molstar 3.8.2 → 3.9.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (516) hide show
  1. package/build/viewer/index.html +4 -1
  2. package/build/viewer/molstar.js +1 -1
  3. package/lib/apps/viewer/app.d.ts +1 -1
  4. package/lib/apps/viewer/app.js +1 -1
  5. package/lib/apps/viewer/index.html +4 -1
  6. package/lib/cli/cif2bcif/converter.js +1 -1
  7. package/lib/commonjs/apps/viewer/app.d.ts +1 -1
  8. package/lib/commonjs/apps/viewer/app.js +2 -1
  9. package/lib/commonjs/cli/cif2bcif/converter.js +1 -1
  10. package/lib/commonjs/examples/alpha-orbitals/index.d.ts +1 -1
  11. package/lib/commonjs/examples/alpha-orbitals/index.js +4 -1
  12. package/lib/commonjs/examples/basic-wrapper/custom-theme.js +1 -1
  13. package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +3 -3
  14. package/lib/commonjs/extensions/alpha-orbitals/density.d.ts +1 -1
  15. package/lib/commonjs/extensions/alpha-orbitals/density.js +6 -2
  16. package/lib/commonjs/extensions/alpha-orbitals/orbitals.d.ts +1 -1
  17. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +6 -3
  18. package/lib/commonjs/extensions/anvil/algorithm.js +1 -1
  19. package/lib/commonjs/extensions/cellpack/color/generate.js +1 -1
  20. package/lib/commonjs/extensions/cellpack/color/provided.js +1 -1
  21. package/lib/commonjs/extensions/cellpack/state.js +1 -1
  22. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +1 -1
  23. package/lib/commonjs/extensions/g3d/model.js +1 -1
  24. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +1 -1
  25. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +1 -1
  26. package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +1 -1
  27. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +4 -4
  28. package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +1 -1
  29. package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +2 -2
  30. package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +1 -1
  31. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +2 -2
  32. package/lib/commonjs/mol-canvas3d/canvas3d.js +4 -0
  33. package/lib/commonjs/mol-canvas3d/controls/trackball.js +7 -7
  34. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +14 -14
  35. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +5 -5
  36. package/lib/commonjs/mol-canvas3d/passes/draw.js +34 -5
  37. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +5 -0
  38. package/lib/commonjs/mol-canvas3d/passes/marking.js +5 -0
  39. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +9 -0
  40. package/lib/commonjs/mol-canvas3d/passes/pick.d.ts +18 -5
  41. package/lib/commonjs/mol-canvas3d/passes/pick.js +125 -24
  42. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +5 -0
  43. package/lib/commonjs/mol-canvas3d/passes/smaa.js +4 -0
  44. package/lib/commonjs/mol-canvas3d/passes/wboit.js +4 -0
  45. package/lib/commonjs/mol-data/db/column.js +5 -5
  46. package/lib/commonjs/mol-data/db/table.js +2 -2
  47. package/lib/commonjs/mol-data/util/array.d.ts +1 -1
  48. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +13 -0
  49. package/lib/commonjs/mol-gl/compute/grid3d.d.ts +2 -2
  50. package/lib/commonjs/mol-gl/compute/grid3d.js +30 -8
  51. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.d.ts +1 -1
  52. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +6 -1
  53. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.d.ts +1 -1
  54. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +6 -1
  55. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.d.ts +1 -1
  56. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +6 -1
  57. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +1 -1
  58. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +10 -10
  59. package/lib/commonjs/mol-gl/renderer.js +77 -32
  60. package/lib/commonjs/mol-gl/scene.js +2 -0
  61. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  62. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  63. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  64. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  65. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  66. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  67. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  68. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  69. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +1 -1
  70. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +1 -1
  71. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  72. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  73. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +1 -1
  74. package/lib/commonjs/mol-gl/shader/image.frag.js +1 -1
  75. package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +1 -1
  76. package/lib/commonjs/mol-gl/shader/lines.frag.js +1 -1
  77. package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
  78. package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
  79. package/lib/commonjs/mol-gl/shader/points.frag.d.ts +1 -1
  80. package/lib/commonjs/mol-gl/shader/points.frag.js +1 -1
  81. package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +1 -1
  82. package/lib/commonjs/mol-gl/shader/spheres.frag.js +1 -1
  83. package/lib/commonjs/mol-gl/shader/text.frag.d.ts +1 -1
  84. package/lib/commonjs/mol-gl/shader/text.frag.js +1 -1
  85. package/lib/commonjs/mol-gl/shader-code.d.ts +1 -1
  86. package/lib/commonjs/mol-gl/shader-code.js +41 -9
  87. package/lib/commonjs/mol-gl/webgl/compat.d.ts +34 -1
  88. package/lib/commonjs/mol-gl/webgl/compat.js +50 -2
  89. package/lib/commonjs/mol-gl/webgl/context.d.ts +2 -0
  90. package/lib/commonjs/mol-gl/webgl/context.js +3 -0
  91. package/lib/commonjs/mol-gl/webgl/extensions.d.ts +3 -2
  92. package/lib/commonjs/mol-gl/webgl/extensions.js +6 -1
  93. package/lib/commonjs/mol-gl/webgl/timer.d.ts +22 -0
  94. package/lib/commonjs/mol-gl/webgl/timer.js +169 -0
  95. package/lib/commonjs/mol-io/common/binary-cif/array-encoder.js +18 -18
  96. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +16 -16
  97. package/lib/commonjs/mol-io/common/binary-cif/encoding.js +9 -9
  98. package/lib/commonjs/mol-io/reader/cif/binary/field.js +3 -3
  99. package/lib/commonjs/mol-io/reader/cif/data-model.js +14 -14
  100. package/lib/commonjs/mol-io/reader/cif/schema.js +1 -1
  101. package/lib/commonjs/mol-io/reader/cif/text/parser.js +23 -23
  102. package/lib/commonjs/mol-io/reader/common/text/column/fixed.js +1 -1
  103. package/lib/commonjs/mol-io/reader/common/text/column/token.js +1 -1
  104. package/lib/commonjs/mol-io/reader/common/text/number-parser.js +6 -6
  105. package/lib/commonjs/mol-io/reader/csv/parser.js +8 -8
  106. package/lib/commonjs/mol-io/writer/cif/encoder/binary.js +10 -10
  107. package/lib/commonjs/mol-io/writer/cif/encoder/text.js +7 -7
  108. package/lib/commonjs/mol-io/writer/cif/encoder.js +8 -8
  109. package/lib/commonjs/mol-io/writer/mol2/encoder.js +4 -4
  110. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +13 -2
  111. package/lib/commonjs/mol-model/sequence/alignment/sequence.js +3 -3
  112. package/lib/commonjs/mol-model/sequence/sequence.js +9 -9
  113. package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js +3 -3
  114. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  115. package/lib/commonjs/mol-model/structure/export/categories/utils.js +1 -1
  116. package/lib/commonjs/mol-model/structure/model/model.js +2 -2
  117. package/lib/commonjs/mol-model/structure/model/properties/custom/indexed.js +6 -6
  118. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js +1 -1
  119. package/lib/commonjs/mol-model/structure/model/types.js +116 -116
  120. package/lib/commonjs/mol-model/structure/query/context.js +1 -1
  121. package/lib/commonjs/mol-model/structure/query/queries/generators.js +5 -5
  122. package/lib/commonjs/mol-model/structure/query/queries/internal.js +4 -4
  123. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +4 -4
  124. package/lib/commonjs/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
  125. package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js +9 -9
  126. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +106 -106
  127. package/lib/commonjs/mol-model/structure/structure/element/loci.js +5 -5
  128. package/lib/commonjs/mol-model/structure/structure/element/stats.js +5 -5
  129. package/lib/commonjs/mol-model/structure/structure/properties.js +5 -5
  130. package/lib/commonjs/mol-model/structure/structure/structure.js +11 -11
  131. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +5 -5
  132. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +4 -4
  133. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +2 -2
  134. package/lib/commonjs/mol-model/structure/structure/unit/resonance.js +1 -1
  135. package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js +6 -6
  136. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +6 -6
  137. package/lib/commonjs/mol-model/structure/structure/unit.js +16 -16
  138. package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.js +1 -1
  139. package/lib/commonjs/mol-model/structure/util.js +4 -4
  140. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -2
  141. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +4 -4
  142. package/lib/commonjs/mol-model-formats/structure/basic/properties.js +1 -1
  143. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +1 -1
  144. package/lib/commonjs/mol-model-formats/structure/basic/util.js +1 -1
  145. package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
  146. package/lib/commonjs/mol-model-formats/structure/common/entity.js +1 -1
  147. package/lib/commonjs/mol-model-formats/structure/cube.js +1 -1
  148. package/lib/commonjs/mol-model-formats/structure/gro.js +1 -1
  149. package/lib/commonjs/mol-model-formats/structure/mol.js +1 -1
  150. package/lib/commonjs/mol-model-formats/structure/mol2.js +4 -4
  151. package/lib/commonjs/mol-model-formats/structure/prmtop.js +1 -1
  152. package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +3 -3
  153. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  154. package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +6 -6
  155. package/lib/commonjs/mol-model-formats/structure/property/secondary-structure.js +8 -8
  156. package/lib/commonjs/mol-model-formats/structure/psf.js +1 -1
  157. package/lib/commonjs/mol-model-formats/structure/top.js +1 -1
  158. package/lib/commonjs/mol-model-formats/structure/xyz.js +1 -1
  159. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +2 -2
  160. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +3 -3
  161. package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +2 -2
  162. package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js +31 -31
  163. package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js +22 -22
  164. package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +32 -32
  165. package/lib/commonjs/mol-model-props/computed/interactions/charged.js +39 -39
  166. package/lib/commonjs/mol-model-props/computed/interactions/common.js +34 -34
  167. package/lib/commonjs/mol-model-props/computed/interactions/contacts-builder.js +1 -1
  168. package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +1 -1
  169. package/lib/commonjs/mol-model-props/computed/interactions/halogen-bonds.js +12 -12
  170. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +32 -32
  171. package/lib/commonjs/mol-model-props/computed/interactions/hydrophobic.js +9 -9
  172. package/lib/commonjs/mol-model-props/computed/interactions/metal.js +26 -26
  173. package/lib/commonjs/mol-model-props/computed/interactions/refine.js +20 -20
  174. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +2 -2
  175. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +2 -2
  176. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bends.js +1 -1
  177. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bridges.js +12 -12
  178. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/helices.js +6 -6
  179. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/ladders.js +3 -3
  180. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/sheets.js +11 -11
  181. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/turns.js +3 -3
  182. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +30 -30
  183. package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js +1 -1
  184. package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js +10 -10
  185. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js +1 -1
  186. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js +3 -3
  187. package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js +1 -1
  188. package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +1 -1
  189. package/lib/commonjs/mol-plugin/animation-loop.d.ts +2 -1
  190. package/lib/commonjs/mol-plugin/animation-loop.js +18 -5
  191. package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +12 -12
  192. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +7 -7
  193. package/lib/commonjs/mol-plugin/context.d.ts +2 -2
  194. package/lib/commonjs/mol-plugin/state.d.ts +1 -14
  195. package/lib/commonjs/mol-plugin-state/formats/volume.d.ts +12 -11
  196. package/lib/commonjs/mol-plugin-state/formats/volume.js +20 -13
  197. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +5 -5
  198. package/lib/commonjs/mol-plugin-state/transforms/representation.js +2 -2
  199. package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts +1 -1
  200. package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +1 -1
  201. package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +1 -1
  202. package/lib/commonjs/mol-plugin-ui/structure/focus.js +1 -1
  203. package/lib/commonjs/mol-plugin-ui/viewport.d.ts +2 -2
  204. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +10 -10
  205. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +10 -10
  206. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +12 -12
  207. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +12 -12
  208. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +16 -16
  209. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +1 -1
  210. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -0
  211. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +4 -4
  212. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
  213. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +2 -2
  214. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +2 -2
  215. package/lib/commonjs/mol-repr/structure/visual/util/common.js +3 -3
  216. package/lib/commonjs/mol-repr/structure/visual/util/link.js +30 -30
  217. package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js +6 -6
  218. package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js +3 -3
  219. package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +20 -20
  220. package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +6 -6
  221. package/lib/commonjs/mol-script/language/symbol-table/core.d.ts +2 -2
  222. package/lib/commonjs/mol-script/runtime/query/table.js +13 -13
  223. package/lib/commonjs/mol-state/object.d.ts +3 -3
  224. package/lib/commonjs/mol-task/util/user-timing.js +1 -1
  225. package/lib/commonjs/mol-theme/clipping.js +19 -19
  226. package/lib/commonjs/mol-theme/color/atom-id.js +1 -1
  227. package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js +1 -1
  228. package/lib/commonjs/mol-theme/color/chain-id.js +4 -4
  229. package/lib/commonjs/mol-theme/color/element-index.js +1 -1
  230. package/lib/commonjs/mol-theme/color/element-symbol.js +1 -1
  231. package/lib/commonjs/mol-theme/color/entity-id.js +4 -4
  232. package/lib/commonjs/mol-theme/color/entity-source.js +5 -4
  233. package/lib/commonjs/mol-theme/color/hydrophobicity.js +1 -1
  234. package/lib/commonjs/mol-theme/color/illustrative.js +1 -1
  235. package/lib/commonjs/mol-theme/color/model-index.js +1 -1
  236. package/lib/commonjs/mol-theme/color/molecule-type.js +8 -8
  237. package/lib/commonjs/mol-theme/color/occupancy.js +1 -1
  238. package/lib/commonjs/mol-theme/color/operator-hkl.js +1 -1
  239. package/lib/commonjs/mol-theme/color/operator-name.js +1 -1
  240. package/lib/commonjs/mol-theme/color/partial-charge.js +1 -1
  241. package/lib/commonjs/mol-theme/color/polymer-id.js +4 -4
  242. package/lib/commonjs/mol-theme/color/polymer-index.js +1 -1
  243. package/lib/commonjs/mol-theme/color/residue-name.js +1 -1
  244. package/lib/commonjs/mol-theme/color/secondary-structure.js +12 -12
  245. package/lib/commonjs/mol-theme/color/sequence-id.js +7 -7
  246. package/lib/commonjs/mol-theme/color/shape-group.js +1 -1
  247. package/lib/commonjs/mol-theme/color/uncertainty.js +1 -1
  248. package/lib/commonjs/mol-theme/color/uniform.js +1 -1
  249. package/lib/commonjs/mol-theme/color/unit-index.js +1 -1
  250. package/lib/commonjs/mol-theme/color/volume-value.js +1 -1
  251. package/lib/commonjs/mol-theme/label.js +3 -3
  252. package/lib/commonjs/mol-util/binding.js +4 -4
  253. package/lib/commonjs/mol-util/debug.d.ts +6 -1
  254. package/lib/commonjs/mol-util/debug.js +11 -1
  255. package/lib/commonjs/mol-util/input/input-observer.js +20 -20
  256. package/lib/commonjs/mol-util/string-builder.js +1 -1
  257. package/lib/commonjs/servers/model/preprocess/converter.js +1 -1
  258. package/lib/commonjs/servers/model/server/query.js +1 -1
  259. package/lib/commonjs/servers/model/utils/fetch-retry.js +3 -2
  260. package/lib/commonjs/servers/volume/server/algebra/coordinate.js +6 -6
  261. package/lib/commonjs/servers/volume/server/query/encode.js +1 -1
  262. package/lib/examples/alpha-orbitals/index.d.ts +1 -1
  263. package/lib/examples/alpha-orbitals/index.html +11 -0
  264. package/lib/examples/alpha-orbitals/index.js +4 -1
  265. package/lib/examples/basic-wrapper/custom-theme.js +1 -1
  266. package/lib/examples/proteopedia-wrapper/coloring.js +3 -3
  267. package/lib/extensions/alpha-orbitals/density.d.ts +1 -1
  268. package/lib/extensions/alpha-orbitals/density.js +6 -2
  269. package/lib/extensions/alpha-orbitals/orbitals.d.ts +1 -1
  270. package/lib/extensions/alpha-orbitals/orbitals.js +6 -3
  271. package/lib/extensions/anvil/algorithm.js +1 -1
  272. package/lib/extensions/cellpack/color/generate.js +1 -1
  273. package/lib/extensions/cellpack/color/provided.js +1 -1
  274. package/lib/extensions/cellpack/state.js +1 -1
  275. package/lib/extensions/dnatco/confal-pyramids/color.js +1 -1
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@@ -30,23 +30,23 @@ var MinMaxDist;
30
30
  ctx.element.element = e;
31
31
  var d = Math.max(0, Vec3.distance(p, position(e, dV)) - eRadius - elementRadius(ctx));
32
32
  if (d < minDist)
33
- return 0 /* BelowMin */;
33
+ return 0 /* Result.BelowMin */;
34
34
  if (d < maxDist)
35
35
  withinRange = true;
36
36
  }
37
- return withinRange ? 1 /* WithinMax */ : 2 /* Miss */;
37
+ return withinRange ? 1 /* Result.WithinMax */ : 2 /* Result.Miss */;
38
38
  }
39
39
  function toPoint(ctx, s, point, radius, minDist, maxDist, elementRadius) {
40
40
  var units = s.units;
41
41
  var withinRange = false;
42
42
  for (var i = 0, _i = units.length; i < _i; i++) {
43
43
  var iu = inUnit(ctx, units[i], point, radius, minDist, maxDist, elementRadius);
44
- if (iu === 0 /* BelowMin */)
45
- return 0 /* BelowMin */;
46
- if (iu === 1 /* WithinMax */)
44
+ if (iu === 0 /* Result.BelowMin */)
45
+ return 0 /* Result.BelowMin */;
46
+ if (iu === 1 /* Result.WithinMax */)
47
47
  withinRange = true;
48
48
  }
49
- return withinRange ? 1 /* WithinMax */ : 2 /* Miss */;
49
+ return withinRange ? 1 /* Result.WithinMax */ : 2 /* Result.Miss */;
50
50
  }
51
51
  MinMaxDist.toPoint = toPoint;
52
52
  var distPivot = Vec3.zero();
@@ -64,9 +64,9 @@ var MinMaxDist;
64
64
  var e = elements[i_1];
65
65
  ctx.element.element = e;
66
66
  var tp = toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), minDist, maxDist, elementRadius);
67
- if (tp === 0 /* BelowMin */)
68
- return 0 /* BelowMin */;
69
- if (tp === 1 /* WithinMax */)
67
+ if (tp === 0 /* Result.BelowMin */)
68
+ return 0 /* Result.BelowMin */;
69
+ if (tp === 1 /* Result.WithinMax */)
70
70
  withinRange = true;
71
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  }
72
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  }
@@ -20,48 +20,48 @@ export var SaccharideColors = ColorMap({
20
20
  Secondary: 0xf1ece1
21
21
  });
22
22
  var SaccharideTypeNameMap = (_a = {},
23
- _a[0 /* Hexose */] = 'Hexose',
24
- _a[1 /* HexNAc */] = 'HexNAc',
25
- _a[2 /* Hexosamine */] = 'Hexosamine',
26
- _a[3 /* Hexuronate */] = 'Hexuronate',
27
- _a[4 /* Deoxyhexose */] = 'Deoxyhexose',
28
- _a[5 /* DeoxyhexNAc */] = 'DeoxyhexNAc',
29
- _a[6 /* DiDeoxyhexose */] = 'Di-deoxyhexose',
30
- _a[7 /* Pentose */] = 'Pentose',
31
- _a[8 /* Deoxynonulosonate */] = 'Deoxynonulosonate',
32
- _a[9 /* DiDeoxynonulosonate */] = 'Di-deoxynonulosonate',
33
- _a[10 /* Unknown */] = 'Unknown',
34
- _a[11 /* Assigned */] = 'Assigned',
23
+ _a[0 /* SaccharideType.Hexose */] = 'Hexose',
24
+ _a[1 /* SaccharideType.HexNAc */] = 'HexNAc',
25
+ _a[2 /* SaccharideType.Hexosamine */] = 'Hexosamine',
26
+ _a[3 /* SaccharideType.Hexuronate */] = 'Hexuronate',
27
+ _a[4 /* SaccharideType.Deoxyhexose */] = 'Deoxyhexose',
28
+ _a[5 /* SaccharideType.DeoxyhexNAc */] = 'DeoxyhexNAc',
29
+ _a[6 /* SaccharideType.DiDeoxyhexose */] = 'Di-deoxyhexose',
30
+ _a[7 /* SaccharideType.Pentose */] = 'Pentose',
31
+ _a[8 /* SaccharideType.Deoxynonulosonate */] = 'Deoxynonulosonate',
32
+ _a[9 /* SaccharideType.DiDeoxynonulosonate */] = 'Di-deoxynonulosonate',
33
+ _a[10 /* SaccharideType.Unknown */] = 'Unknown',
34
+ _a[11 /* SaccharideType.Assigned */] = 'Assigned',
35
35
  _a);
36
36
  export function getSaccharideName(type) {
37
37
  return SaccharideTypeNameMap[type];
38
38
  }
39
39
  var SaccharideTypeShapeMap = (_b = {},
40
- _b[0 /* Hexose */] = 0 /* FilledSphere */,
41
- _b[1 /* HexNAc */] = 1 /* FilledCube */,
42
- _b[2 /* Hexosamine */] = 2 /* CrossedCube */,
43
- _b[3 /* Hexuronate */] = 3 /* DividedDiamond */,
44
- _b[4 /* Deoxyhexose */] = 4 /* FilledCone */,
45
- _b[5 /* DeoxyhexNAc */] = 5 /* DevidedCone */,
46
- _b[6 /* DiDeoxyhexose */] = 6 /* FlatBox */,
47
- _b[7 /* Pentose */] = 7 /* FilledStar */,
48
- _b[8 /* Deoxynonulosonate */] = 8 /* FilledDiamond */,
49
- _b[9 /* DiDeoxynonulosonate */] = 9 /* FlatDiamond */,
50
- _b[10 /* Unknown */] = 10 /* FlatHexagon */,
51
- _b[11 /* Assigned */] = 11 /* Pentagon */,
40
+ _b[0 /* SaccharideType.Hexose */] = 0 /* SaccharideShape.FilledSphere */,
41
+ _b[1 /* SaccharideType.HexNAc */] = 1 /* SaccharideShape.FilledCube */,
42
+ _b[2 /* SaccharideType.Hexosamine */] = 2 /* SaccharideShape.CrossedCube */,
43
+ _b[3 /* SaccharideType.Hexuronate */] = 3 /* SaccharideShape.DividedDiamond */,
44
+ _b[4 /* SaccharideType.Deoxyhexose */] = 4 /* SaccharideShape.FilledCone */,
45
+ _b[5 /* SaccharideType.DeoxyhexNAc */] = 5 /* SaccharideShape.DevidedCone */,
46
+ _b[6 /* SaccharideType.DiDeoxyhexose */] = 6 /* SaccharideShape.FlatBox */,
47
+ _b[7 /* SaccharideType.Pentose */] = 7 /* SaccharideShape.FilledStar */,
48
+ _b[8 /* SaccharideType.Deoxynonulosonate */] = 8 /* SaccharideShape.FilledDiamond */,
49
+ _b[9 /* SaccharideType.DiDeoxynonulosonate */] = 9 /* SaccharideShape.FlatDiamond */,
50
+ _b[10 /* SaccharideType.Unknown */] = 10 /* SaccharideShape.FlatHexagon */,
51
+ _b[11 /* SaccharideType.Assigned */] = 11 /* SaccharideShape.Pentagon */,
52
52
  _b);
53
53
  export function getSaccharideShape(type, ringMemberCount) {
54
- if (type === 10 /* Unknown */) {
54
+ if (type === 10 /* SaccharideType.Unknown */) {
55
55
  if (ringMemberCount === 4)
56
- return 12 /* DiamondPrism */;
56
+ return 12 /* SaccharideShape.DiamondPrism */;
57
57
  else if (ringMemberCount === 5)
58
- return 13 /* PentagonalPrism */;
58
+ return 13 /* SaccharideShape.PentagonalPrism */;
59
59
  else if (ringMemberCount === 6)
60
- return 14 /* HexagonalPrism */;
60
+ return 14 /* SaccharideShape.HexagonalPrism */;
61
61
  else if (ringMemberCount === 7)
62
- return 15 /* HeptagonalPrism */;
62
+ return 15 /* SaccharideShape.HeptagonalPrism */;
63
63
  else
64
- return 10 /* FlatHexagon */;
64
+ return 10 /* SaccharideShape.FlatHexagon */;
65
65
  }
66
66
  else {
67
67
  return SaccharideTypeShapeMap[type];
@@ -71,84 +71,84 @@ export var UnknownSaccharideComponent = {
71
71
  abbr: 'Unk',
72
72
  name: 'Unknown',
73
73
  color: SaccharideColors.Secondary,
74
- type: 10 /* Unknown */
74
+ type: 10 /* SaccharideType.Unknown */
75
75
  };
76
76
  var Monosaccharides = [
77
- { abbr: 'Glc', name: 'Glucose', color: SaccharideColors.Blue, type: 0 /* Hexose */ },
78
- { abbr: 'Man', name: 'Mannose', color: SaccharideColors.Green, type: 0 /* Hexose */ },
79
- { abbr: 'Gal', name: 'Galactose', color: SaccharideColors.Yellow, type: 0 /* Hexose */ },
80
- { abbr: 'Gul', name: 'Gulose', color: SaccharideColors.Orange, type: 0 /* Hexose */ },
81
- { abbr: 'Alt', name: 'Altrose', color: SaccharideColors.Pink, type: 0 /* Hexose */ },
82
- { abbr: 'All', name: 'Allose', color: SaccharideColors.Purple, type: 0 /* Hexose */ },
83
- { abbr: 'Tal', name: 'Talose', color: SaccharideColors.LightBlue, type: 0 /* Hexose */ },
84
- { abbr: 'Ido', name: 'Idose', color: SaccharideColors.Brown, type: 0 /* Hexose */ },
85
- { abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: SaccharideColors.Blue, type: 1 /* HexNAc */ },
86
- { abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: SaccharideColors.Green, type: 1 /* HexNAc */ },
87
- { abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: SaccharideColors.Yellow, type: 1 /* HexNAc */ },
88
- { abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: SaccharideColors.Orange, type: 1 /* HexNAc */ },
89
- { abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: SaccharideColors.Pink, type: 1 /* HexNAc */ },
90
- { abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: SaccharideColors.Purple, type: 1 /* HexNAc */ },
91
- { abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: SaccharideColors.LightBlue, type: 1 /* HexNAc */ },
92
- { abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: SaccharideColors.Brown, type: 1 /* HexNAc */ },
93
- { abbr: 'GlcN', name: 'Glucosamine', color: SaccharideColors.Blue, type: 2 /* Hexosamine */ },
94
- { abbr: 'ManN', name: 'Mannosamine', color: SaccharideColors.Green, type: 2 /* Hexosamine */ },
95
- { abbr: 'GalN', name: 'Galactosamine', color: SaccharideColors.Yellow, type: 2 /* Hexosamine */ },
96
- { abbr: 'GulN', name: 'Gulosamine', color: SaccharideColors.Orange, type: 2 /* Hexosamine */ },
97
- { abbr: 'AltN', name: 'Altrosamine', color: SaccharideColors.Pink, type: 2 /* Hexosamine */ },
98
- { abbr: 'AllN', name: 'Allosamine', color: SaccharideColors.Purple, type: 2 /* Hexosamine */ },
99
- { abbr: 'TalN', name: 'Talosamine', color: SaccharideColors.LightBlue, type: 2 /* Hexosamine */ },
100
- { abbr: 'IdoN', name: 'Idosamine', color: SaccharideColors.Brown, type: 2 /* Hexosamine */ },
101
- { abbr: 'GlcA', name: 'Glucuronic Acid', color: SaccharideColors.Blue, type: 3 /* Hexuronate */ },
102
- { abbr: 'ManA', name: 'Mannuronic Acid', color: SaccharideColors.Green, type: 3 /* Hexuronate */ },
103
- { abbr: 'GalA', name: 'Galacturonic Acid', color: SaccharideColors.Yellow, type: 3 /* Hexuronate */ },
104
- { abbr: 'GulA', name: 'Guluronic Acid', color: SaccharideColors.Orange, type: 3 /* Hexuronate */ },
105
- { abbr: 'AltA', name: 'Altruronic Acid', color: SaccharideColors.Pink, type: 3 /* Hexuronate */ },
106
- { abbr: 'AllA', name: 'Alluronic Acid', color: SaccharideColors.Purple, type: 3 /* Hexuronate */ },
107
- { abbr: 'TalA', name: 'Taluronic Acid', color: SaccharideColors.LightBlue, type: 3 /* Hexuronate */ },
108
- { abbr: 'IdoA', name: 'Iduronic Acid', color: SaccharideColors.Brown, type: 3 /* Hexuronate */ },
109
- { abbr: 'Qui', name: 'Quinovose', color: SaccharideColors.Blue, type: 4 /* Deoxyhexose */ },
110
- { abbr: 'Rha', name: 'Rhamnose', color: SaccharideColors.Green, type: 4 /* Deoxyhexose */ },
111
- { abbr: '6dGul', name: '6-Deoxy Gulose', color: SaccharideColors.Orange, type: 4 /* Deoxyhexose */ },
112
- { abbr: '6dAlt', name: '6-Deoxy Altrose', color: SaccharideColors.Pink, type: 4 /* Deoxyhexose */ },
113
- { abbr: '6dTal', name: '6-Deoxy Talose', color: SaccharideColors.LightBlue, type: 4 /* Deoxyhexose */ },
114
- { abbr: 'Fuc', name: 'Fucose', color: SaccharideColors.Red, type: 4 /* Deoxyhexose */ },
115
- { abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: SaccharideColors.Blue, type: 5 /* DeoxyhexNAc */ },
116
- { abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: SaccharideColors.Green, type: 5 /* DeoxyhexNAc */ },
117
- { abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: SaccharideColors.Pink, type: 5 /* DeoxyhexNAc */ },
118
- { abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: SaccharideColors.LightBlue, type: 5 /* DeoxyhexNAc */ },
119
- { abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: SaccharideColors.Red, type: 5 /* DeoxyhexNAc */ },
120
- { abbr: 'Oli', name: 'Olivose', color: SaccharideColors.Blue, type: 6 /* DiDeoxyhexose */ },
121
- { abbr: 'Tyv', name: 'Tyvelose', color: SaccharideColors.Green, type: 6 /* DiDeoxyhexose */ },
122
- { abbr: 'Abe', name: 'Abequose', color: SaccharideColors.Orange, type: 6 /* DiDeoxyhexose */ },
123
- { abbr: 'Par', name: 'Paratose', color: SaccharideColors.Pink, type: 6 /* DiDeoxyhexose */ },
124
- { abbr: 'Dig', name: 'Digitoxose', color: SaccharideColors.Purple, type: 6 /* DiDeoxyhexose */ },
125
- { abbr: 'Col', name: 'Colitose', color: SaccharideColors.LightBlue, type: 6 /* DiDeoxyhexose */ },
126
- { abbr: 'Ara', name: 'Arabinose', color: SaccharideColors.Green, type: 7 /* Pentose */ },
127
- { abbr: 'Lyx', name: 'Lyxose', color: SaccharideColors.Yellow, type: 7 /* Pentose */ },
128
- { abbr: 'Xyl', name: 'Xylose', color: SaccharideColors.Orange, type: 7 /* Pentose */ },
129
- { abbr: 'Rib', name: 'Ribose', color: SaccharideColors.Pink, type: 7 /* Pentose */ },
130
- { abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: SaccharideColors.Green, type: 8 /* Deoxynonulosonate */ },
131
- { abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: SaccharideColors.Purple, type: 8 /* Deoxynonulosonate */ },
132
- { abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: SaccharideColors.LightBlue, type: 8 /* Deoxynonulosonate */ },
133
- { abbr: 'Neu', name: 'Neuraminic Acid', color: SaccharideColors.Brown, type: 8 /* Deoxynonulosonate */ },
134
- { abbr: 'Sia', name: 'Sialic acid', color: SaccharideColors.Red, type: 8 /* Deoxynonulosonate */ },
135
- { abbr: 'Pse', name: 'Pseudaminic Acid', color: SaccharideColors.Green, type: 9 /* DiDeoxynonulosonate */ },
136
- { abbr: 'Leg', name: 'Legionaminic Acid', color: SaccharideColors.Yellow, type: 9 /* DiDeoxynonulosonate */ },
137
- { abbr: 'Aci', name: 'Acinetaminic Acid', color: SaccharideColors.Pink, type: 9 /* DiDeoxynonulosonate */ },
138
- { abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: SaccharideColors.LightBlue, type: 9 /* DiDeoxynonulosonate */ },
139
- { abbr: 'Bac', name: 'Bacillosamine', color: SaccharideColors.Blue, type: 10 /* Unknown */ },
140
- { abbr: 'LDmanHep', name: 'L-Glycero-D-Manno Heptose', color: SaccharideColors.Green, type: 10 /* Unknown */ },
141
- { abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: SaccharideColors.Yellow, type: 10 /* Unknown */ },
142
- { abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: SaccharideColors.Orange, type: 10 /* Unknown */ },
143
- { abbr: 'DDmanHep', name: 'D-Glycero-D-Manno-Heptose', color: SaccharideColors.Pink, type: 10 /* Unknown */ },
144
- { abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: SaccharideColors.Purple, type: 10 /* Unknown */ },
145
- { abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: SaccharideColors.LightBlue, type: 10 /* Unknown */ },
146
- { abbr: 'Mur', name: 'Muramic Acid', color: SaccharideColors.Brown, type: 10 /* Unknown */ },
147
- { abbr: 'Api', name: 'Apicose', color: SaccharideColors.Green, type: 11 /* Assigned */ },
148
- { abbr: 'Fru', name: 'Fructose', color: SaccharideColors.Green, type: 11 /* Assigned */ },
149
- { abbr: 'Tag', name: 'Tagatose', color: SaccharideColors.Yellow, type: 11 /* Assigned */ },
150
- { abbr: 'Sor', name: 'Sorbose', color: SaccharideColors.Orange, type: 11 /* Assigned */ },
151
- { abbr: 'Psi', name: 'Psicose', color: SaccharideColors.Pink, type: 11 /* Assigned */ },
77
+ { abbr: 'Glc', name: 'Glucose', color: SaccharideColors.Blue, type: 0 /* SaccharideType.Hexose */ },
78
+ { abbr: 'Man', name: 'Mannose', color: SaccharideColors.Green, type: 0 /* SaccharideType.Hexose */ },
79
+ { abbr: 'Gal', name: 'Galactose', color: SaccharideColors.Yellow, type: 0 /* SaccharideType.Hexose */ },
80
+ { abbr: 'Gul', name: 'Gulose', color: SaccharideColors.Orange, type: 0 /* SaccharideType.Hexose */ },
81
+ { abbr: 'Alt', name: 'Altrose', color: SaccharideColors.Pink, type: 0 /* SaccharideType.Hexose */ },
82
+ { abbr: 'All', name: 'Allose', color: SaccharideColors.Purple, type: 0 /* SaccharideType.Hexose */ },
83
+ { abbr: 'Tal', name: 'Talose', color: SaccharideColors.LightBlue, type: 0 /* SaccharideType.Hexose */ },
84
+ { abbr: 'Ido', name: 'Idose', color: SaccharideColors.Brown, type: 0 /* SaccharideType.Hexose */ },
85
+ { abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: SaccharideColors.Blue, type: 1 /* SaccharideType.HexNAc */ },
86
+ { abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: SaccharideColors.Green, type: 1 /* SaccharideType.HexNAc */ },
87
+ { abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: SaccharideColors.Yellow, type: 1 /* SaccharideType.HexNAc */ },
88
+ { abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: SaccharideColors.Orange, type: 1 /* SaccharideType.HexNAc */ },
89
+ { abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: SaccharideColors.Pink, type: 1 /* SaccharideType.HexNAc */ },
90
+ { abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: SaccharideColors.Purple, type: 1 /* SaccharideType.HexNAc */ },
91
+ { abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: SaccharideColors.LightBlue, type: 1 /* SaccharideType.HexNAc */ },
92
+ { abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: SaccharideColors.Brown, type: 1 /* SaccharideType.HexNAc */ },
93
+ { abbr: 'GlcN', name: 'Glucosamine', color: SaccharideColors.Blue, type: 2 /* SaccharideType.Hexosamine */ },
94
+ { abbr: 'ManN', name: 'Mannosamine', color: SaccharideColors.Green, type: 2 /* SaccharideType.Hexosamine */ },
95
+ { abbr: 'GalN', name: 'Galactosamine', color: SaccharideColors.Yellow, type: 2 /* SaccharideType.Hexosamine */ },
96
+ { abbr: 'GulN', name: 'Gulosamine', color: SaccharideColors.Orange, type: 2 /* SaccharideType.Hexosamine */ },
97
+ { abbr: 'AltN', name: 'Altrosamine', color: SaccharideColors.Pink, type: 2 /* SaccharideType.Hexosamine */ },
98
+ { abbr: 'AllN', name: 'Allosamine', color: SaccharideColors.Purple, type: 2 /* SaccharideType.Hexosamine */ },
99
+ { abbr: 'TalN', name: 'Talosamine', color: SaccharideColors.LightBlue, type: 2 /* SaccharideType.Hexosamine */ },
100
+ { abbr: 'IdoN', name: 'Idosamine', color: SaccharideColors.Brown, type: 2 /* SaccharideType.Hexosamine */ },
101
+ { abbr: 'GlcA', name: 'Glucuronic Acid', color: SaccharideColors.Blue, type: 3 /* SaccharideType.Hexuronate */ },
102
+ { abbr: 'ManA', name: 'Mannuronic Acid', color: SaccharideColors.Green, type: 3 /* SaccharideType.Hexuronate */ },
103
+ { abbr: 'GalA', name: 'Galacturonic Acid', color: SaccharideColors.Yellow, type: 3 /* SaccharideType.Hexuronate */ },
104
+ { abbr: 'GulA', name: 'Guluronic Acid', color: SaccharideColors.Orange, type: 3 /* SaccharideType.Hexuronate */ },
105
+ { abbr: 'AltA', name: 'Altruronic Acid', color: SaccharideColors.Pink, type: 3 /* SaccharideType.Hexuronate */ },
106
+ { abbr: 'AllA', name: 'Alluronic Acid', color: SaccharideColors.Purple, type: 3 /* SaccharideType.Hexuronate */ },
107
+ { abbr: 'TalA', name: 'Taluronic Acid', color: SaccharideColors.LightBlue, type: 3 /* SaccharideType.Hexuronate */ },
108
+ { abbr: 'IdoA', name: 'Iduronic Acid', color: SaccharideColors.Brown, type: 3 /* SaccharideType.Hexuronate */ },
109
+ { abbr: 'Qui', name: 'Quinovose', color: SaccharideColors.Blue, type: 4 /* SaccharideType.Deoxyhexose */ },
110
+ { abbr: 'Rha', name: 'Rhamnose', color: SaccharideColors.Green, type: 4 /* SaccharideType.Deoxyhexose */ },
111
+ { abbr: '6dGul', name: '6-Deoxy Gulose', color: SaccharideColors.Orange, type: 4 /* SaccharideType.Deoxyhexose */ },
112
+ { abbr: '6dAlt', name: '6-Deoxy Altrose', color: SaccharideColors.Pink, type: 4 /* SaccharideType.Deoxyhexose */ },
113
+ { abbr: '6dTal', name: '6-Deoxy Talose', color: SaccharideColors.LightBlue, type: 4 /* SaccharideType.Deoxyhexose */ },
114
+ { abbr: 'Fuc', name: 'Fucose', color: SaccharideColors.Red, type: 4 /* SaccharideType.Deoxyhexose */ },
115
+ { abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: SaccharideColors.Blue, type: 5 /* SaccharideType.DeoxyhexNAc */ },
116
+ { abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: SaccharideColors.Green, type: 5 /* SaccharideType.DeoxyhexNAc */ },
117
+ { abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: SaccharideColors.Pink, type: 5 /* SaccharideType.DeoxyhexNAc */ },
118
+ { abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: SaccharideColors.LightBlue, type: 5 /* SaccharideType.DeoxyhexNAc */ },
119
+ { abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: SaccharideColors.Red, type: 5 /* SaccharideType.DeoxyhexNAc */ },
120
+ { abbr: 'Oli', name: 'Olivose', color: SaccharideColors.Blue, type: 6 /* SaccharideType.DiDeoxyhexose */ },
121
+ { abbr: 'Tyv', name: 'Tyvelose', color: SaccharideColors.Green, type: 6 /* SaccharideType.DiDeoxyhexose */ },
122
+ { abbr: 'Abe', name: 'Abequose', color: SaccharideColors.Orange, type: 6 /* SaccharideType.DiDeoxyhexose */ },
123
+ { abbr: 'Par', name: 'Paratose', color: SaccharideColors.Pink, type: 6 /* SaccharideType.DiDeoxyhexose */ },
124
+ { abbr: 'Dig', name: 'Digitoxose', color: SaccharideColors.Purple, type: 6 /* SaccharideType.DiDeoxyhexose */ },
125
+ { abbr: 'Col', name: 'Colitose', color: SaccharideColors.LightBlue, type: 6 /* SaccharideType.DiDeoxyhexose */ },
126
+ { abbr: 'Ara', name: 'Arabinose', color: SaccharideColors.Green, type: 7 /* SaccharideType.Pentose */ },
127
+ { abbr: 'Lyx', name: 'Lyxose', color: SaccharideColors.Yellow, type: 7 /* SaccharideType.Pentose */ },
128
+ { abbr: 'Xyl', name: 'Xylose', color: SaccharideColors.Orange, type: 7 /* SaccharideType.Pentose */ },
129
+ { abbr: 'Rib', name: 'Ribose', color: SaccharideColors.Pink, type: 7 /* SaccharideType.Pentose */ },
130
+ { abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: SaccharideColors.Green, type: 8 /* SaccharideType.Deoxynonulosonate */ },
131
+ { abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: SaccharideColors.Purple, type: 8 /* SaccharideType.Deoxynonulosonate */ },
132
+ { abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: SaccharideColors.LightBlue, type: 8 /* SaccharideType.Deoxynonulosonate */ },
133
+ { abbr: 'Neu', name: 'Neuraminic Acid', color: SaccharideColors.Brown, type: 8 /* SaccharideType.Deoxynonulosonate */ },
134
+ { abbr: 'Sia', name: 'Sialic acid', color: SaccharideColors.Red, type: 8 /* SaccharideType.Deoxynonulosonate */ },
135
+ { abbr: 'Pse', name: 'Pseudaminic Acid', color: SaccharideColors.Green, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
136
+ { abbr: 'Leg', name: 'Legionaminic Acid', color: SaccharideColors.Yellow, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
137
+ { abbr: 'Aci', name: 'Acinetaminic Acid', color: SaccharideColors.Pink, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
138
+ { abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: SaccharideColors.LightBlue, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
139
+ { abbr: 'Bac', name: 'Bacillosamine', color: SaccharideColors.Blue, type: 10 /* SaccharideType.Unknown */ },
140
+ { abbr: 'LDmanHep', name: 'L-Glycero-D-Manno Heptose', color: SaccharideColors.Green, type: 10 /* SaccharideType.Unknown */ },
141
+ { abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: SaccharideColors.Yellow, type: 10 /* SaccharideType.Unknown */ },
142
+ { abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: SaccharideColors.Orange, type: 10 /* SaccharideType.Unknown */ },
143
+ { abbr: 'DDmanHep', name: 'D-Glycero-D-Manno-Heptose', color: SaccharideColors.Pink, type: 10 /* SaccharideType.Unknown */ },
144
+ { abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: SaccharideColors.Purple, type: 10 /* SaccharideType.Unknown */ },
145
+ { abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: SaccharideColors.LightBlue, type: 10 /* SaccharideType.Unknown */ },
146
+ { abbr: 'Mur', name: 'Muramic Acid', color: SaccharideColors.Brown, type: 10 /* SaccharideType.Unknown */ },
147
+ { abbr: 'Api', name: 'Apicose', color: SaccharideColors.Green, type: 11 /* SaccharideType.Assigned */ },
148
+ { abbr: 'Fru', name: 'Fructose', color: SaccharideColors.Green, type: 11 /* SaccharideType.Assigned */ },
149
+ { abbr: 'Tag', name: 'Tagatose', color: SaccharideColors.Yellow, type: 11 /* SaccharideType.Assigned */ },
150
+ { abbr: 'Sor', name: 'Sorbose', color: SaccharideColors.Orange, type: 11 /* SaccharideType.Assigned */ },
151
+ { abbr: 'Psi', name: 'Psicose', color: SaccharideColors.Pink, type: 11 /* SaccharideType.Assigned */ },
152
152
  ];
153
153
  export var SaccharidesSnfgMap = (function () {
154
154
  var map = new Map();
@@ -278,7 +278,7 @@ export function Loci(structure, elements) {
278
278
  elements[elements.length] = lociElement;
279
279
  continue;
280
280
  }
281
- if (lociElement.unit.kind === 0 /* Atomic */) {
281
+ if (lociElement.unit.kind === 0 /* Unit.Kind.Atomic */) {
282
282
  var unitElements = lociElement.unit.elements;
283
283
  var h = lociElement.unit.model.atomicHierarchy;
284
284
  var label_alt_id = lociElement.unit.model.atomicHierarchy.atoms.label_alt_id;
@@ -322,9 +322,9 @@ export function Loci(structure, elements) {
322
322
  Loci.extendToWholeResidues = extendToWholeResidues;
323
323
  function getChainSegments(unit) {
324
324
  switch (unit.kind) {
325
- case 0 /* Atomic */: return unit.model.atomicHierarchy.chainAtomSegments;
326
- case 1 /* Spheres */: return unit.model.coarseHierarchy.spheres.chainElementSegments;
327
- case 2 /* Gaussians */: return unit.model.coarseHierarchy.gaussians.chainElementSegments;
325
+ case 0 /* Unit.Kind.Atomic */: return unit.model.atomicHierarchy.chainAtomSegments;
326
+ case 1 /* Unit.Kind.Spheres */: return unit.model.coarseHierarchy.spheres.chainElementSegments;
327
+ case 2 /* Unit.Kind.Gaussians */: return unit.model.coarseHierarchy.gaussians.chainElementSegments;
328
328
  }
329
329
  }
330
330
  function isWholeUnit(element) {
@@ -389,7 +389,7 @@ export function Loci(structure, elements) {
389
389
  var elements = [];
390
390
  for (var i = 0, len = loci.elements.length; i < len; i++) {
391
391
  var e = loci.elements[i];
392
- if (Unit.Traits.is(e.unit.traits, 2 /* Partitioned */)) {
392
+ if (Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */)) {
393
393
  var start = i;
394
394
  while (i < len && Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
395
395
  i++;
@@ -48,7 +48,7 @@ export var Stats;
48
48
  }
49
49
  }
50
50
  else if (size === 1) {
51
- if (Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
51
+ if (Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
52
52
  // handled in `handleUnitChainsSimple`
53
53
  return;
54
54
  }
@@ -133,7 +133,7 @@ export var Stats;
133
133
  if (size === 0)
134
134
  return;
135
135
  var elements = unit.elements;
136
- if (!Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
136
+ if (!Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
137
137
  if (size === elements.length) {
138
138
  stats.chainCount += 1;
139
139
  if (stats.chainCount === 1) {
@@ -207,7 +207,7 @@ export var Stats;
207
207
  if (size === 0)
208
208
  continue;
209
209
  var elements = unit.elements;
210
- if (!Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
210
+ if (!Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
211
211
  var eI = elements[OrderedSet.start(indices)];
212
212
  addCountHelper(chainCounts, index[eI], elements.length);
213
213
  continue;
@@ -275,7 +275,7 @@ export var Stats;
275
275
  for (var _i = 0, _b = loci.elements; _i < _b.length; _i++) {
276
276
  var e = _b[_i];
277
277
  handleElement(stats, loci.structure, e);
278
- if (!Unit.Traits.is(e.unit.traits, 2 /* Partitioned */)) {
278
+ if (!Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */)) {
279
279
  handleUnitChainsSimple(stats, loci.structure, e);
280
280
  }
281
281
  else {
@@ -286,7 +286,7 @@ export var Stats;
286
286
  if (hasPartitions) {
287
287
  for (var i = 0, len = loci.elements.length; i < len; i++) {
288
288
  var e = loci.elements[i];
289
- if (!Unit.Traits.is(e.unit.traits, 2 /* Partitioned */))
289
+ if (!Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */))
290
290
  continue;
291
291
  var start = i;
292
292
  while (i < len && Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
@@ -87,7 +87,7 @@ var residue = {
87
87
  if (!Unit.isAtomic(l.unit))
88
88
  notAtomic();
89
89
  var secStruc = (_a = SecondaryStructureProvider.get(l.structure).value) === null || _a === void 0 ? void 0 : _a.get(l.unit.invariantId);
90
- return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* NA */;
90
+ return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* SecondaryStructureType.Flag.NA */;
91
91
  }),
92
92
  secondary_structure_key: p(function (l) {
93
93
  var _a;
@@ -121,11 +121,11 @@ var coarse = {
121
121
  };
122
122
  function eK(l) {
123
123
  switch (l.unit.kind) {
124
- case 0 /* Atomic */:
124
+ case 0 /* Unit.Kind.Atomic */:
125
125
  return l.unit.model.atomicHierarchy.index.getEntityFromChain(l.unit.chainIndex[l.element]);
126
- case 1 /* Spheres */:
126
+ case 1 /* Unit.Kind.Spheres */:
127
127
  return l.unit.model.coarseHierarchy.spheres.entityKey[l.element];
128
- case 2 /* Gaussians */:
128
+ case 2 /* Unit.Kind.Gaussians */:
129
129
  return l.unit.model.coarseHierarchy.gaussians.entityKey[l.element];
130
130
  }
131
131
  }
@@ -148,7 +148,7 @@ var _emptyList = [];
148
148
  var unit = {
149
149
  id: p(function (l) { return l.unit.id; }),
150
150
  chainGroupId: p(function (l) { return l.unit.chainGroupId; }),
151
- multiChain: p(function (l) { return Unit.Traits.is(l.unit.traits, 1 /* MultiChain */); }),
151
+ multiChain: p(function (l) { return Unit.Traits.is(l.unit.traits, 1 /* Unit.Trait.MultiChain */); }),
152
152
  object_primitive: p(function (l) { return l.unit.objectPrimitive; }),
153
153
  operator_name: p(function (l) { return l.unit.conformation.operator.name; }),
154
154
  model_index: p(function (l) { return l.unit.model.modelNum; }),
@@ -595,7 +595,7 @@ function getEntityIndices(structure) {
595
595
  var keys = UniqueArray.create();
596
596
  for (var _a = 0, units_2 = units; _a < units_2.length; _a++) {
597
597
  var unit = units_2[_a];
598
- var prop = unit.kind === 0 /* Atomic */ ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
598
+ var prop = unit.kind === 0 /* Unit.Kind.Atomic */ ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
599
599
  l.unit = unit;
600
600
  var elements = unit.elements;
601
601
  var chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
@@ -921,20 +921,20 @@ function getSerialMapping(structure) {
921
921
  partitionAtomicUnitByResidue(model, elements, builder, multiChain, operator);
922
922
  }
923
923
  else {
924
- builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
924
+ builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, elements, multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */);
925
925
  }
926
926
  }
927
927
  else {
928
- builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
928
+ builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, elements, multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */);
929
929
  }
930
930
  }
931
931
  var cs = model.coarseHierarchy;
932
932
  if (cs.isDefined) {
933
933
  if (cs.spheres.count > 0) {
934
- addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Spheres */);
934
+ addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Unit.Kind.Spheres */);
935
935
  }
936
936
  if (cs.gaussians.count > 0) {
937
- addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Gaussians */);
937
+ addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Unit.Kind.Gaussians */);
938
938
  }
939
939
  }
940
940
  return builder.getStructure();
@@ -953,7 +953,7 @@ function getSerialMapping(structure) {
953
953
  var position = { x: x, y: y, z: z, indices: indices };
954
954
  var lookup = GridLookup3D(position, getBoundary(position), 8192);
955
955
  var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
956
- var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
956
+ var traits = (multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */) | (offset.length > 1 ? 2 /* Unit.Trait.Partitioned */ : 0 /* Unit.Trait.None */);
957
957
  builder.beginChainGroup();
958
958
  for (var i = 0, _i = offset.length; i < _i; i++) {
959
959
  var start = offset[i];
@@ -961,7 +961,7 @@ function getSerialMapping(structure) {
961
961
  for (var j = 0, _j = count[i]; j < _j; j++) {
962
962
  set[j] = indices[array[start + j]];
963
963
  }
964
- builder.addUnit(0 /* Atomic */, model, operator, SortedArray.ofSortedArray(set), traits);
964
+ builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, SortedArray.ofSortedArray(set), traits);
965
965
  }
966
966
  builder.endChainGroup();
967
967
  }
@@ -982,7 +982,7 @@ function getSerialMapping(structure) {
982
982
  var position = { x: x, y: y, z: z, indices: SortedArray.ofSortedArray(startIndices) };
983
983
  var lookup = GridLookup3D(position, getBoundary(position), gridCellCount);
984
984
  var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
985
- var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
985
+ var traits = (multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */) | (offset.length > 1 ? 2 /* Unit.Trait.Partitioned */ : 0 /* Unit.Trait.None */);
986
986
  builder.beginChainGroup();
987
987
  for (var i = 0, _i = offset.length; i < _i; i++) {
988
988
  var start = offset[i];
@@ -993,7 +993,7 @@ function getSerialMapping(structure) {
993
993
  set[set.length] = l;
994
994
  }
995
995
  }
996
- builder.addUnit(0 /* Atomic */, model, operator, SortedArray.ofSortedArray(new Int32Array(set)), traits);
996
+ builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, SortedArray.ofSortedArray(new Int32Array(set)), traits);
997
997
  }
998
998
  builder.endChainGroup();
999
999
  }
@@ -1001,7 +1001,7 @@ function getSerialMapping(structure) {
1001
1001
  var chainElementSegments = elements.chainElementSegments;
1002
1002
  for (var cI = 0; cI < chainElementSegments.count; cI++) {
1003
1003
  var elements_1 = SortedArray.ofBounds(chainElementSegments.offsets[cI], chainElementSegments.offsets[cI + 1]);
1004
- builder.addUnit(kind, model, SymmetryOperator.Default, elements_1, 0 /* None */);
1004
+ builder.addUnit(kind, model, SymmetryOperator.Default, elements_1, 0 /* Unit.Trait.None */);
1005
1005
  }
1006
1006
  }
1007
1007
  function transform(s, transform) {
@@ -1278,7 +1278,7 @@ function getSerialMapping(structure) {
1278
1278
  var l = StructureElement.Location.create(structure);
1279
1279
  for (var _b = 0, _c = structure.units; _b < _c.length; _b++) {
1280
1280
  var unit = _c[_b];
1281
- if (unit.kind !== 0 /* Atomic */)
1281
+ if (unit.kind !== 0 /* Unit.Kind.Atomic */)
1282
1282
  continue;
1283
1283
  l.unit = unit;
1284
1284
  var elements = unit.elements;
@@ -156,7 +156,7 @@ function findPairBonds(unitA, unitB, props, builder) {
156
156
  var compIdB = label_comp_idB.value(residueIndexB[bI]);
157
157
  builder.add(_aI, _bI, {
158
158
  order: getInterBondOrderFromTable(compIdA, compIdB, atomIdA, atomIdB),
159
- flag: (isMetal ? 2 /* MetallicCoordination */ : 1 /* Covalent */) | 32 /* Computed */
159
+ flag: (isMetal ? 2 /* BondType.Flag.MetallicCoordination */ : 1 /* BondType.Flag.Covalent */) | 32 /* BondType.Flag.Computed */
160
160
  });
161
161
  }
162
162
  }
@@ -185,10 +185,10 @@ function computeInterUnitBonds(structure, props) {
185
185
  return findBonds(structure, __assign(__assign({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
186
186
  var mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
187
187
  var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
188
- var notWater = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
189
- (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
190
- var notIon = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
191
- (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
188
+ var notWater = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* MoleculeType.Water */) &&
189
+ (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* MoleculeType.Water */));
190
+ var notIon = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* MoleculeType.Ion */) &&
191
+ (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* MoleculeType.Ion */));
192
192
  return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
193
193
  }) }));
194
194
  }
@@ -191,9 +191,9 @@ function findBonds(unit, props) {
191
191
  order[order.length] = e.order;
192
192
  var flag = e.flags;
193
193
  if (isMetal) {
194
- if (flag | 1 /* Covalent */)
195
- flag ^= 1 /* Covalent */;
196
- flag |= 2 /* MetallicCoordination */;
194
+ if (flag | 1 /* BondType.Flag.Covalent */)
195
+ flag ^= 1 /* BondType.Flag.Covalent */;
196
+ flag |= 2 /* BondType.Flag.MetallicCoordination */;
197
197
  }
198
198
  flags[flags.length] = flag;
199
199
  }
@@ -207,7 +207,7 @@ function findBonds(unit, props) {
207
207
  atomA[atomA.length] = _aI;
208
208
  atomB[atomB.length] = _bI;
209
209
  order[order.length] = getIntraBondOrderFromTable(compId, atomIdA, label_atom_id.value(bI));
210
- flags[flags.length] = (isMetal ? 2 /* MetallicCoordination */ : 1 /* Covalent */) | 32 /* Computed */;
210
+ flags[flags.length] = (isMetal ? 2 /* BondType.Flag.MetallicCoordination */ : 1 /* BondType.Flag.Covalent */) | 32 /* BondType.Flag.Computed */;
211
211
  var seqIdB = label_seq_id.value(rbI);
212
212
  if (seqIdA === seqIdB)
213
213
  isDictionaryBased = false;
@@ -125,14 +125,14 @@ var Bond;
125
125
  var bonds = location.aUnit.bonds;
126
126
  var idx = bonds.getEdgeIndex(location.aIndex, location.bIndex);
127
127
  if (idx < 0)
128
- return BondType.create(0 /* None */);
128
+ return BondType.create(0 /* BondType.Flag.None */);
129
129
  return BondType.create(bonds.edgeProps.flags[idx]);
130
130
  }
131
131
  else {
132
132
  var bond = structure.interUnitBonds.getBondFromLocation(location);
133
133
  if (bond)
134
134
  return BondType.create(bond.props.flag);
135
- return BondType.create(0 /* None */);
135
+ return BondType.create(0 /* BondType.Flag.None */);
136
136
  }
137
137
  }
138
138
  Bond.getType = getType;
@@ -37,7 +37,7 @@ function getDelocalizedTriplets(unit) {
37
37
  var deloBonds = [];
38
38
  for (var t = offset[i], _t = offset[i + 1]; t < _t; t++) {
39
39
  var f = _flags[t];
40
- if (!BondType.is(f, 16 /* Aromatic */))
40
+ if (!BondType.is(f, 16 /* BondType.Flag.Aromatic */))
41
41
  continue;
42
42
  deloBonds.push(b[t]);
43
43
  }
@@ -28,8 +28,8 @@ function State(unit, capacity) {
28
28
  queue: new Int32Array(capacity),
29
29
  pred: new Int32Array(capacity),
30
30
  depth: new Int32Array(capacity),
31
- left: new Int32Array(5 /* MaxDepth */),
32
- right: new Int32Array(5 /* MaxDepth */),
31
+ left: new Int32Array(5 /* Constants.MaxDepth */),
32
+ right: new Int32Array(5 /* Constants.MaxDepth */),
33
33
  color: new Int32Array(capacity),
34
34
  currentColor: 0,
35
35
  currentAltLoc: '',
@@ -132,7 +132,7 @@ function addRing(state, a, b, isRingAtom) {
132
132
  var pred = state.pred, color = state.color, left = state.left, right = state.right;
133
133
  var nc = ++state.currentColor;
134
134
  var current = a;
135
- for (var t = 0; t < 5 /* MaxDepth */; t++) {
135
+ for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
136
136
  color[current] = nc;
137
137
  current = pred[current];
138
138
  if (current < 0)
@@ -141,7 +141,7 @@ function addRing(state, a, b, isRingAtom) {
141
141
  var leftOffset = 0, rightOffset = 0;
142
142
  var found = false, target = 0;
143
143
  current = b;
144
- for (var t = 0; t < 5 /* MaxDepth */; t++) {
144
+ for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
145
145
  if (color[current] === nc) {
146
146
  target = current;
147
147
  found = true;
@@ -156,7 +156,7 @@ function addRing(state, a, b, isRingAtom) {
156
156
  return false;
157
157
  }
158
158
  current = a;
159
- for (var t = 0; t < 5 /* MaxDepth */; t++) {
159
+ for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
160
160
  left[leftOffset++] = current;
161
161
  if (target === current)
162
162
  break;
@@ -228,7 +228,7 @@ function findRings(state, from, mark) {
228
228
  continue;
229
229
  }
230
230
  var newDepth = Math.min(depth[other], d + 1);
231
- if (newDepth > 5 /* MaxDepth */)
231
+ if (newDepth > 5 /* Constants.MaxDepth */)
232
232
  continue;
233
233
  depth[other] = newDepth;
234
234
  marked[other] = mark;