molstar 3.2.0 → 3.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +20 -20
- package/README.md +197 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.css +1 -1
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +0 -1
- package/lib/apps/docking-viewer/viewport.js +6 -6
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +2 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/apps/viewer/index.js +0 -1
- package/lib/cli/chem-comp-dict/create-ions.js +0 -1
- package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
- package/lib/cli/chem-comp-dict/create-table.js +0 -1
- package/lib/cli/chem-comp-dict/util.js +0 -1
- package/lib/cli/cif2bcif/converter.js +0 -1
- package/lib/cli/cif2bcif/index.js +0 -1
- package/lib/cli/cifschema/index.js +0 -1
- package/lib/cli/cifschema/util/cif-dic.js +0 -1
- package/lib/cli/cifschema/util/generate.js +0 -1
- package/lib/cli/cifschema/util/helper.js +0 -1
- package/lib/cli/cifschema/util/schema.js +0 -1
- package/lib/cli/lipid-params/index.js +0 -1
- package/lib/cli/state-docs/index.js +0 -1
- package/lib/cli/state-docs/pd-to-md.js +0 -1
- package/lib/cli/structure-info/helpers.js +0 -1
- package/lib/cli/structure-info/model.js +0 -1
- package/lib/cli/structure-info/volume.js +0 -1
- package/lib/commonjs/apps/docking-viewer/index.js +12 -13
- package/lib/commonjs/apps/docking-viewer/viewport.js +38 -38
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +24 -23
- package/lib/commonjs/apps/viewer/index.js +1 -2
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -7
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -9
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -18
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -10
- package/lib/commonjs/cli/cif2bcif/index.js +8 -9
- package/lib/commonjs/cli/cifschema/index.js +27 -28
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -2
- package/lib/commonjs/cli/cifschema/util/generate.js +0 -1
- package/lib/commonjs/cli/cifschema/util/helper.js +0 -1
- package/lib/commonjs/cli/cifschema/util/schema.js +0 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -10
- package/lib/commonjs/cli/state-docs/index.js +2 -3
- package/lib/commonjs/cli/state-docs/pd-to-md.js +0 -1
- package/lib/commonjs/cli/structure-info/helpers.js +11 -12
- package/lib/commonjs/cli/structure-info/model.js +15 -16
- package/lib/commonjs/cli/structure-info/volume.js +9 -10
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -4
- package/lib/commonjs/examples/alpha-orbitals/example-data.js +0 -1
- package/lib/commonjs/examples/alpha-orbitals/index.js +11 -12
- package/lib/commonjs/examples/basic-wrapper/coloring.js +0 -1
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -3
- package/lib/commonjs/examples/basic-wrapper/custom-theme.js +0 -1
- package/lib/commonjs/examples/basic-wrapper/index.js +22 -23
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -9
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -4
- package/lib/commonjs/examples/domain-annotation-server/schemas.js +0 -1
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -7
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -4
- package/lib/commonjs/examples/lighting/index.js +8 -9
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -3
- package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +0 -1
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -5
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -27
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -3
- package/lib/commonjs/examples/task.js +15 -16
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -2
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -3
- package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.js +0 -1
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -14
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -14
- package/lib/commonjs/extensions/anvil/behavior.js +14 -15
- package/lib/commonjs/extensions/anvil/prop.js +7 -8
- package/lib/commonjs/extensions/anvil/representation.js +5 -6
- package/lib/commonjs/extensions/cellpack/color/generate.js +0 -1
- package/lib/commonjs/extensions/cellpack/color/provided.js +0 -1
- package/lib/commonjs/extensions/cellpack/curve.js +0 -1
- package/lib/commonjs/extensions/cellpack/data.js +0 -1
- package/lib/commonjs/extensions/cellpack/index.js +1 -2
- package/lib/commonjs/extensions/cellpack/model.js +26 -25
- package/lib/commonjs/extensions/cellpack/preset.js +6 -7
- package/lib/commonjs/extensions/cellpack/property.js +3 -4
- package/lib/commonjs/extensions/cellpack/representation.js +2 -3
- package/lib/commonjs/extensions/cellpack/state.js +13 -14
- package/lib/commonjs/extensions/cellpack/util.js +14 -15
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +0 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -6
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -3
- package/lib/commonjs/extensions/dnatco/confal-pyramids/types.js +0 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -2
- package/lib/commonjs/extensions/dnatco/index.js +0 -1
- package/lib/commonjs/extensions/g3d/data.js +6 -7
- package/lib/commonjs/extensions/g3d/format.js +14 -15
- package/lib/commonjs/extensions/g3d/model.js +4 -5
- package/lib/commonjs/extensions/geo-export/controls.js +3 -4
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -10
- package/lib/commonjs/extensions/geo-export/index.js +1 -2
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -13
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -8
- package/lib/commonjs/extensions/geo-export/render-object-exporter.js +0 -1
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -8
- package/lib/commonjs/extensions/geo-export/ui.js +7 -8
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -10
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -10
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -5
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -5
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -6
- package/lib/commonjs/extensions/model-export/export.js +4 -5
- package/lib/commonjs/extensions/model-export/index.js +1 -2
- package/lib/commonjs/extensions/model-export/ui.js +5 -6
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -6
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -5
- package/lib/commonjs/extensions/mp4-export/index.js +1 -2
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -6
- package/lib/commonjs/extensions/pdbe/index.js +0 -1
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -3
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -3
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +0 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -18
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -3
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -10
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -7
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -10
- package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.js +0 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +158 -1
- package/lib/commonjs/extensions/rcsb/graphql/types.js +0 -1
- package/lib/commonjs/extensions/rcsb/index.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -18
- package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +0 -1
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -16
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +22 -6
- package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
- package/lib/commonjs/extensions/zenodo/index.js +35 -0
- package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
- package/lib/commonjs/extensions/zenodo/ui.js +306 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -2
- package/lib/commonjs/mol-canvas3d/camera/transition.js +0 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -2
- package/lib/commonjs/mol-canvas3d/camera.js +2 -2
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +3 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.js +46 -39
- package/lib/commonjs/mol-canvas3d/controls/object.js +0 -1
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -6
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -6
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -2
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -3
- package/lib/commonjs/mol-canvas3d/passes/draw.js +15 -13
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -4
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -2
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -7
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts +1 -1
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +23 -10
- package/lib/commonjs/mol-canvas3d/passes/passes.js +0 -1
- package/lib/commonjs/mol-canvas3d/passes/pick.js +0 -1
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +8 -1
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +60 -31
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -10
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -4
- package/lib/commonjs/mol-canvas3d/util.js +2 -3
- package/lib/commonjs/mol-data/db/column-helpers.js +0 -1
- package/lib/commonjs/mol-data/db/column.js +2 -3
- package/lib/commonjs/mol-data/db/database.js +0 -1
- package/lib/commonjs/mol-data/db/table.js +1 -2
- package/lib/commonjs/mol-data/db.js +1 -2
- package/lib/commonjs/mol-data/generic/hash-set.js +0 -1
- package/lib/commonjs/mol-data/generic/linked-list.js +0 -1
- package/lib/commonjs/mol-data/generic/unique-array.js +0 -1
- package/lib/commonjs/mol-data/generic.js +3 -4
- package/lib/commonjs/mol-data/index.js +4 -5
- package/lib/commonjs/mol-data/int/impl/interval.js +0 -1
- package/lib/commonjs/mol-data/int/impl/ordered-set.js +0 -1
- package/lib/commonjs/mol-data/int/impl/segmentation.js +0 -1
- package/lib/commonjs/mol-data/int/impl/sorted-array.js +0 -1
- package/lib/commonjs/mol-data/int/interval.js +1 -2
- package/lib/commonjs/mol-data/int/linked-index.js +0 -1
- package/lib/commonjs/mol-data/int/map.js +0 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -2
- package/lib/commonjs/mol-data/int/segmentation.js +1 -2
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -2
- package/lib/commonjs/mol-data/int/sorted-ranges.js +0 -1
- package/lib/commonjs/mol-data/int/tuple.js +0 -1
- package/lib/commonjs/mol-data/int.js +0 -1
- package/lib/commonjs/mol-data/iterator.js +0 -1
- package/lib/commonjs/mol-data/util/array.js +0 -1
- package/lib/commonjs/mol-data/util/buckets.js +0 -1
- package/lib/commonjs/mol-data/util/chunked-array.js +0 -1
- package/lib/commonjs/mol-data/util/combination.js +0 -1
- package/lib/commonjs/mol-data/util/equivalence-classes.js +0 -1
- package/lib/commonjs/mol-data/util/grouping.js +0 -1
- package/lib/commonjs/mol-data/util/hash-functions.js +0 -1
- package/lib/commonjs/mol-data/util/interval-iterator.js +0 -1
- package/lib/commonjs/mol-data/util/sort.js +0 -1
- package/lib/commonjs/mol-data/util.js +7 -8
- package/lib/commonjs/mol-geo/geometry/base.js +0 -1
- package/lib/commonjs/mol-geo/geometry/clipping-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/color-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -2
- package/lib/commonjs/mol-geo/geometry/geometry.js +0 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -4
- package/lib/commonjs/mol-geo/geometry/lines/lines-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +4 -5
- package/lib/commonjs/mol-geo/geometry/marker-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/axes.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/box.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/cylinder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ellipsoid.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ribbon.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sphere.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -4
- package/lib/commonjs/mol-geo/geometry/overpaint-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/picking.js +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -4
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -2
- package/lib/commonjs/mol-geo/geometry/spheres/spheres-builder.js +0 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -4
- package/lib/commonjs/mol-geo/geometry/substance-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -2
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -3
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -4
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -5
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -4
- package/lib/commonjs/mol-geo/geometry/transform-data.js +0 -1
- package/lib/commonjs/mol-geo/geometry/transparency-data.js +0 -1
- package/lib/commonjs/mol-geo/primitive/box.js +0 -1
- package/lib/commonjs/mol-geo/primitive/cage.js +0 -1
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -2
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -2
- package/lib/commonjs/mol-geo/primitive/dodecahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/icosahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/octahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/plane.js +0 -1
- package/lib/commonjs/mol-geo/primitive/polygon.js +0 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -2
- package/lib/commonjs/mol-geo/primitive/primitive.js +0 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -2
- package/lib/commonjs/mol-geo/primitive/pyramid.js +0 -1
- package/lib/commonjs/mol-geo/primitive/sphere.js +0 -1
- package/lib/commonjs/mol-geo/primitive/spiked-ball.js +0 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -2
- package/lib/commonjs/mol-geo/primitive/tetrahedron.js +0 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -2
- package/lib/commonjs/mol-geo/primitive/wedge.js +0 -1
- package/lib/commonjs/mol-geo/util/location-iterator.js +0 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -10
- package/lib/commonjs/mol-geo/util/marching-cubes/builder.js +0 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/tables.js +0 -1
- package/lib/commonjs/mol-geo/util.js +0 -1
- package/lib/commonjs/mol-gl/commit-queue.js +0 -1
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -6
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -4
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -4
- package/lib/commonjs/mol-gl/compute/marching-cubes/tables.js +0 -1
- package/lib/commonjs/mol-gl/compute/util.js +3 -4
- package/lib/commonjs/mol-gl/object3d.js +0 -1
- package/lib/commonjs/mol-gl/render-object.js +0 -1
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -4
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -4
- package/lib/commonjs/mol-gl/renderable/image.js +3 -4
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -4
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -4
- package/lib/commonjs/mol-gl/renderable/points.js +3 -4
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -2
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -4
- package/lib/commonjs/mol-gl/renderable/text.js +3 -4
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -4
- package/lib/commonjs/mol-gl/renderable/util.js +1 -2
- package/lib/commonjs/mol-gl/renderable.js +0 -1
- package/lib/commonjs/mol-gl/renderer.js +3 -5
- package/lib/commonjs/mol-gl/scene.d.ts +2 -1
- package/lib/commonjs/mol-gl/scene.js +14 -3
- package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/float-to-rgba.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/matrix-scale.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/normal-frag-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/read-from-texture.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/rgba-to-float.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/size-vert-params.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +0 -1
- package/lib/commonjs/mol-gl/shader/compose.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/copy.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/cylinders.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/cylinders.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/depth-merge.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/evaluate-wboit.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/fxaa.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/gaussian-density.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/sum.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/image.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/image.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/lines.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/lines.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/marching-cubes/active-voxels.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/marking/edge.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/marking/overlay.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/mesh.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/mesh.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/outlines.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/points.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/points.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.js +2 -3
- package/lib/commonjs/mol-gl/shader/quad.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/smaa/blend.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/smaa/blend.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/smaa/edges.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/smaa/edges.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/smaa/weights.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/smaa/weights.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/spheres.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/spheres.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/ssao-blur.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/ssao.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/text.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader/text.vert.js +0 -1
- package/lib/commonjs/mol-gl/shader/util/grid3d-template.frag.js +0 -1
- package/lib/commonjs/mol-gl/shader-code.js +2 -2
- package/lib/commonjs/mol-gl/webgl/buffer.js +4 -6
- package/lib/commonjs/mol-gl/webgl/compat.js +0 -1
- package/lib/commonjs/mol-gl/webgl/context.js +3 -4
- package/lib/commonjs/mol-gl/webgl/extensions.js +0 -1
- package/lib/commonjs/mol-gl/webgl/framebuffer.js +0 -1
- package/lib/commonjs/mol-gl/webgl/program.js +0 -1
- package/lib/commonjs/mol-gl/webgl/render-item.js +1 -2
- package/lib/commonjs/mol-gl/webgl/render-target.js +0 -1
- package/lib/commonjs/mol-gl/webgl/renderbuffer.js +0 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +2 -3
- package/lib/commonjs/mol-gl/webgl/shader.js +0 -1
- package/lib/commonjs/mol-gl/webgl/state.js +0 -1
- package/lib/commonjs/mol-gl/webgl/texture.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/texture.js +9 -2
- package/lib/commonjs/mol-gl/webgl/uniform.js +0 -1
- package/lib/commonjs/mol-gl/webgl/vertex-array.js +0 -1
- package/lib/commonjs/mol-io/common/ascii.js +0 -1
- package/lib/commonjs/mol-io/common/binary-cif/array-encoder.js +0 -1
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -7
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -4
- package/lib/commonjs/mol-io/common/binary-cif/encoding.js +0 -1
- package/lib/commonjs/mol-io/common/binary-cif.js +3 -4
- package/lib/commonjs/mol-io/common/binary.js +0 -1
- package/lib/commonjs/mol-io/common/file-handle.js +0 -1
- package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
- package/lib/commonjs/mol-io/common/msgpack/decode.js +0 -1
- package/lib/commonjs/mol-io/common/msgpack/encode.js +0 -1
- package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
- package/lib/commonjs/mol-io/common/simple-buffer.js +0 -1
- package/lib/commonjs/mol-io/common/typed-array.js +2 -3
- package/lib/commonjs/mol-io/common/utf8.js +0 -1
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -9
- package/lib/commonjs/mol-io/reader/ccp4/schema.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/binary/field.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -4
- package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -2
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +1 -2
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +1 -2
- package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ddl.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/schema/density-server.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/schema/dic.js +0 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -3
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +6 -2
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +5 -2
- package/lib/commonjs/mol-io/reader/cif/schema.js +2 -3
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -8
- package/lib/commonjs/mol-io/reader/cif.js +1 -2
- package/lib/commonjs/mol-io/reader/common/binary/column.js +0 -1
- package/lib/commonjs/mol-io/reader/common/text/column/fixed.js +0 -1
- package/lib/commonjs/mol-io/reader/common/text/column/token.js +0 -1
- package/lib/commonjs/mol-io/reader/common/text/number-parser.js +0 -1
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -5
- package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -2
- package/lib/commonjs/mol-io/reader/csv/field.js +0 -1
- package/lib/commonjs/mol-io/reader/csv/parser.js +7 -8
- package/lib/commonjs/mol-io/reader/csv/schema.js +0 -1
- package/lib/commonjs/mol-io/reader/cube/parser.js +2 -3
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -3
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -9
- package/lib/commonjs/mol-io/reader/dsn6/schema.js +0 -1
- package/lib/commonjs/mol-io/reader/dx/parser.js +4 -5
- package/lib/commonjs/mol-io/reader/gro/parser.js +6 -7
- package/lib/commonjs/mol-io/reader/mol/parser.js +2 -3
- package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -9
- package/lib/commonjs/mol-io/reader/mol2/schema.js +0 -1
- package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
- package/lib/commonjs/mol-io/reader/obj/parser.js +4 -5
- package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -3
- package/lib/commonjs/mol-io/reader/pdb/schema.js +0 -1
- package/lib/commonjs/mol-io/reader/ply/parser.js +4 -5
- package/lib/commonjs/mol-io/reader/ply/schema.js +0 -1
- package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
- package/lib/commonjs/mol-io/reader/psf/parser.js +8 -9
- package/lib/commonjs/mol-io/reader/result.js +0 -1
- package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js +0 -1
- package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -3
- package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
- package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -5
- package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -3
- package/lib/commonjs/mol-io/utils/short-string-pool.js +0 -1
- package/lib/commonjs/mol-io/writer/cif/encoder/binary.js +0 -1
- package/lib/commonjs/mol-io/writer/cif/encoder/text.js +0 -1
- package/lib/commonjs/mol-io/writer/cif/encoder/util.js +0 -1
- package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -3
- package/lib/commonjs/mol-io/writer/cif.js +1 -2
- package/lib/commonjs/mol-io/writer/encoder.js +0 -1
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -2
- package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -2
- package/lib/commonjs/mol-io/writer/mol.js +0 -1
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -2
- package/lib/commonjs/mol-io/writer/mol2.js +0 -1
- package/lib/commonjs/mol-io/writer/sdf.js +0 -1
- package/lib/commonjs/mol-io/writer/writer.js +0 -1
- package/lib/commonjs/mol-math/approx.js +0 -1
- package/lib/commonjs/mol-math/easing.js +0 -1
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -6
- package/lib/commonjs/mol-math/geometry/boundary.js +0 -1
- package/lib/commonjs/mol-math/geometry/centroid-helper.js +0 -1
- package/lib/commonjs/mol-math/geometry/common.js +0 -1
- package/lib/commonjs/mol-math/geometry/distance-transform.js +0 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +4 -5
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +1 -2
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +4 -5
- package/lib/commonjs/mol-math/geometry/lookup3d/common.js +0 -1
- package/lib/commonjs/mol-math/geometry/lookup3d/grid.js +0 -1
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +8 -9
- package/lib/commonjs/mol-math/geometry/primitives/axes3d.js +0 -1
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +0 -1
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +1 -2
- package/lib/commonjs/mol-math/geometry/spacegroup/cell.js +0 -1
- package/lib/commonjs/mol-math/geometry/spacegroup/construction.js +0 -1
- package/lib/commonjs/mol-math/geometry/spacegroup/tables.js +0 -1
- package/lib/commonjs/mol-math/geometry/symmetry-operator.js +0 -1
- package/lib/commonjs/mol-math/geometry.js +8 -9
- package/lib/commonjs/mol-math/graph/int-adjacency-graph.js +0 -1
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -2
- package/lib/commonjs/mol-math/graph.js +1 -2
- package/lib/commonjs/mol-math/histogram.js +0 -1
- package/lib/commonjs/mol-math/interpolate.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/common.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/mat3.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/mat4.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/minimize-rmsd.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/quat.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/vec2.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d/vec4.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/3d.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/matrix/evd.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/matrix/matrix.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/matrix/principal-axes.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/matrix/svd.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra/tensor.js +0 -1
- package/lib/commonjs/mol-math/linear-algebra.js +2 -3
- package/lib/commonjs/mol-math/misc.js +0 -1
- package/lib/commonjs/mol-model/custom-property.js +0 -1
- package/lib/commonjs/mol-model/location.js +0 -1
- package/lib/commonjs/mol-model/loci.js +0 -1
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -2
- package/lib/commonjs/mol-model/sequence/alignment/sequence.js +0 -1
- package/lib/commonjs/mol-model/sequence/alignment/substitution-matrix.js +0 -1
- package/lib/commonjs/mol-model/sequence/alignment.js +0 -1
- package/lib/commonjs/mol-model/sequence/constants.js +0 -1
- package/lib/commonjs/mol-model/sequence/sequence.js +2 -2
- package/lib/commonjs/mol-model/sequence.js +1 -2
- package/lib/commonjs/mol-model/shape/provider.js +0 -1
- package/lib/commonjs/mol-model/shape/shape.js +0 -1
- package/lib/commonjs/mol-model/shape.js +1 -2
- package/lib/commonjs/mol-model/structure/coordinates/coordinates.js +0 -1
- package/lib/commonjs/mol-model/structure/coordinates.js +1 -2
- package/lib/commonjs/mol-model/structure/export/categories/atom_site.js +0 -1
- package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js +0 -1
- package/lib/commonjs/mol-model/structure/export/categories/misc.js +0 -1
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -3
- package/lib/commonjs/mol-model/structure/export/categories/sequence.js +0 -1
- package/lib/commonjs/mol-model/structure/export/categories/utils.js +0 -1
- package/lib/commonjs/mol-model/structure/export/mmcif.js +0 -1
- package/lib/commonjs/mol-model/structure/model/indexing.js +0 -1
- package/lib/commonjs/mol-model/structure/model/model.d.ts +5 -1
- package/lib/commonjs/mol-model/structure/model/model.js +41 -29
- package/lib/commonjs/mol-model/structure/model/properties/atomic/bonds.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/atomic/conformation.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/atomic/measures.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/atomic/types.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -4
- package/lib/commonjs/mol-model/structure/model/properties/coarse/conformation.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/coarse/hierarchy.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -3
- package/lib/commonjs/mol-model/structure/model/properties/common.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/custom/indexed.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/global-transform.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/sequence.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/symmetry.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/coarse-keys.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/coarse-ranges.js +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/residue-set.js +0 -1
- package/lib/commonjs/mol-model/structure/model/types/ions.js +0 -1
- package/lib/commonjs/mol-model/structure/model/types/lipids.js +0 -1
- package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
- package/lib/commonjs/mol-model/structure/model/types.js +0 -1
- package/lib/commonjs/mol-model/structure/model/util.js +0 -1
- package/lib/commonjs/mol-model/structure/model.js +3 -4
- package/lib/commonjs/mol-model/structure/query/context.js +0 -1
- package/lib/commonjs/mol-model/structure/query/predicates.js +0 -1
- package/lib/commonjs/mol-model/structure/query/queries/combinators.js +0 -1
- package/lib/commonjs/mol-model/structure/query/queries/filters.js +0 -1
- package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -3
- package/lib/commonjs/mol-model/structure/query/queries/internal.js +0 -1
- package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -3
- package/lib/commonjs/mol-model/structure/query/query.js +0 -1
- package/lib/commonjs/mol-model/structure/query/selection.js +0 -1
- package/lib/commonjs/mol-model/structure/query/utils/builders.js +0 -1
- package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js +0 -1
- package/lib/commonjs/mol-model/structure/query/utils/structure-set.js +0 -1
- package/lib/commonjs/mol-model/structure/query.js +6 -7
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -2
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -10
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/data.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/element/bundle.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -6
- package/lib/commonjs/mol-model/structure/structure/element/location.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/element/loci.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/element/stats.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/element/util.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/element.js +1 -2
- package/lib/commonjs/mol-model/structure/structure/properties.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/structure.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/structure.js +17 -8
- package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -11
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.d.ts +2 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +3 -4
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/element-set-intra-bond-cache.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +6 -5
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +2 -3
- package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -4
- package/lib/commonjs/mol-model/structure/structure/unit/resonance.d.ts +23 -0
- package/lib/commonjs/mol-model/structure/structure/unit/resonance.js +64 -0
- package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js +70 -44
- package/lib/commonjs/mol-model/structure/structure/unit/rings.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/unit.d.ts +4 -1
- package/lib/commonjs/mol-model/structure/structure/unit.js +22 -9
- package/lib/commonjs/mol-model/structure/structure/util/boundary.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/lookup3d.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/polymer.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/principal-axes.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/subset-builder.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -2
- package/lib/commonjs/mol-model/structure/structure/util/unique-subset-builder.js +0 -1
- package/lib/commonjs/mol-model/structure/structure/util/unit-transforms.js +0 -1
- package/lib/commonjs/mol-model/structure/structure.js +2 -3
- package/lib/commonjs/mol-model/structure/topology/topology.js +0 -1
- package/lib/commonjs/mol-model/structure/topology.js +1 -2
- package/lib/commonjs/mol-model/structure/trajectory.js +0 -1
- package/lib/commonjs/mol-model/structure/util.js +0 -1
- package/lib/commonjs/mol-model/structure.js +6 -7
- package/lib/commonjs/mol-model/volume/grid.js +0 -1
- package/lib/commonjs/mol-model/volume/volume.js +0 -1
- package/lib/commonjs/mol-model/volume.js +2 -3
- package/lib/commonjs/mol-model-formats/format.js +0 -1
- package/lib/commonjs/mol-model-formats/shape/ply.js +7 -8
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -16
- package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -4
- package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -2
- package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -11
- package/lib/commonjs/mol-model-formats/structure/basic/properties.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
- package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -3
- package/lib/commonjs/mol-model-formats/structure/basic/sequence.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -3
- package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
- package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -3
- package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -7
- package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/common/component.js +7 -4
- package/lib/commonjs/mol-model-formats/structure/common/entity.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/common/property.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/common/util.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/cube.js +5 -6
- package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -3
- package/lib/commonjs/mol-model-formats/structure/gro.js +5 -4
- package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -3
- package/lib/commonjs/mol-model-formats/structure/mol.js +5 -6
- package/lib/commonjs/mol-model-formats/structure/mol2.js +7 -8
- package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/nctraj.js +60 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/anisotropic.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/pdb/assembly.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/pdb/conect.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/pdb/entity.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +2 -3
- package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -6
- package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts +16 -0
- package/lib/commonjs/mol-model-formats/structure/prmtop.js +147 -0
- package/lib/commonjs/mol-model-formats/structure/property/anisotropic.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/property/assembly.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/property/atoms/chem_comp.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +7 -6
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -2
- package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/property/partial-charge.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/property/secondary-structure.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -2
- package/lib/commonjs/mol-model-formats/structure/psf.js +5 -4
- package/lib/commonjs/mol-model-formats/structure/sdf.js +0 -1
- package/lib/commonjs/mol-model-formats/structure/top.d.ts +16 -0
- package/lib/commonjs/mol-model-formats/structure/top.js +189 -0
- package/lib/commonjs/mol-model-formats/structure/trr.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/trr.js +46 -0
- package/lib/commonjs/mol-model-formats/structure/util.d.ts +2 -2
- package/lib/commonjs/mol-model-formats/structure/util.js +19 -21
- package/lib/commonjs/mol-model-formats/structure/xtc.js +2 -3
- package/lib/commonjs/mol-model-formats/structure/xyz.js +2 -3
- package/lib/commonjs/mol-model-formats/volume/ccp4.js +2 -3
- package/lib/commonjs/mol-model-formats/volume/cube.js +2 -3
- package/lib/commonjs/mol-model-formats/volume/density-server.js +2 -3
- package/lib/commonjs/mol-model-formats/volume/dsn6.js +2 -3
- package/lib/commonjs/mol-model-formats/volume/dx.js +2 -3
- package/lib/commonjs/mol-model-formats/volume/property.js +0 -1
- package/lib/commonjs/mol-model-props/common/custom-element-property.js +2 -3
- package/lib/commonjs/mol-model-props/common/custom-model-property.js +5 -6
- package/lib/commonjs/mol-model-props/common/custom-property.js +1 -2
- package/lib/commonjs/mol-model-props/common/custom-structure-property.js +6 -7
- package/lib/commonjs/mol-model-props/common/wrapper.js +0 -1
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +2 -3
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.js +0 -1
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +0 -1
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +5 -6
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +4 -5
- package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js +0 -1
- package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js +0 -1
- package/lib/commonjs/mol-model-props/computed/chemistry/util.js +0 -1
- package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +3 -4
- package/lib/commonjs/mol-model-props/computed/helix-orientation/helix-orientation.js +0 -1
- package/lib/commonjs/mol-model-props/computed/helix-orientation.js +2 -3
- package/lib/commonjs/mol-model-props/computed/interactions/charged.js +0 -1
- package/lib/commonjs/mol-model-props/computed/interactions/common.js +1 -2
- package/lib/commonjs/mol-model-props/computed/interactions/contacts-builder.js +0 -1
- package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +1 -2
- package/lib/commonjs/mol-model-props/computed/interactions/features.js +1 -2
- package/lib/commonjs/mol-model-props/computed/interactions/halogen-bonds.js +0 -1
- package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +3 -4
- package/lib/commonjs/mol-model-props/computed/interactions/hydrophobic.js +0 -1
- package/lib/commonjs/mol-model-props/computed/interactions/interactions.js +3 -4
- package/lib/commonjs/mol-model-props/computed/interactions/metal.js +0 -1
- package/lib/commonjs/mol-model-props/computed/interactions/refine.js +0 -1
- package/lib/commonjs/mol-model-props/computed/interactions.js +4 -5
- package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +10 -5
- package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +12 -8
- package/lib/commonjs/mol-model-props/computed/representations/interactions.js +1 -2
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/backbone-hbonds.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bends.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bridges.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/common.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/dihedral-angles.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/helices.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/ladders.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/protein-info.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/sheets.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/trace-lookup.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/turns.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +2 -3
- package/lib/commonjs/mol-model-props/computed/secondary-structure/zhang-skolnik.js +0 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure.js +7 -8
- package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js +0 -1
- package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js +0 -1
- package/lib/commonjs/mol-model-props/computed/valence-model.js +4 -5
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js +0 -1
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js +0 -1
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/property.js +2 -3
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js +12 -4
- package/lib/commonjs/mol-model-props/integrative/pair-restraints.js +0 -1
- package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js +2 -3
- package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +3 -4
- package/lib/commonjs/mol-plugin/animation-loop.js +2 -3
- package/lib/commonjs/mol-plugin/behavior/behavior.js +5 -6
- package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +2 -3
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/interactions.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/secondary-structure.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/valence-model.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/sifts-mapping.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/structure-info.js +2 -3
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.js +0 -1
- package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +7 -8
- package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +11 -12
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.js +12 -13
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.js +1 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.js +16 -17
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +20 -14
- package/lib/commonjs/mol-plugin/behavior/static/camera.js +0 -1
- package/lib/commonjs/mol-plugin/behavior/static/misc.js +0 -1
- package/lib/commonjs/mol-plugin/behavior/static/representation.js +0 -1
- package/lib/commonjs/mol-plugin/behavior/static/state.js +6 -7
- package/lib/commonjs/mol-plugin/behavior.js +8 -9
- package/lib/commonjs/mol-plugin/command.js +2 -3
- package/lib/commonjs/mol-plugin/commands.d.ts +1 -0
- package/lib/commonjs/mol-plugin/commands.js +0 -1
- package/lib/commonjs/mol-plugin/config.js +0 -1
- package/lib/commonjs/mol-plugin/context.d.ts +2 -1
- package/lib/commonjs/mol-plugin/context.js +9 -9
- package/lib/commonjs/mol-plugin/features.js +0 -1
- package/lib/commonjs/mol-plugin/layout.js +2 -3
- package/lib/commonjs/mol-plugin/spec.js +1 -2
- package/lib/commonjs/mol-plugin/state.js +5 -6
- package/lib/commonjs/mol-plugin/util/substructure-parent-helper.js +0 -1
- package/lib/commonjs/mol-plugin/util/task-manager.js +4 -5
- package/lib/commonjs/mol-plugin/util/toast.js +1 -2
- package/lib/commonjs/mol-plugin/util/viewport-screenshot.js +17 -18
- package/lib/commonjs/mol-plugin/version.js +0 -1
- package/lib/commonjs/mol-plugin-state/actions/file.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/actions/file.js +94 -62
- package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +11 -2
- package/lib/commonjs/mol-plugin-state/actions/structure.js +190 -21
- package/lib/commonjs/mol-plugin-state/actions/volume.js +5 -5
- package/lib/commonjs/mol-plugin-state/actions.js +3 -4
- package/lib/commonjs/mol-plugin-state/animation/built-in/assembly-unwind.js +2 -3
- package/lib/commonjs/mol-plugin-state/animation/built-in/camera-rock.js +3 -4
- package/lib/commonjs/mol-plugin-state/animation/built-in/camera-spin.js +3 -4
- package/lib/commonjs/mol-plugin-state/animation/built-in/explode-units.js +4 -5
- package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.js +2 -3
- package/lib/commonjs/mol-plugin-state/animation/built-in/spin-structure.js +5 -6
- package/lib/commonjs/mol-plugin-state/animation/built-in/state-interpolation.js +2 -3
- package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js +5 -6
- package/lib/commonjs/mol-plugin-state/animation/helpers.js +0 -1
- package/lib/commonjs/mol-plugin-state/animation/model.js +0 -1
- package/lib/commonjs/mol-plugin-state/builder/data.js +2 -3
- package/lib/commonjs/mol-plugin-state/builder/preset-provider.js +0 -1
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +16 -17
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.js +0 -1
- package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +28 -29
- package/lib/commonjs/mol-plugin-state/builder/structure/representation.js +2 -3
- package/lib/commonjs/mol-plugin-state/builder/structure.js +7 -8
- package/lib/commonjs/mol-plugin-state/component.js +1 -2
- package/lib/commonjs/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
- package/lib/commonjs/mol-plugin-state/formats/coordinates.js +70 -0
- package/lib/commonjs/mol-plugin-state/formats/provider.js +0 -1
- package/lib/commonjs/mol-plugin-state/formats/registry.d.ts +3 -3
- package/lib/commonjs/mol-plugin-state/formats/registry.js +13 -9
- package/lib/commonjs/mol-plugin-state/formats/shape.js +2 -3
- package/lib/commonjs/mol-plugin-state/formats/topology.d.ts +73 -0
- package/lib/commonjs/mol-plugin-state/formats/topology.js +87 -0
- package/lib/commonjs/mol-plugin-state/formats/trajectory.js +6 -7
- package/lib/commonjs/mol-plugin-state/formats/volume.js +21 -22
- package/lib/commonjs/mol-plugin-state/helpers/root-structure.js +15 -16
- package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +7 -8
- package/lib/commonjs/mol-plugin-state/helpers/structure-component.js +2 -2
- package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js +11 -12
- package/lib/commonjs/mol-plugin-state/helpers/structure-query.js +0 -1
- package/lib/commonjs/mol-plugin-state/helpers/structure-representation-params.js +0 -1
- package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +3 -4
- package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js +11 -12
- package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js +11 -12
- package/lib/commonjs/mol-plugin-state/helpers/volume-representation-params.js +0 -1
- package/lib/commonjs/mol-plugin-state/manager/animation.js +17 -18
- package/lib/commonjs/mol-plugin-state/manager/camera.js +1 -2
- package/lib/commonjs/mol-plugin-state/manager/interactivity.d.ts +5 -3
- package/lib/commonjs/mol-plugin-state/manager/interactivity.js +6 -7
- package/lib/commonjs/mol-plugin-state/manager/loci-label.js +0 -1
- package/lib/commonjs/mol-plugin-state/manager/snapshots.js +14 -15
- package/lib/commonjs/mol-plugin-state/manager/structure/component.js +26 -27
- package/lib/commonjs/mol-plugin-state/manager/structure/focus.js +2 -3
- package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js +1 -2
- package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.js +8 -9
- package/lib/commonjs/mol-plugin-state/manager/structure/measurement.js +21 -22
- package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +3 -4
- package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy-state.js +0 -1
- package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy.js +1 -2
- package/lib/commonjs/mol-plugin-state/objects.d.ts +47 -1
- package/lib/commonjs/mol-plugin-state/objects.js +46 -31
- package/lib/commonjs/mol-plugin-state/transforms/data.d.ts +6 -0
- package/lib/commonjs/mol-plugin-state/transforms/data.js +93 -42
- package/lib/commonjs/mol-plugin-state/transforms/helpers.js +0 -1
- package/lib/commonjs/mol-plugin-state/transforms/misc.js +0 -1
- package/lib/commonjs/mol-plugin-state/transforms/model.d.ts +14 -2
- package/lib/commonjs/mol-plugin-state/transforms/model.js +163 -55
- package/lib/commonjs/mol-plugin-state/transforms/representation.js +77 -78
- package/lib/commonjs/mol-plugin-state/transforms/shape.js +2 -3
- package/lib/commonjs/mol-plugin-state/transforms/volume.js +16 -17
- package/lib/commonjs/mol-plugin-state/transforms.js +6 -7
- package/lib/commonjs/mol-plugin-ui/base.js +5 -6
- package/lib/commonjs/mol-plugin-ui/context.js +1 -2
- package/lib/commonjs/mol-plugin-ui/controls/action-menu.js +14 -15
- package/lib/commonjs/mol-plugin-ui/controls/color.js +7 -8
- package/lib/commonjs/mol-plugin-ui/controls/common.js +16 -17
- package/lib/commonjs/mol-plugin-ui/controls/icons.js +70 -71
- package/lib/commonjs/mol-plugin-ui/controls/legend.js +7 -8
- package/lib/commonjs/mol-plugin-ui/controls/line-graph/line-graph-component.js +3 -4
- package/lib/commonjs/mol-plugin-ui/controls/line-graph/point-component.js +2 -3
- package/lib/commonjs/mol-plugin-ui/controls/parameters.js +94 -95
- package/lib/commonjs/mol-plugin-ui/controls/screenshot.js +5 -6
- package/lib/commonjs/mol-plugin-ui/controls/slider.js +16 -17
- package/lib/commonjs/mol-plugin-ui/controls.js +16 -17
- package/lib/commonjs/mol-plugin-ui/custom/volume.js +16 -17
- package/lib/commonjs/mol-plugin-ui/hooks/use-behavior.js +0 -1
- package/lib/commonjs/mol-plugin-ui/index.js +4 -5
- package/lib/commonjs/mol-plugin-ui/left-panel.d.ts +8 -1
- package/lib/commonjs/mol-plugin-ui/left-panel.js +40 -20
- package/lib/commonjs/mol-plugin-ui/plugin.js +17 -18
- package/lib/commonjs/mol-plugin-ui/sequence/chain.js +1 -2
- package/lib/commonjs/mol-plugin-ui/sequence/element.js +1 -2
- package/lib/commonjs/mol-plugin-ui/sequence/hetero.js +1 -2
- package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +1 -2
- package/lib/commonjs/mol-plugin-ui/sequence/sequence.d.ts +2 -2
- package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +10 -12
- package/lib/commonjs/mol-plugin-ui/sequence/wrapper.js +0 -1
- package/lib/commonjs/mol-plugin-ui/sequence.js +9 -10
- package/lib/commonjs/mol-plugin-ui/spec.js +1 -2
- package/lib/commonjs/mol-plugin-ui/state/actions.js +2 -3
- package/lib/commonjs/mol-plugin-ui/state/animation.js +2 -3
- package/lib/commonjs/mol-plugin-ui/state/apply-action.js +1 -2
- package/lib/commonjs/mol-plugin-ui/state/common.js +12 -13
- package/lib/commonjs/mol-plugin-ui/state/snapshots.js +29 -30
- package/lib/commonjs/mol-plugin-ui/state/tree.js +19 -20
- package/lib/commonjs/mol-plugin-ui/state/update-transform.js +3 -4
- package/lib/commonjs/mol-plugin-ui/structure/components.js +19 -20
- package/lib/commonjs/mol-plugin-ui/structure/focus.js +4 -5
- package/lib/commonjs/mol-plugin-ui/structure/generic.js +6 -7
- package/lib/commonjs/mol-plugin-ui/structure/measurements.js +13 -14
- package/lib/commonjs/mol-plugin-ui/structure/quick-styles.js +13 -14
- package/lib/commonjs/mol-plugin-ui/structure/selection.js +13 -14
- package/lib/commonjs/mol-plugin-ui/structure/source.js +12 -13
- package/lib/commonjs/mol-plugin-ui/structure/superposition.js +20 -21
- package/lib/commonjs/mol-plugin-ui/structure/volume.js +12 -13
- package/lib/commonjs/mol-plugin-ui/task.js +8 -9
- package/lib/commonjs/mol-plugin-ui/toast.js +6 -7
- package/lib/commonjs/mol-plugin-ui/viewport/canvas.js +5 -6
- package/lib/commonjs/mol-plugin-ui/viewport/help.js +14 -15
- package/lib/commonjs/mol-plugin-ui/viewport/screenshot.js +8 -9
- package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +6 -7
- package/lib/commonjs/mol-plugin-ui/viewport.js +7 -8
- package/lib/commonjs/mol-repr/representation.js +4 -5
- package/lib/commonjs/mol-repr/shape/loci/angle.js +9 -10
- package/lib/commonjs/mol-repr/shape/loci/common.js +1 -2
- package/lib/commonjs/mol-repr/shape/loci/dihedral.js +14 -15
- package/lib/commonjs/mol-repr/shape/loci/distance.js +5 -6
- package/lib/commonjs/mol-repr/shape/loci/label.js +3 -4
- package/lib/commonjs/mol-repr/shape/loci/orientation.js +4 -5
- package/lib/commonjs/mol-repr/shape/loci/plane.js +2 -3
- package/lib/commonjs/mol-repr/shape/model/unitcell.js +2 -3
- package/lib/commonjs/mol-repr/shape/representation.js +2 -3
- package/lib/commonjs/mol-repr/structure/complex-representation.js +2 -3
- package/lib/commonjs/mol-repr/structure/complex-visual.js +12 -13
- package/lib/commonjs/mol-repr/structure/params.js +8 -9
- package/lib/commonjs/mol-repr/structure/registry.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/backbone.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/cartoon.js +3 -4
- package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/label.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/line.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/representation/line.js +2 -3
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/orientation.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/point.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/putty.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation/spacefill.js +1 -2
- package/lib/commonjs/mol-repr/structure/representation.js +1 -2
- package/lib/commonjs/mol-repr/structure/units-representation.js +2 -3
- package/lib/commonjs/mol-repr/structure/units-visual.js +16 -17
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +21 -12
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +11 -7
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +26 -10
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +18 -7
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js +11 -3
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +11 -3
- package/lib/commonjs/mol-repr/structure/visual/element-cross.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/element-point.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/element-point.js +23 -5
- package/lib/commonjs/mol-repr/structure/visual/element-sphere.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +6 -7
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +11 -12
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +3 -4
- package/lib/commonjs/mol-repr/structure/visual/label-text.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +3 -4
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +3 -4
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/util/bond.js +2 -3
- package/lib/commonjs/mol-repr/structure/visual/util/common.js +1 -2
- package/lib/commonjs/mol-repr/structure/visual/util/element.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/util/element.js +13 -8
- package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js +13 -14
- package/lib/commonjs/mol-repr/structure/visual/util/link.d.ts +13 -3
- package/lib/commonjs/mol-repr/structure/visual/util/link.js +55 -7
- package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js +5 -6
- package/lib/commonjs/mol-repr/structure/visual/util/nucleotide.js +0 -1
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js +0 -1
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/curve-segment.js +0 -1
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js +0 -1
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +0 -1
- package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +4 -5
- package/lib/commonjs/mol-repr/util.js +1 -2
- package/lib/commonjs/mol-repr/visual.js +0 -1
- package/lib/commonjs/mol-repr/volume/direct-volume.js +3 -4
- package/lib/commonjs/mol-repr/volume/isosurface.js +9 -10
- package/lib/commonjs/mol-repr/volume/registry.js +1 -2
- package/lib/commonjs/mol-repr/volume/representation.js +5 -6
- package/lib/commonjs/mol-repr/volume/slice.js +4 -5
- package/lib/commonjs/mol-repr/volume/util.js +0 -1
- package/lib/commonjs/mol-script/compiler.js +0 -1
- package/lib/commonjs/mol-script/language/builder.d.ts +0 -1
- package/lib/commonjs/mol-script/language/builder.js +0 -1
- package/lib/commonjs/mol-script/language/container.js +0 -1
- package/lib/commonjs/mol-script/language/expression-formatter.js +0 -1
- package/lib/commonjs/mol-script/language/expression.js +0 -1
- package/lib/commonjs/mol-script/language/helpers.js +0 -1
- package/lib/commonjs/mol-script/language/parser.js +7 -5
- package/lib/commonjs/mol-script/language/symbol-table/core.js +0 -1
- package/lib/commonjs/mol-script/language/symbol-table/internal.js +1 -2
- package/lib/commonjs/mol-script/language/symbol-table/structure-query.js +1 -2
- package/lib/commonjs/mol-script/language/symbol-table.js +0 -1
- package/lib/commonjs/mol-script/language/symbol.js +0 -1
- package/lib/commonjs/mol-script/language/type.js +0 -1
- package/lib/commonjs/mol-script/runtime/environment.js +0 -1
- package/lib/commonjs/mol-script/runtime/expression.js +0 -1
- package/lib/commonjs/mol-script/runtime/query/base.js +0 -1
- package/lib/commonjs/mol-script/runtime/query/compiler.js +1 -2
- package/lib/commonjs/mol-script/runtime/query/table.js +0 -1
- package/lib/commonjs/mol-script/runtime/runtime-macro.js +0 -1
- package/lib/commonjs/mol-script/runtime/symbol.js +0 -1
- package/lib/commonjs/mol-script/script/mol-script/examples.js +0 -1
- package/lib/commonjs/mol-script/script/mol-script/parser.js +0 -1
- package/lib/commonjs/mol-script/script/mol-script/script-macro.js +0 -1
- package/lib/commonjs/mol-script/script/mol-script/symbols.js +1 -2
- package/lib/commonjs/mol-script/script/parser.js +0 -1
- package/lib/commonjs/mol-script/script.js +0 -1
- package/lib/commonjs/mol-script/util/id-list.js +0 -1
- package/lib/commonjs/mol-state/action/manager.js +0 -1
- package/lib/commonjs/mol-state/action.js +1 -2
- package/lib/commonjs/mol-state/index.js +8 -9
- package/lib/commonjs/mol-state/object.js +0 -1
- package/lib/commonjs/mol-state/state/builder.js +2 -3
- package/lib/commonjs/mol-state/state/selection.js +1 -2
- package/lib/commonjs/mol-state/state.js +21 -22
- package/lib/commonjs/mol-state/transform.js +4 -5
- package/lib/commonjs/mol-state/transformer.js +1 -2
- package/lib/commonjs/mol-state/tree/immutable.js +0 -1
- package/lib/commonjs/mol-state/tree/spine.js +0 -1
- package/lib/commonjs/mol-state/tree/transient.js +0 -1
- package/lib/commonjs/mol-state/tree.js +0 -1
- package/lib/commonjs/mol-task/execution/observable.js +5 -6
- package/lib/commonjs/mol-task/execution/progress.js +0 -1
- package/lib/commonjs/mol-task/execution/runtime-context.js +0 -1
- package/lib/commonjs/mol-task/execution/synchronous.js +0 -1
- package/lib/commonjs/mol-task/index.js +0 -1
- package/lib/commonjs/mol-task/task.js +3 -4
- package/lib/commonjs/mol-task/util/chunked.js +2 -3
- package/lib/commonjs/mol-task/util/multistep.js +1 -2
- package/lib/commonjs/mol-task/util/scheduler.d.ts +2 -2
- package/lib/commonjs/mol-task/util/scheduler.js +8 -9
- package/lib/commonjs/mol-task/util/user-timing.js +0 -1
- package/lib/commonjs/mol-theme/clipping.js +0 -1
- package/lib/commonjs/mol-theme/color/atom-id.js +1 -2
- package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js +0 -1
- package/lib/commonjs/mol-theme/color/chain-id.js +1 -2
- package/lib/commonjs/mol-theme/color/element-index.js +1 -2
- package/lib/commonjs/mol-theme/color/element-symbol.js +0 -1
- package/lib/commonjs/mol-theme/color/entity-id.js +1 -2
- package/lib/commonjs/mol-theme/color/entity-source.js +2 -3
- package/lib/commonjs/mol-theme/color/hydrophobicity.js +2 -3
- package/lib/commonjs/mol-theme/color/illustrative.js +0 -1
- package/lib/commonjs/mol-theme/color/model-index.js +1 -2
- package/lib/commonjs/mol-theme/color/molecule-type.js +0 -1
- package/lib/commonjs/mol-theme/color/occupancy.js +0 -1
- package/lib/commonjs/mol-theme/color/operator-hkl.js +2 -3
- package/lib/commonjs/mol-theme/color/operator-name.js +1 -2
- package/lib/commonjs/mol-theme/color/partial-charge.js +0 -1
- package/lib/commonjs/mol-theme/color/polymer-id.js +2 -3
- package/lib/commonjs/mol-theme/color/polymer-index.js +2 -3
- package/lib/commonjs/mol-theme/color/residue-name.js +0 -1
- package/lib/commonjs/mol-theme/color/secondary-structure.js +0 -1
- package/lib/commonjs/mol-theme/color/sequence-id.js +0 -1
- package/lib/commonjs/mol-theme/color/shape-group.js +0 -1
- package/lib/commonjs/mol-theme/color/uncertainty.js +0 -1
- package/lib/commonjs/mol-theme/color/uniform.js +0 -1
- package/lib/commonjs/mol-theme/color/unit-index.js +2 -3
- package/lib/commonjs/mol-theme/color/volume-value.js +0 -1
- package/lib/commonjs/mol-theme/color.js +0 -1
- package/lib/commonjs/mol-theme/label.js +6 -7
- package/lib/commonjs/mol-theme/overpaint.js +0 -1
- package/lib/commonjs/mol-theme/size/physical.js +0 -1
- package/lib/commonjs/mol-theme/size/shape-group.js +0 -1
- package/lib/commonjs/mol-theme/size/uncertainty.js +0 -1
- package/lib/commonjs/mol-theme/size/uniform.js +0 -1
- package/lib/commonjs/mol-theme/size.js +0 -1
- package/lib/commonjs/mol-theme/substance.js +0 -1
- package/lib/commonjs/mol-theme/theme.js +3 -4
- package/lib/commonjs/mol-theme/transparency.js +0 -1
- package/lib/commonjs/mol-util/array.js +0 -1
- package/lib/commonjs/mol-util/assets.js +7 -8
- package/lib/commonjs/mol-util/async-queue.js +0 -1
- package/lib/commonjs/mol-util/binding.js +0 -1
- package/lib/commonjs/mol-util/bit-flags.js +0 -1
- package/lib/commonjs/mol-util/clip.js +0 -1
- package/lib/commonjs/mol-util/color/color.js +0 -1
- package/lib/commonjs/mol-util/color/distinct.js +1 -2
- package/lib/commonjs/mol-util/color/index.js +0 -1
- package/lib/commonjs/mol-util/color/lists.js +0 -1
- package/lib/commonjs/mol-util/color/names.js +0 -1
- package/lib/commonjs/mol-util/color/palette.js +3 -4
- package/lib/commonjs/mol-util/color/params.js +0 -1
- package/lib/commonjs/mol-util/color/scale.js +2 -3
- package/lib/commonjs/mol-util/color/spaces/hcl.js +0 -1
- package/lib/commonjs/mol-util/color/spaces/lab.js +0 -1
- package/lib/commonjs/mol-util/color/swatches.js +0 -1
- package/lib/commonjs/mol-util/console-logger.js +0 -1
- package/lib/commonjs/mol-util/data-source.js +14 -14
- package/lib/commonjs/mol-util/date.js +0 -1
- package/lib/commonjs/mol-util/debug.js +0 -1
- package/lib/commonjs/mol-util/download.js +0 -1
- package/lib/commonjs/mol-util/file-info.d.ts +1 -3
- package/lib/commonjs/mol-util/file-info.js +2 -11
- package/lib/commonjs/mol-util/graphql-client.js +4 -5
- package/lib/commonjs/mol-util/id-factory.js +0 -1
- package/lib/commonjs/mol-util/image.js +0 -1
- package/lib/commonjs/mol-util/index.d.ts +1 -0
- package/lib/commonjs/mol-util/index.js +8 -3
- package/lib/commonjs/mol-util/input/event-offset.js +0 -1
- package/lib/commonjs/mol-util/input/input-observer.js +6 -7
- package/lib/commonjs/mol-util/is-little-endian.js +0 -1
- package/lib/commonjs/mol-util/legend.js +0 -1
- package/lib/commonjs/mol-util/log-entry.js +0 -1
- package/lib/commonjs/mol-util/lru-cache.js +0 -1
- package/lib/commonjs/mol-util/make-dir.js +1 -2
- package/lib/commonjs/mol-util/map.js +0 -1
- package/lib/commonjs/mol-util/marker-action.js +0 -1
- package/lib/commonjs/mol-util/mask.js +0 -1
- package/lib/commonjs/mol-util/material.js +2 -3
- package/lib/commonjs/mol-util/memoize.js +0 -1
- package/lib/commonjs/mol-util/monadic-parser.js +2 -3
- package/lib/commonjs/mol-util/now.js +0 -1
- package/lib/commonjs/mol-util/number-packing.js +0 -1
- package/lib/commonjs/mol-util/number.js +0 -1
- package/lib/commonjs/mol-util/object.js +0 -1
- package/lib/commonjs/mol-util/param-definition.js +7 -8
- package/lib/commonjs/mol-util/param-mapping.js +0 -1
- package/lib/commonjs/mol-util/performance-monitor.js +0 -1
- package/lib/commonjs/mol-util/polyfill.js +0 -1
- package/lib/commonjs/mol-util/read.js +2 -3
- package/lib/commonjs/mol-util/reference-cache.js +0 -1
- package/lib/commonjs/mol-util/retry-if.js +2 -3
- package/lib/commonjs/mol-util/rx-event-helper.js +0 -1
- package/lib/commonjs/mol-util/set.js +0 -1
- package/lib/commonjs/mol-util/sleep.js +0 -1
- package/lib/commonjs/mol-util/string-builder.js +0 -1
- package/lib/commonjs/mol-util/string.js +1 -2
- package/lib/commonjs/mol-util/type-helpers.js +0 -1
- package/lib/commonjs/mol-util/url.js +0 -1
- package/lib/commonjs/mol-util/uuid.js +0 -1
- package/lib/commonjs/mol-util/value-cell.js +0 -1
- package/lib/commonjs/mol-util/zip/bin.js +0 -1
- package/lib/commonjs/mol-util/zip/checksum.js +0 -1
- package/lib/commonjs/mol-util/zip/deflate.js +4 -4
- package/lib/commonjs/mol-util/zip/huffman.js +0 -1
- package/lib/commonjs/mol-util/zip/inflate.js +2 -3
- package/lib/commonjs/mol-util/zip/util.js +0 -1
- package/lib/commonjs/mol-util/zip/zip.d.ts +7 -1
- package/lib/commonjs/mol-util/zip/zip.js +21 -17
- package/lib/commonjs/servers/common/file-handle.js +1 -2
- package/lib/commonjs/servers/common/swagger-ui/index.js +1 -2
- package/lib/commonjs/servers/common/swagger-ui/indexTemplate.js +0 -1
- package/lib/commonjs/servers/common/util.js +0 -1
- package/lib/commonjs/servers/model/config.d.ts +2 -2
- package/lib/commonjs/servers/model/config.js +5 -6
- package/lib/commonjs/servers/model/preprocess/converter.js +2 -3
- package/lib/commonjs/servers/model/preprocess/master.js +3 -4
- package/lib/commonjs/servers/model/preprocess/parallel.js +6 -7
- package/lib/commonjs/servers/model/preprocess/preprocess.js +4 -5
- package/lib/commonjs/servers/model/preprocess/util.js +0 -1
- package/lib/commonjs/servers/model/preprocess.js +1 -2
- package/lib/commonjs/servers/model/properties/pdbe.js +0 -1
- package/lib/commonjs/servers/model/properties/providers/pdbe.js +8 -9
- package/lib/commonjs/servers/model/properties/providers/wwpdb.js +12 -13
- package/lib/commonjs/servers/model/properties/wwpdb.js +0 -1
- package/lib/commonjs/servers/model/property-provider.js +3 -4
- package/lib/commonjs/servers/model/query/atoms.js +0 -1
- package/lib/commonjs/servers/model/query/schemas.js +0 -1
- package/lib/commonjs/servers/model/query.js +1 -2
- package/lib/commonjs/servers/model/server/api-local.js +2 -3
- package/lib/commonjs/servers/model/server/api-schema.js +2 -3
- package/lib/commonjs/servers/model/server/api-web-multiple.js +0 -1
- package/lib/commonjs/servers/model/server/api-web.js +5 -6
- package/lib/commonjs/servers/model/server/api.js +6 -7
- package/lib/commonjs/servers/model/server/cache.js +0 -1
- package/lib/commonjs/servers/model/server/jobs.js +0 -1
- package/lib/commonjs/servers/model/server/query.js +15 -16
- package/lib/commonjs/servers/model/server/structure-wrapper.js +21 -22
- package/lib/commonjs/servers/model/server.js +2 -3
- package/lib/commonjs/servers/model/test.js +0 -1
- package/lib/commonjs/servers/model/utils/fetch-props-pdbe.js +6 -7
- package/lib/commonjs/servers/model/utils/fetch-retry.js +3 -4
- package/lib/commonjs/servers/model/utils/tar.js +0 -1
- package/lib/commonjs/servers/model/utils/writer.js +3 -4
- package/lib/commonjs/servers/model/version.js +0 -1
- package/lib/commonjs/servers/plugin-state/api-schema.js +0 -1
- package/lib/commonjs/servers/plugin-state/config.js +1 -2
- package/lib/commonjs/servers/plugin-state/index.js +6 -7
- package/lib/commonjs/servers/plugin-state/version.js +0 -1
- package/lib/commonjs/servers/volume/common/binary-schema.js +1 -2
- package/lib/commonjs/servers/volume/common/data-format.js +3 -4
- package/lib/commonjs/servers/volume/common/file.js +8 -9
- package/lib/commonjs/servers/volume/config.js +6 -7
- package/lib/commonjs/servers/volume/pack/data-model.js +0 -1
- package/lib/commonjs/servers/volume/pack/downsampling.js +0 -1
- package/lib/commonjs/servers/volume/pack/format/ccp4.js +4 -5
- package/lib/commonjs/servers/volume/pack/format/dsn6.js +4 -5
- package/lib/commonjs/servers/volume/pack/format.js +3 -4
- package/lib/commonjs/servers/volume/pack/main.js +13 -14
- package/lib/commonjs/servers/volume/pack/sampling.js +13 -14
- package/lib/commonjs/servers/volume/pack/version.js +0 -1
- package/lib/commonjs/servers/volume/pack/writer.js +2 -3
- package/lib/commonjs/servers/volume/pack.js +1 -2
- package/lib/commonjs/servers/volume/query.js +4 -5
- package/lib/commonjs/servers/volume/server/algebra/box.js +1 -2
- package/lib/commonjs/servers/volume/server/algebra/coordinate.js +0 -1
- package/lib/commonjs/servers/volume/server/api.js +8 -9
- package/lib/commonjs/servers/volume/server/local-api.js +8 -9
- package/lib/commonjs/servers/volume/server/query/compose.js +8 -9
- package/lib/commonjs/servers/volume/server/query/data-model.js +0 -1
- package/lib/commonjs/servers/volume/server/query/encode.js +0 -1
- package/lib/commonjs/servers/volume/server/query/execute.js +10 -11
- package/lib/commonjs/servers/volume/server/query/identify.js +2 -3
- package/lib/commonjs/servers/volume/server/state.js +0 -1
- package/lib/commonjs/servers/volume/server/version.js +0 -1
- package/lib/commonjs/servers/volume/server/web-api.js +7 -8
- package/lib/commonjs/servers/volume/server/web-schema.js +0 -1
- package/lib/commonjs/servers/volume/server.js +2 -3
- package/lib/examples/alpha-orbitals/controls.js +2 -3
- package/lib/examples/alpha-orbitals/example-data.js +0 -1
- package/lib/examples/alpha-orbitals/index.html +61 -61
- package/lib/examples/alpha-orbitals/index.js +0 -1
- package/lib/examples/basic-wrapper/coloring.js +0 -1
- package/lib/examples/basic-wrapper/controls.js +1 -2
- package/lib/examples/basic-wrapper/custom-theme.js +0 -1
- package/lib/examples/basic-wrapper/index.html +137 -137
- package/lib/examples/basic-wrapper/index.js +0 -1
- package/lib/examples/basic-wrapper/superposition.js +0 -1
- package/lib/examples/domain-annotation-server/mapping.js +0 -1
- package/lib/examples/domain-annotation-server/schemas.js +0 -1
- package/lib/examples/domain-annotation-server/server.js +0 -1
- package/lib/examples/domain-annotation-server/test.js +0 -1
- package/lib/examples/lighting/index.html +88 -88
- package/lib/examples/lighting/index.js +2 -3
- package/lib/examples/proteopedia-wrapper/annotation.js +0 -1
- package/lib/examples/proteopedia-wrapper/coloring.js +0 -1
- package/lib/examples/proteopedia-wrapper/helpers.js +0 -1
- package/lib/examples/proteopedia-wrapper/index.html +236 -236
- package/lib/examples/proteopedia-wrapper/index.js +0 -1
- package/lib/examples/proteopedia-wrapper/ui/controls.js +1 -2
- package/lib/examples/task.js +0 -1
- package/lib/extensions/alpha-orbitals/collocation.js +0 -1
- package/lib/extensions/alpha-orbitals/data-model.js +0 -1
- package/lib/extensions/alpha-orbitals/density.js +0 -1
- package/lib/extensions/alpha-orbitals/gpu/compute.js +0 -1
- package/lib/extensions/alpha-orbitals/gpu/shader.frag.js +0 -1
- package/lib/extensions/alpha-orbitals/orbitals.js +0 -1
- package/lib/extensions/alpha-orbitals/spherical-functions.js +0 -1
- package/lib/extensions/alpha-orbitals/transforms.js +0 -1
- package/lib/extensions/anvil/algorithm.js +0 -1
- package/lib/extensions/anvil/behavior.js +0 -1
- package/lib/extensions/anvil/prop.js +0 -1
- package/lib/extensions/anvil/representation.js +0 -1
- package/lib/extensions/cellpack/color/generate.js +0 -1
- package/lib/extensions/cellpack/color/provided.js +0 -1
- package/lib/extensions/cellpack/curve.js +0 -1
- package/lib/extensions/cellpack/data.js +0 -1
- package/lib/extensions/cellpack/index.js +0 -1
- package/lib/extensions/cellpack/model.js +4 -3
- package/lib/extensions/cellpack/preset.js +0 -1
- package/lib/extensions/cellpack/property.js +0 -1
- package/lib/extensions/cellpack/representation.js +0 -1
- package/lib/extensions/cellpack/state.js +2 -3
- package/lib/extensions/cellpack/util.js +0 -1
- package/lib/extensions/dnatco/confal-pyramids/behavior.js +0 -1
- package/lib/extensions/dnatco/confal-pyramids/color.js +0 -1
- package/lib/extensions/dnatco/confal-pyramids/property.js +0 -1
- package/lib/extensions/dnatco/confal-pyramids/representation.js +0 -1
- package/lib/extensions/dnatco/confal-pyramids/types.js +0 -1
- package/lib/extensions/dnatco/confal-pyramids/util.js +0 -1
- package/lib/extensions/dnatco/index.js +0 -1
- package/lib/extensions/g3d/data.js +0 -1
- package/lib/extensions/g3d/format.js +0 -1
- package/lib/extensions/g3d/model.js +0 -1
- package/lib/extensions/geo-export/controls.js +0 -1
- package/lib/extensions/geo-export/glb-exporter.js +0 -1
- package/lib/extensions/geo-export/index.js +0 -1
- package/lib/extensions/geo-export/mesh-exporter.js +0 -1
- package/lib/extensions/geo-export/obj-exporter.js +0 -1
- package/lib/extensions/geo-export/render-object-exporter.js +0 -1
- package/lib/extensions/geo-export/stl-exporter.js +0 -1
- package/lib/extensions/geo-export/ui.js +2 -3
- package/lib/extensions/geo-export/usdz-exporter.js +0 -1
- package/lib/extensions/model-archive/quality-assessment/behavior.js +0 -1
- package/lib/extensions/model-archive/quality-assessment/color/plddt.js +0 -1
- package/lib/extensions/model-archive/quality-assessment/color/qmean.js +0 -1
- package/lib/extensions/model-archive/quality-assessment/prop.js +0 -1
- package/lib/extensions/model-export/export.js +0 -1
- package/lib/extensions/model-export/index.js +0 -1
- package/lib/extensions/model-export/ui.js +2 -3
- package/lib/extensions/mp4-export/controls.js +0 -1
- package/lib/extensions/mp4-export/encoder.js +0 -1
- package/lib/extensions/mp4-export/index.js +0 -1
- package/lib/extensions/mp4-export/ui.js +2 -3
- package/lib/extensions/pdbe/index.js +0 -1
- package/lib/extensions/pdbe/preferred-assembly.js +0 -1
- package/lib/extensions/pdbe/struct-ref-domain.js +0 -1
- package/lib/extensions/pdbe/structure-quality-report/behavior.js +0 -1
- package/lib/extensions/pdbe/structure-quality-report/color.js +0 -1
- package/lib/extensions/pdbe/structure-quality-report/prop.js +0 -1
- package/lib/extensions/rcsb/assembly-symmetry/behavior.js +0 -1
- package/lib/extensions/rcsb/assembly-symmetry/color.js +0 -1
- package/lib/extensions/rcsb/assembly-symmetry/prop.js +0 -1
- package/lib/extensions/rcsb/assembly-symmetry/representation.js +0 -1
- package/lib/extensions/rcsb/assembly-symmetry/ui.js +3 -4
- package/lib/extensions/rcsb/graphql/symmetry.gql.js +0 -1
- package/lib/extensions/rcsb/graphql/types.d.ts +158 -1
- package/lib/extensions/rcsb/graphql/types.js +0 -1
- package/lib/extensions/rcsb/index.js +0 -1
- package/lib/extensions/rcsb/validation-report/behavior.js +0 -1
- package/lib/extensions/rcsb/validation-report/color/density-fit.js +0 -1
- package/lib/extensions/rcsb/validation-report/color/geometry-quality.js +0 -1
- package/lib/extensions/rcsb/validation-report/color/random-coil-index.js +0 -1
- package/lib/extensions/rcsb/validation-report/prop.js +0 -1
- package/lib/extensions/rcsb/validation-report/representation.js +19 -3
- package/lib/extensions/zenodo/index.d.ts +7 -0
- package/lib/extensions/zenodo/index.js +32 -0
- package/lib/extensions/zenodo/ui.d.ts +61 -0
- package/lib/extensions/zenodo/ui.js +303 -0
- package/lib/mol-canvas3d/camera/stereo.js +0 -1
- package/lib/mol-canvas3d/camera/transition.js +0 -1
- package/lib/mol-canvas3d/camera/util.js +0 -1
- package/lib/mol-canvas3d/camera.js +2 -2
- package/lib/mol-canvas3d/canvas3d.d.ts +3 -1
- package/lib/mol-canvas3d/canvas3d.js +32 -25
- package/lib/mol-canvas3d/controls/object.js +0 -1
- package/lib/mol-canvas3d/controls/trackball.js +0 -1
- package/lib/mol-canvas3d/helper/bounding-sphere-helper.js +0 -1
- package/lib/mol-canvas3d/helper/camera-helper.js +1 -2
- package/lib/mol-canvas3d/helper/handle-helper.js +1 -2
- package/lib/mol-canvas3d/helper/helper.js +0 -1
- package/lib/mol-canvas3d/helper/interaction-events.js +1 -2
- package/lib/mol-canvas3d/passes/draw.js +12 -10
- package/lib/mol-canvas3d/passes/fxaa.js +0 -1
- package/lib/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/mol-canvas3d/passes/image.js +0 -1
- package/lib/mol-canvas3d/passes/marking.js +0 -1
- package/lib/mol-canvas3d/passes/multi-sample.d.ts +1 -1
- package/lib/mol-canvas3d/passes/multi-sample.js +20 -7
- package/lib/mol-canvas3d/passes/passes.js +0 -1
- package/lib/mol-canvas3d/passes/pick.js +0 -1
- package/lib/mol-canvas3d/passes/postprocessing.d.ts +8 -1
- package/lib/mol-canvas3d/passes/postprocessing.js +51 -22
- package/lib/mol-canvas3d/passes/smaa.js +0 -1
- package/lib/mol-canvas3d/passes/wboit.js +0 -1
- package/lib/mol-canvas3d/util.js +0 -1
- package/lib/mol-data/db/column-helpers.js +0 -1
- package/lib/mol-data/db/column.js +0 -1
- package/lib/mol-data/db/database.js +0 -1
- package/lib/mol-data/db/table.js +0 -1
- package/lib/mol-data/db.js +0 -1
- package/lib/mol-data/generic/hash-set.js +0 -1
- package/lib/mol-data/generic/linked-list.js +0 -1
- package/lib/mol-data/generic/unique-array.js +0 -1
- package/lib/mol-data/generic.js +0 -1
- package/lib/mol-data/index.js +0 -1
- package/lib/mol-data/int/impl/interval.js +0 -1
- package/lib/mol-data/int/impl/ordered-set.js +0 -1
- package/lib/mol-data/int/impl/segmentation.js +0 -1
- package/lib/mol-data/int/impl/sorted-array.js +0 -1
- package/lib/mol-data/int/interval.js +0 -1
- package/lib/mol-data/int/linked-index.js +0 -1
- package/lib/mol-data/int/map.js +0 -1
- package/lib/mol-data/int/ordered-set.js +0 -1
- package/lib/mol-data/int/segmentation.js +0 -1
- package/lib/mol-data/int/sorted-array.js +0 -1
- package/lib/mol-data/int/sorted-ranges.js +0 -1
- package/lib/mol-data/int/tuple.js +0 -1
- package/lib/mol-data/int.js +0 -1
- package/lib/mol-data/iterator.js +0 -1
- package/lib/mol-data/util/array.js +0 -1
- package/lib/mol-data/util/buckets.js +0 -1
- package/lib/mol-data/util/chunked-array.js +0 -1
- package/lib/mol-data/util/combination.js +0 -1
- package/lib/mol-data/util/equivalence-classes.js +0 -1
- package/lib/mol-data/util/grouping.js +0 -1
- package/lib/mol-data/util/hash-functions.js +0 -1
- package/lib/mol-data/util/interval-iterator.js +0 -1
- package/lib/mol-data/util/sort.js +0 -1
- package/lib/mol-data/util.js +0 -1
- package/lib/mol-geo/geometry/base.js +0 -1
- package/lib/mol-geo/geometry/clipping-data.js +0 -1
- package/lib/mol-geo/geometry/color-data.js +0 -1
- package/lib/mol-geo/geometry/cylinders/cylinders-builder.js +0 -1
- package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/mol-geo/geometry/cylinders/cylinders.js +0 -1
- package/lib/mol-geo/geometry/direct-volume/direct-volume.js +0 -1
- package/lib/mol-geo/geometry/direct-volume/transfer-function.js +0 -1
- package/lib/mol-geo/geometry/geometry.js +0 -1
- package/lib/mol-geo/geometry/image/image.js +0 -1
- package/lib/mol-geo/geometry/lines/lines-builder.js +0 -1
- package/lib/mol-geo/geometry/lines/lines.d.ts +2 -1
- package/lib/mol-geo/geometry/lines/lines.js +2 -3
- package/lib/mol-geo/geometry/marker-data.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/axes.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/box.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/cylinder.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/ellipsoid.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/ribbon.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/sheet.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/sphere.js +0 -1
- package/lib/mol-geo/geometry/mesh/builder/tube.js +0 -1
- package/lib/mol-geo/geometry/mesh/color-smoothing.js +0 -1
- package/lib/mol-geo/geometry/mesh/laplacian-smoothing.js +0 -1
- package/lib/mol-geo/geometry/mesh/mesh-builder.js +0 -1
- package/lib/mol-geo/geometry/mesh/mesh.js +0 -1
- package/lib/mol-geo/geometry/overpaint-data.js +0 -1
- package/lib/mol-geo/geometry/picking.js +0 -1
- package/lib/mol-geo/geometry/points/points-builder.js +0 -1
- package/lib/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/mol-geo/geometry/points/points.js +0 -1
- package/lib/mol-geo/geometry/size-data.js +0 -1
- package/lib/mol-geo/geometry/spheres/spheres-builder.js +0 -1
- package/lib/mol-geo/geometry/spheres/spheres.js +0 -1
- package/lib/mol-geo/geometry/substance-data.js +0 -1
- package/lib/mol-geo/geometry/text/font-atlas.js +0 -1
- package/lib/mol-geo/geometry/text/text-builder.js +2 -2
- package/lib/mol-geo/geometry/text/text.js +0 -1
- package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +0 -1
- package/lib/mol-geo/geometry/texture-mesh/texture-mesh.js +0 -1
- package/lib/mol-geo/geometry/transform-data.js +0 -1
- package/lib/mol-geo/geometry/transparency-data.js +0 -1
- package/lib/mol-geo/primitive/box.js +0 -1
- package/lib/mol-geo/primitive/cage.js +0 -1
- package/lib/mol-geo/primitive/circle.js +0 -1
- package/lib/mol-geo/primitive/cylinder.js +0 -1
- package/lib/mol-geo/primitive/dodecahedron.js +0 -1
- package/lib/mol-geo/primitive/icosahedron.js +0 -1
- package/lib/mol-geo/primitive/octahedron.js +0 -1
- package/lib/mol-geo/primitive/plane.js +0 -1
- package/lib/mol-geo/primitive/polygon.js +0 -1
- package/lib/mol-geo/primitive/polyhedron.js +0 -1
- package/lib/mol-geo/primitive/primitive.js +0 -1
- package/lib/mol-geo/primitive/prism.js +0 -1
- package/lib/mol-geo/primitive/pyramid.js +0 -1
- package/lib/mol-geo/primitive/sphere.js +0 -1
- package/lib/mol-geo/primitive/spiked-ball.js +0 -1
- package/lib/mol-geo/primitive/star.js +0 -1
- package/lib/mol-geo/primitive/tetrahedron.js +0 -1
- package/lib/mol-geo/primitive/torus.js +0 -1
- package/lib/mol-geo/primitive/wedge.js +0 -1
- package/lib/mol-geo/util/location-iterator.js +0 -1
- package/lib/mol-geo/util/marching-cubes/algorithm.js +0 -1
- package/lib/mol-geo/util/marching-cubes/builder.js +0 -1
- package/lib/mol-geo/util/marching-cubes/tables.js +0 -1
- package/lib/mol-geo/util.js +0 -1
- package/lib/mol-gl/commit-queue.js +0 -1
- package/lib/mol-gl/compute/grid3d.js +0 -1
- package/lib/mol-gl/compute/histogram-pyramid/reduction.js +0 -1
- package/lib/mol-gl/compute/histogram-pyramid/sum.js +0 -1
- package/lib/mol-gl/compute/marching-cubes/active-voxels.js +0 -1
- package/lib/mol-gl/compute/marching-cubes/isosurface.js +0 -1
- package/lib/mol-gl/compute/marching-cubes/tables.js +0 -1
- package/lib/mol-gl/compute/util.js +0 -1
- package/lib/mol-gl/object3d.js +0 -1
- package/lib/mol-gl/render-object.js +0 -1
- package/lib/mol-gl/renderable/cylinders.js +0 -1
- package/lib/mol-gl/renderable/direct-volume.js +0 -1
- package/lib/mol-gl/renderable/image.js +0 -1
- package/lib/mol-gl/renderable/lines.js +0 -1
- package/lib/mol-gl/renderable/mesh.js +0 -1
- package/lib/mol-gl/renderable/points.js +0 -1
- package/lib/mol-gl/renderable/schema.js +0 -1
- package/lib/mol-gl/renderable/spheres.js +0 -1
- package/lib/mol-gl/renderable/text.js +0 -1
- package/lib/mol-gl/renderable/texture-mesh.js +0 -1
- package/lib/mol-gl/renderable/util.js +0 -1
- package/lib/mol-gl/renderable.js +0 -1
- package/lib/mol-gl/renderer.js +3 -5
- package/lib/mol-gl/scene.d.ts +2 -1
- package/lib/mol-gl/scene.js +14 -3
- package/lib/mol-gl/shader/chunks/apply-fog.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/apply-interior-color.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/apply-marker-color.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-group.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-marker-varying.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-material-color.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-position.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/assign-size.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/check-picking-alpha.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/clip-instance.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/clip-pixel.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/color-frag-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/color-vert-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/common-clip.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/common-frag-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/common-vert-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/common.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/float-to-rgba.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/light-frag-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/matrix-scale.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/normal-frag-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/read-from-texture.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/rgba-to-float.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/size-vert-params.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +0 -1
- package/lib/mol-gl/shader/chunks/wboit-write.glsl.js +0 -1
- package/lib/mol-gl/shader/compose.frag.js +0 -1
- package/lib/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +0 -1
- package/lib/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +0 -1
- package/lib/mol-gl/shader/compute/color-smoothing/normalize.frag.js +0 -1
- package/lib/mol-gl/shader/copy.frag.js +0 -1
- package/lib/mol-gl/shader/cylinders.frag.js +0 -1
- package/lib/mol-gl/shader/cylinders.vert.js +0 -1
- package/lib/mol-gl/shader/depth-merge.frag.js +0 -1
- package/lib/mol-gl/shader/direct-volume.frag.js +0 -1
- package/lib/mol-gl/shader/direct-volume.vert.js +0 -1
- package/lib/mol-gl/shader/evaluate-wboit.frag.js +0 -1
- package/lib/mol-gl/shader/fxaa.frag.js +0 -1
- package/lib/mol-gl/shader/gaussian-density.frag.js +0 -1
- package/lib/mol-gl/shader/gaussian-density.vert.js +0 -1
- package/lib/mol-gl/shader/histogram-pyramid/reduction.frag.js +0 -1
- package/lib/mol-gl/shader/histogram-pyramid/sum.frag.js +0 -1
- package/lib/mol-gl/shader/image.frag.js +0 -1
- package/lib/mol-gl/shader/image.vert.js +0 -1
- package/lib/mol-gl/shader/lines.frag.js +0 -1
- package/lib/mol-gl/shader/lines.vert.js +0 -1
- package/lib/mol-gl/shader/marching-cubes/active-voxels.frag.js +0 -1
- package/lib/mol-gl/shader/marching-cubes/isosurface.frag.js +0 -1
- package/lib/mol-gl/shader/marking/edge.frag.js +0 -1
- package/lib/mol-gl/shader/marking/overlay.frag.js +0 -1
- package/lib/mol-gl/shader/mesh.frag.js +0 -1
- package/lib/mol-gl/shader/mesh.vert.js +0 -1
- package/lib/mol-gl/shader/outlines.frag.js +0 -1
- package/lib/mol-gl/shader/points.frag.js +0 -1
- package/lib/mol-gl/shader/points.vert.js +0 -1
- package/lib/mol-gl/shader/postprocessing.frag.d.ts +2 -2
- package/lib/mol-gl/shader/postprocessing.frag.js +2 -3
- package/lib/mol-gl/shader/quad.vert.js +0 -1
- package/lib/mol-gl/shader/smaa/blend.frag.js +0 -1
- package/lib/mol-gl/shader/smaa/blend.vert.js +0 -1
- package/lib/mol-gl/shader/smaa/edges.frag.js +0 -1
- package/lib/mol-gl/shader/smaa/edges.vert.js +0 -1
- package/lib/mol-gl/shader/smaa/weights.frag.js +0 -1
- package/lib/mol-gl/shader/smaa/weights.vert.js +0 -1
- package/lib/mol-gl/shader/spheres.frag.js +0 -1
- package/lib/mol-gl/shader/spheres.vert.js +0 -1
- package/lib/mol-gl/shader/ssao-blur.frag.js +0 -1
- package/lib/mol-gl/shader/ssao.frag.js +0 -1
- package/lib/mol-gl/shader/text.frag.js +0 -1
- package/lib/mol-gl/shader/text.vert.js +0 -1
- package/lib/mol-gl/shader/util/grid3d-template.frag.js +0 -1
- package/lib/mol-gl/shader-code.js +2 -2
- package/lib/mol-gl/webgl/buffer.js +2 -4
- package/lib/mol-gl/webgl/compat.js +0 -1
- package/lib/mol-gl/webgl/context.js +0 -1
- package/lib/mol-gl/webgl/extensions.js +0 -1
- package/lib/mol-gl/webgl/framebuffer.js +0 -1
- package/lib/mol-gl/webgl/program.js +0 -1
- package/lib/mol-gl/webgl/render-item.js +0 -1
- package/lib/mol-gl/webgl/render-target.js +0 -1
- package/lib/mol-gl/webgl/renderbuffer.js +0 -1
- package/lib/mol-gl/webgl/resources.js +0 -1
- package/lib/mol-gl/webgl/shader.js +0 -1
- package/lib/mol-gl/webgl/state.js +0 -1
- package/lib/mol-gl/webgl/texture.d.ts +1 -1
- package/lib/mol-gl/webgl/texture.js +9 -2
- package/lib/mol-gl/webgl/uniform.js +0 -1
- package/lib/mol-gl/webgl/vertex-array.js +0 -1
- package/lib/mol-io/common/ascii.js +0 -1
- package/lib/mol-io/common/binary-cif/array-encoder.js +0 -1
- package/lib/mol-io/common/binary-cif/classifier.js +3 -3
- package/lib/mol-io/common/binary-cif/decoder.js +4 -4
- package/lib/mol-io/common/binary-cif/encoding.js +0 -1
- package/lib/mol-io/common/binary-cif.js +0 -1
- package/lib/mol-io/common/binary.js +0 -1
- package/lib/mol-io/common/file-handle.js +0 -1
- package/lib/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/mol-io/common/io-buffer.js +405 -0
- package/lib/mol-io/common/msgpack/decode.js +0 -1
- package/lib/mol-io/common/msgpack/encode.js +0 -1
- package/lib/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/mol-io/common/netcdf/reader.js +456 -0
- package/lib/mol-io/common/simple-buffer.js +0 -1
- package/lib/mol-io/common/typed-array.js +0 -1
- package/lib/mol-io/common/utf8.js +0 -1
- package/lib/mol-io/reader/ccp4/parser.js +0 -1
- package/lib/mol-io/reader/ccp4/schema.js +0 -1
- package/lib/mol-io/reader/cif/binary/field.js +0 -1
- package/lib/mol-io/reader/cif/binary/parser.js +0 -1
- package/lib/mol-io/reader/cif/data-model.js +0 -1
- package/lib/mol-io/reader/cif/schema/bird.d.ts +1 -1
- package/lib/mol-io/reader/cif/schema/bird.js +1 -2
- package/lib/mol-io/reader/cif/schema/ccd-extras.js +0 -1
- package/lib/mol-io/reader/cif/schema/ccd.d.ts +1 -1
- package/lib/mol-io/reader/cif/schema/ccd.js +1 -2
- package/lib/mol-io/reader/cif/schema/cif-core.js +0 -1
- package/lib/mol-io/reader/cif/schema/ddl.js +0 -1
- package/lib/mol-io/reader/cif/schema/density-server.js +0 -1
- package/lib/mol-io/reader/cif/schema/dic.js +0 -1
- package/lib/mol-io/reader/cif/schema/mmcif-extras.js +0 -1
- package/lib/mol-io/reader/cif/schema/mmcif.d.ts +6 -2
- package/lib/mol-io/reader/cif/schema/mmcif.js +5 -2
- package/lib/mol-io/reader/cif/schema.js +0 -1
- package/lib/mol-io/reader/cif/text/parser.js +0 -1
- package/lib/mol-io/reader/cif.js +0 -1
- package/lib/mol-io/reader/common/binary/column.js +0 -1
- package/lib/mol-io/reader/common/text/column/fixed.js +0 -1
- package/lib/mol-io/reader/common/text/column/token.js +0 -1
- package/lib/mol-io/reader/common/text/number-parser.js +0 -1
- package/lib/mol-io/reader/common/text/tokenizer.js +0 -1
- package/lib/mol-io/reader/csv/data-model.js +0 -1
- package/lib/mol-io/reader/csv/field.js +0 -1
- package/lib/mol-io/reader/csv/parser.js +0 -1
- package/lib/mol-io/reader/csv/schema.js +0 -1
- package/lib/mol-io/reader/cube/parser.js +0 -1
- package/lib/mol-io/reader/dcd/parser.js +0 -1
- package/lib/mol-io/reader/dsn6/parser.js +0 -1
- package/lib/mol-io/reader/dsn6/schema.js +0 -1
- package/lib/mol-io/reader/dx/parser.js +0 -1
- package/lib/mol-io/reader/gro/parser.js +0 -1
- package/lib/mol-io/reader/mol/parser.js +0 -1
- package/lib/mol-io/reader/mol2/parser.js +0 -1
- package/lib/mol-io/reader/mol2/schema.js +0 -1
- package/lib/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/mol-io/reader/nctraj/parser.js +97 -0
- package/lib/mol-io/reader/obj/parser.js +0 -1
- package/lib/mol-io/reader/pdb/parser.js +0 -1
- package/lib/mol-io/reader/pdb/schema.js +0 -1
- package/lib/mol-io/reader/ply/parser.js +0 -1
- package/lib/mol-io/reader/ply/schema.js +0 -1
- package/lib/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/mol-io/reader/prmtop/parser.js +168 -0
- package/lib/mol-io/reader/psf/parser.js +0 -1
- package/lib/mol-io/reader/result.js +0 -1
- package/lib/mol-io/reader/sdf/parser-v3-util.js +0 -1
- package/lib/mol-io/reader/sdf/parser.js +0 -1
- package/lib/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/mol-io/reader/top/parser.js +299 -0
- package/lib/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/mol-io/reader/trr/parser.js +142 -0
- package/lib/mol-io/reader/xtc/parser.js +0 -1
- package/lib/mol-io/reader/xyz/parser.js +0 -1
- package/lib/mol-io/utils/short-string-pool.js +0 -1
- package/lib/mol-io/writer/cif/encoder/binary.js +0 -1
- package/lib/mol-io/writer/cif/encoder/text.js +0 -1
- package/lib/mol-io/writer/cif/encoder/util.js +0 -1
- package/lib/mol-io/writer/cif/encoder.js +2 -2
- package/lib/mol-io/writer/cif.js +0 -1
- package/lib/mol-io/writer/encoder.js +0 -1
- package/lib/mol-io/writer/ligand-encoder.js +0 -1
- package/lib/mol-io/writer/mol/encoder.js +0 -1
- package/lib/mol-io/writer/mol.js +0 -1
- package/lib/mol-io/writer/mol2/encoder.js +0 -1
- package/lib/mol-io/writer/mol2.js +0 -1
- package/lib/mol-io/writer/sdf.js +0 -1
- package/lib/mol-io/writer/writer.js +0 -1
- package/lib/mol-math/approx.js +0 -1
- package/lib/mol-math/easing.js +0 -1
- package/lib/mol-math/geometry/boundary-helper.js +0 -1
- package/lib/mol-math/geometry/boundary.js +0 -1
- package/lib/mol-math/geometry/centroid-helper.js +0 -1
- package/lib/mol-math/geometry/common.js +0 -1
- package/lib/mol-math/geometry/distance-transform.js +0 -1
- package/lib/mol-math/geometry/gaussian-density/cpu.js +0 -1
- package/lib/mol-math/geometry/gaussian-density/gpu.js +0 -1
- package/lib/mol-math/geometry/gaussian-density.js +0 -1
- package/lib/mol-math/geometry/lookup3d/common.js +0 -1
- package/lib/mol-math/geometry/lookup3d/grid.js +0 -1
- package/lib/mol-math/geometry/molecular-surface.js +0 -1
- package/lib/mol-math/geometry/primitives/axes3d.js +0 -1
- package/lib/mol-math/geometry/primitives/box3d.js +0 -1
- package/lib/mol-math/geometry/primitives/sphere3d.js +0 -1
- package/lib/mol-math/geometry/spacegroup/cell.js +0 -1
- package/lib/mol-math/geometry/spacegroup/construction.js +0 -1
- package/lib/mol-math/geometry/spacegroup/tables.js +0 -1
- package/lib/mol-math/geometry/symmetry-operator.js +0 -1
- package/lib/mol-math/geometry.js +0 -1
- package/lib/mol-math/graph/int-adjacency-graph.js +0 -1
- package/lib/mol-math/graph/inter-unit-graph.js +0 -1
- package/lib/mol-math/graph.js +0 -1
- package/lib/mol-math/histogram.js +0 -1
- package/lib/mol-math/interpolate.js +0 -1
- package/lib/mol-math/linear-algebra/3d/common.js +0 -1
- package/lib/mol-math/linear-algebra/3d/mat3.js +0 -1
- package/lib/mol-math/linear-algebra/3d/mat4.js +0 -1
- package/lib/mol-math/linear-algebra/3d/minimize-rmsd.js +0 -1
- package/lib/mol-math/linear-algebra/3d/quat.js +0 -1
- package/lib/mol-math/linear-algebra/3d/vec2.js +0 -1
- package/lib/mol-math/linear-algebra/3d/vec3.js +0 -1
- package/lib/mol-math/linear-algebra/3d/vec4.js +0 -1
- package/lib/mol-math/linear-algebra/3d.js +0 -1
- package/lib/mol-math/linear-algebra/matrix/evd.js +0 -1
- package/lib/mol-math/linear-algebra/matrix/matrix.js +0 -1
- package/lib/mol-math/linear-algebra/matrix/principal-axes.js +0 -1
- package/lib/mol-math/linear-algebra/matrix/svd.js +0 -1
- package/lib/mol-math/linear-algebra/tensor.js +0 -1
- package/lib/mol-math/linear-algebra.js +0 -1
- package/lib/mol-math/misc.js +0 -1
- package/lib/mol-model/custom-property.js +0 -1
- package/lib/mol-model/location.js +0 -1
- package/lib/mol-model/loci.js +0 -1
- package/lib/mol-model/sequence/alignment/alignment.js +0 -1
- package/lib/mol-model/sequence/alignment/sequence.js +0 -1
- package/lib/mol-model/sequence/alignment/substitution-matrix.js +0 -1
- package/lib/mol-model/sequence/alignment.js +0 -1
- package/lib/mol-model/sequence/constants.js +0 -1
- package/lib/mol-model/sequence/sequence.js +2 -2
- package/lib/mol-model/sequence.js +0 -1
- package/lib/mol-model/shape/provider.js +0 -1
- package/lib/mol-model/shape/shape.js +0 -1
- package/lib/mol-model/shape.js +0 -1
- package/lib/mol-model/structure/coordinates/coordinates.js +0 -1
- package/lib/mol-model/structure/coordinates.js +0 -1
- package/lib/mol-model/structure/export/categories/atom_site.js +0 -1
- package/lib/mol-model/structure/export/categories/atom_site_operator_mapping.js +0 -1
- package/lib/mol-model/structure/export/categories/misc.js +0 -1
- package/lib/mol-model/structure/export/categories/secondary-structure.js +0 -1
- package/lib/mol-model/structure/export/categories/sequence.js +0 -1
- package/lib/mol-model/structure/export/categories/utils.js +0 -1
- package/lib/mol-model/structure/export/mmcif.js +0 -1
- package/lib/mol-model/structure/model/indexing.js +0 -1
- package/lib/mol-model/structure/model/model.d.ts +5 -1
- package/lib/mol-model/structure/model/model.js +38 -26
- package/lib/mol-model/structure/model/properties/atomic/bonds.js +0 -1
- package/lib/mol-model/structure/model/properties/atomic/conformation.js +0 -1
- package/lib/mol-model/structure/model/properties/atomic/hierarchy.js +0 -1
- package/lib/mol-model/structure/model/properties/atomic/measures.js +0 -1
- package/lib/mol-model/structure/model/properties/atomic/types.js +0 -1
- package/lib/mol-model/structure/model/properties/atomic.js +0 -1
- package/lib/mol-model/structure/model/properties/coarse/conformation.js +0 -1
- package/lib/mol-model/structure/model/properties/coarse/hierarchy.js +0 -1
- package/lib/mol-model/structure/model/properties/coarse.js +0 -1
- package/lib/mol-model/structure/model/properties/common.js +0 -1
- package/lib/mol-model/structure/model/properties/custom/indexed.js +0 -1
- package/lib/mol-model/structure/model/properties/global-transform.js +0 -1
- package/lib/mol-model/structure/model/properties/seconday-structure.js +0 -1
- package/lib/mol-model/structure/model/properties/sequence.js +0 -1
- package/lib/mol-model/structure/model/properties/symmetry.js +0 -1
- package/lib/mol-model/structure/model/properties/utils/atomic-derived.js +0 -1
- package/lib/mol-model/structure/model/properties/utils/atomic-index.js +0 -1
- package/lib/mol-model/structure/model/properties/utils/atomic-ranges.js +0 -1
- package/lib/mol-model/structure/model/properties/utils/coarse-keys.js +0 -1
- package/lib/mol-model/structure/model/properties/utils/coarse-ranges.js +0 -1
- package/lib/mol-model/structure/model/properties/utils/residue-set.js +0 -1
- package/lib/mol-model/structure/model/types/ions.js +0 -1
- package/lib/mol-model/structure/model/types/lipids.js +0 -1
- package/lib/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/mol-model/structure/model/types/saccharides.js +8 -0
- package/lib/mol-model/structure/model/types.js +0 -1
- package/lib/mol-model/structure/model/util.js +0 -1
- package/lib/mol-model/structure/model.js +0 -1
- package/lib/mol-model/structure/query/context.js +0 -1
- package/lib/mol-model/structure/query/predicates.js +0 -1
- package/lib/mol-model/structure/query/queries/combinators.js +0 -1
- package/lib/mol-model/structure/query/queries/filters.js +0 -1
- package/lib/mol-model/structure/query/queries/generators.js +0 -1
- package/lib/mol-model/structure/query/queries/internal.js +0 -1
- package/lib/mol-model/structure/query/queries/modifiers.js +0 -1
- package/lib/mol-model/structure/query/query.js +0 -1
- package/lib/mol-model/structure/query/selection.js +0 -1
- package/lib/mol-model/structure/query/utils/builders.js +0 -1
- package/lib/mol-model/structure/query/utils/structure-distance.js +0 -1
- package/lib/mol-model/structure/query/utils/structure-set.js +0 -1
- package/lib/mol-model/structure/query.js +0 -1
- package/lib/mol-model/structure/structure/carbohydrates/compute.js +0 -1
- package/lib/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
- package/lib/mol-model/structure/structure/carbohydrates/constants.js +6 -10
- package/lib/mol-model/structure/structure/carbohydrates/data.js +0 -1
- package/lib/mol-model/structure/structure/element/bundle.js +0 -1
- package/lib/mol-model/structure/structure/element/element.js +0 -1
- package/lib/mol-model/structure/structure/element/location.js +0 -1
- package/lib/mol-model/structure/structure/element/loci.js +0 -1
- package/lib/mol-model/structure/structure/element/stats.js +0 -1
- package/lib/mol-model/structure/structure/element/util.js +0 -1
- package/lib/mol-model/structure/structure/element.js +0 -1
- package/lib/mol-model/structure/structure/properties.js +0 -1
- package/lib/mol-model/structure/structure/structure.d.ts +1 -1
- package/lib/mol-model/structure/structure/structure.js +13 -4
- package/lib/mol-model/structure/structure/symmetry.js +0 -1
- package/lib/mol-model/structure/structure/unit/bonds/common.js +0 -1
- package/lib/mol-model/structure/structure/unit/bonds/data.d.ts +2 -1
- package/lib/mol-model/structure/structure/unit/bonds/data.js +1 -2
- package/lib/mol-model/structure/structure/unit/bonds/element-set-intra-bond-cache.js +0 -1
- package/lib/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
- package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +4 -3
- package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -2
- package/lib/mol-model/structure/structure/unit/bonds.js +0 -1
- package/lib/mol-model/structure/structure/unit/resonance.d.ts +23 -0
- package/lib/mol-model/structure/structure/unit/resonance.js +60 -0
- package/lib/mol-model/structure/structure/unit/rings/compute.js +70 -44
- package/lib/mol-model/structure/structure/unit/rings.js +0 -1
- package/lib/mol-model/structure/structure/unit.d.ts +4 -1
- package/lib/mol-model/structure/structure/unit.js +19 -6
- package/lib/mol-model/structure/structure/util/boundary.js +0 -1
- package/lib/mol-model/structure/structure/util/lookup3d.js +0 -1
- package/lib/mol-model/structure/structure/util/polymer.js +0 -1
- package/lib/mol-model/structure/structure/util/principal-axes.js +0 -1
- package/lib/mol-model/structure/structure/util/subset-builder.js +0 -1
- package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.js +0 -1
- package/lib/mol-model/structure/structure/util/superposition.js +0 -1
- package/lib/mol-model/structure/structure/util/unique-subset-builder.js +0 -1
- package/lib/mol-model/structure/structure/util/unit-transforms.js +0 -1
- package/lib/mol-model/structure/structure.js +0 -1
- package/lib/mol-model/structure/topology/topology.js +0 -1
- package/lib/mol-model/structure/topology.js +0 -1
- package/lib/mol-model/structure/trajectory.js +0 -1
- package/lib/mol-model/structure/util.js +0 -1
- package/lib/mol-model/structure.js +0 -1
- package/lib/mol-model/volume/grid.js +0 -1
- package/lib/mol-model/volume/volume.js +0 -1
- package/lib/mol-model/volume.js +0 -1
- package/lib/mol-model-formats/format.js +0 -1
- package/lib/mol-model-formats/shape/ply.js +0 -1
- package/lib/mol-model-formats/structure/basic/atomic.d.ts +1 -1
- package/lib/mol-model-formats/structure/basic/atomic.js +1 -15
- package/lib/mol-model-formats/structure/basic/coarse.js +0 -1
- package/lib/mol-model-formats/structure/basic/entities.js +0 -1
- package/lib/mol-model-formats/structure/basic/parser.d.ts +1 -1
- package/lib/mol-model-formats/structure/basic/parser.js +1 -2
- package/lib/mol-model-formats/structure/basic/properties.js +0 -1
- package/lib/mol-model-formats/structure/basic/schema.d.ts +2 -2
- package/lib/mol-model-formats/structure/basic/schema.js +7 -3
- package/lib/mol-model-formats/structure/basic/sequence.js +0 -1
- package/lib/mol-model-formats/structure/basic/sort.js +0 -1
- package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
- package/lib/mol-model-formats/structure/basic/util.js +24 -2
- package/lib/mol-model-formats/structure/cif-core.js +4 -5
- package/lib/mol-model-formats/structure/common/component.d.ts +1 -1
- package/lib/mol-model-formats/structure/common/component.js +7 -4
- package/lib/mol-model-formats/structure/common/entity.js +0 -1
- package/lib/mol-model-formats/structure/common/property.js +0 -1
- package/lib/mol-model-formats/structure/common/util.js +0 -1
- package/lib/mol-model-formats/structure/cube.js +3 -4
- package/lib/mol-model-formats/structure/dcd.js +0 -1
- package/lib/mol-model-formats/structure/gro.js +3 -2
- package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
- package/lib/mol-model-formats/structure/mmcif.js +4 -3
- package/lib/mol-model-formats/structure/mol.js +3 -4
- package/lib/mol-model-formats/structure/mol2.js +5 -6
- package/lib/mol-model-formats/structure/nctraj.d.ts +9 -0
- package/lib/mol-model-formats/structure/nctraj.js +56 -0
- package/lib/mol-model-formats/structure/pdb/anisotropic.js +0 -1
- package/lib/mol-model-formats/structure/pdb/assembly.js +0 -1
- package/lib/mol-model-formats/structure/pdb/atom-site.js +0 -1
- package/lib/mol-model-formats/structure/pdb/conect.js +0 -1
- package/lib/mol-model-formats/structure/pdb/entity.js +0 -1
- package/lib/mol-model-formats/structure/pdb/secondary-structure.js +0 -1
- package/lib/mol-model-formats/structure/pdb/to-cif.js +0 -1
- package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/mol-model-formats/structure/pdb.js +5 -4
- package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
- package/lib/mol-model-formats/structure/prmtop.js +144 -0
- package/lib/mol-model-formats/structure/property/anisotropic.js +0 -1
- package/lib/mol-model-formats/structure/property/assembly.js +0 -1
- package/lib/mol-model-formats/structure/property/atoms/chem_comp.js +0 -1
- package/lib/mol-model-formats/structure/property/bonds/chem_comp.d.ts +1 -1
- package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +7 -6
- package/lib/mol-model-formats/structure/property/bonds/index-pair.js +0 -1
- package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +0 -1
- package/lib/mol-model-formats/structure/property/partial-charge.js +0 -1
- package/lib/mol-model-formats/structure/property/secondary-structure.js +0 -1
- package/lib/mol-model-formats/structure/property/symmetry.js +11 -2
- package/lib/mol-model-formats/structure/psf.js +3 -2
- package/lib/mol-model-formats/structure/sdf.js +0 -1
- package/lib/mol-model-formats/structure/top.d.ts +16 -0
- package/lib/mol-model-formats/structure/top.js +186 -0
- package/lib/mol-model-formats/structure/trr.d.ts +9 -0
- package/lib/mol-model-formats/structure/trr.js +42 -0
- package/lib/mol-model-formats/structure/util.d.ts +2 -2
- package/lib/mol-model-formats/structure/util.js +19 -21
- package/lib/mol-model-formats/structure/xtc.js +0 -1
- package/lib/mol-model-formats/structure/xyz.js +2 -3
- package/lib/mol-model-formats/volume/ccp4.js +0 -1
- package/lib/mol-model-formats/volume/cube.js +0 -1
- package/lib/mol-model-formats/volume/density-server.js +0 -1
- package/lib/mol-model-formats/volume/dsn6.js +0 -1
- package/lib/mol-model-formats/volume/dx.js +0 -1
- package/lib/mol-model-formats/volume/property.js +0 -1
- package/lib/mol-model-props/common/custom-element-property.js +0 -1
- package/lib/mol-model-props/common/custom-model-property.js +0 -1
- package/lib/mol-model-props/common/custom-property.js +0 -1
- package/lib/mol-model-props/common/custom-structure-property.js +0 -1
- package/lib/mol-model-props/common/wrapper.js +0 -1
- package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +0 -1
- package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.js +0 -1
- package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +0 -1
- package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +0 -1
- package/lib/mol-model-props/computed/accessible-surface-area.js +0 -1
- package/lib/mol-model-props/computed/chemistry/functional-group.js +0 -1
- package/lib/mol-model-props/computed/chemistry/geometry.js +0 -1
- package/lib/mol-model-props/computed/chemistry/util.js +0 -1
- package/lib/mol-model-props/computed/chemistry/valence-model.js +0 -1
- package/lib/mol-model-props/computed/helix-orientation/helix-orientation.js +0 -1
- package/lib/mol-model-props/computed/helix-orientation.js +0 -1
- package/lib/mol-model-props/computed/interactions/charged.js +0 -1
- package/lib/mol-model-props/computed/interactions/common.js +0 -1
- package/lib/mol-model-props/computed/interactions/contacts-builder.js +0 -1
- package/lib/mol-model-props/computed/interactions/contacts.js +0 -1
- package/lib/mol-model-props/computed/interactions/features.js +0 -1
- package/lib/mol-model-props/computed/interactions/halogen-bonds.js +0 -1
- package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js +0 -1
- package/lib/mol-model-props/computed/interactions/hydrophobic.js +0 -1
- package/lib/mol-model-props/computed/interactions/interactions.js +0 -1
- package/lib/mol-model-props/computed/interactions/metal.js +0 -1
- package/lib/mol-model-props/computed/interactions/refine.js +0 -1
- package/lib/mol-model-props/computed/interactions.js +0 -1
- package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +9 -4
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +10 -6
- package/lib/mol-model-props/computed/representations/interactions.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/backbone-hbonds.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/bends.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/bridges.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/common.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/dihedral-angles.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/helices.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/ladders.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/protein-info.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/sheets.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/trace-lookup.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/turns.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure/zhang-skolnik.js +0 -1
- package/lib/mol-model-props/computed/secondary-structure.js +0 -1
- package/lib/mol-model-props/computed/themes/accessible-surface-area.js +0 -1
- package/lib/mol-model-props/computed/themes/interaction-type.js +0 -1
- package/lib/mol-model-props/computed/valence-model.js +0 -1
- package/lib/mol-model-props/integrative/cross-link-restraint/color.js +0 -1
- package/lib/mol-model-props/integrative/cross-link-restraint/format.js +0 -1
- package/lib/mol-model-props/integrative/cross-link-restraint/property.js +0 -1
- package/lib/mol-model-props/integrative/cross-link-restraint/representation.js +10 -2
- package/lib/mol-model-props/integrative/pair-restraints.js +0 -1
- package/lib/mol-model-props/sequence/sifts-mapping.js +0 -1
- package/lib/mol-model-props/sequence/themes/sifts-mapping.js +0 -1
- package/lib/mol-plugin/animation-loop.js +0 -1
- package/lib/mol-plugin/behavior/behavior.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/camera.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/computed/interactions.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/computed/secondary-structure.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/computed/valence-model.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/sequence/sifts-mapping.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/structure-info.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/representation.js +4 -5
- package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.js +0 -1
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js +10 -4
- package/lib/mol-plugin/behavior/static/camera.js +0 -1
- package/lib/mol-plugin/behavior/static/misc.js +0 -1
- package/lib/mol-plugin/behavior/static/representation.js +0 -1
- package/lib/mol-plugin/behavior/static/state.js +0 -1
- package/lib/mol-plugin/behavior.js +0 -1
- package/lib/mol-plugin/command.js +0 -1
- package/lib/mol-plugin/commands.d.ts +1 -0
- package/lib/mol-plugin/commands.js +0 -1
- package/lib/mol-plugin/config.js +0 -1
- package/lib/mol-plugin/context.d.ts +2 -1
- package/lib/mol-plugin/context.js +4 -4
- package/lib/mol-plugin/features.js +0 -1
- package/lib/mol-plugin/layout.js +0 -1
- package/lib/mol-plugin/spec.js +1 -2
- package/lib/mol-plugin/state.js +0 -1
- package/lib/mol-plugin/util/substructure-parent-helper.js +0 -1
- package/lib/mol-plugin/util/task-manager.js +0 -1
- package/lib/mol-plugin/util/toast.js +0 -1
- package/lib/mol-plugin/util/viewport-screenshot.js +2 -3
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-state/actions/file.d.ts +1 -1
- package/lib/mol-plugin-state/actions/file.js +88 -56
- package/lib/mol-plugin-state/actions/structure.d.ts +11 -2
- package/lib/mol-plugin-state/actions/structure.js +174 -5
- package/lib/mol-plugin-state/actions/volume.js +3 -3
- package/lib/mol-plugin-state/actions.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/assembly-unwind.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/camera-rock.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/camera-spin.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/explode-units.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/model-index.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/spin-structure.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/state-interpolation.js +0 -1
- package/lib/mol-plugin-state/animation/built-in/state-snapshots.js +0 -1
- package/lib/mol-plugin-state/animation/helpers.js +0 -1
- package/lib/mol-plugin-state/animation/model.js +0 -1
- package/lib/mol-plugin-state/builder/data.js +0 -1
- package/lib/mol-plugin-state/builder/preset-provider.js +0 -1
- package/lib/mol-plugin-state/builder/structure/hierarchy-preset.js +0 -1
- package/lib/mol-plugin-state/builder/structure/hierarchy.js +0 -1
- package/lib/mol-plugin-state/builder/structure/representation-preset.js +2 -3
- package/lib/mol-plugin-state/builder/structure/representation.js +0 -1
- package/lib/mol-plugin-state/builder/structure.js +0 -1
- package/lib/mol-plugin-state/component.js +0 -1
- package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
- package/lib/mol-plugin-state/formats/coordinates.js +67 -0
- package/lib/mol-plugin-state/formats/provider.js +0 -1
- package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
- package/lib/mol-plugin-state/formats/registry.js +13 -9
- package/lib/mol-plugin-state/formats/shape.js +0 -1
- package/lib/mol-plugin-state/formats/topology.d.ts +73 -0
- package/lib/mol-plugin-state/formats/topology.js +84 -0
- package/lib/mol-plugin-state/formats/trajectory.js +0 -1
- package/lib/mol-plugin-state/formats/volume.js +0 -1
- package/lib/mol-plugin-state/helpers/root-structure.js +1 -2
- package/lib/mol-plugin-state/helpers/structure-clipping.js +0 -1
- package/lib/mol-plugin-state/helpers/structure-component.js +2 -2
- package/lib/mol-plugin-state/helpers/structure-overpaint.js +0 -1
- package/lib/mol-plugin-state/helpers/structure-query.js +0 -1
- package/lib/mol-plugin-state/helpers/structure-representation-params.js +0 -1
- package/lib/mol-plugin-state/helpers/structure-selection-query.js +0 -1
- package/lib/mol-plugin-state/helpers/structure-substance.js +0 -1
- package/lib/mol-plugin-state/helpers/structure-transparency.js +0 -1
- package/lib/mol-plugin-state/helpers/volume-representation-params.js +0 -1
- package/lib/mol-plugin-state/manager/animation.js +0 -1
- package/lib/mol-plugin-state/manager/camera.js +0 -1
- package/lib/mol-plugin-state/manager/interactivity.d.ts +5 -3
- package/lib/mol-plugin-state/manager/interactivity.js +0 -1
- package/lib/mol-plugin-state/manager/loci-label.js +0 -1
- package/lib/mol-plugin-state/manager/snapshots.js +4 -5
- package/lib/mol-plugin-state/manager/structure/component.js +0 -1
- package/lib/mol-plugin-state/manager/structure/focus.js +0 -1
- package/lib/mol-plugin-state/manager/structure/hierarchy-state.js +0 -1
- package/lib/mol-plugin-state/manager/structure/hierarchy.js +0 -1
- package/lib/mol-plugin-state/manager/structure/measurement.js +0 -1
- package/lib/mol-plugin-state/manager/structure/selection.js +0 -1
- package/lib/mol-plugin-state/manager/volume/hierarchy-state.js +0 -1
- package/lib/mol-plugin-state/manager/volume/hierarchy.js +0 -1
- package/lib/mol-plugin-state/objects.d.ts +47 -1
- package/lib/mol-plugin-state/objects.js +17 -2
- package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
- package/lib/mol-plugin-state/transforms/data.js +61 -10
- package/lib/mol-plugin-state/transforms/helpers.js +0 -1
- package/lib/mol-plugin-state/transforms/misc.js +0 -1
- package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
- package/lib/mol-plugin-state/transforms/model.js +112 -4
- package/lib/mol-plugin-state/transforms/representation.js +0 -1
- package/lib/mol-plugin-state/transforms/shape.js +0 -1
- package/lib/mol-plugin-state/transforms/volume.js +0 -1
- package/lib/mol-plugin-state/transforms.js +0 -1
- package/lib/mol-plugin-ui/base.js +1 -2
- package/lib/mol-plugin-ui/context.js +0 -1
- package/lib/mol-plugin-ui/controls/action-menu.js +7 -8
- package/lib/mol-plugin-ui/controls/color.js +3 -4
- package/lib/mol-plugin-ui/controls/common.js +10 -11
- package/lib/mol-plugin-ui/controls/icons.js +70 -71
- package/lib/mol-plugin-ui/controls/legend.js +3 -4
- package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -2
- package/lib/mol-plugin-ui/controls/line-graph/point-component.js +0 -1
- package/lib/mol-plugin-ui/controls/parameters.js +51 -52
- package/lib/mol-plugin-ui/controls/screenshot.js +2 -3
- package/lib/mol-plugin-ui/controls/slider.js +5 -6
- package/lib/mol-plugin-ui/controls.js +7 -8
- package/lib/mol-plugin-ui/custom/volume.js +4 -5
- package/lib/mol-plugin-ui/hooks/use-behavior.js +0 -1
- package/lib/mol-plugin-ui/index.js +0 -1
- package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
- package/lib/mol-plugin-ui/left-panel.js +33 -13
- package/lib/mol-plugin-ui/plugin.js +10 -11
- package/lib/mol-plugin-ui/sequence/chain.js +0 -1
- package/lib/mol-plugin-ui/sequence/element.js +0 -1
- package/lib/mol-plugin-ui/sequence/hetero.js +0 -1
- package/lib/mol-plugin-ui/sequence/polymer.js +0 -1
- package/lib/mol-plugin-ui/sequence/sequence.d.ts +2 -2
- package/lib/mol-plugin-ui/sequence/sequence.js +6 -8
- package/lib/mol-plugin-ui/sequence/wrapper.js +0 -1
- package/lib/mol-plugin-ui/sequence.js +5 -6
- 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 -643
- 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 +128 -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-plugin-ui/spec.js +0 -1
- package/lib/mol-plugin-ui/state/actions.js +1 -2
- package/lib/mol-plugin-ui/state/animation.js +1 -2
- package/lib/mol-plugin-ui/state/apply-action.js +0 -1
- package/lib/mol-plugin-ui/state/common.js +7 -8
- package/lib/mol-plugin-ui/state/snapshots.js +9 -10
- package/lib/mol-plugin-ui/state/tree.js +14 -15
- package/lib/mol-plugin-ui/state/update-transform.js +1 -2
- package/lib/mol-plugin-ui/structure/components.js +10 -11
- package/lib/mol-plugin-ui/structure/focus.js +1 -2
- package/lib/mol-plugin-ui/structure/generic.js +4 -5
- package/lib/mol-plugin-ui/structure/measurements.js +8 -9
- package/lib/mol-plugin-ui/structure/quick-styles.js +4 -5
- package/lib/mol-plugin-ui/structure/selection.js +7 -8
- package/lib/mol-plugin-ui/structure/source.js +4 -5
- package/lib/mol-plugin-ui/structure/superposition.js +8 -9
- package/lib/mol-plugin-ui/structure/volume.js +4 -5
- package/lib/mol-plugin-ui/task.js +5 -6
- package/lib/mol-plugin-ui/toast.js +4 -5
- package/lib/mol-plugin-ui/viewport/canvas.js +3 -4
- package/lib/mol-plugin-ui/viewport/help.js +8 -9
- package/lib/mol-plugin-ui/viewport/screenshot.js +3 -4
- package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -2
- package/lib/mol-plugin-ui/viewport.js +4 -5
- package/lib/mol-repr/representation.js +0 -1
- package/lib/mol-repr/shape/loci/angle.js +0 -1
- package/lib/mol-repr/shape/loci/common.js +0 -1
- package/lib/mol-repr/shape/loci/dihedral.js +0 -1
- package/lib/mol-repr/shape/loci/distance.js +0 -1
- package/lib/mol-repr/shape/loci/label.js +0 -1
- package/lib/mol-repr/shape/loci/orientation.js +0 -1
- package/lib/mol-repr/shape/loci/plane.js +0 -1
- package/lib/mol-repr/shape/model/unitcell.js +0 -1
- package/lib/mol-repr/shape/representation.js +0 -1
- package/lib/mol-repr/structure/complex-representation.js +0 -1
- package/lib/mol-repr/structure/complex-visual.js +0 -1
- package/lib/mol-repr/structure/params.js +0 -1
- package/lib/mol-repr/structure/registry.js +0 -1
- package/lib/mol-repr/structure/representation/backbone.js +0 -1
- package/lib/mol-repr/structure/representation/ball-and-stick.js +0 -1
- package/lib/mol-repr/structure/representation/carbohydrate.js +0 -1
- package/lib/mol-repr/structure/representation/cartoon.js +0 -1
- package/lib/mol-repr/structure/representation/ellipsoid.js +0 -1
- package/lib/mol-repr/structure/representation/gaussian-surface.js +0 -1
- package/lib/mol-repr/structure/representation/gaussian-volume.js +0 -1
- package/lib/mol-repr/structure/representation/label.js +0 -1
- package/lib/mol-repr/structure/representation/line.d.ts +1 -1
- package/lib/mol-repr/structure/representation/line.js +2 -3
- package/lib/mol-repr/structure/representation/molecular-surface.js +0 -1
- package/lib/mol-repr/structure/representation/orientation.js +0 -1
- package/lib/mol-repr/structure/representation/point.js +0 -1
- package/lib/mol-repr/structure/representation/putty.js +0 -1
- package/lib/mol-repr/structure/representation/spacefill.js +0 -1
- package/lib/mol-repr/structure/representation.js +0 -1
- package/lib/mol-repr/structure/units-representation.js +0 -1
- package/lib/mol-repr/structure/units-visual.js +0 -1
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +20 -11
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -6
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +25 -9
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +17 -6
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js +10 -2
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +10 -2
- package/lib/mol-repr/structure/visual/element-cross.js +0 -1
- package/lib/mol-repr/structure/visual/element-point.d.ts +1 -1
- package/lib/mol-repr/structure/visual/element-point.js +22 -4
- package/lib/mol-repr/structure/visual/element-sphere.js +0 -1
- package/lib/mol-repr/structure/visual/ellipsoid-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +0 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +0 -1
- package/lib/mol-repr/structure/visual/label-text.js +0 -1
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +0 -1
- package/lib/mol-repr/structure/visual/nucleotide-block-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.js +0 -1
- package/lib/mol-repr/structure/visual/polymer-backbone-sphere.js +0 -1
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.js +0 -1
- package/lib/mol-repr/structure/visual/polymer-gap-cylinder.js +0 -1
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/polymer-tube-mesh.js +0 -1
- package/lib/mol-repr/structure/visual/util/bond.js +0 -1
- package/lib/mol-repr/structure/visual/util/common.js +0 -1
- package/lib/mol-repr/structure/visual/util/element.d.ts +1 -1
- package/lib/mol-repr/structure/visual/util/element.js +13 -8
- package/lib/mol-repr/structure/visual/util/gaussian.js +0 -1
- package/lib/mol-repr/structure/visual/util/link.d.ts +13 -3
- package/lib/mol-repr/structure/visual/util/link.js +55 -7
- package/lib/mol-repr/structure/visual/util/molecular-surface.js +0 -1
- package/lib/mol-repr/structure/visual/util/nucleotide.js +0 -1
- package/lib/mol-repr/structure/visual/util/polymer/backbone.js +0 -1
- package/lib/mol-repr/structure/visual/util/polymer/curve-segment.js +0 -1
- package/lib/mol-repr/structure/visual/util/polymer/gap-iterator.js +0 -1
- package/lib/mol-repr/structure/visual/util/polymer/trace-iterator.js +0 -1
- package/lib/mol-repr/structure/visual/util/polymer.js +0 -1
- package/lib/mol-repr/util.js +0 -1
- package/lib/mol-repr/visual.js +0 -1
- package/lib/mol-repr/volume/direct-volume.js +0 -1
- package/lib/mol-repr/volume/isosurface.js +0 -1
- package/lib/mol-repr/volume/registry.js +0 -1
- package/lib/mol-repr/volume/representation.js +0 -1
- package/lib/mol-repr/volume/slice.js +0 -1
- package/lib/mol-repr/volume/util.js +0 -1
- package/lib/mol-script/compiler.js +0 -1
- package/lib/mol-script/language/builder.d.ts +0 -1
- package/lib/mol-script/language/builder.js +0 -1
- package/lib/mol-script/language/container.js +0 -1
- package/lib/mol-script/language/expression-formatter.js +0 -1
- package/lib/mol-script/language/expression.js +0 -1
- package/lib/mol-script/language/helpers.js +0 -1
- package/lib/mol-script/language/parser.js +7 -5
- package/lib/mol-script/language/symbol-table/core.js +0 -1
- package/lib/mol-script/language/symbol-table/internal.js +0 -1
- package/lib/mol-script/language/symbol-table/structure-query.js +0 -1
- package/lib/mol-script/language/symbol-table.js +0 -1
- package/lib/mol-script/language/symbol.js +0 -1
- package/lib/mol-script/language/type.js +0 -1
- package/lib/mol-script/runtime/environment.js +0 -1
- package/lib/mol-script/runtime/expression.js +0 -1
- package/lib/mol-script/runtime/query/base.js +0 -1
- package/lib/mol-script/runtime/query/compiler.js +0 -1
- package/lib/mol-script/runtime/query/table.js +0 -1
- package/lib/mol-script/runtime/runtime-macro.js +0 -1
- package/lib/mol-script/runtime/symbol.js +0 -1
- package/lib/mol-script/script/mol-script/examples.js +0 -1
- package/lib/mol-script/script/mol-script/parser.js +0 -1
- package/lib/mol-script/script/mol-script/script-macro.js +0 -1
- package/lib/mol-script/script/mol-script/symbols.js +0 -1
- package/lib/mol-script/script/parser.js +0 -1
- package/lib/mol-script/script.js +0 -1
- package/lib/mol-script/util/id-list.js +0 -1
- package/lib/mol-state/action/manager.js +0 -1
- package/lib/mol-state/action.js +0 -1
- package/lib/mol-state/index.js +0 -1
- package/lib/mol-state/object.js +0 -1
- package/lib/mol-state/state/builder.js +0 -1
- package/lib/mol-state/state/selection.js +0 -1
- package/lib/mol-state/state.js +0 -1
- package/lib/mol-state/transform.js +0 -1
- package/lib/mol-state/transformer.js +0 -1
- package/lib/mol-state/tree/immutable.js +0 -1
- package/lib/mol-state/tree/spine.js +0 -1
- package/lib/mol-state/tree/transient.js +0 -1
- package/lib/mol-state/tree.js +0 -1
- package/lib/mol-task/execution/observable.js +0 -1
- package/lib/mol-task/execution/progress.js +0 -1
- package/lib/mol-task/execution/runtime-context.js +0 -1
- package/lib/mol-task/execution/synchronous.js +0 -1
- package/lib/mol-task/index.js +0 -1
- package/lib/mol-task/task.js +0 -1
- package/lib/mol-task/util/chunked.js +0 -1
- package/lib/mol-task/util/multistep.js +0 -1
- package/lib/mol-task/util/scheduler.d.ts +2 -2
- package/lib/mol-task/util/scheduler.js +7 -8
- package/lib/mol-task/util/user-timing.js +0 -1
- package/lib/mol-theme/clipping.js +0 -1
- package/lib/mol-theme/color/atom-id.js +0 -1
- package/lib/mol-theme/color/carbohydrate-symbol.js +0 -1
- package/lib/mol-theme/color/chain-id.js +0 -1
- package/lib/mol-theme/color/element-index.js +0 -1
- package/lib/mol-theme/color/element-symbol.js +0 -1
- package/lib/mol-theme/color/entity-id.js +0 -1
- package/lib/mol-theme/color/entity-source.js +0 -1
- package/lib/mol-theme/color/hydrophobicity.js +2 -3
- package/lib/mol-theme/color/illustrative.js +0 -1
- package/lib/mol-theme/color/model-index.js +0 -1
- package/lib/mol-theme/color/molecule-type.js +0 -1
- package/lib/mol-theme/color/occupancy.js +0 -1
- package/lib/mol-theme/color/operator-hkl.js +0 -1
- package/lib/mol-theme/color/operator-name.js +0 -1
- package/lib/mol-theme/color/partial-charge.js +0 -1
- package/lib/mol-theme/color/polymer-id.js +0 -1
- package/lib/mol-theme/color/polymer-index.js +0 -1
- package/lib/mol-theme/color/residue-name.js +0 -1
- package/lib/mol-theme/color/secondary-structure.js +0 -1
- package/lib/mol-theme/color/sequence-id.js +0 -1
- package/lib/mol-theme/color/shape-group.js +0 -1
- package/lib/mol-theme/color/uncertainty.js +0 -1
- package/lib/mol-theme/color/uniform.js +0 -1
- package/lib/mol-theme/color/unit-index.js +0 -1
- package/lib/mol-theme/color/volume-value.js +0 -1
- package/lib/mol-theme/color.js +0 -1
- package/lib/mol-theme/label.js +0 -1
- package/lib/mol-theme/overpaint.js +0 -1
- package/lib/mol-theme/size/physical.js +0 -1
- package/lib/mol-theme/size/shape-group.js +0 -1
- package/lib/mol-theme/size/uncertainty.js +0 -1
- package/lib/mol-theme/size/uniform.js +0 -1
- package/lib/mol-theme/size.js +0 -1
- package/lib/mol-theme/substance.js +0 -1
- package/lib/mol-theme/theme.js +0 -1
- package/lib/mol-theme/transparency.js +0 -1
- package/lib/mol-util/array.js +0 -1
- package/lib/mol-util/assets.js +0 -1
- package/lib/mol-util/async-queue.js +0 -1
- package/lib/mol-util/binding.js +0 -1
- package/lib/mol-util/bit-flags.js +0 -1
- package/lib/mol-util/clip.js +0 -1
- package/lib/mol-util/color/color.js +0 -1
- package/lib/mol-util/color/distinct.js +0 -1
- package/lib/mol-util/color/index.js +0 -1
- package/lib/mol-util/color/lists.js +0 -1
- package/lib/mol-util/color/names.js +0 -1
- package/lib/mol-util/color/palette.js +0 -1
- package/lib/mol-util/color/params.js +0 -1
- package/lib/mol-util/color/scale.js +0 -1
- package/lib/mol-util/color/spaces/hcl.js +0 -1
- package/lib/mol-util/color/spaces/lab.js +0 -1
- package/lib/mol-util/color/swatches.js +0 -1
- package/lib/mol-util/console-logger.js +0 -1
- package/lib/mol-util/data-source.js +2 -2
- package/lib/mol-util/date.js +0 -1
- package/lib/mol-util/debug.js +0 -1
- package/lib/mol-util/download.js +0 -1
- package/lib/mol-util/file-info.d.ts +1 -3
- package/lib/mol-util/file-info.js +2 -11
- package/lib/mol-util/graphql-client.js +0 -1
- package/lib/mol-util/id-factory.js +0 -1
- package/lib/mol-util/image.js +0 -1
- package/lib/mol-util/index.d.ts +1 -0
- package/lib/mol-util/index.js +5 -1
- package/lib/mol-util/input/event-offset.js +0 -1
- package/lib/mol-util/input/input-observer.js +0 -1
- package/lib/mol-util/is-little-endian.js +0 -1
- package/lib/mol-util/legend.js +0 -1
- package/lib/mol-util/log-entry.js +0 -1
- package/lib/mol-util/lru-cache.js +0 -1
- package/lib/mol-util/make-dir.js +0 -1
- package/lib/mol-util/map.js +0 -1
- package/lib/mol-util/marker-action.js +0 -1
- package/lib/mol-util/mask.js +0 -1
- package/lib/mol-util/material.js +0 -1
- package/lib/mol-util/memoize.js +0 -1
- package/lib/mol-util/monadic-parser.js +0 -1
- package/lib/mol-util/now.js +0 -1
- package/lib/mol-util/number-packing.js +0 -1
- package/lib/mol-util/number.js +0 -1
- package/lib/mol-util/object.js +0 -1
- package/lib/mol-util/param-definition.js +0 -1
- package/lib/mol-util/param-mapping.js +0 -1
- package/lib/mol-util/performance-monitor.js +0 -1
- package/lib/mol-util/polyfill.js +0 -1
- package/lib/mol-util/read.js +0 -1
- package/lib/mol-util/reference-cache.js +0 -1
- package/lib/mol-util/retry-if.js +0 -1
- package/lib/mol-util/rx-event-helper.js +0 -1
- package/lib/mol-util/set.js +0 -1
- package/lib/mol-util/sleep.js +0 -1
- package/lib/mol-util/string-builder.js +0 -1
- package/lib/mol-util/string.js +0 -1
- package/lib/mol-util/type-helpers.js +0 -1
- package/lib/mol-util/url.js +0 -1
- package/lib/mol-util/uuid.js +0 -1
- package/lib/mol-util/value-cell.js +0 -1
- package/lib/mol-util/zip/bin.js +0 -1
- package/lib/mol-util/zip/checksum.js +0 -1
- package/lib/mol-util/zip/deflate.js +2 -2
- package/lib/mol-util/zip/huffman.js +0 -1
- package/lib/mol-util/zip/inflate.js +0 -1
- package/lib/mol-util/zip/util.js +0 -1
- package/lib/mol-util/zip/zip.d.ts +7 -1
- package/lib/mol-util/zip/zip.js +5 -2
- package/lib/servers/common/file-handle.js +0 -1
- package/lib/servers/common/swagger-ui/index.js +0 -1
- package/lib/servers/common/swagger-ui/indexTemplate.js +0 -1
- package/lib/servers/common/util.js +0 -1
- package/lib/servers/model/config.d.ts +2 -2
- package/lib/servers/model/config.js +0 -1
- package/lib/servers/model/preprocess/converter.js +0 -1
- package/lib/servers/model/preprocess/master.js +0 -1
- package/lib/servers/model/preprocess/parallel.js +0 -1
- package/lib/servers/model/preprocess/preprocess.js +0 -1
- package/lib/servers/model/preprocess/util.js +0 -1
- package/lib/servers/model/preprocess.js +0 -1
- package/lib/servers/model/properties/pdbe.js +0 -1
- package/lib/servers/model/properties/providers/pdbe.js +0 -1
- package/lib/servers/model/properties/providers/wwpdb.js +0 -1
- package/lib/servers/model/properties/wwpdb.js +0 -1
- package/lib/servers/model/property-provider.js +0 -1
- package/lib/servers/model/query/atoms.js +0 -1
- package/lib/servers/model/query/schemas.js +0 -1
- package/lib/servers/model/query.js +0 -1
- package/lib/servers/model/server/api-local.js +0 -1
- package/lib/servers/model/server/api-schema.js +0 -1
- package/lib/servers/model/server/api-web-multiple.js +0 -1
- package/lib/servers/model/server/api-web.js +0 -1
- package/lib/servers/model/server/api.js +0 -1
- package/lib/servers/model/server/cache.js +0 -1
- package/lib/servers/model/server/jobs.js +0 -1
- package/lib/servers/model/server/query.js +0 -1
- package/lib/servers/model/server/structure-wrapper.js +0 -1
- package/lib/servers/model/server.js +0 -1
- package/lib/servers/model/test.js +0 -1
- package/lib/servers/model/utils/fetch-props-pdbe.js +0 -1
- package/lib/servers/model/utils/fetch-retry.js +0 -1
- package/lib/servers/model/utils/tar.js +0 -1
- package/lib/servers/model/utils/writer.js +0 -1
- package/lib/servers/model/version.js +0 -1
- package/lib/servers/plugin-state/api-schema.js +0 -1
- package/lib/servers/plugin-state/config.js +0 -1
- package/lib/servers/plugin-state/index.js +0 -1
- package/lib/servers/plugin-state/version.js +0 -1
- package/lib/servers/volume/common/binary-schema.js +0 -1
- package/lib/servers/volume/common/data-format.js +0 -1
- package/lib/servers/volume/common/file.js +0 -1
- package/lib/servers/volume/config.js +0 -1
- package/lib/servers/volume/pack/data-model.js +0 -1
- package/lib/servers/volume/pack/downsampling.js +0 -1
- package/lib/servers/volume/pack/format/ccp4.js +0 -1
- package/lib/servers/volume/pack/format/dsn6.js +0 -1
- package/lib/servers/volume/pack/format.js +0 -1
- package/lib/servers/volume/pack/main.js +0 -1
- package/lib/servers/volume/pack/sampling.js +0 -1
- package/lib/servers/volume/pack/version.js +0 -1
- package/lib/servers/volume/pack/writer.js +0 -1
- package/lib/servers/volume/pack.js +0 -1
- package/lib/servers/volume/query.js +0 -1
- package/lib/servers/volume/server/algebra/box.js +0 -1
- package/lib/servers/volume/server/algebra/coordinate.js +0 -1
- package/lib/servers/volume/server/api.js +0 -1
- package/lib/servers/volume/server/local-api.js +0 -1
- package/lib/servers/volume/server/query/compose.js +0 -1
- package/lib/servers/volume/server/query/data-model.js +0 -1
- package/lib/servers/volume/server/query/encode.js +0 -1
- package/lib/servers/volume/server/query/execute.js +0 -1
- package/lib/servers/volume/server/query/identify.js +0 -1
- package/lib/servers/volume/server/state.js +0 -1
- package/lib/servers/volume/server/version.js +0 -1
- package/lib/servers/volume/server/web-api.js +0 -1
- package/lib/servers/volume/server/web-schema.js +0 -1
- package/lib/servers/volume/server.js +0 -1
- package/package.json +160 -160
- package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -65
- package/lib/mol-plugin-state/formats/structure.js +0 -62
|
@@ -9,10 +9,10 @@ var jsx_runtime_1 = require("react/jsx-runtime");
|
|
|
9
9
|
* @author David Sehnal <david.sehnal@gmail.com>
|
|
10
10
|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
11
11
|
*/
|
|
12
|
-
var React =
|
|
12
|
+
var React = tslib_1.__importStar(require("react"));
|
|
13
13
|
var base_1 = require("../base");
|
|
14
14
|
var ViewportCanvas = /** @class */ (function (_super) {
|
|
15
|
-
|
|
15
|
+
tslib_1.__extends(ViewportCanvas, _super);
|
|
16
16
|
function ViewportCanvas() {
|
|
17
17
|
var _this = _super !== null && _super.apply(this, arguments) || this;
|
|
18
18
|
_this.container = React.createRef();
|
|
@@ -42,17 +42,16 @@ var ViewportCanvas = /** @class */ (function (_super) {
|
|
|
42
42
|
ViewportCanvas.prototype.renderMissing = function () {
|
|
43
43
|
if (this.props.noWebGl) {
|
|
44
44
|
var C = this.props.noWebGl;
|
|
45
|
-
return (0, jsx_runtime_1.jsx)(C, {}
|
|
45
|
+
return (0, jsx_runtime_1.jsx)(C, {});
|
|
46
46
|
}
|
|
47
|
-
return (0, jsx_runtime_1.jsx)("div",
|
|
47
|
+
return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-no-webgl' }, { children: (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("p", { children: (0, jsx_runtime_1.jsx)("b", { children: "WebGL does not seem to be available." }) }), (0, jsx_runtime_1.jsx)("p", { children: "This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps." }), (0, jsx_runtime_1.jsxs)("p", { children: ["For a list of supported browsers, refer to ", (0, jsx_runtime_1.jsx)("a", tslib_1.__assign({ href: 'http://caniuse.com/#feat=webgl', target: '_blank' }, { children: "http://caniuse.com/#feat=webgl" })), "."] })] }) }));
|
|
48
48
|
};
|
|
49
49
|
ViewportCanvas.prototype.render = function () {
|
|
50
50
|
if (this.state.noWebGl)
|
|
51
51
|
return this.renderMissing();
|
|
52
52
|
var Logo = this.props.logo;
|
|
53
|
-
return (0, jsx_runtime_1.jsxs)("div",
|
|
53
|
+
return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: this.props.parentClassName || 'msp-viewport', style: this.props.parentStyle }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: this.props.hostClassName || 'msp-viewport-host3d', style: this.props.hostStyle, ref: this.container }, { children: (0, jsx_runtime_1.jsx)("canvas", { ref: this.canvas }) })), (this.state.showLogo && Logo) && (0, jsx_runtime_1.jsx)(Logo, {})] }));
|
|
54
54
|
};
|
|
55
55
|
return ViewportCanvas;
|
|
56
56
|
}(base_1.PluginUIComponent));
|
|
57
57
|
exports.ViewportCanvas = ViewportCanvas;
|
|
58
|
-
//# sourceMappingURL=canvas.js.map
|
|
@@ -8,7 +8,7 @@ var jsx_runtime_1 = require("react/jsx-runtime");
|
|
|
8
8
|
*
|
|
9
9
|
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
10
10
|
*/
|
|
11
|
-
var React =
|
|
11
|
+
var React = tslib_1.__importStar(require("react"));
|
|
12
12
|
var binding_1 = require("../../mol-util/binding");
|
|
13
13
|
var base_1 = require("../base");
|
|
14
14
|
var mol_state_1 = require("../../mol-state");
|
|
@@ -20,7 +20,7 @@ function getBindingsList(bindings) {
|
|
|
20
20
|
return Object.keys(bindings).map(function (k) { return [k, bindings[k]]; });
|
|
21
21
|
}
|
|
22
22
|
var BindingsHelp = /** @class */ (function (_super) {
|
|
23
|
-
|
|
23
|
+
tslib_1.__extends(BindingsHelp, _super);
|
|
24
24
|
function BindingsHelp() {
|
|
25
25
|
return _super !== null && _super.apply(this, arguments) || this;
|
|
26
26
|
}
|
|
@@ -29,29 +29,29 @@ var BindingsHelp = /** @class */ (function (_super) {
|
|
|
29
29
|
return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: bindingsList.map(function (value) {
|
|
30
30
|
var name = value[0], binding = value[1];
|
|
31
31
|
return !binding_1.Binding.isEmpty(binding)
|
|
32
|
-
? (0, jsx_runtime_1.jsxs)("div",
|
|
32
|
+
? (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { marginBottom: '6px' } }, { children: [(0, jsx_runtime_1.jsx)("b", { children: binding.action }), (0, jsx_runtime_1.jsx)("br", {}), (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: binding_1.Binding.format(binding, name) } })] }), name)
|
|
33
33
|
: null;
|
|
34
|
-
}) }
|
|
34
|
+
}) });
|
|
35
35
|
};
|
|
36
36
|
BindingsHelp.prototype.render = function () {
|
|
37
|
-
return (0, jsx_runtime_1.jsx)(HelpText, { children: this.getBindingComponents() }
|
|
37
|
+
return (0, jsx_runtime_1.jsx)(HelpText, { children: this.getBindingComponents() });
|
|
38
38
|
};
|
|
39
39
|
return BindingsHelp;
|
|
40
40
|
}(React.PureComponent));
|
|
41
41
|
exports.BindingsHelp = BindingsHelp;
|
|
42
42
|
var HelpText = /** @class */ (function (_super) {
|
|
43
|
-
|
|
43
|
+
tslib_1.__extends(HelpText, _super);
|
|
44
44
|
function HelpText() {
|
|
45
45
|
return _super !== null && _super.apply(this, arguments) || this;
|
|
46
46
|
}
|
|
47
47
|
HelpText.prototype.render = function () {
|
|
48
|
-
return (0, jsx_runtime_1.jsx)("div",
|
|
48
|
+
return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-help-text' }, { children: (0, jsx_runtime_1.jsx)("div", { children: this.props.children }) }));
|
|
49
49
|
};
|
|
50
50
|
return HelpText;
|
|
51
51
|
}(React.PureComponent));
|
|
52
52
|
exports.HelpText = HelpText;
|
|
53
53
|
var HelpGroup = /** @class */ (function (_super) {
|
|
54
|
-
|
|
54
|
+
tslib_1.__extends(HelpGroup, _super);
|
|
55
55
|
function HelpGroup() {
|
|
56
56
|
var _this = _super !== null && _super.apply(this, arguments) || this;
|
|
57
57
|
_this.state = {
|
|
@@ -62,16 +62,16 @@ var HelpGroup = /** @class */ (function (_super) {
|
|
|
62
62
|
return _this;
|
|
63
63
|
}
|
|
64
64
|
HelpGroup.prototype.render = function () {
|
|
65
|
-
return (0, jsx_runtime_1.jsxs)("div",
|
|
65
|
+
return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-control-group-wrapper' }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-group-header' }, { children: (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ onClick: this.toggleExpanded }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg }), this.props.header] })) })), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset', style: { display: this.state.isExpanded ? 'block' : 'none' } }, { children: this.props.children }))] }));
|
|
66
66
|
};
|
|
67
67
|
return HelpGroup;
|
|
68
68
|
}(React.PureComponent));
|
|
69
69
|
exports.HelpGroup = HelpGroup;
|
|
70
70
|
function HelpSection(props) {
|
|
71
|
-
return (0, jsx_runtime_1.jsx)("div",
|
|
71
|
+
return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-simple-help-section' }, { children: props.header }));
|
|
72
72
|
}
|
|
73
73
|
var ViewportHelpContent = /** @class */ (function (_super) {
|
|
74
|
-
|
|
74
|
+
tslib_1.__extends(ViewportHelpContent, _super);
|
|
75
75
|
function ViewportHelpContent() {
|
|
76
76
|
return _super !== null && _super.apply(this, arguments) || this;
|
|
77
77
|
}
|
|
@@ -86,13 +86,13 @@ var ViewportHelpContent = /** @class */ (function (_super) {
|
|
|
86
86
|
if (bindings)
|
|
87
87
|
Object.assign(interactionBindings, bindings);
|
|
88
88
|
});
|
|
89
|
-
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(!this.props.selectOnly && this.plugin.canvas3d) && (0, jsx_runtime_1.jsx)(HelpGroup,
|
|
89
|
+
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(!this.props.selectOnly && this.plugin.canvas3d) && (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Moving in 3D' }, { children: (0, jsx_runtime_1.jsx)(BindingsHelp, { bindings: this.plugin.canvas3d.props.trackball.bindings }) }), 'trackball'), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Mouse Controls' }, { children: (0, jsx_runtime_1.jsx)(BindingsHelp, { bindings: interactionBindings }) }), 'interactions')] });
|
|
90
90
|
};
|
|
91
91
|
return ViewportHelpContent;
|
|
92
92
|
}(base_1.PluginUIComponent));
|
|
93
93
|
exports.ViewportHelpContent = ViewportHelpContent;
|
|
94
94
|
var HelpContent = /** @class */ (function (_super) {
|
|
95
|
-
|
|
95
|
+
tslib_1.__extends(HelpContent, _super);
|
|
96
96
|
function HelpContent() {
|
|
97
97
|
return _super !== null && _super.apply(this, arguments) || this;
|
|
98
98
|
}
|
|
@@ -115,9 +115,8 @@ var HelpContent = /** @class */ (function (_super) {
|
|
|
115
115
|
var selectToggleTriggers = this.getTriggerFor(representation_1.SelectLoci, 'clickSelectToggle');
|
|
116
116
|
var focusTriggers = this.getTriggerFor(representation_2.FocusLoci, 'clickFocus');
|
|
117
117
|
// TODO: interactive help, for example for density
|
|
118
|
-
return (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(HelpSection, { header: 'Interface Controls' }
|
|
118
|
+
return (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(HelpSection, { header: 'Interface Controls' }), (0, jsx_runtime_1.jsxs)(HelpGroup, tslib_1.__assign({ header: 'Inline Help' }, { children: [(0, jsx_runtime_1.jsx)(HelpText, { children: "Many user interface elements show a little questionmark icon when hovered over. Clicking the icon toggles the display of an inline help text." }), (0, jsx_runtime_1.jsx)(HelpText, { children: "Tooltips may provide additional information on a user interface element and are shown when hovering over it with the mouse." })] })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Selections' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["The viewer allows changing colors and representations for selections of atoms, residues or chains. Selections can be created by", (0, jsx_runtime_1.jsxs)("ul", tslib_1.__assign({ style: { paddingLeft: '20px' } }, { children: [(0, jsx_runtime_1.jsxs)("li", { children: ["picking elements on the 3D canvas or the sequence view using the mouse, e.g. toggle selection using ", selectToggleTriggers, " (for more see help section on ", (0, jsx_runtime_1.jsx)("i", { children: "Mouse Controls" }), ")"] }), (0, jsx_runtime_1.jsxs)("li", { children: ["using the ", (0, jsx_runtime_1.jsx)("i", { children: "Add" }), ", ", (0, jsx_runtime_1.jsx)("i", { children: "Remove" }), " and ", (0, jsx_runtime_1.jsx)("i", { children: "Only" }), " dropdown buttons in the ", (0, jsx_runtime_1.jsx)("i", { children: "Manage Selection" }), " panel which allow modifing the current selection by predefined sets"] })] }))] }) })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Coloring' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["There are two ways to color structures. Every representation (e.g. cartoon or spacefill) has a color theme which can be changed using the dropdown for each representation in the ", (0, jsx_runtime_1.jsx)("i", { children: "Structure Settings" }), " panel. Additionally any selection atoms, residues or chains can by given a custom color. For that, first select the parts of the structure to be colored (see help section on ", (0, jsx_runtime_1.jsx)("i", { children: "Selections" }), ") and, second, choose a color from the color dropdown botton in the ", (0, jsx_runtime_1.jsx)("i", { children: "Selection" }), " row of the ", (0, jsx_runtime_1.jsx)("i", { children: "Change Representation" }), " panel. The theme color can be seen as a base color that is overpainted by the custom color. Custom colors can be removed for a selection with the 'Clear' option in the color dropdown."] }) })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Representations' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["Structures can be shown with many different representations (e.g. cartoon or spacefill). The ", (0, jsx_runtime_1.jsx)("i", { children: "Change Representation" }), " panel offers a collection of predefined styles which can be applied using the ", (0, jsx_runtime_1.jsx)("i", { children: "Preset" }), " dropdown button. Additionally any selection atoms, residues or chains can by shown with a custom representation. For that, first select the parts of the structure to be mofified (see help section on ", (0, jsx_runtime_1.jsx)("i", { children: "Selections" }), ") and, second, choose a representation to hide or show from the ", (0, jsx_runtime_1.jsx)("i", { children: "Show" }), " and ", (0, jsx_runtime_1.jsx)("i", { children: "Hide" }), " dropdown bottons in the ", (0, jsx_runtime_1.jsx)("i", { children: "Selection" }), " row of the ", (0, jsx_runtime_1.jsx)("i", { children: "Change Representation" }), " panel. The ", (0, jsx_runtime_1.jsx)("i", { children: "Everything" }), " row applies the action to the whole structure instead of the current selection."] }) })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Surroundings' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["To show the surroundings of a residue or ligand, click it in the 3D scene or in the sequence widget using ", focusTriggers, "."] }) })), (0, jsx_runtime_1.jsx)(HelpSection, { header: 'How-to Guides' }), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Create an Image' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: [(0, jsx_runtime_1.jsxs)("p", { children: ["Use the ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CameraSvg }), " icon in the viewport to bring up the screenshot controls."] }), (0, jsx_runtime_1.jsxs)("p", { children: ["To adjust the size of the image, use the ", (0, jsx_runtime_1.jsx)("i", { children: "Resolution" }), " dropdown."] })] }) })), (0, jsx_runtime_1.jsx)(HelpSection, { header: 'Mouse Controls' }), (0, jsx_runtime_1.jsx)(ViewportHelpContent, {})] });
|
|
119
119
|
};
|
|
120
120
|
return HelpContent;
|
|
121
121
|
}(base_1.PluginUIComponent));
|
|
122
122
|
exports.HelpContent = HelpContent;
|
|
123
|
-
//# sourceMappingURL=help.js.map
|
|
@@ -12,7 +12,7 @@ var screenshot_1 = require("../controls/screenshot");
|
|
|
12
12
|
var use_behavior_1 = require("../hooks/use-behavior");
|
|
13
13
|
var snapshots_1 = require("../state/snapshots");
|
|
14
14
|
var DownloadScreenshotControls = /** @class */ (function (_super) {
|
|
15
|
-
|
|
15
|
+
tslib_1.__extends(DownloadScreenshotControls, _super);
|
|
16
16
|
function DownloadScreenshotControls() {
|
|
17
17
|
var _this = _super !== null && _super.apply(this, arguments) || this;
|
|
18
18
|
_this.state = {
|
|
@@ -24,10 +24,10 @@ var DownloadScreenshotControls = /** @class */ (function (_super) {
|
|
|
24
24
|
(_a = _this.plugin.helpers.viewportScreenshot) === null || _a === void 0 ? void 0 : _a.download();
|
|
25
25
|
_this.props.close();
|
|
26
26
|
};
|
|
27
|
-
_this.copy = function () { return
|
|
27
|
+
_this.copy = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
28
28
|
var _a;
|
|
29
29
|
var _b;
|
|
30
|
-
return
|
|
30
|
+
return tslib_1.__generator(this, function (_c) {
|
|
31
31
|
switch (_c.label) {
|
|
32
32
|
case 0:
|
|
33
33
|
_c.trys.push([0, 2, , 3]);
|
|
@@ -47,10 +47,10 @@ var DownloadScreenshotControls = /** @class */ (function (_super) {
|
|
|
47
47
|
}
|
|
48
48
|
});
|
|
49
49
|
}); };
|
|
50
|
-
_this.copyImg = function () { return
|
|
50
|
+
_this.copyImg = function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
51
51
|
var src;
|
|
52
52
|
var _a;
|
|
53
|
-
return
|
|
53
|
+
return tslib_1.__generator(this, function (_b) {
|
|
54
54
|
switch (_b.label) {
|
|
55
55
|
case 0: return [4 /*yield*/, ((_a = this.plugin.helpers.viewportScreenshot) === null || _a === void 0 ? void 0 : _a.getImageDataUri())];
|
|
56
56
|
case 1:
|
|
@@ -80,7 +80,7 @@ var DownloadScreenshotControls = /** @class */ (function (_super) {
|
|
|
80
80
|
var _this = this;
|
|
81
81
|
var _a;
|
|
82
82
|
var hasClipboardApi = !!((_a = navigator.clipboard) === null || _a === void 0 ? void 0 : _a.write);
|
|
83
|
-
return (0, jsx_runtime_1.jsxs)("div", { children: [this.state.showPreview && (0, jsx_runtime_1.jsxs)("div",
|
|
83
|
+
return (0, jsx_runtime_1.jsxs)("div", { children: [this.state.showPreview && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-image-preview' }, { children: [(0, jsx_runtime_1.jsx)(screenshot_1.ScreenshotPreview, { plugin: this.plugin }), (0, jsx_runtime_1.jsx)(CropControls, { plugin: this.plugin })] })), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [!this.state.imageData && (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.CopySvg, onClick: hasClipboardApi ? this.copy : this.copyImg, disabled: this.state.isDisabled }, { children: "Copy" })), this.state.imageData && (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: function () { return _this.setState({ imageData: void 0 }); }, disabled: this.state.isDisabled }, { children: "Clear" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.GetAppSvg, onClick: this.download, disabled: this.state.isDisabled }, { children: "Download" }))] })), this.state.imageData && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-row msp-copy-image-wrapper' }, { children: [(0, jsx_runtime_1.jsx)("div", { children: "Right click below + Copy Image" }), (0, jsx_runtime_1.jsx)("img", { src: this.state.imageData, style: { width: '100%', height: 32, display: 'block' } })] })), (0, jsx_runtime_1.jsx)(ScreenshotParams, { plugin: this.plugin, isDisabled: this.state.isDisabled }), (0, jsx_runtime_1.jsxs)(common_1.ExpandGroup, tslib_1.__assign({ header: 'State' }, { children: [(0, jsx_runtime_1.jsx)(snapshots_1.StateExportImportControls, { onAction: this.props.close }), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: 'Save Options', initiallyExpanded: false, noOffset: true }, { children: (0, jsx_runtime_1.jsx)(snapshots_1.LocalStateSnapshotParams, {}) }))] }))] });
|
|
84
84
|
};
|
|
85
85
|
return DownloadScreenshotControls;
|
|
86
86
|
}(base_1.PluginUIComponent));
|
|
@@ -89,7 +89,7 @@ function ScreenshotParams(_a) {
|
|
|
89
89
|
var plugin = _a.plugin, isDisabled = _a.isDisabled;
|
|
90
90
|
var helper = plugin.helpers.viewportScreenshot;
|
|
91
91
|
var values = (0, use_behavior_1.useBehavior)(helper.behaviors.values);
|
|
92
|
-
return (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: helper.params, values: values, onChangeValues: function (v) { return helper.behaviors.values.next(v); }, isDisabled: isDisabled }
|
|
92
|
+
return (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: helper.params, values: values, onChangeValues: function (v) { return helper.behaviors.values.next(v); }, isDisabled: isDisabled });
|
|
93
93
|
}
|
|
94
94
|
function CropControls(_a) {
|
|
95
95
|
var plugin = _a.plugin;
|
|
@@ -98,6 +98,5 @@ function CropControls(_a) {
|
|
|
98
98
|
(0, use_behavior_1.useBehavior)(helper === null || helper === void 0 ? void 0 : helper.behaviors.relativeCrop);
|
|
99
99
|
if (!helper)
|
|
100
100
|
return null;
|
|
101
|
-
return (0, jsx_runtime_1.jsxs)("div",
|
|
101
|
+
return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { width: '100%', height: '24px', marginTop: '8px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.CropOrginalSvg, title: 'Auto-crop', inline: true, isSelected: cropParams.auto, style: { background: 'transparent', float: 'left', width: 'auto', height: '24px', lineHeight: '24px' }, toggle: function () { return helper.toggleAutocrop(); }, label: 'Auto-crop ' + (cropParams.auto ? 'On' : 'Off') }), !cropParams.auto && (0, jsx_runtime_1.jsx)(common_1.Button, { icon: icons_1.CropSvg, title: 'Crop', style: { background: 'transparent', float: 'right', height: '24px', lineHeight: '24px', width: '24px', padding: '0' }, onClick: function () { return helper.autocrop(); } }), !cropParams.auto && !helper.isFullFrame && (0, jsx_runtime_1.jsx)(common_1.Button, { icon: icons_1.CropFreeSvg, title: 'Reset Crop', style: { background: 'transparent', float: 'right', height: '24px', lineHeight: '24px', width: '24px', padding: '0' }, onClick: function () { return helper.resetCrop(); } })] }));
|
|
102
102
|
}
|
|
103
|
-
//# sourceMappingURL=screenshot.js.map
|
|
@@ -20,7 +20,7 @@ var base_1 = require("../base");
|
|
|
20
20
|
var parameters_1 = require("../controls/parameters");
|
|
21
21
|
var help_1 = require("./help");
|
|
22
22
|
var SimpleSettingsControl = /** @class */ (function (_super) {
|
|
23
|
-
|
|
23
|
+
tslib_1.__extends(SimpleSettingsControl, _super);
|
|
24
24
|
function SimpleSettingsControl() {
|
|
25
25
|
return _super !== null && _super.apply(this, arguments) || this;
|
|
26
26
|
}
|
|
@@ -36,7 +36,7 @@ var SimpleSettingsControl = /** @class */ (function (_super) {
|
|
|
36
36
|
SimpleSettingsControl.prototype.render = function () {
|
|
37
37
|
if (!this.plugin.canvas3d)
|
|
38
38
|
return null;
|
|
39
|
-
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterMappingControl, { mapping: SimpleSettingsMapping }
|
|
39
|
+
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterMappingControl, { mapping: SimpleSettingsMapping }), (0, jsx_runtime_1.jsx)(help_1.ViewportHelpContent, {})] });
|
|
40
40
|
};
|
|
41
41
|
return SimpleSettingsControl;
|
|
42
42
|
}(base_1.PluginUIComponent));
|
|
@@ -58,7 +58,7 @@ var SimpleSettingsParams = {
|
|
|
58
58
|
outline: canvas3d_1.Canvas3DParams.postprocessing.params.outline,
|
|
59
59
|
fog: canvas3d_1.Canvas3DParams.cameraFog,
|
|
60
60
|
}, { isFlat: true }),
|
|
61
|
-
clipping: param_definition_1.ParamDefinition.Group(
|
|
61
|
+
clipping: param_definition_1.ParamDefinition.Group(tslib_1.__assign({}, canvas3d_1.Canvas3DParams.cameraClipping.params), { pivot: 'radius' }),
|
|
62
62
|
layout: param_definition_1.ParamDefinition.MultiSelect([], param_definition_1.ParamDefinition.objectToOptions(LayoutOptions)),
|
|
63
63
|
};
|
|
64
64
|
var SimpleSettingsMapping = (0, param_mapping_1.ParamMapping)({
|
|
@@ -108,7 +108,7 @@ var SimpleSettingsMapping = (0, param_mapping_1.ParamMapping)({
|
|
|
108
108
|
outline: canvas.postprocessing.outline,
|
|
109
109
|
fog: canvas.cameraFog,
|
|
110
110
|
},
|
|
111
|
-
clipping:
|
|
111
|
+
clipping: tslib_1.__assign({}, canvas.cameraClipping)
|
|
112
112
|
};
|
|
113
113
|
},
|
|
114
114
|
update: function (s, props) {
|
|
@@ -127,9 +127,9 @@ var SimpleSettingsMapping = (0, param_mapping_1.ParamMapping)({
|
|
|
127
127
|
props.layout = s.layout;
|
|
128
128
|
},
|
|
129
129
|
apply: function (props, ctx) {
|
|
130
|
-
return
|
|
130
|
+
return tslib_1.__awaiter(this, void 0, void 0, function () {
|
|
131
131
|
var hideLeft, state;
|
|
132
|
-
return
|
|
132
|
+
return tslib_1.__generator(this, function (_a) {
|
|
133
133
|
switch (_a.label) {
|
|
134
134
|
case 0: return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(ctx, { settings: props.canvas })];
|
|
135
135
|
case 1:
|
|
@@ -152,4 +152,3 @@ var SimpleSettingsMapping = (0, param_mapping_1.ParamMapping)({
|
|
|
152
152
|
});
|
|
153
153
|
}
|
|
154
154
|
});
|
|
155
|
-
//# sourceMappingURL=simple-settings.js.map
|
|
@@ -13,14 +13,14 @@ var canvas_1 = require("./viewport/canvas");
|
|
|
13
13
|
var screenshot_1 = require("./viewport/screenshot");
|
|
14
14
|
var simple_settings_1 = require("./viewport/simple-settings");
|
|
15
15
|
var ViewportControls = /** @class */ (function (_super) {
|
|
16
|
-
|
|
16
|
+
tslib_1.__extends(ViewportControls, _super);
|
|
17
17
|
function ViewportControls() {
|
|
18
18
|
var _this = _super !== null && _super.apply(this, arguments) || this;
|
|
19
19
|
_this.allCollapsedState = {
|
|
20
20
|
isSettingsExpanded: false,
|
|
21
21
|
isScreenshotExpanded: false
|
|
22
22
|
};
|
|
23
|
-
_this.state =
|
|
23
|
+
_this.state = tslib_1.__assign({}, _this.allCollapsedState);
|
|
24
24
|
_this.resetCamera = function () {
|
|
25
25
|
commands_1.PluginCommands.Camera.Reset(_this.plugin, {});
|
|
26
26
|
};
|
|
@@ -55,7 +55,7 @@ var ViewportControls = /** @class */ (function (_super) {
|
|
|
55
55
|
var _this = this;
|
|
56
56
|
return function (e) {
|
|
57
57
|
var _a;
|
|
58
|
-
_this.setState(
|
|
58
|
+
_this.setState(tslib_1.__assign(tslib_1.__assign({}, _this.allCollapsedState), (_a = {}, _a[panel] = !_this.state[panel], _a)));
|
|
59
59
|
e === null || e === void 0 ? void 0 : e.currentTarget.blur();
|
|
60
60
|
};
|
|
61
61
|
};
|
|
@@ -66,18 +66,17 @@ var ViewportControls = /** @class */ (function (_super) {
|
|
|
66
66
|
};
|
|
67
67
|
ViewportControls.prototype.icon = function (icon, onClick, title, isOn) {
|
|
68
68
|
if (isOn === void 0) { isOn = true; }
|
|
69
|
-
return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icon, toggleState: isOn, onClick: onClick, title: title, style: { background: 'transparent' } }
|
|
69
|
+
return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icon, toggleState: isOn, onClick: onClick, title: title, style: { background: 'transparent' } });
|
|
70
70
|
};
|
|
71
71
|
ViewportControls.prototype.render = function () {
|
|
72
|
-
return (0, jsx_runtime_1.jsxs)("div",
|
|
72
|
+
return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-viewport-controls', onMouseMove: this.onMouseMove }, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-viewport-controls-buttons' }, { children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-semi-transparent-background' }), this.icon(icons_1.AutorenewSvg, this.resetCamera, 'Reset Camera')] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-semi-transparent-background' }), this.icon(icons_1.CameraOutlinedSvg, this.toggleScreenshotExpanded, 'Screenshot / State Snapshot', this.state.isScreenshotExpanded)] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-semi-transparent-background' }), this.plugin.config.get(config_1.PluginConfig.Viewport.ShowControls) && this.icon(icons_1.BuildOutlinedSvg, this.toggleControls, 'Toggle Controls Panel', this.plugin.layout.state.showControls), this.plugin.config.get(config_1.PluginConfig.Viewport.ShowExpand) && this.icon(icons_1.FullscreenSvg, this.toggleExpanded, 'Toggle Expanded Viewport', this.plugin.layout.state.isExpanded), this.plugin.config.get(config_1.PluginConfig.Viewport.ShowSettings) && this.icon(icons_1.TuneSvg, this.toggleSettingsExpanded, 'Settings / Controls Info', this.state.isSettingsExpanded)] }), this.plugin.config.get(config_1.PluginConfig.Viewport.ShowSelectionMode) && (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-semi-transparent-background' }), (0, jsx_runtime_1.jsx)(selection_1.ToggleSelectionModeButton, {})] })] })), this.state.isScreenshotExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-viewport-controls-panel' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, tslib_1.__assign({ header: 'Screenshot / State', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleScreenshotExpanded, topRightIcon: icons_1.CloseSvg, noTopMargin: true, childrenClassName: 'msp-viewport-controls-panel-controls' }, { children: (0, jsx_runtime_1.jsx)(screenshot_1.DownloadScreenshotControls, { close: this.toggleScreenshotExpanded }) })) })), this.state.isSettingsExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-viewport-controls-panel' }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlGroup, tslib_1.__assign({ header: 'Settings / Controls Info', title: 'Click to close.', initialExpanded: true, hideExpander: true, hideOffset: true, onHeaderClick: this.toggleSettingsExpanded, topRightIcon: icons_1.CloseSvg, noTopMargin: true, childrenClassName: 'msp-viewport-controls-panel-controls' }, { children: (0, jsx_runtime_1.jsx)(simple_settings_1.SimpleSettingsControl, {}) })) }))] }));
|
|
73
73
|
};
|
|
74
74
|
return ViewportControls;
|
|
75
75
|
}(base_1.PluginUIComponent));
|
|
76
76
|
exports.ViewportControls = ViewportControls;
|
|
77
77
|
var Logo = function () {
|
|
78
|
-
return (0, jsx_runtime_1.jsx)("a", { className: 'msp-logo', href: 'https://molstar.org', target: '_blank' }
|
|
78
|
+
return (0, jsx_runtime_1.jsx)("a", { className: 'msp-logo', href: 'https://molstar.org', target: '_blank' });
|
|
79
79
|
};
|
|
80
80
|
exports.Logo = Logo;
|
|
81
|
-
var Viewport = function () { return (0, jsx_runtime_1.jsx)(canvas_1.ViewportCanvas, { logo: exports.Logo }
|
|
81
|
+
var Viewport = function () { return (0, jsx_runtime_1.jsx)(canvas_1.ViewportCanvas, { logo: exports.Logo }); };
|
|
82
82
|
exports.Viewport = Viewport;
|
|
83
|
-
//# sourceMappingURL=viewport.js.map
|
|
@@ -242,9 +242,9 @@ var Representation;
|
|
|
242
242
|
var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, currentProps, props), currentData);
|
|
243
243
|
Object.assign(currentProps, props, qualityProps);
|
|
244
244
|
var visuals = currentProps.visuals;
|
|
245
|
-
return mol_task_1.Task.create("Creating or updating '".concat(label, "' representation"), function (runtime) { return
|
|
245
|
+
return mol_task_1.Task.create("Creating or updating '".concat(label, "' representation"), function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
246
246
|
var i, il;
|
|
247
|
-
return
|
|
247
|
+
return tslib_1.__generator(this, function (_a) {
|
|
248
248
|
switch (_a.label) {
|
|
249
249
|
case 0:
|
|
250
250
|
i = 0, il = reprList.length;
|
|
@@ -331,8 +331,8 @@ var Representation;
|
|
|
331
331
|
if (props === void 0) { props = {}; }
|
|
332
332
|
var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, currentProps, props));
|
|
333
333
|
Object.assign(currentProps, props, qualityProps);
|
|
334
|
-
return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return
|
|
335
|
-
return
|
|
334
|
+
return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
335
|
+
return tslib_1.__generator(this, function (_a) {
|
|
336
336
|
// TODO
|
|
337
337
|
geometryState.add(0, renderObject.id);
|
|
338
338
|
geometryState.snapshot();
|
|
@@ -380,4 +380,3 @@ var Representation;
|
|
|
380
380
|
Representation.fromRenderObject = fromRenderObject;
|
|
381
381
|
})(Representation || (Representation = {}));
|
|
382
382
|
exports.Representation = Representation;
|
|
383
|
-
//# sourceMappingURL=representation.js.map
|
|
@@ -31,17 +31,17 @@ var SharedParams = {
|
|
|
31
31
|
color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
|
|
32
32
|
arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
|
|
33
33
|
};
|
|
34
|
-
var LinesParams =
|
|
35
|
-
var VectorsParams =
|
|
36
|
-
var ArcParams =
|
|
37
|
-
var SectorParams =
|
|
34
|
+
var LinesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
35
|
+
var VectorsParams = tslib_1.__assign({}, LinesParams);
|
|
36
|
+
var ArcParams = tslib_1.__assign({}, LinesParams);
|
|
37
|
+
var SectorParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { ignoreLight: param_definition_1.ParamDefinition.Boolean(true), sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }) });
|
|
38
38
|
var AngleVisuals = {
|
|
39
|
-
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
40
|
-
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
41
|
-
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (
|
|
42
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
39
|
+
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
40
|
+
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
41
|
+
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity })); }, modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
42
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
43
43
|
};
|
|
44
|
-
exports.AngleParams =
|
|
44
|
+
exports.AngleParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, VectorsParams), ArcParams), SectorParams), common_1.LociLabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['vectors', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(AngleVisuals)) });
|
|
45
45
|
//
|
|
46
46
|
function getAngleState() {
|
|
47
47
|
return {
|
|
@@ -173,4 +173,3 @@ function AngleRepresentation(ctx, getParams) {
|
|
|
173
173
|
return representation_2.Representation.createMulti('Angle', ctx, getParams, representation_2.Representation.StateBuilder, AngleVisuals);
|
|
174
174
|
}
|
|
175
175
|
exports.AngleRepresentation = AngleRepresentation;
|
|
176
|
-
//# sourceMappingURL=angle.js.map
|
|
@@ -16,5 +16,4 @@ exports.MeasurementRepresentationCommonTextParams = {
|
|
|
16
16
|
textColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black, { isEssential: true }),
|
|
17
17
|
textSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
|
|
18
18
|
};
|
|
19
|
-
exports.LociLabelTextParams =
|
|
20
|
-
//# sourceMappingURL=common.js.map
|
|
19
|
+
exports.LociLabelTextParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, text_1.Text.Params), exports.MeasurementRepresentationCommonTextParams), { borderWidth: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 0.5, step: 0.01 }) });
|
|
@@ -31,22 +31,22 @@ var SharedParams = {
|
|
|
31
31
|
color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
|
|
32
32
|
arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
|
|
33
33
|
};
|
|
34
|
-
var LinesParams =
|
|
35
|
-
var VectorsParams =
|
|
36
|
-
var ExtendersParams =
|
|
37
|
-
var ArmsParams =
|
|
38
|
-
var ArcParams =
|
|
39
|
-
var SectorParams =
|
|
34
|
+
var LinesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
35
|
+
var VectorsParams = tslib_1.__assign({}, LinesParams);
|
|
36
|
+
var ExtendersParams = tslib_1.__assign({}, LinesParams);
|
|
37
|
+
var ArmsParams = tslib_1.__assign({}, LinesParams);
|
|
38
|
+
var ArcParams = tslib_1.__assign({}, LinesParams);
|
|
39
|
+
var SectorParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { ignoreLight: param_definition_1.ParamDefinition.Boolean(true), sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }) });
|
|
40
40
|
var DihedralVisuals = {
|
|
41
|
-
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
42
|
-
'extenders': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
43
|
-
'connector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
44
|
-
'arms': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
45
|
-
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
46
|
-
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (
|
|
47
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
41
|
+
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
42
|
+
'extenders': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
43
|
+
'connector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
44
|
+
'arms': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
45
|
+
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
46
|
+
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity })); }, modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
47
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
48
48
|
};
|
|
49
|
-
exports.DihedralParams =
|
|
49
|
+
exports.DihedralParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, VectorsParams), ExtendersParams), ArmsParams), ArcParams), SectorParams), common_1.LociLabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['extenders', 'arms', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(DihedralVisuals)) });
|
|
50
50
|
//
|
|
51
51
|
function getDihedralState() {
|
|
52
52
|
return {
|
|
@@ -254,4 +254,3 @@ function DihedralRepresentation(ctx, getParams) {
|
|
|
254
254
|
return representation_2.Representation.createMulti('Dihedral', ctx, getParams, representation_2.Representation.StateBuilder, DihedralVisuals);
|
|
255
255
|
}
|
|
256
256
|
exports.DihedralRepresentation = DihedralRepresentation;
|
|
257
|
-
//# sourceMappingURL=dihedral.js.map
|
|
@@ -25,13 +25,13 @@ var geometry_1 = require("../../../mol-math/geometry");
|
|
|
25
25
|
var SharedParams = {
|
|
26
26
|
unitLabel: param_definition_1.ParamDefinition.Text('\u212B', { isEssential: true })
|
|
27
27
|
};
|
|
28
|
-
var LineParams =
|
|
29
|
-
var TextParams =
|
|
28
|
+
var LineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen, { isEssential: true }), linesSize: param_definition_1.ParamDefinition.Numeric(0.075, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
29
|
+
var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), SharedParams);
|
|
30
30
|
var DistanceVisuals = {
|
|
31
|
-
'lines': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getLinesShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
32
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
31
|
+
'lines': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getLinesShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
32
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
33
33
|
};
|
|
34
|
-
exports.DistanceParams =
|
|
34
|
+
exports.DistanceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, LineParams), TextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['lines', 'text'], param_definition_1.ParamDefinition.objectToOptions(DistanceVisuals)) });
|
|
35
35
|
//
|
|
36
36
|
function getDistanceState() {
|
|
37
37
|
return {
|
|
@@ -93,4 +93,3 @@ function DistanceRepresentation(ctx, getParams) {
|
|
|
93
93
|
return representation_2.Representation.createMulti('Distance', ctx, getParams, representation_2.Representation.StateBuilder, DistanceVisuals);
|
|
94
94
|
}
|
|
95
95
|
exports.DistanceRepresentation = DistanceRepresentation;
|
|
96
|
-
//# sourceMappingURL=distance.js.map
|
|
@@ -17,11 +17,11 @@ var text_builder_1 = require("../../../mol-geo/geometry/text/text-builder");
|
|
|
17
17
|
var geometry_1 = require("../../../mol-math/geometry");
|
|
18
18
|
var label_1 = require("../../../mol-theme/label");
|
|
19
19
|
var common_1 = require("./common");
|
|
20
|
-
var TextParams =
|
|
20
|
+
var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), { offsetZ: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }) });
|
|
21
21
|
var LabelVisuals = {
|
|
22
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
22
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
23
23
|
};
|
|
24
|
-
exports.LabelParams =
|
|
24
|
+
exports.LabelParams = tslib_1.__assign(tslib_1.__assign({}, TextParams), { scaleByRadius: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['text'], param_definition_1.ParamDefinition.objectToOptions(LabelVisuals)) });
|
|
25
25
|
//
|
|
26
26
|
var tmpSphere = (0, geometry_1.Sphere3D)();
|
|
27
27
|
function label(info, condensed) {
|
|
@@ -62,4 +62,3 @@ function LabelRepresentation(ctx, getParams) {
|
|
|
62
62
|
return representation_2.Representation.createMulti('Label', ctx, getParams, representation_2.Representation.StateBuilder, LabelVisuals);
|
|
63
63
|
}
|
|
64
64
|
exports.LabelRepresentation = LabelRepresentation;
|
|
65
|
-
//# sourceMappingURL=label.js.map
|
|
@@ -27,15 +27,15 @@ var SharedParams = {
|
|
|
27
27
|
scaleFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
|
|
28
28
|
radiusScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 10, step: 0.1 })
|
|
29
29
|
};
|
|
30
|
-
var AxesParams =
|
|
31
|
-
var BoxParams =
|
|
32
|
-
var EllipsoidParams =
|
|
30
|
+
var AxesParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams);
|
|
31
|
+
var BoxParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams);
|
|
32
|
+
var EllipsoidParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams);
|
|
33
33
|
var OrientationVisuals = {
|
|
34
34
|
'axes': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getAxesShape, mesh_1.Mesh.Utils); },
|
|
35
35
|
'box': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getBoxShape, mesh_1.Mesh.Utils); },
|
|
36
36
|
'ellipsoid': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getEllipsoidShape, mesh_1.Mesh.Utils); },
|
|
37
37
|
};
|
|
38
|
-
exports.OrientationParams =
|
|
38
|
+
exports.OrientationParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, AxesParams), BoxParams), EllipsoidParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['box'], param_definition_1.ParamDefinition.objectToOptions(OrientationVisuals)) });
|
|
39
39
|
//
|
|
40
40
|
function getAxesName(locis) {
|
|
41
41
|
var label = (0, label_1.structureElementLociLabelMany)(locis, { countsOnly: true });
|
|
@@ -100,4 +100,3 @@ function OrientationRepresentation(ctx, getParams) {
|
|
|
100
100
|
return repr;
|
|
101
101
|
}
|
|
102
102
|
exports.OrientationRepresentation = OrientationRepresentation;
|
|
103
|
-
//# sourceMappingURL=orientation.js.map
|
|
@@ -20,11 +20,11 @@ var marker_action_1 = require("../../../mol-util/marker-action");
|
|
|
20
20
|
var plane_1 = require("../../../mol-geo/primitive/plane");
|
|
21
21
|
var structure_1 = require("../../../mol-model/structure");
|
|
22
22
|
var geometry_1 = require("../../../mol-math/geometry");
|
|
23
|
-
var _PlaneParams =
|
|
23
|
+
var _PlaneParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), scaleFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 10, step: 0.1 }) });
|
|
24
24
|
var PlaneVisuals = {
|
|
25
25
|
'plane': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getPlaneShape, mesh_1.Mesh.Utils); },
|
|
26
26
|
};
|
|
27
|
-
exports.PlaneParams =
|
|
27
|
+
exports.PlaneParams = tslib_1.__assign(tslib_1.__assign({}, _PlaneParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['plane'], param_definition_1.ParamDefinition.objectToOptions(PlaneVisuals)) });
|
|
28
28
|
//
|
|
29
29
|
function getPlaneName(locis) {
|
|
30
30
|
var label = (0, label_1.structureElementLociLabelMany)(locis, { countsOnly: true });
|
|
@@ -58,4 +58,3 @@ function PlaneRepresentation(ctx, getParams) {
|
|
|
58
58
|
return repr;
|
|
59
59
|
}
|
|
60
60
|
exports.PlaneRepresentation = PlaneRepresentation;
|
|
61
|
-
//# sourceMappingURL=plane.js.map
|
|
@@ -31,11 +31,11 @@ var CellAttachment = {
|
|
|
31
31
|
corner: 'Corner',
|
|
32
32
|
center: 'Center'
|
|
33
33
|
};
|
|
34
|
-
var CellParams =
|
|
34
|
+
var CellParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { cellColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), cellScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), ref: param_definition_1.ParamDefinition.Select('model', param_definition_1.ParamDefinition.objectToOptions(CellRef), { isEssential: true }), attachment: param_definition_1.ParamDefinition.Select('corner', param_definition_1.ParamDefinition.objectToOptions(CellAttachment), { isEssential: true }) });
|
|
35
35
|
var UnitcellVisuals = {
|
|
36
36
|
'mesh': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getUnitcellShape, mesh_1.Mesh.Utils); },
|
|
37
37
|
};
|
|
38
|
-
exports.UnitcellParams =
|
|
38
|
+
exports.UnitcellParams = tslib_1.__assign({}, CellParams);
|
|
39
39
|
function getUnitcellMesh(data, props, mesh) {
|
|
40
40
|
var state = mesh_builder_1.MeshBuilder.createState(256, 128, mesh);
|
|
41
41
|
var fromFractional = data.symmetry.spacegroup.cell.fromFractional;
|
|
@@ -78,4 +78,3 @@ function UnitcellRepresentation(ctx, getParams) {
|
|
|
78
78
|
return representation_2.Representation.createMulti('Unit Cell', ctx, getParams, representation_2.Representation.StateBuilder, UnitcellVisuals);
|
|
79
79
|
}
|
|
80
80
|
exports.UnitcellRepresentation = UnitcellRepresentation;
|
|
81
|
-
//# sourceMappingURL=unitcell.js.map
|