molstar 3.3.0 → 3.5.0

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 (905) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +202 -194
  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/lib/apps/docking-viewer/index.html +36 -36
  7. package/lib/apps/docking-viewer/viewport.js +1 -1
  8. package/lib/apps/viewer/app.d.ts +7 -6
  9. package/lib/apps/viewer/app.js +2 -0
  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/create-saccharides.d.ts +7 -0
  13. package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
  14. package/lib/cli/cif2bcif/converter.js +1 -1
  15. package/lib/cli/cif2bcif/index.js +4 -4
  16. package/lib/commonjs/apps/docking-viewer/index.js +12 -12
  17. package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
  18. package/lib/commonjs/apps/viewer/app.d.ts +7 -6
  19. package/lib/commonjs/apps/viewer/app.js +24 -22
  20. package/lib/commonjs/apps/viewer/index.js +1 -1
  21. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
  22. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  23. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
  24. package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
  25. package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
  26. package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
  27. package/lib/commonjs/cli/cif2bcif/index.js +12 -12
  28. package/lib/commonjs/cli/cifschema/index.js +27 -27
  29. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
  30. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  31. package/lib/commonjs/cli/state-docs/index.js +2 -2
  32. package/lib/commonjs/cli/structure-info/helpers.js +11 -11
  33. package/lib/commonjs/cli/structure-info/model.js +15 -15
  34. package/lib/commonjs/cli/structure-info/volume.js +9 -9
  35. package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
  36. package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
  37. package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
  38. package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
  39. package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
  40. package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
  41. package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
  42. package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
  43. package/lib/commonjs/examples/lighting/index.js +6 -6
  44. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
  45. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
  46. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
  47. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
  48. package/lib/commonjs/examples/task.js +15 -15
  49. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
  50. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
  51. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
  52. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
  53. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
  54. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
  55. package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
  56. package/lib/commonjs/extensions/anvil/behavior.js +14 -14
  57. package/lib/commonjs/extensions/anvil/prop.js +7 -7
  58. package/lib/commonjs/extensions/anvil/representation.js +5 -5
  59. package/lib/commonjs/extensions/cellpack/index.js +1 -1
  60. package/lib/commonjs/extensions/cellpack/model.js +26 -24
  61. package/lib/commonjs/extensions/cellpack/preset.js +6 -6
  62. package/lib/commonjs/extensions/cellpack/property.js +3 -3
  63. package/lib/commonjs/extensions/cellpack/representation.js +2 -2
  64. package/lib/commonjs/extensions/cellpack/state.js +13 -13
  65. package/lib/commonjs/extensions/cellpack/util.js +14 -14
  66. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
  67. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  68. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
  69. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
  70. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
  71. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
  72. package/lib/commonjs/extensions/g3d/data.js +6 -6
  73. package/lib/commonjs/extensions/g3d/format.js +14 -14
  74. package/lib/commonjs/extensions/g3d/model.js +4 -4
  75. package/lib/commonjs/extensions/geo-export/controls.js +3 -3
  76. package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
  77. package/lib/commonjs/extensions/geo-export/index.js +1 -1
  78. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
  79. package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
  80. package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
  81. package/lib/commonjs/extensions/geo-export/ui.js +7 -7
  82. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
  83. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
  84. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
  85. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
  86. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
  87. package/lib/commonjs/extensions/model-export/export.js +4 -4
  88. package/lib/commonjs/extensions/model-export/index.js +1 -1
  89. package/lib/commonjs/extensions/model-export/ui.js +5 -5
  90. package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
  91. package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
  92. package/lib/commonjs/extensions/mp4-export/index.js +1 -1
  93. package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
  94. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
  95. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
  96. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
  97. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
  98. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
  99. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
  100. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
  101. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
  102. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
  103. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
  104. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
  105. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +22 -5
  106. package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
  107. package/lib/commonjs/extensions/zenodo/index.js +35 -0
  108. package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
  109. package/lib/commonjs/extensions/zenodo/ui.js +306 -0
  110. package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
  111. package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
  112. package/lib/commonjs/mol-canvas3d/camera.js +2 -1
  113. package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
  114. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  115. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
  116. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
  117. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
  118. package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
  119. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
  120. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  121. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
  122. package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
  123. package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
  124. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
  125. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
  126. package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
  127. package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
  128. package/lib/commonjs/mol-canvas3d/util.js +2 -2
  129. package/lib/commonjs/mol-data/db/column.js +2 -2
  130. package/lib/commonjs/mol-data/db/table.js +1 -1
  131. package/lib/commonjs/mol-data/db.js +1 -1
  132. package/lib/commonjs/mol-data/generic.js +3 -3
  133. package/lib/commonjs/mol-data/index.js +4 -4
  134. package/lib/commonjs/mol-data/int/interval.js +1 -1
  135. package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
  136. package/lib/commonjs/mol-data/int/segmentation.js +1 -1
  137. package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
  138. package/lib/commonjs/mol-data/util.js +7 -7
  139. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
  140. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
  141. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
  142. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
  143. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
  144. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  145. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
  146. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  147. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  148. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
  149. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  150. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
  151. package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
  152. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
  153. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
  154. package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
  155. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
  156. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  157. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
  158. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
  159. package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
  160. package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
  161. package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
  162. package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
  163. package/lib/commonjs/mol-geo/primitive/star.js +1 -1
  164. package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
  165. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
  166. package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
  167. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
  168. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
  169. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
  170. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  171. package/lib/commonjs/mol-gl/compute/util.js +3 -3
  172. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  173. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  174. package/lib/commonjs/mol-gl/renderable/image.js +3 -3
  175. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  176. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  177. package/lib/commonjs/mol-gl/renderable/points.js +3 -3
  178. package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
  179. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  180. package/lib/commonjs/mol-gl/renderable/text.js +3 -3
  181. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  182. package/lib/commonjs/mol-gl/renderable/util.js +1 -1
  183. package/lib/commonjs/mol-gl/shader-code.js +2 -1
  184. package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
  185. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  186. package/lib/commonjs/mol-gl/webgl/context.js +5 -5
  187. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
  188. package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
  189. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
  190. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
  191. package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
  192. package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
  193. package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
  194. package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
  195. package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
  196. package/lib/commonjs/mol-io/common/typed-array.js +2 -2
  197. package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
  198. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
  199. package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
  200. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  201. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  202. package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
  203. package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
  204. package/lib/commonjs/mol-io/reader/cif.js +1 -1
  205. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
  206. package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
  207. package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
  208. package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
  209. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
  210. package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
  211. package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
  212. package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
  213. package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
  214. package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
  215. package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
  216. package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
  217. package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
  218. package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
  219. package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
  220. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
  221. package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
  222. package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
  223. package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
  224. package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
  225. package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
  226. package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
  227. package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
  228. package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
  229. package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
  230. package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
  231. package/lib/commonjs/mol-io/writer/cif.js +1 -1
  232. package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
  233. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  234. package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
  235. package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
  236. package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
  237. package/lib/commonjs/mol-math/geometry/common.js +1 -1
  238. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  239. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
  240. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  241. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
  242. package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
  243. package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
  244. package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
  245. package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
  246. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
  247. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
  248. package/lib/commonjs/mol-math/geometry.js +8 -8
  249. package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
  250. package/lib/commonjs/mol-math/graph.js +1 -1
  251. package/lib/commonjs/mol-math/linear-algebra.js +2 -2
  252. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
  253. package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
  254. package/lib/commonjs/mol-model/sequence.js +1 -1
  255. package/lib/commonjs/mol-model/shape.js +1 -1
  256. package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
  257. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  258. package/lib/commonjs/mol-model/structure/model/model.js +3 -3
  259. package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
  260. package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
  261. package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
  262. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
  263. package/lib/commonjs/mol-model/structure/model.js +3 -3
  264. package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
  265. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
  266. package/lib/commonjs/mol-model/structure/query.js +6 -6
  267. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
  268. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  269. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  270. package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
  271. package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
  272. package/lib/commonjs/mol-model/structure/structure/structure.js +9 -6
  273. package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
  274. package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
  275. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
  276. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +6 -4
  277. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  278. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
  279. package/lib/commonjs/mol-model/structure/structure/unit.js +5 -22
  280. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
  281. package/lib/commonjs/mol-model/structure/structure.js +2 -2
  282. package/lib/commonjs/mol-model/structure/topology.js +1 -1
  283. package/lib/commonjs/mol-model/structure.js +6 -6
  284. package/lib/commonjs/mol-model/volume.js +2 -2
  285. package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
  286. package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  287. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
  288. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
  289. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  290. package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
  291. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
  292. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
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  872. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js +10 -1
  873. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +10 -1
  874. package/lib/mol-repr/structure/visual/element-point.d.ts +1 -1
  875. package/lib/mol-repr/structure/visual/element-point.js +22 -3
  876. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  877. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +1 -1
  878. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
  879. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  880. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  881. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
  882. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  883. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
  884. package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
  885. package/lib/mol-repr/structure/visual/util/common.js +1 -24
  886. package/lib/mol-repr/structure/visual/util/element.js +36 -2
  887. package/lib/mol-repr/structure/visual/util/link.d.ts +13 -3
  888. package/lib/mol-repr/structure/visual/util/link.js +55 -6
  889. package/lib/mol-script/language/builder.d.ts +1 -0
  890. package/lib/mol-script/language/parser.js +7 -4
  891. package/lib/mol-task/util/scheduler.d.ts +2 -2
  892. package/lib/mol-task/util/scheduler.js +7 -7
  893. package/lib/mol-theme/color/hydrophobicity.js +2 -2
  894. package/lib/mol-util/data-source.js +2 -1
  895. package/lib/mol-util/file-info.d.ts +1 -3
  896. package/lib/mol-util/file-info.js +2 -10
  897. package/lib/mol-util/index.d.ts +1 -0
  898. package/lib/mol-util/index.js +5 -0
  899. package/lib/mol-util/zip/deflate.js +2 -1
  900. package/lib/mol-util/zip/zip.d.ts +7 -1
  901. package/lib/mol-util/zip/zip.js +5 -1
  902. package/lib/servers/model/config.d.ts +2 -2
  903. package/package.json +160 -160
  904. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  905. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.LeftPanelControls = void 0;
3
+ exports.LeftPanelControls = exports.CustomImportControls = void 0;
4
4
  var tslib_1 = require("tslib");
5
5
  var jsx_runtime_1 = require("react/jsx-runtime");
6
6
  var canvas3d_1 = require("../mol-canvas3d/canvas3d");
@@ -14,30 +14,51 @@ var snapshots_1 = require("./state/snapshots");
14
14
  var tree_1 = require("./state/tree");
15
15
  var help_1 = require("./viewport/help");
16
16
  var icons_1 = require("./controls/icons");
17
+ var CustomImportControls = /** @class */ (function (_super) {
18
+ tslib_1.__extends(CustomImportControls, _super);
19
+ function CustomImportControls() {
20
+ return _super !== null && _super.apply(this, arguments) || this;
21
+ }
22
+ CustomImportControls.prototype.componentDidMount = function () {
23
+ var _this = this;
24
+ this.subscribe(this.plugin.state.behaviors.events.changed, function () { return _this.forceUpdate(); });
25
+ };
26
+ CustomImportControls.prototype.render = function () {
27
+ var _this = this;
28
+ var controls = [];
29
+ this.plugin.customImportControls.forEach(function (Controls, key) {
30
+ controls.push((0, jsx_runtime_1.jsx)(Controls, { initiallyCollapsed: _this.props.initiallyCollapsed }, key));
31
+ });
32
+ return controls.length > 0 ? (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: controls }) : null;
33
+ };
34
+ return CustomImportControls;
35
+ }(base_1.PluginUIComponent));
36
+ exports.CustomImportControls = CustomImportControls;
17
37
  var LeftPanelControls = /** @class */ (function (_super) {
18
- (0, tslib_1.__extends)(LeftPanelControls, _super);
38
+ tslib_1.__extends(LeftPanelControls, _super);
19
39
  function LeftPanelControls() {
40
+ var _this = this;
20
41
  var _a;
21
- var _this = _super.apply(this, arguments) || this;
42
+ _this = _super.apply(this, arguments) || this;
22
43
  _this.state = { tab: _this.plugin.behaviors.layout.leftPanelTabName.value };
23
44
  _this.set = function (tab) {
24
45
  if (_this.state.tab === tab) {
25
46
  _this.setState({ tab: 'none' }, function () { return _this.plugin.behaviors.layout.leftPanelTabName.next('none'); });
26
- commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { regionState: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.layout.state.regionState), { left: 'collapsed' }) } });
47
+ commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { regionState: tslib_1.__assign(tslib_1.__assign({}, _this.plugin.layout.state.regionState), { left: 'collapsed' }) } });
27
48
  return;
28
49
  }
29
50
  _this.setState({ tab: tab }, function () { return _this.plugin.behaviors.layout.leftPanelTabName.next(tab); });
30
51
  if (_this.plugin.layout.state.regionState.left !== 'full') {
31
- commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { regionState: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.layout.state.regionState), { left: 'full' }) } });
52
+ commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { regionState: tslib_1.__assign(tslib_1.__assign({}, _this.plugin.layout.state.regionState), { left: 'full' }) } });
32
53
  }
33
54
  };
34
55
  _this.tabs = {
35
- 'none': (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, {}, void 0),
36
- 'root': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.HomeOutlinedSvg, title: 'Home' }, void 0), (0, jsx_runtime_1.jsx)(actions_1.StateObjectActions, { state: _this.plugin.state.data, nodeRef: mol_state_1.StateTransform.RootRef, hideHeader: true, initiallyCollapsed: true, alwaysExpandFirst: true }, void 0), ((_a = _this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.remoteState) !== 'none' && (0, jsx_runtime_1.jsx)(snapshots_1.RemoteStateSnapshots, { listOnly: true }, void 0)] }, void 0),
37
- 'data': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.AccountTreeOutlinedSvg, title: (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(RemoveAllButton, {}, void 0), " State Tree"] }, void 0) }, void 0), (0, jsx_runtime_1.jsx)(tree_1.StateTree, { state: _this.plugin.state.data }, void 0)] }, void 0),
38
- 'states': (0, jsx_runtime_1.jsx)(snapshots_1.StateSnapshots, {}, void 0),
39
- 'settings': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.TuneSvg, title: 'Plugin Settings' }, void 0), (0, jsx_runtime_1.jsx)(FullSettings, {}, void 0)] }, void 0),
40
- 'help': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.HelpOutlineSvg, title: 'Help' }, void 0), (0, jsx_runtime_1.jsx)(help_1.HelpContent, {}, void 0)] }, void 0)
56
+ 'none': (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, {}),
57
+ 'root': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.HomeOutlinedSvg, title: 'Home' }), (0, jsx_runtime_1.jsx)(actions_1.StateObjectActions, { state: _this.plugin.state.data, nodeRef: mol_state_1.StateTransform.RootRef, hideHeader: true, initiallyCollapsed: true, alwaysExpandFirst: true }), (0, jsx_runtime_1.jsx)(CustomImportControls, {}), ((_a = _this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.remoteState) !== 'none' && (0, jsx_runtime_1.jsx)(snapshots_1.RemoteStateSnapshots, { listOnly: true })] }),
58
+ 'data': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.AccountTreeOutlinedSvg, title: (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(RemoveAllButton, {}), " State Tree"] }) }), (0, jsx_runtime_1.jsx)(tree_1.StateTree, { state: _this.plugin.state.data })] }),
59
+ 'states': (0, jsx_runtime_1.jsx)(snapshots_1.StateSnapshots, {}),
60
+ 'settings': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.TuneSvg, title: 'Plugin Settings' }), (0, jsx_runtime_1.jsx)(FullSettings, {})] }),
61
+ 'help': (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { icon: icons_1.HelpOutlineSvg, title: 'Help' }), (0, jsx_runtime_1.jsx)(help_1.HelpContent, {})] })
41
62
  };
42
63
  return _this;
43
64
  }
@@ -47,7 +68,7 @@ var LeftPanelControls = /** @class */ (function (_super) {
47
68
  if (_this.state.tab !== tab)
48
69
  _this.setState({ tab: tab });
49
70
  if (tab === 'none' && _this.plugin.layout.state.regionState.left !== 'collapsed') {
50
- commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { regionState: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.layout.state.regionState), { left: 'collapsed' }) } });
71
+ commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { regionState: tslib_1.__assign(tslib_1.__assign({}, _this.plugin.layout.state.regionState), { left: 'collapsed' }) } });
51
72
  }
52
73
  });
53
74
  this.subscribe(this.plugin.state.data.events.changed, function (_a) {
@@ -61,13 +82,13 @@ var LeftPanelControls = /** @class */ (function (_super) {
61
82
  LeftPanelControls.prototype.render = function () {
62
83
  var _this = this;
63
84
  var tab = this.state.tab;
64
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-left-panel-controls' }, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-left-panel-controls-buttons' }, { children: [(0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.HomeOutlinedSvg, toggleState: tab === 'root', transparent: true, onClick: function () { return _this.set('root'); }, title: 'Home' }, void 0), (0, jsx_runtime_1.jsx)(DataIcon, { set: this.set }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.SaveOutlinedSvg, toggleState: tab === 'states', transparent: true, onClick: function () { return _this.set('states'); }, title: 'Plugin State' }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.HelpOutlineSvg, toggleState: tab === 'help', transparent: true, onClick: function () { return _this.set('help'); }, title: 'Help' }, void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-left-panel-controls-buttons-bottom' }, { children: (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.TuneSvg, toggleState: tab === 'settings', transparent: true, onClick: function () { return _this.set('settings'); }, title: 'Settings' }, void 0) }), void 0)] }), void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-scrollable-container' }, { children: this.tabs[tab] }), void 0)] }), void 0);
85
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-left-panel-controls' }, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-left-panel-controls-buttons' }, { children: [(0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.HomeOutlinedSvg, toggleState: tab === 'root', transparent: true, onClick: function () { return _this.set('root'); }, title: 'Home' }), (0, jsx_runtime_1.jsx)(DataIcon, { set: this.set }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.SaveOutlinedSvg, toggleState: tab === 'states', transparent: true, onClick: function () { return _this.set('states'); }, title: 'Plugin State' }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.HelpOutlineSvg, toggleState: tab === 'help', transparent: true, onClick: function () { return _this.set('help'); }, title: 'Help' }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-left-panel-controls-buttons-bottom' }, { children: (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.TuneSvg, toggleState: tab === 'settings', transparent: true, onClick: function () { return _this.set('settings'); }, title: 'Settings' }) }))] })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-scrollable-container' }, { children: this.tabs[tab] }))] }));
65
86
  };
66
87
  return LeftPanelControls;
67
88
  }(base_1.PluginUIComponent));
68
89
  exports.LeftPanelControls = LeftPanelControls;
69
90
  var DataIcon = /** @class */ (function (_super) {
70
- (0, tslib_1.__extends)(DataIcon, _super);
91
+ tslib_1.__extends(DataIcon, _super);
71
92
  function DataIcon() {
72
93
  var _this = _super !== null && _super.apply(this, arguments) || this;
73
94
  _this.state = { changed: false };
@@ -95,12 +116,12 @@ var DataIcon = /** @class */ (function (_super) {
95
116
  };
96
117
  DataIcon.prototype.render = function () {
97
118
  var _this = this;
98
- return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.AccountTreeOutlinedSvg, toggleState: this.tab === 'data', transparent: true, onClick: function () { return _this.props.set('data'); }, title: 'State Tree', style: { position: 'relative' }, extraContent: this.state.changed ? (0, jsx_runtime_1.jsx)("div", { className: 'msp-left-panel-controls-button-data-dirty' }, void 0) : void 0 }, void 0);
119
+ return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.AccountTreeOutlinedSvg, toggleState: this.tab === 'data', transparent: true, onClick: function () { return _this.props.set('data'); }, title: 'State Tree', style: { position: 'relative' }, extraContent: this.state.changed ? (0, jsx_runtime_1.jsx)("div", { className: 'msp-left-panel-controls-button-data-dirty' }) : void 0 });
99
120
  };
100
121
  return DataIcon;
101
122
  }(base_1.PluginUIComponent));
102
123
  var FullSettings = /** @class */ (function (_super) {
103
- (0, tslib_1.__extends)(FullSettings, _super);
124
+ tslib_1.__extends(FullSettings, _super);
104
125
  function FullSettings() {
105
126
  var _this = _super !== null && _super.apply(this, arguments) || this;
106
127
  _this.setSettings = function (p) {
@@ -120,12 +141,12 @@ var FullSettings = /** @class */ (function (_super) {
120
141
  });
121
142
  };
122
143
  FullSettings.prototype.render = function () {
123
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [this.plugin.canvas3d && (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { title: 'Viewport' }, void 0), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: canvas3d_1.Canvas3DParams, values: this.plugin.canvas3d.props, onChange: this.setSettings }, void 0)] }, void 0), (0, jsx_runtime_1.jsx)(common_1.SectionHeader, { title: 'Behavior' }, void 0), (0, jsx_runtime_1.jsx)(tree_1.StateTree, { state: this.plugin.state.behaviors }, void 0)] }, void 0);
144
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [this.plugin.canvas3d && (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.SectionHeader, { title: 'Viewport' }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: canvas3d_1.Canvas3DParams, values: this.plugin.canvas3d.props, onChange: this.setSettings })] }), (0, jsx_runtime_1.jsx)(common_1.SectionHeader, { title: 'Behavior' }), (0, jsx_runtime_1.jsx)(tree_1.StateTree, { state: this.plugin.state.behaviors })] });
124
145
  };
125
146
  return FullSettings;
126
147
  }(base_1.PluginUIComponent));
127
148
  var RemoveAllButton = /** @class */ (function (_super) {
128
- (0, tslib_1.__extends)(RemoveAllButton, _super);
149
+ tslib_1.__extends(RemoveAllButton, _super);
129
150
  function RemoveAllButton() {
130
151
  var _this = _super !== null && _super.apply(this, arguments) || this;
131
152
  _this.remove = function (e) {
@@ -149,7 +170,7 @@ var RemoveAllButton = /** @class */ (function (_super) {
149
170
  var count = this.plugin.state.data.tree.children.get(mol_state_1.StateTransform.RootRef).size;
150
171
  if (count === 0)
151
172
  return null;
152
- return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, title: 'Remove All', style: { display: 'inline-block' }, small: true, className: 'msp-no-hover-outline', transparent: true }, void 0);
173
+ return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, title: 'Remove All', style: { display: 'inline-block' }, small: true, className: 'msp-no-hover-outline', transparent: true });
153
174
  };
154
175
  return RemoveAllButton;
155
176
  }(base_1.PluginUIComponent));
@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.Log = exports.DefaultViewport = exports.ControlsWrapper = exports.PluginContextContainer = exports.Plugin = void 0;
4
4
  var tslib_1 = require("tslib");
5
5
  var jsx_runtime_1 = require("react/jsx-runtime");
6
- var React = (0, tslib_1.__importStar)(require("react"));
6
+ var React = tslib_1.__importStar(require("react"));
7
7
  var mol_util_1 = require("../mol-util");
8
8
  var base_1 = require("./base");
9
9
  var controls_1 = require("./controls");
@@ -18,32 +18,32 @@ var assets_1 = require("../mol-util/assets");
18
18
  var rxjs_1 = require("rxjs");
19
19
  var use_behavior_1 = require("./hooks/use-behavior");
20
20
  var Plugin = /** @class */ (function (_super) {
21
- (0, tslib_1.__extends)(Plugin, _super);
21
+ tslib_1.__extends(Plugin, _super);
22
22
  function Plugin() {
23
23
  return _super !== null && _super.apply(this, arguments) || this;
24
24
  }
25
25
  Plugin.prototype.region = function (kind, element) {
26
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: "msp-layout-region msp-layout-".concat(kind) }, { children: (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-layout-static' }, { children: element }), void 0) }), void 0);
26
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: "msp-layout-region msp-layout-".concat(kind) }, { children: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-layout-static' }, { children: element })) }));
27
27
  };
28
28
  Plugin.prototype.render = function () {
29
- return (0, jsx_runtime_1.jsx)(base_1.PluginReactContext.Provider, (0, tslib_1.__assign)({ value: this.props.plugin }, { children: (0, jsx_runtime_1.jsx)(Layout, {}, void 0) }), void 0);
29
+ return (0, jsx_runtime_1.jsx)(base_1.PluginReactContext.Provider, tslib_1.__assign({ value: this.props.plugin }, { children: (0, jsx_runtime_1.jsx)(Layout, {}) }));
30
30
  };
31
31
  return Plugin;
32
32
  }(React.Component));
33
33
  exports.Plugin = Plugin;
34
34
  var PluginContextContainer = /** @class */ (function (_super) {
35
- (0, tslib_1.__extends)(PluginContextContainer, _super);
35
+ tslib_1.__extends(PluginContextContainer, _super);
36
36
  function PluginContextContainer() {
37
37
  return _super !== null && _super.apply(this, arguments) || this;
38
38
  }
39
39
  PluginContextContainer.prototype.render = function () {
40
- return (0, jsx_runtime_1.jsx)(base_1.PluginReactContext.Provider, (0, tslib_1.__assign)({ value: this.props.plugin }, { children: (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-plugin' }, { children: this.props.children }), void 0) }), void 0);
40
+ return (0, jsx_runtime_1.jsx)(base_1.PluginReactContext.Provider, tslib_1.__assign({ value: this.props.plugin }, { children: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-plugin' }, { children: this.props.children })) }));
41
41
  };
42
42
  return PluginContextContainer;
43
43
  }(React.Component));
44
44
  exports.PluginContextContainer = PluginContextContainer;
45
45
  var Layout = /** @class */ (function (_super) {
46
- (0, tslib_1.__extends)(Layout, _super);
46
+ tslib_1.__extends(Layout, _super);
47
47
  function Layout() {
48
48
  var _this = _super !== null && _super.apply(this, arguments) || this;
49
49
  _this.onDrop = function (ev) {
@@ -93,7 +93,7 @@ var Layout = /** @class */ (function (_super) {
93
93
  this.subscribe(this.plugin.layout.events.updated, function () { return _this.forceUpdate(); });
94
94
  };
95
95
  Layout.prototype.region = function (kind, Element) {
96
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: "msp-layout-region msp-layout-".concat(kind) }, { children: (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-layout-static' }, { children: Element ? (0, jsx_runtime_1.jsx)(Element, {}, void 0) : null }), void 0) }), void 0);
96
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: "msp-layout-region msp-layout-".concat(kind) }, { children: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-layout-static' }, { children: Element ? (0, jsx_runtime_1.jsx)(Element, {}) : null })) }));
97
97
  };
98
98
  Object.defineProperty(Layout.prototype, "layoutVisibilityClassName", {
99
99
  get: function () {
@@ -141,7 +141,7 @@ var Layout = /** @class */ (function (_super) {
141
141
  var layout = this.plugin.layout.state;
142
142
  var controls = ((_a = this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.controls) || {};
143
143
  var viewport = ((_c = (_b = this.plugin.spec.components) === null || _b === void 0 ? void 0 : _b.viewport) === null || _c === void 0 ? void 0 : _c.view) || DefaultViewport;
144
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-plugin' }, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: this.layoutClassName, onDragEnter: this.onDragEnter }, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: this.layoutVisibilityClassName }, { children: [this.region('main', viewport), layout.showControls && controls.top !== 'none' && this.region('top', controls.top || sequence_1.SequenceView), layout.showControls && controls.left !== 'none' && this.region('left', controls.left || left_panel_1.LeftPanelControls), layout.showControls && controls.right !== 'none' && this.region('right', controls.right || ControlsWrapper), layout.showControls && controls.bottom !== 'none' && this.region('bottom', controls.bottom || Log)] }), void 0), !((_d = this.plugin.spec.components) === null || _d === void 0 ? void 0 : _d.hideTaskOverlay) && (0, jsx_runtime_1.jsx)(task_1.OverlayTaskProgress, {}, void 0), (0, jsx_runtime_1.jsx)(DragOverlay, { plugin: this.plugin, showDragOverlay: this.showDragOverlay }, void 0)] }), void 0) }), void 0);
144
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-plugin' }, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: this.layoutClassName, onDragEnter: this.onDragEnter }, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: this.layoutVisibilityClassName }, { children: [this.region('main', viewport), layout.showControls && controls.top !== 'none' && this.region('top', controls.top || sequence_1.SequenceView), layout.showControls && controls.left !== 'none' && this.region('left', controls.left || left_panel_1.LeftPanelControls), layout.showControls && controls.right !== 'none' && this.region('right', controls.right || ControlsWrapper), layout.showControls && controls.bottom !== 'none' && this.region('bottom', controls.bottom || Log)] })), !((_d = this.plugin.spec.components) === null || _d === void 0 ? void 0 : _d.hideTaskOverlay) && (0, jsx_runtime_1.jsx)(task_1.OverlayTaskProgress, {}), (0, jsx_runtime_1.jsx)(DragOverlay, { plugin: this.plugin, showDragOverlay: this.showDragOverlay })] })) }));
145
145
  };
146
146
  return Layout;
147
147
  }(base_1.PluginUIComponent));
@@ -190,36 +190,36 @@ function DragOverlay(_a) {
190
190
  e.preventDefault();
191
191
  e.stopPropagation();
192
192
  };
193
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-drag-drop-overlay', style: { display: show ? 'flex' : 'none' }, onDragEnter: preventDrag, onDragOver: preventDrag, onDragLeave: function () { return showDragOverlay.next(false); }, onDrop: function (e) { return dropFiles(e, plugin, showDragOverlay); } }, { children: "Load File(s)" }), void 0);
193
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-drag-drop-overlay', style: { display: show ? 'flex' : 'none' }, onDragEnter: preventDrag, onDragOver: preventDrag, onDragLeave: function () { return showDragOverlay.next(false); }, onDrop: function (e) { return dropFiles(e, plugin, showDragOverlay); } }, { children: "Load File(s)" }));
194
194
  }
195
195
  var ControlsWrapper = /** @class */ (function (_super) {
196
- (0, tslib_1.__extends)(ControlsWrapper, _super);
196
+ tslib_1.__extends(ControlsWrapper, _super);
197
197
  function ControlsWrapper() {
198
198
  return _super !== null && _super.apply(this, arguments) || this;
199
199
  }
200
200
  ControlsWrapper.prototype.render = function () {
201
201
  var _a;
202
202
  var StructureTools = ((_a = this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.structureTools) || controls_1.DefaultStructureTools;
203
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-scrollable-container' }, { children: (0, jsx_runtime_1.jsx)(StructureTools, {}, void 0) }), void 0);
203
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-scrollable-container' }, { children: (0, jsx_runtime_1.jsx)(StructureTools, {}) }));
204
204
  };
205
205
  return ControlsWrapper;
206
206
  }(base_1.PluginUIComponent));
207
207
  exports.ControlsWrapper = ControlsWrapper;
208
208
  var DefaultViewport = /** @class */ (function (_super) {
209
- (0, tslib_1.__extends)(DefaultViewport, _super);
209
+ tslib_1.__extends(DefaultViewport, _super);
210
210
  function DefaultViewport() {
211
211
  return _super !== null && _super.apply(this, arguments) || this;
212
212
  }
213
213
  DefaultViewport.prototype.render = function () {
214
214
  var _a, _b;
215
215
  var VPControls = ((_b = (_a = this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.viewport) === null || _b === void 0 ? void 0 : _b.controls) || viewport_1.ViewportControls;
216
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(viewport_1.Viewport, {}, void 0), (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-viewport-top-left-controls' }, { children: [(0, jsx_runtime_1.jsx)(controls_1.AnimationViewportControls, {}, void 0), (0, jsx_runtime_1.jsx)(controls_1.TrajectoryViewportControls, {}, void 0), (0, jsx_runtime_1.jsx)(controls_1.StateSnapshotViewportControls, {}, void 0)] }), void 0), (0, jsx_runtime_1.jsx)(controls_1.SelectionViewportControls, {}, void 0), (0, jsx_runtime_1.jsx)(VPControls, {}, void 0), (0, jsx_runtime_1.jsx)(task_1.BackgroundTaskProgress, {}, void 0), (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-highlight-toast-wrapper' }, { children: [(0, jsx_runtime_1.jsx)(controls_1.LociLabels, {}, void 0), (0, jsx_runtime_1.jsx)(toast_1.Toasts, {}, void 0)] }), void 0)] }, void 0);
216
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(viewport_1.Viewport, {}), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-viewport-top-left-controls' }, { children: [(0, jsx_runtime_1.jsx)(controls_1.AnimationViewportControls, {}), (0, jsx_runtime_1.jsx)(controls_1.TrajectoryViewportControls, {}), (0, jsx_runtime_1.jsx)(controls_1.StateSnapshotViewportControls, {})] })), (0, jsx_runtime_1.jsx)(controls_1.SelectionViewportControls, {}), (0, jsx_runtime_1.jsx)(VPControls, {}), (0, jsx_runtime_1.jsx)(task_1.BackgroundTaskProgress, {}), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-highlight-toast-wrapper' }, { children: [(0, jsx_runtime_1.jsx)(controls_1.LociLabels, {}), (0, jsx_runtime_1.jsx)(toast_1.Toasts, {})] }))] });
217
217
  };
218
218
  return DefaultViewport;
219
219
  }(base_1.PluginUIComponent));
220
220
  exports.DefaultViewport = DefaultViewport;
221
221
  var Log = /** @class */ (function (_super) {
222
- (0, tslib_1.__extends)(Log, _super);
222
+ tslib_1.__extends(Log, _super);
223
223
  function Log() {
224
224
  var _this = _super !== null && _super.apply(this, arguments) || this;
225
225
  _this.wrapper = React.createRef();
@@ -246,9 +246,9 @@ var Log = /** @class */ (function (_super) {
246
246
  var entries = [];
247
247
  for (var i = Math.max(0, l - maxEntries), o = 0; i < l; i++) {
248
248
  var e = xs.get(i);
249
- entries.push((0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-log-entry-badge msp-log-entry-' + e.type }, void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-log-timestamp' }, { children: (0, mol_util_1.formatTime)(e.timestamp) }), void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-log-entry' }, { children: e.message }), void 0)] }, o++));
249
+ entries.push((0, jsx_runtime_1.jsxs)("li", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-log-entry-badge msp-log-entry-' + e.type }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-log-timestamp' }, { children: (0, mol_util_1.formatTime)(e.timestamp) })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-log-entry' }, { children: e.message }))] }, o++));
250
250
  }
251
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ ref: this.wrapper, className: 'msp-log', style: { position: 'absolute', top: '0', right: '0', bottom: '0', left: '0', overflowY: 'auto' } }, { children: (0, jsx_runtime_1.jsx)("ul", (0, tslib_1.__assign)({ className: 'msp-list-unstyled' }, { children: entries }), void 0) }), void 0);
251
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ ref: this.wrapper, className: 'msp-log', style: { position: 'absolute', top: '0', right: '0', bottom: '0', left: '0', overflowY: 'auto' } }, { children: (0, jsx_runtime_1.jsx)("ul", tslib_1.__assign({ className: 'msp-list-unstyled' }, { children: entries })) }));
252
252
  };
253
253
  return Log;
254
254
  }(base_1.PluginUIComponent));
@@ -13,7 +13,7 @@ var int_1 = require("../../mol-data/int");
13
13
  var names_1 = require("../../mol-util/color/names");
14
14
  var marker_action_1 = require("../../mol-util/marker-action");
15
15
  var ChainSequenceWrapper = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(ChainSequenceWrapper, _super);
16
+ tslib_1.__extends(ChainSequenceWrapper, _super);
17
17
  function ChainSequenceWrapper(data) {
18
18
  var _this = this;
19
19
  var residueCount = 0;
@@ -13,7 +13,7 @@ var int_1 = require("../../mol-data/int");
13
13
  var names_1 = require("../../mol-util/color/names");
14
14
  var marker_action_1 = require("../../mol-util/marker-action");
15
15
  var ElementSequenceWrapper = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(ElementSequenceWrapper, _super);
16
+ tslib_1.__extends(ElementSequenceWrapper, _super);
17
17
  function ElementSequenceWrapper(data) {
18
18
  var _this = this;
19
19
  var length = 0;
@@ -13,7 +13,7 @@ var int_1 = require("../../mol-data/int");
13
13
  var names_1 = require("../../mol-util/color/names");
14
14
  var marker_action_1 = require("../../mol-util/marker-action");
15
15
  var HeteroSequenceWrapper = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(HeteroSequenceWrapper, _super);
16
+ tslib_1.__extends(HeteroSequenceWrapper, _super);
17
17
  function HeteroSequenceWrapper(data) {
18
18
  var _this = this;
19
19
  var sequence = [];
@@ -13,7 +13,7 @@ var int_1 = require("../../mol-data/int");
13
13
  var names_1 = require("../../mol-util/color/names");
14
14
  var marker_action_1 = require("../../mol-util/marker-action");
15
15
  var PolymerSequenceWrapper = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(PolymerSequenceWrapper, _super);
16
+ tslib_1.__extends(PolymerSequenceWrapper, _super);
17
17
  function PolymerSequenceWrapper(data) {
18
18
  var _this = this;
19
19
  var l = structure_1.StructureElement.Location.create(data.structure, data.units[0], data.units[0].elements[0]);
@@ -9,7 +9,7 @@ var jsx_runtime_1 = require("react/jsx-runtime");
9
9
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
10
10
  * @author David Sehnal <david.sehnal@gmail.com>
11
11
  */
12
- var React = (0, tslib_1.__importStar)(require("react"));
12
+ var React = tslib_1.__importStar(require("react"));
13
13
  var rxjs_1 = require("rxjs");
14
14
  var operators_1 = require("rxjs/operators");
15
15
  var int_1 = require("../../mol-data/int");
@@ -21,7 +21,7 @@ var base_1 = require("../base");
21
21
  var MaxSequenceNumberSize = 5;
22
22
  // TODO: this is somewhat inefficient and should be done using a canvas.
23
23
  var Sequence = /** @class */ (function (_super) {
24
- (0, tslib_1.__extends)(Sequence, _super);
24
+ tslib_1.__extends(Sequence, _super);
25
25
  function Sequence() {
26
26
  var _this = _super !== null && _super.apply(this, arguments) || this;
27
27
  _this.parentDiv = React.createRef();
@@ -96,7 +96,7 @@ var Sequence = /** @class */ (function (_super) {
96
96
  _this.lastMouseOverSeqIdx = seqIdx;
97
97
  if (_this.mouseDownLoci !== undefined) {
98
98
  var loci = _this.getLoci(seqIdx);
99
- _this.hover(loci, 0 /* None */, 0 /* None */, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, modifiers), { shift: true }));
99
+ _this.hover(loci, 0 /* None */, 0 /* None */, tslib_1.__assign(tslib_1.__assign({}, modifiers), { shift: true }));
100
100
  }
101
101
  else {
102
102
  _this.highlightQueue.next({ seqIdx: seqIdx, buttons: buttons, button: button, modifiers: modifiers });
@@ -190,7 +190,7 @@ var Sequence = /** @class */ (function (_super) {
190
190
  : this.props.sequenceWrapper.residueClass(seqIdx);
191
191
  };
192
192
  Sequence.prototype.residue = function (seqIdx, label, marker) {
193
- return (0, jsx_runtime_1.jsx)("span", (0, tslib_1.__assign)({ "data-seqid": seqIdx, style: { backgroundColor: this.getBackgroundColor(marker) }, className: this.getResidueClass(seqIdx, label) }, { children: "\u200B".concat(label, "\u200B") }), seqIdx);
193
+ return (0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ "data-seqid": seqIdx, style: { backgroundColor: this.getBackgroundColor(marker) }, className: this.getResidueClass(seqIdx, label) }, { children: "\u200B".concat(label, "\u200B") }), seqIdx);
194
194
  };
195
195
  Sequence.prototype.getSequenceNumberClass = function (seqIdx, seqNum, label) {
196
196
  var classList = ['msp-sequence-number'];
@@ -229,7 +229,7 @@ var Sequence = /** @class */ (function (_super) {
229
229
  };
230
230
  Sequence.prototype.getSequenceNumberSpan = function (seqIdx, label) {
231
231
  var seqNum = this.getSequenceNumber(seqIdx);
232
- return (0, jsx_runtime_1.jsx)("span", (0, tslib_1.__assign)({ className: this.getSequenceNumberClass(seqIdx, seqNum, label) }, { children: this.padSeqNum(seqNum) }), "marker-".concat(seqIdx));
232
+ return (0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ className: this.getSequenceNumberClass(seqIdx, seqNum, label) }, { children: this.padSeqNum(seqNum) }), "marker-".concat(seqIdx));
233
233
  };
234
234
  Sequence.prototype.updateMarker = function () {
235
235
  if (!this.parentDiv.current)
@@ -273,7 +273,7 @@ var Sequence = /** @class */ (function (_super) {
273
273
  // calling .updateMarker here is neccesary to ensure existing
274
274
  // residue spans are updated as react won't update them
275
275
  this.updateMarker();
276
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-sequence-wrapper', onContextMenu: this.contextMenu, onMouseDown: this.mouseDown, onMouseUp: this.mouseUp, onMouseMove: this.mouseMove, onMouseLeave: this.mouseLeave, ref: this.parentDiv }, { children: elems }), void 0);
276
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-wrapper', onContextMenu: this.contextMenu, onMouseDown: this.mouseDown, onMouseUp: this.mouseUp, onMouseMove: this.mouseMove, onMouseLeave: this.mouseLeave, ref: this.parentDiv }, { children: elems }));
277
277
  };
278
278
  return Sequence;
279
279
  }(base_1.PluginUIComponent));
@@ -9,7 +9,7 @@ var jsx_runtime_1 = require("react/jsx-runtime");
9
9
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
10
10
  * @author David Sehnal <david.sehnal@gmail.com>
11
11
  */
12
- var React = (0, tslib_1.__importStar)(require("react"));
12
+ var React = tslib_1.__importStar(require("react"));
13
13
  var base_1 = require("./base");
14
14
  var objects_1 = require("../mol-plugin-state/objects");
15
15
  var sequence_1 = require("./sequence/sequence");
@@ -208,12 +208,12 @@ function getStructureOptions(state) {
208
208
  }
209
209
  var SequenceViewModeParam = param_definition_1.ParamDefinition.Select('single', [['single', 'Chain'], ['polymers', 'Polymers'], ['all', 'Everything']]);
210
210
  var SequenceView = /** @class */ (function (_super) {
211
- (0, tslib_1.__extends)(SequenceView, _super);
211
+ tslib_1.__extends(SequenceView, _super);
212
212
  function SequenceView() {
213
213
  var _this = _super !== null && _super.apply(this, arguments) || this;
214
214
  _this.state = { structureOptions: { options: [], all: [] }, structure: structure_1.Structure.Empty, structureRef: '', modelEntityId: '', chainGroupId: -1, operatorKey: '', mode: 'single' };
215
215
  _this.setParamProps = function (p) {
216
- var state = (0, tslib_1.__assign)({}, _this.state);
216
+ var state = tslib_1.__assign({}, _this.state);
217
217
  switch (p.name) {
218
218
  case 'mode':
219
219
  state.mode = p.value;
@@ -363,24 +363,24 @@ var SequenceView = /** @class */ (function (_super) {
363
363
  });
364
364
  SequenceView.prototype.render = function () {
365
365
  if (this.getStructure(this.state.structureRef) === structure_1.Structure.Empty) {
366
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-sequence' }, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-sequence-select' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, style: { cursor: 'help', position: 'absolute', right: 0, top: 0 }, title: 'Shows a sequence of one or more chains. Use the controls to alter selection.' }, void 0), (0, jsx_runtime_1.jsx)("span", { children: "Sequence" }, void 0), (0, jsx_runtime_1.jsx)("span", (0, tslib_1.__assign)({ style: { fontWeight: 'normal' } }, { children: "No structure available" }), void 0)] }), void 0) }), void 0);
366
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence' }, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-sequence-select' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, style: { cursor: 'help', position: 'absolute', right: 0, top: 0 }, title: 'Shows a sequence of one or more chains. Use the controls to alter selection.' }), (0, jsx_runtime_1.jsx)("span", { children: "Sequence" }), (0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ style: { fontWeight: 'normal' } }, { children: "No structure available" }))] })) }));
367
367
  }
368
368
  var params = this.params;
369
369
  var values = this.values;
370
370
  var sequenceWrappers = this.getSequenceWrappers(params);
371
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-sequence' }, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-sequence-select' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, style: { cursor: 'help', position: 'absolute', right: 0, top: 0 }, title: 'This shows a single sequence. Use the controls to show a different sequence.' }, void 0), (0, jsx_runtime_1.jsx)("span", { children: "Sequence of" }, void 0), (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Structure] ".concat(param_definition_1.ParamDefinition.optionLabel(params.structure, values.structure)), param: params.structure, name: 'structure', value: values.structure, onChange: this.setParamProps }, void 0), (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Mode]", param: SequenceViewModeParam, name: 'mode', value: values.mode, onChange: this.setParamProps }, void 0), values.mode === 'single' && (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Entity] ".concat(param_definition_1.ParamDefinition.optionLabel(params.entity, values.entity)), param: params.entity, name: 'entity', value: values.entity, onChange: this.setParamProps }, void 0), values.mode === 'single' && (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Chain] ".concat(param_definition_1.ParamDefinition.optionLabel(params.chain, values.chain)), param: params.chain, name: 'chain', value: values.chain, onChange: this.setParamProps }, void 0), params.operator.options.length > 1 && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Instance] ".concat(param_definition_1.ParamDefinition.optionLabel(params.operator, values.operator)), param: params.operator, name: 'operator', value: values.operator, onChange: this.setParamProps }, void 0) }, void 0)] }), void 0), (0, jsx_runtime_1.jsx)(NonEmptySequenceWrapper, { children: sequenceWrappers.map(function (s, i) {
371
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-sequence' }, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-sequence-select' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, style: { cursor: 'help', position: 'absolute', right: 0, top: 0 }, title: 'This shows a single sequence. Use the controls to show a different sequence.' }), (0, jsx_runtime_1.jsx)("span", { children: "Sequence of" }), (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Structure] ".concat(param_definition_1.ParamDefinition.optionLabel(params.structure, values.structure)), param: params.structure, name: 'structure', value: values.structure, onChange: this.setParamProps }), (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Mode]", param: SequenceViewModeParam, name: 'mode', value: values.mode, onChange: this.setParamProps }), values.mode === 'single' && (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Entity] ".concat(param_definition_1.ParamDefinition.optionLabel(params.entity, values.entity)), param: params.entity, name: 'entity', value: values.entity, onChange: this.setParamProps }), values.mode === 'single' && (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Chain] ".concat(param_definition_1.ParamDefinition.optionLabel(params.chain, values.chain)), param: params.chain, name: 'chain', value: values.chain, onChange: this.setParamProps }), params.operator.options.length > 1 && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "[Instance] ".concat(param_definition_1.ParamDefinition.optionLabel(params.operator, values.operator)), param: params.operator, name: 'operator', value: values.operator, onChange: this.setParamProps }) })] })), (0, jsx_runtime_1.jsx)(NonEmptySequenceWrapper, { children: sequenceWrappers.map(function (s, i) {
372
372
  var elem = typeof s.wrapper === 'string'
373
- ? (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-sequence-wrapper' }, { children: s.wrapper }), i)
373
+ ? (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-wrapper' }, { children: s.wrapper }), i)
374
374
  : (0, jsx_runtime_1.jsx)(sequence_1.Sequence, { sequenceWrapper: s.wrapper }, i);
375
375
  if (values.mode === 'single')
376
376
  return elem;
377
- return (0, jsx_runtime_1.jsxs)(React.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-sequence-chain-label' }, { children: s.label }), void 0), elem] }, i);
378
- }) }, void 0)] }), void 0);
377
+ return (0, jsx_runtime_1.jsxs)(React.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-chain-label' }, { children: s.label })), elem] }, i);
378
+ }) })] }));
379
379
  };
380
380
  return SequenceView;
381
381
  }(base_1.PluginUIComponent));
382
382
  exports.SequenceView = SequenceView;
383
383
  function NonEmptySequenceWrapper(_a) {
384
384
  var children = _a.children;
385
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-sequence-wrapper-non-empty' }, { children: children }), void 0);
385
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-sequence-wrapper-non-empty' }, { children: children }));
386
386
  }
@@ -11,7 +11,7 @@ var tslib_1 = require("tslib");
11
11
  var transformers_1 = require("../mol-plugin/behavior/dynamic/volume-streaming/transformers");
12
12
  var spec_1 = require("../mol-plugin/spec");
13
13
  var volume_1 = require("./custom/volume");
14
- var DefaultPluginUISpec = function () { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginSpec)()), { customParamEditors: [
14
+ var DefaultPluginUISpec = function () { return (tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginSpec)()), { customParamEditors: [
15
15
  [transformers_1.CreateVolumeStreamingBehavior, volume_1.VolumeStreamingCustomControls]
16
16
  ] })); };
17
17
  exports.DefaultPluginUISpec = DefaultPluginUISpec;
@@ -7,7 +7,7 @@ var base_1 = require("../base");
7
7
  var icons_1 = require("../controls/icons");
8
8
  var apply_action_1 = require("./apply-action");
9
9
  var StateObjectActions = /** @class */ (function (_super) {
10
- (0, tslib_1.__extends)(StateObjectActions, _super);
10
+ tslib_1.__extends(StateObjectActions, _super);
11
11
  function StateObjectActions() {
12
12
  return _super !== null && _super.apply(this, arguments) || this;
13
13
  }
@@ -43,7 +43,7 @@ var StateObjectActions = /** @class */ (function (_super) {
43
43
  return null;
44
44
  var def = cell.transform.transformer.definition;
45
45
  var display = cell.obj ? cell.obj.label : (def.display && def.display.name) || def.name;
46
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-state-actions' }, { children: [!this.props.hideHeader && (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-section-header' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CodeSvg }, void 0), " ", "Actions (".concat(display, ")")] }), void 0), actions.map(function (act, i) { return (0, jsx_runtime_1.jsx)(apply_action_1.ApplyActionControl, { state: state, action: act, nodeRef: ref, initiallyCollapsed: i === 0 ? !_this.props.alwaysExpandFirst && _this.props.initiallyCollapsed : _this.props.initiallyCollapsed }, "".concat(act.id)); })] }), void 0);
46
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-state-actions' }, { children: [!this.props.hideHeader && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-section-header' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CodeSvg }), " ", "Actions (".concat(display, ")")] })), actions.map(function (act, i) { return (0, jsx_runtime_1.jsx)(apply_action_1.ApplyActionControl, { state: state, action: act, nodeRef: ref, initiallyCollapsed: i === 0 ? !_this.props.alwaysExpandFirst && _this.props.initiallyCollapsed : _this.props.initiallyCollapsed }, "".concat(act.id)); })] }));
47
47
  };
48
48
  return StateObjectActions;
49
49
  }(base_1.PluginUIComponent));
@@ -13,7 +13,7 @@ var parameters_1 = require("../controls/parameters");
13
13
  var common_1 = require("../controls/common");
14
14
  var icons_1 = require("../controls/icons");
15
15
  var AnimationControls = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(AnimationControls, _super);
16
+ tslib_1.__extends(AnimationControls, _super);
17
17
  function AnimationControls() {
18
18
  var _this = _super !== null && _super.apply(this, arguments) || this;
19
19
  _this.updateParams = function (p) {
@@ -47,7 +47,7 @@ var AnimationControls = /** @class */ (function (_super) {
47
47
  return null;
48
48
  var isDisabled = anim.state.animationState === 'playing';
49
49
  var canApply = (_b = (_a = anim.current.anim).canApply) === null || _b === void 0 ? void 0 : _b.call(_a, this.plugin);
50
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.getParams(), values: anim.state.params, onChange: this.updateParams, isDisabled: isDisabled }, void 0), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.current.params, values: anim.current.paramValues, onChange: this.updateCurrentParams, isDisabled: isDisabled }, void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: anim.state.animationState !== 'playing' ? void 0 : icons_1.PlayArrowSvg, onClick: this.startOrStop, disabled: canApply !== void 0 && canApply.canApply === false }, { children: anim.state.animationState === 'playing' ? 'Stop' : canApply === void 0 || canApply.canApply ? 'Start' : canApply.reason || 'Start' }), void 0) }), void 0)] }, void 0);
50
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.getParams(), values: anim.state.params, onChange: this.updateParams, isDisabled: isDisabled }), (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: anim.current.params, values: anim.current.paramValues, onChange: this.updateCurrentParams, isDisabled: isDisabled }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: anim.state.animationState !== 'playing' ? void 0 : icons_1.PlayArrowSvg, onClick: this.startOrStop, disabled: canApply !== void 0 && canApply.canApply === false }, { children: anim.state.animationState === 'playing' ? 'Stop' : canApply === void 0 || canApply.canApply ? 'Start' : canApply.reason || 'Start' })) }))] });
51
51
  };
52
52
  return AnimationControls;
53
53
  }(base_1.PluginUIComponent));
@@ -12,7 +12,7 @@ var memoize_1 = require("../../mol-util/memoize");
12
12
  var common_1 = require("./common");
13
13
  var param_definition_1 = require("../../mol-util/param-definition");
14
14
  var ApplyActionControl = /** @class */ (function (_super) {
15
- (0, tslib_1.__extends)(ApplyActionControl, _super);
15
+ tslib_1.__extends(ApplyActionControl, _super);
16
16
  function ApplyActionControl() {
17
17
  var _this = _super !== null && _super.apply(this, arguments) || this;
18
18
  _this._getInfo = (0, memoize_1.memoizeLatest)(function (t, v) { return common_1.StateTransformParameters.infoFromAction(_this.plugin, _this.props.state, _this.props.action, _this.props.nodeRef); });
@@ -10,13 +10,13 @@ var rxjs_1 = require("rxjs");
10
10
  var icons_1 = require("../controls/icons");
11
11
  var common_1 = require("../controls/common");
12
12
  var StateTransformParameters = /** @class */ (function (_super) {
13
- (0, tslib_1.__extends)(StateTransformParameters, _super);
13
+ tslib_1.__extends(StateTransformParameters, _super);
14
14
  function StateTransformParameters() {
15
15
  var _this = _super !== null && _super.apply(this, arguments) || this;
16
16
  _this.onChange = function (_a) {
17
17
  var _b;
18
18
  var name = _a.name, value = _a.value;
19
- var params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.props.params), (_b = {}, _b[name] = value, _b));
19
+ var params = tslib_1.__assign(tslib_1.__assign({}, _this.props.params), (_b = {}, _b[name] = value, _b));
20
20
  _this.props.events.onChange(params, _this.areInitial(params), _this.validate(params));
21
21
  };
22
22
  return _this;
@@ -29,7 +29,7 @@ var StateTransformParameters = /** @class */ (function (_super) {
29
29
  return param_definition_1.ParamDefinition.areEqual(this.props.info.params, params, this.props.info.initialValues);
30
30
  };
31
31
  StateTransformParameters.prototype.render = function () {
32
- return (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: this.props.info.params, values: this.props.params, onChange: this.onChange, onEnter: this.props.events.onEnter, isDisabled: this.props.isDisabled }, void 0);
32
+ return (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: this.props.info.params, values: this.props.params, onChange: this.onChange, onEnter: this.props.events.onEnter, isDisabled: this.props.isDisabled });
33
33
  };
34
34
  return StateTransformParameters;
35
35
  }(base_1.PurePluginUIComponent));
@@ -72,7 +72,7 @@ exports.StateTransformParameters = StateTransformParameters;
72
72
  })(StateTransformParameters || (StateTransformParameters = {}));
73
73
  exports.StateTransformParameters = StateTransformParameters;
74
74
  var TransformControlBase = /** @class */ (function (_super) {
75
- (0, tslib_1.__extends)(TransformControlBase, _super);
75
+ tslib_1.__extends(TransformControlBase, _super);
76
76
  function TransformControlBase() {
77
77
  var _this = _super !== null && _super.apply(this, arguments) || this;
78
78
  _this.busy = new rxjs_1.Subject();
@@ -94,10 +94,10 @@ var TransformControlBase = /** @class */ (function (_super) {
94
94
  });
95
95
  }
96
96
  };
97
- _this.apply = function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
97
+ _this.apply = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
98
98
  var e_1;
99
99
  var _a, _b;
100
- return (0, tslib_1.__generator)(this, function (_c) {
100
+ return tslib_1.__generator(this, function (_c) {
101
101
  switch (_c.label) {
102
102
  case 0:
103
103
  this.clearAutoApply();
@@ -155,7 +155,7 @@ var TransformControlBase = /** @class */ (function (_super) {
155
155
  var canApply = this.canApply();
156
156
  if (this.props.autoHideApply && (!canApply || this.canAutoApply(this.state.params)))
157
157
  return null;
158
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-transform-apply-wrap' }, { children: [(0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.RefreshSvg, className: 'msp-transform-default-params', onClick: this.setDefault, disabled: this.state.busy, title: 'Set default params' }, void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: "msp-transform-apply-wider" }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: canApply ? icons_1.CheckSvg : void 0, className: "msp-btn-commit msp-btn-commit-".concat(canApply ? 'on' : 'off'), onClick: this.apply, disabled: !canApply }, { children: this.props.applyLabel || this.applyText() }), void 0) }), void 0)] }), void 0);
158
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-transform-apply-wrap' }, { children: [(0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.RefreshSvg, className: 'msp-transform-default-params', onClick: this.setDefault, disabled: this.state.busy, title: 'Set default params' }), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: "msp-transform-apply-wider" }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: canApply ? icons_1.CheckSvg : void 0, className: "msp-btn-commit msp-btn-commit-".concat(canApply ? 'on' : 'off'), onClick: this.apply, disabled: !canApply }, { children: this.props.applyLabel || this.applyText() })) }))] }));
159
159
  };
160
160
  TransformControlBase.prototype.renderDefault = function () {
161
161
  var info = this.getInfo();
@@ -172,18 +172,18 @@ var TransformControlBase = /** @class */ (function (_super) {
172
172
  if (!isEmpty && !this.state.isCollapsed) {
173
173
  var _a = this.getSourceAndTarget(), a = _a.a, b = _a.b, bCell = _a.bCell;
174
174
  var applyControl = this.renderApply();
175
- params = (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy }, void 0), applyControl] }, void 0);
175
+ params = (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy }), applyControl] });
176
176
  }
177
- var ctrl = (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: wrapClass, style: { marginBottom: this.props.noMargin ? 0 : void 0 } }, { children: [display !== 'none' && !this.props.wrapInExpander && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-transform-header' }, { children: (0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.toggleExpanded, title: display.description }, { children: [!isEmpty && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isCollapsed ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg }, void 0), display.name] }), void 0) }), void 0), params] }), void 0);
177
+ var ctrl = (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: wrapClass, style: { marginBottom: this.props.noMargin ? 0 : void 0 } }, { children: [display !== 'none' && !this.props.wrapInExpander && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-transform-header' }, { children: (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ onClick: this.toggleExpanded, title: display.description }, { children: [!isEmpty && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isCollapsed ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg }), display.name] })) })), params] }));
178
178
  if (isEmpty || !this.props.wrapInExpander)
179
179
  return ctrl;
180
- return (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, (0, tslib_1.__assign)({ header: this.isUpdate() ? "Update ".concat(display === 'none' ? '' : display.name) : "Apply ".concat(display === 'none' ? '' : display.name), headerLeftMargin: this.props.expanderHeaderLeftMargin }, { children: ctrl }), void 0);
180
+ return (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: this.isUpdate() ? "Update ".concat(display === 'none' ? '' : display.name) : "Apply ".concat(display === 'none' ? '' : display.name), headerLeftMargin: this.props.expanderHeaderLeftMargin }, { children: ctrl }));
181
181
  };
182
182
  TransformControlBase.prototype.renderSimple = function () {
183
183
  var _a, _b, _c;
184
184
  var info = this.getInfo();
185
185
  var canApply = this.canApply();
186
- var apply = (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: (_a = this.props.simpleApply) === null || _a === void 0 ? void 0 : _a.icon, title: (_b = this.props.simpleApply) === null || _b === void 0 ? void 0 : _b.title, disabled: this.state.busy || !canApply, onClick: this.apply, className: 'msp-btn-apply-simple' }, { children: (_c = this.props.simpleApply) === null || _c === void 0 ? void 0 : _c.header }), void 0), !info.isEmpty && (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.TuneSvg, label: '', title: 'Options', toggle: this.toggleExpanded, isSelected: !this.state.isCollapsed, disabled: this.state.busy, style: { flex: '0 0 40px', padding: 0 } }, void 0)] }), void 0);
186
+ var apply = (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: (_a = this.props.simpleApply) === null || _a === void 0 ? void 0 : _a.icon, title: (_b = this.props.simpleApply) === null || _b === void 0 ? void 0 : _b.title, disabled: this.state.busy || !canApply, onClick: this.apply, className: 'msp-btn-apply-simple' }, { children: (_c = this.props.simpleApply) === null || _c === void 0 ? void 0 : _c.header })), !info.isEmpty && (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.TuneSvg, label: '', title: 'Options', toggle: this.toggleExpanded, isSelected: !this.state.isCollapsed, disabled: this.state.busy, style: { flex: '0 0 40px', padding: 0 } })] }));
187
187
  if (this.state.isCollapsed)
188
188
  return apply;
189
189
  var tId = this.getTransformerId();
@@ -191,7 +191,7 @@ var TransformControlBase = /** @class */ (function (_super) {
191
191
  ? this.plugin.customParamEditors.get(tId)
192
192
  : StateTransformParameters;
193
193
  var _d = this.getSourceAndTarget(), a = _d.a, b = _d.b, bCell = _d.bCell;
194
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [apply, (0, jsx_runtime_1.jsx)(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy }, void 0)] }, void 0);
194
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [apply, (0, jsx_runtime_1.jsx)(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy })] });
195
195
  };
196
196
  TransformControlBase.prototype.render = function () {
197
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  // console.log('rendering', ((this.props as any)?.transform?.transformer || (this.props as any)?.action)?.definition.display.name, +new Date)