molstar 4.0.1 → 4.2.0

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 (907) 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 +0 -9
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/docking-viewer/viewport.d.ts +8 -8
  9. package/lib/apps/mesoscale-explorer/behavior/camera.d.ts +1 -1
  10. package/lib/apps/mesoscale-explorer/behavior/select.d.ts +1 -1
  11. package/lib/apps/mesoscale-explorer/data/cellpack/model.d.ts +2 -2
  12. package/lib/apps/mesoscale-explorer/data/cellpack/preset.d.ts +1 -1
  13. package/lib/apps/mesoscale-explorer/data/cellpack/preset.js +5 -5
  14. package/lib/apps/mesoscale-explorer/data/generic/preset.d.ts +1 -1
  15. package/lib/apps/mesoscale-explorer/data/generic/preset.js +3 -3
  16. package/lib/apps/mesoscale-explorer/data/mmcif/preset.d.ts +1 -1
  17. package/lib/apps/mesoscale-explorer/data/mmcif/preset.js +3 -3
  18. package/lib/apps/mesoscale-explorer/data/petworld/preset.d.ts +1 -1
  19. package/lib/apps/mesoscale-explorer/data/petworld/preset.js +3 -3
  20. package/lib/apps/mesoscale-explorer/data/state.d.ts +19 -10
  21. package/lib/apps/mesoscale-explorer/data/state.js +14 -2
  22. package/lib/apps/mesoscale-explorer/index.html +100 -100
  23. package/lib/apps/mesoscale-explorer/style.scss +33 -33
  24. package/lib/apps/mesoscale-explorer/ui/entities.d.ts +19 -13
  25. package/lib/apps/mesoscale-explorer/ui/entities.js +23 -4
  26. package/lib/apps/viewer/app.d.ts +30 -24
  27. package/lib/apps/viewer/app.js +6 -6
  28. package/lib/apps/viewer/embedded.html +52 -52
  29. package/lib/apps/viewer/index.html +129 -129
  30. package/lib/cli/chem-comp-dict/create-ions.js +9 -9
  31. package/lib/cli/chem-comp-dict/create-saccharides.js +9 -9
  32. package/lib/cli/chem-comp-dict/util.d.ts +112 -112
  33. package/lib/cli/cifschema/util/cif-dic.js +1 -0
  34. package/lib/cli/cifschema/util/generate.js +12 -12
  35. package/lib/cli/lipid-params/index.js +9 -9
  36. package/lib/cli/mvs/mvs-print-schema.d.ts +1 -0
  37. package/lib/cli/mvs/mvs-print-schema.js +1 -0
  38. package/lib/cli/mvs/mvs-render.d.ts +1 -0
  39. package/lib/cli/mvs/mvs-render.js +1 -0
  40. package/lib/cli/mvs/mvs-validate.d.ts +1 -0
  41. package/lib/cli/mvs/mvs-validate.js +1 -0
  42. package/lib/commonjs/apps/docking-viewer/viewport.d.ts +8 -8
  43. package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.d.ts +1 -1
  44. package/lib/commonjs/apps/mesoscale-explorer/behavior/select.d.ts +1 -1
  45. package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/model.d.ts +2 -2
  46. package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.d.ts +1 -1
  47. package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.js +5 -5
  48. package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.d.ts +1 -1
  49. package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.js +3 -3
  50. package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.d.ts +1 -1
  51. package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.js +3 -3
  52. package/lib/commonjs/apps/mesoscale-explorer/data/petworld/preset.d.ts +1 -1
  53. package/lib/commonjs/apps/mesoscale-explorer/data/petworld/preset.js +3 -3
  54. package/lib/commonjs/apps/mesoscale-explorer/data/state.d.ts +19 -10
  55. package/lib/commonjs/apps/mesoscale-explorer/data/state.js +15 -3
  56. package/lib/commonjs/apps/mesoscale-explorer/ui/entities.d.ts +19 -13
  57. package/lib/commonjs/apps/mesoscale-explorer/ui/entities.js +22 -3
  58. package/lib/commonjs/apps/viewer/app.d.ts +30 -24
  59. package/lib/commonjs/apps/viewer/app.js +6 -6
  60. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +9 -9
  61. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +9 -9
  62. package/lib/commonjs/cli/chem-comp-dict/util.d.ts +112 -112
  63. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -0
  64. package/lib/commonjs/cli/cifschema/util/generate.js +12 -12
  65. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  66. package/lib/commonjs/cli/mvs/mvs-print-schema.d.ts +1 -0
  67. package/lib/commonjs/cli/mvs/mvs-print-schema.js +1 -0
  68. package/lib/commonjs/cli/mvs/mvs-render.d.ts +1 -0
  69. package/lib/commonjs/cli/mvs/mvs-render.js +1 -0
  70. package/lib/commonjs/cli/mvs/mvs-validate.d.ts +1 -0
  71. package/lib/commonjs/cli/mvs/mvs-validate.js +1 -0
  72. package/lib/commonjs/examples/alpha-orbitals/example-data.js +160 -160
  73. package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +136 -136
  74. package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts +2 -2
  75. package/lib/commonjs/extensions/anvil/behavior.d.ts +10 -9
  76. package/lib/commonjs/extensions/anvil/representation.d.ts +5 -0
  77. package/lib/commonjs/extensions/assembly-symmetry/behavior.d.ts +2 -1
  78. package/lib/commonjs/extensions/assembly-symmetry/prop.js +24 -24
  79. package/lib/commonjs/extensions/assembly-symmetry/representation.d.ts +1 -0
  80. package/lib/commonjs/extensions/backgrounds/index.d.ts +2 -2
  81. package/lib/commonjs/extensions/backgrounds/index.js +2 -1
  82. package/lib/commonjs/extensions/dnatco/behavior.d.ts +1 -1
  83. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts +10 -10
  84. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +5 -5
  85. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  86. package/lib/commonjs/extensions/dnatco/ntc-tube/behavior.d.ts +10 -10
  87. package/lib/commonjs/extensions/dnatco/ntc-tube/behavior.js +5 -5
  88. package/lib/commonjs/extensions/dnatco/ntc-tube/representation.d.ts +3 -0
  89. package/lib/commonjs/extensions/g3d/format.d.ts +6 -6
  90. package/lib/commonjs/extensions/geo-export/glb-exporter.d.ts +1 -1
  91. package/lib/commonjs/extensions/geo-export/glb-exporter.js +6 -4
  92. package/lib/commonjs/extensions/geo-export/index.d.ts +1 -1
  93. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +41 -41
  94. package/lib/commonjs/extensions/meshes/mesh-extension.d.ts +2 -3
  95. package/lib/commonjs/extensions/meshes/mesh-streaming/behavior.d.ts +1 -1
  96. package/lib/commonjs/extensions/meshes/mesh-streaming/server-info.d.ts +2 -2
  97. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +9 -9
  98. package/lib/commonjs/extensions/model-export/index.d.ts +1 -1
  99. package/lib/commonjs/extensions/mp4-export/index.d.ts +1 -1
  100. package/lib/commonjs/extensions/mvs/behavior.d.ts +1 -1
  101. package/lib/commonjs/extensions/mvs/camera.d.ts +2 -0
  102. package/lib/commonjs/extensions/mvs/camera.js +29 -2
  103. package/lib/commonjs/extensions/mvs/components/annotation-label/representation.d.ts +4 -0
  104. package/lib/commonjs/extensions/mvs/components/annotation-label/visual.d.ts +1 -0
  105. package/lib/commonjs/extensions/mvs/components/custom-label/representation.d.ts +4 -2
  106. package/lib/commonjs/extensions/mvs/components/custom-label/visual.d.ts +1 -0
  107. package/lib/commonjs/extensions/mvs/components/formats.d.ts +6 -4
  108. package/lib/commonjs/extensions/mvs/components/formats.js +2 -1
  109. package/lib/commonjs/extensions/mvs/load-helpers.d.ts +1 -1
  110. package/lib/commonjs/extensions/mvs/load.d.ts +2 -0
  111. package/lib/commonjs/extensions/mvs/load.js +12 -6
  112. package/lib/commonjs/extensions/mvs/tree/mvs/mvs-builder.d.ts +2 -8
  113. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.d.ts +1 -1
  114. package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts +22 -22
  115. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
  116. package/lib/commonjs/extensions/sb-ncbr/partial-charges/behavior.d.ts +1 -1
  117. package/lib/commonjs/extensions/sb-ncbr/partial-charges/preset.d.ts +4 -4
  118. package/lib/commonjs/extensions/volumes-and-segmentations/entry-meshes.d.ts +1 -1
  119. package/lib/commonjs/extensions/volumes-and-segmentations/entry-root.d.ts +5 -5
  120. package/lib/commonjs/extensions/volumes-and-segmentations/entry-segmentation.d.ts +1 -1
  121. package/lib/commonjs/extensions/volumes-and-segmentations/entry-state.d.ts +2 -2
  122. package/lib/commonjs/extensions/volumes-and-segmentations/global-state.d.ts +2 -2
  123. package/lib/commonjs/extensions/volumes-and-segmentations/helpers.d.ts +1 -1
  124. package/lib/commonjs/extensions/volumes-and-segmentations/index.d.ts +1 -1
  125. package/lib/commonjs/extensions/wwpdb/ccd/behavior.d.ts +1 -1
  126. package/lib/commonjs/extensions/wwpdb/ccd/representation.d.ts +4 -4
  127. package/lib/commonjs/extensions/zenodo/index.d.ts +1 -1
  128. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +14 -2
  129. package/lib/commonjs/mol-canvas3d/canvas3d.js +2 -2
  130. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  131. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  132. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  133. package/lib/commonjs/mol-canvas3d/passes/background.d.ts +6 -1
  134. package/lib/commonjs/mol-canvas3d/passes/background.js +13 -1
  135. package/lib/commonjs/mol-canvas3d/passes/bloom.d.ts +37 -0
  136. package/lib/commonjs/mol-canvas3d/passes/bloom.js +272 -0
  137. package/lib/commonjs/mol-canvas3d/passes/dpoit.js +4 -2
  138. package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +11 -7
  139. package/lib/commonjs/mol-canvas3d/passes/draw.js +29 -3
  140. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +6 -0
  141. package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +31 -5
  142. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +35 -40
  143. package/lib/commonjs/mol-geo/geometry/base.d.ts +3 -1
  144. package/lib/commonjs/mol-geo/geometry/base.js +4 -1
  145. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -1
  146. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -1
  147. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +2 -1
  148. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +4 -1
  149. package/lib/commonjs/mol-geo/geometry/emissive-data.d.ts +26 -0
  150. package/lib/commonjs/mol-geo/geometry/emissive-data.js +80 -0
  151. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +2 -1
  152. package/lib/commonjs/mol-geo/geometry/image/image.js +4 -1
  153. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +3 -2
  154. package/lib/commonjs/mol-geo/geometry/lines/lines.js +4 -1
  155. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +2 -1
  156. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +36 -2
  157. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  158. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +11 -4
  159. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +3 -2
  160. package/lib/commonjs/mol-geo/geometry/points/points.js +4 -1
  161. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -2
  162. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +7 -3
  163. package/lib/commonjs/mol-geo/geometry/text/text.d.ts +2 -1
  164. package/lib/commonjs/mol-geo/geometry/text/text.js +4 -1
  165. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +2 -1
  166. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +34 -2
  167. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +3 -1
  168. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +14 -4
  169. package/lib/commonjs/mol-geo/util/location-iterator.d.ts +5 -2
  170. package/lib/commonjs/mol-geo/util/location-iterator.js +8 -3
  171. package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +10 -0
  172. package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +10 -0
  173. package/lib/commonjs/mol-gl/renderable/image.d.ts +10 -0
  174. package/lib/commonjs/mol-gl/renderable/lines.d.ts +10 -0
  175. package/lib/commonjs/mol-gl/renderable/mesh.d.ts +10 -0
  176. package/lib/commonjs/mol-gl/renderable/points.d.ts +10 -0
  177. package/lib/commonjs/mol-gl/renderable/schema.d.ts +24 -1
  178. package/lib/commonjs/mol-gl/renderable/schema.js +15 -2
  179. package/lib/commonjs/mol-gl/renderable/spheres.d.ts +10 -0
  180. package/lib/commonjs/mol-gl/renderable/text.d.ts +10 -0
  181. package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +10 -0
  182. package/lib/commonjs/mol-gl/renderable.d.ts +1 -1
  183. package/lib/commonjs/mol-gl/renderable.js +2 -2
  184. package/lib/commonjs/mol-gl/renderer.d.ts +2 -1
  185. package/lib/commonjs/mol-gl/renderer.js +58 -49
  186. package/lib/commonjs/mol-gl/scene.d.ts +3 -1
  187. package/lib/commonjs/mol-gl/scene.js +26 -1
  188. package/lib/commonjs/mol-gl/shader/background.frag.d.ts +1 -1
  189. package/lib/commonjs/mol-gl/shader/background.frag.js +95 -94
  190. package/lib/commonjs/mol-gl/shader/background.vert.js +11 -11
  191. package/lib/commonjs/mol-gl/shader/blend-back-dpoit.frag.js +13 -13
  192. package/lib/commonjs/mol-gl/shader/bloom/blur.frag.d.ts +1 -0
  193. package/lib/commonjs/mol-gl/shader/bloom/blur.frag.js +32 -0
  194. package/lib/commonjs/mol-gl/shader/bloom/composite.frag.d.ts +1 -0
  195. package/lib/commonjs/mol-gl/shader/bloom/composite.frag.js +37 -0
  196. package/lib/commonjs/mol-gl/shader/bloom/luminosity.frag.d.ts +1 -0
  197. package/lib/commonjs/mol-gl/shader/bloom/luminosity.frag.js +56 -0
  198. package/lib/commonjs/mol-gl/shader/cas.frag.js +144 -144
  199. package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +31 -31
  200. package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +12 -12
  201. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +2 -2
  202. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +78 -70
  203. package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +16 -16
  204. package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +8 -8
  205. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  206. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +140 -112
  207. package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +6 -6
  208. package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +8 -8
  209. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  210. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +112 -123
  211. package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +14 -14
  212. package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +18 -18
  213. package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +12 -12
  214. package/lib/commonjs/mol-gl/shader/chunks/check-transparency.glsl.d.ts +1 -0
  215. package/lib/commonjs/mol-gl/shader/chunks/check-transparency.glsl.js +20 -0
  216. package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +7 -7
  217. package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +5 -5
  218. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  219. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +60 -51
  220. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  221. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +122 -92
  222. package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js +104 -104
  223. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
  224. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +150 -149
  225. package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +61 -61
  226. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +234 -234
  227. package/lib/commonjs/mol-gl/shader/chunks/dpoit-write.glsl.js +62 -62
  228. package/lib/commonjs/mol-gl/shader/chunks/fade-lod.glsl.js +42 -42
  229. package/lib/commonjs/mol-gl/shader/chunks/float-to-rgba.glsl.js +39 -39
  230. package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +127 -127
  231. package/lib/commonjs/mol-gl/shader/chunks/matrix-scale.glsl.js +5 -5
  232. package/lib/commonjs/mol-gl/shader/chunks/normal-frag-params.glsl.js +2 -2
  233. package/lib/commonjs/mol-gl/shader/chunks/read-from-texture.glsl.js +14 -14
  234. package/lib/commonjs/mol-gl/shader/chunks/rgba-to-float.glsl.js +84 -84
  235. package/lib/commonjs/mol-gl/shader/chunks/size-vert-params.glsl.js +11 -11
  236. package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +23 -23
  237. package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +17 -17
  238. package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +8 -8
  239. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +25 -25
  240. package/lib/commonjs/mol-gl/shader/compose.frag.js +12 -12
  241. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +23 -23
  242. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +43 -43
  243. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js +15 -15
  244. package/lib/commonjs/mol-gl/shader/copy.frag.js +11 -11
  245. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +2 -2
  246. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +267 -264
  247. package/lib/commonjs/mol-gl/shader/cylinders.vert.js +89 -89
  248. package/lib/commonjs/mol-gl/shader/depth-merge.frag.js +23 -23
  249. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  250. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +362 -356
  251. package/lib/commonjs/mol-gl/shader/direct-volume.vert.js +41 -41
  252. package/lib/commonjs/mol-gl/shader/evaluate-dpoit.frag.js +10 -10
  253. package/lib/commonjs/mol-gl/shader/evaluate-wboit.frag.js +17 -17
  254. package/lib/commonjs/mol-gl/shader/fxaa.frag.js +228 -228
  255. package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +49 -49
  256. package/lib/commonjs/mol-gl/shader/gaussian-density.vert.js +27 -27
  257. package/lib/commonjs/mol-gl/shader/hi-z.frag.js +18 -18
  258. package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +58 -58
  259. package/lib/commonjs/mol-gl/shader/histogram-pyramid/sum.frag.js +19 -19
  260. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
  261. package/lib/commonjs/mol-gl/shader/image.frag.js +170 -161
  262. package/lib/commonjs/mol-gl/shader/image.vert.js +21 -21
  263. package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
  264. package/lib/commonjs/mol-gl/shader/lines.frag.js +43 -40
  265. package/lib/commonjs/mol-gl/shader/lines.vert.js +117 -117
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  821. package/lib/mol-repr/shape/loci/common.d.ts +1 -0
  822. package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
  823. package/lib/mol-repr/shape/loci/distance.d.ts +1 -0
  824. package/lib/mol-repr/shape/loci/label.d.ts +1 -0
  825. package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
  826. package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
  827. package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
  828. package/lib/mol-repr/structure/complex-representation.d.ts +1 -1
  829. package/lib/mol-repr/structure/complex-representation.js +7 -1
  830. package/lib/mol-repr/structure/complex-visual.d.ts +8 -1
  831. package/lib/mol-repr/structure/complex-visual.js +5 -1
  832. package/lib/mol-repr/structure/params.d.ts +8 -0
  833. package/lib/mol-repr/structure/registry.d.ts +14 -0
  834. package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
  835. package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  836. package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  837. package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
  838. package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  839. package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  840. package/lib/mol-repr/structure/representation/gaussian-volume.d.ts +3 -0
  841. package/lib/mol-repr/structure/representation/label.d.ts +3 -0
  842. package/lib/mol-repr/structure/representation/line.d.ts +3 -0
  843. package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  844. package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
  845. package/lib/mol-repr/structure/representation/point.d.ts +3 -0
  846. package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
  847. package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
  848. package/lib/mol-repr/structure/units-representation.d.ts +1 -1
  849. package/lib/mol-repr/structure/units-representation.js +9 -3
  850. package/lib/mol-repr/structure/units-visual.d.ts +9 -1
  851. package/lib/mol-repr/structure/units-visual.js +5 -1
  852. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  853. package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -0
  854. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  855. package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts +1 -0
  856. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  857. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  858. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  859. package/lib/mol-repr/structure/visual/element-cross.d.ts +1 -0
  860. package/lib/mol-repr/structure/visual/element-point.d.ts +1 -0
  861. package/lib/mol-repr/structure/visual/element-sphere.d.ts +4 -0
  862. package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  863. package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -0
  864. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +4 -0
  865. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +1 -1
  866. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -0
  867. package/lib/mol-repr/structure/visual/label-text.d.ts +1 -0
  868. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  869. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -0
  870. package/lib/mol-repr/structure/visual/nucleotide-atomic-bond.d.ts +2 -0
  871. package/lib/mol-repr/structure/visual/nucleotide-atomic-element.d.ts +2 -0
  872. package/lib/mol-repr/structure/visual/nucleotide-atomic-ring-fill.d.ts +1 -0
  873. package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  874. package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  875. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  876. package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  877. package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  878. package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  879. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  880. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  881. package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  882. package/lib/mol-repr/visual.d.ts +6 -1
  883. package/lib/mol-repr/visual.js +57 -3
  884. package/lib/mol-repr/volume/direct-volume.d.ts +3 -0
  885. package/lib/mol-repr/volume/isosurface.d.ts +6 -0
  886. package/lib/mol-repr/volume/registry.d.ts +4 -0
  887. package/lib/mol-repr/volume/representation.d.ts +2 -1
  888. package/lib/mol-repr/volume/representation.js +9 -2
  889. package/lib/mol-repr/volume/segment.d.ts +5 -0
  890. package/lib/mol-repr/volume/slice.d.ts +3 -0
  891. package/lib/mol-script/language/symbol-table/core.d.ts +3 -3
  892. package/lib/mol-state/tree/immutable.d.ts +1 -1
  893. package/lib/mol-state/tree/transient.d.ts +2 -2
  894. package/lib/mol-theme/color/external-volume.d.ts +3 -1
  895. package/lib/mol-theme/color/external-volume.js +8 -2
  896. package/lib/mol-theme/color.d.ts +1 -0
  897. package/lib/mol-theme/emissive.d.ts +40 -0
  898. package/lib/mol-theme/emissive.js +134 -0
  899. package/lib/mol-theme/substance.d.ts +1 -1
  900. package/lib/mol-theme/substance.js +2 -2
  901. package/lib/mol-theme/transparency.d.ts +0 -1
  902. package/lib/mol-util/input/input-observer.js +2 -0
  903. package/lib/mol-util/set.d.ts +1 -1
  904. package/lib/mol-util/set.js +17 -1
  905. package/lib/servers/common/swagger-ui/indexTemplate.js +66 -66
  906. package/lib/servers/volume/config.js +5 -5
  907. package/package.json +195 -193
package/LICENSE CHANGED
@@ -1,21 +1,21 @@
1
- The MIT License
2
-
3
- Copyright (c) 2017 - now, Mol* contributors
4
-
5
- Permission is hereby granted, free of charge, to any person obtaining a copy
6
- of this software and associated documentation files (the "Software"), to deal
7
- in the Software without restriction, including without limitation the rights
8
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
- copies of the Software, and to permit persons to whom the Software is
10
- furnished to do so, subject to the following conditions:
11
-
12
- The above copyright notice and this permission notice shall be included in
13
- all copies or substantial portions of the Software.
14
-
15
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
1
+ The MIT License
2
+
3
+ Copyright (c) 2017 - now, Mol* contributors
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in
13
+ all copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
21
21
  THE SOFTWARE.
package/README.md CHANGED
@@ -1,197 +1,197 @@
1
- [![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)
2
- [![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)
3
- [![Build](https://github.com/molstar/molstar/actions/workflows/node.yml/badge.svg)](https://github.com/molstar/molstar/actions/workflows/node.yml)
4
- [![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)
5
-
6
- # Mol*
7
-
8
- The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
9
-
10
- When using Mol*, please cite:
11
-
12
- David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
13
-
14
- ### Protein Data Bank Integrations
15
-
16
- - The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
17
-
18
- - [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
19
-
20
-
21
- ## Project Structure Overview
22
-
23
- The core of Mol* consists of these modules (see under `src/`):
24
-
25
- - `mol-task` Computation abstraction with progress tracking and cancellation support.
26
- - `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
27
- - `mol-math` Math related (loosely) algorithms and data structures.
28
- - `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
29
- - `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
30
- - `mol-model-formats` Data format parsers for `mol-model`.
31
- - `mol-model-props` Common "custom properties".
32
- - `mol-script` A scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
33
- - `mol-geo` Creating (molecular) geometries.
34
- - `mol-theme` Theming for structure, volume and shape representations.
35
- - `mol-repr` Molecular representations for structures, volumes and shapes.
36
- - `mol-gl` A wrapper around WebGL.
37
- - `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
38
- - `mol-state` State representation tree with state saving and automatic updates.
39
- - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
40
- - `mol-plugin-state` State transformations, builders, and managers.
41
- - `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
42
- - `mol-util` Useful things that do not fit elsewhere.
43
-
44
- Moreover, the project contains the implementation of `servers`, including
45
-
46
- - `servers/model` A tool for accessing coordinate and annotation data of molecular structures.
47
- - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
48
- - `servers/plugin-state` A basic server to store Mol* Plugin states.
49
-
50
- The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
51
-
52
- ## Previous Work
53
- This project builds on experience from previous solutions:
54
- - [LiteMol Suite](https://www.litemol.org)
55
- - [WebChemistry](https://webchem.ncbr.muni.cz)
56
- - [NGL Viewer](http://nglviewer.org)
57
- - [MMTF](http://mmtf.rcsb.org)
58
- - [MolQL](http://molql.org)
59
- - [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)
60
- - And many others (list will be continuously expanded).
61
-
62
- ## Building & Running
63
-
64
- ### Build:
65
- npm install
66
- npm run build
67
-
68
- ### Build automatically on file save:
69
- npm run watch
70
-
71
- If working on just the viewer, ``npm run watch-viewer`` will provide shorter compile times.
72
-
73
- ### Build with debug mode enabled:
74
- DEBUG=molstar npm run watch
75
-
76
- Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
77
-
78
- ### Cleaning and forcing a full rebuild
79
- npm run clean
80
-
81
- Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
82
-
83
- npm run rebuild
84
-
85
- Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
86
-
87
- Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
88
-
89
- ### Build for production:
90
- NODE_ENV=production npm run build
91
-
92
- **Run**
93
-
94
- If not installed previously:
95
-
96
- npm install -g http-server
97
-
98
- ...or a similar solution.
99
-
100
- From the root of the project:
101
-
102
- http-server -p PORT-NUMBER
103
-
104
- and navigate to `build/viewer`
105
-
106
-
107
- ### Code generation
108
- **CIF schemas**
109
-
110
- node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
111
- node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
112
- node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
113
- node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
114
-
115
- **Lipid names**
116
-
117
- node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
118
-
119
- **Ion names**
120
-
121
- node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
122
-
123
- **Saccharide names**
124
-
125
- node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts
126
-
127
- ### Other scripts
128
- **Create chem comp bond table**
129
-
130
- node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
131
-
132
- **Test model server**
133
-
134
- export NODE_PATH="lib"; node build/src/servers/model/test.js
135
-
136
- **State Transformer Docs**
137
-
138
- export NODE_PATH="lib"; node build/state-docs
139
-
140
- **Convert any CIF to BinaryCIF (or vice versa)**
141
-
142
- node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
143
-
144
- To see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.
145
-
146
- Or
147
-
148
- node lib/commonjs/cli/cif2bcif
149
-
150
- E.g.
151
-
152
- node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
153
- node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif
154
-
155
- ## Development
156
-
157
- ### Installation
158
-
159
- If node complains about a missing acorn peer dependency, run the following commands
160
-
161
- npm update acorn --depth 20
162
- npm dedupe
163
-
164
- ### Editor
165
-
166
- To get syntax highlighting for shader files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
167
-
168
- "files.associations": {
169
- "*.glsl.ts": "glsl",
170
- "*.frag.ts": "glsl",
171
- "*.vert.ts": "glsl"
172
- },
173
-
174
- ## Publish
175
-
176
- ### Prerelease
177
- npm version prerelease # assumes the current version ends with '-dev.X'
178
- npm publish --tag next
179
-
180
- ### Release
181
- npm version 0.X.0 # provide valid semver string
182
- npm publish
183
-
184
- ## Deploy
185
- npm run test
186
- npm run build
187
- node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
188
-
189
- ## Contributing
190
- Just open an issue or make a pull request. All contributions are welcome.
191
-
192
- ## Funding
193
- Funding sources include but are not limited to:
194
- * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
195
- * [PDBe, EMBL-EBI](https://pdbe.org)
196
- * [CEITEC](https://www.ceitec.eu/)
197
- * [EntosAI](https://www.entos.ai)
1
+ [![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)
2
+ [![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)
3
+ [![Build](https://github.com/molstar/molstar/actions/workflows/node.yml/badge.svg)](https://github.com/molstar/molstar/actions/workflows/node.yml)
4
+ [![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)
5
+
6
+ # Mol*
7
+
8
+ The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
9
+
10
+ When using Mol*, please cite:
11
+
12
+ David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
13
+
14
+ ### Protein Data Bank Integrations
15
+
16
+ - The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
17
+
18
+ - [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
19
+
20
+
21
+ ## Project Structure Overview
22
+
23
+ The core of Mol* consists of these modules (see under `src/`):
24
+
25
+ - `mol-task` Computation abstraction with progress tracking and cancellation support.
26
+ - `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
27
+ - `mol-math` Math related (loosely) algorithms and data structures.
28
+ - `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
29
+ - `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
30
+ - `mol-model-formats` Data format parsers for `mol-model`.
31
+ - `mol-model-props` Common "custom properties".
32
+ - `mol-script` A scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
33
+ - `mol-geo` Creating (molecular) geometries.
34
+ - `mol-theme` Theming for structure, volume and shape representations.
35
+ - `mol-repr` Molecular representations for structures, volumes and shapes.
36
+ - `mol-gl` A wrapper around WebGL.
37
+ - `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
38
+ - `mol-state` State representation tree with state saving and automatic updates.
39
+ - `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
40
+ - `mol-plugin-state` State transformations, builders, and managers.
41
+ - `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
42
+ - `mol-util` Useful things that do not fit elsewhere.
43
+
44
+ Moreover, the project contains the implementation of `servers`, including
45
+
46
+ - `servers/model` A tool for accessing coordinate and annotation data of molecular structures.
47
+ - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
48
+ - `servers/plugin-state` A basic server to store Mol* Plugin states.
49
+
50
+ The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
51
+
52
+ ## Previous Work
53
+ This project builds on experience from previous solutions:
54
+ - [LiteMol Suite](https://www.litemol.org)
55
+ - [WebChemistry](https://webchem.ncbr.muni.cz)
56
+ - [NGL Viewer](http://nglviewer.org)
57
+ - [MMTF](http://mmtf.rcsb.org)
58
+ - [MolQL](http://molql.org)
59
+ - [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)
60
+ - And many others (list will be continuously expanded).
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+
62
+ ## Building & Running
63
+
64
+ ### Build:
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+ npm install
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+ npm run build
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+
68
+ ### Build automatically on file save:
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+ npm run watch
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+
71
+ If working on just the viewer, ``npm run watch-viewer`` will provide shorter compile times.
72
+
73
+ ### Build with debug mode enabled:
74
+ DEBUG=molstar npm run watch
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+
76
+ Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
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+
78
+ ### Cleaning and forcing a full rebuild
79
+ npm run clean
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+
81
+ Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
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+
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+ npm run rebuild
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+
85
+ Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
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+
87
+ Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
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+
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+ ### Build for production:
90
+ NODE_ENV=production npm run build
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+
92
+ **Run**
93
+
94
+ If not installed previously:
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+
96
+ npm install -g http-server
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+
98
+ ...or a similar solution.
99
+
100
+ From the root of the project:
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+
102
+ http-server -p PORT-NUMBER
103
+
104
+ and navigate to `build/viewer`
105
+
106
+
107
+ ### Code generation
108
+ **CIF schemas**
109
+
110
+ node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
111
+ node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
112
+ node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
113
+ node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
114
+
115
+ **Lipid names**
116
+
117
+ node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
118
+
119
+ **Ion names**
120
+
121
+ node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
122
+
123
+ **Saccharide names**
124
+
125
+ node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts
126
+
127
+ ### Other scripts
128
+ **Create chem comp bond table**
129
+
130
+ node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
131
+
132
+ **Test model server**
133
+
134
+ export NODE_PATH="lib"; node build/src/servers/model/test.js
135
+
136
+ **State Transformer Docs**
137
+
138
+ export NODE_PATH="lib"; node build/state-docs
139
+
140
+ **Convert any CIF to BinaryCIF (or vice versa)**
141
+
142
+ node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
143
+
144
+ To see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.
145
+
146
+ Or
147
+
148
+ node lib/commonjs/cli/cif2bcif
149
+
150
+ E.g.
151
+
152
+ node lib/commonjs/cli/cif2bcif src.cif out.bcif.gz
153
+ node lib/commonjs/cli/cif2bcif src.bcif.gz out.cif
154
+
155
+ ## Development
156
+
157
+ ### Installation
158
+
159
+ If node complains about a missing acorn peer dependency, run the following commands
160
+
161
+ npm update acorn --depth 20
162
+ npm dedupe
163
+
164
+ ### Editor
165
+
166
+ To get syntax highlighting for shader files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
167
+
168
+ "files.associations": {
169
+ "*.glsl.ts": "glsl",
170
+ "*.frag.ts": "glsl",
171
+ "*.vert.ts": "glsl"
172
+ },
173
+
174
+ ## Publish
175
+
176
+ ### Prerelease
177
+ npm version prerelease # assumes the current version ends with '-dev.X'
178
+ npm publish --tag next
179
+
180
+ ### Release
181
+ npm version 0.X.0 # provide valid semver string
182
+ npm publish
183
+
184
+ ## Deploy
185
+ npm run test
186
+ npm run build
187
+ node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
188
+
189
+ ## Contributing
190
+ Just open an issue or make a pull request. All contributions are welcome.
191
+
192
+ ## Funding
193
+ Funding sources include but are not limited to:
194
+ * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
195
+ * [PDBe, EMBL-EBI](https://pdbe.org)
196
+ * [CEITEC](https://www.ceitec.eu/)
197
+ * [EntosAI](https://www.entos.ai)
@@ -1,53 +1,53 @@
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>Embedded Mol* Viewer</title>
8
- <style>
9
- #app {
10
- position: absolute;
11
- left: 100px;
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- top: 100px;
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- width: 800px;
14
- height: 600px;
15
- }
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- </style>
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- <link rel="stylesheet" type="text/css" href="molstar.css" />
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- </head>
19
- <body>
20
- <div id="app"></div>
21
- <script type="text/javascript" src="./molstar.js"></script>
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- <script type="text/javascript">
23
- molstar.Viewer.create('app', {
24
- layoutIsExpanded: true,
25
- layoutShowControls: false,
26
- layoutShowRemoteState: false,
27
- layoutShowSequence: true,
28
- layoutShowLog: false,
29
- layoutShowLeftPanel: true,
30
-
31
- viewportShowExpand: true,
32
- viewportShowSelectionMode: false,
33
- viewportShowAnimation: false,
34
-
35
- pdbProvider: 'rcsb',
36
- emdbProvider: 'rcsb',
37
- }).then(viewer => {
38
- viewer.loadPdb('7bv2');
39
- viewer.loadEmdb('EMD-30210', { detail: 6 });
40
- // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
41
- // viewer.loadStructureFromUrl('my url', 'pdb', false, {
42
- // representationParams: {
43
- // theme: {
44
- // globalName: 'uniform',
45
- // globalColorParams: { value: 0xff0000 }
46
- // }
47
- // },
48
- // label: 'my structure'
49
- // });
50
- });
51
- </script>
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- </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>Embedded Mol* Viewer</title>
8
+ <style>
9
+ #app {
10
+ position: absolute;
11
+ left: 100px;
12
+ top: 100px;
13
+ width: 800px;
14
+ height: 600px;
15
+ }
16
+ </style>
17
+ <link rel="stylesheet" type="text/css" href="molstar.css" />
18
+ </head>
19
+ <body>
20
+ <div id="app"></div>
21
+ <script type="text/javascript" src="./molstar.js"></script>
22
+ <script type="text/javascript">
23
+ molstar.Viewer.create('app', {
24
+ layoutIsExpanded: true,
25
+ layoutShowControls: false,
26
+ layoutShowRemoteState: false,
27
+ layoutShowSequence: true,
28
+ layoutShowLog: false,
29
+ layoutShowLeftPanel: true,
30
+
31
+ viewportShowExpand: true,
32
+ viewportShowSelectionMode: false,
33
+ viewportShowAnimation: false,
34
+
35
+ pdbProvider: 'rcsb',
36
+ emdbProvider: 'rcsb',
37
+ }).then(viewer => {
38
+ viewer.loadPdb('7bv2');
39
+ viewer.loadEmdb('EMD-30210', { detail: 6 });
40
+ // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
41
+ // viewer.loadStructureFromUrl('my url', 'pdb', false, {
42
+ // representationParams: {
43
+ // theme: {
44
+ // globalName: 'uniform',
45
+ // globalColorParams: { value: 0xff0000 }
46
+ // }
47
+ // },
48
+ // label: 'my structure'
49
+ // });
50
+ });
51
+ </script>
52
+ </body>
53
53
  </html>