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
package/lib/apps/viewer/index.html CHANGED
@@ -1,130 +1,130 @@
1
- <!DOCTYPE html>
2
- <html lang="en">
3
- <head>
4
- <meta charset="utf-8" />
5
- <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
6
- <link rel="icon" href="./favicon.ico" type="image/x-icon">
7
- <title>Mol* Viewer</title>
8
- <style>
9
- * {
10
- margin: 0;
11
- padding: 0;
12
- box-sizing: border-box;
13
- }
14
- html, body {
15
- width: 100%;
16
- height: 100%;
17
- overflow: hidden;
18
- }
19
- hr {
20
- margin: 10px;
21
- }
22
- h1, h2, h3, h4, h5 {
23
- margin-top: 5px;
24
- margin-bottom: 3px;
25
- }
26
- button {
27
- padding: 2px;
28
- }
29
- #app {
30
- position: absolute;
31
- left: 100px;
32
- top: 100px;
33
- width: 800px;
34
- height: 600px;
35
- }
36
- </style>
37
- <link rel="stylesheet" type="text/css" href="molstar.css" />
38
- </head>
39
- <body>
40
- <div id="app"></div>
41
- <script type="text/javascript" src="./molstar.js"></script>
42
- <script type="text/javascript">
43
- function getParam(name, regex) {
44
- var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
45
- return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
46
- }
47
-
48
- var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
49
- if (debugMode) molstar.setDebugMode(debugMode);
50
-
51
- var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
52
- if (timingMode) molstar.setTimingMode(timingMode);
53
-
54
- var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
55
- var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
56
- var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
57
- var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
58
- var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
59
- var pixelScale = getParam('pixel-scale', '[^&]+').trim();
60
- var pickScale = getParam('pick-scale', '[^&]+').trim();
61
- var pickPadding = getParam('pick-padding', '[^&]+').trim();
62
- var transparency = getParam('transparency', '[^&]+').trim().toLowerCase();
63
- var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
64
- var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
65
- var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
66
-
67
- // console.log('Available extensions: ', Object.keys(molstar.ExtensionMap));
68
-
69
- molstar.Viewer.create('app', {
70
- disabledExtensions: [], // anything from Object.keys(molstar.ExtensionMap)
71
- layoutShowControls: !hideControls,
72
- viewportShowExpand: false,
73
- collapseLeftPanel: collapseLeftPanel,
74
- pdbProvider: pdbProvider || 'pdbe',
75
- emdbProvider: emdbProvider || 'pdbe',
76
- volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
77
- ? 'https://maps.rcsb.org'
78
- : 'https://www.ebi.ac.uk/pdbe/densities',
79
- pixelScale: parseFloat(pixelScale) || 1,
80
- pickScale: parseFloat(pickScale) || 0.25,
81
- pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
82
- transparency: transparency || undefined,
83
- preferWebgl1: preferWebgl1,
84
- allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
85
- powerPreference: powerPreference || 'high-performance',
86
- }).then(viewer => {
87
- var snapshotId = getParam('snapshot-id', '[^&]+').trim();
88
- if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
89
-
90
- var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
91
- var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
92
- if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
93
-
94
- var structureUrl = getParam('structure-url', '[^&]+').trim();
95
- var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
96
- var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
97
- if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
98
-
99
- var mvsUrl = getParam('mvs-url', '[^&]+').trim();
100
- var mvsData = getParam('mvs-data', '[^&]+').trim();
101
- var mvsFormat = getParam('mvs-format', '[^&]+').trim() || 'mvsj';
102
- if (mvsUrl && mvsData) console.error('Cannot specify mvs-url and mvs-data URL parameters at the same time. Ignoring both.');
103
- else if (mvsUrl) viewer.loadMvsFromUrl(mvsUrl, mvsFormat);
104
- else if (mvsData) viewer.loadMvsData(mvsData, mvsFormat);
105
-
106
-
107
- var pdb = getParam('pdb', '[^&]+').trim();
108
- if (pdb) viewer.loadPdb(pdb);
109
-
110
- var pdbDev = getParam('pdb-dev', '[^&]+').trim();
111
- if (pdbDev) viewer.loadPdbDev(pdbDev);
112
-
113
- var emdb = getParam('emdb', '[^&]+').trim();
114
- if (emdb) viewer.loadEmdb(emdb);
115
-
116
- var afdb = getParam('afdb', '[^&]+').trim();
117
- if (afdb) viewer.loadAlphaFoldDb(afdb);
118
-
119
- var modelArchive = getParam('model-archive', '[^&]+').trim();
120
- if (modelArchive) viewer.loadModelArchive(modelArchive);
121
-
122
- window.addEventListener('unload', () => {
123
- // to aid GC
124
- viewer.dispose();
125
- });
126
- });
127
- </script>
128
- <!-- __MOLSTAR_ANALYTICS__ -->
129
- </body>
1
+ <!DOCTYPE html>
2
+ <html lang="en">
3
+ <head>
4
+ <meta charset="utf-8" />
5
+ <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
6
+ <link rel="icon" href="./favicon.ico" type="image/x-icon">
7
+ <title>Mol* Viewer</title>
8
+ <style>
9
+ * {
10
+ margin: 0;
11
+ padding: 0;
12
+ box-sizing: border-box;
13
+ }
14
+ html, body {
15
+ width: 100%;
16
+ height: 100%;
17
+ overflow: hidden;
18
+ }
19
+ hr {
20
+ margin: 10px;
21
+ }
22
+ h1, h2, h3, h4, h5 {
23
+ margin-top: 5px;
24
+ margin-bottom: 3px;
25
+ }
26
+ button {
27
+ padding: 2px;
28
+ }
29
+ #app {
30
+ position: absolute;
31
+ left: 100px;
32
+ top: 100px;
33
+ width: 800px;
34
+ height: 600px;
35
+ }
36
+ </style>
37
+ <link rel="stylesheet" type="text/css" href="molstar.css" />
38
+ </head>
39
+ <body>
40
+ <div id="app"></div>
41
+ <script type="text/javascript" src="./molstar.js"></script>
42
+ <script type="text/javascript">
43
+ function getParam(name, regex) {
44
+ var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
45
+ return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
46
+ }
47
+
48
+ var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
49
+ if (debugMode) molstar.setDebugMode(debugMode);
50
+
51
+ var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
52
+ if (timingMode) molstar.setTimingMode(timingMode);
53
+
54
+ var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
55
+ var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
56
+ var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
57
+ var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
58
+ var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
59
+ var pixelScale = getParam('pixel-scale', '[^&]+').trim();
60
+ var pickScale = getParam('pick-scale', '[^&]+').trim();
61
+ var pickPadding = getParam('pick-padding', '[^&]+').trim();
62
+ var transparency = getParam('transparency', '[^&]+').trim().toLowerCase();
63
+ var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
64
+ var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
65
+ var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
66
+
67
+ // console.log('Available extensions: ', Object.keys(molstar.ExtensionMap));
68
+
69
+ molstar.Viewer.create('app', {
70
+ disabledExtensions: [], // anything from Object.keys(molstar.ExtensionMap)
71
+ layoutShowControls: !hideControls,
72
+ viewportShowExpand: false,
73
+ collapseLeftPanel: collapseLeftPanel,
74
+ pdbProvider: pdbProvider || 'pdbe',
75
+ emdbProvider: emdbProvider || 'pdbe',
76
+ volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
77
+ ? 'https://maps.rcsb.org'
78
+ : 'https://www.ebi.ac.uk/pdbe/densities',
79
+ pixelScale: parseFloat(pixelScale) || 1,
80
+ pickScale: parseFloat(pickScale) || 0.25,
81
+ pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
82
+ transparency: transparency || undefined,
83
+ preferWebgl1: preferWebgl1,
84
+ allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
85
+ powerPreference: powerPreference || 'high-performance',
86
+ }).then(viewer => {
87
+ var snapshotId = getParam('snapshot-id', '[^&]+').trim();
88
+ if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
89
+
90
+ var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
91
+ var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
92
+ if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
93
+
94
+ var structureUrl = getParam('structure-url', '[^&]+').trim();
95
+ var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
96
+ var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
97
+ if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
98
+
99
+ var mvsUrl = getParam('mvs-url', '[^&]+').trim();
100
+ var mvsData = getParam('mvs-data', '[^&]+').trim();
101
+ var mvsFormat = getParam('mvs-format', '[^&]+').trim() || 'mvsj';
102
+ if (mvsUrl && mvsData) console.error('Cannot specify mvs-url and mvs-data URL parameters at the same time. Ignoring both.');
103
+ else if (mvsUrl) viewer.loadMvsFromUrl(mvsUrl, mvsFormat);
104
+ else if (mvsData) viewer.loadMvsData(mvsData, mvsFormat);
105
+
106
+
107
+ var pdb = getParam('pdb', '[^&]+').trim();
108
+ if (pdb) viewer.loadPdb(pdb);
109
+
110
+ var pdbDev = getParam('pdb-dev', '[^&]+').trim();
111
+ if (pdbDev) viewer.loadPdbDev(pdbDev);
112
+
113
+ var emdb = getParam('emdb', '[^&]+').trim();
114
+ if (emdb) viewer.loadEmdb(emdb);
115
+
116
+ var afdb = getParam('afdb', '[^&]+').trim();
117
+ if (afdb) viewer.loadAlphaFoldDb(afdb);
118
+
119
+ var modelArchive = getParam('model-archive', '[^&]+').trim();
120
+ if (modelArchive) viewer.loadModelArchive(modelArchive);
121
+
122
+ window.addEventListener('unload', () => {
123
+ // to aid GC
124
+ viewer.dispose();
125
+ });
126
+ });
127
+ </script>
128
+ <!-- __MOLSTAR_ANALYTICS__ -->
129
+ </body>
130
130
  </html>
package/lib/cli/chem-comp-dict/create-ions.js CHANGED
@@ -25,15 +25,15 @@ function extractIonNames(ccd) {
25
25
  return ionNames;
26
26
  }
27
27
  function writeIonNamesFile(filePath, ionNames) {
28
- const output = `/**
29
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
30
- *
31
- * Code-generated ion names params file. Names extracted from CCD components.
32
- *
33
- * @author molstar/chem-comp-dict/create-ions cli
34
- */
35
-
36
- export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
28
+ const output = `/**
29
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
30
+ *
31
+ * Code-generated ion names params file. Names extracted from CCD components.
32
+ *
33
+ * @author molstar/chem-comp-dict/create-ions cli
34
+ */
35
+
36
+ export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
37
37
  `;
38
38
  writeFile(filePath, output);
39
39
  }
package/lib/cli/chem-comp-dict/create-saccharides.js CHANGED
@@ -26,15 +26,15 @@ function extractSaccharideNames(ccd) {
26
26
  return saccharideNames;
27
27
  }
28
28
  function writeSaccharideNamesFile(filePath, ionNames) {
29
- const output = `/**
30
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
31
- *
32
- * Code-generated ion names params file. Names extracted from CCD components.
33
- *
34
- * @author molstar/cli/chem-comp-dict/create-saccharides
35
- */
36
-
37
- export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
29
+ const output = `/**
30
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
31
+ *
32
+ * Code-generated ion names params file. Names extracted from CCD components.
33
+ *
34
+ * @author molstar/cli/chem-comp-dict/create-saccharides
35
+ */
36
+
37
+ export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
38
38
  `;
39
39
  writeFile(filePath, output);
40
40
  }
package/lib/cli/cifschema/util/generate.js CHANGED
@@ -6,21 +6,21 @@
6
6
  import { indentString } from '../../../mol-util/string';
7
7
  import { FieldPath } from '../../../mol-io/reader/cif/schema';
8
8
  function header(name, info, moldataImportPath) {
9
- return `/**
10
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
11
- *
12
- * Code-generated '${name}' schema file. ${info}
13
- *
14
- * @author molstar/ciftools package
15
- */
16
-
17
- import { Database, Column } from '${moldataImportPath}/db';
18
-
9
+ return `/**
10
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
11
+ *
12
+ * Code-generated '${name}' schema file. ${info}
13
+ *
14
+ * @author molstar/ciftools package
15
+ */
16
+
17
+ import { Database, Column } from '${moldataImportPath}/db';
18
+
19
19
  import Schema = Column.Schema;`;
20
20
  }
21
21
  function footer(name) {
22
- return `
23
- export type ${name}_Schema = typeof ${name}_Schema;
22
+ return `
23
+ export type ${name}_Schema = typeof ${name}_Schema;
24
24
  export interface ${name}_Database extends Database<${name}_Schema> {};`;
25
25
  }
26
26
  function getTypeShorthands(schema, fields) {
package/lib/cli/lipid-params/index.js CHANGED
@@ -41,15 +41,15 @@ async function run(out) {
41
41
  }
42
42
  const lipidNames = JSON.stringify(lipids.array);
43
43
  if (out) {
44
- const output = `/**
45
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
46
- *
47
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
48
- *
49
- * @author molstar/lipid-params cli
50
- */
51
-
52
- export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
44
+ const output = `/**
45
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
46
+ *
47
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
48
+ *
49
+ * @author molstar/lipid-params cli
50
+ */
51
+
52
+ export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
53
53
  `;
54
54
  fs.writeFileSync(out, output);
55
55
  }
package/lib/commonjs/apps/viewer/app.d.ts CHANGED
@@ -41,10 +41,11 @@ export declare const ExtensionMap: {
41
41
  'sb-ncbr-partial-charges': PluginSpec.Behavior;
42
42
  'wwpdb-chemical-component-dictionary': PluginSpec.Behavior;
43
43
  mvs: PluginSpec.Behavior;
44
+ tunnels: PluginSpec.Behavior;
44
45
  };
45
46
  declare const DefaultViewerOptions: {
46
47
  customFormats: [string, DataFormatProvider<any, any, any>][];
47
- extensions: ("mp4-export" | "backgrounds" | "dnatco-ntcs" | "g3d" | "geo-export" | "model-export" | "mvs" | "pdbe-structure-quality-report" | "sb-ncbr-partial-charges" | "volseg" | "wwpdb-chemical-component-dictionary" | "zenodo-import" | "assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
48
+ extensions: ("mp4-export" | "backgrounds" | "dnatco-ntcs" | "g3d" | "geo-export" | "model-export" | "mvs" | "pdbe-structure-quality-report" | "sb-ncbr-partial-charges" | "volseg" | "wwpdb-chemical-component-dictionary" | "zenodo-import" | "assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment" | "tunnels")[];
48
49
  disabledExtensions: string[];
49
50
  layoutIsExpanded: boolean;
50
51
  layoutShowControls: boolean;
package/lib/commonjs/apps/viewer/app.js CHANGED
@@ -73,6 +73,7 @@ exports.ExtensionMap = {
73
73
  'sb-ncbr-partial-charges': spec_2.PluginSpec.Behavior(sb_ncbr_1.SbNcbrPartialCharges),
74
74
  'wwpdb-chemical-component-dictionary': spec_2.PluginSpec.Behavior(behavior_4.wwPDBChemicalComponentDictionary),
75
75
  'mvs': spec_2.PluginSpec.Behavior(behavior_3.MolViewSpec),
76
+ 'tunnels': spec_2.PluginSpec.Behavior(sb_ncbr_1.SbNcbrTunnels),
76
77
  };
77
78
  const DefaultViewerOptions = {
78
79
  customFormats: CustomFormats,
package/lib/commonjs/cli/chem-comp-dict/create-ions.js CHANGED
@@ -28,15 +28,15 @@ function extractIonNames(ccd) {
28
28
  return ionNames;
29
29
  }
30
30
  function writeIonNamesFile(filePath, ionNames) {
31
- const output = `/**
32
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
33
- *
34
- * Code-generated ion names params file. Names extracted from CCD components.
35
- *
36
- * @author molstar/chem-comp-dict/create-ions cli
37
- */
38
-
39
- export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
31
+ const output = `/**
32
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
33
+ *
34
+ * Code-generated ion names params file. Names extracted from CCD components.
35
+ *
36
+ * @author molstar/chem-comp-dict/create-ions cli
37
+ */
38
+
39
+ export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
40
40
  `;
41
41
  writeFile(filePath, output);
42
42
  }
package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js CHANGED
@@ -29,15 +29,15 @@ function extractSaccharideNames(ccd) {
29
29
  return saccharideNames;
30
30
  }
31
31
  function writeSaccharideNamesFile(filePath, ionNames) {
32
- const output = `/**
33
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
34
- *
35
- * Code-generated ion names params file. Names extracted from CCD components.
36
- *
37
- * @author molstar/cli/chem-comp-dict/create-saccharides
38
- */
39
-
40
- export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
32
+ const output = `/**
33
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
34
+ *
35
+ * Code-generated ion names params file. Names extracted from CCD components.
36
+ *
37
+ * @author molstar/cli/chem-comp-dict/create-saccharides
38
+ */
39
+
40
+ export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
41
41
  `;
42
42
  writeFile(filePath, output);
43
43
  }
package/lib/commonjs/cli/cifschema/util/generate.js CHANGED
@@ -9,21 +9,21 @@ exports.generate = void 0;
9
9
  const string_1 = require("../../../mol-util/string");
10
10
  const schema_1 = require("../../../mol-io/reader/cif/schema");
11
11
  function header(name, info, moldataImportPath) {
12
- return `/**
13
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
14
- *
15
- * Code-generated '${name}' schema file. ${info}
16
- *
17
- * @author molstar/ciftools package
18
- */
19
-
20
- import { Database, Column } from '${moldataImportPath}/db';
21
-
12
+ return `/**
13
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
14
+ *
15
+ * Code-generated '${name}' schema file. ${info}
16
+ *
17
+ * @author molstar/ciftools package
18
+ */
19
+
20
+ import { Database, Column } from '${moldataImportPath}/db';
21
+
22
22
  import Schema = Column.Schema;`;
23
23
  }
24
24
  function footer(name) {
25
- return `
26
- export type ${name}_Schema = typeof ${name}_Schema;
25
+ return `
26
+ export type ${name}_Schema = typeof ${name}_Schema;
27
27
  export interface ${name}_Database extends Database<${name}_Schema> {};`;
28
28
  }
29
29
  function getTypeShorthands(schema, fields) {
package/lib/commonjs/cli/lipid-params/index.js CHANGED
@@ -44,15 +44,15 @@ async function run(out) {
44
44
  }
45
45
  const lipidNames = JSON.stringify(lipids.array);
46
46
  if (out) {
47
- const output = `/**
48
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
49
- *
50
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
51
- *
52
- * @author molstar/lipid-params cli
53
- */
54
-
55
- export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
47
+ const output = `/**
48
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
49
+ *
50
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
51
+ *
52
+ * @author molstar/lipid-params cli
53
+ */
54
+
55
+ export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
56
56
  `;
57
57
  fs.writeFileSync(out, output);
58
58
  }