molstar 3.0.0-dev.5 → 3.0.0-dev.9

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 (688) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +187 -187
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +106 -95
  5. package/build/viewer/molstar.js +1 -1
  6. package/lib/apps/docking-viewer/index.d.ts +2 -1
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/docking-viewer/index.js +87 -74
  9. package/lib/apps/viewer/app.d.ts +230 -0
  10. package/lib/apps/viewer/app.js +515 -0
  11. package/lib/apps/viewer/embedded.html +43 -43
  12. package/lib/apps/viewer/index.d.ts +2 -403
  13. package/lib/apps/viewer/index.html +106 -95
  14. package/lib/apps/viewer/index.js +2 -420
  15. package/lib/cli/cifschema/index.d.ts +1 -1
  16. package/lib/cli/cifschema/index.js +15 -35
  17. package/lib/commonjs/apps/docking-viewer/index.d.ts +2 -1
  18. package/lib/commonjs/apps/docking-viewer/index.js +86 -73
  19. package/lib/commonjs/apps/viewer/app.d.ts +230 -0
  20. package/lib/commonjs/apps/viewer/app.js +521 -0
  21. package/lib/commonjs/apps/viewer/index.d.ts +2 -403
  22. package/lib/commonjs/apps/viewer/index.js +2 -423
  23. package/lib/commonjs/cli/cifschema/index.d.ts +1 -1
  24. package/lib/commonjs/cli/cifschema/index.js +15 -35
  25. package/lib/commonjs/examples/alpha-orbitals/index.js +3 -4
  26. package/lib/commonjs/examples/basic-wrapper/index.js +23 -11
  27. package/lib/commonjs/examples/lighting/index.d.ts +1 -1
  28. package/lib/commonjs/examples/lighting/index.js +57 -41
  29. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -14
  30. package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts +0 -1
  31. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +1 -14
  32. package/lib/commonjs/extensions/anvil/behavior.d.ts +4 -0
  33. package/lib/commonjs/extensions/anvil/representation.d.ts +50 -0
  34. package/lib/commonjs/extensions/cellpack/representation.d.ts +10 -0
  35. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +30 -0
  36. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +4 -4
  37. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +68 -0
  38. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +236 -0
  39. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.d.ts +14 -0
  40. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +125 -0
  41. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.d.ts +12 -0
  42. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +111 -0
  43. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.d.ts +28 -0
  44. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +130 -0
  45. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +1 -1
  46. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +6 -2
  47. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +1 -1
  48. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +10 -0
  49. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +1 -1
  50. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +50 -0
  51. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +3 -9
  52. package/lib/commonjs/mol-canvas3d/canvas3d.js +34 -23
  53. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +3 -2
  54. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +4 -0
  55. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +2 -2
  56. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +4 -0
  57. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +2 -2
  58. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  59. package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +13 -1
  60. package/lib/commonjs/mol-canvas3d/passes/draw.js +16 -15
  61. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
  62. package/lib/commonjs/mol-canvas3d/passes/image.js +3 -2
  63. package/lib/commonjs/mol-canvas3d/passes/marking.js +1 -1
  64. package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +10 -2
  65. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +18 -14
  66. package/lib/commonjs/mol-canvas3d/passes/pick.js +12 -12
  67. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +3 -3
  68. package/lib/commonjs/mol-canvas3d/passes/smaa.js +1 -1
  69. package/lib/commonjs/mol-geo/geometry/base.d.ts +18 -0
  70. package/lib/commonjs/mol-geo/geometry/base.js +18 -1
  71. package/lib/commonjs/mol-geo/geometry/clipping-data.d.ts +1 -3
  72. package/lib/commonjs/mol-geo/geometry/clipping-data.js +3 -8
  73. package/lib/commonjs/mol-geo/geometry/color-data.d.ts +1 -1
  74. package/lib/commonjs/mol-geo/geometry/color-data.js +22 -0
  75. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +12 -2
  76. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +2 -2
  77. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +15 -38
  78. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +21 -66
  79. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.d.ts +2 -4
  80. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +4 -7
  81. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +10 -0
  82. package/lib/commonjs/mol-geo/geometry/image/image.js +1 -1
  83. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +11 -0
  84. package/lib/commonjs/mol-geo/geometry/lines/lines.js +1 -1
  85. package/lib/commonjs/mol-geo/geometry/marker-data.d.ts +0 -1
  86. package/lib/commonjs/mol-geo/geometry/marker-data.js +13 -9
  87. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +10 -0
  88. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +2 -2
  89. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +11 -1
  90. package/lib/commonjs/mol-geo/geometry/points/points.js +1 -1
  91. package/lib/commonjs/mol-geo/geometry/size-data.js +5 -5
  92. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +10 -0
  93. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +2 -2
  94. package/lib/commonjs/mol-geo/geometry/text/text.d.ts +10 -0
  95. package/lib/commonjs/mol-geo/geometry/text/text.js +1 -1
  96. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +10 -0
  97. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  98. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +2 -2
  99. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +2 -2
  100. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +10 -9
  101. package/lib/commonjs/mol-gl/render-object.d.ts +2 -1
  102. package/lib/commonjs/mol-gl/render-object.js +10 -10
  103. package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +11 -5
  104. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  105. package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +15 -14
  106. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  107. package/lib/commonjs/mol-gl/renderable/image.d.ts +10 -4
  108. package/lib/commonjs/mol-gl/renderable/image.js +2 -2
  109. package/lib/commonjs/mol-gl/renderable/lines.d.ts +39 -33
  110. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  111. package/lib/commonjs/mol-gl/renderable/mesh.d.ts +11 -5
  112. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  113. package/lib/commonjs/mol-gl/renderable/points.d.ts +10 -4
  114. package/lib/commonjs/mol-gl/renderable/points.js +2 -2
  115. package/lib/commonjs/mol-gl/renderable/schema.d.ts +10 -11
  116. package/lib/commonjs/mol-gl/renderable/schema.js +4 -10
  117. package/lib/commonjs/mol-gl/renderable/spheres.d.ts +11 -5
  118. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  119. package/lib/commonjs/mol-gl/renderable/text.d.ts +10 -4
  120. package/lib/commonjs/mol-gl/renderable/text.js +2 -2
  121. package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +11 -6
  122. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  123. package/lib/commonjs/mol-gl/renderable.d.ts +0 -1
  124. package/lib/commonjs/mol-gl/renderer.d.ts +12 -12
  125. package/lib/commonjs/mol-gl/renderer.js +23 -92
  126. package/lib/commonjs/mol-gl/scene.d.ts +2 -2
  127. package/lib/commonjs/mol-gl/scene.js +7 -5
  128. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +1 -1
  129. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +1 -1
  130. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  131. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  132. package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.d.ts +1 -1
  133. package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +1 -1
  134. package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.d.ts +1 -1
  135. package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +1 -1
  136. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  137. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  138. package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.d.ts +1 -1
  139. package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +1 -1
  140. package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.d.ts +1 -1
  141. package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +1 -1
  142. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  143. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  144. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  145. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  146. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
  147. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +1 -1
  148. package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.d.ts +1 -1
  149. package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +1 -1
  150. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
  151. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +1 -1
  152. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +1 -1
  153. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +1 -1
  154. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.d.ts +1 -1
  155. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +1 -1
  156. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +1 -1
  157. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +1 -1
  158. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  159. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  160. package/lib/commonjs/mol-gl/shader/gaussian-density.frag.d.ts +1 -1
  161. package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +1 -1
  162. package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.d.ts +1 -1
  163. package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +1 -1
  164. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +1 -1
  165. package/lib/commonjs/mol-gl/shader/image.frag.js +1 -1
  166. package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.d.ts +1 -1
  167. package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +1 -1
  168. package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
  169. package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
  170. package/lib/commonjs/mol-gl/shader/mesh.vert.d.ts +1 -1
  171. package/lib/commonjs/mol-gl/shader/mesh.vert.js +1 -1
  172. package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +1 -1
  173. package/lib/commonjs/mol-gl/shader/spheres.frag.js +1 -1
  174. package/lib/commonjs/mol-gl/shader-code.d.ts +3 -1
  175. package/lib/commonjs/mol-gl/shader-code.js +43 -14
  176. package/lib/commonjs/mol-gl/webgl/render-item.d.ts +7 -6
  177. package/lib/commonjs/mol-gl/webgl/render-item.js +10 -8
  178. package/lib/commonjs/mol-gl/webgl/resources.js +8 -1
  179. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +326 -1
  180. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +326 -1
  181. package/lib/commonjs/mol-io/reader/mol2/parser.d.ts +1 -1
  182. package/lib/commonjs/mol-io/reader/mol2/parser.js +33 -3
  183. package/lib/commonjs/mol-io/reader/mol2/schema.d.ts +12 -1
  184. package/lib/commonjs/mol-io/reader/mol2/schema.js +1 -1
  185. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +2 -2
  186. package/lib/commonjs/mol-math/geometry/symmetry-operator.js +3 -2
  187. package/lib/commonjs/mol-math/linear-algebra/3d/quat.d.ts +9 -1
  188. package/lib/commonjs/mol-math/linear-algebra/3d/quat.js +20 -1
  189. package/lib/commonjs/mol-model/structure/model/model.d.ts +1 -0
  190. package/lib/commonjs/mol-model/structure/model/model.js +8 -2
  191. package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.d.ts +6 -1
  192. package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.js +1 -1
  193. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.d.ts +1 -1
  194. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.js +4 -1
  195. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.d.ts +1 -1
  196. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js +12 -1
  197. package/lib/commonjs/mol-model/structure/model/types.js +9 -0
  198. package/lib/commonjs/mol-model/structure/structure/element/stats.js +8 -0
  199. package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.d.ts +2 -1
  200. package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js +11 -2
  201. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -1
  202. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +20 -10
  203. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.d.ts +1 -1
  204. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +21 -11
  205. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +2 -0
  206. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +20 -0
  207. package/lib/commonjs/mol-model-formats/structure/mol2.d.ts +1 -1
  208. package/lib/commonjs/mol-model-formats/structure/mol2.js +37 -7
  209. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts +18 -1
  210. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +18 -5
  211. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +10 -0
  212. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +10 -0
  213. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +30 -0
  214. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +40 -0
  215. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +4 -6
  216. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +11 -0
  217. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +3 -1
  218. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
  219. package/lib/commonjs/mol-plugin/commands.d.ts +1 -4
  220. package/lib/commonjs/mol-plugin/config.d.ts +2 -2
  221. package/lib/commonjs/mol-plugin/config.js +5 -25
  222. package/lib/commonjs/mol-plugin/features.d.ts +9 -0
  223. package/lib/commonjs/mol-plugin/features.js +38 -0
  224. package/lib/commonjs/mol-plugin/spec.js +1 -0
  225. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +12 -0
  226. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +8 -1
  227. package/lib/commonjs/mol-plugin-state/actions/structure.js +183 -72
  228. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +5 -355
  229. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +13 -8
  230. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -71
  231. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +4 -4
  232. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.d.ts +1 -1
  233. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +1 -1
  234. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +33 -19
  235. package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +13 -1
  236. package/lib/commonjs/mol-plugin-state/manager/structure/component.js +13 -8
  237. package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +3 -1
  238. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +32 -0
  239. package/lib/commonjs/mol-plugin-state/transforms/representation.js +2 -2
  240. package/lib/commonjs/mol-plugin-ui/index.d.ts +4 -4
  241. package/lib/commonjs/mol-plugin-ui/index.js +13 -16
  242. package/lib/commonjs/mol-plugin-ui/plugin.js +1 -1
  243. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +2 -6
  244. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +10 -0
  245. package/lib/commonjs/mol-repr/shape/loci/common.d.ts +10 -0
  246. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +10 -0
  247. package/lib/commonjs/mol-repr/shape/loci/distance.d.ts +10 -0
  248. package/lib/commonjs/mol-repr/shape/loci/label.d.ts +10 -0
  249. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +10 -0
  250. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +10 -0
  251. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +10 -0
  252. package/lib/commonjs/mol-repr/structure/complex-representation.js +1 -1
  253. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +61 -19
  254. package/lib/commonjs/mol-repr/structure/params.d.ts +81 -19
  255. package/lib/commonjs/mol-repr/structure/registry.d.ts +141 -19
  256. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +30 -0
  257. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +30 -0
  258. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +30 -0
  259. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +30 -0
  260. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +30 -0
  261. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +30 -0
  262. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +1 -1
  263. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +34 -58
  264. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +2 -7
  265. package/lib/commonjs/mol-repr/structure/representation/label.d.ts +30 -0
  266. package/lib/commonjs/mol-repr/structure/representation/label.js +1 -1
  267. package/lib/commonjs/mol-repr/structure/representation/line.d.ts +30 -0
  268. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +30 -0
  269. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +1 -1
  270. package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +30 -0
  271. package/lib/commonjs/mol-repr/structure/representation/point.d.ts +30 -0
  272. package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +30 -0
  273. package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +30 -0
  274. package/lib/commonjs/mol-repr/structure/units-representation.js +1 -1
  275. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +81 -19
  276. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +20 -0
  277. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +10 -0
  278. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +20 -0
  279. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +2 -2
  280. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.d.ts +10 -0
  281. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +2 -2
  282. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +10 -0
  283. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +10 -0
  284. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +10 -0
  285. package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts +10 -0
  286. package/lib/commonjs/mol-repr/structure/visual/element-point.d.ts +10 -0
  287. package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +20 -0
  288. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +10 -0
  289. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.d.ts +22 -38
  290. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +8 -6
  291. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +40 -0
  292. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +11 -8
  293. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +10 -0
  294. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +1 -1
  295. package/lib/commonjs/mol-repr/structure/visual/label-text.d.ts +10 -0
  296. package/lib/commonjs/mol-repr/structure/visual/label-text.js +1 -2
  297. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +10 -0
  298. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +1 -1
  299. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +10 -0
  300. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +1 -1
  301. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +10 -0
  302. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +10 -0
  303. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +10 -0
  304. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +20 -0
  305. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +20 -0
  306. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +10 -0
  307. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +10 -0
  308. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +10 -0
  309. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
  310. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +10 -0
  311. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +1 -1
  312. package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts +3 -2
  313. package/lib/commonjs/mol-repr/structure/visual/util/common.js +2 -5
  314. package/lib/commonjs/mol-repr/structure/visual/util/gaussian.d.ts +7 -6
  315. package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js +12 -12
  316. package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.d.ts +2 -1
  317. package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js +4 -4
  318. package/lib/commonjs/mol-repr/visual.js +11 -7
  319. package/lib/commonjs/mol-repr/volume/direct-volume.d.ts +33 -57
  320. package/lib/commonjs/mol-repr/volume/direct-volume.js +8 -12
  321. package/lib/commonjs/mol-repr/volume/isosurface.d.ts +60 -0
  322. package/lib/commonjs/mol-repr/volume/isosurface.js +11 -2
  323. package/lib/commonjs/mol-repr/volume/registry.d.ts +31 -19
  324. package/lib/commonjs/mol-repr/volume/representation.d.ts +10 -0
  325. package/lib/commonjs/mol-repr/volume/slice.d.ts +30 -0
  326. package/lib/commonjs/mol-repr/volume/slice.js +2 -2
  327. package/lib/commonjs/mol-repr/volume/util.js +2 -2
  328. package/lib/commonjs/mol-script/language/builder.d.ts +0 -1
  329. package/lib/commonjs/mol-theme/clipping.d.ts +7 -15
  330. package/lib/commonjs/mol-theme/clipping.js +5 -12
  331. package/lib/commonjs/mol-theme/color/volume-value.d.ts +17 -0
  332. package/lib/commonjs/mol-theme/color/volume-value.js +57 -0
  333. package/lib/commonjs/mol-theme/color.d.ts +3 -0
  334. package/lib/commonjs/mol-theme/color.js +2 -0
  335. package/lib/commonjs/mol-util/clip.d.ts +49 -0
  336. package/lib/commonjs/mol-util/clip.js +97 -0
  337. package/lib/commonjs/mol-util/number-packing.d.ts +11 -0
  338. package/lib/commonjs/mol-util/{float-packing.js → number-packing.js} +10 -19
  339. package/lib/examples/alpha-orbitals/index.html +61 -60
  340. package/lib/examples/alpha-orbitals/index.js +4 -5
  341. package/lib/examples/basic-wrapper/index.html +137 -136
  342. package/lib/examples/basic-wrapper/index.js +24 -12
  343. package/lib/examples/lighting/index.d.ts +1 -1
  344. package/lib/examples/lighting/index.html +88 -86
  345. package/lib/examples/lighting/index.js +58 -42
  346. package/lib/examples/proteopedia-wrapper/index.html +236 -235
  347. package/lib/examples/proteopedia-wrapper/index.js +27 -15
  348. package/lib/extensions/alpha-orbitals/transforms.d.ts +0 -1
  349. package/lib/extensions/alpha-orbitals/transforms.js +1 -14
  350. package/lib/extensions/anvil/behavior.d.ts +4 -0
  351. package/lib/extensions/anvil/representation.d.ts +50 -0
  352. package/lib/extensions/cellpack/representation.d.ts +10 -0
  353. package/lib/extensions/dnatco/confal-pyramids/representation.d.ts +30 -0
  354. package/lib/extensions/geo-export/mesh-exporter.js +4 -4
  355. package/lib/extensions/model-archive/quality-assessment/behavior.d.ts +68 -0
  356. package/lib/extensions/model-archive/quality-assessment/behavior.js +233 -0
  357. package/lib/extensions/model-archive/quality-assessment/color/plddt.d.ts +14 -0
  358. package/lib/extensions/model-archive/quality-assessment/color/plddt.js +120 -0
  359. package/lib/extensions/model-archive/quality-assessment/color/qmean.d.ts +12 -0
  360. package/lib/extensions/model-archive/quality-assessment/color/qmean.js +106 -0
  361. package/lib/extensions/model-archive/quality-assessment/prop.d.ts +28 -0
  362. package/lib/extensions/model-archive/quality-assessment/prop.js +127 -0
  363. package/lib/extensions/pdbe/structure-quality-report/prop.js +1 -1
  364. package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +6 -2
  365. package/lib/extensions/rcsb/assembly-symmetry/prop.js +1 -1
  366. package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts +10 -0
  367. package/lib/extensions/rcsb/validation-report/prop.js +1 -1
  368. package/lib/extensions/rcsb/validation-report/representation.d.ts +50 -0
  369. package/lib/mol-canvas3d/canvas3d.d.ts +3 -9
  370. package/lib/mol-canvas3d/canvas3d.js +34 -23
  371. package/lib/mol-canvas3d/helper/bounding-sphere-helper.js +3 -2
  372. package/lib/mol-canvas3d/helper/camera-helper.d.ts +4 -0
  373. package/lib/mol-canvas3d/helper/camera-helper.js +2 -2
  374. package/lib/mol-canvas3d/helper/handle-helper.d.ts +4 -0
  375. package/lib/mol-canvas3d/helper/handle-helper.js +2 -2
  376. package/lib/mol-canvas3d/helper/helper.d.ts +2 -0
  377. package/lib/mol-canvas3d/passes/draw.d.ts +13 -1
  378. package/lib/mol-canvas3d/passes/draw.js +16 -15
  379. package/lib/mol-canvas3d/passes/image.d.ts +1 -0
  380. package/lib/mol-canvas3d/passes/image.js +3 -2
  381. package/lib/mol-canvas3d/passes/marking.js +1 -1
  382. package/lib/mol-canvas3d/passes/multi-sample.d.ts +10 -2
  383. package/lib/mol-canvas3d/passes/multi-sample.js +18 -14
  384. package/lib/mol-canvas3d/passes/pick.js +11 -11
  385. package/lib/mol-canvas3d/passes/postprocessing.js +3 -3
  386. package/lib/mol-canvas3d/passes/smaa.js +1 -1
  387. package/lib/mol-geo/geometry/base.d.ts +18 -0
  388. package/lib/mol-geo/geometry/base.js +18 -1
  389. package/lib/mol-geo/geometry/clipping-data.d.ts +1 -3
  390. package/lib/mol-geo/geometry/clipping-data.js +3 -8
  391. package/lib/mol-geo/geometry/color-data.d.ts +1 -1
  392. package/lib/mol-geo/geometry/color-data.js +22 -0
  393. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +12 -2
  394. package/lib/mol-geo/geometry/cylinders/cylinders.js +2 -2
  395. package/lib/mol-geo/geometry/direct-volume/direct-volume.d.ts +15 -38
  396. package/lib/mol-geo/geometry/direct-volume/direct-volume.js +22 -67
  397. package/lib/mol-geo/geometry/direct-volume/transfer-function.d.ts +2 -4
  398. package/lib/mol-geo/geometry/direct-volume/transfer-function.js +4 -7
  399. package/lib/mol-geo/geometry/image/image.d.ts +10 -0
  400. package/lib/mol-geo/geometry/image/image.js +1 -1
  401. package/lib/mol-geo/geometry/lines/lines.d.ts +11 -0
  402. package/lib/mol-geo/geometry/lines/lines.js +1 -1
  403. package/lib/mol-geo/geometry/marker-data.d.ts +0 -1
  404. package/lib/mol-geo/geometry/marker-data.js +13 -9
  405. package/lib/mol-geo/geometry/mesh/mesh.d.ts +10 -0
  406. package/lib/mol-geo/geometry/mesh/mesh.js +2 -2
  407. package/lib/mol-geo/geometry/points/points.d.ts +11 -1
  408. package/lib/mol-geo/geometry/points/points.js +1 -1
  409. package/lib/mol-geo/geometry/size-data.js +5 -5
  410. package/lib/mol-geo/geometry/spheres/spheres.d.ts +10 -0
  411. package/lib/mol-geo/geometry/spheres/spheres.js +2 -2
  412. package/lib/mol-geo/geometry/text/text.d.ts +10 -0
  413. package/lib/mol-geo/geometry/text/text.js +1 -1
  414. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +10 -0
  415. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  416. package/lib/mol-gl/compute/histogram-pyramid/sum.js +2 -2
  417. package/lib/mol-gl/compute/marching-cubes/isosurface.d.ts +2 -2
  418. package/lib/mol-gl/compute/marching-cubes/isosurface.js +10 -9
  419. package/lib/mol-gl/render-object.d.ts +2 -1
  420. package/lib/mol-gl/render-object.js +10 -10
  421. package/lib/mol-gl/renderable/cylinders.d.ts +11 -5
  422. package/lib/mol-gl/renderable/cylinders.js +3 -3
  423. package/lib/mol-gl/renderable/direct-volume.d.ts +15 -14
  424. package/lib/mol-gl/renderable/direct-volume.js +3 -3
  425. package/lib/mol-gl/renderable/image.d.ts +10 -4
  426. package/lib/mol-gl/renderable/image.js +2 -2
  427. package/lib/mol-gl/renderable/lines.d.ts +39 -33
  428. package/lib/mol-gl/renderable/lines.js +4 -4
  429. package/lib/mol-gl/renderable/mesh.d.ts +11 -5
  430. package/lib/mol-gl/renderable/mesh.js +3 -3
  431. package/lib/mol-gl/renderable/points.d.ts +10 -4
  432. package/lib/mol-gl/renderable/points.js +2 -2
  433. package/lib/mol-gl/renderable/schema.d.ts +10 -11
  434. package/lib/mol-gl/renderable/schema.js +4 -10
  435. package/lib/mol-gl/renderable/spheres.d.ts +11 -5
  436. package/lib/mol-gl/renderable/spheres.js +3 -3
  437. package/lib/mol-gl/renderable/text.d.ts +10 -4
  438. package/lib/mol-gl/renderable/text.js +2 -2
  439. package/lib/mol-gl/renderable/texture-mesh.d.ts +11 -6
  440. package/lib/mol-gl/renderable/texture-mesh.js +3 -3
  441. package/lib/mol-gl/renderable.d.ts +0 -1
  442. package/lib/mol-gl/renderer.d.ts +12 -12
  443. package/lib/mol-gl/renderer.js +24 -93
  444. package/lib/mol-gl/scene.d.ts +2 -2
  445. package/lib/mol-gl/scene.js +7 -5
  446. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +1 -1
  447. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js +1 -1
  448. package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  449. package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  450. package/lib/mol-gl/shader/chunks/assign-group.glsl.d.ts +1 -1
  451. package/lib/mol-gl/shader/chunks/assign-group.glsl.js +1 -1
  452. package/lib/mol-gl/shader/chunks/assign-marker-varying.glsl.d.ts +1 -1
  453. package/lib/mol-gl/shader/chunks/assign-marker-varying.glsl.js +1 -1
  454. package/lib/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  455. package/lib/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  456. package/lib/mol-gl/shader/chunks/assign-position.glsl.d.ts +1 -1
  457. package/lib/mol-gl/shader/chunks/assign-position.glsl.js +1 -1
  458. package/lib/mol-gl/shader/chunks/assign-size.glsl.d.ts +1 -1
  459. package/lib/mol-gl/shader/chunks/assign-size.glsl.js +1 -1
  460. package/lib/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  461. package/lib/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  462. package/lib/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  463. package/lib/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  464. package/lib/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
  465. package/lib/mol-gl/shader/chunks/common-frag-params.glsl.js +1 -1
  466. package/lib/mol-gl/shader/chunks/common-vert-params.glsl.d.ts +1 -1
  467. package/lib/mol-gl/shader/chunks/common-vert-params.glsl.js +1 -1
  468. package/lib/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
  469. package/lib/mol-gl/shader/chunks/common.glsl.js +1 -1
  470. package/lib/mol-gl/shader/chunks/wboit-write.glsl.d.ts +1 -1
  471. package/lib/mol-gl/shader/chunks/wboit-write.glsl.js +1 -1
  472. package/lib/mol-gl/shader/compute/color-smoothing/accumulate.vert.d.ts +1 -1
  473. package/lib/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +1 -1
  474. package/lib/mol-gl/shader/cylinders.frag.d.ts +1 -1
  475. package/lib/mol-gl/shader/cylinders.frag.js +1 -1
  476. package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  477. package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
  478. package/lib/mol-gl/shader/gaussian-density.frag.d.ts +1 -1
  479. package/lib/mol-gl/shader/gaussian-density.frag.js +1 -1
  480. package/lib/mol-gl/shader/histogram-pyramid/reduction.frag.d.ts +1 -1
  481. package/lib/mol-gl/shader/histogram-pyramid/reduction.frag.js +1 -1
  482. package/lib/mol-gl/shader/image.frag.d.ts +1 -1
  483. package/lib/mol-gl/shader/image.frag.js +1 -1
  484. package/lib/mol-gl/shader/marching-cubes/isosurface.frag.d.ts +1 -1
  485. package/lib/mol-gl/shader/marching-cubes/isosurface.frag.js +1 -1
  486. package/lib/mol-gl/shader/mesh.frag.d.ts +1 -1
  487. package/lib/mol-gl/shader/mesh.frag.js +1 -1
  488. package/lib/mol-gl/shader/mesh.vert.d.ts +1 -1
  489. package/lib/mol-gl/shader/mesh.vert.js +1 -1
  490. package/lib/mol-gl/shader/spheres.frag.d.ts +1 -1
  491. package/lib/mol-gl/shader/spheres.frag.js +1 -1
  492. package/lib/mol-gl/shader-code.d.ts +3 -1
  493. package/lib/mol-gl/shader-code.js +43 -14
  494. package/lib/mol-gl/webgl/render-item.d.ts +7 -6
  495. package/lib/mol-gl/webgl/render-item.js +8 -6
  496. package/lib/mol-gl/webgl/resources.js +8 -1
  497. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +326 -1
  498. package/lib/mol-io/reader/cif/schema/mmcif.js +326 -1
  499. package/lib/mol-io/reader/mol2/parser.d.ts +1 -1
  500. package/lib/mol-io/reader/mol2/parser.js +33 -3
  501. package/lib/mol-io/reader/mol2/schema.d.ts +12 -1
  502. package/lib/mol-io/reader/mol2/schema.js +1 -1
  503. package/lib/mol-math/geometry/gaussian-density/gpu.js +2 -2
  504. package/lib/mol-math/geometry/symmetry-operator.js +3 -2
  505. package/lib/mol-math/linear-algebra/3d/quat.d.ts +9 -1
  506. package/lib/mol-math/linear-algebra/3d/quat.js +20 -1
  507. package/lib/mol-model/structure/model/model.d.ts +1 -0
  508. package/lib/mol-model/structure/model/model.js +8 -2
  509. package/lib/mol-model/structure/model/properties/atomic/hierarchy.d.ts +6 -1
  510. package/lib/mol-model/structure/model/properties/atomic/hierarchy.js +1 -1
  511. package/lib/mol-model/structure/model/properties/utils/atomic-derived.d.ts +1 -1
  512. package/lib/mol-model/structure/model/properties/utils/atomic-derived.js +5 -2
  513. package/lib/mol-model/structure/model/properties/utils/atomic-index.d.ts +1 -1
  514. package/lib/mol-model/structure/model/properties/utils/atomic-index.js +12 -1
  515. package/lib/mol-model/structure/model/types.js +9 -0
  516. package/lib/mol-model/structure/structure/element/stats.js +8 -0
  517. package/lib/mol-model/structure/structure/unit/bonds/common.d.ts +2 -1
  518. package/lib/mol-model/structure/structure/unit/bonds/common.js +9 -1
  519. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -1
  520. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +21 -11
  521. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.d.ts +1 -1
  522. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +22 -12
  523. package/lib/mol-model/structure/structure/unit/rings.js +2 -0
  524. package/lib/mol-model-formats/shape/ply.d.ts +20 -0
  525. package/lib/mol-model-formats/structure/mol2.d.ts +1 -1
  526. package/lib/mol-model-formats/structure/mol2.js +37 -7
  527. package/lib/mol-model-formats/structure/property/bonds/index-pair.d.ts +18 -1
  528. package/lib/mol-model-formats/structure/property/bonds/index-pair.js +18 -5
  529. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +10 -0
  530. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +10 -0
  531. package/lib/mol-model-props/computed/representations/interactions.d.ts +30 -0
  532. package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +40 -0
  533. package/lib/mol-plugin/behavior/dynamic/representation.js +4 -6
  534. package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +11 -0
  535. package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +3 -1
  536. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
  537. package/lib/mol-plugin/commands.d.ts +1 -4
  538. package/lib/mol-plugin/config.d.ts +2 -2
  539. package/lib/mol-plugin/config.js +4 -23
  540. package/lib/mol-plugin/features.d.ts +9 -0
  541. package/lib/mol-plugin/features.js +35 -0
  542. package/lib/mol-plugin/spec.js +1 -0
  543. package/lib/mol-plugin/util/viewport-screenshot.d.ts +12 -0
  544. package/lib/mol-plugin/version.js +2 -2
  545. package/lib/mol-plugin-state/actions/structure.d.ts +8 -1
  546. package/lib/mol-plugin-state/actions/structure.js +183 -72
  547. package/lib/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +5 -355
  548. package/lib/mol-plugin-state/builder/structure/hierarchy-preset.js +14 -9
  549. package/lib/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -71
  550. package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts +4 -4
  551. package/lib/mol-plugin-state/helpers/structure-clipping.d.ts +1 -1
  552. package/lib/mol-plugin-state/helpers/structure-clipping.js +1 -1
  553. package/lib/mol-plugin-state/helpers/structure-selection-query.js +34 -20
  554. package/lib/mol-plugin-state/manager/structure/component.d.ts +13 -1
  555. package/lib/mol-plugin-state/manager/structure/component.js +14 -9
  556. package/lib/mol-plugin-state/manager/structure/selection.js +3 -1
  557. package/lib/mol-plugin-state/transforms/representation.d.ts +32 -0
  558. package/lib/mol-plugin-state/transforms/representation.js +2 -2
  559. package/lib/mol-plugin-ui/index.d.ts +4 -4
  560. package/lib/mol-plugin-ui/index.js +11 -13
  561. package/lib/mol-plugin-ui/plugin.js +1 -1
  562. package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
  563. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  564. package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
  565. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  566. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  567. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  568. package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
  569. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  570. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  571. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  572. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  573. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  574. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +127 -127
  575. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  576. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  577. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  578. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  579. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  580. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  581. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  582. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  583. package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
  584. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  585. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  586. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  587. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  588. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  589. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  590. package/lib/mol-plugin-ui/viewport/simple-settings.js +2 -6
  591. package/lib/mol-repr/shape/loci/angle.d.ts +10 -0
  592. package/lib/mol-repr/shape/loci/common.d.ts +10 -0
  593. package/lib/mol-repr/shape/loci/dihedral.d.ts +10 -0
  594. package/lib/mol-repr/shape/loci/distance.d.ts +10 -0
  595. package/lib/mol-repr/shape/loci/label.d.ts +10 -0
  596. package/lib/mol-repr/shape/loci/orientation.d.ts +10 -0
  597. package/lib/mol-repr/shape/loci/plane.d.ts +10 -0
  598. package/lib/mol-repr/shape/model/unitcell.d.ts +10 -0
  599. package/lib/mol-repr/structure/complex-representation.js +1 -1
  600. package/lib/mol-repr/structure/complex-visual.d.ts +61 -19
  601. package/lib/mol-repr/structure/params.d.ts +81 -19
  602. package/lib/mol-repr/structure/registry.d.ts +141 -19
  603. package/lib/mol-repr/structure/representation/backbone.d.ts +30 -0
  604. package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +30 -0
  605. package/lib/mol-repr/structure/representation/carbohydrate.d.ts +30 -0
  606. package/lib/mol-repr/structure/representation/cartoon.d.ts +30 -0
  607. package/lib/mol-repr/structure/representation/ellipsoid.d.ts +30 -0
  608. package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +30 -0
  609. package/lib/mol-repr/structure/representation/gaussian-surface.js +1 -1
  610. package/lib/mol-repr/structure/representation/gaussian-volume.d.ts +34 -58
  611. package/lib/mol-repr/structure/representation/gaussian-volume.js +2 -7
  612. package/lib/mol-repr/structure/representation/label.d.ts +30 -0
  613. package/lib/mol-repr/structure/representation/label.js +1 -1
  614. package/lib/mol-repr/structure/representation/line.d.ts +30 -0
  615. package/lib/mol-repr/structure/representation/molecular-surface.d.ts +30 -0
  616. package/lib/mol-repr/structure/representation/molecular-surface.js +1 -1
  617. package/lib/mol-repr/structure/representation/orientation.d.ts +30 -0
  618. package/lib/mol-repr/structure/representation/point.d.ts +30 -0
  619. package/lib/mol-repr/structure/representation/putty.d.ts +30 -0
  620. package/lib/mol-repr/structure/representation/spacefill.d.ts +30 -0
  621. package/lib/mol-repr/structure/units-representation.js +1 -1
  622. package/lib/mol-repr/structure/units-visual.d.ts +81 -19
  623. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +20 -0
  624. package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +10 -0
  625. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +20 -0
  626. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +2 -2
  627. package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts +10 -0
  628. package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +2 -2
  629. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +10 -0
  630. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +10 -0
  631. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +10 -0
  632. package/lib/mol-repr/structure/visual/element-cross.d.ts +10 -0
  633. package/lib/mol-repr/structure/visual/element-point.d.ts +10 -0
  634. package/lib/mol-repr/structure/visual/element-sphere.d.ts +20 -0
  635. package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +10 -0
  636. package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts +22 -38
  637. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +8 -6
  638. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +40 -0
  639. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +11 -8
  640. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +10 -0
  641. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +1 -1
  642. package/lib/mol-repr/structure/visual/label-text.d.ts +10 -0
  643. package/lib/mol-repr/structure/visual/label-text.js +1 -2
  644. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +10 -0
  645. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +1 -1
  646. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +10 -0
  647. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +1 -1
  648. package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +10 -0
  649. package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +10 -0
  650. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +10 -0
  651. package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +20 -0
  652. package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +20 -0
  653. package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +10 -0
  654. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +10 -0
  655. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +10 -0
  656. package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
  657. package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +10 -0
  658. package/lib/mol-repr/structure/visual/util/bond.js +1 -1
  659. package/lib/mol-repr/structure/visual/util/common.d.ts +3 -2
  660. package/lib/mol-repr/structure/visual/util/common.js +2 -5
  661. package/lib/mol-repr/structure/visual/util/gaussian.d.ts +7 -6
  662. package/lib/mol-repr/structure/visual/util/gaussian.js +12 -12
  663. package/lib/mol-repr/structure/visual/util/molecular-surface.d.ts +2 -1
  664. package/lib/mol-repr/structure/visual/util/molecular-surface.js +4 -4
  665. package/lib/mol-repr/visual.js +11 -7
  666. package/lib/mol-repr/volume/direct-volume.d.ts +33 -57
  667. package/lib/mol-repr/volume/direct-volume.js +8 -12
  668. package/lib/mol-repr/volume/isosurface.d.ts +60 -0
  669. package/lib/mol-repr/volume/isosurface.js +11 -2
  670. package/lib/mol-repr/volume/registry.d.ts +31 -19
  671. package/lib/mol-repr/volume/representation.d.ts +10 -0
  672. package/lib/mol-repr/volume/slice.d.ts +30 -0
  673. package/lib/mol-repr/volume/slice.js +2 -2
  674. package/lib/mol-repr/volume/util.js +2 -2
  675. package/lib/mol-script/language/builder.d.ts +0 -1
  676. package/lib/mol-theme/clipping.d.ts +7 -15
  677. package/lib/mol-theme/clipping.js +5 -12
  678. package/lib/mol-theme/color/volume-value.d.ts +17 -0
  679. package/lib/mol-theme/color/volume-value.js +52 -0
  680. package/lib/mol-theme/color.d.ts +3 -0
  681. package/lib/mol-theme/color.js +2 -0
  682. package/lib/mol-util/clip.d.ts +49 -0
  683. package/lib/mol-util/clip.js +93 -0
  684. package/lib/mol-util/number-packing.d.ts +11 -0
  685. package/lib/mol-util/{float-packing.js → number-packing.js} +7 -14
  686. package/package.json +162 -162
  687. package/lib/commonjs/mol-util/float-packing.d.ts +0 -15
  688. package/lib/mol-util/float-packing.d.ts +0 -15
@@ -30,6 +30,16 @@ export declare namespace StructureRepresentationRegistry {
30
30
  roughness: number;
31
31
  bumpiness: number;
32
32
  }>>;
33
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
34
+ variant: import("../../mol-util/clip").Clip.Variant;
35
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
36
+ type: any;
37
+ invert: any;
38
+ position: any;
39
+ rotation: any;
40
+ scale: any;
41
+ }>[];
42
+ }>>;
33
43
  radialSegments: import("../../mol-util/param-definition").ParamDefinition.Numeric;
34
44
  detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
35
45
  aspectRatio: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -59,6 +69,16 @@ export declare namespace StructureRepresentationRegistry {
59
69
  roughness: number;
60
70
  bumpiness: number;
61
71
  }>>;
72
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
73
+ variant: import("../../mol-util/clip").Clip.Variant;
74
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
75
+ type: any;
76
+ invert: any;
77
+ position: any;
78
+ rotation: any;
79
+ scale: any;
80
+ }>[];
81
+ }>>;
62
82
  tryUseImpostor: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
63
83
  detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
64
84
  }, "backbone">;
@@ -98,6 +118,16 @@ export declare namespace StructureRepresentationRegistry {
98
118
  roughness: number;
99
119
  bumpiness: number;
100
120
  }>>;
121
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
122
+ variant: import("../../mol-util/clip").Clip.Variant;
123
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
124
+ type: any;
125
+ invert: any;
126
+ position: any;
127
+ rotation: any;
128
+ scale: any;
129
+ }>[];
130
+ }>>;
101
131
  flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
102
132
  flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
103
133
  traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -133,6 +163,16 @@ export declare namespace StructureRepresentationRegistry {
133
163
  roughness: number;
134
164
  bumpiness: number;
135
165
  }>>;
166
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
167
+ variant: import("../../mol-util/clip").Clip.Variant;
168
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
169
+ type: any;
170
+ invert: any;
171
+ position: any;
172
+ rotation: any;
173
+ scale: any;
174
+ }>[];
175
+ }>>;
136
176
  linkSizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
137
177
  detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
138
178
  sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -173,6 +213,16 @@ export declare namespace StructureRepresentationRegistry {
173
213
  roughness: number;
174
214
  bumpiness: number;
175
215
  }>>;
216
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
217
+ variant: import("../../mol-util/clip").Clip.Variant;
218
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
219
+ type: any;
220
+ invert: any;
221
+ position: any;
222
+ rotation: any;
223
+ scale: any;
224
+ }>[];
225
+ }>>;
176
226
  flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
177
227
  flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
178
228
  detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -196,6 +246,16 @@ export declare namespace StructureRepresentationRegistry {
196
246
  roughness: number;
197
247
  bumpiness: number;
198
248
  }>>;
249
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
250
+ variant: import("../../mol-util/clip").Clip.Variant;
251
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
252
+ type: any;
253
+ invert: any;
254
+ position: any;
255
+ rotation: any;
256
+ scale: any;
257
+ }>[];
258
+ }>>;
199
259
  tryUseGpu: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
200
260
  smoothColors: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
201
261
  resolutionFactor: number;
@@ -217,27 +277,9 @@ export declare namespace StructureRepresentationRegistry {
217
277
  radiusOffset: import("../../mol-util/param-definition").ParamDefinition.Numeric;
218
278
  smoothness: import("../../mol-util/param-definition").ParamDefinition.Numeric;
219
279
  unitKinds: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"spheres" | "gaussians" | "atomic">;
220
- doubleSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
221
- flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
222
- flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
223
280
  ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
224
281
  xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
225
- renderMode: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
226
- controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
227
- list: {
228
- kind: "set" | "interpolate";
229
- colors: import("../../mol-util/color/color").ColorListEntry[];
230
- };
231
- }>, "volume"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
232
- isoValue: Readonly<{
233
- kind: "absolute";
234
- absoluteValue: number;
235
- }> | Readonly<{
236
- kind: "relative";
237
- relativeValue: number;
238
- }>;
239
- singleLayer: boolean;
240
- }>, "isosurface">>;
282
+ controlPoints: import("../../mol-util/param-definition").ParamDefinition.LineGraph;
241
283
  stepsPerCell: import("../../mol-util/param-definition").ParamDefinition.Numeric;
242
284
  jumpLength: import("../../mol-util/param-definition").ParamDefinition.Numeric;
243
285
  alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -247,6 +289,16 @@ export declare namespace StructureRepresentationRegistry {
247
289
  roughness: number;
248
290
  bumpiness: number;
249
291
  }>>;
292
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
293
+ variant: import("../../mol-util/clip").Clip.Variant;
294
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
295
+ type: any;
296
+ invert: any;
297
+ position: any;
298
+ rotation: any;
299
+ scale: any;
300
+ }>[];
301
+ }>>;
250
302
  }, "gaussian-volume">;
251
303
  label: import("./representation").StructureRepresentationProvider<{
252
304
  visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"label-text">;
@@ -282,6 +334,16 @@ export declare namespace StructureRepresentationRegistry {
282
334
  roughness: number;
283
335
  bumpiness: number;
284
336
  }>>;
337
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
338
+ variant: import("../../mol-util/clip").Clip.Variant;
339
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
340
+ type: any;
341
+ invert: any;
342
+ position: any;
343
+ rotation: any;
344
+ scale: any;
345
+ }>[];
346
+ }>>;
285
347
  }, "label">;
286
348
  line: import("./representation").StructureRepresentationProvider<{
287
349
  multipleBonds: import("../../mol-util/param-definition").ParamDefinition.Select<"offset" | "off" | "symmetric">;
@@ -301,6 +363,16 @@ export declare namespace StructureRepresentationRegistry {
301
363
  roughness: number;
302
364
  bumpiness: number;
303
365
  }>>;
366
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
367
+ variant: import("../../mol-util/clip").Clip.Variant;
368
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
369
+ type: any;
370
+ invert: any;
371
+ position: any;
372
+ rotation: any;
373
+ scale: any;
374
+ }>[];
375
+ }>>;
304
376
  pointSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
305
377
  pointStyle: import("../../mol-util/param-definition").ParamDefinition.Select<"circle" | "square" | "fuzzy">;
306
378
  includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -330,6 +402,16 @@ export declare namespace StructureRepresentationRegistry {
330
402
  roughness: number;
331
403
  bumpiness: number;
332
404
  }>>;
405
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
406
+ variant: import("../../mol-util/clip").Clip.Variant;
407
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
408
+ type: any;
409
+ invert: any;
410
+ position: any;
411
+ rotation: any;
412
+ scale: any;
413
+ }>[];
414
+ }>>;
333
415
  smoothColors: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
334
416
  resolutionFactor: number;
335
417
  sampleStride: number;
@@ -361,6 +443,16 @@ export declare namespace StructureRepresentationRegistry {
361
443
  roughness: number;
362
444
  bumpiness: number;
363
445
  }>>;
446
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
447
+ variant: import("../../mol-util/clip").Clip.Variant;
448
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
449
+ type: any;
450
+ invert: any;
451
+ position: any;
452
+ rotation: any;
453
+ scale: any;
454
+ }>[];
455
+ }>>;
364
456
  }, "orientation">;
365
457
  point: import("./representation").StructureRepresentationProvider<{
366
458
  pointSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -377,6 +469,16 @@ export declare namespace StructureRepresentationRegistry {
377
469
  roughness: number;
378
470
  bumpiness: number;
379
471
  }>>;
472
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
473
+ variant: import("../../mol-util/clip").Clip.Variant;
474
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
475
+ type: any;
476
+ invert: any;
477
+ position: any;
478
+ rotation: any;
479
+ scale: any;
480
+ }>[];
481
+ }>>;
380
482
  }, "point">;
381
483
  putty: import("./representation").StructureRepresentationProvider<{
382
484
  sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -398,6 +500,16 @@ export declare namespace StructureRepresentationRegistry {
398
500
  roughness: number;
399
501
  bumpiness: number;
400
502
  }>>;
503
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
504
+ variant: import("../../mol-util/clip").Clip.Variant;
505
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
506
+ type: any;
507
+ invert: any;
508
+ position: any;
509
+ rotation: any;
510
+ scale: any;
511
+ }>[];
512
+ }>>;
401
513
  detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
402
514
  linearSegments: import("../../mol-util/param-definition").ParamDefinition.Numeric;
403
515
  }, "putty">;
@@ -421,6 +533,16 @@ export declare namespace StructureRepresentationRegistry {
421
533
  roughness: number;
422
534
  bumpiness: number;
423
535
  }>>;
536
+ clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
537
+ variant: import("../../mol-util/clip").Clip.Variant;
538
+ objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
539
+ type: any;
540
+ invert: any;
541
+ position: any;
542
+ rotation: any;
543
+ scale: any;
544
+ }>[];
545
+ }>>;
424
546
  flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
425
547
  flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
426
548
  }, "spacefill">;
@@ -29,6 +29,16 @@ export declare const BackboneParams: {
29
29
  roughness: number;
30
30
  bumpiness: number;
31
31
  }>>;
32
+ clip: PD.Group<PD.Normalize<{
33
+ variant: import("../../../mol-util/clip").Clip.Variant;
34
+ objects: PD.Normalize<{
35
+ type: any;
36
+ invert: any;
37
+ position: any;
38
+ rotation: any;
39
+ scale: any;
40
+ }>[];
41
+ }>>;
32
42
  tryUseImpostor: PD.BooleanParam;
33
43
  detail: PD.Numeric;
34
44
  };
@@ -54,6 +64,16 @@ export declare function getBackboneParams(ctx: ThemeRegistryContext, structure:
54
64
  roughness: number;
55
65
  bumpiness: number;
56
66
  }>>;
67
+ clip: PD.Group<PD.Normalize<{
68
+ variant: import("../../../mol-util/clip").Clip.Variant;
69
+ objects: PD.Normalize<{
70
+ type: any;
71
+ invert: any;
72
+ position: any;
73
+ rotation: any;
74
+ scale: any;
75
+ }>[];
76
+ }>>;
57
77
  tryUseImpostor: PD.BooleanParam;
58
78
  detail: PD.Numeric;
59
79
  };
@@ -80,6 +100,16 @@ export declare const BackboneRepresentationProvider: StructureRepresentationProv
80
100
  roughness: number;
81
101
  bumpiness: number;
82
102
  }>>;
103
+ clip: PD.Group<PD.Normalize<{
104
+ variant: import("../../../mol-util/clip").Clip.Variant;
105
+ objects: PD.Normalize<{
106
+ type: any;
107
+ invert: any;
108
+ position: any;
109
+ rotation: any;
110
+ scale: any;
111
+ }>[];
112
+ }>>;
83
113
  tryUseImpostor: PD.BooleanParam;
84
114
  detail: PD.Numeric;
85
115
  }, "backbone">;
@@ -44,6 +44,16 @@ export declare const BallAndStickParams: {
44
44
  roughness: number;
45
45
  bumpiness: number;
46
46
  }>>;
47
+ clip: PD.Group<PD.Normalize<{
48
+ variant: import("../../../mol-util/clip").Clip.Variant;
49
+ objects: PD.Normalize<{
50
+ type: any;
51
+ invert: any;
52
+ position: any;
53
+ rotation: any;
54
+ scale: any;
55
+ }>[];
56
+ }>>;
47
57
  flipSided: PD.BooleanParam;
48
58
  flatShaded: PD.BooleanParam;
49
59
  traceOnly: PD.BooleanParam;
@@ -86,6 +96,16 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
86
96
  roughness: number;
87
97
  bumpiness: number;
88
98
  }>>;
99
+ clip: PD.Group<PD.Normalize<{
100
+ variant: import("../../../mol-util/clip").Clip.Variant;
101
+ objects: PD.Normalize<{
102
+ type: any;
103
+ invert: any;
104
+ position: any;
105
+ rotation: any;
106
+ scale: any;
107
+ }>[];
108
+ }>>;
89
109
  flipSided: PD.BooleanParam;
90
110
  flatShaded: PD.BooleanParam;
91
111
  traceOnly: PD.BooleanParam;
@@ -129,6 +149,16 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
129
149
  roughness: number;
130
150
  bumpiness: number;
131
151
  }>>;
152
+ clip: PD.Group<PD.Normalize<{
153
+ variant: import("../../../mol-util/clip").Clip.Variant;
154
+ objects: PD.Normalize<{
155
+ type: any;
156
+ invert: any;
157
+ position: any;
158
+ rotation: any;
159
+ scale: any;
160
+ }>[];
161
+ }>>;
132
162
  flipSided: PD.BooleanParam;
133
163
  flatShaded: PD.BooleanParam;
134
164
  traceOnly: PD.BooleanParam;
@@ -38,6 +38,16 @@ export declare const CarbohydrateParams: {
38
38
  roughness: number;
39
39
  bumpiness: number;
40
40
  }>>;
41
+ clip: PD.Group<PD.Normalize<{
42
+ variant: import("../../../mol-util/clip").Clip.Variant;
43
+ objects: PD.Normalize<{
44
+ type: any;
45
+ invert: any;
46
+ position: any;
47
+ rotation: any;
48
+ scale: any;
49
+ }>[];
50
+ }>>;
41
51
  linkSizeFactor: PD.Numeric;
42
52
  detail: PD.Numeric;
43
53
  sizeFactor: PD.Numeric;
@@ -73,6 +83,16 @@ export declare function getCarbohydrateParams(ctx: ThemeRegistryContext, structu
73
83
  roughness: number;
74
84
  bumpiness: number;
75
85
  }>>;
86
+ clip: PD.Group<PD.Normalize<{
87
+ variant: import("../../../mol-util/clip").Clip.Variant;
88
+ objects: PD.Normalize<{
89
+ type: any;
90
+ invert: any;
91
+ position: any;
92
+ rotation: any;
93
+ scale: any;
94
+ }>[];
95
+ }>>;
76
96
  linkSizeFactor: PD.Numeric;
77
97
  detail: PD.Numeric;
78
98
  sizeFactor: PD.Numeric;
@@ -109,6 +129,16 @@ export declare const CarbohydrateRepresentationProvider: StructureRepresentation
109
129
  roughness: number;
110
130
  bumpiness: number;
111
131
  }>>;
132
+ clip: PD.Group<PD.Normalize<{
133
+ variant: import("../../../mol-util/clip").Clip.Variant;
134
+ objects: PD.Normalize<{
135
+ type: any;
136
+ invert: any;
137
+ position: any;
138
+ rotation: any;
139
+ scale: any;
140
+ }>[];
141
+ }>>;
112
142
  linkSizeFactor: PD.Numeric;
113
143
  detail: PD.Numeric;
114
144
  sizeFactor: PD.Numeric;
@@ -27,6 +27,16 @@ export declare const CartoonParams: {
27
27
  roughness: number;
28
28
  bumpiness: number;
29
29
  }>>;
30
+ clip: PD.Group<PD.Normalize<{
31
+ variant: import("../../../mol-util/clip").Clip.Variant;
32
+ objects: PD.Normalize<{
33
+ type: any;
34
+ invert: any;
35
+ position: any;
36
+ rotation: any;
37
+ scale: any;
38
+ }>[];
39
+ }>>;
30
40
  radialSegments: PD.Numeric;
31
41
  detail: PD.Numeric;
32
42
  aspectRatio: PD.Numeric;
@@ -55,6 +65,16 @@ export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: S
55
65
  roughness: number;
56
66
  bumpiness: number;
57
67
  }>>;
68
+ clip: PD.Group<PD.Normalize<{
69
+ variant: import("../../../mol-util/clip").Clip.Variant;
70
+ objects: PD.Normalize<{
71
+ type: any;
72
+ invert: any;
73
+ position: any;
74
+ rotation: any;
75
+ scale: any;
76
+ }>[];
77
+ }>>;
58
78
  radialSegments: PD.Numeric;
59
79
  detail: PD.Numeric;
60
80
  aspectRatio: PD.Numeric;
@@ -84,6 +104,16 @@ export declare const CartoonRepresentationProvider: StructureRepresentationProvi
84
104
  roughness: number;
85
105
  bumpiness: number;
86
106
  }>>;
107
+ clip: PD.Group<PD.Normalize<{
108
+ variant: import("../../../mol-util/clip").Clip.Variant;
109
+ objects: PD.Normalize<{
110
+ type: any;
111
+ invert: any;
112
+ position: any;
113
+ rotation: any;
114
+ scale: any;
115
+ }>[];
116
+ }>>;
87
117
  radialSegments: PD.Numeric;
88
118
  detail: PD.Numeric;
89
119
  aspectRatio: PD.Numeric;
@@ -44,6 +44,16 @@ export declare const EllipsoidParams: {
44
44
  roughness: number;
45
45
  bumpiness: number;
46
46
  }>>;
47
+ clip: PD.Group<PD.Normalize<{
48
+ variant: import("../../../mol-util/clip").Clip.Variant;
49
+ objects: PD.Normalize<{
50
+ type: any;
51
+ invert: any;
52
+ position: any;
53
+ rotation: any;
54
+ scale: any;
55
+ }>[];
56
+ }>>;
47
57
  flipSided: PD.BooleanParam;
48
58
  flatShaded: PD.BooleanParam;
49
59
  detail: PD.Numeric;
@@ -85,6 +95,16 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
85
95
  roughness: number;
86
96
  bumpiness: number;
87
97
  }>>;
98
+ clip: PD.Group<PD.Normalize<{
99
+ variant: import("../../../mol-util/clip").Clip.Variant;
100
+ objects: PD.Normalize<{
101
+ type: any;
102
+ invert: any;
103
+ position: any;
104
+ rotation: any;
105
+ scale: any;
106
+ }>[];
107
+ }>>;
88
108
  flipSided: PD.BooleanParam;
89
109
  flatShaded: PD.BooleanParam;
90
110
  detail: PD.Numeric;
@@ -127,6 +147,16 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
127
147
  roughness: number;
128
148
  bumpiness: number;
129
149
  }>>;
150
+ clip: PD.Group<PD.Normalize<{
151
+ variant: import("../../../mol-util/clip").Clip.Variant;
152
+ objects: PD.Normalize<{
153
+ type: any;
154
+ invert: any;
155
+ position: any;
156
+ rotation: any;
157
+ scale: any;
158
+ }>[];
159
+ }>>;
130
160
  flipSided: PD.BooleanParam;
131
161
  flatShaded: PD.BooleanParam;
132
162
  detail: PD.Numeric;
@@ -27,6 +27,16 @@ export declare const GaussianSurfaceParams: {
27
27
  roughness: number;
28
28
  bumpiness: number;
29
29
  }>>;
30
+ clip: PD.Group<PD.Normalize<{
31
+ variant: import("../../../mol-util/clip").Clip.Variant;
32
+ objects: PD.Normalize<{
33
+ type: any;
34
+ invert: any;
35
+ position: any;
36
+ rotation: any;
37
+ scale: any;
38
+ }>[];
39
+ }>>;
30
40
  tryUseGpu: PD.BooleanParam;
31
41
  smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
32
42
  resolutionFactor: number;
@@ -59,6 +69,16 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
59
69
  roughness: number;
60
70
  bumpiness: number;
61
71
  }>>;
72
+ clip: PD.Group<PD.Normalize<{
73
+ variant: import("../../../mol-util/clip").Clip.Variant;
74
+ objects: PD.Normalize<{
75
+ type: any;
76
+ invert: any;
77
+ position: any;
78
+ rotation: any;
79
+ scale: any;
80
+ }>[];
81
+ }>>;
62
82
  tryUseGpu: PD.BooleanParam;
63
83
  smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
64
84
  resolutionFactor: number;
@@ -92,6 +112,16 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
92
112
  roughness: number;
93
113
  bumpiness: number;
94
114
  }>>;
115
+ clip: PD.Group<PD.Normalize<{
116
+ variant: import("../../../mol-util/clip").Clip.Variant;
117
+ objects: PD.Normalize<{
118
+ type: any;
119
+ invert: any;
120
+ position: any;
121
+ rotation: any;
122
+ scale: any;
123
+ }>[];
124
+ }>>;
95
125
  tryUseGpu: PD.BooleanParam;
96
126
  smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
97
127
  resolutionFactor: number;
@@ -31,7 +31,7 @@ export var GaussianSurfaceRepresentationProvider = StructureRepresentationProvid
31
31
  getParams: getGaussianSurfaceParams,
32
32
  defaultValues: PD.getDefaultValues(GaussianSurfaceParams),
33
33
  defaultColorTheme: { name: 'chain-id' },
34
- defaultSizeTheme: { name: 'uniform' },
34
+ defaultSizeTheme: { name: 'physical' },
35
35
  isApplicable: function (structure) { return structure.elementCount > 0; }
36
36
  });
37
37
  //# sourceMappingURL=gaussian-surface.js.map