molstar 4.2.0 → 4.3.0

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 (339) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +197 -197
  3. package/build/viewer/embedded.html +52 -52
  4. package/build/viewer/index.html +129 -129
  5. package/build/viewer/molstar.js +1 -1
  6. package/build/viewer/molstar.js.LICENSE.txt +9 -0
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/mesoscale-explorer/index.html +100 -100
  9. package/lib/apps/mesoscale-explorer/style.scss +33 -33
  10. package/lib/apps/viewer/app.d.ts +2 -1
  11. package/lib/apps/viewer/app.js +2 -1
  12. package/lib/apps/viewer/embedded.html +52 -52
  13. package/lib/apps/viewer/index.html +129 -129
  14. package/lib/cli/chem-comp-dict/create-ions.js +9 -9
  15. package/lib/cli/chem-comp-dict/create-saccharides.js +9 -9
  16. package/lib/cli/cifschema/util/generate.js +12 -12
  17. package/lib/cli/lipid-params/index.js +9 -9
  18. package/lib/commonjs/apps/viewer/app.d.ts +2 -1
  19. package/lib/commonjs/apps/viewer/app.js +1 -0
  20. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +9 -9
  21. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +9 -9
  22. package/lib/commonjs/cli/cifschema/util/generate.js +12 -12
  23. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  24. package/lib/commonjs/examples/alpha-orbitals/example-data.js +160 -160
  25. package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +136 -136
  26. package/lib/commonjs/extensions/assembly-symmetry/prop.js +24 -24
  27. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +5 -5
  28. package/lib/commonjs/extensions/dnatco/ntc-tube/behavior.js +5 -5
  29. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +41 -41
  30. package/lib/commonjs/extensions/meshes/mesh-extension.d.ts +1 -0
  31. package/lib/commonjs/extensions/mp4-export/encoder.js +1 -1
  32. package/lib/commonjs/extensions/mvs/components/annotation-label/representation.d.ts +0 -2
  33. package/lib/commonjs/extensions/mvs/components/custom-label/representation.d.ts +2 -2
  34. package/lib/commonjs/extensions/mvs/tree/mvs/mvs-builder.d.ts +8 -2
  35. package/lib/commonjs/extensions/sb-ncbr/index.d.ts +8 -0
  36. package/lib/commonjs/extensions/sb-ncbr/index.js +14 -1
  37. package/lib/commonjs/extensions/sb-ncbr/tunnels/actions.d.ts +20 -0
  38. package/lib/commonjs/extensions/sb-ncbr/tunnels/actions.js +89 -0
  39. package/lib/commonjs/extensions/sb-ncbr/tunnels/algorithm.d.ts +26 -0
  40. package/lib/commonjs/extensions/sb-ncbr/tunnels/algorithm.js +474 -0
  41. package/lib/commonjs/extensions/sb-ncbr/tunnels/behavior.d.ts +40 -0
  42. package/lib/commonjs/extensions/sb-ncbr/tunnels/behavior.js +96 -0
  43. package/lib/commonjs/extensions/sb-ncbr/tunnels/data-model.d.ts +146 -0
  44. package/lib/commonjs/extensions/sb-ncbr/tunnels/data-model.js +28 -0
  45. package/lib/commonjs/extensions/sb-ncbr/tunnels/examples.d.ts +12 -0
  46. package/lib/commonjs/extensions/sb-ncbr/tunnels/examples.js +54 -0
  47. package/lib/commonjs/extensions/sb-ncbr/tunnels/props.d.ts +19 -0
  48. package/lib/commonjs/extensions/sb-ncbr/tunnels/props.js +26 -0
  49. package/lib/commonjs/extensions/sb-ncbr/tunnels/representation.d.ts +29 -0
  50. package/lib/commonjs/extensions/sb-ncbr/tunnels/representation.js +99 -0
  51. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +17 -0
  52. package/lib/commonjs/mol-canvas3d/canvas3d.js +4 -0
  53. package/lib/commonjs/mol-canvas3d/passes/dof.d.ts +34 -0
  54. package/lib/commonjs/mol-canvas3d/passes/dof.js +167 -0
  55. package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +2 -0
  56. package/lib/commonjs/mol-canvas3d/passes/draw.js +31 -8
  57. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +8 -0
  58. package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +8 -0
  59. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +5 -0
  60. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  61. package/lib/commonjs/mol-gl/shader/background.frag.js +95 -95
  62. package/lib/commonjs/mol-gl/shader/background.vert.js +11 -11
  63. package/lib/commonjs/mol-gl/shader/blend-back-dpoit.frag.js +13 -13
  64. package/lib/commonjs/mol-gl/shader/bloom/blur.frag.js +28 -28
  65. package/lib/commonjs/mol-gl/shader/bloom/composite.frag.js +33 -33
  66. package/lib/commonjs/mol-gl/shader/bloom/luminosity.frag.js +52 -52
  67. package/lib/commonjs/mol-gl/shader/cas.frag.js +144 -144
  68. package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +31 -31
  69. package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +12 -12
  70. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +77 -77
  71. package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +16 -16
  72. package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +8 -8
  73. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +140 -140
  74. package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +6 -6
  75. package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +8 -8
  76. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +112 -112
  77. package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +14 -14
  78. package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +18 -18
  79. package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +12 -12
  80. package/lib/commonjs/mol-gl/shader/chunks/check-transparency.glsl.js +16 -16
  81. package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +7 -7
  82. package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +5 -5
  83. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +60 -60
  84. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +122 -122
  85. package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js +104 -104
  86. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +150 -150
  87. package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +61 -61
  88. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +234 -234
  89. package/lib/commonjs/mol-gl/shader/chunks/dpoit-write.glsl.js +62 -62
  90. package/lib/commonjs/mol-gl/shader/chunks/fade-lod.glsl.js +42 -42
  91. package/lib/commonjs/mol-gl/shader/chunks/float-to-rgba.glsl.js +39 -39
  92. package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +127 -127
  93. package/lib/commonjs/mol-gl/shader/chunks/matrix-scale.glsl.js +5 -5
  94. package/lib/commonjs/mol-gl/shader/chunks/normal-frag-params.glsl.js +2 -2
  95. package/lib/commonjs/mol-gl/shader/chunks/read-from-texture.glsl.js +14 -14
  96. package/lib/commonjs/mol-gl/shader/chunks/rgba-to-float.glsl.js +84 -84
  97. package/lib/commonjs/mol-gl/shader/chunks/size-vert-params.glsl.js +11 -11
  98. package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +23 -23
  99. package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +17 -17
  100. package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +8 -8
  101. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +25 -25
  102. package/lib/commonjs/mol-gl/shader/compose.frag.js +12 -12
  103. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +23 -23
  104. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +43 -43
  105. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js +15 -15
  106. package/lib/commonjs/mol-gl/shader/copy.frag.js +11 -11
  107. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +266 -266
  108. package/lib/commonjs/mol-gl/shader/cylinders.vert.js +89 -89
  109. package/lib/commonjs/mol-gl/shader/depth-merge.frag.js +23 -23
  110. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +362 -362
  111. package/lib/commonjs/mol-gl/shader/direct-volume.vert.js +41 -41
  112. package/lib/commonjs/mol-gl/shader/dof.frag.d.ts +7 -0
  113. package/lib/commonjs/mol-gl/shader/dof.frag.js +122 -0
  114. package/lib/commonjs/mol-gl/shader/evaluate-dpoit.frag.js +10 -10
  115. package/lib/commonjs/mol-gl/shader/evaluate-wboit.frag.js +17 -17
  116. package/lib/commonjs/mol-gl/shader/fxaa.frag.js +228 -228
  117. package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +49 -49
  118. package/lib/commonjs/mol-gl/shader/gaussian-density.vert.js +27 -27
  119. package/lib/commonjs/mol-gl/shader/hi-z.frag.js +18 -18
  120. package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +58 -58
  121. package/lib/commonjs/mol-gl/shader/histogram-pyramid/sum.frag.js +19 -19
  122. package/lib/commonjs/mol-gl/shader/image.frag.js +169 -169
  123. package/lib/commonjs/mol-gl/shader/image.vert.js +21 -21
  124. package/lib/commonjs/mol-gl/shader/lines.frag.js +42 -42
  125. package/lib/commonjs/mol-gl/shader/lines.vert.js +117 -117
  126. package/lib/commonjs/mol-gl/shader/marching-cubes/active-voxels.frag.js +70 -70
  127. package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +311 -311
  128. package/lib/commonjs/mol-gl/shader/marking/edge.frag.js +28 -28
  129. package/lib/commonjs/mol-gl/shader/marking/overlay.frag.js +26 -26
  130. package/lib/commonjs/mol-gl/shader/mesh.frag.js +65 -65
  131. package/lib/commonjs/mol-gl/shader/mesh.vert.js +49 -49
  132. package/lib/commonjs/mol-gl/shader/outlines.frag.js +95 -95
  133. package/lib/commonjs/mol-gl/shader/points.frag.js +59 -59
  134. package/lib/commonjs/mol-gl/shader/points.vert.js +38 -38
  135. package/lib/commonjs/mol-gl/shader/postprocessing.frag.js +150 -150
  136. package/lib/commonjs/mol-gl/shader/quad.vert.js +10 -10
  137. package/lib/commonjs/mol-gl/shader/shadows.frag.js +123 -123
  138. package/lib/commonjs/mol-gl/shader/smaa/blend.frag.js +56 -56
  139. package/lib/commonjs/mol-gl/shader/smaa/blend.vert.js +25 -25
  140. package/lib/commonjs/mol-gl/shader/smaa/edges.frag.js +66 -66
  141. package/lib/commonjs/mol-gl/shader/smaa/edges.vert.js +26 -26
  142. package/lib/commonjs/mol-gl/shader/smaa/weights.frag.js +206 -206
  143. package/lib/commonjs/mol-gl/shader/smaa/weights.vert.js +32 -32
  144. package/lib/commonjs/mol-gl/shader/spheres.frag.js +148 -148
  145. package/lib/commonjs/mol-gl/shader/spheres.vert.js +132 -132
  146. package/lib/commonjs/mol-gl/shader/ssao-blur.frag.js +97 -97
  147. package/lib/commonjs/mol-gl/shader/ssao.frag.js +211 -211
  148. package/lib/commonjs/mol-gl/shader/text.frag.js +85 -85
  149. package/lib/commonjs/mol-gl/shader/text.vert.js +85 -85
  150. package/lib/commonjs/mol-gl/shader/util/grid3d-template.frag.js +46 -46
  151. package/lib/commonjs/mol-gl/shader-code.js +15 -15
  152. package/lib/commonjs/mol-gl/webgl/compat.js +12 -12
  153. package/lib/commonjs/mol-gl/webgl/context.js +1 -0
  154. package/lib/commonjs/mol-gl/webgl/timer.d.ts +1 -1
  155. package/lib/commonjs/mol-gl/webgl/timer.js +8 -1
  156. package/lib/commonjs/mol-math/linear-algebra/3d/minimize-rmsd.js +2 -1
  157. package/lib/commonjs/mol-plugin/animation-loop.d.ts +1 -0
  158. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +6 -6
  159. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +1 -1
  160. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +3 -3
  161. package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js +7 -3
  162. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +3 -0
  163. package/lib/commonjs/servers/common/swagger-ui/indexTemplate.js +66 -66
  164. package/lib/commonjs/servers/volume/config.js +5 -5
  165. package/lib/examples/alpha-orbitals/example-data.js +160 -160
  166. package/lib/examples/alpha-orbitals/index.html +72 -72
  167. package/lib/examples/basic-wrapper/index.html +137 -137
  168. package/lib/examples/lighting/index.html +88 -88
  169. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  170. package/lib/extensions/alpha-orbitals/gpu/shader.frag.js +136 -136
  171. package/lib/extensions/assembly-symmetry/prop.js +24 -24
  172. package/lib/extensions/dnatco/confal-pyramids/behavior.js +5 -5
  173. package/lib/extensions/dnatco/ntc-tube/behavior.js +5 -5
  174. package/lib/extensions/geo-export/usdz-exporter.js +41 -41
  175. package/lib/extensions/meshes/mesh-extension.d.ts +1 -0
  176. package/lib/extensions/mp4-export/encoder.js +1 -1
  177. package/lib/extensions/mvs/components/annotation-label/representation.d.ts +0 -2
  178. package/lib/extensions/mvs/components/custom-label/representation.d.ts +2 -2
  179. package/lib/extensions/mvs/tree/mvs/mvs-builder.d.ts +8 -2
  180. package/lib/extensions/sb-ncbr/index.d.ts +8 -0
  181. package/lib/extensions/sb-ncbr/index.js +8 -0
  182. package/lib/extensions/sb-ncbr/tunnels/actions.d.ts +20 -0
  183. package/lib/extensions/sb-ncbr/tunnels/actions.js +86 -0
  184. package/lib/extensions/sb-ncbr/tunnels/algorithm.d.ts +26 -0
  185. package/lib/extensions/sb-ncbr/tunnels/algorithm.js +469 -0
  186. package/lib/extensions/sb-ncbr/tunnels/behavior.d.ts +40 -0
  187. package/lib/extensions/sb-ncbr/tunnels/behavior.js +92 -0
  188. package/lib/extensions/sb-ncbr/tunnels/data-model.d.ts +146 -0
  189. package/lib/extensions/sb-ncbr/tunnels/data-model.js +23 -0
  190. package/lib/extensions/sb-ncbr/tunnels/examples.d.ts +12 -0
  191. package/lib/extensions/sb-ncbr/tunnels/examples.js +49 -0
  192. package/lib/extensions/sb-ncbr/tunnels/props.d.ts +19 -0
  193. package/lib/extensions/sb-ncbr/tunnels/props.js +22 -0
  194. package/lib/extensions/sb-ncbr/tunnels/representation.d.ts +29 -0
  195. package/lib/extensions/sb-ncbr/tunnels/representation.js +96 -0
  196. package/lib/mol-canvas3d/canvas3d.d.ts +17 -0
  197. package/lib/mol-canvas3d/canvas3d.js +4 -0
  198. package/lib/mol-canvas3d/passes/dof.d.ts +34 -0
  199. package/lib/mol-canvas3d/passes/dof.js +163 -0
  200. package/lib/mol-canvas3d/passes/draw.d.ts +2 -0
  201. package/lib/mol-canvas3d/passes/draw.js +31 -8
  202. package/lib/mol-canvas3d/passes/image.d.ts +8 -0
  203. package/lib/mol-canvas3d/passes/postprocessing.d.ts +8 -0
  204. package/lib/mol-canvas3d/passes/postprocessing.js +5 -0
  205. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  206. package/lib/mol-gl/shader/background.frag.js +95 -95
  207. package/lib/mol-gl/shader/background.vert.js +11 -11
  208. package/lib/mol-gl/shader/blend-back-dpoit.frag.js +13 -13
  209. package/lib/mol-gl/shader/bloom/blur.frag.js +28 -28
  210. package/lib/mol-gl/shader/bloom/composite.frag.js +33 -33
  211. package/lib/mol-gl/shader/bloom/luminosity.frag.js +52 -52
  212. package/lib/mol-gl/shader/cas.frag.js +144 -144
  213. package/lib/mol-gl/shader/chunks/apply-fog.glsl.js +31 -31
  214. package/lib/mol-gl/shader/chunks/apply-interior-color.glsl.js +12 -12
  215. package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js +77 -77
  216. package/lib/mol-gl/shader/chunks/apply-marker-color.glsl.js +16 -16
  217. package/lib/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +8 -8
  218. package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.js +140 -140
  219. package/lib/mol-gl/shader/chunks/assign-group.glsl.js +6 -6
  220. package/lib/mol-gl/shader/chunks/assign-marker-varying.glsl.js +8 -8
  221. package/lib/mol-gl/shader/chunks/assign-material-color.glsl.js +112 -112
  222. package/lib/mol-gl/shader/chunks/assign-position.glsl.js +14 -14
  223. package/lib/mol-gl/shader/chunks/assign-size.glsl.js +18 -18
  224. package/lib/mol-gl/shader/chunks/check-picking-alpha.glsl.js +12 -12
  225. package/lib/mol-gl/shader/chunks/check-transparency.glsl.js +16 -16
  226. package/lib/mol-gl/shader/chunks/clip-instance.glsl.js +7 -7
  227. package/lib/mol-gl/shader/chunks/clip-pixel.glsl.js +5 -5
  228. package/lib/mol-gl/shader/chunks/color-frag-params.glsl.js +60 -60
  229. package/lib/mol-gl/shader/chunks/color-vert-params.glsl.js +122 -122
  230. package/lib/mol-gl/shader/chunks/common-clip.glsl.js +104 -104
  231. package/lib/mol-gl/shader/chunks/common-frag-params.glsl.js +150 -150
  232. package/lib/mol-gl/shader/chunks/common-vert-params.glsl.js +61 -61
  233. package/lib/mol-gl/shader/chunks/common.glsl.js +234 -234
  234. package/lib/mol-gl/shader/chunks/dpoit-write.glsl.js +62 -62
  235. package/lib/mol-gl/shader/chunks/fade-lod.glsl.js +42 -42
  236. package/lib/mol-gl/shader/chunks/float-to-rgba.glsl.js +39 -39
  237. package/lib/mol-gl/shader/chunks/light-frag-params.glsl.js +127 -127
  238. package/lib/mol-gl/shader/chunks/matrix-scale.glsl.js +5 -5
  239. package/lib/mol-gl/shader/chunks/normal-frag-params.glsl.js +2 -2
  240. package/lib/mol-gl/shader/chunks/read-from-texture.glsl.js +14 -14
  241. package/lib/mol-gl/shader/chunks/rgba-to-float.glsl.js +84 -84
  242. package/lib/mol-gl/shader/chunks/size-vert-params.glsl.js +11 -11
  243. package/lib/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +23 -23
  244. package/lib/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +17 -17
  245. package/lib/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +8 -8
  246. package/lib/mol-gl/shader/chunks/wboit-write.glsl.js +25 -25
  247. package/lib/mol-gl/shader/compose.frag.js +12 -12
  248. package/lib/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +23 -23
  249. package/lib/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +43 -43
  250. package/lib/mol-gl/shader/compute/color-smoothing/normalize.frag.js +15 -15
  251. package/lib/mol-gl/shader/copy.frag.js +11 -11
  252. package/lib/mol-gl/shader/cylinders.frag.js +266 -266
  253. package/lib/mol-gl/shader/cylinders.vert.js +89 -89
  254. package/lib/mol-gl/shader/depth-merge.frag.js +23 -23
  255. package/lib/mol-gl/shader/direct-volume.frag.js +362 -362
  256. package/lib/mol-gl/shader/direct-volume.vert.js +41 -41
  257. package/lib/mol-gl/shader/dof.frag.d.ts +7 -0
  258. package/lib/mol-gl/shader/dof.frag.js +119 -0
  259. package/lib/mol-gl/shader/evaluate-dpoit.frag.js +10 -10
  260. package/lib/mol-gl/shader/evaluate-wboit.frag.js +17 -17
  261. package/lib/mol-gl/shader/fxaa.frag.js +228 -228
  262. package/lib/mol-gl/shader/gaussian-density.frag.js +49 -49
  263. package/lib/mol-gl/shader/gaussian-density.vert.js +27 -27
  264. package/lib/mol-gl/shader/hi-z.frag.js +18 -18
  265. package/lib/mol-gl/shader/histogram-pyramid/reduction.frag.js +58 -58
  266. package/lib/mol-gl/shader/histogram-pyramid/sum.frag.js +19 -19
  267. package/lib/mol-gl/shader/image.frag.js +169 -169
  268. package/lib/mol-gl/shader/image.vert.js +21 -21
  269. package/lib/mol-gl/shader/lines.frag.js +42 -42
  270. package/lib/mol-gl/shader/lines.vert.js +117 -117
  271. package/lib/mol-gl/shader/marching-cubes/active-voxels.frag.js +70 -70
  272. package/lib/mol-gl/shader/marching-cubes/isosurface.frag.js +311 -311
  273. package/lib/mol-gl/shader/marking/edge.frag.js +28 -28
  274. package/lib/mol-gl/shader/marking/overlay.frag.js +26 -26
  275. package/lib/mol-gl/shader/mesh.frag.js +65 -65
  276. package/lib/mol-gl/shader/mesh.vert.js +49 -49
  277. package/lib/mol-gl/shader/outlines.frag.js +95 -95
  278. package/lib/mol-gl/shader/points.frag.js +59 -59
  279. package/lib/mol-gl/shader/points.vert.js +38 -38
  280. package/lib/mol-gl/shader/postprocessing.frag.js +150 -150
  281. package/lib/mol-gl/shader/quad.vert.js +10 -10
  282. package/lib/mol-gl/shader/shadows.frag.js +123 -123
  283. package/lib/mol-gl/shader/smaa/blend.frag.js +56 -56
  284. package/lib/mol-gl/shader/smaa/blend.vert.js +25 -25
  285. package/lib/mol-gl/shader/smaa/edges.frag.js +66 -66
  286. package/lib/mol-gl/shader/smaa/edges.vert.js +26 -26
  287. package/lib/mol-gl/shader/smaa/weights.frag.js +206 -206
  288. package/lib/mol-gl/shader/smaa/weights.vert.js +32 -32
  289. package/lib/mol-gl/shader/spheres.frag.js +148 -148
  290. package/lib/mol-gl/shader/spheres.vert.js +132 -132
  291. package/lib/mol-gl/shader/ssao-blur.frag.js +97 -97
  292. package/lib/mol-gl/shader/ssao.frag.js +211 -211
  293. package/lib/mol-gl/shader/text.frag.js +85 -85
  294. package/lib/mol-gl/shader/text.vert.js +85 -85
  295. package/lib/mol-gl/shader/util/grid3d-template.frag.js +46 -46
  296. package/lib/mol-gl/shader-code.js +15 -15
  297. package/lib/mol-gl/webgl/compat.js +12 -12
  298. package/lib/mol-gl/webgl/context.js +1 -0
  299. package/lib/mol-gl/webgl/timer.d.ts +1 -1
  300. package/lib/mol-gl/webgl/timer.js +8 -1
  301. package/lib/mol-math/linear-algebra/3d/minimize-rmsd.js +2 -1
  302. package/lib/mol-plugin/animation-loop.d.ts +1 -0
  303. package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +6 -6
  304. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +1 -1
  305. package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +3 -3
  306. package/lib/mol-plugin/version.js +2 -2
  307. package/lib/mol-plugin-state/animation/built-in/state-snapshots.js +7 -3
  308. package/lib/mol-plugin-ui/skin/base/base.scss +37 -37
  309. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  310. package/lib/mol-plugin-ui/skin/base/components/controls.scss +445 -445
  311. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  312. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  313. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  314. package/lib/mol-plugin-ui/skin/base/components/misc.scss +663 -663
  315. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  316. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  317. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  318. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  319. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  320. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +194 -194
  321. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  322. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  323. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  324. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  325. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  326. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  327. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  328. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  329. package/lib/mol-plugin-ui/skin/base/variables.scss +88 -88
  330. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  331. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  332. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  333. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  334. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  335. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  336. package/lib/mol-plugin-ui/viewport/simple-settings.js +3 -0
  337. package/lib/servers/common/swagger-ui/indexTemplate.js +66 -66
  338. package/lib/servers/volume/config.js +5 -5
  339. package/package.json +196 -195
@@ -1,126 +1,126 @@
1
- .msp-sequence {
2
- position: absolute;
3
- right: 0;
4
- top: 0;
5
- left: 0;
6
- bottom: 0;
7
- background: $sequence-background;
8
- }
9
-
10
- $sequence-select-height: 24px;
11
- .msp-sequence-select {
12
- position: relative;
13
- height: $sequence-select-height;
14
- width: 100%;
15
- margin-bottom: 1px;
16
- background: $control-background;
17
- text-align: left;
18
-
19
- > span {
20
- display: inline-block;
21
- line-height: $sequence-select-height;
22
- padding: 0 $control-spacing;
23
- font-size: 85%;
24
- font-weight: bold;
25
- cursor: default;
26
- }
27
-
28
- > select {
29
- display: inline-block;
30
- max-width: 120px;
31
- width: auto;
32
- text-overflow: ellipsis;
33
- font-size: 85%;
34
- height: $sequence-select-height;
35
- line-height: $sequence-select-height;
36
- background-size: 6px 8px;
37
- background-color: $control-background;
38
- }
39
- }
40
-
41
- .msp-sequence-wrapper {
42
- word-break: break-word;
43
- // use $control-spacing for top to have space for sequence numebrs
44
- padding: $control-spacing $control-spacing $info-vertical-padding $control-spacing;
45
- user-select: none;
46
- }
47
-
48
- .msp-sequence-wrapper-non-empty {
49
- font-size: 85%;
50
- line-height: 180%;
51
- font-family: "Courier New", monospace;
52
- background: $msp-form-control-background;
53
-
54
- width: 100%;
55
- overflow-y: auto;
56
- overflow-x: hidden;
57
- position: absolute;
58
- top: $sequence-select-height + 1px;
59
- left: 0;
60
- bottom: 0;
61
- right: 0;
62
- }
63
-
64
- .msp-sequence-chain-label {
65
- margin-left: $control-spacing;
66
- margin-top: $control-spacing;
67
- user-select: none;
68
- color: $sequence-number-color;
69
- font-size: 90%;
70
- line-height: 90%;
71
- padding-left: 0.2em;
72
- }
73
-
74
- .msp-sequence-wrapper {
75
- span {
76
- cursor: pointer;
77
- }
78
-
79
- .msp-sequence-residue-long {
80
- margin: 0em 0.2em 0em 0.2em;
81
- }
82
-
83
- .msp-sequence-residue-long-begin {
84
- margin: 0em 0.2em 0em 0em;
85
- }
86
-
87
- .msp-sequence-label {
88
- color: $sequence-number-color;
89
- font-size: 90%;
90
- line-height: 90%;
91
- padding-bottom: 1em;
92
- padding-left: 0.2em;
93
- }
94
-
95
- .msp-sequence-number {
96
- color: $sequence-number-color;
97
- word-break: keep-all;
98
- cursor: default;
99
- position: relative;
100
- top: -1.1em;
101
- left: 3.1em;
102
- padding: 0px;
103
- margin-left: -3em;
104
- font-size: 80%;
105
- }
106
-
107
- .msp-sequence-number-long {
108
- left: 3.3em;
109
- }
110
-
111
- .msp-sequence-number-long-negative {
112
- left: 2.7em;
113
- }
114
-
115
- .msp-sequence-number-negative {
116
- left: 2.5em;
117
- }
118
-
119
- .msp-sequence-present {
120
- color: $font-color;
121
- }
122
-
123
- .msp-sequence-missing {
124
- color: color-lower-contrast($font-color, 33%);
125
- }
1
+ .msp-sequence {
2
+ position: absolute;
3
+ right: 0;
4
+ top: 0;
5
+ left: 0;
6
+ bottom: 0;
7
+ background: $sequence-background;
8
+ }
9
+
10
+ $sequence-select-height: 24px;
11
+ .msp-sequence-select {
12
+ position: relative;
13
+ height: $sequence-select-height;
14
+ width: 100%;
15
+ margin-bottom: 1px;
16
+ background: $control-background;
17
+ text-align: left;
18
+
19
+ > span {
20
+ display: inline-block;
21
+ line-height: $sequence-select-height;
22
+ padding: 0 $control-spacing;
23
+ font-size: 85%;
24
+ font-weight: bold;
25
+ cursor: default;
26
+ }
27
+
28
+ > select {
29
+ display: inline-block;
30
+ max-width: 120px;
31
+ width: auto;
32
+ text-overflow: ellipsis;
33
+ font-size: 85%;
34
+ height: $sequence-select-height;
35
+ line-height: $sequence-select-height;
36
+ background-size: 6px 8px;
37
+ background-color: $control-background;
38
+ }
39
+ }
40
+
41
+ .msp-sequence-wrapper {
42
+ word-break: break-word;
43
+ // use $control-spacing for top to have space for sequence numebrs
44
+ padding: $control-spacing $control-spacing $info-vertical-padding $control-spacing;
45
+ user-select: none;
46
+ }
47
+
48
+ .msp-sequence-wrapper-non-empty {
49
+ font-size: 85%;
50
+ line-height: 180%;
51
+ font-family: "Courier New", monospace;
52
+ background: $msp-form-control-background;
53
+
54
+ width: 100%;
55
+ overflow-y: auto;
56
+ overflow-x: hidden;
57
+ position: absolute;
58
+ top: $sequence-select-height + 1px;
59
+ left: 0;
60
+ bottom: 0;
61
+ right: 0;
62
+ }
63
+
64
+ .msp-sequence-chain-label {
65
+ margin-left: $control-spacing;
66
+ margin-top: $control-spacing;
67
+ user-select: none;
68
+ color: $sequence-number-color;
69
+ font-size: 90%;
70
+ line-height: 90%;
71
+ padding-left: 0.2em;
72
+ }
73
+
74
+ .msp-sequence-wrapper {
75
+ span {
76
+ cursor: pointer;
77
+ }
78
+
79
+ .msp-sequence-residue-long {
80
+ margin: 0em 0.2em 0em 0.2em;
81
+ }
82
+
83
+ .msp-sequence-residue-long-begin {
84
+ margin: 0em 0.2em 0em 0em;
85
+ }
86
+
87
+ .msp-sequence-label {
88
+ color: $sequence-number-color;
89
+ font-size: 90%;
90
+ line-height: 90%;
91
+ padding-bottom: 1em;
92
+ padding-left: 0.2em;
93
+ }
94
+
95
+ .msp-sequence-number {
96
+ color: $sequence-number-color;
97
+ word-break: keep-all;
98
+ cursor: default;
99
+ position: relative;
100
+ top: -1.1em;
101
+ left: 3.1em;
102
+ padding: 0px;
103
+ margin-left: -3em;
104
+ font-size: 80%;
105
+ }
106
+
107
+ .msp-sequence-number-long {
108
+ left: 3.3em;
109
+ }
110
+
111
+ .msp-sequence-number-long-negative {
112
+ left: 2.7em;
113
+ }
114
+
115
+ .msp-sequence-number-negative {
116
+ left: 2.5em;
117
+ }
118
+
119
+ .msp-sequence-present {
120
+ color: $font-color;
121
+ }
122
+
123
+ .msp-sequence-missing {
124
+ color: color-lower-contrast($font-color, 33%);
125
+ }
126
126
  }
@@ -1,166 +1,166 @@
1
- @mixin borderBox {
2
- box-sizing: border-box;
3
- -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
4
-
5
- * {
6
- box-sizing: border-box;
7
- -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
8
- }
9
- }
10
-
11
- .msp-slider-base {
12
- position: relative;
13
- height: 14px;
14
- padding: 5px 0;
15
- width: 100%;
16
- border-radius: $slider-border-radius-base;
17
- align-self: center;
18
- @include borderBox;
19
-
20
- &-rail {
21
- position: absolute;
22
- width: 100%;
23
- background-color: $control-background;
24
- height: 4px;
25
- border-radius: 2px;
26
- }
27
-
28
- &-track {
29
- position: absolute;
30
- left: 0;
31
- height: 4px;
32
- border-radius: $slider-border-radius-base;
33
- background-color: tint($font-color, 60%);
34
- }
35
-
36
- &-handle {
37
- position: absolute;
38
- margin-left: -11px;
39
- margin-top: -9px;
40
- width: 22px;
41
- height: 22px;
42
- cursor: pointer;
43
- border-radius: 50%;
44
- background-color: $font-color;
45
- border: 4px solid $control-background;
46
-
47
- &:hover {
48
- background-color: $hover-font-color;
49
- }
50
- }
51
-
52
- &-mark {
53
- position: absolute;
54
- top: 18px;
55
- left: 0;
56
- width: 100%;
57
- font-size: 12px;
58
- }
59
-
60
- &-mark-text {
61
- position: absolute;
62
- display: inline-block;
63
- vertical-align: middle;
64
- text-align: center;
65
- cursor: pointer;
66
- color: #999;
67
-
68
- &-active {
69
- color: #666;
70
- }
71
- }
72
-
73
- &-step {
74
- position: absolute;
75
- width: 100%;
76
- height: 4px;
77
- background: transparent;
78
- }
79
-
80
- &-dot {
81
- position: absolute;
82
- bottom: -2px;
83
- margin-left: -4px;
84
- width: 8px;
85
- height: 8px;
86
- border: 2px solid #e9e9e9;
87
- background-color: #fff;
88
- cursor: pointer;
89
- border-radius: 50%;
90
- vertical-align: middle;
91
- &:first-child {
92
- margin-left: -4px;
93
- }
94
- &:last-child {
95
- margin-left: -4px;
96
- }
97
- &-active {
98
- border-color: tint($font-color, 50%);
99
- }
100
- }
101
-
102
- &-disabled {
103
- background: $default-background;
104
- opacity: 0.35;
105
-
106
- // .msp-slider-base-track {
107
- // background-color: $slider-disabledColor;
108
- // }
109
-
110
- .msp-slider-base-handle, .msp-slider-base-dot {
111
- // border-color: $slider-disabledColor;
112
- // background-color: color-lower-contrast($font-color, 10%);
113
- cursor: not-allowed;
114
- }
115
-
116
- .msp-slider-base-mark-text, .msp-slider-base-dot {
117
- cursor: not-allowed!important;
118
- }
119
- }
120
- }
121
-
122
- // .msp-slider-base-vertical {
123
- // width: 14px;
124
- // height: 100%;
125
- // padding: 0 5px;
126
-
127
- // .msp-slider-base {
128
- // &-rail {
129
- // height: 100%;
130
- // width: 4px;
131
- // }
132
-
133
- // &-track {
134
- // left: 5px;
135
- // bottom: 0;
136
- // width: 4px;
137
- // }
138
-
139
- // &-handle {
140
- // margin-left: -5px;
141
- // margin-bottom: -7px;
142
- // }
143
-
144
- // &-mark {
145
- // top: 0;
146
- // left: 18px;
147
- // height: 100%;
148
- // }
149
-
150
- // &-step {
151
- // height: 100%;
152
- // width: 4px;
153
- // }
154
-
155
- // &-dot {
156
- // left: 2px;
157
- // margin-bottom: -4px;
158
- // &:first-child {
159
- // margin-bottom: -4px;
160
- // }
161
- // &:last-child {
162
- // margin-bottom: -4px;
163
- // }
164
- // }
165
- // }
1
+ @mixin borderBox {
2
+ box-sizing: border-box;
3
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
4
+
5
+ * {
6
+ box-sizing: border-box;
7
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
8
+ }
9
+ }
10
+
11
+ .msp-slider-base {
12
+ position: relative;
13
+ height: 14px;
14
+ padding: 5px 0;
15
+ width: 100%;
16
+ border-radius: $slider-border-radius-base;
17
+ align-self: center;
18
+ @include borderBox;
19
+
20
+ &-rail {
21
+ position: absolute;
22
+ width: 100%;
23
+ background-color: $control-background;
24
+ height: 4px;
25
+ border-radius: 2px;
26
+ }
27
+
28
+ &-track {
29
+ position: absolute;
30
+ left: 0;
31
+ height: 4px;
32
+ border-radius: $slider-border-radius-base;
33
+ background-color: tint($font-color, 60%);
34
+ }
35
+
36
+ &-handle {
37
+ position: absolute;
38
+ margin-left: -11px;
39
+ margin-top: -9px;
40
+ width: 22px;
41
+ height: 22px;
42
+ cursor: pointer;
43
+ border-radius: 50%;
44
+ background-color: $font-color;
45
+ border: 4px solid $control-background;
46
+
47
+ &:hover {
48
+ background-color: $hover-font-color;
49
+ }
50
+ }
51
+
52
+ &-mark {
53
+ position: absolute;
54
+ top: 18px;
55
+ left: 0;
56
+ width: 100%;
57
+ font-size: 12px;
58
+ }
59
+
60
+ &-mark-text {
61
+ position: absolute;
62
+ display: inline-block;
63
+ vertical-align: middle;
64
+ text-align: center;
65
+ cursor: pointer;
66
+ color: #999;
67
+
68
+ &-active {
69
+ color: #666;
70
+ }
71
+ }
72
+
73
+ &-step {
74
+ position: absolute;
75
+ width: 100%;
76
+ height: 4px;
77
+ background: transparent;
78
+ }
79
+
80
+ &-dot {
81
+ position: absolute;
82
+ bottom: -2px;
83
+ margin-left: -4px;
84
+ width: 8px;
85
+ height: 8px;
86
+ border: 2px solid #e9e9e9;
87
+ background-color: #fff;
88
+ cursor: pointer;
89
+ border-radius: 50%;
90
+ vertical-align: middle;
91
+ &:first-child {
92
+ margin-left: -4px;
93
+ }
94
+ &:last-child {
95
+ margin-left: -4px;
96
+ }
97
+ &-active {
98
+ border-color: tint($font-color, 50%);
99
+ }
100
+ }
101
+
102
+ &-disabled {
103
+ background: $default-background;
104
+ opacity: 0.35;
105
+
106
+ // .msp-slider-base-track {
107
+ // background-color: $slider-disabledColor;
108
+ // }
109
+
110
+ .msp-slider-base-handle, .msp-slider-base-dot {
111
+ // border-color: $slider-disabledColor;
112
+ // background-color: color-lower-contrast($font-color, 10%);
113
+ cursor: not-allowed;
114
+ }
115
+
116
+ .msp-slider-base-mark-text, .msp-slider-base-dot {
117
+ cursor: not-allowed!important;
118
+ }
119
+ }
120
+ }
121
+
122
+ // .msp-slider-base-vertical {
123
+ // width: 14px;
124
+ // height: 100%;
125
+ // padding: 0 5px;
126
+
127
+ // .msp-slider-base {
128
+ // &-rail {
129
+ // height: 100%;
130
+ // width: 4px;
131
+ // }
132
+
133
+ // &-track {
134
+ // left: 5px;
135
+ // bottom: 0;
136
+ // width: 4px;
137
+ // }
138
+
139
+ // &-handle {
140
+ // margin-left: -5px;
141
+ // margin-bottom: -7px;
142
+ // }
143
+
144
+ // &-mark {
145
+ // top: 0;
146
+ // left: 18px;
147
+ // height: 100%;
148
+ // }
149
+
150
+ // &-step {
151
+ // height: 100%;
152
+ // width: 4px;
153
+ // }
154
+
155
+ // &-dot {
156
+ // left: 2px;
157
+ // margin-bottom: -4px;
158
+ // &:first-child {
159
+ // margin-bottom: -4px;
160
+ // }
161
+ // &:last-child {
162
+ // margin-bottom: -4px;
163
+ // }
164
+ // }
165
+ // }
166
166
  // }