molstar 3.3.1 → 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/README.md +3 -0
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/viewport.js +1 -1
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +2 -0
- 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/commonjs/apps/docking-viewer/index.js +12 -12
- package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +24 -22
- package/lib/commonjs/apps/viewer/index.js +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
- 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 -8
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
- package/lib/commonjs/cli/cif2bcif/index.js +8 -8
- package/lib/commonjs/cli/cifschema/index.js +27 -27
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +1 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -9
- package/lib/commonjs/cli/state-docs/index.js +2 -2
- package/lib/commonjs/cli/structure-info/helpers.js +11 -11
- package/lib/commonjs/cli/structure-info/model.js +15 -15
- package/lib/commonjs/cli/structure-info/volume.js +9 -9
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
- package/lib/commonjs/examples/alpha-orbitals/index.js +11 -11
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
- package/lib/commonjs/examples/basic-wrapper/index.js +22 -22
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
- package/lib/commonjs/examples/lighting/index.js +6 -6
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +26 -26
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
- package/lib/commonjs/examples/task.js +15 -15
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
- package/lib/commonjs/extensions/anvil/behavior.js +14 -14
- package/lib/commonjs/extensions/anvil/prop.js +7 -7
- package/lib/commonjs/extensions/anvil/representation.js +5 -5
- package/lib/commonjs/extensions/cellpack/index.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.js +26 -24
- package/lib/commonjs/extensions/cellpack/preset.js +6 -6
- package/lib/commonjs/extensions/cellpack/property.js +3 -3
- package/lib/commonjs/extensions/cellpack/representation.js +2 -2
- package/lib/commonjs/extensions/cellpack/state.js +13 -13
- package/lib/commonjs/extensions/cellpack/util.js +14 -14
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +5 -5
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +1 -1
- package/lib/commonjs/extensions/g3d/data.js +6 -6
- package/lib/commonjs/extensions/g3d/format.js +14 -14
- package/lib/commonjs/extensions/g3d/model.js +4 -4
- package/lib/commonjs/extensions/geo-export/controls.js +3 -3
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
- package/lib/commonjs/extensions/geo-export/index.js +1 -1
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/ui.js +7 -7
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
- package/lib/commonjs/extensions/model-export/export.js +4 -4
- package/lib/commonjs/extensions/model-export/index.js +1 -1
- package/lib/commonjs/extensions/model-export/ui.js +5 -5
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
- package/lib/commonjs/extensions/mp4-export/index.js +1 -1
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
- 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 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera.js +2 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
- package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
- package/lib/commonjs/mol-canvas3d/util.js +2 -2
- package/lib/commonjs/mol-data/db/column.js +2 -2
- package/lib/commonjs/mol-data/db/table.js +1 -1
- package/lib/commonjs/mol-data/db.js +1 -1
- package/lib/commonjs/mol-data/generic.js +3 -3
- package/lib/commonjs/mol-data/index.js +4 -4
- package/lib/commonjs/mol-data/int/interval.js +1 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
- package/lib/commonjs/mol-data/int/segmentation.js +1 -1
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
- package/lib/commonjs/mol-data/util.js +7 -7
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +3 -3
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +3 -3
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +4 -4
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +3 -3
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
- package/lib/commonjs/mol-gl/compute/util.js +3 -3
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.js +3 -3
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/points.js +3 -3
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
- package/lib/commonjs/mol-gl/renderable/text.js +3 -3
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/util.js +1 -1
- package/lib/commonjs/mol-gl/shader-code.js +2 -1
- package/lib/commonjs/mol-gl/webgl/buffer.js +4 -5
- package/lib/commonjs/mol-gl/webgl/context.js +3 -3
- package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
- package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
- 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/netcdf/reader.d.ts +78 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
- package/lib/commonjs/mol-io/common/typed-array.js +2 -2
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
- package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +2 -2
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema.js +2 -2
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cif.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
- package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
- package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
- 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 -4
- package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
- 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 -8
- package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
- 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 -4
- package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
- package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
- package/lib/commonjs/mol-io/writer/cif.js +1 -1
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol/encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +4 -4
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +4 -4
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +8 -8
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +1 -1
- package/lib/commonjs/mol-math/geometry.js +8 -8
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
- package/lib/commonjs/mol-math/graph.js +1 -1
- package/lib/commonjs/mol-math/linear-algebra.js +2 -2
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
- package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
- package/lib/commonjs/mol-model/sequence.js +1 -1
- package/lib/commonjs/mol-model/shape.js +1 -1
- package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/commonjs/mol-model/structure/model/model.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
- 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.js +3 -3
- package/lib/commonjs/mol-model/structure/query/queries/generators.js +2 -2
- package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +2 -2
- package/lib/commonjs/mol-model/structure/query.js +6 -6
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +6 -9
- package/lib/commonjs/mol-model/structure/structure/element/element.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/element.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/structure.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/symmetry.js +10 -10
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +2 -2
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +3 -3
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +3 -3
- package/lib/commonjs/mol-model/structure/structure/unit.js +4 -4
- package/lib/commonjs/mol-model/structure/structure/util/superposition.js +1 -1
- package/lib/commonjs/mol-model/structure/structure.js +2 -2
- package/lib/commonjs/mol-model/structure/topology.js +1 -1
- package/lib/commonjs/mol-model/structure.js +6 -6
- package/lib/commonjs/mol-model/volume.js +2 -2
- package/lib/commonjs/mol-model-formats/shape/ply.js +7 -7
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -15
- package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +3 -3
- package/lib/commonjs/mol-model-formats/structure/basic/entities.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/parser.js +10 -10
- package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +2 -2
- package/lib/commonjs/mol-model-formats/structure/basic/schema.js +7 -2
- package/lib/commonjs/mol-model-formats/structure/basic/sort.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +33 -2
- package/lib/commonjs/mol-model-formats/structure/basic/util.js +26 -2
- package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
- package/lib/commonjs/mol-model-formats/structure/common/component.js +5 -1
- package/lib/commonjs/mol-model-formats/structure/cube.js +5 -5
- package/lib/commonjs/mol-model-formats/structure/dcd.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/gro.js +5 -3
- package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/mmcif.js +4 -2
- package/lib/commonjs/mol-model-formats/structure/mol.js +5 -5
- package/lib/commonjs/mol-model-formats/structure/mol2.js +6 -6
- 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/to-cif.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/commonjs/mol-model-formats/structure/pdb.js +7 -5
- 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/bonds/index-pair.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +11 -1
- package/lib/commonjs/mol-model-formats/structure/psf.js +5 -3
- 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 -20
- package/lib/commonjs/mol-model-formats/structure/xtc.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/xyz.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/ccp4.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/cube.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/density-server.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/dsn6.js +2 -2
- package/lib/commonjs/mol-model-formats/volume/dx.js +2 -2
- package/lib/commonjs/mol-model-props/common/custom-element-property.js +2 -2
- package/lib/commonjs/mol-model-props/common/custom-model-property.js +5 -5
- package/lib/commonjs/mol-model-props/common/custom-property.js +1 -1
- package/lib/commonjs/mol-model-props/common/custom-structure-property.js +6 -6
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +2 -2
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +5 -5
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +4 -4
- package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +3 -3
- package/lib/commonjs/mol-model-props/computed/helix-orientation.js +2 -2
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- package/lib/commonjs/servers/volume/pack.js +1 -1
- package/lib/commonjs/servers/volume/query.js +4 -4
- package/lib/commonjs/servers/volume/server/algebra/box.js +1 -1
- package/lib/commonjs/servers/volume/server/api.js +8 -8
- package/lib/commonjs/servers/volume/server/local-api.js +8 -8
- package/lib/commonjs/servers/volume/server/query/compose.js +8 -8
- package/lib/commonjs/servers/volume/server/query/execute.js +10 -10
- package/lib/commonjs/servers/volume/server/query/identify.js +2 -2
- package/lib/commonjs/servers/volume/server/web-api.js +7 -7
- package/lib/commonjs/servers/volume/server.js +2 -2
- package/lib/examples/alpha-orbitals/controls.js +2 -2
- package/lib/examples/basic-wrapper/controls.js +1 -1
- package/lib/examples/proteopedia-wrapper/ui/controls.js +1 -1
- package/lib/extensions/cellpack/model.js +4 -2
- package/lib/extensions/cellpack/state.js +2 -2
- package/lib/extensions/geo-export/ui.js +2 -2
- package/lib/extensions/model-export/ui.js +2 -2
- package/lib/extensions/mp4-export/ui.js +2 -2
- package/lib/extensions/rcsb/assembly-symmetry/ui.js +3 -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.js +2 -1
- package/lib/mol-canvas3d/helper/camera-helper.js +1 -1
- package/lib/mol-canvas3d/helper/handle-helper.js +1 -1
- package/lib/mol-canvas3d/helper/interaction-events.js +1 -1
- package/lib/mol-geo/geometry/text/text-builder.js +2 -1
- package/lib/mol-gl/shader-code.js +2 -1
- package/lib/mol-gl/webgl/buffer.js +2 -3
- package/lib/mol-io/common/binary-cif/classifier.js +3 -2
- package/lib/mol-io/common/binary-cif/decoder.js +4 -3
- 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/netcdf/reader.d.ts +78 -0
- package/lib/mol-io/common/netcdf/reader.js +456 -0
- package/lib/mol-io/reader/cif/schema/mmcif.d.ts +1 -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/prmtop/parser.d.ts +58 -0
- package/lib/mol-io/reader/prmtop/parser.js +168 -0
- 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/writer/cif/encoder.js +2 -1
- package/lib/mol-model/sequence/sequence.js +2 -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/structure/carbohydrates/constants.d.ts +1 -1
- package/lib/mol-model/structure/structure/carbohydrates/constants.js +6 -9
- package/lib/mol-model-formats/structure/basic/atomic.d.ts +1 -1
- package/lib/mol-model-formats/structure/basic/atomic.js +1 -14
- package/lib/mol-model-formats/structure/basic/parser.d.ts +1 -1
- package/lib/mol-model-formats/structure/basic/parser.js +1 -1
- package/lib/mol-model-formats/structure/basic/schema.d.ts +2 -2
- package/lib/mol-model-formats/structure/basic/schema.js +7 -2
- package/lib/mol-model-formats/structure/basic/util.d.ts +33 -2
- package/lib/mol-model-formats/structure/basic/util.js +24 -1
- package/lib/mol-model-formats/structure/cif-core.js +4 -4
- package/lib/mol-model-formats/structure/common/component.js +5 -1
- package/lib/mol-model-formats/structure/cube.js +3 -3
- package/lib/mol-model-formats/structure/gro.js +3 -1
- package/lib/mol-model-formats/structure/mmcif.d.ts +1 -1
- package/lib/mol-model-formats/structure/mmcif.js +4 -2
- package/lib/mol-model-formats/structure/mol.js +3 -3
- package/lib/mol-model-formats/structure/mol2.js +4 -4
- 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.d.ts +1 -1
- package/lib/mol-model-formats/structure/pdb.js +5 -3
- 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/symmetry.js +11 -1
- package/lib/mol-model-formats/structure/psf.js +3 -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 -20
- package/lib/mol-model-formats/structure/xyz.js +2 -2
- package/lib/mol-plugin/context.d.ts +2 -1
- package/lib/mol-plugin/context.js +4 -3
- package/lib/mol-plugin/spec.js +1 -1
- 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 -55
- package/lib/mol-plugin-state/actions/structure.d.ts +11 -2
- package/lib/mol-plugin-state/actions/structure.js +174 -4
- package/lib/mol-plugin-state/actions/volume.js +3 -2
- 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/registry.d.ts +3 -3
- package/lib/mol-plugin-state/formats/registry.js +13 -8
- 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/helpers/structure-component.js +2 -1
- package/lib/mol-plugin-state/manager/snapshots.js +4 -4
- package/lib/mol-plugin-state/objects.d.ts +47 -1
- package/lib/mol-plugin-state/objects.js +17 -1
- package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
- package/lib/mol-plugin-state/transforms/data.js +61 -9
- package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
- package/lib/mol-plugin-state/transforms/model.js +112 -3
- package/lib/mol-plugin-ui/base.js +1 -1
- package/lib/mol-plugin-ui/controls/action-menu.js +7 -7
- package/lib/mol-plugin-ui/controls/color.js +3 -3
- package/lib/mol-plugin-ui/controls/common.js +10 -10
- package/lib/mol-plugin-ui/controls/icons.js +70 -70
- package/lib/mol-plugin-ui/controls/legend.js +3 -3
- package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -1
- package/lib/mol-plugin-ui/controls/parameters.js +51 -51
- package/lib/mol-plugin-ui/controls/screenshot.js +2 -2
- package/lib/mol-plugin-ui/controls/slider.js +5 -5
- package/lib/mol-plugin-ui/controls.js +7 -7
- package/lib/mol-plugin-ui/custom/volume.js +4 -4
- package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
- package/lib/mol-plugin-ui/left-panel.js +33 -12
- package/lib/mol-plugin-ui/plugin.js +10 -10
- package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/mol-plugin-ui/sequence.js +5 -5
- package/lib/mol-plugin-ui/state/actions.js +1 -1
- package/lib/mol-plugin-ui/state/animation.js +1 -1
- package/lib/mol-plugin-ui/state/common.js +7 -7
- package/lib/mol-plugin-ui/state/snapshots.js +9 -9
- package/lib/mol-plugin-ui/state/tree.js +14 -14
- package/lib/mol-plugin-ui/state/update-transform.js +1 -1
- package/lib/mol-plugin-ui/structure/components.js +10 -10
- package/lib/mol-plugin-ui/structure/focus.js +1 -1
- package/lib/mol-plugin-ui/structure/generic.js +4 -4
- package/lib/mol-plugin-ui/structure/measurements.js +8 -8
- package/lib/mol-plugin-ui/structure/quick-styles.js +2 -2
- package/lib/mol-plugin-ui/structure/selection.js +7 -7
- package/lib/mol-plugin-ui/structure/source.js +4 -4
- package/lib/mol-plugin-ui/structure/superposition.js +8 -8
- package/lib/mol-plugin-ui/structure/volume.js +4 -4
- package/lib/mol-plugin-ui/task.js +5 -5
- package/lib/mol-plugin-ui/toast.js +4 -4
- package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
- package/lib/mol-plugin-ui/viewport/help.js +8 -8
- package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
- package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
- package/lib/mol-plugin-ui/viewport.js +4 -4
- package/lib/mol-script/language/parser.js +7 -4
- package/lib/mol-task/util/scheduler.d.ts +2 -2
- package/lib/mol-task/util/scheduler.js +7 -7
- package/lib/mol-theme/color/hydrophobicity.js +2 -2
- package/lib/mol-util/data-source.js +2 -1
- package/lib/mol-util/file-info.d.ts +1 -3
- package/lib/mol-util/file-info.js +2 -10
- package/lib/mol-util/index.d.ts +1 -0
- package/lib/mol-util/index.js +5 -0
- package/lib/mol-util/zip/deflate.js +2 -1
- package/lib/mol-util/zip/zip.d.ts +7 -1
- package/lib/mol-util/zip/zip.js +5 -1
- package/lib/servers/model/config.d.ts +2 -2
- package/package.json +16 -16
- package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
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return [2 /*return*/];
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@@ -342,7 +342,7 @@ var RemoteStateSnapshotList = /** @class */ (function (_super) {
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return (0, jsx_runtime_1.jsx)("ul", tslib_1.__assign({ style: { listStyle: 'none', marginTop: '10px' }, className: 'msp-state-list' }, { children: this.props.entries.valueSeq().map(function (e) { return (0, jsx_runtime_1.jsxs)("li", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ "data-id": e.id, onClick: _this.props.fetch, disabled: _this.props.isBusy, onContextMenu: _this.open, title: 'Click to download, right-click to open in a new tab.' }, { children: [e.name || new Date(e.timestamp).toLocaleString(), " ", (0, jsx_runtime_1.jsx)("small", { children: e.description })] })), !e.isSticky && _this.props.remove && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, "data-id": e.id, title: 'Remove', onClick: _this.props.remove, disabled: _this.props.isBusy, small: true })] }), e.id); }) }));
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { margin: '10px', cursor: 'default' } }, { children: [(0, jsx_runtime_1.jsx)("p", { children: "Nothing to see here yet." }), (0, jsx_runtime_1.jsxs)("p", { children: ["Structures and Volumes can be loaded from the ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HomeOutlinedSvg }), " tab."] })] }));
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decorators.push((0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: cell.parent, transform: d.transform, noMargin: true, wrapInExpander: true, expanderHeaderLeftMargin: margin }, "".concat(d.transform.transformer.id, "-").concat(i)));
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|
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|
|
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|
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|
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|
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|
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label = (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ className: 'msp-btn-tree-label msp-no-hover-outline', noOverflow: true, title: name_1, onClick: this.state.isCurrent ? this.setCurrentRoot : this.setCurrent, disabled: disabled }, { children: [cell.status === 'error' && (0, jsx_runtime_1.jsxs)("b", { children: ["[", cell.status, "]"] }), " ", (0, jsx_runtime_1.jsx)("span", { children: name_1 })] }));
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label = (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ className: "msp-btn-tree-label msp-type-class-".concat(obj.type.typeClass), noOverflow: true, disabled: disabled, title: title, onClick: this.state.isCurrent ? this.setCurrentRoot : this.setCurrent }, { children: [(0, jsx_runtime_1.jsx)("span", { children: obj.label }), " ", obj.description ? (0, jsx_runtime_1.jsx)("small", { children: obj.description }) : void 0] }));
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var expand = (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cellState.isCollapsed ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg, flex: '20px', disabled: disabled, onClick: this.toggleExpanded, transparent: true, className: 'msp-no-hover-outline', style: { visibility: children.size > 0 ? 'visible' : 'hidden' } }
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var remove = !cell.state.isLocked ? (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, disabled: disabled, small: true, toggleState: false }
|
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var visibility = (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cellState.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, disabled: disabled, small: true, onClick: this.toggleVisible }
|
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var expand = (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cellState.isCollapsed ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg, flex: '20px', disabled: disabled, onClick: this.toggleExpanded, transparent: true, className: 'msp-no-hover-outline', style: { visibility: children.size > 0 ? 'visible' : 'hidden' } });
|
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|
+
var remove = !cell.state.isLocked ? (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, disabled: disabled, small: true, toggleState: false }) : void 0;
|
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var visibility = (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cellState.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, disabled: disabled, small: true, onClick: this.toggleVisible });
|
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var marginStyle = {
|
|
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|
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|
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|
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|
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var row = (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: "msp-flex-row msp-tree-row".concat(isCurrent ? ' msp-tree-row-current' : ''), onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: marginStyle }, { children: [expand, label, remove, visibility] }));
|
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|
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|
return row;
|
|
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|
if (this.state.action === 'apply' && this.state.currentAction) {
|
|
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|
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|
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, (0, jsx_runtime_1.jsx)("small", tslib_1.__assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: reprLabel }))] })), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(cell.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, toggleState: false, onClick: this.remove, title: 'Remove', small: true, className: 'msp-form-control', flex: true }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.MoreHorizSvg, onClick: this.toggleAction, title: 'Actions', toggleState: this.state.action === 'action', className: 'msp-form-control', flex: true })] })), this.state.action === 'label' && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset', style: { marginBottom: '6px' } }, { children: (0, jsx_runtime_1.jsx)(common_1.ControlRow, { label: 'Label', control: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.updateLabel, value: label, style: { flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', blurOnEnter: true, blurOnEscape: true }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.CheckSvg, onClick: this.toggleLabel, className: 'msp-form-control msp-control-button-label', flex: true })] })) }) })), this.state.action === 'action' && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-accent-offset' }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginBottom: '6px' } }, { children: (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }) })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginBottom: '6px' } }, { children: component.representations.map(function (r) { return (0, jsx_runtime_1.jsx)(StructureRepresentationEntry, { group: _this.props.group, representation: r }, r.cell.transform.ref); }) }))] }))] });
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_this.remove = function () { return _this.plugin.managers.structure.component.removeRepresentations(_this.props.group, _this.props.representation); };
|
|
@@ -356,11 +356,11 @@ var StructureRepresentationEntry = /** @class */ (function (_super) {
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StructureRepresentationEntry.prototype.render = function () {
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-representation-entry' }, { children: [repr.parent && (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: "".concat(((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) || '', " Representation"), noOffset: true }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', customUpdate: this.update, noMargin: true }) })), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true, className: 'msp-default-bg', toggleState: false, style: {
|
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position: 'absolute', top: 0, right: '32px', lineHeight: '24px', height: '24px', textAlign: 'right', width: '44px', paddingRight: '6px', background: 'none'
|
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} }
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|
+
} }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: this.props.representation.cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: 'Toggle Visibility', small: true, className: 'msp-default-bg', style: {
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position: 'absolute', top: 0, right: 0, lineHeight: '24px', height: '24px', textAlign: 'right', width: '32px', paddingRight: '6px', background: 'none'
|
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} }
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|
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|
+
} })] }));
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};
|
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return StructureRepresentationEntry;
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|
|
@@ -92,7 +92,7 @@ function getFocusEntries(structure) {
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|
return entries;
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|
}
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var StructureFocusControls = /** @class */ (function (_super) {
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|
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tslib_1.__extends(StructureFocusControls, _super);
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function StructureFocusControls() {
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_this.state = { isBusy: false, showAction: false };
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@@ -105,7 +105,7 @@ var StructureFocusControls = /** @class */ (function (_super) {
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if (d) {
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var entries = getFocusEntries(d);
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if (entries.length > 0) {
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-
presetItems.push(
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+
presetItems.push(tslib_1.__spreadArray([
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action_menu_1.ActionMenu.Header(d.label, { description: d.label })
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], action_menu_1.ActionMenu.createItems(entries, {
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label: function (f) { return f.label; },
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@@ -177,7 +177,7 @@ var StructureFocusControls = /** @class */ (function (_super) {
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var historyItems = [];
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var history = this.plugin.managers.structure.focus.history;
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if (history.length > 0) {
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-
historyItems.push(
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+
historyItems.push(tslib_1.__spreadArray([
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action_menu_1.ActionMenu.Header('History', { description: 'Previously focused on items.' })
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], action_menu_1.ActionMenu.createItems(history, {
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label: function (f) { return f.label; },
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@@ -225,7 +225,7 @@ var StructureFocusControls = /** @class */ (function (_super) {
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title += "\nor use '".concat(binding, "' on element");
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}
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}
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-
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div",
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+
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label })), current && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true, disabled: this.isDisabled }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.CenterFocusStrongSvg, title: 'Select a focus target to center on an show its surroundings. Hold shift to focus on multiple targets.', toggle: this.toggleAction, isSelected: this.state.showAction, disabled: this.isDisabled, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.showAction && (0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actionItems, onSelect: this.selectAction })] });
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};
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return StructureFocusControls;
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}(base_1.PluginUIComponent));
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