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.
- package/LICENSE +20 -20
- package/README.md +187 -187
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -95
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.d.ts +2 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +87 -74
- package/lib/apps/viewer/app.d.ts +230 -0
- package/lib/apps/viewer/app.js +515 -0
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.d.ts +2 -403
- package/lib/apps/viewer/index.html +106 -95
- package/lib/apps/viewer/index.js +2 -420
- package/lib/cli/cifschema/index.d.ts +1 -1
- package/lib/cli/cifschema/index.js +15 -35
- package/lib/commonjs/apps/docking-viewer/index.d.ts +2 -1
- package/lib/commonjs/apps/docking-viewer/index.js +86 -73
- package/lib/commonjs/apps/viewer/app.d.ts +230 -0
- package/lib/commonjs/apps/viewer/app.js +521 -0
- package/lib/commonjs/apps/viewer/index.d.ts +2 -403
- package/lib/commonjs/apps/viewer/index.js +2 -423
- package/lib/commonjs/cli/cifschema/index.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/index.js +15 -35
- package/lib/commonjs/examples/alpha-orbitals/index.js +3 -4
- package/lib/commonjs/examples/basic-wrapper/index.js +23 -11
- package/lib/commonjs/examples/lighting/index.d.ts +1 -1
- package/lib/commonjs/examples/lighting/index.js +57 -41
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -14
- package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +1 -14
- package/lib/commonjs/extensions/anvil/behavior.d.ts +4 -0
- package/lib/commonjs/extensions/anvil/representation.d.ts +50 -0
- package/lib/commonjs/extensions/cellpack/representation.d.ts +10 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +30 -0
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +68 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +236 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.d.ts +14 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +125 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.d.ts +12 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +111 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.d.ts +28 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +130 -0
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +6 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +10 -0
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +50 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +3 -9
- package/lib/commonjs/mol-canvas3d/canvas3d.js +34 -23
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +3 -2
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +4 -0
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +2 -2
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +4 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +2 -2
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +13 -1
- package/lib/commonjs/mol-canvas3d/passes/draw.js +16 -15
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +3 -2
- package/lib/commonjs/mol-canvas3d/passes/marking.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +10 -2
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +18 -14
- package/lib/commonjs/mol-canvas3d/passes/pick.js +12 -12
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +1 -1
- package/lib/commonjs/mol-geo/geometry/base.d.ts +18 -0
- package/lib/commonjs/mol-geo/geometry/base.js +18 -1
- package/lib/commonjs/mol-geo/geometry/clipping-data.d.ts +1 -3
- package/lib/commonjs/mol-geo/geometry/clipping-data.js +3 -8
- package/lib/commonjs/mol-geo/geometry/color-data.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/color-data.js +22 -0
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +12 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +2 -2
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +15 -38
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +21 -66
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.d.ts +2 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +4 -7
- package/lib/commonjs/mol-geo/geometry/image/image.d.ts +10 -0
- package/lib/commonjs/mol-geo/geometry/image/image.js +1 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +11 -0
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +1 -1
- package/lib/commonjs/mol-geo/geometry/marker-data.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/marker-data.js +13 -9
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +10 -0
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +2 -2
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +11 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +1 -1
- package/lib/commonjs/mol-geo/geometry/size-data.js +5 -5
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +10 -0
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +2 -2
- package/lib/commonjs/mol-geo/geometry/text/text.d.ts +10 -0
- package/lib/commonjs/mol-geo/geometry/text/text.js +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +10 -0
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +2 -2
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +2 -2
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +2 -2
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +10 -9
- package/lib/commonjs/mol-gl/render-object.d.ts +2 -1
- package/lib/commonjs/mol-gl/render-object.js +10 -10
- package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +11 -5
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
- package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +15 -14
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.d.ts +10 -4
- package/lib/commonjs/mol-gl/renderable/image.js +2 -2
- package/lib/commonjs/mol-gl/renderable/lines.d.ts +39 -33
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.d.ts +11 -5
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/points.d.ts +10 -4
- package/lib/commonjs/mol-gl/renderable/points.js +2 -2
- package/lib/commonjs/mol-gl/renderable/schema.d.ts +10 -11
- package/lib/commonjs/mol-gl/renderable/schema.js +4 -10
- package/lib/commonjs/mol-gl/renderable/spheres.d.ts +11 -5
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
- package/lib/commonjs/mol-gl/renderable/text.d.ts +10 -4
- package/lib/commonjs/mol-gl/renderable/text.js +2 -2
- package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +11 -6
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable.d.ts +0 -1
- package/lib/commonjs/mol-gl/renderer.d.ts +12 -12
- package/lib/commonjs/mol-gl/renderer.js +23 -92
- package/lib/commonjs/mol-gl/scene.d.ts +2 -2
- package/lib/commonjs/mol-gl/scene.js +7 -5
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +1 -1
- 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 +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +1 -1
- 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 +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +1 -1
- 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 +1 -1
- 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 +1 -1
- 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 +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +1 -1
- package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/cylinders.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/gaussian-density.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.vert.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.vert.js +1 -1
- package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/spheres.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader-code.d.ts +3 -1
- package/lib/commonjs/mol-gl/shader-code.js +43 -14
- package/lib/commonjs/mol-gl/webgl/render-item.d.ts +7 -6
- package/lib/commonjs/mol-gl/webgl/render-item.js +10 -8
- package/lib/commonjs/mol-gl/webgl/resources.js +8 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +326 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +326 -1
- package/lib/commonjs/mol-io/reader/mol2/parser.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/mol2/parser.js +33 -3
- package/lib/commonjs/mol-io/reader/mol2/schema.d.ts +12 -1
- package/lib/commonjs/mol-io/reader/mol2/schema.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +2 -2
- package/lib/commonjs/mol-math/geometry/symmetry-operator.js +3 -2
- package/lib/commonjs/mol-math/linear-algebra/3d/quat.d.ts +9 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/quat.js +20 -1
- package/lib/commonjs/mol-model/structure/model/model.d.ts +1 -0
- package/lib/commonjs/mol-model/structure/model/model.js +8 -2
- package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.d.ts +6 -1
- package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.js +1 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.js +4 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js +12 -1
- package/lib/commonjs/mol-model/structure/model/types.js +9 -0
- package/lib/commonjs/mol-model/structure/structure/element/stats.js +8 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.d.ts +2 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js +11 -2
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +20 -10
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +21 -11
- package/lib/commonjs/mol-model/structure/structure/unit/rings.js +2 -0
- package/lib/commonjs/mol-model-formats/shape/ply.d.ts +20 -0
- package/lib/commonjs/mol-model-formats/structure/mol2.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/mol2.js +37 -7
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts +18 -1
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +18 -5
- package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +10 -0
- package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +10 -0
- package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +30 -0
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +40 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +4 -6
- package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +11 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +3 -1
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/commonjs/mol-plugin/commands.d.ts +1 -4
- package/lib/commonjs/mol-plugin/config.d.ts +2 -2
- package/lib/commonjs/mol-plugin/config.js +5 -25
- package/lib/commonjs/mol-plugin/features.d.ts +9 -0
- package/lib/commonjs/mol-plugin/features.js +38 -0
- package/lib/commonjs/mol-plugin/spec.js +1 -0
- package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +12 -0
- package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +8 -1
- package/lib/commonjs/mol-plugin-state/actions/structure.js +183 -72
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +5 -355
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +13 -8
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -71
- package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +4 -4
- package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +1 -1
- package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +33 -19
- package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +13 -1
- package/lib/commonjs/mol-plugin-state/manager/structure/component.js +13 -8
- package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +3 -1
- package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +32 -0
- package/lib/commonjs/mol-plugin-state/transforms/representation.js +2 -2
- package/lib/commonjs/mol-plugin-ui/index.d.ts +4 -4
- package/lib/commonjs/mol-plugin-ui/index.js +13 -16
- package/lib/commonjs/mol-plugin-ui/plugin.js +1 -1
- package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +2 -6
- package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/loci/common.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/loci/distance.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/loci/label.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +10 -0
- package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/complex-representation.js +1 -1
- package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +61 -19
- package/lib/commonjs/mol-repr/structure/params.d.ts +81 -19
- package/lib/commonjs/mol-repr/structure/registry.d.ts +141 -19
- package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +1 -1
- package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +34 -58
- package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +2 -7
- package/lib/commonjs/mol-repr/structure/representation/label.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/label.js +1 -1
- package/lib/commonjs/mol-repr/structure/representation/line.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +1 -1
- package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/point.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +30 -0
- package/lib/commonjs/mol-repr/structure/units-representation.js +1 -1
- package/lib/commonjs/mol-repr/structure/units-visual.d.ts +81 -19
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +20 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +20 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +2 -2
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +2 -2
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/element-point.d.ts +10 -0
- package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +20 -0
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- package/lib/mol-repr/shape/loci/plane.d.ts +10 -0
- package/lib/mol-repr/shape/model/unitcell.d.ts +10 -0
- package/lib/mol-repr/structure/complex-representation.js +1 -1
- package/lib/mol-repr/structure/complex-visual.d.ts +61 -19
- package/lib/mol-repr/structure/params.d.ts +81 -19
- package/lib/mol-repr/structure/registry.d.ts +141 -19
- package/lib/mol-repr/structure/representation/backbone.d.ts +30 -0
- package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +30 -0
- package/lib/mol-repr/structure/representation/carbohydrate.d.ts +30 -0
- package/lib/mol-repr/structure/representation/cartoon.d.ts +30 -0
- package/lib/mol-repr/structure/representation/ellipsoid.d.ts +30 -0
- package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +30 -0
- package/lib/mol-repr/structure/representation/gaussian-surface.js +1 -1
- package/lib/mol-repr/structure/representation/gaussian-volume.d.ts +34 -58
- package/lib/mol-repr/structure/representation/gaussian-volume.js +2 -7
- package/lib/mol-repr/structure/representation/label.d.ts +30 -0
- package/lib/mol-repr/structure/representation/label.js +1 -1
- package/lib/mol-repr/structure/representation/line.d.ts +30 -0
- package/lib/mol-repr/structure/representation/molecular-surface.d.ts +30 -0
- package/lib/mol-repr/structure/representation/molecular-surface.js +1 -1
- package/lib/mol-repr/structure/representation/orientation.d.ts +30 -0
- package/lib/mol-repr/structure/representation/point.d.ts +30 -0
- package/lib/mol-repr/structure/representation/putty.d.ts +30 -0
- package/lib/mol-repr/structure/representation/spacefill.d.ts +30 -0
- package/lib/mol-repr/structure/units-representation.js +1 -1
- package/lib/mol-repr/structure/units-visual.d.ts +81 -19
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +20 -0
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +10 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +20 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +2 -2
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts +10 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +2 -2
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +10 -0
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +10 -0
- package/lib/mol-repr/structure/visual/element-cross.d.ts +10 -0
- package/lib/mol-repr/structure/visual/element-point.d.ts +10 -0
- package/lib/mol-repr/structure/visual/element-sphere.d.ts +20 -0
- package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts +22 -38
- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +8 -6
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +40 -0
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +11 -8
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +10 -0
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +1 -1
- package/lib/mol-repr/structure/visual/label-text.d.ts +10 -0
- package/lib/mol-repr/structure/visual/label-text.js +1 -2
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +1 -1
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +10 -0
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +1 -1
- package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +20 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +20 -0
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +10 -0
- package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +10 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
- package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +10 -0
- package/lib/mol-repr/structure/visual/util/bond.js +1 -1
- package/lib/mol-repr/structure/visual/util/common.d.ts +3 -2
- package/lib/mol-repr/structure/visual/util/common.js +2 -5
- package/lib/mol-repr/structure/visual/util/gaussian.d.ts +7 -6
- package/lib/mol-repr/structure/visual/util/gaussian.js +12 -12
- package/lib/mol-repr/structure/visual/util/molecular-surface.d.ts +2 -1
- package/lib/mol-repr/structure/visual/util/molecular-surface.js +4 -4
- package/lib/mol-repr/visual.js +11 -7
- package/lib/mol-repr/volume/direct-volume.d.ts +33 -57
- package/lib/mol-repr/volume/direct-volume.js +8 -12
- package/lib/mol-repr/volume/isosurface.d.ts +60 -0
- package/lib/mol-repr/volume/isosurface.js +11 -2
- package/lib/mol-repr/volume/registry.d.ts +31 -19
- package/lib/mol-repr/volume/representation.d.ts +10 -0
- package/lib/mol-repr/volume/slice.d.ts +30 -0
- package/lib/mol-repr/volume/slice.js +2 -2
- package/lib/mol-repr/volume/util.js +2 -2
- package/lib/mol-script/language/builder.d.ts +0 -1
- package/lib/mol-theme/clipping.d.ts +7 -15
- package/lib/mol-theme/clipping.js +5 -12
- package/lib/mol-theme/color/volume-value.d.ts +17 -0
- package/lib/mol-theme/color/volume-value.js +52 -0
- package/lib/mol-theme/color.d.ts +3 -0
- package/lib/mol-theme/color.js +2 -0
- package/lib/mol-util/clip.d.ts +49 -0
- package/lib/mol-util/clip.js +93 -0
- package/lib/mol-util/number-packing.d.ts +11 -0
- package/lib/mol-util/{float-packing.js → number-packing.js} +7 -14
- package/package.json +162 -162
- package/lib/commonjs/mol-util/float-packing.d.ts +0 -15
- package/lib/mol-util/float-packing.d.ts +0 -15
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clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
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variant: import("../../mol-util/clip").Clip.Variant;
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}>[];
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}>>;
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}, "orientation">;
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clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
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}>[];
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}>>;
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}, "point">;
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putty: import("./representation").StructureRepresentationProvider<{
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@@ -398,6 +500,16 @@ export declare namespace StructureRepresentationRegistry {
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clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
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}>[];
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}>>;
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detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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linearSegments: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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}, "putty">;
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@@ -421,6 +533,16 @@ export declare namespace StructureRepresentationRegistry {
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}>>;
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clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
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objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
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}>[];
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}>>;
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flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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}, "spacefill">;
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@@ -29,6 +29,16 @@ export declare const BackboneParams: {
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clip: PD.Group<PD.Normalize<{
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}>[];
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}>>;
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};
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@@ -54,6 +64,16 @@ export declare function getBackboneParams(ctx: ThemeRegistryContext, structure:
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bumpiness: number;
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}>>;
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}>[];
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}>>;
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};
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|
@@ -80,6 +100,16 @@ export declare const BackboneRepresentationProvider: StructureRepresentationProv
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}>>;
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}>[];
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}>>;
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tryUseImpostor: PD.BooleanParam;
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detail: PD.Numeric;
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}, "backbone">;
|
|
@@ -44,6 +44,16 @@ export declare const BallAndStickParams: {
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bumpiness: number;
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|
}>>;
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clip: PD.Group<PD.Normalize<{
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variant: import("../../../mol-util/clip").Clip.Variant;
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objects: PD.Normalize<{
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type: any;
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scale: any;
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}>[];
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}>>;
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flipSided: PD.BooleanParam;
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|
flatShaded: PD.BooleanParam;
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|
traceOnly: PD.BooleanParam;
|
|
@@ -86,6 +96,16 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
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roughness: number;
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bumpiness: number;
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}>>;
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}>[];
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}>>;
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flipSided: PD.BooleanParam;
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|
flatShaded: PD.BooleanParam;
|
|
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|
traceOnly: PD.BooleanParam;
|
|
@@ -129,6 +149,16 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
|
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}>>;
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clip: PD.Group<PD.Normalize<{
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}>[];
|
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}>>;
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flipSided: PD.BooleanParam;
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|
flatShaded: PD.BooleanParam;
|
|
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traceOnly: PD.BooleanParam;
|
|
@@ -38,6 +38,16 @@ export declare const CarbohydrateParams: {
|
|
|
38
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|
roughness: number;
|
|
39
39
|
bumpiness: number;
|
|
40
40
|
}>>;
|
|
41
|
+
clip: PD.Group<PD.Normalize<{
|
|
42
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
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|
+
objects: PD.Normalize<{
|
|
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|
+
type: any;
|
|
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|
+
invert: any;
|
|
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|
+
position: any;
|
|
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|
+
rotation: any;
|
|
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|
+
scale: any;
|
|
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|
+
}>[];
|
|
50
|
+
}>>;
|
|
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51
|
linkSizeFactor: PD.Numeric;
|
|
42
52
|
detail: PD.Numeric;
|
|
43
53
|
sizeFactor: PD.Numeric;
|
|
@@ -73,6 +83,16 @@ export declare function getCarbohydrateParams(ctx: ThemeRegistryContext, structu
|
|
|
73
83
|
roughness: number;
|
|
74
84
|
bumpiness: number;
|
|
75
85
|
}>>;
|
|
86
|
+
clip: PD.Group<PD.Normalize<{
|
|
87
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
88
|
+
objects: PD.Normalize<{
|
|
89
|
+
type: any;
|
|
90
|
+
invert: any;
|
|
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|
+
position: any;
|
|
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|
+
rotation: any;
|
|
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|
+
scale: any;
|
|
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|
+
}>[];
|
|
95
|
+
}>>;
|
|
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96
|
linkSizeFactor: PD.Numeric;
|
|
77
97
|
detail: PD.Numeric;
|
|
78
98
|
sizeFactor: PD.Numeric;
|
|
@@ -109,6 +129,16 @@ export declare const CarbohydrateRepresentationProvider: StructureRepresentation
|
|
|
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|
roughness: number;
|
|
110
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|
bumpiness: number;
|
|
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|
}>>;
|
|
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|
+
clip: PD.Group<PD.Normalize<{
|
|
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|
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|
|
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|
+
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|
|
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|
+
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|
|
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|
+
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|
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|
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+
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|
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|
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|
|
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|
+
}>[];
|
|
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|
+
}>>;
|
|
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|
linkSizeFactor: PD.Numeric;
|
|
113
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|
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|
|
114
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|
sizeFactor: PD.Numeric;
|
|
@@ -27,6 +27,16 @@ export declare const CartoonParams: {
|
|
|
27
27
|
roughness: number;
|
|
28
28
|
bumpiness: number;
|
|
29
29
|
}>>;
|
|
30
|
+
clip: PD.Group<PD.Normalize<{
|
|
31
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
32
|
+
objects: PD.Normalize<{
|
|
33
|
+
type: any;
|
|
34
|
+
invert: any;
|
|
35
|
+
position: any;
|
|
36
|
+
rotation: any;
|
|
37
|
+
scale: any;
|
|
38
|
+
}>[];
|
|
39
|
+
}>>;
|
|
30
40
|
radialSegments: PD.Numeric;
|
|
31
41
|
detail: PD.Numeric;
|
|
32
42
|
aspectRatio: PD.Numeric;
|
|
@@ -55,6 +65,16 @@ export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: S
|
|
|
55
65
|
roughness: number;
|
|
56
66
|
bumpiness: number;
|
|
57
67
|
}>>;
|
|
68
|
+
clip: PD.Group<PD.Normalize<{
|
|
69
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
70
|
+
objects: PD.Normalize<{
|
|
71
|
+
type: any;
|
|
72
|
+
invert: any;
|
|
73
|
+
position: any;
|
|
74
|
+
rotation: any;
|
|
75
|
+
scale: any;
|
|
76
|
+
}>[];
|
|
77
|
+
}>>;
|
|
58
78
|
radialSegments: PD.Numeric;
|
|
59
79
|
detail: PD.Numeric;
|
|
60
80
|
aspectRatio: PD.Numeric;
|
|
@@ -84,6 +104,16 @@ export declare const CartoonRepresentationProvider: StructureRepresentationProvi
|
|
|
84
104
|
roughness: number;
|
|
85
105
|
bumpiness: number;
|
|
86
106
|
}>>;
|
|
107
|
+
clip: PD.Group<PD.Normalize<{
|
|
108
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
109
|
+
objects: PD.Normalize<{
|
|
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|
+
type: any;
|
|
111
|
+
invert: any;
|
|
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|
+
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|
|
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|
+
rotation: any;
|
|
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|
+
scale: any;
|
|
115
|
+
}>[];
|
|
116
|
+
}>>;
|
|
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117
|
radialSegments: PD.Numeric;
|
|
88
118
|
detail: PD.Numeric;
|
|
89
119
|
aspectRatio: PD.Numeric;
|
|
@@ -44,6 +44,16 @@ export declare const EllipsoidParams: {
|
|
|
44
44
|
roughness: number;
|
|
45
45
|
bumpiness: number;
|
|
46
46
|
}>>;
|
|
47
|
+
clip: PD.Group<PD.Normalize<{
|
|
48
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
49
|
+
objects: PD.Normalize<{
|
|
50
|
+
type: any;
|
|
51
|
+
invert: any;
|
|
52
|
+
position: any;
|
|
53
|
+
rotation: any;
|
|
54
|
+
scale: any;
|
|
55
|
+
}>[];
|
|
56
|
+
}>>;
|
|
47
57
|
flipSided: PD.BooleanParam;
|
|
48
58
|
flatShaded: PD.BooleanParam;
|
|
49
59
|
detail: PD.Numeric;
|
|
@@ -85,6 +95,16 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
|
|
|
85
95
|
roughness: number;
|
|
86
96
|
bumpiness: number;
|
|
87
97
|
}>>;
|
|
98
|
+
clip: PD.Group<PD.Normalize<{
|
|
99
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
100
|
+
objects: PD.Normalize<{
|
|
101
|
+
type: any;
|
|
102
|
+
invert: any;
|
|
103
|
+
position: any;
|
|
104
|
+
rotation: any;
|
|
105
|
+
scale: any;
|
|
106
|
+
}>[];
|
|
107
|
+
}>>;
|
|
88
108
|
flipSided: PD.BooleanParam;
|
|
89
109
|
flatShaded: PD.BooleanParam;
|
|
90
110
|
detail: PD.Numeric;
|
|
@@ -127,6 +147,16 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
|
|
|
127
147
|
roughness: number;
|
|
128
148
|
bumpiness: number;
|
|
129
149
|
}>>;
|
|
150
|
+
clip: PD.Group<PD.Normalize<{
|
|
151
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
152
|
+
objects: PD.Normalize<{
|
|
153
|
+
type: any;
|
|
154
|
+
invert: any;
|
|
155
|
+
position: any;
|
|
156
|
+
rotation: any;
|
|
157
|
+
scale: any;
|
|
158
|
+
}>[];
|
|
159
|
+
}>>;
|
|
130
160
|
flipSided: PD.BooleanParam;
|
|
131
161
|
flatShaded: PD.BooleanParam;
|
|
132
162
|
detail: PD.Numeric;
|
|
@@ -27,6 +27,16 @@ export declare const GaussianSurfaceParams: {
|
|
|
27
27
|
roughness: number;
|
|
28
28
|
bumpiness: number;
|
|
29
29
|
}>>;
|
|
30
|
+
clip: PD.Group<PD.Normalize<{
|
|
31
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
32
|
+
objects: PD.Normalize<{
|
|
33
|
+
type: any;
|
|
34
|
+
invert: any;
|
|
35
|
+
position: any;
|
|
36
|
+
rotation: any;
|
|
37
|
+
scale: any;
|
|
38
|
+
}>[];
|
|
39
|
+
}>>;
|
|
30
40
|
tryUseGpu: PD.BooleanParam;
|
|
31
41
|
smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
|
|
32
42
|
resolutionFactor: number;
|
|
@@ -59,6 +69,16 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
|
|
|
59
69
|
roughness: number;
|
|
60
70
|
bumpiness: number;
|
|
61
71
|
}>>;
|
|
72
|
+
clip: PD.Group<PD.Normalize<{
|
|
73
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
74
|
+
objects: PD.Normalize<{
|
|
75
|
+
type: any;
|
|
76
|
+
invert: any;
|
|
77
|
+
position: any;
|
|
78
|
+
rotation: any;
|
|
79
|
+
scale: any;
|
|
80
|
+
}>[];
|
|
81
|
+
}>>;
|
|
62
82
|
tryUseGpu: PD.BooleanParam;
|
|
63
83
|
smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
|
|
64
84
|
resolutionFactor: number;
|
|
@@ -92,6 +112,16 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
|
|
|
92
112
|
roughness: number;
|
|
93
113
|
bumpiness: number;
|
|
94
114
|
}>>;
|
|
115
|
+
clip: PD.Group<PD.Normalize<{
|
|
116
|
+
variant: import("../../../mol-util/clip").Clip.Variant;
|
|
117
|
+
objects: PD.Normalize<{
|
|
118
|
+
type: any;
|
|
119
|
+
invert: any;
|
|
120
|
+
position: any;
|
|
121
|
+
rotation: any;
|
|
122
|
+
scale: any;
|
|
123
|
+
}>[];
|
|
124
|
+
}>>;
|
|
95
125
|
tryUseGpu: PD.BooleanParam;
|
|
96
126
|
smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
|
|
97
127
|
resolutionFactor: number;
|
|
@@ -31,7 +31,7 @@ export var GaussianSurfaceRepresentationProvider = StructureRepresentationProvid
|
|
|
31
31
|
getParams: getGaussianSurfaceParams,
|
|
32
32
|
defaultValues: PD.getDefaultValues(GaussianSurfaceParams),
|
|
33
33
|
defaultColorTheme: { name: 'chain-id' },
|
|
34
|
-
defaultSizeTheme: { name: '
|
|
34
|
+
defaultSizeTheme: { name: 'physical' },
|
|
35
35
|
isApplicable: function (structure) { return structure.elementCount > 0; }
|
|
36
36
|
});
|
|
37
37
|
//# sourceMappingURL=gaussian-surface.js.map
|