molstar 3.0.0-dev.5 → 3.0.0-dev.9

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 (688) hide show
  1. package/LICENSE +20 -20
  2. package/README.md +187 -187
  3. package/build/viewer/embedded.html +43 -43
  4. package/build/viewer/index.html +106 -95
  5. package/build/viewer/molstar.js +1 -1
  6. package/lib/apps/docking-viewer/index.d.ts +2 -1
  7. package/lib/apps/docking-viewer/index.html +36 -36
  8. package/lib/apps/docking-viewer/index.js +87 -74
  9. package/lib/apps/viewer/app.d.ts +230 -0
  10. package/lib/apps/viewer/app.js +515 -0
  11. package/lib/apps/viewer/embedded.html +43 -43
  12. package/lib/apps/viewer/index.d.ts +2 -403
  13. package/lib/apps/viewer/index.html +106 -95
  14. package/lib/apps/viewer/index.js +2 -420
  15. package/lib/cli/cifschema/index.d.ts +1 -1
  16. package/lib/cli/cifschema/index.js +15 -35
  17. package/lib/commonjs/apps/docking-viewer/index.d.ts +2 -1
  18. package/lib/commonjs/apps/docking-viewer/index.js +86 -73
  19. package/lib/commonjs/apps/viewer/app.d.ts +230 -0
  20. package/lib/commonjs/apps/viewer/app.js +521 -0
  21. package/lib/commonjs/apps/viewer/index.d.ts +2 -403
  22. package/lib/commonjs/apps/viewer/index.js +2 -423
  23. package/lib/commonjs/cli/cifschema/index.d.ts +1 -1
  24. package/lib/commonjs/cli/cifschema/index.js +15 -35
  25. package/lib/commonjs/examples/alpha-orbitals/index.js +3 -4
  26. package/lib/commonjs/examples/basic-wrapper/index.js +23 -11
  27. package/lib/commonjs/examples/lighting/index.d.ts +1 -1
  28. package/lib/commonjs/examples/lighting/index.js +57 -41
  29. package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -14
  30. package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts +0 -1
  31. package/lib/commonjs/extensions/alpha-orbitals/transforms.js +1 -14
  32. package/lib/commonjs/extensions/anvil/behavior.d.ts +4 -0
  33. package/lib/commonjs/extensions/anvil/representation.d.ts +50 -0
  34. package/lib/commonjs/extensions/cellpack/representation.d.ts +10 -0
  35. package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +30 -0
  36. package/lib/commonjs/extensions/geo-export/mesh-exporter.js +4 -4
  37. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +68 -0
  38. package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +236 -0
  39. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.d.ts +14 -0
  40. package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +125 -0
  41. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.d.ts +12 -0
  42. package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +111 -0
  43. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.d.ts +28 -0
  44. package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +130 -0
  45. package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +1 -1
  46. package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +6 -2
  47. package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +1 -1
  48. package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +10 -0
  49. package/lib/commonjs/extensions/rcsb/validation-report/prop.js +1 -1
  50. package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +50 -0
  51. package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +3 -9
  52. package/lib/commonjs/mol-canvas3d/canvas3d.js +34 -23
  53. package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +3 -2
  54. package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +4 -0
  55. package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +2 -2
  56. package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +4 -0
  57. package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +2 -2
  58. package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
  59. package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +13 -1
  60. package/lib/commonjs/mol-canvas3d/passes/draw.js +16 -15
  61. package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
  62. package/lib/commonjs/mol-canvas3d/passes/image.js +3 -2
  63. package/lib/commonjs/mol-canvas3d/passes/marking.js +1 -1
  64. package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +10 -2
  65. package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +18 -14
  66. package/lib/commonjs/mol-canvas3d/passes/pick.js +12 -12
  67. package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +3 -3
  68. package/lib/commonjs/mol-canvas3d/passes/smaa.js +1 -1
  69. package/lib/commonjs/mol-geo/geometry/base.d.ts +18 -0
  70. package/lib/commonjs/mol-geo/geometry/base.js +18 -1
  71. package/lib/commonjs/mol-geo/geometry/clipping-data.d.ts +1 -3
  72. package/lib/commonjs/mol-geo/geometry/clipping-data.js +3 -8
  73. package/lib/commonjs/mol-geo/geometry/color-data.d.ts +1 -1
  74. package/lib/commonjs/mol-geo/geometry/color-data.js +22 -0
  75. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +12 -2
  76. package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +2 -2
  77. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +15 -38
  78. package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +21 -66
  79. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.d.ts +2 -4
  80. package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +4 -7
  81. package/lib/commonjs/mol-geo/geometry/image/image.d.ts +10 -0
  82. package/lib/commonjs/mol-geo/geometry/image/image.js +1 -1
  83. package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +11 -0
  84. package/lib/commonjs/mol-geo/geometry/lines/lines.js +1 -1
  85. package/lib/commonjs/mol-geo/geometry/marker-data.d.ts +0 -1
  86. package/lib/commonjs/mol-geo/geometry/marker-data.js +13 -9
  87. package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +10 -0
  88. package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +2 -2
  89. package/lib/commonjs/mol-geo/geometry/points/points.d.ts +11 -1
  90. package/lib/commonjs/mol-geo/geometry/points/points.js +1 -1
  91. package/lib/commonjs/mol-geo/geometry/size-data.js +5 -5
  92. package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +10 -0
  93. package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +2 -2
  94. package/lib/commonjs/mol-geo/geometry/text/text.d.ts +10 -0
  95. package/lib/commonjs/mol-geo/geometry/text/text.js +1 -1
  96. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +10 -0
  97. package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
  98. package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +2 -2
  99. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +2 -2
  100. package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +10 -9
  101. package/lib/commonjs/mol-gl/render-object.d.ts +2 -1
  102. package/lib/commonjs/mol-gl/render-object.js +10 -10
  103. package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +11 -5
  104. package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
  105. package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +15 -14
  106. package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
  107. package/lib/commonjs/mol-gl/renderable/image.d.ts +10 -4
  108. package/lib/commonjs/mol-gl/renderable/image.js +2 -2
  109. package/lib/commonjs/mol-gl/renderable/lines.d.ts +39 -33
  110. package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
  111. package/lib/commonjs/mol-gl/renderable/mesh.d.ts +11 -5
  112. package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
  113. package/lib/commonjs/mol-gl/renderable/points.d.ts +10 -4
  114. package/lib/commonjs/mol-gl/renderable/points.js +2 -2
  115. package/lib/commonjs/mol-gl/renderable/schema.d.ts +10 -11
  116. package/lib/commonjs/mol-gl/renderable/schema.js +4 -10
  117. package/lib/commonjs/mol-gl/renderable/spheres.d.ts +11 -5
  118. package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
  119. package/lib/commonjs/mol-gl/renderable/text.d.ts +10 -4
  120. package/lib/commonjs/mol-gl/renderable/text.js +2 -2
  121. package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +11 -6
  122. package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
  123. package/lib/commonjs/mol-gl/renderable.d.ts +0 -1
  124. package/lib/commonjs/mol-gl/renderer.d.ts +12 -12
  125. package/lib/commonjs/mol-gl/renderer.js +23 -92
  126. package/lib/commonjs/mol-gl/scene.d.ts +2 -2
  127. package/lib/commonjs/mol-gl/scene.js +7 -5
  128. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +1 -1
  129. package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +1 -1
  130. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
  131. package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
  132. package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.d.ts +1 -1
  133. package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +1 -1
  134. package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.d.ts +1 -1
  135. package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +1 -1
  136. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
  137. package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
  138. package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.d.ts +1 -1
  139. package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +1 -1
  140. package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.d.ts +1 -1
  141. package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +1 -1
  142. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
  143. package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
  144. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
  145. package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
  146. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
  147. package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +1 -1
  148. package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.d.ts +1 -1
  149. package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +1 -1
  150. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
  151. package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +1 -1
  152. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +1 -1
  153. package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +1 -1
  154. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.d.ts +1 -1
  155. package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +1 -1
  156. package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +1 -1
  157. package/lib/commonjs/mol-gl/shader/cylinders.frag.js +1 -1
  158. package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
  159. package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
  160. package/lib/commonjs/mol-gl/shader/gaussian-density.frag.d.ts +1 -1
  161. package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +1 -1
  162. package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.d.ts +1 -1
  163. package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +1 -1
  164. package/lib/commonjs/mol-gl/shader/image.frag.d.ts +1 -1
  165. package/lib/commonjs/mol-gl/shader/image.frag.js +1 -1
  166. package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.d.ts +1 -1
  167. package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +1 -1
  168. package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
  169. package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
  170. package/lib/commonjs/mol-gl/shader/mesh.vert.d.ts +1 -1
  171. package/lib/commonjs/mol-gl/shader/mesh.vert.js +1 -1
  172. package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +1 -1
  173. package/lib/commonjs/mol-gl/shader/spheres.frag.js +1 -1
  174. package/lib/commonjs/mol-gl/shader-code.d.ts +3 -1
  175. package/lib/commonjs/mol-gl/shader-code.js +43 -14
  176. package/lib/commonjs/mol-gl/webgl/render-item.d.ts +7 -6
  177. package/lib/commonjs/mol-gl/webgl/render-item.js +10 -8
  178. package/lib/commonjs/mol-gl/webgl/resources.js +8 -1
  179. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +326 -1
  180. package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +326 -1
  181. package/lib/commonjs/mol-io/reader/mol2/parser.d.ts +1 -1
  182. package/lib/commonjs/mol-io/reader/mol2/parser.js +33 -3
  183. package/lib/commonjs/mol-io/reader/mol2/schema.d.ts +12 -1
  184. package/lib/commonjs/mol-io/reader/mol2/schema.js +1 -1
  185. package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +2 -2
  186. package/lib/commonjs/mol-math/geometry/symmetry-operator.js +3 -2
  187. package/lib/commonjs/mol-math/linear-algebra/3d/quat.d.ts +9 -1
  188. package/lib/commonjs/mol-math/linear-algebra/3d/quat.js +20 -1
  189. package/lib/commonjs/mol-model/structure/model/model.d.ts +1 -0
  190. package/lib/commonjs/mol-model/structure/model/model.js +8 -2
  191. package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.d.ts +6 -1
  192. package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.js +1 -1
  193. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.d.ts +1 -1
  194. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.js +4 -1
  195. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.d.ts +1 -1
  196. package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js +12 -1
  197. package/lib/commonjs/mol-model/structure/model/types.js +9 -0
  198. package/lib/commonjs/mol-model/structure/structure/element/stats.js +8 -0
  199. package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.d.ts +2 -1
  200. package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js +11 -2
  201. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -1
  202. package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +20 -10
  203. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.d.ts +1 -1
  204. package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +21 -11
  205. package/lib/commonjs/mol-model/structure/structure/unit/rings.js +2 -0
  206. package/lib/commonjs/mol-model-formats/shape/ply.d.ts +20 -0
  207. package/lib/commonjs/mol-model-formats/structure/mol2.d.ts +1 -1
  208. package/lib/commonjs/mol-model-formats/structure/mol2.js +37 -7
  209. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts +18 -1
  210. package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +18 -5
  211. package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +10 -0
  212. package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +10 -0
  213. package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +30 -0
  214. package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +40 -0
  215. package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +4 -6
  216. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +11 -0
  217. package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +3 -1
  218. package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
  219. package/lib/commonjs/mol-plugin/commands.d.ts +1 -4
  220. package/lib/commonjs/mol-plugin/config.d.ts +2 -2
  221. package/lib/commonjs/mol-plugin/config.js +5 -25
  222. package/lib/commonjs/mol-plugin/features.d.ts +9 -0
  223. package/lib/commonjs/mol-plugin/features.js +38 -0
  224. package/lib/commonjs/mol-plugin/spec.js +1 -0
  225. package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +12 -0
  226. package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +8 -1
  227. package/lib/commonjs/mol-plugin-state/actions/structure.js +183 -72
  228. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +5 -355
  229. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +13 -8
  230. package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -71
  231. package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +4 -4
  232. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.d.ts +1 -1
  233. package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +1 -1
  234. package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +33 -19
  235. package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +13 -1
  236. package/lib/commonjs/mol-plugin-state/manager/structure/component.js +13 -8
  237. package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +3 -1
  238. package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +32 -0
  239. package/lib/commonjs/mol-plugin-state/transforms/representation.js +2 -2
  240. package/lib/commonjs/mol-plugin-ui/index.d.ts +4 -4
  241. package/lib/commonjs/mol-plugin-ui/index.js +13 -16
  242. package/lib/commonjs/mol-plugin-ui/plugin.js +1 -1
  243. package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +2 -6
  244. package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +10 -0
  245. package/lib/commonjs/mol-repr/shape/loci/common.d.ts +10 -0
  246. package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +10 -0
  247. package/lib/commonjs/mol-repr/shape/loci/distance.d.ts +10 -0
  248. package/lib/commonjs/mol-repr/shape/loci/label.d.ts +10 -0
  249. package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +10 -0
  250. package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +10 -0
  251. package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +10 -0
  252. package/lib/commonjs/mol-repr/structure/complex-representation.js +1 -1
  253. package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +61 -19
  254. package/lib/commonjs/mol-repr/structure/params.d.ts +81 -19
  255. package/lib/commonjs/mol-repr/structure/registry.d.ts +141 -19
  256. package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +30 -0
  257. package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +30 -0
  258. package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +30 -0
  259. package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +30 -0
  260. package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +30 -0
  261. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +30 -0
  262. package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +1 -1
  263. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +34 -58
  264. package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +2 -7
  265. package/lib/commonjs/mol-repr/structure/representation/label.d.ts +30 -0
  266. package/lib/commonjs/mol-repr/structure/representation/label.js +1 -1
  267. package/lib/commonjs/mol-repr/structure/representation/line.d.ts +30 -0
  268. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +30 -0
  269. package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +1 -1
  270. package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +30 -0
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  687. package/lib/commonjs/mol-util/float-packing.d.ts +0 -15
  688. package/lib/mol-util/float-packing.d.ts +0 -15
@@ -1,210 +1,210 @@
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-
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- //
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- // 1. Set default font family to sans-serif.
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- //
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- * {
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- }
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- //
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- // Address `[hidden]` styling not present in IE 8/9/10.
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- // Hide the `template` element in IE 8/9/10/11, Safari, and Firefox < 22.
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- //
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- template {
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- }
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-
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- // Links
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- // ==========================================================================
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-
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- //
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- //
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- a {
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- //
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- // Improve readability of focused elements when they are also in an
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- // active/hover state.
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- //
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- outline: 0;
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- }
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-
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- // Text-level semantics
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- // ==========================================================================
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-
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- //
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- // Address styling not present in IE 8/9/10/11, Safari, and Chrome.
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- //
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-
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- abbr[title] {
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- border-bottom: 1px dotted;
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- }
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-
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- //
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- // Address style set to `bolder` in Firefox 4+, Safari, and Chrome.
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- //
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-
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- b,
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- strong {
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- font-weight: bold;
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- }
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-
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- //
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- // Address inconsistent and variable font size in all browsers.
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- //
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-
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- small {
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- font-size: 80%;
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- }
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-
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- // Embedded content
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- // ==========================================================================
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-
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- //
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- //
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-
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- img {
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- border: 0;
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- }
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-
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- //
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- // Correct overflow not hidden in IE 9/10/11.
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- //
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-
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- svg:not(:root) {
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- overflow: hidden;
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- }
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-
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- // Forms
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- // ==========================================================================
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-
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- //
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- // Known limitation: by default, Chrome and Safari on OS X allow very limited
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- // styling of `select`, unless a `border` property is set.
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- //
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-
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- //
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- // 1. Correct color not being inherited.
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- // Known issue: affects color of disabled elements.
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- // 2. Correct font properties not being inherited.
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- // 3. Address margins set differently in Firefox 4+, Safari, and Chrome.
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- //
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- button,
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- input,
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- color: inherit; // 1
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- font: inherit; // 2
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- margin: 0; // 3
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- }
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-
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- //
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- // Address `overflow` set to `hidden` in IE 8/9/10/11.
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- //
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- button {
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- overflow: visible;
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- }
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-
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- //
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- // Address inconsistent `text-transform` inheritance for `button` and `select`.
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- // All other form control elements do not inherit `text-transform` values.
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- // Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.
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- // Correct `select` style inheritance in Firefox.
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- //
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- button,
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- select {
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- text-transform: none;
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- }
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-
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- //
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- // 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
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- // and `video` controls.
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- // 2. Correct inability to style clickable `input` types in iOS.
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- // 3. Improve usability and consistency of cursor style between image-type
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- // `input` and others.
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- //
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- cursor: pointer; // 3
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- }
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- //
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- }
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- //
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- // It's recommended that you don't attempt to style these elements.
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- // Firefox's implementation doesn't respect box-sizing, padding, or width.
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- //
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- // 1. Address box sizing set to `content-box` in IE 8/9/10.
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- // 2. Remove excess padding in IE 8/9/10.
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- input[type="checkbox"],
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- box-sizing: border-box; // 1
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- padding: 0; // 2
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- }
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- //
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- // Fix the cursor style for Chrome's increment/decrement buttons. For certain
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- // `font-size` values of the `input`, it causes the cursor style of the
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- // decrement button to change from `default` to `text`.
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- overflow: auto;
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+ /*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */
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+
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+ //
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+ // 1. Set default font family to sans-serif.
5
+ // 2. Prevent iOS and IE text size adjust after device orientation change,
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+ // without disabling user zoom.
7
+ //
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+ * {
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+ box-sizing: border-box; // 1
10
+ }
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+
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+ //
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+ // Address `[hidden]` styling not present in IE 8/9/10.
14
+ // Hide the `template` element in IE 8/9/10/11, Safari, and Firefox < 22.
15
+ //
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+
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+ [hidden],
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+ template {
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+ display: none;
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+ }
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+
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+ // Links
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+ // ==========================================================================
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+
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+ //
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+ // Remove the gray background color from active links in IE 10.
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+ //
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+
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+ a {
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+ background-color: transparent;
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+ }
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+
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+ //
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+ // Improve readability of focused elements when they are also in an
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+ // active/hover state.
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+ //
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+
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+ a:active,
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+ a:hover {
40
+ outline: 0;
41
+ }
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+
43
+ // Text-level semantics
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+ // ==========================================================================
45
+
46
+ //
47
+ // Address styling not present in IE 8/9/10/11, Safari, and Chrome.
48
+ //
49
+
50
+ abbr[title] {
51
+ border-bottom: 1px dotted;
52
+ }
53
+
54
+ //
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+ // Address style set to `bolder` in Firefox 4+, Safari, and Chrome.
56
+ //
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+
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+ b,
59
+ strong {
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+ font-weight: bold;
61
+ }
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+
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+ //
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+ // Address inconsistent and variable font size in all browsers.
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+ //
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+
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+ small {
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+ font-size: 80%;
69
+ }
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+
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+ // Embedded content
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+ // ==========================================================================
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+
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+ //
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+ // Remove border when inside `a` element in IE 8/9/10.
76
+ //
77
+
78
+ img {
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+ border: 0;
80
+ }
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+
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+ //
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+ // Correct overflow not hidden in IE 9/10/11.
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+ //
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+
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+ svg:not(:root) {
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+ overflow: hidden;
88
+ }
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+
90
+ // Forms
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+ // ==========================================================================
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+
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+ //
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+ // Known limitation: by default, Chrome and Safari on OS X allow very limited
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+ // styling of `select`, unless a `border` property is set.
96
+ //
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+
98
+ //
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+ // 1. Correct color not being inherited.
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+ // Known issue: affects color of disabled elements.
101
+ // 2. Correct font properties not being inherited.
102
+ // 3. Address margins set differently in Firefox 4+, Safari, and Chrome.
103
+ //
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+
105
+ button,
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+ input,
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+ optgroup,
108
+ select,
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+ textarea {
110
+ color: inherit; // 1
111
+ font: inherit; // 2
112
+ margin: 0; // 3
113
+ }
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+
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+ //
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+ // Address `overflow` set to `hidden` in IE 8/9/10/11.
117
+ //
118
+
119
+ button {
120
+ overflow: visible;
121
+ }
122
+
123
+ //
124
+ // Address inconsistent `text-transform` inheritance for `button` and `select`.
125
+ // All other form control elements do not inherit `text-transform` values.
126
+ // Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.
127
+ // Correct `select` style inheritance in Firefox.
128
+ //
129
+
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+ button,
131
+ select {
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+ text-transform: none;
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+ }
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+
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+ //
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+ // 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
137
+ // and `video` controls.
138
+ // 2. Correct inability to style clickable `input` types in iOS.
139
+ // 3. Improve usability and consistency of cursor style between image-type
140
+ // `input` and others.
141
+ //
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+
143
+ button,
144
+ html input[type="button"], // 1
145
+ input[type="reset"],
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+ input[type="submit"] {
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+ -webkit-appearance: button; // 2
148
+ cursor: pointer; // 3
149
+ }
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+
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+ //
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+ // Re-set default cursor for disabled elements.
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+ //
154
+
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+ button[disabled],
156
+ html input[disabled] {
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+ cursor: default;
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+ }
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+
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+ //
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+ // Remove inner padding and border in Firefox 4+.
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+ //
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+
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+ button::-moz-focus-inner,
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+ input::-moz-focus-inner {
166
+ border: 0;
167
+ padding: 0;
168
+ }
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+
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+ //
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+ // Address Firefox 4+ setting `line-height` on `input` using `!important` in
172
+ // the UA stylesheet.
173
+ //
174
+
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+ input {
176
+ line-height: normal;
177
+ }
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+
179
+ //
180
+ // It's recommended that you don't attempt to style these elements.
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+ // Firefox's implementation doesn't respect box-sizing, padding, or width.
182
+ //
183
+ // 1. Address box sizing set to `content-box` in IE 8/9/10.
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+ // 2. Remove excess padding in IE 8/9/10.
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+ //
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+
187
+ input[type="checkbox"],
188
+ input[type="radio"] {
189
+ box-sizing: border-box; // 1
190
+ padding: 0; // 2
191
+ }
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+
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+ //
194
+ // Fix the cursor style for Chrome's increment/decrement buttons. For certain
195
+ // `font-size` values of the `input`, it causes the cursor style of the
196
+ // decrement button to change from `default` to `text`.
197
+ //
198
+
199
+ input[type="number"]::-webkit-inner-spin-button,
200
+ input[type="number"]::-webkit-outer-spin-button {
201
+ height: auto;
202
+ }
203
+
204
+ //
205
+ // Remove default vertical scrollbar in IE 8/9/10/11.
206
+ //
207
+
208
+ textarea {
209
+ overflow: auto;
210
210
  }
@@ -1,41 +1,41 @@
1
-
2
- @mixin non-selectable {
3
- -webkit-user-select: none; /* Chrome/Safari */
4
- -moz-user-select: none; /* Firefox */
5
- -ms-user-select: none; /* IE10+ */
6
- /* Rules below not implemented in browsers yet */
7
- -o-user-select: none;
8
- user-select: none;
9
-
10
- cursor: default;
11
- }
12
-
13
- ::-webkit-scrollbar {
14
- width: 10px;
15
- height:10px;
16
- }
17
-
18
- ::-webkit-scrollbar-track {
19
- //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.8);
20
- border-radius: 0;
21
- background-color: color-lower-contrast($control-background, 4%);
22
- }
23
-
24
- ::-webkit-scrollbar-thumb {
25
- border-radius: 0;
26
- //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.9);
27
- background-color: color-lower-contrast($control-background, 8%);
28
- }
29
-
30
- @import 'components/controls-base';
31
- @import 'components/controls';
32
- @import 'components/slider';
33
- @import 'components/misc';
34
- @import 'components/tasks';
35
- @import 'components/viewport';
36
- @import 'components/log';
37
- @import 'components/sequence';
38
- @import 'components/transformer';
39
- @import 'components/toast';
40
- @import 'components/help';
1
+
2
+ @mixin non-selectable {
3
+ -webkit-user-select: none; /* Chrome/Safari */
4
+ -moz-user-select: none; /* Firefox */
5
+ -ms-user-select: none; /* IE10+ */
6
+ /* Rules below not implemented in browsers yet */
7
+ -o-user-select: none;
8
+ user-select: none;
9
+
10
+ cursor: default;
11
+ }
12
+
13
+ ::-webkit-scrollbar {
14
+ width: 10px;
15
+ height:10px;
16
+ }
17
+
18
+ ::-webkit-scrollbar-track {
19
+ //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.8);
20
+ border-radius: 0;
21
+ background-color: color-lower-contrast($control-background, 4%);
22
+ }
23
+
24
+ ::-webkit-scrollbar-thumb {
25
+ border-radius: 0;
26
+ //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.9);
27
+ background-color: color-lower-contrast($control-background, 8%);
28
+ }
29
+
30
+ @import 'components/controls-base';
31
+ @import 'components/controls';
32
+ @import 'components/slider';
33
+ @import 'components/misc';
34
+ @import 'components/tasks';
35
+ @import 'components/viewport';
36
+ @import 'components/log';
37
+ @import 'components/sequence';
38
+ @import 'components/transformer';
39
+ @import 'components/toast';
40
+ @import 'components/help';
41
41
  @import 'components/line-graph';
@@ -1,86 +1,86 @@
1
-
2
- // measures
3
-
4
- $control-label-width: 110px;
5
- $control-label-short-width: 70px;
6
- $row-height: 32px;
7
- $control-spacing: 10px;
8
- $entity-subtree-offset: 8px;
9
- $info-vertical-padding: 3px;
10
- $slider-border-radius-base: 6px;
11
-
12
- // layout
13
- $expanded-top-height: 100px;
14
- $expanded-bottom-height: 70px; // 3 * $row-height + 2;
15
- $expanded-right-width: 300px;
16
- $expanded-left-width: 330px;
17
-
18
- $collapsed-left-width: $row-height;
19
-
20
- $expanded-portrait-bottom-height: 10 * ($row-height + 1) + 3 * $control-spacing + 1;
21
- $expanded-portrait-top-height: 3 * $row-height + 1;
22
-
23
- $standard-bottom-height: 8 * ($row-height + 1) + 3 * $control-spacing + 1;
24
- $standard-top-height: 3 * $row-height + 1;
25
-
26
-
27
- $color-accent-cyan: color-lower-contrast(#95a5a6, 15%);
28
- $color-accent-red: color-lower-contrast(#e74c3c, 15%);
29
- $color-accent-gray: color-lower-contrast(#34495e, 10%);
30
- $color-accent-green: color-lower-contrast(#2ecc71, 10%);
31
- $color-accent-purple: color-lower-contrast(#9b59b6, 10%);
32
- $color-accent-blue: color-lower-contrast(#3498db, 5%);
33
- $color-accent-orange: color-lower-contrast(#e67e22, 5%);
34
-
35
- // TypeClass = 'Root' | 'Group' | 'Data' | 'Object' | 'Representation3D' | 'Behavior'
36
-
37
- $type-class-Root: $default-background;
38
- $type-class-Data: color-lower-contrast(#95a5a6, 15%);
39
- $type-class-Object: color-lower-contrast(#2ecc71, 10%);
40
- $type-class-Behavior: color-lower-contrast(#9b59b6, 10%);
41
- $type-class-Representation3D: color-lower-contrast(#3498db, 5%);
42
- $type-class-Group: color-lower-contrast(#e67e22, 5%);
43
-
44
- //////////////////////////////////////////////////
45
- // COLORS and COMPUTED COLORS
46
-
47
- $slider-disabledColor: #ccc;
48
-
49
- $control-background: color-increase-contrast($default-background, 6.5%);
50
- $border-color: color-increase-contrast($default-background, 15%);
51
- $msp-form-control-background: color-lower-contrast($default-background, 2.5%);
52
-
53
- // buttons
54
- $msp-btn-link-font-color: $font-color;
55
- $msp-btn-link-toggle-on-font-color: $font-color;
56
- $msp-btn-link-toggle-off-font-color: color-lower-contrast($font-color, 33%);
57
-
58
- // used for "actions" -- i.e. + in selection
59
- $msp-btn-remove-font-color: $font-color;
60
-
61
- $msp-btn-action-background: $msp-form-control-background;
62
-
63
- // update selection etc
64
- //!! $msp-btn-commit-on-font-color: $entity-current-font-color;
65
- $msp-btn-commit-on-hover-font-color: color-lower-contrast($msp-btn-commit-on-font-color, 20%); //!!Change
66
- $msp-btn-commit-on-background: color-lower-contrast($default-background, 2%);
67
- $msp-btn-commit-off-background: color-lower-contrast($default-background, 4%); //$control-background;
68
- $msp-btn-commit-off-font-color: $font-color;
69
-
70
- // log
71
- $log-font-color: color-lower-contrast($font-color, 5%);
72
- $log-timestamp-font-color: color-lower-contrast($font-color, 20%);
73
-
74
- // highlight
75
- $highlight-info-font-color: $hover-font-color;
76
- $highlight-info-additional-font-color: color-lower-contrast($hover-font-color, 20%);
77
-
78
- // entity state
79
- $entity-color-fully-visible: $font-color;
80
- $entity-color-not-visible: color-lower-contrast($font-color, 66%);
81
- $entity-color-partialy-visible: color-lower-contrast($font-color, 33%);
82
- $entity-tag-color: color-lower-contrast($font-color, 20%);
83
-
84
- // sequence
85
- $sequence-background: $default-background;
1
+
2
+ // measures
3
+
4
+ $control-label-width: 110px;
5
+ $control-label-short-width: 70px;
6
+ $row-height: 32px;
7
+ $control-spacing: 10px;
8
+ $entity-subtree-offset: 8px;
9
+ $info-vertical-padding: 3px;
10
+ $slider-border-radius-base: 6px;
11
+
12
+ // layout
13
+ $expanded-top-height: 100px;
14
+ $expanded-bottom-height: 70px; // 3 * $row-height + 2;
15
+ $expanded-right-width: 300px;
16
+ $expanded-left-width: 330px;
17
+
18
+ $collapsed-left-width: $row-height;
19
+
20
+ $expanded-portrait-bottom-height: 10 * ($row-height + 1) + 3 * $control-spacing + 1;
21
+ $expanded-portrait-top-height: 3 * $row-height + 1;
22
+
23
+ $standard-bottom-height: 8 * ($row-height + 1) + 3 * $control-spacing + 1;
24
+ $standard-top-height: 3 * $row-height + 1;
25
+
26
+
27
+ $color-accent-cyan: color-lower-contrast(#95a5a6, 15%);
28
+ $color-accent-red: color-lower-contrast(#e74c3c, 15%);
29
+ $color-accent-gray: color-lower-contrast(#34495e, 10%);
30
+ $color-accent-green: color-lower-contrast(#2ecc71, 10%);
31
+ $color-accent-purple: color-lower-contrast(#9b59b6, 10%);
32
+ $color-accent-blue: color-lower-contrast(#3498db, 5%);
33
+ $color-accent-orange: color-lower-contrast(#e67e22, 5%);
34
+
35
+ // TypeClass = 'Root' | 'Group' | 'Data' | 'Object' | 'Representation3D' | 'Behavior'
36
+
37
+ $type-class-Root: $default-background;
38
+ $type-class-Data: color-lower-contrast(#95a5a6, 15%);
39
+ $type-class-Object: color-lower-contrast(#2ecc71, 10%);
40
+ $type-class-Behavior: color-lower-contrast(#9b59b6, 10%);
41
+ $type-class-Representation3D: color-lower-contrast(#3498db, 5%);
42
+ $type-class-Group: color-lower-contrast(#e67e22, 5%);
43
+
44
+ //////////////////////////////////////////////////
45
+ // COLORS and COMPUTED COLORS
46
+
47
+ $slider-disabledColor: #ccc;
48
+
49
+ $control-background: color-increase-contrast($default-background, 6.5%);
50
+ $border-color: color-increase-contrast($default-background, 15%);
51
+ $msp-form-control-background: color-lower-contrast($default-background, 2.5%);
52
+
53
+ // buttons
54
+ $msp-btn-link-font-color: $font-color;
55
+ $msp-btn-link-toggle-on-font-color: $font-color;
56
+ $msp-btn-link-toggle-off-font-color: color-lower-contrast($font-color, 33%);
57
+
58
+ // used for "actions" -- i.e. + in selection
59
+ $msp-btn-remove-font-color: $font-color;
60
+
61
+ $msp-btn-action-background: $msp-form-control-background;
62
+
63
+ // update selection etc
64
+ //!! $msp-btn-commit-on-font-color: $entity-current-font-color;
65
+ $msp-btn-commit-on-hover-font-color: color-lower-contrast($msp-btn-commit-on-font-color, 20%); //!!Change
66
+ $msp-btn-commit-on-background: color-lower-contrast($default-background, 2%);
67
+ $msp-btn-commit-off-background: color-lower-contrast($default-background, 4%); //$control-background;
68
+ $msp-btn-commit-off-font-color: $font-color;
69
+
70
+ // log
71
+ $log-font-color: color-lower-contrast($font-color, 5%);
72
+ $log-timestamp-font-color: color-lower-contrast($font-color, 20%);
73
+
74
+ // highlight
75
+ $highlight-info-font-color: $hover-font-color;
76
+ $highlight-info-additional-font-color: color-lower-contrast($hover-font-color, 20%);
77
+
78
+ // entity state
79
+ $entity-color-fully-visible: $font-color;
80
+ $entity-color-not-visible: color-lower-contrast($font-color, 66%);
81
+ $entity-color-partialy-visible: color-lower-contrast($font-color, 33%);
82
+ $entity-tag-color: color-lower-contrast($font-color, 20%);
83
+
84
+ // sequence
85
+ $sequence-background: $default-background;
86
86
  $sequence-number-color: $hover-font-color;
@@ -1,2 +1,2 @@
1
- @import 'colors/blue';
1
+ @import 'colors/blue';
2
2
  @import 'base/base';