molstar 3.4.0 → 3.6.1

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 (401) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +202 -197
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +106 -106
  5. package/build/viewer/molstar.js +1 -1
  6. package/build/viewer/molstar.js.LICENSE.txt +12 -14
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/docking-viewer/index.js +1 -1
  9. package/lib/apps/viewer/app.js +1 -1
  10. package/lib/apps/viewer/embedded.html +43 -43
  11. package/lib/apps/viewer/index.html +106 -106
  12. package/lib/cli/chem-comp-dict/util.d.ts +20 -20
  13. package/lib/cli/cif2bcif/converter.js +1 -1
  14. package/lib/cli/cif2bcif/index.js +4 -4
  15. package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
  16. package/lib/cli/cifschema/util/cif-dic.js +7 -5
  17. package/lib/cli/cifschema/util/generate.d.ts +1 -1
  18. package/lib/cli/cifschema/util/generate.js +12 -3
  19. package/lib/cli/cifschema/util/schema.d.ts +3 -3
  20. package/lib/cli/cifschema/util/schema.js +1 -1
  21. package/lib/commonjs/apps/docking-viewer/index.js +2 -2
  22. package/lib/commonjs/apps/viewer/app.js +2 -2
  23. package/lib/commonjs/cli/chem-comp-dict/util.d.ts +20 -20
  24. package/lib/commonjs/cli/cif2bcif/converter.js +1 -1
  25. package/lib/commonjs/cli/cif2bcif/index.js +4 -4
  26. package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
  27. package/lib/commonjs/cli/cifschema/util/cif-dic.js +7 -5
  28. package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
  29. package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
  30. package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
  31. package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
  32. package/lib/commonjs/examples/alpha-orbitals/index.js +2 -2
  33. package/lib/commonjs/examples/basic-wrapper/index.js +2 -2
  34. package/lib/commonjs/examples/lighting/index.js +2 -2
  35. package/lib/commonjs/examples/proteopedia-wrapper/index.js +2 -2
  36. package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
  37. package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
  38. package/lib/commonjs/extensions/cellpack/representation.d.ts +1 -0
  39. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  40. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
  41. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +1 -3
  42. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  43. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +18 -19
  44. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
  45. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
  46. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
  47. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +2 -0
  48. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  49. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  50. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  51. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
  52. package/lib/commonjs/mol-data/db/column.d.ts +10 -3
  53. package/lib/commonjs/mol-data/db/column.js +39 -17
  54. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
  55. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +2 -2
  56. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  57. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  58. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  59. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  60. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +2 -2
  61. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  62. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -1
  63. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +2 -2
  64. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  65. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
  66. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
  67. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  68. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
  69. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
  70. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  71. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  72. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
  73. package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
  74. package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
  75. package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
  76. package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
  77. package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
  78. package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
  79. package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
  80. package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
  81. package/lib/commonjs/mol-gl/webgl/buffer.js +12 -12
  82. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  83. package/lib/commonjs/mol-gl/webgl/context.js +2 -2
  84. package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
  85. package/lib/commonjs/mol-gl/webgl/program.js +10 -4
  86. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +8 -8
  87. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
  88. package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
  89. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
  90. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
  91. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
  92. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  93. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +30 -26
  94. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
  95. package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
  96. package/lib/commonjs/mol-io/reader/cif/schema.js +22 -2
  97. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  98. package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
  99. package/lib/commonjs/mol-math/geometry/common.js +1 -1
  100. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  101. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +2 -2
  102. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  103. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +7 -7
  104. package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
  105. package/lib/commonjs/mol-math/geometry/gaussian-density.js +1 -1
  106. package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
  107. package/lib/commonjs/mol-math/geometry/molecular-surface.js +2 -2
  108. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
  109. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +12 -6
  110. package/lib/commonjs/mol-model/structure/model/model.js +14 -6
  111. package/lib/commonjs/mol-model/structure/model/properties/common.js +1 -1
  112. package/lib/commonjs/mol-model/structure/model/types.d.ts +19 -17
  113. package/lib/commonjs/mol-model/structure/model/types.js +30 -31
  114. package/lib/commonjs/mol-model/structure/query/queries/generators.js +1 -1
  115. package/lib/commonjs/mol-model/structure/structure/properties.d.ts +1 -1
  116. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +2 -4
  117. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -3
  118. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +3 -0
  119. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +2 -0
  120. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  121. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
  122. package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +3 -3
  123. package/lib/commonjs/mol-model-formats/structure/common/component.js +46 -46
  124. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.d.ts +2 -2
  125. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js +72 -7
  126. package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js +11 -11
  127. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +7 -2
  128. package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
  129. package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
  130. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  131. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  132. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +3 -0
  133. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  134. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  135. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +4 -2
  136. package/lib/commonjs/mol-plugin/commands.d.ts +1 -0
  137. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +3 -0
  138. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +6 -6
  139. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
  140. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +1 -1
  141. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +6 -0
  142. package/lib/commonjs/mol-plugin-ui/react18.d.ts +11 -0
  143. package/lib/commonjs/mol-plugin-ui/react18.js +38 -0
  144. package/lib/commonjs/mol-plugin-ui/state/common.js +6 -7
  145. package/lib/commonjs/mol-plugin-ui/structure/focus.d.ts +1 -1
  146. package/lib/commonjs/mol-plugin-ui/structure/focus.js +2 -2
  147. package/lib/commonjs/mol-plugin-ui/task.d.ts +2 -21
  148. package/lib/commonjs/mol-plugin-ui/task.js +39 -43
  149. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +1 -0
  150. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +1 -0
  151. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +1 -0
  152. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +1 -0
  153. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +1 -0
  154. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +3 -0
  155. package/lib/commonjs/mol-repr/structure/params.d.ts +4 -0
  156. package/lib/commonjs/mol-repr/structure/registry.d.ts +10 -0
  157. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +3 -0
  158. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  159. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  160. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +3 -0
  161. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  162. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  163. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  164. package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +3 -0
  165. package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +3 -0
  166. package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +3 -0
  167. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +4 -0
  168. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  169. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  170. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  171. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  172. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  173. package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +2 -0
  174. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  175. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  176. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
  177. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -9
  178. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  179. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  180. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  181. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +3 -3
  182. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  183. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +4 -4
  184. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  185. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  186. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  187. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  188. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  189. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  190. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  191. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  192. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  193. package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts +1 -3
  194. package/lib/commonjs/mol-repr/structure/visual/util/common.js +2 -27
  195. package/lib/commonjs/mol-repr/util.d.ts +2 -1
  196. package/lib/commonjs/mol-repr/util.js +2 -2
  197. package/lib/commonjs/mol-repr/volume/isosurface.d.ts +5 -0
  198. package/lib/commonjs/mol-repr/volume/registry.d.ts +1 -0
  199. package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
  200. package/lib/examples/alpha-orbitals/index.html +61 -61
  201. package/lib/examples/alpha-orbitals/index.js +1 -1
  202. package/lib/examples/basic-wrapper/index.html +137 -137
  203. package/lib/examples/basic-wrapper/index.js +1 -1
  204. package/lib/examples/lighting/index.html +88 -88
  205. package/lib/examples/lighting/index.js +1 -1
  206. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  207. package/lib/examples/proteopedia-wrapper/index.js +1 -1
  208. package/lib/extensions/anvil/behavior.d.ts +1 -0
  209. package/lib/extensions/anvil/representation.d.ts +4 -0
  210. package/lib/extensions/cellpack/representation.d.ts +1 -0
  211. package/lib/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  212. package/lib/extensions/dnatco/confal-pyramids/color.js +224 -132
  213. package/lib/extensions/dnatco/confal-pyramids/property.js +1 -3
  214. package/lib/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  215. package/lib/extensions/dnatco/confal-pyramids/util.js +19 -20
  216. package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
  217. package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
  218. package/lib/extensions/rcsb/validation-report/representation.d.ts +5 -0
  219. package/lib/mol-canvas3d/canvas3d.d.ts +2 -0
  220. package/lib/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  221. package/lib/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  222. package/lib/mol-canvas3d/helper/helper.d.ts +2 -0
  223. package/lib/mol-canvas3d/passes/image.d.ts +1 -0
  224. package/lib/mol-data/db/column.d.ts +10 -3
  225. package/lib/mol-data/db/column.js +39 -18
  226. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
  227. package/lib/mol-geo/geometry/cylinders/cylinders.js +2 -2
  228. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  229. package/lib/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  230. package/lib/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  231. package/lib/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  232. package/lib/mol-geo/geometry/mesh/mesh.js +2 -2
  233. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  234. package/lib/mol-geo/geometry/spheres/spheres.d.ts +2 -1
  235. package/lib/mol-geo/geometry/spheres/spheres.js +2 -2
  236. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  237. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
  238. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
  239. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  240. package/lib/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
  241. package/lib/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
  242. package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  243. package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
  244. package/lib/mol-gl/shader/image.frag.d.ts +2 -2
  245. package/lib/mol-gl/shader/image.frag.js +2 -2
  246. package/lib/mol-gl/shader/lines.frag.d.ts +2 -2
  247. package/lib/mol-gl/shader/lines.frag.js +2 -2
  248. package/lib/mol-gl/shader/points.frag.d.ts +2 -2
  249. package/lib/mol-gl/shader/points.frag.js +2 -2
  250. package/lib/mol-gl/shader/text.frag.d.ts +2 -2
  251. package/lib/mol-gl/shader/text.frag.js +2 -2
  252. package/lib/mol-gl/webgl/buffer.d.ts +2 -2
  253. package/lib/mol-gl/webgl/buffer.js +12 -12
  254. package/lib/mol-gl/webgl/context.d.ts +1 -1
  255. package/lib/mol-gl/webgl/context.js +2 -2
  256. package/lib/mol-gl/webgl/program.d.ts +1 -1
  257. package/lib/mol-gl/webgl/program.js +10 -4
  258. package/lib/mol-io/reader/cif/schema/bird.d.ts +8 -8
  259. package/lib/mol-io/reader/cif/schema/bird.js +12 -11
  260. package/lib/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
  261. package/lib/mol-io/reader/cif/schema/ccd.d.ts +12 -12
  262. package/lib/mol-io/reader/cif/schema/ccd.js +13 -12
  263. package/lib/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
  264. package/lib/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  265. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +30 -26
  266. package/lib/mol-io/reader/cif/schema/mmcif.js +44 -39
  267. package/lib/mol-io/reader/cif/schema.d.ts +1 -1
  268. package/lib/mol-io/reader/cif/schema.js +22 -2
  269. package/lib/mol-io/writer/mol/encoder.js +1 -1
  270. package/lib/mol-math/geometry/common.d.ts +2 -1
  271. package/lib/mol-math/geometry/common.js +1 -1
  272. package/lib/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  273. package/lib/mol-math/geometry/gaussian-density/cpu.js +2 -2
  274. package/lib/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  275. package/lib/mol-math/geometry/gaussian-density/gpu.js +7 -7
  276. package/lib/mol-math/geometry/gaussian-density.d.ts +2 -2
  277. package/lib/mol-math/geometry/gaussian-density.js +1 -1
  278. package/lib/mol-math/geometry/molecular-surface.d.ts +2 -1
  279. package/lib/mol-math/geometry/molecular-surface.js +2 -2
  280. package/lib/mol-math/geometry/primitives/box3d.js +2 -1
  281. package/lib/mol-math/geometry/primitives/sphere3d.js +12 -6
  282. package/lib/mol-model/structure/model/model.js +14 -6
  283. package/lib/mol-model/structure/model/properties/common.js +1 -1
  284. package/lib/mol-model/structure/model/types.d.ts +19 -17
  285. package/lib/mol-model/structure/model/types.js +30 -31
  286. package/lib/mol-model/structure/query/queries/generators.js +1 -1
  287. package/lib/mol-model/structure/structure/properties.d.ts +1 -1
  288. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +2 -4
  289. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -3
  290. package/lib/mol-model/structure/structure/unit/rings.js +3 -0
  291. package/lib/mol-model-formats/shape/ply.d.ts +2 -0
  292. package/lib/mol-model-formats/structure/basic/entities.js +1 -1
  293. package/lib/mol-model-formats/structure/basic/schema.d.ts +2 -2
  294. package/lib/mol-model-formats/structure/common/component.d.ts +3 -3
  295. package/lib/mol-model-formats/structure/common/component.js +46 -46
  296. package/lib/mol-model-formats/structure/pdb/atom-site.d.ts +2 -2
  297. package/lib/mol-model-formats/structure/pdb/atom-site.js +72 -7
  298. package/lib/mol-model-formats/structure/pdb/secondary-structure.js +11 -11
  299. package/lib/mol-model-formats/structure/pdb/to-cif.js +7 -2
  300. package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
  301. package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
  302. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  303. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  304. package/lib/mol-model-props/computed/representations/interactions.d.ts +3 -0
  305. package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  306. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  307. package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js +4 -2
  308. package/lib/mol-plugin/commands.d.ts +1 -0
  309. package/lib/mol-plugin/util/viewport-screenshot.d.ts +3 -0
  310. package/lib/mol-plugin/version.js +2 -2
  311. package/lib/mol-plugin-state/actions/structure.d.ts +6 -6
  312. package/lib/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
  313. package/lib/mol-plugin-state/helpers/structure-selection-query.js +1 -1
  314. package/lib/mol-plugin-state/transforms/representation.d.ts +6 -0
  315. package/lib/mol-plugin-ui/react18.d.ts +11 -0
  316. package/lib/mol-plugin-ui/react18.js +34 -0
  317. package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
  318. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  319. package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
  320. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  321. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  322. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  323. package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
  324. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  325. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  326. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  327. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  328. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  329. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +128 -128
  330. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  331. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  332. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  333. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  334. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  335. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  336. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  337. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  338. package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
  339. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  340. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  341. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  342. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  343. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  344. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  345. package/lib/mol-plugin-ui/state/common.js +7 -8
  346. package/lib/mol-plugin-ui/structure/focus.d.ts +1 -1
  347. package/lib/mol-plugin-ui/structure/focus.js +2 -2
  348. package/lib/mol-plugin-ui/task.d.ts +2 -21
  349. package/lib/mol-plugin-ui/task.js +40 -46
  350. package/lib/mol-repr/shape/loci/angle.d.ts +1 -0
  351. package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
  352. package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
  353. package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
  354. package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
  355. package/lib/mol-repr/structure/complex-visual.d.ts +3 -0
  356. package/lib/mol-repr/structure/params.d.ts +4 -0
  357. package/lib/mol-repr/structure/registry.d.ts +10 -0
  358. package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
  359. package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  360. package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  361. package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
  362. package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  363. package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  364. package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  365. package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
  366. package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
  367. package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
  368. package/lib/mol-repr/structure/units-visual.d.ts +4 -0
  369. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  370. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  371. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  372. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  373. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  374. package/lib/mol-repr/structure/visual/element-sphere.d.ts +2 -0
  375. package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  376. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  377. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
  378. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
  379. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  380. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  381. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  382. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
  383. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  384. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
  385. package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  386. package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  387. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  388. package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  389. package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  390. package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  391. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  392. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  393. package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  394. package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
  395. package/lib/mol-repr/structure/visual/util/common.js +1 -24
  396. package/lib/mol-repr/util.d.ts +2 -1
  397. package/lib/mol-repr/util.js +2 -2
  398. package/lib/mol-repr/volume/isosurface.d.ts +5 -0
  399. package/lib/mol-repr/volume/registry.d.ts +1 -0
  400. package/lib/mol-script/language/builder.d.ts +1 -0
  401. package/package.json +162 -160
@@ -1,6 +1,6 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
- export declare const lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n bool interior = false;\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
6
+ export declare const lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
@@ -1,6 +1,6 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
- export var lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n bool interior = false;\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
6
+ export var lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
@@ -1,6 +1,6 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
- export declare const points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n bool interior = false;\n #include assign_material_color\n\n #if defined(dPointStyle_circle)\n float dist = distance(gl_PointCoord, center);\n if (dist > radius) discard;\n #elif defined(dPointStyle_fuzzy)\n float dist = distance(gl_PointCoord, center);\n float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);\n if (fuzzyAlpha < 0.0001) discard;\n #endif\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #if defined(dPointStyle_fuzzy)\n gl_FragColor.a *= fuzzyAlpha;\n #endif\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
6
+ export declare const points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dPointStyle_circle)\n float dist = distance(gl_PointCoord, center);\n if (dist > radius) discard;\n #elif defined(dPointStyle_fuzzy)\n float dist = distance(gl_PointCoord, center);\n float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);\n if (fuzzyAlpha < 0.0001) discard;\n #endif\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #if defined(dPointStyle_fuzzy)\n gl_FragColor.a *= fuzzyAlpha;\n #endif\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
@@ -1,6 +1,6 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
- export var points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n bool interior = false;\n #include assign_material_color\n\n #if defined(dPointStyle_circle)\n float dist = distance(gl_PointCoord, center);\n if (dist > radius) discard;\n #elif defined(dPointStyle_fuzzy)\n float dist = distance(gl_PointCoord, center);\n float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);\n if (fuzzyAlpha < 0.0001) discard;\n #endif\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #if defined(dPointStyle_fuzzy)\n gl_FragColor.a *= fuzzyAlpha;\n #endif\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
6
+ export var points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dPointStyle_circle)\n float dist = distance(gl_PointCoord, center);\n if (dist > radius) discard;\n #elif defined(dPointStyle_fuzzy)\n float dist = distance(gl_PointCoord, center);\n float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);\n if (fuzzyAlpha < 0.0001) discard;\n #endif\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #if defined(dPointStyle_fuzzy)\n gl_FragColor.a *= fuzzyAlpha;\n #endif\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
@@ -1,6 +1,6 @@
1
1
  /**
2
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
- export declare const text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n bool interior = false;\n #include assign_material_color\n\n if (vTexCoord.x > 1.0) {\n gl_FragColor = vec4(uBackgroundColor, uBackgroundOpacity * material.a);\n } else {\n // retrieve signed distance\n float sdf = texture2D(tFont, vTexCoord).a + uBorderWidth;\n\n // perform adaptive anti-aliasing of the edges\n float w = clamp(smoothness * (abs(dFdx(vTexCoord.x)) + abs(dFdy(vTexCoord.y))), 0.0, 0.5);\n float a = smoothstep(0.5 - w, 0.5 + w, sdf);\n\n // gamma correction for linear attenuation\n a = pow(a, 1.0 / gamma);\n\n if (a < 0.5) discard;\n material.a *= a;\n\n // add border\n float t = 0.5 + uBorderWidth;\n if (uBorderWidth > 0.0 && sdf < t) {\n material.xyz = mix(uBorderColor, material.xyz, smoothstep(t - w, t, sdf));\n }\n\n gl_FragColor = material;\n }\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
6
+ export declare const text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n if (vTexCoord.x > 1.0) {\n gl_FragColor = vec4(uBackgroundColor, uBackgroundOpacity * material.a);\n } else {\n // retrieve signed distance\n float sdf = texture2D(tFont, vTexCoord).a + uBorderWidth;\n\n // perform adaptive anti-aliasing of the edges\n float w = clamp(smoothness * (abs(dFdx(vTexCoord.x)) + abs(dFdy(vTexCoord.y))), 0.0, 0.5);\n float a = smoothstep(0.5 - w, 0.5 + w, sdf);\n\n // gamma correction for linear attenuation\n a = pow(a, 1.0 / gamma);\n\n if (a < 0.5) discard;\n material.a *= a;\n\n // add border\n float t = 0.5 + uBorderWidth;\n if (uBorderWidth > 0.0 && sdf < t) {\n material.xyz = mix(uBorderColor, material.xyz, smoothstep(t - w, t, sdf));\n }\n\n gl_FragColor = material;\n }\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
@@ -1,6 +1,6 @@
1
1
  /**
2
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
- export var text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n bool interior = false;\n #include assign_material_color\n\n if (vTexCoord.x > 1.0) {\n gl_FragColor = vec4(uBackgroundColor, uBackgroundOpacity * material.a);\n } else {\n // retrieve signed distance\n float sdf = texture2D(tFont, vTexCoord).a + uBorderWidth;\n\n // perform adaptive anti-aliasing of the edges\n float w = clamp(smoothness * (abs(dFdx(vTexCoord.x)) + abs(dFdy(vTexCoord.y))), 0.0, 0.5);\n float a = smoothstep(0.5 - w, 0.5 + w, sdf);\n\n // gamma correction for linear attenuation\n a = pow(a, 1.0 / gamma);\n\n if (a < 0.5) discard;\n material.a *= a;\n\n // add border\n float t = 0.5 + uBorderWidth;\n if (uBorderWidth > 0.0 && sdf < t) {\n material.xyz = mix(uBorderColor, material.xyz, smoothstep(t - w, t, sdf));\n }\n\n gl_FragColor = material;\n }\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
6
+ export var text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n if (vTexCoord.x > 1.0) {\n gl_FragColor = vec4(uBackgroundColor, uBackgroundOpacity * material.a);\n } else {\n // retrieve signed distance\n float sdf = texture2D(tFont, vTexCoord).a + uBorderWidth;\n\n // perform adaptive anti-aliasing of the edges\n float w = clamp(smoothness * (abs(dFdx(vTexCoord.x)) + abs(dFdy(vTexCoord.y))), 0.0, 0.5);\n float a = smoothstep(0.5 - w, 0.5 + w, sdf);\n\n // gamma correction for linear attenuation\n a = pow(a, 1.0 / gamma);\n\n if (a < 0.5) discard;\n material.a *= a;\n\n // add border\n float t = 0.5 + uBorderWidth;\n if (uBorderWidth > 0.0 && sdf < t) {\n material.xyz = mix(uBorderColor, material.xyz, smoothstep(t - w, t, sdf));\n }\n\n gl_FragColor = material;\n }\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
@@ -41,7 +41,7 @@ export interface Buffer {
41
41
  destroy: () => void;
42
42
  }
43
43
  export declare type AttributeItemSize = 1 | 2 | 3 | 4 | 16;
44
- export declare type AttributeKind = 'float32' | 'int32';
44
+ export declare type AttributeKind = 'float32';
45
45
  export declare function getAttribType(gl: GLRenderingContext, kind: AttributeKind, itemSize: AttributeItemSize): number;
46
46
  export declare type AttributeDefs = {
47
47
  [k: string]: {
@@ -1,11 +1,12 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
6
6
  import { __assign } from "tslib";
7
7
  import { idFactory } from '../../mol-util/id-factory';
8
8
  import { assertUnreachable } from '../../mol-util/type-helpers';
9
+ import { isWebGL2 } from './compat';
9
10
  var getNextBufferId = idFactory();
10
11
  export function getUsageHint(gl, usageHint) {
11
12
  switch (usageHint) {
@@ -23,6 +24,7 @@ export function getDataType(gl, dataType) {
23
24
  case 'uint32': return gl.UNSIGNED_INT;
24
25
  case 'int32': return gl.INT;
25
26
  case 'float32': return gl.FLOAT;
27
+ default: assertUnreachable(dataType);
26
28
  }
27
29
  }
28
30
  function dataTypeFromArray(gl, array) {
@@ -53,7 +55,13 @@ export function getBufferType(gl, bufferType) {
53
55
  switch (bufferType) {
54
56
  case 'attribute': return gl.ARRAY_BUFFER;
55
57
  case 'elements': return gl.ELEMENT_ARRAY_BUFFER;
56
- case 'uniform': return gl.UNIFORM_BUFFER;
58
+ case 'uniform':
59
+ if (isWebGL2(gl)) {
60
+ return gl.UNIFORM_BUFFER;
61
+ }
62
+ else {
63
+ throw new Error('WebGL2 is required for uniform buffers');
64
+ }
57
65
  }
58
66
  }
59
67
  function getBuffer(gl) {
@@ -108,14 +116,6 @@ function createBuffer(gl, array, usageHint, bufferType) {
108
116
  }
109
117
  export function getAttribType(gl, kind, itemSize) {
110
118
  switch (kind) {
111
- case 'int32':
112
- switch (itemSize) {
113
- case 1: return gl.INT;
114
- case 2: return gl.INT_VEC2;
115
- case 3: return gl.INT_VEC3;
116
- case 4: return gl.INT_VEC4;
117
- }
118
- break;
119
119
  case 'float32':
120
120
  switch (itemSize) {
121
121
  case 1: return gl.FLOAT;
@@ -124,9 +124,9 @@ export function getAttribType(gl, kind, itemSize) {
124
124
  case 4: return gl.FLOAT_VEC4;
125
125
  case 16: return gl.FLOAT_MAT4;
126
126
  }
127
- break;
127
+ default:
128
+ assertUnreachable(kind);
128
129
  }
129
- throw new Error("unknown attribute type for kind '".concat(kind, "' and itemSize '").concat(itemSize, "'"));
130
130
  }
131
131
  export function createAttributeBuffer(gl, state, extensions, array, itemSize, divisor, usageHint) {
132
132
  if (usageHint === void 0) { usageHint = 'dynamic'; }
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
@@ -226,7 +226,7 @@ export function createContext(gl, props) {
226
226
  gl: gl,
227
227
  isWebGL2: isWebGL2(gl),
228
228
  get pixelRatio() {
229
- var dpr = (typeof window !== 'undefined') ? window.devicePixelRatio : 1;
229
+ var dpr = (typeof window !== 'undefined') ? (window.devicePixelRatio || 1) : 1;
230
230
  return dpr * (props.pixelScale || 1);
231
231
  },
232
232
  extensions: extensions,
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
5
5
  */
@@ -8,6 +8,7 @@ import { getUniformSetters, getUniformType } from './uniform';
8
8
  import { getAttribType } from './buffer';
9
9
  import { idFactory } from '../../mol-util/id-factory';
10
10
  import { isDebugMode } from '../../mol-util/debug';
11
+ import { isWebGL2 } from './compat';
11
12
  var getNextProgramId = idFactory();
12
13
  function getLocations(gl, program, schema) {
13
14
  var locations = {};
@@ -51,7 +52,7 @@ function checkActiveAttributes(gl, program, schema) {
51
52
  }
52
53
  var attribType = getAttribType(gl, spec.kind, spec.itemSize);
53
54
  if (attribType !== type) {
54
- throw new Error("unexpected attribute type for ".concat(name_1));
55
+ throw new Error("unexpected attribute type '".concat(attribType, "' for ").concat(name_1, ", expected '").concat(type, "'"));
55
56
  }
56
57
  }
57
58
  }
@@ -84,8 +85,13 @@ function checkActiveUniforms(gl, program, schema) {
84
85
  }
85
86
  }
86
87
  else if (spec.kind === 'volume-float32' || spec.kind === 'volume-uint8') {
87
- if (type !== gl.SAMPLER_3D) {
88
- throw new Error("unexpected sampler type for '".concat(name_2, "'"));
88
+ if (isWebGL2(gl)) {
89
+ if (type !== gl.SAMPLER_3D) {
90
+ throw new Error("unexpected sampler type for '".concat(name_2, "'"));
91
+ }
92
+ }
93
+ else {
94
+ throw new Error("WebGL2 is required to use SAMPLER_3D");
89
95
  }
90
96
  }
91
97
  else {
@@ -1,7 +1,7 @@
1
1
  /**
2
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
4
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
5
5
  *
6
6
  * @author molstar/ciftools package
7
7
  */
@@ -50,7 +50,7 @@ export declare const BIRD_Schema: {
50
50
  /**
51
51
  * Defines the structural classification of the entity.
52
52
  */
53
- type: Schema.Aliased<"Unknown" | "Amino acid" | "Aminoglycoside" | "Anthracycline" | "Anthraquinone" | "Ansamycin" | "Chalkophore" | "Chromophore" | "Glycopeptide" | "Cyclic depsipeptide" | "Cyclic lipopeptide" | "Cyclic peptide" | "Heterocyclic" | "Imino sugar" | "Keto acid" | "Lipoglycopeptide" | "Lipopeptide" | "Macrolide" | "Non-polymer" | "Nucleoside" | "Oligopeptide" | "Oligosaccharide" | "Peptaibol" | "Peptide-like" | "Polycyclic" | "Polypeptide" | "Polysaccharide" | "Quinolone" | "Thiolactone" | "Thiopeptide" | "Siderophore" | "Chalkophore, Polypeptide">;
53
+ type: Schema.Aliased<"unknown" | "non-polymer" | "peptide-like" | "macrolide" | "amino acid" | "aminoglycoside" | "anthracycline" | "anthraquinone" | "ansamycin" | "chalkophore" | "chromophore" | "glycopeptide" | "cyclic depsipeptide" | "cyclic lipopeptide" | "cyclic peptide" | "heterocyclic" | "imino sugar" | "keto acid" | "lipoglycopeptide" | "lipopeptide" | "nucleoside" | "oligopeptide" | "oligosaccharide" | "peptaibol" | "polycyclic" | "polypeptide" | "polysaccharide" | "quinolone" | "thiolactone" | "thiopeptide" | "siderophore" | "chalkophore, polypeptide">;
54
54
  /**
55
55
  * Evidence for the assignment of _pdbx_reference_molecule.type
56
56
  */
@@ -58,7 +58,7 @@ export declare const BIRD_Schema: {
58
58
  /**
59
59
  * Broadly defines the function of the entity.
60
60
  */
61
- class: Schema.Aliased<"Antagonist" | "Antibiotic" | "Anticancer" | "Anticoagulant" | "Antifungal" | "Antigen" | "Antiinflammatory" | "Antimicrobial" | "Antineoplastic" | "Antiparasitic" | "Antiretroviral" | "Anthelmintic" | "Antithrombotic" | "Antitumor" | "Antiviral" | "CASPASE inhibitor" | "Chaperone binding" | "Enzyme inhibitor" | "Drug delivery" | "Glycan component" | "Growth factor" | "Immunosuppressant" | "Inducer" | "Inhibitor" | "Lantibiotic" | "Metabolism" | "Metal transport" | "Nutrient" | "Oxidation-reduction" | "Protein binding" | "Receptor" | "Substrate analog" | "Synthetic opioid" | "Thrombin inhibitor" | "Transition state mimetic" | "Transport activator" | "Trypsin inhibitor" | "Toxin" | "Unknown" | "Water retention" | "Anticoagulant, Antithrombotic" | "Antibiotic, Antimicrobial" | "Antibiotic, Anthelmintic" | "Antibiotic, Antineoplastic" | "Antimicrobial, Antiretroviral" | "Antimicrobial, Antitumor" | "Antimicrobial, Antiparasitic, Antibiotic" | "Thrombin inhibitor, Trypsin inhibitor">;
61
+ class: Schema.Aliased<"unknown" | "antagonist" | "antibiotic" | "anticancer" | "anticoagulant" | "antifungal" | "antigen" | "antiinflammatory" | "antimicrobial" | "antineoplastic" | "antiparasitic" | "antiretroviral" | "anthelmintic" | "antithrombotic" | "antitumor" | "antiviral" | "caspase inhibitor" | "chaperone binding" | "enzyme inhibitor" | "drug delivery" | "glycan component" | "growth factor" | "immunosuppressant" | "inducer" | "inhibitor" | "lantibiotic" | "metabolism" | "metal transport" | "nutrient" | "oxidation-reduction" | "protein binding" | "receptor" | "substrate analog" | "synthetic opioid" | "thrombin inhibitor" | "transition state mimetic" | "transport activator" | "trypsin inhibitor" | "toxin" | "water retention" | "anticoagulant, antithrombotic" | "antibiotic, antimicrobial" | "antibiotic, anthelmintic" | "antibiotic, antineoplastic" | "antimicrobial, antiretroviral" | "antimicrobial, antitumor" | "antimicrobial, antiparasitic, antibiotic" | "thrombin inhibitor, trypsin inhibitor">;
62
62
  /**
63
63
  * Evidence for the assignment of _pdbx_reference_molecule.class
64
64
  */
@@ -91,7 +91,7 @@ export declare const BIRD_Schema: {
91
91
  /**
92
92
  * Defines the current PDB release status for this molecule definition.
93
93
  */
94
- release_status: Schema.Aliased<"WAIT" | "REL" | "HOLD" | "OBS">;
94
+ release_status: Schema.Aliased<"wait" | "rel" | "hold" | "obs">;
95
95
  /**
96
96
  * Assigns the identifier for the reference molecule which have been replaced
97
97
  * by this reference molecule.
@@ -392,11 +392,11 @@ export declare const BIRD_Schema: {
392
392
  /**
393
393
  * A flag to indicate that this monomer is observed in the instance example.
394
394
  */
395
- observed: Schema.Aliased<"N" | "Y">;
395
+ observed: Schema.Aliased<"y" | "n">;
396
396
  /**
397
397
  * A flag to indicate that sequence heterogeneity at this monomer position.
398
398
  */
399
- hetero: Schema.Aliased<"N" | "Y">;
399
+ hetero: Schema.Aliased<"y" | "n">;
400
400
  };
401
401
  /**
402
402
  * Additional features associated with the reference entity.
@@ -479,7 +479,7 @@ export declare const BIRD_Schema: {
479
479
  /**
480
480
  * An identifier for the wwPDB site creating or modifying the molecule.
481
481
  */
482
- processing_site: Schema.Aliased<"RCSB" | "PDBE" | "BMRB" | "PDBJ" | "PDBC">;
482
+ processing_site: Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "BMRB" | "PDBC">;
483
483
  /**
484
484
  * The action associated with this audit record.
485
485
  */
@@ -1,7 +1,7 @@
1
1
  /**
2
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
4
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
5
5
  *
6
6
  * @author molstar/ciftools package
7
7
  */
@@ -9,6 +9,7 @@ import { Column } from '../../../../mol-data/db';
9
9
  var Schema = Column.Schema;
10
10
  var str = Schema.str;
11
11
  var float = Schema.float;
12
+ var lstr = Schema.lstr;
12
13
  var Aliased = Schema.Aliased;
13
14
  var int = Schema.int;
14
15
  export var BIRD_Schema = {
@@ -54,7 +55,7 @@ export var BIRD_Schema = {
54
55
  /**
55
56
  * Defines the structural classification of the entity.
56
57
  */
57
- type: Aliased(str),
58
+ type: Aliased(lstr),
58
59
  /**
59
60
  * Evidence for the assignment of _pdbx_reference_molecule.type
60
61
  */
@@ -62,7 +63,7 @@ export var BIRD_Schema = {
62
63
  /**
63
64
  * Broadly defines the function of the entity.
64
65
  */
65
- class: Aliased(str),
66
+ class: Aliased(lstr),
66
67
  /**
67
68
  * Evidence for the assignment of _pdbx_reference_molecule.class
68
69
  */
@@ -74,7 +75,7 @@ export var BIRD_Schema = {
74
75
  /**
75
76
  * Defines how this entity is represented in PDB data files.
76
77
  */
77
- represent_as: Aliased(str),
78
+ represent_as: Aliased(lstr),
78
79
  /**
79
80
  * For entities represented as single molecules, the identifier
80
81
  * corresponding to the chemical definition for the molecule.
@@ -95,7 +96,7 @@ export var BIRD_Schema = {
95
96
  /**
96
97
  * Defines the current PDB release status for this molecule definition.
97
98
  */
98
- release_status: Aliased(str),
99
+ release_status: Aliased(lstr),
99
100
  /**
100
101
  * Assigns the identifier for the reference molecule which have been replaced
101
102
  * by this reference molecule.
@@ -125,7 +126,7 @@ export var BIRD_Schema = {
125
126
  /**
126
127
  * Defines the polymer characteristic of the entity.
127
128
  */
128
- type: Aliased(str),
129
+ type: Aliased(lstr),
129
130
  /**
130
131
  * Additional details about this entity.
131
132
  */
@@ -245,7 +246,7 @@ export var BIRD_Schema = {
245
246
  /**
246
247
  * The bond order target for the chemical linkage.
247
248
  */
248
- value_order: Aliased(str),
249
+ value_order: Aliased(lstr),
249
250
  /**
250
251
  * The entity component identifier for the first of two entities containing the linkage.
251
252
  */
@@ -331,7 +332,7 @@ export var BIRD_Schema = {
331
332
  /**
332
333
  * The bond order target for the non-standard linkage.
333
334
  */
334
- value_order: Aliased(str),
335
+ value_order: Aliased(lstr),
335
336
  },
336
337
  /**
337
338
  * Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about
@@ -396,11 +397,11 @@ export var BIRD_Schema = {
396
397
  /**
397
398
  * A flag to indicate that this monomer is observed in the instance example.
398
399
  */
399
- observed: Aliased(str),
400
+ observed: Aliased(lstr),
400
401
  /**
401
402
  * A flag to indicate that sequence heterogeneity at this monomer position.
402
403
  */
403
- hetero: Aliased(str),
404
+ hetero: Aliased(lstr),
404
405
  },
405
406
  /**
406
407
  * Additional features associated with the reference entity.
@@ -8,5 +8,5 @@ export declare const ccd_chemCompAtom_schema: {
8
8
  comp_id: import("../../../../mol-data/db/column").Column.Schema.Str;
9
9
  atom_id: import("../../../../mol-data/db/column").Column.Schema.Str;
10
10
  charge: import("../../../../mol-data/db/column").Column.Schema.Int;
11
- pdbx_stereo_config: import("../../../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
11
+ pdbx_stereo_config: import("../../../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
12
12
  };
@@ -1,7 +1,7 @@
1
1
  /**
2
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
4
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
5
5
  *
6
6
  * @author molstar/ciftools package
7
7
  */
@@ -93,7 +93,7 @@ export declare const CCD_Schema: {
93
93
  * linking monomers, monomers with some type of N-terminal (or 5')
94
94
  * cap and monomers with some type of C-terminal (or 3') cap.
95
95
  */
96
- type: Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
96
+ type: Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
97
97
  /**
98
98
  * Synonym list for the component.
99
99
  */
@@ -144,11 +144,11 @@ export declare const CCD_Schema: {
144
144
  /**
145
145
  * This data item identifies if ideal coordinates are missing in this definition.
146
146
  */
147
- pdbx_ideal_coordinates_missing_flag: Schema.Aliased<"N" | "Y">;
147
+ pdbx_ideal_coordinates_missing_flag: Schema.Aliased<"y" | "n">;
148
148
  /**
149
149
  * This data item identifies if model coordinates are missing in this definition.
150
150
  */
151
- pdbx_model_coordinates_missing_flag: Schema.Aliased<"N" | "Y">;
151
+ pdbx_model_coordinates_missing_flag: Schema.Aliased<"y" | "n">;
152
152
  /**
153
153
  * Date component was added to database.
154
154
  */
@@ -165,7 +165,7 @@ export declare const CCD_Schema: {
165
165
  * This data item identifies the deposition site that processed
166
166
  * this chemical component defintion.
167
167
  */
168
- pdbx_processing_site: Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
168
+ pdbx_processing_site: Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
169
169
  };
170
170
  /**
171
171
  * Data items in the CHEM_COMP_ATOM category record details about
@@ -269,15 +269,15 @@ export declare const CCD_Schema: {
269
269
  /**
270
270
  * The chiral configuration of the atom that is a chiral center.
271
271
  */
272
- pdbx_stereo_config: Schema.Aliased<"N" | "R" | "S">;
272
+ pdbx_stereo_config: Schema.Aliased<"s" | "r" | "n">;
273
273
  /**
274
274
  * A flag indicating an aromatic atom.
275
275
  */
276
- pdbx_aromatic_flag: Schema.Aliased<"N" | "Y">;
276
+ pdbx_aromatic_flag: Schema.Aliased<"y" | "n">;
277
277
  /**
278
278
  * A flag indicating a leaving atom.
279
279
  */
280
- pdbx_leaving_atom_flag: Schema.Aliased<"N" | "Y">;
280
+ pdbx_leaving_atom_flag: Schema.Aliased<"y" | "n">;
281
281
  };
282
282
  /**
283
283
  * Data items in the CHEM_COMP_BOND category record details about
@@ -318,11 +318,11 @@ export declare const CCD_Schema: {
318
318
  /**
319
319
  * Stereochemical configuration across a double bond.
320
320
  */
321
- pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
321
+ pdbx_stereo_config: Schema.Aliased<"z" | "n" | "e">;
322
322
  /**
323
323
  * A flag indicating an aromatic bond.
324
324
  */
325
- pdbx_aromatic_flag: Schema.Aliased<"N" | "Y">;
325
+ pdbx_aromatic_flag: Schema.Aliased<"y" | "n">;
326
326
  };
327
327
  /**
328
328
  * Data items in the CHEM_COMP_DESCRIPTOR category provide
@@ -342,7 +342,7 @@ export declare const CCD_Schema: {
342
342
  /**
343
343
  * This data item contains the descriptor type.
344
344
  */
345
- type: Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
345
+ type: Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
346
346
  /**
347
347
  * This data item contains the name of the program
348
348
  * or library used to compute the descriptor.
@@ -1,7 +1,7 @@
1
1
  /**
2
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
4
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
5
5
  *
6
6
  * @author molstar/ciftools package
7
7
  */
@@ -10,6 +10,7 @@ var Schema = Column.Schema;
10
10
  var str = Schema.str;
11
11
  var float = Schema.float;
12
12
  var List = Schema.List;
13
+ var lstr = Schema.lstr;
13
14
  var Aliased = Schema.Aliased;
14
15
  var int = Schema.int;
15
16
  var coord = Schema.coord;
@@ -99,7 +100,7 @@ export var CCD_Schema = {
99
100
  * linking monomers, monomers with some type of N-terminal (or 5')
100
101
  * cap and monomers with some type of C-terminal (or 3') cap.
101
102
  */
102
- type: Aliased(str),
103
+ type: Aliased(lstr),
103
104
  /**
104
105
  * Synonym list for the component.
105
106
  */
@@ -150,11 +151,11 @@ export var CCD_Schema = {
150
151
  /**
151
152
  * This data item identifies if ideal coordinates are missing in this definition.
152
153
  */
153
- pdbx_ideal_coordinates_missing_flag: Aliased(str),
154
+ pdbx_ideal_coordinates_missing_flag: Aliased(lstr),
154
155
  /**
155
156
  * This data item identifies if model coordinates are missing in this definition.
156
157
  */
157
- pdbx_model_coordinates_missing_flag: Aliased(str),
158
+ pdbx_model_coordinates_missing_flag: Aliased(lstr),
158
159
  /**
159
160
  * Date component was added to database.
160
161
  */
@@ -275,15 +276,15 @@ export var CCD_Schema = {
275
276
  /**
276
277
  * The chiral configuration of the atom that is a chiral center.
277
278
  */
278
- pdbx_stereo_config: Aliased(str),
279
+ pdbx_stereo_config: Aliased(lstr),
279
280
  /**
280
281
  * A flag indicating an aromatic atom.
281
282
  */
282
- pdbx_aromatic_flag: Aliased(str),
283
+ pdbx_aromatic_flag: Aliased(lstr),
283
284
  /**
284
285
  * A flag indicating a leaving atom.
285
286
  */
286
- pdbx_leaving_atom_flag: Aliased(str),
287
+ pdbx_leaving_atom_flag: Aliased(lstr),
287
288
  },
288
289
  /**
289
290
  * Data items in the CHEM_COMP_BOND category record details about
@@ -316,7 +317,7 @@ export var CCD_Schema = {
316
317
  * bond associated with the specified atoms, expressed as a bond
317
318
  * order.
318
319
  */
319
- value_order: Aliased(str),
320
+ value_order: Aliased(lstr),
320
321
  /**
321
322
  * Ordinal index for the component bond list.
322
323
  */
@@ -324,11 +325,11 @@ export var CCD_Schema = {
324
325
  /**
325
326
  * Stereochemical configuration across a double bond.
326
327
  */
327
- pdbx_stereo_config: Aliased(str),
328
+ pdbx_stereo_config: Aliased(lstr),
328
329
  /**
329
330
  * A flag indicating an aromatic bond.
330
331
  */
331
- pdbx_aromatic_flag: Aliased(str),
332
+ pdbx_aromatic_flag: Aliased(lstr),
332
333
  },
333
334
  /**
334
335
  * Data items in the CHEM_COMP_DESCRIPTOR category provide
@@ -348,7 +349,7 @@ export var CCD_Schema = {
348
349
  /**
349
350
  * This data item contains the descriptor type.
350
351
  */
351
- type: Aliased(str),
352
+ type: Aliased(lstr),
352
353
  /**
353
354
  * This data item contains the name of the program
354
355
  * or library used to compute the descriptor.
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author David Sehnal <david.sehnal@gmail.com>
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -23,12 +23,12 @@ export declare const mmCIF_chemCompBond_schema: {
23
23
  comp_id: Column.Schema.Str;
24
24
  value_order: Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
25
25
  pdbx_ordinal: Column.Schema.Int;
26
- pdbx_stereo_config: Column.Schema.Aliased<"N" | "E" | "Z">;
27
- pdbx_aromatic_flag: Column.Schema.Aliased<"N" | "Y">;
26
+ pdbx_stereo_config: Column.Schema.Aliased<"z" | "n" | "e">;
27
+ pdbx_aromatic_flag: Column.Schema.Aliased<"y" | "n">;
28
28
  };
29
- /** Has `type` extended with 'Ion' and 'Lipid' */
29
+ /** Has `type` extended with 'ION' and 'LIPID' */
30
30
  export declare const mmCIF_chemComp_schema: {
31
- type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
31
+ type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
32
32
  formula: Column.Schema.Str;
33
33
  formula_weight: Column.Schema.Float;
34
34
  id: Column.Schema.Str;
@@ -1,5 +1,5 @@
1
1
  /**
2
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
2
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
3
  *
4
4
  * @author David Sehnal <david.sehnal@gmail.com>
5
5
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -20,5 +20,5 @@ export var mmCIF_residueId_schema = {
20
20
  export var mmCIF_chemCompBond_schema = __assign(__assign({}, mmCIF_Schema.chem_comp_bond), {
21
21
  /** Indicates if the bond entry was taken from the protonation variant dictionary */
22
22
  molstar_protonation_variant: Column.Schema.Str() });
23
- /** Has `type` extended with 'Ion' and 'Lipid' */
23
+ /** Has `type` extended with 'ION' and 'LIPID' */
24
24
  export var mmCIF_chemComp_schema = __assign(__assign({}, mmCIF_Schema.chem_comp), { type: Column.Schema.Aliased(Column.Schema.str) });