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
  280. package/lib/commonjs/mol-geo/primitive/tetrahedron.js +3 -3
  281. package/lib/commonjs/mol-geo/primitive/torus.js +2 -2
  282. package/lib/commonjs/mol-geo/primitive/wedge.js +3 -4
  283. package/lib/commonjs/mol-geo/util/location-iterator.js +3 -4
  284. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +2 -3
  285. package/lib/commonjs/mol-geo/util/marching-cubes/builder.js +2 -3
  286. package/lib/commonjs/mol-geo/util/marching-cubes/tables.js +3 -3
  287. package/lib/commonjs/mol-geo/util.js +7 -8
  288. package/lib/commonjs/mol-gl/compute/grid3d.js +2 -3
  289. package/lib/commonjs/mol-gl/compute/hi-z.js +1 -2
  290. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +1 -2
  291. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +1 -2
  292. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +1 -2
  293. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +2 -3
  294. package/lib/commonjs/mol-gl/compute/marching-cubes/tables.js +2 -3
  295. package/lib/commonjs/mol-gl/compute/util.js +5 -5
  296. package/lib/commonjs/mol-gl/render-object.js +3 -3
  297. package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +1 -0
  298. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -2
  299. package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +1 -0
  300. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -2
  301. package/lib/commonjs/mol-gl/renderable/image.js +2 -2
  302. package/lib/commonjs/mol-gl/renderable/lines.js +2 -2
  303. package/lib/commonjs/mol-gl/renderable/mesh.d.ts +1 -0
  304. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -2
  305. package/lib/commonjs/mol-gl/renderable/points.js +2 -2
  306. package/lib/commonjs/mol-gl/renderable/schema.d.ts +1 -0
  307. package/lib/commonjs/mol-gl/renderable/schema.js +10 -9
  308. package/lib/commonjs/mol-gl/renderable/spheres.d.ts +1 -0
  309. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -2
  310. package/lib/commonjs/mol-gl/renderable/text.js +2 -2
  311. package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +1 -0
  312. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -2
  313. package/lib/commonjs/mol-gl/renderable/util.js +7 -8
  314. package/lib/commonjs/mol-gl/renderable.js +2 -3
  315. package/lib/commonjs/mol-gl/renderer.d.ts +1 -0
  316. package/lib/commonjs/mol-gl/renderer.js +6 -0
  317. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +2 -1
  318. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +57 -24
  319. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
  320. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +1 -0
  321. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
  322. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +6 -0
  323. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +2 -1
  324. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +11 -2
  325. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  326. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -0
  327. package/lib/commonjs/mol-gl/shader/dof.frag.d.ts +7 -0
  328. package/lib/commonjs/mol-gl/shader/dof.frag.js +122 -0
  329. package/lib/commonjs/mol-gl/shader/ssao-blur.frag.d.ts +1 -1
  330. package/lib/commonjs/mol-gl/shader/ssao-blur.frag.js +9 -6
  331. package/lib/commonjs/mol-gl/shader-code.js +4 -4
  332. package/lib/commonjs/mol-gl/webgl/buffer.js +8 -9
  333. package/lib/commonjs/mol-gl/webgl/compat.js +32 -33
  334. package/lib/commonjs/mol-gl/webgl/context.js +7 -7
  335. package/lib/commonjs/mol-gl/webgl/extensions.js +1 -2
  336. package/lib/commonjs/mol-gl/webgl/framebuffer.js +3 -4
  337. package/lib/commonjs/mol-gl/webgl/program.js +2 -3
  338. package/lib/commonjs/mol-gl/webgl/render-item.d.ts +2 -2
  339. package/lib/commonjs/mol-gl/webgl/render-item.js +5 -5
  340. package/lib/commonjs/mol-gl/webgl/render-target.js +2 -3
  341. package/lib/commonjs/mol-gl/webgl/renderbuffer.js +3 -4
  342. package/lib/commonjs/mol-gl/webgl/resources.js +1 -2
  343. package/lib/commonjs/mol-gl/webgl/shader.js +2 -3
  344. package/lib/commonjs/mol-gl/webgl/state.js +1 -2
  345. package/lib/commonjs/mol-gl/webgl/texture.js +13 -14
  346. package/lib/commonjs/mol-gl/webgl/timer.d.ts +1 -1
  347. package/lib/commonjs/mol-gl/webgl/timer.js +10 -4
  348. package/lib/commonjs/mol-gl/webgl/uniform.js +6 -7
  349. package/lib/commonjs/mol-gl/webgl/vertex-array.js +1 -2
  350. package/lib/commonjs/mol-io/common/ascii.js +1 -2
  351. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +2 -3
  352. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +1 -2
  353. package/lib/commonjs/mol-io/common/binary.js +3 -3
  354. package/lib/commonjs/mol-io/common/msgpack/decode.js +1 -2
  355. package/lib/commonjs/mol-io/common/msgpack/encode.js +1 -2
  356. package/lib/commonjs/mol-io/common/simple-buffer.d.ts +0 -1
  357. package/lib/commonjs/mol-io/common/typed-array.js +6 -6
  358. package/lib/commonjs/mol-io/common/utf8.js +3 -4
  359. package/lib/commonjs/mol-io/reader/ccp4/parser.js +6 -7
  360. package/lib/commonjs/mol-io/reader/cif/binary/field.js +1 -2
  361. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +1 -2
  362. package/lib/commonjs/mol-io/reader/cif/data-model.js +8 -8
  363. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +1 -1
  364. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +1 -1
  365. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  366. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +1 -1
  367. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +9 -1
  368. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +9 -1
  369. package/lib/commonjs/mol-io/reader/cif/schema.js +4 -4
  370. package/lib/commonjs/mol-io/reader/cif/text/parser.js +1 -2
  371. package/lib/commonjs/mol-io/reader/common/text/column/fixed.d.ts +1 -1
  372. package/lib/commonjs/mol-io/reader/common/text/column/fixed.js +2 -3
  373. package/lib/commonjs/mol-io/reader/common/text/column/token.d.ts +1 -1
  374. package/lib/commonjs/mol-io/reader/common/text/column/token.js +4 -5
  375. package/lib/commonjs/mol-io/reader/common/text/number-parser.js +6 -6
  376. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +3 -3
  377. package/lib/commonjs/mol-io/reader/csv/data-model.js +3 -3
  378. package/lib/commonjs/mol-io/reader/csv/parser.js +1 -2
  379. package/lib/commonjs/mol-io/reader/cube/parser.js +1 -2
  380. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -3
  381. package/lib/commonjs/mol-io/reader/dsn6/parser.js +6 -6
  382. package/lib/commonjs/mol-io/reader/dx/parser.js +1 -2
  383. package/lib/commonjs/mol-io/reader/gro/parser.js +1 -2
  384. package/lib/commonjs/mol-io/reader/mol/parser.js +6 -7
  385. package/lib/commonjs/mol-io/reader/mol2/parser.js +1 -2
  386. package/lib/commonjs/mol-io/reader/nctraj/parser.js +1 -2
  387. package/lib/commonjs/mol-io/reader/obj/parser.js +1 -2
  388. package/lib/commonjs/mol-io/reader/pdb/parser.js +1 -2
  389. package/lib/commonjs/mol-io/reader/ply/parser.js +1 -2
  390. package/lib/commonjs/mol-io/reader/ply/schema.d.ts +1 -1
  391. package/lib/commonjs/mol-io/reader/ply/schema.js +3 -3
  392. package/lib/commonjs/mol-io/reader/prmtop/parser.js +1 -2
  393. package/lib/commonjs/mol-io/reader/psf/parser.js +1 -2
  394. package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js +4 -5
  395. package/lib/commonjs/mol-io/reader/sdf/parser.js +1 -2
  396. package/lib/commonjs/mol-io/reader/top/parser.js +1 -2
  397. package/lib/commonjs/mol-io/reader/trr/parser.js +1 -2
  398. package/lib/commonjs/mol-io/reader/xtc/parser.js +1 -2
  399. package/lib/commonjs/mol-io/reader/xyz/parser.js +1 -2
  400. package/lib/commonjs/mol-io/writer/cif/encoder/util.js +3 -4
  401. package/lib/commonjs/mol-math/approx.js +24 -25
  402. package/lib/commonjs/mol-math/easing.js +18 -19
  403. package/lib/commonjs/mol-math/geometry/boundary.js +2 -3
  404. package/lib/commonjs/mol-math/geometry/common.js +2 -3
  405. package/lib/commonjs/mol-math/geometry/distance-transform.js +1 -2
  406. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +1 -2
  407. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +4 -5
  408. package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
  409. package/lib/commonjs/mol-math/geometry/instance-grid.js +2 -3
  410. package/lib/commonjs/mol-math/geometry/lookup3d/grid.js +1 -2
  411. package/lib/commonjs/mol-math/geometry/molecular-surface.js +2 -2
  412. package/lib/commonjs/mol-math/geometry/polygon.js +1 -2
  413. package/lib/commonjs/mol-math/geometry/primitives/axes3d.js +1 -2
  414. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +1 -2
  415. package/lib/commonjs/mol-math/geometry/primitives/frustum3d.js +1 -2
  416. package/lib/commonjs/mol-math/geometry/primitives/plane3d.js +1 -2
  417. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +1 -2
  418. package/lib/commonjs/mol-math/geometry/spacegroup/cell.js +1 -2
  419. package/lib/commonjs/mol-math/geometry/spacegroup/tables.js +4 -4
  420. package/lib/commonjs/mol-math/histogram.js +1 -2
  421. package/lib/commonjs/mol-math/interpolate.js +12 -13
  422. package/lib/commonjs/mol-math/linear-algebra/3d/common.js +2 -2
  423. package/lib/commonjs/mol-math/linear-algebra/3d/euler.js +1 -2
  424. package/lib/commonjs/mol-math/linear-algebra/3d/mat3.js +1 -2
  425. package/lib/commonjs/mol-math/linear-algebra/3d/mat4.js +1 -2
  426. package/lib/commonjs/mol-math/linear-algebra/3d/minimize-rmsd.js +2 -1
  427. package/lib/commonjs/mol-math/linear-algebra/3d/quat.js +1 -2
  428. package/lib/commonjs/mol-math/linear-algebra/3d/vec2.js +1 -2
  429. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js +1 -2
  430. package/lib/commonjs/mol-math/linear-algebra/3d/vec4.js +1 -2
  431. package/lib/commonjs/mol-math/linear-algebra/matrix/svd.js +4 -5
  432. package/lib/commonjs/mol-math/misc.js +7 -7
  433. package/lib/commonjs/mol-model/custom-property.js +2 -2
  434. package/lib/commonjs/mol-model/location.js +4 -4
  435. package/lib/commonjs/mol-model/loci.d.ts +1 -1
  436. package/lib/commonjs/mol-model/loci.js +7 -7
  437. package/lib/commonjs/mol-model/sequence/alignment/alignment.d.ts +2 -1
  438. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -2
  439. package/lib/commonjs/mol-model/sequence/alignment/sequence.js +3 -3
  440. package/lib/commonjs/mol-model/sequence/constants.js +3 -4
  441. package/lib/commonjs/mol-model/structure/coordinates/coordinates.js +2 -2
  442. package/lib/commonjs/mol-model/structure/export/categories/atom_site.js +5 -5
  443. package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js +2 -2
  444. package/lib/commonjs/mol-model/structure/export/categories/utils.js +6 -7
  445. package/lib/commonjs/mol-model/structure/export/mmcif.js +3 -3
  446. package/lib/commonjs/mol-model/structure/model/properties/atomic/bonds.js +2 -3
  447. package/lib/commonjs/mol-model/structure/model/properties/atomic/measures.js +4 -4
  448. package/lib/commonjs/mol-model/structure/model/properties/atomic/types.js +14 -14
  449. package/lib/commonjs/mol-model/structure/model/properties/secondary-structure.js +1 -2
  450. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.js +1 -2
  451. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js +1 -2
  452. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js +1 -2
  453. package/lib/commonjs/mol-model/structure/model/properties/utils/coarse-keys.js +1 -2
  454. package/lib/commonjs/mol-model/structure/model/properties/utils/coarse-ranges.js +1 -2
  455. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +1 -1
  456. package/lib/commonjs/mol-model/structure/model/types.d.ts +3 -3
  457. package/lib/commonjs/mol-model/structure/model/types.js +12 -12
  458. package/lib/commonjs/mol-model/structure/model/util.js +2 -3
  459. package/lib/commonjs/mol-model/structure/query/queries/atom-set.js +3 -4
  460. package/lib/commonjs/mol-model/structure/query/queries/combinators.js +2 -3
  461. package/lib/commonjs/mol-model/structure/query/queries/filters.js +7 -8
  462. package/lib/commonjs/mol-model/structure/query/queries/generators.js +9 -9
  463. package/lib/commonjs/mol-model/structure/query/queries/internal.js +7 -8
  464. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +9 -10
  465. package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js +2 -3
  466. package/lib/commonjs/mol-model/structure/query/utils/structure-set.js +5 -6
  467. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -2
  468. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +4 -4
  469. package/lib/commonjs/mol-model/structure/structure/element/loci.js +1 -2
  470. package/lib/commonjs/mol-model/structure/structure/element/util.js +6 -7
  471. package/lib/commonjs/mol-model/structure/structure/properties.d.ts +1 -0
  472. package/lib/commonjs/mol-model/structure/structure/properties.js +1 -0
  473. package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js +6 -6
  474. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +1 -2
  475. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -2
  476. package/lib/commonjs/mol-model/structure/structure/unit/resonance.js +1 -2
  477. package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js +3 -4
  478. package/lib/commonjs/mol-model/structure/structure/util/boundary.js +1 -2
  479. package/lib/commonjs/mol-model/structure/structure/util/lookup3d.js +2 -2
  480. package/lib/commonjs/mol-model/structure/structure/util/polymer.js +6 -7
  481. package/lib/commonjs/mol-model/structure/structure/util/principal-axes.js +2 -3
  482. package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.js +1 -2
  483. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +3 -4
  484. package/lib/commonjs/mol-model/structure/util.js +5 -6
  485. package/lib/commonjs/mol-model/volume/volume.d.ts +6 -6
  486. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +2 -0
  487. package/lib/commonjs/mol-model-formats/shape/ply.js +2 -2
  488. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +1 -2
  489. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +2 -2
  490. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +2 -3
  491. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +1 -2
  492. package/lib/commonjs/mol-model-formats/structure/basic/properties.js +4 -5
  493. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +1 -0
  494. package/lib/commonjs/mol-model-formats/structure/basic/schema.js +2 -2
  495. package/lib/commonjs/mol-model-formats/structure/basic/sequence.js +1 -2
  496. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +1 -2
  497. package/lib/commonjs/mol-model-formats/structure/basic/util.js +2 -3
  498. package/lib/commonjs/mol-model-formats/structure/cif-core.js +2 -2
  499. package/lib/commonjs/mol-model-formats/structure/common/entity.d.ts +1 -0
  500. package/lib/commonjs/mol-model-formats/structure/cube.js +1 -2
  501. package/lib/commonjs/mol-model-formats/structure/dcd.js +1 -2
  502. package/lib/commonjs/mol-model-formats/structure/gro.js +2 -2
  503. package/lib/commonjs/mol-model-formats/structure/mmcif.js +3 -3
  504. package/lib/commonjs/mol-model-formats/structure/mol.js +3 -3
  505. package/lib/commonjs/mol-model-formats/structure/mol2.js +2 -2
  506. package/lib/commonjs/mol-model-formats/structure/nctraj.js +1 -2
  507. package/lib/commonjs/mol-model-formats/structure/pdb/anisotropic.js +3 -4
  508. package/lib/commonjs/mol-model-formats/structure/pdb/assembly.js +3 -4
  509. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js +3 -4
  510. package/lib/commonjs/mol-model-formats/structure/pdb/conect.js +1 -2
  511. package/lib/commonjs/mol-model-formats/structure/pdb/entity.js +2 -3
  512. package/lib/commonjs/mol-model-formats/structure/pdb/header.js +1 -2
  513. package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js +2 -3
  514. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +1 -2
  515. package/lib/commonjs/mol-model-formats/structure/pdb.js +2 -2
  516. package/lib/commonjs/mol-model-formats/structure/prmtop.js +2 -2
  517. package/lib/commonjs/mol-model-formats/structure/property/assembly.js +3 -4
  518. package/lib/commonjs/mol-model-formats/structure/psf.js +2 -2
  519. package/lib/commonjs/mol-model-formats/structure/sdf.js +2 -2
  520. package/lib/commonjs/mol-model-formats/structure/top.js +2 -2
  521. package/lib/commonjs/mol-model-formats/structure/trr.js +1 -2
  522. package/lib/commonjs/mol-model-formats/structure/util.js +2 -3
  523. package/lib/commonjs/mol-model-formats/structure/xtc.js +1 -2
  524. package/lib/commonjs/mol-model-formats/structure/xyz.js +2 -2
  525. package/lib/commonjs/mol-model-formats/volume/ccp4.js +3 -3
  526. package/lib/commonjs/mol-model-formats/volume/cube.js +2 -2
  527. package/lib/commonjs/mol-model-formats/volume/density-server.js +2 -2
  528. package/lib/commonjs/mol-model-formats/volume/dsn6.js +2 -2
  529. package/lib/commonjs/mol-model-formats/volume/dx.js +2 -2
  530. package/lib/commonjs/mol-model-formats/volume/segmentation.js +2 -2
  531. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +1 -2
  532. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +1 -2
  533. package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js +16 -17
  534. package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js +5 -5
  535. package/lib/commonjs/mol-model-props/computed/chemistry/util.js +16 -17
  536. package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +4 -4
  537. package/lib/commonjs/mol-model-props/computed/helix-orientation/helix-orientation.js +1 -2
  538. package/lib/commonjs/mol-model-props/computed/interactions/common.js +4 -4
  539. package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +3 -3
  540. package/lib/commonjs/mol-model-props/computed/interactions/interactions.js +2 -2
  541. package/lib/commonjs/mol-model-props/computed/interactions/refine.js +1 -2
  542. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  543. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +2 -2
  544. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  545. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +2 -2
  546. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +3 -0
  547. package/lib/commonjs/mol-model-props/computed/representations/interactions.js +3 -3
  548. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/backbone-hbonds.js +1 -2
  549. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bends.js +1 -2
  550. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bridges.js +1 -2
  551. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/dihedral-angles.js +1 -2
  552. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/helices.js +1 -2
  553. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/ladders.js +1 -2
  554. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/protein-info.js +1 -2
  555. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/sheets.js +1 -2
  556. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/trace-lookup.js +1 -2
  557. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/turns.js +1 -2
  558. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +2 -2
  559. package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js +3 -3
  560. package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js +3 -3
  561. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js +3 -3
  562. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  563. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js +4 -4
  564. package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.d.ts +2 -2
  565. package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +3 -3
  566. package/lib/commonjs/mol-plugin/animation-loop.d.ts +1 -0
  567. package/lib/commonjs/mol-plugin/behavior/behavior.d.ts +9 -9
  568. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +9 -9
  569. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -3
  570. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +3 -3
  571. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +8 -9
  572. package/lib/commonjs/mol-plugin/behavior/static/camera.js +6 -7
  573. package/lib/commonjs/mol-plugin/behavior/static/misc.js +2 -3
  574. package/lib/commonjs/mol-plugin/behavior/static/representation.js +4 -5
  575. package/lib/commonjs/mol-plugin/behavior/static/state.js +12 -13
  576. package/lib/commonjs/mol-plugin/command.js +2 -2
  577. package/lib/commonjs/mol-plugin/commands.d.ts +23 -87
  578. package/lib/commonjs/mol-plugin/context.d.ts +3 -2
  579. package/lib/commonjs/mol-plugin/context.js +4 -2
  580. package/lib/commonjs/mol-plugin/state.d.ts +7 -7
  581. package/lib/commonjs/mol-plugin/util/headless-screenshot.d.ts +1 -1
  582. package/lib/commonjs/mol-plugin/util/headless-screenshot.js +7 -5
  583. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +1 -1
  584. package/lib/commonjs/mol-plugin/util/viewport-screenshot.js +2 -1
  585. package/lib/commonjs/mol-plugin-state/actions/volume.d.ts +1 -1
  586. package/lib/commonjs/mol-plugin-state/actions/volume.js +4 -12
  587. package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.d.ts +2 -2
  588. package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js +7 -3
  589. package/lib/commonjs/mol-plugin-state/animation/helpers.js +5 -5
  590. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +2 -2
  591. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +4 -4
  592. package/lib/commonjs/mol-plugin-state/formats/provider.js +2 -3
  593. package/lib/commonjs/mol-plugin-state/formats/registry.d.ts +1 -1
  594. package/lib/commonjs/mol-plugin-state/formats/trajectory.d.ts +9 -9
  595. package/lib/commonjs/mol-plugin-state/formats/volume.d.ts +0 -1
  596. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +1 -2
  597. package/lib/commonjs/mol-plugin-state/helpers/structure-component.js +3 -3
  598. package/lib/commonjs/mol-plugin-state/helpers/structure-emissive.js +2 -3
  599. package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js +2 -3
  600. package/lib/commonjs/mol-plugin-state/helpers/structure-representation-params.js +4 -5
  601. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +9 -9
  602. package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js +2 -3
  603. package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js +2 -3
  604. package/lib/commonjs/mol-plugin-state/helpers/volume-representation-params.js +4 -5
  605. package/lib/commonjs/mol-plugin-state/manager/focus-camera/focus-first-residue.js +2 -3
  606. package/lib/commonjs/mol-plugin-state/manager/focus-camera/orient-axes.js +4 -4
  607. package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js +2 -3
  608. package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.d.ts +3 -3
  609. package/lib/commonjs/mol-plugin-state/manager/structure/measurement.d.ts +4 -0
  610. package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy-state.js +2 -3
  611. package/lib/commonjs/mol-plugin-state/objects.d.ts +97 -97
  612. package/lib/commonjs/mol-plugin-state/transforms/data.d.ts +10 -1
  613. package/lib/commonjs/mol-plugin-state/transforms/data.js +31 -2
  614. package/lib/commonjs/mol-plugin-state/transforms/helpers.js +6 -7
  615. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +6 -0
  616. package/lib/commonjs/mol-plugin-state/transforms/shape.js +2 -2
  617. package/lib/commonjs/mol-plugin-ui/base.js +2 -1
  618. package/lib/commonjs/mol-plugin-ui/controls/color.js +3 -3
  619. package/lib/commonjs/mol-plugin-ui/controls/common.js +5 -5
  620. package/lib/commonjs/mol-plugin-ui/controls/icons.d.ts +5 -0
  621. package/lib/commonjs/mol-plugin-ui/controls/icons.js +87 -73
  622. package/lib/commonjs/mol-plugin-ui/controls/legend.js +2 -2
  623. package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts +3 -3
  624. package/lib/commonjs/mol-plugin-ui/controls/parameters.js +2 -2
  625. package/lib/commonjs/mol-plugin-ui/controls.js +3 -3
  626. package/lib/commonjs/mol-plugin-ui/hooks/use-behavior.js +1 -2
  627. package/lib/commonjs/mol-plugin-ui/index.js +1 -2
  628. package/lib/commonjs/mol-plugin-ui/left-panel.d.ts +0 -1
  629. package/lib/commonjs/mol-plugin-ui/plugin.js +5 -4
  630. package/lib/commonjs/mol-plugin-ui/react18.js +1 -2
  631. package/lib/commonjs/mol-plugin-ui/sequence.js +8 -8
  632. package/lib/commonjs/mol-plugin-ui/spec.d.ts +10 -10
  633. package/lib/commonjs/mol-plugin-ui/spec.js +1 -1
  634. package/lib/commonjs/mol-plugin-ui/state/apply-action.d.ts +1 -1
  635. package/lib/commonjs/mol-plugin-ui/state/update-transform.d.ts +1 -1
  636. package/lib/commonjs/mol-plugin-ui/structure/quick-styles.d.ts +2 -1
  637. package/lib/commonjs/mol-plugin-ui/structure/quick-styles.js +5 -2
  638. package/lib/commonjs/mol-plugin-ui/structure/selection.d.ts +2 -2
  639. package/lib/commonjs/mol-plugin-ui/task.js +2 -3
  640. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +3 -0
  641. package/lib/commonjs/mol-repr/representation.d.ts +3 -3
  642. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +1 -0
  643. package/lib/commonjs/mol-repr/shape/loci/angle.js +2 -2
  644. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +1 -0
  645. package/lib/commonjs/mol-repr/shape/loci/dihedral.js +2 -2
  646. package/lib/commonjs/mol-repr/shape/loci/distance.js +2 -2
  647. package/lib/commonjs/mol-repr/shape/loci/label.js +2 -2
  648. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +1 -0
  649. package/lib/commonjs/mol-repr/shape/loci/orientation.js +2 -2
  650. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +1 -0
  651. package/lib/commonjs/mol-repr/shape/loci/plane.js +2 -2
  652. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +1 -0
  653. package/lib/commonjs/mol-repr/shape/model/unitcell.js +3 -3
  654. package/lib/commonjs/mol-repr/shape/representation.js +1 -2
  655. package/lib/commonjs/mol-repr/structure/complex-representation.js +1 -2
  656. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +5 -0
  657. package/lib/commonjs/mol-repr/structure/complex-visual.js +9 -9
  658. package/lib/commonjs/mol-repr/structure/params.d.ts +5 -0
  659. package/lib/commonjs/mol-repr/structure/params.js +2 -2
  660. package/lib/commonjs/mol-repr/structure/registry.d.ts +11 -0
  661. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +3 -0
  662. package/lib/commonjs/mol-repr/structure/representation/backbone.js +3 -3
  663. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  664. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js +3 -3
  665. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  666. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js +3 -3
  667. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +3 -0
  668. package/lib/commonjs/mol-repr/structure/representation/cartoon.js +3 -3
  669. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  670. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js +3 -3
  671. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  672. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +3 -3
  673. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +3 -0
  674. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +3 -3
  675. package/lib/commonjs/mol-repr/structure/representation/label.js +3 -3
  676. package/lib/commonjs/mol-repr/structure/representation/line.js +3 -3
  677. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  678. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +3 -3
  679. package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +3 -0
  680. package/lib/commonjs/mol-repr/structure/representation/orientation.js +3 -3
  681. package/lib/commonjs/mol-repr/structure/representation/point.js +3 -3
  682. package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +3 -0
  683. package/lib/commonjs/mol-repr/structure/representation/putty.js +3 -3
  684. package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +3 -0
  685. package/lib/commonjs/mol-repr/structure/representation/spacefill.js +3 -3
  686. package/lib/commonjs/mol-repr/structure/representation.js +2 -2
  687. package/lib/commonjs/mol-repr/structure/units-representation.js +1 -2
  688. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +5 -0
  689. package/lib/commonjs/mol-repr/structure/units-visual.js +10 -10
  690. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  691. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +4 -4
  692. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +2 -2
  693. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  694. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +4 -4
  695. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +2 -2
  696. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  697. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js +2 -2
  698. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  699. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +2 -2
  700. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  701. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +2 -2
  702. package/lib/commonjs/mol-repr/structure/visual/element-cross.js +3 -3
  703. package/lib/commonjs/mol-repr/structure/visual/element-point.js +3 -3
  704. package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +4 -0
  705. package/lib/commonjs/mol-repr/structure/visual/element-sphere.js +7 -7
  706. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  707. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.js +3 -3
  708. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -0
  709. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +3 -3
  710. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +4 -0
  711. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +7 -7
  712. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +2 -2
  713. package/lib/commonjs/mol-repr/structure/visual/label-text.js +2 -2
  714. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  715. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +3 -3
  716. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +2 -2
  717. package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-bond.d.ts +2 -0
  718. package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-bond.js +4 -4
  719. package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-element.d.ts +2 -0
  720. package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-element.js +4 -4
  721. package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-ring-fill.d.ts +1 -0
  722. package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-ring-fill.js +2 -2
  723. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  724. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.js +2 -2
  725. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  726. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.js +2 -2
  727. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  728. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +3 -3
  729. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  730. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.js +4 -4
  731. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  732. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.js +4 -4
  733. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  734. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +2 -2
  735. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  736. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.js +2 -2
  737. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  738. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +2 -2
  739. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  740. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js +2 -2
  741. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +8 -8
  742. package/lib/commonjs/mol-repr/structure/visual/util/common.js +14 -14
  743. package/lib/commonjs/mol-repr/structure/visual/util/element.js +10 -10
  744. package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js +8 -8
  745. package/lib/commonjs/mol-repr/structure/visual/util/link.js +5 -5
  746. package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js +2 -3
  747. package/lib/commonjs/mol-repr/structure/visual/util/nucleotide.d.ts +60 -60
  748. package/lib/commonjs/mol-repr/structure/visual/util/nucleotide.js +11 -11
  749. package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js +3 -4
  750. package/lib/commonjs/mol-repr/structure/visual/util/polymer/curve-segment.js +5 -6
  751. package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js +2 -2
  752. package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +2 -2
  753. package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +8 -8
  754. package/lib/commonjs/mol-repr/util.js +3 -3
  755. package/lib/commonjs/mol-repr/volume/direct-volume.d.ts +48 -45
  756. package/lib/commonjs/mol-repr/volume/direct-volume.js +9 -9
  757. package/lib/commonjs/mol-repr/volume/isosurface.d.ts +95 -90
  758. package/lib/commonjs/mol-repr/volume/isosurface.js +10 -10
  759. package/lib/commonjs/mol-repr/volume/registry.d.ts +63 -60
  760. package/lib/commonjs/mol-repr/volume/representation.js +4 -4
  761. package/lib/commonjs/mol-repr/volume/segment.d.ts +80 -75
  762. package/lib/commonjs/mol-repr/volume/segment.js +8 -8
  763. package/lib/commonjs/mol-repr/volume/slice.d.ts +45 -45
  764. package/lib/commonjs/mol-repr/volume/slice.js +5 -5
  765. package/lib/commonjs/mol-repr/volume/util.js +5 -6
  766. package/lib/commonjs/mol-script/language/expression-formatter.js +1 -2
  767. package/lib/commonjs/mol-script/language/helpers.js +3 -4
  768. package/lib/commonjs/mol-script/language/parser.js +1 -2
  769. package/lib/commonjs/mol-script/language/symbol-table/core.d.ts +1 -1
  770. package/lib/commonjs/mol-script/language/symbol.js +5 -5
  771. package/lib/commonjs/mol-script/runtime/query/base.js +2 -2
  772. package/lib/commonjs/mol-script/script/mol-script/script-macro.js +4 -5
  773. package/lib/commonjs/mol-script/script/mol-script/symbols.js +3 -3
  774. package/lib/commonjs/mol-script/script.js +1 -2
  775. package/lib/commonjs/mol-script/transpile.js +1 -2
  776. package/lib/commonjs/mol-script/transpilers/helper.js +28 -28
  777. package/lib/commonjs/mol-script/transpilers/jmol/properties.js +2 -2
  778. package/lib/commonjs/mol-script/transpilers/vmd/properties.js +2 -2
  779. package/lib/commonjs/mol-script/util/id-list.js +1 -2
  780. package/lib/commonjs/mol-state/object.d.ts +4 -4
  781. package/lib/commonjs/mol-state/state.d.ts +4 -4
  782. package/lib/commonjs/mol-state/transform.d.ts +1 -1
  783. package/lib/commonjs/mol-state/transformer.d.ts +1 -1
  784. package/lib/commonjs/mol-task/execution/observable.js +4 -5
  785. package/lib/commonjs/mol-task/util/chunked.js +1 -2
  786. package/lib/commonjs/mol-task/util/multistep.js +1 -2
  787. package/lib/commonjs/mol-task/util/scheduler.d.ts +0 -1
  788. package/lib/commonjs/mol-theme/clipping.js +1 -2
  789. package/lib/commonjs/mol-theme/color/atom-id.d.ts +2 -2
  790. package/lib/commonjs/mol-theme/color/atom-id.js +3 -3
  791. package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js +3 -3
  792. package/lib/commonjs/mol-theme/color/cartoon.js +3 -3
  793. package/lib/commonjs/mol-theme/color/chain-id.d.ts +2 -2
  794. package/lib/commonjs/mol-theme/color/chain-id.js +3 -3
  795. package/lib/commonjs/mol-theme/color/element-index.d.ts +2 -2
  796. package/lib/commonjs/mol-theme/color/element-index.js +3 -3
  797. package/lib/commonjs/mol-theme/color/element-symbol.js +4 -4
  798. package/lib/commonjs/mol-theme/color/entity-id.d.ts +2 -2
  799. package/lib/commonjs/mol-theme/color/entity-id.js +3 -3
  800. package/lib/commonjs/mol-theme/color/entity-source.d.ts +2 -2
  801. package/lib/commonjs/mol-theme/color/entity-source.js +3 -3
  802. package/lib/commonjs/mol-theme/color/external-volume.d.ts +2 -2
  803. package/lib/commonjs/mol-theme/color/external-volume.js +2 -2
  804. package/lib/commonjs/mol-theme/color/hydrophobicity.js +4 -4
  805. package/lib/commonjs/mol-theme/color/illustrative.js +3 -3
  806. package/lib/commonjs/mol-theme/color/model-index.d.ts +2 -2
  807. package/lib/commonjs/mol-theme/color/model-index.js +3 -3
  808. package/lib/commonjs/mol-theme/color/molecule-type.js +4 -4
  809. package/lib/commonjs/mol-theme/color/occupancy.js +4 -4
  810. package/lib/commonjs/mol-theme/color/operator-hkl.d.ts +2 -2
  811. package/lib/commonjs/mol-theme/color/operator-hkl.js +3 -3
  812. package/lib/commonjs/mol-theme/color/operator-name.d.ts +2 -2
  813. package/lib/commonjs/mol-theme/color/operator-name.js +3 -3
  814. package/lib/commonjs/mol-theme/color/partial-charge.js +3 -3
  815. package/lib/commonjs/mol-theme/color/polymer-id.d.ts +2 -2
  816. package/lib/commonjs/mol-theme/color/polymer-id.js +3 -3
  817. package/lib/commonjs/mol-theme/color/polymer-index.d.ts +2 -2
  818. package/lib/commonjs/mol-theme/color/polymer-index.js +3 -3
  819. package/lib/commonjs/mol-theme/color/residue-name.js +4 -4
  820. package/lib/commonjs/mol-theme/color/secondary-structure.js +4 -4
  821. package/lib/commonjs/mol-theme/color/sequence-id.js +3 -3
  822. package/lib/commonjs/mol-theme/color/shape-group.js +3 -3
  823. package/lib/commonjs/mol-theme/color/structure-index.d.ts +2 -2
  824. package/lib/commonjs/mol-theme/color/structure-index.js +3 -3
  825. package/lib/commonjs/mol-theme/color/trajectory-index.d.ts +2 -2
  826. package/lib/commonjs/mol-theme/color/trajectory-index.js +3 -3
  827. package/lib/commonjs/mol-theme/color/uncertainty.js +4 -4
  828. package/lib/commonjs/mol-theme/color/uniform.js +3 -3
  829. package/lib/commonjs/mol-theme/color/unit-index.d.ts +2 -2
  830. package/lib/commonjs/mol-theme/color/unit-index.js +3 -3
  831. package/lib/commonjs/mol-theme/color/volume-segment.d.ts +2 -2
  832. package/lib/commonjs/mol-theme/color/volume-segment.js +3 -3
  833. package/lib/commonjs/mol-theme/color/volume-value.js +3 -3
  834. package/lib/commonjs/mol-theme/color.d.ts +16 -16
  835. package/lib/commonjs/mol-theme/color.js +2 -2
  836. package/lib/commonjs/mol-theme/emissive.js +1 -2
  837. package/lib/commonjs/mol-theme/label.js +11 -11
  838. package/lib/commonjs/mol-theme/overpaint.js +1 -2
  839. package/lib/commonjs/mol-theme/size/physical.js +4 -4
  840. package/lib/commonjs/mol-theme/size/shape-group.js +3 -3
  841. package/lib/commonjs/mol-theme/size/uncertainty.js +4 -4
  842. package/lib/commonjs/mol-theme/size/uniform.js +3 -3
  843. package/lib/commonjs/mol-theme/substance.js +1 -2
  844. package/lib/commonjs/mol-theme/theme.d.ts +3 -3
  845. package/lib/commonjs/mol-theme/transparency.js +1 -2
  846. package/lib/commonjs/mol-util/array.js +22 -23
  847. package/lib/commonjs/mol-util/binding.js +1 -2
  848. package/lib/commonjs/mol-util/clip.js +1 -2
  849. package/lib/commonjs/mol-util/color/color.js +6 -7
  850. package/lib/commonjs/mol-util/color/distinct.js +2 -2
  851. package/lib/commonjs/mol-util/color/lists.js +2 -2
  852. package/lib/commonjs/mol-util/color/palette.d.ts +4 -3
  853. package/lib/commonjs/mol-util/color/palette.js +2 -3
  854. package/lib/commonjs/mol-util/color/params.js +1 -2
  855. package/lib/commonjs/mol-util/color/scale.d.ts +2 -1
  856. package/lib/commonjs/mol-util/color/spaces/hcl.js +1 -2
  857. package/lib/commonjs/mol-util/color/spaces/lab.js +1 -2
  858. package/lib/commonjs/mol-util/data-source.d.ts +0 -1
  859. package/lib/commonjs/mol-util/data-source.js +7 -7
  860. package/lib/commonjs/mol-util/date.js +2 -3
  861. package/lib/commonjs/mol-util/debug.js +7 -7
  862. package/lib/commonjs/mol-util/download.js +1 -2
  863. package/lib/commonjs/mol-util/file-info.js +1 -2
  864. package/lib/commonjs/mol-util/id-factory.js +1 -2
  865. package/lib/commonjs/mol-util/index.js +13 -13
  866. package/lib/commonjs/mol-util/input/event-offset.js +1 -2
  867. package/lib/commonjs/mol-util/input/input-observer.js +4 -4
  868. package/lib/commonjs/mol-util/is-little-endian.js +1 -2
  869. package/lib/commonjs/mol-util/json.js +2 -3
  870. package/lib/commonjs/mol-util/legend.js +2 -3
  871. package/lib/commonjs/mol-util/make-dir.js +1 -2
  872. package/lib/commonjs/mol-util/map.js +1 -2
  873. package/lib/commonjs/mol-util/marker-action.js +6 -6
  874. package/lib/commonjs/mol-util/mask.js +2 -2
  875. package/lib/commonjs/mol-util/material.js +1 -2
  876. package/lib/commonjs/mol-util/memoize.js +2 -3
  877. package/lib/commonjs/mol-util/nodejs-shims.d.ts +1 -1
  878. package/lib/commonjs/mol-util/now.js +2 -2
  879. package/lib/commonjs/mol-util/number-packing.js +3 -4
  880. package/lib/commonjs/mol-util/number.js +7 -8
  881. package/lib/commonjs/mol-util/object.js +14 -15
  882. package/lib/commonjs/mol-util/param-mapping.js +1 -2
  883. package/lib/commonjs/mol-util/read.js +6 -7
  884. package/lib/commonjs/mol-util/reference-cache.js +3 -4
  885. package/lib/commonjs/mol-util/retry-if.js +1 -2
  886. package/lib/commonjs/mol-util/sleep.js +1 -2
  887. package/lib/commonjs/mol-util/string.js +18 -18
  888. package/lib/commonjs/mol-util/type-helpers.js +3 -4
  889. package/lib/commonjs/mol-util/url.js +2 -3
  890. package/lib/commonjs/mol-util/zip/bin.js +9 -10
  891. package/lib/commonjs/mol-util/zip/checksum.js +2 -3
  892. package/lib/commonjs/mol-util/zip/deflate.js +1 -2
  893. package/lib/commonjs/mol-util/zip/huffman.js +1 -2
  894. package/lib/commonjs/mol-util/zip/inflate.js +1 -2
  895. package/lib/commonjs/mol-util/zip/util.js +4 -4
  896. package/lib/commonjs/mol-util/zip/zip.js +8 -9
  897. package/lib/commonjs/servers/common/file-handle.js +1 -2
  898. package/lib/commonjs/servers/common/swagger-ui/index.js +2 -3
  899. package/lib/commonjs/servers/common/util.js +1 -2
  900. package/lib/commonjs/servers/model/config.d.ts +4 -4
  901. package/lib/commonjs/servers/model/config.js +2 -2
  902. package/lib/commonjs/servers/model/preprocess/converter.js +1 -2
  903. package/lib/commonjs/servers/model/preprocess/parallel.js +2 -3
  904. package/lib/commonjs/servers/model/preprocess/preprocess.js +1 -2
  905. package/lib/commonjs/servers/model/preprocess/util.js +2 -3
  906. package/lib/commonjs/servers/model/property-provider.js +2 -3
  907. package/lib/commonjs/servers/model/query/atoms.js +1 -2
  908. package/lib/commonjs/servers/model/server/api-local.js +1 -2
  909. package/lib/commonjs/servers/model/server/api-schema.js +2 -2
  910. package/lib/commonjs/servers/model/server/api-web-multiple.js +1 -2
  911. package/lib/commonjs/servers/model/server/api-web.js +2 -3
  912. package/lib/commonjs/servers/model/server/api.js +4 -4
  913. package/lib/commonjs/servers/model/server/jobs.js +3 -3
  914. package/lib/commonjs/servers/model/server/query.js +2 -3
  915. package/lib/commonjs/servers/model/server/structure-wrapper.js +6 -6
  916. package/lib/commonjs/servers/model/utils/fetch-retry.js +1 -2
  917. package/lib/commonjs/servers/model/utils/tar.d.ts +0 -1
  918. package/lib/commonjs/servers/model/utils/tar.js +2 -2
  919. package/lib/commonjs/servers/plugin-state/api-schema.js +2 -2
  920. package/lib/commonjs/servers/plugin-state/config.js +1 -2
  921. package/lib/commonjs/servers/volume/common/binary-schema.d.ts +0 -1
  922. package/lib/commonjs/servers/volume/common/binary-schema.js +5 -5
  923. package/lib/commonjs/servers/volume/common/data-format.d.ts +0 -1
  924. package/lib/commonjs/servers/volume/common/data-format.js +2 -3
  925. package/lib/commonjs/servers/volume/common/file.js +4 -5
  926. package/lib/commonjs/servers/volume/config.d.ts +1 -5
  927. package/lib/commonjs/servers/volume/config.js +3 -3
  928. package/lib/commonjs/servers/volume/pack/data-model.js +2 -3
  929. package/lib/commonjs/servers/volume/pack/downsampling.js +2 -3
  930. package/lib/commonjs/servers/volume/pack/format/ccp4.js +2 -2
  931. package/lib/commonjs/servers/volume/pack/format/dsn6.js +2 -2
  932. package/lib/commonjs/servers/volume/pack/format.js +4 -5
  933. package/lib/commonjs/servers/volume/pack/main.js +1 -2
  934. package/lib/commonjs/servers/volume/pack/sampling.js +2 -3
  935. package/lib/commonjs/servers/volume/pack/writer.js +1 -2
  936. package/lib/commonjs/servers/volume/server/algebra/box.js +14 -15
  937. package/lib/commonjs/servers/volume/server/algebra/coordinate.js +17 -18
  938. package/lib/commonjs/servers/volume/server/api.js +3 -4
  939. package/lib/commonjs/servers/volume/server/local-api.js +1 -2
  940. package/lib/commonjs/servers/volume/server/query/compose.js +1 -2
  941. package/lib/commonjs/servers/volume/server/query/encode.js +1 -2
  942. package/lib/commonjs/servers/volume/server/query/execute.js +1 -2
  943. package/lib/commonjs/servers/volume/server/query/identify.js +1 -2
  944. package/lib/commonjs/servers/volume/server/web-api.js +1 -2
  945. package/lib/commonjs/servers/volume/server/web-schema.js +2 -2
  946. package/lib/examples/lighting/index.d.ts +1 -1
  947. package/lib/examples/lighting/index.js +2 -1
  948. package/lib/examples/proteopedia-wrapper/coloring.d.ts +5 -20
  949. package/lib/extensions/alpha-orbitals/transforms.d.ts +3 -3
  950. package/lib/extensions/anvil/behavior.d.ts +1 -0
  951. package/lib/extensions/anvil/representation.d.ts +4 -0
  952. package/lib/extensions/assembly-symmetry/behavior.d.ts +1 -0
  953. package/lib/extensions/assembly-symmetry/color.d.ts +2 -2
  954. package/lib/extensions/assembly-symmetry/representation.d.ts +1 -0
  955. package/lib/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  956. package/lib/extensions/dnatco/ntc-tube/representation.d.ts +3 -0
  957. package/lib/extensions/g3d/format.d.ts +3 -3
  958. package/lib/extensions/geo-export/mesh-exporter.d.ts +2 -2
  959. package/lib/extensions/geo-export/ui.d.ts +0 -1
  960. package/lib/extensions/meshes/mesh-extension.d.ts +3 -5
  961. package/lib/extensions/meshes/mesh-streaming/behavior.d.ts +3 -3
  962. package/lib/extensions/meshes/mesh-streaming/server-info.d.ts +3 -3
  963. package/lib/extensions/model-archive/quality-assessment/color/plddt.d.ts +1 -1
  964. package/lib/extensions/model-archive/quality-assessment/color/plddt.js +8 -5
  965. package/lib/extensions/model-export/ui.d.ts +0 -1
  966. package/lib/extensions/mp4-export/controls.d.ts +1 -1
  967. package/lib/extensions/mp4-export/encoder.js +1 -1
  968. package/lib/extensions/mp4-export/ui.d.ts +0 -1
  969. package/lib/extensions/mvs/components/annotation-label/representation.d.ts +32 -34
  970. package/lib/extensions/mvs/components/annotation-label/visual.d.ts +16 -16
  971. package/lib/extensions/mvs/components/custom-label/representation.d.ts +32 -32
  972. package/lib/extensions/mvs/components/custom-label/visual.d.ts +16 -16
  973. package/lib/extensions/mvs/components/formats.d.ts +6 -6
  974. package/lib/extensions/mvs/helpers/indexing.d.ts +2 -2
  975. package/lib/extensions/mvs/helpers/schemas.d.ts +1 -1
  976. package/lib/extensions/mvs/helpers/utils.d.ts +1 -1
  977. package/lib/extensions/mvs/load-helpers.d.ts +1 -1
  978. package/lib/extensions/mvs/tree/mvs/mvs-builder.d.ts +0 -2
  979. package/lib/extensions/rcsb/validation-report/representation.d.ts +5 -0
  980. package/lib/extensions/sb-ncbr/index.d.ts +8 -0
  981. package/lib/extensions/sb-ncbr/index.js +8 -0
  982. package/lib/extensions/sb-ncbr/tunnels/actions.d.ts +20 -0
  983. package/lib/extensions/sb-ncbr/tunnels/actions.js +86 -0
  984. package/lib/extensions/sb-ncbr/tunnels/algorithm.d.ts +26 -0
  985. package/lib/extensions/sb-ncbr/tunnels/algorithm.js +469 -0
  986. package/lib/extensions/sb-ncbr/tunnels/behavior.d.ts +40 -0
  987. package/lib/extensions/sb-ncbr/tunnels/behavior.js +92 -0
  988. package/lib/extensions/sb-ncbr/tunnels/data-model.d.ts +146 -0
  989. package/lib/extensions/sb-ncbr/tunnels/data-model.js +23 -0
  990. package/lib/extensions/sb-ncbr/tunnels/examples.d.ts +12 -0
  991. package/lib/extensions/sb-ncbr/tunnels/examples.js +49 -0
  992. package/lib/extensions/sb-ncbr/tunnels/props.d.ts +19 -0
  993. package/lib/extensions/sb-ncbr/tunnels/props.js +22 -0
  994. package/lib/extensions/sb-ncbr/tunnels/representation.d.ts +29 -0
  995. package/lib/extensions/sb-ncbr/tunnels/representation.js +96 -0
  996. package/lib/extensions/volumes-and-segmentations/entry-root.d.ts +3 -3
  997. package/lib/extensions/volumes-and-segmentations/entry-state.d.ts +3 -3
  998. package/lib/extensions/volumes-and-segmentations/global-state.d.ts +3 -3
  999. package/lib/extensions/volumes-and-segmentations/ui.d.ts +0 -1
  1000. package/lib/extensions/zenodo/ui.d.ts +0 -1
  1001. package/lib/mol-canvas3d/camera/transition.d.ts +1 -1
  1002. package/lib/mol-canvas3d/camera/transition.js +23 -6
  1003. package/lib/mol-canvas3d/canvas3d.d.ts +26 -1
  1004. package/lib/mol-canvas3d/canvas3d.js +4 -0
  1005. package/lib/mol-canvas3d/helper/bounding-sphere-helper.d.ts +1 -6
  1006. package/lib/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  1007. package/lib/mol-canvas3d/helper/helper.d.ts +2 -0
  1008. package/lib/mol-canvas3d/passes/dof.d.ts +34 -0
  1009. package/lib/mol-canvas3d/passes/dof.js +163 -0
  1010. package/lib/mol-canvas3d/passes/draw.d.ts +2 -0
  1011. package/lib/mol-canvas3d/passes/draw.js +31 -8
  1012. package/lib/mol-canvas3d/passes/image.d.ts +10 -0
  1013. package/lib/mol-canvas3d/passes/multi-sample.d.ts +2 -1
  1014. package/lib/mol-canvas3d/passes/multi-sample.js +4 -3
  1015. package/lib/mol-canvas3d/passes/postprocessing.d.ts +9 -0
  1016. package/lib/mol-canvas3d/passes/postprocessing.js +10 -0
  1017. package/lib/mol-data/db/column.d.ts +1 -1
  1018. package/lib/mol-geo/geometry/base.d.ts +1 -1
  1019. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +1 -0
  1020. package/lib/mol-geo/geometry/cylinders/cylinders.js +3 -0
  1021. package/lib/mol-geo/geometry/direct-volume/direct-volume.d.ts +1 -0
  1022. package/lib/mol-geo/geometry/direct-volume/direct-volume.js +3 -0
  1023. package/lib/mol-geo/geometry/image/image.d.ts +1 -1
  1024. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  1025. package/lib/mol-geo/geometry/mesh/mesh.d.ts +1 -0
  1026. package/lib/mol-geo/geometry/mesh/mesh.js +3 -0
  1027. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  1028. package/lib/mol-geo/geometry/spheres/spheres.d.ts +1 -0
  1029. package/lib/mol-geo/geometry/spheres/spheres.js +3 -0
  1030. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +1 -0
  1031. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -0
  1032. package/lib/mol-gl/renderable/cylinders.d.ts +1 -0
  1033. package/lib/mol-gl/renderable/cylinders.js +1 -0
  1034. package/lib/mol-gl/renderable/direct-volume.d.ts +1 -0
  1035. package/lib/mol-gl/renderable/direct-volume.js +1 -0
  1036. package/lib/mol-gl/renderable/mesh.d.ts +1 -0
  1037. package/lib/mol-gl/renderable/mesh.js +1 -0
  1038. package/lib/mol-gl/renderable/schema.d.ts +1 -0
  1039. package/lib/mol-gl/renderable/schema.js +1 -0
  1040. package/lib/mol-gl/renderable/spheres.d.ts +1 -0
  1041. package/lib/mol-gl/renderable/spheres.js +1 -0
  1042. package/lib/mol-gl/renderable/texture-mesh.d.ts +1 -0
  1043. package/lib/mol-gl/renderable/texture-mesh.js +1 -0
  1044. package/lib/mol-gl/renderer.d.ts +1 -0
  1045. package/lib/mol-gl/renderer.js +6 -0
  1046. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +2 -1
  1047. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js +57 -24
  1048. package/lib/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
  1049. package/lib/mol-gl/shader/chunks/common-frag-params.glsl.js +1 -0
  1050. package/lib/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
  1051. package/lib/mol-gl/shader/chunks/common.glsl.js +6 -0
  1052. package/lib/mol-gl/shader/cylinders.frag.d.ts +2 -1
  1053. package/lib/mol-gl/shader/cylinders.frag.js +11 -2
  1054. package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  1055. package/lib/mol-gl/shader/direct-volume.frag.js +1 -0
  1056. package/lib/mol-gl/shader/dof.frag.d.ts +7 -0
  1057. package/lib/mol-gl/shader/dof.frag.js +119 -0
  1058. package/lib/mol-gl/shader/ssao-blur.frag.d.ts +1 -1
  1059. package/lib/mol-gl/shader/ssao-blur.frag.js +9 -6
  1060. package/lib/mol-gl/shader-code.js +1 -1
  1061. package/lib/mol-gl/webgl/context.js +1 -0
  1062. package/lib/mol-gl/webgl/render-item.d.ts +2 -2
  1063. package/lib/mol-gl/webgl/timer.d.ts +1 -1
  1064. package/lib/mol-gl/webgl/timer.js +8 -1
  1065. package/lib/mol-io/common/simple-buffer.d.ts +0 -1
  1066. package/lib/mol-io/reader/cif/schema/bird.d.ts +1 -1
  1067. package/lib/mol-io/reader/cif/schema/bird.js +1 -1
  1068. package/lib/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  1069. package/lib/mol-io/reader/cif/schema/ccd.js +1 -1
  1070. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +9 -1
  1071. package/lib/mol-io/reader/cif/schema/mmcif.js +9 -1
  1072. package/lib/mol-io/reader/common/text/column/fixed.d.ts +1 -1
  1073. package/lib/mol-io/reader/common/text/column/token.d.ts +1 -1
  1074. package/lib/mol-io/reader/ply/schema.d.ts +1 -1
  1075. package/lib/mol-math/linear-algebra/3d/minimize-rmsd.js +2 -1
  1076. package/lib/mol-model/loci.d.ts +1 -1
  1077. package/lib/mol-model/sequence/alignment/alignment.d.ts +2 -1
  1078. package/lib/mol-model/structure/model/types/saccharides.js +1 -1
  1079. package/lib/mol-model/structure/model/types.d.ts +3 -3
  1080. package/lib/mol-model/structure/query/queries/generators.js +2 -2
  1081. package/lib/mol-model/structure/structure/properties.d.ts +1 -0
  1082. package/lib/mol-model/structure/structure/properties.js +1 -0
  1083. package/lib/mol-model/volume/volume.d.ts +6 -6
  1084. package/lib/mol-model-formats/shape/ply.d.ts +2 -0
  1085. package/lib/mol-model-formats/structure/basic/schema.d.ts +1 -0
  1086. package/lib/mol-model-formats/structure/common/entity.d.ts +1 -0
  1087. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  1088. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  1089. package/lib/mol-model-props/computed/representations/interactions.d.ts +3 -0
  1090. package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  1091. package/lib/mol-model-props/sequence/themes/sifts-mapping.d.ts +2 -2
  1092. package/lib/mol-plugin/animation-loop.d.ts +1 -0
  1093. package/lib/mol-plugin/behavior/behavior.d.ts +9 -9
  1094. package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +9 -9
  1095. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -3
  1096. package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +3 -3
  1097. package/lib/mol-plugin/commands.d.ts +23 -87
  1098. package/lib/mol-plugin/context.d.ts +3 -2
  1099. package/lib/mol-plugin/context.js +4 -2
  1100. package/lib/mol-plugin/state.d.ts +7 -7
  1101. package/lib/mol-plugin/util/headless-screenshot.d.ts +1 -1
  1102. package/lib/mol-plugin/util/headless-screenshot.js +3 -1
  1103. package/lib/mol-plugin/util/viewport-screenshot.d.ts +1 -1
  1104. package/lib/mol-plugin/util/viewport-screenshot.js +2 -1
  1105. package/lib/mol-plugin/version.js +2 -2
  1106. package/lib/mol-plugin-state/actions/volume.d.ts +1 -1
  1107. package/lib/mol-plugin-state/actions/volume.js +4 -12
  1108. package/lib/mol-plugin-state/animation/built-in/model-index.d.ts +2 -2
  1109. package/lib/mol-plugin-state/animation/built-in/state-snapshots.js +7 -3
  1110. package/lib/mol-plugin-state/formats/registry.d.ts +1 -1
  1111. package/lib/mol-plugin-state/formats/trajectory.d.ts +9 -9
  1112. package/lib/mol-plugin-state/formats/volume.d.ts +0 -1
  1113. package/lib/mol-plugin-state/manager/structure/hierarchy.d.ts +3 -3
  1114. package/lib/mol-plugin-state/manager/structure/measurement.d.ts +4 -0
  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
@@ -5,7 +5,9 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.WedgeCage = exports.Wedge = exports.createWedge = void 0;
8
+ exports.createWedge = createWedge;
9
+ exports.Wedge = Wedge;
10
+ exports.WedgeCage = WedgeCage;
9
11
  const linear_algebra_1 = require("../../mol-math/linear-algebra");
10
12
  const primitive_1 = require("./primitive");
11
13
  const polygon_1 = require("./polygon");
@@ -38,18 +40,15 @@ function createWedge() {
38
40
  builder.add(a, b, c);
39
41
  return builder.getPrimitive();
40
42
  }
41
- exports.createWedge = createWedge;
42
43
  let wedge;
43
44
  function Wedge() {
44
45
  if (!wedge)
45
46
  wedge = createWedge();
46
47
  return wedge;
47
48
  }
48
- exports.Wedge = Wedge;
49
49
  let wedgeCage;
50
50
  function WedgeCage() {
51
51
  if (!wedgeCage)
52
52
  wedgeCage = (0, prism_1.PrismCage)(points);
53
53
  return wedgeCage;
54
54
  }
55
- exports.WedgeCage = WedgeCage;
@@ -7,7 +7,9 @@
7
7
  * @author Cai Huiyu <szmun.caihy@gmail.com>
8
8
  */
9
9
  Object.defineProperty(exports, "__esModule", { value: true });
10
- exports.isPositionLocation = exports.PositionLocation = exports.LocationIterator = void 0;
10
+ exports.LocationIterator = LocationIterator;
11
+ exports.PositionLocation = PositionLocation;
12
+ exports.isPositionLocation = isPositionLocation;
11
13
  const linear_algebra_1 = require("../../mol-math/linear-algebra");
12
14
  const location_1 = require("../../mol-model/location");
13
15
  function LocationIterator(groupCount, instanceCount, stride, getLocation, nonInstanceable = false, isSecondary = () => false, getLocation2) {
@@ -85,7 +87,6 @@ function LocationIterator(groupCount, instanceCount, stride, getLocation, nonIns
85
87
  }
86
88
  };
87
89
  }
88
- exports.LocationIterator = LocationIterator;
89
90
  function PositionLocation(position, normal) {
90
91
  return {
91
92
  kind: 'position-location',
@@ -93,8 +94,6 @@ function PositionLocation(position, normal) {
93
94
  normal: normal ? linear_algebra_1.Vec3.clone(normal) : (0, linear_algebra_1.Vec3)()
94
95
  };
95
96
  }
96
- exports.PositionLocation = PositionLocation;
97
97
  function isPositionLocation(x) {
98
98
  return !!x && x.kind === 'position-location';
99
99
  }
100
- exports.isPositionLocation = isPositionLocation;
@@ -6,7 +6,8 @@
6
6
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
7
7
  */
8
8
  Object.defineProperty(exports, "__esModule", { value: true });
9
- exports.computeMarchingCubesLines = exports.computeMarchingCubesMesh = void 0;
9
+ exports.computeMarchingCubesMesh = computeMarchingCubesMesh;
10
+ exports.computeMarchingCubesLines = computeMarchingCubesLines;
10
11
  const mol_task_1 = require("../../../mol-task");
11
12
  const tables_1 = require("./tables");
12
13
  const mol_util_1 = require("../../../mol-util");
@@ -36,7 +37,6 @@ function computeMarchingCubesMesh(params, mesh) {
36
37
  return builder.get();
37
38
  });
38
39
  }
39
- exports.computeMarchingCubesMesh = computeMarchingCubesMesh;
40
40
  function computeMarchingCubesLines(params, lines) {
41
41
  return mol_task_1.Task.create('Marching Cubes Lines', async (ctx) => {
42
42
  const inputParams = getInputParams(params);
@@ -48,7 +48,6 @@ function computeMarchingCubesLines(params, lines) {
48
48
  return builder.get();
49
49
  });
50
50
  }
51
- exports.computeMarchingCubesLines = computeMarchingCubesLines;
52
51
  class MarchingCubesComputation {
53
52
  async doSlices() {
54
53
  let done = 0;
@@ -7,7 +7,8 @@
7
7
  * @author Fred Ludlow <fred.ludlow@gmail.com>
8
8
  */
9
9
  Object.defineProperty(exports, "__esModule", { value: true });
10
- exports.MarchinCubesLinesBuilder = exports.MarchinCubesMeshBuilder = void 0;
10
+ exports.MarchinCubesMeshBuilder = MarchinCubesMeshBuilder;
11
+ exports.MarchinCubesLinesBuilder = MarchinCubesLinesBuilder;
11
12
  const util_1 = require("../../../mol-data/util");
12
13
  const mol_util_1 = require("../../../mol-util");
13
14
  const mesh_1 = require("../../geometry/mesh/mesh");
@@ -50,7 +51,6 @@ function MarchinCubesMeshBuilder(vertexChunkSize, mesh) {
50
51
  }
51
52
  };
52
53
  }
53
- exports.MarchinCubesMeshBuilder = MarchinCubesMeshBuilder;
54
54
  function MarchinCubesLinesBuilder(vertexChunkSize, lines) {
55
55
  const vertices = util_1.ChunkedArray.create(Float32Array, 3, vertexChunkSize);
56
56
  const groups = util_1.ChunkedArray.create(Float32Array, 1, vertexChunkSize);
@@ -96,4 +96,3 @@ function MarchinCubesLinesBuilder(vertexChunkSize, lines) {
96
96
  }
97
97
  };
98
98
  }
99
- exports.MarchinCubesLinesBuilder = MarchinCubesLinesBuilder;
@@ -6,11 +6,11 @@
6
6
  * @author Fred Ludlow <fred.ludlow@gmail.com>
7
7
  */
8
8
  Object.defineProperty(exports, "__esModule", { value: true });
9
- exports.AllowedContours = exports.TriTable = exports.EdgeTable = exports.EdgeIdInfo = exports.CubeEdges = exports.CubeVertices = exports.EdgesYZ = exports.EdgesXZ = exports.EdgesXY = exports.IndexPair = exports.Index = void 0;
10
- function Index(i, j, k) { return { i, j, k }; }
9
+ exports.AllowedContours = exports.TriTable = exports.EdgeTable = exports.EdgeIdInfo = exports.CubeEdges = exports.CubeVertices = exports.EdgesYZ = exports.EdgesXZ = exports.EdgesXY = void 0;
11
10
  exports.Index = Index;
12
- function IndexPair(a, b) { return { a, b }; }
13
11
  exports.IndexPair = IndexPair;
12
+ function Index(i, j, k) { return { i, j, k }; }
13
+ function IndexPair(a, b) { return { a, b }; }
14
14
  exports.EdgesXY = [
15
15
  [],
16
16
  [0, 3],
@@ -5,7 +5,13 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.createGroupMapping = exports.computeVertexNormals = exports.computeIndexedVertexNormals = exports.appplyRadius = exports.transformDirectionArray = exports.transformPositionArray = exports.normalizeVec3Array = void 0;
8
+ exports.normalizeVec3Array = normalizeVec3Array;
9
+ exports.transformPositionArray = transformPositionArray;
10
+ exports.transformDirectionArray = transformDirectionArray;
11
+ exports.appplyRadius = appplyRadius;
12
+ exports.computeIndexedVertexNormals = computeIndexedVertexNormals;
13
+ exports.computeVertexNormals = computeVertexNormals;
14
+ exports.createGroupMapping = createGroupMapping;
9
15
  const linear_algebra_1 = require("../mol-math/linear-algebra");
10
16
  const array_1 = require("../mol-util/array");
11
17
  function normalizeVec3Array(a, count) {
@@ -20,7 +26,6 @@ function normalizeVec3Array(a, count) {
20
26
  }
21
27
  return a;
22
28
  }
23
- exports.normalizeVec3Array = normalizeVec3Array;
24
29
  const tmpV3 = (0, linear_algebra_1.Vec3)();
25
30
  function transformPositionArray(t, array, offset, count) {
26
31
  for (let i = 0, il = count * 3; i < il; i += 3) {
@@ -29,7 +34,6 @@ function transformPositionArray(t, array, offset, count) {
29
34
  linear_algebra_1.Vec3.toArray(tmpV3, array, offset + i);
30
35
  }
31
36
  }
32
- exports.transformPositionArray = transformPositionArray;
33
37
  function transformDirectionArray(n, array, offset, count) {
34
38
  for (let i = 0, il = count * 3; i < il; i += 3) {
35
39
  linear_algebra_1.Vec3.fromArray(tmpV3, array, offset + i);
@@ -37,7 +41,6 @@ function transformDirectionArray(n, array, offset, count) {
37
41
  linear_algebra_1.Vec3.toArray(tmpV3, array, offset + i);
38
42
  }
39
43
  }
40
- exports.transformDirectionArray = transformDirectionArray;
41
44
  /** iterate over the entire array and apply the radius to each vertex */
42
45
  function appplyRadius(vertices, radius) {
43
46
  for (let i = 0, il = vertices.length; i < il; i += 3) {
@@ -47,7 +50,6 @@ function appplyRadius(vertices, radius) {
47
50
  linear_algebra_1.Vec3.toArray(tmpV3, vertices, i);
48
51
  }
49
52
  }
50
- exports.appplyRadius = appplyRadius;
51
53
  const a = (0, linear_algebra_1.Vec3)();
52
54
  const b = (0, linear_algebra_1.Vec3)();
53
55
  const c = (0, linear_algebra_1.Vec3)();
@@ -81,7 +83,6 @@ function computeIndexedVertexNormals(vertices, indices, normals, vertexCount, tr
81
83
  }
82
84
  return normalizeVec3Array(normals, vertexCount);
83
85
  }
84
- exports.computeIndexedVertexNormals = computeIndexedVertexNormals;
85
86
  /**
86
87
  * vertex normals for unindexed triangle soup
87
88
  * - normals array must contain only zeros
@@ -106,7 +107,6 @@ function computeVertexNormals(vertices, normals, vertexCount) {
106
107
  }
107
108
  return normalizeVec3Array(normals, vertexCount);
108
109
  }
109
- exports.computeVertexNormals = computeVertexNormals;
110
110
  /**
111
111
  * The `step` parameter allows to skip over repeated values in `groups`
112
112
  */
@@ -132,4 +132,3 @@ function createGroupMapping(groups, dataCount, step = 1) {
132
132
  }
133
133
  return { indices, offsets };
134
134
  }
135
- exports.createGroupMapping = createGroupMapping;
@@ -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.createGrid3dComputeRenderable = exports.canComputeGrid3dOnGPU = void 0;
8
+ exports.canComputeGrid3dOnGPU = canComputeGrid3dOnGPU;
9
+ exports.createGrid3dComputeRenderable = createGrid3dComputeRenderable;
9
10
  const schema_1 = require("../renderable/schema");
10
11
  const common_1 = require("../../mol-math/geometry/common");
11
12
  const grid3d_template_frag_1 = require("../shader/util/grid3d-template.frag");
@@ -22,7 +23,6 @@ const debug_1 = require("../../mol-util/debug");
22
23
  function canComputeGrid3dOnGPU(webgl) {
23
24
  return !!(webgl === null || webgl === void 0 ? void 0 : webgl.extensions.textureFloat);
24
25
  }
25
- exports.canComputeGrid3dOnGPU = canComputeGrid3dOnGPU;
26
26
  const FrameBufferName = 'grid3d-computable';
27
27
  const Texture0Name = 'grid3d-computable-0';
28
28
  const Texture1Name = 'grid3d-computable-1';
@@ -196,7 +196,6 @@ function createGrid3dComputeRenderable(spec) {
196
196
  return new Float32Array(array.buffer, array.byteOffset, nx * ny * nz);
197
197
  };
198
198
  }
199
- exports.createGrid3dComputeRenderable = createGrid3dComputeRenderable;
200
199
  function resetGl(webgl, w) {
201
200
  const { gl, state } = webgl;
202
201
  state.viewport(0, 0, w, w);
@@ -5,7 +5,7 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.createHiZRenderable = void 0;
8
+ exports.createHiZRenderable = createHiZRenderable;
9
9
  const vec2_1 = require("../../mol-math/linear-algebra/3d/vec2");
10
10
  const value_cell_1 = require("../../mol-util/value-cell");
11
11
  const renderable_1 = require("../renderable");
@@ -33,4 +33,3 @@ function createHiZRenderable(ctx, previousLevel) {
33
33
  const renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', HiZShaderCode, schema, values);
34
34
  return (0, renderable_1.createComputeRenderable)(renderItem, values);
35
35
  }
36
- exports.createHiZRenderable = createHiZRenderable;
@@ -5,7 +5,7 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.createHistogramPyramid = void 0;
8
+ exports.createHistogramPyramid = createHistogramPyramid;
9
9
  const renderable_1 = require("../../renderable");
10
10
  const render_item_1 = require("../../webgl/render-item");
11
11
  const schema_1 = require("../../renderable/schema");
@@ -171,4 +171,3 @@ function createHistogramPyramid(ctx, inputTexture, scale, gridTexDim) {
171
171
  // console.log({ height, count, scale });
172
172
  return { pyramidTex, count, height, levels, scale };
173
173
  }
174
- exports.createHistogramPyramid = createHistogramPyramid;
@@ -5,7 +5,7 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.getHistopyramidSum = void 0;
8
+ exports.getHistopyramidSum = getHistopyramidSum;
9
9
  const renderable_1 = require("../../renderable");
10
10
  const render_item_1 = require("../../webgl/render-item");
11
11
  const schema_1 = require("../../renderable/schema");
@@ -85,4 +85,3 @@ function getHistopyramidSum(ctx, pyramidTopTexture) {
85
85
  ? sumInts[0]
86
86
  : (0, number_packing_1.unpackRGBToInt)(sumBytes[0], sumBytes[1], sumBytes[2]);
87
87
  }
88
- exports.getHistopyramidSum = getHistopyramidSum;
@@ -5,7 +5,7 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.calcActiveVoxels = void 0;
8
+ exports.calcActiveVoxels = calcActiveVoxels;
9
9
  const renderable_1 = require("../../renderable");
10
10
  const render_item_1 = require("../../webgl/render-item");
11
11
  const schema_1 = require("../../renderable/schema");
@@ -102,4 +102,3 @@ function calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridSc
102
102
  ctx.timer.markEnd('calcActiveVoxels');
103
103
  return activeVoxelsTex;
104
104
  }
105
- exports.calcActiveVoxels = calcActiveVoxels;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.extractIsosurface = exports.createIsosurfaceBuffers = void 0;
8
+ exports.createIsosurfaceBuffers = createIsosurfaceBuffers;
9
+ exports.extractIsosurface = extractIsosurface;
9
10
  const renderable_1 = require("../../renderable");
10
11
  const render_item_1 = require("../../webgl/render-item");
11
12
  const schema_1 = require("../../renderable/schema");
@@ -168,7 +169,6 @@ function createIsosurfaceBuffers(ctx, activeVoxelsBase, volumeData, histogramPyr
168
169
  // printTextureImage(readTexture(ctx, normalTexture, new Float32Array(width * height * 4)), { scale: 0.75, normalize: true });
169
170
  return { vertexTexture, groupTexture, normalTexture, vertexCount: count };
170
171
  }
171
- exports.createIsosurfaceBuffers = createIsosurfaceBuffers;
172
172
  //
173
173
  /**
174
174
  * GPU isosurface extraction
@@ -189,4 +189,3 @@ function extractIsosurface(ctx, volumeData, gridDim, gridTexDim, gridTexScale, t
189
189
  ctx.timer.markEnd('extractIsosurface');
190
190
  return gv;
191
191
  }
192
- exports.extractIsosurface = extractIsosurface;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.getTriIndices = exports.getTriCount = void 0;
8
+ exports.getTriCount = getTriCount;
9
+ exports.getTriIndices = getTriIndices;
9
10
  const tables_1 = require("../../../mol-geo/util/marching-cubes/tables");
10
11
  const util_1 = require("../../../mol-gl/renderable/util");
11
12
  let TriCount;
@@ -19,7 +20,6 @@ function getTriCount() {
19
20
  }
20
21
  return TriCount;
21
22
  }
22
- exports.getTriCount = getTriCount;
23
23
  let TriIndices;
24
24
  function getTriIndices() {
25
25
  if (TriIndices !== undefined)
@@ -38,4 +38,3 @@ function getTriIndices() {
38
38
  }
39
39
  return TriIndices;
40
40
  }
41
- exports.getTriIndices = getTriIndices;
@@ -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.readAlphaTexture = exports.readTexture = exports.getSharedCopyRenderable = exports.createCopyRenderable = exports.QuadValues = exports.QuadSchema = exports.QuadPositions = void 0;
8
+ exports.QuadValues = exports.QuadSchema = exports.QuadPositions = void 0;
9
+ exports.createCopyRenderable = createCopyRenderable;
10
+ exports.getSharedCopyRenderable = getSharedCopyRenderable;
11
+ exports.readTexture = readTexture;
12
+ exports.readAlphaTexture = readAlphaTexture;
9
13
  const texture_1 = require("../../mol-gl/webgl/texture");
10
14
  const mol_util_1 = require("../../mol-util");
11
15
  const schema_1 = require("../../mol-gl/renderable/schema");
@@ -48,7 +52,6 @@ function createCopyRenderable(ctx, texture) {
48
52
  const renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', CopyShaderCode, schema, values);
49
53
  return (0, renderable_1.createComputeRenderable)(renderItem, values);
50
54
  }
51
- exports.createCopyRenderable = createCopyRenderable;
52
55
  const SharedCopyName = 'shared-copy';
53
56
  function getSharedCopyRenderable(ctx, texture) {
54
57
  if (!ctx.namedComputeRenderables[SharedCopyName]) {
@@ -60,7 +63,6 @@ function getSharedCopyRenderable(ctx, texture) {
60
63
  copy.update();
61
64
  return copy;
62
65
  }
63
- exports.getSharedCopyRenderable = getSharedCopyRenderable;
64
66
  //
65
67
  const ReadTextureName = 'read-texture';
66
68
  const ReadAlphaTextureName = 'read-alpha-texture';
@@ -81,7 +83,6 @@ function readTexture(ctx, texture, array) {
81
83
  ctx.readPixels(0, 0, width, height, array);
82
84
  return { array, width, height };
83
85
  }
84
- exports.readTexture = readTexture;
85
86
  function readAlphaTexture(ctx, texture) {
86
87
  const { gl, state, resources } = ctx;
87
88
  if (texture.type !== gl.UNSIGNED_BYTE)
@@ -117,4 +118,3 @@ function readAlphaTexture(ctx, texture) {
117
118
  ctx.readPixels(0, 0, width, height, array);
118
119
  return { array, width, height };
119
120
  }
120
- exports.readAlphaTexture = readAlphaTexture;
@@ -5,7 +5,9 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.createRenderable = exports.createRenderObject = exports.getNextMaterialId = void 0;
8
+ exports.getNextMaterialId = void 0;
9
+ exports.createRenderObject = createRenderObject;
10
+ exports.createRenderable = createRenderable;
9
11
  const id_factory_1 = require("../mol-util/id-factory");
10
12
  const direct_volume_1 = require("./renderable/direct-volume");
11
13
  const mesh_1 = require("./renderable/mesh");
@@ -22,7 +24,6 @@ exports.getNextMaterialId = (0, id_factory_1.idFactory)(0, 0x7FFFFFFF);
22
24
  function createRenderObject(type, values, state, materialId) {
23
25
  return { id: getNextId(), type, values, state, materialId };
24
26
  }
25
- exports.createRenderObject = createRenderObject;
26
27
  function createRenderable(ctx, o, transparency) {
27
28
  switch (o.type) {
28
29
  case 'mesh': return (0, mesh_1.MeshRenderable)(ctx, o.id, o.values, o.state, o.materialId, transparency);
@@ -37,4 +38,3 @@ function createRenderable(ctx, o, transparency) {
37
38
  }
38
39
  throw new Error('unsupported type');
39
40
  }
40
- exports.createRenderable = createRenderable;
@@ -19,6 +19,7 @@ export declare const CylindersSchema: {
19
19
  padding: ValueSpec<"number">;
20
20
  uDoubleSided: UniformSpec<"b">;
21
21
  dIgnoreLight: DefineSpec<"boolean">;
22
+ dCelShaded: DefineSpec<"boolean">;
22
23
  dXrayShaded: DefineSpec<"string">;
23
24
  dTransparentBackfaces: DefineSpec<"string">;
24
25
  dSolidInterior: DefineSpec<"boolean">;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.CylindersRenderable = exports.CylindersSchema = void 0;
8
+ exports.CylindersSchema = void 0;
9
+ exports.CylindersRenderable = CylindersRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -25,6 +26,7 @@ exports.CylindersSchema = {
25
26
  padding: (0, schema_1.ValueSpec)('number'),
26
27
  uDoubleSided: (0, schema_1.UniformSpec)('b', 'material'),
27
28
  dIgnoreLight: (0, schema_1.DefineSpec)('boolean'),
29
+ dCelShaded: (0, schema_1.DefineSpec)('boolean'),
28
30
  dXrayShaded: (0, schema_1.DefineSpec)('string', ['off', 'on', 'inverted']),
29
31
  dTransparentBackfaces: (0, schema_1.DefineSpec)('string', ['off', 'on', 'opaque']),
30
32
  dSolidInterior: (0, schema_1.DefineSpec)('boolean'),
@@ -41,4 +43,3 @@ function CylindersRenderable(ctx, id, values, state, materialId, transparency) {
41
43
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
42
44
  return (0, renderable_1.createRenderable)(renderItem, values, state);
43
45
  }
44
- exports.CylindersRenderable = CylindersRenderable;
@@ -30,6 +30,7 @@ export declare const DirectVolumeSchema: {
30
30
  dPackedGroup: DefineSpec<"boolean">;
31
31
  dAxisOrder: DefineSpec<"string">;
32
32
  dIgnoreLight: DefineSpec<"boolean">;
33
+ dCelShaded: DefineSpec<"boolean">;
33
34
  dXrayShaded: DefineSpec<"string">;
34
35
  dLightCount: DefineSpec<"number">;
35
36
  dColorMarker: DefineSpec<"boolean">;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.DirectVolumeRenderable = exports.DirectVolumeSchema = void 0;
8
+ exports.DirectVolumeSchema = void 0;
9
+ exports.DirectVolumeRenderable = DirectVolumeRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -35,6 +36,7 @@ exports.DirectVolumeSchema = {
35
36
  dPackedGroup: (0, schema_1.DefineSpec)('boolean'),
36
37
  dAxisOrder: (0, schema_1.DefineSpec)('string', ['012', '021', '102', '120', '201', '210']),
37
38
  dIgnoreLight: (0, schema_1.DefineSpec)('boolean'),
39
+ dCelShaded: (0, schema_1.DefineSpec)('boolean'),
38
40
  dXrayShaded: (0, schema_1.DefineSpec)('string', ['off', 'on', 'inverted']),
39
41
  };
40
42
  function DirectVolumeRenderable(ctx, id, values, state, materialId, transparency) {
@@ -50,4 +52,3 @@ function DirectVolumeRenderable(ctx, id, values, state, materialId, transparency
50
52
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
51
53
  return (0, renderable_1.createRenderable)(renderItem, values, state);
52
54
  }
53
- exports.DirectVolumeRenderable = DirectVolumeRenderable;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.ImageRenderable = exports.ImageSchema = void 0;
8
+ exports.ImageSchema = void 0;
9
+ exports.ImageRenderable = ImageRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -32,4 +33,3 @@ function ImageRenderable(ctx, id, values, state, materialId, transparency) {
32
33
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
33
34
  return (0, renderable_1.createRenderable)(renderItem, values, state);
34
35
  }
35
- exports.ImageRenderable = ImageRenderable;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.LinesRenderable = exports.LinesSchema = void 0;
8
+ exports.LinesSchema = void 0;
9
+ exports.LinesRenderable = LinesRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -32,4 +33,3 @@ function LinesRenderable(ctx, id, values, state, materialId, transparency) {
32
33
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
33
34
  return (0, renderable_1.createRenderable)(renderItem, values, state);
34
35
  }
35
- exports.LinesRenderable = LinesRenderable;
@@ -17,6 +17,7 @@ export declare const MeshSchema: {
17
17
  readonly uDoubleSided: UniformSpec<"b">;
18
18
  readonly dFlipSided: DefineSpec<"boolean">;
19
19
  readonly dIgnoreLight: DefineSpec<"boolean">;
20
+ readonly dCelShaded: DefineSpec<"boolean">;
20
21
  readonly dXrayShaded: DefineSpec<"string">;
21
22
  readonly dTransparentBackfaces: DefineSpec<"string">;
22
23
  readonly uBumpFrequency: UniformSpec<"f">;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.MeshRenderable = exports.MeshSchema = void 0;
8
+ exports.MeshSchema = void 0;
9
+ exports.MeshRenderable = MeshRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -22,6 +23,7 @@ exports.MeshSchema = {
22
23
  uDoubleSided: (0, schema_1.UniformSpec)('b', 'material'),
23
24
  dFlipSided: (0, schema_1.DefineSpec)('boolean'),
24
25
  dIgnoreLight: (0, schema_1.DefineSpec)('boolean'),
26
+ dCelShaded: (0, schema_1.DefineSpec)('boolean'),
25
27
  dXrayShaded: (0, schema_1.DefineSpec)('string', ['off', 'on', 'inverted']),
26
28
  dTransparentBackfaces: (0, schema_1.DefineSpec)('string', ['off', 'on', 'opaque']),
27
29
  uBumpFrequency: (0, schema_1.UniformSpec)('f', 'material'),
@@ -37,4 +39,3 @@ function MeshRenderable(ctx, id, values, state, materialId, transparency) {
37
39
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
38
40
  return (0, renderable_1.createRenderable)(renderItem, values, state);
39
41
  }
40
- exports.MeshRenderable = MeshRenderable;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.PointsRenderable = exports.PointsSchema = void 0;
8
+ exports.PointsSchema = void 0;
9
+ exports.PointsRenderable = PointsRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -28,4 +29,3 @@ function PointsRenderable(ctx, id, values, state, materialId, transparency) {
28
29
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'points', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
29
30
  return (0, renderable_1.createRenderable)(renderItem, values, state);
30
31
  }
31
- exports.PointsRenderable = PointsRenderable;
@@ -133,6 +133,7 @@ export declare const GlobalUniformSchema: {
133
133
  readonly uMarkerPriority: UniformSpec<"i">;
134
134
  readonly uMarkerAverage: UniformSpec<"f">;
135
135
  readonly uXrayEdgeFalloff: UniformSpec<"f">;
136
+ readonly uCelSteps: UniformSpec<"f">;
136
137
  readonly uExposure: UniformSpec<"f">;
137
138
  readonly uRenderMask: UniformSpec<"i">;
138
139
  readonly uMarkingDepthTest: UniformSpec<"b">;
@@ -6,7 +6,15 @@
6
6
  * @author Gianluca Tomasello <giagitom@gmail.com>
7
7
  */
8
8
  Object.defineProperty(exports, "__esModule", { value: true });
9
- exports.BaseSchema = exports.ClippingSchema = exports.SubstanceSchema = exports.EmissiveSchema = exports.TransparencySchema = exports.OverpaintSchema = exports.MarkerSchema = exports.SizeSchema = exports.ColorSchema = exports.InternalSchema = exports.GlobalTextureSchema = exports.GlobalUniformSchema = exports.ValueSpec = exports.DefineSpec = exports.ElementsSpec = exports.TextureSpec = exports.UniformSpec = exports.AttributeSpec = exports.getValueVersions = exports.splitValues = void 0;
9
+ exports.BaseSchema = exports.ClippingSchema = exports.SubstanceSchema = exports.EmissiveSchema = exports.TransparencySchema = exports.OverpaintSchema = exports.MarkerSchema = exports.SizeSchema = exports.ColorSchema = exports.InternalSchema = exports.GlobalTextureSchema = exports.GlobalUniformSchema = void 0;
10
+ exports.splitValues = splitValues;
11
+ exports.getValueVersions = getValueVersions;
12
+ exports.AttributeSpec = AttributeSpec;
13
+ exports.UniformSpec = UniformSpec;
14
+ exports.TextureSpec = TextureSpec;
15
+ exports.ElementsSpec = ElementsSpec;
16
+ exports.DefineSpec = DefineSpec;
17
+ exports.ValueSpec = ValueSpec;
10
18
  function splitValues(schema, values) {
11
19
  const attributeValues = {};
12
20
  const defineValues = {};
@@ -40,7 +48,6 @@ function splitValues(schema, values) {
40
48
  });
41
49
  return { attributeValues, defineValues, textureValues, materialTextureValues, uniformValues, materialUniformValues, bufferedUniformValues };
42
50
  }
43
- exports.splitValues = splitValues;
44
51
  function getValueVersions(values) {
45
52
  const versions = {};
46
53
  Object.keys(values).forEach(k => {
@@ -48,31 +55,24 @@ function getValueVersions(values) {
48
55
  });
49
56
  return versions;
50
57
  }
51
- exports.getValueVersions = getValueVersions;
52
58
  function AttributeSpec(kind, itemSize, divisor) {
53
59
  return { type: 'attribute', kind, itemSize, divisor };
54
60
  }
55
- exports.AttributeSpec = AttributeSpec;
56
61
  function UniformSpec(kind, variant) {
57
62
  return { type: 'uniform', kind, variant };
58
63
  }
59
- exports.UniformSpec = UniformSpec;
60
64
  function TextureSpec(kind, format, dataType, filter, variant) {
61
65
  return { type: 'texture', kind, format, dataType, filter, variant };
62
66
  }
63
- exports.TextureSpec = TextureSpec;
64
67
  function ElementsSpec(kind) {
65
68
  return { type: 'elements', kind };
66
69
  }
67
- exports.ElementsSpec = ElementsSpec;
68
70
  function DefineSpec(kind, options) {
69
71
  return { type: 'define', kind, options };
70
72
  }
71
- exports.DefineSpec = DefineSpec;
72
73
  function ValueSpec(kind) {
73
74
  return { type: 'value', kind };
74
75
  }
75
- exports.ValueSpec = ValueSpec;
76
76
  //
77
77
  exports.GlobalUniformSchema = {
78
78
  uDrawId: UniformSpec('i'),
@@ -116,6 +116,7 @@ exports.GlobalUniformSchema = {
116
116
  uMarkerPriority: UniformSpec('i'),
117
117
  uMarkerAverage: UniformSpec('f'),
118
118
  uXrayEdgeFalloff: UniformSpec('f'),
119
+ uCelSteps: UniformSpec('f'),
119
120
  uExposure: UniformSpec('f'),
120
121
  uRenderMask: UniformSpec('i'),
121
122
  uMarkingDepthTest: UniformSpec('b'),
@@ -13,6 +13,7 @@ export declare const SpheresSchema: {
13
13
  padding: ValueSpec<"number">;
14
14
  uDoubleSided: UniformSpec<"b">;
15
15
  dIgnoreLight: DefineSpec<"boolean">;
16
+ dCelShaded: DefineSpec<"boolean">;
16
17
  dXrayShaded: DefineSpec<"string">;
17
18
  dTransparentBackfaces: DefineSpec<"string">;
18
19
  dSolidInterior: DefineSpec<"boolean">;
@@ -5,7 +5,8 @@
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
6
6
  */
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
- exports.SpheresRenderable = exports.SpheresSchema = void 0;
8
+ exports.SpheresSchema = void 0;
9
+ exports.SpheresRenderable = SpheresRenderable;
9
10
  const renderable_1 = require("../renderable");
10
11
  const render_item_1 = require("../webgl/render-item");
11
12
  const schema_1 = require("./schema");
@@ -19,6 +20,7 @@ exports.SpheresSchema = {
19
20
  padding: (0, schema_1.ValueSpec)('number'),
20
21
  uDoubleSided: (0, schema_1.UniformSpec)('b', 'material'),
21
22
  dIgnoreLight: (0, schema_1.DefineSpec)('boolean'),
23
+ dCelShaded: (0, schema_1.DefineSpec)('boolean'),
22
24
  dXrayShaded: (0, schema_1.DefineSpec)('string', ['off', 'on', 'inverted']),
23
25
  dTransparentBackfaces: (0, schema_1.DefineSpec)('string', ['off', 'on', 'opaque']),
24
26
  dSolidInterior: (0, schema_1.DefineSpec)('boolean'),
@@ -40,4 +42,3 @@ function SpheresRenderable(ctx, id, values, state, materialId, transparency) {
40
42
  const renderItem = (0, render_item_1.createGraphicsRenderItem)(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
41
43
  return (0, renderable_1.createRenderable)(renderItem, values, state);
42
44
  }
43
- exports.SpheresRenderable = SpheresRenderable;