molstar 4.0.1 → 4.2.0
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.
- package/LICENSE +20 -20
- package/README.md +197 -197
- package/build/viewer/embedded.html +52 -52
- package/build/viewer/index.html +129 -129
- package/build/viewer/molstar.js +1 -1
- package/build/viewer/molstar.js.LICENSE.txt +0 -9
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/viewport.d.ts +8 -8
- package/lib/apps/mesoscale-explorer/behavior/camera.d.ts +1 -1
- package/lib/apps/mesoscale-explorer/behavior/select.d.ts +1 -1
- package/lib/apps/mesoscale-explorer/data/cellpack/model.d.ts +2 -2
- package/lib/apps/mesoscale-explorer/data/cellpack/preset.d.ts +1 -1
- package/lib/apps/mesoscale-explorer/data/cellpack/preset.js +5 -5
- package/lib/apps/mesoscale-explorer/data/generic/preset.d.ts +1 -1
- package/lib/apps/mesoscale-explorer/data/generic/preset.js +3 -3
- package/lib/apps/mesoscale-explorer/data/mmcif/preset.d.ts +1 -1
- package/lib/apps/mesoscale-explorer/data/mmcif/preset.js +3 -3
- package/lib/apps/mesoscale-explorer/data/petworld/preset.d.ts +1 -1
- package/lib/apps/mesoscale-explorer/data/petworld/preset.js +3 -3
- package/lib/apps/mesoscale-explorer/data/state.d.ts +19 -10
- package/lib/apps/mesoscale-explorer/data/state.js +14 -2
- package/lib/apps/mesoscale-explorer/index.html +100 -100
- package/lib/apps/mesoscale-explorer/style.scss +33 -33
- package/lib/apps/mesoscale-explorer/ui/entities.d.ts +19 -13
- package/lib/apps/mesoscale-explorer/ui/entities.js +23 -4
- package/lib/apps/viewer/app.d.ts +30 -24
- package/lib/apps/viewer/app.js +6 -6
- package/lib/apps/viewer/embedded.html +52 -52
- package/lib/apps/viewer/index.html +129 -129
- package/lib/cli/chem-comp-dict/create-ions.js +9 -9
- package/lib/cli/chem-comp-dict/create-saccharides.js +9 -9
- package/lib/cli/chem-comp-dict/util.d.ts +112 -112
- package/lib/cli/cifschema/util/cif-dic.js +1 -0
- package/lib/cli/cifschema/util/generate.js +12 -12
- package/lib/cli/lipid-params/index.js +9 -9
- package/lib/cli/mvs/mvs-print-schema.d.ts +1 -0
- package/lib/cli/mvs/mvs-print-schema.js +1 -0
- package/lib/cli/mvs/mvs-render.d.ts +1 -0
- package/lib/cli/mvs/mvs-render.js +1 -0
- package/lib/cli/mvs/mvs-validate.d.ts +1 -0
- package/lib/cli/mvs/mvs-validate.js +1 -0
- package/lib/commonjs/apps/docking-viewer/viewport.d.ts +8 -8
- package/lib/commonjs/apps/mesoscale-explorer/behavior/camera.d.ts +1 -1
- package/lib/commonjs/apps/mesoscale-explorer/behavior/select.d.ts +1 -1
- package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/model.d.ts +2 -2
- package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.d.ts +1 -1
- package/lib/commonjs/apps/mesoscale-explorer/data/cellpack/preset.js +5 -5
- package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.d.ts +1 -1
- package/lib/commonjs/apps/mesoscale-explorer/data/generic/preset.js +3 -3
- package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.d.ts +1 -1
- package/lib/commonjs/apps/mesoscale-explorer/data/mmcif/preset.js +3 -3
- package/lib/commonjs/apps/mesoscale-explorer/data/petworld/preset.d.ts +1 -1
- package/lib/commonjs/apps/mesoscale-explorer/data/petworld/preset.js +3 -3
- package/lib/commonjs/apps/mesoscale-explorer/data/state.d.ts +19 -10
- package/lib/commonjs/apps/mesoscale-explorer/data/state.js +15 -3
- package/lib/commonjs/apps/mesoscale-explorer/ui/entities.d.ts +19 -13
- package/lib/commonjs/apps/mesoscale-explorer/ui/entities.js +22 -3
- package/lib/commonjs/apps/viewer/app.d.ts +30 -24
- package/lib/commonjs/apps/viewer/app.js +6 -6
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +9 -9
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +9 -9
- package/lib/commonjs/cli/chem-comp-dict/util.d.ts +112 -112
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -0
- package/lib/commonjs/cli/cifschema/util/generate.js +12 -12
- package/lib/commonjs/cli/lipid-params/index.js +9 -9
- package/lib/commonjs/cli/mvs/mvs-print-schema.d.ts +1 -0
- package/lib/commonjs/cli/mvs/mvs-print-schema.js +1 -0
- package/lib/commonjs/cli/mvs/mvs-render.d.ts +1 -0
- package/lib/commonjs/cli/mvs/mvs-render.js +1 -0
- package/lib/commonjs/cli/mvs/mvs-validate.d.ts +1 -0
- package/lib/commonjs/cli/mvs/mvs-validate.js +1 -0
- package/lib/commonjs/examples/alpha-orbitals/example-data.js +160 -160
- package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +136 -136
- package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts +2 -2
- package/lib/commonjs/extensions/anvil/behavior.d.ts +10 -9
- package/lib/commonjs/extensions/anvil/representation.d.ts +5 -0
- package/lib/commonjs/extensions/assembly-symmetry/behavior.d.ts +2 -1
- package/lib/commonjs/extensions/assembly-symmetry/prop.js +24 -24
- package/lib/commonjs/extensions/assembly-symmetry/representation.d.ts +1 -0
- package/lib/commonjs/extensions/backgrounds/index.d.ts +2 -2
- package/lib/commonjs/extensions/backgrounds/index.js +2 -1
- package/lib/commonjs/extensions/dnatco/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts +10 -10
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +5 -5
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
- package/lib/commonjs/extensions/dnatco/ntc-tube/behavior.d.ts +10 -10
- package/lib/commonjs/extensions/dnatco/ntc-tube/behavior.js +5 -5
- package/lib/commonjs/extensions/dnatco/ntc-tube/representation.d.ts +3 -0
- package/lib/commonjs/extensions/g3d/format.d.ts +6 -6
- package/lib/commonjs/extensions/geo-export/glb-exporter.d.ts +1 -1
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +6 -4
- package/lib/commonjs/extensions/geo-export/index.d.ts +1 -1
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +41 -41
- package/lib/commonjs/extensions/meshes/mesh-extension.d.ts +2 -3
- package/lib/commonjs/extensions/meshes/mesh-streaming/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/meshes/mesh-streaming/server-info.d.ts +2 -2
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +9 -9
- package/lib/commonjs/extensions/model-export/index.d.ts +1 -1
- package/lib/commonjs/extensions/mp4-export/index.d.ts +1 -1
- package/lib/commonjs/extensions/mvs/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/mvs/camera.d.ts +2 -0
- package/lib/commonjs/extensions/mvs/camera.js +29 -2
- package/lib/commonjs/extensions/mvs/components/annotation-label/representation.d.ts +4 -0
- package/lib/commonjs/extensions/mvs/components/annotation-label/visual.d.ts +1 -0
- package/lib/commonjs/extensions/mvs/components/custom-label/representation.d.ts +4 -2
- package/lib/commonjs/extensions/mvs/components/custom-label/visual.d.ts +1 -0
- package/lib/commonjs/extensions/mvs/components/formats.d.ts +6 -4
- package/lib/commonjs/extensions/mvs/components/formats.js +2 -1
- package/lib/commonjs/extensions/mvs/load-helpers.d.ts +1 -1
- package/lib/commonjs/extensions/mvs/load.d.ts +2 -0
- package/lib/commonjs/extensions/mvs/load.js +12 -6
- package/lib/commonjs/extensions/mvs/tree/mvs/mvs-builder.d.ts +2 -8
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts +22 -22
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
- package/lib/commonjs/extensions/sb-ncbr/partial-charges/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/sb-ncbr/partial-charges/preset.d.ts +4 -4
- package/lib/commonjs/extensions/volumes-and-segmentations/entry-meshes.d.ts +1 -1
- package/lib/commonjs/extensions/volumes-and-segmentations/entry-root.d.ts +5 -5
- package/lib/commonjs/extensions/volumes-and-segmentations/entry-segmentation.d.ts +1 -1
- package/lib/commonjs/extensions/volumes-and-segmentations/entry-state.d.ts +2 -2
- package/lib/commonjs/extensions/volumes-and-segmentations/global-state.d.ts +2 -2
- package/lib/commonjs/extensions/volumes-and-segmentations/helpers.d.ts +1 -1
- package/lib/commonjs/extensions/volumes-and-segmentations/index.d.ts +1 -1
- package/lib/commonjs/extensions/wwpdb/ccd/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/wwpdb/ccd/representation.d.ts +4 -4
- package/lib/commonjs/extensions/zenodo/index.d.ts +1 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +14 -2
- package/lib/commonjs/mol-canvas3d/canvas3d.js +2 -2
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/passes/background.d.ts +6 -1
- package/lib/commonjs/mol-canvas3d/passes/background.js +13 -1
- package/lib/commonjs/mol-canvas3d/passes/bloom.d.ts +37 -0
- package/lib/commonjs/mol-canvas3d/passes/bloom.js +272 -0
- package/lib/commonjs/mol-canvas3d/passes/dpoit.js +4 -2
- package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +11 -7
- package/lib/commonjs/mol-canvas3d/passes/draw.js +29 -3
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +6 -0
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +31 -5
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +35 -40
- package/lib/commonjs/mol-geo/geometry/base.d.ts +3 -1
- package/lib/commonjs/mol-geo/geometry/base.js +4 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -1
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +4 -1
- package/lib/commonjs/mol-geo/geometry/emissive-data.d.ts +26 -0
- package/lib/commonjs/mol-geo/geometry/emissive-data.js +80 -0
- package/lib/commonjs/mol-geo/geometry/image/image.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +4 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +3 -2
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +4 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +36 -2
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +11 -4
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +3 -2
- package/lib/commonjs/mol-geo/geometry/points/points.js +4 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +7 -3
- package/lib/commonjs/mol-geo/geometry/text/text.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/text/text.js +4 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +34 -2
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +3 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +14 -4
- package/lib/commonjs/mol-geo/util/location-iterator.d.ts +5 -2
- package/lib/commonjs/mol-geo/util/location-iterator.js +8 -3
- package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/image.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/lines.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/mesh.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/points.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/schema.d.ts +24 -1
- package/lib/commonjs/mol-gl/renderable/schema.js +15 -2
- package/lib/commonjs/mol-gl/renderable/spheres.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/text.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +10 -0
- package/lib/commonjs/mol-gl/renderable.d.ts +1 -1
- package/lib/commonjs/mol-gl/renderable.js +2 -2
- package/lib/commonjs/mol-gl/renderer.d.ts +2 -1
- package/lib/commonjs/mol-gl/renderer.js +58 -49
- package/lib/commonjs/mol-gl/scene.d.ts +3 -1
- package/lib/commonjs/mol-gl/scene.js +26 -1
- package/lib/commonjs/mol-gl/shader/background.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/background.frag.js +95 -94
- package/lib/commonjs/mol-gl/shader/background.vert.js +11 -11
- package/lib/commonjs/mol-gl/shader/blend-back-dpoit.frag.js +13 -13
- package/lib/commonjs/mol-gl/shader/bloom/blur.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/bloom/blur.frag.js +32 -0
- package/lib/commonjs/mol-gl/shader/bloom/composite.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/bloom/composite.frag.js +37 -0
- package/lib/commonjs/mol-gl/shader/bloom/luminosity.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/bloom/luminosity.frag.js +56 -0
- package/lib/commonjs/mol-gl/shader/cas.frag.js +144 -144
- package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +31 -31
- package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +12 -12
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +78 -70
- package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +16 -16
- package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +8 -8
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +140 -112
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +6 -6
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +8 -8
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +112 -123
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +14 -14
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +18 -18
- package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +12 -12
- package/lib/commonjs/mol-gl/shader/chunks/check-transparency.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/check-transparency.glsl.js +20 -0
- package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +7 -7
- package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +5 -5
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +60 -51
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +122 -92
- package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js +104 -104
- package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +150 -149
- package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +61 -61
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +234 -234
- package/lib/commonjs/mol-gl/shader/chunks/dpoit-write.glsl.js +62 -62
- package/lib/commonjs/mol-gl/shader/chunks/fade-lod.glsl.js +42 -42
- package/lib/commonjs/mol-gl/shader/chunks/float-to-rgba.glsl.js +39 -39
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +127 -127
- package/lib/commonjs/mol-gl/shader/chunks/matrix-scale.glsl.js +5 -5
- package/lib/commonjs/mol-gl/shader/chunks/normal-frag-params.glsl.js +2 -2
- package/lib/commonjs/mol-gl/shader/chunks/read-from-texture.glsl.js +14 -14
- package/lib/commonjs/mol-gl/shader/chunks/rgba-to-float.glsl.js +84 -84
- package/lib/commonjs/mol-gl/shader/chunks/size-vert-params.glsl.js +11 -11
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +23 -23
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +17 -17
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +8 -8
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +25 -25
- package/lib/commonjs/mol-gl/shader/compose.frag.js +12 -12
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +23 -23
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +43 -43
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js +15 -15
- package/lib/commonjs/mol-gl/shader/copy.frag.js +11 -11
- package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/cylinders.frag.js +267 -264
- package/lib/commonjs/mol-gl/shader/cylinders.vert.js +89 -89
- package/lib/commonjs/mol-gl/shader/depth-merge.frag.js +23 -23
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +362 -356
- package/lib/commonjs/mol-gl/shader/direct-volume.vert.js +41 -41
- package/lib/commonjs/mol-gl/shader/evaluate-dpoit.frag.js +10 -10
- package/lib/commonjs/mol-gl/shader/evaluate-wboit.frag.js +17 -17
- package/lib/commonjs/mol-gl/shader/fxaa.frag.js +228 -228
- package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +49 -49
- package/lib/commonjs/mol-gl/shader/gaussian-density.vert.js +27 -27
- package/lib/commonjs/mol-gl/shader/hi-z.frag.js +18 -18
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +58 -58
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/sum.frag.js +19 -19
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/image.frag.js +170 -161
- package/lib/commonjs/mol-gl/shader/image.vert.js +21 -21
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.js +43 -40
- package/lib/commonjs/mol-gl/shader/lines.vert.js +117 -117
- package/lib/commonjs/mol-gl/shader/marching-cubes/active-voxels.frag.js +70 -70
- package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +311 -311
- package/lib/commonjs/mol-gl/shader/marking/edge.frag.js +28 -28
- package/lib/commonjs/mol-gl/shader/marking/overlay.frag.js +26 -26
- package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/mesh.frag.js +66 -63
- package/lib/commonjs/mol-gl/shader/mesh.vert.js +49 -49
- package/lib/commonjs/mol-gl/shader/outlines.frag.js +95 -95
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.js +60 -56
- package/lib/commonjs/mol-gl/shader/points.vert.js +38 -38
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.js +150 -150
- package/lib/commonjs/mol-gl/shader/quad.vert.js +10 -10
- package/lib/commonjs/mol-gl/shader/shadows.frag.js +123 -123
- package/lib/commonjs/mol-gl/shader/smaa/blend.frag.js +56 -56
- package/lib/commonjs/mol-gl/shader/smaa/blend.vert.js +25 -25
- package/lib/commonjs/mol-gl/shader/smaa/edges.frag.js +66 -66
- package/lib/commonjs/mol-gl/shader/smaa/edges.vert.js +26 -26
- package/lib/commonjs/mol-gl/shader/smaa/weights.frag.js +206 -206
- package/lib/commonjs/mol-gl/shader/smaa/weights.vert.js +32 -32
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- package/lib/mol-repr/visual.d.ts +6 -1
- package/lib/mol-repr/visual.js +57 -3
- package/lib/mol-repr/volume/direct-volume.d.ts +3 -0
- package/lib/mol-repr/volume/isosurface.d.ts +6 -0
- package/lib/mol-repr/volume/registry.d.ts +4 -0
- package/lib/mol-repr/volume/representation.d.ts +2 -1
- package/lib/mol-repr/volume/representation.js +9 -2
- package/lib/mol-repr/volume/segment.d.ts +5 -0
- package/lib/mol-repr/volume/slice.d.ts +3 -0
- package/lib/mol-script/language/symbol-table/core.d.ts +3 -3
- package/lib/mol-state/tree/immutable.d.ts +1 -1
- package/lib/mol-state/tree/transient.d.ts +2 -2
- package/lib/mol-theme/color/external-volume.d.ts +3 -1
- package/lib/mol-theme/color/external-volume.js +8 -2
- package/lib/mol-theme/color.d.ts +1 -0
- package/lib/mol-theme/emissive.d.ts +40 -0
- package/lib/mol-theme/emissive.js +134 -0
- package/lib/mol-theme/substance.d.ts +1 -1
- package/lib/mol-theme/substance.js +2 -2
- package/lib/mol-theme/transparency.d.ts +0 -1
- package/lib/mol-util/input/input-observer.js +2 -0
- package/lib/mol-util/set.d.ts +1 -1
- package/lib/mol-util/set.js +17 -1
- package/lib/servers/common/swagger-ui/indexTemplate.js +66 -66
- package/lib/servers/volume/config.js +5 -5
- package/package.json +195 -193
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import { ParamDefinition as PD } from '../../../mol-util/param-definition';
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polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
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all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
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updateOpacity(opacity: number): Promise<import("../../mol-state").StateObjectSelector<import("../../mol-state
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updateOpacity(opacity: number): Promise<import("../../mol-state").StateObjectSelector<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>>;
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/** Make visible the specified set of mesh segments */
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} | undefined): {
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id: import("../../mol-util
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id: import("../../mol-util").UUID;
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type: PluginStateObject.TypeInfo;
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label: string;
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data: VolsegEntryData;
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};
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is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<VolsegEntryData, PluginStateObject.TypeInfo>;
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findNodesByTags(...tags: string[]): StateSelection.CellSeq<StateObjectCell<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, StateTransform<import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>>>;
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newUpdate(): import("../../mol-state").StateBuilder.To<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
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constructor(rootData: VolsegEntryData);
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loadSegmentation(): Promise<void>;
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private createPalette;
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updateOpacity(opacity: number): Promise<import("../../mol-state").StateObjectSelector<import("../../mol-state
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updateOpacity(opacity: number): Promise<import("../../mol-state").StateObjectSelector<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>>;
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selectSegment(segment?: number): Promise<void>;
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@@ -41,7 +41,7 @@ declare const VolsegState_base: {
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} | undefined): {
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id: import("../../mol-util
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id: import("../../mol-util").UUID;
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type: PluginStateObject.TypeInfo;
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is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<PD.Values<{
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volumeType: PD.Select<"off" | "direct-volume" | "isosurface">;
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volumeIsovalueKind: PD.Select<string>;
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volumeIsovalueValue: PD.Numeric;
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@@ -18,14 +18,14 @@ declare const VolsegGlobalState_base: {
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description?: string | undefined;
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} | undefined): {
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id: import("../../mol-util
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id: import("../../mol-util").UUID;
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type: PluginStateObject.TypeInfo;
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data: VolsegGlobalStateData;
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type: PluginStateObject.TypeInfo;
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is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<VolsegGlobalStateData, PluginStateObject.TypeInfo>;
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};
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export declare class VolsegGlobalState extends VolsegGlobalState_base {
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deleteAllNodes(update: StateBuilder.Root): void;
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hideAllNodes(): void;
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showNode(key: string, factory: () => StateObjectSelector | Promise<StateObjectSelector>, forceVisible?: boolean): Promise<StateObjectSelector<import("../../mol-state
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showNode(key: string, factory: () => StateObjectSelector | Promise<StateObjectSelector>, forceVisible?: boolean): Promise<StateObjectSelector<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>>;
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export declare const CreateVolume: StateTransformer<PluginStateObject.Root, PluginStateObject.Volume.Data, ParamDefinition.Normalize<{
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label: string;
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@@ -10,7 +10,7 @@ import { StateAction } from '../../mol-state';
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export declare const VolsegVolumeServerConfig: {
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DefaultServer: PluginConfigItem<string>;
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};
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export declare const Volseg: import("../../mol-state
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export declare const Volseg: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
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autoAttach: boolean;
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showTooltip: boolean;
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}>;
|
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@@ -4,4 +4,4 @@
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* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
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*/
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import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
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export declare const wwPDBChemicalComponentDictionary: import("../../../mol-state
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|
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|
+
export declare const wwPDBChemicalComponentDictionary: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
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|
@@ -32,8 +32,8 @@ export declare const ChemicalCompontentTrajectoryHierarchyPreset: TrajectoryHier
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structures?: undefined;
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} | {
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models: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Model, import("../../../mol-state
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structures: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state
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models: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Model, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>[];
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structures: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>[];
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}>;
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export declare const ChemicalComponentPreset: StructureRepresentationPresetProvider<{
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aromaticBonds: boolean;
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|
@@ -56,9 +56,9 @@ export declare const ChemicalComponentPreset: StructureRepresentationPresetProvi
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} | {
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components: {
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[x: string]: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state
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[x: string]: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
|
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};
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representations: {
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|
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[x: string]: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state
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[x: string]: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
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}>;
|
|
@@ -4,4 +4,4 @@
|
|
|
4
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|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
5
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|
*/
|
|
6
6
|
import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
|
|
7
|
-
export declare const ZenodoImport: import("../../mol-state
|
|
7
|
+
export declare const ZenodoImport: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
|
|
@@ -103,6 +103,12 @@ export declare const Canvas3DParams: {
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background: PD.Normalize<{
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variant: any;
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|
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|
}>;
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bloom: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
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|
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|
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strength: any;
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radius: any;
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threshold: any;
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mode: any;
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|
+
}>, "on">;
|
|
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|
}>>;
|
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marking: PD.Group<PD.Normalize<{
|
|
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|
enabled: boolean;
|
|
@@ -138,7 +144,6 @@ export declare const Canvas3DParams: {
|
|
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light: PD.Normalize<{
|
|
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|
inclination: number;
|
|
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azimuth: number;
|
|
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|
-
/** Can be used to create multiple Canvas3D objects */
|
|
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|
color: import("../mol-util/color").Color;
|
|
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|
intensity: number;
|
|
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|
}>[];
|
|
@@ -225,6 +230,7 @@ export declare const Canvas3DParams: {
|
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quality: any;
|
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material: any;
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|
clip: any;
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|
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emissive: any;
|
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|
instanceGranularity: any;
|
|
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|
lod: any;
|
|
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|
cellSize: any;
|
|
@@ -312,6 +318,12 @@ export declare const DefaultCanvas3DParams: PD.Values<{
|
|
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|
background: PD.Normalize<{
|
|
313
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|
variant: any;
|
|
314
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|
}>;
|
|
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|
+
bloom: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
|
|
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|
+
strength: any;
|
|
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|
+
radius: any;
|
|
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|
+
threshold: any;
|
|
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|
+
mode: any;
|
|
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|
+
}>, "on">;
|
|
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|
}>>;
|
|
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|
marking: PD.Group<PD.Normalize<{
|
|
317
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|
enabled: boolean;
|
|
@@ -347,7 +359,6 @@ export declare const DefaultCanvas3DParams: PD.Values<{
|
|
|
347
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|
light: PD.Normalize<{
|
|
348
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|
inclination: number;
|
|
349
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|
azimuth: number;
|
|
350
|
-
/** Can be used to create multiple Canvas3D objects */
|
|
351
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|
color: import("../mol-util/color").Color;
|
|
352
363
|
intensity: number;
|
|
353
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|
}>[];
|
|
@@ -434,6 +445,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
|
|
|
434
445
|
quality: any;
|
|
435
446
|
material: any;
|
|
436
447
|
clip: any;
|
|
448
|
+
emissive: any;
|
|
437
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|
instanceGranularity: any;
|
|
438
450
|
lod: any;
|
|
439
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|
cellSize: any;
|
|
@@ -248,7 +248,7 @@ var Canvas3D;
|
|
|
248
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|
let forceNextRender = false;
|
|
249
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|
let currentTime = 0;
|
|
250
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|
updateViewport();
|
|
251
|
-
const scene = scene_1.Scene.create(webgl,
|
|
251
|
+
const scene = scene_1.Scene.create(webgl, passes.draw.transparency);
|
|
252
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|
function getSceneRadius() {
|
|
253
253
|
return scene.boundingSphere.radius * p.sceneRadiusFactor;
|
|
254
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|
}
|
|
@@ -638,7 +638,7 @@ var Canvas3D;
|
|
|
638
638
|
}
|
|
639
639
|
(0, debug_1.addConsoleStatsProvider)(consoleStats);
|
|
640
640
|
const ctxChangedSub = (_a = ctx.changed) === null || _a === void 0 ? void 0 : _a.subscribe(() => {
|
|
641
|
-
scene.setTransparency(
|
|
641
|
+
scene.setTransparency(passes.draw.transparency);
|
|
642
642
|
requestDraw();
|
|
643
643
|
});
|
|
644
644
|
//
|
|
@@ -142,7 +142,7 @@ var TrackballControls;
|
|
|
142
142
|
);
|
|
143
143
|
}
|
|
144
144
|
function getRotateFactor() {
|
|
145
|
-
const aspectRatio = input.width / input.height;
|
|
145
|
+
const aspectRatio = (input.width / input.height) || 1;
|
|
146
146
|
return p.rotateSpeed * input.pixelRatio * aspectRatio;
|
|
147
147
|
}
|
|
148
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|
const rotAxis = (0, linear_algebra_1.Vec3)();
|
|
@@ -39,6 +39,7 @@ export declare const HelperParams: {
|
|
|
39
39
|
quality: any;
|
|
40
40
|
material: any;
|
|
41
41
|
clip: any;
|
|
42
|
+
emissive: any;
|
|
42
43
|
instanceGranularity: any;
|
|
43
44
|
lod: any;
|
|
44
45
|
cellSize: any;
|
|
@@ -76,6 +77,7 @@ export declare const DefaultHelperProps: PD.Values<{
|
|
|
76
77
|
quality: any;
|
|
77
78
|
material: any;
|
|
78
79
|
clip: any;
|
|
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|
+
emissive: any;
|
|
79
81
|
instanceGranularity: any;
|
|
80
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|
lod: any;
|
|
81
83
|
cellSize: any;
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
/**
|
|
2
|
-
* Copyright (c) 2022-
|
|
2
|
+
* Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
3
3
|
*
|
|
4
4
|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
5
5
|
*/
|
|
@@ -42,6 +42,11 @@ export declare const BackgroundParams: {
|
|
|
42
42
|
pz: any;
|
|
43
43
|
}>, "files">;
|
|
44
44
|
blur: number;
|
|
45
|
+
rotation: PD.Normalize<{
|
|
46
|
+
x: any;
|
|
47
|
+
y: any;
|
|
48
|
+
z: any;
|
|
49
|
+
}>;
|
|
45
50
|
}>, "skybox"> | PD.NamedParams<PD.Normalize<{
|
|
46
51
|
topColor: Color;
|
|
47
52
|
bottomColor: Color;
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
/**
|
|
3
|
-
* Copyright (c) 2022-
|
|
3
|
+
* Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
4
4
|
*
|
|
5
5
|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
6
6
|
*/
|
|
@@ -25,6 +25,8 @@ const color_1 = require("../../mol-util/color");
|
|
|
25
25
|
const assets_1 = require("../../mol-util/assets");
|
|
26
26
|
const vec4_1 = require("../../mol-math/linear-algebra/3d/vec4");
|
|
27
27
|
const misc_1 = require("../../mol-math/misc");
|
|
28
|
+
const mat3_1 = require("../../mol-math/linear-algebra/3d/mat3");
|
|
29
|
+
const euler_1 = require("../../mol-math/linear-algebra/3d/euler");
|
|
28
30
|
const SharedParams = {
|
|
29
31
|
opacity: param_definition_1.ParamDefinition.Numeric(1, { min: 0.0, max: 1.0, step: 0.01 }),
|
|
30
32
|
saturation: param_definition_1.ParamDefinition.Numeric(0, { min: -1, max: 1, step: 0.01 }),
|
|
@@ -50,6 +52,11 @@ const SkyboxParams = {
|
|
|
50
52
|
}, { isExpanded: true, label: 'Files' }),
|
|
51
53
|
}),
|
|
52
54
|
blur: param_definition_1.ParamDefinition.Numeric(0, { min: 0.0, max: 1.0, step: 0.01 }, { description: 'Note, this only works in WebGL2 or when "EXT_shader_texture_lod" is available.' }),
|
|
55
|
+
rotation: param_definition_1.ParamDefinition.Group({
|
|
56
|
+
x: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 360, step: 1 }, { immediateUpdate: true }),
|
|
57
|
+
y: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 360, step: 1 }, { immediateUpdate: true }),
|
|
58
|
+
z: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 360, step: 1 }, { immediateUpdate: true }),
|
|
59
|
+
}),
|
|
53
60
|
...SharedParams,
|
|
54
61
|
};
|
|
55
62
|
const ImageParams = {
|
|
@@ -144,6 +151,9 @@ class BackgroundPass {
|
|
|
144
151
|
mat4_1.Mat4.mul(m, cam.projection, m);
|
|
145
152
|
mat4_1.Mat4.invert(m, m);
|
|
146
153
|
value_cell_1.ValueCell.update(this.renderable.values.uViewDirectionProjectionInverse, m);
|
|
154
|
+
const r = this.renderable.values.uRotation.ref.value;
|
|
155
|
+
mat3_1.Mat3.fromEuler(r, euler_1.Euler.create((0, misc_1.degToRad)(props.rotation.x), (0, misc_1.degToRad)(props.rotation.y), (0, misc_1.degToRad)(props.rotation.z)), 'XYZ');
|
|
156
|
+
value_cell_1.ValueCell.update(this.renderable.values.uRotation, r);
|
|
147
157
|
value_cell_1.ValueCell.updateIfChanged(this.renderable.values.uBlur, props.blur);
|
|
148
158
|
value_cell_1.ValueCell.updateIfChanged(this.renderable.values.uOpacity, props.opacity);
|
|
149
159
|
value_cell_1.ValueCell.updateIfChanged(this.renderable.values.uSaturation, props.saturation);
|
|
@@ -402,6 +412,7 @@ const BackgroundSchema = {
|
|
|
402
412
|
uOpacity: (0, schema_1.UniformSpec)('f'),
|
|
403
413
|
uSaturation: (0, schema_1.UniformSpec)('f'),
|
|
404
414
|
uLightness: (0, schema_1.UniformSpec)('f'),
|
|
415
|
+
uRotation: (0, schema_1.UniformSpec)('m3'),
|
|
405
416
|
dVariant: (0, schema_1.DefineSpec)('string', ['skybox', 'image', 'verticalGradient', 'horizontalGradient', 'radialGradient']),
|
|
406
417
|
};
|
|
407
418
|
const SkyboxShaderCode = (0, shader_code_1.ShaderCode)('background', background_vert_1.background_vert, background_frag_1.background_frag, {
|
|
@@ -427,6 +438,7 @@ function getBackgroundRenderable(ctx, width, height) {
|
|
|
427
438
|
uOpacity: value_cell_1.ValueCell.create(1),
|
|
428
439
|
uSaturation: value_cell_1.ValueCell.create(0),
|
|
429
440
|
uLightness: value_cell_1.ValueCell.create(0),
|
|
441
|
+
uRotation: value_cell_1.ValueCell.create(mat3_1.Mat3.identity()),
|
|
430
442
|
dVariant: value_cell_1.ValueCell.create('skybox'),
|
|
431
443
|
};
|
|
432
444
|
const schema = { ...BackgroundSchema };
|
|
@@ -0,0 +1,37 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
3
|
+
*
|
|
4
|
+
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
5
|
+
*
|
|
6
|
+
* Partially adapted from three.js, The MIT License, Copyright © 2010-2024 three.js authors
|
|
7
|
+
*/
|
|
8
|
+
import { WebGLContext } from '../../mol-gl/webgl/context';
|
|
9
|
+
import { Texture } from '../../mol-gl/webgl/texture';
|
|
10
|
+
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
|
11
|
+
import { Viewport } from '../camera/util';
|
|
12
|
+
import { RenderTarget } from '../../mol-gl/webgl/render-target';
|
|
13
|
+
import { PostprocessingProps } from './postprocessing';
|
|
14
|
+
export declare const BloomParams: {
|
|
15
|
+
strength: PD.Numeric;
|
|
16
|
+
radius: PD.Numeric;
|
|
17
|
+
threshold: PD.Numeric;
|
|
18
|
+
mode: PD.Select<"luminosity" | "emissive">;
|
|
19
|
+
};
|
|
20
|
+
export type BloomProps = PD.Values<typeof BloomParams>;
|
|
21
|
+
export declare class BloomPass {
|
|
22
|
+
private webgl;
|
|
23
|
+
static isEnabled(props: PostprocessingProps): boolean;
|
|
24
|
+
readonly emissiveTarget: RenderTarget;
|
|
25
|
+
private readonly luminosityTarget;
|
|
26
|
+
private readonly horizontalBlurTargets;
|
|
27
|
+
private readonly verticalBlurTargets;
|
|
28
|
+
private readonly compositeTarget;
|
|
29
|
+
private readonly luminosityRenderable;
|
|
30
|
+
private readonly blurRenderable;
|
|
31
|
+
private readonly compositeRenderable;
|
|
32
|
+
private readonly copyRenderable;
|
|
33
|
+
constructor(webgl: WebGLContext, width: number, height: number);
|
|
34
|
+
setSize(width: number, height: number): void;
|
|
35
|
+
update(input: Texture, emissive: Texture, depth: Texture, props: BloomProps): void;
|
|
36
|
+
render(viewport: Viewport, target: RenderTarget | undefined): void;
|
|
37
|
+
}
|