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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  610. package/lib/commonjs/servers/volume/common/file.js +8 -8
  611. package/lib/commonjs/servers/volume/config.js +6 -6
  612. package/lib/commonjs/servers/volume/pack/format/ccp4.js +4 -4
  613. package/lib/commonjs/servers/volume/pack/format/dsn6.js +4 -4
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  616. package/lib/commonjs/servers/volume/pack/sampling.js +13 -13
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  620. package/lib/commonjs/servers/volume/server/algebra/box.js +1 -1
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  622. package/lib/commonjs/servers/volume/server/local-api.js +8 -8
  623. package/lib/commonjs/servers/volume/server/query/compose.js +8 -8
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  625. package/lib/commonjs/servers/volume/server/query/identify.js +2 -2
  626. package/lib/commonjs/servers/volume/server/web-api.js +7 -7
  627. package/lib/commonjs/servers/volume/server.js +2 -2
  628. package/lib/examples/alpha-orbitals/controls.js +2 -2
  629. package/lib/examples/basic-wrapper/controls.js +1 -1
  630. package/lib/examples/proteopedia-wrapper/ui/controls.js +1 -1
  631. package/lib/extensions/cellpack/model.js +4 -2
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  635. package/lib/extensions/mp4-export/ui.js +2 -2
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  637. package/lib/extensions/zenodo/index.d.ts +7 -0
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  639. package/lib/extensions/zenodo/ui.d.ts +61 -0
  640. package/lib/extensions/zenodo/ui.js +303 -0
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  642. package/lib/mol-canvas3d/helper/camera-helper.js +1 -1
  643. package/lib/mol-canvas3d/helper/handle-helper.js +1 -1
  644. package/lib/mol-canvas3d/helper/interaction-events.js +1 -1
  645. package/lib/mol-geo/geometry/text/text-builder.js +2 -1
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  647. package/lib/mol-gl/webgl/buffer.js +2 -3
  648. package/lib/mol-io/common/binary-cif/classifier.js +3 -2
  649. package/lib/mol-io/common/binary-cif/decoder.js +4 -3
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  652. package/lib/mol-io/common/netcdf/reader.d.ts +78 -0
  653. package/lib/mol-io/common/netcdf/reader.js +456 -0
  654. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  655. package/lib/mol-io/reader/nctraj/parser.d.ts +18 -0
  656. package/lib/mol-io/reader/nctraj/parser.js +97 -0
  657. package/lib/mol-io/reader/prmtop/parser.d.ts +58 -0
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  663. package/lib/mol-io/writer/cif/encoder.js +2 -1
  664. package/lib/mol-model/sequence/sequence.js +2 -1
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  667. package/lib/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
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  675. package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
  676. package/lib/mol-model-formats/structure/basic/util.js +24 -1
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  679. package/lib/mol-model-formats/structure/cube.js +3 -3
  680. package/lib/mol-model-formats/structure/gro.js +3 -1
  681. package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
  682. package/lib/mol-model-formats/structure/mmcif.js +4 -2
  683. package/lib/mol-model-formats/structure/mol.js +3 -3
  684. package/lib/mol-model-formats/structure/mol2.js +4 -4
  685. package/lib/mol-model-formats/structure/nctraj.d.ts +9 -0
  686. package/lib/mol-model-formats/structure/nctraj.js +56 -0
  687. package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
  688. package/lib/mol-model-formats/structure/pdb.js +5 -3
  689. package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
  690. package/lib/mol-model-formats/structure/prmtop.js +144 -0
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  692. package/lib/mol-model-formats/structure/psf.js +3 -1
  693. package/lib/mol-model-formats/structure/top.d.ts +16 -0
  694. package/lib/mol-model-formats/structure/top.js +186 -0
  695. package/lib/mol-model-formats/structure/trr.d.ts +9 -0
  696. package/lib/mol-model-formats/structure/trr.js +42 -0
  697. package/lib/mol-model-formats/structure/util.d.ts +2 -2
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  699. package/lib/mol-model-formats/structure/xyz.js +2 -2
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  709. package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
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  711. package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
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  746. package/lib/mol-plugin-ui/structure/components.js +10 -10
  747. package/lib/mol-plugin-ui/structure/focus.js +1 -1
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  767. package/lib/mol-util/file-info.d.ts +1 -3
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  774. package/lib/servers/model/config.d.ts +2 -2
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  776. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  777. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -33,7 +33,7 @@ var StructureComponentControls = /** @class */ (function (_super) {
33
33
  }); });
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  };
35
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  StructureComponentControls.prototype.renderControls = function () {
36
- return _jsxs(_Fragment, { children: [_jsx(ComponentEditorControls, {}, void 0), _jsx(ComponentListControls, {}, void 0), _jsx(GenericEntryListControls, {}, void 0)] }, void 0);
36
+ return _jsxs(_Fragment, { children: [_jsx(ComponentEditorControls, {}), _jsx(ComponentListControls, {}), _jsx(GenericEntryListControls, {})] });
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  };
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  return StructureComponentControls;
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  }(CollapsableControls));
@@ -96,7 +96,7 @@ var ComponentEditorControls = /** @class */ (function (_super) {
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  };
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  Object.defineProperty(ComponentEditorControls.prototype, "presetControls", {
98
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  get: function () {
99
- return _jsx(ActionMenu, { items: this.presetActions, onSelect: this.applyPreset }, void 0);
99
+ return _jsx(ActionMenu, { items: this.presetActions, onSelect: this.applyPreset });
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  },
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  enumerable: false,
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  configurable: true
@@ -114,7 +114,7 @@ var ComponentEditorControls = /** @class */ (function (_super) {
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  var undoTitle = this.state.canUndo
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  ? "Undo ".concat(this.plugin.state.data.latestUndoLabel)
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  : 'Some mistakes of the past can be undone.';
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- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: BookmarksOutlinedSvg, label: 'Preset', title: 'Apply a representation preset for the current structure(s).', toggle: this.togglePreset, isSelected: this.state.action === 'preset', disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: AddSvg, label: 'Add', title: 'Add a new representation component for a selection.', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options that are applied to all applicable representations.', style: { flex: '0 0 40px', padding: 0 }, toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.isDisabled }, void 0), _jsx(IconButton, { svg: RestoreSvg, className: 'msp-flex-item', flex: '40px', onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle }, void 0)] }), void 0), this.state.action === 'preset' && this.presetControls, this.state.action === 'add' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(AddComponentControls, { onApply: this.hideAction }, void 0) }), void 0), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ComponentOptionsControls, { isDisabled: this.isDisabled }, void 0) }), void 0)] }, void 0);
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+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: BookmarksOutlinedSvg, label: 'Preset', title: 'Apply a representation preset for the current structure(s).', toggle: this.togglePreset, isSelected: this.state.action === 'preset', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: AddSvg, label: 'Add', title: 'Add a new representation component for a selection.', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options that are applied to all applicable representations.', style: { flex: '0 0 40px', padding: 0 }, toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.isDisabled }), _jsx(IconButton, { svg: RestoreSvg, className: 'msp-flex-item', flex: '40px', onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle })] })), this.state.action === 'preset' && this.presetControls, this.state.action === 'add' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(AddComponentControls, { onApply: this.hideAction }) })), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ComponentOptionsControls, { isDisabled: this.isDisabled }) }))] });
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  };
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  return ComponentEditorControls;
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  }(PurePluginUIComponent));
@@ -150,7 +150,7 @@ var AddComponentControls = /** @class */ (function (_super) {
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  configurable: true
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  });
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  AddComponentControls.prototype.render = function () {
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- return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.state.params, values: this.state.values, onChangeValues: this.paramsChanged }, void 0), _jsx(Button, __assign({ icon: AddSvg, title: 'Use Selection and optional Representation to create a new Component.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Create Component" }), void 0)] }, void 0);
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+ return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.state.params, values: this.state.values, onChangeValues: this.paramsChanged }), _jsx(Button, __assign({ icon: AddSvg, title: 'Use Selection and optional Representation to create a new Component.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Create Component" }))] });
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  };
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  return AddComponentControls;
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  }(PurePluginUIComponent));
@@ -167,7 +167,7 @@ var ComponentOptionsControls = /** @class */ (function (_super) {
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  this.subscribe(this.plugin.managers.structure.component.events.optionsUpdated, function () { return _this.forceUpdate(); });
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  };
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  ComponentOptionsControls.prototype.render = function () {
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- return _jsx(ParameterControls, { params: StructureComponentManager.OptionsParams, values: this.plugin.managers.structure.component.state.options, onChangeValues: this.update, isDisabled: this.props.isDisabled }, void 0);
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+ return _jsx(ParameterControls, { params: StructureComponentManager.OptionsParams, values: this.plugin.managers.structure.component.state.options, onChangeValues: this.update, isDisabled: this.props.isDisabled });
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  };
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  return ComponentOptionsControls;
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  }(PurePluginUIComponent));
@@ -186,7 +186,7 @@ var ComponentListControls = /** @class */ (function (_super) {
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  var componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
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  if (componentGroups.length === 0)
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  return null;
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- return _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: componentGroups.map(function (g) { return _jsx(StructureComponentGroup, { group: g }, g[0].cell.transform.ref); }) }), void 0);
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+ return _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: componentGroups.map(function (g) { return _jsx(StructureComponentGroup, { group: g }, g[0].cell.transform.ref); }) }));
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  };
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  return ComponentListControls;
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  }(PurePluginUIComponent));
@@ -326,7 +326,7 @@ var StructureComponentGroup = /** @class */ (function (_super) {
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  var cell = component.cell;
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  var label = (_a = cell.obj) === null || _a === void 0 ? void 0 : _a.label;
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  var reprLabel = this.reprLabel;
329
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: reprLabel }), void 0)] }), void 0), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(cell.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, toggleState: false, onClick: this.remove, title: 'Remove', small: true, className: 'msp-form-control', flex: true }, void 0), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleAction, title: 'Actions', toggleState: this.state.action === 'action', className: 'msp-form-control', flex: true }, void 0)] }), void 0), this.state.action === 'label' && _jsx("div", __assign({ className: 'msp-control-offset', style: { marginBottom: '6px' } }, { children: _jsx(ControlRow, { label: 'Label', control: _jsxs("div", __assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [_jsx(TextInput, { onChange: this.updateLabel, value: label, style: { flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', blurOnEnter: true, blurOnEscape: true }, void 0), _jsx(IconButton, { svg: CheckSvg, onClick: this.toggleLabel, className: 'msp-form-control msp-control-button-label', flex: true }, void 0)] }), void 0) }, void 0) }), void 0), this.state.action === 'action' && _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: _jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }, void 0) }), void 0), _jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: component.representations.map(function (r) { return _jsx(StructureRepresentationEntry, { group: _this.props.group, representation: r }, r.cell.transform.ref); }) }), void 0)] }), void 0)] }, void 0);
329
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: reprLabel }))] })), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(cell.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: DeleteOutlinedSvg, toggleState: false, onClick: this.remove, title: 'Remove', small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleAction, title: 'Actions', toggleState: this.state.action === 'action', className: 'msp-form-control', flex: true })] })), this.state.action === 'label' && _jsx("div", __assign({ className: 'msp-control-offset', style: { marginBottom: '6px' } }, { children: _jsx(ControlRow, { label: 'Label', control: _jsxs("div", __assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [_jsx(TextInput, { onChange: this.updateLabel, value: label, style: { flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', blurOnEnter: true, blurOnEscape: true }), _jsx(IconButton, { svg: CheckSvg, onClick: this.toggleLabel, className: 'msp-form-control msp-control-button-label', flex: true })] })) }) })), this.state.action === 'action' && _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: _jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }) })), _jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: component.representations.map(function (r) { return _jsx(StructureRepresentationEntry, { group: _this.props.group, representation: r }, r.cell.transform.ref); }) }))] }))] });
330
330
  };
331
331
  return StructureComponentGroup;
332
332
  }(PurePluginUIComponent));
@@ -353,11 +353,11 @@ var StructureRepresentationEntry = /** @class */ (function (_super) {
353
353
  StructureRepresentationEntry.prototype.render = function () {
354
354
  var _a;
355
355
  var repr = this.props.representation.cell;
356
- return _jsxs("div", __assign({ className: 'msp-representation-entry' }, { children: [repr.parent && _jsx(ExpandGroup, __assign({ header: "".concat(((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) || '', " Representation"), noOffset: true }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', customUpdate: this.update, noMargin: true }, void 0) }), void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true, className: 'msp-default-bg', toggleState: false, style: {
356
+ return _jsxs("div", __assign({ className: 'msp-representation-entry' }, { children: [repr.parent && _jsx(ExpandGroup, __assign({ header: "".concat(((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) || '', " Representation"), noOffset: true }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', customUpdate: this.update, noMargin: true }) })), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true, className: 'msp-default-bg', toggleState: false, style: {
357
357
  position: 'absolute', top: 0, right: '32px', lineHeight: '24px', height: '24px', textAlign: 'right', width: '44px', paddingRight: '6px', background: 'none'
358
- } }, void 0), _jsx(IconButton, { svg: this.props.representation.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: 'Toggle Visibility', small: true, className: 'msp-default-bg', style: {
358
+ } }), _jsx(IconButton, { svg: this.props.representation.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: 'Toggle Visibility', small: true, className: 'msp-default-bg', style: {
359
359
  position: 'absolute', top: 0, right: 0, lineHeight: '24px', height: '24px', textAlign: 'right', width: '32px', paddingRight: '6px', background: 'none'
360
- } }, void 0)] }), void 0);
360
+ } })] }));
361
361
  };
362
362
  return StructureRepresentationEntry;
363
363
  }(PurePluginUIComponent));
@@ -222,7 +222,7 @@ var StructureFocusControls = /** @class */ (function (_super) {
222
222
  title += "\nor use '".concat(binding, "' on element");
223
223
  }
224
224
  }
225
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label }), void 0), current && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true, disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: CenterFocusStrongSvg, title: 'Select a focus target to center on an show its surroundings. Hold shift to focus on multiple targets.', toggle: this.toggleAction, isSelected: this.state.showAction, disabled: this.isDisabled, style: { flex: '0 0 40px', padding: 0 } }, void 0)] }), void 0), this.state.showAction && _jsx(ActionMenu, { items: this.actionItems, onSelect: this.selectAction }, void 0)] }, void 0);
225
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label })), current && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true, disabled: this.isDisabled }), _jsx(ToggleButton, { icon: CenterFocusStrongSvg, title: 'Select a focus target to center on an show its surroundings. Hold shift to focus on multiple targets.', toggle: this.toggleAction, isSelected: this.state.showAction, disabled: this.isDisabled, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.showAction && _jsx(ActionMenu, { items: this.actionItems, onSelect: this.selectAction })] });
226
226
  };
227
227
  return StructureFocusControls;
228
228
  }(PluginUIComponent));
@@ -37,7 +37,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
37
37
  }
38
38
  if (refs.length === 0)
39
39
  return null;
40
- return _jsx(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' }, void 0);
40
+ return _jsx(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' });
41
41
  },
42
42
  enumerable: false,
43
43
  configurable: true
@@ -49,7 +49,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
49
49
  this.plugin.genericRepresentationControls.forEach(function (provider, key) {
50
50
  var _a = provider(_this.plugin.managers.structure.hierarchy.selection), refs = _a[0], labelMultiple = _a[1];
51
51
  if (refs.length > 0) {
52
- controls.push(_jsx("div", { children: _jsx(GenericEntry, { refs: refs, labelMultiple: labelMultiple }, void 0) }, key));
52
+ controls.push(_jsx("div", { children: _jsx(GenericEntry, { refs: refs, labelMultiple: labelMultiple }) }, key));
53
53
  }
54
54
  });
55
55
  return controls.length > 0 ? controls : null;
@@ -58,7 +58,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
58
58
  configurable: true
59
59
  });
60
60
  GenericEntryListControls.prototype.render = function () {
61
- return _jsx(_Fragment, { children: _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] }), void 0) }, void 0);
61
+ return _jsx(_Fragment, { children: _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] })) });
62
62
  };
63
63
  return GenericEntryListControls;
64
64
  }(PurePluginUIComponent));
@@ -144,7 +144,7 @@ var GenericEntry = /** @class */ (function (_super) {
144
144
  else {
145
145
  label = "".concat(refs.length, " ").concat(labelMultiple || 'Objects');
146
146
  }
147
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs("button", __assign({ className: 'msp-form-control msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, " ", _jsx("small", { children: description }, void 0)] }), void 0), _jsx(IconButton, { svg: pivot.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, className: 'msp-form-control', onClick: this.toggleVisibility, title: "".concat(pivot.cell.state.isHidden ? 'Show' : 'Hide'), small: true, flex: true }, void 0), refs.length === 1 && _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleOptions, title: 'Options', toggleState: this.state.showOptions, flex: true }, void 0)] }), void 0), (refs.length === 1 && this.state.showOptions && pivot.cell.parent) && _jsx(_Fragment, { children: _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }, void 0) }), void 0) }, void 0)] }, void 0);
147
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs("button", __assign({ className: 'msp-form-control msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, " ", _jsx("small", { children: description })] })), _jsx(IconButton, { svg: pivot.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, className: 'msp-form-control', onClick: this.toggleVisibility, title: "".concat(pivot.cell.state.isHidden ? 'Show' : 'Hide'), small: true, flex: true }), refs.length === 1 && _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleOptions, title: 'Options', toggleState: this.state.showOptions, flex: true })] })), (refs.length === 1 && this.state.showOptions && pivot.cell.parent) && _jsx(_Fragment, { children: _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }) })) })] });
148
148
  };
149
149
  return GenericEntry;
150
150
  }(PurePluginUIComponent));
@@ -25,7 +25,7 @@ var StructureMeasurementsControls = /** @class */ (function (_super) {
25
25
  };
26
26
  };
27
27
  StructureMeasurementsControls.prototype.renderControls = function () {
28
- return _jsxs(_Fragment, { children: [_jsx(MeasurementControls, {}, void 0), _jsx(MeasurementList, {}, void 0)] }, void 0);
28
+ return _jsxs(_Fragment, { children: [_jsx(MeasurementControls, {}), _jsx(MeasurementList, {})] });
29
29
  };
30
30
  return StructureMeasurementsControls;
31
31
  }(CollapsableControls));
@@ -48,11 +48,11 @@ var MeasurementList = /** @class */ (function (_super) {
48
48
  if (cell.obj)
49
49
  group.push(_jsx(MeasurementEntry, { cell: cell }, cell.obj.id));
50
50
  }
51
- return group.length ? _jsx(ExpandGroup, __assign({ header: header, initiallyExpanded: true }, { children: group }), void 0) : null;
51
+ return group.length ? _jsx(ExpandGroup, __assign({ header: header, initiallyExpanded: true }, { children: group })) : null;
52
52
  };
53
53
  MeasurementList.prototype.render = function () {
54
54
  var measurements = this.plugin.managers.structure.measurement.state;
55
- return _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals'), this.renderGroup(measurements.orientations, 'Orientations'), this.renderGroup(measurements.planes, 'Planes')] }), void 0);
55
+ return _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals'), this.renderGroup(measurements.orientations, 'Orientations'), this.renderGroup(measurements.planes, 'Planes')] }));
56
56
  };
57
57
  return MeasurementList;
58
58
  }(PurePluginUIComponent));
@@ -169,7 +169,7 @@ var MeasurementControls = /** @class */ (function (_super) {
169
169
  MeasurementControls.prototype.historyEntry = function (e, idx) {
170
170
  var _this = this;
171
171
  var history = this.plugin.managers.structure.selection.additionsHistory;
172
- return _jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }, void 0)] }), void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }, void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' }, void 0)] }), e.id);
172
+ return _jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } })] })), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' })] }), e.id);
173
173
  };
174
174
  MeasurementControls.prototype.add = function () {
175
175
  var history = this.plugin.managers.structure.selection.additionsHistory;
@@ -177,10 +177,10 @@ var MeasurementControls = /** @class */ (function (_super) {
177
177
  for (var i = 0, _i = Math.min(history.length, 4); i < _i; i++) {
178
178
  entries.push(this.historyEntry(history[i], i + 1));
179
179
  }
180
- return _jsxs(_Fragment, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction }, void 0), entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries }), void 0), entries.length === 0 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }, void 0), "Add one or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }, void 0), " mode)"] }), void 0) }), void 0)] }, void 0);
180
+ return _jsxs(_Fragment, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction }), entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries })), entries.length === 0 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }), "Add one or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }), " mode)"] })) }))] });
181
181
  };
182
182
  MeasurementControls.prototype.render = function () {
183
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }, void 0), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } }, void 0)] }), void 0), this.state.action === 'add' && this.add(), this.state.action === 'options' && _jsx(MeasurementsOptions, {}, void 0)] }, void 0);
183
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.action === 'add' && this.add(), this.state.action === 'options' && _jsx(MeasurementsOptions, {})] });
184
184
  };
185
185
  return MeasurementControls;
186
186
  }(PurePluginUIComponent));
@@ -206,7 +206,7 @@ var MeasurementsOptions = /** @class */ (function (_super) {
206
206
  };
207
207
  MeasurementsOptions.prototype.render = function () {
208
208
  var measurements = this.plugin.managers.structure.measurement.state;
209
- return _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }, void 0) }), void 0);
209
+ return _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }) }));
210
210
  };
211
211
  return MeasurementsOptions;
212
212
  }(PurePluginUIComponent));
@@ -324,7 +324,7 @@ var MeasurementEntry = /** @class */ (function (_super) {
324
324
  var obj = cell.obj;
325
325
  if (!obj)
326
326
  return null;
327
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [_jsx("button", __assign({ className: 'msp-form-control msp-control-button-label msp-no-overflow', title: 'Click to focus. Hover to highlight.', onClick: this.focus, style: { width: 'auto', textAlign: 'left' } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: this.label } }, void 0) }), void 0), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, small: true, className: 'msp-form-control', onClick: this.toggleVisibility, flex: true, title: cell.state.isHidden ? 'Show' : 'Hide' }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: this.delete, flex: true, title: 'Delete', toggleState: false }, void 0), _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleUpdate, flex: true, title: 'Actions', toggleState: this.state.showUpdate }, void 0)] }), obj.id), this.state.showUpdate && cell.parent && _jsx(_Fragment, { children: _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }, void 0), _jsx(ExpandGroup, __assign({ header: 'Options', noOffset: true }, { children: _jsx(UpdateTransformControl, { state: cell.parent, transform: cell.transform, customHeader: 'none', autoHideApply: true }, void 0) }), void 0)] }), void 0) }, void 0)] }, void 0);
327
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [_jsx("button", __assign({ className: 'msp-form-control msp-control-button-label msp-no-overflow', title: 'Click to focus. Hover to highlight.', onClick: this.focus, style: { width: 'auto', textAlign: 'left' } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: this.label } }) })), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, small: true, className: 'msp-form-control', onClick: this.toggleVisibility, flex: true, title: cell.state.isHidden ? 'Show' : 'Hide' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: this.delete, flex: true, title: 'Delete', toggleState: false }), _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleUpdate, flex: true, title: 'Actions', toggleState: this.state.showUpdate })] }), obj.id), this.state.showUpdate && cell.parent && _jsx(_Fragment, { children: _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }), _jsx(ExpandGroup, __assign({ header: 'Options', noOffset: true }, { children: _jsx(UpdateTransformControl, { state: cell.parent, transform: cell.transform, customHeader: 'none', autoHideApply: true }) }))] })) })] });
328
328
  };
329
329
  return MeasurementEntry;
330
330
  }(PurePluginUIComponent));
@@ -27,7 +27,7 @@ var StructureQuickStylesControls = /** @class */ (function (_super) {
27
27
  };
28
28
  };
29
29
  StructureQuickStylesControls.prototype.renderControls = function () {
30
- return _jsx(_Fragment, { children: _jsx(QuickStyles, {}, void 0) }, void 0);
30
+ return _jsx(_Fragment, { children: _jsx(QuickStyles, {}) });
31
31
  };
32
32
  return StructureQuickStylesControls;
33
33
  }(CollapsableControls));
@@ -120,7 +120,7 @@ var QuickStyles = /** @class */ (function (_super) {
120
120
  };
121
121
  QuickStyles.prototype.render = function () {
122
122
  var _this = this;
123
- return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" }), void 0), _jsx(Button, __assign({ noOverflow: true, title: 'Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.', onClick: function () { return _this.stylized(); }, style: { width: 'auto' } }, { children: "Stylized" }), void 0), _jsx(Button, __assign({ noOverflow: true, title: 'Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.', onClick: function () { return _this.illustrative(); }, style: { width: 'auto' } }, { children: "Illustrative" }), void 0)] }), void 0);
123
+ return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" })), _jsx(Button, __assign({ noOverflow: true, title: 'Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.', onClick: function () { return _this.stylized(); }, style: { width: 'auto' } }, { children: "Stylized" })), _jsx(Button, __assign({ noOverflow: true, title: 'Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.', onClick: function () { return _this.illustrative(); }, style: { width: 'auto' } }, { children: "Illustrative" }))] }));
124
124
  };
125
125
  return QuickStyles;
126
126
  }(PurePluginUIComponent));
@@ -40,7 +40,7 @@ var ToggleSelectionModeButton = /** @class */ (function (_super) {
40
40
  var style = this.props.inline
41
41
  ? { background: 'transparent', width: 'auto', height: 'auto', lineHeight: 'unset' }
42
42
  : { background: 'transparent' };
43
- return _jsx(IconButton, { svg: SelectionModeSvg, onClick: this._toggleSelMode, title: 'Toggle Selection Mode', style: style, toggleState: this.plugin.selectionMode }, void 0);
43
+ return _jsx(IconButton, { svg: SelectionModeSvg, onClick: this._toggleSelMode, title: 'Toggle Selection Mode', style: style, toggleState: this.plugin.selectionMode });
44
44
  };
45
45
  return ToggleSelectionModeButton;
46
46
  }(PurePluginUIComponent));
@@ -219,13 +219,13 @@ var StructureSelectionActionsControls = /** @class */ (function (_super) {
219
219
  : 'Some mistakes of the past can be undone.';
220
220
  var children = void 0;
221
221
  if (this.state.action && !this.state.helper) {
222
- children = _jsxs(_Fragment, { children: [(this.state.action && this.state.action !== 'theme' && this.state.action !== 'add-component' && this.state.action !== 'help') && _jsxs("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: [_jsx(ActionMenu, { header: ActionHeader.get(this.state.action), title: 'Click to close.', items: this.queries, onSelect: this.selectQuery, noOffset: true }, void 0), _jsx(ActionMenu, { items: this.helpers, onSelect: this.selectHelper, noOffset: true }, void 0)] }), void 0), this.state.action === 'theme' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Theme', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleTheme, topRightIcon: CloseSvg }, { children: _jsx(ApplyThemeControls, { onApply: this.toggleTheme }, void 0) }), void 0) }), void 0), this.state.action === 'add-component' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Add Component', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleAddComponent, topRightIcon: CloseSvg }, { children: _jsx(AddComponentControls, { onApply: this.toggleAddComponent, forSelection: true }, void 0) }), void 0) }), void 0), this.state.action === 'help' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsxs(ControlGroup, __assign({ header: 'Help', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleHelp, topRightIcon: CloseSvg, maxHeight: '300px' }, { children: [_jsx(HelpGroup, __assign({ header: 'Selection Operations' }, { children: _jsxs(HelpText, { children: ["Use ", _jsx(Icon, { svg: UnionSvg, inline: true }, void 0), " ", _jsx(Icon, { svg: SubtractSvg, inline: true }, void 0), " ", _jsx(Icon, { svg: IntersectSvg, inline: true }, void 0), " ", _jsx(Icon, { svg: SetSvg, inline: true }, void 0), " to modify the selection."] }, void 0) }), void 0), _jsx(HelpGroup, __assign({ header: 'Representation Operations' }, { children: _jsxs(HelpText, { children: ["Use ", _jsx(Icon, { svg: BrushSvg, inline: true }, void 0), " ", _jsx(Icon, { svg: CubeOutlineSvg, inline: true }, void 0), " ", _jsx(Icon, { svg: RemoveSvg, inline: true }, void 0), " ", _jsx(Icon, { svg: RestoreSvg, inline: true }, void 0), " to color, create components, remove from components, or undo actions."] }, void 0) }), void 0), _jsx(ViewportHelpContent, { selectOnly: true }, void 0)] }), void 0) }), void 0)] }, void 0);
222
+ children = _jsxs(_Fragment, { children: [(this.state.action && this.state.action !== 'theme' && this.state.action !== 'add-component' && this.state.action !== 'help') && _jsxs("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: [_jsx(ActionMenu, { header: ActionHeader.get(this.state.action), title: 'Click to close.', items: this.queries, onSelect: this.selectQuery, noOffset: true }), _jsx(ActionMenu, { items: this.helpers, onSelect: this.selectHelper, noOffset: true })] })), this.state.action === 'theme' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Theme', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleTheme, topRightIcon: CloseSvg }, { children: _jsx(ApplyThemeControls, { onApply: this.toggleTheme }) })) })), this.state.action === 'add-component' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Add Component', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleAddComponent, topRightIcon: CloseSvg }, { children: _jsx(AddComponentControls, { onApply: this.toggleAddComponent, forSelection: true }) })) })), this.state.action === 'help' && _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsxs(ControlGroup, __assign({ header: 'Help', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleHelp, topRightIcon: CloseSvg, maxHeight: '300px' }, { children: [_jsx(HelpGroup, __assign({ header: 'Selection Operations' }, { children: _jsxs(HelpText, { children: ["Use ", _jsx(Icon, { svg: UnionSvg, inline: true }), " ", _jsx(Icon, { svg: SubtractSvg, inline: true }), " ", _jsx(Icon, { svg: IntersectSvg, inline: true }), " ", _jsx(Icon, { svg: SetSvg, inline: true }), " to modify the selection."] }) })), _jsx(HelpGroup, __assign({ header: 'Representation Operations' }, { children: _jsxs(HelpText, { children: ["Use ", _jsx(Icon, { svg: BrushSvg, inline: true }), " ", _jsx(Icon, { svg: CubeOutlineSvg, inline: true }), " ", _jsx(Icon, { svg: RemoveSvg, inline: true }), " ", _jsx(Icon, { svg: RestoreSvg, inline: true }), " to color, create components, remove from components, or undo actions."] }) })), _jsx(ViewportHelpContent, { selectOnly: true })] })) }))] });
223
223
  }
224
224
  else if (ActionHeader.has(this.state.action) && this.state.helper === 'residue-list') {
225
225
  var close_1 = function () { return _this.setState({ action: void 0, helper: void 0 }); };
226
- children = _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Atom/Residue Identifier List', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: close_1, topRightIcon: CloseSvg }, { children: _jsx(ResidueListSelectionHelper, { modifier: this.state.action, plugin: this.plugin, close: close_1 }, void 0) }), void 0) }), void 0);
226
+ children = _jsx("div", __assign({ className: 'msp-selection-viewport-controls-actions' }, { children: _jsx(ControlGroup, __assign({ header: 'Atom/Residue Identifier List', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: close_1, topRightIcon: CloseSvg }, { children: _jsx(ResidueListSelectionHelper, { modifier: this.state.action, plugin: this.plugin, close: close_1 }) })) }));
227
227
  }
228
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { background: 'none' } }, { children: [_jsx(PureSelectControl, { title: "Picking Level for selecting and highlighting", param: StructureSelectionParams.granularity, name: 'granularity', value: granularity, onChange: this.setGranuality, isDisabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: UnionSvg, title: "".concat(ActionHeader.get('add'), ". Hold shift key to keep menu open."), toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: SubtractSvg, title: "".concat(ActionHeader.get('remove'), ". Hold shift key to keep menu open."), toggle: this.toggleRemove, isSelected: this.state.action === 'remove', disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: IntersectSvg, title: "".concat(ActionHeader.get('intersect'), ". Hold shift key to keep menu open."), toggle: this.toggleIntersect, isSelected: this.state.action === 'intersect', disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: SetSvg, title: "".concat(ActionHeader.get('set'), ". Hold shift key to keep menu open."), toggle: this.toggleSet, isSelected: this.state.action === 'set', disabled: this.isDisabled }, void 0), _jsx(ToggleButton, { icon: BrushSvg, title: 'Apply Theme to Selection', toggle: this.toggleTheme, isSelected: this.state.action === 'theme', disabled: this.isDisabled, style: { marginLeft: '10px' } }, void 0), _jsx(ToggleButton, { icon: CubeOutlineSvg, title: 'Create Component of Selection with Representation', toggle: this.toggleAddComponent, isSelected: this.state.action === 'add-component', disabled: this.isDisabled }, void 0), _jsx(IconButton, { svg: RemoveSvg, title: 'Remove/subtract Selection from all Components', onClick: this.subtract, disabled: this.isDisabled }, void 0), _jsx(IconButton, { svg: RestoreSvg, onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle }, void 0), _jsx(ToggleButton, { icon: HelpOutlineSvg, title: 'Show/hide help', toggle: this.toggleHelp, style: { marginLeft: '10px' }, isSelected: this.state.action === 'help' }, void 0), _jsx(IconButton, { svg: CancelOutlinedSvg, title: 'Turn selection mode off', onClick: this.turnOff }, void 0)] }), void 0), children] }, void 0);
228
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { background: 'none' } }, { children: [_jsx(PureSelectControl, { title: "Picking Level for selecting and highlighting", param: StructureSelectionParams.granularity, name: 'granularity', value: granularity, onChange: this.setGranuality, isDisabled: this.isDisabled }), _jsx(ToggleButton, { icon: UnionSvg, title: "".concat(ActionHeader.get('add'), ". Hold shift key to keep menu open."), toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: SubtractSvg, title: "".concat(ActionHeader.get('remove'), ". Hold shift key to keep menu open."), toggle: this.toggleRemove, isSelected: this.state.action === 'remove', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: IntersectSvg, title: "".concat(ActionHeader.get('intersect'), ". Hold shift key to keep menu open."), toggle: this.toggleIntersect, isSelected: this.state.action === 'intersect', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: SetSvg, title: "".concat(ActionHeader.get('set'), ". Hold shift key to keep menu open."), toggle: this.toggleSet, isSelected: this.state.action === 'set', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: BrushSvg, title: 'Apply Theme to Selection', toggle: this.toggleTheme, isSelected: this.state.action === 'theme', disabled: this.isDisabled, style: { marginLeft: '10px' } }), _jsx(ToggleButton, { icon: CubeOutlineSvg, title: 'Create Component of Selection with Representation', toggle: this.toggleAddComponent, isSelected: this.state.action === 'add-component', disabled: this.isDisabled }), _jsx(IconButton, { svg: RemoveSvg, title: 'Remove/subtract Selection from all Components', onClick: this.subtract, disabled: this.isDisabled }), _jsx(IconButton, { svg: RestoreSvg, onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle }), _jsx(ToggleButton, { icon: HelpOutlineSvg, title: 'Show/hide help', toggle: this.toggleHelp, style: { marginLeft: '10px' }, isSelected: this.state.action === 'help' }), _jsx(IconButton, { svg: CancelOutlinedSvg, title: 'Turn selection mode off', onClick: this.turnOff })] })), children] });
229
229
  };
230
230
  return StructureSelectionActionsControls;
231
231
  }(PluginUIComponent));
@@ -296,7 +296,7 @@ var StructureSelectionStatsControls = /** @class */ (function (_super) {
296
296
  var empty = stats.structureCount === 0 || stats.elementCount === 0;
297
297
  if (empty && this.props.hideOnEmpty)
298
298
  return null;
299
- return _jsx(_Fragment, { children: _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focus, title: 'Click to Focus Selection', disabled: empty, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlignLast: !empty ? 'left' : void 0 } }, { children: this.stats }), void 0), !empty && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true }, void 0)] }), void 0) }, void 0);
299
+ return _jsx(_Fragment, { children: _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focus, title: 'Click to Focus Selection', disabled: empty, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlignLast: !empty ? 'left' : void 0 } }, { children: this.stats })), !empty && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true })] })) });
300
300
  };
301
301
  return StructureSelectionStatsControls;
302
302
  }(PluginUIComponent));
@@ -321,7 +321,7 @@ var ApplyThemeControls = /** @class */ (function (_super) {
321
321
  configurable: true
322
322
  });
323
323
  ApplyThemeControls.prototype.render = function () {
324
- return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.params, values: this.state.values, onChangeValues: this.paramsChanged }, void 0), _jsx(Button, __assign({ icon: BrushSvg, className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Apply Theme" }), void 0)] }, void 0);
324
+ return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.params, values: this.state.values, onChangeValues: this.paramsChanged }), _jsx(Button, __assign({ icon: BrushSvg, className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Apply Theme" }))] });
325
325
  };
326
326
  return ApplyThemeControls;
327
327
  }(PurePluginUIComponent));
@@ -346,5 +346,5 @@ function ResidueListSelectionHelper(_a) {
346
346
  plugin.log.error('Failed to create selection');
347
347
  }
348
348
  };
349
- return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: ResidueListIdTypeParams, values: state, onChangeValues: setState, onEnter: apply }, void 0), _jsxs(Button, __assign({ className: 'msp-btn-commit msp-btn-commit-on', disabled: state.identifiers.trim().length === 0, onClick: apply, style: { marginTop: '1px' } }, { children: [capitalize(modifier), " Selection"] }), void 0)] }, void 0);
349
+ return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: ResidueListIdTypeParams, values: state, onChangeValues: setState, onEnter: apply }), _jsxs(Button, __assign({ className: 'msp-btn-commit msp-btn-commit-on', disabled: state.identifiers.trim().length === 0, onClick: apply, style: { marginTop: '1px' } }, { children: [capitalize(modifier), " Selection"] }))] });
350
350
  }
@@ -289,7 +289,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
289
289
  var params = (_a = m.cell.params) === null || _a === void 0 ? void 0 : _a.definition;
290
290
  if (!params)
291
291
  return null;
292
- return _jsx(ParameterControls, { params: params, values: (_b = m.cell.params) === null || _b === void 0 ? void 0 : _b.values, onChangeValues: this.updateStructureModel, isDisabled: this.state.isBusy }, void 0);
292
+ return _jsx(ParameterControls, { params: params, values: (_b = m.cell.params) === null || _b === void 0 ? void 0 : _b.values, onChangeValues: this.updateStructureModel, isDisabled: this.state.isBusy });
293
293
  },
294
294
  enumerable: false,
295
295
  configurable: true
@@ -304,7 +304,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
304
304
  var params = (_a = s.cell.params) === null || _a === void 0 ? void 0 : _a.definition;
305
305
  if (!params || !s.cell.parent)
306
306
  return null;
307
- return _jsx(UpdateTransformControl, { state: s.cell.parent, transform: s.cell.transform, customHeader: 'none', customUpdate: this.updateStructure, noMargin: true, autoHideApply: true }, void 0);
307
+ return _jsx(UpdateTransformControl, { state: s.cell.parent, transform: s.cell.transform, customHeader: 'none', customUpdate: this.updateStructure, noMargin: true, autoHideApply: true });
308
308
  },
309
309
  enumerable: false,
310
310
  configurable: true
@@ -320,7 +320,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
320
320
  var t = StateSelection.tryFindDecorator(this.plugin.state.data, pivot.cell.transform.ref, StateTransforms.Model.TransformStructureConformation);
321
321
  if (!t)
322
322
  return;
323
- return _jsx(ExpandGroup, __assign({ header: "Conformation Transform" }, { children: _jsx(UpdateTransformControl, { state: t.parent, transform: t.transform, customHeader: 'none', noMargin: true, autoHideApply: true }, void 0) }), void 0);
323
+ return _jsx(ExpandGroup, __assign({ header: "Conformation Transform" }, { children: _jsx(UpdateTransformControl, { state: t.parent, transform: t.transform, customHeader: 'none', noMargin: true, autoHideApply: true }) }));
324
324
  },
325
325
  enumerable: false,
326
326
  configurable: true
@@ -329,7 +329,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
329
329
  var disabled = this.state.isBusy || this.isEmpty;
330
330
  var presets = this.presetActions;
331
331
  var label = this.label;
332
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label }), void 0), presets.length > 0 && _jsx(IconButton, { svg: BookmarksOutlinedSvg, className: 'msp-form-control', flex: '40px', onClick: this.togglePreset, title: 'Apply a structure presets to the current hierarchy.', toggleState: this.state.show === 'presets', disabled: disabled }, void 0)] }), void 0), this.state.show === 'hierarchy' && _jsx(ActionMenu, { items: this.hierarchyItems, onSelect: this.selectHierarchy, multiselect: true }, void 0), this.state.show === 'presets' && _jsx(ActionMenu, { items: presets, onSelect: this.applyPreset }, void 0), this.modelIndex, this.structureType, this.transform, _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [_jsx(StructureFocusControls, {}, void 0), _jsx(StructureSelectionStatsControls, { hideOnEmpty: true }, void 0)] }), void 0)] }, void 0);
332
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })), presets.length > 0 && _jsx(IconButton, { svg: BookmarksOutlinedSvg, className: 'msp-form-control', flex: '40px', onClick: this.togglePreset, title: 'Apply a structure presets to the current hierarchy.', toggleState: this.state.show === 'presets', disabled: disabled })] })), this.state.show === 'hierarchy' && _jsx(ActionMenu, { items: this.hierarchyItems, onSelect: this.selectHierarchy, multiselect: true }), this.state.show === 'presets' && _jsx(ActionMenu, { items: presets, onSelect: this.applyPreset }), this.modelIndex, this.structureType, this.transform, _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [_jsx(StructureFocusControls, {}), _jsx(StructureSelectionStatsControls, { hideOnEmpty: true })] }))] });
333
333
  };
334
334
  return StructureSourceControls;
335
335
  }(CollapsableControls));
@@ -42,7 +42,7 @@ var StructureSuperpositionControls = /** @class */ (function (_super) {
42
42
  });
43
43
  };
44
44
  StructureSuperpositionControls.prototype.renderControls = function () {
45
- return _jsx(_Fragment, { children: _jsx(SuperpositionControls, {}, void 0) }, void 0);
45
+ return _jsx(_Fragment, { children: _jsx(SuperpositionControls, {}) });
46
46
  };
47
47
  return StructureSuperpositionControls;
48
48
  }(CollapsableControls));
@@ -274,16 +274,16 @@ var SuperpositionControls = /** @class */ (function (_super) {
274
274
  };
275
275
  SuperpositionControls.prototype.lociEntry = function (e, idx) {
276
276
  var _this = this;
277
- return _jsx("div", __assign({ className: 'msp-flex-row' }, { children: _jsx(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }, void 0) }), void 0) }), idx);
277
+ return _jsx("div", __assign({ className: 'msp-flex-row' }, { children: _jsx(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }) })) }), idx);
278
278
  };
279
279
  SuperpositionControls.prototype.historyEntry = function (e, idx) {
280
280
  var _this = this;
281
281
  var history = this.plugin.managers.structure.selection.additionsHistory;
282
- return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } }, void 0)] }), void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }, void 0), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' }, void 0)] }), e.id);
282
+ return _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' }, onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [idx, ". ", _jsx("span", { dangerouslySetInnerHTML: { __html: e.label } })] })), history.length > 1 && _jsx(IconButton, { svg: ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }), history.length > 1 && _jsx(IconButton, { svg: ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' })] }), e.id);
283
283
  };
284
284
  SuperpositionControls.prototype.atomsLociEntry = function (e, idx) {
285
285
  var _this = this;
286
- return _jsxs("div", { children: [_jsx("div", __assign({ className: 'msp-control-group-header' }, { children: _jsx("div", __assign({ className: 'msp-no-overflow', title: e.label }, { children: e.label }), void 0) }), void 0), _jsx("div", __assign({ className: 'msp-control-offset' }, { children: e.atoms.map(function (h, i) { return _this.historyEntry(h, i); }) }), void 0)] }, idx);
286
+ return _jsxs("div", { children: [_jsx("div", __assign({ className: 'msp-control-group-header' }, { children: _jsx("div", __assign({ className: 'msp-no-overflow', title: e.label }, { children: e.label })) })), _jsx("div", __assign({ className: 'msp-control-offset' }, { children: e.atoms.map(function (h, i) { return _this.historyEntry(h, i); }) }))] }, idx);
287
287
  };
288
288
  Object.defineProperty(SuperpositionControls.prototype, "chainEntries", {
289
289
  get: function () {
@@ -346,18 +346,18 @@ var SuperpositionControls = /** @class */ (function (_super) {
346
346
  SuperpositionControls.prototype.addByChains = function () {
347
347
  var _this = this;
348
348
  var entries = this.chainEntries;
349
- return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.lociEntry(e, i); }) }), void 0), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }, void 0), "Add 2 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }, void 0), " mode) from separate structures. Selections must be limited to single polymer chains or residues therein."] }), void 0) }), void 0), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected chains.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeChains, style: { marginTop: '1px' } }, { children: "Superpose" }), void 0)] }, void 0);
349
+ return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.lociEntry(e, i); }) })), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }), "Add 2 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }), " mode) from separate structures. Selections must be limited to single polymer chains or residues therein."] })) })), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected chains.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeChains, style: { marginTop: '1px' } }, { children: "Superpose" }))] });
350
350
  };
351
351
  SuperpositionControls.prototype.addByAtoms = function () {
352
352
  var _this = this;
353
353
  var entries = this.atomEntries;
354
- return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.atomsLociEntry(e, i); }) }), void 0), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }, void 0), "Add 1 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }, void 0), " mode) from separate structures. Selections must be limited to single atoms."] }), void 0) }), void 0), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected atoms.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeAtoms, style: { marginTop: '1px' } }, { children: "Superpose" }), void 0)] }, void 0);
354
+ return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.atomsLociEntry(e, i); }) })), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }), "Add 1 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }), " mode) from separate structures. Selections must be limited to single atoms."] })) })), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected atoms.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeAtoms, style: { marginTop: '1px' } }, { children: "Superpose" }))] });
355
355
  };
356
356
  SuperpositionControls.prototype.superposeByDbMapping = function () {
357
- return _jsx(_Fragment, { children: _jsx(Button, __assign({ icon: SuperposeChainsSvg, title: 'Superpose structures using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px' }, disabled: this.state.isBusy }, { children: "Uniprot" }), void 0) }, void 0);
357
+ return _jsx(_Fragment, { children: _jsx(Button, __assign({ icon: SuperposeChainsSvg, title: 'Superpose structures using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px' }, disabled: this.state.isBusy }, { children: "Uniprot" })) });
358
358
  };
359
359
  SuperpositionControls.prototype.render = function () {
360
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: SuperposeChainsSvg, label: 'Chains', toggle: this.toggleByChains, isSelected: this.state.action === 'byChains', disabled: this.state.isBusy }, void 0), _jsx(ToggleButton, { icon: SuperposeAtomsSvg, label: 'Atoms', toggle: this.toggleByAtoms, isSelected: this.state.action === 'byAtoms', disabled: this.state.isBusy }, void 0), this.state.canUseDb && this.superposeByDbMapping(), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } }, void 0)] }), void 0), this.state.action === 'byChains' && this.addByChains(), this.state.action === 'byAtoms' && this.addByAtoms(), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }, void 0) }), void 0)] }, void 0);
360
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: SuperposeChainsSvg, label: 'Chains', toggle: this.toggleByChains, isSelected: this.state.action === 'byChains', disabled: this.state.isBusy }), _jsx(ToggleButton, { icon: SuperposeAtomsSvg, label: 'Atoms', toggle: this.toggleByAtoms, isSelected: this.state.action === 'byAtoms', disabled: this.state.isBusy }), this.state.canUseDb && this.superposeByDbMapping(), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.action === 'byChains' && this.addByChains(), this.state.action === 'byAtoms' && this.addByAtoms(), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }) }))] });
361
361
  };
362
362
  return SuperpositionControls;
363
363
  }(PurePluginUIComponent));
@@ -76,7 +76,7 @@ var VolumeStreamingControls = /** @class */ (function (_super) {
76
76
  : rootCell && ((_b = rootCell.obj) === null || _b === void 0 ? void 0 : _b.data.entries.length) === 0
77
77
  ? { header: 'Error Enabling', icon: ErrorSvg, title: 'No Entry for Streaming Found' }
78
78
  : { header: 'Enable', icon: CheckSvg, title: 'Enable' };
79
- return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: InitVolumeStreaming, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: simpleApply }, void 0);
79
+ return _jsx(ApplyActionControl, { state: pivot.cell.parent, action: InitVolumeStreaming, initiallyCollapsed: true, nodeRef: pivot.cell.transform.ref, simpleApply: simpleApply });
80
80
  };
81
81
  VolumeStreamingControls.prototype.renderParams = function () {
82
82
  var _a, _b, _c, _d, _e;
@@ -84,7 +84,7 @@ var VolumeStreamingControls = /** @class */ (function (_super) {
84
84
  if (!pivot.cell.parent)
85
85
  return null;
86
86
  var bindings = ((_b = (_a = pivot.volumeStreaming) === null || _a === void 0 ? void 0 : _a.cell.transform.params) === null || _b === void 0 ? void 0 : _b.entry.params.view.name) === 'selection-box' && ((_e = (_d = (_c = this.plugin.state.behaviors.cells.get(FocusLoci.id)) === null || _c === void 0 ? void 0 : _c.params) === null || _d === void 0 ? void 0 : _d.values) === null || _e === void 0 ? void 0 : _e.bindings);
87
- return _jsxs(_Fragment, { children: [_jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.volumeStreaming.cell.transform, customHeader: 'none', noMargin: true }, void 0), bindings && _jsx(ExpandGroup, __assign({ header: 'Controls Help' }, { children: _jsx(BindingsHelp, { bindings: bindings }, void 0) }), void 0)] }, void 0);
87
+ return _jsxs(_Fragment, { children: [_jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.volumeStreaming.cell.transform, customHeader: 'none', noMargin: true }), bindings && _jsx(ExpandGroup, __assign({ header: 'Controls Help' }, { children: _jsx(BindingsHelp, { bindings: bindings }) }))] });
88
88
  };
89
89
  VolumeStreamingControls.prototype.renderControls = function () {
90
90
  var pivot = this.pivot;
@@ -267,7 +267,7 @@ var VolumeSourceControls = /** @class */ (function (_super) {
267
267
  var disabled = this.state.isBusy || this.isEmpty;
268
268
  var label = this.label;
269
269
  var selected = this.plugin.managers.volume.hierarchy.selection;
270
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label }), void 0), !this.isEmpty && selected && _jsx(IconButton, { svg: AddSvg, onClick: this.toggleAddRepr, title: 'Apply a structure presets to the current hierarchy.', toggleState: this.state.show === 'add-repr', disabled: disabled }, void 0)] }), void 0), this.state.show === 'hierarchy' && _jsx(ActionMenu, { items: this.hierarchyItems, onSelect: this.selectCurrent }, void 0), this.state.show === 'add-repr' && _jsx(ActionMenu, { items: this.addActions, onSelect: this.selectAdd }, void 0), selected && selected.representations.length > 0 && _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: selected.representations.map(function (r) { return _jsx(VolumeRepresentationControls, { representation: r }, r.cell.transform.ref); }) }), void 0)] }, void 0);
270
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [_jsx(Button, __assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })), !this.isEmpty && selected && _jsx(IconButton, { svg: AddSvg, onClick: this.toggleAddRepr, title: 'Apply a structure presets to the current hierarchy.', toggleState: this.state.show === 'add-repr', disabled: disabled })] })), this.state.show === 'hierarchy' && _jsx(ActionMenu, { items: this.hierarchyItems, onSelect: this.selectCurrent }), this.state.show === 'add-repr' && _jsx(ActionMenu, { items: this.addActions, onSelect: this.selectAdd }), selected && selected.representations.length > 0 && _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: selected.representations.map(function (r) { return _jsx(VolumeRepresentationControls, { representation: r }, r.cell.transform.ref); }) }))] });
271
271
  };
272
272
  return VolumeSourceControls;
273
273
  }(CollapsableControls));
@@ -314,7 +314,7 @@ var VolumeRepresentationControls = /** @class */ (function (_super) {
314
314
  VolumeRepresentationControls.prototype.render = function () {
315
315
  var _a, _b, _c;
316
316
  var repr = this.props.representation.cell;
317
- return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [(_b = repr.obj) === null || _b === void 0 ? void 0 : _b.label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: (_c = repr.obj) === null || _c === void 0 ? void 0 : _c.description }), void 0)] }), void 0), _jsx(IconButton, { svg: repr.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(repr.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }, void 0), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true }, void 0), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleUpdate, title: 'Actions', toggleState: this.state.action === 'update' }, void 0)] }), void 0), this.state.action === 'update' && !!repr.parent && _jsx("div", __assign({ style: { marginBottom: '6px' }, className: 'msp-accent-offset' }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', noMargin: true }, void 0) }), void 0)] }, void 0);
317
+ return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [(_b = repr.obj) === null || _b === void 0 ? void 0 : _b.label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: (_c = repr.obj) === null || _c === void 0 ? void 0 : _c.description }))] })), _jsx(IconButton, { svg: repr.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(repr.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true }), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleUpdate, title: 'Actions', toggleState: this.state.action === 'update' })] })), this.state.action === 'update' && !!repr.parent && _jsx("div", __assign({ style: { marginBottom: '6px' }, className: 'msp-accent-offset' }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', noMargin: true }) }))] });
318
318
  };
319
319
  return VolumeRepresentationControls;
320
320
  }(PurePluginUIComponent));
@@ -30,7 +30,7 @@ var BackgroundTaskProgress = /** @class */ (function (_super) {
30
30
  });
31
31
  };
32
32
  BackgroundTaskProgress.prototype.render = function () {
33
- return _jsx("div", __assign({ className: 'msp-background-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) }), void 0);
33
+ return _jsx("div", __assign({ className: 'msp-background-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) }));
34
34
  };
35
35
  return BackgroundTaskProgress;
36
36
  }(PluginUIComponent));
@@ -49,11 +49,11 @@ var ProgressEntry = /** @class */ (function (_super) {
49
49
  var subtaskCount = countSubtasks(this.props.event.progress.root) - 1;
50
50
  var pr = root.progress.isIndeterminate
51
51
  ? void 0
52
- : _jsxs(_Fragment, { children: ["[", root.progress.current, "/", root.progress.max, "]"] }, void 0);
52
+ : _jsxs(_Fragment, { children: ["[", root.progress.current, "/", root.progress.max, "]"] });
53
53
  var subtasks = subtaskCount > 0
54
- ? _jsxs(_Fragment, { children: ["[", subtaskCount, " subtask(s)]"] }, void 0)
54
+ ? _jsxs(_Fragment, { children: ["[", subtaskCount, " subtask(s)]"] })
55
55
  : void 0;
56
- return _jsx("div", __assign({ className: 'msp-task-state' }, { children: _jsxs("div", { children: [root.progress.canAbort && _jsx(IconButton, { svg: CancelSvg, onClick: this.abort, title: 'Abort' }, void 0), _jsxs("div", { children: [root.progress.message, " ", pr, " ", subtasks] }, void 0)] }, void 0) }), void 0);
56
+ return _jsx("div", __assign({ className: 'msp-task-state' }, { children: _jsxs("div", { children: [root.progress.canAbort && _jsx(IconButton, { svg: CancelSvg, onClick: this.abort, title: 'Abort' }), _jsxs("div", { children: [root.progress.message, " ", pr, " ", subtasks] })] }) }));
57
57
  };
58
58
  return ProgressEntry;
59
59
  }(PluginUIComponent));
@@ -87,7 +87,7 @@ var OverlayTaskProgress = /** @class */ (function (_super) {
87
87
  OverlayTaskProgress.prototype.render = function () {
88
88
  if (this.state.tracked.size === 0)
89
89
  return null;
90
- return _jsx("div", __assign({ className: 'msp-overlay-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) }), void 0);
90
+ return _jsx("div", __assign({ className: 'msp-overlay-tasks' }, { children: this.state.tracked.valueSeq().map(function (e) { return _jsx(ProgressEntry, { event: e }, e.id); }) }));
91
91
  };
92
92
  return OverlayTaskProgress;
93
93
  }(PluginUIComponent));
@@ -24,9 +24,9 @@ var ToastEntry = /** @class */ (function (_super) {
24
24
  var _this = this;
25
25
  var entry = this.props.entry;
26
26
  var message = typeof entry.message === 'string'
27
- ? _jsx("div", { dangerouslySetInnerHTML: { __html: entry.message } }, void 0)
28
- : _jsx("div", { children: _jsx(entry.message, {}, void 0) }, void 0);
29
- return _jsxs("div", __assign({ className: 'msp-toast-entry' }, { children: [_jsx("div", __assign({ className: 'msp-toast-title', onClick: function () { return _this.hide(); } }, { children: entry.title }), void 0), _jsx("div", __assign({ className: 'msp-toast-message' }, { children: message }), void 0), _jsx("div", { className: 'msp-toast-clear' }, void 0), _jsx("div", __assign({ className: 'msp-toast-hide' }, { children: _jsx(IconButton, { svg: CancelSvg, onClick: this.hide, title: 'Hide', className: 'msp-no-hover-outline' }, void 0) }), void 0)] }), void 0);
27
+ ? _jsx("div", { dangerouslySetInnerHTML: { __html: entry.message } })
28
+ : _jsx("div", { children: _jsx(entry.message, {}) });
29
+ return _jsxs("div", __assign({ className: 'msp-toast-entry' }, { children: [_jsx("div", __assign({ className: 'msp-toast-title', onClick: function () { return _this.hide(); } }, { children: entry.title })), _jsx("div", __assign({ className: 'msp-toast-message' }, { children: message })), _jsx("div", { className: 'msp-toast-clear' }), _jsx("div", __assign({ className: 'msp-toast-hide' }, { children: _jsx(IconButton, { svg: CancelSvg, onClick: this.hide, title: 'Hide', className: 'msp-no-hover-outline' }) }))] }));
30
30
  };
31
31
  return ToastEntry;
32
32
  }(PluginUIComponent));
@@ -46,7 +46,7 @@ var Toasts = /** @class */ (function (_super) {
46
46
  var entries = [];
47
47
  state.entries.forEach(function (t, k) { return entries.push(t); });
48
48
  entries.sort(function (x, y) { return x.serialNumber - y.serialNumber; });
49
- return _jsx("div", __assign({ className: 'msp-toast-container' }, { children: entries.map(function (e) { return _jsx(ToastEntry, { entry: e }, e.serialNumber); }) }), void 0);
49
+ return _jsx("div", __assign({ className: 'msp-toast-container' }, { children: entries.map(function (e) { return _jsx(ToastEntry, { entry: e }, e.serialNumber); }) }));
50
50
  };
51
51
  return Toasts;
52
52
  }(PluginUIComponent));
@@ -39,15 +39,15 @@ var ViewportCanvas = /** @class */ (function (_super) {
39
39
  ViewportCanvas.prototype.renderMissing = function () {
40
40
  if (this.props.noWebGl) {
41
41
  var C = this.props.noWebGl;
42
- return _jsx(C, {}, void 0);
42
+ return _jsx(C, {});
43
43
  }
44
- return _jsx("div", __assign({ className: 'msp-no-webgl' }, { children: _jsxs("div", { children: [_jsx("p", { children: _jsx("b", { children: "WebGL does not seem to be available." }, void 0) }, void 0), _jsx("p", { children: "This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps." }, void 0), _jsxs("p", { children: ["For a list of supported browsers, refer to ", _jsx("a", __assign({ href: 'http://caniuse.com/#feat=webgl', target: '_blank' }, { children: "http://caniuse.com/#feat=webgl" }), void 0), "."] }, void 0)] }, void 0) }), void 0);
44
+ return _jsx("div", __assign({ className: 'msp-no-webgl' }, { children: _jsxs("div", { children: [_jsx("p", { children: _jsx("b", { children: "WebGL does not seem to be available." }) }), _jsx("p", { children: "This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps." }), _jsxs("p", { children: ["For a list of supported browsers, refer to ", _jsx("a", __assign({ href: 'http://caniuse.com/#feat=webgl', target: '_blank' }, { children: "http://caniuse.com/#feat=webgl" })), "."] })] }) }));
45
45
  };
46
46
  ViewportCanvas.prototype.render = function () {
47
47
  if (this.state.noWebGl)
48
48
  return this.renderMissing();
49
49
  var Logo = this.props.logo;
50
- return _jsxs("div", __assign({ className: this.props.parentClassName || 'msp-viewport', style: this.props.parentStyle }, { children: [_jsx("div", __assign({ className: this.props.hostClassName || 'msp-viewport-host3d', style: this.props.hostStyle, ref: this.container }, { children: _jsx("canvas", { ref: this.canvas }, void 0) }), void 0), (this.state.showLogo && Logo) && _jsx(Logo, {}, void 0)] }), void 0);
50
+ return _jsxs("div", __assign({ className: this.props.parentClassName || 'msp-viewport', style: this.props.parentStyle }, { children: [_jsx("div", __assign({ className: this.props.hostClassName || 'msp-viewport-host3d', style: this.props.hostStyle, ref: this.container }, { children: _jsx("canvas", { ref: this.canvas }) })), (this.state.showLogo && Logo) && _jsx(Logo, {})] }));
51
51
  };
52
52
  return ViewportCanvas;
53
53
  }(PluginUIComponent));