molstar 3.3.0 → 3.5.0

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 (905) 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/lib/apps/docking-viewer/index.html +36 -36
  7. package/lib/apps/docking-viewer/viewport.js +1 -1
  8. package/lib/apps/viewer/app.d.ts +7 -6
  9. package/lib/apps/viewer/app.js +2 -0
  10. package/lib/apps/viewer/embedded.html +43 -43
  11. package/lib/apps/viewer/index.html +106 -106
  12. package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  13. package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
  14. package/lib/cli/cif2bcif/converter.js +1 -1
  15. package/lib/cli/cif2bcif/index.js +4 -4
  16. package/lib/commonjs/apps/docking-viewer/index.js +12 -12
  17. package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
  18. package/lib/commonjs/apps/viewer/app.d.ts +7 -6
  19. package/lib/commonjs/apps/viewer/app.js +24 -22
  20. package/lib/commonjs/apps/viewer/index.js +1 -1
  21. package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
  22. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
  23. package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
  24. package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
  25. package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
  26. package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
  27. package/lib/commonjs/cli/cif2bcif/index.js +12 -12
  28. package/lib/commonjs/cli/cifschema/index.js +27 -27
  29. package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
  30. package/lib/commonjs/cli/lipid-params/index.js +9 -9
  31. package/lib/commonjs/cli/state-docs/index.js +2 -2
  32. package/lib/commonjs/cli/structure-info/helpers.js +11 -11
  33. package/lib/commonjs/cli/structure-info/model.js +15 -15
  34. package/lib/commonjs/cli/structure-info/volume.js +9 -9
  35. package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
  36. package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
  37. package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
  38. package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
  39. package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
  40. package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
  41. package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
  42. package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
  43. package/lib/commonjs/examples/lighting/index.js +6 -6
  44. package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
  45. package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
  46. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
  47. package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
  48. package/lib/commonjs/examples/task.js +15 -15
  49. package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
  50. package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
  51. package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
  52. package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
  53. package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
  54. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
  55. package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
  56. package/lib/commonjs/extensions/anvil/behavior.js +14 -14
  57. package/lib/commonjs/extensions/anvil/prop.js +7 -7
  58. package/lib/commonjs/extensions/anvil/representation.js +5 -5
  59. package/lib/commonjs/extensions/cellpack/index.js +1 -1
  60. package/lib/commonjs/extensions/cellpack/model.js +26 -24
  61. package/lib/commonjs/extensions/cellpack/preset.js +6 -6
  62. package/lib/commonjs/extensions/cellpack/property.js +3 -3
  63. package/lib/commonjs/extensions/cellpack/representation.js +2 -2
  64. package/lib/commonjs/extensions/cellpack/state.js +13 -13
  65. package/lib/commonjs/extensions/cellpack/util.js +14 -14
  66. package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
  67. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
  68. package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
  69. package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
  70. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
  71. package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
  72. package/lib/commonjs/extensions/g3d/data.js +6 -6
  73. package/lib/commonjs/extensions/g3d/format.js +14 -14
  74. package/lib/commonjs/extensions/g3d/model.js +4 -4
  75. package/lib/commonjs/extensions/geo-export/controls.js +3 -3
  76. package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
  77. package/lib/commonjs/extensions/geo-export/index.js +1 -1
  78. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
  79. package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
  80. package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
  81. package/lib/commonjs/extensions/geo-export/ui.js +7 -7
  82. package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
  83. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
  84. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
  85. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
  86. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
  87. package/lib/commonjs/extensions/model-export/export.js +4 -4
  88. package/lib/commonjs/extensions/model-export/index.js +1 -1
  89. package/lib/commonjs/extensions/model-export/ui.js +5 -5
  90. package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
  91. package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
  92. package/lib/commonjs/extensions/mp4-export/index.js +1 -1
  93. package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
  94. package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
  95. package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
  96. package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
  97. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
  98. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
  99. package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
  100. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
  101. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
  102. package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
  103. package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
  104. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
  105. package/lib/commonjs/extensions/rcsb/validation-report/representation.js +22 -5
  106. package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
  107. package/lib/commonjs/extensions/zenodo/index.js +35 -0
  108. package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
  109. package/lib/commonjs/extensions/zenodo/ui.js +306 -0
  110. package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
  111. package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
  112. package/lib/commonjs/mol-canvas3d/camera.js +2 -1
  113. package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
  114. package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
  115. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
  116. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
  117. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
  118. package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
  119. package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
  120. package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
  121. package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
  122. package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
  123. package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
  124. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
  125. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
  126. package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
  127. package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
  128. package/lib/commonjs/mol-canvas3d/util.js +2 -2
  129. package/lib/commonjs/mol-data/db/column.js +2 -2
  130. package/lib/commonjs/mol-data/db/table.js +1 -1
  131. package/lib/commonjs/mol-data/db.js +1 -1
  132. package/lib/commonjs/mol-data/generic.js +3 -3
  133. package/lib/commonjs/mol-data/index.js +4 -4
  134. package/lib/commonjs/mol-data/int/interval.js +1 -1
  135. package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
  136. package/lib/commonjs/mol-data/int/segmentation.js +1 -1
  137. package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
  138. package/lib/commonjs/mol-data/util.js +7 -7
  139. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
  140. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
  141. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
  142. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
  143. package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
  144. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
  145. package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
  146. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
  147. package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
  148. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
  149. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
  150. package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
  151. package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
  152. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
  153. package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
  154. package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
  155. package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
  156. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
  157. package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
  158. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
  159. package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
  160. package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
  161. package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
  162. package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
  163. package/lib/commonjs/mol-geo/primitive/star.js +1 -1
  164. package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
  165. package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
  166. package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
  167. package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
  168. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
  169. package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
  170. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
  171. package/lib/commonjs/mol-gl/compute/util.js +3 -3
  172. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  173. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  174. package/lib/commonjs/mol-gl/renderable/image.js +3 -3
  175. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  176. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  177. package/lib/commonjs/mol-gl/renderable/points.js +3 -3
  178. package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
  179. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  180. package/lib/commonjs/mol-gl/renderable/text.js +3 -3
  181. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  182. package/lib/commonjs/mol-gl/renderable/util.js +1 -1
  183. package/lib/commonjs/mol-gl/shader-code.js +2 -1
  184. package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
  185. package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
  186. package/lib/commonjs/mol-gl/webgl/context.js +5 -5
  187. package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
  188. package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
  189. package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
  190. package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
  191. package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
  192. package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
  193. package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
  194. package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
  195. package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
  196. package/lib/commonjs/mol-io/common/typed-array.js +2 -2
  197. package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
  198. package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
  199. package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
  200. package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
  201. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
  202. package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
  203. package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
  204. package/lib/commonjs/mol-io/reader/cif.js +1 -1
  205. package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
  206. package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
  207. package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
  208. package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
  209. package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
  210. package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
  211. package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
  212. package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
  213. package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
  214. package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
  215. package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
  216. package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
  217. package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
  218. package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
  219. package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
  220. package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
  221. package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
  222. package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
  223. package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
  224. package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
  225. package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
  226. package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
  227. package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
  228. package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
  229. package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
  230. package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
  231. package/lib/commonjs/mol-io/writer/cif.js +1 -1
  232. package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
  233. package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
  234. package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
  235. package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
  236. package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
  237. package/lib/commonjs/mol-math/geometry/common.js +1 -1
  238. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
  239. package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
  240. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
  241. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
  242. package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
  243. package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
  244. package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
  245. package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
  246. package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
  247. package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
  248. package/lib/commonjs/mol-math/geometry.js +8 -8
  249. package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
  250. package/lib/commonjs/mol-math/graph.js +1 -1
  251. package/lib/commonjs/mol-math/linear-algebra.js +2 -2
  252. package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
  253. package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
  254. package/lib/commonjs/mol-model/sequence.js +1 -1
  255. package/lib/commonjs/mol-model/shape.js +1 -1
  256. package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
  257. package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
  258. package/lib/commonjs/mol-model/structure/model/model.js +3 -3
  259. package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
  260. package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
  261. package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
  262. package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
  263. package/lib/commonjs/mol-model/structure/model.js +3 -3
  264. package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
  265. package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
  266. package/lib/commonjs/mol-model/structure/query.js +6 -6
  267. package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
  268. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
  269. package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
  270. package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
  271. package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
  272. package/lib/commonjs/mol-model/structure/structure/structure.js +9 -6
  273. package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
  274. package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
  275. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
  276. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +6 -4
  277. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
  278. package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
  279. package/lib/commonjs/mol-model/structure/structure/unit.js +5 -22
  280. package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
  281. package/lib/commonjs/mol-model/structure/structure.js +2 -2
  282. package/lib/commonjs/mol-model/structure/topology.js +1 -1
  283. package/lib/commonjs/mol-model/structure.js +6 -6
  284. package/lib/commonjs/mol-model/volume.js +2 -2
  285. package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
  286. package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
  287. package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
  288. package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
  289. package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
  290. package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
  291. package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
  292. package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
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  872. package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js +10 -1
  873. package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +10 -1
  874. package/lib/mol-repr/structure/visual/element-point.d.ts +1 -1
  875. package/lib/mol-repr/structure/visual/element-point.js +22 -3
  876. package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
  877. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +1 -1
  878. package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
  879. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
  880. package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
  881. package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
  882. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
  883. package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
  884. package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
  885. package/lib/mol-repr/structure/visual/util/common.js +1 -24
  886. package/lib/mol-repr/structure/visual/util/element.js +36 -2
  887. package/lib/mol-repr/structure/visual/util/link.d.ts +13 -3
  888. package/lib/mol-repr/structure/visual/util/link.js +55 -6
  889. package/lib/mol-script/language/builder.d.ts +1 -0
  890. package/lib/mol-script/language/parser.js +7 -4
  891. package/lib/mol-task/util/scheduler.d.ts +2 -2
  892. package/lib/mol-task/util/scheduler.js +7 -7
  893. package/lib/mol-theme/color/hydrophobicity.js +2 -2
  894. package/lib/mol-util/data-source.js +2 -1
  895. package/lib/mol-util/file-info.d.ts +1 -3
  896. package/lib/mol-util/file-info.js +2 -10
  897. package/lib/mol-util/index.d.ts +1 -0
  898. package/lib/mol-util/index.js +5 -0
  899. package/lib/mol-util/zip/deflate.js +2 -1
  900. package/lib/mol-util/zip/zip.d.ts +7 -1
  901. package/lib/mol-util/zip/zip.js +5 -1
  902. package/lib/servers/model/config.d.ts +2 -2
  903. package/package.json +160 -160
  904. package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
  905. package/lib/mol-plugin-state/formats/structure.js +0 -61
@@ -1,126 +1,126 @@
1
- .msp-sequence {
2
- position: absolute;
3
- right: 0;
4
- top: 0;
5
- left: 0;
6
- bottom: 0;
7
- background: $sequence-background;
8
- }
9
-
10
- $sequence-select-height: 24px;
11
- .msp-sequence-select {
12
- position: relative;
13
- height: $sequence-select-height;
14
- width: 100%;
15
- margin-bottom: 1px;
16
- background: $control-background;
17
- text-align: left;
18
-
19
- > span {
20
- display: inline-block;
21
- line-height: $sequence-select-height;
22
- padding: 0 $control-spacing;
23
- font-size: 85%;
24
- font-weight: bold;
25
- cursor: default;
26
- }
27
-
28
- > select {
29
- display: inline-block;
30
- max-width: 120px;
31
- width: auto;
32
- text-overflow: ellipsis;
33
- font-size: 85%;
34
- height: $sequence-select-height;
35
- line-height: $sequence-select-height;
36
- background-size: 6px 8px;
37
- background-color: $control-background;
38
- }
39
- }
40
-
41
- .msp-sequence-wrapper {
42
- word-break: break-word;
43
- // use $control-spacing for top to have space for sequence numebrs
44
- padding: $control-spacing $control-spacing $info-vertical-padding $control-spacing;
45
- user-select: none;
46
- }
47
-
48
- .msp-sequence-wrapper-non-empty {
49
- font-size: 85%;
50
- line-height: 180%;
51
- font-family: "Courier New", monospace;
52
- background: $msp-form-control-background;
53
-
54
- width: 100%;
55
- overflow-y: auto;
56
- overflow-x: hidden;
57
- position: absolute;
58
- top: $sequence-select-height + 1px;
59
- left: 0;
60
- bottom: 0;
61
- right: 0;
62
- }
63
-
64
- .msp-sequence-chain-label {
65
- margin-left: $control-spacing;
66
- margin-top: $control-spacing;
67
- user-select: none;
68
- color: $sequence-number-color;
69
- font-size: 90%;
70
- line-height: 90%;
71
- padding-left: 0.2em;
72
- }
73
-
74
- .msp-sequence-wrapper {
75
- span {
76
- cursor: pointer;
77
- }
78
-
79
- .msp-sequence-residue-long {
80
- margin: 0em 0.2em 0em 0.2em;
81
- }
82
-
83
- .msp-sequence-residue-long-begin {
84
- margin: 0em 0.2em 0em 0em;
85
- }
86
-
87
- .msp-sequence-label {
88
- color: $sequence-number-color;
89
- font-size: 90%;
90
- line-height: 90%;
91
- padding-bottom: 1em;
92
- padding-left: 0.2em;
93
- }
94
-
95
- .msp-sequence-number {
96
- color: $sequence-number-color;
97
- word-break: keep-all;
98
- cursor: default;
99
- position: relative;
100
- top: -1.1em;
101
- left: 3.1em;
102
- padding: 0px;
103
- margin-left: -3em;
104
- font-size: 80%;
105
- }
106
-
107
- .msp-sequence-number-long {
108
- left: 3.3em;
109
- }
110
-
111
- .msp-sequence-number-long-negative {
112
- left: 2.7em;
113
- }
114
-
115
- .msp-sequence-number-negative {
116
- left: 2.5em;
117
- }
118
-
119
- .msp-sequence-present {
120
- color: $font-color;
121
- }
122
-
123
- .msp-sequence-missing {
124
- color: color-lower-contrast($font-color, 33%);
125
- }
1
+ .msp-sequence {
2
+ position: absolute;
3
+ right: 0;
4
+ top: 0;
5
+ left: 0;
6
+ bottom: 0;
7
+ background: $sequence-background;
8
+ }
9
+
10
+ $sequence-select-height: 24px;
11
+ .msp-sequence-select {
12
+ position: relative;
13
+ height: $sequence-select-height;
14
+ width: 100%;
15
+ margin-bottom: 1px;
16
+ background: $control-background;
17
+ text-align: left;
18
+
19
+ > span {
20
+ display: inline-block;
21
+ line-height: $sequence-select-height;
22
+ padding: 0 $control-spacing;
23
+ font-size: 85%;
24
+ font-weight: bold;
25
+ cursor: default;
26
+ }
27
+
28
+ > select {
29
+ display: inline-block;
30
+ max-width: 120px;
31
+ width: auto;
32
+ text-overflow: ellipsis;
33
+ font-size: 85%;
34
+ height: $sequence-select-height;
35
+ line-height: $sequence-select-height;
36
+ background-size: 6px 8px;
37
+ background-color: $control-background;
38
+ }
39
+ }
40
+
41
+ .msp-sequence-wrapper {
42
+ word-break: break-word;
43
+ // use $control-spacing for top to have space for sequence numebrs
44
+ padding: $control-spacing $control-spacing $info-vertical-padding $control-spacing;
45
+ user-select: none;
46
+ }
47
+
48
+ .msp-sequence-wrapper-non-empty {
49
+ font-size: 85%;
50
+ line-height: 180%;
51
+ font-family: "Courier New", monospace;
52
+ background: $msp-form-control-background;
53
+
54
+ width: 100%;
55
+ overflow-y: auto;
56
+ overflow-x: hidden;
57
+ position: absolute;
58
+ top: $sequence-select-height + 1px;
59
+ left: 0;
60
+ bottom: 0;
61
+ right: 0;
62
+ }
63
+
64
+ .msp-sequence-chain-label {
65
+ margin-left: $control-spacing;
66
+ margin-top: $control-spacing;
67
+ user-select: none;
68
+ color: $sequence-number-color;
69
+ font-size: 90%;
70
+ line-height: 90%;
71
+ padding-left: 0.2em;
72
+ }
73
+
74
+ .msp-sequence-wrapper {
75
+ span {
76
+ cursor: pointer;
77
+ }
78
+
79
+ .msp-sequence-residue-long {
80
+ margin: 0em 0.2em 0em 0.2em;
81
+ }
82
+
83
+ .msp-sequence-residue-long-begin {
84
+ margin: 0em 0.2em 0em 0em;
85
+ }
86
+
87
+ .msp-sequence-label {
88
+ color: $sequence-number-color;
89
+ font-size: 90%;
90
+ line-height: 90%;
91
+ padding-bottom: 1em;
92
+ padding-left: 0.2em;
93
+ }
94
+
95
+ .msp-sequence-number {
96
+ color: $sequence-number-color;
97
+ word-break: keep-all;
98
+ cursor: default;
99
+ position: relative;
100
+ top: -1.1em;
101
+ left: 3.1em;
102
+ padding: 0px;
103
+ margin-left: -3em;
104
+ font-size: 80%;
105
+ }
106
+
107
+ .msp-sequence-number-long {
108
+ left: 3.3em;
109
+ }
110
+
111
+ .msp-sequence-number-long-negative {
112
+ left: 2.7em;
113
+ }
114
+
115
+ .msp-sequence-number-negative {
116
+ left: 2.5em;
117
+ }
118
+
119
+ .msp-sequence-present {
120
+ color: $font-color;
121
+ }
122
+
123
+ .msp-sequence-missing {
124
+ color: color-lower-contrast($font-color, 33%);
125
+ }
126
126
  }
@@ -1,166 +1,166 @@
1
- @mixin borderBox {
2
- box-sizing: border-box;
3
- -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
4
-
5
- * {
6
- box-sizing: border-box;
7
- -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
8
- }
9
- }
10
-
11
- .msp-slider-base {
12
- position: relative;
13
- height: 14px;
14
- padding: 5px 0;
15
- width: 100%;
16
- border-radius: $slider-border-radius-base;
17
- align-self: center;
18
- @include borderBox;
19
-
20
- &-rail {
21
- position: absolute;
22
- width: 100%;
23
- background-color: $control-background;
24
- height: 4px;
25
- border-radius: 2px;
26
- }
27
-
28
- &-track {
29
- position: absolute;
30
- left: 0;
31
- height: 4px;
32
- border-radius: $slider-border-radius-base;
33
- background-color: tint($font-color, 60%);
34
- }
35
-
36
- &-handle {
37
- position: absolute;
38
- margin-left: -11px;
39
- margin-top: -9px;
40
- width: 22px;
41
- height: 22px;
42
- cursor: pointer;
43
- border-radius: 50%;
44
- background-color: $font-color;
45
- border: 4px solid $control-background;
46
-
47
- &:hover {
48
- background-color: $hover-font-color;
49
- }
50
- }
51
-
52
- &-mark {
53
- position: absolute;
54
- top: 18px;
55
- left: 0;
56
- width: 100%;
57
- font-size: 12px;
58
- }
59
-
60
- &-mark-text {
61
- position: absolute;
62
- display: inline-block;
63
- vertical-align: middle;
64
- text-align: center;
65
- cursor: pointer;
66
- color: #999;
67
-
68
- &-active {
69
- color: #666;
70
- }
71
- }
72
-
73
- &-step {
74
- position: absolute;
75
- width: 100%;
76
- height: 4px;
77
- background: transparent;
78
- }
79
-
80
- &-dot {
81
- position: absolute;
82
- bottom: -2px;
83
- margin-left: -4px;
84
- width: 8px;
85
- height: 8px;
86
- border: 2px solid #e9e9e9;
87
- background-color: #fff;
88
- cursor: pointer;
89
- border-radius: 50%;
90
- vertical-align: middle;
91
- &:first-child {
92
- margin-left: -4px;
93
- }
94
- &:last-child {
95
- margin-left: -4px;
96
- }
97
- &-active {
98
- border-color: tint($font-color, 50%);
99
- }
100
- }
101
-
102
- &-disabled {
103
- background: $default-background;
104
- opacity: 0.35;
105
-
106
- // .msp-slider-base-track {
107
- // background-color: $slider-disabledColor;
108
- // }
109
-
110
- .msp-slider-base-handle, .msp-slider-base-dot {
111
- // border-color: $slider-disabledColor;
112
- // background-color: color-lower-contrast($font-color, 10%);
113
- cursor: not-allowed;
114
- }
115
-
116
- .msp-slider-base-mark-text, .msp-slider-base-dot {
117
- cursor: not-allowed!important;
118
- }
119
- }
120
- }
121
-
122
- // .msp-slider-base-vertical {
123
- // width: 14px;
124
- // height: 100%;
125
- // padding: 0 5px;
126
-
127
- // .msp-slider-base {
128
- // &-rail {
129
- // height: 100%;
130
- // width: 4px;
131
- // }
132
-
133
- // &-track {
134
- // left: 5px;
135
- // bottom: 0;
136
- // width: 4px;
137
- // }
138
-
139
- // &-handle {
140
- // margin-left: -5px;
141
- // margin-bottom: -7px;
142
- // }
143
-
144
- // &-mark {
145
- // top: 0;
146
- // left: 18px;
147
- // height: 100%;
148
- // }
149
-
150
- // &-step {
151
- // height: 100%;
152
- // width: 4px;
153
- // }
154
-
155
- // &-dot {
156
- // left: 2px;
157
- // margin-bottom: -4px;
158
- // &:first-child {
159
- // margin-bottom: -4px;
160
- // }
161
- // &:last-child {
162
- // margin-bottom: -4px;
163
- // }
164
- // }
165
- // }
1
+ @mixin borderBox {
2
+ box-sizing: border-box;
3
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
4
+
5
+ * {
6
+ box-sizing: border-box;
7
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0); // remove tap highlight color for mobile safari
8
+ }
9
+ }
10
+
11
+ .msp-slider-base {
12
+ position: relative;
13
+ height: 14px;
14
+ padding: 5px 0;
15
+ width: 100%;
16
+ border-radius: $slider-border-radius-base;
17
+ align-self: center;
18
+ @include borderBox;
19
+
20
+ &-rail {
21
+ position: absolute;
22
+ width: 100%;
23
+ background-color: $control-background;
24
+ height: 4px;
25
+ border-radius: 2px;
26
+ }
27
+
28
+ &-track {
29
+ position: absolute;
30
+ left: 0;
31
+ height: 4px;
32
+ border-radius: $slider-border-radius-base;
33
+ background-color: tint($font-color, 60%);
34
+ }
35
+
36
+ &-handle {
37
+ position: absolute;
38
+ margin-left: -11px;
39
+ margin-top: -9px;
40
+ width: 22px;
41
+ height: 22px;
42
+ cursor: pointer;
43
+ border-radius: 50%;
44
+ background-color: $font-color;
45
+ border: 4px solid $control-background;
46
+
47
+ &:hover {
48
+ background-color: $hover-font-color;
49
+ }
50
+ }
51
+
52
+ &-mark {
53
+ position: absolute;
54
+ top: 18px;
55
+ left: 0;
56
+ width: 100%;
57
+ font-size: 12px;
58
+ }
59
+
60
+ &-mark-text {
61
+ position: absolute;
62
+ display: inline-block;
63
+ vertical-align: middle;
64
+ text-align: center;
65
+ cursor: pointer;
66
+ color: #999;
67
+
68
+ &-active {
69
+ color: #666;
70
+ }
71
+ }
72
+
73
+ &-step {
74
+ position: absolute;
75
+ width: 100%;
76
+ height: 4px;
77
+ background: transparent;
78
+ }
79
+
80
+ &-dot {
81
+ position: absolute;
82
+ bottom: -2px;
83
+ margin-left: -4px;
84
+ width: 8px;
85
+ height: 8px;
86
+ border: 2px solid #e9e9e9;
87
+ background-color: #fff;
88
+ cursor: pointer;
89
+ border-radius: 50%;
90
+ vertical-align: middle;
91
+ &:first-child {
92
+ margin-left: -4px;
93
+ }
94
+ &:last-child {
95
+ margin-left: -4px;
96
+ }
97
+ &-active {
98
+ border-color: tint($font-color, 50%);
99
+ }
100
+ }
101
+
102
+ &-disabled {
103
+ background: $default-background;
104
+ opacity: 0.35;
105
+
106
+ // .msp-slider-base-track {
107
+ // background-color: $slider-disabledColor;
108
+ // }
109
+
110
+ .msp-slider-base-handle, .msp-slider-base-dot {
111
+ // border-color: $slider-disabledColor;
112
+ // background-color: color-lower-contrast($font-color, 10%);
113
+ cursor: not-allowed;
114
+ }
115
+
116
+ .msp-slider-base-mark-text, .msp-slider-base-dot {
117
+ cursor: not-allowed!important;
118
+ }
119
+ }
120
+ }
121
+
122
+ // .msp-slider-base-vertical {
123
+ // width: 14px;
124
+ // height: 100%;
125
+ // padding: 0 5px;
126
+
127
+ // .msp-slider-base {
128
+ // &-rail {
129
+ // height: 100%;
130
+ // width: 4px;
131
+ // }
132
+
133
+ // &-track {
134
+ // left: 5px;
135
+ // bottom: 0;
136
+ // width: 4px;
137
+ // }
138
+
139
+ // &-handle {
140
+ // margin-left: -5px;
141
+ // margin-bottom: -7px;
142
+ // }
143
+
144
+ // &-mark {
145
+ // top: 0;
146
+ // left: 18px;
147
+ // height: 100%;
148
+ // }
149
+
150
+ // &-step {
151
+ // height: 100%;
152
+ // width: 4px;
153
+ // }
154
+
155
+ // &-dot {
156
+ // left: 2px;
157
+ // margin-bottom: -4px;
158
+ // &:first-child {
159
+ // margin-bottom: -4px;
160
+ // }
161
+ // &:last-child {
162
+ // margin-bottom: -4px;
163
+ // }
164
+ // }
165
+ // }
166
166
  // }