molstar 3.0.0-dev.2 → 3.0.0-dev.6
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 +102 -94
- package/build/viewer/molstar.css +1 -1
- 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/docking-viewer/viewport.js +2 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.d.ts +36 -215
- package/lib/apps/viewer/index.html +102 -94
- package/lib/apps/viewer/index.js +139 -52
- 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/docking-viewer/viewport.js +2 -1
- package/lib/commonjs/apps/viewer/index.d.ts +36 -215
- package/lib/commonjs/apps/viewer/index.js +139 -52
- 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 +2 -3
- 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 +58 -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 +3 -0
- package/lib/commonjs/extensions/anvil/representation.d.ts +13 -0
- package/lib/commonjs/extensions/cellpack/representation.d.ts +3 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +9 -0
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +1 -1
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +1 -1
- 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/mp4-export/controls.d.ts +1 -0
- package/lib/commonjs/extensions/mp4-export/controls.js +9 -7
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +3 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +3 -0
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +15 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +6 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.js +10 -3
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +3 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +3 -0
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +4 -0
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +3 -0
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +2 -1
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +4 -2
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +4 -2
- package/lib/commonjs/mol-geo/geometry/base.d.ts +2 -0
- package/lib/commonjs/mol-geo/geometry/base.js +2 -0
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -2
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +1 -0
- package/lib/commonjs/mol-geo/geometry/image/image.d.ts +1 -0
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +2 -0
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +3 -0
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +4 -2
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -0
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +3 -0
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +4 -2
- package/lib/commonjs/mol-geo/geometry/substance-data.js +3 -3
- package/lib/commonjs/mol-geo/geometry/text/text.d.ts +1 -0
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +3 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +3 -0
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -2
- package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +31 -28
- package/lib/commonjs/mol-gl/renderable/cylinders.js +2 -2
- package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +1 -0
- package/lib/commonjs/mol-gl/renderable/image.d.ts +1 -0
- package/lib/commonjs/mol-gl/renderable/lines.d.ts +1 -0
- package/lib/commonjs/mol-gl/renderable/mesh.d.ts +28 -25
- package/lib/commonjs/mol-gl/renderable/mesh.js +2 -2
- package/lib/commonjs/mol-gl/renderable/points.d.ts +1 -0
- package/lib/commonjs/mol-gl/renderable/schema.d.ts +1 -0
- package/lib/commonjs/mol-gl/renderable/schema.js +3 -3
- package/lib/commonjs/mol-gl/renderable/spheres.d.ts +31 -28
- package/lib/commonjs/mol-gl/renderable/spheres.js +2 -2
- package/lib/commonjs/mol-gl/renderable/text.d.ts +1 -0
- package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +3 -0
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +1 -1
- 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-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/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.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.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/mesh.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.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-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-math/geometry/symmetry-operator.js +3 -2
- package/lib/commonjs/mol-model/structure/model/model.d.ts +1 -0
- package/lib/commonjs/mol-model/structure/model/model.js +15 -5
- 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/unit/rings.js +2 -0
- package/lib/commonjs/mol-model-formats/shape/ply.d.ts +6 -0
- package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +3 -0
- package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +3 -0
- package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +9 -0
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +12 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +1 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/commonjs/mol-plugin/commands.d.ts +3 -0
- package/lib/commonjs/mol-plugin/config.d.ts +2 -0
- package/lib/commonjs/mol-plugin/config.js +10 -3
- package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +9 -0
- package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +7 -1
- package/lib/commonjs/mol-plugin-state/actions/structure.js +150 -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/helpers/structure-selection-query.js +33 -19
- package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +2 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/component.js +1 -1
- package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +22 -0
- package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts +3 -2
- package/lib/commonjs/mol-plugin-ui/controls/parameters.js +11 -6
- package/lib/commonjs/mol-plugin-ui/hooks/use-behavior.d.ts +1 -1
- package/lib/commonjs/mol-plugin-ui/hooks/use-behavior.js +8 -17
- 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.d.ts +1 -1
- package/lib/commonjs/mol-plugin-ui/plugin.js +76 -10
- package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +3 -0
- package/lib/commonjs/mol-repr/shape/loci/common.d.ts +1 -0
- package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +3 -0
- package/lib/commonjs/mol-repr/shape/loci/distance.d.ts +1 -0
- package/lib/commonjs/mol-repr/shape/loci/label.d.ts +1 -0
- package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +3 -0
- package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +3 -0
- package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +12 -0
- package/lib/commonjs/mol-repr/structure/params.d.ts +16 -0
- package/lib/commonjs/mol-repr/structure/registry.d.ts +35 -1
- package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/backbone.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/cartoon.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/representation/label.d.ts +6 -3
- package/lib/commonjs/mol-repr/structure/representation/line.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/orientation.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/point.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/putty.js +2 -1
- package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +9 -0
- package/lib/commonjs/mol-repr/structure/representation/spacefill.js +2 -1
- package/lib/commonjs/mol-repr/structure/units-visual.d.ts +16 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +6 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +6 -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 +1 -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 +3 -0
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts +1 -0
- package/lib/commonjs/mol-repr/structure/visual/element-point.d.ts +1 -0
- package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +6 -0
- package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -0
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +12 -0
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -0
- package/lib/commonjs/mol-repr/structure/visual/label-text.d.ts +3 -2
- package/lib/commonjs/mol-repr/structure/visual/label-text.js +2 -2
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -0
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +6 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +6 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
- package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +3 -0
- package/lib/commonjs/mol-repr/structure/visual/util/bond.js +1 -1
- package/lib/commonjs/mol-repr/volume/direct-volume.d.ts +3 -0
- package/lib/commonjs/mol-repr/volume/isosurface.d.ts +16 -0
- package/lib/commonjs/mol-repr/volume/isosurface.js +2 -1
- package/lib/commonjs/mol-repr/volume/registry.d.ts +5 -0
- package/lib/commonjs/mol-repr/volume/representation.d.ts +1 -0
- package/lib/commonjs/mol-repr/volume/slice.d.ts +3 -0
- package/lib/commonjs/mol-script/language/builder.d.ts +0 -1
- package/lib/commonjs/mol-theme/color/illustrative.d.ts +2 -0
- package/lib/commonjs/mol-theme/color/illustrative.js +2 -2
- package/lib/commonjs/mol-theme/color.d.ts +1 -0
- package/lib/commonjs/mol-util/material.d.ts +5 -1
- package/lib/commonjs/mol-util/material.js +9 -7
- package/lib/examples/alpha-orbitals/index.html +61 -60
- package/lib/examples/alpha-orbitals/index.js +3 -4
- package/lib/examples/basic-wrapper/index.html +137 -136
- package/lib/examples/basic-wrapper/index.js +24 -12
- package/lib/examples/lighting/index.d.ts +1 -1
- package/lib/examples/lighting/index.html +88 -86
- package/lib/examples/lighting/index.js +59 -42
- package/lib/examples/proteopedia-wrapper/index.html +236 -235
- package/lib/examples/proteopedia-wrapper/index.js +27 -15
- package/lib/extensions/alpha-orbitals/transforms.d.ts +0 -1
- package/lib/extensions/alpha-orbitals/transforms.js +1 -14
- package/lib/extensions/anvil/behavior.d.ts +3 -0
- package/lib/extensions/anvil/representation.d.ts +13 -0
- package/lib/extensions/cellpack/representation.d.ts +3 -0
- package/lib/extensions/dnatco/confal-pyramids/representation.d.ts +9 -0
- package/lib/extensions/geo-export/obj-exporter.js +1 -1
- package/lib/extensions/geo-export/usdz-exporter.js +1 -1
- package/lib/extensions/model-archive/quality-assessment/behavior.d.ts +68 -0
- package/lib/extensions/model-archive/quality-assessment/behavior.js +233 -0
- package/lib/extensions/model-archive/quality-assessment/color/plddt.d.ts +14 -0
- package/lib/extensions/model-archive/quality-assessment/color/plddt.js +120 -0
- package/lib/extensions/model-archive/quality-assessment/color/qmean.d.ts +12 -0
- package/lib/extensions/model-archive/quality-assessment/color/qmean.js +106 -0
- package/lib/extensions/model-archive/quality-assessment/prop.d.ts +28 -0
- package/lib/extensions/model-archive/quality-assessment/prop.js +127 -0
- package/lib/extensions/mp4-export/controls.d.ts +1 -0
- package/lib/extensions/mp4-export/controls.js +9 -7
- package/lib/extensions/pdbe/structure-quality-report/prop.js +1 -1
- package/lib/extensions/rcsb/assembly-symmetry/behavior.d.ts +3 -0
- package/lib/extensions/rcsb/assembly-symmetry/prop.js +1 -1
- package/lib/extensions/rcsb/assembly-symmetry/representation.d.ts +3 -0
- package/lib/extensions/rcsb/validation-report/prop.js +1 -1
- package/lib/extensions/rcsb/validation-report/representation.d.ts +15 -0
- package/lib/mol-canvas3d/canvas3d.d.ts +6 -0
- package/lib/mol-canvas3d/canvas3d.js +10 -3
- package/lib/mol-canvas3d/helper/camera-helper.d.ts +3 -0
- package/lib/mol-canvas3d/helper/handle-helper.d.ts +3 -0
- package/lib/mol-canvas3d/helper/helper.d.ts +4 -0
- package/lib/mol-canvas3d/passes/image.d.ts +3 -0
- package/lib/mol-canvas3d/passes/multi-sample.d.ts +2 -1
- package/lib/mol-canvas3d/passes/multi-sample.js +4 -2
- package/lib/mol-canvas3d/passes/postprocessing.d.ts +1 -0
- package/lib/mol-canvas3d/passes/postprocessing.js +4 -2
- package/lib/mol-geo/geometry/base.d.ts +2 -0
- package/lib/mol-geo/geometry/base.js +2 -0
- package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +4 -1
- package/lib/mol-geo/geometry/cylinders/cylinders.js +4 -2
- package/lib/mol-geo/geometry/direct-volume/direct-volume.d.ts +1 -0
- package/lib/mol-geo/geometry/image/image.d.ts +1 -0
- package/lib/mol-geo/geometry/lines/lines.d.ts +2 -0
- package/lib/mol-geo/geometry/mesh/color-smoothing.js +1 -1
- package/lib/mol-geo/geometry/mesh/mesh.d.ts +3 -0
- package/lib/mol-geo/geometry/mesh/mesh.js +4 -2
- package/lib/mol-geo/geometry/points/points.d.ts +1 -0
- package/lib/mol-geo/geometry/spheres/spheres.d.ts +3 -0
- package/lib/mol-geo/geometry/spheres/spheres.js +4 -2
- package/lib/mol-geo/geometry/substance-data.js +3 -3
- package/lib/mol-geo/geometry/text/text.d.ts +1 -0
- package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +3 -3
- package/lib/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +3 -0
- package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -2
- package/lib/mol-gl/renderable/cylinders.d.ts +31 -28
- package/lib/mol-gl/renderable/cylinders.js +3 -3
- package/lib/mol-gl/renderable/direct-volume.d.ts +1 -0
- package/lib/mol-gl/renderable/image.d.ts +1 -0
- package/lib/mol-gl/renderable/lines.d.ts +1 -0
- package/lib/mol-gl/renderable/mesh.d.ts +28 -25
- package/lib/mol-gl/renderable/mesh.js +3 -3
- package/lib/mol-gl/renderable/points.d.ts +1 -0
- package/lib/mol-gl/renderable/schema.d.ts +1 -0
- package/lib/mol-gl/renderable/schema.js +3 -3
- package/lib/mol-gl/renderable/spheres.d.ts +31 -28
- package/lib/mol-gl/renderable/spheres.js +3 -3
- package/lib/mol-gl/renderable/text.d.ts +1 -0
- package/lib/mol-gl/renderable/texture-mesh.d.ts +3 -0
- package/lib/mol-gl/renderable/texture-mesh.js +1 -1
- package/lib/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/common-frag-params.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/common.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/common.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/light-frag-params.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/light-frag-params.glsl.js +1 -1
- package/lib/mol-gl/shader/cylinders.frag.d.ts +1 -1
- package/lib/mol-gl/shader/cylinders.frag.js +1 -1
- package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/mol-gl/shader/mesh.frag.d.ts +1 -1
- package/lib/mol-gl/shader/mesh.frag.js +1 -1
- package/lib/mol-gl/shader/postprocessing.frag.d.ts +1 -1
- package/lib/mol-gl/shader/postprocessing.frag.js +1 -1
- package/lib/mol-gl/shader/spheres.frag.d.ts +1 -1
- package/lib/mol-gl/shader/spheres.frag.js +1 -1
- package/lib/mol-io/reader/cif/schema/mmcif.d.ts +326 -1
- package/lib/mol-io/reader/cif/schema/mmcif.js +326 -1
- package/lib/mol-math/geometry/symmetry-operator.js +3 -2
- package/lib/mol-model/structure/model/model.d.ts +1 -0
- package/lib/mol-model/structure/model/model.js +15 -5
- package/lib/mol-model/structure/model/properties/atomic/hierarchy.d.ts +6 -1
- package/lib/mol-model/structure/model/properties/atomic/hierarchy.js +1 -1
- package/lib/mol-model/structure/model/properties/utils/atomic-derived.d.ts +1 -1
- package/lib/mol-model/structure/model/properties/utils/atomic-derived.js +5 -2
- package/lib/mol-model/structure/model/properties/utils/atomic-index.d.ts +1 -1
- package/lib/mol-model/structure/model/properties/utils/atomic-index.js +12 -1
- package/lib/mol-model/structure/model/types.js +9 -0
- package/lib/mol-model/structure/structure/unit/rings.js +2 -0
- package/lib/mol-model-formats/shape/ply.d.ts +6 -0
- package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +3 -0
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +3 -0
- package/lib/mol-model-props/computed/representations/interactions.d.ts +9 -0
- package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +12 -0
- package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +1 -0
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/mol-plugin/commands.d.ts +3 -0
- package/lib/mol-plugin/config.d.ts +2 -0
- package/lib/mol-plugin/config.js +9 -3
- package/lib/mol-plugin/util/viewport-screenshot.d.ts +9 -0
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-state/actions/structure.d.ts +7 -1
- package/lib/mol-plugin-state/actions/structure.js +150 -72
- package/lib/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +5 -355
- package/lib/mol-plugin-state/builder/structure/hierarchy-preset.js +14 -9
- package/lib/mol-plugin-state/builder/structure/hierarchy.d.ts +1 -71
- package/lib/mol-plugin-state/helpers/structure-selection-query.js +34 -20
- package/lib/mol-plugin-state/manager/structure/component.d.ts +2 -0
- package/lib/mol-plugin-state/manager/structure/component.js +2 -2
- package/lib/mol-plugin-state/transforms/representation.d.ts +22 -0
- package/lib/mol-plugin-ui/controls/parameters.d.ts +3 -2
- package/lib/mol-plugin-ui/controls/parameters.js +12 -7
- package/lib/mol-plugin-ui/hooks/use-behavior.d.ts +1 -1
- package/lib/mol-plugin-ui/hooks/use-behavior.js +9 -18
- package/lib/mol-plugin-ui/index.d.ts +4 -4
- package/lib/mol-plugin-ui/index.js +11 -13
- package/lib/mol-plugin-ui/plugin.d.ts +1 -1
- package/lib/mol-plugin-ui/plugin.js +76 -10
- package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
- package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
- package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
- package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
- package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
- package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
- package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -616
- package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
- package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
- package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
- package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
- package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
- package/lib/mol-plugin-ui/skin/base/components/viewport.scss +127 -127
- package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
- package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
- package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
- package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
- package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
- package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
- package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
- package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
- package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
- package/lib/mol-plugin-ui/skin/blue.scss +1 -1
- package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
- package/lib/mol-plugin-ui/skin/dark.scss +1 -1
- package/lib/mol-plugin-ui/skin/light.scss +1 -1
- package/lib/mol-repr/shape/loci/angle.d.ts +3 -0
- package/lib/mol-repr/shape/loci/common.d.ts +1 -0
- package/lib/mol-repr/shape/loci/dihedral.d.ts +3 -0
- package/lib/mol-repr/shape/loci/distance.d.ts +1 -0
- package/lib/mol-repr/shape/loci/label.d.ts +1 -0
- package/lib/mol-repr/shape/loci/orientation.d.ts +3 -0
- package/lib/mol-repr/shape/loci/plane.d.ts +3 -0
- package/lib/mol-repr/shape/model/unitcell.d.ts +3 -0
- package/lib/mol-repr/structure/complex-visual.d.ts +12 -0
- package/lib/mol-repr/structure/params.d.ts +16 -0
- package/lib/mol-repr/structure/registry.d.ts +35 -1
- package/lib/mol-repr/structure/representation/backbone.d.ts +9 -0
- package/lib/mol-repr/structure/representation/backbone.js +2 -1
- package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +9 -0
- package/lib/mol-repr/structure/representation/ball-and-stick.js +2 -1
- package/lib/mol-repr/structure/representation/carbohydrate.d.ts +9 -0
- package/lib/mol-repr/structure/representation/carbohydrate.js +2 -1
- package/lib/mol-repr/structure/representation/cartoon.d.ts +9 -0
- package/lib/mol-repr/structure/representation/cartoon.js +2 -1
- package/lib/mol-repr/structure/representation/ellipsoid.d.ts +9 -0
- package/lib/mol-repr/structure/representation/ellipsoid.js +2 -1
- package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +9 -0
- package/lib/mol-repr/structure/representation/gaussian-surface.js +2 -1
- package/lib/mol-repr/structure/representation/gaussian-volume.d.ts +3 -0
- package/lib/mol-repr/structure/representation/label.d.ts +6 -3
- package/lib/mol-repr/structure/representation/line.d.ts +3 -0
- package/lib/mol-repr/structure/representation/molecular-surface.d.ts +9 -0
- package/lib/mol-repr/structure/representation/molecular-surface.js +2 -1
- package/lib/mol-repr/structure/representation/orientation.d.ts +9 -0
- package/lib/mol-repr/structure/representation/orientation.js +2 -1
- package/lib/mol-repr/structure/representation/point.d.ts +3 -0
- package/lib/mol-repr/structure/representation/putty.d.ts +9 -0
- package/lib/mol-repr/structure/representation/putty.js +2 -1
- package/lib/mol-repr/structure/representation/spacefill.d.ts +9 -0
- package/lib/mol-repr/structure/representation/spacefill.js +2 -1
- package/lib/mol-repr/structure/units-visual.d.ts +16 -0
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +6 -0
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +6 -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 +1 -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 +3 -0
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +3 -0
- package/lib/mol-repr/structure/visual/element-cross.d.ts +1 -0
- package/lib/mol-repr/structure/visual/element-point.d.ts +1 -0
- package/lib/mol-repr/structure/visual/element-sphere.d.ts +6 -0
- package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -0
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +12 -0
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -0
- package/lib/mol-repr/structure/visual/label-text.d.ts +3 -2
- package/lib/mol-repr/structure/visual/label-text.js +2 -2
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -0
- package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +6 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +6 -0
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +3 -0
- package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +3 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +1 -1
- package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +3 -0
- package/lib/mol-repr/structure/visual/util/bond.js +1 -1
- package/lib/mol-repr/volume/direct-volume.d.ts +3 -0
- package/lib/mol-repr/volume/isosurface.d.ts +16 -0
- package/lib/mol-repr/volume/isosurface.js +2 -1
- package/lib/mol-repr/volume/registry.d.ts +5 -0
- package/lib/mol-repr/volume/representation.d.ts +1 -0
- package/lib/mol-repr/volume/slice.d.ts +3 -0
- package/lib/mol-script/language/builder.d.ts +0 -1
- package/lib/mol-theme/color/illustrative.d.ts +2 -0
- package/lib/mol-theme/color/illustrative.js +2 -2
- package/lib/mol-theme/color.d.ts +1 -0
- package/lib/mol-util/material.d.ts +5 -1
- package/lib/mol-util/material.js +9 -7
- package/package.json +162 -160
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includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
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@@ -361,16 +390,19 @@ export declare namespace StructureRepresentationRegistry {
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flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
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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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spacefill: import("./representation").StructureRepresentationProvider<{
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|
+
bumpFrequency: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
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@@ -381,11 +413,13 @@ export declare namespace StructureRepresentationRegistry {
|
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doubleSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
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xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
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+
bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
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quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
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material: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
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metalness: number;
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roughness: number;
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+
bumpiness: number;
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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;
|
|
@@ -11,6 +11,7 @@ import { Structure } from '../../../mol-model/structure';
|
|
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11
11
|
export declare const BackboneParams: {
|
|
12
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|
sizeAspectRatio: PD.Numeric;
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13
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|
visuals: PD.MultiSelect<"polymer-gap" | "polymer-backbone-cylinder" | "polymer-backbone-sphere">;
|
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14
|
+
bumpFrequency: PD.Numeric;
|
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14
15
|
sizeFactor: PD.Numeric;
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15
16
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radialSegments: PD.Numeric;
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16
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unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
|
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@@ -20,11 +21,13 @@ export declare const BackboneParams: {
|
|
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20
21
|
flatShaded: PD.BooleanParam;
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21
22
|
ignoreLight: PD.BooleanParam;
|
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22
23
|
xrayShaded: PD.BooleanParam;
|
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24
|
+
bumpAmplitude: PD.Numeric;
|
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23
25
|
alpha: PD.Numeric;
|
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26
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
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|
material: PD.Group<PD.Normalize<{
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|
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|
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|
+
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28
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|
}>>;
|
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|
tryUseImpostor: PD.BooleanParam;
|
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|
detail: PD.Numeric;
|
|
@@ -33,6 +36,7 @@ export declare type BackboneParams = typeof BackboneParams;
|
|
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33
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|
export declare function getBackboneParams(ctx: ThemeRegistryContext, structure: Structure): {
|
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34
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|
sizeAspectRatio: PD.Numeric;
|
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35
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|
visuals: PD.MultiSelect<"polymer-gap" | "polymer-backbone-cylinder" | "polymer-backbone-sphere">;
|
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39
|
+
bumpFrequency: PD.Numeric;
|
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36
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|
sizeFactor: PD.Numeric;
|
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|
radialSegments: PD.Numeric;
|
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38
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|
unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
|
|
@@ -42,11 +46,13 @@ export declare function getBackboneParams(ctx: ThemeRegistryContext, structure:
|
|
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42
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|
flatShaded: PD.BooleanParam;
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43
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|
ignoreLight: PD.BooleanParam;
|
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44
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|
xrayShaded: PD.BooleanParam;
|
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49
|
+
bumpAmplitude: PD.Numeric;
|
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|
alpha: PD.Numeric;
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46
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|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
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47
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|
material: PD.Group<PD.Normalize<{
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|
metalness: number;
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49
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|
roughness: number;
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55
|
+
bumpiness: number;
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|
}>>;
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|
tryUseImpostor: PD.BooleanParam;
|
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|
detail: PD.Numeric;
|
|
@@ -56,6 +62,7 @@ export declare function BackboneRepresentation(ctx: RepresentationContext, getPa
|
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56
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|
export declare const BackboneRepresentationProvider: StructureRepresentationProvider<{
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|
57
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|
sizeAspectRatio: PD.Numeric;
|
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58
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exports.BackboneParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_backbone_sphere_1.PolymerBackboneSphereParams), polymer_backbone_cylinder_1.PolymerBackboneCylinderParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 3, step: 0.1 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(BackboneVisuals)) });
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exports.BackboneParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_backbone_sphere_1.PolymerBackboneSphereParams), polymer_backbone_cylinder_1.PolymerBackboneCylinderParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 3, step: 0.1 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(BackboneVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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}>>;
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@@ -93,6 +99,7 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
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visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
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includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
|
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@@ -114,11 +121,13 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
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doubleSided: PD.BooleanParam;
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ignoreLight: PD.BooleanParam;
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xrayShaded: PD.BooleanParam;
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alpha: PD.Numeric;
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}>>;
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@@ -16,12 +16,13 @@ var complex_representation_1 = require("../complex-representation");
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var params_1 = require("../params");
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var base_1 = require("../../../mol-geo/geometry/base");
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var BallAndStickVisuals = {
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'element-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Element sphere', ctx, getParams, element_sphere_1.ElementSphereVisual); },
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'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
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'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
|
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};
|
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exports.BallAndStickParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)) });
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exports.BallAndStickParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
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|
function getBallAndStickParams(ctx, structure) {
|
|
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|
return param_definition_1.ParamDefinition.clone(exports.BallAndStickParams);
|
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}
|
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@@ -10,6 +10,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
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import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
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export declare const CarbohydrateParams: {
|
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visuals: PD.MultiSelect<"carbohydrate-symbol" | "carbohydrate-link" | "carbohydrate-terminal-link">;
|
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+
bumpFrequency: PD.Numeric;
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terminalLinkSizeFactor: PD.Numeric;
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linkScale: PD.Numeric;
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linkSpacing: PD.Numeric;
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|
@@ -29,11 +30,13 @@ export declare const CarbohydrateParams: {
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flatShaded: PD.BooleanParam;
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xrayShaded: PD.BooleanParam;
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|
+
bumpAmplitude: PD.Numeric;
|
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alpha: PD.Numeric;
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quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
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material: PD.Group<PD.Normalize<{
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metalness: number;
|
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roughness: number;
|
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+
bumpiness: number;
|
|
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|
}>>;
|
|
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linkSizeFactor: PD.Numeric;
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|
detail: PD.Numeric;
|
|
@@ -42,6 +45,7 @@ export declare const CarbohydrateParams: {
|
|
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42
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|
export declare type CarbohydrateParams = typeof CarbohydrateParams;
|
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46
|
export declare function getCarbohydrateParams(ctx: ThemeRegistryContext, structure: Structure): {
|
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visuals: PD.MultiSelect<"carbohydrate-symbol" | "carbohydrate-link" | "carbohydrate-terminal-link">;
|
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|
+
bumpFrequency: PD.Numeric;
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|
terminalLinkSizeFactor: PD.Numeric;
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|
linkScale: PD.Numeric;
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linkSpacing: PD.Numeric;
|
|
@@ -61,11 +65,13 @@ export declare function getCarbohydrateParams(ctx: ThemeRegistryContext, structu
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flatShaded: PD.BooleanParam;
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|
xrayShaded: PD.BooleanParam;
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|
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|
+
bumpAmplitude: PD.Numeric;
|
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alpha: PD.Numeric;
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quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
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|
roughness: number;
|
|
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+
bumpiness: number;
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|
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|
}>>;
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linkSizeFactor: PD.Numeric;
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detail: PD.Numeric;
|
|
@@ -75,6 +81,7 @@ export declare type CarbohydrateRepresentation = StructureRepresentation<Carbohy
|
|
|
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|
export declare function CarbohydrateRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CarbohydrateParams>): CarbohydrateRepresentation;
|
|
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|
export declare const CarbohydrateRepresentationProvider: StructureRepresentationProvider<{
|
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|
visuals: PD.MultiSelect<"carbohydrate-symbol" | "carbohydrate-link" | "carbohydrate-terminal-link">;
|
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|
+
bumpFrequency: PD.Numeric;
|
|
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|
terminalLinkSizeFactor: PD.Numeric;
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|
linkScale: PD.Numeric;
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|
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|
linkSpacing: PD.Numeric;
|
|
@@ -94,11 +101,13 @@ export declare const CarbohydrateRepresentationProvider: StructureRepresentation
|
|
|
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|
flatShaded: PD.BooleanParam;
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|
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|
ignoreLight: PD.BooleanParam;
|
|
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|
xrayShaded: PD.BooleanParam;
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|
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bumpAmplitude: PD.Numeric;
|
|
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|
alpha: PD.Numeric;
|
|
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|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
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|
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|
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|
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bumpiness: number;
|
|
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|
}>>;
|
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|
linkSizeFactor: PD.Numeric;
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detail: PD.Numeric;
|
|
@@ -7,6 +7,7 @@
|
|
|
7
7
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
8
8
|
exports.CarbohydrateRepresentationProvider = exports.CarbohydrateRepresentation = exports.getCarbohydrateParams = exports.CarbohydrateParams = void 0;
|
|
9
9
|
var tslib_1 = require("tslib");
|
|
10
|
+
var base_1 = require("../../../mol-geo/geometry/base");
|
|
10
11
|
var structure_1 = require("../../../mol-model/structure");
|
|
11
12
|
var representation_1 = require("../../../mol-repr/representation");
|
|
12
13
|
var param_definition_1 = require("../../../mol-util/param-definition");
|
|
@@ -20,7 +21,7 @@ var CarbohydrateVisuals = {
|
|
|
20
21
|
'carbohydrate-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate link cylinder', ctx, getParams, carbohydrate_link_cylinder_1.CarbohydrateLinkVisual); },
|
|
21
22
|
'carbohydrate-terminal-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate terminal link cylinder', ctx, getParams, carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkVisual); },
|
|
22
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|
};
|
|
23
|
-
exports.CarbohydrateParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, carbohydrate_symbol_mesh_1.CarbohydrateSymbolParams), carbohydrate_link_cylinder_1.CarbohydrateLinkParams), carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], param_definition_1.ParamDefinition.objectToOptions(CarbohydrateVisuals)) });
|
|
24
|
+
exports.CarbohydrateParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, carbohydrate_symbol_mesh_1.CarbohydrateSymbolParams), carbohydrate_link_cylinder_1.CarbohydrateLinkParams), carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], param_definition_1.ParamDefinition.objectToOptions(CarbohydrateVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
24
25
|
function getCarbohydrateParams(ctx, structure) {
|
|
25
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|
return param_definition_1.ParamDefinition.clone(exports.CarbohydrateParams);
|
|
26
27
|
}
|
|
@@ -11,6 +11,7 @@ import { StructureRepresentation, StructureRepresentationProvider } from '../rep
|
|
|
11
11
|
export declare const CartoonParams: {
|
|
12
12
|
sizeFactor: PD.Numeric;
|
|
13
13
|
visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
|
|
14
|
+
bumpFrequency: PD.Numeric;
|
|
14
15
|
unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
|
|
15
16
|
includeParent: PD.BooleanParam;
|
|
16
17
|
doubleSided: PD.BooleanParam;
|
|
@@ -18,11 +19,13 @@ export declare const CartoonParams: {
|
|
|
18
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|
flatShaded: PD.BooleanParam;
|
|
19
20
|
ignoreLight: PD.BooleanParam;
|
|
20
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|
xrayShaded: PD.BooleanParam;
|
|
22
|
+
bumpAmplitude: PD.Numeric;
|
|
21
23
|
alpha: PD.Numeric;
|
|
22
24
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
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material: PD.Group<PD.Normalize<{
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metalness: number;
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roughness: number;
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bumpiness: number;
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}>>;
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radialSegments: PD.Numeric;
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detail: PD.Numeric;
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@@ -36,6 +39,7 @@ export declare type CartoonParams = typeof CartoonParams;
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export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure): {
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sizeFactor: PD.Numeric;
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visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
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bumpFrequency: PD.Numeric;
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unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
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includeParent: PD.BooleanParam;
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doubleSided: PD.BooleanParam;
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@@ -43,11 +47,13 @@ export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: S
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flatShaded: PD.BooleanParam;
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ignoreLight: PD.BooleanParam;
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xrayShaded: PD.BooleanParam;
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bumpAmplitude: PD.Numeric;
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alpha: PD.Numeric;
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quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
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material: PD.Group<PD.Normalize<{
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metalness: number;
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roughness: number;
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bumpiness: number;
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}>>;
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radialSegments: PD.Numeric;
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detail: PD.Numeric;
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@@ -62,6 +68,7 @@ export declare function CartoonRepresentation(ctx: RepresentationContext, getPar
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export declare const CartoonRepresentationProvider: StructureRepresentationProvider<{
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sizeFactor: PD.Numeric;
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visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
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+
bumpFrequency: PD.Numeric;
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unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
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includeParent: PD.BooleanParam;
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doubleSided: PD.BooleanParam;
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@@ -69,11 +76,13 @@ export declare const CartoonRepresentationProvider: StructureRepresentationProvi
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flatShaded: PD.BooleanParam;
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ignoreLight: PD.BooleanParam;
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xrayShaded: PD.BooleanParam;
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79
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+
bumpAmplitude: PD.Numeric;
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alpha: PD.Numeric;
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quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
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material: PD.Group<PD.Normalize<{
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metalness: number;
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roughness: number;
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85
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+
bumpiness: number;
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}>>;
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radialSegments: PD.Numeric;
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detail: PD.Numeric;
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@@ -19,6 +19,7 @@ var polymer_gap_cylinder_1 = require("../visual/polymer-gap-cylinder");
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var polymer_trace_mesh_1 = require("../visual/polymer-trace-mesh");
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var secondary_structure_1 = require("../../../mol-model-props/computed/secondary-structure");
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var helix_orientation_1 = require("../../../mol-model-props/computed/helix-orientation");
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+
var base_1 = require("../../../mol-geo/geometry/base");
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var CartoonVisuals = {
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'polymer-trace': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer trace mesh', ctx, getParams, polymer_trace_mesh_1.PolymerTraceVisual); },
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'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
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@@ -26,7 +27,7 @@ var CartoonVisuals = {
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'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
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|
'direction-wedge': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer direction wedge', ctx, getParams, polymer_direction_wedge_1.PolymerDirectionVisual); }
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28
29
|
};
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-
exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)) });
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30
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+
exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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function getCartoonParams(ctx, structure) {
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var params = param_definition_1.ParamDefinition.clone(exports.CartoonParams);
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var hasNucleotides = false;
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