molstar 3.3.1 → 3.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (777) hide show
  1. package/README.md +3 -0
  2. package/build/viewer/molstar.js +1 -1
  3. package/lib/apps/docking-viewer/viewport.js +1 -1
  4. package/lib/apps/viewer/app.d.ts +7 -6
  5. package/lib/apps/viewer/app.js +2 -0
  6. package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  7. package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
  8. package/lib/commonjs/apps/docking-viewer/index.js +12 -12
  9. package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
  10. package/lib/commonjs/apps/viewer/app.d.ts +7 -6
  11. package/lib/commonjs/apps/viewer/app.js +24 -22
  12. package/lib/commonjs/apps/viewer/index.js +1 -1
  13. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
  14. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  15. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
  16. package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
  17. package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
  18. package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
  19. package/lib/commonjs/cli/cif2bcif/index.js +8 -8
  20. package/lib/commonjs/cli/cifschema/index.js +27 -27
  21. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
  22. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  23. package/lib/commonjs/cli/state-docs/index.js +2 -2
  24. package/lib/commonjs/cli/structure-info/helpers.js +11 -11
  25. package/lib/commonjs/cli/structure-info/model.js +15 -15
  26. package/lib/commonjs/cli/structure-info/volume.js +9 -9
  27. package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
  28. package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
  29. package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
  30. package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
  31. package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
  32. package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
  33. package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
  34. package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
  35. package/lib/commonjs/examples/lighting/index.js +6 -6
  36. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
  37. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
  38. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
  39. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
  40. package/lib/commonjs/examples/task.js +15 -15
  41. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
  42. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
  43. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
  44. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
  45. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
  46. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
  47. package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
  48. package/lib/commonjs/extensions/anvil/behavior.js +14 -14
  49. package/lib/commonjs/extensions/anvil/prop.js +7 -7
  50. package/lib/commonjs/extensions/anvil/representation.js +5 -5
  51. package/lib/commonjs/extensions/cellpack/index.js +1 -1
  52. package/lib/commonjs/extensions/cellpack/model.js +26 -24
  53. package/lib/commonjs/extensions/cellpack/preset.js +6 -6
  54. package/lib/commonjs/extensions/cellpack/property.js +3 -3
  55. package/lib/commonjs/extensions/cellpack/representation.js +2 -2
  56. package/lib/commonjs/extensions/cellpack/state.js +13 -13
  57. package/lib/commonjs/extensions/cellpack/util.js +14 -14
  58. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
  59. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -5
  60. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
  61. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -1
  62. package/lib/commonjs/extensions/g3d/data.js +6 -6
  63. package/lib/commonjs/extensions/g3d/format.js +14 -14
  64. package/lib/commonjs/extensions/g3d/model.js +4 -4
  65. package/lib/commonjs/extensions/geo-export/controls.js +3 -3
  66. package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
  67. package/lib/commonjs/extensions/geo-export/index.js +1 -1
  68. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
  69. package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
  70. package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
  71. package/lib/commonjs/extensions/geo-export/ui.js +7 -7
  72. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
  73. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
  74. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
  75. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
  76. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
  77. package/lib/commonjs/extensions/model-export/export.js +4 -4
  78. package/lib/commonjs/extensions/model-export/index.js +1 -1
  79. package/lib/commonjs/extensions/model-export/ui.js +5 -5
  80. package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
  81. package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
  82. package/lib/commonjs/extensions/mp4-export/index.js +1 -1
  83. package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
  84. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
  85. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
  86. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
  87. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
  88. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
  89. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
  90. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
  91. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
  92. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
  93. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
  94. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
  95. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
  96. package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
  97. package/lib/commonjs/extensions/zenodo/index.js +35 -0
  98. package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
  99. package/lib/commonjs/extensions/zenodo/ui.js +306 -0
  100. package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
  101. package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
  102. package/lib/commonjs/mol-canvas3d/camera.js +2 -1
  103. package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
  104. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  105. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
  106. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
  107. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
  108. package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
  109. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
  110. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  111. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
  112. package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
  113. package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
  114. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
  115. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
  116. package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
  117. package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
  118. package/lib/commonjs/mol-canvas3d/util.js +2 -2
  119. package/lib/commonjs/mol-data/db/column.js +2 -2
  120. package/lib/commonjs/mol-data/db/table.js +1 -1
  121. package/lib/commonjs/mol-data/db.js +1 -1
  122. package/lib/commonjs/mol-data/generic.js +3 -3
  123. package/lib/commonjs/mol-data/index.js +4 -4
  124. package/lib/commonjs/mol-data/int/interval.js +1 -1
  125. package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
  126. package/lib/commonjs/mol-data/int/segmentation.js +1 -1
  127. package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
  128. package/lib/commonjs/mol-data/util.js +7 -7
  129. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
  130. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
  131. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
  132. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
  133. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
  134. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
  135. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
  136. package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
  137. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
  138. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
  139. package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
  140. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
  141. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -4
  142. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
  143. package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
  144. package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
  145. package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
  146. package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
  147. package/lib/commonjs/mol-geo/primitive/star.js +1 -1
  148. package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
  149. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
  150. package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
  151. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
  152. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
  153. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
  154. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  155. package/lib/commonjs/mol-gl/compute/util.js +3 -3
  156. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  157. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  158. package/lib/commonjs/mol-gl/renderable/image.js +3 -3
  159. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  160. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  161. package/lib/commonjs/mol-gl/renderable/points.js +3 -3
  162. package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
  163. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  164. package/lib/commonjs/mol-gl/renderable/text.js +3 -3
  165. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  166. package/lib/commonjs/mol-gl/renderable/util.js +1 -1
  167. package/lib/commonjs/mol-gl/shader-code.js +2 -1
  168. package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
  169. package/lib/commonjs/mol-gl/webgl/context.js +3 -3
  170. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
  171. package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
  172. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
  173. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
  174. package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
  175. package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
  176. package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
  177. package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
  178. package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
  179. package/lib/commonjs/mol-io/common/typed-array.js +2 -2
  180. package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
  181. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
  182. package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
  183. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  184. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  185. package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
  186. package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
  187. package/lib/commonjs/mol-io/reader/cif.js +1 -1
  188. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
  189. package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
  190. package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
  191. package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
  192. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
  193. package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
  194. package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
  195. package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
  196. package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
  197. package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
  198. package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
  199. package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
  200. package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
  201. package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
  202. package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
  203. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
  204. package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
  205. package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
  206. package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
  207. package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
  208. package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
  209. package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
  210. package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
  211. package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
  212. package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
  213. package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
  214. package/lib/commonjs/mol-io/writer/cif.js +1 -1
  215. package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
  216. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  217. package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
  218. package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
  219. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +4 -4
  220. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +1 -1
  221. package/lib/commonjs/mol-math/geometry/gaussian-density.js +4 -4
  222. package/lib/commonjs/mol-math/geometry/molecular-surface.js +8 -8
  223. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +1 -1
  224. package/lib/commonjs/mol-math/geometry.js +8 -8
  225. package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
  226. package/lib/commonjs/mol-math/graph.js +1 -1
  227. package/lib/commonjs/mol-math/linear-algebra.js +2 -2
  228. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
  229. package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
  230. package/lib/commonjs/mol-model/sequence.js +1 -1
  231. package/lib/commonjs/mol-model/shape.js +1 -1
  232. package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
  233. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  234. package/lib/commonjs/mol-model/structure/model/model.js +3 -3
  235. package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
  236. package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
  237. package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
  238. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
  239. package/lib/commonjs/mol-model/structure/model.js +3 -3
  240. package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
  241. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
  242. package/lib/commonjs/mol-model/structure/query.js +6 -6
  243. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
  244. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  245. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  246. package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
  247. package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
  248. package/lib/commonjs/mol-model/structure/structure/structure.js +5 -5
  249. package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
  250. package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
  251. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +3 -3
  252. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  253. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
  254. package/lib/commonjs/mol-model/structure/structure/unit.js +4 -4
  255. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
  256. package/lib/commonjs/mol-model/structure/structure.js +2 -2
  257. package/lib/commonjs/mol-model/structure/topology.js +1 -1
  258. package/lib/commonjs/mol-model/structure.js +6 -6
  259. package/lib/commonjs/mol-model/volume.js +2 -2
  260. package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
  261. package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  262. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
  263. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
  264. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  265. package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
  266. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
  267. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
  268. package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -2
  269. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -2
  270. package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
  271. package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -2
  272. package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
  273. package/lib/commonjs/mol-model-formats/structure/common/component.js +5 -1
  274. package/lib/commonjs/mol-model-formats/structure/cube.js +5 -5
  275. package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -2
  276. package/lib/commonjs/mol-model-formats/structure/gro.js +5 -3
  277. package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
  278. package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -2
  279. package/lib/commonjs/mol-model-formats/structure/mol.js +5 -5
  280. package/lib/commonjs/mol-model-formats/structure/mol2.js +6 -6
  281. package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts +9 -0
  282. package/lib/commonjs/mol-model-formats/structure/nctraj.js +60 -0
  283. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +2 -2
  284. package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
  285. package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -5
  286. package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts +16 -0
  287. package/lib/commonjs/mol-model-formats/structure/prmtop.js +147 -0
  288. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  289. package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -1
  290. package/lib/commonjs/mol-model-formats/structure/psf.js +5 -3
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  647. package/lib/mol-gl/webgl/buffer.js +2 -3
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  649. package/lib/mol-io/common/binary-cif/decoder.js +4 -3
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  654. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  655. package/lib/mol-io/reader/nctraj/parser.d.ts +18 -0
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  657. package/lib/mol-io/reader/prmtop/parser.d.ts +58 -0
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  663. package/lib/mol-io/writer/cif/encoder.js +2 -1
  664. package/lib/mol-model/sequence/sequence.js +2 -1
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  675. package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
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  680. package/lib/mol-model-formats/structure/gro.js +3 -1
  681. package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
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  687. package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
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  695. package/lib/mol-model-formats/structure/trr.d.ts +9 -0
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  759. package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
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  762. package/lib/mol-script/language/parser.js +7 -4
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  764. package/lib/mol-task/util/scheduler.js +7 -7
  765. package/lib/mol-theme/color/hydrophobicity.js +2 -2
  766. package/lib/mol-util/data-source.js +2 -1
  767. package/lib/mol-util/file-info.d.ts +1 -3
  768. package/lib/mol-util/file-info.js +2 -10
  769. package/lib/mol-util/index.d.ts +1 -0
  770. package/lib/mol-util/index.js +5 -0
  771. package/lib/mol-util/zip/deflate.js +2 -1
  772. package/lib/mol-util/zip/zip.d.ts +7 -1
  773. package/lib/mol-util/zip/zip.js +5 -1
  774. package/lib/servers/model/config.d.ts +2 -2
  775. package/package.json +16 -16
  776. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  777. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -62,9 +62,9 @@ exports.InitVolumeStreaming = mol_state_1.StateAction.build({
62
62
  }
63
63
  })(function (_a, plugin) {
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  var ref = _a.ref, state = _a.state, params = _a.params;
65
- return mol_task_1.Task.create('Volume Streaming', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
65
+ return mol_task_1.Task.create('Volume Streaming', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
66
66
  var entries, i, il, dataId, emDefaultContourLevel, emdbIds, j, jl, emdbId, contourLevel, e_1, e_2, infoTree, info, children, infoObj, behTree;
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- return (0, tslib_1.__generator)(this, function (_a) {
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+ return tslib_1.__generator(this, function (_a) {
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  switch (_a.label) {
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  case 0:
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  entries = [];
@@ -171,9 +171,9 @@ exports.BoxifyVolumeStreaming = mol_state_1.StateAction.build({
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  var box = geometry_1.Box3D.create(linear_algebra_1.Vec3.clone(params.entry.params.view.params.bottomLeft), linear_algebra_1.Vec3.clone(params.entry.params.view.params.topRight));
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  var r = params.entry.params.view.params.radius;
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  geometry_1.Box3D.expand(box, box, linear_algebra_1.Vec3.create(r, r, r));
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- var newParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { entry: {
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+ var newParams = tslib_1.__assign(tslib_1.__assign({}, params), { entry: {
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  name: params.entry.name,
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- params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.entry.params), { view: {
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+ params: tslib_1.__assign(tslib_1.__assign({}, params.entry.params), { view: {
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  name: 'box',
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  params: {
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  bottomLeft: box.min,
@@ -211,9 +211,9 @@ var CreateVolumeStreamingInfo = objects_1.PluginStateTransform.BuiltIn({
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  })({
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  apply: function (_a, plugin) {
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  var a = _a.a, params = _a.params;
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- return mol_task_1.Task.create('', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
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+ return mol_task_1.Task.create('', function (taskCtx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
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  var entries, i, il, e, dataId, emDefaultContourLevel, header, data;
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- return (0, tslib_1.__generator)(this, function (_a) {
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+ return tslib_1.__generator(this, function (_a) {
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  switch (_a.label) {
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  case 0:
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  entries = [];
@@ -270,9 +270,9 @@ var CreateVolumeStreamingBehavior = objects_1.PluginStateTransform.BuiltIn({
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  },
271
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  apply: function (_a, plugin) {
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  var a = _a.a, params = _a.params;
273
- return mol_task_1.Task.create('Volume streaming', function (_) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
273
+ return mol_task_1.Task.create('Volume streaming', function (_) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
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  var behavior;
275
- return (0, tslib_1.__generator)(this, function (_a) {
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+ return tslib_1.__generator(this, function (_a) {
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  switch (_a.label) {
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  case 0:
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  behavior = new behavior_1.VolumeStreaming.Behavior(plugin, a.data);
@@ -287,9 +287,9 @@ var CreateVolumeStreamingBehavior = objects_1.PluginStateTransform.BuiltIn({
287
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  update: function (_a) {
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  var _this = this;
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289
  var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
290
- return mol_task_1.Task.create('Update Volume Streaming', function (_) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
290
+ return mol_task_1.Task.create('Update Volume Streaming', function (_) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
291
291
  var emDefaultContourLevel, ret;
292
- return (0, tslib_1.__generator)(this, function (_a) {
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+ return tslib_1.__generator(this, function (_a) {
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  switch (_a.label) {
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  case 0:
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  if (oldParams.entry.name !== newParams.entry.name) {
@@ -322,10 +322,10 @@ var VolumeStreamingVisual = objects_1.PluginStateTransform.BuiltIn({
322
322
  })({
323
323
  apply: function (_a, plugin) {
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324
  var a = _a.a, srcParams = _a.params, spine = _a.spine;
325
- return mol_task_1.Task.create('Volume Representation', function (ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
325
+ return mol_task_1.Task.create('Volume Representation', function (ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
326
326
  var channel, params, provider, props, repr, structure, transform;
327
327
  var _a, _b;
328
- return (0, tslib_1.__generator)(this, function (_c) {
328
+ return tslib_1.__generator(this, function (_c) {
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  switch (_c.label) {
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  case 0:
331
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  channel = a.data.channels[srcParams.channel];
@@ -334,7 +334,7 @@ var VolumeStreamingVisual = objects_1.PluginStateTransform.BuiltIn({
334
334
  params = createVolumeProps(a.data, srcParams.channel);
335
335
  provider = registry_1.VolumeRepresentationRegistry.BuiltIn.isosurface;
336
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  props = params.type.params || {};
337
- repr = provider.factory((0, tslib_1.__assign)({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.volume.themes), provider.getParams);
337
+ repr = provider.factory(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.volume.themes), provider.getParams);
338
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  repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
339
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  structure = (_b = spine.getAncestorOfType(objects_1.PluginStateObject.Molecule.Structure)) === null || _b === void 0 ? void 0 : _b.data;
340
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  transform = (structure === null || structure === void 0 ? void 0 : structure.models.length) === 0 ? void 0 : global_transform_1.GlobalModelTransformInfo.get(structure === null || structure === void 0 ? void 0 : structure.models[0]);
@@ -350,9 +350,9 @@ var VolumeStreamingVisual = objects_1.PluginStateTransform.BuiltIn({
350
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  },
351
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  update: function (_a, plugin) {
352
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  var a = _a.a, b = _a.b, newParams = _a.newParams, spine = _a.spine;
353
- return mol_task_1.Task.create('Volume Representation', function (ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
353
+ return mol_task_1.Task.create('Volume Representation', function (ctx) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
354
354
  var channel, visible, params, props;
355
- return (0, tslib_1.__generator)(this, function (_a) {
355
+ return tslib_1.__generator(this, function (_a) {
356
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  switch (_a.label) {
357
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  case 0:
358
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  channel = a.data.channels[newParams.channel];
@@ -361,7 +361,7 @@ var VolumeStreamingVisual = objects_1.PluginStateTransform.BuiltIn({
361
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  return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Unchanged];
362
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  visible = b.data.repr.state.visible;
363
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  params = createVolumeProps(a.data, newParams.channel);
364
- props = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, b.data.repr.props), params.type.params);
364
+ props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), params.type.params);
365
365
  b.data.repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
366
366
  return [4 /*yield*/, b.data.repr.createOrUpdate(props, channel.data).runInContext(ctx)];
367
367
  case 1:
@@ -63,8 +63,8 @@ function getIds(method, s) {
63
63
  }
64
64
  exports.getIds = getIds;
65
65
  function getContourLevel(provider, plugin, taskCtx, emdbId) {
66
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
67
- return (0, tslib_1.__generator)(this, function (_a) {
66
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
67
+ return tslib_1.__generator(this, function (_a) {
68
68
  switch (provider) {
69
69
  case 'emdb': return [2 /*return*/, getContourLevelEmdb(plugin, taskCtx, emdbId)];
70
70
  case 'pdbe': return [2 /*return*/, getContourLevelPdbe(plugin, taskCtx, emdbId)];
@@ -75,9 +75,9 @@ function getContourLevel(provider, plugin, taskCtx, emdbId) {
75
75
  }
76
76
  exports.getContourLevel = getContourLevel;
77
77
  function getContourLevelEmdb(plugin, taskCtx, emdbId) {
78
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
78
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
79
79
  var emdbHeaderServer, header, contours, primaryContour, i, contourLevel;
80
- return (0, tslib_1.__generator)(this, function (_a) {
80
+ return tslib_1.__generator(this, function (_a) {
81
81
  switch (_a.label) {
82
82
  case 0:
83
83
  emdbHeaderServer = plugin.config.get(config_1.PluginConfig.VolumeStreaming.EmdbHeaderServer);
@@ -101,9 +101,9 @@ function getContourLevelEmdb(plugin, taskCtx, emdbId) {
101
101
  exports.getContourLevelEmdb = getContourLevelEmdb;
102
102
  function getContourLevelPdbe(plugin, taskCtx, emdbId) {
103
103
  var _a, _b, _c, _d;
104
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
104
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
105
105
  var header, contours;
106
- return (0, tslib_1.__generator)(this, function (_e) {
106
+ return tslib_1.__generator(this, function (_e) {
107
107
  switch (_e.label) {
108
108
  case 0:
109
109
  // TODO: parametrize URL in plugin settings?
@@ -124,9 +124,9 @@ function getContourLevelPdbe(plugin, taskCtx, emdbId) {
124
124
  exports.getContourLevelPdbe = getContourLevelPdbe;
125
125
  function getContourLevelPdbeLegacy(plugin, taskCtx, emdbId) {
126
126
  var _a, _b, _c;
127
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
127
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
128
128
  var header, emdbEntry, contourLevel;
129
- return (0, tslib_1.__generator)(this, function (_d) {
129
+ return tslib_1.__generator(this, function (_d) {
130
130
  switch (_d.label) {
131
131
  case 0:
132
132
  // TODO: parametrize URL in plugin settings?
@@ -146,9 +146,9 @@ function getContourLevelPdbeLegacy(plugin, taskCtx, emdbId) {
146
146
  }
147
147
  function getEmdbIds(plugin, taskCtx, pdbId) {
148
148
  var _a;
149
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
149
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
150
150
  var summary, summaryEntry, emdbIds, emdb;
151
- return (0, tslib_1.__generator)(this, function (_b) {
151
+ return tslib_1.__generator(this, function (_b) {
152
152
  switch (_b.label) {
153
153
  case 0: return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/".concat(pdbId), type: 'json' }).runInContext(taskCtx)];
154
154
  case 1:
@@ -204,9 +204,9 @@ function Snapshots(ctx) {
204
204
  });
205
205
  commands_1.PluginCommands.State.Snapshots.Fetch.subscribe(ctx, function (_a) {
206
206
  var url = _a.url;
207
- return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
207
+ return tslib_1.__awaiter(_this, void 0, void 0, function () {
208
208
  var json;
209
- return (0, tslib_1.__generator)(this, function (_b) {
209
+ return tslib_1.__generator(this, function (_b) {
210
210
  switch (_b.label) {
211
211
  case 0: return [4 /*yield*/, ctx.runTask(ctx.fetch({ url: url, type: 'json' }))];
212
212
  case 1:
@@ -221,9 +221,9 @@ function Snapshots(ctx) {
221
221
  });
222
222
  commands_1.PluginCommands.State.Snapshots.DownloadToFile.subscribe(ctx, function (_a) {
223
223
  var name = _a.name, type = _a.type, params = _a.params;
224
- return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
224
+ return tslib_1.__awaiter(_this, void 0, void 0, function () {
225
225
  var filename, data;
226
- return (0, tslib_1.__generator)(this, function (_b) {
226
+ return tslib_1.__generator(this, function (_b) {
227
227
  switch (_b.label) {
228
228
  case 0:
229
229
  filename = "mol-star_state_".concat((name || (0, date_1.getFormattedTime)()), ".").concat(type === 'json' ? 'molj' : 'molx');
@@ -242,9 +242,9 @@ function Snapshots(ctx) {
242
242
  });
243
243
  commands_1.PluginCommands.State.Snapshots.OpenUrl.subscribe(ctx, function (_a) {
244
244
  var url = _a.url, type = _a.type;
245
- return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
245
+ return tslib_1.__awaiter(_this, void 0, void 0, function () {
246
246
  var data;
247
- return (0, tslib_1.__generator)(this, function (_b) {
247
+ return tslib_1.__generator(this, function (_b) {
248
248
  switch (_b.label) {
249
249
  case 0: return [4 /*yield*/, ctx.runTask(ctx.fetch({ url: url, type: 'binary' }))];
250
250
  case 1:
@@ -7,14 +7,14 @@
7
7
  Object.defineProperty(exports, "__esModule", { value: true });
8
8
  exports.PluginBehaviors = exports.BuiltInPluginBehaviors = void 0;
9
9
  var tslib_1 = require("tslib");
10
- (0, tslib_1.__exportStar)(require("./behavior/behavior"), exports);
11
- var StaticState = (0, tslib_1.__importStar)(require("./behavior/static/state"));
12
- var StaticRepresentation = (0, tslib_1.__importStar)(require("./behavior/static/representation"));
13
- var StaticCamera = (0, tslib_1.__importStar)(require("./behavior/static/camera"));
14
- var StaticMisc = (0, tslib_1.__importStar)(require("./behavior/static/misc"));
15
- var DynamicRepresentation = (0, tslib_1.__importStar)(require("./behavior/dynamic/representation"));
16
- var DynamicCamera = (0, tslib_1.__importStar)(require("./behavior/dynamic/camera"));
17
- var DynamicCustomProps = (0, tslib_1.__importStar)(require("./behavior/dynamic/custom-props"));
10
+ tslib_1.__exportStar(require("./behavior/behavior"), exports);
11
+ var StaticState = tslib_1.__importStar(require("./behavior/static/state"));
12
+ var StaticRepresentation = tslib_1.__importStar(require("./behavior/static/representation"));
13
+ var StaticCamera = tslib_1.__importStar(require("./behavior/static/camera"));
14
+ var StaticMisc = tslib_1.__importStar(require("./behavior/static/misc"));
15
+ var DynamicRepresentation = tslib_1.__importStar(require("./behavior/dynamic/representation"));
16
+ var DynamicCamera = tslib_1.__importStar(require("./behavior/dynamic/camera"));
17
+ var DynamicCustomProps = tslib_1.__importStar(require("./behavior/dynamic/custom-props"));
18
18
  exports.BuiltInPluginBehaviors = {
19
19
  State: StaticState,
20
20
  Representation: StaticRepresentation,
@@ -63,9 +63,9 @@ var PluginCommandManager = /** @class */ (function () {
63
63
  this.subs.clear();
64
64
  };
65
65
  PluginCommandManager.prototype.resolve = function (instance) {
66
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
66
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
67
67
  var actions, _i, actions_1, a, e_1;
68
- return (0, tslib_1.__generator)(this, function (_a) {
68
+ return tslib_1.__generator(this, function (_a) {
69
69
  switch (_a.label) {
70
70
  case 0:
71
71
  actions = this.subs.get(instance.cmd.id);
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author David Sehnal <david.sehnal@gmail.com>
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -143,6 +143,7 @@ export declare class PluginContext {
143
143
  readonly customModelProperties: CustomProperty.Registry<Model>;
144
144
  readonly customStructureProperties: CustomProperty.Registry<Structure>;
145
145
  readonly customStructureControls: Map<string, new () => any>;
146
+ readonly customImportControls: Map<string, new () => any>;
146
147
  readonly genericRepresentationControls: Map<string, (selection: StructureHierarchyManager['selection']) => [StructureHierarchyRef[], string]>;
147
148
  /**
148
149
  * Used to store application specific custom state which is then available
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  /**
3
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
4
4
  *
5
5
  * @author David Sehnal <david.sehnal@gmail.com>
6
6
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,7 +8,7 @@
8
8
  Object.defineProperty(exports, "__esModule", { value: true });
9
9
  exports.PluginContext = void 0;
10
10
  var tslib_1 = require("tslib");
11
- var immer_1 = (0, tslib_1.__importStar)(require("immer"));
11
+ var immer_1 = tslib_1.__importStar(require("immer"));
12
12
  var immutable_1 = require("immutable");
13
13
  var rxjs_1 = require("rxjs");
14
14
  var operators_1 = require("rxjs/operators");
@@ -159,6 +159,7 @@ var PluginContext = /** @class */ (function () {
159
159
  this.customModelProperties = new custom_property_1.CustomProperty.Registry();
160
160
  this.customStructureProperties = new custom_property_1.CustomProperty.Registry();
161
161
  this.customStructureControls = new Map();
162
+ this.customImportControls = new Map();
162
163
  this.genericRepresentationControls = new Map();
163
164
  /**
164
165
  * Used to store application specific custom state which is then available
@@ -294,8 +295,8 @@ var PluginContext = /** @class */ (function () {
294
295
  this.state.dispose();
295
296
  this.managers.task.dispose();
296
297
  this.helpers.substructureParent.dispose();
297
- (0, object_1.objectForEach)(this.managers, function (m) { var _a, _b; return (_b = (_a = m) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a); });
298
- (0, object_1.objectForEach)(this.managers.structure, function (m) { var _a, _b; return (_b = (_a = m) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a); });
298
+ (0, object_1.objectForEach)(this.managers, function (m) { var _a; return (_a = m === null || m === void 0 ? void 0 : m.dispose) === null || _a === void 0 ? void 0 : _a.call(m); });
299
+ (0, object_1.objectForEach)(this.managers.structure, function (m) { var _a; return (_a = m === null || m === void 0 ? void 0 : m.dispose) === null || _a === void 0 ? void 0 : _a.call(m); });
299
300
  this.disposed = true;
300
301
  };
301
302
  PluginContext.prototype.initBehaviorEvents = function () {
@@ -346,9 +347,9 @@ var PluginContext = /** @class */ (function () {
346
347
  this.subs.push((0, rxjs_1.merge)(this.state.data.events.log, this.state.behaviors.events.log).subscribe(function (e) { return _this.events.log.next(e); }));
347
348
  };
348
349
  PluginContext.prototype.initBehaviors = function () {
349
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
350
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
350
351
  var tree, _i, _a, cat, _b, _c, b, cat, _d, _e, b, cat;
351
- return (0, tslib_1.__generator)(this, function (_f) {
352
+ return tslib_1.__generator(this, function (_f) {
352
353
  switch (_f.label) {
353
354
  case 0:
354
355
  tree = this.state.behaviors.build();
@@ -408,9 +409,9 @@ var PluginContext = /** @class */ (function () {
408
409
  }
409
410
  };
410
411
  PluginContext.prototype.init = function () {
411
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
412
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
412
413
  var _this = this;
413
- return (0, tslib_1.__generator)(this, function (_a) {
414
+ return tslib_1.__generator(this, function (_a) {
414
415
  switch (_a.label) {
415
416
  case 0:
416
417
  this.subs.push(this.events.log.subscribe(function (e) { return _this.log.entries = _this.log.entries.push(e); }));
@@ -32,9 +32,9 @@ exports.PluginLayoutStateParams = {
32
32
  controlsDisplay: param_definition_1.ParamDefinition.Value('outside', { isHidden: true })
33
33
  };
34
34
  var PluginLayout = /** @class */ (function (_super) {
35
- (0, tslib_1.__extends)(PluginLayout, _super);
35
+ tslib_1.__extends(PluginLayout, _super);
36
36
  function PluginLayout(context) {
37
- var _this = _super.call(this, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.PluginLayoutStateParams)), (context.spec.layout && context.spec.layout.initial))) || this;
37
+ var _this = _super.call(this, tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.PluginLayoutStateParams)), (context.spec.layout && context.spec.layout.initial))) || this;
38
38
  _this.context = context;
39
39
  _this.events = {
40
40
  updated: _this.ev()
@@ -36,10 +36,10 @@ exports.PluginSpec = PluginSpec;
36
36
  var DefaultPluginSpec = function () { return ({
37
37
  actions: [
38
38
  PluginSpec.Action(actions_1.StateActions.Structure.DownloadStructure),
39
- PluginSpec.Action(actions_1.StateActions.Structure.AddTrajectory),
40
39
  PluginSpec.Action(actions_1.StateActions.Volume.DownloadDensity),
41
40
  PluginSpec.Action(actions_1.StateActions.DataFormat.DownloadFile),
42
41
  PluginSpec.Action(actions_1.StateActions.DataFormat.OpenFiles),
42
+ PluginSpec.Action(actions_1.StateActions.Structure.LoadTrajectory),
43
43
  PluginSpec.Action(actions_1.StateActions.Structure.EnableModelCustomProps),
44
44
  PluginSpec.Action(actions_1.StateActions.Structure.EnableStructureCustomProps),
45
45
  // Volume streaming
@@ -19,7 +19,7 @@ var rxjs_1 = require("rxjs");
19
19
  var component_1 = require("../mol-plugin-state/component");
20
20
  var config_1 = require("./config");
21
21
  var PluginState = /** @class */ (function (_super) {
22
- (0, tslib_1.__extends)(PluginState, _super);
22
+ tslib_1.__extends(PluginState, _super);
23
23
  function PluginState(plugin) {
24
24
  var _this = _super.call(this) || this;
25
25
  _this.plugin = plugin;
@@ -39,7 +39,7 @@ var PluginState = /** @class */ (function (_super) {
39
39
  };
40
40
  _this.snapshotParams = _this.ev.behavior(PluginState.DefaultSnapshotParams);
41
41
  _this.setSnapshotParams = function (params) {
42
- _this.snapshotParams.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, PluginState.DefaultSnapshotParams), params));
42
+ _this.snapshotParams.next(tslib_1.__assign(tslib_1.__assign({}, PluginState.DefaultSnapshotParams), params));
43
43
  };
44
44
  return _this;
45
45
  }
@@ -50,7 +50,7 @@ var PluginState = /** @class */ (function (_super) {
50
50
  });
51
51
  PluginState.prototype.getSnapshot = function (params) {
52
52
  var _a, _b;
53
- var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.snapshotParams.value), params);
53
+ var p = tslib_1.__assign(tslib_1.__assign({}, this.snapshotParams.value), params);
54
54
  return {
55
55
  id: mol_util_1.UUID.create22(),
56
56
  data: p.data ? this.data.getSnapshot() : void 0,
@@ -73,9 +73,9 @@ var PluginState = /** @class */ (function (_super) {
73
73
  };
74
74
  PluginState.prototype.setSnapshot = function (snapshot) {
75
75
  var _a, _b, _c;
76
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
76
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
77
77
  var settings;
78
- return (0, tslib_1.__generator)(this, function (_d) {
78
+ return tslib_1.__generator(this, function (_d) {
79
79
  switch (_d.label) {
80
80
  case 0: return [4 /*yield*/, this.animation.stop()];
81
81
  case 1:
@@ -55,9 +55,9 @@ var TaskManager = /** @class */ (function () {
55
55
  };
56
56
  };
57
57
  TaskManager.prototype.run = function (task, params) {
58
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
58
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
59
59
  var id, ctx, ret;
60
- return (0, tslib_1.__generator)(this, function (_a) {
60
+ return tslib_1.__generator(this, function (_a) {
61
61
  switch (_a.label) {
62
62
  case 0:
63
63
  id = this.id++;
@@ -113,9 +113,9 @@ exports.TaskManager = TaskManager;
113
113
  }
114
114
  function testTask(N) {
115
115
  var _this = this;
116
- return mol_task_1.Task.create('Test', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
116
+ return mol_task_1.Task.create('Test', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
117
117
  var i;
118
- return (0, tslib_1.__generator)(this, function (_a) {
118
+ return tslib_1.__generator(this, function (_a) {
119
119
  switch (_a.label) {
120
120
  case 0:
121
121
  i = 0;
@@ -13,7 +13,7 @@ var component_1 = require("../../mol-plugin-state/component");
13
13
  var immutable_1 = require("immutable");
14
14
  var commands_1 = require("../commands");
15
15
  var PluginToastManager = /** @class */ (function (_super) {
16
- (0, tslib_1.__extends)(PluginToastManager, _super);
16
+ tslib_1.__extends(PluginToastManager, _super);
17
17
  function PluginToastManager(plugin) {
18
18
  var _this = _super.call(this, { entries: (0, immutable_1.OrderedMap)() }) || this;
19
19
  _this.events = {
@@ -20,7 +20,7 @@ var download_1 = require("../../mol-util/download");
20
20
  var param_definition_1 = require("../../mol-util/param-definition");
21
21
  var set_1 = require("../../mol-util/set");
22
22
  var ViewportScreenshotHelper = /** @class */ (function (_super) {
23
- (0, tslib_1.__extends)(ViewportScreenshotHelper, _super);
23
+ tslib_1.__extends(ViewportScreenshotHelper, _super);
24
24
  function ViewportScreenshotHelper(plugin) {
25
25
  var _this = _super.call(this) || this;
26
26
  _this.plugin = plugin;
@@ -135,10 +135,10 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
135
135
  mode: mutlisample ? 'on' : 'off',
136
136
  sampleLevel: colorBufferFloat && textureFloat ? 4 : 2
137
137
  },
138
- postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
139
- ? { name: 'on', params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
138
+ postprocessing: tslib_1.__assign(tslib_1.__assign({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
139
+ ? { name: 'on', params: tslib_1.__assign(tslib_1.__assign({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
140
140
  : aoProps }),
141
- marking: (0, tslib_1.__assign)({}, c.props.marking)
141
+ marking: tslib_1.__assign({}, c.props.marking)
142
142
  });
143
143
  };
144
144
  Object.defineProperty(ViewportScreenshotHelper.prototype, "previewPass", {
@@ -157,10 +157,10 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
157
157
  cameraHelper: { axes: this.values.axes },
158
158
  transparentBackground: this.values.transparent,
159
159
  // TODO: optimize because this creates a copy of a large object!
160
- postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
161
- ? { name: 'on', params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
160
+ postprocessing: tslib_1.__assign(tslib_1.__assign({}, c.props.postprocessing), { occlusion: aoProps.name === 'on'
161
+ ? { name: 'on', params: tslib_1.__assign(tslib_1.__assign({}, aoProps.params), { samples: 128, resolutionScale: 1 }) }
162
162
  : aoProps }),
163
- marking: (0, tslib_1.__assign)({}, c.props.marking)
163
+ marking: tslib_1.__assign({}, c.props.marking)
164
164
  });
165
165
  return this._imagePass;
166
166
  }
@@ -182,11 +182,11 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
182
182
  };
183
183
  ViewportScreenshotHelper.prototype.toggleAutocrop = function () {
184
184
  if (this.cropParams.auto) {
185
- this.behaviors.cropParams.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.cropParams), { auto: false }));
185
+ this.behaviors.cropParams.next(tslib_1.__assign(tslib_1.__assign({}, this.cropParams), { auto: false }));
186
186
  this.resetCrop();
187
187
  }
188
188
  else {
189
- this.behaviors.cropParams.next((0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.cropParams), { auto: true }));
189
+ this.behaviors.cropParams.next(tslib_1.__assign(tslib_1.__assign({}, this.cropParams), { auto: true }));
190
190
  }
191
191
  };
192
192
  Object.defineProperty(ViewportScreenshotHelper.prototype, "isFullFrame", {
@@ -304,9 +304,9 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
304
304
  return { width: width, height: height, viewport: viewport };
305
305
  };
306
306
  ViewportScreenshotHelper.prototype.draw = function (ctx) {
307
- return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
307
+ return tslib_1.__awaiter(this, void 0, void 0, function () {
308
308
  var _a, width, height, viewport, imageData, canvas, canvasCtx;
309
- return (0, tslib_1.__generator)(this, function (_b) {
309
+ return tslib_1.__generator(this, function (_b) {
310
310
  switch (_b.label) {
311
311
  case 0:
312
312
  _a = this.getSizeAndViewport(), width = _a.width, height = _a.height, viewport = _a.viewport;
@@ -338,9 +338,9 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
338
338
  this.plugin.log.error('clipboard.write not supported!');
339
339
  return;
340
340
  }
341
- return mol_task_1.Task.create('Copy Image', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
341
+ return mol_task_1.Task.create('Copy Image', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
342
342
  var blob, item;
343
- return (0, tslib_1.__generator)(this, function (_a) {
343
+ return tslib_1.__generator(this, function (_a) {
344
344
  switch (_a.label) {
345
345
  case 0: return [4 /*yield*/, this.draw(ctx)];
346
346
  case 1:
@@ -363,8 +363,8 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
363
363
  };
364
364
  ViewportScreenshotHelper.prototype.getImageDataUri = function () {
365
365
  var _this = this;
366
- return this.plugin.runTask(mol_task_1.Task.create('Generate Image', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
367
- return (0, tslib_1.__generator)(this, function (_a) {
366
+ return this.plugin.runTask(mol_task_1.Task.create('Generate Image', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
367
+ return tslib_1.__generator(this, function (_a) {
368
368
  switch (_a.label) {
369
369
  case 0: return [4 /*yield*/, this.draw(ctx)];
370
370
  case 1:
@@ -385,9 +385,9 @@ var ViewportScreenshotHelper = /** @class */ (function (_super) {
385
385
  };
386
386
  ViewportScreenshotHelper.prototype.downloadTask = function (filename) {
387
387
  var _this = this;
388
- return mol_task_1.Task.create('Download Image', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
388
+ return mol_task_1.Task.create('Download Image', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
389
389
  var blob;
390
- return (0, tslib_1.__generator)(this, function (_a) {
390
+ return tslib_1.__generator(this, function (_a) {
391
391
  switch (_a.label) {
392
392
  case 0: return [4 /*yield*/, this.draw(ctx)];
393
393
  case 1:
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */