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
@@ -1,334 +1,334 @@
1
-
2
-
3
- .msp-form-control {
4
- display: block;
5
- width: 100%;
6
- background: $msp-form-control-background;
7
- // color: $font-color;
8
- border: none; // !important;
9
- padding: 0 $control-spacing;
10
- line-height: $row-height - 2px;
11
- height: $row-height;
12
- -webkit-appearance: none;
13
- -moz-appearance: none;
14
- appearance: none;
15
- -webkit-box-shadow: none; // iOS <4.3 & Android <4.1
16
- box-shadow: none;
17
- // box-shadow: none !important;
18
- background-image: none;
19
-
20
- // Firefox
21
- &::-moz-placeholder {
22
- color: color-lower-contrast($font-color, 33%);
23
- opacity: 1; // Override Firefox's unusual default opacity; see https://github.com/twbs/bootstrap/pull/11526
24
- }
25
- &:-ms-input-placeholder { color: color-lower-contrast($font-color, 33%); } // Internet Explorer 10+
26
- &::-webkit-input-placeholder { color: color-lower-contrast($font-color, 33%); } // Safari and Chrome
27
-
28
- &:hover {
29
- color: $hover-font-color;
30
- background-color: color-increase-contrast($msp-form-control-background, 5%);
31
- border: none;
32
- outline-offset: -1px !important;
33
- outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
34
- }
35
-
36
- &:active, &:focus {
37
- color: $font-color;
38
- background-color: $msp-form-control-background;
39
- border: none;
40
- outline-offset: 0;
41
- outline: none;
42
- }
43
-
44
- // Disabled and read-only inputs
45
- //
46
- // HTML5 says that controls under a fieldset > legend:first-child won't be
47
- // disabled if the fieldset is disabled. Due to implementation difficulty, we
48
- // don't honor that edge case; we style them as disabled anyway.
49
- &[disabled],
50
- &[readonly],
51
- fieldset[disabled] & {
52
- background: $default-background;
53
- opacity: 0.35;
54
- }
55
- }
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-
57
- .msp-btn {
58
- @extend .msp-form-control;
59
-
60
- display: inline-block;
61
- margin-bottom: 0; // For input.msp-btn
62
- text-align: center;
63
- touch-action: manipulation;
64
- cursor: pointer;
65
- background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214
66
- white-space: nowrap;
67
- @include user-select(none);
68
-
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-
70
- padding: 0 $control-spacing;
71
- line-height: $row-height;
72
- border: none;
73
- -moz-box-sizing: border-box;
74
- box-sizing: border-box;
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-
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- &[disabled] {
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- background: $default-background;
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- opacity: 0.35;
79
- }
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- }
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-
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- .msp-btn-block {
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- display: block;
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- width: 100%;
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- }
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-
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- .msp-btn, .msp-btn:active, .msp-btn-link:focus, .msp-btn:hover {
88
- outline: none;
89
- }
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-
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- .msp-material-icon {
92
- svg {
93
- display: inline-flex;
94
- vertical-align: middle;
95
- font-size: 1.2em;
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- margin-bottom: 3px;
97
-
98
- fill: currentColor;
99
- width: 1em;
100
- height: 1em;
101
- flex-shrink: 0;
102
- user-select: none;
103
- }
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- }
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-
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- .msp-btn-block {
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- > .msp-material-icon {
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- margin-left: 0;
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- margin-right: .4em;
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- }
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- }
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-
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- .msp-btn-childless {
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- > .msp-material-icon {
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- margin-left: 0;
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- margin-right: 0;
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- }
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- }
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-
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- .msp-btn-icon {
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- border: none;
122
- height: $row-height;
123
- width: $row-height;
124
- line-height: $row-height;
125
- padding: 0;
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- text-align: center;
127
-
128
- &:hover {
129
- color: $hover-font-color;
130
- background-color: color-increase-contrast($msp-form-control-background, 5%);
131
- border: none;
132
- outline-offset: -1px !important;
133
- outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
134
- }
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-
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- &[disabled], &[disabled]:hover, &[disabled]:active {
137
- color: $msp-btn-link-toggle-off-font-color;
138
- }
139
- }
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-
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- .msp-btn-icon-small {
142
- border: none;
143
- height: $row-height;
144
- width: 20px;
145
- // font-size: 85%;
146
- line-height: $row-height;
147
- padding: 0;
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- text-align: center;
149
-
150
- &:hover {
151
- color: $hover-font-color;
152
- background-color: color-increase-contrast($msp-form-control-background, 5%);
153
- border: none;
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- outline-offset: -1px !important;
155
- outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
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- }
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-
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- &[disabled], &[disabled]:hover, &[disabled]:active {
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- color: $msp-btn-link-toggle-off-font-color;
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- }
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- }
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-
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- .msp-btn-link {
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- font-weight: normal;
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- border-radius: 0;
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-
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- &,
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- &:active,
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- &.active,
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- &[disabled],
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- fieldset[disabled] & {
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- background-color: transparent;
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- -webkit-box-shadow: none; // iOS <4.3 & Android <4.1
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- box-shadow: none;
175
- }
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- &,
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- &:hover,
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- &:focus,
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- &:active {
180
- border-color: transparent;
181
- }
182
- &:hover,
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- &:focus {
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- text-decoration: none;
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- background-color: transparent;
186
- }
187
- &[disabled],
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- fieldset[disabled] & {
189
- &:hover,
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- &:focus {
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- text-decoration: none;
192
- }
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- }
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-
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- .msp-icon {
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- font-size: 100%;
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- }
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- }
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-
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- .msp-btn-link, .msp-btn-link:active, .msp-btn-link:focus {
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- color: $msp-btn-link-font-color;
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- text-decoration: none;
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- }
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-
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- .msp-btn-link:hover {
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- color: $hover-font-color;
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- text-decoration: none;
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- }
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-
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- .msp-btn-link-toggle-on {
211
- color: $msp-btn-link-toggle-on-font-color;
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- }
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-
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- .msp-btn-link-toggle-off, .msp-btn-link-toggle-off:active, .msp-btn-link-toggle-off:focus {
215
- color: $msp-btn-link-toggle-off-font-color !important;
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- }
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-
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- .msp-btn-link-toggle-off:hover, .msp-btn-link-toggle-on:hover {
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- color: $hover-font-color !important;
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- }
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-
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- @mixin msp-btn($name, $font, $bg) {
223
- .msp-btn-#{$name}, .msp-btn-#{$name}:active, .msp-btn-#{$name}:focus {
224
- color: $font;
225
- background: $bg;
226
- }
227
- .msp-btn-#{$name}:hover {
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- color: $hover-font-color;
229
- background: color-lower-contrast($bg, 2.5%);
230
- }
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-
232
- .msp-btn-#{$name}[disabled], .msp-btn-#{$name}[disabled]:hover,
233
- .msp-btn-#{$name}[disabled]:active, .msp-btn-#{$name}[disabled]:focus {
234
- color: color-lower-contrast($font, 1%);
235
- }
236
- }
237
-
238
- // @include msp-btn('remove', $msp-btn-remove-font-color, $msp-btn-remove-background);
239
- @include msp-btn('action', $font-color, $msp-btn-action-background);
240
- @include msp-btn('commit-on', $msp-btn-commit-on-font-color, $msp-btn-commit-on-background);
241
- @include msp-btn('commit-off', $msp-btn-commit-off-font-color, $msp-btn-commit-off-background);
242
-
243
- .msp-btn-remove:hover {
244
- color: $msp-btn-remove-hover-font-color;
245
- }
246
- .msp-btn-commit-on:hover {
247
- color: $msp-btn-commit-on-hover-font-color;
248
- }
249
-
250
- .msp-btn-action {
251
- height: $row-height;
252
- line-height: $row-height;
253
- }
254
-
255
- input[type="file"] {
256
- display: block;
257
- }
258
-
259
- // Make range inputs behave like textual form controls
260
- input[type="range"] {
261
- display: block;
262
- width: 100%;
263
- }
264
-
265
- // Make multiple select elements height not fixed
266
- select[multiple],
267
- select[size] {
268
- height: auto;
269
- }
270
-
271
- // Reset height for `textarea`s
272
- textarea.msp-form-control {
273
- height: auto;
274
- }
275
-
276
- .msp-control-top-offset {
277
- margin-top: 1px;
278
- }
279
-
280
- .msp-btn-commit {
281
- text-align: right;
282
- padding-top: 0;
283
- padding-bottom: 0;
284
- padding-right: $control-spacing;
285
- padding-left: 0;
286
- line-height: $row-height;
287
- border: none;
288
- overflow: hidden;
289
- font-weight: bold;
290
-
291
- .msp-icon {
292
- display: block-inline;
293
- line-height: $row-height;
294
- width: $row-height;
295
- text-align: center;
296
- }
297
- }
298
-
299
- select.msp-form-control {
300
- background: none;
301
- background-color: $msp-form-control-background;
302
- background-size: 8px 12px;
303
- background-image: url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAUCAMAAACzvE1FAAAADFBMVEUzMzMzMzMzMzMzMzMKAG/3AAAAA3RSTlMAf4C/aSLHAAAAPElEQVR42q3NMQ4AIAgEQTn//2cLdRKppSGzBYwzVXvznNWs8C58CiussPJj8h6NwgorrKRdTvuV9v16Afn0AYFOB7aYAAAAAElFTkSuQmCC);
304
- background-repeat: no-repeat;
305
- background-position: right $control-spacing center;
306
- padding-right: ($row-height - 8px);
307
- }
308
-
309
- select.msp-form-control:-moz-focusring {
310
- color: transparent;
311
- text-shadow: 0 0 0 $font-color;
312
- }
313
-
314
- .msp-default-bg {
315
- background: $default-background;
316
- }
317
-
318
- .msp-transparent-bg {
319
- background: transparent;
320
- }
321
-
322
- .msp-no-hover-outline {
323
- &:hover {
324
- color: $hover-font-color;
325
- background-color: inherit;
326
- border: none;
327
- outline-offset: 0 !important;
328
- outline: none !important;
329
- }
330
- }
331
-
332
- .msp-icon-inline {
333
- margin-right: 8px;
1
+
2
+
3
+ .msp-form-control {
4
+ display: block;
5
+ width: 100%;
6
+ background: $msp-form-control-background;
7
+ // color: $font-color;
8
+ border: none; // !important;
9
+ padding: 0 $control-spacing;
10
+ line-height: $row-height - 2px;
11
+ height: $row-height;
12
+ -webkit-appearance: none;
13
+ -moz-appearance: none;
14
+ appearance: none;
15
+ -webkit-box-shadow: none; // iOS <4.3 & Android <4.1
16
+ box-shadow: none;
17
+ // box-shadow: none !important;
18
+ background-image: none;
19
+
20
+ // Firefox
21
+ &::-moz-placeholder {
22
+ color: color-lower-contrast($font-color, 33%);
23
+ opacity: 1; // Override Firefox's unusual default opacity; see https://github.com/twbs/bootstrap/pull/11526
24
+ }
25
+ &:-ms-input-placeholder { color: color-lower-contrast($font-color, 33%); } // Internet Explorer 10+
26
+ &::-webkit-input-placeholder { color: color-lower-contrast($font-color, 33%); } // Safari and Chrome
27
+
28
+ &:hover {
29
+ color: $hover-font-color;
30
+ background-color: color-increase-contrast($msp-form-control-background, 5%);
31
+ border: none;
32
+ outline-offset: -1px !important;
33
+ outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
34
+ }
35
+
36
+ &:active, &:focus {
37
+ color: $font-color;
38
+ background-color: $msp-form-control-background;
39
+ border: none;
40
+ outline-offset: 0;
41
+ outline: none;
42
+ }
43
+
44
+ // Disabled and read-only inputs
45
+ //
46
+ // HTML5 says that controls under a fieldset > legend:first-child won't be
47
+ // disabled if the fieldset is disabled. Due to implementation difficulty, we
48
+ // don't honor that edge case; we style them as disabled anyway.
49
+ &[disabled],
50
+ &[readonly],
51
+ fieldset[disabled] & {
52
+ background: $default-background;
53
+ opacity: 0.35;
54
+ }
55
+ }
56
+
57
+ .msp-btn {
58
+ @extend .msp-form-control;
59
+
60
+ display: inline-block;
61
+ margin-bottom: 0; // For input.msp-btn
62
+ text-align: center;
63
+ touch-action: manipulation;
64
+ cursor: pointer;
65
+ background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214
66
+ white-space: nowrap;
67
+ @include user-select(none);
68
+
69
+
70
+ padding: 0 $control-spacing;
71
+ line-height: $row-height;
72
+ border: none;
73
+ -moz-box-sizing: border-box;
74
+ box-sizing: border-box;
75
+
76
+ &[disabled] {
77
+ background: $default-background;
78
+ opacity: 0.35;
79
+ }
80
+ }
81
+
82
+ .msp-btn-block {
83
+ display: block;
84
+ width: 100%;
85
+ }
86
+
87
+ .msp-btn, .msp-btn:active, .msp-btn-link:focus, .msp-btn:hover {
88
+ outline: none;
89
+ }
90
+
91
+ .msp-material-icon {
92
+ svg {
93
+ display: inline-flex;
94
+ vertical-align: middle;
95
+ font-size: 1.2em;
96
+ margin-bottom: 3px;
97
+
98
+ fill: currentColor;
99
+ width: 1em;
100
+ height: 1em;
101
+ flex-shrink: 0;
102
+ user-select: none;
103
+ }
104
+ }
105
+
106
+ .msp-btn-block {
107
+ > .msp-material-icon {
108
+ margin-left: 0;
109
+ margin-right: .4em;
110
+ }
111
+ }
112
+
113
+ .msp-btn-childless {
114
+ > .msp-material-icon {
115
+ margin-left: 0;
116
+ margin-right: 0;
117
+ }
118
+ }
119
+
120
+ .msp-btn-icon {
121
+ border: none;
122
+ height: $row-height;
123
+ width: $row-height;
124
+ line-height: $row-height;
125
+ padding: 0;
126
+ text-align: center;
127
+
128
+ &:hover {
129
+ color: $hover-font-color;
130
+ background-color: color-increase-contrast($msp-form-control-background, 5%);
131
+ border: none;
132
+ outline-offset: -1px !important;
133
+ outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
134
+ }
135
+
136
+ &[disabled], &[disabled]:hover, &[disabled]:active {
137
+ color: $msp-btn-link-toggle-off-font-color;
138
+ }
139
+ }
140
+
141
+ .msp-btn-icon-small {
142
+ border: none;
143
+ height: $row-height;
144
+ width: 20px;
145
+ // font-size: 85%;
146
+ line-height: $row-height;
147
+ padding: 0;
148
+ text-align: center;
149
+
150
+ &:hover {
151
+ color: $hover-font-color;
152
+ background-color: color-increase-contrast($msp-form-control-background, 5%);
153
+ border: none;
154
+ outline-offset: -1px !important;
155
+ outline: 1px solid color-increase-contrast($msp-form-control-background, 20%) !important;
156
+ }
157
+
158
+ &[disabled], &[disabled]:hover, &[disabled]:active {
159
+ color: $msp-btn-link-toggle-off-font-color;
160
+ }
161
+ }
162
+
163
+ .msp-btn-link {
164
+ font-weight: normal;
165
+ border-radius: 0;
166
+
167
+ &,
168
+ &:active,
169
+ &.active,
170
+ &[disabled],
171
+ fieldset[disabled] & {
172
+ background-color: transparent;
173
+ -webkit-box-shadow: none; // iOS <4.3 & Android <4.1
174
+ box-shadow: none;
175
+ }
176
+ &,
177
+ &:hover,
178
+ &:focus,
179
+ &:active {
180
+ border-color: transparent;
181
+ }
182
+ &:hover,
183
+ &:focus {
184
+ text-decoration: none;
185
+ background-color: transparent;
186
+ }
187
+ &[disabled],
188
+ fieldset[disabled] & {
189
+ &:hover,
190
+ &:focus {
191
+ text-decoration: none;
192
+ }
193
+ }
194
+
195
+ .msp-icon {
196
+ font-size: 100%;
197
+ }
198
+ }
199
+
200
+ .msp-btn-link, .msp-btn-link:active, .msp-btn-link:focus {
201
+ color: $msp-btn-link-font-color;
202
+ text-decoration: none;
203
+ }
204
+
205
+ .msp-btn-link:hover {
206
+ color: $hover-font-color;
207
+ text-decoration: none;
208
+ }
209
+
210
+ .msp-btn-link-toggle-on {
211
+ color: $msp-btn-link-toggle-on-font-color;
212
+ }
213
+
214
+ .msp-btn-link-toggle-off, .msp-btn-link-toggle-off:active, .msp-btn-link-toggle-off:focus {
215
+ color: $msp-btn-link-toggle-off-font-color !important;
216
+ }
217
+
218
+ .msp-btn-link-toggle-off:hover, .msp-btn-link-toggle-on:hover {
219
+ color: $hover-font-color !important;
220
+ }
221
+
222
+ @mixin msp-btn($name, $font, $bg) {
223
+ .msp-btn-#{$name}, .msp-btn-#{$name}:active, .msp-btn-#{$name}:focus {
224
+ color: $font;
225
+ background: $bg;
226
+ }
227
+ .msp-btn-#{$name}:hover {
228
+ color: $hover-font-color;
229
+ background: color-lower-contrast($bg, 2.5%);
230
+ }
231
+
232
+ .msp-btn-#{$name}[disabled], .msp-btn-#{$name}[disabled]:hover,
233
+ .msp-btn-#{$name}[disabled]:active, .msp-btn-#{$name}[disabled]:focus {
234
+ color: color-lower-contrast($font, 1%);
235
+ }
236
+ }
237
+
238
+ // @include msp-btn('remove', $msp-btn-remove-font-color, $msp-btn-remove-background);
239
+ @include msp-btn('action', $font-color, $msp-btn-action-background);
240
+ @include msp-btn('commit-on', $msp-btn-commit-on-font-color, $msp-btn-commit-on-background);
241
+ @include msp-btn('commit-off', $msp-btn-commit-off-font-color, $msp-btn-commit-off-background);
242
+
243
+ .msp-btn-remove:hover {
244
+ color: $msp-btn-remove-hover-font-color;
245
+ }
246
+ .msp-btn-commit-on:hover {
247
+ color: $msp-btn-commit-on-hover-font-color;
248
+ }
249
+
250
+ .msp-btn-action {
251
+ height: $row-height;
252
+ line-height: $row-height;
253
+ }
254
+
255
+ input[type="file"] {
256
+ display: block;
257
+ }
258
+
259
+ // Make range inputs behave like textual form controls
260
+ input[type="range"] {
261
+ display: block;
262
+ width: 100%;
263
+ }
264
+
265
+ // Make multiple select elements height not fixed
266
+ select[multiple],
267
+ select[size] {
268
+ height: auto;
269
+ }
270
+
271
+ // Reset height for `textarea`s
272
+ textarea.msp-form-control {
273
+ height: auto;
274
+ }
275
+
276
+ .msp-control-top-offset {
277
+ margin-top: 1px;
278
+ }
279
+
280
+ .msp-btn-commit {
281
+ text-align: right;
282
+ padding-top: 0;
283
+ padding-bottom: 0;
284
+ padding-right: $control-spacing;
285
+ padding-left: 0;
286
+ line-height: $row-height;
287
+ border: none;
288
+ overflow: hidden;
289
+ font-weight: bold;
290
+
291
+ .msp-icon {
292
+ display: block-inline;
293
+ line-height: $row-height;
294
+ width: $row-height;
295
+ text-align: center;
296
+ }
297
+ }
298
+
299
+ select.msp-form-control {
300
+ background: none;
301
+ background-color: $msp-form-control-background;
302
+ background-size: 8px 12px;
303
+ background-image: url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAUCAMAAACzvE1FAAAADFBMVEUzMzMzMzMzMzMzMzMKAG/3AAAAA3RSTlMAf4C/aSLHAAAAPElEQVR42q3NMQ4AIAgEQTn//2cLdRKppSGzBYwzVXvznNWs8C58CiussPJj8h6NwgorrKRdTvuV9v16Afn0AYFOB7aYAAAAAElFTkSuQmCC);
304
+ background-repeat: no-repeat;
305
+ background-position: right $control-spacing center;
306
+ padding-right: ($row-height - 8px);
307
+ }
308
+
309
+ select.msp-form-control:-moz-focusring {
310
+ color: transparent;
311
+ text-shadow: 0 0 0 $font-color;
312
+ }
313
+
314
+ .msp-default-bg {
315
+ background: $default-background;
316
+ }
317
+
318
+ .msp-transparent-bg {
319
+ background: transparent;
320
+ }
321
+
322
+ .msp-no-hover-outline {
323
+ &:hover {
324
+ color: $hover-font-color;
325
+ background-color: inherit;
326
+ border: none;
327
+ outline-offset: 0 !important;
328
+ outline: none !important;
329
+ }
330
+ }
331
+
332
+ .msp-icon-inline {
333
+ margin-right: 8px;
334
334
  }