extends Type>(t?: T, alias?: string) => Type.Container<(env: any) => T["@type"]>;
20
20
  const Flags: <T extends Type>(t: T, alias?: string) => Type.Container<number>;
21
21
  const BitFlags: Type.Container<number>;
22
22
  }
@@ -5,13 +5,16 @@
5
5
  * @author David Sehnal <david.sehnal@gmail.com>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.isSymbol = exports.CustomPropSymbol = exports.MSymbol = exports.Arguments = exports.Argument = void 0;
8
+ exports.Arguments = void 0;
9
+ exports.Argument = Argument;
10
+ exports.MSymbol = MSymbol;
11
+ exports.CustomPropSymbol = CustomPropSymbol;
12
+ exports.isSymbol = isSymbol;
9
13
  const expression_1 = require("./expression");
10
14
  function Argument(type, params) {
11
15
  const { description = void 0, isOptional = false, isRest = false, defaultValue = void 0 } = params || {};
12
16
  return { type, isOptional, isRest, defaultValue, description };
13
17
  }
14
- exports.Argument = Argument;
15
18
  var Arguments;
16
19
  (function (Arguments) {
17
20
  Arguments.None = Dictionary({});
@@ -35,7 +38,6 @@ function MSymbol(name, args, type, description) {
35
38
  symbol.type = type;
36
39
  return symbol;
37
40
  }
38
- exports.MSymbol = MSymbol;
39
41
  function CustomPropSymbol(namespace, name, type, description) {
40
42
  const symbol = function (args) {
41
43
  return expression_1.Expression.Apply(expression_1.Expression.Symbol(symbol.id), args);
@@ -46,9 +48,7 @@ function CustomPropSymbol(namespace, name, type, description) {
46
48
  symbol.type = type;
47
49
  return symbol;
48
50
  }
49
- exports.CustomPropSymbol = CustomPropSymbol;
50
51
  function isSymbol(x) {
51
52
  const s = x;
52
53
  return typeof s === 'function' && !!s.info && !!s.args && typeof s.info.namespace === 'string' && !!s.type;
53
54
  }
54
- exports.isSymbol = isSymbol;
@@ -5,7 +5,8 @@
5
5
  * @author David Sehnal <david.sehnal@gmail.com>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.compile = exports.QuerySymbolRuntime = exports.QueryRuntimeArguments = exports.CompiledQueryFn = exports.QueryCompiledSymbol = exports.QueryCompilerCtx = exports.DefaultQueryRuntimeTable = exports.QueryRuntimeTable = void 0;
8
+ exports.QuerySymbolRuntime = exports.QueryRuntimeArguments = exports.CompiledQueryFn = exports.QueryCompiledSymbol = exports.QueryCompilerCtx = exports.DefaultQueryRuntimeTable = exports.QueryRuntimeTable = void 0;
9
+ exports.compile = compile;
9
10
  const expression_1 = require("../../language/expression");
10
11
  const structure_1 = require("../../../mol-model/structure");
11
12
  class QueryRuntimeTable {
@@ -162,4 +163,3 @@ function compile(expression) {
162
163
  const ctx = new QueryCompilerCtx(exports.DefaultQueryRuntimeTable);
163
164
  return _compile(ctx, expression).fn;
164
165
  }
165
- exports.compile = compile;