molstar 2.3.8 → 3.0.0-dev.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 (701) hide show
  1. package/build/viewer/molstar.js +1 -1
  2. package/lib/apps/docking-viewer/viewport.d.ts +2 -2
  3. package/lib/apps/docking-viewer/viewport.js +14 -14
  4. package/lib/apps/docking-viewer/viewport.js.map +1 -1
  5. package/lib/cli/chem-comp-dict/util.d.ts +4 -4
  6. package/lib/cli/cifschema/util/cif-dic.js +1 -0
  7. package/lib/cli/cifschema/util/cif-dic.js.map +1 -1
  8. package/lib/commonjs/apps/docking-viewer/viewport.js +14 -14
  9. package/lib/commonjs/apps/docking-viewer/viewport.js.map +1 -1
  10. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -0
  11. package/lib/commonjs/cli/cifschema/util/cif-dic.js.map +1 -1
  12. package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
  13. package/lib/commonjs/extensions/anvil/representation.d.ts +20 -0
  14. package/lib/commonjs/extensions/cellpack/representation.d.ts +4 -0
  15. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +12 -0
  16. package/lib/commonjs/extensions/geo-export/controls.js +16 -18
  17. package/lib/commonjs/extensions/geo-export/controls.js.map +1 -1
  18. package/lib/commonjs/extensions/geo-export/glb-exporter.d.ts +5 -3
  19. package/lib/commonjs/extensions/geo-export/glb-exporter.js +49 -27
  20. package/lib/commonjs/extensions/geo-export/glb-exporter.js.map +1 -1
  21. package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts +31 -2
  22. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +87 -15
  23. package/lib/commonjs/extensions/geo-export/mesh-exporter.js.map +1 -1
  24. package/lib/commonjs/extensions/geo-export/obj-exporter.d.ts +1 -0
  25. package/lib/commonjs/extensions/geo-export/obj-exporter.js +24 -15
  26. package/lib/commonjs/extensions/geo-export/obj-exporter.js.map +1 -1
  27. package/lib/commonjs/extensions/geo-export/ui.js +24 -20
  28. package/lib/commonjs/extensions/geo-export/ui.js.map +1 -1
  29. package/lib/commonjs/extensions/geo-export/usdz-exporter.d.ts +3 -5
  30. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +39 -30
  31. package/lib/commonjs/extensions/geo-export/usdz-exporter.js.map +1 -1
  32. package/lib/commonjs/extensions/mp4-export/controls.js +1 -1
  33. package/lib/commonjs/extensions/mp4-export/controls.js.map +1 -1
  34. package/lib/commonjs/extensions/mp4-export/ui.js +7 -6
  35. package/lib/commonjs/extensions/mp4-export/ui.js.map +1 -1
  36. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +3 -2
  37. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +4 -0
  38. package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +22 -21
  39. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +20 -0
  40. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +22 -18
  41. package/lib/commonjs/mol-canvas3d/controls/trackball.d.ts +2 -2
  42. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  43. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  44. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  45. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -11
  46. package/lib/commonjs/mol-canvas3d/passes/draw.js.map +1 -1
  47. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
  48. package/lib/commonjs/mol-geo/geometry/base.d.ts +24 -3
  49. package/lib/commonjs/mol-geo/geometry/base.js +51 -6
  50. package/lib/commonjs/mol-geo/geometry/base.js.map +1 -1
  51. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -0
  52. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -1
  53. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js.map +1 -1
  54. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +4 -0
  55. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +4 -3
  56. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js.map +1 -1
  57. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +4 -0
  58. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -1
  59. package/lib/commonjs/mol-geo/geometry/image/image.js.map +1 -1
  60. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +4 -0
  61. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -1
  62. package/lib/commonjs/mol-geo/geometry/lines/lines.js.map +1 -1
  63. package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +18 -8
  64. package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js.map +1 -1
  65. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +10 -2
  66. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +188 -35
  67. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js.map +1 -1
  68. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +4 -0
  69. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -1
  70. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js.map +1 -1
  71. package/lib/commonjs/mol-geo/geometry/overpaint-data.d.ts +7 -2
  72. package/lib/commonjs/mol-geo/geometry/overpaint-data.js +10 -1
  73. package/lib/commonjs/mol-geo/geometry/overpaint-data.js.map +1 -1
  74. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +4 -0
  75. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -1
  76. package/lib/commonjs/mol-geo/geometry/points/points.js.map +1 -1
  77. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +4 -1
  78. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -1
  79. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js.map +1 -1
  80. package/lib/commonjs/mol-geo/geometry/substance-data.d.ts +23 -0
  81. package/lib/commonjs/mol-geo/geometry/substance-data.js +68 -0
  82. package/lib/commonjs/mol-geo/geometry/substance-data.js.map +1 -0
  83. package/lib/commonjs/mol-geo/geometry/text/text.d.ts +4 -0
  84. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -1
  85. package/lib/commonjs/mol-geo/geometry/text/text.js.map +1 -1
  86. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +8 -3
  87. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +194 -27
  88. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js.map +1 -1
  89. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +7 -1
  90. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -1
  91. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js.map +1 -1
  92. package/lib/commonjs/mol-geo/geometry/transparency-data.d.ts +7 -2
  93. package/lib/commonjs/mol-geo/geometry/transparency-data.js +10 -1
  94. package/lib/commonjs/mol-geo/geometry/transparency-data.js.map +1 -1
  95. package/lib/commonjs/mol-gl/_spec/renderer.spec.js +2 -2
  96. package/lib/commonjs/mol-gl/_spec/renderer.spec.js.map +1 -1
  97. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  98. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js.map +1 -1
  99. package/lib/commonjs/mol-gl/compute/util.d.ts +25 -6
  100. package/lib/commonjs/mol-gl/compute/util.js +76 -21
  101. package/lib/commonjs/mol-gl/compute/util.js.map +1 -1
  102. package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +18 -0
  103. package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +18 -0
  104. package/lib/commonjs/mol-gl/renderable/image.d.ts +18 -0
  105. package/lib/commonjs/mol-gl/renderable/lines.d.ts +18 -0
  106. package/lib/commonjs/mol-gl/renderable/mesh.d.ts +18 -0
  107. package/lib/commonjs/mol-gl/renderable/points.d.ts +18 -0
  108. package/lib/commonjs/mol-gl/renderable/points.js +1 -2
  109. package/lib/commonjs/mol-gl/renderable/points.js.map +1 -1
  110. package/lib/commonjs/mol-gl/renderable/schema.d.ts +40 -5
  111. package/lib/commonjs/mol-gl/renderable/schema.js +23 -11
  112. package/lib/commonjs/mol-gl/renderable/schema.js.map +1 -1
  113. package/lib/commonjs/mol-gl/renderable/spheres.d.ts +18 -0
  114. package/lib/commonjs/mol-gl/renderable/text.d.ts +18 -0
  115. package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +32 -13
  116. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +1 -1
  117. package/lib/commonjs/mol-gl/renderable/texture-mesh.js.map +1 -1
  118. package/lib/commonjs/mol-gl/renderer.d.ts +9 -15
  119. package/lib/commonjs/mol-gl/renderer.js +56 -61
  120. package/lib/commonjs/mol-gl/renderer.js.map +1 -1
  121. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +3 -3
  122. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +3 -3
  123. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js.map +1 -1
  124. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  125. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  126. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js.map +1 -1
  127. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  128. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  129. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js.map +1 -1
  130. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  131. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  132. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js.map +1 -1
  133. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  134. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  135. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js.map +1 -1
  136. package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.d.ts +1 -1
  137. package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js +1 -1
  138. package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js.map +1 -1
  139. package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.d.ts +3 -3
  140. package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +3 -3
  141. package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js.map +1 -1
  142. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.d.ts +1 -1
  143. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +1 -1
  144. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js.map +1 -1
  145. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.d.ts +1 -1
  146. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +1 -1
  147. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js.map +1 -1
  148. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.d.ts +1 -1
  149. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js +1 -1
  150. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js.map +1 -1
  151. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  152. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  153. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js.map +1 -1
  154. package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
  155. package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
  156. package/lib/commonjs/mol-gl/shader/mesh.frag.js.map +1 -1
  157. package/lib/commonjs/mol-gl/shader/mesh.vert.d.ts +1 -1
  158. package/lib/commonjs/mol-gl/shader/mesh.vert.js +1 -1
  159. package/lib/commonjs/mol-gl/shader/mesh.vert.js.map +1 -1
  160. package/lib/commonjs/mol-gl/shader-code.d.ts +0 -1
  161. package/lib/commonjs/mol-gl/shader-code.js +31 -13
  162. package/lib/commonjs/mol-gl/shader-code.js.map +1 -1
  163. package/lib/commonjs/mol-gl/webgl/extensions.js +2 -4
  164. package/lib/commonjs/mol-gl/webgl/extensions.js.map +1 -1
  165. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -4
  166. package/lib/commonjs/mol-gl/webgl/render-item.js.map +1 -1
  167. package/lib/commonjs/mol-gl/webgl/resources.js +1 -1
  168. package/lib/commonjs/mol-gl/webgl/resources.js.map +1 -1
  169. package/lib/commonjs/mol-gl/webgl/vertex-array.d.ts +3 -2
  170. package/lib/commonjs/mol-gl/webgl/vertex-array.js +9 -2
  171. package/lib/commonjs/mol-gl/webgl/vertex-array.js.map +1 -1
  172. package/lib/commonjs/mol-io/reader/_spec/sdf.spec.js +51 -0
  173. package/lib/commonjs/mol-io/reader/_spec/sdf.spec.js.map +1 -1
  174. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +2 -2
  175. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +1 -1
  176. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +1 -1
  177. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +1 -1
  178. package/lib/commonjs/mol-io/reader/cif/schema/cif-core.d.ts +8 -5
  179. package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js +15 -5
  180. package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js.map +1 -1
  181. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  182. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +1 -1
  183. package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.d.ts +9 -0
  184. package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js +91 -0
  185. package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js.map +1 -0
  186. package/lib/commonjs/mol-io/reader/sdf/parser.d.ts +1 -1
  187. package/lib/commonjs/mol-io/reader/sdf/parser.js +12 -4
  188. package/lib/commonjs/mol-io/reader/sdf/parser.js.map +1 -1
  189. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.d.ts +6 -0
  190. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js +9 -0
  191. package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js.map +1 -1
  192. package/lib/commonjs/mol-model/loci.d.ts +18 -18
  193. package/lib/commonjs/mol-model/structure/structure/properties.d.ts +1 -1
  194. package/lib/commonjs/mol-model/structure/structure/properties.js +5 -5
  195. package/lib/commonjs/mol-model/structure/structure/properties.js.map +1 -1
  196. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +8 -0
  197. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.d.ts +1 -1
  198. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +1 -7
  199. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js.map +1 -1
  200. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +4 -0
  201. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +4 -0
  202. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +12 -0
  203. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +16 -0
  204. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.d.ts +2 -2
  205. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +5 -0
  206. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +4 -2
  207. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js.map +1 -1
  208. package/lib/commonjs/mol-plugin/commands.d.ts +11 -9
  209. package/lib/commonjs/mol-plugin/spec.js +1 -0
  210. package/lib/commonjs/mol-plugin/spec.js.map +1 -1
  211. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +3 -0
  212. package/lib/commonjs/mol-plugin-state/actions/file.js +4 -2
  213. package/lib/commonjs/mol-plugin-state/actions/file.js.map +1 -1
  214. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +4 -4
  215. package/lib/commonjs/mol-plugin-state/formats/volume.js +1 -0
  216. package/lib/commonjs/mol-plugin-state/formats/volume.js.map +1 -1
  217. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
  218. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +14 -3
  219. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js.map +1 -1
  220. package/lib/commonjs/mol-plugin-state/helpers/structure-substance.d.ts +13 -0
  221. package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js +126 -0
  222. package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js.map +1 -0
  223. package/lib/commonjs/mol-plugin-state/manager/snapshots.js +2 -1
  224. package/lib/commonjs/mol-plugin-state/manager/snapshots.js.map +1 -1
  225. package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +9 -2
  226. package/lib/commonjs/mol-plugin-state/manager/structure/component.js +44 -22
  227. package/lib/commonjs/mol-plugin-state/manager/structure/component.js.map +1 -1
  228. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +31 -4
  229. package/lib/commonjs/mol-plugin-state/transforms/representation.js +160 -15
  230. package/lib/commonjs/mol-plugin-state/transforms/representation.js.map +1 -1
  231. package/lib/commonjs/mol-plugin-ui/state/common.js +10 -9
  232. package/lib/commonjs/mol-plugin-ui/state/common.js.map +1 -1
  233. package/lib/commonjs/mol-plugin-ui/state/snapshots.js +10 -8
  234. package/lib/commonjs/mol-plugin-ui/state/snapshots.js.map +1 -1
  235. package/lib/commonjs/mol-plugin-ui/structure/selection.js +2 -1
  236. package/lib/commonjs/mol-plugin-ui/structure/selection.js.map +1 -1
  237. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +2 -5
  238. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js.map +1 -1
  239. package/lib/commonjs/mol-repr/representation.d.ts +12 -0
  240. package/lib/commonjs/mol-repr/representation.js +50 -5
  241. package/lib/commonjs/mol-repr/representation.js.map +1 -1
  242. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +5 -1
  243. package/lib/commonjs/mol-repr/shape/loci/common.d.ts +5 -1
  244. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +5 -1
  245. package/lib/commonjs/mol-repr/shape/loci/distance.d.ts +5 -1
  246. package/lib/commonjs/mol-repr/shape/loci/label.d.ts +5 -1
  247. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +4 -0
  248. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +4 -0
  249. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +4 -0
  250. package/lib/commonjs/mol-repr/shape/representation.js +8 -0
  251. package/lib/commonjs/mol-repr/shape/representation.js.map +1 -1
  252. package/lib/commonjs/mol-repr/structure/complex-representation.js +17 -4
  253. package/lib/commonjs/mol-repr/structure/complex-representation.js.map +1 -1
  254. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +25 -1
  255. package/lib/commonjs/mol-repr/structure/complex-visual.js +15 -5
  256. package/lib/commonjs/mol-repr/structure/complex-visual.js.map +1 -1
  257. package/lib/commonjs/mol-repr/structure/params.d.ts +33 -1
  258. package/lib/commonjs/mol-repr/structure/registry.d.ts +61 -5
  259. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +12 -0
  260. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +12 -0
  261. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +12 -0
  262. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +12 -0
  263. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +12 -0
  264. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +18 -6
  265. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +12 -0
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package/lib/mol-task/execution/observable.js CHANGED
@@ -8,7 +8,6 @@ import { Task } from '../task';
8
8
  import { now } from '../../mol-util/now';
9
9
  import { Scheduler } from '../util/scheduler';
10
10
  import { UserTiming } from '../util/user-timing';
11
- import { isDebugMode } from '../../mol-util/debug';
12
11
  export function ExecuteObservable(task, observer, updateRateMs) {
13
12
  if (updateRateMs === void 0) { updateRateMs = 250; }
14
13
  var info = ProgressInfo(task, observer, updateRateMs);
@@ -99,10 +98,7 @@ function execute(task, ctx) {
99
98
  task.onAbort();
100
99
  }
101
100
  _a.label = 6;
102
- case 6:
103
- if (isDebugMode)
104
- console.error(e_1);
105
- throw e_1;
101
+ case 6: throw e_1;
106
102
  case 7: return [2 /*return*/];
107
103
  }
108
104
  });
package/lib/mol-task/execution/observable.js.map CHANGED
@@ -1 +1 @@
1
- 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package/lib/mol-theme/overpaint.js CHANGED
@@ -67,7 +67,7 @@ function Overpaint(layers) {
67
67
  var layers = [];
68
68
  map.forEach(function (loci, colorOrClear) {
69
69
  var clear = colorOrClear === -1;
70
- var color = colorOrClear === -1 ? Color(0) : colorOrClear;
70
+ var color = clear ? Color(0) : colorOrClear;
71
71
  layers.push({ loci: loci, color: color, clear: clear });
72
72
  });
73
73
  return { layers: layers };
package/lib/mol-theme/overpaint.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/lib/mol-theme/substance.d.ts ADDED
@@ -0,0 +1,43 @@
1
+ /**
2
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ *
4
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
+ */
6
+ import { Structure, StructureElement } from '../mol-model/structure';
7
+ import { Script } from '../mol-script/script';
8
+ import { Material } from '../mol-util/material';
9
+ export { Substance };
10
+ declare type Substance = {
11
+ readonly layers: ReadonlyArray<Substance.Layer>;
12
+ };
13
+ declare function Substance(layers: ReadonlyArray<Substance.Layer>): Substance;
14
+ declare namespace Substance {
15
+ type Layer = {
16
+ readonly loci: StructureElement.Loci;
17
+ readonly material: Material;
18
+ readonly clear: boolean;
19
+ };
20
+ const Empty: Substance;
21
+ function areEqual(sA: Substance, sB: Substance): boolean;
22
+ function isEmpty(overpaint: Substance): boolean;
23
+ function remap(substance: Substance, structure: Structure): {
24
+ layers: Layer[];
25
+ };
26
+ function merge(substance: Substance): Substance;
27
+ function filter(substance: Substance, filter: Structure): Substance;
28
+ type ScriptLayer = {
29
+ script: Script;
30
+ material: Material;
31
+ clear: boolean;
32
+ };
33
+ function ofScript(scriptLayers: ScriptLayer[], structure: Structure): Substance;
34
+ type BundleLayer = {
35
+ bundle: StructureElement.Bundle;
36
+ material: Material;
37
+ clear: boolean;
38
+ };
39
+ function ofBundle(bundleLayers: BundleLayer[], structure: Structure): Substance;
40
+ function toBundle(overpaint: Substance): {
41
+ layers: BundleLayer[];
42
+ };
43
+ }
package/lib/mol-theme/substance.js ADDED
@@ -0,0 +1,128 @@
1
+ /**
2
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ *
4
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
+ */
6
+ import { Loci } from '../mol-model/loci';
7
+ import { StructureElement } from '../mol-model/structure';
8
+ import { Script } from '../mol-script/script';
9
+ import { Material } from '../mol-util/material';
10
+ export { Substance };
11
+ function Substance(layers) {
12
+ return { layers: layers };
13
+ }
14
+ (function (Substance) {
15
+ Substance.Empty = { layers: [] };
16
+ function areEqual(sA, sB) {
17
+ if (sA.layers.length === 0 && sB.layers.length === 0)
18
+ return true;
19
+ if (sA.layers.length !== sB.layers.length)
20
+ return false;
21
+ for (var i = 0, il = sA.layers.length; i < il; ++i) {
22
+ if (sA.layers[i].clear !== sB.layers[i].clear)
23
+ return false;
24
+ if (sA.layers[i].material !== sB.layers[i].material)
25
+ return false;
26
+ if (!Loci.areEqual(sA.layers[i].loci, sB.layers[i].loci))
27
+ return false;
28
+ }
29
+ return true;
30
+ }
31
+ Substance.areEqual = areEqual;
32
+ function isEmpty(overpaint) {
33
+ return overpaint.layers.length === 0;
34
+ }
35
+ Substance.isEmpty = isEmpty;
36
+ function remap(substance, structure) {
37
+ var layers = [];
38
+ for (var _i = 0, _a = substance.layers; _i < _a.length; _i++) {
39
+ var layer = _a[_i];
40
+ var loci = layer.loci, material = layer.material, clear = layer.clear;
41
+ loci = StructureElement.Loci.remap(loci, structure);
42
+ if (!StructureElement.Loci.isEmpty(loci)) {
43
+ layers.push({ loci: loci, material: material, clear: clear });
44
+ }
45
+ }
46
+ return { layers: layers };
47
+ }
48
+ Substance.remap = remap;
49
+ function merge(substance) {
50
+ if (isEmpty(substance))
51
+ return substance;
52
+ var structure = substance.layers[0].loci.structure;
53
+ var map = new Map();
54
+ var shadowed = StructureElement.Loci.none(structure);
55
+ for (var i = 0, il = substance.layers.length; i < il; ++i) {
56
+ var _a = substance.layers[il - i - 1], loci = _a.loci, material = _a.material, clear = _a.clear; // process from end
57
+ loci = StructureElement.Loci.subtract(loci, shadowed);
58
+ shadowed = StructureElement.Loci.union(loci, shadowed);
59
+ if (!StructureElement.Loci.isEmpty(loci)) {
60
+ var materialOrClear = clear ? -1 : material;
61
+ if (map.has(materialOrClear)) {
62
+ loci = StructureElement.Loci.union(loci, map.get(materialOrClear));
63
+ }
64
+ map.set(materialOrClear, loci);
65
+ }
66
+ }
67
+ var layers = [];
68
+ map.forEach(function (loci, materialOrClear) {
69
+ var clear = materialOrClear === -1;
70
+ var material = clear ? Material(0) : materialOrClear;
71
+ layers.push({ loci: loci, material: material, clear: clear });
72
+ });
73
+ return { layers: layers };
74
+ }
75
+ Substance.merge = merge;
76
+ function filter(substance, filter) {
77
+ if (isEmpty(substance))
78
+ return substance;
79
+ var structure = substance.layers[0].loci.structure;
80
+ var layers = [];
81
+ for (var _i = 0, _a = substance.layers; _i < _a.length; _i++) {
82
+ var layer = _a[_i];
83
+ var loci = layer.loci, material = layer.material, clear = layer.clear;
84
+ // filter by first map to the `filter` structure and
85
+ // then map back to the original structure of the substance loci
86
+ var filtered = StructureElement.Loci.remap(loci, filter);
87
+ loci = StructureElement.Loci.remap(filtered, structure);
88
+ if (!StructureElement.Loci.isEmpty(loci)) {
89
+ layers.push({ loci: loci, material: material, clear: clear });
90
+ }
91
+ }
92
+ return { layers: layers };
93
+ }
94
+ Substance.filter = filter;
95
+ function ofScript(scriptLayers, structure) {
96
+ var layers = [];
97
+ for (var i = 0, il = scriptLayers.length; i < il; ++i) {
98
+ var _a = scriptLayers[i], script = _a.script, material = _a.material, clear = _a.clear;
99
+ var loci = Script.toLoci(script, structure);
100
+ if (!StructureElement.Loci.isEmpty(loci)) {
101
+ layers.push({ loci: loci, material: material, clear: clear });
102
+ }
103
+ }
104
+ return { layers: layers };
105
+ }
106
+ Substance.ofScript = ofScript;
107
+ function ofBundle(bundleLayers, structure) {
108
+ var layers = [];
109
+ for (var i = 0, il = bundleLayers.length; i < il; ++i) {
110
+ var _a = bundleLayers[i], bundle = _a.bundle, material = _a.material, clear = _a.clear;
111
+ var loci = StructureElement.Bundle.toLoci(bundle, structure.root);
112
+ layers.push({ loci: loci, material: material, clear: clear });
113
+ }
114
+ return { layers: layers };
115
+ }
116
+ Substance.ofBundle = ofBundle;
117
+ function toBundle(overpaint) {
118
+ var layers = [];
119
+ for (var i = 0, il = overpaint.layers.length; i < il; ++i) {
120
+ var _a = overpaint.layers[i], loci = _a.loci, material = _a.material, clear = _a.clear;
121
+ var bundle = StructureElement.Bundle.fromLoci(loci);
122
+ layers.push({ bundle: bundle, material: material, clear: clear });
123
+ }
124
+ return { layers: layers };
125
+ }
126
+ Substance.toBundle = toBundle;
127
+ })(Substance || (Substance = {}));
128
+ //# sourceMappingURL=substance.js.map
package/lib/mol-theme/substance.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/lib/mol-util/color/names.d.ts CHANGED
@@ -164,4 +164,4 @@ export declare const ColorNames: ColorMap<{
164
164
  }>;
165
165
  export declare type ColorNames = typeof ColorNames;
166
166
  export declare type ColorName = keyof ColorNames;
167
- export declare const ColorNamesValueMap: Map<Color, "aliceblue" | "antiquewhite" | "aqua" | "aquamarine" | "azure" | "beige" | "bisque" | "black" | "blanchedalmond" | "blue" | "blueviolet" | "brown" | "burlywood" | "cadetblue" | "chartreuse" | "chocolate" | "coral" | "cornflower" | "cornflowerblue" | "cornsilk" | "crimson" | "cyan" | "darkblue" | "darkcyan" | "darkgoldenrod" | "darkgray" | "darkgreen" | "darkgrey" | "darkkhaki" | "darkmagenta" | "darkolivegreen" | "darkorange" | "darkorchid" | "darkred" | "darksalmon" | "darkseagreen" | "darkslateblue" | "darkslategray" | "darkslategrey" | "darkturquoise" | "darkviolet" | "deeppink" | "deepskyblue" | "dimgray" | "dimgrey" | "dodgerblue" | "firebrick" | "floralwhite" | "forestgreen" | "fuchsia" | "gainsboro" | "ghostwhite" | "gold" | "goldenrod" | "gray" | "green" | "greenyellow" | "grey" | "honeydew" | "hotpink" | "indianred" | "indigo" | "ivory" | "khaki" | "laserlemon" | "lavender" | "lavenderblush" | "lawngreen" | "lemonchiffon" | "lightblue" | "lightcoral" | "lightcyan" | "lightgoldenrod" | "lightgoldenrodyellow" | "lightgray" | "lightgreen" | "lightgrey" | "lightpink" | "lightsalmon" | "lightseagreen" | "lightskyblue" | "lightslategray" | "lightslategrey" | "lightsteelblue" | "lightyellow" | "lime" | "limegreen" | "linen" | "magenta" | "maroon" | "maroon2" | "maroon3" | "mediumaquamarine" | "mediumblue" | "mediumorchid" | "mediumpurple" | "mediumseagreen" | "mediumslateblue" | "mediumspringgreen" | "mediumturquoise" | "mediumvioletred" | "midnightblue" | "mintcream" | "mistyrose" | "moccasin" | "navajowhite" | "navy" | "oldlace" | "olive" | "olivedrab" | "orange" | "orangered" | "orchid" | "palegoldenrod" | "palegreen" | "paleturquoise" | "palevioletred" | "papayawhip" | "peachpuff" | "peru" | "pink" | "plum" | "powderblue" | "purple" | "purple2" | "purple3" | "rebeccapurple" | "red" | "rosybrown" | "royalblue" | "saddlebrown" | "salmon" | "sandybrown" | "seagreen" | "seashell" | "sienna" | "silver" | "skyblue" | "slateblue" | "slategray" | "slategrey" | "snow" | "springgreen" | "steelblue" | "tan" | "teal" | "thistle" | "tomato" | "turquoise" | "violet" | "wheat" | "white" | "whitesmoke" | "yellow" | "yellowgreen">;
167
+ export declare const ColorNamesValueMap: Map<Color, "aliceblue" | "antiquewhite" | "aqua" | "aquamarine" | "azure" | "beige" | "bisque" | "black" | "blanchedalmond" | "blue" | "blueviolet" | "brown" | "burlywood" | "cadetblue" | "chartreuse" | "chocolate" | "coral" | "cornflowerblue" | "cornsilk" | "crimson" | "cyan" | "darkblue" | "darkcyan" | "darkgoldenrod" | "darkgray" | "darkgreen" | "darkgrey" | "darkkhaki" | "darkmagenta" | "darkolivegreen" | "darkorange" | "darkorchid" | "darkred" | "darksalmon" | "darkseagreen" | "darkslateblue" | "darkslategray" | "darkslategrey" | "darkturquoise" | "darkviolet" | "deeppink" | "deepskyblue" | "dimgray" | "dimgrey" | "dodgerblue" | "firebrick" | "floralwhite" | "forestgreen" | "fuchsia" | "gainsboro" | "ghostwhite" | "gold" | "goldenrod" | "gray" | "green" | "greenyellow" | "grey" | "honeydew" | "hotpink" | "indianred" | "indigo" | "ivory" | "khaki" | "lavender" | "lavenderblush" | "lawngreen" | "lemonchiffon" | "lightblue" | "lightcoral" | "lightcyan" | "lightgoldenrodyellow" | "lightgray" | "lightgreen" | "lightgrey" | "lightpink" | "lightsalmon" | "lightseagreen" | "lightskyblue" | "lightslategray" | "lightslategrey" | "lightsteelblue" | "lightyellow" | "lime" | "limegreen" | "linen" | "magenta" | "maroon" | "mediumaquamarine" | "mediumblue" | "mediumorchid" | "mediumpurple" | "mediumseagreen" | "mediumslateblue" | "mediumspringgreen" | "mediumturquoise" | "mediumvioletred" | "midnightblue" | "mintcream" | "mistyrose" | "moccasin" | "navajowhite" | "navy" | "oldlace" | "olive" | "olivedrab" | "orange" | "orangered" | "orchid" | "palegoldenrod" | "palegreen" | "paleturquoise" | "palevioletred" | "papayawhip" | "peachpuff" | "peru" | "pink" | "plum" | "powderblue" | "purple" | "rebeccapurple" | "red" | "rosybrown" | "royalblue" | "saddlebrown" | "salmon" | "sandybrown" | "seagreen" | "seashell" | "sienna" | "silver" | "skyblue" | "slateblue" | "slategray" | "slategrey" | "snow" | "springgreen" | "steelblue" | "tan" | "teal" | "thistle" | "tomato" | "turquoise" | "violet" | "wheat" | "white" | "whitesmoke" | "yellow" | "yellowgreen" | "cornflower" | "laserlemon" | "lightgoldenrod" | "maroon2" | "maroon3" | "purple2" | "purple3">;
package/lib/mol-util/material.d.ts ADDED
@@ -0,0 +1,32 @@
1
+ /**
2
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ *
4
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
+ */
6
+ import { NumberArray } from './type-helpers';
7
+ import { ParamDefinition as PD } from './param-definition';
8
+ /** Material properties expressed as a single number */
9
+ export declare type Material = {
10
+ readonly '@type': 'material';
11
+ } & number;
12
+ export declare function Material(hex: number): Material;
13
+ export declare namespace Material {
14
+ function fromNormalized(metalness: number, roughness: number): Material;
15
+ function fromObjectNormalized(v: {
16
+ metalness: number;
17
+ roughness: number;
18
+ }): Material;
19
+ function toObjectNormalized(material: Material, fractionDigits?: number): {
20
+ metalness: number;
21
+ roughness: number;
22
+ };
23
+ function toArray(material: Material, array: NumberArray, offset: number): NumberArray;
24
+ function toString(material: Material): string;
25
+ function getParam(info?: {
26
+ isExpanded?: boolean;
27
+ isFlat?: boolean;
28
+ }): PD.Converted<Material, PD.Normalize<{
29
+ metalness: number;
30
+ roughness: number;
31
+ }>>;
32
+ }
package/lib/mol-util/material.js ADDED
@@ -0,0 +1,47 @@
1
+ /**
2
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ *
4
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
+ */
6
+ import { ParamDefinition as PD } from './param-definition';
7
+ import { toFixed } from './number';
8
+ export function Material(hex) { return hex; }
9
+ (function (Material) {
10
+ function fromNormalized(metalness, roughness) {
11
+ return (((metalness * 255) << 16) | ((roughness * 255) << 8));
12
+ }
13
+ Material.fromNormalized = fromNormalized;
14
+ function fromObjectNormalized(v) {
15
+ return fromNormalized(v.metalness, v.roughness);
16
+ }
17
+ Material.fromObjectNormalized = fromObjectNormalized;
18
+ function toObjectNormalized(material, fractionDigits) {
19
+ var metalness = (material >> 16 & 255) / 255;
20
+ var roughness = (material >> 8 & 255) / 255;
21
+ return {
22
+ metalness: fractionDigits ? toFixed(metalness, fractionDigits) : metalness,
23
+ roughness: fractionDigits ? toFixed(roughness, fractionDigits) : roughness
24
+ };
25
+ }
26
+ Material.toObjectNormalized = toObjectNormalized;
27
+ function toArray(material, array, offset) {
28
+ array[offset] = (material >> 16 & 255);
29
+ array[offset + 1] = (material >> 8 & 255);
30
+ return array;
31
+ }
32
+ Material.toArray = toArray;
33
+ function toString(material) {
34
+ var metalness = (material >> 16 & 255) / 255;
35
+ var roughness = (material >> 8 & 255) / 255;
36
+ return "M ".concat(metalness, " | R ").concat(roughness);
37
+ }
38
+ Material.toString = toString;
39
+ function getParam(info) {
40
+ return PD.Converted(function (v) { return toObjectNormalized(v, 2); }, function (v) { return fromObjectNormalized(v); }, PD.Group({
41
+ metalness: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
42
+ roughness: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
43
+ }, info));
44
+ }
45
+ Material.getParam = getParam;
46
+ })(Material || (Material = {}));
47
+ //# sourceMappingURL=material.js.map
package/lib/mol-util/material.js.map ADDED
@@ -0,0 +1 @@
1
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package/lib/mol-util/number.d.ts CHANGED
@@ -23,3 +23,4 @@ export declare function getArrayDigitCount(xs: ArrayLike<number>, maxDigits: num
23
23
  export declare function isInteger(s: string): boolean;
24
24
  export declare function getPrecision(v: number): number;
25
25
  export declare function toPrecision(v: number, precision: number): number;
26
+ export declare function toFixed(v: number, fractionDigits: number): number;
package/lib/mol-util/number.js CHANGED
@@ -69,4 +69,7 @@ export function getPrecision(v) {
69
69
  export function toPrecision(v, precision) {
70
70
  return parseFloat(v.toPrecision(precision));
71
71
  }
72
+ export function toFixed(v, fractionDigits) {
73
+ return parseFloat(v.toFixed(fractionDigits));
74
+ }
72
75
  //# sourceMappingURL=number.js.map
package/lib/mol-util/number.js.map CHANGED
@@ -1 +1 @@
1
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package/lib/servers/model/config.d.ts CHANGED
@@ -53,7 +53,7 @@ declare const DefaultModelServerConfig: {
53
53
  *
54
54
  * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
55
55
  */
56
- sourceMap: ([string, string] | [string, string, "cif" | "bcif" | "cif.gz" | "bcif.gz"])[];
56
+ sourceMap: ([string, string] | [string, string, "bcif" | "cif" | "cif.gz" | "bcif.gz"])[];
57
57
  };
58
58
  export declare const ModelServerFetchFormats: readonly ["cif", "bcif", "cif.gz", "bcif.gz"];
59
59
  export declare type ModelServerFetchFormats = (typeof ModelServerFetchFormats)[number];
@@ -108,7 +108,7 @@ export declare const ModelServerConfig: {
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  *
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  * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
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  */
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- sourceMap: ([string, string] | [string, string, "cif" | "bcif" | "cif.gz" | "bcif.gz"])[];
111
+ sourceMap: ([string, string] | [string, string, "bcif" | "cif" | "cif.gz" | "bcif.gz"])[];
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  };
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  export declare const ModelServerConfigTemplate: ModelServerConfig;
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  export declare function configureServer(): void;