molstar 3.8.2 → 3.10.0

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 (596) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +202 -202
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +109 -106
  5. package/build/viewer/molstar.js +1 -1
  6. package/lib/apps/docking-viewer/index.html +36 -36
  7. package/lib/apps/viewer/app.d.ts +5 -2
  8. package/lib/apps/viewer/app.js +11 -7
  9. package/lib/apps/viewer/embedded.html +43 -43
  10. package/lib/apps/viewer/index.html +109 -106
  11. package/lib/cli/cif2bcif/converter.js +1 -1
  12. package/lib/commonjs/apps/viewer/app.d.ts +5 -2
  13. package/lib/commonjs/apps/viewer/app.js +12 -7
  14. package/lib/commonjs/cli/cif2bcif/converter.js +1 -1
  15. package/lib/commonjs/examples/alpha-orbitals/index.d.ts +1 -1
  16. package/lib/commonjs/examples/alpha-orbitals/index.js +4 -1
  17. package/lib/commonjs/examples/basic-wrapper/custom-theme.js +1 -1
  18. package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +3 -3
  19. package/lib/commonjs/extensions/alpha-orbitals/density.d.ts +1 -1
  20. package/lib/commonjs/extensions/alpha-orbitals/density.js +6 -2
  21. package/lib/commonjs/extensions/alpha-orbitals/orbitals.d.ts +1 -1
  22. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +6 -3
  23. package/lib/commonjs/extensions/anvil/algorithm.js +1 -1
  24. package/lib/commonjs/extensions/cellpack/color/generate.js +1 -1
  25. package/lib/commonjs/extensions/cellpack/color/provided.js +1 -1
  26. package/lib/commonjs/extensions/cellpack/state.js +1 -1
  27. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +1 -1
  28. package/lib/commonjs/extensions/g3d/model.js +1 -1
  29. package/lib/commonjs/extensions/geo-export/ui.js +1 -0
  30. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +1 -1
  31. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +1 -1
  32. package/lib/commonjs/extensions/mp4-export/ui.js +1 -0
  33. package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +1 -1
  34. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +4 -4
  35. package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +1 -1
  36. package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +2 -2
  37. package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +1 -1
  38. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +2 -2
  39. package/lib/commonjs/mol-canvas3d/canvas3d.js +4 -0
  40. package/lib/commonjs/mol-canvas3d/controls/trackball.js +7 -7
  41. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +14 -14
  42. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +5 -5
  43. package/lib/commonjs/mol-canvas3d/passes/draw.js +34 -5
  44. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +5 -0
  45. package/lib/commonjs/mol-canvas3d/passes/marking.js +5 -0
  46. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +9 -0
  47. package/lib/commonjs/mol-canvas3d/passes/pick.d.ts +18 -5
  48. package/lib/commonjs/mol-canvas3d/passes/pick.js +125 -24
  49. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +5 -0
  50. package/lib/commonjs/mol-canvas3d/passes/smaa.js +4 -0
  51. package/lib/commonjs/mol-canvas3d/passes/wboit.js +4 -0
  52. package/lib/commonjs/mol-data/db/column.js +5 -5
  53. package/lib/commonjs/mol-data/db/table.js +2 -2
  54. package/lib/commonjs/mol-data/util/array.d.ts +1 -1
  55. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +1 -1
  56. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  57. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  58. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +13 -0
  59. package/lib/commonjs/mol-gl/compute/grid3d.d.ts +2 -2
  60. package/lib/commonjs/mol-gl/compute/grid3d.js +30 -8
  61. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.d.ts +1 -1
  62. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +6 -1
  63. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.d.ts +1 -1
  64. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +6 -1
  65. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.d.ts +1 -1
  66. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +6 -1
  67. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +1 -1
  68. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +10 -10
  69. package/lib/commonjs/mol-gl/renderer.js +77 -32
  70. package/lib/commonjs/mol-gl/scene.js +2 -0
  71. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  72. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  73. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  74. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  75. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  76. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  77. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  78. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  79. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +1 -1
  80. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +1 -1
  81. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  82. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  83. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +1 -1
  84. package/lib/commonjs/mol-gl/shader/image.frag.js +1 -1
  85. package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +1 -1
  86. package/lib/commonjs/mol-gl/shader/lines.frag.js +1 -1
  87. package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
  88. package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
  89. package/lib/commonjs/mol-gl/shader/points.frag.d.ts +1 -1
  90. package/lib/commonjs/mol-gl/shader/points.frag.js +1 -1
  91. package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +1 -1
  92. package/lib/commonjs/mol-gl/shader/spheres.frag.js +1 -1
  93. package/lib/commonjs/mol-gl/shader/text.frag.d.ts +1 -1
  94. package/lib/commonjs/mol-gl/shader/text.frag.js +1 -1
  95. package/lib/commonjs/mol-gl/shader-code.d.ts +1 -1
  96. package/lib/commonjs/mol-gl/shader-code.js +41 -9
  97. package/lib/commonjs/mol-gl/webgl/compat.d.ts +34 -1
  98. package/lib/commonjs/mol-gl/webgl/compat.js +50 -2
  99. package/lib/commonjs/mol-gl/webgl/context.d.ts +2 -0
  100. package/lib/commonjs/mol-gl/webgl/context.js +3 -0
  101. package/lib/commonjs/mol-gl/webgl/extensions.d.ts +3 -2
  102. package/lib/commonjs/mol-gl/webgl/extensions.js +6 -1
  103. package/lib/commonjs/mol-gl/webgl/timer.d.ts +22 -0
  104. package/lib/commonjs/mol-gl/webgl/timer.js +169 -0
  105. package/lib/commonjs/mol-io/common/binary-cif/array-encoder.js +18 -18
  106. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +16 -16
  107. package/lib/commonjs/mol-io/common/binary-cif/encoding.js +9 -9
  108. package/lib/commonjs/mol-io/reader/cif/binary/field.js +3 -3
  109. package/lib/commonjs/mol-io/reader/cif/data-model.js +14 -14
  110. package/lib/commonjs/mol-io/reader/cif/schema.js +1 -1
  111. package/lib/commonjs/mol-io/reader/cif/text/parser.js +23 -23
  112. package/lib/commonjs/mol-io/reader/common/text/column/fixed.js +1 -1
  113. package/lib/commonjs/mol-io/reader/common/text/column/token.js +1 -1
  114. package/lib/commonjs/mol-io/reader/common/text/number-parser.js +6 -6
  115. package/lib/commonjs/mol-io/reader/csv/parser.js +8 -8
  116. package/lib/commonjs/mol-io/writer/cif/encoder/binary.js +10 -10
  117. package/lib/commonjs/mol-io/writer/cif/encoder/text.js +7 -7
  118. package/lib/commonjs/mol-io/writer/cif/encoder.js +8 -8
  119. package/lib/commonjs/mol-io/writer/mol2/encoder.js +4 -4
  120. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +13 -2
  121. package/lib/commonjs/mol-model/sequence/alignment/sequence.js +3 -3
  122. package/lib/commonjs/mol-model/sequence/sequence.js +9 -9
  123. package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js +3 -3
  124. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  125. package/lib/commonjs/mol-model/structure/export/categories/utils.js +1 -1
  126. package/lib/commonjs/mol-model/structure/model/model.js +2 -2
  127. package/lib/commonjs/mol-model/structure/model/properties/custom/indexed.js +6 -6
  128. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js +1 -1
  129. package/lib/commonjs/mol-model/structure/model/types.js +116 -116
  130. package/lib/commonjs/mol-model/structure/query/context.js +1 -1
  131. package/lib/commonjs/mol-model/structure/query/queries/generators.js +5 -5
  132. package/lib/commonjs/mol-model/structure/query/queries/internal.js +4 -4
  133. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +4 -4
  134. package/lib/commonjs/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
  135. package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js +9 -9
  136. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +3 -1
  137. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +192 -108
  138. package/lib/commonjs/mol-model/structure/structure/element/loci.js +5 -5
  139. package/lib/commonjs/mol-model/structure/structure/element/stats.js +5 -5
  140. package/lib/commonjs/mol-model/structure/structure/properties.js +5 -5
  141. package/lib/commonjs/mol-model/structure/structure/structure.js +11 -11
  142. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +5 -5
  143. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +4 -4
  144. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +2 -2
  145. package/lib/commonjs/mol-model/structure/structure/unit/resonance.js +1 -1
  146. package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js +6 -6
  147. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +6 -6
  148. package/lib/commonjs/mol-model/structure/structure/unit.js +16 -16
  149. package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.js +1 -1
  150. package/lib/commonjs/mol-model/structure/util.js +4 -4
  151. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -2
  152. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +4 -4
  153. package/lib/commonjs/mol-model-formats/structure/basic/properties.js +1 -1
  154. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +1 -1
  155. package/lib/commonjs/mol-model-formats/structure/basic/util.js +1 -1
  156. package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
  157. package/lib/commonjs/mol-model-formats/structure/common/entity.js +1 -1
  158. package/lib/commonjs/mol-model-formats/structure/cube.js +1 -1
  159. package/lib/commonjs/mol-model-formats/structure/gro.js +1 -1
  160. package/lib/commonjs/mol-model-formats/structure/mol.js +1 -1
  161. package/lib/commonjs/mol-model-formats/structure/mol2.js +4 -4
  162. package/lib/commonjs/mol-model-formats/structure/prmtop.js +1 -1
  163. package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +3 -3
  164. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  165. package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +6 -6
  166. package/lib/commonjs/mol-model-formats/structure/property/secondary-structure.js +8 -8
  167. package/lib/commonjs/mol-model-formats/structure/psf.js +1 -1
  168. package/lib/commonjs/mol-model-formats/structure/top.js +1 -1
  169. package/lib/commonjs/mol-model-formats/structure/xyz.js +1 -1
  170. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +2 -2
  171. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +3 -3
  172. package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +2 -2
  173. package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js +31 -31
  174. package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js +22 -22
  175. package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +32 -32
  176. package/lib/commonjs/mol-model-props/computed/interactions/charged.js +39 -39
  177. package/lib/commonjs/mol-model-props/computed/interactions/common.js +34 -34
  178. package/lib/commonjs/mol-model-props/computed/interactions/contacts-builder.js +1 -1
  179. package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +1 -1
  180. package/lib/commonjs/mol-model-props/computed/interactions/halogen-bonds.js +12 -12
  181. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +32 -32
  182. package/lib/commonjs/mol-model-props/computed/interactions/hydrophobic.js +9 -9
  183. package/lib/commonjs/mol-model-props/computed/interactions/metal.js +26 -26
  184. package/lib/commonjs/mol-model-props/computed/interactions/refine.js +20 -20
  185. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +2 -2
  186. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +2 -2
  187. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bends.js +1 -1
  188. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bridges.js +12 -12
  189. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/helices.js +6 -6
  190. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/ladders.js +3 -3
  191. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/sheets.js +11 -11
  192. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/turns.js +3 -3
  193. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +30 -30
  194. package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js +1 -1
  195. package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js +10 -10
  196. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js +1 -1
  197. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js +3 -3
  198. package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js +1 -1
  199. package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +1 -1
  200. package/lib/commonjs/mol-plugin/animation-loop.d.ts +2 -1
  201. package/lib/commonjs/mol-plugin/animation-loop.js +18 -5
  202. package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +12 -12
  203. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +7 -7
  204. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  205. package/lib/commonjs/mol-plugin/config.d.ts +3 -0
  206. package/lib/commonjs/mol-plugin/config.js +3 -1
  207. package/lib/commonjs/mol-plugin/context.d.ts +2 -2
  208. package/lib/commonjs/mol-plugin/context.js +3 -0
  209. package/lib/commonjs/mol-plugin/state.d.ts +1 -14
  210. package/lib/commonjs/mol-plugin-state/formats/volume.d.ts +12 -11
  211. package/lib/commonjs/mol-plugin-state/formats/volume.js +20 -13
  212. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +5 -5
  213. package/lib/commonjs/mol-plugin-state/transforms/representation.js +2 -2
  214. package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts +1 -1
  215. package/lib/commonjs/mol-plugin-ui/controls.js +1 -1
  216. package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +1 -1
  217. package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +1 -1
  218. package/lib/commonjs/mol-plugin-ui/state/snapshots.js +1 -0
  219. package/lib/commonjs/mol-plugin-ui/structure/focus.js +1 -1
  220. package/lib/commonjs/mol-plugin-ui/viewport/screenshot.js +1 -0
  221. package/lib/commonjs/mol-plugin-ui/viewport.d.ts +2 -2
  222. package/lib/commonjs/mol-repr/shape/representation.d.ts +1 -1
  223. package/lib/commonjs/mol-repr/shape/representation.js +2 -1
  224. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +1 -1
  225. package/lib/commonjs/mol-repr/structure/complex-visual.js +2 -1
  226. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +1 -1
  227. package/lib/commonjs/mol-repr/structure/units-visual.js +2 -1
  228. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +10 -10
  229. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +10 -10
  230. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +12 -15
  231. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +12 -15
  232. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +16 -16
  233. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +1 -1
  234. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -0
  235. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +4 -4
  236. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
  237. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +2 -2
  238. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +2 -2
  239. package/lib/commonjs/mol-repr/structure/visual/util/common.js +3 -3
  240. package/lib/commonjs/mol-repr/structure/visual/util/link.js +30 -30
  241. package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js +6 -6
  242. package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js +3 -3
  243. package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +20 -20
  244. package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +6 -6
  245. package/lib/commonjs/mol-repr/volume/representation.d.ts +1 -1
  246. package/lib/commonjs/mol-repr/volume/representation.js +2 -1
  247. package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
  248. package/lib/commonjs/mol-script/language/symbol-table/core.d.ts +2 -2
  249. package/lib/commonjs/mol-script/runtime/query/table.js +13 -13
  250. package/lib/commonjs/mol-state/object.d.ts +3 -3
  251. package/lib/commonjs/mol-task/util/user-timing.js +1 -1
  252. package/lib/commonjs/mol-theme/clipping.js +19 -19
  253. package/lib/commonjs/mol-theme/color/atom-id.js +1 -1
  254. package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js +1 -1
  255. package/lib/commonjs/mol-theme/color/chain-id.js +4 -4
  256. package/lib/commonjs/mol-theme/color/element-index.js +1 -1
  257. package/lib/commonjs/mol-theme/color/element-symbol.js +1 -1
  258. package/lib/commonjs/mol-theme/color/entity-id.js +4 -4
  259. package/lib/commonjs/mol-theme/color/entity-source.js +5 -4
  260. package/lib/commonjs/mol-theme/color/hydrophobicity.js +1 -1
  261. package/lib/commonjs/mol-theme/color/illustrative.js +1 -1
  262. package/lib/commonjs/mol-theme/color/model-index.js +1 -1
  263. package/lib/commonjs/mol-theme/color/molecule-type.js +8 -8
  264. package/lib/commonjs/mol-theme/color/occupancy.js +1 -1
  265. package/lib/commonjs/mol-theme/color/operator-hkl.js +1 -1
  266. package/lib/commonjs/mol-theme/color/operator-name.js +1 -1
  267. package/lib/commonjs/mol-theme/color/partial-charge.js +1 -1
  268. package/lib/commonjs/mol-theme/color/polymer-id.js +4 -4
  269. package/lib/commonjs/mol-theme/color/polymer-index.js +1 -1
  270. package/lib/commonjs/mol-theme/color/residue-name.js +1 -1
  271. package/lib/commonjs/mol-theme/color/secondary-structure.js +12 -12
  272. package/lib/commonjs/mol-theme/color/sequence-id.js +7 -7
  273. package/lib/commonjs/mol-theme/color/shape-group.js +1 -1
  274. package/lib/commonjs/mol-theme/color/uncertainty.js +1 -1
  275. package/lib/commonjs/mol-theme/color/uniform.js +1 -1
  276. package/lib/commonjs/mol-theme/color/unit-index.js +1 -1
  277. package/lib/commonjs/mol-theme/color/volume-value.js +1 -1
  278. package/lib/commonjs/mol-theme/label.js +3 -3
  279. package/lib/commonjs/mol-util/binding.js +4 -4
  280. package/lib/commonjs/mol-util/debug.d.ts +6 -1
  281. package/lib/commonjs/mol-util/debug.js +11 -1
  282. package/lib/commonjs/mol-util/input/input-observer.js +20 -20
  283. package/lib/commonjs/mol-util/string-builder.js +1 -1
  284. package/lib/commonjs/servers/model/preprocess/converter.js +1 -1
  285. package/lib/commonjs/servers/model/server/query.js +1 -1
  286. package/lib/commonjs/servers/model/utils/fetch-retry.js +3 -2
  287. package/lib/commonjs/servers/volume/server/algebra/coordinate.js +6 -6
  288. package/lib/commonjs/servers/volume/server/query/encode.js +1 -1
  289. package/lib/examples/alpha-orbitals/index.d.ts +1 -1
  290. package/lib/examples/alpha-orbitals/index.html +72 -61
  291. package/lib/examples/alpha-orbitals/index.js +4 -1
  292. package/lib/examples/basic-wrapper/custom-theme.js +1 -1
  293. package/lib/examples/basic-wrapper/index.html +137 -137
  294. package/lib/examples/lighting/index.html +88 -88
  295. package/lib/examples/proteopedia-wrapper/coloring.js +3 -3
  296. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  297. package/lib/extensions/alpha-orbitals/density.d.ts +1 -1
  298. package/lib/extensions/alpha-orbitals/density.js +6 -2
  299. package/lib/extensions/alpha-orbitals/orbitals.d.ts +1 -1
  300. package/lib/extensions/alpha-orbitals/orbitals.js +6 -3
  301. package/lib/extensions/anvil/algorithm.js +1 -1
  302. package/lib/extensions/cellpack/color/generate.js +1 -1
  303. package/lib/extensions/cellpack/color/provided.js +1 -1
  304. package/lib/extensions/cellpack/state.js +1 -1
  305. package/lib/extensions/dnatco/confal-pyramids/color.js +1 -1
  306. package/lib/extensions/g3d/model.js +1 -1
  307. package/lib/extensions/geo-export/ui.js +1 -0
  308. package/lib/extensions/model-archive/quality-assessment/color/plddt.js +1 -1
  309. package/lib/extensions/model-archive/quality-assessment/color/qmean.js +1 -1
  310. package/lib/extensions/mp4-export/ui.js +1 -0
  311. package/lib/extensions/pdbe/structure-quality-report/color.js +1 -1
  312. package/lib/extensions/rcsb/assembly-symmetry/color.js +4 -4
  313. package/lib/extensions/rcsb/validation-report/color/density-fit.js +1 -1
  314. package/lib/extensions/rcsb/validation-report/color/geometry-quality.js +2 -2
  315. package/lib/extensions/rcsb/validation-report/color/random-coil-index.js +1 -1
  316. package/lib/extensions/rcsb/validation-report/representation.js +2 -2
  317. package/lib/mol-canvas3d/canvas3d.js +5 -1
  318. package/lib/mol-canvas3d/controls/trackball.js +7 -7
  319. package/lib/mol-canvas3d/helper/camera-helper.js +14 -14
  320. package/lib/mol-canvas3d/helper/interaction-events.js +5 -5
  321. package/lib/mol-canvas3d/passes/draw.js +34 -5
  322. package/lib/mol-canvas3d/passes/fxaa.js +5 -0
  323. package/lib/mol-canvas3d/passes/marking.js +5 -0
  324. package/lib/mol-canvas3d/passes/multi-sample.js +9 -0
  325. package/lib/mol-canvas3d/passes/pick.d.ts +18 -5
  326. package/lib/mol-canvas3d/passes/pick.js +125 -24
  327. package/lib/mol-canvas3d/passes/postprocessing.js +5 -0
  328. package/lib/mol-canvas3d/passes/smaa.js +5 -1
  329. package/lib/mol-canvas3d/passes/wboit.js +5 -1
  330. package/lib/mol-data/db/column.js +5 -5
  331. package/lib/mol-data/db/table.js +2 -2
  332. package/lib/mol-data/util/array.d.ts +1 -1
  333. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +1 -1
  334. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  335. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  336. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +13 -0
  337. package/lib/mol-gl/compute/grid3d.d.ts +2 -2
  338. package/lib/mol-gl/compute/grid3d.js +30 -8
  339. package/lib/mol-gl/compute/histogram-pyramid/reduction.d.ts +1 -1
  340. package/lib/mol-gl/compute/histogram-pyramid/reduction.js +6 -1
  341. package/lib/mol-gl/compute/histogram-pyramid/sum.d.ts +1 -1
  342. package/lib/mol-gl/compute/histogram-pyramid/sum.js +6 -1
  343. package/lib/mol-gl/compute/marching-cubes/active-voxels.d.ts +1 -1
  344. package/lib/mol-gl/compute/marching-cubes/active-voxels.js +6 -1
  345. package/lib/mol-gl/compute/marching-cubes/isosurface.d.ts +1 -1
  346. package/lib/mol-gl/compute/marching-cubes/isosurface.js +10 -10
  347. package/lib/mol-gl/renderer.js +77 -32
  348. package/lib/mol-gl/scene.js +2 -0
  349. package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  350. package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  351. package/lib/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  352. package/lib/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  353. package/lib/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  354. package/lib/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  355. package/lib/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  356. package/lib/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  357. package/lib/mol-gl/shader/cylinders.frag.d.ts +1 -1
  358. package/lib/mol-gl/shader/cylinders.frag.js +1 -1
  359. package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  360. package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
  361. package/lib/mol-gl/shader/image.frag.d.ts +1 -1
  362. package/lib/mol-gl/shader/image.frag.js +1 -1
  363. package/lib/mol-gl/shader/lines.frag.d.ts +1 -1
  364. package/lib/mol-gl/shader/lines.frag.js +1 -1
  365. package/lib/mol-gl/shader/mesh.frag.d.ts +1 -1
  366. package/lib/mol-gl/shader/mesh.frag.js +1 -1
  367. package/lib/mol-gl/shader/points.frag.d.ts +1 -1
  368. package/lib/mol-gl/shader/points.frag.js +1 -1
  369. package/lib/mol-gl/shader/spheres.frag.d.ts +1 -1
  370. package/lib/mol-gl/shader/spheres.frag.js +1 -1
  371. package/lib/mol-gl/shader/text.frag.d.ts +1 -1
  372. package/lib/mol-gl/shader/text.frag.js +1 -1
  373. package/lib/mol-gl/shader-code.d.ts +1 -1
  374. package/lib/mol-gl/shader-code.js +41 -9
  375. package/lib/mol-gl/webgl/compat.d.ts +34 -1
  376. package/lib/mol-gl/webgl/compat.js +48 -1
  377. package/lib/mol-gl/webgl/context.d.ts +2 -0
  378. package/lib/mol-gl/webgl/context.js +3 -0
  379. package/lib/mol-gl/webgl/extensions.d.ts +3 -2
  380. package/lib/mol-gl/webgl/extensions.js +7 -2
  381. package/lib/mol-gl/webgl/timer.d.ts +22 -0
  382. package/lib/mol-gl/webgl/timer.js +164 -0
  383. package/lib/mol-io/common/binary-cif/array-encoder.js +18 -18
  384. package/lib/mol-io/common/binary-cif/decoder.js +16 -16
  385. package/lib/mol-io/common/binary-cif/encoding.js +9 -9
  386. package/lib/mol-io/reader/cif/binary/field.js +3 -3
  387. package/lib/mol-io/reader/cif/data-model.js +14 -14
  388. package/lib/mol-io/reader/cif/schema.js +1 -1
  389. package/lib/mol-io/reader/cif/text/parser.js +23 -23
  390. package/lib/mol-io/reader/common/text/column/fixed.js +1 -1
  391. package/lib/mol-io/reader/common/text/column/token.js +1 -1
  392. package/lib/mol-io/reader/common/text/number-parser.js +6 -6
  393. package/lib/mol-io/reader/csv/parser.js +8 -8
  394. package/lib/mol-io/writer/cif/encoder/binary.js +10 -10
  395. package/lib/mol-io/writer/cif/encoder/text.js +7 -7
  396. package/lib/mol-io/writer/cif/encoder.js +8 -8
  397. package/lib/mol-io/writer/mol2/encoder.js +4 -4
  398. package/lib/mol-math/geometry/gaussian-density/gpu.js +13 -2
  399. package/lib/mol-model/sequence/alignment/sequence.js +3 -3
  400. package/lib/mol-model/sequence/sequence.js +9 -9
  401. package/lib/mol-model/structure/export/categories/atom_site_operator_mapping.js +3 -3
  402. package/lib/mol-model/structure/export/categories/secondary-structure.js +2 -2
  403. package/lib/mol-model/structure/export/categories/utils.js +1 -1
  404. package/lib/mol-model/structure/model/model.js +2 -2
  405. package/lib/mol-model/structure/model/properties/custom/indexed.js +6 -6
  406. package/lib/mol-model/structure/model/properties/utils/atomic-ranges.js +1 -1
  407. package/lib/mol-model/structure/model/types.js +116 -116
  408. package/lib/mol-model/structure/query/context.js +1 -1
  409. package/lib/mol-model/structure/query/queries/generators.js +5 -5
  410. package/lib/mol-model/structure/query/queries/internal.js +4 -4
  411. package/lib/mol-model/structure/query/queries/modifiers.js +4 -4
  412. package/lib/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
  413. package/lib/mol-model/structure/query/utils/structure-distance.js +9 -9
  414. package/lib/mol-model/structure/structure/carbohydrates/constants.d.ts +3 -1
  415. package/lib/mol-model/structure/structure/carbohydrates/constants.js +190 -107
  416. package/lib/mol-model/structure/structure/element/loci.js +5 -5
  417. package/lib/mol-model/structure/structure/element/stats.js +5 -5
  418. package/lib/mol-model/structure/structure/properties.js +5 -5
  419. package/lib/mol-model/structure/structure/structure.js +11 -11
  420. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +5 -5
  421. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +4 -4
  422. package/lib/mol-model/structure/structure/unit/bonds.js +2 -2
  423. package/lib/mol-model/structure/structure/unit/resonance.js +1 -1
  424. package/lib/mol-model/structure/structure/unit/rings/compute.js +6 -6
  425. package/lib/mol-model/structure/structure/unit/rings.js +6 -6
  426. package/lib/mol-model/structure/structure/unit.js +16 -16
  427. package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.js +1 -1
  428. package/lib/mol-model/structure/util.js +4 -4
  429. package/lib/mol-model-formats/structure/basic/atomic.js +2 -2
  430. package/lib/mol-model-formats/structure/basic/parser.js +4 -4
  431. package/lib/mol-model-formats/structure/basic/properties.js +1 -1
  432. package/lib/mol-model-formats/structure/basic/sort.js +1 -1
  433. package/lib/mol-model-formats/structure/basic/util.js +1 -1
  434. package/lib/mol-model-formats/structure/cif-core.js +6 -6
  435. package/lib/mol-model-formats/structure/common/entity.js +1 -1
  436. package/lib/mol-model-formats/structure/cube.js +1 -1
  437. package/lib/mol-model-formats/structure/gro.js +1 -1
  438. package/lib/mol-model-formats/structure/mol.js +1 -1
  439. package/lib/mol-model-formats/structure/mol2.js +4 -4
  440. package/lib/mol-model-formats/structure/prmtop.js +1 -1
  441. package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +3 -3
  442. package/lib/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  443. package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +6 -6
  444. package/lib/mol-model-formats/structure/property/secondary-structure.js +8 -8
  445. package/lib/mol-model-formats/structure/psf.js +1 -1
  446. package/lib/mol-model-formats/structure/top.js +1 -1
  447. package/lib/mol-model-formats/structure/xyz.js +1 -1
  448. package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +2 -2
  449. package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +3 -3
  450. package/lib/mol-model-props/computed/accessible-surface-area.js +2 -2
  451. package/lib/mol-model-props/computed/chemistry/functional-group.js +31 -31
  452. package/lib/mol-model-props/computed/chemistry/geometry.js +22 -22
  453. package/lib/mol-model-props/computed/chemistry/valence-model.js +32 -32
  454. package/lib/mol-model-props/computed/interactions/charged.js +39 -39
  455. package/lib/mol-model-props/computed/interactions/common.js +34 -34
  456. package/lib/mol-model-props/computed/interactions/contacts-builder.js +1 -1
  457. package/lib/mol-model-props/computed/interactions/contacts.js +1 -1
  458. package/lib/mol-model-props/computed/interactions/halogen-bonds.js +12 -12
  459. package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js +32 -32
  460. package/lib/mol-model-props/computed/interactions/hydrophobic.js +9 -9
  461. package/lib/mol-model-props/computed/interactions/metal.js +26 -26
  462. package/lib/mol-model-props/computed/interactions/refine.js +20 -20
  463. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +2 -2
  464. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +2 -2
  465. package/lib/mol-model-props/computed/secondary-structure/dssp/bends.js +1 -1
  466. package/lib/mol-model-props/computed/secondary-structure/dssp/bridges.js +12 -12
  467. package/lib/mol-model-props/computed/secondary-structure/dssp/helices.js +6 -6
  468. package/lib/mol-model-props/computed/secondary-structure/dssp/ladders.js +3 -3
  469. package/lib/mol-model-props/computed/secondary-structure/dssp/sheets.js +11 -11
  470. package/lib/mol-model-props/computed/secondary-structure/dssp/turns.js +3 -3
  471. package/lib/mol-model-props/computed/secondary-structure/dssp.js +30 -30
  472. package/lib/mol-model-props/computed/themes/accessible-surface-area.js +1 -1
  473. package/lib/mol-model-props/computed/themes/interaction-type.js +10 -10
  474. package/lib/mol-model-props/integrative/cross-link-restraint/color.js +1 -1
  475. package/lib/mol-model-props/integrative/cross-link-restraint/format.js +3 -3
  476. package/lib/mol-model-props/sequence/sifts-mapping.js +1 -1
  477. package/lib/mol-model-props/sequence/themes/sifts-mapping.js +1 -1
  478. package/lib/mol-plugin/animation-loop.d.ts +2 -1
  479. package/lib/mol-plugin/animation-loop.js +18 -5
  480. package/lib/mol-plugin/behavior/dynamic/camera.js +12 -12
  481. package/lib/mol-plugin/behavior/dynamic/representation.js +7 -7
  482. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  483. package/lib/mol-plugin/config.d.ts +3 -0
  484. package/lib/mol-plugin/config.js +3 -1
  485. package/lib/mol-plugin/context.d.ts +2 -2
  486. package/lib/mol-plugin/context.js +3 -0
  487. package/lib/mol-plugin/state.d.ts +1 -14
  488. package/lib/mol-plugin/version.js +2 -2
  489. package/lib/mol-plugin-state/formats/volume.d.ts +12 -11
  490. package/lib/mol-plugin-state/formats/volume.js +20 -13
  491. package/lib/mol-plugin-state/helpers/structure-selection-query.js +5 -5
  492. package/lib/mol-plugin-state/transforms/representation.js +2 -2
  493. package/lib/mol-plugin-ui/controls/parameters.d.ts +1 -1
  494. package/lib/mol-plugin-ui/controls.js +1 -1
  495. package/lib/mol-plugin-ui/sequence/polymer.js +1 -1
  496. package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
  497. package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
  498. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  499. package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
  500. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  501. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  502. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  503. package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
  504. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  505. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  506. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  507. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  508. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  509. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +128 -128
  510. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  511. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  512. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  513. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  514. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  515. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  516. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  517. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  518. package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
  519. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  520. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  521. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  522. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  523. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  524. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  525. package/lib/mol-plugin-ui/state/snapshots.js +1 -0
  526. package/lib/mol-plugin-ui/structure/focus.js +1 -1
  527. package/lib/mol-plugin-ui/viewport/screenshot.js +1 -0
  528. package/lib/mol-plugin-ui/viewport.d.ts +2 -2
  529. package/lib/mol-repr/shape/representation.d.ts +1 -1
  530. package/lib/mol-repr/shape/representation.js +2 -1
  531. package/lib/mol-repr/structure/complex-visual.d.ts +1 -1
  532. package/lib/mol-repr/structure/complex-visual.js +2 -1
  533. package/lib/mol-repr/structure/units-visual.d.ts +1 -1
  534. package/lib/mol-repr/structure/units-visual.js +2 -1
  535. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +10 -10
  536. package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -10
  537. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +12 -15
  538. package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +12 -15
  539. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +16 -16
  540. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +1 -1
  541. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -0
  542. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +4 -4
  543. package/lib/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
  544. package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +2 -2
  545. package/lib/mol-repr/structure/visual/util/bond.js +2 -2
  546. package/lib/mol-repr/structure/visual/util/common.js +3 -3
  547. package/lib/mol-repr/structure/visual/util/link.js +30 -30
  548. package/lib/mol-repr/structure/visual/util/polymer/backbone.js +6 -6
  549. package/lib/mol-repr/structure/visual/util/polymer/gap-iterator.js +3 -3
  550. package/lib/mol-repr/structure/visual/util/polymer/trace-iterator.js +20 -20
  551. package/lib/mol-repr/structure/visual/util/polymer.js +6 -6
  552. package/lib/mol-repr/volume/representation.d.ts +1 -1
  553. package/lib/mol-repr/volume/representation.js +2 -1
  554. package/lib/mol-script/language/builder.d.ts +1 -0
  555. package/lib/mol-script/language/symbol-table/core.d.ts +2 -2
  556. package/lib/mol-script/runtime/query/table.js +13 -13
  557. package/lib/mol-state/object.d.ts +3 -3
  558. package/lib/mol-task/util/user-timing.js +1 -1
  559. package/lib/mol-theme/clipping.js +19 -19
  560. package/lib/mol-theme/color/atom-id.js +1 -1
  561. package/lib/mol-theme/color/carbohydrate-symbol.js +1 -1
  562. package/lib/mol-theme/color/chain-id.js +4 -4
  563. package/lib/mol-theme/color/element-index.js +1 -1
  564. package/lib/mol-theme/color/element-symbol.js +1 -1
  565. package/lib/mol-theme/color/entity-id.js +4 -4
  566. package/lib/mol-theme/color/entity-source.js +5 -4
  567. package/lib/mol-theme/color/hydrophobicity.js +1 -1
  568. package/lib/mol-theme/color/illustrative.js +1 -1
  569. package/lib/mol-theme/color/model-index.js +1 -1
  570. package/lib/mol-theme/color/molecule-type.js +8 -8
  571. package/lib/mol-theme/color/occupancy.js +1 -1
  572. package/lib/mol-theme/color/operator-hkl.js +1 -1
  573. package/lib/mol-theme/color/operator-name.js +1 -1
  574. package/lib/mol-theme/color/partial-charge.js +1 -1
  575. package/lib/mol-theme/color/polymer-id.js +4 -4
  576. package/lib/mol-theme/color/polymer-index.js +1 -1
  577. package/lib/mol-theme/color/residue-name.js +1 -1
  578. package/lib/mol-theme/color/secondary-structure.js +12 -12
  579. package/lib/mol-theme/color/sequence-id.js +7 -7
  580. package/lib/mol-theme/color/shape-group.js +1 -1
  581. package/lib/mol-theme/color/uncertainty.js +1 -1
  582. package/lib/mol-theme/color/uniform.js +1 -1
  583. package/lib/mol-theme/color/unit-index.js +1 -1
  584. package/lib/mol-theme/color/volume-value.js +1 -1
  585. package/lib/mol-theme/label.js +3 -3
  586. package/lib/mol-util/binding.js +4 -4
  587. package/lib/mol-util/debug.d.ts +6 -1
  588. package/lib/mol-util/debug.js +9 -1
  589. package/lib/mol-util/input/input-observer.js +20 -20
  590. package/lib/mol-util/string-builder.js +1 -1
  591. package/lib/servers/model/preprocess/converter.js +1 -1
  592. package/lib/servers/model/server/query.js +1 -1
  593. package/lib/servers/model/utils/fetch-retry.js +3 -2
  594. package/lib/servers/volume/server/algebra/coordinate.js +6 -6
  595. package/lib/servers/volume/server/query/encode.js +1 -1
  596. package/package.json +162 -162
@@ -1,99 +1,99 @@
1
- .msp-task-state {
2
-
3
- line-height: $row-height;
4
- //height: $row-height;
5
- //position: relative;
6
- //margin-top: 1px;
7
-
8
- > span {
9
- @include non-selectable;
10
- //display: inline-block;
11
- //padding: 0 $control-spacing;
12
- }
13
- }
14
-
15
- .msp-overlay-tasks {
16
- position: absolute;
17
- display: flex;
18
- top: 0;
19
- left: 0;
20
- bottom: 0;
21
- right: 0;
22
- height: 100%;
23
- width: 100%;
24
- z-index: 1000;
25
- justify-content: center;
26
- align-items: center;
27
- background: rgba(0, 0, 0, 0.25);
28
-
29
- .msp-task-state {
30
- $size: $row-height;
31
-
32
- > div {
33
- height: $size;
34
- margin-top: 1px;
35
- position: relative;
36
- width: 100%;
37
- background: $default-background;
38
-
39
- > div {
40
- height: $size;
41
- line-height: $size;
42
- display: inline-block;
43
- padding: 0 ($control-spacing);
44
- @include non-selectable;
45
- white-space: nowrap;
46
- background: $default-background;
47
- position: absolute;
48
- }
49
-
50
- > button {
51
- display: inline-block;
52
- margin-top: -3px;
53
- // font-size: 140%;
54
- }
55
- }
56
- }
57
- }
58
-
59
- /* background */
60
-
61
- .msp-background-tasks {
62
- position: absolute;
63
- left: 0;
64
- bottom: 0;
65
- z-index: 1000;
66
-
67
- .msp-task-state {
68
- $size: $row-height;
69
-
70
- > div {
71
- height: $size;
72
- margin-top: 1px;
73
- position: relative;
74
- width: 100%;
75
- background: $default-background;
76
-
77
- > div {
78
- height: $size;
79
- line-height: $size;
80
- display: inline-block;
81
- padding: 0 ($control-spacing);
82
- @include non-selectable;
83
- white-space: nowrap;
84
- background: $default-background;
85
- position: absolute;
86
- }
87
-
88
- > button {
89
- display: inline-block;
90
- margin-top: -3px;
91
- // font-size: 140%;
92
- }
93
- }
94
- }
95
- }
96
-
97
- // .msp-background-tasks .msp-task-state {
98
- // color:
99
- // }
1
+ .msp-task-state {
2
+
3
+ line-height: $row-height;
4
+ //height: $row-height;
5
+ //position: relative;
6
+ //margin-top: 1px;
7
+
8
+ > span {
9
+ @include non-selectable;
10
+ //display: inline-block;
11
+ //padding: 0 $control-spacing;
12
+ }
13
+ }
14
+
15
+ .msp-overlay-tasks {
16
+ position: absolute;
17
+ display: flex;
18
+ top: 0;
19
+ left: 0;
20
+ bottom: 0;
21
+ right: 0;
22
+ height: 100%;
23
+ width: 100%;
24
+ z-index: 1000;
25
+ justify-content: center;
26
+ align-items: center;
27
+ background: rgba(0, 0, 0, 0.25);
28
+
29
+ .msp-task-state {
30
+ $size: $row-height;
31
+
32
+ > div {
33
+ height: $size;
34
+ margin-top: 1px;
35
+ position: relative;
36
+ width: 100%;
37
+ background: $default-background;
38
+
39
+ > div {
40
+ height: $size;
41
+ line-height: $size;
42
+ display: inline-block;
43
+ padding: 0 ($control-spacing);
44
+ @include non-selectable;
45
+ white-space: nowrap;
46
+ background: $default-background;
47
+ position: absolute;
48
+ }
49
+
50
+ > button {
51
+ display: inline-block;
52
+ margin-top: -3px;
53
+ // font-size: 140%;
54
+ }
55
+ }
56
+ }
57
+ }
58
+
59
+ /* background */
60
+
61
+ .msp-background-tasks {
62
+ position: absolute;
63
+ left: 0;
64
+ bottom: 0;
65
+ z-index: 1000;
66
+
67
+ .msp-task-state {
68
+ $size: $row-height;
69
+
70
+ > div {
71
+ height: $size;
72
+ margin-top: 1px;
73
+ position: relative;
74
+ width: 100%;
75
+ background: $default-background;
76
+
77
+ > div {
78
+ height: $size;
79
+ line-height: $size;
80
+ display: inline-block;
81
+ padding: 0 ($control-spacing);
82
+ @include non-selectable;
83
+ white-space: nowrap;
84
+ background: $default-background;
85
+ position: absolute;
86
+ }
87
+
88
+ > button {
89
+ display: inline-block;
90
+ margin-top: -3px;
91
+ // font-size: 140%;
92
+ }
93
+ }
94
+ }
95
+ }
96
+
97
+ // .msp-background-tasks .msp-task-state {
98
+ // color:
99
+ // }
@@ -1,84 +1,84 @@
1
-
2
- @use "sass:math";
3
-
4
- .msp-toast-container {
5
- position: relative;
6
- // bottom: $control-spacing;
7
- // right: $control-spacing;
8
- // margin-left: $control-spacing;
9
- z-index: 1001;
10
-
11
- .msp-toast-entry {
12
- color: $font-color;
13
- background: $control-background;
14
- position: relative;
15
- float: right;
16
- min-height: $row-height;
17
- margin-top: $control-spacing;
18
- border: 1px solid $border-color;
19
- display: table;
20
-
21
- .msp-toast-title {
22
- height: 100%;
23
- line-height: $row-height;
24
- padding: 0 $control-spacing;
25
- background: $default-background;
26
- font-weight: bold;
27
- display: table-cell;
28
-
29
- -webkit-user-select: none; /* Chrome/Safari */
30
- -moz-user-select: none; /* Firefox */
31
- -ms-user-select: none; /* IE10+ */
32
-
33
- /* Rules below not implemented in browsers yet */
34
- -o-user-select: none;
35
- user-select: none;
36
-
37
- font-weight: light;
38
-
39
- cursor: pointer;
40
- }
41
-
42
- .msp-toast-message {
43
- padding: $info-vertical-padding ($control-spacing + $row-height) $info-vertical-padding $control-spacing;
44
- display: table-cell;
45
-
46
- a {
47
- text-decoration: none;
48
- color: $msp-btn-commit-on-font-color;
49
- font-weight: bold;
50
-
51
- &:hover {
52
- text-decoration: underline;
53
- color: $msp-btn-commit-on-hover-font-color;
54
- }
55
-
56
- &:active, &:focus {
57
- color: $msp-btn-commit-on-font-color;
58
- outline-offset: 0;
59
- outline: none;
60
- }
61
- }
62
- }
63
-
64
- .msp-toast-hide {
65
- position: absolute;
66
- width: $row-height + $control-spacing;
67
- right: 0;
68
- top: 0;
69
- bottom: 0;
70
-
71
- .msp-btn-icon {
72
- background: transparent;
73
- position: absolute;
74
- top: 1px;
75
- right: 0;
76
- left: 0;
77
- bottom: 0;
78
- width: 100%;
79
- text-align: right;
80
- padding-right: math.div($control-spacing, 2);
81
- }
82
- }
83
- }
1
+
2
+ @use "sass:math";
3
+
4
+ .msp-toast-container {
5
+ position: relative;
6
+ // bottom: $control-spacing;
7
+ // right: $control-spacing;
8
+ // margin-left: $control-spacing;
9
+ z-index: 1001;
10
+
11
+ .msp-toast-entry {
12
+ color: $font-color;
13
+ background: $control-background;
14
+ position: relative;
15
+ float: right;
16
+ min-height: $row-height;
17
+ margin-top: $control-spacing;
18
+ border: 1px solid $border-color;
19
+ display: table;
20
+
21
+ .msp-toast-title {
22
+ height: 100%;
23
+ line-height: $row-height;
24
+ padding: 0 $control-spacing;
25
+ background: $default-background;
26
+ font-weight: bold;
27
+ display: table-cell;
28
+
29
+ -webkit-user-select: none; /* Chrome/Safari */
30
+ -moz-user-select: none; /* Firefox */
31
+ -ms-user-select: none; /* IE10+ */
32
+
33
+ /* Rules below not implemented in browsers yet */
34
+ -o-user-select: none;
35
+ user-select: none;
36
+
37
+ font-weight: light;
38
+
39
+ cursor: pointer;
40
+ }
41
+
42
+ .msp-toast-message {
43
+ padding: $info-vertical-padding ($control-spacing + $row-height) $info-vertical-padding $control-spacing;
44
+ display: table-cell;
45
+
46
+ a {
47
+ text-decoration: none;
48
+ color: $msp-btn-commit-on-font-color;
49
+ font-weight: bold;
50
+
51
+ &:hover {
52
+ text-decoration: underline;
53
+ color: $msp-btn-commit-on-hover-font-color;
54
+ }
55
+
56
+ &:active, &:focus {
57
+ color: $msp-btn-commit-on-font-color;
58
+ outline-offset: 0;
59
+ outline: none;
60
+ }
61
+ }
62
+ }
63
+
64
+ .msp-toast-hide {
65
+ position: absolute;
66
+ width: $row-height + $control-spacing;
67
+ right: 0;
68
+ top: 0;
69
+ bottom: 0;
70
+
71
+ .msp-btn-icon {
72
+ background: transparent;
73
+ position: absolute;
74
+ top: 1px;
75
+ right: 0;
76
+ left: 0;
77
+ bottom: 0;
78
+ width: 100%;
79
+ text-align: right;
80
+ padding-right: math.div($control-spacing, 2);
81
+ }
82
+ }
83
+ }
84
84
  }
@@ -1,164 +1,164 @@
1
- .msp-transformer {
2
-
3
- .msp-entity-badge {
4
- position: absolute;
5
- top: 0;
6
- right: 0;
7
- height: $row-height;
8
- line-height: $row-height;
9
- width: $row-height;
10
- }
11
- }
12
-
13
- .msp-layout-right, .msp-layout-left {
14
- background: $control-background;
15
- }
16
-
17
- .msp-transformer-wrapper {
18
- position: relative;
19
- }
20
-
21
- .msp-transformer-wrapper {
22
-
23
- .msp-entity-badge {
24
- left: 0;
25
- top: 0;
26
- }
27
-
28
- &:first-child {
29
- .msp-panel-description-content {
30
- top: $row-height + 1;
31
- }
32
- }
33
-
34
- &:not(:first-child) {
35
- .msp-panel-description-content {
36
- bottom: $row-height + 1;
37
- }
38
- }
39
- }
40
-
41
- .msp-transform-wrapper {
42
- margin-bottom: $control-spacing;
43
- }
44
-
45
- .msp-transform-wrapper-collapsed {
46
- margin-bottom: 1px;
47
- }
48
-
49
- .msp-transform-update-wrapper {
50
- margin-bottom: 1px;
51
- }
52
-
53
- .msp-transform-update-wrapper-collapsed {
54
- margin-bottom: 1px;
55
- }
56
-
57
- .msp-transform-update-wrapper, .msp-transform-update-wrapper-collapsed {
58
- > .msp-transform-header > button {
59
- text-align: left;
60
- padding-left: $row-height;
61
- line-height: 24px;
62
- background: color-lower-contrast($control-background, 4%); // $control-background; // color-lower-contrast($default-background, 4%);
63
- // font-weight: bold;
64
- }
65
- }
66
-
67
- .msp-transform-wrapper > .msp-transform-header > button {
68
- text-align: left;
69
- background: $default-background; // color-lower-contrast($default-background, 4%);
70
- font-weight: bold;
71
- padding-right: 5px;
72
- }
73
-
74
- .msp-transform-header {
75
- position: relative;
76
- // border-top: 1px solid $entity-color-Behaviour; // TODO: separate color
77
-
78
- // > button {
79
- // text-align: left;
80
- // padding-left: $row-height;
81
- // background: $control-background; // color-lower-contrast($default-background, 4%);
82
- // font-weight: bold;
83
- // }
84
-
85
- > button > small {
86
- font-weight: normal;
87
- float: right;
88
- }
89
-
90
- > button {
91
- > span:first-child {
92
- margin-right: 10px;
93
- }
94
- }
95
-
96
- > button:hover {
97
- color: color-lower-contrast($font-color, 15%);
98
- }
99
- }
100
-
101
- .msp-transform-header-brand {
102
- // padding-left: 42px;
103
- margin-bottom: -1px;
104
- svg {
105
- fill: $font-color;
106
- stroke: $font-color;
107
- }
108
- // > div {
109
- // position: absolute;
110
- // height: 32px;
111
- // line-height: 32px;
112
- // width: 32px;
113
- // top: 0;
114
- // left: 0;
115
- // text-align: center;
116
- // color: #eceff3;
117
- // fill: #eceff3;
118
- // stroke: #eceff3;
119
- // font-size: 85%;
120
- // }
121
- }
122
-
123
- .msp-transform-default-params {
124
- background: $default-background;
125
- position: absolute;
126
- left: 0;
127
- top: 0;
128
- width: $row-height;
129
- padding: 0;
130
- }
131
-
132
- .msp-transform-default-params:hover {
133
- background: color-lower-contrast($default-background, 20%);
134
- }
135
-
136
- .msp-transform-apply-wrap {
137
- position: relative;
138
- margin-top: 1px;
139
- width: 100%;
140
- height: $row-height;
141
- }
142
-
143
- .msp-transform-refresh {
144
- width: $control-label-width + $control-spacing - $row-height - 1;
145
- margin-left: $row-height + 1;
146
- background: $default-background;
147
- text-align: right;
148
- }
149
-
150
- .msp-transform-apply {
151
- display: block;
152
- position: absolute;
153
- left: $control-label-width + $control-spacing;
154
- right: 0;
155
- top: 0;
156
- }
157
-
158
- .msp-transform-apply-wider {
159
- margin-left: $row-height + 1px;
160
- }
161
-
162
- .msp-data-beh {
163
- margin: $control-spacing 0 !important;
1
+ .msp-transformer {
2
+
3
+ .msp-entity-badge {
4
+ position: absolute;
5
+ top: 0;
6
+ right: 0;
7
+ height: $row-height;
8
+ line-height: $row-height;
9
+ width: $row-height;
10
+ }
11
+ }
12
+
13
+ .msp-layout-right, .msp-layout-left {
14
+ background: $control-background;
15
+ }
16
+
17
+ .msp-transformer-wrapper {
18
+ position: relative;
19
+ }
20
+
21
+ .msp-transformer-wrapper {
22
+
23
+ .msp-entity-badge {
24
+ left: 0;
25
+ top: 0;
26
+ }
27
+
28
+ &:first-child {
29
+ .msp-panel-description-content {
30
+ top: $row-height + 1;
31
+ }
32
+ }
33
+
34
+ &:not(:first-child) {
35
+ .msp-panel-description-content {
36
+ bottom: $row-height + 1;
37
+ }
38
+ }
39
+ }
40
+
41
+ .msp-transform-wrapper {
42
+ margin-bottom: $control-spacing;
43
+ }
44
+
45
+ .msp-transform-wrapper-collapsed {
46
+ margin-bottom: 1px;
47
+ }
48
+
49
+ .msp-transform-update-wrapper {
50
+ margin-bottom: 1px;
51
+ }
52
+
53
+ .msp-transform-update-wrapper-collapsed {
54
+ margin-bottom: 1px;
55
+ }
56
+
57
+ .msp-transform-update-wrapper, .msp-transform-update-wrapper-collapsed {
58
+ > .msp-transform-header > button {
59
+ text-align: left;
60
+ padding-left: $row-height;
61
+ line-height: 24px;
62
+ background: color-lower-contrast($control-background, 4%); // $control-background; // color-lower-contrast($default-background, 4%);
63
+ // font-weight: bold;
64
+ }
65
+ }
66
+
67
+ .msp-transform-wrapper > .msp-transform-header > button {
68
+ text-align: left;
69
+ background: $default-background; // color-lower-contrast($default-background, 4%);
70
+ font-weight: bold;
71
+ padding-right: 5px;
72
+ }
73
+
74
+ .msp-transform-header {
75
+ position: relative;
76
+ // border-top: 1px solid $entity-color-Behaviour; // TODO: separate color
77
+
78
+ // > button {
79
+ // text-align: left;
80
+ // padding-left: $row-height;
81
+ // background: $control-background; // color-lower-contrast($default-background, 4%);
82
+ // font-weight: bold;
83
+ // }
84
+
85
+ > button > small {
86
+ font-weight: normal;
87
+ float: right;
88
+ }
89
+
90
+ > button {
91
+ > span:first-child {
92
+ margin-right: 10px;
93
+ }
94
+ }
95
+
96
+ > button:hover {
97
+ color: color-lower-contrast($font-color, 15%);
98
+ }
99
+ }
100
+
101
+ .msp-transform-header-brand {
102
+ // padding-left: 42px;
103
+ margin-bottom: -1px;
104
+ svg {
105
+ fill: $font-color;
106
+ stroke: $font-color;
107
+ }
108
+ // > div {
109
+ // position: absolute;
110
+ // height: 32px;
111
+ // line-height: 32px;
112
+ // width: 32px;
113
+ // top: 0;
114
+ // left: 0;
115
+ // text-align: center;
116
+ // color: #eceff3;
117
+ // fill: #eceff3;
118
+ // stroke: #eceff3;
119
+ // font-size: 85%;
120
+ // }
121
+ }
122
+
123
+ .msp-transform-default-params {
124
+ background: $default-background;
125
+ position: absolute;
126
+ left: 0;
127
+ top: 0;
128
+ width: $row-height;
129
+ padding: 0;
130
+ }
131
+
132
+ .msp-transform-default-params:hover {
133
+ background: color-lower-contrast($default-background, 20%);
134
+ }
135
+
136
+ .msp-transform-apply-wrap {
137
+ position: relative;
138
+ margin-top: 1px;
139
+ width: 100%;
140
+ height: $row-height;
141
+ }
142
+
143
+ .msp-transform-refresh {
144
+ width: $control-label-width + $control-spacing - $row-height - 1;
145
+ margin-left: $row-height + 1;
146
+ background: $default-background;
147
+ text-align: right;
148
+ }
149
+
150
+ .msp-transform-apply {
151
+ display: block;
152
+ position: absolute;
153
+ left: $control-label-width + $control-spacing;
154
+ right: 0;
155
+ top: 0;
156
+ }
157
+
158
+ .msp-transform-apply-wider {
159
+ margin-left: $row-height + 1px;
160
+ }
161
+
162
+ .msp-data-beh {
163
+ margin: $control-spacing 0 !important;
164
164
  }