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
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  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
@@ -1,128 +1,128 @@
1
- .msp-viewport {
2
- position: absolute;
3
- left: 0;
4
- top: 0;
5
- right: 0;
6
- bottom: 0;
7
- background: black;
8
-
9
- .msp-btn-link {
10
- background: rgba(0,0,0,0.2);
11
- }
12
-
13
- }
14
-
15
- .msp-viewport-expanded {
16
- position: fixed;
17
- z-index: 1000;
18
- }
19
-
20
- .msp-viewport-host3d {
21
- position: absolute;
22
- left: 0;
23
- top: 0;
24
- right: 0;
25
- bottom: 0;
26
- -webkit-user-select: none;
27
- user-select: none;
28
- -webkit-tap-highlight-color: rgba(0,0,0,0);
29
- -webkit-touch-callout: none;
30
- touch-action: manipulation;
31
-
32
- > canvas {
33
- background-color: $default-background;
34
- background-image: linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey),
35
- linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey);
36
- background-size: 60px 60px;
37
- background-position: 0 0, 30px 30px;
38
- }
39
- }
40
-
41
- .msp-viewport-controls {
42
- position: absolute;
43
- right: $control-spacing;
44
- top: $control-spacing;
45
- width: 32px;
46
- }
47
-
48
- .msp-viewport-controls-buttons {
49
- text-align: right;
50
- position: relative;
51
- // opacity: 0.5;
52
- // &:hover { opacity: 1.0; }
53
-
54
- > div {
55
- position: relative;
56
- margin-bottom: 4px;
57
- }
58
-
59
- button {
60
- padding: 0;
61
- text-align: center;
62
- width: $row-height;
63
- position: relative;
64
- }
65
-
66
- .msp-btn-link-toggle-off {
67
- color: $msp-btn-link-toggle-off-font-color;
68
- }
69
-
70
- .msp-btn-link:hover {
71
- color: $hover-font-color;
72
- }
73
- }
74
-
75
- .msp-semi-transparent-background {
76
- background: $default-background;
77
- opacity: 0.5;
78
- position: absolute;
79
- top: 0;
80
- left: 0;
81
- width: 100%;
82
- height: 100%;
83
- }
84
-
85
- .msp-viewport-controls-panel {
86
- width: 290px;
87
- top: 0;
88
- right: $row-height + 4px;
89
- position: absolute;
90
- background: $control-background;
91
-
92
- .msp-control-group-wrapper:first-child {
93
- padding-top: 0;
94
- }
95
-
96
- .msp-viewport-controls-panel-controls {
97
- overflow-y: auto;
98
- max-height: 400px;
99
- }
100
- }
101
-
102
- /* highlight & toasts */
103
-
104
- .msp-highlight-toast-wrapper {
105
- position: absolute;
106
- right: $control-spacing;
107
- bottom: $control-spacing;
108
- max-width: 95%;
109
-
110
- z-index: 10000;
111
- }
112
-
113
- .msp-highlight-info {
114
- color: $highlight-info-font-color;
115
- padding: $info-vertical-padding $control-spacing;
116
- background: $default-background; //$highlight-info-background;
117
-
118
- // min-height: $row-height;
119
- text-align: right;
120
-
121
- @include non-selectable;
122
- }
123
-
124
- .msp-highlight-info-additional {
125
- font-size: 85%;
126
- display: inline-block;
127
- color: $highlight-info-additional-font-color;
128
- }
1
+ .msp-viewport {
2
+ position: absolute;
3
+ left: 0;
4
+ top: 0;
5
+ right: 0;
6
+ bottom: 0;
7
+ background: black;
8
+
9
+ .msp-btn-link {
10
+ background: rgba(0,0,0,0.2);
11
+ }
12
+
13
+ }
14
+
15
+ .msp-viewport-expanded {
16
+ position: fixed;
17
+ z-index: 1000;
18
+ }
19
+
20
+ .msp-viewport-host3d {
21
+ position: absolute;
22
+ left: 0;
23
+ top: 0;
24
+ right: 0;
25
+ bottom: 0;
26
+ -webkit-user-select: none;
27
+ user-select: none;
28
+ -webkit-tap-highlight-color: rgba(0,0,0,0);
29
+ -webkit-touch-callout: none;
30
+ touch-action: manipulation;
31
+
32
+ > canvas {
33
+ background-color: $default-background;
34
+ background-image: linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey),
35
+ linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey);
36
+ background-size: 60px 60px;
37
+ background-position: 0 0, 30px 30px;
38
+ }
39
+ }
40
+
41
+ .msp-viewport-controls {
42
+ position: absolute;
43
+ right: $control-spacing;
44
+ top: $control-spacing;
45
+ width: 32px;
46
+ }
47
+
48
+ .msp-viewport-controls-buttons {
49
+ text-align: right;
50
+ position: relative;
51
+ // opacity: 0.5;
52
+ // &:hover { opacity: 1.0; }
53
+
54
+ > div {
55
+ position: relative;
56
+ margin-bottom: 4px;
57
+ }
58
+
59
+ button {
60
+ padding: 0;
61
+ text-align: center;
62
+ width: $row-height;
63
+ position: relative;
64
+ }
65
+
66
+ .msp-btn-link-toggle-off {
67
+ color: $msp-btn-link-toggle-off-font-color;
68
+ }
69
+
70
+ .msp-btn-link:hover {
71
+ color: $hover-font-color;
72
+ }
73
+ }
74
+
75
+ .msp-semi-transparent-background {
76
+ background: $default-background;
77
+ opacity: 0.5;
78
+ position: absolute;
79
+ top: 0;
80
+ left: 0;
81
+ width: 100%;
82
+ height: 100%;
83
+ }
84
+
85
+ .msp-viewport-controls-panel {
86
+ width: 290px;
87
+ top: 0;
88
+ right: $row-height + 4px;
89
+ position: absolute;
90
+ background: $control-background;
91
+
92
+ .msp-control-group-wrapper:first-child {
93
+ padding-top: 0;
94
+ }
95
+
96
+ .msp-viewport-controls-panel-controls {
97
+ overflow-y: auto;
98
+ max-height: 400px;
99
+ }
100
+ }
101
+
102
+ /* highlight & toasts */
103
+
104
+ .msp-highlight-toast-wrapper {
105
+ position: absolute;
106
+ right: $control-spacing;
107
+ bottom: $control-spacing;
108
+ max-width: 95%;
109
+
110
+ z-index: 10000;
111
+ }
112
+
113
+ .msp-highlight-info {
114
+ color: $highlight-info-font-color;
115
+ padding: $info-vertical-padding $control-spacing;
116
+ background: $default-background; //$highlight-info-background;
117
+
118
+ // min-height: $row-height;
119
+ text-align: right;
120
+
121
+ @include non-selectable;
122
+ }
123
+
124
+ .msp-highlight-info-additional {
125
+ font-size: 85%;
126
+ display: inline-block;
127
+ color: $highlight-info-additional-font-color;
128
+ }
@@ -1,72 +1,72 @@
1
-
2
-
3
- .msp-layout-expanded, .msp-layout-standard {
4
- left: 0;
5
- right: 0;
6
- top: 0;
7
- bottom: 0;
8
- }
9
-
10
- .msp-layout-standard {
11
- border: 1px solid $border-color;
12
- }
13
-
14
- .msp-layout-region {
15
- overflow: hidden;
16
- }
17
-
18
- .msp-layout-static, .msp-layout-scrollable {
19
- position: absolute;
20
- }
21
-
22
- .msp-scrollable {
23
- overflow-y: auto;
24
- }
25
-
26
- .msp-scrollable-container {
27
- position: absolute;
28
- left: 0;
29
- right: 0;
30
- top: 0;
31
- bottom: 0;
32
- overflow-y: auto;
33
- }
34
-
35
- .msp-layout-static {
36
- overflow: hidden;
37
- }
38
-
39
- .msp-layout-top, .msp-layout-main, .msp-layout-bottom {
40
- .msp-layout-static {
41
- left: 0;
42
- right: 0;
43
- top: 0;
44
- bottom: 0;
45
- }
46
- }
47
-
48
- .msp-layout-right {
49
- .msp-layout-static {
50
- left: 0;
51
- right: 0;
52
- top: 0;
53
- bottom: 0; // height: $row-height + $control-spacing;
54
- }
55
-
56
- .msp-layout-scrollable {
57
- left: 0;
58
- right: 0;
59
- top: $row-height + $control-spacing + 1;
60
- bottom: 0;
61
- }
62
-
63
- }
64
-
65
- .msp-layout-left {
66
- .msp-layout-static {
67
- left: 0;
68
- right: 0;
69
- bottom: 0;
70
- top: 0;
71
- }
1
+
2
+
3
+ .msp-layout-expanded, .msp-layout-standard {
4
+ left: 0;
5
+ right: 0;
6
+ top: 0;
7
+ bottom: 0;
8
+ }
9
+
10
+ .msp-layout-standard {
11
+ border: 1px solid $border-color;
12
+ }
13
+
14
+ .msp-layout-region {
15
+ overflow: hidden;
16
+ }
17
+
18
+ .msp-layout-static, .msp-layout-scrollable {
19
+ position: absolute;
20
+ }
21
+
22
+ .msp-scrollable {
23
+ overflow-y: auto;
24
+ }
25
+
26
+ .msp-scrollable-container {
27
+ position: absolute;
28
+ left: 0;
29
+ right: 0;
30
+ top: 0;
31
+ bottom: 0;
32
+ overflow-y: auto;
33
+ }
34
+
35
+ .msp-layout-static {
36
+ overflow: hidden;
37
+ }
38
+
39
+ .msp-layout-top, .msp-layout-main, .msp-layout-bottom {
40
+ .msp-layout-static {
41
+ left: 0;
42
+ right: 0;
43
+ top: 0;
44
+ bottom: 0;
45
+ }
46
+ }
47
+
48
+ .msp-layout-right {
49
+ .msp-layout-static {
50
+ left: 0;
51
+ right: 0;
52
+ top: 0;
53
+ bottom: 0; // height: $row-height + $control-spacing;
54
+ }
55
+
56
+ .msp-layout-scrollable {
57
+ left: 0;
58
+ right: 0;
59
+ top: $row-height + $control-spacing + 1;
60
+ bottom: 0;
61
+ }
62
+
63
+ }
64
+
65
+ .msp-layout-left {
66
+ .msp-layout-static {
67
+ left: 0;
68
+ right: 0;
69
+ bottom: 0;
70
+ top: 0;
71
+ }
72
72
  }
@@ -1,90 +1,90 @@
1
- 
2
- .msp-layout-main {
3
- position: absolute;
4
- left: $expanded-left-width;
5
- right: $expanded-right-width;
6
- bottom: $expanded-bottom-height;
7
- top: $expanded-top-height;
8
- }
9
-
10
- .msp-layout-top {
11
- position: absolute;
12
- left: $expanded-left-width;
13
- right: $expanded-right-width;
14
- height: $expanded-top-height;
15
- top: 0;
16
- border-bottom: 1px solid $border-color;
17
- }
18
-
19
- .msp-layout-bottom {
20
- position: absolute;
21
- left: $expanded-left-width;
22
- right: $expanded-right-width;
23
- height: $expanded-bottom-height;
24
- bottom: 0;
25
- border-top: 1px solid $border-color;
26
- }
27
-
28
- .msp-layout-right {
29
- position: absolute;
30
- width: $expanded-right-width;
31
- right: 0;
32
- bottom: 0;
33
- top: 0;
34
- border-left: 1px solid $border-color;
35
- }
36
-
37
- .msp-layout-left {
38
- position: absolute;
39
- width: $expanded-left-width;
40
- left: 0;
41
- bottom: 0;
42
- top: 0;
43
- border-right: 1px solid $border-color;
44
- }
45
-
46
- .msp-layout-hide-right {
47
- .msp-layout-right {
48
- display: none;
49
- }
50
- .msp-layout-main, .msp-layout-top, .msp-layout-bottom {
51
- right: 0;
52
- }
53
- }
54
-
55
-
56
- .msp-layout-hide-left {
57
- .msp-layout-left {
58
- display: none;
59
- }
60
- .msp-layout-main, .msp-layout-top, .msp-layout-bottom {
61
- left: 0;
62
- }
63
- }
64
-
65
- .msp-layout-collapse-left {
66
- .msp-layout-left {
67
- width: $collapsed-left-width;
68
- }
69
- .msp-layout-main, .msp-layout-top, .msp-layout-bottom {
70
- left: $collapsed-left-width;
71
- }
72
- }
73
-
74
- .msp-layout-hide-bottom {
75
- .msp-layout-bottom {
76
- display: none;
77
- }
78
- .msp-layout-main {
79
- bottom: 0;
80
- }
81
- }
82
-
83
- .msp-layout-hide-top {
84
- .msp-layout-top {
85
- display: none;
86
- }
87
- .msp-layout-main {
88
- top: 0;
89
- }
1
+ 
2
+ .msp-layout-main {
3
+ position: absolute;
4
+ left: $expanded-left-width;
5
+ right: $expanded-right-width;
6
+ bottom: $expanded-bottom-height;
7
+ top: $expanded-top-height;
8
+ }
9
+
10
+ .msp-layout-top {
11
+ position: absolute;
12
+ left: $expanded-left-width;
13
+ right: $expanded-right-width;
14
+ height: $expanded-top-height;
15
+ top: 0;
16
+ border-bottom: 1px solid $border-color;
17
+ }
18
+
19
+ .msp-layout-bottom {
20
+ position: absolute;
21
+ left: $expanded-left-width;
22
+ right: $expanded-right-width;
23
+ height: $expanded-bottom-height;
24
+ bottom: 0;
25
+ border-top: 1px solid $border-color;
26
+ }
27
+
28
+ .msp-layout-right {
29
+ position: absolute;
30
+ width: $expanded-right-width;
31
+ right: 0;
32
+ bottom: 0;
33
+ top: 0;
34
+ border-left: 1px solid $border-color;
35
+ }
36
+
37
+ .msp-layout-left {
38
+ position: absolute;
39
+ width: $expanded-left-width;
40
+ left: 0;
41
+ bottom: 0;
42
+ top: 0;
43
+ border-right: 1px solid $border-color;
44
+ }
45
+
46
+ .msp-layout-hide-right {
47
+ .msp-layout-right {
48
+ display: none;
49
+ }
50
+ .msp-layout-main, .msp-layout-top, .msp-layout-bottom {
51
+ right: 0;
52
+ }
53
+ }
54
+
55
+
56
+ .msp-layout-hide-left {
57
+ .msp-layout-left {
58
+ display: none;
59
+ }
60
+ .msp-layout-main, .msp-layout-top, .msp-layout-bottom {
61
+ left: 0;
62
+ }
63
+ }
64
+
65
+ .msp-layout-collapse-left {
66
+ .msp-layout-left {
67
+ width: $collapsed-left-width;
68
+ }
69
+ .msp-layout-main, .msp-layout-top, .msp-layout-bottom {
70
+ left: $collapsed-left-width;
71
+ }
72
+ }
73
+
74
+ .msp-layout-hide-bottom {
75
+ .msp-layout-bottom {
76
+ display: none;
77
+ }
78
+ .msp-layout-main {
79
+ bottom: 0;
80
+ }
81
+ }
82
+
83
+ .msp-layout-hide-top {
84
+ .msp-layout-top {
85
+ display: none;
86
+ }
87
+ .msp-layout-main {
88
+ top: 0;
89
+ }
90
90
  }