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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  612. package/lib/commonjs/servers/volume/pack/format/ccp4.js +4 -4
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  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
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  637. package/lib/extensions/zenodo/index.d.ts +7 -0
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  647. package/lib/mol-gl/webgl/buffer.js +2 -3
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  652. package/lib/mol-io/common/netcdf/reader.d.ts +78 -0
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  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
  658. package/lib/mol-io/reader/prmtop/parser.js +168 -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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  669. package/lib/mol-model-formats/structure/basic/atomic.d.ts +1 -1
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  676. package/lib/mol-model-formats/structure/basic/util.js +24 -1
  677. package/lib/mol-model-formats/structure/cif-core.js +4 -4
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  680. package/lib/mol-model-formats/structure/gro.js +3 -1
  681. package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
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  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
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  693. package/lib/mol-model-formats/structure/top.d.ts +16 -0
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  695. package/lib/mol-model-formats/structure/trr.d.ts +9 -0
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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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  754. package/lib/mol-plugin-ui/structure/volume.js +4 -4
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  757. package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
  758. package/lib/mol-plugin-ui/viewport/help.js +8 -8
  759. package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
  760. package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
  761. package/lib/mol-plugin-ui/viewport.js +4 -4
  762. package/lib/mol-script/language/parser.js +7 -4
  763. package/lib/mol-task/util/scheduler.d.ts +2 -2
  764. package/lib/mol-task/util/scheduler.js +7 -7
  765. package/lib/mol-theme/color/hydrophobicity.js +2 -2
  766. package/lib/mol-util/data-source.js +2 -1
  767. package/lib/mol-util/file-info.d.ts +1 -3
  768. package/lib/mol-util/file-info.js +2 -10
  769. package/lib/mol-util/index.d.ts +1 -0
  770. package/lib/mol-util/index.js +5 -0
  771. package/lib/mol-util/zip/deflate.js +2 -1
  772. package/lib/mol-util/zip/zip.d.ts +7 -1
  773. package/lib/mol-util/zip/zip.js +5 -1
  774. package/lib/servers/model/config.d.ts +2 -2
  775. package/package.json +16 -16
  776. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  777. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -10,7 +10,7 @@ var common_1 = require("../controls/common");
10
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  var update_transform_1 = require("../state/update-transform");
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  var icons_1 = require("../controls/icons");
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  var GenericEntryListControls = /** @class */ (function (_super) {
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- (0, tslib_1.__extends)(GenericEntryListControls, _super);
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+ tslib_1.__extends(GenericEntryListControls, _super);
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  function GenericEntryListControls() {
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  return _super !== null && _super.apply(this, arguments) || this;
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  }
@@ -40,7 +40,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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  }
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  if (refs.length === 0)
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  return null;
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- return (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' }, void 0);
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+ return (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' });
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  },
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  enumerable: false,
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  configurable: true
@@ -52,7 +52,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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  this.plugin.genericRepresentationControls.forEach(function (provider, key) {
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  var _a = provider(_this.plugin.managers.structure.hierarchy.selection), refs = _a[0], labelMultiple = _a[1];
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  if (refs.length > 0) {
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- controls.push((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: labelMultiple }, void 0) }, key));
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+ controls.push((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: labelMultiple }) }, key));
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  }
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  });
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  return controls.length > 0 ? controls : null;
@@ -61,13 +61,13 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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  configurable: true
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  });
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  GenericEntryListControls.prototype.render = function () {
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- return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] }), void 0) }, void 0);
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+ return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] })) });
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  };
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  return GenericEntryListControls;
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  }(base_1.PurePluginUIComponent));
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  exports.GenericEntryListControls = GenericEntryListControls;
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  var GenericEntry = /** @class */ (function (_super) {
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- (0, tslib_1.__extends)(GenericEntry, _super);
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+ tslib_1.__extends(GenericEntry, _super);
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  function GenericEntry() {
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  var _this = _super !== null && _super.apply(this, arguments) || this;
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  _this.state = { showOptions: false };
@@ -147,7 +147,7 @@ var GenericEntry = /** @class */ (function (_super) {
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  else {
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  label = "".concat(refs.length, " ").concat(labelMultiple || 'Objects');
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  }
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- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsxs)("button", (0, tslib_1.__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, " ", (0, jsx_runtime_1.jsx)("small", { children: description }, void 0)] }), void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: pivot.cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.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 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.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) && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset' }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }, void 0) }), void 0) }, void 0)] }, void 0);
150
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsxs)("button", tslib_1.__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, " ", (0, jsx_runtime_1.jsx)("small", { children: description })] })), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: pivot.cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.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 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.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) && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }) })) })] });
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  };
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  return GenericEntry;
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  }(base_1.PurePluginUIComponent));
@@ -16,7 +16,7 @@ var update_transform_1 = require("../state/update-transform");
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  var selection_1 = require("./selection");
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  // TODO details, options (e.g. change text for labels)
18
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  var StructureMeasurementsControls = /** @class */ (function (_super) {
19
- (0, tslib_1.__extends)(StructureMeasurementsControls, _super);
19
+ tslib_1.__extends(StructureMeasurementsControls, _super);
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  function StructureMeasurementsControls() {
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  return _super !== null && _super.apply(this, arguments) || this;
22
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  }
@@ -28,13 +28,13 @@ var StructureMeasurementsControls = /** @class */ (function (_super) {
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  };
29
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  };
30
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  StructureMeasurementsControls.prototype.renderControls = function () {
31
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(MeasurementControls, {}, void 0), (0, jsx_runtime_1.jsx)(MeasurementList, {}, void 0)] }, void 0);
31
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(MeasurementControls, {}), (0, jsx_runtime_1.jsx)(MeasurementList, {})] });
32
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  };
33
33
  return StructureMeasurementsControls;
34
34
  }(base_1.CollapsableControls));
35
35
  exports.StructureMeasurementsControls = StructureMeasurementsControls;
36
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  var MeasurementList = /** @class */ (function (_super) {
37
- (0, tslib_1.__extends)(MeasurementList, _super);
37
+ tslib_1.__extends(MeasurementList, _super);
38
38
  function MeasurementList() {
39
39
  return _super !== null && _super.apply(this, arguments) || this;
40
40
  }
@@ -51,17 +51,17 @@ var MeasurementList = /** @class */ (function (_super) {
51
51
  if (cell.obj)
52
52
  group.push((0, jsx_runtime_1.jsx)(MeasurementEntry, { cell: cell }, cell.obj.id));
53
53
  }
54
- return group.length ? (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, (0, tslib_1.__assign)({ header: header, initiallyExpanded: true }, { children: group }), void 0) : null;
54
+ return group.length ? (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: header, initiallyExpanded: true }, { children: group })) : null;
55
55
  };
56
56
  MeasurementList.prototype.render = function () {
57
57
  var measurements = this.plugin.managers.structure.measurement.state;
58
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__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);
58
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__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')] }));
59
59
  };
60
60
  return MeasurementList;
61
61
  }(base_1.PurePluginUIComponent));
62
62
  exports.MeasurementList = MeasurementList;
63
63
  var MeasurementControls = /** @class */ (function (_super) {
64
- (0, tslib_1.__extends)(MeasurementControls, _super);
64
+ tslib_1.__extends(MeasurementControls, _super);
65
65
  function MeasurementControls() {
66
66
  var _this = _super !== null && _super.apply(this, arguments) || this;
67
67
  _this.state = { isBusy: false, action: void 0 };
@@ -172,7 +172,7 @@ var MeasurementControls = /** @class */ (function (_super) {
172
172
  MeasurementControls.prototype.historyEntry = function (e, idx) {
173
173
  var _this = this;
174
174
  var history = this.plugin.managers.structure.selection.additionsHistory;
175
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: e.label } }, void 0)] }), void 0), history.length > 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }, void 0), history.length > 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.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);
175
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: e.label } })] })), history.length > 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }), history.length > 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' })] }), e.id);
176
176
  };
177
177
  MeasurementControls.prototype.add = function () {
178
178
  var history = this.plugin.managers.structure.selection.additionsHistory;
@@ -180,16 +180,16 @@ var MeasurementControls = /** @class */ (function (_super) {
180
180
  for (var i = 0, _i = Math.min(history.length, 4); i < _i; i++) {
181
181
  entries.push(this.historyEntry(history[i], i + 1));
182
182
  }
183
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction }, void 0), entries.length > 0 && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset' }, { children: entries }), void 0), entries.length === 0 && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-help-description' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, inline: true }, void 0), "Add one or more selections (toggle ", (0, jsx_runtime_1.jsx)(selection_1.ToggleSelectionModeButton, { inline: true }, void 0), " mode)"] }), void 0) }), void 0)] }, void 0);
183
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction }), entries.length > 0 && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: entries })), entries.length === 0 && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-help-description' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, inline: true }), "Add one or more selections (toggle ", (0, jsx_runtime_1.jsx)(selection_1.ToggleSelectionModeButton, { inline: true }), " mode)"] })) }))] });
184
184
  };
185
185
  MeasurementControls.prototype.render = function () {
186
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }, void 0), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.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' && (0, jsx_runtime_1.jsx)(MeasurementsOptions, {}, void 0)] }, void 0);
186
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.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' && (0, jsx_runtime_1.jsx)(MeasurementsOptions, {})] });
187
187
  };
188
188
  return MeasurementControls;
189
189
  }(base_1.PurePluginUIComponent));
190
190
  exports.MeasurementControls = MeasurementControls;
191
191
  var MeasurementsOptions = /** @class */ (function (_super) {
192
- (0, tslib_1.__extends)(MeasurementsOptions, _super);
192
+ tslib_1.__extends(MeasurementsOptions, _super);
193
193
  function MeasurementsOptions() {
194
194
  var _this = _super !== null && _super.apply(this, arguments) || this;
195
195
  _this.state = { isDisabled: false };
@@ -209,12 +209,12 @@ var MeasurementsOptions = /** @class */ (function (_super) {
209
209
  };
210
210
  MeasurementsOptions.prototype.render = function () {
211
211
  var measurements = this.plugin.managers.structure.measurement.state;
212
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset' }, { children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: measurement_1.StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }, void 0) }), void 0);
212
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: measurement_1.StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }) }));
213
213
  };
214
214
  return MeasurementsOptions;
215
215
  }(base_1.PurePluginUIComponent));
216
216
  var MeasurementEntry = /** @class */ (function (_super) {
217
- (0, tslib_1.__extends)(MeasurementEntry, _super);
217
+ tslib_1.__extends(MeasurementEntry, _super);
218
218
  function MeasurementEntry() {
219
219
  var _this = _super !== null && _super.apply(this, arguments) || this;
220
220
  _this.state = { showUpdate: false };
@@ -327,7 +327,7 @@ var MeasurementEntry = /** @class */ (function (_super) {
327
327
  var obj = cell.obj;
328
328
  if (!obj)
329
329
  return null;
330
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [(0, jsx_runtime_1.jsx)("button", (0, tslib_1.__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: (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: this.label } }, void 0) }), void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, small: true, className: 'msp-form-control', onClick: this.toggleVisibility, flex: true, title: cell.state.isHidden ? 'Show' : 'Hide' }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: this.delete, flex: true, title: 'Delete', toggleState: false }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.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 && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-accent-offset' }, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, (0, tslib_1.__assign)({ header: 'Options', noOffset: true }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: cell.parent, transform: cell.transform, customHeader: 'none', autoHideApply: true }, void 0) }), void 0)] }), void 0) }, void 0)] }, void 0);
330
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [(0, jsx_runtime_1.jsx)("button", tslib_1.__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: (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: this.label } }) })), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, small: true, className: 'msp-form-control', onClick: this.toggleVisibility, flex: true, title: cell.state.isHidden ? 'Show' : 'Hide' }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: this.delete, flex: true, title: 'Delete', toggleState: false }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleUpdate, flex: true, title: 'Actions', toggleState: this.state.showUpdate })] }), obj.id), this.state.showUpdate && cell.parent && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-accent-offset' }, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: 'Options', noOffset: true }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: cell.parent, transform: cell.transform, customHeader: 'none', autoHideApply: true }) }))] })) })] });
331
331
  };
332
332
  return MeasurementEntry;
333
333
  }(base_1.PurePluginUIComponent));
@@ -18,7 +18,7 @@ var postprocessing_1 = require("../../mol-canvas3d/passes/postprocessing");
18
18
  var config_1 = require("../../mol-plugin/config");
19
19
  var component_1 = require("../../mol-plugin-state/manager/structure/component");
20
20
  var StructureQuickStylesControls = /** @class */ (function (_super) {
21
- (0, tslib_1.__extends)(StructureQuickStylesControls, _super);
21
+ tslib_1.__extends(StructureQuickStylesControls, _super);
22
22
  function StructureQuickStylesControls() {
23
23
  return _super !== null && _super.apply(this, arguments) || this;
24
24
  }
@@ -30,20 +30,20 @@ var StructureQuickStylesControls = /** @class */ (function (_super) {
30
30
  };
31
31
  };
32
32
  StructureQuickStylesControls.prototype.renderControls = function () {
33
- return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(QuickStyles, {}, void 0) }, void 0);
33
+ return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(QuickStyles, {}) });
34
34
  };
35
35
  return StructureQuickStylesControls;
36
36
  }(base_1.CollapsableControls));
37
37
  exports.StructureQuickStylesControls = StructureQuickStylesControls;
38
38
  var QuickStyles = /** @class */ (function (_super) {
39
- (0, tslib_1.__extends)(QuickStyles, _super);
39
+ tslib_1.__extends(QuickStyles, _super);
40
40
  function QuickStyles() {
41
41
  return _super !== null && _super.apply(this, arguments) || this;
42
42
  }
43
43
  QuickStyles.prototype.default = function () {
44
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
44
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
45
45
  var structures, preset, provider, p;
46
- return (0, tslib_1.__generator)(this, function (_a) {
46
+ return tslib_1.__generator(this, function (_a) {
47
47
  switch (_a.label) {
48
48
  case 0:
49
49
  structures = this.plugin.managers.structure.hierarchy.selection.structures;
@@ -65,9 +65,9 @@ var QuickStyles = /** @class */ (function (_super) {
65
65
  });
66
66
  };
67
67
  QuickStyles.prototype.illustrative = function () {
68
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
68
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
69
69
  var structures;
70
- return (0, tslib_1.__generator)(this, function (_a) {
70
+ return tslib_1.__generator(this, function (_a) {
71
71
  switch (_a.label) {
72
72
  case 0:
73
73
  structures = this.plugin.managers.structure.hierarchy.selection.structures;
@@ -94,10 +94,10 @@ var QuickStyles = /** @class */ (function (_super) {
94
94
  });
95
95
  };
96
96
  QuickStyles.prototype.stylized = function () {
97
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
97
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
98
98
  var pp;
99
- return (0, tslib_1.__generator)(this, function (_a) {
100
- this.plugin.managers.structure.component.setOptions((0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.plugin.managers.structure.component.state.options), { ignoreLight: true }));
99
+ return tslib_1.__generator(this, function (_a) {
100
+ this.plugin.managers.structure.component.setOptions(tslib_1.__assign(tslib_1.__assign({}, this.plugin.managers.structure.component.state.options), { ignoreLight: true }));
101
101
  if (this.plugin.canvas3d) {
102
102
  pp = this.plugin.canvas3d.props.postprocessing;
103
103
  this.plugin.canvas3d.setProps({
@@ -123,7 +123,7 @@ var QuickStyles = /** @class */ (function (_super) {
123
123
  };
124
124
  QuickStyles.prototype.render = function () {
125
125
  var _this = this;
126
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ 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), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__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), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__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);
126
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ noOverflow: true, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__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" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__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" }))] }));
127
127
  };
128
128
  return QuickStyles;
129
129
  }(base_1.PurePluginUIComponent));
@@ -9,7 +9,7 @@ var jsx_runtime_1 = require("react/jsx-runtime");
9
9
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
10
10
  * @author David Sehnal <david.sehnal@gmail.com>
11
11
  */
12
- var React = (0, tslib_1.__importStar)(require("react"));
12
+ var React = tslib_1.__importStar(require("react"));
13
13
  var structure_selection_query_1 = require("../../mol-plugin-state/helpers/structure-selection-query");
14
14
  var interactivity_1 = require("../../mol-plugin-state/manager/interactivity");
15
15
  var component_1 = require("../../mol-plugin-state/manager/structure/component");
@@ -25,7 +25,7 @@ var parameters_1 = require("../controls/parameters");
25
25
  var help_1 = require("../viewport/help");
26
26
  var components_1 = require("./components");
27
27
  var ToggleSelectionModeButton = /** @class */ (function (_super) {
28
- (0, tslib_1.__extends)(ToggleSelectionModeButton, _super);
28
+ tslib_1.__extends(ToggleSelectionModeButton, _super);
29
29
  function ToggleSelectionModeButton() {
30
30
  var _this = _super !== null && _super.apply(this, arguments) || this;
31
31
  _this._toggleSelMode = function () {
@@ -43,7 +43,7 @@ var ToggleSelectionModeButton = /** @class */ (function (_super) {
43
43
  var style = this.props.inline
44
44
  ? { background: 'transparent', width: 'auto', height: 'auto', lineHeight: 'unset' }
45
45
  : { background: 'transparent' };
46
- return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.SelectionModeSvg, onClick: this._toggleSelMode, title: 'Toggle Selection Mode', style: style, toggleState: this.plugin.selectionMode }, void 0);
46
+ return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.SelectionModeSvg, onClick: this._toggleSelMode, title: 'Toggle Selection Mode', style: style, toggleState: this.plugin.selectionMode });
47
47
  };
48
48
  return ToggleSelectionModeButton;
49
49
  }(base_1.PurePluginUIComponent));
@@ -58,7 +58,7 @@ var ActionHeader = new Map([
58
58
  ['set', 'Set Selection']
59
59
  ]);
60
60
  var StructureSelectionActionsControls = /** @class */ (function (_super) {
61
- (0, tslib_1.__extends)(StructureSelectionActionsControls, _super);
61
+ tslib_1.__extends(StructureSelectionActionsControls, _super);
62
62
  function StructureSelectionActionsControls() {
63
63
  var _this = _super !== null && _super.apply(this, arguments) || this;
64
64
  _this.state = {
@@ -176,7 +176,7 @@ var StructureSelectionActionsControls = /** @class */ (function (_super) {
176
176
  var registry = this.plugin.query.structure.registry;
177
177
  if (registry.version !== this.queriesVersion) {
178
178
  var structures = this.structures;
179
- var queries = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], registry.list, true), (0, structure_selection_query_1.getPolymerAndBranchedEntityQueries)(structures), true), (0, structure_selection_query_1.getNonStandardResidueQueries)(structures), true), (0, structure_selection_query_1.getElementQueries)(structures), true).sort(function (a, b) { return b.priority - a.priority; });
179
+ var queries = tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], registry.list, true), (0, structure_selection_query_1.getPolymerAndBranchedEntityQueries)(structures), true), (0, structure_selection_query_1.getNonStandardResidueQueries)(structures), true), (0, structure_selection_query_1.getElementQueries)(structures), true).sort(function (a, b) { return b.priority - a.priority; });
180
180
  this.queriesItems = action_menu_1.ActionMenu.createItems(queries, {
181
181
  filter: function (q) { return q !== structure_selection_query_1.StructureSelectionQueries.current && !q.isHidden; },
182
182
  label: function (q) { return q.label; },
@@ -222,19 +222,19 @@ var StructureSelectionActionsControls = /** @class */ (function (_super) {
222
222
  : 'Some mistakes of the past can be undone.';
223
223
  var children = void 0;
224
224
  if (this.state.action && !this.state.helper) {
225
- children = (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(this.state.action && this.state.action !== 'theme' && this.state.action !== 'add-component' && this.state.action !== 'help') && (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-selection-viewport-controls-actions' }, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { header: ActionHeader.get(this.state.action), title: 'Click to close.', items: this.queries, onSelect: this.selectQuery, noOffset: true }, void 0), (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.helpers, onSelect: this.selectHelper, noOffset: true }, void 0)] }), void 0), this.state.action === 'theme' && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, (0, tslib_1.__assign)({ header: 'Theme', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleTheme, topRightIcon: icons_1.CloseSvg }, { children: (0, jsx_runtime_1.jsx)(ApplyThemeControls, { onApply: this.toggleTheme }, void 0) }), void 0) }), void 0), this.state.action === 'add-component' && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, (0, tslib_1.__assign)({ header: 'Add Component', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleAddComponent, topRightIcon: icons_1.CloseSvg }, { children: (0, jsx_runtime_1.jsx)(components_1.AddComponentControls, { onApply: this.toggleAddComponent, forSelection: true }, void 0) }), void 0) }), void 0), this.state.action === 'help' && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsxs)(common_1.ControlGroup, (0, tslib_1.__assign)({ header: 'Help', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleHelp, topRightIcon: icons_1.CloseSvg, maxHeight: '300px' }, { children: [(0, jsx_runtime_1.jsx)(help_1.HelpGroup, (0, tslib_1.__assign)({ header: 'Selection Operations' }, { children: (0, jsx_runtime_1.jsxs)(help_1.HelpText, { children: ["Use ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.UnionSvg, inline: true }, void 0), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.SubtractSvg, inline: true }, void 0), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.IntersectSvg, inline: true }, void 0), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.SetSvg, inline: true }, void 0), " to modify the selection."] }, void 0) }), void 0), (0, jsx_runtime_1.jsx)(help_1.HelpGroup, (0, tslib_1.__assign)({ header: 'Representation Operations' }, { children: (0, jsx_runtime_1.jsxs)(help_1.HelpText, { children: ["Use ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.BrushSvg, inline: true }, void 0), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CubeOutlineSvg, inline: true }, void 0), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.RemoveSvg, inline: true }, void 0), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.RestoreSvg, inline: true }, void 0), " to color, create components, remove from components, or undo actions."] }, void 0) }), void 0), (0, jsx_runtime_1.jsx)(help_1.ViewportHelpContent, { selectOnly: true }, void 0)] }), void 0) }), void 0)] }, void 0);
225
+ children = (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(this.state.action && this.state.action !== 'theme' && this.state.action !== 'add-component' && this.state.action !== 'help') && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-selection-viewport-controls-actions' }, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { header: ActionHeader.get(this.state.action), title: 'Click to close.', items: this.queries, onSelect: this.selectQuery, noOffset: true }), (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.helpers, onSelect: this.selectHelper, noOffset: true })] })), this.state.action === 'theme' && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, tslib_1.__assign({ header: 'Theme', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleTheme, topRightIcon: icons_1.CloseSvg }, { children: (0, jsx_runtime_1.jsx)(ApplyThemeControls, { onApply: this.toggleTheme }) })) })), this.state.action === 'add-component' && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, tslib_1.__assign({ header: 'Add Component', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleAddComponent, topRightIcon: icons_1.CloseSvg }, { children: (0, jsx_runtime_1.jsx)(components_1.AddComponentControls, { onApply: this.toggleAddComponent, forSelection: true }) })) })), this.state.action === 'help' && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsxs)(common_1.ControlGroup, tslib_1.__assign({ header: 'Help', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleHelp, topRightIcon: icons_1.CloseSvg, maxHeight: '300px' }, { children: [(0, jsx_runtime_1.jsx)(help_1.HelpGroup, tslib_1.__assign({ header: 'Selection Operations' }, { children: (0, jsx_runtime_1.jsxs)(help_1.HelpText, { children: ["Use ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.UnionSvg, inline: true }), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.SubtractSvg, inline: true }), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.IntersectSvg, inline: true }), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.SetSvg, inline: true }), " to modify the selection."] }) })), (0, jsx_runtime_1.jsx)(help_1.HelpGroup, tslib_1.__assign({ header: 'Representation Operations' }, { children: (0, jsx_runtime_1.jsxs)(help_1.HelpText, { children: ["Use ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.BrushSvg, inline: true }), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CubeOutlineSvg, inline: true }), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.RemoveSvg, inline: true }), " ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.RestoreSvg, inline: true }), " to color, create components, remove from components, or undo actions."] }) })), (0, jsx_runtime_1.jsx)(help_1.ViewportHelpContent, { selectOnly: true })] })) }))] });
226
226
  }
227
227
  else if (ActionHeader.has(this.state.action) && this.state.helper === 'residue-list') {
228
228
  var close_1 = function () { return _this.setState({ action: void 0, helper: void 0 }); };
229
- children = (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, (0, tslib_1.__assign)({ header: 'Atom/Residue Identifier List', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: close_1, topRightIcon: icons_1.CloseSvg }, { children: (0, jsx_runtime_1.jsx)(ResidueListSelectionHelper, { modifier: this.state.action, plugin: this.plugin, close: close_1 }, void 0) }), void 0) }), void 0);
229
+ children = (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-selection-viewport-controls-actions' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, tslib_1.__assign({ header: 'Atom/Residue Identifier List', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: close_1, topRightIcon: icons_1.CloseSvg }, { children: (0, jsx_runtime_1.jsx)(ResidueListSelectionHelper, { modifier: this.state.action, plugin: this.plugin, close: close_1 }) })) }));
230
230
  }
231
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row', style: { background: 'none' } }, { children: [(0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "Picking Level for selecting and highlighting", param: StructureSelectionParams.granularity, name: 'granularity', value: granularity, onChange: this.setGranuality, isDisabled: this.isDisabled }, void 0), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.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), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.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), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.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), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.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), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.BrushSvg, title: 'Apply Theme to Selection', toggle: this.toggleTheme, isSelected: this.state.action === 'theme', disabled: this.isDisabled, style: { marginLeft: '10px' } }, void 0), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.CubeOutlineSvg, title: 'Create Component of Selection with Representation', toggle: this.toggleAddComponent, isSelected: this.state.action === 'add-component', disabled: this.isDisabled }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.RemoveSvg, title: 'Remove/subtract Selection from all Components', onClick: this.subtract, disabled: this.isDisabled }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.RestoreSvg, onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle }, void 0), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.HelpOutlineSvg, title: 'Show/hide help', toggle: this.toggleHelp, style: { marginLeft: '10px' }, isSelected: this.state.action === 'help' }, void 0), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.CancelOutlinedSvg, title: 'Turn selection mode off', onClick: this.turnOff }, void 0)] }), void 0), children] }, void 0);
231
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row', style: { background: 'none' } }, { children: [(0, jsx_runtime_1.jsx)(parameters_1.PureSelectControl, { title: "Picking Level for selecting and highlighting", param: StructureSelectionParams.granularity, name: 'granularity', value: granularity, onChange: this.setGranuality, isDisabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.UnionSvg, title: "".concat(ActionHeader.get('add'), ". Hold shift key to keep menu open."), toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.SubtractSvg, title: "".concat(ActionHeader.get('remove'), ". Hold shift key to keep menu open."), toggle: this.toggleRemove, isSelected: this.state.action === 'remove', disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.IntersectSvg, title: "".concat(ActionHeader.get('intersect'), ". Hold shift key to keep menu open."), toggle: this.toggleIntersect, isSelected: this.state.action === 'intersect', disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.SetSvg, title: "".concat(ActionHeader.get('set'), ". Hold shift key to keep menu open."), toggle: this.toggleSet, isSelected: this.state.action === 'set', disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.BrushSvg, title: 'Apply Theme to Selection', toggle: this.toggleTheme, isSelected: this.state.action === 'theme', disabled: this.isDisabled, style: { marginLeft: '10px' } }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.CubeOutlineSvg, title: 'Create Component of Selection with Representation', toggle: this.toggleAddComponent, isSelected: this.state.action === 'add-component', disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.RemoveSvg, title: 'Remove/subtract Selection from all Components', onClick: this.subtract, disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.RestoreSvg, onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.HelpOutlineSvg, title: 'Show/hide help', toggle: this.toggleHelp, style: { marginLeft: '10px' }, isSelected: this.state.action === 'help' }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.CancelOutlinedSvg, title: 'Turn selection mode off', onClick: this.turnOff })] })), children] });
232
232
  };
233
233
  return StructureSelectionActionsControls;
234
234
  }(base_1.PluginUIComponent));
235
235
  exports.StructureSelectionActionsControls = StructureSelectionActionsControls;
236
236
  var StructureSelectionStatsControls = /** @class */ (function (_super) {
237
- (0, tslib_1.__extends)(StructureSelectionStatsControls, _super);
237
+ tslib_1.__extends(StructureSelectionStatsControls, _super);
238
238
  function StructureSelectionStatsControls() {
239
239
  var _this = _super !== null && _super.apply(this, arguments) || this;
240
240
  _this.state = {
@@ -299,13 +299,13 @@ var StructureSelectionStatsControls = /** @class */ (function (_super) {
299
299
  var empty = stats.structureCount === 0 || stats.elementCount === 0;
300
300
  if (empty && this.props.hideOnEmpty)
301
301
  return null;
302
- return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ 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 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true }, void 0)] }), void 0) }, void 0);
302
+ return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ 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 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true })] })) });
303
303
  };
304
304
  return StructureSelectionStatsControls;
305
305
  }(base_1.PluginUIComponent));
306
306
  exports.StructureSelectionStatsControls = StructureSelectionStatsControls;
307
307
  var ApplyThemeControls = /** @class */ (function (_super) {
308
- (0, tslib_1.__extends)(ApplyThemeControls, _super);
308
+ tslib_1.__extends(ApplyThemeControls, _super);
309
309
  function ApplyThemeControls() {
310
310
  var _this = _super !== null && _super.apply(this, arguments) || this;
311
311
  _this._params = (0, memoize_1.memoizeLatest)(function (pivot) { return component_1.StructureComponentManager.getThemeParams(_this.plugin, pivot); });
@@ -324,7 +324,7 @@ var ApplyThemeControls = /** @class */ (function (_super) {
324
324
  configurable: true
325
325
  });
326
326
  ApplyThemeControls.prototype.render = function () {
327
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: this.params, values: this.state.values, onChangeValues: this.paramsChanged }, void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: icons_1.BrushSvg, className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Apply Theme" }), void 0)] }, void 0);
327
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: this.params, values: this.state.values, onChangeValues: this.paramsChanged }), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.BrushSvg, className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Apply Theme" }))] });
328
328
  };
329
329
  return ApplyThemeControls;
330
330
  }(base_1.PurePluginUIComponent));
@@ -349,5 +349,5 @@ function ResidueListSelectionHelper(_a) {
349
349
  plugin.log.error('Failed to create selection');
350
350
  }
351
351
  };
352
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: ResidueListIdTypeParams, values: state, onChangeValues: setState, onEnter: apply }, void 0), (0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ className: 'msp-btn-commit msp-btn-commit-on', disabled: state.identifiers.trim().length === 0, onClick: apply, style: { marginTop: '1px' } }, { children: [(0, string_1.capitalize)(modifier), " Selection"] }), void 0)] }, void 0);
352
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: ResidueListIdTypeParams, values: state, onChangeValues: setState, onEnter: apply }), (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ className: 'msp-btn-commit msp-btn-commit-on', disabled: state.identifiers.trim().length === 0, onClick: apply, style: { marginTop: '1px' } }, { children: [(0, string_1.capitalize)(modifier), " Selection"] }))] });
353
353
  }
@@ -21,7 +21,7 @@ var update_transform_1 = require("../state/update-transform");
21
21
  var focus_1 = require("./focus");
22
22
  var selection_1 = require("./selection");
23
23
  var StructureSourceControls = /** @class */ (function (_super) {
24
- (0, tslib_1.__extends)(StructureSourceControls, _super);
24
+ tslib_1.__extends(StructureSourceControls, _super);
25
25
  function StructureSourceControls() {
26
26
  var _this = _super !== null && _super.apply(this, arguments) || this;
27
27
  _this.item = function (ref) {
@@ -63,7 +63,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
63
63
  var _a;
64
64
  if (t.models.length === 0)
65
65
  return _this.item(t);
66
- return (0, tslib_1.__spreadArray)([action_menu_1.ActionMenu.Header((_a = t.cell.obj) === null || _a === void 0 ? void 0 : _a.label)], t.models.map(_this.getModelItems), true);
66
+ return tslib_1.__spreadArray([action_menu_1.ActionMenu.Header((_a = t.cell.obj) === null || _a === void 0 ? void 0 : _a.label)], t.models.map(_this.getModelItems), true);
67
67
  };
68
68
  _this.getModelItems = function (m) {
69
69
  var _a, _b, _c;
@@ -74,7 +74,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
74
74
  var ref = m.structures[0];
75
75
  return { label: "".concat((_a = m.cell.obj) === null || _a === void 0 ? void 0 : _a.label, " | ").concat((_b = ref.cell.obj) === null || _b === void 0 ? void 0 : _b.label), selected: selected.has(ref.cell.transform.ref), value: [m, ref] };
76
76
  }
77
- return (0, tslib_1.__spreadArray)([action_menu_1.ActionMenu.Header((_c = m.cell.obj) === null || _c === void 0 ? void 0 : _c.label)], m.structures.map(_this.item), true);
77
+ return tslib_1.__spreadArray([action_menu_1.ActionMenu.Header((_c = m.cell.obj) === null || _c === void 0 ? void 0 : _c.label)], m.structures.map(_this.item), true);
78
78
  };
79
79
  _this.selectHierarchy = function (items) {
80
80
  if (!items || items.length === 0)
@@ -133,12 +133,12 @@ var StructureSourceControls = /** @class */ (function (_super) {
133
133
  var current = mng.current;
134
134
  var ret = [];
135
135
  if (current.trajectories.length > 1) {
136
- ret.push((0, tslib_1.__spreadArray)([
136
+ ret.push(tslib_1.__spreadArray([
137
137
  action_menu_1.ActionMenu.Header('Trajectories')
138
138
  ], current.trajectories.map(this.item), true));
139
139
  }
140
140
  if (current.models.length > 1 || current.trajectories.length > 1) {
141
- ret.push((0, tslib_1.__spreadArray)([
141
+ ret.push(tslib_1.__spreadArray([
142
142
  action_menu_1.ActionMenu.Header('Models')
143
143
  ], current.models.map(this.item), true));
144
144
  }
@@ -146,7 +146,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
146
146
  ret.push.apply(ret, current.structures.map(this.item));
147
147
  }
148
148
  else if (current.structures.length > 0) {
149
- ret.push((0, tslib_1.__spreadArray)([
149
+ ret.push(tslib_1.__spreadArray([
150
150
  action_menu_1.ActionMenu.Header('Structures')
151
151
  ], current.structures.map(this.item), true));
152
152
  }
@@ -250,9 +250,9 @@ var StructureSourceControls = /** @class */ (function (_super) {
250
250
  configurable: true
251
251
  });
252
252
  StructureSourceControls.prototype._updateStructureModel = function () {
253
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
253
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
254
254
  var params, selection, m;
255
- return (0, tslib_1.__generator)(this, function (_a) {
255
+ return tslib_1.__generator(this, function (_a) {
256
256
  switch (_a.label) {
257
257
  case 0:
258
258
  if (!this.updateModelQueueParams || this.isUpdatingModel)
@@ -292,7 +292,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
292
292
  var params = (_a = m.cell.params) === null || _a === void 0 ? void 0 : _a.definition;
293
293
  if (!params)
294
294
  return null;
295
- return (0, jsx_runtime_1.jsx)(parameters_1.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);
295
+ return (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: params, values: (_b = m.cell.params) === null || _b === void 0 ? void 0 : _b.values, onChangeValues: this.updateStructureModel, isDisabled: this.state.isBusy });
296
296
  },
297
297
  enumerable: false,
298
298
  configurable: true
@@ -307,7 +307,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
307
307
  var params = (_a = s.cell.params) === null || _a === void 0 ? void 0 : _a.definition;
308
308
  if (!params || !s.cell.parent)
309
309
  return null;
310
- return (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: s.cell.parent, transform: s.cell.transform, customHeader: 'none', customUpdate: this.updateStructure, noMargin: true, autoHideApply: true }, void 0);
310
+ return (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: s.cell.parent, transform: s.cell.transform, customHeader: 'none', customUpdate: this.updateStructure, noMargin: true, autoHideApply: true });
311
311
  },
312
312
  enumerable: false,
313
313
  configurable: true
@@ -323,7 +323,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
323
323
  var t = mol_state_1.StateSelection.tryFindDecorator(this.plugin.state.data, pivot.cell.transform.ref, transforms_1.StateTransforms.Model.TransformStructureConformation);
324
324
  if (!t)
325
325
  return;
326
- return (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, (0, tslib_1.__assign)({ header: "Conformation Transform" }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: t.parent, transform: t.transform, customHeader: 'none', noMargin: true, autoHideApply: true }, void 0) }), void 0);
326
+ return (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: "Conformation Transform" }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: t.parent, transform: t.transform, customHeader: 'none', noMargin: true, autoHideApply: true }) }));
327
327
  },
328
328
  enumerable: false,
329
329
  configurable: true
@@ -332,7 +332,7 @@ var StructureSourceControls = /** @class */ (function (_super) {
332
332
  var disabled = this.state.isBusy || this.isEmpty;
333
333
  var presets = this.presetActions;
334
334
  var label = this.label;
335
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label }), void 0), presets.length > 0 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.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' && (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.hierarchyItems, onSelect: this.selectHierarchy, multiselect: true }, void 0), this.state.show === 'presets' && (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: presets, onSelect: this.applyPreset }, void 0), this.modelIndex, this.structureType, this.transform, (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ style: { marginTop: '6px' } }, { children: [(0, jsx_runtime_1.jsx)(focus_1.StructureFocusControls, {}, void 0), (0, jsx_runtime_1.jsx)(selection_1.StructureSelectionStatsControls, { hideOnEmpty: true }, void 0)] }), void 0)] }, void 0);
335
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row', style: { marginTop: '1px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ noOverflow: true, flex: true, onClick: this.toggleHierarchy, disabled: disabled, title: label }, { children: label })), presets.length > 0 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.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' && (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.hierarchyItems, onSelect: this.selectHierarchy, multiselect: true }), this.state.show === 'presets' && (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: presets, onSelect: this.applyPreset }), this.modelIndex, this.structureType, this.transform, (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { marginTop: '6px' } }, { children: [(0, jsx_runtime_1.jsx)(focus_1.StructureFocusControls, {}), (0, jsx_runtime_1.jsx)(selection_1.StructureSelectionStatsControls, { hideOnEmpty: true })] }))] });
336
336
  };
337
337
  return StructureSourceControls;
338
338
  }(base_1.CollapsableControls));