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
|
@@ -87,10 +87,10 @@ var StructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
87
87
|
apply: function (_a, plugin) {
|
|
88
88
|
var _this = this;
|
|
89
89
|
var a = _a.a, params = _a.params, cache = _a.cache;
|
|
90
|
-
return mol_task_1.Task.create('Structure Representation', function (ctx) { return
|
|
90
|
+
return mol_task_1.Task.create('Structure Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
91
91
|
var propertyCtx, provider, data, repr, props;
|
|
92
92
|
var _a, _b;
|
|
93
|
-
return
|
|
93
|
+
return tslib_1.__generator(this, function (_c) {
|
|
94
94
|
switch (_c.label) {
|
|
95
95
|
case 0:
|
|
96
96
|
propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
|
|
@@ -102,7 +102,7 @@ var StructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
102
102
|
_c.sent();
|
|
103
103
|
_c.label = 2;
|
|
104
104
|
case 2:
|
|
105
|
-
repr = provider.factory(
|
|
105
|
+
repr = provider.factory(tslib_1.__assign({ webgl: (_b = plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.webgl }, plugin.representation.structure.themes), provider.getParams);
|
|
106
106
|
return [4 /*yield*/, theme_1.Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: data }, params)];
|
|
107
107
|
case 3:
|
|
108
108
|
_c.sent();
|
|
@@ -119,10 +119,10 @@ var StructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
119
119
|
update: function (_a, plugin) {
|
|
120
120
|
var _this = this;
|
|
121
121
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams, cache = _a.cache;
|
|
122
|
-
return mol_task_1.Task.create('Structure Representation', function (ctx) { return
|
|
122
|
+
return mol_task_1.Task.create('Structure Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
123
123
|
var provider, data, propertyCtx, props;
|
|
124
124
|
var _a, _b;
|
|
125
|
-
return
|
|
125
|
+
return tslib_1.__generator(this, function (_c) {
|
|
126
126
|
switch (_c.label) {
|
|
127
127
|
case 0:
|
|
128
128
|
if (newParams.type.name !== oldParams.type.name)
|
|
@@ -145,7 +145,7 @@ var StructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
145
145
|
case 3:
|
|
146
146
|
_c.sent();
|
|
147
147
|
b.data.repr.setTheme(theme_1.Theme.create(plugin.representation.structure.themes, { structure: data }, newParams));
|
|
148
|
-
props =
|
|
148
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams.type.params);
|
|
149
149
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
150
150
|
case 4:
|
|
151
151
|
_c.sent();
|
|
@@ -262,7 +262,7 @@ var SpinStructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
262
262
|
display: 'Spin 3D Representation',
|
|
263
263
|
from: objects_1.PluginStateObject.Molecule.Structure.Representation3D,
|
|
264
264
|
to: objects_1.PluginStateObject.Molecule.Structure.Representation3DState,
|
|
265
|
-
params:
|
|
265
|
+
params: tslib_1.__assign({ t: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }) }, helpers_1.SpinStructureParams)
|
|
266
266
|
})({
|
|
267
267
|
canAutoUpdate: function () {
|
|
268
268
|
return true;
|
|
@@ -754,7 +754,7 @@ var VolumeRepresentation3DHelpers;
|
|
|
754
754
|
var sizeParams = ctx.representation.volume.themes.sizeThemeRegistry.get(type.defaultSizeTheme.name).getParams(themeDataCtx);
|
|
755
755
|
var volumeDefaultParams = param_definition_1.ParamDefinition.getDefaultValues(type.getParams(ctx.representation.volume.themes, volume));
|
|
756
756
|
return ({
|
|
757
|
-
type: { name: name, params: volumeParams ?
|
|
757
|
+
type: { name: name, params: volumeParams ? tslib_1.__assign(tslib_1.__assign({}, volumeDefaultParams), volumeParams) : volumeDefaultParams },
|
|
758
758
|
colorTheme: { name: type.defaultColorTheme.name, params: param_definition_1.ParamDefinition.getDefaultValues(colorParams) },
|
|
759
759
|
sizeTheme: { name: type.defaultSizeTheme.name, params: param_definition_1.ParamDefinition.getDefaultValues(sizeParams) }
|
|
760
760
|
});
|
|
@@ -765,9 +765,9 @@ var VolumeRepresentation3DHelpers;
|
|
|
765
765
|
var colorType = ctx.representation.volume.themes.colorThemeRegistry.get(colorName || type.defaultColorTheme.name);
|
|
766
766
|
var sizeType = ctx.representation.volume.themes.sizeThemeRegistry.get(sizeName || type.defaultSizeTheme.name);
|
|
767
767
|
return ({
|
|
768
|
-
type: { name: name, params: volumeParams ?
|
|
769
|
-
colorTheme: { name: type.defaultColorTheme.name, params: colorParams ?
|
|
770
|
-
sizeTheme: { name: type.defaultSizeTheme.name, params: sizeParams ?
|
|
768
|
+
type: { name: name, params: volumeParams ? tslib_1.__assign(tslib_1.__assign({}, type.defaultValues), volumeParams) : type.defaultValues },
|
|
769
|
+
colorTheme: { name: type.defaultColorTheme.name, params: colorParams ? tslib_1.__assign(tslib_1.__assign({}, colorType.defaultValues), colorParams) : colorType.defaultValues },
|
|
770
|
+
sizeTheme: { name: type.defaultSizeTheme.name, params: sizeParams ? tslib_1.__assign(tslib_1.__assign({}, sizeType.defaultValues), sizeParams) : sizeType.defaultValues }
|
|
771
771
|
});
|
|
772
772
|
}
|
|
773
773
|
VolumeRepresentation3DHelpers.getDefaultParamsStatic = getDefaultParamsStatic;
|
|
@@ -812,10 +812,10 @@ var VolumeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
812
812
|
apply: function (_a, plugin) {
|
|
813
813
|
var _this = this;
|
|
814
814
|
var a = _a.a, params = _a.params;
|
|
815
|
-
return mol_task_1.Task.create('Volume Representation', function (ctx) { return
|
|
815
|
+
return mol_task_1.Task.create('Volume Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
816
816
|
var propertyCtx, provider, repr, props;
|
|
817
817
|
var _a;
|
|
818
|
-
return
|
|
818
|
+
return tslib_1.__generator(this, function (_b) {
|
|
819
819
|
switch (_b.label) {
|
|
820
820
|
case 0:
|
|
821
821
|
propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
|
|
@@ -826,7 +826,7 @@ var VolumeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
826
826
|
_b.sent();
|
|
827
827
|
_b.label = 2;
|
|
828
828
|
case 2:
|
|
829
|
-
repr = provider.factory(
|
|
829
|
+
repr = provider.factory(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.volume.themes), provider.getParams);
|
|
830
830
|
repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
|
|
831
831
|
props = params.type.params || {};
|
|
832
832
|
return [4 /*yield*/, repr.createOrUpdate(props, a.data).runInContext(ctx)];
|
|
@@ -840,10 +840,10 @@ var VolumeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
840
840
|
update: function (_a, plugin) {
|
|
841
841
|
var _this = this;
|
|
842
842
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
843
|
-
return mol_task_1.Task.create('Volume Representation', function (ctx) { return
|
|
843
|
+
return mol_task_1.Task.create('Volume Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
844
844
|
var oldProvider, props;
|
|
845
845
|
var _a;
|
|
846
|
-
return
|
|
846
|
+
return tslib_1.__generator(this, function (_b) {
|
|
847
847
|
switch (_b.label) {
|
|
848
848
|
case 0:
|
|
849
849
|
if (newParams.type.name !== oldParams.type.name) {
|
|
@@ -851,7 +851,7 @@ var VolumeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
851
851
|
(_a = oldProvider.ensureCustomProperties) === null || _a === void 0 ? void 0 : _a.detach(a.data);
|
|
852
852
|
return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Recreate];
|
|
853
853
|
}
|
|
854
|
-
props =
|
|
854
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams.type.params);
|
|
855
855
|
b.data.repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
|
|
856
856
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, a.data).runInContext(ctx)];
|
|
857
857
|
case 1:
|
|
@@ -880,12 +880,12 @@ var ShapeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
880
880
|
apply: function (_a, plugin) {
|
|
881
881
|
var _this = this;
|
|
882
882
|
var a = _a.a, params = _a.params;
|
|
883
|
-
return mol_task_1.Task.create('Shape Representation', function (ctx) { return
|
|
883
|
+
return mol_task_1.Task.create('Shape Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
884
884
|
var props, repr;
|
|
885
|
-
return
|
|
885
|
+
return tslib_1.__generator(this, function (_a) {
|
|
886
886
|
switch (_a.label) {
|
|
887
887
|
case 0:
|
|
888
|
-
props =
|
|
888
|
+
props = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(a.data.params)), params);
|
|
889
889
|
repr = (0, representation_1.ShapeRepresentation)(a.data.getShape, a.data.geometryUtils);
|
|
890
890
|
return [4 /*yield*/, repr.createOrUpdate(props, a.data.data).runInContext(ctx)];
|
|
891
891
|
case 1:
|
|
@@ -898,12 +898,12 @@ var ShapeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
898
898
|
update: function (_a, plugin) {
|
|
899
899
|
var _this = this;
|
|
900
900
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
901
|
-
return mol_task_1.Task.create('Shape Representation', function (ctx) { return
|
|
901
|
+
return mol_task_1.Task.create('Shape Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
902
902
|
var props;
|
|
903
|
-
return
|
|
903
|
+
return tslib_1.__generator(this, function (_a) {
|
|
904
904
|
switch (_a.label) {
|
|
905
905
|
case 0:
|
|
906
|
-
props =
|
|
906
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
907
907
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, a.data.data).runInContext(ctx)];
|
|
908
908
|
case 1:
|
|
909
909
|
_a.sent();
|
|
@@ -920,7 +920,7 @@ var ModelUnitcell3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
920
920
|
display: 'Model Unit Cell',
|
|
921
921
|
from: objects_1.PluginStateObject.Molecule.Model,
|
|
922
922
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
923
|
-
params: function () { return (
|
|
923
|
+
params: function () { return (tslib_1.__assign({}, unitcell_1.UnitcellParams)); }
|
|
924
924
|
})({
|
|
925
925
|
isApplicable: function (a) { return !!symmetry_1.ModelSymmetry.Provider.get(a.data); },
|
|
926
926
|
canAutoUpdate: function (_a) {
|
|
@@ -930,17 +930,17 @@ var ModelUnitcell3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
930
930
|
apply: function (_a, plugin) {
|
|
931
931
|
var _this = this;
|
|
932
932
|
var a = _a.a, params = _a.params;
|
|
933
|
-
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return
|
|
933
|
+
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
934
934
|
var symmetry, data, repr;
|
|
935
935
|
var _a;
|
|
936
|
-
return
|
|
936
|
+
return tslib_1.__generator(this, function (_b) {
|
|
937
937
|
switch (_b.label) {
|
|
938
938
|
case 0:
|
|
939
939
|
symmetry = symmetry_1.ModelSymmetry.Provider.get(a.data);
|
|
940
940
|
if (!symmetry)
|
|
941
941
|
return [2 /*return*/, mol_state_1.StateObject.Null];
|
|
942
942
|
data = (0, unitcell_1.getUnitcellData)(a.data, symmetry, params);
|
|
943
|
-
repr = (0, unitcell_1.UnitcellRepresentation)(
|
|
943
|
+
repr = (0, unitcell_1.UnitcellRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return unitcell_1.UnitcellParams; });
|
|
944
944
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
945
945
|
case 1:
|
|
946
946
|
_b.sent();
|
|
@@ -952,15 +952,15 @@ var ModelUnitcell3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
952
952
|
update: function (_a) {
|
|
953
953
|
var _this = this;
|
|
954
954
|
var a = _a.a, b = _a.b, newParams = _a.newParams;
|
|
955
|
-
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return
|
|
955
|
+
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
956
956
|
var symmetry, props, data;
|
|
957
|
-
return
|
|
957
|
+
return tslib_1.__generator(this, function (_a) {
|
|
958
958
|
switch (_a.label) {
|
|
959
959
|
case 0:
|
|
960
960
|
symmetry = symmetry_1.ModelSymmetry.Provider.get(a.data);
|
|
961
961
|
if (!symmetry)
|
|
962
962
|
return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Null];
|
|
963
|
-
props =
|
|
963
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
964
964
|
data = (0, unitcell_1.getUnitcellData)(a.data, symmetry, props);
|
|
965
965
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
966
966
|
case 1:
|
|
@@ -978,7 +978,7 @@ var StructureBoundingBox3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
978
978
|
display: 'Bounding Box',
|
|
979
979
|
from: objects_1.PluginStateObject.Molecule.Structure,
|
|
980
980
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
981
|
-
params:
|
|
981
|
+
params: tslib_1.__assign({ radius: param_definition_1.ParamDefinition.Numeric(0.05, { min: 0.01, max: 4, step: 0.01 }, { isEssential: true }), color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.red, { isEssential: true }) }, mesh_1.Mesh.Params)
|
|
982
982
|
})({
|
|
983
983
|
canAutoUpdate: function () {
|
|
984
984
|
return true;
|
|
@@ -986,9 +986,9 @@ var StructureBoundingBox3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
986
986
|
apply: function (_a, plugin) {
|
|
987
987
|
var _this = this;
|
|
988
988
|
var a = _a.a, params = _a.params;
|
|
989
|
-
return mol_task_1.Task.create('Bounding Box', function (ctx) { return
|
|
989
|
+
return mol_task_1.Task.create('Bounding Box', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
990
990
|
var repr;
|
|
991
|
-
return
|
|
991
|
+
return tslib_1.__generator(this, function (_a) {
|
|
992
992
|
switch (_a.label) {
|
|
993
993
|
case 0:
|
|
994
994
|
repr = (0, representation_1.ShapeRepresentation)(function (_, data, __, shape) {
|
|
@@ -1006,8 +1006,8 @@ var StructureBoundingBox3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1006
1006
|
update: function (_a, plugin) {
|
|
1007
1007
|
var _this = this;
|
|
1008
1008
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1009
|
-
return mol_task_1.Task.create('Bounding Box', function (ctx) { return
|
|
1010
|
-
return
|
|
1009
|
+
return mol_task_1.Task.create('Bounding Box', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1010
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1011
1011
|
switch (_a.label) {
|
|
1012
1012
|
case 0: return [4 /*yield*/, b.data.repr.createOrUpdate(newParams, { box: a.data.boundary.box, radius: newParams.radius, color: newParams.color }).runInContext(ctx)];
|
|
1013
1013
|
case 1:
|
|
@@ -1025,7 +1025,7 @@ var StructureSelectionsDistance3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1025
1025
|
display: '3D Distance',
|
|
1026
1026
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1027
1027
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1028
|
-
params: function () { return (
|
|
1028
|
+
params: function () { return (tslib_1.__assign({}, distance_1.DistanceParams)); }
|
|
1029
1029
|
})({
|
|
1030
1030
|
canAutoUpdate: function (_a) {
|
|
1031
1031
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1034,14 +1034,14 @@ var StructureSelectionsDistance3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1034
1034
|
apply: function (_a, plugin) {
|
|
1035
1035
|
var _this = this;
|
|
1036
1036
|
var a = _a.a, params = _a.params;
|
|
1037
|
-
return mol_task_1.Task.create('Structure Distance', function (ctx) { return
|
|
1037
|
+
return mol_task_1.Task.create('Structure Distance', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1038
1038
|
var data, repr;
|
|
1039
1039
|
var _a;
|
|
1040
|
-
return
|
|
1040
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1041
1041
|
switch (_b.label) {
|
|
1042
1042
|
case 0:
|
|
1043
1043
|
data = (0, helpers_2.getDistanceDataFromStructureSelections)(a.data);
|
|
1044
|
-
repr = (0, distance_1.DistanceRepresentation)(
|
|
1044
|
+
repr = (0, distance_1.DistanceRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return distance_1.DistanceParams; });
|
|
1045
1045
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1046
1046
|
case 1:
|
|
1047
1047
|
_b.sent();
|
|
@@ -1053,12 +1053,12 @@ var StructureSelectionsDistance3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1053
1053
|
update: function (_a, plugin) {
|
|
1054
1054
|
var _this = this;
|
|
1055
1055
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1056
|
-
return mol_task_1.Task.create('Structure Distance', function (ctx) { return
|
|
1056
|
+
return mol_task_1.Task.create('Structure Distance', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1057
1057
|
var props, data;
|
|
1058
|
-
return
|
|
1058
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1059
1059
|
switch (_a.label) {
|
|
1060
1060
|
case 0:
|
|
1061
|
-
props =
|
|
1061
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1062
1062
|
data = (0, helpers_2.getDistanceDataFromStructureSelections)(a.data);
|
|
1063
1063
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1064
1064
|
case 1:
|
|
@@ -1076,7 +1076,7 @@ var StructureSelectionsAngle3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1076
1076
|
display: '3D Angle',
|
|
1077
1077
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1078
1078
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1079
|
-
params: function () { return (
|
|
1079
|
+
params: function () { return (tslib_1.__assign({}, angle_1.AngleParams)); }
|
|
1080
1080
|
})({
|
|
1081
1081
|
canAutoUpdate: function (_a) {
|
|
1082
1082
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1085,14 +1085,14 @@ var StructureSelectionsAngle3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1085
1085
|
apply: function (_a, plugin) {
|
|
1086
1086
|
var _this = this;
|
|
1087
1087
|
var a = _a.a, params = _a.params;
|
|
1088
|
-
return mol_task_1.Task.create('Structure Angle', function (ctx) { return
|
|
1088
|
+
return mol_task_1.Task.create('Structure Angle', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1089
1089
|
var data, repr;
|
|
1090
1090
|
var _a;
|
|
1091
|
-
return
|
|
1091
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1092
1092
|
switch (_b.label) {
|
|
1093
1093
|
case 0:
|
|
1094
1094
|
data = (0, helpers_2.getAngleDataFromStructureSelections)(a.data);
|
|
1095
|
-
repr = (0, angle_1.AngleRepresentation)(
|
|
1095
|
+
repr = (0, angle_1.AngleRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return angle_1.AngleParams; });
|
|
1096
1096
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1097
1097
|
case 1:
|
|
1098
1098
|
_b.sent();
|
|
@@ -1104,12 +1104,12 @@ var StructureSelectionsAngle3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1104
1104
|
update: function (_a, plugin) {
|
|
1105
1105
|
var _this = this;
|
|
1106
1106
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1107
|
-
return mol_task_1.Task.create('Structure Angle', function (ctx) { return
|
|
1107
|
+
return mol_task_1.Task.create('Structure Angle', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1108
1108
|
var props, data;
|
|
1109
|
-
return
|
|
1109
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1110
1110
|
switch (_a.label) {
|
|
1111
1111
|
case 0:
|
|
1112
|
-
props =
|
|
1112
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1113
1113
|
data = (0, helpers_2.getAngleDataFromStructureSelections)(a.data);
|
|
1114
1114
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1115
1115
|
case 1:
|
|
@@ -1127,7 +1127,7 @@ var StructureSelectionsDihedral3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1127
1127
|
display: '3D Dihedral',
|
|
1128
1128
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1129
1129
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1130
|
-
params: function () { return (
|
|
1130
|
+
params: function () { return (tslib_1.__assign({}, dihedral_1.DihedralParams)); }
|
|
1131
1131
|
})({
|
|
1132
1132
|
canAutoUpdate: function (_a) {
|
|
1133
1133
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1136,14 +1136,14 @@ var StructureSelectionsDihedral3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1136
1136
|
apply: function (_a, plugin) {
|
|
1137
1137
|
var _this = this;
|
|
1138
1138
|
var a = _a.a, params = _a.params;
|
|
1139
|
-
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return
|
|
1139
|
+
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1140
1140
|
var data, repr;
|
|
1141
1141
|
var _a;
|
|
1142
|
-
return
|
|
1142
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1143
1143
|
switch (_b.label) {
|
|
1144
1144
|
case 0:
|
|
1145
1145
|
data = (0, helpers_2.getDihedralDataFromStructureSelections)(a.data);
|
|
1146
|
-
repr = (0, dihedral_1.DihedralRepresentation)(
|
|
1146
|
+
repr = (0, dihedral_1.DihedralRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return dihedral_1.DihedralParams; });
|
|
1147
1147
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1148
1148
|
case 1:
|
|
1149
1149
|
_b.sent();
|
|
@@ -1155,12 +1155,12 @@ var StructureSelectionsDihedral3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1155
1155
|
update: function (_a, plugin) {
|
|
1156
1156
|
var _this = this;
|
|
1157
1157
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1158
|
-
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return
|
|
1158
|
+
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1159
1159
|
var props, data;
|
|
1160
|
-
return
|
|
1160
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1161
1161
|
switch (_a.label) {
|
|
1162
1162
|
case 0:
|
|
1163
|
-
props =
|
|
1163
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1164
1164
|
data = (0, helpers_2.getDihedralDataFromStructureSelections)(a.data);
|
|
1165
1165
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1166
1166
|
case 1:
|
|
@@ -1178,7 +1178,7 @@ var StructureSelectionsLabel3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1178
1178
|
display: '3D Label',
|
|
1179
1179
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1180
1180
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1181
|
-
params: function () { return (
|
|
1181
|
+
params: function () { return (tslib_1.__assign({}, label_1.LabelParams)); }
|
|
1182
1182
|
})({
|
|
1183
1183
|
canAutoUpdate: function (_a) {
|
|
1184
1184
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1187,14 +1187,14 @@ var StructureSelectionsLabel3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1187
1187
|
apply: function (_a, plugin) {
|
|
1188
1188
|
var _this = this;
|
|
1189
1189
|
var a = _a.a, params = _a.params;
|
|
1190
|
-
return mol_task_1.Task.create('Structure Label', function (ctx) { return
|
|
1190
|
+
return mol_task_1.Task.create('Structure Label', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1191
1191
|
var data, repr;
|
|
1192
1192
|
var _a;
|
|
1193
|
-
return
|
|
1193
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1194
1194
|
switch (_b.label) {
|
|
1195
1195
|
case 0:
|
|
1196
1196
|
data = (0, helpers_2.getLabelDataFromStructureSelections)(a.data);
|
|
1197
|
-
repr = (0, label_1.LabelRepresentation)(
|
|
1197
|
+
repr = (0, label_1.LabelRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return label_1.LabelParams; });
|
|
1198
1198
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1199
1199
|
case 1:
|
|
1200
1200
|
_b.sent();
|
|
@@ -1206,12 +1206,12 @@ var StructureSelectionsLabel3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1206
1206
|
update: function (_a, plugin) {
|
|
1207
1207
|
var _this = this;
|
|
1208
1208
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1209
|
-
return mol_task_1.Task.create('Structure Label', function (ctx) { return
|
|
1209
|
+
return mol_task_1.Task.create('Structure Label', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1210
1210
|
var props, data;
|
|
1211
|
-
return
|
|
1211
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1212
1212
|
switch (_a.label) {
|
|
1213
1213
|
case 0:
|
|
1214
|
-
props =
|
|
1214
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1215
1215
|
data = (0, helpers_2.getLabelDataFromStructureSelections)(a.data);
|
|
1216
1216
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1217
1217
|
case 1:
|
|
@@ -1229,7 +1229,7 @@ var StructureSelectionsOrientation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1229
1229
|
display: '3D Orientation',
|
|
1230
1230
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1231
1231
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1232
|
-
params: function () { return (
|
|
1232
|
+
params: function () { return (tslib_1.__assign({}, orientation_1.OrientationParams)); }
|
|
1233
1233
|
})({
|
|
1234
1234
|
canAutoUpdate: function (_a) {
|
|
1235
1235
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1238,14 +1238,14 @@ var StructureSelectionsOrientation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1238
1238
|
apply: function (_a, plugin) {
|
|
1239
1239
|
var _this = this;
|
|
1240
1240
|
var a = _a.a, params = _a.params;
|
|
1241
|
-
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return
|
|
1241
|
+
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1242
1242
|
var data, repr;
|
|
1243
1243
|
var _a;
|
|
1244
|
-
return
|
|
1244
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1245
1245
|
switch (_b.label) {
|
|
1246
1246
|
case 0:
|
|
1247
1247
|
data = (0, helpers_2.getOrientationDataFromStructureSelections)(a.data);
|
|
1248
|
-
repr = (0, orientation_1.OrientationRepresentation)(
|
|
1248
|
+
repr = (0, orientation_1.OrientationRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return orientation_1.OrientationParams; });
|
|
1249
1249
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1250
1250
|
case 1:
|
|
1251
1251
|
_b.sent();
|
|
@@ -1257,12 +1257,12 @@ var StructureSelectionsOrientation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1257
1257
|
update: function (_a, plugin) {
|
|
1258
1258
|
var _this = this;
|
|
1259
1259
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1260
|
-
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return
|
|
1260
|
+
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1261
1261
|
var props, data;
|
|
1262
|
-
return
|
|
1262
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1263
1263
|
switch (_a.label) {
|
|
1264
1264
|
case 0:
|
|
1265
|
-
props =
|
|
1265
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1266
1266
|
data = (0, helpers_2.getOrientationDataFromStructureSelections)(a.data);
|
|
1267
1267
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1268
1268
|
case 1:
|
|
@@ -1280,7 +1280,7 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1280
1280
|
display: '3D Plane',
|
|
1281
1281
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1282
1282
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1283
|
-
params: function () { return (
|
|
1283
|
+
params: function () { return (tslib_1.__assign({}, plane_1.PlaneParams)); }
|
|
1284
1284
|
})({
|
|
1285
1285
|
canAutoUpdate: function (_a) {
|
|
1286
1286
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1289,14 +1289,14 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1289
1289
|
apply: function (_a, plugin) {
|
|
1290
1290
|
var _this = this;
|
|
1291
1291
|
var a = _a.a, params = _a.params;
|
|
1292
|
-
return mol_task_1.Task.create('Structure Plane', function (ctx) { return
|
|
1292
|
+
return mol_task_1.Task.create('Structure Plane', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1293
1293
|
var data, repr;
|
|
1294
1294
|
var _a;
|
|
1295
|
-
return
|
|
1295
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1296
1296
|
switch (_b.label) {
|
|
1297
1297
|
case 0:
|
|
1298
1298
|
data = (0, helpers_2.getPlaneDataFromStructureSelections)(a.data);
|
|
1299
|
-
repr = (0, plane_1.PlaneRepresentation)(
|
|
1299
|
+
repr = (0, plane_1.PlaneRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return plane_1.PlaneParams; });
|
|
1300
1300
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1301
1301
|
case 1:
|
|
1302
1302
|
_b.sent();
|
|
@@ -1308,12 +1308,12 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1308
1308
|
update: function (_a, plugin) {
|
|
1309
1309
|
var _this = this;
|
|
1310
1310
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1311
|
-
return mol_task_1.Task.create('Structure Plane', function (ctx) { return
|
|
1311
|
+
return mol_task_1.Task.create('Structure Plane', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1312
1312
|
var props, data;
|
|
1313
|
-
return
|
|
1313
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1314
1314
|
switch (_a.label) {
|
|
1315
1315
|
case 0:
|
|
1316
|
-
props =
|
|
1316
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1317
1317
|
data = (0, helpers_2.getPlaneDataFromStructureSelections)(a.data);
|
|
1318
1318
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1319
1319
|
case 1:
|
|
@@ -1326,4 +1326,3 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1326
1326
|
},
|
|
1327
1327
|
});
|
|
1328
1328
|
exports.StructureSelectionsPlane3D = StructureSelectionsPlane3D;
|
|
1329
|
-
//# sourceMappingURL=representation.js.map
|
|
@@ -35,8 +35,8 @@ var BoxShape3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
35
35
|
apply: function (_a) {
|
|
36
36
|
var _this = this;
|
|
37
37
|
var params = _a.params;
|
|
38
|
-
return mol_task_1.Task.create('Shape Representation', function (ctx) { return
|
|
39
|
-
return
|
|
38
|
+
return mol_task_1.Task.create('Shape Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
39
|
+
return tslib_1.__generator(this, function (_a) {
|
|
40
40
|
return [2 /*return*/, new objects_1.PluginStateObject.Shape.Provider({
|
|
41
41
|
label: 'Box',
|
|
42
42
|
data: params,
|
|
@@ -69,4 +69,3 @@ function getBoxMesh(box, radius, oldMesh) {
|
|
|
69
69
|
return mesh;
|
|
70
70
|
}
|
|
71
71
|
exports.getBoxMesh = getBoxMesh;
|
|
72
|
-
//# sourceMappingURL=shape.js.map
|
|
@@ -35,11 +35,11 @@ var VolumeFromCcp4 = objects_1.PluginStateTransform.BuiltIn({
|
|
|
35
35
|
apply: function (_a) {
|
|
36
36
|
var _this = this;
|
|
37
37
|
var a = _a.a, params = _a.params;
|
|
38
|
-
return mol_task_1.Task.create('Create volume from CCP4/MRC/MAP', function (ctx) { return
|
|
38
|
+
return mol_task_1.Task.create('Create volume from CCP4/MRC/MAP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
39
39
|
var volume, props;
|
|
40
|
-
return
|
|
40
|
+
return tslib_1.__generator(this, function (_a) {
|
|
41
41
|
switch (_a.label) {
|
|
42
|
-
case 0: return [4 /*yield*/, (0, ccp4_1.volumeFromCcp4)(a.data,
|
|
42
|
+
case 0: return [4 /*yield*/, (0, ccp4_1.volumeFromCcp4)(a.data, tslib_1.__assign(tslib_1.__assign({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
|
|
43
43
|
case 1:
|
|
44
44
|
volume = _a.sent();
|
|
45
45
|
props = { label: volume.label || 'Volume', description: "Volume ".concat(a.data.header.NX, "\u00D7").concat(a.data.header.NX, "\u00D7").concat(a.data.header.NX) };
|
|
@@ -69,11 +69,11 @@ var VolumeFromDsn6 = objects_1.PluginStateTransform.BuiltIn({
|
|
|
69
69
|
apply: function (_a) {
|
|
70
70
|
var _this = this;
|
|
71
71
|
var a = _a.a, params = _a.params;
|
|
72
|
-
return mol_task_1.Task.create('Create volume from DSN6/BRIX', function (ctx) { return
|
|
72
|
+
return mol_task_1.Task.create('Create volume from DSN6/BRIX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
73
73
|
var volume, props;
|
|
74
|
-
return
|
|
74
|
+
return tslib_1.__generator(this, function (_a) {
|
|
75
75
|
switch (_a.label) {
|
|
76
|
-
case 0: return [4 /*yield*/, (0, dsn6_1.volumeFromDsn6)(a.data,
|
|
76
|
+
case 0: return [4 /*yield*/, (0, dsn6_1.volumeFromDsn6)(a.data, tslib_1.__assign(tslib_1.__assign({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
|
|
77
77
|
case 1:
|
|
78
78
|
volume = _a.sent();
|
|
79
79
|
props = { label: volume.label || 'Volume', description: "Volume ".concat(a.data.header.xExtent, "\u00D7").concat(a.data.header.yExtent, "\u00D7").concat(a.data.header.zExtent) };
|
|
@@ -104,11 +104,11 @@ var VolumeFromCube = objects_1.PluginStateTransform.BuiltIn({
|
|
|
104
104
|
apply: function (_a) {
|
|
105
105
|
var _this = this;
|
|
106
106
|
var a = _a.a, params = _a.params;
|
|
107
|
-
return mol_task_1.Task.create('Create volume from Cube', function (ctx) { return
|
|
107
|
+
return mol_task_1.Task.create('Create volume from Cube', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
108
108
|
var volume, props;
|
|
109
|
-
return
|
|
109
|
+
return tslib_1.__generator(this, function (_a) {
|
|
110
110
|
switch (_a.label) {
|
|
111
|
-
case 0: return [4 /*yield*/, (0, cube_1.volumeFromCube)(a.data,
|
|
111
|
+
case 0: return [4 /*yield*/, (0, cube_1.volumeFromCube)(a.data, tslib_1.__assign(tslib_1.__assign({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
|
|
112
112
|
case 1:
|
|
113
113
|
volume = _a.sent();
|
|
114
114
|
props = { label: volume.label || 'Volume', description: "Volume ".concat(a.data.header.dim[0], "\u00D7").concat(a.data.header.dim[1], "\u00D7").concat(a.data.header.dim[2]) };
|
|
@@ -132,9 +132,9 @@ var VolumeFromDx = objects_1.PluginStateTransform.BuiltIn({
|
|
|
132
132
|
apply: function (_a) {
|
|
133
133
|
var _this = this;
|
|
134
134
|
var a = _a.a;
|
|
135
|
-
return mol_task_1.Task.create('Parse DX', function (ctx) { return
|
|
135
|
+
return mol_task_1.Task.create('Parse DX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
136
136
|
var volume, props;
|
|
137
|
-
return
|
|
137
|
+
return tslib_1.__generator(this, function (_a) {
|
|
138
138
|
switch (_a.label) {
|
|
139
139
|
case 0: return [4 /*yield*/, (0, dx_1.volumeFromDx)(a.data, { label: a.data.name || a.label }).runInContext(ctx)];
|
|
140
140
|
case 1:
|
|
@@ -174,10 +174,10 @@ var VolumeFromDensityServerCif = objects_1.PluginStateTransform.BuiltIn({
|
|
|
174
174
|
apply: function (_a) {
|
|
175
175
|
var _this = this;
|
|
176
176
|
var a = _a.a, params = _a.params;
|
|
177
|
-
return mol_task_1.Task.create('Parse density-server CIF', function (ctx) { return
|
|
177
|
+
return mol_task_1.Task.create('Parse density-server CIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
178
178
|
var header, block, densityServerCif, volume, _a, x, y, z, props;
|
|
179
179
|
var _b;
|
|
180
|
-
return
|
|
180
|
+
return tslib_1.__generator(this, function (_c) {
|
|
181
181
|
switch (_c.label) {
|
|
182
182
|
case 0:
|
|
183
183
|
header = params.blockHeader || a.data.blocks[1].header;
|
|
@@ -219,14 +219,14 @@ var AssignColorVolume = objects_1.PluginStateTransform.BuiltIn({
|
|
|
219
219
|
apply: function (_a) {
|
|
220
220
|
var _this = this;
|
|
221
221
|
var a = _a.a, params = _a.params, dependencies = _a.dependencies;
|
|
222
|
-
return mol_task_1.Task.create('Assign Color Volume', function (ctx) { return
|
|
222
|
+
return mol_task_1.Task.create('Assign Color Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
223
223
|
var colorVolume, volume, props;
|
|
224
|
-
return
|
|
224
|
+
return tslib_1.__generator(this, function (_a) {
|
|
225
225
|
if (!dependencies || !dependencies[params.ref]) {
|
|
226
226
|
throw new Error('Dependency not available.');
|
|
227
227
|
}
|
|
228
228
|
colorVolume = dependencies[params.ref].data;
|
|
229
|
-
volume =
|
|
229
|
+
volume = tslib_1.__assign(tslib_1.__assign({}, a.data), { colorVolume: colorVolume });
|
|
230
230
|
props = { label: a.label, description: 'Volume + Colors' };
|
|
231
231
|
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
|
|
232
232
|
});
|
|
@@ -234,4 +234,3 @@ var AssignColorVolume = objects_1.PluginStateTransform.BuiltIn({
|
|
|
234
234
|
}
|
|
235
235
|
});
|
|
236
236
|
exports.AssignColorVolume = AssignColorVolume;
|
|
237
|
-
//# sourceMappingURL=volume.js.map
|
|
@@ -7,12 +7,12 @@
|
|
|
7
7
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
8
8
|
exports.StateTransforms = void 0;
|
|
9
9
|
var tslib_1 = require("tslib");
|
|
10
|
-
var Data =
|
|
11
|
-
var Misc =
|
|
12
|
-
var Model =
|
|
13
|
-
var Volume =
|
|
14
|
-
var Representation =
|
|
15
|
-
var Shape =
|
|
10
|
+
var Data = tslib_1.__importStar(require("./transforms/data"));
|
|
11
|
+
var Misc = tslib_1.__importStar(require("./transforms/misc"));
|
|
12
|
+
var Model = tslib_1.__importStar(require("./transforms/model"));
|
|
13
|
+
var Volume = tslib_1.__importStar(require("./transforms/volume"));
|
|
14
|
+
var Representation = tslib_1.__importStar(require("./transforms/representation"));
|
|
15
|
+
var Shape = tslib_1.__importStar(require("./transforms/shape"));
|
|
16
16
|
exports.StateTransforms = {
|
|
17
17
|
Data: Data,
|
|
18
18
|
Misc: Misc,
|
|
@@ -21,4 +21,3 @@ exports.StateTransforms = {
|
|
|
21
21
|
Representation: Representation,
|
|
22
22
|
Shape: Shape
|
|
23
23
|
};
|
|
24
|
-
//# sourceMappingURL=transforms.js.map
|