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
@@ -1,419 +1,419 @@
1
- @use "sass:math";
2
-
3
- .msp-control-row {
4
- position: relative;
5
- height: $row-height;
6
- background: $default-background;
7
- margin-top: 1px;
8
-
9
- select, button, input[type=text] {
10
- @extend .msp-form-control;
11
- }
12
-
13
- button {
14
- @extend .msp-btn;
15
- @extend .msp-btn-block;
16
- }
17
-
18
- > span.msp-control-row-label, > button.msp-control-button-label {
19
- line-height: $row-height;
20
- display: block;
21
- width: $control-label-width + $control-spacing;
22
- text-align: right;
23
- padding: 0 $control-spacing;
24
- color: color-lower-contrast($font-color, 15%);
25
- overflow: hidden;
26
- text-overflow: ellipsis;
27
- white-space: nowrap;
28
- position: relative;
29
-
30
- @include non-selectable;
31
- }
32
-
33
- > button.msp-control-button-label {
34
- background: $default-background;
35
- cursor: pointer;
36
- }
37
-
38
- .msp-control-current {
39
- background: $default-background;
40
- }
41
-
42
- > div.msp-control-row-ctrl {
43
- position: absolute;
44
- left: $control-label-width + $control-spacing;
45
- top: 0;
46
- right: 0;
47
- bottom: 0;
48
- }
49
-
50
- > div {
51
- background: $msp-form-control-background;
52
- }
53
-
54
- > .msp-flex-row {
55
- background: $default-background;
56
- }
57
- }
58
-
59
- .msp-control-label-short {
60
- > span {
61
- width: $control-label-short-width + $control-spacing !important;
62
- }
63
-
64
- > div:nth-child(2) {
65
- left: $control-label-short-width + $control-spacing !important;
66
- }
67
- }
68
-
69
- .msp-control-col-2 {
70
- float: left;
71
- width: 50%;
72
- }
73
-
74
- .msp-control-group {
75
- position: relative;
76
- }
77
-
78
- .msp-toggle-button {
79
- .msp-icon {
80
- display: inline-block;
81
- margin-right: 6px;
82
- }
83
-
84
- > div > button:hover {
85
- border-color: color-increase-contrast($msp-form-control-background, 5%) !important;
86
- border: none;
87
- outline-offset: -1px !important;
88
- outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
89
- }
90
- }
91
-
92
- .msp-slider {
93
- > div:first-child {
94
- position: absolute;
95
- top: 0;
96
- left: 18px;
97
- bottom: 0;
98
- right: 62px;
99
- display: flex;
100
- }
101
- > div:last-child {
102
- position: absolute;
103
- height: $row-height;
104
- line-height: $row-height;
105
- text-align: center;
106
- right: 0;
107
- width: 50px;
108
- top: 0;
109
- bottom: 0;
110
- }
111
-
112
- input[type=text] {
113
- padding-right: 6px;
114
- padding-left: 4px;
115
- font-size: 80%;
116
- text-align: right;
117
- }
118
-
119
- // input[type=range] {
120
- // width: 100%;
121
- // }
122
- }
123
-
124
- .msp-slider2 {
125
- > div:first-child {
126
- position: absolute;
127
- height: $row-height;
128
- line-height: $row-height;
129
- text-align: center;
130
- left: 0;
131
- width: 25px;
132
- top: 0;
133
- bottom: 0;
134
- font-size: 80%;
135
- }
136
- > div:nth-child(2) {
137
- position: absolute;
138
- top: 0;
139
- left: 35px;
140
- bottom: 0;
141
- right: 37px;
142
- display: flex;
143
- }
144
- > div:last-child {
145
- position: absolute;
146
- height: $row-height;
147
- line-height: $row-height;
148
- text-align: center;
149
- right: 0;
150
- width: 25px;
151
- top: 0;
152
- bottom: 0;
153
- font-size: 80%;
154
- }
155
-
156
- input[type=text] {
157
- padding-right: 4px;
158
- padding-left: 4px;
159
- font-size: 80%;
160
- text-align: center;
161
- }
162
-
163
- // input[type=range] {
164
- // width: 100%;
165
- // }
166
- }
167
-
168
- .msp-toggle-color-picker {
169
- button {
170
- border: $control-spacing solid $msp-form-control-background !important;
171
- margin: 0;
172
- text-align: center;
173
- padding-right: $control-spacing;
174
- padding-left: $control-spacing;
175
-
176
- &:hover {
177
- border-color: color-increase-contrast($msp-form-control-background, 5%) !important;
178
- border: none;
179
- outline-offset: -1px !important;
180
- outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
181
- }
182
- }
183
-
184
- .msp-color-picker {
185
- position: absolute;
186
- z-index: 100000;
187
- background: $default-background;
188
- border-top: 1px solid $default-background;
189
- padding-bottom: math.div($control-spacing, 2);
190
- width: 100%;
191
-
192
- // input[type=text] {
193
- // background: $msp-form-control-background !important;
194
- // }
195
- }
196
- }
197
-
198
- .msp-toggle-color-picker-above {
199
- .msp-color-picker {
200
- top: -2 * 32px - 16px - math.div($control-spacing, 2);
201
- height: 2 * 32px + 16px + math.div($control-spacing, 2);
202
- }
203
- }
204
-
205
- .msp-toggle-color-picker-below {
206
- .msp-color-picker {
207
- top: $row-height;
208
- height: 2 * 32px + 16px;
209
- }
210
- }
211
-
212
- .msp-control-offset {
213
- padding-left: $control-spacing;
214
- }
215
-
216
- .msp-accent-offset {
217
- padding-left: 1px;
218
- margin-left: $control-spacing - 2;
219
- border-left: 2px solid $color-accent-orange;
220
- }
221
-
222
- // .msp-accent-offset-right {
223
- // margin-left: $control-spacing;
224
- // padding-right: 1px;
225
- // border-right: 2px solid $color-accent-orange;
226
- // }
227
-
228
- .msp-control-group-wrapper {
229
- //border-left-width: math.div($control-spacing, 2);
230
- //border-left-style: solid;
231
- //border-left-color: color-increase-contrast($default-background, 10%);
232
-
233
- margin-bottom: 0px;
234
- margin-top: 1px;
235
- }
236
-
237
- // TODO : get rid of the important
238
- .msp-control-group-header {
239
- background: $default-background;
240
- > button, div {
241
- padding-left: 4px; // math.div($control-spacing, 2) !important;
242
- text-align: left;
243
- height: 24px !important;
244
- line-height: 24px !important;
245
- font-size: 85% !important;
246
- background: $default-background !important;
247
- color: color-lower-contrast($font-color, 15%);
248
- }
249
- .msp-icon {
250
- height: 24px !important;
251
- line-height: 24px !important;
252
- }
253
- > span {
254
- padding-left: math.div($control-spacing, 2);
255
- line-height: math.div(2 * $row-height, 3);
256
- font-size: 70%;
257
- background: $default-background;
258
- color: color-lower-contrast($font-color, 15%);
259
- }
260
- }
261
-
262
- .msp-control-current {
263
- background: $default-background;
264
- }
265
-
266
- .msp-control-group-footer {
267
- background: color-increase-contrast($default-background, 5%);
268
- height: math.div($control-spacing, 2);
269
- font-size: 1px;
270
- margin-top: 1px;
271
- }
272
-
273
- .msp-control-group-expander {
274
- display: block;
275
- position: absolute;
276
- line-height: $row-height;
277
- padding: 0;
278
- left: 0;
279
- top: 0;
280
- width: $control-label-width + $control-spacing;
281
- text-align: left;
282
- background: transparent;
283
-
284
- .msp-icon {
285
- line-height: $row-height - 3;
286
- width: $row-height - 1;
287
- text-align: center;
288
- // display: inline-block;
289
- font-size: 100%;
290
- }
291
- }
292
-
293
- .msp-plugin-layout_controls {
294
- position: absolute;
295
- left: $control-spacing;
296
- top: $control-spacing;
297
- }
298
-
299
- .msp-plugin-layout_controls > button:first-child {
300
- margin-right: 6px;
301
- }
302
-
303
- .msp-empty-control {
304
- display: none;
305
- }
306
-
307
- .msp-control .msp-btn-block {
308
- margin-bottom: 0px;
309
- margin-top: 0px;
310
- }
311
-
312
- .msp-row-text {
313
- height: $row-height;
314
- position: relative;
315
- background: $default-background;
316
- margin-top: 1px;
317
-
318
- > div {
319
- line-height: $row-height;
320
- text-align: center;
321
- color: color-lower-contrast($font-color, 15%);
322
- }
323
- }
324
-
325
- .msp-help span {
326
- display: none;
327
- }
328
-
329
- .msp-help:hover span {
330
- display: inline-block;
331
- background: linear-gradient($default-background, change-color($default-background, $alpha: 0.8));
332
- }
333
-
334
- .msp-help-text {
335
- position: relative;
336
- background: $default-background;
337
- margin-top: 1px;
338
-
339
- > div {
340
- padding: (math.div($control-spacing, 2)) $control-spacing;
341
- text-align: left;
342
- color: color-lower-contrast($font-color, 15%);
343
- }
344
- }
345
-
346
- .msp-help-description {
347
- font-style: italic;
348
- }
349
-
350
- .msp-help-legend {
351
- padding-top: $control-spacing;
352
- }
353
-
354
- .msp-scale-legend {
355
- > div {
356
- width: 100%;
357
- height: $control-spacing * 3;
358
-
359
- > span {
360
- padding: math.div($control-spacing, 2);
361
- color: white;
362
- font-weight: bold;
363
- background-color: rgba(0, 0, 0, 0.2);
364
- }
365
- }
366
- }
367
-
368
- .msp-table-legend {
369
- > div {
370
- // min-width: 60px;
371
- margin-right: math.div($control-spacing, 2);
372
- display: inline-flex;
373
-
374
- .msp-table-legend-color {
375
- width: $control-spacing * 3;
376
- height: $control-spacing * 2;
377
- }
378
-
379
- .msp-table-legend-text {
380
- margin: 0 (math.div($control-spacing, 2));
381
- }
382
- }
383
- }
384
-
385
- .msp-image-preview {
386
- position: relative;
387
- background: $default-background;
388
- margin-top: 1px;
389
- padding: $control-spacing;
390
-
391
- canvas {
392
- @include user-select(none);
393
- }
394
-
395
- > span {
396
- margin-top: 6px;
397
- display: block;
398
- text-align: center;
399
- font-size: 80%;
400
- line-height: 15px;
401
- }
402
- }
403
-
404
- .msp-copy-image-wrapper {
405
- position: relative;
406
-
407
- div {
408
- font-weight: bold;
409
- padding: 3px;
410
- margin: 1px 0;
411
- width: 100%;
412
- background: $msp-form-control-background;
413
- text-align: center;
414
- }
415
-
416
- img {
417
- margin-top: 1px;
418
- }
1
+ @use "sass:math";
2
+
3
+ .msp-control-row {
4
+ position: relative;
5
+ height: $row-height;
6
+ background: $default-background;
7
+ margin-top: 1px;
8
+
9
+ select, button, input[type=text] {
10
+ @extend .msp-form-control;
11
+ }
12
+
13
+ button {
14
+ @extend .msp-btn;
15
+ @extend .msp-btn-block;
16
+ }
17
+
18
+ > span.msp-control-row-label, > button.msp-control-button-label {
19
+ line-height: $row-height;
20
+ display: block;
21
+ width: $control-label-width + $control-spacing;
22
+ text-align: right;
23
+ padding: 0 $control-spacing;
24
+ color: color-lower-contrast($font-color, 15%);
25
+ overflow: hidden;
26
+ text-overflow: ellipsis;
27
+ white-space: nowrap;
28
+ position: relative;
29
+
30
+ @include non-selectable;
31
+ }
32
+
33
+ > button.msp-control-button-label {
34
+ background: $default-background;
35
+ cursor: pointer;
36
+ }
37
+
38
+ .msp-control-current {
39
+ background: $default-background;
40
+ }
41
+
42
+ > div.msp-control-row-ctrl {
43
+ position: absolute;
44
+ left: $control-label-width + $control-spacing;
45
+ top: 0;
46
+ right: 0;
47
+ bottom: 0;
48
+ }
49
+
50
+ > div {
51
+ background: $msp-form-control-background;
52
+ }
53
+
54
+ > .msp-flex-row {
55
+ background: $default-background;
56
+ }
57
+ }
58
+
59
+ .msp-control-label-short {
60
+ > span {
61
+ width: $control-label-short-width + $control-spacing !important;
62
+ }
63
+
64
+ > div:nth-child(2) {
65
+ left: $control-label-short-width + $control-spacing !important;
66
+ }
67
+ }
68
+
69
+ .msp-control-col-2 {
70
+ float: left;
71
+ width: 50%;
72
+ }
73
+
74
+ .msp-control-group {
75
+ position: relative;
76
+ }
77
+
78
+ .msp-toggle-button {
79
+ .msp-icon {
80
+ display: inline-block;
81
+ margin-right: 6px;
82
+ }
83
+
84
+ > div > button:hover {
85
+ border-color: color-increase-contrast($msp-form-control-background, 5%) !important;
86
+ border: none;
87
+ outline-offset: -1px !important;
88
+ outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
89
+ }
90
+ }
91
+
92
+ .msp-slider {
93
+ > div:first-child {
94
+ position: absolute;
95
+ top: 0;
96
+ left: 18px;
97
+ bottom: 0;
98
+ right: 62px;
99
+ display: flex;
100
+ }
101
+ > div:last-child {
102
+ position: absolute;
103
+ height: $row-height;
104
+ line-height: $row-height;
105
+ text-align: center;
106
+ right: 0;
107
+ width: 50px;
108
+ top: 0;
109
+ bottom: 0;
110
+ }
111
+
112
+ input[type=text] {
113
+ padding-right: 6px;
114
+ padding-left: 4px;
115
+ font-size: 80%;
116
+ text-align: right;
117
+ }
118
+
119
+ // input[type=range] {
120
+ // width: 100%;
121
+ // }
122
+ }
123
+
124
+ .msp-slider2 {
125
+ > div:first-child {
126
+ position: absolute;
127
+ height: $row-height;
128
+ line-height: $row-height;
129
+ text-align: center;
130
+ left: 0;
131
+ width: 25px;
132
+ top: 0;
133
+ bottom: 0;
134
+ font-size: 80%;
135
+ }
136
+ > div:nth-child(2) {
137
+ position: absolute;
138
+ top: 0;
139
+ left: 35px;
140
+ bottom: 0;
141
+ right: 37px;
142
+ display: flex;
143
+ }
144
+ > div:last-child {
145
+ position: absolute;
146
+ height: $row-height;
147
+ line-height: $row-height;
148
+ text-align: center;
149
+ right: 0;
150
+ width: 25px;
151
+ top: 0;
152
+ bottom: 0;
153
+ font-size: 80%;
154
+ }
155
+
156
+ input[type=text] {
157
+ padding-right: 4px;
158
+ padding-left: 4px;
159
+ font-size: 80%;
160
+ text-align: center;
161
+ }
162
+
163
+ // input[type=range] {
164
+ // width: 100%;
165
+ // }
166
+ }
167
+
168
+ .msp-toggle-color-picker {
169
+ button {
170
+ border: $control-spacing solid $msp-form-control-background !important;
171
+ margin: 0;
172
+ text-align: center;
173
+ padding-right: $control-spacing;
174
+ padding-left: $control-spacing;
175
+
176
+ &:hover {
177
+ border-color: color-increase-contrast($msp-form-control-background, 5%) !important;
178
+ border: none;
179
+ outline-offset: -1px !important;
180
+ outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
181
+ }
182
+ }
183
+
184
+ .msp-color-picker {
185
+ position: absolute;
186
+ z-index: 100000;
187
+ background: $default-background;
188
+ border-top: 1px solid $default-background;
189
+ padding-bottom: math.div($control-spacing, 2);
190
+ width: 100%;
191
+
192
+ // input[type=text] {
193
+ // background: $msp-form-control-background !important;
194
+ // }
195
+ }
196
+ }
197
+
198
+ .msp-toggle-color-picker-above {
199
+ .msp-color-picker {
200
+ top: -2 * 32px - 16px - math.div($control-spacing, 2);
201
+ height: 2 * 32px + 16px + math.div($control-spacing, 2);
202
+ }
203
+ }
204
+
205
+ .msp-toggle-color-picker-below {
206
+ .msp-color-picker {
207
+ top: $row-height;
208
+ height: 2 * 32px + 16px;
209
+ }
210
+ }
211
+
212
+ .msp-control-offset {
213
+ padding-left: $control-spacing;
214
+ }
215
+
216
+ .msp-accent-offset {
217
+ padding-left: 1px;
218
+ margin-left: $control-spacing - 2;
219
+ border-left: 2px solid $color-accent-orange;
220
+ }
221
+
222
+ // .msp-accent-offset-right {
223
+ // margin-left: $control-spacing;
224
+ // padding-right: 1px;
225
+ // border-right: 2px solid $color-accent-orange;
226
+ // }
227
+
228
+ .msp-control-group-wrapper {
229
+ //border-left-width: math.div($control-spacing, 2);
230
+ //border-left-style: solid;
231
+ //border-left-color: color-increase-contrast($default-background, 10%);
232
+
233
+ margin-bottom: 0px;
234
+ margin-top: 1px;
235
+ }
236
+
237
+ // TODO : get rid of the important
238
+ .msp-control-group-header {
239
+ background: $default-background;
240
+ > button, div {
241
+ padding-left: 4px; // math.div($control-spacing, 2) !important;
242
+ text-align: left;
243
+ height: 24px !important;
244
+ line-height: 24px !important;
245
+ font-size: 85% !important;
246
+ background: $default-background !important;
247
+ color: color-lower-contrast($font-color, 15%);
248
+ }
249
+ .msp-icon {
250
+ height: 24px !important;
251
+ line-height: 24px !important;
252
+ }
253
+ > span {
254
+ padding-left: math.div($control-spacing, 2);
255
+ line-height: math.div(2 * $row-height, 3);
256
+ font-size: 70%;
257
+ background: $default-background;
258
+ color: color-lower-contrast($font-color, 15%);
259
+ }
260
+ }
261
+
262
+ .msp-control-current {
263
+ background: $default-background;
264
+ }
265
+
266
+ .msp-control-group-footer {
267
+ background: color-increase-contrast($default-background, 5%);
268
+ height: math.div($control-spacing, 2);
269
+ font-size: 1px;
270
+ margin-top: 1px;
271
+ }
272
+
273
+ .msp-control-group-expander {
274
+ display: block;
275
+ position: absolute;
276
+ line-height: $row-height;
277
+ padding: 0;
278
+ left: 0;
279
+ top: 0;
280
+ width: $control-label-width + $control-spacing;
281
+ text-align: left;
282
+ background: transparent;
283
+
284
+ .msp-icon {
285
+ line-height: $row-height - 3;
286
+ width: $row-height - 1;
287
+ text-align: center;
288
+ // display: inline-block;
289
+ font-size: 100%;
290
+ }
291
+ }
292
+
293
+ .msp-plugin-layout_controls {
294
+ position: absolute;
295
+ left: $control-spacing;
296
+ top: $control-spacing;
297
+ }
298
+
299
+ .msp-plugin-layout_controls > button:first-child {
300
+ margin-right: 6px;
301
+ }
302
+
303
+ .msp-empty-control {
304
+ display: none;
305
+ }
306
+
307
+ .msp-control .msp-btn-block {
308
+ margin-bottom: 0px;
309
+ margin-top: 0px;
310
+ }
311
+
312
+ .msp-row-text {
313
+ height: $row-height;
314
+ position: relative;
315
+ background: $default-background;
316
+ margin-top: 1px;
317
+
318
+ > div {
319
+ line-height: $row-height;
320
+ text-align: center;
321
+ color: color-lower-contrast($font-color, 15%);
322
+ }
323
+ }
324
+
325
+ .msp-help span {
326
+ display: none;
327
+ }
328
+
329
+ .msp-help:hover span {
330
+ display: inline-block;
331
+ background: linear-gradient($default-background, change-color($default-background, $alpha: 0.8));
332
+ }
333
+
334
+ .msp-help-text {
335
+ position: relative;
336
+ background: $default-background;
337
+ margin-top: 1px;
338
+
339
+ > div {
340
+ padding: (math.div($control-spacing, 2)) $control-spacing;
341
+ text-align: left;
342
+ color: color-lower-contrast($font-color, 15%);
343
+ }
344
+ }
345
+
346
+ .msp-help-description {
347
+ font-style: italic;
348
+ }
349
+
350
+ .msp-help-legend {
351
+ padding-top: $control-spacing;
352
+ }
353
+
354
+ .msp-scale-legend {
355
+ > div {
356
+ width: 100%;
357
+ height: $control-spacing * 3;
358
+
359
+ > span {
360
+ padding: math.div($control-spacing, 2);
361
+ color: white;
362
+ font-weight: bold;
363
+ background-color: rgba(0, 0, 0, 0.2);
364
+ }
365
+ }
366
+ }
367
+
368
+ .msp-table-legend {
369
+ > div {
370
+ // min-width: 60px;
371
+ margin-right: math.div($control-spacing, 2);
372
+ display: inline-flex;
373
+
374
+ .msp-table-legend-color {
375
+ width: $control-spacing * 3;
376
+ height: $control-spacing * 2;
377
+ }
378
+
379
+ .msp-table-legend-text {
380
+ margin: 0 (math.div($control-spacing, 2));
381
+ }
382
+ }
383
+ }
384
+
385
+ .msp-image-preview {
386
+ position: relative;
387
+ background: $default-background;
388
+ margin-top: 1px;
389
+ padding: $control-spacing;
390
+
391
+ canvas {
392
+ @include user-select(none);
393
+ }
394
+
395
+ > span {
396
+ margin-top: 6px;
397
+ display: block;
398
+ text-align: center;
399
+ font-size: 80%;
400
+ line-height: 15px;
401
+ }
402
+ }
403
+
404
+ .msp-copy-image-wrapper {
405
+ position: relative;
406
+
407
+ div {
408
+ font-weight: bold;
409
+ padding: 3px;
410
+ margin: 1px 0;
411
+ width: 100%;
412
+ background: $msp-form-control-background;
413
+ text-align: center;
414
+ }
415
+
416
+ img {
417
+ margin-top: 1px;
418
+ }
419
419
  }