molstar 3.3.1 → 3.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (777) hide show
  1. package/README.md +3 -0
  2. package/build/viewer/molstar.js +1 -1
  3. package/lib/apps/docking-viewer/viewport.js +1 -1
  4. package/lib/apps/viewer/app.d.ts +7 -6
  5. package/lib/apps/viewer/app.js +2 -0
  6. package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  7. package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
  8. package/lib/commonjs/apps/docking-viewer/index.js +12 -12
  9. package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
  10. package/lib/commonjs/apps/viewer/app.d.ts +7 -6
  11. package/lib/commonjs/apps/viewer/app.js +24 -22
  12. package/lib/commonjs/apps/viewer/index.js +1 -1
  13. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
  14. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  15. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
  16. package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
  17. package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
  18. package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
  19. package/lib/commonjs/cli/cif2bcif/index.js +8 -8
  20. package/lib/commonjs/cli/cifschema/index.js +27 -27
  21. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
  22. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  23. package/lib/commonjs/cli/state-docs/index.js +2 -2
  24. package/lib/commonjs/cli/structure-info/helpers.js +11 -11
  25. package/lib/commonjs/cli/structure-info/model.js +15 -15
  26. package/lib/commonjs/cli/structure-info/volume.js +9 -9
  27. package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
  28. package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
  29. package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
  30. package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
  31. package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
  32. package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
  33. package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
  34. package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
  35. package/lib/commonjs/examples/lighting/index.js +6 -6
  36. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
  37. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
  38. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
  39. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
  40. package/lib/commonjs/examples/task.js +15 -15
  41. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
  42. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
  43. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
  44. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
  45. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
  46. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
  47. package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
  48. package/lib/commonjs/extensions/anvil/behavior.js +14 -14
  49. package/lib/commonjs/extensions/anvil/prop.js +7 -7
  50. package/lib/commonjs/extensions/anvil/representation.js +5 -5
  51. package/lib/commonjs/extensions/cellpack/index.js +1 -1
  52. package/lib/commonjs/extensions/cellpack/model.js +26 -24
  53. package/lib/commonjs/extensions/cellpack/preset.js +6 -6
  54. package/lib/commonjs/extensions/cellpack/property.js +3 -3
  55. package/lib/commonjs/extensions/cellpack/representation.js +2 -2
  56. package/lib/commonjs/extensions/cellpack/state.js +13 -13
  57. package/lib/commonjs/extensions/cellpack/util.js +14 -14
  58. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
  59. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -5
  60. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
  61. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -1
  62. package/lib/commonjs/extensions/g3d/data.js +6 -6
  63. package/lib/commonjs/extensions/g3d/format.js +14 -14
  64. package/lib/commonjs/extensions/g3d/model.js +4 -4
  65. package/lib/commonjs/extensions/geo-export/controls.js +3 -3
  66. package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
  67. package/lib/commonjs/extensions/geo-export/index.js +1 -1
  68. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
  69. package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
  70. package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
  71. package/lib/commonjs/extensions/geo-export/ui.js +7 -7
  72. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
  73. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
  74. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
  75. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
  76. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
  77. package/lib/commonjs/extensions/model-export/export.js +4 -4
  78. package/lib/commonjs/extensions/model-export/index.js +1 -1
  79. package/lib/commonjs/extensions/model-export/ui.js +5 -5
  80. package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
  81. package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
  82. package/lib/commonjs/extensions/mp4-export/index.js +1 -1
  83. package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
  84. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
  85. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
  86. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
  87. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
  88. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
  89. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
  90. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
  91. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
  92. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
  93. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
  94. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
  95. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
  96. package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
  97. package/lib/commonjs/extensions/zenodo/index.js +35 -0
  98. package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
  99. package/lib/commonjs/extensions/zenodo/ui.js +306 -0
  100. package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
  101. package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
  102. package/lib/commonjs/mol-canvas3d/camera.js +2 -1
  103. package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
  104. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  105. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
  106. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
  107. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
  108. package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
  109. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
  110. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  111. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
  112. package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
  113. package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
  114. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
  115. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
  116. package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
  117. package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
  118. package/lib/commonjs/mol-canvas3d/util.js +2 -2
  119. package/lib/commonjs/mol-data/db/column.js +2 -2
  120. package/lib/commonjs/mol-data/db/table.js +1 -1
  121. package/lib/commonjs/mol-data/db.js +1 -1
  122. package/lib/commonjs/mol-data/generic.js +3 -3
  123. package/lib/commonjs/mol-data/index.js +4 -4
  124. package/lib/commonjs/mol-data/int/interval.js +1 -1
  125. package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
  126. package/lib/commonjs/mol-data/int/segmentation.js +1 -1
  127. package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
  128. package/lib/commonjs/mol-data/util.js +7 -7
  129. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
  130. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
  131. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
  132. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
  133. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
  134. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
  135. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
  136. package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
  137. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
  138. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
  139. package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
  140. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
  141. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -4
  142. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
  143. package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
  144. package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
  145. package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
  146. package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
  147. package/lib/commonjs/mol-geo/primitive/star.js +1 -1
  148. package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
  149. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
  150. package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
  151. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
  152. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
  153. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
  154. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  155. package/lib/commonjs/mol-gl/compute/util.js +3 -3
  156. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  157. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  158. package/lib/commonjs/mol-gl/renderable/image.js +3 -3
  159. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  160. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  161. package/lib/commonjs/mol-gl/renderable/points.js +3 -3
  162. package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
  163. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  164. package/lib/commonjs/mol-gl/renderable/text.js +3 -3
  165. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  166. package/lib/commonjs/mol-gl/renderable/util.js +1 -1
  167. package/lib/commonjs/mol-gl/shader-code.js +2 -1
  168. package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
  169. package/lib/commonjs/mol-gl/webgl/context.js +3 -3
  170. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
  171. package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
  172. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
  173. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
  174. package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
  175. package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
  176. package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
  177. package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
  178. package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
  179. package/lib/commonjs/mol-io/common/typed-array.js +2 -2
  180. package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
  181. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
  182. package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
  183. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  184. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  185. package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
  186. package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
  187. package/lib/commonjs/mol-io/reader/cif.js +1 -1
  188. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
  189. package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
  190. package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
  191. package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
  192. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
  193. package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
  194. package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
  195. package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
  196. package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
  197. package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
  198. package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
  199. package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
  200. package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
  201. package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
  202. package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
  203. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
  204. package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
  205. package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
  206. package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
  207. package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
  208. package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
  209. package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
  210. package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
  211. package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
  212. package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
  213. package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
  214. package/lib/commonjs/mol-io/writer/cif.js +1 -1
  215. package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
  216. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  217. package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
  218. package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
  219. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +4 -4
  220. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +1 -1
  221. package/lib/commonjs/mol-math/geometry/gaussian-density.js +4 -4
  222. package/lib/commonjs/mol-math/geometry/molecular-surface.js +8 -8
  223. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +1 -1
  224. package/lib/commonjs/mol-math/geometry.js +8 -8
  225. package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
  226. package/lib/commonjs/mol-math/graph.js +1 -1
  227. package/lib/commonjs/mol-math/linear-algebra.js +2 -2
  228. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
  229. package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
  230. package/lib/commonjs/mol-model/sequence.js +1 -1
  231. package/lib/commonjs/mol-model/shape.js +1 -1
  232. package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
  233. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  234. package/lib/commonjs/mol-model/structure/model/model.js +3 -3
  235. package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
  236. package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
  237. package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
  238. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
  239. package/lib/commonjs/mol-model/structure/model.js +3 -3
  240. package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
  241. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
  242. package/lib/commonjs/mol-model/structure/query.js +6 -6
  243. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
  244. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  245. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  246. package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
  247. package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
  248. package/lib/commonjs/mol-model/structure/structure/structure.js +5 -5
  249. package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
  250. package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
  251. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +3 -3
  252. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  253. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
  254. package/lib/commonjs/mol-model/structure/structure/unit.js +4 -4
  255. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
  256. package/lib/commonjs/mol-model/structure/structure.js +2 -2
  257. package/lib/commonjs/mol-model/structure/topology.js +1 -1
  258. package/lib/commonjs/mol-model/structure.js +6 -6
  259. package/lib/commonjs/mol-model/volume.js +2 -2
  260. package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
  261. package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  262. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
  263. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
  264. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  265. package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
  266. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
  267. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
  268. package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -2
  269. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -2
  270. package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
  271. package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -2
  272. package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
  273. package/lib/commonjs/mol-model-formats/structure/common/component.js +5 -1
  274. package/lib/commonjs/mol-model-formats/structure/cube.js +5 -5
  275. package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -2
  276. package/lib/commonjs/mol-model-formats/structure/gro.js +5 -3
  277. package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
  278. package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -2
  279. package/lib/commonjs/mol-model-formats/structure/mol.js +5 -5
  280. package/lib/commonjs/mol-model-formats/structure/mol2.js +6 -6
  281. package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts +9 -0
  282. package/lib/commonjs/mol-model-formats/structure/nctraj.js +60 -0
  283. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +2 -2
  284. package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
  285. package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -5
  286. package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts +16 -0
  287. package/lib/commonjs/mol-model-formats/structure/prmtop.js +147 -0
  288. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  289. package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -1
  290. package/lib/commonjs/mol-model-formats/structure/psf.js +5 -3
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  774. package/lib/servers/model/config.d.ts +2 -2
  775. package/package.json +16 -16
  776. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  777. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -18,7 +18,7 @@ var MolecularSurfaceVisuals = {
18
18
  'molecular-surface-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Molecular surface mesh', ctx, getParams, molecular_surface_mesh_1.MolecularSurfaceMeshVisual); },
19
19
  'molecular-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Molecular surface wireframe', ctx, getParams, molecular_surface_wireframe_1.MolecularSurfaceWireframeVisual); },
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  };
21
- exports.MolecularSurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, molecular_surface_mesh_1.MolecularSurfaceMeshParams), molecular_surface_wireframe_1.MolecularSurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['molecular-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(MolecularSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
21
+ exports.MolecularSurfaceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, molecular_surface_mesh_1.MolecularSurfaceMeshParams), molecular_surface_wireframe_1.MolecularSurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['molecular-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(MolecularSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
22
22
  function getMolecularSurfaceParams(ctx, structure) {
23
23
  return param_definition_1.ParamDefinition.clone(exports.MolecularSurfaceParams);
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  }
@@ -16,7 +16,7 @@ var base_1 = require("../../../mol-geo/geometry/base");
16
16
  var OrientationVisuals = {
17
17
  'orientation-ellipsoid-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Orientation ellipsoid mesh', ctx, getParams, orientation_ellipsoid_mesh_1.OrientationEllipsoidMeshVisual); },
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  };
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- exports.OrientationParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, orientation_ellipsoid_mesh_1.OrientationEllipsoidMeshParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['orientation-ellipsoid-mesh'], param_definition_1.ParamDefinition.objectToOptions(OrientationVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
19
+ exports.OrientationParams = tslib_1.__assign(tslib_1.__assign({}, orientation_ellipsoid_mesh_1.OrientationEllipsoidMeshParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['orientation-ellipsoid-mesh'], param_definition_1.ParamDefinition.objectToOptions(OrientationVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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20
  function getOrientationParams(ctx, structure) {
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21
  return param_definition_1.ParamDefinition.clone(exports.OrientationParams);
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  }
@@ -15,7 +15,7 @@ var representation_2 = require("../../../mol-repr/representation");
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15
  var PointVisuals = {
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  'element-point': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Points', ctx, getParams, element_point_1.ElementPointVisual); },
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  };
18
- exports.PointParams = (0, tslib_1.__assign)({}, element_point_1.ElementPointParams);
18
+ exports.PointParams = tslib_1.__assign({}, element_point_1.ElementPointParams);
19
19
  function getPointParams(ctx, structure) {
20
20
  return param_definition_1.ParamDefinition.clone(exports.PointParams);
21
21
  }
@@ -19,7 +19,7 @@ var PuttyVisuals = {
19
19
  'polymer-tube': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer tube mesh', ctx, getParams, polymer_tube_mesh_1.PolymerTubeVisual); },
20
20
  'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
21
21
  };
22
- exports.PuttyParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_tube_mesh_1.PolymerTubeParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-tube', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(PuttyVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
22
+ exports.PuttyParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, polymer_tube_mesh_1.PolymerTubeParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-tube', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(PuttyVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
23
23
  function getPuttyParams(ctx, structure) {
24
24
  var params = param_definition_1.ParamDefinition.clone(exports.PuttyParams);
25
25
  var hasNucleotides = false;
@@ -16,7 +16,7 @@ var base_1 = require("../../../mol-geo/geometry/base");
16
16
  var SpacefillVisuals = {
17
17
  'element-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Sphere mesh', ctx, getParams, element_sphere_1.ElementSphereVisual); },
18
18
  };
19
- exports.SpacefillParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
19
+ exports.SpacefillParams = tslib_1.__assign(tslib_1.__assign({}, element_sphere_1.ElementSphereParams), { bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
20
20
  function getSpacefillParams(ctx, structure) {
21
21
  var params = param_definition_1.ParamDefinition.clone(exports.SpacefillParams);
22
22
  if (structure.isCoarseGrained) {
@@ -11,7 +11,7 @@ var tslib_1 = require("tslib");
11
11
  var representation_1 = require("../representation");
12
12
  exports.StructureRepresentationStateBuilder = {
13
13
  create: function () {
14
- return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, representation_1.Representation.createState()), { unitTransforms: null, unitTransformsVersion: -1 });
14
+ return tslib_1.__assign(tslib_1.__assign({}, representation_1.Representation.createState()), { unitTransforms: null, unitTransformsVersion: -1 });
15
15
  },
16
16
  update: function (state, update) {
17
17
  representation_1.Representation.updateState(state, update);
@@ -47,10 +47,10 @@ function UnitsRepresentation(label, ctx, getParams, visualCtor) {
47
47
  _props = param_definition_1.ParamDefinition.getDefaultValues(_params);
48
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  }
49
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  _props = Object.assign({}, _props, props);
50
- return mol_task_1.Task.create('Creating or updating UnitsRepresentation', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
50
+ return mol_task_1.Task.create('Creating or updating UnitsRepresentation', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
51
51
  var i, group, visual, promise, oldVisuals, i, group, visualGroup, visual, promise, promise, arr, visual, promise, i, group, visualGroup, visual, promise, promise, visualsList_1, i, il, _a, visual, group, promise, promise;
52
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  var _b, _c, _d;
53
- return (0, tslib_1.__generator)(this, function (_e) {
53
+ return tslib_1.__generator(this, function (_e) {
54
54
  switch (_e.label) {
55
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  case 0:
56
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  if (!(!_structure && !structure)) return [3 /*break*/, 1];
@@ -300,9 +300,9 @@ function UnitsVisual(builder, materialId) {
300
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  }
301
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  exports.UnitsVisual = UnitsVisual;
302
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  // mesh
303
- exports.UnitsMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureMeshParams), params_1.StructureParams);
303
+ exports.UnitsMeshParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureMeshParams), params_1.StructureParams);
304
304
  function UnitsMeshVisual(builder, materialId) {
305
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
305
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
306
306
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
307
307
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
308
308
  state.createGeometry = true;
@@ -310,9 +310,9 @@ function UnitsMeshVisual(builder, materialId) {
310
310
  }
311
311
  exports.UnitsMeshVisual = UnitsMeshVisual;
312
312
  // spheres
313
- exports.UnitsSpheresParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureSpheresParams), params_1.StructureParams);
313
+ exports.UnitsSpheresParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureSpheresParams), params_1.StructureParams);
314
314
  function UnitsSpheresVisual(builder, materialId) {
315
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
315
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
316
316
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
317
317
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
318
318
  state.updateSize = true;
@@ -320,9 +320,9 @@ function UnitsSpheresVisual(builder, materialId) {
320
320
  }
321
321
  exports.UnitsSpheresVisual = UnitsSpheresVisual;
322
322
  // cylinders
323
- exports.UnitsCylindersParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureCylindersParams), params_1.StructureParams);
323
+ exports.UnitsCylindersParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureCylindersParams), params_1.StructureParams);
324
324
  function UnitsCylindersVisual(builder, materialId) {
325
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
325
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
326
326
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
327
327
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
328
328
  state.updateSize = true;
@@ -330,9 +330,9 @@ function UnitsCylindersVisual(builder, materialId) {
330
330
  }
331
331
  exports.UnitsCylindersVisual = UnitsCylindersVisual;
332
332
  // points
333
- exports.UnitsPointsParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructurePointsParams), params_1.StructureParams);
333
+ exports.UnitsPointsParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructurePointsParams), params_1.StructureParams);
334
334
  function UnitsPointsVisual(builder, materialId) {
335
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
335
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
336
336
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
337
337
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
338
338
  state.updateSize = true;
@@ -340,9 +340,9 @@ function UnitsPointsVisual(builder, materialId) {
340
340
  }
341
341
  exports.UnitsPointsVisual = UnitsPointsVisual;
342
342
  // lines
343
- exports.UnitsLinesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureLinesParams), params_1.StructureParams);
343
+ exports.UnitsLinesParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureLinesParams), params_1.StructureParams);
344
344
  function UnitsLinesVisual(builder, materialId) {
345
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
345
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
346
346
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
347
347
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
348
348
  state.updateSize = true;
@@ -350,9 +350,9 @@ function UnitsLinesVisual(builder, materialId) {
350
350
  }
351
351
  exports.UnitsLinesVisual = UnitsLinesVisual;
352
352
  // text
353
- exports.UnitsTextParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureTextParams), params_1.StructureParams);
353
+ exports.UnitsTextParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureTextParams), params_1.StructureParams);
354
354
  function UnitsTextVisual(builder, materialId) {
355
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
355
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
356
356
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
357
357
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
358
358
  state.updateSize = true;
@@ -382,9 +382,9 @@ function UnitsTextVisual(builder, materialId) {
382
382
  }
383
383
  exports.UnitsTextVisual = UnitsTextVisual;
384
384
  // direct-volume
385
- exports.UnitsDirectVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureDirectVolumeParams), params_1.StructureParams);
385
+ exports.UnitsDirectVolumeParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureDirectVolumeParams), params_1.StructureParams);
386
386
  function UnitsDirectVolumeVisual(builder, materialId) {
387
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
387
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
388
388
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
389
389
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
390
390
  state.createGeometry = true;
@@ -392,9 +392,9 @@ function UnitsDirectVolumeVisual(builder, materialId) {
392
392
  }
393
393
  exports.UnitsDirectVolumeVisual = UnitsDirectVolumeVisual;
394
394
  // texture-mesh
395
- exports.UnitsTextureMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureTextureMeshParams), params_1.StructureParams);
395
+ exports.UnitsTextureMeshParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureTextureMeshParams), params_1.StructureParams);
396
396
  function UnitsTextureMeshVisual(builder, materialId) {
397
- return UnitsVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
397
+ return UnitsVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
398
398
  builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup);
399
399
  if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
400
400
  state.createGeometry = true;
@@ -171,7 +171,7 @@ function createInterUnitBondCylinderMesh(ctx, structure, theme, props, mesh) {
171
171
  }
172
172
  return m;
173
173
  }
174
- exports.InterUnitBondCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexCylindersParams), bond_1.BondCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
174
+ exports.InterUnitBondCylinderParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexCylindersParams), bond_1.BondCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
175
175
  function InterUnitBondCylinderVisual(materialId, structure, props, webgl) {
176
176
  return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
177
177
  ? InterUnitBondCylinderImpostorVisual(materialId)
@@ -110,7 +110,7 @@ function createInterUnitBondLines(ctx, structure, theme, props, lines) {
110
110
  }
111
111
  return l;
112
112
  }
113
- exports.InterUnitBondLineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });
113
+ exports.InterUnitBondLineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });
114
114
  function InterUnitBondLineVisual(materialId) {
115
115
  return (0, complex_visual_1.ComplexLinesVisual)({
116
116
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitBondLineParams),
@@ -195,7 +195,7 @@ function createIntraUnitBondCylinderMesh(ctx, unit, structure, theme, props, mes
195
195
  }
196
196
  return m;
197
197
  }
198
- exports.IntraUnitBondCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsCylindersParams), bond_1.BondCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
198
+ exports.IntraUnitBondCylinderParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsCylindersParams), bond_1.BondCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0, max: 3, step: 0.01 }), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
199
199
  function IntraUnitBondCylinderVisual(materialId, structure, props, webgl) {
200
200
  return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
201
201
  ? IntraUnitBondCylinderImpostorVisual(materialId)
@@ -135,7 +135,7 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
135
135
  }
136
136
  return l;
137
137
  }
138
- exports.IntraUnitBondLineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });
138
+ exports.IntraUnitBondLineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), bond_1.BondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false) });
139
139
  function IntraUnitBondLineVisual(materialId) {
140
140
  return (0, units_visual_1.UnitsLinesVisual)({
141
141
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitBondLineParams),
@@ -48,7 +48,7 @@ function createCarbohydrateLinkCylinderMesh(ctx, structure, theme, props, mesh)
48
48
  }
49
49
  return m;
50
50
  }
51
- exports.CarbohydrateLinkParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkSizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 3, step: 0.01 }) });
51
+ exports.CarbohydrateLinkParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkSizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 3, step: 0.01 }) });
52
52
  function CarbohydrateLinkVisual(materialId) {
53
53
  return (0, complex_visual_1.ComplexMeshVisual)({
54
54
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.CarbohydrateLinkParams),
@@ -145,7 +145,7 @@ function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) {
145
145
  }
146
146
  return mesh_builder_1.MeshBuilder.getMesh(builderState);
147
147
  }
148
- exports.CarbohydrateSymbolParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), { detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), sizeFactor: param_definition_1.ParamDefinition.Numeric(1.75, { min: 0, max: 10, step: 0.01 }) });
148
+ exports.CarbohydrateSymbolParams = tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), { detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), sizeFactor: param_definition_1.ParamDefinition.Numeric(1.75, { min: 0, max: 10, step: 0.01 }) });
149
149
  function CarbohydrateSymbolVisual(materialId) {
150
150
  return (0, complex_visual_1.ComplexMeshVisual)({
151
151
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.CarbohydrateSymbolParams),
@@ -67,7 +67,7 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props
67
67
  }
68
68
  return m;
69
69
  }
70
- exports.CarbohydrateTerminalLinkParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { terminalLinkSizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 3, step: 0.01 }) });
70
+ exports.CarbohydrateTerminalLinkParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { terminalLinkSizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 3, step: 0.01 }) });
71
71
  function CarbohydrateTerminalLinkVisual(materialId) {
72
72
  return (0, complex_visual_1.ComplexMeshVisual)({
73
73
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.CarbohydrateTerminalLinkParams),
@@ -21,7 +21,7 @@ var v3scaleAndAdd = linear_algebra_1.Vec3.scaleAndAdd;
21
21
  var v3unitX = linear_algebra_1.Vec3.unitX;
22
22
  var v3unitY = linear_algebra_1.Vec3.unitY;
23
23
  var v3unitZ = linear_algebra_1.Vec3.unitZ;
24
- exports.ElementCrossParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsLinesParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false), crosses: param_definition_1.ParamDefinition.Select('lone', param_definition_1.ParamDefinition.arrayToOptions(['lone', 'all'])), crossSize: param_definition_1.ParamDefinition.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
24
+ exports.ElementCrossParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false), crosses: param_definition_1.ParamDefinition.Select('lone', param_definition_1.ParamDefinition.arrayToOptions(['lone', 'all'])), crossSize: param_definition_1.ParamDefinition.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
25
25
  function createElementCross(ctx, unit, structure, theme, props, lines) {
26
26
  var child = structure.child;
27
27
  if (child && !child.unitMap.get(unit.id))
@@ -16,7 +16,7 @@ var element_1 = require("./util/element");
16
16
  var geometry_1 = require("../../../mol-math/geometry");
17
17
  // avoiding namespace lookup improved performance in Chrome (Aug 2020)
18
18
  var v3add = linear_algebra_1.Vec3.add;
19
- exports.ElementPointParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsPointsParams), { pointSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false) });
19
+ exports.ElementPointParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsPointsParams), { pointSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false) });
20
20
  // TODO size
21
21
  function createElementPoint(ctx, unit, structure, theme, props, points) {
22
22
  // TODO sizeFactor
@@ -12,7 +12,7 @@ var param_definition_1 = require("../../../mol-util/param-definition");
12
12
  var units_visual_1 = require("../units-visual");
13
13
  var element_1 = require("./util/element");
14
14
  var base_1 = require("../../../mol-geo/geometry/base");
15
- exports.ElementSphereParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsSpheresParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
15
+ exports.ElementSphereParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsSpheresParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
16
16
  function ElementSphereVisual(materialId, structure, props, webgl) {
17
17
  return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
18
18
  ? ElementSphereImpostorVisual(materialId)
@@ -23,7 +23,7 @@ var sphere_2 = require("../../../mol-geo/geometry/mesh/builder/sphere");
23
23
  var geometry_1 = require("../../../mol-math/geometry");
24
24
  var base_1 = require("../../../mol-geo/geometry/base");
25
25
  var sorted_array_1 = require("../../../mol-data/int/sorted-array");
26
- exports.EllipsoidMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false) });
26
+ exports.EllipsoidMeshParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false) });
27
27
  function EllipsoidMeshVisual(materialId) {
28
28
  return (0, units_visual_1.UnitsMeshVisual)({
29
29
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.EllipsoidMeshParams),
@@ -17,9 +17,9 @@ var geometry_1 = require("../../../mol-math/geometry");
17
17
  var units_visual_1 = require("../units-visual");
18
18
  var common_1 = require("./util/common");
19
19
  function createGaussianDensityVolume(ctx, structure, theme, props, directVolume) {
20
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
20
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
21
21
  var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
22
- return (0, tslib_1.__generator)(this, function (_a) {
22
+ return tslib_1.__generator(this, function (_a) {
23
23
  switch (_a.label) {
24
24
  case 0:
25
25
  runtime = ctx.runtime, webgl = ctx.webgl;
@@ -43,7 +43,7 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
43
43
  });
44
44
  });
45
45
  }
46
- exports.GaussianDensityVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
46
+ exports.GaussianDensityVolumeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
47
47
  function GaussianDensityVolumeVisual(materialId) {
48
48
  return (0, complex_visual_1.ComplexDirectVolumeVisual)({
49
49
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianDensityVolumeParams),
@@ -73,9 +73,9 @@ function GaussianDensityVolumeVisual(materialId) {
73
73
  exports.GaussianDensityVolumeVisual = GaussianDensityVolumeVisual;
74
74
  //
75
75
  function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, directVolume) {
76
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
76
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
77
77
  var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
78
- return (0, tslib_1.__generator)(this, function (_a) {
78
+ return tslib_1.__generator(this, function (_a) {
79
79
  switch (_a.label) {
80
80
  case 0:
81
81
  runtime = ctx.runtime, webgl = ctx.webgl;
@@ -102,7 +102,7 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
102
102
  });
103
103
  });
104
104
  }
105
- exports.UnitsGaussianDensityVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
105
+ exports.UnitsGaussianDensityVolumeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
106
106
  function UnitsGaussianDensityVolumeVisual(materialId) {
107
107
  return (0, units_visual_1.UnitsDirectVolumeVisual)({
108
108
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.UnitsGaussianDensityVolumeParams),
@@ -22,9 +22,9 @@ var color_smoothing_1 = require("../../../mol-geo/geometry/mesh/color-smoothing"
22
22
  var color_smoothing_2 = require("../../../mol-geo/geometry/texture-mesh/color-smoothing");
23
23
  var base_1 = require("../../../mol-geo/geometry/base");
24
24
  var linear_algebra_1 = require("../../../mol-math/linear-algebra");
25
- var SharedParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussian_1.GaussianDensityParams), base_1.ColorSmoothingParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
26
- exports.GaussianSurfaceMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsTextureMeshParams), SharedParams);
27
- exports.StructureGaussianSurfaceMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexTextureMeshParams), SharedParams);
25
+ var SharedParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_1.GaussianDensityParams), base_1.ColorSmoothingParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
26
+ exports.GaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsTextureMeshParams), SharedParams);
27
+ exports.StructureGaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexTextureMeshParams), SharedParams);
28
28
  function gpuSupport(webgl) {
29
29
  return webgl.extensions.colorBufferFloat && webgl.extensions.textureFloat && webgl.extensions.blendMinMax && webgl.extensions.drawBuffers;
30
30
  }
@@ -55,9 +55,9 @@ function StructureGaussianSurfaceVisual(materialId, structure, props, webgl) {
55
55
  exports.StructureGaussianSurfaceVisual = StructureGaussianSurfaceVisual;
56
56
  //
57
57
  function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
58
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
58
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
59
59
  var smoothness, _a, transform, field, idField, radiusFactor, resolution, params, surface, sphere;
60
- return (0, tslib_1.__generator)(this, function (_b) {
60
+ return tslib_1.__generator(this, function (_b) {
61
61
  switch (_b.label) {
62
62
  case 0:
63
63
  smoothness = props.smoothness;
@@ -133,9 +133,9 @@ function GaussianSurfaceMeshVisual(materialId) {
133
133
  exports.GaussianSurfaceMeshVisual = GaussianSurfaceMeshVisual;
134
134
  //
135
135
  function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh) {
136
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
136
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
137
137
  var smoothness, _a, transform, field, idField, radiusFactor, resolution, params, surface, sphere;
138
- return (0, tslib_1.__generator)(this, function (_b) {
138
+ return tslib_1.__generator(this, function (_b) {
139
139
  switch (_b.label) {
140
140
  case 0:
141
141
  smoothness = props.smoothness;
@@ -210,9 +210,9 @@ exports.StructureGaussianSurfaceMeshVisual = StructureGaussianSurfaceMeshVisual;
210
210
  //
211
211
  var GaussianSurfaceName = 'gaussian-surface';
212
212
  function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, textureMesh) {
213
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
213
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
214
214
  var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, axisOrder, buffer, gv, boundingSphere, surface;
215
- return (0, tslib_1.__generator)(this, function (_c) {
215
+ return tslib_1.__generator(this, function (_c) {
216
216
  switch (_c.label) {
217
217
  case 0:
218
218
  if (!ctx.webgl)
@@ -294,9 +294,9 @@ function GaussianSurfaceTextureMeshVisual(materialId) {
294
294
  exports.GaussianSurfaceTextureMeshVisual = GaussianSurfaceTextureMeshVisual;
295
295
  //
296
296
  function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props, textureMesh) {
297
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
297
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
298
298
  var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, axisOrder, buffer, gv, boundingSphere, surface;
299
- return (0, tslib_1.__generator)(this, function (_c) {
299
+ return tslib_1.__generator(this, function (_c) {
300
300
  switch (_c.label) {
301
301
  case 0:
302
302
  if (!ctx.webgl)
@@ -16,9 +16,9 @@ var element_1 = require("./util/element");
16
16
  var geometry_1 = require("../../../mol-math/geometry");
17
17
  var common_1 = require("./util/common");
18
18
  function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
19
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
19
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
20
20
  var smoothness, _a, transform, field, idField, params, wireframe, sphere;
21
- return (0, tslib_1.__generator)(this, function (_b) {
21
+ return tslib_1.__generator(this, function (_b) {
22
22
  switch (_b.label) {
23
23
  case 0:
24
24
  smoothness = props.smoothness;
@@ -41,7 +41,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
41
41
  });
42
42
  });
43
43
  }
44
- exports.GaussianWireframeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsLinesParams), gaussian_1.GaussianDensityParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }), lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
44
+ exports.GaussianWireframeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), gaussian_1.GaussianDensityParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }), lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
45
45
  function GaussianWireframeVisual(materialId) {
46
46
  return (0, units_visual_1.UnitsLinesVisual)({
47
47
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianWireframeParams),
@@ -16,7 +16,7 @@ var element_1 = require("./util/element");
16
16
  var names_1 = require("../../../mol-util/color/names");
17
17
  var linear_algebra_1 = require("../../../mol-math/linear-algebra");
18
18
  var boundary_helper_1 = require("../../../mol-math/geometry/boundary-helper");
19
- exports.LabelTextParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexTextParams), { background: param_definition_1.ParamDefinition.Boolean(false), backgroundMargin: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }), backgroundColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black), backgroundOpacity: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }), borderWidth: param_definition_1.ParamDefinition.Numeric(0.25, { min: 0, max: 0.5, step: 0.01 }), level: param_definition_1.ParamDefinition.Select('residue', [['chain', 'Chain'], ['residue', 'Residue'], ['element', 'Element']], { isEssential: true }), chainScale: param_definition_1.ParamDefinition.Numeric(10, { min: 0, max: 20, step: 0.1 }), residueScale: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 20, step: 0.1 }), elementScale: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 20, step: 0.1 }) });
19
+ exports.LabelTextParams = tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexTextParams), { background: param_definition_1.ParamDefinition.Boolean(false), backgroundMargin: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }), backgroundColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black), backgroundOpacity: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }), borderWidth: param_definition_1.ParamDefinition.Numeric(0.25, { min: 0, max: 0.5, step: 0.01 }), level: param_definition_1.ParamDefinition.Select('residue', [['chain', 'Chain'], ['residue', 'Residue'], ['element', 'Element']], { isEssential: true }), chainScale: param_definition_1.ParamDefinition.Numeric(10, { min: 0, max: 20, step: 0.1 }), residueScale: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 20, step: 0.1 }), elementScale: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 20, step: 0.1 }) });
20
20
  function LabelTextVisual(materialId) {
21
21
  return (0, complex_visual_1.ComplexTextVisual)({
22
22
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.LabelTextParams),
@@ -18,12 +18,12 @@ var common_1 = require("./util/common");
18
18
  var geometry_1 = require("../../../mol-math/geometry");
19
19
  var color_smoothing_1 = require("../../../mol-geo/geometry/mesh/color-smoothing");
20
20
  var base_1 = require("../../../mol-geo/geometry/base");
21
- exports.MolecularSurfaceMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), molecular_surface_1.MolecularSurfaceCalculationParams), common_1.CommonSurfaceParams), base_1.ColorSmoothingParams);
21
+ exports.MolecularSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), molecular_surface_1.MolecularSurfaceCalculationParams), common_1.CommonSurfaceParams), base_1.ColorSmoothingParams);
22
22
  //
23
23
  function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
24
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
24
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
25
25
  var _a, transform, field, idField, resolution, params, surface, iterations, sphere;
26
- return (0, tslib_1.__generator)(this, function (_b) {
26
+ return tslib_1.__generator(this, function (_b) {
27
27
  switch (_b.label) {
28
28
  case 0: return [4 /*yield*/, (0, molecular_surface_2.computeUnitMolecularSurface)(structure, unit, theme.size, props).runInContext(ctx.runtime)];
29
29
  case 1:
@@ -16,12 +16,12 @@ var algorithm_1 = require("../../../mol-geo/util/marching-cubes/algorithm");
16
16
  var element_1 = require("./util/element");
17
17
  var common_1 = require("./util/common");
18
18
  var geometry_1 = require("../../../mol-math/geometry");
19
- exports.MolecularSurfaceWireframeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsLinesParams), molecular_surface_1.MolecularSurfaceCalculationParams), common_1.CommonSurfaceParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 10, step: 0.1 }) });
19
+ exports.MolecularSurfaceWireframeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), molecular_surface_1.MolecularSurfaceCalculationParams), common_1.CommonSurfaceParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 10, step: 0.1 }) });
20
20
  //
21
21
  function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lines) {
22
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
22
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
23
23
  var _a, transform, field, idField, params, wireframe, sphere;
24
- return (0, tslib_1.__generator)(this, function (_b) {
24
+ return tslib_1.__generator(this, function (_b) {
25
25
  switch (_b.label) {
26
26
  case 0: return [4 /*yield*/, (0, molecular_surface_2.computeUnitMolecularSurface)(structure, unit, theme.size, props).runInContext(ctx.runtime)];
27
27
  case 1:
@@ -130,7 +130,7 @@ function createNucleotideBlockMesh(ctx, unit, structure, theme, props, mesh) {
130
130
  m.setBoundingSphere(sphere);
131
131
  return m;
132
132
  }
133
- exports.NucleotideBlockParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.NucleotideBlockMeshParams);
133
+ exports.NucleotideBlockParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.NucleotideBlockMeshParams);
134
134
  function NucleotideBlockVisual(materialId) {
135
135
  return (0, units_visual_1.UnitsMeshVisual)({
136
136
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideBlockParams),
@@ -184,7 +184,7 @@ function createNucleotideRingMesh(ctx, unit, structure, theme, props, mesh) {
184
184
  m.setBoundingSphere(sphere);
185
185
  return m;
186
186
  }
187
- exports.NucleotideRingParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.NucleotideRingMeshParams);
187
+ exports.NucleotideRingParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.NucleotideRingMeshParams);
188
188
  function NucleotideRingVisual(materialId) {
189
189
  return (0, units_visual_1.UnitsMeshVisual)({
190
190
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.NucleotideRingParams),
@@ -19,7 +19,7 @@ var int_1 = require("../../../mol-data/int");
19
19
  var loci_1 = require("../../../mol-model/loci");
20
20
  var location_iterator_1 = require("../../../mol-geo/util/location-iterator");
21
21
  var base_1 = require("../../../mol-geo/geometry/base");
22
- exports.OrientationEllipsoidMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 2, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo) });
22
+ exports.OrientationEllipsoidMeshParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 2, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo) });
23
23
  function OrientationEllipsoidMeshVisual(materialId) {
24
24
  return (0, units_visual_1.UnitsMeshVisual)({
25
25
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.OrientationEllipsoidMeshParams),
@@ -25,7 +25,7 @@ var backbone_1 = require("./util/polymer/backbone");
25
25
  var v3scale = linear_algebra_1.Vec3.scale;
26
26
  var v3add = linear_algebra_1.Vec3.add;
27
27
  var v3sub = linear_algebra_1.Vec3.sub;
28
- exports.PolymerBackboneCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsCylindersParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
28
+ exports.PolymerBackboneCylinderParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsCylindersParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
29
29
  function PolymerBackboneCylinderVisual(materialId, structure, props, webgl) {
30
30
  return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
31
31
  ? PolymerBackboneCylinderImpostorVisual(materialId)
@@ -21,7 +21,7 @@ var sphere_2 = require("../../../mol-geo/primitive/sphere");
21
21
  var spheres_1 = require("../../../mol-geo/geometry/spheres/spheres");
22
22
  var spheres_builder_1 = require("../../../mol-geo/geometry/spheres/spheres-builder");
23
23
  var backbone_1 = require("./util/polymer/backbone");
24
- exports.PolymerBackboneSphereParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsSpheresParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
24
+ exports.PolymerBackboneSphereParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsSpheresParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
25
25
  function PolymerBackboneSphereVisual(materialId, structure, props, webgl) {
26
26
  return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
27
27
  ? PolymerBackboneSphereImpostorVisual(materialId)
@@ -71,7 +71,7 @@ function createPolymerDirectionWedgeMesh(ctx, unit, structure, theme, props, mes
71
71
  m.setBoundingSphere(sphere);
72
72
  return m;
73
73
  }
74
- exports.PolymerDirectionParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.PolymerDirectionWedgeParams);
74
+ exports.PolymerDirectionParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.PolymerDirectionWedgeParams);
75
75
  function PolymerDirectionVisual(materialId) {
76
76
  return (0, units_visual_1.UnitsMeshVisual)({
77
77
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerDirectionParams),
@@ -71,7 +71,7 @@ function createPolymerGapCylinderMesh(ctx, unit, structure, theme, props, mesh)
71
71
  m.setBoundingSphere(sphere);
72
72
  return m;
73
73
  }
74
- exports.PolymerGapParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.PolymerGapCylinderParams);
74
+ exports.PolymerGapParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.PolymerGapCylinderParams);
75
75
  function PolymerGapVisual(materialId) {
76
76
  return (0, units_visual_1.UnitsMeshVisual)({
77
77
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerGapParams),
@@ -162,7 +162,7 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
162
162
  m.setBoundingSphere(sphere);
163
163
  return m;
164
164
  }
165
- exports.PolymerTraceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.PolymerTraceMeshParams);
165
+ exports.PolymerTraceParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.PolymerTraceMeshParams);
166
166
  function PolymerTraceVisual(materialId) {
167
167
  return (0, units_visual_1.UnitsMeshVisual)({
168
168
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerTraceParams),
@@ -91,7 +91,7 @@ function createPolymerTubeMesh(ctx, unit, structure, theme, props, mesh) {
91
91
  m.setBoundingSphere(sphere);
92
92
  return m;
93
93
  }
94
- exports.PolymerTubeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), exports.PolymerTubeMeshParams);
94
+ exports.PolymerTubeParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), exports.PolymerTubeMeshParams);
95
95
  function PolymerTubeVisual(materialId) {
96
96
  return (0, units_visual_1.UnitsMeshVisual)({
97
97
  defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerTubeParams),