molstar 3.3.0 → 3.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (905) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +202 -194
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +106 -106
  5. package/build/viewer/molstar.js +1 -1
  6. package/lib/apps/docking-viewer/index.html +36 -36
  7. package/lib/apps/docking-viewer/viewport.js +1 -1
  8. package/lib/apps/viewer/app.d.ts +7 -6
  9. package/lib/apps/viewer/app.js +2 -0
  10. package/lib/apps/viewer/embedded.html +43 -43
  11. package/lib/apps/viewer/index.html +106 -106
  12. package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  13. package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
  14. package/lib/cli/cif2bcif/converter.js +1 -1
  15. package/lib/cli/cif2bcif/index.js +4 -4
  16. package/lib/commonjs/apps/docking-viewer/index.js +12 -12
  17. package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
  18. package/lib/commonjs/apps/viewer/app.d.ts +7 -6
  19. package/lib/commonjs/apps/viewer/app.js +24 -22
  20. package/lib/commonjs/apps/viewer/index.js +1 -1
  21. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
  22. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  23. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
  24. package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
  25. package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
  26. package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
  27. package/lib/commonjs/cli/cif2bcif/index.js +12 -12
  28. package/lib/commonjs/cli/cifschema/index.js +27 -27
  29. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
  30. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  31. package/lib/commonjs/cli/state-docs/index.js +2 -2
  32. package/lib/commonjs/cli/structure-info/helpers.js +11 -11
  33. package/lib/commonjs/cli/structure-info/model.js +15 -15
  34. package/lib/commonjs/cli/structure-info/volume.js +9 -9
  35. package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
  36. package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
  37. package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
  38. package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
  39. package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
  40. package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
  41. package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
  42. package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
  43. package/lib/commonjs/examples/lighting/index.js +6 -6
  44. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
  45. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
  46. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
  47. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
  48. package/lib/commonjs/examples/task.js +15 -15
  49. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
  50. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
  51. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
  52. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
  53. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
  54. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
  55. package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
  56. package/lib/commonjs/extensions/anvil/behavior.js +14 -14
  57. package/lib/commonjs/extensions/anvil/prop.js +7 -7
  58. package/lib/commonjs/extensions/anvil/representation.js +5 -5
  59. package/lib/commonjs/extensions/cellpack/index.js +1 -1
  60. package/lib/commonjs/extensions/cellpack/model.js +26 -24
  61. package/lib/commonjs/extensions/cellpack/preset.js +6 -6
  62. package/lib/commonjs/extensions/cellpack/property.js +3 -3
  63. package/lib/commonjs/extensions/cellpack/representation.js +2 -2
  64. package/lib/commonjs/extensions/cellpack/state.js +13 -13
  65. package/lib/commonjs/extensions/cellpack/util.js +14 -14
  66. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
  67. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  68. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
  69. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
  70. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
  71. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
  72. package/lib/commonjs/extensions/g3d/data.js +6 -6
  73. package/lib/commonjs/extensions/g3d/format.js +14 -14
  74. package/lib/commonjs/extensions/g3d/model.js +4 -4
  75. package/lib/commonjs/extensions/geo-export/controls.js +3 -3
  76. package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
  77. package/lib/commonjs/extensions/geo-export/index.js +1 -1
  78. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
  79. package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
  80. package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
  81. package/lib/commonjs/extensions/geo-export/ui.js +7 -7
  82. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
  83. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
  84. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
  85. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
  86. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
  87. package/lib/commonjs/extensions/model-export/export.js +4 -4
  88. package/lib/commonjs/extensions/model-export/index.js +1 -1
  89. package/lib/commonjs/extensions/model-export/ui.js +5 -5
  90. package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
  91. package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
  92. package/lib/commonjs/extensions/mp4-export/index.js +1 -1
  93. package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
  94. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
  95. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
  96. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
  97. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
  98. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
  99. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
  100. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
  101. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
  102. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
  103. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
  104. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
  105. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +22 -5
  106. package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
  107. package/lib/commonjs/extensions/zenodo/index.js +35 -0
  108. package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
  109. package/lib/commonjs/extensions/zenodo/ui.js +306 -0
  110. package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
  111. package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
  112. package/lib/commonjs/mol-canvas3d/camera.js +2 -1
  113. package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
  114. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  115. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
  116. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
  117. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
  118. package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
  119. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
  120. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  121. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
  122. package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
  123. package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
  124. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
  125. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
  126. package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
  127. package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
  128. package/lib/commonjs/mol-canvas3d/util.js +2 -2
  129. package/lib/commonjs/mol-data/db/column.js +2 -2
  130. package/lib/commonjs/mol-data/db/table.js +1 -1
  131. package/lib/commonjs/mol-data/db.js +1 -1
  132. package/lib/commonjs/mol-data/generic.js +3 -3
  133. package/lib/commonjs/mol-data/index.js +4 -4
  134. package/lib/commonjs/mol-data/int/interval.js +1 -1
  135. package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
  136. package/lib/commonjs/mol-data/int/segmentation.js +1 -1
  137. package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
  138. package/lib/commonjs/mol-data/util.js +7 -7
  139. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
  140. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
  141. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
  142. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
  143. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
  144. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  145. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
  146. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  147. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  148. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
  149. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  150. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
  151. package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
  152. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
  153. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
  154. package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
  155. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
  156. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  157. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
  158. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
  159. package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
  160. package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
  161. package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
  162. package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
  163. package/lib/commonjs/mol-geo/primitive/star.js +1 -1
  164. package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
  165. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
  166. package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
  167. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
  168. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
  169. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
  170. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  171. package/lib/commonjs/mol-gl/compute/util.js +3 -3
  172. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  173. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  174. package/lib/commonjs/mol-gl/renderable/image.js +3 -3
  175. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  176. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  177. package/lib/commonjs/mol-gl/renderable/points.js +3 -3
  178. package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
  179. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  180. package/lib/commonjs/mol-gl/renderable/text.js +3 -3
  181. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  182. package/lib/commonjs/mol-gl/renderable/util.js +1 -1
  183. package/lib/commonjs/mol-gl/shader-code.js +2 -1
  184. package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
  185. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  186. package/lib/commonjs/mol-gl/webgl/context.js +5 -5
  187. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
  188. package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
  189. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
  190. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
  191. package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
  192. package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
  193. package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
  194. package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
  195. package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
  196. package/lib/commonjs/mol-io/common/typed-array.js +2 -2
  197. package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
  198. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
  199. package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
  200. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  201. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  202. package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
  203. package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
  204. package/lib/commonjs/mol-io/reader/cif.js +1 -1
  205. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
  206. package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
  207. package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
  208. package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
  209. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
  210. package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
  211. package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
  212. package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
  213. package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
  214. package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
  215. package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
  216. package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
  217. package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
  218. package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
  219. package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
  220. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
  221. package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
  222. package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
  223. package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
  224. package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
  225. package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
  226. package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
  227. package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
  228. package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
  229. package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
  230. package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
  231. package/lib/commonjs/mol-io/writer/cif.js +1 -1
  232. package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
  233. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  234. package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
  235. package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
  236. package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
  237. package/lib/commonjs/mol-math/geometry/common.js +1 -1
  238. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  239. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
  240. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  241. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
  242. package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
  243. package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
  244. package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
  245. package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
  246. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
  247. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
  248. package/lib/commonjs/mol-math/geometry.js +8 -8
  249. package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
  250. package/lib/commonjs/mol-math/graph.js +1 -1
  251. package/lib/commonjs/mol-math/linear-algebra.js +2 -2
  252. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
  253. package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
  254. package/lib/commonjs/mol-model/sequence.js +1 -1
  255. package/lib/commonjs/mol-model/shape.js +1 -1
  256. package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
  257. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  258. package/lib/commonjs/mol-model/structure/model/model.js +3 -3
  259. package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
  260. package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
  261. package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
  262. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
  263. package/lib/commonjs/mol-model/structure/model.js +3 -3
  264. package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
  265. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
  266. package/lib/commonjs/mol-model/structure/query.js +6 -6
  267. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
  268. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  269. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  270. package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
  271. package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
  272. package/lib/commonjs/mol-model/structure/structure/structure.js +9 -6
  273. package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
  274. package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
  275. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
  276. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +6 -4
  277. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  278. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
  279. package/lib/commonjs/mol-model/structure/structure/unit.js +5 -22
  280. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
  281. package/lib/commonjs/mol-model/structure/structure.js +2 -2
  282. package/lib/commonjs/mol-model/structure/topology.js +1 -1
  283. package/lib/commonjs/mol-model/structure.js +6 -6
  284. package/lib/commonjs/mol-model/volume.js +2 -2
  285. package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
  286. package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  287. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
  288. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
  289. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  290. package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
  291. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
  292. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
  293. package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -2
  294. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -2
  295. package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
  296. package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -2
  297. package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
  298. package/lib/commonjs/mol-model-formats/structure/common/component.js +5 -1
  299. package/lib/commonjs/mol-model-formats/structure/cube.js +5 -5
  300. package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -2
  301. package/lib/commonjs/mol-model-formats/structure/gro.js +5 -3
  302. package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
  303. package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -2
  304. package/lib/commonjs/mol-model-formats/structure/mol.js +5 -5
  305. package/lib/commonjs/mol-model-formats/structure/mol2.js +6 -6
  306. package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts +9 -0
  307. package/lib/commonjs/mol-model-formats/structure/nctraj.js +60 -0
  308. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +2 -2
  309. package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
  310. package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -5
  311. package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts +16 -0
  312. package/lib/commonjs/mol-model-formats/structure/prmtop.js +147 -0
  313. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  314. package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -1
  315. package/lib/commonjs/mol-model-formats/structure/psf.js +5 -3
  316. package/lib/commonjs/mol-model-formats/structure/top.d.ts +16 -0
  317. package/lib/commonjs/mol-model-formats/structure/top.js +189 -0
  318. package/lib/commonjs/mol-model-formats/structure/trr.d.ts +9 -0
  319. package/lib/commonjs/mol-model-formats/structure/trr.js +46 -0
  320. package/lib/commonjs/mol-model-formats/structure/util.d.ts +2 -2
  321. package/lib/commonjs/mol-model-formats/structure/util.js +19 -20
  322. package/lib/commonjs/mol-model-formats/structure/xtc.js +2 -2
  323. package/lib/commonjs/mol-model-formats/structure/xyz.js +2 -2
  324. package/lib/commonjs/mol-model-formats/volume/ccp4.js +2 -2
  325. package/lib/commonjs/mol-model-formats/volume/cube.js +2 -2
  326. package/lib/commonjs/mol-model-formats/volume/density-server.js +2 -2
  327. package/lib/commonjs/mol-model-formats/volume/dsn6.js +2 -2
  328. package/lib/commonjs/mol-model-formats/volume/dx.js +2 -2
  329. package/lib/commonjs/mol-model-props/common/custom-element-property.js +2 -2
  330. package/lib/commonjs/mol-model-props/common/custom-model-property.js +5 -5
  331. package/lib/commonjs/mol-model-props/common/custom-property.js +1 -1
  332. package/lib/commonjs/mol-model-props/common/custom-structure-property.js +6 -6
  333. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +2 -2
  334. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +5 -5
  335. package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +4 -4
  336. package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +3 -3
  337. package/lib/commonjs/mol-model-props/computed/helix-orientation.js +2 -2
  338. package/lib/commonjs/mol-model-props/computed/interactions/common.js +1 -1
  339. package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +1 -1
  340. package/lib/commonjs/mol-model-props/computed/interactions/features.js +1 -1
  341. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +3 -3
  342. package/lib/commonjs/mol-model-props/computed/interactions/interactions.js +3 -3
  343. package/lib/commonjs/mol-model-props/computed/interactions.js +4 -4
  344. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +10 -4
  345. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +12 -7
  346. package/lib/commonjs/mol-model-props/computed/representations/interactions.js +1 -1
  347. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +2 -2
  348. package/lib/commonjs/mol-model-props/computed/secondary-structure.js +7 -7
  349. package/lib/commonjs/mol-model-props/computed/valence-model.js +4 -4
  350. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/property.js +2 -2
  351. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js +12 -3
  352. package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js +2 -2
  353. package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +3 -3
  354. package/lib/commonjs/mol-plugin/animation-loop.js +2 -2
  355. package/lib/commonjs/mol-plugin/behavior/behavior.js +5 -5
  356. package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +2 -2
  357. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.js +1 -1
  358. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/interactions.js +1 -1
  359. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/secondary-structure.js +1 -1
  360. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/valence-model.js +1 -1
  361. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.js +1 -1
  362. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/sifts-mapping.js +1 -1
  363. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/structure-info.js +2 -2
  364. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +3 -3
  365. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +11 -11
  366. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.js +12 -12
  367. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  368. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.js +1 -1
  369. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.js +16 -16
  370. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +10 -10
  371. package/lib/commonjs/mol-plugin/behavior/static/state.js +6 -6
  372. package/lib/commonjs/mol-plugin/behavior.js +8 -8
  373. package/lib/commonjs/mol-plugin/command.js +2 -2
  374. package/lib/commonjs/mol-plugin/context.d.ts +2 -1
  375. package/lib/commonjs/mol-plugin/context.js +9 -8
  376. package/lib/commonjs/mol-plugin/layout.js +2 -2
  377. package/lib/commonjs/mol-plugin/spec.js +1 -1
  378. package/lib/commonjs/mol-plugin/state.js +5 -5
  379. package/lib/commonjs/mol-plugin/util/task-manager.js +4 -4
  380. package/lib/commonjs/mol-plugin/util/toast.js +1 -1
  381. package/lib/commonjs/mol-plugin/util/viewport-screenshot.js +17 -17
  382. package/lib/commonjs/mol-plugin-state/actions/file.d.ts +1 -1
  383. package/lib/commonjs/mol-plugin-state/actions/file.js +94 -61
  384. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +11 -2
  385. package/lib/commonjs/mol-plugin-state/actions/structure.js +190 -20
  386. package/lib/commonjs/mol-plugin-state/actions/volume.js +5 -4
  387. package/lib/commonjs/mol-plugin-state/actions.js +3 -3
  388. package/lib/commonjs/mol-plugin-state/animation/built-in/assembly-unwind.js +2 -2
  389. package/lib/commonjs/mol-plugin-state/animation/built-in/camera-rock.js +3 -3
  390. package/lib/commonjs/mol-plugin-state/animation/built-in/camera-spin.js +3 -3
  391. package/lib/commonjs/mol-plugin-state/animation/built-in/explode-units.js +4 -4
  392. package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.js +2 -2
  393. package/lib/commonjs/mol-plugin-state/animation/built-in/spin-structure.js +5 -5
  394. package/lib/commonjs/mol-plugin-state/animation/built-in/state-interpolation.js +2 -2
  395. package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js +5 -5
  396. package/lib/commonjs/mol-plugin-state/builder/data.js +2 -2
  397. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +16 -16
  398. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +28 -28
  399. package/lib/commonjs/mol-plugin-state/builder/structure/representation.js +2 -2
  400. package/lib/commonjs/mol-plugin-state/builder/structure.js +7 -7
  401. package/lib/commonjs/mol-plugin-state/component.js +1 -1
  402. package/lib/commonjs/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
  403. package/lib/commonjs/mol-plugin-state/formats/coordinates.js +70 -0
  404. package/lib/commonjs/mol-plugin-state/formats/registry.d.ts +3 -3
  405. package/lib/commonjs/mol-plugin-state/formats/registry.js +13 -8
  406. package/lib/commonjs/mol-plugin-state/formats/shape.js +2 -2
  407. package/lib/commonjs/mol-plugin-state/formats/topology.d.ts +73 -0
  408. package/lib/commonjs/mol-plugin-state/formats/topology.js +87 -0
  409. package/lib/commonjs/mol-plugin-state/formats/trajectory.js +6 -6
  410. package/lib/commonjs/mol-plugin-state/formats/volume.js +21 -21
  411. package/lib/commonjs/mol-plugin-state/helpers/root-structure.js +15 -15
  412. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +7 -7
  413. package/lib/commonjs/mol-plugin-state/helpers/structure-component.js +2 -1
  414. package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js +11 -11
  415. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +3 -3
  416. package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js +11 -11
  417. package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js +11 -11
  418. package/lib/commonjs/mol-plugin-state/manager/animation.js +17 -17
  419. package/lib/commonjs/mol-plugin-state/manager/camera.js +1 -1
  420. package/lib/commonjs/mol-plugin-state/manager/interactivity.js +6 -6
  421. package/lib/commonjs/mol-plugin-state/manager/snapshots.js +14 -14
  422. package/lib/commonjs/mol-plugin-state/manager/structure/component.js +26 -26
  423. package/lib/commonjs/mol-plugin-state/manager/structure/focus.js +2 -2
  424. package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js +1 -1
  425. package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.js +8 -8
  426. package/lib/commonjs/mol-plugin-state/manager/structure/measurement.js +21 -21
  427. package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +3 -3
  428. package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy.js +1 -1
  429. package/lib/commonjs/mol-plugin-state/objects.d.ts +47 -1
  430. package/lib/commonjs/mol-plugin-state/objects.js +46 -30
  431. package/lib/commonjs/mol-plugin-state/transforms/data.d.ts +6 -0
  432. package/lib/commonjs/mol-plugin-state/transforms/data.js +93 -41
  433. package/lib/commonjs/mol-plugin-state/transforms/model.d.ts +14 -2
  434. package/lib/commonjs/mol-plugin-state/transforms/model.js +163 -54
  435. package/lib/commonjs/mol-plugin-state/transforms/representation.js +77 -77
  436. package/lib/commonjs/mol-plugin-state/transforms/shape.js +2 -2
  437. package/lib/commonjs/mol-plugin-state/transforms/volume.js +16 -16
  438. package/lib/commonjs/mol-plugin-state/transforms.js +6 -6
  439. package/lib/commonjs/mol-plugin-ui/base.js +5 -5
  440. package/lib/commonjs/mol-plugin-ui/context.js +1 -1
  441. package/lib/commonjs/mol-plugin-ui/controls/action-menu.js +14 -14
  442. package/lib/commonjs/mol-plugin-ui/controls/color.js +7 -7
  443. package/lib/commonjs/mol-plugin-ui/controls/common.js +16 -16
  444. package/lib/commonjs/mol-plugin-ui/controls/icons.js +70 -70
  445. package/lib/commonjs/mol-plugin-ui/controls/legend.js +7 -7
  446. package/lib/commonjs/mol-plugin-ui/controls/line-graph/line-graph-component.js +3 -3
  447. package/lib/commonjs/mol-plugin-ui/controls/line-graph/point-component.js +2 -2
  448. package/lib/commonjs/mol-plugin-ui/controls/parameters.js +94 -94
  449. package/lib/commonjs/mol-plugin-ui/controls/screenshot.js +5 -5
  450. package/lib/commonjs/mol-plugin-ui/controls/slider.js +16 -16
  451. package/lib/commonjs/mol-plugin-ui/controls.js +16 -16
  452. package/lib/commonjs/mol-plugin-ui/custom/volume.js +16 -16
  453. package/lib/commonjs/mol-plugin-ui/index.js +4 -4
  454. package/lib/commonjs/mol-plugin-ui/left-panel.d.ts +8 -1
  455. package/lib/commonjs/mol-plugin-ui/left-panel.js +40 -19
  456. package/lib/commonjs/mol-plugin-ui/plugin.js +17 -17
  457. package/lib/commonjs/mol-plugin-ui/sequence/chain.js +1 -1
  458. package/lib/commonjs/mol-plugin-ui/sequence/element.js +1 -1
  459. package/lib/commonjs/mol-plugin-ui/sequence/hetero.js +1 -1
  460. package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +1 -1
  461. package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +6 -6
  462. package/lib/commonjs/mol-plugin-ui/sequence.js +9 -9
  463. package/lib/commonjs/mol-plugin-ui/spec.js +1 -1
  464. package/lib/commonjs/mol-plugin-ui/state/actions.js +2 -2
  465. package/lib/commonjs/mol-plugin-ui/state/animation.js +2 -2
  466. package/lib/commonjs/mol-plugin-ui/state/apply-action.js +1 -1
  467. package/lib/commonjs/mol-plugin-ui/state/common.js +12 -12
  468. package/lib/commonjs/mol-plugin-ui/state/snapshots.js +29 -29
  469. package/lib/commonjs/mol-plugin-ui/state/tree.js +19 -19
  470. package/lib/commonjs/mol-plugin-ui/state/update-transform.js +3 -3
  471. package/lib/commonjs/mol-plugin-ui/structure/components.js +19 -19
  472. package/lib/commonjs/mol-plugin-ui/structure/focus.js +4 -4
  473. package/lib/commonjs/mol-plugin-ui/structure/generic.js +6 -6
  474. package/lib/commonjs/mol-plugin-ui/structure/measurements.js +13 -13
  475. package/lib/commonjs/mol-plugin-ui/structure/quick-styles.js +11 -11
  476. package/lib/commonjs/mol-plugin-ui/structure/selection.js +13 -13
  477. package/lib/commonjs/mol-plugin-ui/structure/source.js +12 -12
  478. package/lib/commonjs/mol-plugin-ui/structure/superposition.js +20 -20
  479. package/lib/commonjs/mol-plugin-ui/structure/volume.js +12 -12
  480. package/lib/commonjs/mol-plugin-ui/task.js +8 -8
  481. package/lib/commonjs/mol-plugin-ui/toast.js +6 -6
  482. package/lib/commonjs/mol-plugin-ui/viewport/canvas.js +5 -5
  483. package/lib/commonjs/mol-plugin-ui/viewport/help.js +14 -14
  484. package/lib/commonjs/mol-plugin-ui/viewport/screenshot.js +8 -8
  485. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +6 -6
  486. package/lib/commonjs/mol-plugin-ui/viewport.js +7 -7
  487. package/lib/commonjs/mol-repr/representation.js +4 -4
  488. package/lib/commonjs/mol-repr/shape/loci/angle.js +9 -9
  489. package/lib/commonjs/mol-repr/shape/loci/common.js +1 -1
  490. package/lib/commonjs/mol-repr/shape/loci/dihedral.js +14 -14
  491. package/lib/commonjs/mol-repr/shape/loci/distance.js +5 -5
  492. package/lib/commonjs/mol-repr/shape/loci/label.js +3 -3
  493. package/lib/commonjs/mol-repr/shape/loci/orientation.js +4 -4
  494. package/lib/commonjs/mol-repr/shape/loci/plane.js +2 -2
  495. package/lib/commonjs/mol-repr/shape/model/unitcell.js +2 -2
  496. package/lib/commonjs/mol-repr/shape/representation.js +2 -2
  497. package/lib/commonjs/mol-repr/structure/complex-representation.js +2 -2
  498. package/lib/commonjs/mol-repr/structure/complex-visual.js +12 -12
  499. package/lib/commonjs/mol-repr/structure/params.js +8 -8
  500. package/lib/commonjs/mol-repr/structure/registry.js +1 -1
  501. package/lib/commonjs/mol-repr/structure/representation/backbone.js +1 -1
  502. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js +1 -1
  503. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js +1 -1
  504. package/lib/commonjs/mol-repr/structure/representation/cartoon.js +3 -3
  505. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js +1 -1
  506. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +1 -1
  507. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +1 -1
  508. package/lib/commonjs/mol-repr/structure/representation/label.js +1 -1
  509. package/lib/commonjs/mol-repr/structure/representation/line.js +1 -1
  510. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +1 -1
  511. package/lib/commonjs/mol-repr/structure/representation/orientation.js +1 -1
  512. package/lib/commonjs/mol-repr/structure/representation/point.js +1 -1
  513. package/lib/commonjs/mol-repr/structure/representation/putty.js +1 -1
  514. package/lib/commonjs/mol-repr/structure/representation/spacefill.js +1 -1
  515. package/lib/commonjs/mol-repr/structure/representation.js +1 -1
  516. package/lib/commonjs/mol-repr/structure/units-representation.js +2 -2
  517. package/lib/commonjs/mol-repr/structure/units-visual.js +16 -16
  518. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +1 -1
  519. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +21 -11
  520. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -1
  521. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +11 -6
  522. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +17 -7
  523. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +9 -4
  524. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js +11 -2
  525. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +1 -1
  526. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +11 -2
  527. package/lib/commonjs/mol-repr/structure/visual/element-cross.js +1 -1
  528. package/lib/commonjs/mol-repr/structure/visual/element-point.d.ts +1 -1
  529. package/lib/commonjs/mol-repr/structure/visual/element-point.js +23 -4
  530. package/lib/commonjs/mol-repr/structure/visual/element-sphere.js +1 -1
  531. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.js +1 -1
  532. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +8 -9
  533. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +1 -1
  534. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +20 -20
  535. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  536. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +7 -8
  537. package/lib/commonjs/mol-repr/structure/visual/label-text.js +1 -1
  538. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +6 -6
  539. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  540. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +7 -7
  541. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.js +1 -1
  542. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.js +1 -1
  543. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +1 -1
  544. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.js +1 -1
  545. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.js +1 -1
  546. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
  547. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.js +1 -1
  548. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
  549. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js +1 -1
  550. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +2 -2
  551. package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts +1 -3
  552. package/lib/commonjs/mol-repr/structure/visual/util/common.js +3 -28
  553. package/lib/commonjs/mol-repr/structure/visual/util/element.js +36 -2
  554. package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js +13 -13
  555. package/lib/commonjs/mol-repr/structure/visual/util/link.d.ts +13 -3
  556. package/lib/commonjs/mol-repr/structure/visual/util/link.js +55 -6
  557. package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js +5 -5
  558. package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +4 -4
  559. package/lib/commonjs/mol-repr/util.js +1 -1
  560. package/lib/commonjs/mol-repr/volume/direct-volume.js +3 -3
  561. package/lib/commonjs/mol-repr/volume/isosurface.js +9 -9
  562. package/lib/commonjs/mol-repr/volume/registry.js +1 -1
  563. package/lib/commonjs/mol-repr/volume/representation.js +5 -5
  564. package/lib/commonjs/mol-repr/volume/slice.js +4 -4
  565. package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
  566. package/lib/commonjs/mol-script/language/parser.js +7 -4
  567. package/lib/commonjs/mol-script/language/symbol-table/internal.js +1 -1
  568. package/lib/commonjs/mol-script/language/symbol-table/structure-query.js +1 -1
  569. package/lib/commonjs/mol-script/runtime/query/compiler.js +1 -1
  570. package/lib/commonjs/mol-script/script/mol-script/symbols.js +1 -1
  571. package/lib/commonjs/mol-state/action.js +1 -1
  572. package/lib/commonjs/mol-state/index.js +8 -8
  573. package/lib/commonjs/mol-state/state/builder.js +2 -2
  574. package/lib/commonjs/mol-state/state/selection.js +1 -1
  575. package/lib/commonjs/mol-state/state.js +21 -21
  576. package/lib/commonjs/mol-state/transform.js +4 -4
  577. package/lib/commonjs/mol-state/transformer.js +1 -1
  578. package/lib/commonjs/mol-task/execution/observable.js +5 -5
  579. package/lib/commonjs/mol-task/task.js +3 -3
  580. package/lib/commonjs/mol-task/util/chunked.js +2 -2
  581. package/lib/commonjs/mol-task/util/multistep.js +1 -1
  582. package/lib/commonjs/mol-task/util/scheduler.d.ts +2 -2
  583. package/lib/commonjs/mol-task/util/scheduler.js +8 -8
  584. package/lib/commonjs/mol-theme/color/atom-id.js +1 -1
  585. package/lib/commonjs/mol-theme/color/chain-id.js +1 -1
  586. package/lib/commonjs/mol-theme/color/element-index.js +1 -1
  587. package/lib/commonjs/mol-theme/color/entity-id.js +1 -1
  588. package/lib/commonjs/mol-theme/color/entity-source.js +2 -2
  589. package/lib/commonjs/mol-theme/color/hydrophobicity.js +2 -2
  590. package/lib/commonjs/mol-theme/color/model-index.js +1 -1
  591. package/lib/commonjs/mol-theme/color/operator-hkl.js +2 -2
  592. package/lib/commonjs/mol-theme/color/operator-name.js +1 -1
  593. package/lib/commonjs/mol-theme/color/polymer-id.js +2 -2
  594. package/lib/commonjs/mol-theme/color/polymer-index.js +2 -2
  595. package/lib/commonjs/mol-theme/color/unit-index.js +2 -2
  596. package/lib/commonjs/mol-theme/label.js +6 -6
  597. package/lib/commonjs/mol-theme/theme.js +3 -3
  598. package/lib/commonjs/mol-util/assets.js +7 -7
  599. package/lib/commonjs/mol-util/color/distinct.js +1 -1
  600. package/lib/commonjs/mol-util/color/palette.js +3 -3
  601. package/lib/commonjs/mol-util/color/scale.js +2 -2
  602. package/lib/commonjs/mol-util/data-source.js +14 -13
  603. package/lib/commonjs/mol-util/file-info.d.ts +1 -3
  604. package/lib/commonjs/mol-util/file-info.js +2 -10
  605. package/lib/commonjs/mol-util/graphql-client.js +4 -4
  606. package/lib/commonjs/mol-util/index.d.ts +1 -0
  607. package/lib/commonjs/mol-util/index.js +8 -2
  608. package/lib/commonjs/mol-util/input/input-observer.js +6 -6
  609. package/lib/commonjs/mol-util/make-dir.js +1 -1
  610. package/lib/commonjs/mol-util/material.js +2 -2
  611. package/lib/commonjs/mol-util/monadic-parser.js +2 -2
  612. package/lib/commonjs/mol-util/param-definition.js +7 -7
  613. package/lib/commonjs/mol-util/read.js +2 -2
  614. package/lib/commonjs/mol-util/retry-if.js +2 -2
  615. package/lib/commonjs/mol-util/string.js +1 -1
  616. package/lib/commonjs/mol-util/zip/deflate.js +4 -3
  617. package/lib/commonjs/mol-util/zip/inflate.js +2 -2
  618. package/lib/commonjs/mol-util/zip/zip.d.ts +7 -1
  619. package/lib/commonjs/mol-util/zip/zip.js +21 -16
  620. package/lib/commonjs/servers/common/file-handle.js +1 -1
  621. package/lib/commonjs/servers/common/swagger-ui/index.js +1 -1
  622. package/lib/commonjs/servers/model/config.d.ts +2 -2
  623. package/lib/commonjs/servers/model/config.js +5 -5
  624. package/lib/commonjs/servers/model/preprocess/converter.js +2 -2
  625. package/lib/commonjs/servers/model/preprocess/master.js +3 -3
  626. package/lib/commonjs/servers/model/preprocess/parallel.js +6 -6
  627. package/lib/commonjs/servers/model/preprocess/preprocess.js +4 -4
  628. package/lib/commonjs/servers/model/preprocess.js +1 -1
  629. package/lib/commonjs/servers/model/properties/providers/pdbe.js +8 -8
  630. package/lib/commonjs/servers/model/properties/providers/wwpdb.js +12 -12
  631. package/lib/commonjs/servers/model/property-provider.js +3 -3
  632. package/lib/commonjs/servers/model/query.js +1 -1
  633. package/lib/commonjs/servers/model/server/api-local.js +2 -2
  634. package/lib/commonjs/servers/model/server/api-schema.js +2 -2
  635. package/lib/commonjs/servers/model/server/api-web.js +5 -5
  636. package/lib/commonjs/servers/model/server/api.js +6 -6
  637. package/lib/commonjs/servers/model/server/query.js +15 -15
  638. package/lib/commonjs/servers/model/server/structure-wrapper.js +21 -21
  639. package/lib/commonjs/servers/model/server.js +2 -2
  640. package/lib/commonjs/servers/model/utils/fetch-props-pdbe.js +6 -6
  641. package/lib/commonjs/servers/model/utils/fetch-retry.js +3 -3
  642. package/lib/commonjs/servers/model/utils/writer.js +3 -3
  643. package/lib/commonjs/servers/plugin-state/config.js +1 -1
  644. package/lib/commonjs/servers/plugin-state/index.js +6 -6
  645. package/lib/commonjs/servers/volume/common/binary-schema.js +1 -1
  646. package/lib/commonjs/servers/volume/common/data-format.js +3 -3
  647. package/lib/commonjs/servers/volume/common/file.js +8 -8
  648. package/lib/commonjs/servers/volume/config.js +6 -6
  649. package/lib/commonjs/servers/volume/pack/format/ccp4.js +4 -4
  650. package/lib/commonjs/servers/volume/pack/format/dsn6.js +4 -4
  651. package/lib/commonjs/servers/volume/pack/format.js +3 -3
  652. package/lib/commonjs/servers/volume/pack/main.js +13 -13
  653. package/lib/commonjs/servers/volume/pack/sampling.js +13 -13
  654. package/lib/commonjs/servers/volume/pack/writer.js +2 -2
  655. package/lib/commonjs/servers/volume/pack.js +1 -1
  656. package/lib/commonjs/servers/volume/query.js +4 -4
  657. package/lib/commonjs/servers/volume/server/algebra/box.js +1 -1
  658. package/lib/commonjs/servers/volume/server/api.js +8 -8
  659. package/lib/commonjs/servers/volume/server/local-api.js +8 -8
  660. package/lib/commonjs/servers/volume/server/query/compose.js +8 -8
  661. package/lib/commonjs/servers/volume/server/query/execute.js +10 -10
  662. package/lib/commonjs/servers/volume/server/query/identify.js +2 -2
  663. package/lib/commonjs/servers/volume/server/web-api.js +7 -7
  664. package/lib/commonjs/servers/volume/server.js +2 -2
  665. package/lib/examples/alpha-orbitals/controls.js +2 -2
  666. package/lib/examples/alpha-orbitals/index.html +61 -61
  667. package/lib/examples/basic-wrapper/controls.js +1 -1
  668. package/lib/examples/basic-wrapper/index.html +137 -137
  669. package/lib/examples/lighting/index.html +88 -88
  670. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  671. package/lib/examples/proteopedia-wrapper/ui/controls.js +1 -1
  672. package/lib/extensions/cellpack/model.js +4 -2
  673. package/lib/extensions/cellpack/state.js +2 -2
  674. package/lib/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  675. package/lib/extensions/dnatco/confal-pyramids/color.js +224 -132
  676. package/lib/extensions/dnatco/confal-pyramids/property.js +1 -3
  677. package/lib/extensions/dnatco/confal-pyramids/util.js +19 -20
  678. package/lib/extensions/geo-export/ui.js +2 -2
  679. package/lib/extensions/model-export/ui.js +2 -2
  680. package/lib/extensions/mp4-export/ui.js +2 -2
  681. package/lib/extensions/rcsb/assembly-symmetry/ui.js +3 -3
  682. package/lib/extensions/rcsb/validation-report/representation.js +19 -2
  683. package/lib/extensions/zenodo/index.d.ts +7 -0
  684. package/lib/extensions/zenodo/index.js +32 -0
  685. package/lib/extensions/zenodo/ui.d.ts +61 -0
  686. package/lib/extensions/zenodo/ui.js +303 -0
  687. package/lib/mol-canvas3d/camera.js +2 -1
  688. package/lib/mol-canvas3d/helper/camera-helper.js +1 -1
  689. package/lib/mol-canvas3d/helper/handle-helper.js +1 -1
  690. package/lib/mol-canvas3d/helper/interaction-events.js +1 -1
  691. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
  692. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  693. package/lib/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  694. package/lib/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  695. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  696. package/lib/mol-geo/geometry/text/text-builder.js +2 -1
  697. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  698. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
  699. package/lib/mol-gl/shader-code.js +2 -1
  700. package/lib/mol-gl/webgl/buffer.js +2 -3
  701. package/lib/mol-gl/webgl/context.d.ts +1 -1
  702. package/lib/mol-gl/webgl/context.js +2 -2
  703. package/lib/mol-io/common/binary-cif/classifier.js +3 -2
  704. package/lib/mol-io/common/binary-cif/decoder.js +4 -3
  705. package/lib/mol-io/common/io-buffer.d.ts +206 -0
  706. package/lib/mol-io/common/io-buffer.js +405 -0
  707. package/lib/mol-io/common/netcdf/reader.d.ts +78 -0
  708. package/lib/mol-io/common/netcdf/reader.js +456 -0
  709. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  710. package/lib/mol-io/reader/nctraj/parser.d.ts +18 -0
  711. package/lib/mol-io/reader/nctraj/parser.js +97 -0
  712. package/lib/mol-io/reader/prmtop/parser.d.ts +58 -0
  713. package/lib/mol-io/reader/prmtop/parser.js +168 -0
  714. package/lib/mol-io/reader/top/parser.d.ts +37 -0
  715. package/lib/mol-io/reader/top/parser.js +299 -0
  716. package/lib/mol-io/reader/trr/parser.d.ts +22 -0
  717. package/lib/mol-io/reader/trr/parser.js +142 -0
  718. package/lib/mol-io/writer/cif/encoder.js +2 -1
  719. package/lib/mol-math/geometry/common.d.ts +2 -1
  720. package/lib/mol-math/geometry/common.js +1 -1
  721. package/lib/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  722. package/lib/mol-math/geometry/gaussian-density/cpu.js +2 -2
  723. package/lib/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  724. package/lib/mol-math/geometry/gaussian-density/gpu.js +7 -7
  725. package/lib/mol-math/geometry/gaussian-density.d.ts +2 -2
  726. package/lib/mol-math/geometry/gaussian-density.js +1 -1
  727. package/lib/mol-math/geometry/molecular-surface.d.ts +2 -1
  728. package/lib/mol-math/geometry/molecular-surface.js +2 -2
  729. package/lib/mol-math/geometry/primitives/box3d.js +2 -1
  730. package/lib/mol-math/geometry/primitives/sphere3d.js +12 -6
  731. package/lib/mol-model/sequence/sequence.js +2 -1
  732. package/lib/mol-model/structure/model/types/saccharides.d.ts +8 -0
  733. package/lib/mol-model/structure/model/types/saccharides.js +8 -0
  734. package/lib/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  735. package/lib/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  736. package/lib/mol-model/structure/structure/structure.js +4 -1
  737. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
  738. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +4 -2
  739. package/lib/mol-model/structure/structure/unit.js +1 -18
  740. package/lib/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  741. package/lib/mol-model-formats/structure/basic/atomic.js +1 -14
  742. package/lib/mol-model-formats/structure/basic/parser.d.ts +1 -1
  743. package/lib/mol-model-formats/structure/basic/parser.js +1 -1
  744. package/lib/mol-model-formats/structure/basic/schema.d.ts +2 -2
  745. package/lib/mol-model-formats/structure/basic/schema.js +7 -2
  746. package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
  747. package/lib/mol-model-formats/structure/basic/util.js +24 -1
  748. package/lib/mol-model-formats/structure/cif-core.js +4 -4
  749. package/lib/mol-model-formats/structure/common/component.js +5 -1
  750. package/lib/mol-model-formats/structure/cube.js +3 -3
  751. package/lib/mol-model-formats/structure/gro.js +3 -1
  752. package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
  753. package/lib/mol-model-formats/structure/mmcif.js +4 -2
  754. package/lib/mol-model-formats/structure/mol.js +3 -3
  755. package/lib/mol-model-formats/structure/mol2.js +4 -4
  756. package/lib/mol-model-formats/structure/nctraj.d.ts +9 -0
  757. package/lib/mol-model-formats/structure/nctraj.js +56 -0
  758. package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
  759. package/lib/mol-model-formats/structure/pdb.js +5 -3
  760. package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
  761. package/lib/mol-model-formats/structure/prmtop.js +144 -0
  762. package/lib/mol-model-formats/structure/property/symmetry.js +11 -1
  763. package/lib/mol-model-formats/structure/psf.js +3 -1
  764. package/lib/mol-model-formats/structure/top.d.ts +16 -0
  765. package/lib/mol-model-formats/structure/top.js +186 -0
  766. package/lib/mol-model-formats/structure/trr.d.ts +9 -0
  767. package/lib/mol-model-formats/structure/trr.js +42 -0
  768. package/lib/mol-model-formats/structure/util.d.ts +2 -2
  769. package/lib/mol-model-formats/structure/util.js +19 -20
  770. package/lib/mol-model-formats/structure/xyz.js +2 -2
  771. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +9 -3
  772. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +10 -5
  773. package/lib/mol-model-props/integrative/cross-link-restraint/representation.js +10 -1
  774. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  775. package/lib/mol-plugin/context.d.ts +2 -1
  776. package/lib/mol-plugin/context.js +4 -3
  777. package/lib/mol-plugin/spec.js +1 -1
  778. package/lib/mol-plugin/version.js +2 -2
  779. package/lib/mol-plugin-state/actions/file.d.ts +1 -1
  780. package/lib/mol-plugin-state/actions/file.js +88 -55
  781. package/lib/mol-plugin-state/actions/structure.d.ts +11 -2
  782. package/lib/mol-plugin-state/actions/structure.js +174 -4
  783. package/lib/mol-plugin-state/actions/volume.js +3 -2
  784. package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
  785. package/lib/mol-plugin-state/formats/coordinates.js +67 -0
  786. package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
  787. package/lib/mol-plugin-state/formats/registry.js +13 -8
  788. package/lib/mol-plugin-state/formats/topology.d.ts +73 -0
  789. package/lib/mol-plugin-state/formats/topology.js +84 -0
  790. package/lib/mol-plugin-state/helpers/root-structure.js +1 -1
  791. package/lib/mol-plugin-state/helpers/structure-component.js +2 -1
  792. package/lib/mol-plugin-state/manager/snapshots.js +4 -4
  793. package/lib/mol-plugin-state/objects.d.ts +47 -1
  794. package/lib/mol-plugin-state/objects.js +17 -1
  795. package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
  796. package/lib/mol-plugin-state/transforms/data.js +61 -9
  797. package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
  798. package/lib/mol-plugin-state/transforms/model.js +112 -3
  799. package/lib/mol-plugin-ui/base.js +1 -1
  800. package/lib/mol-plugin-ui/controls/action-menu.js +7 -7
  801. package/lib/mol-plugin-ui/controls/color.js +3 -3
  802. package/lib/mol-plugin-ui/controls/common.js +10 -10
  803. package/lib/mol-plugin-ui/controls/icons.js +70 -70
  804. package/lib/mol-plugin-ui/controls/legend.js +3 -3
  805. package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -1
  806. package/lib/mol-plugin-ui/controls/parameters.js +51 -51
  807. package/lib/mol-plugin-ui/controls/screenshot.js +2 -2
  808. package/lib/mol-plugin-ui/controls/slider.js +5 -5
  809. package/lib/mol-plugin-ui/controls.js +7 -7
  810. package/lib/mol-plugin-ui/custom/volume.js +4 -4
  811. package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
  812. package/lib/mol-plugin-ui/left-panel.js +33 -12
  813. package/lib/mol-plugin-ui/plugin.js +10 -10
  814. package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
  815. package/lib/mol-plugin-ui/sequence.js +5 -5
  816. package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
  817. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  818. package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
  819. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  820. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  821. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  822. package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
  823. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  824. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  825. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  826. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  827. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  828. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +128 -128
  829. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  830. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  831. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  832. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  833. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  834. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  835. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  836. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  837. package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
  838. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  839. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  840. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  841. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  842. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  843. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  844. package/lib/mol-plugin-ui/state/actions.js +1 -1
  845. package/lib/mol-plugin-ui/state/animation.js +1 -1
  846. package/lib/mol-plugin-ui/state/common.js +7 -7
  847. package/lib/mol-plugin-ui/state/snapshots.js +9 -9
  848. package/lib/mol-plugin-ui/state/tree.js +14 -14
  849. package/lib/mol-plugin-ui/state/update-transform.js +1 -1
  850. package/lib/mol-plugin-ui/structure/components.js +10 -10
  851. package/lib/mol-plugin-ui/structure/focus.js +1 -1
  852. package/lib/mol-plugin-ui/structure/generic.js +4 -4
  853. package/lib/mol-plugin-ui/structure/measurements.js +8 -8
  854. package/lib/mol-plugin-ui/structure/quick-styles.js +2 -2
  855. package/lib/mol-plugin-ui/structure/selection.js +7 -7
  856. package/lib/mol-plugin-ui/structure/source.js +4 -4
  857. package/lib/mol-plugin-ui/structure/superposition.js +8 -8
  858. package/lib/mol-plugin-ui/structure/volume.js +4 -4
  859. package/lib/mol-plugin-ui/task.js +5 -5
  860. package/lib/mol-plugin-ui/toast.js +4 -4
  861. package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
  862. package/lib/mol-plugin-ui/viewport/help.js +8 -8
  863. package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
  864. package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
  865. package/lib/mol-plugin-ui/viewport.js +4 -4
  866. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +1 -1
  867. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +20 -10
  868. package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -1
  869. package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -5
  870. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +16 -6
  871. package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +8 -3
  872. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js +10 -1
  873. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +10 -1
  874. package/lib/mol-repr/structure/visual/element-point.d.ts +1 -1
  875. package/lib/mol-repr/structure/visual/element-point.js +22 -3
  876. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  877. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +1 -1
  878. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
  879. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  880. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  881. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
  882. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  883. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
  884. package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
  885. package/lib/mol-repr/structure/visual/util/common.js +1 -24
  886. package/lib/mol-repr/structure/visual/util/element.js +36 -2
  887. package/lib/mol-repr/structure/visual/util/link.d.ts +13 -3
  888. package/lib/mol-repr/structure/visual/util/link.js +55 -6
  889. package/lib/mol-script/language/builder.d.ts +1 -0
  890. package/lib/mol-script/language/parser.js +7 -4
  891. package/lib/mol-task/util/scheduler.d.ts +2 -2
  892. package/lib/mol-task/util/scheduler.js +7 -7
  893. package/lib/mol-theme/color/hydrophobicity.js +2 -2
  894. package/lib/mol-util/data-source.js +2 -1
  895. package/lib/mol-util/file-info.d.ts +1 -3
  896. package/lib/mol-util/file-info.js +2 -10
  897. package/lib/mol-util/index.d.ts +1 -0
  898. package/lib/mol-util/index.js +5 -0
  899. package/lib/mol-util/zip/deflate.js +2 -1
  900. package/lib/mol-util/zip/zip.d.ts +7 -1
  901. package/lib/mol-util/zip/zip.js +5 -1
  902. package/lib/servers/model/config.d.ts +2 -2
  903. package/package.json +160 -160
  904. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  905. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -9,12 +9,12 @@ var jsx_runtime_1 = require("react/jsx-runtime");
9
9
  * @author David Sehnal <david.sehnal@gmail.com>
10
10
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
11
11
  */
12
- var React = (0, tslib_1.__importStar)(require("react"));
12
+ var React = tslib_1.__importStar(require("react"));
13
13
  var common_1 = require("./controls/common");
14
14
  var icons_1 = require("./controls/icons");
15
15
  exports.PluginReactContext = React.createContext(void 0);
16
16
  var PluginUIComponent = /** @class */ (function (_super) {
17
- (0, tslib_1.__extends)(PluginUIComponent, _super);
17
+ tslib_1.__extends(PluginUIComponent, _super);
18
18
  function PluginUIComponent(props, context) {
19
19
  var _this = _super.call(this, props) || this;
20
20
  _this.subs = void 0;
@@ -42,7 +42,7 @@ var PluginUIComponent = /** @class */ (function (_super) {
42
42
  }(React.Component));
43
43
  exports.PluginUIComponent = PluginUIComponent;
44
44
  var PurePluginUIComponent = /** @class */ (function (_super) {
45
- (0, tslib_1.__extends)(PurePluginUIComponent, _super);
45
+ tslib_1.__extends(PurePluginUIComponent, _super);
46
46
  function PurePluginUIComponent(props, context) {
47
47
  var _this = _super.call(this, props, context) || this;
48
48
  _this.subs = void 0;
@@ -70,7 +70,7 @@ var PurePluginUIComponent = /** @class */ (function (_super) {
70
70
  }(React.PureComponent));
71
71
  exports.PurePluginUIComponent = PurePluginUIComponent;
72
72
  var CollapsableControls = /** @class */ (function (_super) {
73
- (0, tslib_1.__extends)(CollapsableControls, _super);
73
+ tslib_1.__extends(CollapsableControls, _super);
74
74
  function CollapsableControls(props, context) {
75
75
  var _this = _super.call(this, props, context) || this;
76
76
  _this.toggleCollapsed = function () {
@@ -96,7 +96,7 @@ var CollapsableControls = /** @class */ (function (_super) {
96
96
  var wrapClass = this.state.isCollapsed
97
97
  ? 'msp-transform-wrapper msp-transform-wrapper-collapsed'
98
98
  : 'msp-transform-wrapper';
99
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: wrapClass }, { children: [(0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-transform-header' }, { children: (0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ icon: this.state.brand ? void 0 : this.state.isCollapsed ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg, noOverflow: true, onClick: this.toggleCollapsed, className: this.state.brand ? "msp-transform-header-brand msp-transform-header-brand-".concat(this.state.brand.accent) : void 0, title: "Click to ".concat(this.state.isCollapsed ? 'expand' : 'collapse') }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: (_a = this.state.brand) === null || _a === void 0 ? void 0 : _a.svg, inline: true }, void 0), this.state.header, (0, jsx_runtime_1.jsx)("small", (0, tslib_1.__assign)({ style: { margin: '0 6px' } }, { children: this.state.isCollapsed ? '' : this.state.description }), void 0)] }), void 0) }), void 0), !this.state.isCollapsed && this.renderControls()] }), void 0);
99
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: wrapClass }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-transform-header' }, { children: (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ icon: this.state.brand ? void 0 : this.state.isCollapsed ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg, noOverflow: true, onClick: this.toggleCollapsed, className: this.state.brand ? "msp-transform-header-brand msp-transform-header-brand-".concat(this.state.brand.accent) : void 0, title: "Click to ".concat(this.state.isCollapsed ? 'expand' : 'collapse') }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: (_a = this.state.brand) === null || _a === void 0 ? void 0 : _a.svg, inline: true }), this.state.header, (0, jsx_runtime_1.jsx)("small", tslib_1.__assign({ style: { margin: '0 6px' } }, { children: this.state.isCollapsed ? '' : this.state.description }))] })) })), !this.state.isCollapsed && this.renderControls()] }));
100
100
  };
101
101
  return CollapsableControls;
102
102
  }(PluginUIComponent));
@@ -9,7 +9,7 @@ exports.PluginUIContext = void 0;
9
9
  var tslib_1 = require("tslib");
10
10
  var context_1 = require("../mol-plugin/context");
11
11
  var PluginUIContext = /** @class */ (function (_super) {
12
- (0, tslib_1.__extends)(PluginUIContext, _super);
12
+ tslib_1.__extends(PluginUIContext, _super);
13
13
  function PluginUIContext(spec) {
14
14
  var _this = _super.call(this, spec) || this;
15
15
  _this.spec = spec;
@@ -9,11 +9,11 @@ var jsx_runtime_1 = require("react/jsx-runtime");
9
9
  * @author David Sehnal <david.sehnal@gmail.com>
10
10
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
11
11
  */
12
- var React = (0, tslib_1.__importStar)(require("react"));
12
+ var React = tslib_1.__importStar(require("react"));
13
13
  var common_1 = require("./common");
14
14
  var icons_1 = require("./icons");
15
15
  var ActionMenu = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(ActionMenu, _super);
16
+ tslib_1.__extends(ActionMenu, _super);
17
17
  function ActionMenu() {
18
18
  var _this = _super !== null && _super.apply(this, arguments) || this;
19
19
  _this.hide = function () { return _this.props.onSelect(void 0); };
@@ -21,19 +21,19 @@ var ActionMenu = /** @class */ (function (_super) {
21
21
  }
22
22
  ActionMenu.prototype.render = function () {
23
23
  var cmd = this.props;
24
- var section = (0, jsx_runtime_1.jsx)(Section, { items: cmd.items, onSelect: cmd.onSelect, current: cmd.current, multiselect: this.props.multiselect, noOffset: this.props.noOffset, noAccent: this.props.noAccent }, void 0);
25
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: "msp-action-menu-options".concat(cmd.header ? '' : ' msp-action-menu-options-no-header') }, { children: [cmd.header && (0, jsx_runtime_1.jsx)(common_1.ControlGroup, (0, tslib_1.__assign)({ header: cmd.header, title: cmd.title, initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.hide, topRightIcon: icons_1.CloseSvg }, { children: section }), void 0), !cmd.header && section] }), void 0);
24
+ var section = (0, jsx_runtime_1.jsx)(Section, { items: cmd.items, onSelect: cmd.onSelect, current: cmd.current, multiselect: this.props.multiselect, noOffset: this.props.noOffset, noAccent: this.props.noAccent });
25
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: "msp-action-menu-options".concat(cmd.header ? '' : ' msp-action-menu-options-no-header') }, { children: [cmd.header && (0, jsx_runtime_1.jsx)(common_1.ControlGroup, tslib_1.__assign({ header: cmd.header, title: cmd.title, initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.hide, topRightIcon: icons_1.CloseSvg }, { children: section })), !cmd.header && section] }));
26
26
  };
27
27
  return ActionMenu;
28
28
  }(React.PureComponent));
29
29
  exports.ActionMenu = ActionMenu;
30
30
  (function (ActionMenu) {
31
31
  function Header(label, options) {
32
- return options ? (0, tslib_1.__assign)({ kind: 'header', label: label }, options) : { kind: 'header', label: label };
32
+ return options ? tslib_1.__assign({ kind: 'header', label: label }, options) : { kind: 'header', label: label };
33
33
  }
34
34
  ActionMenu.Header = Header;
35
35
  function Item(label, value, options) {
36
- return (0, tslib_1.__assign)({ kind: 'item', label: label, value: value }, options);
36
+ return tslib_1.__assign({ kind: 'item', label: label, value: value }, options);
37
37
  }
38
38
  ActionMenu.Item = Item;
39
39
  function createItems(xs, params) {
@@ -71,7 +71,7 @@ exports.ActionMenu = ActionMenu;
71
71
  ActionMenu.createItems = createItems;
72
72
  var _selectOptions = { value: function (o) { return o[0]; }, label: function (o) { return o[1]; }, category: function (o) { return o[2]; } };
73
73
  function createItemsFromSelectOptions(options, params) {
74
- return createItems(options, params ? (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _selectOptions), params) : _selectOptions);
74
+ return createItems(options, params ? tslib_1.__assign(tslib_1.__assign({}, _selectOptions), params) : _selectOptions);
75
75
  }
76
76
  ActionMenu.createItemsFromSelectOptions = createItemsFromSelectOptions;
77
77
  function hasSelectedItem(items) {
@@ -143,7 +143,7 @@ exports.ActionMenu = ActionMenu;
143
143
  })(ActionMenu = exports.ActionMenu || (exports.ActionMenu = {}));
144
144
  exports.ActionMenu = ActionMenu;
145
145
  var Section = /** @class */ (function (_super) {
146
- (0, tslib_1.__extends)(Section, _super);
146
+ tslib_1.__extends(Section, _super);
147
147
  function Section() {
148
148
  var _this = _super !== null && _super.apply(this, arguments) || this;
149
149
  _this.state = Section.createState(_this.props);
@@ -186,7 +186,7 @@ var Section = /** @class */ (function (_super) {
186
186
  Object.defineProperty(Section.prototype, "multiselectHeader", {
187
187
  get: function () {
188
188
  var _a = this.state, header = _a.header, hasCurrent = _a.hasCurrent;
189
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-flex-row msp-control-group-header' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg, flex: true, noOverflow: true, onClick: this.toggleExpanded, title: "Click to ".concat(this.state.isExpanded ? 'collapse' : 'expand', ".").concat((header === null || header === void 0 ? void 0 : header.description) ? " ".concat(header === null || header === void 0 ? void 0 : header.description) : '') }, { children: hasCurrent ? (0, jsx_runtime_1.jsx)("b", { children: header === null || header === void 0 ? void 0 : header.label }, void 0) : header === null || header === void 0 ? void 0 : header.label }), void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: icons_1.CheckSvg, flex: true, onClick: this.selectAll, style: { flex: '0 0 50px', textAlign: 'right' } }, { children: "All" }), void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ icon: icons_1.CloseSvg, flex: true, onClick: this.selectNone, style: { flex: '0 0 50px', textAlign: 'right' } }, { children: "None" }), void 0)] }), void 0);
189
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row msp-control-group-header' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg, flex: true, noOverflow: true, onClick: this.toggleExpanded, title: "Click to ".concat(this.state.isExpanded ? 'collapse' : 'expand', ".").concat((header === null || header === void 0 ? void 0 : header.description) ? " ".concat(header === null || header === void 0 ? void 0 : header.description) : '') }, { children: hasCurrent ? (0, jsx_runtime_1.jsx)("b", { children: header === null || header === void 0 ? void 0 : header.label }) : header === null || header === void 0 ? void 0 : header.label })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.CheckSvg, flex: true, onClick: this.selectAll, style: { flex: '0 0 50px', textAlign: 'right' } }, { children: "All" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.CloseSvg, flex: true, onClick: this.selectNone, style: { flex: '0 0 50px', textAlign: 'right' } }, { children: "None" }))] }));
190
190
  },
191
191
  enumerable: false,
192
192
  configurable: true
@@ -194,7 +194,7 @@ var Section = /** @class */ (function (_super) {
194
194
  Object.defineProperty(Section.prototype, "basicHeader", {
195
195
  get: function () {
196
196
  var _a = this.state, header = _a.header, hasCurrent = _a.hasCurrent;
197
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-group-header', style: { marginTop: '1px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ noOverflow: true, icon: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg, onClick: this.toggleExpanded, title: "Click to ".concat(this.state.isExpanded ? 'collapse' : 'expand', ". ").concat((header === null || header === void 0 ? void 0 : header.description) ? header === null || header === void 0 ? void 0 : header.description : '') }, { children: hasCurrent ? (0, jsx_runtime_1.jsx)("b", { children: header === null || header === void 0 ? void 0 : header.label }, void 0) : header === null || header === void 0 ? void 0 : header.label }), void 0) }), void 0);
197
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-group-header', style: { marginTop: '1px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ noOverflow: true, icon: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg, onClick: this.toggleExpanded, title: "Click to ".concat(this.state.isExpanded ? 'collapse' : 'expand', ". ").concat((header === null || header === void 0 ? void 0 : header.description) ? header === null || header === void 0 ? void 0 : header.description : '') }, { children: hasCurrent ? (0, jsx_runtime_1.jsx)("b", { children: header === null || header === void 0 ? void 0 : header.label }) : header === null || header === void 0 ? void 0 : header.label })) }));
198
198
  },
199
199
  enumerable: false,
200
200
  configurable: true
@@ -205,15 +205,15 @@ var Section = /** @class */ (function (_super) {
205
205
  if (isHeader(items))
206
206
  return null;
207
207
  if (isItem(items))
208
- return (0, jsx_runtime_1.jsx)(Action, { item: items, onSelect: onSelect, current: current, multiselect: this.props.multiselect }, void 0);
208
+ return (0, jsx_runtime_1.jsx)(Action, { item: items, onSelect: onSelect, current: current, multiselect: this.props.multiselect });
209
209
  var header = this.state.header;
210
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [header && (this.props.multiselect && this.state.isExpanded ? this.multiselectHeader : this.basicHeader), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: this.props.noOffset ? void 0 : this.props.noAccent ? 'msp-control-offset' : 'msp-accent-offset' }, { children: (!header || this.state.isExpanded) && items.map(function (x, i) {
210
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [header && (this.props.multiselect && this.state.isExpanded ? this.multiselectHeader : this.basicHeader), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: this.props.noOffset ? void 0 : this.props.noAccent ? 'msp-control-offset' : 'msp-accent-offset' }, { children: (!header || this.state.isExpanded) && items.map(function (x, i) {
211
211
  if (isHeader(x))
212
212
  return null;
213
213
  if (isItem(x))
214
214
  return (0, jsx_runtime_1.jsx)(Action, { item: x, onSelect: onSelect, current: current, multiselect: _this.props.multiselect }, i);
215
215
  return (0, jsx_runtime_1.jsx)(Section, { items: x, onSelect: onSelect, current: current, multiselect: _this.props.multiselect, noAccent: true }, i);
216
- }) }), void 0)] }, void 0);
216
+ }) }))] });
217
217
  };
218
218
  return Section;
219
219
  }(React.PureComponent));
@@ -221,7 +221,7 @@ var Action = function (_a) {
221
221
  var item = _a.item, onSelect = _a.onSelect, current = _a.current, multiselect = _a.multiselect;
222
222
  var isCurrent = current === item;
223
223
  var style = item.addOn ? { position: 'relative' } : void 0;
224
- return (0, jsx_runtime_1.jsxs)(common_1.Button, (0, tslib_1.__assign)({ icon: item.icon, noOverflow: true, className: 'msp-action-menu-button', onClick: function (e) { return onSelect(multiselect ? [item] : item, e); }, disabled: item.disabled, style: style, title: item.description }, { children: [isCurrent || item.selected ? (0, jsx_runtime_1.jsx)("b", { children: item.label }, void 0) : item.label, item.addOn] }), void 0);
224
+ return (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ icon: item.icon, noOverflow: true, className: 'msp-action-menu-button', onClick: function (e) { return onSelect(multiselect ? [item] : item, e); }, disabled: item.disabled, style: style, title: item.description }, { children: [isCurrent || item.selected ? (0, jsx_runtime_1.jsx)("b", { children: item.label }) : item.label, item.addOn] }));
225
225
  };
226
226
  function isItems(x) {
227
227
  return !!x && Array.isArray(x);
@@ -11,11 +11,11 @@ var jsx_runtime_1 = require("react/jsx-runtime");
11
11
  */
12
12
  var color_1 = require("../../mol-util/color");
13
13
  var string_1 = require("../../mol-util/string");
14
- var React = (0, tslib_1.__importStar)(require("react"));
14
+ var React = tslib_1.__importStar(require("react"));
15
15
  var common_1 = require("./common");
16
16
  var swatches_1 = require("../../mol-util/color/swatches");
17
17
  var CombinedColorControl = /** @class */ (function (_super) {
18
- (0, tslib_1.__extends)(CombinedColorControl, _super);
18
+ tslib_1.__extends(CombinedColorControl, _super);
19
19
  function CombinedColorControl() {
20
20
  var _this = _super !== null && _super.apply(this, arguments) || this;
21
21
  _this.state = {
@@ -65,12 +65,12 @@ var CombinedColorControl = /** @class */ (function (_super) {
65
65
  };
66
66
  CombinedColorControl.prototype.swatch = function () {
67
67
  var _this = this;
68
- return (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-combined-color-swatch' }, { children: swatches_1.DefaultColorSwatch.map(function (c) { return (0, jsx_runtime_1.jsx)(common_1.Button, { inline: true, "data-color": c[1], onClick: _this.onClickSwatch, style: { background: color_1.Color.toStyle(c[1]) } }, c[1]); }) }), void 0);
68
+ return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-combined-color-swatch' }, { children: swatches_1.DefaultColorSwatch.map(function (c) { return (0, jsx_runtime_1.jsx)(common_1.Button, { inline: true, "data-color": c[1], onClick: _this.onClickSwatch, style: { background: color_1.Color.toStyle(c[1]) } }, c[1]); }) }));
69
69
  };
70
70
  CombinedColorControl.prototype.render = function () {
71
71
  var label = this.props.param.label || (0, string_1.camelCaseToWords)(this.props.name);
72
72
  var _a = color_1.Color.toRgb(this.props.value), r = _a[0], g = _a[1], b = _a[2];
73
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.ControlRow, { title: this.props.param.description, label: label, control: (0, jsx_runtime_1.jsx)(common_1.Button, { onClick: this.toggleExpanded, inline: true, className: 'msp-combined-color-button', style: { background: color_1.Color.toStyle(this.props.value) } }, void 0) }, void 0), this.state.isExpanded && (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset' }, { children: [this.swatch(), (0, jsx_runtime_1.jsx)(common_1.ControlRow, { label: 'RGB', className: 'msp-control-label-short', control: (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ style: { display: 'flex', textAlignLast: 'center', left: '80px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onR, numeric: true, value: r, delayMs: 250, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onG, numeric: true, value: g, delayMs: 250, style: { order: 2, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }, void 0), (0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onB, numeric: true, value: b, delayMs: 250, style: { order: 3, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }, void 0)] }), void 0) }, void 0), (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.onLighten, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control' }, { children: "Lighten" }), void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: this.onDarken, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control' }, { children: "Darken" }), void 0)] }), void 0)] }), void 0)] }, void 0);
73
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.ControlRow, { title: this.props.param.description, label: label, control: (0, jsx_runtime_1.jsx)(common_1.Button, { onClick: this.toggleExpanded, inline: true, className: 'msp-combined-color-button', style: { background: color_1.Color.toStyle(this.props.value) } }) }), this.state.isExpanded && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: [this.swatch(), (0, jsx_runtime_1.jsx)(common_1.ControlRow, { label: 'RGB', className: 'msp-control-label-short', control: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { display: 'flex', textAlignLast: 'center', left: '80px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onR, numeric: true, value: r, delayMs: 250, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }), (0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onG, numeric: true, value: g, delayMs: 250, style: { order: 2, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }), (0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onB, numeric: true, value: b, delayMs: 250, style: { order: 3, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true })] })) }), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.onLighten, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control' }, { children: "Lighten" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.onDarken, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control' }, { children: "Darken" }))] }))] }))] });
74
74
  };
75
75
  return CombinedColorControl;
76
76
  }(React.PureComponent));
@@ -80,8 +80,8 @@ function ColorOptions() {
80
80
  if (_colors)
81
81
  return _colors;
82
82
  _colors = (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: swatches_1.DefaultColorSwatch.map(function (v) {
83
- return (0, jsx_runtime_1.jsx)("option", (0, tslib_1.__assign)({ value: v[1], style: { background: "".concat(color_1.Color.toStyle(v[1])) } }, { children: (0, string_1.stringToWords)(v[0]) }), v[1]);
84
- }) }, void 0);
83
+ return (0, jsx_runtime_1.jsx)("option", tslib_1.__assign({ value: v[1], style: { background: "".concat(color_1.Color.toStyle(v[1])) } }, { children: (0, string_1.stringToWords)(v[0]) }), v[1]);
84
+ }) });
85
85
  return _colors;
86
86
  }
87
87
  exports.ColorOptions = ColorOptions;
@@ -94,6 +94,6 @@ var DefaultColorSwatchMap = (function () {
94
94
  return map;
95
95
  })();
96
96
  function ColorValueOption(color) {
97
- return !DefaultColorSwatchMap.has(color) ? (0, jsx_runtime_1.jsx)("option", (0, tslib_1.__assign)({ value: color, style: { background: "".concat(color_1.Color.toStyle(color)) } }, { children: color_1.Color.toRgbString(color) }), color_1.Color.toHexString(color)) : null;
97
+ return !DefaultColorSwatchMap.has(color) ? (0, jsx_runtime_1.jsx)("option", tslib_1.__assign({ value: color, style: { background: "".concat(color_1.Color.toStyle(color)) } }, { children: color_1.Color.toRgbString(color) }), color_1.Color.toHexString(color)) : null;
98
98
  }
99
99
  exports.ColorValueOption = ColorValueOption;
@@ -8,11 +8,11 @@ var jsx_runtime_1 = require("react/jsx-runtime");
8
8
  *
9
9
  * @author David Sehnal <david.sehnal@gmail.com>
10
10
  */
11
- var React = (0, tslib_1.__importStar)(require("react"));
11
+ var React = tslib_1.__importStar(require("react"));
12
12
  var color_1 = require("../../mol-util/color");
13
13
  var icons_1 = require("./icons");
14
14
  var ControlGroup = /** @class */ (function (_super) {
15
- (0, tslib_1.__extends)(ControlGroup, _super);
15
+ tslib_1.__extends(ControlGroup, _super);
16
16
  function ControlGroup() {
17
17
  var _this = _super !== null && _super.apply(this, arguments) || this;
18
18
  _this.state = { isExpanded: !!_this.props.initialExpanded };
@@ -31,14 +31,14 @@ var ControlGroup = /** @class */ (function (_super) {
31
31
  if (this.props.childrenClassName)
32
32
  groupClassName += ' ' + this.props.childrenClassName;
33
33
  // TODO: customize header style (bg color, togle button etc)
34
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: 'msp-control-group-wrapper', style: { position: 'relative', marginTop: this.props.noTopMargin ? 0 : void 0 } }, { children: [(0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-group-header', style: { marginLeft: this.props.headerLeftMargin }, title: this.props.title }, { children: (0, jsx_runtime_1.jsxs)(Button, (0, tslib_1.__assign)({ onClick: this.headerClicked }, { children: [!this.props.hideExpander && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg }, void 0), this.props.topRightIcon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.props.topRightIcon, style: { position: 'absolute', right: '2px', top: 0 } }, void 0), (0, jsx_runtime_1.jsx)("b", { children: this.props.header }, void 0)] }), void 0) }), void 0), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: groupClassName, style: { display: this.state.isExpanded ? 'block' : 'none', maxHeight: this.props.maxHeight, overflow: 'hidden', overflowY: 'auto' } }, { children: this.props.children }), void 0)] }), void 0);
34
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-control-group-wrapper', style: { position: 'relative', marginTop: this.props.noTopMargin ? 0 : void 0 } }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-group-header', style: { marginLeft: this.props.headerLeftMargin }, title: this.props.title }, { children: (0, jsx_runtime_1.jsxs)(Button, tslib_1.__assign({ onClick: this.headerClicked }, { children: [!this.props.hideExpander && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg }), this.props.topRightIcon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.props.topRightIcon, style: { position: 'absolute', right: '2px', top: 0 } }), (0, jsx_runtime_1.jsx)("b", { children: this.props.header })] })) })), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: groupClassName, style: { display: this.state.isExpanded ? 'block' : 'none', maxHeight: this.props.maxHeight, overflow: 'hidden', overflowY: 'auto' } }, { children: this.props.children }))] }));
35
35
  };
36
36
  return ControlGroup;
37
37
  }(React.Component));
38
38
  exports.ControlGroup = ControlGroup;
39
39
  function _id(x) { return x; }
40
40
  var TextInput = /** @class */ (function (_super) {
41
- (0, tslib_1.__extends)(TextInput, _super);
41
+ tslib_1.__extends(TextInput, _super);
42
42
  function TextInput() {
43
43
  var _this = _super !== null && _super.apply(this, arguments) || this;
44
44
  _this.input = React.createRef();
@@ -126,13 +126,13 @@ var TextInput = /** @class */ (function (_super) {
126
126
  return { originalValue: value, value: value };
127
127
  };
128
128
  TextInput.prototype.render = function () {
129
- return (0, jsx_runtime_1.jsx)("input", { type: 'text', className: this.props.className, style: this.props.style, ref: this.input, onBlur: this.onBlur, value: this.state.value, placeholder: this.props.placeholder, onChange: this.onChange, onKeyPress: this.props.onEnter || this.props.blurOnEnter || this.props.blurOnEscape ? this.onKeyPress : void 0, onKeyDown: this.props.blurOnEscape ? this.onKeyUp : void 0, disabled: !!this.props.isDisabled }, void 0);
129
+ return (0, jsx_runtime_1.jsx)("input", { type: 'text', className: this.props.className, style: this.props.style, ref: this.input, onBlur: this.onBlur, value: this.state.value, placeholder: this.props.placeholder, onChange: this.onChange, onKeyPress: this.props.onEnter || this.props.blurOnEnter || this.props.blurOnEscape ? this.onKeyPress : void 0, onKeyDown: this.props.blurOnEscape ? this.onKeyUp : void 0, disabled: !!this.props.isDisabled });
130
130
  };
131
131
  return TextInput;
132
132
  }(React.PureComponent));
133
133
  exports.TextInput = TextInput;
134
134
  var ExpandableControlRow = /** @class */ (function (_super) {
135
- (0, tslib_1.__extends)(ExpandableControlRow, _super);
135
+ tslib_1.__extends(ExpandableControlRow, _super);
136
136
  function ExpandableControlRow() {
137
137
  var _this = _super !== null && _super.apply(this, arguments) || this;
138
138
  _this.state = { isExpanded: false };
@@ -142,13 +142,13 @@ var ExpandableControlRow = /** @class */ (function (_super) {
142
142
  ExpandableControlRow.prototype.render = function () {
143
143
  var _a = this.props, label = _a.label, pivot = _a.pivot, controls = _a.controls;
144
144
  // TODO: fix the inline CSS
145
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ControlRow, (0, tslib_1.__assign)({ label: (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [label, (0, jsx_runtime_1.jsx)("button", (0, tslib_1.__assign)({ className: 'msp-btn-link msp-btn-icon msp-control-group-expander', onClick: this.toggleExpanded, title: "".concat(this.state.isExpanded ? 'Less' : 'More', " options"), style: { background: 'transparent', textAlign: 'left', padding: '0' } }, { children: (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.RemoveSvg : icons_1.AddSvg, style: { display: 'inline-block' } }, void 0) }), void 0)] }, void 0), control: pivot }, { children: this.props.colorStripe && (0, jsx_runtime_1.jsx)("div", { className: 'msp-expandable-group-color-stripe', style: { backgroundColor: color_1.Color.toStyle(this.props.colorStripe) } }, void 0) }), void 0), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-offset' }, { children: controls }), void 0)] }, void 0);
145
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ControlRow, tslib_1.__assign({ label: (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [label, (0, jsx_runtime_1.jsx)("button", tslib_1.__assign({ className: 'msp-btn-link msp-btn-icon msp-control-group-expander', onClick: this.toggleExpanded, title: "".concat(this.state.isExpanded ? 'Less' : 'More', " options"), style: { background: 'transparent', textAlign: 'left', padding: '0' } }, { children: (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.RemoveSvg : icons_1.AddSvg, style: { display: 'inline-block' } }) }))] }), control: pivot }, { children: this.props.colorStripe && (0, jsx_runtime_1.jsx)("div", { className: 'msp-expandable-group-color-stripe', style: { backgroundColor: color_1.Color.toStyle(this.props.colorStripe) } }) })), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: controls }))] });
146
146
  };
147
147
  return ExpandableControlRow;
148
148
  }(React.Component));
149
149
  exports.ExpandableControlRow = ExpandableControlRow;
150
150
  function SectionHeader(props) {
151
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: "msp-section-header".concat(props.accent ? ' msp-transform-header-brand-' + props.accent : '') }, { children: [props.icon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.icon }, void 0), props.title, " ", (0, jsx_runtime_1.jsx)("small", { children: props.desc }, void 0)] }), void 0);
151
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: "msp-section-header".concat(props.accent ? ' msp-transform-header-brand-' + props.accent : '') }, { children: [props.icon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.icon }), props.title, " ", (0, jsx_runtime_1.jsx)("small", { children: props.desc })] }));
152
152
  }
153
153
  exports.SectionHeader = SectionHeader;
154
154
  function Button(props) {
@@ -180,7 +180,7 @@ function Button(props) {
180
180
  else
181
181
  style = props.style;
182
182
  }
183
- return (0, jsx_runtime_1.jsxs)("button", (0, tslib_1.__assign)({ onClick: props.onClick, title: props.title, disabled: props.disabled, style: style, className: className, "data-id": props['data-id'], "data-color": props['data-color'], onContextMenu: props.onContextMenu, onMouseEnter: props.onMouseEnter, onMouseLeave: props.onMouseLeave }, { children: [props.icon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.icon }, void 0), props.children] }), void 0);
183
+ return (0, jsx_runtime_1.jsxs)("button", tslib_1.__assign({ onClick: props.onClick, title: props.title, disabled: props.disabled, style: style, className: className, "data-id": props['data-id'], "data-color": props['data-color'], onContextMenu: props.onContextMenu, onMouseEnter: props.onMouseEnter, onMouseLeave: props.onMouseLeave }, { children: [props.icon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.icon }), props.children] }));
184
184
  }
185
185
  exports.Button = Button;
186
186
  function IconButton(props) {
@@ -206,11 +206,11 @@ function IconButton(props) {
206
206
  else
207
207
  style = props.style;
208
208
  }
209
- return (0, jsx_runtime_1.jsxs)("button", (0, tslib_1.__assign)({ className: className, onClick: props.onClick, title: props.title, disabled: props.disabled, "data-id": props['data-id'], style: style }, { children: [props.svg && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.svg }, void 0), props.extraContent] }), void 0);
209
+ return (0, jsx_runtime_1.jsxs)("button", tslib_1.__assign({ className: className, onClick: props.onClick, title: props.title, disabled: props.disabled, "data-id": props['data-id'], style: style }, { children: [props.svg && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.svg }), props.extraContent] }));
210
210
  }
211
211
  exports.IconButton = IconButton;
212
212
  var ToggleButton = /** @class */ (function (_super) {
213
- (0, tslib_1.__extends)(ToggleButton, _super);
213
+ tslib_1.__extends(ToggleButton, _super);
214
214
  function ToggleButton() {
215
215
  var _this = _super !== null && _super.apply(this, arguments) || this;
216
216
  _this.onClick = function (e) {
@@ -223,13 +223,13 @@ var ToggleButton = /** @class */ (function (_super) {
223
223
  var props = this.props;
224
224
  var label = props.label;
225
225
  var className = props.isSelected ? "".concat(props.className || '', " msp-control-current") : props.className;
226
- return (0, jsx_runtime_1.jsx)(Button, (0, tslib_1.__assign)({ icon: this.props.icon, onClick: this.onClick, title: this.props.title, inline: this.props.inline, disabled: props.disabled, style: props.style, className: className }, { children: label && this.props.isSelected ? (0, jsx_runtime_1.jsx)("b", { children: label }, void 0) : label }), void 0);
226
+ return (0, jsx_runtime_1.jsx)(Button, tslib_1.__assign({ icon: this.props.icon, onClick: this.onClick, title: this.props.title, inline: this.props.inline, disabled: props.disabled, style: props.style, className: className }, { children: label && this.props.isSelected ? (0, jsx_runtime_1.jsx)("b", { children: label }) : label }));
227
227
  };
228
228
  return ToggleButton;
229
229
  }(React.PureComponent));
230
230
  exports.ToggleButton = ToggleButton;
231
231
  var ExpandGroup = /** @class */ (function (_super) {
232
- (0, tslib_1.__extends)(ExpandGroup, _super);
232
+ tslib_1.__extends(ExpandGroup, _super);
233
233
  function ExpandGroup() {
234
234
  var _this = _super !== null && _super.apply(this, arguments) || this;
235
235
  _this.state = { isExpanded: !!_this.props.initiallyExpanded };
@@ -237,10 +237,10 @@ var ExpandGroup = /** @class */ (function (_super) {
237
237
  return _this;
238
238
  }
239
239
  ExpandGroup.prototype.render = function () {
240
- return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-group-header', style: { marginTop: this.props.marginTop !== void 0 ? this.props.marginTop : '1px', marginLeft: this.props.headerLeftMargin } }, { children: (0, jsx_runtime_1.jsxs)("button", (0, tslib_1.__assign)({ className: 'msp-btn msp-form-control msp-btn-block', onClick: this.toggleExpanded, style: this.props.headerStyle }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg }, void 0), this.props.header] }), void 0) }), void 0), this.state.isExpanded &&
240
+ return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-group-header', style: { marginTop: this.props.marginTop !== void 0 ? this.props.marginTop : '1px', marginLeft: this.props.headerLeftMargin } }, { children: (0, jsx_runtime_1.jsxs)("button", tslib_1.__assign({ className: 'msp-btn msp-form-control msp-btn-block', onClick: this.toggleExpanded, style: this.props.headerStyle }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg }), this.props.header] })) })), this.state.isExpanded &&
241
241
  (this.props.noOffset
242
242
  ? this.props.children
243
- : (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: this.props.accent ? 'msp-accent-offset' : 'msp-control-offset' }, { children: this.props.children }), void 0))] }, void 0);
243
+ : (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: this.props.accent ? 'msp-accent-offset' : 'msp-control-offset' }, { children: this.props.children })))] });
244
244
  };
245
245
  return ExpandGroup;
246
246
  }(React.PureComponent));
@@ -249,6 +249,6 @@ function ControlRow(props) {
249
249
  var className = 'msp-control-row';
250
250
  if (props.className)
251
251
  className += ' ' + props.className;
252
- return (0, jsx_runtime_1.jsxs)("div", (0, tslib_1.__assign)({ className: className }, { children: [(0, jsx_runtime_1.jsx)("span", (0, tslib_1.__assign)({ className: 'msp-control-row-label', title: props.title }, { children: props.label }), void 0), (0, jsx_runtime_1.jsx)("div", (0, tslib_1.__assign)({ className: 'msp-control-row-ctrl' }, { children: props.control }), void 0), props.children] }), void 0);
252
+ return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: className }, { children: [(0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ className: 'msp-control-row-label', title: props.title }, { children: props.label })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-row-ctrl' }, { children: props.control })), props.children] }));
253
253
  }
254
254
  exports.ControlRow = ControlRow;