molstar 3.4.0 → 3.6.1

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 (401) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +202 -197
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +106 -106
  5. package/build/viewer/molstar.js +1 -1
  6. package/build/viewer/molstar.js.LICENSE.txt +12 -14
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/docking-viewer/index.js +1 -1
  9. package/lib/apps/viewer/app.js +1 -1
  10. package/lib/apps/viewer/embedded.html +43 -43
  11. package/lib/apps/viewer/index.html +106 -106
  12. package/lib/cli/chem-comp-dict/util.d.ts +20 -20
  13. package/lib/cli/cif2bcif/converter.js +1 -1
  14. package/lib/cli/cif2bcif/index.js +4 -4
  15. package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
  16. package/lib/cli/cifschema/util/cif-dic.js +7 -5
  17. package/lib/cli/cifschema/util/generate.d.ts +1 -1
  18. package/lib/cli/cifschema/util/generate.js +12 -3
  19. package/lib/cli/cifschema/util/schema.d.ts +3 -3
  20. package/lib/cli/cifschema/util/schema.js +1 -1
  21. package/lib/commonjs/apps/docking-viewer/index.js +2 -2
  22. package/lib/commonjs/apps/viewer/app.js +2 -2
  23. package/lib/commonjs/cli/chem-comp-dict/util.d.ts +20 -20
  24. package/lib/commonjs/cli/cif2bcif/converter.js +1 -1
  25. package/lib/commonjs/cli/cif2bcif/index.js +4 -4
  26. package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
  27. package/lib/commonjs/cli/cifschema/util/cif-dic.js +7 -5
  28. package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
  29. package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
  30. package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
  31. package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
  32. package/lib/commonjs/examples/alpha-orbitals/index.js +2 -2
  33. package/lib/commonjs/examples/basic-wrapper/index.js +2 -2
  34. package/lib/commonjs/examples/lighting/index.js +2 -2
  35. package/lib/commonjs/examples/proteopedia-wrapper/index.js +2 -2
  36. package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
  37. package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
  38. package/lib/commonjs/extensions/cellpack/representation.d.ts +1 -0
  39. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  40. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
  41. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +1 -3
  42. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  43. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +18 -19
  44. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
  45. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
  46. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
  47. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +2 -0
  48. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  49. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  50. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  51. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
  52. package/lib/commonjs/mol-data/db/column.d.ts +10 -3
  53. package/lib/commonjs/mol-data/db/column.js +39 -17
  54. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
  55. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +2 -2
  56. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  57. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  58. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  59. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  60. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +2 -2
  61. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  62. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -1
  63. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +2 -2
  64. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  65. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
  66. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
  67. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  68. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
  69. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
  70. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  71. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  72. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
  73. package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
  74. package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
  75. package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
  76. package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
  77. package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
  78. package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
  79. package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
  80. package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
  81. package/lib/commonjs/mol-gl/webgl/buffer.js +12 -12
  82. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  83. package/lib/commonjs/mol-gl/webgl/context.js +2 -2
  84. package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
  85. package/lib/commonjs/mol-gl/webgl/program.js +10 -4
  86. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +8 -8
  87. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
  88. package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
  89. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
  90. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
  91. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
  92. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  93. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +30 -26
  94. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
  95. package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
  96. package/lib/commonjs/mol-io/reader/cif/schema.js +22 -2
  97. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  98. package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
  99. package/lib/commonjs/mol-math/geometry/common.js +1 -1
  100. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  101. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +2 -2
  102. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  103. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +7 -7
  104. package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
  105. package/lib/commonjs/mol-math/geometry/gaussian-density.js +1 -1
  106. package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
  107. package/lib/commonjs/mol-math/geometry/molecular-surface.js +2 -2
  108. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
  109. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +12 -6
  110. package/lib/commonjs/mol-model/structure/model/model.js +14 -6
  111. package/lib/commonjs/mol-model/structure/model/properties/common.js +1 -1
  112. package/lib/commonjs/mol-model/structure/model/types.d.ts +19 -17
  113. package/lib/commonjs/mol-model/structure/model/types.js +30 -31
  114. package/lib/commonjs/mol-model/structure/query/queries/generators.js +1 -1
  115. package/lib/commonjs/mol-model/structure/structure/properties.d.ts +1 -1
  116. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +2 -4
  117. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -3
  118. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +3 -0
  119. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +2 -0
  120. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  121. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
  122. package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +3 -3
  123. package/lib/commonjs/mol-model-formats/structure/common/component.js +46 -46
  124. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.d.ts +2 -2
  125. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js +72 -7
  126. package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js +11 -11
  127. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +7 -2
  128. package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
  129. package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
  130. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  131. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  132. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +3 -0
  133. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  134. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  135. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +4 -2
  136. package/lib/commonjs/mol-plugin/commands.d.ts +1 -0
  137. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +3 -0
  138. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +6 -6
  139. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
  140. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +1 -1
  141. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +6 -0
  142. package/lib/commonjs/mol-plugin-ui/react18.d.ts +11 -0
  143. package/lib/commonjs/mol-plugin-ui/react18.js +38 -0
  144. package/lib/commonjs/mol-plugin-ui/state/common.js +6 -7
  145. package/lib/commonjs/mol-plugin-ui/structure/focus.d.ts +1 -1
  146. package/lib/commonjs/mol-plugin-ui/structure/focus.js +2 -2
  147. package/lib/commonjs/mol-plugin-ui/task.d.ts +2 -21
  148. package/lib/commonjs/mol-plugin-ui/task.js +39 -43
  149. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +1 -0
  150. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +1 -0
  151. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +1 -0
  152. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +1 -0
  153. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +1 -0
  154. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +3 -0
  155. package/lib/commonjs/mol-repr/structure/params.d.ts +4 -0
  156. package/lib/commonjs/mol-repr/structure/registry.d.ts +10 -0
  157. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +3 -0
  158. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  159. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  160. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +3 -0
  161. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  162. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  163. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  164. package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +3 -0
  165. package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +3 -0
  166. package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +3 -0
  167. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +4 -0
  168. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  169. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  170. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  171. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  172. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  173. package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +2 -0
  174. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  175. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  176. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
  177. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -9
  178. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  179. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  180. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  181. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +3 -3
  182. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  183. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +4 -4
  184. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  185. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  186. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  187. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  188. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  189. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  190. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  191. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  192. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  193. package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts +1 -3
  194. package/lib/commonjs/mol-repr/structure/visual/util/common.js +2 -27
  195. package/lib/commonjs/mol-repr/util.d.ts +2 -1
  196. package/lib/commonjs/mol-repr/util.js +2 -2
  197. package/lib/commonjs/mol-repr/volume/isosurface.d.ts +5 -0
  198. package/lib/commonjs/mol-repr/volume/registry.d.ts +1 -0
  199. package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
  200. package/lib/examples/alpha-orbitals/index.html +61 -61
  201. package/lib/examples/alpha-orbitals/index.js +1 -1
  202. package/lib/examples/basic-wrapper/index.html +137 -137
  203. package/lib/examples/basic-wrapper/index.js +1 -1
  204. package/lib/examples/lighting/index.html +88 -88
  205. package/lib/examples/lighting/index.js +1 -1
  206. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  207. package/lib/examples/proteopedia-wrapper/index.js +1 -1
  208. package/lib/extensions/anvil/behavior.d.ts +1 -0
  209. package/lib/extensions/anvil/representation.d.ts +4 -0
  210. package/lib/extensions/cellpack/representation.d.ts +1 -0
  211. package/lib/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  212. package/lib/extensions/dnatco/confal-pyramids/color.js +224 -132
  213. package/lib/extensions/dnatco/confal-pyramids/property.js +1 -3
  214. package/lib/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  215. package/lib/extensions/dnatco/confal-pyramids/util.js +19 -20
  216. package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
  217. package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
  218. package/lib/extensions/rcsb/validation-report/representation.d.ts +5 -0
  219. package/lib/mol-canvas3d/canvas3d.d.ts +2 -0
  220. package/lib/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  221. package/lib/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  222. package/lib/mol-canvas3d/helper/helper.d.ts +2 -0
  223. package/lib/mol-canvas3d/passes/image.d.ts +1 -0
  224. package/lib/mol-data/db/column.d.ts +10 -3
  225. package/lib/mol-data/db/column.js +39 -18
  226. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
  227. package/lib/mol-geo/geometry/cylinders/cylinders.js +2 -2
  228. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  229. package/lib/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  230. package/lib/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  231. package/lib/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  232. package/lib/mol-geo/geometry/mesh/mesh.js +2 -2
  233. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  234. package/lib/mol-geo/geometry/spheres/spheres.d.ts +2 -1
  235. package/lib/mol-geo/geometry/spheres/spheres.js +2 -2
  236. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  237. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
  238. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
  239. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  240. package/lib/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
  241. package/lib/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
  242. package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  243. package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
  244. package/lib/mol-gl/shader/image.frag.d.ts +2 -2
  245. package/lib/mol-gl/shader/image.frag.js +2 -2
  246. package/lib/mol-gl/shader/lines.frag.d.ts +2 -2
  247. package/lib/mol-gl/shader/lines.frag.js +2 -2
  248. package/lib/mol-gl/shader/points.frag.d.ts +2 -2
  249. package/lib/mol-gl/shader/points.frag.js +2 -2
  250. package/lib/mol-gl/shader/text.frag.d.ts +2 -2
  251. package/lib/mol-gl/shader/text.frag.js +2 -2
  252. package/lib/mol-gl/webgl/buffer.d.ts +2 -2
  253. package/lib/mol-gl/webgl/buffer.js +12 -12
  254. package/lib/mol-gl/webgl/context.d.ts +1 -1
  255. package/lib/mol-gl/webgl/context.js +2 -2
  256. package/lib/mol-gl/webgl/program.d.ts +1 -1
  257. package/lib/mol-gl/webgl/program.js +10 -4
  258. package/lib/mol-io/reader/cif/schema/bird.d.ts +8 -8
  259. package/lib/mol-io/reader/cif/schema/bird.js +12 -11
  260. package/lib/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
  261. package/lib/mol-io/reader/cif/schema/ccd.d.ts +12 -12
  262. package/lib/mol-io/reader/cif/schema/ccd.js +13 -12
  263. package/lib/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
  264. package/lib/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  265. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +30 -26
  266. package/lib/mol-io/reader/cif/schema/mmcif.js +44 -39
  267. package/lib/mol-io/reader/cif/schema.d.ts +1 -1
  268. package/lib/mol-io/reader/cif/schema.js +22 -2
  269. package/lib/mol-io/writer/mol/encoder.js +1 -1
  270. package/lib/mol-math/geometry/common.d.ts +2 -1
  271. package/lib/mol-math/geometry/common.js +1 -1
  272. package/lib/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  273. package/lib/mol-math/geometry/gaussian-density/cpu.js +2 -2
  274. package/lib/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  275. package/lib/mol-math/geometry/gaussian-density/gpu.js +7 -7
  276. package/lib/mol-math/geometry/gaussian-density.d.ts +2 -2
  277. package/lib/mol-math/geometry/gaussian-density.js +1 -1
  278. package/lib/mol-math/geometry/molecular-surface.d.ts +2 -1
  279. package/lib/mol-math/geometry/molecular-surface.js +2 -2
  280. package/lib/mol-math/geometry/primitives/box3d.js +2 -1
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  295. package/lib/mol-model-formats/structure/common/component.js +46 -46
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  300. package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
  301. package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
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  303. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
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  351. package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
  352. package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
  353. package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
  354. package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
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  370. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
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  372. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  373. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  374. package/lib/mol-repr/structure/visual/element-sphere.d.ts +2 -0
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  376. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  377. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
  378. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
  379. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  380. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  381. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  382. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
  383. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  384. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
  385. package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  386. package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  387. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  388. package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  389. package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  390. package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  391. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  392. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  393. package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  394. package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
  395. package/lib/mol-repr/structure/visual/util/common.js +1 -24
  396. package/lib/mol-repr/util.d.ts +2 -1
  397. package/lib/mol-repr/util.js +2 -2
  398. package/lib/mol-repr/volume/isosurface.d.ts +5 -0
  399. package/lib/mol-repr/volume/registry.d.ts +1 -0
  400. package/lib/mol-script/language/builder.d.ts +1 -0
  401. package/package.json +162 -160
@@ -1,107 +1,107 @@
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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- <meta charset="utf-8" />
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- <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
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- <link rel="icon" href="./favicon.ico" type="image/x-icon">
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- <title>Mol* Viewer</title>
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- <style>
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- * {
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- margin: 0;
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- padding: 0;
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- box-sizing: border-box;
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- }
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- html, body {
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- width: 100%;
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- height: 100%;
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- overflow: hidden;
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- }
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- hr {
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- margin: 10px;
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- }
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- h1, h2, h3, h4, h5 {
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- margin-top: 5px;
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- margin-bottom: 3px;
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- }
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- button {
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- padding: 2px;
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- }
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- #app {
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- position: absolute;
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- left: 100px;
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- top: 100px;
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- width: 800px;
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- height: 600px;
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- }
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- </style>
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- <link rel="stylesheet" type="text/css" href="molstar.css" />
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- </head>
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- <body>
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- <div id="app"></div>
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- <script type="text/javascript" src="./molstar.js"></script>
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- <script type="text/javascript">
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- function getParam(name, regex) {
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- var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
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- return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
46
- }
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-
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- var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
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- if (debugMode) molstar.setDebugMode(debugMode, debugMode);
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-
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- var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
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- var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
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- var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
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- var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
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- var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
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- var pixelScale = getParam('pixel-scale', '[^&]+').trim();
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- var pickScale = getParam('pick-scale', '[^&]+').trim();
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- var pickPadding = getParam('pick-padding', '[^&]+').trim();
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- var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
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- var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
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-
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- molstar.Viewer.create('app', {
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- layoutShowControls: !hideControls,
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- viewportShowExpand: false,
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- collapseLeftPanel: collapseLeftPanel,
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- pdbProvider: pdbProvider || 'pdbe',
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- emdbProvider: emdbProvider || 'pdbe',
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- volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
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- ? 'https://maps.rcsb.org'
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- : 'https://www.ebi.ac.uk/pdbe/densities',
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- pixelScale: parseFloat(pixelScale) || 1,
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- pickScale: parseFloat(pickScale) || 0.25,
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- pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
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- enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
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- preferWebgl1: preferWebgl1,
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- }).then(viewer => {
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- var snapshotId = getParam('snapshot-id', '[^&]+').trim();
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- if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
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-
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- var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
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- var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
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- if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
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-
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- var structureUrl = getParam('structure-url', '[^&]+').trim();
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- var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
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- var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
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- if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
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-
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- var pdb = getParam('pdb', '[^&]+').trim();
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- if (pdb) viewer.loadPdb(pdb);
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-
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- var pdbDev = getParam('pdb-dev', '[^&]+').trim();
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- if (pdbDev) viewer.loadPdbDev(pdbDev);
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-
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- var emdb = getParam('emdb', '[^&]+').trim();
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- if (emdb) viewer.loadEmdb(emdb);
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-
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- var afdb = getParam('afdb', '[^&]+').trim();
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- if (afdb) viewer.loadAlphaFoldDb(afdb);
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-
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- var modelArchive = getParam('model-archive', '[^&]+').trim();
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- if (modelArchive) viewer.loadModelArchive(modelArchive);
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- });
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- </script>
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- <!-- __MOLSTAR_ANALYTICS__ -->
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- </body>
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="utf-8" />
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+ <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
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+ <link rel="icon" href="./favicon.ico" type="image/x-icon">
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+ <title>Mol* Viewer</title>
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+ <style>
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+ * {
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+ margin: 0;
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+ padding: 0;
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+ box-sizing: border-box;
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+ }
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+ html, body {
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+ width: 100%;
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+ height: 100%;
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+ overflow: hidden;
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+ }
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+ hr {
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+ margin: 10px;
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+ }
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+ h1, h2, h3, h4, h5 {
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+ margin-top: 5px;
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+ margin-bottom: 3px;
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+ }
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+ button {
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+ padding: 2px;
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+ }
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+ #app {
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+ position: absolute;
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+ left: 100px;
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+ top: 100px;
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+ width: 800px;
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+ height: 600px;
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+ }
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+ </style>
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+ <link rel="stylesheet" type="text/css" href="molstar.css" />
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+ </head>
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+ <body>
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+ <div id="app"></div>
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+ <script type="text/javascript" src="./molstar.js"></script>
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+ <script type="text/javascript">
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+ function getParam(name, regex) {
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+ var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
45
+ return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
46
+ }
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+
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+ var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
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+ if (debugMode) molstar.setDebugMode(debugMode, debugMode);
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+
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+ var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
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+ var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
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+ var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
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+ var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
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+ var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
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+ var pixelScale = getParam('pixel-scale', '[^&]+').trim();
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+ var pickScale = getParam('pick-scale', '[^&]+').trim();
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+ var pickPadding = getParam('pick-padding', '[^&]+').trim();
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+ var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
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+ var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
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+
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+ molstar.Viewer.create('app', {
63
+ layoutShowControls: !hideControls,
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+ viewportShowExpand: false,
65
+ collapseLeftPanel: collapseLeftPanel,
66
+ pdbProvider: pdbProvider || 'pdbe',
67
+ emdbProvider: emdbProvider || 'pdbe',
68
+ volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
69
+ ? 'https://maps.rcsb.org'
70
+ : 'https://www.ebi.ac.uk/pdbe/densities',
71
+ pixelScale: parseFloat(pixelScale) || 1,
72
+ pickScale: parseFloat(pickScale) || 0.25,
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+ pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
74
+ enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
75
+ preferWebgl1: preferWebgl1,
76
+ }).then(viewer => {
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+ var snapshotId = getParam('snapshot-id', '[^&]+').trim();
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+ if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
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+
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+ var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
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+ var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
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+ if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
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+
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+ var structureUrl = getParam('structure-url', '[^&]+').trim();
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+ var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
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+ var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
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+ if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
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+
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+ var pdb = getParam('pdb', '[^&]+').trim();
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+ if (pdb) viewer.loadPdb(pdb);
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+
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+ var pdbDev = getParam('pdb-dev', '[^&]+').trim();
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+ if (pdbDev) viewer.loadPdbDev(pdbDev);
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+
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+ var emdb = getParam('emdb', '[^&]+').trim();
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+ if (emdb) viewer.loadEmdb(emdb);
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+
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+ var afdb = getParam('afdb', '[^&]+').trim();
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+ if (afdb) viewer.loadAlphaFoldDb(afdb);
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+
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+ var modelArchive = getParam('model-archive', '[^&]+').trim();
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+ if (modelArchive) viewer.loadModelArchive(modelArchive);
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+ });
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+ </script>
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+ <!-- __MOLSTAR_ANALYTICS__ -->
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+ </body>
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  </html>