molstar 3.0.1 → 3.0.2

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 (1754) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +194 -194
  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/lib/apps/docking-viewer/index.html +36 -36
  7. package/lib/apps/viewer/embedded.html +43 -43
  8. package/lib/apps/viewer/index.html +106 -106
  9. package/lib/commonjs/apps/docking-viewer/index.js +253 -0
  10. package/lib/commonjs/apps/docking-viewer/viewport.d.ts +2 -2
  11. package/lib/commonjs/apps/docking-viewer/viewport.js +326 -0
  12. package/lib/commonjs/apps/viewer/app.d.ts +3 -3
  13. package/lib/commonjs/cli/chem-comp-dict/create-ions.d.ts +7 -0
  14. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +68 -0
  15. package/lib/commonjs/cli/chem-comp-dict/create-table.d.ts +7 -0
  16. package/lib/commonjs/cli/chem-comp-dict/create-table.js +282 -0
  17. package/lib/commonjs/cli/chem-comp-dict/util.d.ts +146 -0
  18. package/lib/commonjs/cli/chem-comp-dict/util.js +144 -0
  19. package/lib/commonjs/cli/cif2bcif/converter.d.ts +8 -0
  20. package/lib/commonjs/cli/cif2bcif/converter.js +187 -0
  21. package/lib/commonjs/cli/cif2bcif/index.d.ts +8 -0
  22. package/lib/commonjs/cli/cif2bcif/index.js +81 -0
  23. package/lib/commonjs/cli/cifschema/index.d.ts +7 -0
  24. package/lib/commonjs/cli/cifschema/index.js +397 -0
  25. package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +11 -0
  26. package/lib/commonjs/cli/cifschema/util/cif-dic.js +456 -0
  27. package/lib/commonjs/cli/cifschema/util/generate.d.ts +7 -0
  28. package/lib/commonjs/cli/cifschema/util/generate.js +158 -0
  29. package/lib/commonjs/cli/cifschema/util/helper.d.ts +10 -0
  30. package/lib/commonjs/cli/cifschema/util/helper.js +22 -0
  31. package/lib/commonjs/cli/cifschema/util/schema.d.ts +70 -0
  32. package/lib/commonjs/cli/cifschema/util/schema.js +64 -0
  33. package/lib/commonjs/cli/lipid-params/index.d.ts +7 -0
  34. package/lib/commonjs/cli/lipid-params/index.js +104 -0
  35. package/lib/commonjs/cli/state-docs/index.js +64 -0
  36. package/lib/commonjs/cli/state-docs/pd-to-md.js +80 -0
  37. package/lib/commonjs/cli/structure-info/helpers.d.ts +7 -0
  38. package/lib/commonjs/cli/structure-info/helpers.js +92 -0
  39. package/lib/commonjs/cli/structure-info/model.js +336 -0
  40. package/lib/commonjs/cli/structure-info/volume.js +115 -0
  41. package/lib/commonjs/examples/alpha-orbitals/controls.js +25 -0
  42. package/lib/commonjs/examples/alpha-orbitals/example-data.js +60260 -0
  43. package/lib/commonjs/examples/alpha-orbitals/index.js +230 -0
  44. package/lib/commonjs/examples/basic-wrapper/coloring.js +31 -0
  45. package/lib/commonjs/examples/basic-wrapper/controls.js +23 -0
  46. package/lib/commonjs/examples/basic-wrapper/custom-theme.js +49 -0
  47. package/lib/commonjs/examples/basic-wrapper/index.js +265 -0
  48. package/lib/commonjs/examples/basic-wrapper/superposition.js +191 -0
  49. package/lib/commonjs/examples/domain-annotation-server/mapping.d.ts +6 -0
  50. package/lib/commonjs/examples/domain-annotation-server/mapping.js +111 -0
  51. package/lib/commonjs/examples/domain-annotation-server/schemas.d.ts +103 -0
  52. package/lib/commonjs/examples/domain-annotation-server/schemas.js +73 -0
  53. package/lib/commonjs/examples/domain-annotation-server/server.d.ts +6 -0
  54. package/lib/commonjs/examples/domain-annotation-server/server.js +65 -0
  55. package/lib/commonjs/examples/domain-annotation-server/test.d.ts +6 -0
  56. package/lib/commonjs/examples/domain-annotation-server/test.js +28 -0
  57. package/lib/commonjs/examples/lighting/index.js +145 -0
  58. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +88 -0
  59. package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +97 -0
  60. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +109 -0
  61. package/lib/commonjs/examples/proteopedia-wrapper/index.js +498 -0
  62. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +19 -0
  63. package/lib/commonjs/examples/task.d.ts +19 -0
  64. package/lib/commonjs/examples/task.js +221 -0
  65. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +134 -0
  66. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +69 -0
  67. package/lib/commonjs/extensions/alpha-orbitals/density.js +113 -0
  68. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +157 -0
  69. package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.d.ts +7 -0
  70. package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +11 -0
  71. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +121 -0
  72. package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.d.ts +11 -0
  73. package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.js +66 -0
  74. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +261 -0
  75. package/lib/commonjs/extensions/anvil/algorithm.js +578 -0
  76. package/lib/commonjs/extensions/anvil/behavior.d.ts +2 -2
  77. package/lib/commonjs/extensions/anvil/behavior.js +209 -0
  78. package/lib/commonjs/extensions/anvil/prop.js +82 -0
  79. package/lib/commonjs/extensions/anvil/representation.d.ts +5 -5
  80. package/lib/commonjs/extensions/anvil/representation.js +118 -0
  81. package/lib/commonjs/extensions/cellpack/color/generate.js +86 -0
  82. package/lib/commonjs/extensions/cellpack/color/provided.js +68 -0
  83. package/lib/commonjs/extensions/cellpack/curve.d.ts +9 -0
  84. package/lib/commonjs/extensions/cellpack/curve.js +203 -0
  85. package/lib/commonjs/extensions/cellpack/data.d.ts +107 -0
  86. package/lib/commonjs/extensions/cellpack/data.js +8 -0
  87. package/lib/commonjs/extensions/cellpack/index.js +39 -0
  88. package/lib/commonjs/extensions/cellpack/model.js +903 -0
  89. package/lib/commonjs/extensions/cellpack/preset.js +109 -0
  90. package/lib/commonjs/extensions/cellpack/property.js +31 -0
  91. package/lib/commonjs/extensions/cellpack/representation.d.ts +2 -2
  92. package/lib/commonjs/extensions/cellpack/representation.js +47 -0
  93. package/lib/commonjs/extensions/cellpack/state.js +397 -0
  94. package/lib/commonjs/extensions/cellpack/util.js +181 -0
  95. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts +1 -1
  96. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +121 -0
  97. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +178 -0
  98. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +160 -0
  99. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -3
  100. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +159 -0
  101. package/lib/commonjs/extensions/dnatco/confal-pyramids/types.js +27 -0
  102. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +234 -0
  103. package/lib/commonjs/extensions/dnatco/index.js +12 -0
  104. package/lib/commonjs/extensions/g3d/data.js +71 -0
  105. package/lib/commonjs/extensions/g3d/format.js +232 -0
  106. package/lib/commonjs/extensions/g3d/model.js +215 -0
  107. package/lib/commonjs/extensions/geo-export/controls.js +109 -0
  108. package/lib/commonjs/extensions/geo-export/glb-exporter.js +323 -0
  109. package/lib/commonjs/extensions/geo-export/index.js +36 -0
  110. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +457 -0
  111. package/lib/commonjs/extensions/geo-export/obj-exporter.js +212 -0
  112. package/lib/commonjs/extensions/geo-export/render-object-exporter.js +8 -0
  113. package/lib/commonjs/extensions/geo-export/stl-exporter.js +131 -0
  114. package/lib/commonjs/extensions/geo-export/ui.js +116 -0
  115. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +222 -0
  116. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +2 -2
  117. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +236 -0
  118. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +125 -0
  119. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +111 -0
  120. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +130 -0
  121. package/lib/commonjs/extensions/model-export/export.js +129 -0
  122. package/lib/commonjs/extensions/model-export/index.js +36 -0
  123. package/lib/commonjs/extensions/model-export/ui.js +77 -0
  124. package/lib/commonjs/extensions/mp4-export/controls.js +142 -0
  125. package/lib/commonjs/extensions/mp4-export/encoder.js +119 -0
  126. package/lib/commonjs/extensions/mp4-export/index.js +36 -0
  127. package/lib/commonjs/extensions/mp4-export/ui.js +94 -0
  128. package/lib/commonjs/extensions/pdbe/index.js +15 -0
  129. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +98 -0
  130. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +128 -0
  131. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +75 -0
  132. package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +113 -0
  133. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +288 -0
  134. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +5 -5
  135. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +255 -0
  136. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts +2 -2
  137. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +101 -0
  138. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +220 -0
  139. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -1
  140. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +363 -0
  141. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +215 -0
  142. package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.d.ts +1 -0
  143. package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.js +5 -0
  144. package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +12874 -0
  145. package/lib/commonjs/extensions/rcsb/graphql/types.js +3 -0
  146. package/lib/commonjs/extensions/rcsb/index.js +13 -0
  147. package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts +3 -3
  148. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +421 -0
  149. package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +79 -0
  150. package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +110 -0
  151. package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +67 -0
  152. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +490 -0
  153. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -5
  154. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +243 -0
  155. package/lib/commonjs/mol-canvas3d/camera/stereo.js +129 -0
  156. package/lib/commonjs/mol-canvas3d/camera/transition.js +103 -0
  157. package/lib/commonjs/mol-canvas3d/camera/util.d.ts +31 -0
  158. package/lib/commonjs/mol-canvas3d/camera/util.js +94 -0
  159. package/lib/commonjs/mol-canvas3d/camera.js +334 -0
  160. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +4 -4
  161. package/lib/commonjs/mol-canvas3d/controls/object.js +49 -0
  162. package/lib/commonjs/mol-canvas3d/controls/trackball.js +426 -0
  163. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +157 -0
  164. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -1
  165. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +217 -0
  166. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -1
  167. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +184 -0
  168. package/lib/commonjs/mol-canvas3d/helper/helper.js +33 -0
  169. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +94 -0
  170. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +2 -2
  171. package/lib/commonjs/mol-canvas3d/passes/marking.js +131 -0
  172. package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +2 -2
  173. package/lib/commonjs/mol-canvas3d/passes/smaa.js +167 -0
  174. package/lib/commonjs/mol-canvas3d/passes/wboit.d.ts +23 -0
  175. package/lib/commonjs/mol-canvas3d/passes/wboit.js +115 -0
  176. package/lib/commonjs/mol-canvas3d/util.d.ts +10 -0
  177. package/lib/commonjs/mol-canvas3d/util.js +70 -0
  178. package/lib/commonjs/mol-data/db/column-helpers.d.ts +19 -0
  179. package/lib/commonjs/mol-data/db/column-helpers.js +44 -0
  180. package/lib/commonjs/mol-data/db/column.d.ts +135 -0
  181. package/lib/commonjs/mol-data/db/column.js +425 -0
  182. package/lib/commonjs/mol-data/db/database.d.ts +25 -0
  183. package/lib/commonjs/mol-data/db/database.js +40 -0
  184. package/lib/commonjs/mol-data/db/table.d.ts +57 -0
  185. package/lib/commonjs/mol-data/db/table.js +302 -0
  186. package/lib/commonjs/mol-data/db.d.ts +14 -0
  187. package/lib/commonjs/mol-data/db.js +19 -0
  188. package/lib/commonjs/mol-data/generic/hash-set.d.ts +12 -0
  189. package/lib/commonjs/mol-data/generic/hash-set.js +52 -0
  190. package/lib/commonjs/mol-data/generic/linked-list.d.ts +26 -0
  191. package/lib/commonjs/mol-data/generic/linked-list.js +95 -0
  192. package/lib/commonjs/mol-data/generic/unique-array.d.ts +15 -0
  193. package/lib/commonjs/mol-data/generic/unique-array.js +31 -0
  194. package/lib/commonjs/mol-data/generic.d.ts +8 -0
  195. package/lib/commonjs/mol-data/generic.js +12 -0
  196. package/lib/commonjs/mol-data/index.d.ts +11 -0
  197. package/lib/commonjs/mol-data/index.js +20 -0
  198. package/lib/commonjs/mol-data/int/impl/interval.d.ts +30 -0
  199. package/lib/commonjs/mol-data/int/impl/interval.js +84 -0
  200. package/lib/commonjs/mol-data/int/impl/ordered-set.d.ts +40 -0
  201. package/lib/commonjs/mol-data/int/impl/ordered-set.js +423 -0
  202. package/lib/commonjs/mol-data/int/impl/segmentation.d.ts +41 -0
  203. package/lib/commonjs/mol-data/int/impl/segmentation.js +109 -0
  204. package/lib/commonjs/mol-data/int/impl/sorted-array.d.ts +45 -0
  205. package/lib/commonjs/mol-data/int/impl/sorted-array.js +477 -0
  206. package/lib/commonjs/mol-data/int/interval.d.ts +53 -0
  207. package/lib/commonjs/mol-data/int/interval.js +56 -0
  208. package/lib/commonjs/mol-data/int/linked-index.d.ts +13 -0
  209. package/lib/commonjs/mol-data/int/linked-index.js +48 -0
  210. package/lib/commonjs/mol-data/int/map.d.ts +25 -0
  211. package/lib/commonjs/mol-data/int/map.js +50 -0
  212. package/lib/commonjs/mol-data/int/ordered-set.d.ts +55 -0
  213. package/lib/commonjs/mol-data/int/ordered-set.js +80 -0
  214. package/lib/commonjs/mol-data/int/segmentation.d.ts +32 -0
  215. package/lib/commonjs/mol-data/int/segmentation.js +22 -0
  216. package/lib/commonjs/mol-data/int/sorted-array.d.ts +49 -0
  217. package/lib/commonjs/mol-data/int/sorted-array.js +52 -0
  218. package/lib/commonjs/mol-data/int/sorted-ranges.d.ts +42 -0
  219. package/lib/commonjs/mol-data/int/sorted-ranges.js +125 -0
  220. package/lib/commonjs/mol-data/int/tuple.d.ts +28 -0
  221. package/lib/commonjs/mol-data/int/tuple.js +86 -0
  222. package/lib/commonjs/mol-data/int.d.ts +14 -0
  223. package/lib/commonjs/mol-data/int.js +25 -0
  224. package/lib/commonjs/mol-data/iterator.d.ts +25 -0
  225. package/lib/commonjs/mol-data/iterator.js +113 -0
  226. package/lib/commonjs/mol-data/util/array.d.ts +19 -0
  227. package/lib/commonjs/mol-data/util/array.js +56 -0
  228. package/lib/commonjs/mol-data/util/buckets.d.ts +16 -0
  229. package/lib/commonjs/mol-data/util/buckets.js +81 -0
  230. package/lib/commonjs/mol-data/util/chunked-array.d.ts +49 -0
  231. package/lib/commonjs/mol-data/util/chunked-array.js +175 -0
  232. package/lib/commonjs/mol-data/util/combination.d.ts +17 -0
  233. package/lib/commonjs/mol-data/util/combination.js +61 -0
  234. package/lib/commonjs/mol-data/util/equivalence-classes.d.ts +16 -0
  235. package/lib/commonjs/mol-data/util/equivalence-classes.js +52 -0
  236. package/lib/commonjs/mol-data/util/grouping.d.ts +23 -0
  237. package/lib/commonjs/mol-data/util/grouping.js +53 -0
  238. package/lib/commonjs/mol-data/util/hash-functions.d.ts +26 -0
  239. package/lib/commonjs/mol-data/util/hash-functions.js +96 -0
  240. package/lib/commonjs/mol-data/util/interval-iterator.d.ts +19 -0
  241. package/lib/commonjs/mol-data/util/interval-iterator.js +45 -0
  242. package/lib/commonjs/mol-data/util/sort.d.ts +12 -0
  243. package/lib/commonjs/mol-data/util/sort.js +164 -0
  244. package/lib/commonjs/mol-data/util.d.ts +12 -0
  245. package/lib/commonjs/mol-data/util.js +16 -0
  246. package/lib/commonjs/mol-geo/geometry/base.d.ts +5 -5
  247. package/lib/commonjs/mol-geo/geometry/base.js +152 -0
  248. package/lib/commonjs/mol-geo/geometry/clipping-data.js +55 -0
  249. package/lib/commonjs/mol-geo/geometry/color-data.js +235 -0
  250. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders-builder.js +114 -0
  251. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +3 -3
  252. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +197 -0
  253. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +1 -1
  254. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +220 -0
  255. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.d.ts +15 -0
  256. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +61 -0
  257. package/lib/commonjs/mol-geo/geometry/geometry.js +89 -0
  258. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +3 -3
  259. package/lib/commonjs/mol-geo/geometry/image/image.js +176 -0
  260. package/lib/commonjs/mol-geo/geometry/lines/lines-builder.js +110 -0
  261. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +2 -1
  262. package/lib/commonjs/mol-geo/geometry/lines/lines.js +195 -0
  263. package/lib/commonjs/mol-geo/geometry/marker-data.d.ts +24 -0
  264. package/lib/commonjs/mol-geo/geometry/marker-data.js +103 -0
  265. package/lib/commonjs/mol-geo/geometry/mesh/builder/axes.js +32 -0
  266. package/lib/commonjs/mol-geo/geometry/mesh/builder/box.js +100 -0
  267. package/lib/commonjs/mol-geo/geometry/mesh/builder/cylinder.js +119 -0
  268. package/lib/commonjs/mol-geo/geometry/mesh/builder/ellipsoid.js +24 -0
  269. package/lib/commonjs/mol-geo/geometry/mesh/builder/ribbon.js +85 -0
  270. package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +187 -0
  271. package/lib/commonjs/mol-geo/geometry/mesh/builder/sphere.js +30 -0
  272. package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +175 -0
  273. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +325 -0
  274. package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.d.ts +5 -0
  275. package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.js +75 -0
  276. package/lib/commonjs/mol-geo/geometry/mesh/mesh-builder.js +154 -0
  277. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +1 -1
  278. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +638 -0
  279. package/lib/commonjs/mol-geo/geometry/overpaint-data.d.ts +23 -0
  280. package/lib/commonjs/mol-geo/geometry/overpaint-data.js +68 -0
  281. package/lib/commonjs/mol-geo/geometry/picking.d.ts +13 -0
  282. package/lib/commonjs/mol-geo/geometry/picking.js +16 -0
  283. package/lib/commonjs/mol-geo/geometry/points/points-builder.js +35 -0
  284. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +4 -4
  285. package/lib/commonjs/mol-geo/geometry/points/points.js +175 -0
  286. package/lib/commonjs/mol-geo/geometry/size-data.js +123 -0
  287. package/lib/commonjs/mol-geo/geometry/spheres/spheres-builder.js +58 -0
  288. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +1 -1
  289. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +180 -0
  290. package/lib/commonjs/mol-geo/geometry/substance-data.js +68 -0
  291. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +124 -0
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@@ -0,0 +1,684 @@
1
+ /**
2
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
3
+ *
4
+ * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
5
+ *
6
+ * @author molstar/ciftools package
7
+ */
8
+ import { Database, Column } from '../../../../mol-data/db';
9
+ import Schema = Column.Schema;
10
+ export declare const CifCore_Schema: {
11
+ /**
12
+ * The CATEGORY of data items used to describe the parameters of
13
+ * the crystal unit cell and their measurement.
14
+ */
15
+ cell: {
16
+ /**
17
+ * The angle between the bounding cell axes.
18
+ */
19
+ angle_alpha: Schema.Float;
20
+ /**
21
+ * The angle between the bounding cell axes.
22
+ */
23
+ angle_beta: Schema.Float;
24
+ /**
25
+ * The angle between the bounding cell axes.
26
+ */
27
+ angle_gamma: Schema.Float;
28
+ /**
29
+ * The number of the formula units in the unit cell as specified
30
+ * by _chemical_formula.structural, _chemical_formula.moiety or
31
+ * _chemical_formula.sum.
32
+ */
33
+ formula_units_z: Schema.Int;
34
+ /**
35
+ * The length of each cell axis.
36
+ */
37
+ length_a: Schema.Float;
38
+ /**
39
+ * The length of each cell axis.
40
+ */
41
+ length_b: Schema.Float;
42
+ /**
43
+ * The length of each cell axis.
44
+ */
45
+ length_c: Schema.Float;
46
+ /**
47
+ * Volume of the crystal unit cell.
48
+ */
49
+ volume: Schema.Float;
50
+ };
51
+ /**
52
+ * The CATEGORY of data items which describe the composition and
53
+ * chemical properties of the compound under study. The formula data
54
+ * items must be consistent with the density, unit-cell and Z values.
55
+ */
56
+ chemical: {
57
+ /**
58
+ * The temperature at which a crystalline solid changes to a liquid.
59
+ */
60
+ melting_point: Schema.Float;
61
+ /**
62
+ * Trivial name by which the compound is commonly known.
63
+ */
64
+ name_common: Schema.Str;
65
+ /**
66
+ * IUPAC or Chemical Abstracts full name of compound.
67
+ */
68
+ name_systematic: Schema.Str;
69
+ };
70
+ /**
71
+ * The CATEGORY of data items which specify the composition and chemical
72
+ * properties of the compound. The formula data items must agree
73
+ * with those that specify the density, unit-cell and Z values.
74
+ *
75
+ * The following rules apply to the construction of the data items
76
+ * _chemical_formula.analytical, *.structural and *.sum. For the
77
+ * data item *.moiety the formula construction is broken up into
78
+ * residues or moieties, i.e. groups of atoms that form a molecular
79
+ * unit or molecular ion. The rules given below apply within each
80
+ * moiety but different requirements apply to the way that moieties
81
+ * are connected (see _chemical_formula.moiety).
82
+ *
83
+ * 1. Only recognized element symbols may be used.
84
+ *
85
+ * 2. Each element symbol is followed by a 'count' number. A count of
86
+ * '1' may be omitted.
87
+ *
88
+ * 3. A space or parenthesis must separate each cluster of (element
89
+ * symbol + count).
90
+ *
91
+ * 4. Where a group of elements is enclosed in parentheses, the
92
+ * multiplier for the group must follow the closing parentheses.
93
+ * That is, all element and group multipliers are assumed to be
94
+ * printed as subscripted numbers. [An exception to this rule
95
+ * exists for *.moiety formulae where pre- and post-multipliers
96
+ * are permitted for molecular units].
97
+ *
98
+ * 5. Unless the elements are ordered in a manner that corresponds to
99
+ * their chemical structure, as in _chemical_formula.structural,
100
+ * the order of the elements within any group or moiety
101
+ * depends on whether or not carbon is present. If carbon is
102
+ * present, the order should be: C, then H, then the other
103
+ * elements in alphabetical order of their symbol. If carbon is
104
+ * not present, the elements are listed purely in alphabetic order
105
+ * of their symbol. This is the 'Hill' system used by Chemical
106
+ * Abstracts. This ordering is used in _chemical_formula.moiety
107
+ * and _chemical_formula.sum.
108
+ *
109
+ * _chemical_formula.IUPAC '[Mo (C O)4 (C18 H33 P)2]'
110
+ * _chemical_formula.moiety 'C40 H66 Mo O4 P2'
111
+ * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
112
+ * _chemical_formula.sum 'C40 H66 Mo O4 P2'
113
+ * _chemical_formula.weight 768.81
114
+ */
115
+ chemical_formula: {
116
+ /**
117
+ * Formula with each discrete bonded residue or ion shown as a
118
+ * separate moiety. See above CHEMICAL_FORMULA for rules
119
+ * for writing chemical formulae. In addition to the general
120
+ * formulae requirements, the following rules apply:
121
+ * 1. Moieties are separated by commas ','.
122
+ * 2. The order of elements within a moiety follows general rule
123
+ * 5 in CHEMICAL_FORMULA.
124
+ * 3. Parentheses are not used within moieties but may surround
125
+ * a moiety. Parentheses may not be nested.
126
+ * 4. Charges should be placed at the end of the moiety. The
127
+ * Singlege '+' or '-' may be preceded by a numerical multiplier
128
+ * and should be separated from the last (element symbol +
129
+ * count) by a space. Pre- or post-multipliers may be used for
130
+ * individual moieties.
131
+ */
132
+ moiety: Schema.Str;
133
+ /**
134
+ * Chemical formulae in which all discrete bonded residues and ions are
135
+ * summed over the constituent elements, following the ordering given
136
+ * in rule 5 of the CATEGORY description. Parentheses normally not used.
137
+ */
138
+ sum: Schema.Str;
139
+ /**
140
+ * Mass corresponding to the formulae _chemical_formula.structural,
141
+ * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
142
+ * parameters yield the density given as _exptl_crystal.density_diffrn.
143
+ */
144
+ weight: Schema.Float;
145
+ };
146
+ /**
147
+ * The CATEGORY of data items used to specify space group
148
+ * information about the crystal used in the diffraction measurements.
149
+ *
150
+ * Space-group types are identified by their number as listed in
151
+ * International Tables for Crystallography Volume A, or by their
152
+ * Schoenflies symbol. Specific settings of the space groups can
153
+ * be identified by their Hall symbol, by specifying their
154
+ * symmetry operations or generators, or by giving the
155
+ * transformation that relates the specific setting to the
156
+ * reference setting based on International Tables Volume A and
157
+ * stored in this dictionary.
158
+ *
159
+ * The commonly used Hermann-Mauguin symbol determines the
160
+ * space-group type uniquely but several different Hermann-Mauguin
161
+ * symbols may refer to the same space-group type. A
162
+ * Hermann-Mauguin symbol contains information on the choice of
163
+ * the basis, but not on the choice of origin.
164
+ *
165
+ * Ref: International Tables for Crystallography (2002). Volume A,
166
+ * Space-group symmetry, edited by Th. Hahn, 5th ed.
167
+ * Dordrecht: Kluwer Academic Publishers.
168
+ */
169
+ space_group: {
170
+ /**
171
+ * The name of the system of geometric crystal classes of space
172
+ * groups (crystal system) to which the space group belongs.
173
+ * Note that rhombohedral space groups belong to the
174
+ * trigonal system.
175
+ */
176
+ crystal_system: Schema.Str;
177
+ /**
178
+ * The number as assigned in International Tables for Crystallography
179
+ * Vol. A, specifying the proper affine class (i.e. the orientation
180
+ * preserving affine class) of space groups (crystallographic space
181
+ * group type) to which the space group belongs. This number defines
182
+ * the space group type but not the coordinate system expressed.
183
+ */
184
+ it_number: Schema.Int;
185
+ /**
186
+ * The full international Hermann-Mauguin space-group symbol as
187
+ * defined in Section 2.2.3 and given as the second item of the
188
+ * second line of each of the space-group tables of Part 7 of
189
+ * International Tables for Crystallography Volume A (2002).
190
+ *
191
+ * Each component of the space-group name is separated by a
192
+ * space or an underscore character. The use of a space is
193
+ * strongly recommended. The underscore is only retained
194
+ * because it was used in old CIFs. It should not be used in
195
+ * new CIFs.
196
+ *
197
+ * Subscripts should appear without special symbols. Bars should
198
+ * be given as negative signs before the numbers to which they
199
+ * apply. The commonly used Hermann-Mauguin symbol determines the
200
+ * space-group type uniquely but a given space-group type may
201
+ * be described by more than one Hermann-Mauguin symbol. The
202
+ * space-group type is best described using
203
+ * _space_group.IT_number or _space_group.name_Schoenflies. The
204
+ * full international Hermann-Mauguin symbol contains information
205
+ * about the choice of basis for monoclinic and orthorhombic
206
+ * space groups but does not give information about the choice
207
+ * of origin. To define the setting uniquely use
208
+ * _space_group.name_Hall, or list the symmetry operations
209
+ * or generators.
210
+ *
211
+ * Ref: International Tables for Crystallography (2002). Volume A,
212
+ * Space-group symmetry, edited by Th. Hahn, 5th ed.
213
+ * Dordrecht: Kluwer Academic Publishers.
214
+ */
215
+ 'name_h-m_full': Schema.Str;
216
+ };
217
+ /**
218
+ * The CATEGORY of data items used to describe symmetry equivalent sites
219
+ * in the crystal unit cell.
220
+ */
221
+ space_group_symop: {
222
+ /**
223
+ * A parsable string giving one of the symmetry operations of the
224
+ * space group in algebraic form. If W is a matrix representation
225
+ * of the rotational part of the symmetry operation defined by the
226
+ * positions and signs of x, y and z, and w is a column of
227
+ * translations defined by fractions, an equivalent position
228
+ * X' is generated from a given position X by the equation
229
+ *
230
+ * X' = WX + w
231
+ *
232
+ * (Note: X is used to represent bold_italics_x in International
233
+ * Tables for Crystallography Vol. A, Part 5)
234
+ *
235
+ * When a list of symmetry operations is given, it must contain
236
+ * a complete set of coordinate representatives which generates
237
+ * all the operations of the space group by the addition of
238
+ * all primitive translations of the space group. Such
239
+ * representatives are to be found as the coordinates of
240
+ * the general-equivalent position in International Tables for
241
+ * Crystallography Vol. A (2002), to which it is necessary to
242
+ * add any centring translations shown above the
243
+ * general-equivalent position.
244
+ *
245
+ * That is to say, it is necessary to list explicitly all the
246
+ * symmetry operations required to generate all the atoms in
247
+ * the unit cell defined by the setting used.
248
+ */
249
+ operation_xyz: Schema.Str;
250
+ };
251
+ /**
252
+ * The CATEGORY of data items used to specify the geometry bonds in the
253
+ * structural model as derived from the atomic sites.
254
+ */
255
+ geom_bond: {
256
+ /**
257
+ * This label is a unique identifier for a particular site in the
258
+ * asymmetric unit of the crystal unit cell.
259
+ */
260
+ atom_site_label_1: Schema.Str;
261
+ /**
262
+ * This label is a unique identifier for a particular site in the
263
+ * asymmetric unit of the crystal unit cell.
264
+ */
265
+ atom_site_label_2: Schema.Str;
266
+ /**
267
+ * Intramolecular bond distance between the sites identified
268
+ * by _geom_bond.id
269
+ */
270
+ distance: Schema.Float;
271
+ /**
272
+ * This code signals whether the angle is referred to in a
273
+ * publication or should be placed in a table of significant angles.
274
+ */
275
+ publ_flag: Schema.Str;
276
+ /**
277
+ * The set of data items which specify the symmetry operation codes
278
+ * which must be applied to the atom sites involved in the geometry angle.
279
+ *
280
+ * The symmetry code of each atom site as the symmetry-equivalent position
281
+ * number 'n' and the cell translation number 'pqr'. These numbers are
282
+ * combined to form the code 'n pqr' or n_pqr.
283
+ *
284
+ * The character string n_pqr is composed as follows:
285
+ *
286
+ * n refers to the symmetry operation that is applied to the
287
+ * coordinates stored in _atom_site.fract_xyz. It must match a
288
+ * number given in _symmetry_equiv.pos_site_id.
289
+ *
290
+ * p, q and r refer to the translations that are subsequently
291
+ * applied to the symmetry transformed coordinates to generate
292
+ * the atom used in calculating the angle. These translations
293
+ * (x,y,z) are related to (p,q,r) by the relations
294
+ * p = 5 + x
295
+ * q = 5 + y
296
+ * r = 5 + z
297
+ */
298
+ site_symmetry_1: Schema.Str;
299
+ /**
300
+ * The set of data items which specify the symmetry operation codes
301
+ * which must be applied to the atom sites involved in the geometry angle.
302
+ *
303
+ * The symmetry code of each atom site as the symmetry-equivalent position
304
+ * number 'n' and the cell translation number 'pqr'. These numbers are
305
+ * combined to form the code 'n pqr' or n_pqr.
306
+ *
307
+ * The character string n_pqr is composed as follows:
308
+ *
309
+ * n refers to the symmetry operation that is applied to the
310
+ * coordinates stored in _atom_site.fract_xyz. It must match a
311
+ * number given in _symmetry_equiv.pos_site_id.
312
+ *
313
+ * p, q and r refer to the translations that are subsequently
314
+ * applied to the symmetry transformed coordinates to generate
315
+ * the atom used in calculating the angle. These translations
316
+ * (x,y,z) are related to (p,q,r) by the relations
317
+ * p = 5 + x
318
+ * q = 5 + y
319
+ * r = 5 + z
320
+ */
321
+ site_symmetry_2: Schema.Str;
322
+ /**
323
+ * Bond valence calculated from the bond distance.
324
+ */
325
+ valence: Schema.Float;
326
+ };
327
+ /**
328
+ * The CATEGORY of data items used to record details about the
329
+ * creation and subsequent updating of the data block.
330
+ */
331
+ audit: {
332
+ /**
333
+ * The digital object identifier (DOI) registered to identify
334
+ * the data set publication represented by the current
335
+ * data block. This can be used as a unique identifier for
336
+ * the data block so long as the code used is a valid DOI
337
+ * (i.e. begins with a valid publisher prefix assigned by a
338
+ * Registration Agency and a suffix guaranteed to be unique
339
+ * by the publisher) and has had its metadata deposited
340
+ * with a DOI Registration Agency.
341
+ *
342
+ * A DOI is a unique character string identifying any
343
+ * object of intellectual property. It provides a
344
+ * persistent identifier for an object on a digital network
345
+ * and permits the association of related current data in a
346
+ * structured extensible way. A DOI is an implementation
347
+ * of the Internet concepts of Uniform Resource Name and
348
+ * Universal Resource Locator managed according to the
349
+ * specifications of the International DOI Foundation
350
+ * (see http://www.doi.org).
351
+ */
352
+ block_doi: Schema.Str;
353
+ };
354
+ /**
355
+ * The CATEGORY of data items recording database deposition. These data items
356
+ * are assigned by database managers and should only appear in a CIF if they
357
+ * originate from that source.
358
+ */
359
+ database_code: {
360
+ /**
361
+ * Code assigned by the Crystallography Open Database (COD).
362
+ */
363
+ cod: Schema.Str;
364
+ /**
365
+ * Code assigned by the Cambridge Structural Database.
366
+ */
367
+ csd: Schema.Str;
368
+ /**
369
+ * Deposition numbers assigned by the Cambridge Crystallographic
370
+ * Data Centre (CCDC) to files containing structural information
371
+ * archived by the CCDC.
372
+ */
373
+ depnum_ccdc_archive: Schema.Str;
374
+ /**
375
+ * Deposition numbers assigned by the Fachinformationszentrum
376
+ * Karlsruhe (FIZ) to files containing structural information
377
+ * archived by the Cambridge Crystallographic Data Centre (CCDC).
378
+ */
379
+ depnum_ccdc_fiz: Schema.Str;
380
+ /**
381
+ * Code assigned by the Inorganic Crystal Structure Database.
382
+ */
383
+ icsd: Schema.Str;
384
+ /**
385
+ * Code assigned in the Metals Data File.
386
+ */
387
+ mdf: Schema.Str;
388
+ /**
389
+ * Code assigned by the NBS (NIST) Crystal Data Database.
390
+ */
391
+ nbs: Schema.Str;
392
+ };
393
+ /**
394
+ * The CATEGORY of data items used to describe atom site information
395
+ * used in crystallographic structure studies.
396
+ */
397
+ atom_site: {
398
+ /**
399
+ * Code for type of atomic displacement parameters used for the site.
400
+ */
401
+ adp_type: Schema.Str;
402
+ /**
403
+ * A standard code to signal if the site coordinates have been
404
+ * determined from the intensities or calculated from the geometry
405
+ * of surrounding sites, or have been assigned dummy coordinates.
406
+ */
407
+ calc_flag: Schema.Str;
408
+ /**
409
+ * A code which identifies a cluster of atoms that show long range
410
+ * positional disorder but are locally ordered. Within each such
411
+ * cluster of atoms, _atom_site.disorder_group is used to identify
412
+ * the sites that are simultaneously occupied. This field is only
413
+ * needed if there is more than one cluster of disordered atoms
414
+ * showing independent local order.
415
+ */
416
+ disorder_assembly: Schema.Str;
417
+ /**
418
+ * A code that identifies a group of positionally disordered atom
419
+ * sites that are locally simultaneously occupied. Atoms that are
420
+ * positionally disordered over two or more sites (e.g. the H
421
+ * atoms of a methyl group that exists in two orientations) can
422
+ * be assigned to two or more groups. Sites belonging to the same
423
+ * group are simultaneously occupied, but those belonging to
424
+ * different groups are not. A minus prefix (e.g. "-1") is used to
425
+ * indicate sites disordered about a special position.
426
+ */
427
+ disorder_group: Schema.Str;
428
+ /**
429
+ * Atom site coordinates as fractions of the cell length values.
430
+ */
431
+ fract_x: Schema.Float;
432
+ /**
433
+ * Atom site coordinates as fractions of the cell length values.
434
+ */
435
+ fract_y: Schema.Float;
436
+ /**
437
+ * Atom site coordinates as fractions of the cell length values.
438
+ */
439
+ fract_z: Schema.Float;
440
+ /**
441
+ * This label is a unique identifier for a particular site in the
442
+ * asymmetric unit of the crystal unit cell. It is made up of
443
+ * components, _atom_site.label_component_0 to *_6, which may be
444
+ * specified as separate data items. Component 0 usually matches one
445
+ * of the specified _atom_type.symbol codes. This is not mandatory
446
+ * if an _atom_site.type_symbol item is included in the atom site
447
+ * list. The _atom_site.type_symbol always takes precedence over
448
+ * an _atom_site.label in the identification of the atom type. The
449
+ * label components 1 to 6 are optional, and normally only
450
+ * components 0 and 1 are used. Note that components 0 and 1 are
451
+ * concatenated, while all other components, if specified, are
452
+ * separated by an underline character. Underline separators are
453
+ * only used if higher-order components exist. If an intermediate
454
+ * component is not used it may be omitted provided the underline
455
+ * separators are inserted. For example the label 'C233__ggg' is
456
+ * acceptable and represents the components C, 233, '', and ggg.
457
+ * Each label may have a different number of components.
458
+ */
459
+ label: Schema.Str;
460
+ /**
461
+ * The fraction of the atom type present at this site.
462
+ * The sum of the occupancies of all the atom types at this site
463
+ * may not significantly exceed 1.0 unless it is a dummy site. The
464
+ * value must lie in the 99.97% Gaussian confidence interval
465
+ * -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
466
+ * correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
467
+ */
468
+ occupancy: Schema.Float;
469
+ /**
470
+ * A concatenated series of single-letter codes which indicate the
471
+ * refinement restraints or constraints applied to this site. This
472
+ * item should not be used. It has been replaced by
473
+ * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
474
+ * retained in this dictionary only to provide compatibility with
475
+ * legacy CIFs.
476
+ */
477
+ refinement_flags: Schema.Str;
478
+ /**
479
+ * The number of different sites that are generated by the
480
+ * application of the space-group symmetry to the coordinates
481
+ * given for this site. It is equal to the multiplicity given
482
+ * for this Wyckoff site in International Tables for Cryst.
483
+ * Vol. A (2002). It is equal to the multiplicity of the general
484
+ * position divided by the order of the site symmetry given in
485
+ * _atom_site.site_symmetry_order.
486
+ */
487
+ site_symmetry_multiplicity: Schema.Int;
488
+ /**
489
+ * A code to identify the atom specie(s) occupying this site.
490
+ * This code must match a corresponding _atom_type.symbol. The
491
+ * specification of this code is optional if component_0 of the
492
+ * _atom_site.label is used for this purpose. See _atom_type.symbol.
493
+ */
494
+ type_symbol: Schema.Str;
495
+ /**
496
+ * Isotropic atomic displacement parameter, or equivalent isotropic
497
+ * atomic displacement parameter, U(equiv), in angstroms squared,
498
+ * calculated from anisotropic atomic displacement parameters.
499
+ *
500
+ * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
501
+ *
502
+ * a = the real-space cell vectors
503
+ * a* = the reciprocal-space cell lengths
504
+ * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
505
+ */
506
+ u_iso_or_equiv: Schema.Float;
507
+ };
508
+ /**
509
+ * The CATEGORY of data items used to describe the anisotropic
510
+ * thermal parameters of the atomic sites in a crystal structure.
511
+ */
512
+ atom_site_aniso: {
513
+ /**
514
+ * Anisotropic atomic displacement parameters are usually looped in
515
+ * a separate list. If this is the case, this code must match the
516
+ * _atom_site.label of the associated atom in the atom coordinate
517
+ * list and conform with the same rules described in _atom_site.label.
518
+ */
519
+ label: Schema.Str;
520
+ /**
521
+ * These are the standard anisotropic atomic displacement
522
+ * components in angstroms squared which appear in the
523
+ * structure factor term:
524
+ *
525
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
526
+ *
527
+ * h = the Miller indices
528
+ * a* = the reciprocal-space cell lengths
529
+ *
530
+ * The unique elements of the real symmetric matrix are entered by row.
531
+ */
532
+ u_11: Schema.Float;
533
+ /**
534
+ * These are the standard anisotropic atomic displacement
535
+ * components in angstroms squared which appear in the
536
+ * structure factor term:
537
+ *
538
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
539
+ *
540
+ * h = the Miller indices
541
+ * a* = the reciprocal-space cell lengths
542
+ *
543
+ * The unique elements of the real symmetric matrix are entered by row.
544
+ */
545
+ u: Schema.Tensor;
546
+ /**
547
+ * These are the standard anisotropic atomic displacement
548
+ * components in angstroms squared which appear in the
549
+ * structure factor term:
550
+ *
551
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
552
+ *
553
+ * h = the Miller indices
554
+ * a* = the reciprocal-space cell lengths
555
+ *
556
+ * The unique elements of the real symmetric matrix are entered by row.
557
+ */
558
+ u_12: Schema.Float;
559
+ /**
560
+ * These are the standard anisotropic atomic displacement
561
+ * components in angstroms squared which appear in the
562
+ * structure factor term:
563
+ *
564
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
565
+ *
566
+ * h = the Miller indices
567
+ * a* = the reciprocal-space cell lengths
568
+ *
569
+ * The unique elements of the real symmetric matrix are entered by row.
570
+ */
571
+ u_13: Schema.Float;
572
+ /**
573
+ * These are the standard anisotropic atomic displacement
574
+ * components in angstroms squared which appear in the
575
+ * structure factor term:
576
+ *
577
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
578
+ *
579
+ * h = the Miller indices
580
+ * a* = the reciprocal-space cell lengths
581
+ *
582
+ * The unique elements of the real symmetric matrix are entered by row.
583
+ */
584
+ u_22: Schema.Float;
585
+ /**
586
+ * These are the standard anisotropic atomic displacement
587
+ * components in angstroms squared which appear in the
588
+ * structure factor term:
589
+ *
590
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
591
+ *
592
+ * h = the Miller indices
593
+ * a* = the reciprocal-space cell lengths
594
+ *
595
+ * The unique elements of the real symmetric matrix are entered by row.
596
+ */
597
+ u_23: Schema.Float;
598
+ /**
599
+ * These are the standard anisotropic atomic displacement
600
+ * components in angstroms squared which appear in the
601
+ * structure factor term:
602
+ *
603
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
604
+ *
605
+ * h = the Miller indices
606
+ * a* = the reciprocal-space cell lengths
607
+ *
608
+ * The unique elements of the real symmetric matrix are entered by row.
609
+ */
610
+ u_33: Schema.Float;
611
+ };
612
+ /**
613
+ * The CATEGORY of data items used to describe atomic type information
614
+ * used in crystallographic structure studies.
615
+ */
616
+ atom_type: {
617
+ /**
618
+ * A description of the atom(s) designated by this atom type. In
619
+ * most cases this will be the element name and oxidation state of
620
+ * a single atom species. For disordered or nonstoichiometric
621
+ * structures it will describe a combination of atom species.
622
+ */
623
+ description: Schema.Str;
624
+ /**
625
+ * The identity of the atom specie(s) representing this atom type.
626
+ * Normally this code is the element symbol followed by the charge
627
+ * if there is one. The symbol may be composed of any character except
628
+ * an underline or a blank, with the proviso that digits designate an
629
+ * oxidation state and must be followed by a + or - character.
630
+ */
631
+ symbol: Schema.Str;
632
+ };
633
+ /**
634
+ * The CATEGORY of data items used to describe atomic scattering
635
+ * information used in crystallographic structure studies.
636
+ */
637
+ atom_type_scat: {
638
+ /**
639
+ * The imaginary component of the anomalous dispersion scattering factors
640
+ * for this atom type and radiation by _diffrn_radiation_wavelength.value
641
+ */
642
+ dispersion_imag: Schema.Float;
643
+ /**
644
+ * The real component of the anomalous dispersion scattering factors
645
+ * for this atom type and radiation by _diffrn_radiation_wavelength.value
646
+ */
647
+ dispersion_real: Schema.Float;
648
+ /**
649
+ * Reference to source of scattering factors used for this atom type.
650
+ */
651
+ source: Schema.Str;
652
+ };
653
+ };
654
+ export declare const CifCore_Aliases: {
655
+ 'cell.formula_units_z': string[];
656
+ 'space_group.it_number': string[];
657
+ 'space_group.name_h-m_full': string[];
658
+ 'space_group_symop.operation_xyz': string[];
659
+ 'geom_bond.atom_site_label_1': string[];
660
+ 'geom_bond.atom_site_label_2': string[];
661
+ 'geom_bond.distance': string[];
662
+ 'audit.block_doi': string[];
663
+ 'database_code.cod': string[];
664
+ 'database_code.csd': string[];
665
+ 'database_code.depnum_ccdc_archive': string[];
666
+ 'database_code.depnum_ccdc_fiz': string[];
667
+ 'database_code.icsd': string[];
668
+ 'database_code.mdf': string[];
669
+ 'database_code.nbs': string[];
670
+ 'atom_site.adp_type': string[];
671
+ 'atom_site.label': string[];
672
+ 'atom_site.site_symmetry_multiplicity': string[];
673
+ 'atom_site.u_iso_or_equiv': string[];
674
+ 'atom_site_aniso.label': string[];
675
+ 'atom_site_aniso.u_11': string[];
676
+ 'atom_site_aniso.u_12': string[];
677
+ 'atom_site_aniso.u_13': string[];
678
+ 'atom_site_aniso.u_22': string[];
679
+ 'atom_site_aniso.u_23': string[];
680
+ 'atom_site_aniso.u_33': string[];
681
+ };
682
+ export declare type CifCore_Schema = typeof CifCore_Schema;
683
+ export interface CifCore_Database extends Database<CifCore_Schema> {
684
+ }