molstar 2.3.9 → 3.0.0-dev.10
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/README.md +18 -0
- package/build/viewer/embedded.html +5 -5
- package/build/viewer/index.html +29 -17
- 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 +8 -8
- package/lib/apps/docking-viewer/index.js +87 -74
- package/lib/apps/docking-viewer/viewport.d.ts +2 -2
- package/lib/apps/docking-viewer/viewport.js +18 -15
- package/lib/apps/viewer/app.d.ts +230 -0
- package/lib/apps/viewer/app.js +515 -0
- package/lib/apps/viewer/embedded.html +5 -5
- package/lib/apps/viewer/index.d.ts +2 -403
- package/lib/apps/viewer/index.html +29 -17
- package/lib/apps/viewer/index.js +2 -420
- package/lib/cli/chem-comp-dict/util.d.ts +4 -4
- package/lib/cli/cifschema/index.d.ts +1 -1
- package/lib/cli/cifschema/index.js +15 -35
- package/lib/cli/cifschema/util/cif-dic.js +1 -0
- 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.d.ts +2 -2
- package/lib/commonjs/apps/docking-viewer/viewport.js +18 -15
- 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/chem-comp-dict/util.d.ts +4 -4
- package/lib/commonjs/cli/cifschema/index.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/index.js +15 -35
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -0
- package/lib/commonjs/examples/alpha-orbitals/index.js +3 -4
- package/lib/commonjs/examples/basic-wrapper/index.js +30 -14
- 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 +33 -15
- 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 +13 -2
- package/lib/commonjs/extensions/anvil/representation.d.ts +88 -5
- package/lib/commonjs/extensions/anvil/representation.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.d.ts +1 -1
- package/lib/commonjs/extensions/cellpack/representation.d.ts +19 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +57 -6
- package/lib/commonjs/extensions/geo-export/controls.js +16 -18
- package/lib/commonjs/extensions/geo-export/glb-exporter.d.ts +5 -3
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +49 -27
- package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts +31 -2
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +91 -19
- package/lib/commonjs/extensions/geo-export/obj-exporter.d.ts +1 -0
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +24 -15
- package/lib/commonjs/extensions/geo-export/ui.js +24 -20
- package/lib/commonjs/extensions/geo-export/usdz-exporter.d.ts +3 -5
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +39 -30
- 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 +10 -8
- package/lib/commonjs/extensions/mp4-export/encoder.js +1 -1
- package/lib/commonjs/extensions/mp4-export/ui.js +7 -6
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +17 -6
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts +12 -12
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +18 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +24 -23
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts +3 -3
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +95 -10
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +39 -27
- package/lib/commonjs/mol-canvas3d/canvas3d.js +37 -25
- package/lib/commonjs/mol-canvas3d/controls/trackball.d.ts +9 -4
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +50 -11
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +3 -2
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +14 -3
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +2 -2
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +12 -1
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +2 -2
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +8 -0
- package/lib/commonjs/mol-canvas3d/passes/draw.d.ts +13 -1
- package/lib/commonjs/mol-canvas3d/passes/draw.js +19 -26
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +7 -2
- 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.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +6 -4
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +1 -1
- package/lib/commonjs/mol-data/int/impl/sorted-array.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/base.d.ts +46 -6
- package/lib/commonjs/mol-geo/geometry/base.js +69 -7
- 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 +18 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +7 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +21 -39
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +24 -68
- 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 +16 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +17 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -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/builder/tube.js +18 -8
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +10 -2
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +188 -35
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +18 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +7 -3
- package/lib/commonjs/mol-geo/geometry/overpaint-data.d.ts +7 -2
- package/lib/commonjs/mol-geo/geometry/overpaint-data.js +10 -1
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +18 -3
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -1
- package/lib/commonjs/mol-geo/geometry/size-data.js +5 -5
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +18 -2
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +7 -3
- package/lib/commonjs/mol-geo/geometry/substance-data.d.ts +23 -0
- package/lib/commonjs/mol-geo/geometry/substance-data.js +68 -0
- package/lib/commonjs/mol-geo/geometry/text/text.d.ts +16 -1
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +8 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +194 -27
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +21 -2
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +8 -3
- package/lib/commonjs/mol-geo/geometry/transparency-data.d.ts +7 -2
- package/lib/commonjs/mol-geo/geometry/transparency-data.js +10 -1
- 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 +13 -12
- package/lib/commonjs/mol-gl/compute/util.d.ts +25 -6
- package/lib/commonjs/mol-gl/compute/util.js +76 -21
- 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 +51 -24
- package/lib/commonjs/mol-gl/renderable/cylinders.js +4 -4
- package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +34 -14
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.d.ts +29 -4
- package/lib/commonjs/mol-gl/renderable/image.js +2 -2
- package/lib/commonjs/mol-gl/renderable/lines.d.ts +48 -23
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.d.ts +48 -21
- package/lib/commonjs/mol-gl/renderable/mesh.js +4 -4
- package/lib/commonjs/mol-gl/renderable/points.d.ts +29 -4
- package/lib/commonjs/mol-gl/renderable/points.js +3 -4
- package/lib/commonjs/mol-gl/renderable/schema.d.ts +51 -16
- package/lib/commonjs/mol-gl/renderable/schema.js +26 -20
- package/lib/commonjs/mol-gl/renderable/spheres.d.ts +51 -24
- package/lib/commonjs/mol-gl/renderable/spheres.js +4 -4
- package/lib/commonjs/mol-gl/renderable/text.d.ts +29 -4
- package/lib/commonjs/mol-gl/renderable/text.js +2 -2
- package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +46 -19
- 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 +20 -26
- package/lib/commonjs/mol-gl/renderer.js +76 -150
- 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 +3 -3
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +3 -3
- 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-clip.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-clip.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/light-frag-params.glsl.d.ts +3 -3
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +3 -3
- 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.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.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/compute/color-smoothing/normalize.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.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/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-gl/shader-code.d.ts +3 -2
- package/lib/commonjs/mol-gl/shader-code.js +70 -23
- package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/extensions.js +3 -9
- 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 +9 -2
- package/lib/commonjs/mol-gl/webgl/vertex-array.d.ts +3 -2
- package/lib/commonjs/mol-gl/webgl/vertex-array.js +9 -2
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +2 -2
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +3 -3
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/cif-core.d.ts +8 -5
- package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js +15 -5
- package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts +3 -3
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +3 -3
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +341 -16
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +326 -1
- package/lib/commonjs/mol-io/reader/mol/parser.d.ts +23 -1
- package/lib/commonjs/mol-io/reader/mol/parser.js +116 -4
- 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-io/reader/ply/schema.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.d.ts +15 -0
- package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js +100 -0
- package/lib/commonjs/mol-io/reader/sdf/parser.d.ts +4 -2
- package/lib/commonjs/mol-io/reader/sdf/parser.js +23 -6
- 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-math/linear-algebra/3d/vec3.d.ts +6 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js +9 -0
- package/lib/commonjs/mol-model/loci.d.ts +30 -30
- package/lib/commonjs/mol-model/shape/shape.d.ts +1 -1
- 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/query/utils/structure-distance.d.ts +54 -5
- package/lib/commonjs/mol-model/structure/structure/element/stats.js +8 -0
- package/lib/commonjs/mol-model/structure/structure/properties.d.ts +2 -2
- package/lib/commonjs/mol-model/structure/structure/properties.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/symmetry.js +1 -3
- 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/structure/structure/unit.d.ts +2 -2
- package/lib/commonjs/mol-model-formats/shape/ply.d.ts +40 -6
- package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +6 -6
- package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +8 -8
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- package/lib/servers/model/properties/wwpdb.js.map +0 -1
- package/lib/servers/model/property-provider.js.map +0 -1
- package/lib/servers/model/query/atoms.js.map +0 -1
- package/lib/servers/model/query/schemas.js.map +0 -1
- package/lib/servers/model/query.js.map +0 -1
- package/lib/servers/model/server/api-local.js.map +0 -1
- package/lib/servers/model/server/api-schema.js.map +0 -1
- package/lib/servers/model/server/api-web-multiple.js.map +0 -1
- package/lib/servers/model/server/api-web.js.map +0 -1
- package/lib/servers/model/server/api.js.map +0 -1
- package/lib/servers/model/server/cache.js.map +0 -1
- package/lib/servers/model/server/jobs.js.map +0 -1
- package/lib/servers/model/server/query.js.map +0 -1
- package/lib/servers/model/server/structure-wrapper.js.map +0 -1
- package/lib/servers/model/server.js.map +0 -1
- package/lib/servers/model/test.js.map +0 -1
- package/lib/servers/model/utils/fetch-props-pdbe.js.map +0 -1
- package/lib/servers/model/utils/fetch-retry.js.map +0 -1
- package/lib/servers/model/utils/tar.js.map +0 -1
- package/lib/servers/model/utils/writer.js.map +0 -1
- package/lib/servers/model/version.js.map +0 -1
- package/lib/servers/plugin-state/api-schema.js.map +0 -1
- package/lib/servers/plugin-state/config.js.map +0 -1
- package/lib/servers/plugin-state/index.js.map +0 -1
- package/lib/servers/plugin-state/version.js.map +0 -1
- package/lib/servers/volume/common/binary-schema.js.map +0 -1
- package/lib/servers/volume/common/data-format.js.map +0 -1
- package/lib/servers/volume/common/file.js.map +0 -1
- package/lib/servers/volume/config.js.map +0 -1
- package/lib/servers/volume/pack/data-model.js.map +0 -1
- package/lib/servers/volume/pack/downsampling.js.map +0 -1
- package/lib/servers/volume/pack/format/ccp4.js.map +0 -1
- package/lib/servers/volume/pack/format/dsn6.js.map +0 -1
- package/lib/servers/volume/pack/format.js.map +0 -1
- package/lib/servers/volume/pack/main.js.map +0 -1
- package/lib/servers/volume/pack/sampling.js.map +0 -1
- package/lib/servers/volume/pack/version.js.map +0 -1
- package/lib/servers/volume/pack/writer.js.map +0 -1
- package/lib/servers/volume/pack.js.map +0 -1
- package/lib/servers/volume/query.js.map +0 -1
- package/lib/servers/volume/server/algebra/box.js.map +0 -1
- package/lib/servers/volume/server/algebra/coordinate.js.map +0 -1
- package/lib/servers/volume/server/api.js.map +0 -1
- package/lib/servers/volume/server/local-api.js.map +0 -1
- package/lib/servers/volume/server/query/compose.js.map +0 -1
- package/lib/servers/volume/server/query/data-model.js.map +0 -1
- package/lib/servers/volume/server/query/encode.js.map +0 -1
- package/lib/servers/volume/server/query/execute.js.map +0 -1
- package/lib/servers/volume/server/query/identify.js.map +0 -1
- package/lib/servers/volume/server/state.js.map +0 -1
- package/lib/servers/volume/server/version.js.map +0 -1
- package/lib/servers/volume/server/web-api.js.map +0 -1
- package/lib/servers/volume/server/web-schema.js.map +0 -1
- package/lib/servers/volume/server.js.map +0 -1
- package/lib/tests/browser/font-atlas.d.ts +0 -6
- package/lib/tests/browser/font-atlas.js +0 -36
- package/lib/tests/browser/font-atlas.js.map +0 -1
- package/lib/tests/browser/index.html +0 -37
- package/lib/tests/browser/marching-cubes.d.ts +0 -6
- package/lib/tests/browser/marching-cubes.js +0 -142
- package/lib/tests/browser/marching-cubes.js.map +0 -1
- package/lib/tests/browser/parse-xtc.d.ts +0 -6
- package/lib/tests/browser/parse-xtc.js +0 -40
- package/lib/tests/browser/parse-xtc.js.map +0 -1
- package/lib/tests/browser/render-lines.d.ts +0 -6
- package/lib/tests/browser/render-lines.js +0 -40
- package/lib/tests/browser/render-lines.js.map +0 -1
- package/lib/tests/browser/render-mesh.d.ts +0 -6
- package/lib/tests/browser/render-mesh.js +0 -49
- package/lib/tests/browser/render-mesh.js.map +0 -1
- package/lib/tests/browser/render-shape.d.ts +0 -7
- package/lib/tests/browser/render-shape.js +0 -164
- package/lib/tests/browser/render-shape.js.map +0 -1
- package/lib/tests/browser/render-spheres.d.ts +0 -6
- package/lib/tests/browser/render-spheres.js +0 -39
- package/lib/tests/browser/render-spheres.js.map +0 -1
- package/lib/tests/browser/render-structure.d.ts +0 -6
- package/lib/tests/browser/render-structure.js +0 -287
- package/lib/tests/browser/render-structure.js.map +0 -1
- package/lib/tests/browser/render-text.d.ts +0 -6
- package/lib/tests/browser/render-text.js +0 -59
- package/lib/tests/browser/render-text.js.map +0 -1
- package/lib/tsconfig.commonjs.tsbuildinfo +0 -1
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assembly_ids: ReadonlyArray<
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assembly_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
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export declare type RcsbUniprotAlignmentsCoreEntityAlignments = {
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readonly aligned_regions
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readonly scores
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export declare type AssemblySymmetryQuery = {
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readonly assembly?:
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readonly rcsb_struct_symmetry?:
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readonly assembly?: {
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} | null | undefined>;
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} | null | undefined>;
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} | null | undefined> | null | undefined;
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@@ -12,7 +12,7 @@ export declare const RCSBValidationReport: import("../../../mol-state/transforme
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export declare const ValidationReportDensityFitPreset: StructureRepresentationPresetProvider<{
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export declare const ValidationReportRandomCoilIndexPreset: StructureRepresentationPresetProvider<{
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ValidationReport.getEntryUrl = getEntryUrl;
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function isApplicable(model) {
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ValidationReport.isApplicable = isApplicable;
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function fromXml(xml, model) {
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}>>;
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}>>;
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};
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alpha: PD.Numeric;
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quality: PD.Select<"
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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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}>>;
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}>[];
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}>>;
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};
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export declare type ClashesParams = typeof ClashesParams;
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export declare function getClashesParams(ctx: ThemeRegistryContext, structure: Structure): {
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@@ -107,8 +158,25 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
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flatShaded: PD.BooleanParam;
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ignoreLight: PD.BooleanParam;
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bumpFrequency: PD.Numeric;
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alpha: PD.Numeric;
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quality: PD.Select<"
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intensity: number;
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+
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|
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|
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}>, "spin"> | PD.NamedParams<PD.Normalize<{
|
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}>, "rock">;
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|
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|
@@ -309,7 +317,11 @@ export declare const DefaultCanvas3DParams: PD.Values<{
|
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|
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|
}>, "on">;
|
|
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|
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|
|
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|
}>;
|
|
@@ -370,7 +382,7 @@ interface Canvas3D {
|
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|
update(repr?: Representation.Any, keepBoundingSphere?: boolean): void;
|
|
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|
clear(): void;
|
|
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|
syncVisibility(): void;
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|
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|
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requestDraw(
|
|
385
|
+
requestDraw(): void;
|
|
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|
/** Reset the timers, used by "animate" */
|
|
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|
resetTime(t: number): void;
|
|
376
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|
animate(): void;
|
|
@@ -35,6 +35,7 @@ import { Helper } from './helper/helper';
|
|
|
35
35
|
import { Passes } from './passes/passes';
|
|
36
36
|
import { shallowEqual } from '../mol-util';
|
|
37
37
|
import { MarkingParams } from './passes/marking';
|
|
38
|
+
import { GraphicsRenderVariantsBlended, GraphicsRenderVariantsWboit } from '../mol-gl/webgl/render-item';
|
|
38
39
|
export var Canvas3DParams = {
|
|
39
40
|
camera: PD.Group({
|
|
40
41
|
mode: PD.Select('perspective', PD.arrayToOptions(['perspective', 'orthographic']), { label: 'Camera' }),
|
|
@@ -200,7 +201,7 @@ var Canvas3D;
|
|
|
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201
|
var width = 128;
|
|
201
202
|
var height = 128;
|
|
202
203
|
updateViewport();
|
|
203
|
-
var scene = Scene.create(webgl);
|
|
204
|
+
var scene = Scene.create(webgl, passes.draw.wboitEnabled ? GraphicsRenderVariantsWboit : GraphicsRenderVariantsBlended);
|
|
204
205
|
var camera = new Camera({
|
|
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206
|
position: Vec3.create(0, 0, 100),
|
|
206
207
|
mode: p.camera.mode,
|
|
@@ -252,16 +253,24 @@ var Canvas3D;
|
|
|
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253
|
changed = helper.camera.mark(loci, action) || changed;
|
|
253
254
|
reprRenderObjects.forEach(function (_, _repr) { changed = _repr.mark(loci, action) || changed; });
|
|
254
255
|
}
|
|
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|
-
if (changed
|
|
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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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|
-
|
|
256
|
+
if (changed) {
|
|
257
|
+
if (noDraw) {
|
|
258
|
+
// Even with `noDraw` make sure changes will be rendered.
|
|
259
|
+
// Note that with this calling mark (with or without `noDraw`) multiple times
|
|
260
|
+
// during a JS event loop iteration will only result in a single render call.
|
|
261
|
+
forceNextRender = true;
|
|
262
|
+
}
|
|
263
|
+
else {
|
|
264
|
+
scene.update(void 0, true);
|
|
265
|
+
helper.handle.scene.update(void 0, true);
|
|
266
|
+
helper.camera.scene.update(void 0, true);
|
|
267
|
+
var prevPickDirty = pickHelper.dirty;
|
|
268
|
+
draw({ force: true, allowMulti: true });
|
|
269
|
+
pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
|
|
270
|
+
}
|
|
262
271
|
}
|
|
263
272
|
}
|
|
264
|
-
function render(force) {
|
|
273
|
+
function render(force, allowMulti) {
|
|
265
274
|
if (webgl.isContextLost)
|
|
266
275
|
return false;
|
|
267
276
|
var resized = false;
|
|
@@ -285,11 +294,13 @@ var Canvas3D;
|
|
|
285
294
|
stereoCamera.update();
|
|
286
295
|
cam = stereoCamera;
|
|
287
296
|
}
|
|
297
|
+
var ctx = { renderer: renderer, camera: cam, scene: scene, helper: helper };
|
|
288
298
|
if (MultiSamplePass.isEnabled(p.multiSample)) {
|
|
289
|
-
|
|
299
|
+
var forceOn = !cameraChanged && allowMulti && !controls.isAnimating;
|
|
300
|
+
multiSampleHelper.render(ctx, p, true, forceOn);
|
|
290
301
|
}
|
|
291
302
|
else {
|
|
292
|
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passes.draw.render(
|
|
303
|
+
passes.draw.render(ctx, p, true);
|
|
293
304
|
}
|
|
294
305
|
pickHelper.dirty = true;
|
|
295
306
|
didRender = true;
|
|
@@ -300,15 +311,15 @@ var Canvas3D;
|
|
|
300
311
|
var forceDrawAfterAllCommited = false;
|
|
301
312
|
var currentTime = 0;
|
|
302
313
|
var drawPaused = false;
|
|
303
|
-
function draw(
|
|
314
|
+
function draw(options) {
|
|
304
315
|
if (drawPaused)
|
|
305
316
|
return;
|
|
306
|
-
if (render(!!force) && notifyDidDraw) {
|
|
317
|
+
if (render(!!(options === null || options === void 0 ? void 0 : options.force), !!(options === null || options === void 0 ? void 0 : options.allowMulti)) && notifyDidDraw) {
|
|
307
318
|
didDraw.next(now() - startTime);
|
|
308
319
|
}
|
|
309
320
|
}
|
|
310
|
-
function requestDraw(
|
|
311
|
-
forceNextRender =
|
|
321
|
+
function requestDraw() {
|
|
322
|
+
forceNextRender = true;
|
|
312
323
|
}
|
|
313
324
|
var animationFrameHandle = 0;
|
|
314
325
|
function tick(t, options) {
|
|
@@ -318,7 +329,7 @@ var Canvas3D;
|
|
|
318
329
|
if (options === null || options === void 0 ? void 0 : options.manualDraw) {
|
|
319
330
|
return;
|
|
320
331
|
}
|
|
321
|
-
draw(
|
|
332
|
+
draw();
|
|
322
333
|
if (!camera.transition.inTransition && !webgl.isContextLost) {
|
|
323
334
|
interactionHelper.tick(currentTime);
|
|
324
335
|
}
|
|
@@ -356,7 +367,7 @@ var Canvas3D;
|
|
|
356
367
|
if (forceDrawAfterAllCommited) {
|
|
357
368
|
if (helper.debug.isEnabled)
|
|
358
369
|
helper.debug.update();
|
|
359
|
-
draw(true);
|
|
370
|
+
draw({ force: true });
|
|
360
371
|
forceDrawAfterAllCommited = false;
|
|
361
372
|
}
|
|
362
373
|
commited.next(now());
|
|
@@ -391,7 +402,7 @@ var Canvas3D;
|
|
|
391
402
|
return true;
|
|
392
403
|
if (camera.transition.inTransition || nextCameraResetSnapshot)
|
|
393
404
|
return false;
|
|
394
|
-
var cameraSphereOverlapsNone = true;
|
|
405
|
+
var cameraSphereOverlapsNone = true, isEmpty = true;
|
|
395
406
|
Sphere3D.set(cameraSphere, camera.state.target, camera.state.radius);
|
|
396
407
|
// check if any renderable has moved outside of the old bounding sphere
|
|
397
408
|
// and if no renderable is overlapping with the camera sphere
|
|
@@ -402,13 +413,14 @@ var Canvas3D;
|
|
|
402
413
|
var b = r.values.boundingSphere.ref.value;
|
|
403
414
|
if (!b.radius)
|
|
404
415
|
continue;
|
|
416
|
+
isEmpty = false;
|
|
405
417
|
var cameraDist = Vec3.distance(cameraSphere.center, b.center);
|
|
406
418
|
if ((cameraDist > cameraSphere.radius || cameraDist > b.radius || b.radius > camera.state.radiusMax) && !Sphere3D.includes(oldBoundingSphereVisible, b))
|
|
407
419
|
return true;
|
|
408
420
|
if (Sphere3D.overlaps(cameraSphere, b))
|
|
409
421
|
cameraSphereOverlapsNone = false;
|
|
410
422
|
}
|
|
411
|
-
return cameraSphereOverlapsNone;
|
|
423
|
+
return cameraSphereOverlapsNone || (!isEmpty && cameraSphere.radius <= 0.1);
|
|
412
424
|
}
|
|
413
425
|
var sceneCommitTimeoutMs = 250;
|
|
414
426
|
function commitScene(isSynchronous) {
|
|
@@ -524,11 +536,11 @@ var Canvas3D;
|
|
|
524
536
|
}
|
|
525
537
|
var contextRestoredSub = contextRestored.subscribe(function () {
|
|
526
538
|
pickHelper.dirty = true;
|
|
527
|
-
draw(true);
|
|
539
|
+
draw({ force: true });
|
|
528
540
|
// Unclear why, but in Chrome with wboit enabled the first `draw` only clears
|
|
529
541
|
// the drawingBuffer. Note that in Firefox the drawingBuffer is preserved after
|
|
530
542
|
// context loss so it is unclear if it behaves the same.
|
|
531
|
-
draw(true);
|
|
543
|
+
draw({ force: true });
|
|
532
544
|
});
|
|
533
545
|
var resized = new BehaviorSubject(0);
|
|
534
546
|
function handleResize(draw) {
|
|
@@ -537,7 +549,7 @@ var Canvas3D;
|
|
|
537
549
|
updateViewport();
|
|
538
550
|
syncViewport();
|
|
539
551
|
if (draw)
|
|
540
|
-
requestDraw(
|
|
552
|
+
requestDraw();
|
|
541
553
|
resized.next(+new Date());
|
|
542
554
|
}
|
|
543
555
|
return {
|
|
@@ -562,7 +574,7 @@ var Canvas3D;
|
|
|
562
574
|
reprRenderObjects.clear();
|
|
563
575
|
scene.clear();
|
|
564
576
|
helper.debug.clear();
|
|
565
|
-
requestDraw(
|
|
577
|
+
requestDraw();
|
|
566
578
|
reprCount.next(reprRenderObjects.size);
|
|
567
579
|
},
|
|
568
580
|
syncVisibility: function () {
|
|
@@ -574,7 +586,7 @@ var Canvas3D;
|
|
|
574
586
|
if (helper.debug.isEnabled)
|
|
575
587
|
helper.debug.update();
|
|
576
588
|
}
|
|
577
|
-
requestDraw(
|
|
589
|
+
requestDraw();
|
|
578
590
|
},
|
|
579
591
|
requestDraw: requestDraw,
|
|
580
592
|
tick: tick,
|
|
@@ -671,7 +683,7 @@ var Canvas3D;
|
|
|
671
683
|
p.camera.stereo.name = 'off';
|
|
672
684
|
}
|
|
673
685
|
if (!doNotRequestDraw) {
|
|
674
|
-
requestDraw(
|
|
686
|
+
requestDraw();
|
|
675
687
|
}
|
|
676
688
|
},
|
|
677
689
|
getImagePass: function (props) {
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
/**
|
|
2
|
-
* Copyright (c) 2018-
|
|
2
|
+
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
3
3
|
*
|
|
4
4
|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
5
5
|
* @author David Sehnal <david.sehnal@gmail.com>
|
|
@@ -28,8 +28,12 @@ export declare const TrackballControlsParams: {
|
|
|
28
28
|
rotateSpeed: PD.Numeric;
|
|
29
29
|
zoomSpeed: PD.Numeric;
|
|
30
30
|
panSpeed: PD.Numeric;
|
|
31
|
-
|
|
32
|
-
|
|
31
|
+
animate: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
|
|
32
|
+
speed: number;
|
|
33
|
+
}>, "spin"> | PD.NamedParams<PD.Normalize<{
|
|
34
|
+
speed: number;
|
|
35
|
+
angle: number;
|
|
36
|
+
}>, "rock">>;
|
|
33
37
|
staticMoving: PD.BooleanParam;
|
|
34
38
|
dynamicDampingFactor: PD.Numeric;
|
|
35
39
|
minDistance: PD.Numeric;
|
|
@@ -61,7 +65,8 @@ export declare const TrackballControlsParams: {
|
|
|
61
65
|
export declare type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>;
|
|
62
66
|
export { TrackballControls };
|
|
63
67
|
interface TrackballControls {
|
|
64
|
-
viewport: Viewport;
|
|
68
|
+
readonly viewport: Viewport;
|
|
69
|
+
readonly isAnimating: boolean;
|
|
65
70
|
readonly props: Readonly<TrackballControlsProps>;
|
|
66
71
|
setProps: (props: Partial<TrackballControlsProps>) => void;
|
|
67
72
|
start: (t: number) => void;
|