molstar 3.3.1 → 3.6.0

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 (1114) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +202 -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/build/viewer/molstar.js.LICENSE.txt +12 -14
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/docking-viewer/index.js +1 -1
  9. package/lib/apps/docking-viewer/viewport.js +1 -1
  10. package/lib/apps/viewer/app.d.ts +7 -6
  11. package/lib/apps/viewer/app.js +3 -1
  12. package/lib/apps/viewer/embedded.html +43 -43
  13. package/lib/apps/viewer/index.html +106 -106
  14. package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  15. package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
  16. package/lib/cli/chem-comp-dict/util.d.ts +20 -20
  17. package/lib/cli/cif2bcif/converter.js +1 -1
  18. package/lib/cli/cif2bcif/index.js +4 -4
  19. package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
  20. package/lib/cli/cifschema/util/cif-dic.js +7 -5
  21. package/lib/cli/cifschema/util/generate.d.ts +1 -1
  22. package/lib/cli/cifschema/util/generate.js +12 -3
  23. package/lib/cli/cifschema/util/schema.d.ts +3 -3
  24. package/lib/cli/cifschema/util/schema.js +1 -1
  25. package/lib/commonjs/apps/docking-viewer/index.js +14 -14
  26. package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
  27. package/lib/commonjs/apps/viewer/app.d.ts +7 -6
  28. package/lib/commonjs/apps/viewer/app.js +26 -24
  29. package/lib/commonjs/apps/viewer/index.js +1 -1
  30. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
  31. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  32. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
  33. package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
  34. package/lib/commonjs/cli/chem-comp-dict/util.d.ts +20 -20
  35. package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
  36. package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
  37. package/lib/commonjs/cli/cif2bcif/index.js +12 -12
  38. package/lib/commonjs/cli/cifschema/index.js +27 -27
  39. package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
  40. package/lib/commonjs/cli/cifschema/util/cif-dic.js +8 -6
  41. package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
  42. package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
  43. package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
  44. package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
  45. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  46. package/lib/commonjs/cli/state-docs/index.js +2 -2
  47. package/lib/commonjs/cli/structure-info/helpers.js +11 -11
  48. package/lib/commonjs/cli/structure-info/model.js +15 -15
  49. package/lib/commonjs/cli/structure-info/volume.js +9 -9
  50. package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
  51. package/lib/commonjs/examples/alpha-orbitals/index.js +12 -12
  52. package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
  53. package/lib/commonjs/examples/basic-wrapper/index.js +23 -23
  54. package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
  55. package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
  56. package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
  57. package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
  58. package/lib/commonjs/examples/lighting/index.js +7 -7
  59. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
  60. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
  61. package/lib/commonjs/examples/proteopedia-wrapper/index.js +27 -27
  62. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
  63. package/lib/commonjs/examples/task.js +15 -15
  64. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
  65. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
  66. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
  67. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
  68. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
  69. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
  70. package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
  71. package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
  72. package/lib/commonjs/extensions/anvil/behavior.js +14 -14
  73. package/lib/commonjs/extensions/anvil/prop.js +7 -7
  74. package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
  75. package/lib/commonjs/extensions/anvil/representation.js +5 -5
  76. package/lib/commonjs/extensions/cellpack/index.js +1 -1
  77. package/lib/commonjs/extensions/cellpack/model.js +26 -24
  78. package/lib/commonjs/extensions/cellpack/preset.js +6 -6
  79. package/lib/commonjs/extensions/cellpack/property.js +3 -3
  80. package/lib/commonjs/extensions/cellpack/representation.d.ts +1 -0
  81. package/lib/commonjs/extensions/cellpack/representation.js +2 -2
  82. package/lib/commonjs/extensions/cellpack/state.js +13 -13
  83. package/lib/commonjs/extensions/cellpack/util.js +14 -14
  84. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
  85. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  86. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
  87. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
  88. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  89. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
  90. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
  91. package/lib/commonjs/extensions/g3d/data.js +6 -6
  92. package/lib/commonjs/extensions/g3d/format.js +14 -14
  93. package/lib/commonjs/extensions/g3d/model.js +4 -4
  94. package/lib/commonjs/extensions/geo-export/controls.js +3 -3
  95. package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
  96. package/lib/commonjs/extensions/geo-export/index.js +1 -1
  97. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
  98. package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
  99. package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
  100. package/lib/commonjs/extensions/geo-export/ui.js +7 -7
  101. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
  102. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
  103. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
  104. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
  105. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
  106. package/lib/commonjs/extensions/model-export/export.js +4 -4
  107. package/lib/commonjs/extensions/model-export/index.js +1 -1
  108. package/lib/commonjs/extensions/model-export/ui.js +5 -5
  109. package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
  110. package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
  111. package/lib/commonjs/extensions/mp4-export/index.js +1 -1
  112. package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
  113. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
  114. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
  115. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
  116. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
  117. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
  118. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
  119. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
  120. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
  121. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
  122. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
  123. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
  124. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
  125. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
  126. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
  127. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
  128. package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
  129. package/lib/commonjs/extensions/zenodo/index.js +35 -0
  130. package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
  131. package/lib/commonjs/extensions/zenodo/ui.js +306 -0
  132. package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
  133. package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
  134. package/lib/commonjs/mol-canvas3d/camera.js +2 -1
  135. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +2 -0
  136. package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
  137. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  138. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
  139. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  140. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
  141. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  142. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
  143. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  144. package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
  145. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
  146. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  147. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
  148. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
  149. package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
  150. package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
  151. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
  152. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
  153. package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
  154. package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
  155. package/lib/commonjs/mol-canvas3d/util.js +2 -2
  156. package/lib/commonjs/mol-data/db/column.d.ts +10 -3
  157. package/lib/commonjs/mol-data/db/column.js +40 -18
  158. package/lib/commonjs/mol-data/db/table.js +1 -1
  159. package/lib/commonjs/mol-data/db.js +1 -1
  160. package/lib/commonjs/mol-data/generic.js +3 -3
  161. package/lib/commonjs/mol-data/index.js +4 -4
  162. package/lib/commonjs/mol-data/int/interval.js +1 -1
  163. package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
  164. package/lib/commonjs/mol-data/int/segmentation.js +1 -1
  165. package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
  166. package/lib/commonjs/mol-data/util.js +7 -7
  167. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
  168. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -4
  169. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
  170. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
  171. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
  172. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  173. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
  174. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  175. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  176. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  177. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +4 -4
  178. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  179. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
  180. package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
  181. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -1
  182. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +4 -4
  183. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
  184. package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
  185. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
  186. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  187. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
  188. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
  189. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -4
  190. package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
  191. package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
  192. package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
  193. package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
  194. package/lib/commonjs/mol-geo/primitive/star.js +1 -1
  195. package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
  196. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
  197. package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
  198. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
  199. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
  200. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
  201. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  202. package/lib/commonjs/mol-gl/compute/util.js +3 -3
  203. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  204. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  205. package/lib/commonjs/mol-gl/renderable/image.js +3 -3
  206. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  207. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  208. package/lib/commonjs/mol-gl/renderable/points.js +3 -3
  209. package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
  210. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  211. package/lib/commonjs/mol-gl/renderable/text.js +3 -3
  212. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  213. package/lib/commonjs/mol-gl/renderable/util.js +1 -1
  214. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
  215. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
  216. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  217. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  218. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
  219. package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
  220. package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
  221. package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
  222. package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
  223. package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
  224. package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
  225. package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
  226. package/lib/commonjs/mol-gl/shader-code.js +2 -1
  227. package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
  228. package/lib/commonjs/mol-gl/webgl/buffer.js +16 -17
  229. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  230. package/lib/commonjs/mol-gl/webgl/context.js +5 -5
  231. package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
  232. package/lib/commonjs/mol-gl/webgl/program.js +10 -4
  233. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
  234. package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
  235. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
  236. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
  237. package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
  238. package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
  239. package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
  240. package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
  241. package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
  242. package/lib/commonjs/mol-io/common/typed-array.js +2 -2
  243. package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
  244. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
  245. package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
  246. package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +8 -8
  247. package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
  248. package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
  249. package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
  250. package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
  251. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
  252. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +4 -4
  253. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +31 -27
  254. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
  255. package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
  256. package/lib/commonjs/mol-io/reader/cif/schema.js +24 -4
  257. package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
  258. package/lib/commonjs/mol-io/reader/cif.js +1 -1
  259. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
  260. package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
  261. package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
  262. package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
  263. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
  264. package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
  265. package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
  266. package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
  267. package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
  268. package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
  269. package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
  270. package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
  271. package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
  272. package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
  273. package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
  274. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
  275. package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
  276. package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
  277. package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
  278. package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
  279. package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
  280. package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
  281. package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
  282. package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
  283. package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
  284. package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
  285. package/lib/commonjs/mol-io/writer/cif.js +1 -1
  286. package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
  287. package/lib/commonjs/mol-io/writer/mol/encoder.js +2 -2
  288. package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
  289. package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
  290. package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
  291. package/lib/commonjs/mol-math/geometry/common.js +1 -1
  292. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  293. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
  294. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  295. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
  296. package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
  297. package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
  298. package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
  299. package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
  300. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
  301. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
  302. package/lib/commonjs/mol-math/geometry.js +8 -8
  303. package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
  304. package/lib/commonjs/mol-math/graph.js +1 -1
  305. package/lib/commonjs/mol-math/linear-algebra.js +2 -2
  306. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
  307. package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
  308. package/lib/commonjs/mol-model/sequence.js +1 -1
  309. package/lib/commonjs/mol-model/shape.js +1 -1
  310. package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
  311. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  312. package/lib/commonjs/mol-model/structure/model/model.js +17 -9
  313. package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
  314. package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
  315. package/lib/commonjs/mol-model/structure/model/properties/common.js +1 -1
  316. package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
  317. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
  318. package/lib/commonjs/mol-model/structure/model/types.d.ts +19 -17
  319. package/lib/commonjs/mol-model/structure/model/types.js +30 -31
  320. package/lib/commonjs/mol-model/structure/model.js +3 -3
  321. package/lib/commonjs/mol-model/structure/query/queries/generators.js +3 -3
  322. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
  323. package/lib/commonjs/mol-model/structure/query.js +6 -6
  324. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
  325. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  326. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  327. package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
  328. package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
  329. package/lib/commonjs/mol-model/structure/structure/properties.d.ts +1 -1
  330. package/lib/commonjs/mol-model/structure/structure/structure.js +5 -5
  331. package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
  332. package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
  333. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +5 -7
  334. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +2 -4
  335. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
  336. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +3 -0
  337. package/lib/commonjs/mol-model/structure/structure/unit.js +4 -4
  338. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
  339. package/lib/commonjs/mol-model/structure/structure.js +2 -2
  340. package/lib/commonjs/mol-model/structure/topology.js +1 -1
  341. package/lib/commonjs/mol-model/structure.js +6 -6
  342. package/lib/commonjs/mol-model/volume.js +2 -2
  343. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +2 -0
  344. package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
  345. package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  346. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
  347. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
  348. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +2 -2
  349. package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
  350. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
  351. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +4 -4
  352. package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -2
  353. package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -2
  354. package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
  355. package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -2
  356. package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
  357. package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +3 -3
  358. package/lib/commonjs/mol-model-formats/structure/common/component.js +51 -47
  359. package/lib/commonjs/mol-model-formats/structure/cube.js +5 -5
  360. package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -2
  361. package/lib/commonjs/mol-model-formats/structure/gro.js +5 -3
  362. package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
  363. package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -2
  364. package/lib/commonjs/mol-model-formats/structure/mol.js +5 -5
  365. package/lib/commonjs/mol-model-formats/structure/mol2.js +6 -6
  366. package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts +9 -0
  367. package/lib/commonjs/mol-model-formats/structure/nctraj.js +60 -0
  368. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.d.ts +2 -2
  369. package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js +72 -7
  370. package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js +11 -11
  371. package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +9 -4
  372. package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
  373. package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -5
  374. package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts +16 -0
  375. package/lib/commonjs/mol-model-formats/structure/prmtop.js +147 -0
  376. package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
  377. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
  378. package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
  379. package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -1
  380. package/lib/commonjs/mol-model-formats/structure/psf.js +5 -3
  381. package/lib/commonjs/mol-model-formats/structure/top.d.ts +16 -0
  382. package/lib/commonjs/mol-model-formats/structure/top.js +189 -0
  383. package/lib/commonjs/mol-model-formats/structure/trr.d.ts +9 -0
  384. package/lib/commonjs/mol-model-formats/structure/trr.js +46 -0
  385. package/lib/commonjs/mol-model-formats/structure/util.d.ts +2 -2
  386. package/lib/commonjs/mol-model-formats/structure/util.js +19 -20
  387. package/lib/commonjs/mol-model-formats/structure/xtc.js +2 -2
  388. package/lib/commonjs/mol-model-formats/structure/xyz.js +2 -2
  389. package/lib/commonjs/mol-model-formats/volume/ccp4.js +2 -2
  390. package/lib/commonjs/mol-model-formats/volume/cube.js +2 -2
  391. package/lib/commonjs/mol-model-formats/volume/density-server.js +2 -2
  392. package/lib/commonjs/mol-model-formats/volume/dsn6.js +2 -2
  393. package/lib/commonjs/mol-model-formats/volume/dx.js +2 -2
  394. package/lib/commonjs/mol-model-props/common/custom-element-property.js +2 -2
  395. package/lib/commonjs/mol-model-props/common/custom-model-property.js +5 -5
  396. package/lib/commonjs/mol-model-props/common/custom-property.js +1 -1
  397. package/lib/commonjs/mol-model-props/common/custom-structure-property.js +6 -6
  398. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +2 -2
  399. package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +5 -5
  400. package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +4 -4
  401. package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +3 -3
  402. package/lib/commonjs/mol-model-props/computed/helix-orientation.js +2 -2
  403. package/lib/commonjs/mol-model-props/computed/interactions/common.js +1 -1
  404. package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +1 -1
  405. package/lib/commonjs/mol-model-props/computed/interactions/features.js +1 -1
  406. package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +3 -3
  407. package/lib/commonjs/mol-model-props/computed/interactions/interactions.js +3 -3
  408. package/lib/commonjs/mol-model-props/computed/interactions.js +4 -4
  409. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  410. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +1 -1
  411. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  412. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +3 -3
  413. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +3 -0
  414. package/lib/commonjs/mol-model-props/computed/representations/interactions.js +1 -1
  415. package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +2 -2
  416. package/lib/commonjs/mol-model-props/computed/secondary-structure.js +7 -7
  417. package/lib/commonjs/mol-model-props/computed/valence-model.js +4 -4
  418. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/property.js +2 -2
  419. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  420. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js +2 -2
  421. package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js +2 -2
  422. package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +3 -3
  423. package/lib/commonjs/mol-plugin/animation-loop.js +2 -2
  424. package/lib/commonjs/mol-plugin/behavior/behavior.js +5 -5
  425. package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +2 -2
  426. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.js +1 -1
  427. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/interactions.js +1 -1
  428. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/secondary-structure.js +1 -1
  429. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/valence-model.js +1 -1
  430. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.js +1 -1
  431. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/sifts-mapping.js +1 -1
  432. package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/structure-info.js +2 -2
  433. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +3 -3
  434. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +11 -11
  435. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.js +12 -12
  436. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  437. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.js +1 -1
  438. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.js +16 -16
  439. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +13 -12
  440. package/lib/commonjs/mol-plugin/behavior/static/state.js +6 -6
  441. package/lib/commonjs/mol-plugin/behavior.js +8 -8
  442. package/lib/commonjs/mol-plugin/command.js +2 -2
  443. package/lib/commonjs/mol-plugin/commands.d.ts +1 -0
  444. package/lib/commonjs/mol-plugin/context.d.ts +2 -1
  445. package/lib/commonjs/mol-plugin/context.js +9 -8
  446. package/lib/commonjs/mol-plugin/layout.js +2 -2
  447. package/lib/commonjs/mol-plugin/spec.js +1 -1
  448. package/lib/commonjs/mol-plugin/state.js +5 -5
  449. package/lib/commonjs/mol-plugin/util/task-manager.js +4 -4
  450. package/lib/commonjs/mol-plugin/util/toast.js +1 -1
  451. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +3 -0
  452. package/lib/commonjs/mol-plugin/util/viewport-screenshot.js +17 -17
  453. package/lib/commonjs/mol-plugin-state/actions/file.d.ts +1 -1
  454. package/lib/commonjs/mol-plugin-state/actions/file.js +94 -61
  455. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +17 -8
  456. package/lib/commonjs/mol-plugin-state/actions/structure.js +190 -20
  457. package/lib/commonjs/mol-plugin-state/actions/volume.js +5 -4
  458. package/lib/commonjs/mol-plugin-state/actions.js +3 -3
  459. package/lib/commonjs/mol-plugin-state/animation/built-in/assembly-unwind.js +2 -2
  460. package/lib/commonjs/mol-plugin-state/animation/built-in/camera-rock.js +3 -3
  461. package/lib/commonjs/mol-plugin-state/animation/built-in/camera-spin.js +3 -3
  462. package/lib/commonjs/mol-plugin-state/animation/built-in/explode-units.js +4 -4
  463. package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.js +2 -2
  464. package/lib/commonjs/mol-plugin-state/animation/built-in/spin-structure.js +5 -5
  465. package/lib/commonjs/mol-plugin-state/animation/built-in/state-interpolation.js +2 -2
  466. package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js +5 -5
  467. package/lib/commonjs/mol-plugin-state/builder/data.js +2 -2
  468. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +16 -16
  469. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +28 -28
  470. package/lib/commonjs/mol-plugin-state/builder/structure/representation.js +2 -2
  471. package/lib/commonjs/mol-plugin-state/builder/structure.js +7 -7
  472. package/lib/commonjs/mol-plugin-state/component.js +1 -1
  473. package/lib/commonjs/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
  474. package/lib/commonjs/mol-plugin-state/formats/coordinates.js +70 -0
  475. package/lib/commonjs/mol-plugin-state/formats/registry.d.ts +3 -3
  476. package/lib/commonjs/mol-plugin-state/formats/registry.js +13 -8
  477. package/lib/commonjs/mol-plugin-state/formats/shape.js +2 -2
  478. package/lib/commonjs/mol-plugin-state/formats/topology.d.ts +73 -0
  479. package/lib/commonjs/mol-plugin-state/formats/topology.js +87 -0
  480. package/lib/commonjs/mol-plugin-state/formats/trajectory.js +6 -6
  481. package/lib/commonjs/mol-plugin-state/formats/volume.js +21 -21
  482. package/lib/commonjs/mol-plugin-state/helpers/root-structure.js +14 -14
  483. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +7 -7
  484. package/lib/commonjs/mol-plugin-state/helpers/structure-component.js +2 -1
  485. package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js +11 -11
  486. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
  487. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +4 -4
  488. package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js +11 -11
  489. package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js +11 -11
  490. package/lib/commonjs/mol-plugin-state/manager/animation.js +17 -17
  491. package/lib/commonjs/mol-plugin-state/manager/camera.js +1 -1
  492. package/lib/commonjs/mol-plugin-state/manager/interactivity.js +6 -6
  493. package/lib/commonjs/mol-plugin-state/manager/snapshots.js +14 -14
  494. package/lib/commonjs/mol-plugin-state/manager/structure/component.js +26 -26
  495. package/lib/commonjs/mol-plugin-state/manager/structure/focus.js +2 -2
  496. package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js +1 -1
  497. package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.js +8 -8
  498. package/lib/commonjs/mol-plugin-state/manager/structure/measurement.js +21 -21
  499. package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +3 -3
  500. package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy.js +1 -1
  501. package/lib/commonjs/mol-plugin-state/objects.d.ts +47 -1
  502. package/lib/commonjs/mol-plugin-state/objects.js +46 -30
  503. package/lib/commonjs/mol-plugin-state/transforms/data.d.ts +6 -0
  504. package/lib/commonjs/mol-plugin-state/transforms/data.js +93 -41
  505. package/lib/commonjs/mol-plugin-state/transforms/model.d.ts +14 -2
  506. package/lib/commonjs/mol-plugin-state/transforms/model.js +163 -54
  507. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +6 -0
  508. package/lib/commonjs/mol-plugin-state/transforms/representation.js +77 -77
  509. package/lib/commonjs/mol-plugin-state/transforms/shape.js +2 -2
  510. package/lib/commonjs/mol-plugin-state/transforms/volume.js +16 -16
  511. package/lib/commonjs/mol-plugin-state/transforms.js +6 -6
  512. package/lib/commonjs/mol-plugin-ui/base.js +5 -5
  513. package/lib/commonjs/mol-plugin-ui/context.js +1 -1
  514. package/lib/commonjs/mol-plugin-ui/controls/action-menu.js +14 -14
  515. package/lib/commonjs/mol-plugin-ui/controls/color.js +7 -7
  516. package/lib/commonjs/mol-plugin-ui/controls/common.js +16 -16
  517. package/lib/commonjs/mol-plugin-ui/controls/icons.js +70 -70
  518. package/lib/commonjs/mol-plugin-ui/controls/legend.js +7 -7
  519. package/lib/commonjs/mol-plugin-ui/controls/line-graph/line-graph-component.js +3 -3
  520. package/lib/commonjs/mol-plugin-ui/controls/line-graph/point-component.js +2 -2
  521. package/lib/commonjs/mol-plugin-ui/controls/parameters.js +94 -94
  522. package/lib/commonjs/mol-plugin-ui/controls/screenshot.js +5 -5
  523. package/lib/commonjs/mol-plugin-ui/controls/slider.js +16 -16
  524. package/lib/commonjs/mol-plugin-ui/controls.js +16 -16
  525. package/lib/commonjs/mol-plugin-ui/custom/volume.js +16 -16
  526. package/lib/commonjs/mol-plugin-ui/index.js +4 -4
  527. package/lib/commonjs/mol-plugin-ui/left-panel.d.ts +8 -1
  528. package/lib/commonjs/mol-plugin-ui/left-panel.js +40 -19
  529. package/lib/commonjs/mol-plugin-ui/plugin.js +17 -17
  530. package/lib/commonjs/mol-plugin-ui/react18.d.ts +11 -0
  531. package/lib/commonjs/mol-plugin-ui/react18.js +38 -0
  532. package/lib/commonjs/mol-plugin-ui/sequence/chain.js +1 -1
  533. package/lib/commonjs/mol-plugin-ui/sequence/element.js +1 -1
  534. package/lib/commonjs/mol-plugin-ui/sequence/hetero.js +1 -1
  535. package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +1 -1
  536. package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +6 -6
  537. package/lib/commonjs/mol-plugin-ui/sequence.js +9 -9
  538. package/lib/commonjs/mol-plugin-ui/spec.js +1 -1
  539. package/lib/commonjs/mol-plugin-ui/state/actions.js +2 -2
  540. package/lib/commonjs/mol-plugin-ui/state/animation.js +2 -2
  541. package/lib/commonjs/mol-plugin-ui/state/apply-action.js +1 -1
  542. package/lib/commonjs/mol-plugin-ui/state/common.js +12 -12
  543. package/lib/commonjs/mol-plugin-ui/state/snapshots.js +29 -29
  544. package/lib/commonjs/mol-plugin-ui/state/tree.js +19 -19
  545. package/lib/commonjs/mol-plugin-ui/state/update-transform.js +3 -3
  546. package/lib/commonjs/mol-plugin-ui/structure/components.js +19 -19
  547. package/lib/commonjs/mol-plugin-ui/structure/focus.d.ts +1 -1
  548. package/lib/commonjs/mol-plugin-ui/structure/focus.js +6 -6
  549. package/lib/commonjs/mol-plugin-ui/structure/generic.js +6 -6
  550. package/lib/commonjs/mol-plugin-ui/structure/measurements.js +13 -13
  551. package/lib/commonjs/mol-plugin-ui/structure/quick-styles.js +11 -11
  552. package/lib/commonjs/mol-plugin-ui/structure/selection.js +13 -13
  553. package/lib/commonjs/mol-plugin-ui/structure/source.js +12 -12
  554. package/lib/commonjs/mol-plugin-ui/structure/superposition.js +20 -20
  555. package/lib/commonjs/mol-plugin-ui/structure/volume.js +12 -12
  556. package/lib/commonjs/mol-plugin-ui/task.js +8 -8
  557. package/lib/commonjs/mol-plugin-ui/toast.js +6 -6
  558. package/lib/commonjs/mol-plugin-ui/viewport/canvas.js +5 -5
  559. package/lib/commonjs/mol-plugin-ui/viewport/help.js +14 -14
  560. package/lib/commonjs/mol-plugin-ui/viewport/screenshot.js +8 -8
  561. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +6 -6
  562. package/lib/commonjs/mol-plugin-ui/viewport.js +7 -7
  563. package/lib/commonjs/mol-repr/representation.js +4 -4
  564. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +1 -0
  565. package/lib/commonjs/mol-repr/shape/loci/angle.js +9 -9
  566. package/lib/commonjs/mol-repr/shape/loci/common.js +1 -1
  567. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +1 -0
  568. package/lib/commonjs/mol-repr/shape/loci/dihedral.js +14 -14
  569. package/lib/commonjs/mol-repr/shape/loci/distance.js +5 -5
  570. package/lib/commonjs/mol-repr/shape/loci/label.js +3 -3
  571. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +1 -0
  572. package/lib/commonjs/mol-repr/shape/loci/orientation.js +4 -4
  573. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +1 -0
  574. package/lib/commonjs/mol-repr/shape/loci/plane.js +2 -2
  575. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +1 -0
  576. package/lib/commonjs/mol-repr/shape/model/unitcell.js +2 -2
  577. package/lib/commonjs/mol-repr/shape/representation.js +2 -2
  578. package/lib/commonjs/mol-repr/structure/complex-representation.js +2 -2
  579. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +3 -0
  580. package/lib/commonjs/mol-repr/structure/complex-visual.js +12 -12
  581. package/lib/commonjs/mol-repr/structure/params.d.ts +4 -0
  582. package/lib/commonjs/mol-repr/structure/params.js +8 -8
  583. package/lib/commonjs/mol-repr/structure/registry.d.ts +10 -0
  584. package/lib/commonjs/mol-repr/structure/registry.js +1 -1
  585. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +3 -0
  586. package/lib/commonjs/mol-repr/structure/representation/backbone.js +1 -1
  587. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  588. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js +1 -1
  589. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  590. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js +1 -1
  591. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +3 -0
  592. package/lib/commonjs/mol-repr/structure/representation/cartoon.js +3 -3
  593. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  594. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js +1 -1
  595. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  596. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +1 -1
  597. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +1 -1
  598. package/lib/commonjs/mol-repr/structure/representation/label.js +1 -1
  599. package/lib/commonjs/mol-repr/structure/representation/line.js +1 -1
  600. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  601. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +1 -1
  602. package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +3 -0
  603. package/lib/commonjs/mol-repr/structure/representation/orientation.js +1 -1
  604. package/lib/commonjs/mol-repr/structure/representation/point.js +1 -1
  605. package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +3 -0
  606. package/lib/commonjs/mol-repr/structure/representation/putty.js +1 -1
  607. package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +3 -0
  608. package/lib/commonjs/mol-repr/structure/representation/spacefill.js +1 -1
  609. package/lib/commonjs/mol-repr/structure/representation.js +1 -1
  610. package/lib/commonjs/mol-repr/structure/units-representation.js +2 -2
  611. package/lib/commonjs/mol-repr/structure/units-visual.d.ts +4 -0
  612. package/lib/commonjs/mol-repr/structure/units-visual.js +16 -16
  613. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  614. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +1 -1
  615. package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +1 -1
  616. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  617. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +1 -1
  618. package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +1 -1
  619. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  620. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js +1 -1
  621. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  622. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +1 -1
  623. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  624. package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +1 -1
  625. package/lib/commonjs/mol-repr/structure/visual/element-cross.js +1 -1
  626. package/lib/commonjs/mol-repr/structure/visual/element-point.js +1 -1
  627. package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +2 -0
  628. package/lib/commonjs/mol-repr/structure/visual/element-sphere.js +1 -1
  629. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  630. package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.js +1 -1
  631. package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +8 -9
  632. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
  633. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +20 -20
  634. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  635. package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +7 -8
  636. package/lib/commonjs/mol-repr/structure/visual/label-text.js +1 -1
  637. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  638. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +6 -6
  639. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  640. package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +7 -7
  641. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  642. package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.js +1 -1
  643. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  644. package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.js +1 -1
  645. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  646. package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +1 -1
  647. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  648. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.js +1 -1
  649. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  650. package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.js +1 -1
  651. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  652. package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
  653. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  654. package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.js +1 -1
  655. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  656. package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
  657. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  658. package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js +1 -1
  659. package/lib/commonjs/mol-repr/structure/visual/util/bond.js +2 -2
  660. package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts +1 -3
  661. package/lib/commonjs/mol-repr/structure/visual/util/common.js +3 -28
  662. package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js +13 -13
  663. package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js +5 -5
  664. package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +4 -4
  665. package/lib/commonjs/mol-repr/util.d.ts +2 -1
  666. package/lib/commonjs/mol-repr/util.js +3 -3
  667. package/lib/commonjs/mol-repr/volume/direct-volume.js +3 -3
  668. package/lib/commonjs/mol-repr/volume/isosurface.d.ts +5 -0
  669. package/lib/commonjs/mol-repr/volume/isosurface.js +9 -9
  670. package/lib/commonjs/mol-repr/volume/registry.d.ts +1 -0
  671. package/lib/commonjs/mol-repr/volume/registry.js +1 -1
  672. package/lib/commonjs/mol-repr/volume/representation.js +5 -5
  673. package/lib/commonjs/mol-repr/volume/slice.js +4 -4
  674. package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
  675. package/lib/commonjs/mol-script/language/parser.js +7 -4
  676. package/lib/commonjs/mol-script/language/symbol-table/internal.js +1 -1
  677. package/lib/commonjs/mol-script/language/symbol-table/structure-query.js +1 -1
  678. package/lib/commonjs/mol-script/runtime/query/compiler.js +1 -1
  679. package/lib/commonjs/mol-script/script/mol-script/symbols.js +1 -1
  680. package/lib/commonjs/mol-state/action.js +1 -1
  681. package/lib/commonjs/mol-state/index.js +8 -8
  682. package/lib/commonjs/mol-state/state/builder.js +2 -2
  683. package/lib/commonjs/mol-state/state/selection.js +1 -1
  684. package/lib/commonjs/mol-state/state.js +21 -21
  685. package/lib/commonjs/mol-state/transform.js +4 -4
  686. package/lib/commonjs/mol-state/transformer.js +1 -1
  687. package/lib/commonjs/mol-task/execution/observable.js +5 -5
  688. package/lib/commonjs/mol-task/task.js +3 -3
  689. package/lib/commonjs/mol-task/util/chunked.js +2 -2
  690. package/lib/commonjs/mol-task/util/multistep.js +1 -1
  691. package/lib/commonjs/mol-task/util/scheduler.d.ts +2 -2
  692. package/lib/commonjs/mol-task/util/scheduler.js +8 -8
  693. package/lib/commonjs/mol-theme/color/atom-id.js +1 -1
  694. package/lib/commonjs/mol-theme/color/chain-id.js +1 -1
  695. package/lib/commonjs/mol-theme/color/element-index.js +1 -1
  696. package/lib/commonjs/mol-theme/color/entity-id.js +1 -1
  697. package/lib/commonjs/mol-theme/color/entity-source.js +2 -2
  698. package/lib/commonjs/mol-theme/color/hydrophobicity.js +2 -2
  699. package/lib/commonjs/mol-theme/color/model-index.js +1 -1
  700. package/lib/commonjs/mol-theme/color/operator-hkl.js +2 -2
  701. package/lib/commonjs/mol-theme/color/operator-name.js +1 -1
  702. package/lib/commonjs/mol-theme/color/polymer-id.js +2 -2
  703. package/lib/commonjs/mol-theme/color/polymer-index.js +2 -2
  704. package/lib/commonjs/mol-theme/color/unit-index.js +2 -2
  705. package/lib/commonjs/mol-theme/label.js +6 -6
  706. package/lib/commonjs/mol-theme/theme.js +3 -3
  707. package/lib/commonjs/mol-util/assets.js +7 -7
  708. package/lib/commonjs/mol-util/color/distinct.js +1 -1
  709. package/lib/commonjs/mol-util/color/palette.js +3 -3
  710. package/lib/commonjs/mol-util/color/scale.js +2 -2
  711. package/lib/commonjs/mol-util/data-source.js +14 -13
  712. package/lib/commonjs/mol-util/file-info.d.ts +1 -3
  713. package/lib/commonjs/mol-util/file-info.js +2 -10
  714. package/lib/commonjs/mol-util/graphql-client.js +4 -4
  715. package/lib/commonjs/mol-util/index.d.ts +1 -0
  716. package/lib/commonjs/mol-util/index.js +8 -2
  717. package/lib/commonjs/mol-util/input/input-observer.js +6 -6
  718. package/lib/commonjs/mol-util/make-dir.js +1 -1
  719. package/lib/commonjs/mol-util/material.js +2 -2
  720. package/lib/commonjs/mol-util/monadic-parser.js +2 -2
  721. package/lib/commonjs/mol-util/param-definition.js +7 -7
  722. package/lib/commonjs/mol-util/read.js +2 -2
  723. package/lib/commonjs/mol-util/retry-if.js +2 -2
  724. package/lib/commonjs/mol-util/string.js +1 -1
  725. package/lib/commonjs/mol-util/zip/deflate.js +4 -3
  726. package/lib/commonjs/mol-util/zip/inflate.js +2 -2
  727. package/lib/commonjs/mol-util/zip/zip.d.ts +7 -1
  728. package/lib/commonjs/mol-util/zip/zip.js +21 -16
  729. package/lib/commonjs/servers/common/file-handle.js +1 -1
  730. package/lib/commonjs/servers/common/swagger-ui/index.js +1 -1
  731. package/lib/commonjs/servers/model/config.d.ts +2 -2
  732. package/lib/commonjs/servers/model/config.js +5 -5
  733. package/lib/commonjs/servers/model/preprocess/converter.js +2 -2
  734. package/lib/commonjs/servers/model/preprocess/master.js +3 -3
  735. package/lib/commonjs/servers/model/preprocess/parallel.js +6 -6
  736. package/lib/commonjs/servers/model/preprocess/preprocess.js +4 -4
  737. package/lib/commonjs/servers/model/preprocess.js +1 -1
  738. package/lib/commonjs/servers/model/properties/providers/pdbe.js +8 -8
  739. package/lib/commonjs/servers/model/properties/providers/wwpdb.js +12 -12
  740. package/lib/commonjs/servers/model/property-provider.js +3 -3
  741. package/lib/commonjs/servers/model/query.js +1 -1
  742. package/lib/commonjs/servers/model/server/api-local.js +2 -2
  743. package/lib/commonjs/servers/model/server/api-schema.js +2 -2
  744. package/lib/commonjs/servers/model/server/api-web.js +5 -5
  745. package/lib/commonjs/servers/model/server/api.js +6 -6
  746. package/lib/commonjs/servers/model/server/query.js +15 -15
  747. package/lib/commonjs/servers/model/server/structure-wrapper.js +21 -21
  748. package/lib/commonjs/servers/model/server.js +2 -2
  749. package/lib/commonjs/servers/model/utils/fetch-props-pdbe.js +6 -6
  750. package/lib/commonjs/servers/model/utils/fetch-retry.js +3 -3
  751. package/lib/commonjs/servers/model/utils/writer.js +3 -3
  752. package/lib/commonjs/servers/plugin-state/config.js +1 -1
  753. package/lib/commonjs/servers/plugin-state/index.js +6 -6
  754. package/lib/commonjs/servers/volume/common/binary-schema.js +1 -1
  755. package/lib/commonjs/servers/volume/common/data-format.js +3 -3
  756. package/lib/commonjs/servers/volume/common/file.js +8 -8
  757. package/lib/commonjs/servers/volume/config.js +6 -6
  758. package/lib/commonjs/servers/volume/pack/format/ccp4.js +4 -4
  759. package/lib/commonjs/servers/volume/pack/format/dsn6.js +4 -4
  760. package/lib/commonjs/servers/volume/pack/format.js +3 -3
  761. package/lib/commonjs/servers/volume/pack/main.js +13 -13
  762. package/lib/commonjs/servers/volume/pack/sampling.js +13 -13
  763. package/lib/commonjs/servers/volume/pack/writer.js +2 -2
  764. package/lib/commonjs/servers/volume/pack.js +1 -1
  765. package/lib/commonjs/servers/volume/query.js +4 -4
  766. package/lib/commonjs/servers/volume/server/algebra/box.js +1 -1
  767. package/lib/commonjs/servers/volume/server/api.js +8 -8
  768. package/lib/commonjs/servers/volume/server/local-api.js +8 -8
  769. package/lib/commonjs/servers/volume/server/query/compose.js +8 -8
  770. package/lib/commonjs/servers/volume/server/query/execute.js +10 -10
  771. package/lib/commonjs/servers/volume/server/query/identify.js +2 -2
  772. package/lib/commonjs/servers/volume/server/web-api.js +7 -7
  773. package/lib/commonjs/servers/volume/server.js +2 -2
  774. package/lib/examples/alpha-orbitals/controls.js +2 -2
  775. package/lib/examples/alpha-orbitals/index.html +61 -61
  776. package/lib/examples/alpha-orbitals/index.js +1 -1
  777. package/lib/examples/basic-wrapper/controls.js +1 -1
  778. package/lib/examples/basic-wrapper/index.html +137 -137
  779. package/lib/examples/basic-wrapper/index.js +1 -1
  780. package/lib/examples/lighting/index.html +88 -88
  781. package/lib/examples/lighting/index.js +1 -1
  782. package/lib/examples/proteopedia-wrapper/index.html +236 -236
  783. package/lib/examples/proteopedia-wrapper/index.js +1 -1
  784. package/lib/examples/proteopedia-wrapper/ui/controls.js +1 -1
  785. package/lib/extensions/anvil/behavior.d.ts +1 -0
  786. package/lib/extensions/anvil/representation.d.ts +4 -0
  787. package/lib/extensions/cellpack/model.js +4 -2
  788. package/lib/extensions/cellpack/representation.d.ts +1 -0
  789. package/lib/extensions/cellpack/state.js +2 -2
  790. package/lib/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  791. package/lib/extensions/dnatco/confal-pyramids/color.js +224 -132
  792. package/lib/extensions/dnatco/confal-pyramids/property.js +1 -3
  793. package/lib/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
  794. package/lib/extensions/dnatco/confal-pyramids/util.js +19 -20
  795. package/lib/extensions/geo-export/ui.js +2 -2
  796. package/lib/extensions/model-export/ui.js +2 -2
  797. package/lib/extensions/mp4-export/ui.js +2 -2
  798. package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
  799. package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
  800. package/lib/extensions/rcsb/assembly-symmetry/ui.js +3 -3
  801. package/lib/extensions/rcsb/validation-report/representation.d.ts +5 -0
  802. package/lib/extensions/zenodo/index.d.ts +7 -0
  803. package/lib/extensions/zenodo/index.js +32 -0
  804. package/lib/extensions/zenodo/ui.d.ts +61 -0
  805. package/lib/extensions/zenodo/ui.js +303 -0
  806. package/lib/mol-canvas3d/camera.js +2 -1
  807. package/lib/mol-canvas3d/canvas3d.d.ts +2 -0
  808. package/lib/mol-canvas3d/helper/camera-helper.d.ts +1 -0
  809. package/lib/mol-canvas3d/helper/camera-helper.js +1 -1
  810. package/lib/mol-canvas3d/helper/handle-helper.d.ts +1 -0
  811. package/lib/mol-canvas3d/helper/handle-helper.js +1 -1
  812. package/lib/mol-canvas3d/helper/helper.d.ts +2 -0
  813. package/lib/mol-canvas3d/helper/interaction-events.js +1 -1
  814. package/lib/mol-canvas3d/passes/image.d.ts +1 -0
  815. package/lib/mol-data/db/column.d.ts +10 -3
  816. package/lib/mol-data/db/column.js +39 -18
  817. package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
  818. package/lib/mol-geo/geometry/cylinders/cylinders.js +2 -2
  819. package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
  820. package/lib/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  821. package/lib/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  822. package/lib/mol-geo/geometry/mesh/mesh.d.ts +2 -1
  823. package/lib/mol-geo/geometry/mesh/mesh.js +2 -2
  824. package/lib/mol-geo/geometry/points/points.d.ts +1 -1
  825. package/lib/mol-geo/geometry/spheres/spheres.d.ts +2 -1
  826. package/lib/mol-geo/geometry/spheres/spheres.js +2 -2
  827. package/lib/mol-geo/geometry/text/text-builder.js +2 -1
  828. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  829. package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
  830. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
  831. package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  832. package/lib/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
  833. package/lib/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
  834. package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  835. package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
  836. package/lib/mol-gl/shader/image.frag.d.ts +2 -2
  837. package/lib/mol-gl/shader/image.frag.js +2 -2
  838. package/lib/mol-gl/shader/lines.frag.d.ts +2 -2
  839. package/lib/mol-gl/shader/lines.frag.js +2 -2
  840. package/lib/mol-gl/shader/points.frag.d.ts +2 -2
  841. package/lib/mol-gl/shader/points.frag.js +2 -2
  842. package/lib/mol-gl/shader/text.frag.d.ts +2 -2
  843. package/lib/mol-gl/shader/text.frag.js +2 -2
  844. package/lib/mol-gl/shader-code.js +2 -1
  845. package/lib/mol-gl/webgl/buffer.d.ts +2 -2
  846. package/lib/mol-gl/webgl/buffer.js +14 -15
  847. package/lib/mol-gl/webgl/context.d.ts +1 -1
  848. package/lib/mol-gl/webgl/context.js +2 -2
  849. package/lib/mol-gl/webgl/program.d.ts +1 -1
  850. package/lib/mol-gl/webgl/program.js +10 -4
  851. package/lib/mol-io/common/binary-cif/classifier.js +3 -2
  852. package/lib/mol-io/common/binary-cif/decoder.js +4 -3
  853. package/lib/mol-io/common/io-buffer.d.ts +206 -0
  854. package/lib/mol-io/common/io-buffer.js +405 -0
  855. package/lib/mol-io/common/netcdf/reader.d.ts +78 -0
  856. package/lib/mol-io/common/netcdf/reader.js +456 -0
  857. package/lib/mol-io/reader/cif/schema/bird.d.ts +8 -8
  858. package/lib/mol-io/reader/cif/schema/bird.js +12 -11
  859. package/lib/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
  860. package/lib/mol-io/reader/cif/schema/ccd.d.ts +12 -12
  861. package/lib/mol-io/reader/cif/schema/ccd.js +13 -12
  862. package/lib/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
  863. package/lib/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  864. package/lib/mol-io/reader/cif/schema/mmcif.d.ts +31 -27
  865. package/lib/mol-io/reader/cif/schema/mmcif.js +44 -39
  866. package/lib/mol-io/reader/cif/schema.d.ts +1 -1
  867. package/lib/mol-io/reader/cif/schema.js +22 -2
  868. package/lib/mol-io/reader/nctraj/parser.d.ts +18 -0
  869. package/lib/mol-io/reader/nctraj/parser.js +97 -0
  870. package/lib/mol-io/reader/prmtop/parser.d.ts +58 -0
  871. package/lib/mol-io/reader/prmtop/parser.js +168 -0
  872. package/lib/mol-io/reader/top/parser.d.ts +37 -0
  873. package/lib/mol-io/reader/top/parser.js +299 -0
  874. package/lib/mol-io/reader/trr/parser.d.ts +22 -0
  875. package/lib/mol-io/reader/trr/parser.js +142 -0
  876. package/lib/mol-io/writer/cif/encoder.js +2 -1
  877. package/lib/mol-io/writer/mol/encoder.js +1 -1
  878. package/lib/mol-math/geometry/common.d.ts +2 -1
  879. package/lib/mol-math/geometry/common.js +1 -1
  880. package/lib/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  881. package/lib/mol-math/geometry/gaussian-density/cpu.js +2 -2
  882. package/lib/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  883. package/lib/mol-math/geometry/gaussian-density/gpu.js +7 -7
  884. package/lib/mol-math/geometry/gaussian-density.d.ts +2 -2
  885. package/lib/mol-math/geometry/gaussian-density.js +1 -1
  886. package/lib/mol-math/geometry/molecular-surface.d.ts +2 -1
  887. package/lib/mol-math/geometry/molecular-surface.js +2 -2
  888. package/lib/mol-math/geometry/primitives/box3d.js +2 -1
  889. package/lib/mol-math/geometry/primitives/sphere3d.js +12 -6
  890. package/lib/mol-model/sequence/sequence.js +2 -1
  891. package/lib/mol-model/structure/model/model.js +14 -6
  892. package/lib/mol-model/structure/model/properties/common.js +1 -1
  893. package/lib/mol-model/structure/model/types/saccharides.d.ts +8 -0
  894. package/lib/mol-model/structure/model/types/saccharides.js +8 -0
  895. package/lib/mol-model/structure/model/types.d.ts +19 -17
  896. package/lib/mol-model/structure/model/types.js +30 -31
  897. package/lib/mol-model/structure/query/queries/generators.js +1 -1
  898. package/lib/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  899. package/lib/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  900. package/lib/mol-model/structure/structure/properties.d.ts +1 -1
  901. package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +2 -4
  902. package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -3
  903. package/lib/mol-model/structure/structure/unit/rings.js +3 -0
  904. package/lib/mol-model-formats/shape/ply.d.ts +2 -0
  905. package/lib/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  906. package/lib/mol-model-formats/structure/basic/atomic.js +1 -14
  907. package/lib/mol-model-formats/structure/basic/entities.js +1 -1
  908. package/lib/mol-model-formats/structure/basic/parser.d.ts +1 -1
  909. package/lib/mol-model-formats/structure/basic/parser.js +1 -1
  910. package/lib/mol-model-formats/structure/basic/schema.d.ts +4 -4
  911. package/lib/mol-model-formats/structure/basic/schema.js +7 -2
  912. package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
  913. package/lib/mol-model-formats/structure/basic/util.js +24 -1
  914. package/lib/mol-model-formats/structure/cif-core.js +4 -4
  915. package/lib/mol-model-formats/structure/common/component.d.ts +3 -3
  916. package/lib/mol-model-formats/structure/common/component.js +51 -47
  917. package/lib/mol-model-formats/structure/cube.js +3 -3
  918. package/lib/mol-model-formats/structure/gro.js +3 -1
  919. package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
  920. package/lib/mol-model-formats/structure/mmcif.js +4 -2
  921. package/lib/mol-model-formats/structure/mol.js +3 -3
  922. package/lib/mol-model-formats/structure/mol2.js +4 -4
  923. package/lib/mol-model-formats/structure/nctraj.d.ts +9 -0
  924. package/lib/mol-model-formats/structure/nctraj.js +56 -0
  925. package/lib/mol-model-formats/structure/pdb/atom-site.d.ts +2 -2
  926. package/lib/mol-model-formats/structure/pdb/atom-site.js +72 -7
  927. package/lib/mol-model-formats/structure/pdb/secondary-structure.js +11 -11
  928. package/lib/mol-model-formats/structure/pdb/to-cif.js +7 -2
  929. package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
  930. package/lib/mol-model-formats/structure/pdb.js +5 -3
  931. package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
  932. package/lib/mol-model-formats/structure/prmtop.js +144 -0
  933. package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
  934. package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
  935. package/lib/mol-model-formats/structure/property/symmetry.js +11 -1
  936. package/lib/mol-model-formats/structure/psf.js +3 -1
  937. package/lib/mol-model-formats/structure/top.d.ts +16 -0
  938. package/lib/mol-model-formats/structure/top.js +186 -0
  939. package/lib/mol-model-formats/structure/trr.d.ts +9 -0
  940. package/lib/mol-model-formats/structure/trr.js +42 -0
  941. package/lib/mol-model-formats/structure/util.d.ts +2 -2
  942. package/lib/mol-model-formats/structure/util.js +19 -20
  943. package/lib/mol-model-formats/structure/xyz.js +2 -2
  944. package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
  945. package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
  946. package/lib/mol-model-props/computed/representations/interactions.d.ts +3 -0
  947. package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
  948. package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
  949. package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js +3 -2
  950. package/lib/mol-plugin/commands.d.ts +1 -0
  951. package/lib/mol-plugin/context.d.ts +2 -1
  952. package/lib/mol-plugin/context.js +4 -3
  953. package/lib/mol-plugin/spec.js +1 -1
  954. package/lib/mol-plugin/util/viewport-screenshot.d.ts +3 -0
  955. package/lib/mol-plugin/version.js +2 -2
  956. package/lib/mol-plugin-state/actions/file.d.ts +1 -1
  957. package/lib/mol-plugin-state/actions/file.js +88 -55
  958. package/lib/mol-plugin-state/actions/structure.d.ts +17 -8
  959. package/lib/mol-plugin-state/actions/structure.js +174 -4
  960. package/lib/mol-plugin-state/actions/volume.js +3 -2
  961. package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
  962. package/lib/mol-plugin-state/formats/coordinates.js +67 -0
  963. package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
  964. package/lib/mol-plugin-state/formats/registry.js +13 -8
  965. package/lib/mol-plugin-state/formats/topology.d.ts +73 -0
  966. package/lib/mol-plugin-state/formats/topology.js +84 -0
  967. package/lib/mol-plugin-state/helpers/structure-component.js +2 -1
  968. package/lib/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
  969. package/lib/mol-plugin-state/helpers/structure-selection-query.js +1 -1
  970. package/lib/mol-plugin-state/manager/snapshots.js +4 -4
  971. package/lib/mol-plugin-state/objects.d.ts +47 -1
  972. package/lib/mol-plugin-state/objects.js +17 -1
  973. package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
  974. package/lib/mol-plugin-state/transforms/data.js +61 -9
  975. package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
  976. package/lib/mol-plugin-state/transforms/model.js +112 -3
  977. package/lib/mol-plugin-state/transforms/representation.d.ts +6 -0
  978. package/lib/mol-plugin-ui/base.js +1 -1
  979. package/lib/mol-plugin-ui/controls/action-menu.js +7 -7
  980. package/lib/mol-plugin-ui/controls/color.js +3 -3
  981. package/lib/mol-plugin-ui/controls/common.js +10 -10
  982. package/lib/mol-plugin-ui/controls/icons.js +70 -70
  983. package/lib/mol-plugin-ui/controls/legend.js +3 -3
  984. package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -1
  985. package/lib/mol-plugin-ui/controls/parameters.js +51 -51
  986. package/lib/mol-plugin-ui/controls/screenshot.js +2 -2
  987. package/lib/mol-plugin-ui/controls/slider.js +5 -5
  988. package/lib/mol-plugin-ui/controls.js +7 -7
  989. package/lib/mol-plugin-ui/custom/volume.js +4 -4
  990. package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
  991. package/lib/mol-plugin-ui/left-panel.js +33 -12
  992. package/lib/mol-plugin-ui/plugin.js +10 -10
  993. package/lib/mol-plugin-ui/react18.d.ts +11 -0
  994. package/lib/mol-plugin-ui/react18.js +34 -0
  995. package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
  996. package/lib/mol-plugin-ui/sequence.js +5 -5
  997. package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
  998. package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
  999. package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
  1000. package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
  1001. package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
  1002. package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
  1003. package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
  1004. package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
  1005. package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
  1006. package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
  1007. package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
  1008. package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
  1009. package/lib/mol-plugin-ui/skin/base/components/viewport.scss +128 -128
  1010. package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
  1011. package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
  1012. package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
  1013. package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
  1014. package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
  1015. package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
  1016. package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
  1017. package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
  1018. package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
  1019. package/lib/mol-plugin-ui/skin/blue.scss +1 -1
  1020. package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
  1021. package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
  1022. package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
  1023. package/lib/mol-plugin-ui/skin/dark.scss +1 -1
  1024. package/lib/mol-plugin-ui/skin/light.scss +1 -1
  1025. package/lib/mol-plugin-ui/state/actions.js +1 -1
  1026. package/lib/mol-plugin-ui/state/animation.js +1 -1
  1027. package/lib/mol-plugin-ui/state/common.js +7 -7
  1028. package/lib/mol-plugin-ui/state/snapshots.js +9 -9
  1029. package/lib/mol-plugin-ui/state/tree.js +14 -14
  1030. package/lib/mol-plugin-ui/state/update-transform.js +1 -1
  1031. package/lib/mol-plugin-ui/structure/components.js +10 -10
  1032. package/lib/mol-plugin-ui/structure/focus.d.ts +1 -1
  1033. package/lib/mol-plugin-ui/structure/focus.js +3 -3
  1034. package/lib/mol-plugin-ui/structure/generic.js +4 -4
  1035. package/lib/mol-plugin-ui/structure/measurements.js +8 -8
  1036. package/lib/mol-plugin-ui/structure/quick-styles.js +2 -2
  1037. package/lib/mol-plugin-ui/structure/selection.js +7 -7
  1038. package/lib/mol-plugin-ui/structure/source.js +4 -4
  1039. package/lib/mol-plugin-ui/structure/superposition.js +8 -8
  1040. package/lib/mol-plugin-ui/structure/volume.js +4 -4
  1041. package/lib/mol-plugin-ui/task.js +5 -5
  1042. package/lib/mol-plugin-ui/toast.js +4 -4
  1043. package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
  1044. package/lib/mol-plugin-ui/viewport/help.js +8 -8
  1045. package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
  1046. package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
  1047. package/lib/mol-plugin-ui/viewport.js +4 -4
  1048. package/lib/mol-repr/shape/loci/angle.d.ts +1 -0
  1049. package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
  1050. package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
  1051. package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
  1052. package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
  1053. package/lib/mol-repr/structure/complex-visual.d.ts +3 -0
  1054. package/lib/mol-repr/structure/params.d.ts +4 -0
  1055. package/lib/mol-repr/structure/registry.d.ts +10 -0
  1056. package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
  1057. package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
  1058. package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
  1059. package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
  1060. package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
  1061. package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
  1062. package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
  1063. package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
  1064. package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
  1065. package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
  1066. package/lib/mol-repr/structure/units-visual.d.ts +4 -0
  1067. package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
  1068. package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
  1069. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
  1070. package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
  1071. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
  1072. package/lib/mol-repr/structure/visual/element-sphere.d.ts +2 -0
  1073. package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
  1074. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  1075. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
  1076. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
  1077. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  1078. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  1079. package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
  1080. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
  1081. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  1082. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
  1083. package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
  1084. package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
  1085. package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
  1086. package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
  1087. package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
  1088. package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
  1089. package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
  1090. package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
  1091. package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
  1092. package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
  1093. package/lib/mol-repr/structure/visual/util/common.js +1 -24
  1094. package/lib/mol-repr/util.d.ts +2 -1
  1095. package/lib/mol-repr/util.js +2 -2
  1096. package/lib/mol-repr/volume/isosurface.d.ts +5 -0
  1097. package/lib/mol-repr/volume/registry.d.ts +1 -0
  1098. package/lib/mol-script/language/builder.d.ts +1 -0
  1099. package/lib/mol-script/language/parser.js +7 -4
  1100. package/lib/mol-task/util/scheduler.d.ts +2 -2
  1101. package/lib/mol-task/util/scheduler.js +7 -7
  1102. package/lib/mol-theme/color/hydrophobicity.js +2 -2
  1103. package/lib/mol-util/data-source.js +2 -1
  1104. package/lib/mol-util/file-info.d.ts +1 -3
  1105. package/lib/mol-util/file-info.js +2 -10
  1106. package/lib/mol-util/index.d.ts +1 -0
  1107. package/lib/mol-util/index.js +5 -0
  1108. package/lib/mol-util/zip/deflate.js +2 -1
  1109. package/lib/mol-util/zip/zip.d.ts +7 -1
  1110. package/lib/mol-util/zip/zip.js +5 -1
  1111. package/lib/servers/model/config.d.ts +2 -2
  1112. package/package.json +162 -160
  1113. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  1114. package/lib/mol-plugin-state/formats/structure.js +0 -61

There are too many changes on this page to be displayed.


The amount of changes on this page would crash your brower.

You can still verify the content by downloading the package file manually.