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 +1,750 @@
1
+ "use strict";
2
+ /**
3
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
4
+ *
5
+ * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
6
+ *
7
+ * @author molstar/ciftools package
8
+ */
9
+ Object.defineProperty(exports, "__esModule", { value: true });
10
+ exports.CifCore_Aliases = exports.CifCore_Schema = void 0;
11
+ var db_1 = require("../../../../mol-data/db");
12
+ var Schema = db_1.Column.Schema;
13
+ var float = Schema.float;
14
+ var int = Schema.int;
15
+ var str = Schema.str;
16
+ var Matrix = Schema.Matrix;
17
+ exports.CifCore_Schema = {
18
+ /**
19
+ * The CATEGORY of data items used to describe the parameters of
20
+ * the crystal unit cell and their measurement.
21
+ */
22
+ cell: {
23
+ /**
24
+ * The angle between the bounding cell axes.
25
+ */
26
+ angle_alpha: float,
27
+ /**
28
+ * The angle between the bounding cell axes.
29
+ */
30
+ angle_beta: float,
31
+ /**
32
+ * The angle between the bounding cell axes.
33
+ */
34
+ angle_gamma: float,
35
+ /**
36
+ * The number of the formula units in the unit cell as specified
37
+ * by _chemical_formula.structural, _chemical_formula.moiety or
38
+ * _chemical_formula.sum.
39
+ */
40
+ formula_units_z: int,
41
+ /**
42
+ * The length of each cell axis.
43
+ */
44
+ length_a: float,
45
+ /**
46
+ * The length of each cell axis.
47
+ */
48
+ length_b: float,
49
+ /**
50
+ * The length of each cell axis.
51
+ */
52
+ length_c: float,
53
+ /**
54
+ * Volume of the crystal unit cell.
55
+ */
56
+ volume: float,
57
+ },
58
+ /**
59
+ * The CATEGORY of data items which describe the composition and
60
+ * chemical properties of the compound under study. The formula data
61
+ * items must be consistent with the density, unit-cell and Z values.
62
+ */
63
+ chemical: {
64
+ /**
65
+ * The temperature at which a crystalline solid changes to a liquid.
66
+ */
67
+ melting_point: float,
68
+ /**
69
+ * Trivial name by which the compound is commonly known.
70
+ */
71
+ name_common: str,
72
+ /**
73
+ * IUPAC or Chemical Abstracts full name of compound.
74
+ */
75
+ name_systematic: str,
76
+ },
77
+ /**
78
+ * The CATEGORY of data items which specify the composition and chemical
79
+ * properties of the compound. The formula data items must agree
80
+ * with those that specify the density, unit-cell and Z values.
81
+ *
82
+ * The following rules apply to the construction of the data items
83
+ * _chemical_formula.analytical, *.structural and *.sum. For the
84
+ * data item *.moiety the formula construction is broken up into
85
+ * residues or moieties, i.e. groups of atoms that form a molecular
86
+ * unit or molecular ion. The rules given below apply within each
87
+ * moiety but different requirements apply to the way that moieties
88
+ * are connected (see _chemical_formula.moiety).
89
+ *
90
+ * 1. Only recognized element symbols may be used.
91
+ *
92
+ * 2. Each element symbol is followed by a 'count' number. A count of
93
+ * '1' may be omitted.
94
+ *
95
+ * 3. A space or parenthesis must separate each cluster of (element
96
+ * symbol + count).
97
+ *
98
+ * 4. Where a group of elements is enclosed in parentheses, the
99
+ * multiplier for the group must follow the closing parentheses.
100
+ * That is, all element and group multipliers are assumed to be
101
+ * printed as subscripted numbers. [An exception to this rule
102
+ * exists for *.moiety formulae where pre- and post-multipliers
103
+ * are permitted for molecular units].
104
+ *
105
+ * 5. Unless the elements are ordered in a manner that corresponds to
106
+ * their chemical structure, as in _chemical_formula.structural,
107
+ * the order of the elements within any group or moiety
108
+ * depends on whether or not carbon is present. If carbon is
109
+ * present, the order should be: C, then H, then the other
110
+ * elements in alphabetical order of their symbol. If carbon is
111
+ * not present, the elements are listed purely in alphabetic order
112
+ * of their symbol. This is the 'Hill' system used by Chemical
113
+ * Abstracts. This ordering is used in _chemical_formula.moiety
114
+ * and _chemical_formula.sum.
115
+ *
116
+ * _chemical_formula.IUPAC '[Mo (C O)4 (C18 H33 P)2]'
117
+ * _chemical_formula.moiety 'C40 H66 Mo O4 P2'
118
+ * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
119
+ * _chemical_formula.sum 'C40 H66 Mo O4 P2'
120
+ * _chemical_formula.weight 768.81
121
+ */
122
+ chemical_formula: {
123
+ /**
124
+ * Formula with each discrete bonded residue or ion shown as a
125
+ * separate moiety. See above CHEMICAL_FORMULA for rules
126
+ * for writing chemical formulae. In addition to the general
127
+ * formulae requirements, the following rules apply:
128
+ * 1. Moieties are separated by commas ','.
129
+ * 2. The order of elements within a moiety follows general rule
130
+ * 5 in CHEMICAL_FORMULA.
131
+ * 3. Parentheses are not used within moieties but may surround
132
+ * a moiety. Parentheses may not be nested.
133
+ * 4. Charges should be placed at the end of the moiety. The
134
+ * Singlege '+' or '-' may be preceded by a numerical multiplier
135
+ * and should be separated from the last (element symbol +
136
+ * count) by a space. Pre- or post-multipliers may be used for
137
+ * individual moieties.
138
+ */
139
+ moiety: str,
140
+ /**
141
+ * Chemical formulae in which all discrete bonded residues and ions are
142
+ * summed over the constituent elements, following the ordering given
143
+ * in rule 5 of the CATEGORY description. Parentheses normally not used.
144
+ */
145
+ sum: str,
146
+ /**
147
+ * Mass corresponding to the formulae _chemical_formula.structural,
148
+ * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
149
+ * parameters yield the density given as _exptl_crystal.density_diffrn.
150
+ */
151
+ weight: float,
152
+ },
153
+ /**
154
+ * The CATEGORY of data items used to specify space group
155
+ * information about the crystal used in the diffraction measurements.
156
+ *
157
+ * Space-group types are identified by their number as listed in
158
+ * International Tables for Crystallography Volume A, or by their
159
+ * Schoenflies symbol. Specific settings of the space groups can
160
+ * be identified by their Hall symbol, by specifying their
161
+ * symmetry operations or generators, or by giving the
162
+ * transformation that relates the specific setting to the
163
+ * reference setting based on International Tables Volume A and
164
+ * stored in this dictionary.
165
+ *
166
+ * The commonly used Hermann-Mauguin symbol determines the
167
+ * space-group type uniquely but several different Hermann-Mauguin
168
+ * symbols may refer to the same space-group type. A
169
+ * Hermann-Mauguin symbol contains information on the choice of
170
+ * the basis, but not on the choice of origin.
171
+ *
172
+ * Ref: International Tables for Crystallography (2002). Volume A,
173
+ * Space-group symmetry, edited by Th. Hahn, 5th ed.
174
+ * Dordrecht: Kluwer Academic Publishers.
175
+ */
176
+ space_group: {
177
+ /**
178
+ * The name of the system of geometric crystal classes of space
179
+ * groups (crystal system) to which the space group belongs.
180
+ * Note that rhombohedral space groups belong to the
181
+ * trigonal system.
182
+ */
183
+ crystal_system: str,
184
+ /**
185
+ * The number as assigned in International Tables for Crystallography
186
+ * Vol. A, specifying the proper affine class (i.e. the orientation
187
+ * preserving affine class) of space groups (crystallographic space
188
+ * group type) to which the space group belongs. This number defines
189
+ * the space group type but not the coordinate system expressed.
190
+ */
191
+ it_number: int,
192
+ /**
193
+ * The full international Hermann-Mauguin space-group symbol as
194
+ * defined in Section 2.2.3 and given as the second item of the
195
+ * second line of each of the space-group tables of Part 7 of
196
+ * International Tables for Crystallography Volume A (2002).
197
+ *
198
+ * Each component of the space-group name is separated by a
199
+ * space or an underscore character. The use of a space is
200
+ * strongly recommended. The underscore is only retained
201
+ * because it was used in old CIFs. It should not be used in
202
+ * new CIFs.
203
+ *
204
+ * Subscripts should appear without special symbols. Bars should
205
+ * be given as negative signs before the numbers to which they
206
+ * apply. The commonly used Hermann-Mauguin symbol determines the
207
+ * space-group type uniquely but a given space-group type may
208
+ * be described by more than one Hermann-Mauguin symbol. The
209
+ * space-group type is best described using
210
+ * _space_group.IT_number or _space_group.name_Schoenflies. The
211
+ * full international Hermann-Mauguin symbol contains information
212
+ * about the choice of basis for monoclinic and orthorhombic
213
+ * space groups but does not give information about the choice
214
+ * of origin. To define the setting uniquely use
215
+ * _space_group.name_Hall, or list the symmetry operations
216
+ * or generators.
217
+ *
218
+ * Ref: International Tables for Crystallography (2002). Volume A,
219
+ * Space-group symmetry, edited by Th. Hahn, 5th ed.
220
+ * Dordrecht: Kluwer Academic Publishers.
221
+ */
222
+ 'name_h-m_full': str,
223
+ },
224
+ /**
225
+ * The CATEGORY of data items used to describe symmetry equivalent sites
226
+ * in the crystal unit cell.
227
+ */
228
+ space_group_symop: {
229
+ /**
230
+ * A parsable string giving one of the symmetry operations of the
231
+ * space group in algebraic form. If W is a matrix representation
232
+ * of the rotational part of the symmetry operation defined by the
233
+ * positions and signs of x, y and z, and w is a column of
234
+ * translations defined by fractions, an equivalent position
235
+ * X' is generated from a given position X by the equation
236
+ *
237
+ * X' = WX + w
238
+ *
239
+ * (Note: X is used to represent bold_italics_x in International
240
+ * Tables for Crystallography Vol. A, Part 5)
241
+ *
242
+ * When a list of symmetry operations is given, it must contain
243
+ * a complete set of coordinate representatives which generates
244
+ * all the operations of the space group by the addition of
245
+ * all primitive translations of the space group. Such
246
+ * representatives are to be found as the coordinates of
247
+ * the general-equivalent position in International Tables for
248
+ * Crystallography Vol. A (2002), to which it is necessary to
249
+ * add any centring translations shown above the
250
+ * general-equivalent position.
251
+ *
252
+ * That is to say, it is necessary to list explicitly all the
253
+ * symmetry operations required to generate all the atoms in
254
+ * the unit cell defined by the setting used.
255
+ */
256
+ operation_xyz: str,
257
+ },
258
+ /**
259
+ * The CATEGORY of data items used to specify the geometry bonds in the
260
+ * structural model as derived from the atomic sites.
261
+ */
262
+ geom_bond: {
263
+ /**
264
+ * This label is a unique identifier for a particular site in the
265
+ * asymmetric unit of the crystal unit cell.
266
+ */
267
+ atom_site_label_1: str,
268
+ /**
269
+ * This label is a unique identifier for a particular site in the
270
+ * asymmetric unit of the crystal unit cell.
271
+ */
272
+ atom_site_label_2: str,
273
+ /**
274
+ * Intramolecular bond distance between the sites identified
275
+ * by _geom_bond.id
276
+ */
277
+ distance: float,
278
+ /**
279
+ * This code signals whether the angle is referred to in a
280
+ * publication or should be placed in a table of significant angles.
281
+ */
282
+ publ_flag: str,
283
+ /**
284
+ * The set of data items which specify the symmetry operation codes
285
+ * which must be applied to the atom sites involved in the geometry angle.
286
+ *
287
+ * The symmetry code of each atom site as the symmetry-equivalent position
288
+ * number 'n' and the cell translation number 'pqr'. These numbers are
289
+ * combined to form the code 'n pqr' or n_pqr.
290
+ *
291
+ * The character string n_pqr is composed as follows:
292
+ *
293
+ * n refers to the symmetry operation that is applied to the
294
+ * coordinates stored in _atom_site.fract_xyz. It must match a
295
+ * number given in _symmetry_equiv.pos_site_id.
296
+ *
297
+ * p, q and r refer to the translations that are subsequently
298
+ * applied to the symmetry transformed coordinates to generate
299
+ * the atom used in calculating the angle. These translations
300
+ * (x,y,z) are related to (p,q,r) by the relations
301
+ * p = 5 + x
302
+ * q = 5 + y
303
+ * r = 5 + z
304
+ */
305
+ site_symmetry_1: str,
306
+ /**
307
+ * The set of data items which specify the symmetry operation codes
308
+ * which must be applied to the atom sites involved in the geometry angle.
309
+ *
310
+ * The symmetry code of each atom site as the symmetry-equivalent position
311
+ * number 'n' and the cell translation number 'pqr'. These numbers are
312
+ * combined to form the code 'n pqr' or n_pqr.
313
+ *
314
+ * The character string n_pqr is composed as follows:
315
+ *
316
+ * n refers to the symmetry operation that is applied to the
317
+ * coordinates stored in _atom_site.fract_xyz. It must match a
318
+ * number given in _symmetry_equiv.pos_site_id.
319
+ *
320
+ * p, q and r refer to the translations that are subsequently
321
+ * applied to the symmetry transformed coordinates to generate
322
+ * the atom used in calculating the angle. These translations
323
+ * (x,y,z) are related to (p,q,r) by the relations
324
+ * p = 5 + x
325
+ * q = 5 + y
326
+ * r = 5 + z
327
+ */
328
+ site_symmetry_2: str,
329
+ /**
330
+ * Bond valence calculated from the bond distance.
331
+ */
332
+ valence: float,
333
+ },
334
+ /**
335
+ * The CATEGORY of data items used to record details about the
336
+ * creation and subsequent updating of the data block.
337
+ */
338
+ audit: {
339
+ /**
340
+ * The digital object identifier (DOI) registered to identify
341
+ * the data set publication represented by the current
342
+ * data block. This can be used as a unique identifier for
343
+ * the data block so long as the code used is a valid DOI
344
+ * (i.e. begins with a valid publisher prefix assigned by a
345
+ * Registration Agency and a suffix guaranteed to be unique
346
+ * by the publisher) and has had its metadata deposited
347
+ * with a DOI Registration Agency.
348
+ *
349
+ * A DOI is a unique character string identifying any
350
+ * object of intellectual property. It provides a
351
+ * persistent identifier for an object on a digital network
352
+ * and permits the association of related current data in a
353
+ * structured extensible way. A DOI is an implementation
354
+ * of the Internet concepts of Uniform Resource Name and
355
+ * Universal Resource Locator managed according to the
356
+ * specifications of the International DOI Foundation
357
+ * (see http://www.doi.org).
358
+ */
359
+ block_doi: str,
360
+ },
361
+ /**
362
+ * The CATEGORY of data items recording database deposition. These data items
363
+ * are assigned by database managers and should only appear in a CIF if they
364
+ * originate from that source.
365
+ */
366
+ database_code: {
367
+ /**
368
+ * Code assigned by the Crystallography Open Database (COD).
369
+ */
370
+ cod: str,
371
+ /**
372
+ * Code assigned by the Cambridge Structural Database.
373
+ */
374
+ csd: str,
375
+ /**
376
+ * Deposition numbers assigned by the Cambridge Crystallographic
377
+ * Data Centre (CCDC) to files containing structural information
378
+ * archived by the CCDC.
379
+ */
380
+ depnum_ccdc_archive: str,
381
+ /**
382
+ * Deposition numbers assigned by the Fachinformationszentrum
383
+ * Karlsruhe (FIZ) to files containing structural information
384
+ * archived by the Cambridge Crystallographic Data Centre (CCDC).
385
+ */
386
+ depnum_ccdc_fiz: str,
387
+ /**
388
+ * Code assigned by the Inorganic Crystal Structure Database.
389
+ */
390
+ icsd: str,
391
+ /**
392
+ * Code assigned in the Metals Data File.
393
+ */
394
+ mdf: str,
395
+ /**
396
+ * Code assigned by the NBS (NIST) Crystal Data Database.
397
+ */
398
+ nbs: str,
399
+ },
400
+ /**
401
+ * The CATEGORY of data items used to describe atom site information
402
+ * used in crystallographic structure studies.
403
+ */
404
+ atom_site: {
405
+ /**
406
+ * Code for type of atomic displacement parameters used for the site.
407
+ */
408
+ adp_type: str,
409
+ /**
410
+ * A standard code to signal if the site coordinates have been
411
+ * determined from the intensities or calculated from the geometry
412
+ * of surrounding sites, or have been assigned dummy coordinates.
413
+ */
414
+ calc_flag: str,
415
+ /**
416
+ * A code which identifies a cluster of atoms that show long range
417
+ * positional disorder but are locally ordered. Within each such
418
+ * cluster of atoms, _atom_site.disorder_group is used to identify
419
+ * the sites that are simultaneously occupied. This field is only
420
+ * needed if there is more than one cluster of disordered atoms
421
+ * showing independent local order.
422
+ */
423
+ disorder_assembly: str,
424
+ /**
425
+ * A code that identifies a group of positionally disordered atom
426
+ * sites that are locally simultaneously occupied. Atoms that are
427
+ * positionally disordered over two or more sites (e.g. the H
428
+ * atoms of a methyl group that exists in two orientations) can
429
+ * be assigned to two or more groups. Sites belonging to the same
430
+ * group are simultaneously occupied, but those belonging to
431
+ * different groups are not. A minus prefix (e.g. "-1") is used to
432
+ * indicate sites disordered about a special position.
433
+ */
434
+ disorder_group: str,
435
+ /**
436
+ * Atom site coordinates as fractions of the cell length values.
437
+ */
438
+ fract_x: float,
439
+ /**
440
+ * Atom site coordinates as fractions of the cell length values.
441
+ */
442
+ fract_y: float,
443
+ /**
444
+ * Atom site coordinates as fractions of the cell length values.
445
+ */
446
+ fract_z: float,
447
+ /**
448
+ * This label is a unique identifier for a particular site in the
449
+ * asymmetric unit of the crystal unit cell. It is made up of
450
+ * components, _atom_site.label_component_0 to *_6, which may be
451
+ * specified as separate data items. Component 0 usually matches one
452
+ * of the specified _atom_type.symbol codes. This is not mandatory
453
+ * if an _atom_site.type_symbol item is included in the atom site
454
+ * list. The _atom_site.type_symbol always takes precedence over
455
+ * an _atom_site.label in the identification of the atom type. The
456
+ * label components 1 to 6 are optional, and normally only
457
+ * components 0 and 1 are used. Note that components 0 and 1 are
458
+ * concatenated, while all other components, if specified, are
459
+ * separated by an underline character. Underline separators are
460
+ * only used if higher-order components exist. If an intermediate
461
+ * component is not used it may be omitted provided the underline
462
+ * separators are inserted. For example the label 'C233__ggg' is
463
+ * acceptable and represents the components C, 233, '', and ggg.
464
+ * Each label may have a different number of components.
465
+ */
466
+ label: str,
467
+ /**
468
+ * The fraction of the atom type present at this site.
469
+ * The sum of the occupancies of all the atom types at this site
470
+ * may not significantly exceed 1.0 unless it is a dummy site. The
471
+ * value must lie in the 99.97% Gaussian confidence interval
472
+ * -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
473
+ * correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
474
+ */
475
+ occupancy: float,
476
+ /**
477
+ * A concatenated series of single-letter codes which indicate the
478
+ * refinement restraints or constraints applied to this site. This
479
+ * item should not be used. It has been replaced by
480
+ * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
481
+ * retained in this dictionary only to provide compatibility with
482
+ * legacy CIFs.
483
+ */
484
+ refinement_flags: str,
485
+ /**
486
+ * The number of different sites that are generated by the
487
+ * application of the space-group symmetry to the coordinates
488
+ * given for this site. It is equal to the multiplicity given
489
+ * for this Wyckoff site in International Tables for Cryst.
490
+ * Vol. A (2002). It is equal to the multiplicity of the general
491
+ * position divided by the order of the site symmetry given in
492
+ * _atom_site.site_symmetry_order.
493
+ */
494
+ site_symmetry_multiplicity: int,
495
+ /**
496
+ * A code to identify the atom specie(s) occupying this site.
497
+ * This code must match a corresponding _atom_type.symbol. The
498
+ * specification of this code is optional if component_0 of the
499
+ * _atom_site.label is used for this purpose. See _atom_type.symbol.
500
+ */
501
+ type_symbol: str,
502
+ /**
503
+ * Isotropic atomic displacement parameter, or equivalent isotropic
504
+ * atomic displacement parameter, U(equiv), in angstroms squared,
505
+ * calculated from anisotropic atomic displacement parameters.
506
+ *
507
+ * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
508
+ *
509
+ * a = the real-space cell vectors
510
+ * a* = the reciprocal-space cell lengths
511
+ * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
512
+ */
513
+ u_iso_or_equiv: float,
514
+ },
515
+ /**
516
+ * The CATEGORY of data items used to describe the anisotropic
517
+ * thermal parameters of the atomic sites in a crystal structure.
518
+ */
519
+ atom_site_aniso: {
520
+ /**
521
+ * Anisotropic atomic displacement parameters are usually looped in
522
+ * a separate list. If this is the case, this code must match the
523
+ * _atom_site.label of the associated atom in the atom coordinate
524
+ * list and conform with the same rules described in _atom_site.label.
525
+ */
526
+ label: str,
527
+ /**
528
+ * These are the standard anisotropic atomic displacement
529
+ * components in angstroms squared which appear in the
530
+ * structure factor term:
531
+ *
532
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
533
+ *
534
+ * h = the Miller indices
535
+ * a* = the reciprocal-space cell lengths
536
+ *
537
+ * The unique elements of the real symmetric matrix are entered by row.
538
+ */
539
+ u_11: float,
540
+ /**
541
+ * These are the standard anisotropic atomic displacement
542
+ * components in angstroms squared which appear in the
543
+ * structure factor term:
544
+ *
545
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
546
+ *
547
+ * h = the Miller indices
548
+ * a* = the reciprocal-space cell lengths
549
+ *
550
+ * The unique elements of the real symmetric matrix are entered by row.
551
+ */
552
+ u: Matrix(3, 3),
553
+ /**
554
+ * These are the standard anisotropic atomic displacement
555
+ * components in angstroms squared which appear in the
556
+ * structure factor term:
557
+ *
558
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
559
+ *
560
+ * h = the Miller indices
561
+ * a* = the reciprocal-space cell lengths
562
+ *
563
+ * The unique elements of the real symmetric matrix are entered by row.
564
+ */
565
+ u_12: float,
566
+ /**
567
+ * These are the standard anisotropic atomic displacement
568
+ * components in angstroms squared which appear in the
569
+ * structure factor term:
570
+ *
571
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
572
+ *
573
+ * h = the Miller indices
574
+ * a* = the reciprocal-space cell lengths
575
+ *
576
+ * The unique elements of the real symmetric matrix are entered by row.
577
+ */
578
+ u_13: float,
579
+ /**
580
+ * These are the standard anisotropic atomic displacement
581
+ * components in angstroms squared which appear in the
582
+ * structure factor term:
583
+ *
584
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
585
+ *
586
+ * h = the Miller indices
587
+ * a* = the reciprocal-space cell lengths
588
+ *
589
+ * The unique elements of the real symmetric matrix are entered by row.
590
+ */
591
+ u_22: float,
592
+ /**
593
+ * These are the standard anisotropic atomic displacement
594
+ * components in angstroms squared which appear in the
595
+ * structure factor term:
596
+ *
597
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
598
+ *
599
+ * h = the Miller indices
600
+ * a* = the reciprocal-space cell lengths
601
+ *
602
+ * The unique elements of the real symmetric matrix are entered by row.
603
+ */
604
+ u_23: float,
605
+ /**
606
+ * These are the standard anisotropic atomic displacement
607
+ * components in angstroms squared which appear in the
608
+ * structure factor term:
609
+ *
610
+ * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
611
+ *
612
+ * h = the Miller indices
613
+ * a* = the reciprocal-space cell lengths
614
+ *
615
+ * The unique elements of the real symmetric matrix are entered by row.
616
+ */
617
+ u_33: float,
618
+ },
619
+ /**
620
+ * The CATEGORY of data items used to describe atomic type information
621
+ * used in crystallographic structure studies.
622
+ */
623
+ atom_type: {
624
+ /**
625
+ * A description of the atom(s) designated by this atom type. In
626
+ * most cases this will be the element name and oxidation state of
627
+ * a single atom species. For disordered or nonstoichiometric
628
+ * structures it will describe a combination of atom species.
629
+ */
630
+ description: str,
631
+ /**
632
+ * The identity of the atom specie(s) representing this atom type.
633
+ * Normally this code is the element symbol followed by the charge
634
+ * if there is one. The symbol may be composed of any character except
635
+ * an underline or a blank, with the proviso that digits designate an
636
+ * oxidation state and must be followed by a + or - character.
637
+ */
638
+ symbol: str,
639
+ },
640
+ /**
641
+ * The CATEGORY of data items used to describe atomic scattering
642
+ * information used in crystallographic structure studies.
643
+ */
644
+ atom_type_scat: {
645
+ /**
646
+ * The imaginary component of the anomalous dispersion scattering factors
647
+ * for this atom type and radiation by _diffrn_radiation_wavelength.value
648
+ */
649
+ dispersion_imag: float,
650
+ /**
651
+ * The real component of the anomalous dispersion scattering factors
652
+ * for this atom type and radiation by _diffrn_radiation_wavelength.value
653
+ */
654
+ dispersion_real: float,
655
+ /**
656
+ * Reference to source of scattering factors used for this atom type.
657
+ */
658
+ source: str,
659
+ },
660
+ };
661
+ exports.CifCore_Aliases = {
662
+ 'cell.formula_units_z': [
663
+ 'cell_formula_units_Z',
664
+ ],
665
+ 'space_group.it_number': [
666
+ 'space_group_IT_number',
667
+ 'symmetry_Int_Tables_number',
668
+ ],
669
+ 'space_group.name_h-m_full': [
670
+ 'symmetry_space_group_name_H-M',
671
+ ],
672
+ 'space_group_symop.operation_xyz': [
673
+ 'symmetry_equiv_pos_as_xyz',
674
+ ],
675
+ 'geom_bond.atom_site_label_1': [
676
+ 'geom_bond_atom_site_id_1',
677
+ ],
678
+ 'geom_bond.atom_site_label_2': [
679
+ 'geom_bond_atom_site_id_2',
680
+ ],
681
+ 'geom_bond.distance': [
682
+ 'geom_bond_dist',
683
+ ],
684
+ 'audit.block_doi': [
685
+ 'audit_block_DOI',
686
+ ],
687
+ 'database_code.cod': [
688
+ 'database_code_COD',
689
+ ],
690
+ 'database_code.csd': [
691
+ 'database_code_CSD',
692
+ ],
693
+ 'database_code.depnum_ccdc_archive': [
694
+ 'database_code_depnum_CCDC_archive',
695
+ ],
696
+ 'database_code.depnum_ccdc_fiz': [
697
+ 'database_code_depnum_CCDC_fiz',
698
+ ],
699
+ 'database_code.icsd': [
700
+ 'database_code_ICSD',
701
+ ],
702
+ 'database_code.mdf': [
703
+ 'database_code_MDF',
704
+ ],
705
+ 'database_code.nbs': [
706
+ 'database_code_NBS',
707
+ ],
708
+ 'atom_site.adp_type': [
709
+ 'atom_site_ADP_type',
710
+ 'atom_site_thermal_displace_type',
711
+ ],
712
+ 'atom_site.label': [
713
+ 'atom_site_id',
714
+ ],
715
+ 'atom_site.site_symmetry_multiplicity': [
716
+ 'atom_site_symmetry_multiplicity',
717
+ ],
718
+ 'atom_site.u_iso_or_equiv': [
719
+ 'atom_site_U_iso_or_equiv',
720
+ ],
721
+ 'atom_site_aniso.label': [
722
+ 'atom_site_anisotrop_id',
723
+ ],
724
+ 'atom_site_aniso.u_11': [
725
+ 'atom_site_aniso_U_11',
726
+ 'atom_site_anisotrop_U_11',
727
+ ],
728
+ 'atom_site_aniso.u_12': [
729
+ 'atom_site_aniso_U_12',
730
+ 'atom_site_anisotrop_U_12',
731
+ ],
732
+ 'atom_site_aniso.u_13': [
733
+ 'atom_site_aniso_U_13',
734
+ 'atom_site_anisotrop_U_13',
735
+ ],
736
+ 'atom_site_aniso.u_22': [
737
+ 'atom_site_aniso_U_22',
738
+ 'atom_site_anisotrop_U_22',
739
+ ],
740
+ 'atom_site_aniso.u_23': [
741
+ 'atom_site_aniso_U_23',
742
+ 'atom_site_anisotrop_U_23',
743
+ ],
744
+ 'atom_site_aniso.u_33': [
745
+ 'atom_site_aniso_U_33',
746
+ 'atom_site_anisotrop_U_33',
747
+ ],
748
+ };
749
+ ;
750
+ //# sourceMappingURL=cif-core.js.map