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
@@ -1,210 +1,210 @@
1
- /*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */
2
-
3
- //
4
- // 1. Set default font family to sans-serif.
5
- // 2. Prevent iOS and IE text size adjust after device orientation change,
6
- // without disabling user zoom.
7
- //
8
- * {
9
- box-sizing: border-box; // 1
10
- }
11
-
12
- //
13
- // Address `[hidden]` styling not present in IE 8/9/10.
14
- // Hide the `template` element in IE 8/9/10/11, Safari, and Firefox < 22.
15
- //
16
-
17
- [hidden],
18
- template {
19
- display: none;
20
- }
21
-
22
- // Links
23
- // ==========================================================================
24
-
25
- //
26
- // Remove the gray background color from active links in IE 10.
27
- //
28
-
29
- a {
30
- background-color: transparent;
31
- }
32
-
33
- //
34
- // Improve readability of focused elements when they are also in an
35
- // active/hover state.
36
- //
37
-
38
- a:active,
39
- a:hover {
40
- outline: 0;
41
- }
42
-
43
- // Text-level semantics
44
- // ==========================================================================
45
-
46
- //
47
- // Address styling not present in IE 8/9/10/11, Safari, and Chrome.
48
- //
49
-
50
- abbr[title] {
51
- border-bottom: 1px dotted;
52
- }
53
-
54
- //
55
- // Address style set to `bolder` in Firefox 4+, Safari, and Chrome.
56
- //
57
-
58
- b,
59
- strong {
60
- font-weight: bold;
61
- }
62
-
63
- //
64
- // Address inconsistent and variable font size in all browsers.
65
- //
66
-
67
- small {
68
- font-size: 80%;
69
- }
70
-
71
- // Embedded content
72
- // ==========================================================================
73
-
74
- //
75
- // Remove border when inside `a` element in IE 8/9/10.
76
- //
77
-
78
- img {
79
- border: 0;
80
- }
81
-
82
- //
83
- // Correct overflow not hidden in IE 9/10/11.
84
- //
85
-
86
- svg:not(:root) {
87
- overflow: hidden;
88
- }
89
-
90
- // Forms
91
- // ==========================================================================
92
-
93
- //
94
- // Known limitation: by default, Chrome and Safari on OS X allow very limited
95
- // styling of `select`, unless a `border` property is set.
96
- //
97
-
98
- //
99
- // 1. Correct color not being inherited.
100
- // Known issue: affects color of disabled elements.
101
- // 2. Correct font properties not being inherited.
102
- // 3. Address margins set differently in Firefox 4+, Safari, and Chrome.
103
- //
104
-
105
- button,
106
- input,
107
- optgroup,
108
- select,
109
- textarea {
110
- color: inherit; // 1
111
- font: inherit; // 2
112
- margin: 0; // 3
113
- }
114
-
115
- //
116
- // Address `overflow` set to `hidden` in IE 8/9/10/11.
117
- //
118
-
119
- button {
120
- overflow: visible;
121
- }
122
-
123
- //
124
- // Address inconsistent `text-transform` inheritance for `button` and `select`.
125
- // All other form control elements do not inherit `text-transform` values.
126
- // Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.
127
- // Correct `select` style inheritance in Firefox.
128
- //
129
-
130
- button,
131
- select {
132
- text-transform: none;
133
- }
134
-
135
- //
136
- // 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
137
- // and `video` controls.
138
- // 2. Correct inability to style clickable `input` types in iOS.
139
- // 3. Improve usability and consistency of cursor style between image-type
140
- // `input` and others.
141
- //
142
-
143
- button,
144
- html input[type="button"], // 1
145
- input[type="reset"],
146
- input[type="submit"] {
147
- -webkit-appearance: button; // 2
148
- cursor: pointer; // 3
149
- }
150
-
151
- //
152
- // Re-set default cursor for disabled elements.
153
- //
154
-
155
- button[disabled],
156
- html input[disabled] {
157
- cursor: default;
158
- }
159
-
160
- //
161
- // Remove inner padding and border in Firefox 4+.
162
- //
163
-
164
- button::-moz-focus-inner,
165
- input::-moz-focus-inner {
166
- border: 0;
167
- padding: 0;
168
- }
169
-
170
- //
171
- // Address Firefox 4+ setting `line-height` on `input` using `!important` in
172
- // the UA stylesheet.
173
- //
174
-
175
- input {
176
- line-height: normal;
177
- }
178
-
179
- //
180
- // It's recommended that you don't attempt to style these elements.
181
- // Firefox's implementation doesn't respect box-sizing, padding, or width.
182
- //
183
- // 1. Address box sizing set to `content-box` in IE 8/9/10.
184
- // 2. Remove excess padding in IE 8/9/10.
185
- //
186
-
187
- input[type="checkbox"],
188
- input[type="radio"] {
189
- box-sizing: border-box; // 1
190
- padding: 0; // 2
191
- }
192
-
193
- //
194
- // Fix the cursor style for Chrome's increment/decrement buttons. For certain
195
- // `font-size` values of the `input`, it causes the cursor style of the
196
- // decrement button to change from `default` to `text`.
197
- //
198
-
199
- input[type="number"]::-webkit-inner-spin-button,
200
- input[type="number"]::-webkit-outer-spin-button {
201
- height: auto;
202
- }
203
-
204
- //
205
- // Remove default vertical scrollbar in IE 8/9/10/11.
206
- //
207
-
208
- textarea {
209
- overflow: auto;
1
+ /*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */
2
+
3
+ //
4
+ // 1. Set default font family to sans-serif.
5
+ // 2. Prevent iOS and IE text size adjust after device orientation change,
6
+ // without disabling user zoom.
7
+ //
8
+ * {
9
+ box-sizing: border-box; // 1
10
+ }
11
+
12
+ //
13
+ // Address `[hidden]` styling not present in IE 8/9/10.
14
+ // Hide the `template` element in IE 8/9/10/11, Safari, and Firefox < 22.
15
+ //
16
+
17
+ [hidden],
18
+ template {
19
+ display: none;
20
+ }
21
+
22
+ // Links
23
+ // ==========================================================================
24
+
25
+ //
26
+ // Remove the gray background color from active links in IE 10.
27
+ //
28
+
29
+ a {
30
+ background-color: transparent;
31
+ }
32
+
33
+ //
34
+ // Improve readability of focused elements when they are also in an
35
+ // active/hover state.
36
+ //
37
+
38
+ a:active,
39
+ a:hover {
40
+ outline: 0;
41
+ }
42
+
43
+ // Text-level semantics
44
+ // ==========================================================================
45
+
46
+ //
47
+ // Address styling not present in IE 8/9/10/11, Safari, and Chrome.
48
+ //
49
+
50
+ abbr[title] {
51
+ border-bottom: 1px dotted;
52
+ }
53
+
54
+ //
55
+ // Address style set to `bolder` in Firefox 4+, Safari, and Chrome.
56
+ //
57
+
58
+ b,
59
+ strong {
60
+ font-weight: bold;
61
+ }
62
+
63
+ //
64
+ // Address inconsistent and variable font size in all browsers.
65
+ //
66
+
67
+ small {
68
+ font-size: 80%;
69
+ }
70
+
71
+ // Embedded content
72
+ // ==========================================================================
73
+
74
+ //
75
+ // Remove border when inside `a` element in IE 8/9/10.
76
+ //
77
+
78
+ img {
79
+ border: 0;
80
+ }
81
+
82
+ //
83
+ // Correct overflow not hidden in IE 9/10/11.
84
+ //
85
+
86
+ svg:not(:root) {
87
+ overflow: hidden;
88
+ }
89
+
90
+ // Forms
91
+ // ==========================================================================
92
+
93
+ //
94
+ // Known limitation: by default, Chrome and Safari on OS X allow very limited
95
+ // styling of `select`, unless a `border` property is set.
96
+ //
97
+
98
+ //
99
+ // 1. Correct color not being inherited.
100
+ // Known issue: affects color of disabled elements.
101
+ // 2. Correct font properties not being inherited.
102
+ // 3. Address margins set differently in Firefox 4+, Safari, and Chrome.
103
+ //
104
+
105
+ button,
106
+ input,
107
+ optgroup,
108
+ select,
109
+ textarea {
110
+ color: inherit; // 1
111
+ font: inherit; // 2
112
+ margin: 0; // 3
113
+ }
114
+
115
+ //
116
+ // Address `overflow` set to `hidden` in IE 8/9/10/11.
117
+ //
118
+
119
+ button {
120
+ overflow: visible;
121
+ }
122
+
123
+ //
124
+ // Address inconsistent `text-transform` inheritance for `button` and `select`.
125
+ // All other form control elements do not inherit `text-transform` values.
126
+ // Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.
127
+ // Correct `select` style inheritance in Firefox.
128
+ //
129
+
130
+ button,
131
+ select {
132
+ text-transform: none;
133
+ }
134
+
135
+ //
136
+ // 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
137
+ // and `video` controls.
138
+ // 2. Correct inability to style clickable `input` types in iOS.
139
+ // 3. Improve usability and consistency of cursor style between image-type
140
+ // `input` and others.
141
+ //
142
+
143
+ button,
144
+ html input[type="button"], // 1
145
+ input[type="reset"],
146
+ input[type="submit"] {
147
+ -webkit-appearance: button; // 2
148
+ cursor: pointer; // 3
149
+ }
150
+
151
+ //
152
+ // Re-set default cursor for disabled elements.
153
+ //
154
+
155
+ button[disabled],
156
+ html input[disabled] {
157
+ cursor: default;
158
+ }
159
+
160
+ //
161
+ // Remove inner padding and border in Firefox 4+.
162
+ //
163
+
164
+ button::-moz-focus-inner,
165
+ input::-moz-focus-inner {
166
+ border: 0;
167
+ padding: 0;
168
+ }
169
+
170
+ //
171
+ // Address Firefox 4+ setting `line-height` on `input` using `!important` in
172
+ // the UA stylesheet.
173
+ //
174
+
175
+ input {
176
+ line-height: normal;
177
+ }
178
+
179
+ //
180
+ // It's recommended that you don't attempt to style these elements.
181
+ // Firefox's implementation doesn't respect box-sizing, padding, or width.
182
+ //
183
+ // 1. Address box sizing set to `content-box` in IE 8/9/10.
184
+ // 2. Remove excess padding in IE 8/9/10.
185
+ //
186
+
187
+ input[type="checkbox"],
188
+ input[type="radio"] {
189
+ box-sizing: border-box; // 1
190
+ padding: 0; // 2
191
+ }
192
+
193
+ //
194
+ // Fix the cursor style for Chrome's increment/decrement buttons. For certain
195
+ // `font-size` values of the `input`, it causes the cursor style of the
196
+ // decrement button to change from `default` to `text`.
197
+ //
198
+
199
+ input[type="number"]::-webkit-inner-spin-button,
200
+ input[type="number"]::-webkit-outer-spin-button {
201
+ height: auto;
202
+ }
203
+
204
+ //
205
+ // Remove default vertical scrollbar in IE 8/9/10/11.
206
+ //
207
+
208
+ textarea {
209
+ overflow: auto;
210
210
  }
@@ -1,41 +1,41 @@
1
-
2
- @mixin non-selectable {
3
- -webkit-user-select: none; /* Chrome/Safari */
4
- -moz-user-select: none; /* Firefox */
5
- -ms-user-select: none; /* IE10+ */
6
- /* Rules below not implemented in browsers yet */
7
- -o-user-select: none;
8
- user-select: none;
9
-
10
- cursor: default;
11
- }
12
-
13
- ::-webkit-scrollbar {
14
- width: 10px;
15
- height:10px;
16
- }
17
-
18
- ::-webkit-scrollbar-track {
19
- //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.8);
20
- border-radius: 0;
21
- background-color: color-lower-contrast($control-background, 4%);
22
- }
23
-
24
- ::-webkit-scrollbar-thumb {
25
- border-radius: 0;
26
- //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.9);
27
- background-color: color-lower-contrast($control-background, 8%);
28
- }
29
-
30
- @import 'components/controls-base';
31
- @import 'components/controls';
32
- @import 'components/slider';
33
- @import 'components/misc';
34
- @import 'components/tasks';
35
- @import 'components/viewport';
36
- @import 'components/log';
37
- @import 'components/sequence';
38
- @import 'components/transformer';
39
- @import 'components/toast';
40
- @import 'components/help';
1
+
2
+ @mixin non-selectable {
3
+ -webkit-user-select: none; /* Chrome/Safari */
4
+ -moz-user-select: none; /* Firefox */
5
+ -ms-user-select: none; /* IE10+ */
6
+ /* Rules below not implemented in browsers yet */
7
+ -o-user-select: none;
8
+ user-select: none;
9
+
10
+ cursor: default;
11
+ }
12
+
13
+ ::-webkit-scrollbar {
14
+ width: 10px;
15
+ height:10px;
16
+ }
17
+
18
+ ::-webkit-scrollbar-track {
19
+ //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.8);
20
+ border-radius: 0;
21
+ background-color: color-lower-contrast($control-background, 4%);
22
+ }
23
+
24
+ ::-webkit-scrollbar-thumb {
25
+ border-radius: 0;
26
+ //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.9);
27
+ background-color: color-lower-contrast($control-background, 8%);
28
+ }
29
+
30
+ @import 'components/controls-base';
31
+ @import 'components/controls';
32
+ @import 'components/slider';
33
+ @import 'components/misc';
34
+ @import 'components/tasks';
35
+ @import 'components/viewport';
36
+ @import 'components/log';
37
+ @import 'components/sequence';
38
+ @import 'components/transformer';
39
+ @import 'components/toast';
40
+ @import 'components/help';
41
41
  @import 'components/line-graph';
@@ -1,86 +1,86 @@
1
-
2
- // measures
3
-
4
- $control-label-width: 110px;
5
- $control-label-short-width: 70px;
6
- $row-height: 32px;
7
- $control-spacing: 10px;
8
- $entity-subtree-offset: 8px;
9
- $info-vertical-padding: 3px;
10
- $slider-border-radius-base: 6px;
11
-
12
- // layout
13
- $expanded-top-height: 100px;
14
- $expanded-bottom-height: 70px; // 3 * $row-height + 2;
15
- $expanded-right-width: 300px;
16
- $expanded-left-width: 330px;
17
-
18
- $collapsed-left-width: $row-height;
19
-
20
- $expanded-portrait-bottom-height: 10 * ($row-height + 1) + 3 * $control-spacing + 1;
21
- $expanded-portrait-top-height: 3 * $row-height + 1;
22
-
23
- $standard-bottom-height: 8 * ($row-height + 1) + 3 * $control-spacing + 1;
24
- $standard-top-height: 3 * $row-height + 1;
25
-
26
-
27
- $color-accent-cyan: color-lower-contrast(#95a5a6, 15%);
28
- $color-accent-red: color-lower-contrast(#e74c3c, 15%);
29
- $color-accent-gray: color-lower-contrast(#34495e, 10%);
30
- $color-accent-green: color-lower-contrast(#2ecc71, 10%);
31
- $color-accent-purple: color-lower-contrast(#9b59b6, 10%);
32
- $color-accent-blue: color-lower-contrast(#3498db, 5%);
33
- $color-accent-orange: color-lower-contrast(#e67e22, 5%);
34
-
35
- // TypeClass = 'Root' | 'Group' | 'Data' | 'Object' | 'Representation3D' | 'Behavior'
36
-
37
- $type-class-Root: $default-background;
38
- $type-class-Data: color-lower-contrast(#95a5a6, 15%);
39
- $type-class-Object: color-lower-contrast(#2ecc71, 10%);
40
- $type-class-Behavior: color-lower-contrast(#9b59b6, 10%);
41
- $type-class-Representation3D: color-lower-contrast(#3498db, 5%);
42
- $type-class-Group: color-lower-contrast(#e67e22, 5%);
43
-
44
- //////////////////////////////////////////////////
45
- // COLORS and COMPUTED COLORS
46
-
47
- $slider-disabledColor: #ccc;
48
-
49
- $control-background: color-increase-contrast($default-background, 6.5%);
50
- $border-color: color-increase-contrast($default-background, 15%);
51
- $msp-form-control-background: color-lower-contrast($default-background, 2.5%);
52
-
53
- // buttons
54
- $msp-btn-link-font-color: $font-color;
55
- $msp-btn-link-toggle-on-font-color: $font-color;
56
- $msp-btn-link-toggle-off-font-color: color-lower-contrast($font-color, 33%);
57
-
58
- // used for "actions" -- i.e. + in selection
59
- $msp-btn-remove-font-color: $font-color;
60
-
61
- $msp-btn-action-background: $msp-form-control-background;
62
-
63
- // update selection etc
64
- //!! $msp-btn-commit-on-font-color: $entity-current-font-color;
65
- $msp-btn-commit-on-hover-font-color: color-lower-contrast($msp-btn-commit-on-font-color, 20%); //!!Change
66
- $msp-btn-commit-on-background: color-lower-contrast($default-background, 2%);
67
- $msp-btn-commit-off-background: color-lower-contrast($default-background, 4%); //$control-background;
68
- $msp-btn-commit-off-font-color: $font-color;
69
-
70
- // log
71
- $log-font-color: color-lower-contrast($font-color, 5%);
72
- $log-timestamp-font-color: color-lower-contrast($font-color, 20%);
73
-
74
- // highlight
75
- $highlight-info-font-color: $hover-font-color;
76
- $highlight-info-additional-font-color: color-lower-contrast($hover-font-color, 20%);
77
-
78
- // entity state
79
- $entity-color-fully-visible: $font-color;
80
- $entity-color-not-visible: color-lower-contrast($font-color, 66%);
81
- $entity-color-partialy-visible: color-lower-contrast($font-color, 33%);
82
- $entity-tag-color: color-lower-contrast($font-color, 20%);
83
-
84
- // sequence
85
- $sequence-background: $default-background;
1
+
2
+ // measures
3
+
4
+ $control-label-width: 110px;
5
+ $control-label-short-width: 70px;
6
+ $row-height: 32px;
7
+ $control-spacing: 10px;
8
+ $entity-subtree-offset: 8px;
9
+ $info-vertical-padding: 3px;
10
+ $slider-border-radius-base: 6px;
11
+
12
+ // layout
13
+ $expanded-top-height: 100px;
14
+ $expanded-bottom-height: 70px; // 3 * $row-height + 2;
15
+ $expanded-right-width: 300px;
16
+ $expanded-left-width: 330px;
17
+
18
+ $collapsed-left-width: $row-height;
19
+
20
+ $expanded-portrait-bottom-height: 10 * ($row-height + 1) + 3 * $control-spacing + 1;
21
+ $expanded-portrait-top-height: 3 * $row-height + 1;
22
+
23
+ $standard-bottom-height: 8 * ($row-height + 1) + 3 * $control-spacing + 1;
24
+ $standard-top-height: 3 * $row-height + 1;
25
+
26
+
27
+ $color-accent-cyan: color-lower-contrast(#95a5a6, 15%);
28
+ $color-accent-red: color-lower-contrast(#e74c3c, 15%);
29
+ $color-accent-gray: color-lower-contrast(#34495e, 10%);
30
+ $color-accent-green: color-lower-contrast(#2ecc71, 10%);
31
+ $color-accent-purple: color-lower-contrast(#9b59b6, 10%);
32
+ $color-accent-blue: color-lower-contrast(#3498db, 5%);
33
+ $color-accent-orange: color-lower-contrast(#e67e22, 5%);
34
+
35
+ // TypeClass = 'Root' | 'Group' | 'Data' | 'Object' | 'Representation3D' | 'Behavior'
36
+
37
+ $type-class-Root: $default-background;
38
+ $type-class-Data: color-lower-contrast(#95a5a6, 15%);
39
+ $type-class-Object: color-lower-contrast(#2ecc71, 10%);
40
+ $type-class-Behavior: color-lower-contrast(#9b59b6, 10%);
41
+ $type-class-Representation3D: color-lower-contrast(#3498db, 5%);
42
+ $type-class-Group: color-lower-contrast(#e67e22, 5%);
43
+
44
+ //////////////////////////////////////////////////
45
+ // COLORS and COMPUTED COLORS
46
+
47
+ $slider-disabledColor: #ccc;
48
+
49
+ $control-background: color-increase-contrast($default-background, 6.5%);
50
+ $border-color: color-increase-contrast($default-background, 15%);
51
+ $msp-form-control-background: color-lower-contrast($default-background, 2.5%);
52
+
53
+ // buttons
54
+ $msp-btn-link-font-color: $font-color;
55
+ $msp-btn-link-toggle-on-font-color: $font-color;
56
+ $msp-btn-link-toggle-off-font-color: color-lower-contrast($font-color, 33%);
57
+
58
+ // used for "actions" -- i.e. + in selection
59
+ $msp-btn-remove-font-color: $font-color;
60
+
61
+ $msp-btn-action-background: $msp-form-control-background;
62
+
63
+ // update selection etc
64
+ //!! $msp-btn-commit-on-font-color: $entity-current-font-color;
65
+ $msp-btn-commit-on-hover-font-color: color-lower-contrast($msp-btn-commit-on-font-color, 20%); //!!Change
66
+ $msp-btn-commit-on-background: color-lower-contrast($default-background, 2%);
67
+ $msp-btn-commit-off-background: color-lower-contrast($default-background, 4%); //$control-background;
68
+ $msp-btn-commit-off-font-color: $font-color;
69
+
70
+ // log
71
+ $log-font-color: color-lower-contrast($font-color, 5%);
72
+ $log-timestamp-font-color: color-lower-contrast($font-color, 20%);
73
+
74
+ // highlight
75
+ $highlight-info-font-color: $hover-font-color;
76
+ $highlight-info-additional-font-color: color-lower-contrast($hover-font-color, 20%);
77
+
78
+ // entity state
79
+ $entity-color-fully-visible: $font-color;
80
+ $entity-color-not-visible: color-lower-contrast($font-color, 66%);
81
+ $entity-color-partialy-visible: color-lower-contrast($font-color, 33%);
82
+ $entity-tag-color: color-lower-contrast($font-color, 20%);
83
+
84
+ // sequence
85
+ $sequence-background: $default-background;
86
86
  $sequence-number-color: $hover-font-color;
@@ -1,2 +1,2 @@
1
- @import 'colors/blue';
1
+ @import 'colors/blue';
2
2
  @import 'base/base';