molstar 3.3.1 → 3.6.0
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 +202 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/build/viewer/molstar.js.LICENSE.txt +12 -14
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.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 +3 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- 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/util.d.ts +20 -20
- package/lib/cli/cif2bcif/converter.js +1 -1
- package/lib/cli/cif2bcif/index.js +4 -4
- package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/cli/cifschema/util/cif-dic.js +7 -5
- package/lib/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/cli/cifschema/util/generate.js +12 -3
- package/lib/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/apps/docking-viewer/index.js +14 -14
- 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 +26 -24
- 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.d.ts +20 -20
- 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 +12 -12
- package/lib/commonjs/cli/cifschema/index.js +27 -27
- package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +8 -6
- package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
- package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/commonjs/cli/cifschema/util/schema.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 +12 -12
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
- package/lib/commonjs/examples/basic-wrapper/index.js +23 -23
- 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 +7 -7
- 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 +27 -27
- 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.d.ts +1 -0
- package/lib/commonjs/extensions/anvil/behavior.js +14 -14
- package/lib/commonjs/extensions/anvil/prop.js +7 -7
- package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
- 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.d.ts +1 -0
- 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/color.d.ts +397 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
- 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.d.ts +1 -0
- 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.d.ts +1 -0
- 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.d.ts +5 -0
- 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.d.ts +2 -0
- 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.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
- 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.d.ts +1 -0
- 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.d.ts +10 -3
- package/lib/commonjs/mol-data/db/column.js +40 -18
- 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.d.ts +4 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -4
- 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.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +4 -4
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- 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.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +4 -4
- 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.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -4
- 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/chunks/wboit-write.glsl.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader-code.js +2 -1
- package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
- package/lib/commonjs/mol-gl/webgl/buffer.js +16 -17
- package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +5 -5
- package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/program.js +10 -4
- 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/bird.d.ts +8 -8
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +4 -4
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +31 -27
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
- package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema.js +24 -4
- 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 +2 -2
- 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/common.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/common.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
- package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
- package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
- 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 +17 -9
- 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/properties/common.js +1 -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
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- package/lib/mol-model-formats/structure/pdb/to-cif.js +7 -2
- 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/bonds/chem_comp.js +1 -1
- package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
- 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-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
- package/lib/mol-model-props/computed/representations/interactions.d.ts +3 -0
- package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js +3 -2
- package/lib/mol-plugin/commands.d.ts +1 -0
- 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/util/viewport-screenshot.d.ts +3 -0
- 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 +17 -8
- 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/helpers/structure-selection-query.d.ts +1 -1
- package/lib/mol-plugin-state/helpers/structure-selection-query.js +1 -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-state/transforms/representation.d.ts +6 -0
- 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/react18.d.ts +11 -0
- package/lib/mol-plugin-ui/react18.js +34 -0
- package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/mol-plugin-ui/sequence.js +5 -5
- 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 -128
- 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/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.d.ts +1 -1
- package/lib/mol-plugin-ui/structure/focus.js +3 -3
- 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-repr/shape/loci/angle.d.ts +1 -0
- package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
- package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
- package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
- package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
- package/lib/mol-repr/structure/complex-visual.d.ts +3 -0
- package/lib/mol-repr/structure/params.d.ts +4 -0
- package/lib/mol-repr/structure/registry.d.ts +10 -0
- package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
- package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
- package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
- package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
- package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
- package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
- package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
- package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
- package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
- package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
- package/lib/mol-repr/structure/units-visual.d.ts +4 -0
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/element-sphere.d.ts +2 -0
- package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
- package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
- package/lib/mol-repr/structure/visual/util/common.js +1 -24
- package/lib/mol-repr/util.d.ts +2 -1
- package/lib/mol-repr/util.js +2 -2
- package/lib/mol-repr/volume/isosurface.d.ts +5 -0
- package/lib/mol-repr/volume/registry.d.ts +1 -0
- package/lib/mol-script/language/builder.d.ts +1 -0
- 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 +162 -160
- package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
- package/lib/mol-plugin-state/formats/structure.js +0 -61
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return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ style: { marginTop: '6px' } }, { children: componentGroups.map(function (g) { return (0, jsx_runtime_1.jsx)(StructureComponentGroup, { group: g }, g[0].cell.transform.ref); }) }));
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.map(function (t) { return action_menu_1.ActionMenu.Item(t[1], function () { return mng.addRepresentation(_this.props.group, t[0]); }); }), true)
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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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} }), (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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} }
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} })] }));
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/**
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* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
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* Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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*/
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Object.defineProperty(StructureFocusControls.prototype, "isDisabled", {
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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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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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|
|
@@ -10,7 +10,7 @@ var common_1 = require("../controls/common");
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return _super !== null && _super.apply(this, arguments) || this;
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|
}
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|
@@ -40,7 +40,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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return null;
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|
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return (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' }
|
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|
+
return (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' });
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},
|
|
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|
|
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|
|
@@ -52,7 +52,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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|
this.plugin.genericRepresentationControls.forEach(function (provider, key) {
|
|
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|
var _a = provider(_this.plugin.managers.structure.hierarchy.selection), refs = _a[0], labelMultiple = _a[1];
|
|
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|
if (refs.length > 0) {
|
|
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|
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controls.push((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: labelMultiple }
|
|
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|
+
controls.push((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(GenericEntry, { refs: refs, labelMultiple: labelMultiple }) }, key));
|
|
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|
}
|
|
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|
});
|
|
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|
return controls.length > 0 ? controls : null;
|
|
@@ -61,13 +61,13 @@ var GenericEntryListControls = /** @class */ (function (_super) {
|
|
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configurable: true
|
|
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|
});
|
|
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|
GenericEntryListControls.prototype.render = function () {
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|
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|
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return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div",
|
|
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|
+
return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] })) });
|
|
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|
};
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|
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return GenericEntryListControls;
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|
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|
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|
exports.GenericEntryListControls = GenericEntryListControls;
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var GenericEntry = /** @class */ (function (_super) {
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|
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tslib_1.__extends(GenericEntry, _super);
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|
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function GenericEntry() {
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_this.state = { showOptions: false };
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|
@@ -147,7 +147,7 @@ var GenericEntry = /** @class */ (function (_super) {
|
|
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else {
|
|
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|
label = "".concat(refs.length, " ").concat(labelMultiple || 'Objects');
|
|
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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.jsxs)("button", tslib_1.__assign({ className: 'msp-form-control 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", { children: description })] })), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: pivot.cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, className: 'msp-form-control', onClick: this.toggleVisibility, title: "".concat(pivot.cell.state.isHidden ? 'Show' : 'Hide'), small: true, flex: true }), refs.length === 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleOptions, title: 'Options', toggleState: this.state.showOptions, flex: true })] })), (refs.length === 1 && this.state.showOptions && pivot.cell.parent) && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }) })) })] });
|
|
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|
};
|
|
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|
return GenericEntry;
|
|
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|
}(base_1.PurePluginUIComponent));
|
|
@@ -16,7 +16,7 @@ var update_transform_1 = require("../state/update-transform");
|
|
|
16
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|
var selection_1 = require("./selection");
|
|
17
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|
// TODO details, options (e.g. change text for labels)
|
|
18
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|
var StructureMeasurementsControls = /** @class */ (function (_super) {
|
|
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|
-
|
|
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|
+
tslib_1.__extends(StructureMeasurementsControls, _super);
|
|
20
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|
function StructureMeasurementsControls() {
|
|
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|
return _super !== null && _super.apply(this, arguments) || this;
|
|
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|
}
|
|
@@ -28,13 +28,13 @@ var StructureMeasurementsControls = /** @class */ (function (_super) {
|
|
|
28
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|
};
|
|
29
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|
};
|
|
30
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|
StructureMeasurementsControls.prototype.renderControls = function () {
|
|
31
|
-
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(MeasurementControls, {}
|
|
31
|
+
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(MeasurementControls, {}), (0, jsx_runtime_1.jsx)(MeasurementList, {})] });
|
|
32
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|
};
|
|
33
33
|
return StructureMeasurementsControls;
|
|
34
34
|
}(base_1.CollapsableControls));
|
|
35
35
|
exports.StructureMeasurementsControls = StructureMeasurementsControls;
|
|
36
36
|
var MeasurementList = /** @class */ (function (_super) {
|
|
37
|
-
|
|
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|
+
tslib_1.__extends(MeasurementList, _super);
|
|
38
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|
function MeasurementList() {
|
|
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|
return _super !== null && _super.apply(this, arguments) || this;
|
|
40
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|
}
|
|
@@ -51,17 +51,17 @@ var MeasurementList = /** @class */ (function (_super) {
|
|
|
51
51
|
if (cell.obj)
|
|
52
52
|
group.push((0, jsx_runtime_1.jsx)(MeasurementEntry, { cell: cell }, cell.obj.id));
|
|
53
53
|
}
|
|
54
|
-
return group.length ? (0, jsx_runtime_1.jsx)(common_1.ExpandGroup,
|
|
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|
+
return group.length ? (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: header, initiallyExpanded: true }, { children: group })) : null;
|
|
55
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|
};
|
|
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|
MeasurementList.prototype.render = function () {
|
|
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|
var measurements = this.plugin.managers.structure.measurement.state;
|
|
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { marginTop: '6px' } }, { children: [this.renderGroup(measurements.labels, 'Labels'), this.renderGroup(measurements.distances, 'Distances'), this.renderGroup(measurements.angles, 'Angles'), this.renderGroup(measurements.dihedrals, 'Dihedrals'), this.renderGroup(measurements.orientations, 'Orientations'), this.renderGroup(measurements.planes, 'Planes')] }));
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row', onMouseEnter: function () { return _this.highlight(e.loci); }, onMouseLeave: function () { return _this.plugin.managers.interactivity.lociHighlights.clearHighlights(); } }, { children: [(0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ noOverflow: true, title: 'Click to focus. Hover to highlight.', onClick: function () { return _this.focusLoci(e.loci); }, style: { width: 'auto', textAlign: 'left' } }, { children: [idx, ". ", (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: e.label } })] })), history.length > 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ArrowUpwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'up'); }, flex: '20px', title: 'Move up' }), history.length > 1 && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.ArrowDownwardSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.moveHistory(e, 'down'); }, flex: '20px', title: 'Move down' }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: function () { return _this.plugin.managers.structure.selection.modifyHistory(e, 'remove'); }, flex: true, title: 'Remove' })] }), e.id);
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction }), entries.length > 0 && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: entries })), entries.length === 0 && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset msp-help-text' }, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-help-description' }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.HelpOutlineSvg, inline: true }), "Add one or more selections (toggle ", (0, jsx_runtime_1.jsx)(selection_1.ToggleSelectionModeButton, { inline: true }), " mode)"] })) }))] });
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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.ToggleButton, { icon: icons_1.AddSvg, label: 'Add', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.state.isBusy, className: 'msp-btn-apply-simple' }), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.action === 'add' && this.add(), this.state.action === 'options' && (0, jsx_runtime_1.jsx)(MeasurementsOptions, {})] });
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return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: measurement_1.StructureMeasurementParams, values: measurements.options, onChangeValues: this.changed, isDisabled: this.state.isDisabled }) }));
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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', onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight }, { children: [(0, jsx_runtime_1.jsx)("button", tslib_1.__assign({ className: 'msp-form-control msp-control-button-label msp-no-overflow', title: 'Click to focus. Hover to highlight.', onClick: this.focus, style: { width: 'auto', textAlign: 'left' } }, { children: (0, jsx_runtime_1.jsx)("span", { dangerouslySetInnerHTML: { __html: this.label } }) })), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: cell.state.isHidden ? icons_1.VisibilityOffOutlinedSvg : icons_1.VisibilityOutlinedSvg, toggleState: false, small: true, className: 'msp-form-control', onClick: this.toggleVisibility, flex: true, title: cell.state.isHidden ? 'Show' : 'Hide' }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.DeleteOutlinedSvg, small: true, className: 'msp-form-control', onClick: this.delete, flex: true, title: 'Delete', toggleState: false }), (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleUpdate, flex: true, title: 'Actions', toggleState: this.state.showUpdate })] }), obj.id), this.state.showUpdate && cell.parent && (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-accent-offset' }, { children: [(0, jsx_runtime_1.jsx)(action_menu_1.ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: 'Options', noOffset: true }, { children: (0, jsx_runtime_1.jsx)(update_transform_1.UpdateTransformControl, { state: cell.parent, transform: cell.transform, customHeader: 'none', autoHideApply: true }) }))] })) })] });
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var config_1 = require("../../mol-plugin/config");
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var component_1 = require("../../mol-plugin-state/manager/structure/component");
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var StructureQuickStylesControls = /** @class */ (function (_super) {
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tslib_1.__extends(StructureQuickStylesControls, _super);
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function StructureQuickStylesControls() {
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return _super !== null && _super.apply(this, arguments) || this;
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@@ -30,20 +30,20 @@ var StructureQuickStylesControls = /** @class */ (function (_super) {
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return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(QuickStyles, {}) });
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return StructureQuickStylesControls;
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}(base_1.CollapsableControls));
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exports.StructureQuickStylesControls = StructureQuickStylesControls;
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var QuickStyles = /** @class */ (function (_super) {
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tslib_1.__extends(QuickStyles, _super);
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function QuickStyles() {
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}
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QuickStyles.prototype.default = function () {
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return
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return tslib_1.__awaiter(this, void 0, void 0, function () {
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return
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return tslib_1.__generator(this, function (_a) {
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switch (_a.label) {
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case 0:
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structures = this.plugin.managers.structure.hierarchy.selection.structures;
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@@ -65,9 +65,9 @@ var QuickStyles = /** @class */ (function (_super) {
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});
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};
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QuickStyles.prototype.illustrative = function () {
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return
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return
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return tslib_1.__generator(this, function (_a) {
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switch (_a.label) {
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case 0:
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structures = this.plugin.managers.structure.hierarchy.selection.structures;
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@@ -94,10 +94,10 @@ var QuickStyles = /** @class */ (function (_super) {
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});
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};
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QuickStyles.prototype.stylized = function () {
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return
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return tslib_1.__awaiter(this, void 0, void 0, function () {
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var pp;
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return
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return tslib_1.__generator(this, function (_a) {
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this.plugin.managers.structure.component.setOptions(tslib_1.__assign(tslib_1.__assign({}, this.plugin.managers.structure.component.state.options), { ignoreLight: true }));
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pp = this.plugin.canvas3d.props.postprocessing;
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this.plugin.canvas3d.setProps({
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@@ -123,7 +123,7 @@ var QuickStyles = /** @class */ (function (_super) {
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};
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return (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, title: 'Applies default representation preset. Set outline and occlusion effects to defaults.', onClick: function () { return _this.default(); }, style: { width: 'auto' } }, { children: "Default" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ noOverflow: true, title: 'Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.', onClick: function () { return _this.stylized(); }, style: { width: 'auto' } }, { children: "Stylized" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ noOverflow: true, title: 'Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.', onClick: function () { return _this.illustrative(); }, style: { width: 'auto' } }, { children: "Illustrative" }))] }));
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};
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return QuickStyles;
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}(base_1.PurePluginUIComponent));
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