molstar 3.3.0 → 3.5.0
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/lib/apps/docking-viewer/index.html +36 -36
- 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/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/cif2bcif/converter.js +1 -1
- package/lib/cli/cif2bcif/index.js +4 -4
- 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 +12 -12
- 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/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.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.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 +22 -5
- 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.d.ts +2 -2
- 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.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.js +3 -3
- 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.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.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.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.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +5 -5
- 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/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 +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 +9 -6
- 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.d.ts +1 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +6 -4
- 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 +5 -22
- 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
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- package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +6 -4
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- package/lib/mol-gl/webgl/context.d.ts +1 -1
- package/lib/mol-gl/webgl/context.js +2 -2
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- 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-math/geometry/common.d.ts +2 -1
- package/lib/mol-math/geometry/common.js +1 -1
- package/lib/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
- package/lib/mol-math/geometry/gaussian-density/cpu.js +2 -2
- package/lib/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
- package/lib/mol-math/geometry/gaussian-density/gpu.js +7 -7
- package/lib/mol-math/geometry/gaussian-density.d.ts +2 -2
- package/lib/mol-math/geometry/gaussian-density.js +1 -1
- package/lib/mol-math/geometry/molecular-surface.d.ts +2 -1
- package/lib/mol-math/geometry/molecular-surface.js +2 -2
- package/lib/mol-math/geometry/primitives/box3d.js +2 -1
- package/lib/mol-math/geometry/primitives/sphere3d.js +12 -6
- 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/structure/structure/structure.js +4 -1
- package/lib/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
- package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +4 -2
- package/lib/mol-model/structure/structure/unit.js +1 -18
- 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-model-props/computed/representations/interactions-inter-unit-cylinder.js +9 -3
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +10 -5
- package/lib/mol-model-props/integrative/cross-link-restraint/representation.js +10 -1
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
- 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/root-structure.js +1 -1
- 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/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.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-repr/structure/visual/bond-inter-unit-cylinder.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +20 -10
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts +1 -1
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -5
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +16 -6
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +8 -3
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.js +10 -1
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +10 -1
- package/lib/mol-repr/structure/visual/element-point.d.ts +1 -1
- package/lib/mol-repr/structure/visual/element-point.js +22 -3
- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +1 -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.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/util/common.d.ts +1 -3
- package/lib/mol-repr/structure/visual/util/common.js +1 -24
- package/lib/mol-repr/structure/visual/util/element.js +36 -2
- package/lib/mol-repr/structure/visual/util/link.d.ts +13 -3
- package/lib/mol-repr/structure/visual/util/link.js +55 -6
- 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 +160 -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)("a", { className: 'msp-logo', href: 'https://molstar.org', target: '_blank' }
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return (0, jsx_runtime_1.jsx)("a", { className: 'msp-logo', href: 'https://molstar.org', target: '_blank' });
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var Viewport = function () { return (0, jsx_runtime_1.jsx)(canvas_1.ViewportCanvas, { logo: exports.Logo }
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var Viewport = function () { return (0, jsx_runtime_1.jsx)(canvas_1.ViewportCanvas, { logo: exports.Logo }); };
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exports.Viewport = Viewport;
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@@ -242,9 +242,9 @@ var Representation;
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var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, currentProps, props), currentData);
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Object.assign(currentProps, props, qualityProps);
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return mol_task_1.Task.create("Creating or updating '".concat(label, "' representation"), function (runtime) { return
|
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return mol_task_1.Task.create("Creating or updating '".concat(label, "' representation"), function (runtime) { 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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case 0:
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i = 0, il = reprList.length;
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|
@@ -331,8 +331,8 @@ var Representation;
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if (props === void 0) { props = {}; }
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var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, currentProps, props));
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Object.assign(currentProps, props, qualityProps);
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return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return
|
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return
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+
return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
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return tslib_1.__generator(this, function (_a) {
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// TODO
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geometryState.add(0, renderObject.id);
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geometryState.snapshot();
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@@ -31,17 +31,17 @@ var SharedParams = {
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color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
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arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
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};
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var LinesParams =
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var VectorsParams =
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var ArcParams =
|
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var SectorParams =
|
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+
var LinesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }) });
|
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+
var VectorsParams = tslib_1.__assign({}, LinesParams);
|
|
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+
var ArcParams = tslib_1.__assign({}, LinesParams);
|
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+
var SectorParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { ignoreLight: param_definition_1.ParamDefinition.Boolean(true), sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }) });
|
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|
var AngleVisuals = {
|
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'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
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'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
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'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (
|
|
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'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
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|
+
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
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+
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
41
|
+
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity })); }, modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
42
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
43
43
|
};
|
|
44
|
-
exports.AngleParams =
|
|
44
|
+
exports.AngleParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, VectorsParams), ArcParams), SectorParams), common_1.LociLabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['vectors', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(AngleVisuals)) });
|
|
45
45
|
//
|
|
46
46
|
function getAngleState() {
|
|
47
47
|
return {
|
|
@@ -16,4 +16,4 @@ exports.MeasurementRepresentationCommonTextParams = {
|
|
|
16
16
|
textColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black, { isEssential: true }),
|
|
17
17
|
textSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
|
|
18
18
|
};
|
|
19
|
-
exports.LociLabelTextParams =
|
|
19
|
+
exports.LociLabelTextParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, text_1.Text.Params), exports.MeasurementRepresentationCommonTextParams), { borderWidth: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 0.5, step: 0.01 }) });
|
|
@@ -31,22 +31,22 @@ var SharedParams = {
|
|
|
31
31
|
color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
|
|
32
32
|
arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
|
|
33
33
|
};
|
|
34
|
-
var LinesParams =
|
|
35
|
-
var VectorsParams =
|
|
36
|
-
var ExtendersParams =
|
|
37
|
-
var ArmsParams =
|
|
38
|
-
var ArcParams =
|
|
39
|
-
var SectorParams =
|
|
34
|
+
var LinesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
35
|
+
var VectorsParams = tslib_1.__assign({}, LinesParams);
|
|
36
|
+
var ExtendersParams = tslib_1.__assign({}, LinesParams);
|
|
37
|
+
var ArmsParams = tslib_1.__assign({}, LinesParams);
|
|
38
|
+
var ArcParams = tslib_1.__assign({}, LinesParams);
|
|
39
|
+
var SectorParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { ignoreLight: param_definition_1.ParamDefinition.Boolean(true), sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }) });
|
|
40
40
|
var DihedralVisuals = {
|
|
41
|
-
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
42
|
-
'extenders': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
43
|
-
'connector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
44
|
-
'arms': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
45
|
-
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
46
|
-
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (
|
|
47
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
41
|
+
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
42
|
+
'extenders': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
43
|
+
'connector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
44
|
+
'arms': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
45
|
+
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
46
|
+
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity })); }, modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
47
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
48
48
|
};
|
|
49
|
-
exports.DihedralParams =
|
|
49
|
+
exports.DihedralParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, VectorsParams), ExtendersParams), ArmsParams), ArcParams), SectorParams), common_1.LociLabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['extenders', 'arms', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(DihedralVisuals)) });
|
|
50
50
|
//
|
|
51
51
|
function getDihedralState() {
|
|
52
52
|
return {
|
|
@@ -25,13 +25,13 @@ var geometry_1 = require("../../../mol-math/geometry");
|
|
|
25
25
|
var SharedParams = {
|
|
26
26
|
unitLabel: param_definition_1.ParamDefinition.Text('\u212B', { isEssential: true })
|
|
27
27
|
};
|
|
28
|
-
var LineParams =
|
|
29
|
-
var TextParams =
|
|
28
|
+
var LineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen, { isEssential: true }), linesSize: param_definition_1.ParamDefinition.Numeric(0.075, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
29
|
+
var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), SharedParams);
|
|
30
30
|
var DistanceVisuals = {
|
|
31
|
-
'lines': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getLinesShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
32
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
31
|
+
'lines': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getLinesShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
32
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
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exports.DistanceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, LineParams), TextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['lines', 'text'], param_definition_1.ParamDefinition.objectToOptions(DistanceVisuals)) });
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function getDistanceState() {
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@@ -17,11 +17,11 @@ var text_builder_1 = require("../../../mol-geo/geometry/text/text-builder");
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var label_1 = require("../../../mol-theme/label");
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var TextParams =
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var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), { offsetZ: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }) });
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'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
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'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
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exports.LabelParams =
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exports.LabelParams = tslib_1.__assign(tslib_1.__assign({}, TextParams), { scaleByRadius: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['text'], param_definition_1.ParamDefinition.objectToOptions(LabelVisuals)) });
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//
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function label(info, condensed) {
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scaleFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
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radiusScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 10, step: 0.1 })
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var AxesParams =
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var EllipsoidParams =
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'box': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getBoxShape, mesh_1.Mesh.Utils); },
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'ellipsoid': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getEllipsoidShape, mesh_1.Mesh.Utils); },
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exports.OrientationParams =
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exports.OrientationParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, AxesParams), BoxParams), EllipsoidParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['box'], param_definition_1.ParamDefinition.objectToOptions(OrientationVisuals)) });
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//
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function getAxesName(locis) {
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var _PlaneParams =
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var _PlaneParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), scaleFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 10, step: 0.1 }) });
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exports.PlaneParams =
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exports.PlaneParams = tslib_1.__assign(tslib_1.__assign({}, _PlaneParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['plane'], param_definition_1.ParamDefinition.objectToOptions(PlaneVisuals)) });
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function getPlaneName(locis) {
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@@ -31,11 +31,11 @@ var CellAttachment = {
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corner: 'Corner',
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var CellParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { cellColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), cellScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), ref: param_definition_1.ParamDefinition.Select('model', param_definition_1.ParamDefinition.objectToOptions(CellRef), { isEssential: true }), attachment: param_definition_1.ParamDefinition.Select('corner', param_definition_1.ParamDefinition.objectToOptions(CellAttachment), { isEssential: true }) });
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'mesh': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getUnitcellShape, mesh_1.Mesh.Utils); },
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exports.UnitcellParams =
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exports.UnitcellParams = tslib_1.__assign({}, CellParams);
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function getUnitcellMesh(data, props, mesh) {
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@@ -84,9 +84,9 @@ function ShapeRepresentation(getShape, geometryUtils, builder) {
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return mol_task_1.Task.create('ShapeRepresentation.create', function (runtime) { return
|
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return mol_task_1.Task.create('ShapeRepresentation.create', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
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|
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return
|
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return tslib_1.__generator(this, function (_b) {
|
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@@ -45,10 +45,10 @@ function ComplexRepresentation(label, ctx, getParams, visualCtor) {
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|
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}
|
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|
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return mol_task_1.Task.create('Creating or updating ComplexRepresentation', function (runtime) { return
|
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+
return mol_task_1.Task.create('Creating or updating ComplexRepresentation', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
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var newVisual, promise;
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|
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return
|
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return tslib_1.__generator(this, function (_b) {
|
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|
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|
@@ -241,9 +241,9 @@ function ComplexVisual(builder, materialId) {
|
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}
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exports.ComplexVisual = ComplexVisual;
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// mesh
|
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exports.ComplexMeshParams =
|
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exports.ComplexMeshParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureMeshParams), params_1.StructureParams);
|
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|
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return ComplexVisual(
|
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+
return ComplexVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
|
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builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
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state.createGeometry = true;
|
|
@@ -251,9 +251,9 @@ function ComplexMeshVisual(builder, materialId) {
|
|
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}
|
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exports.ComplexMeshVisual = ComplexMeshVisual;
|
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|
// cylinders
|
|
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|
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exports.ComplexCylindersParams =
|
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|
+
exports.ComplexCylindersParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureCylindersParams), params_1.StructureParams);
|
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|
|
256
|
-
return ComplexVisual(
|
|
256
|
+
return ComplexVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
|
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|
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|
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state.updateSize = true;
|
|
@@ -261,9 +261,9 @@ function ComplexCylindersVisual(builder, materialId) {
|
|
|
261
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|
}
|
|
262
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|
exports.ComplexCylindersVisual = ComplexCylindersVisual;
|
|
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|
// lines
|
|
264
|
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exports.ComplexLinesParams =
|
|
264
|
+
exports.ComplexLinesParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureLinesParams), params_1.StructureParams);
|
|
265
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|
function ComplexLinesVisual(builder, materialId) {
|
|
266
|
-
return ComplexVisual(
|
|
266
|
+
return ComplexVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
|
|
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|
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
|
|
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|
if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
|
|
269
269
|
state.updateSize = true;
|
|
@@ -271,9 +271,9 @@ function ComplexLinesVisual(builder, materialId) {
|
|
|
271
271
|
}
|
|
272
272
|
exports.ComplexLinesVisual = ComplexLinesVisual;
|
|
273
273
|
// text
|
|
274
|
-
exports.ComplexTextParams =
|
|
274
|
+
exports.ComplexTextParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureTextParams), params_1.StructureParams);
|
|
275
275
|
function ComplexTextVisual(builder, materialId) {
|
|
276
|
-
return ComplexVisual(
|
|
276
|
+
return ComplexVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
|
|
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|
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
|
|
278
278
|
if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
|
|
279
279
|
state.updateSize = true;
|
|
@@ -303,9 +303,9 @@ function ComplexTextVisual(builder, materialId) {
|
|
|
303
303
|
}
|
|
304
304
|
exports.ComplexTextVisual = ComplexTextVisual;
|
|
305
305
|
// direct-volume
|
|
306
|
-
exports.ComplexDirectVolumeParams =
|
|
306
|
+
exports.ComplexDirectVolumeParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureDirectVolumeParams), params_1.StructureParams);
|
|
307
307
|
function ComplexDirectVolumeVisual(builder, materialId) {
|
|
308
|
-
return ComplexVisual(
|
|
308
|
+
return ComplexVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
|
|
309
309
|
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
|
|
310
310
|
if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
|
|
311
311
|
state.createGeometry = true;
|
|
@@ -313,9 +313,9 @@ function ComplexDirectVolumeVisual(builder, materialId) {
|
|
|
313
313
|
}
|
|
314
314
|
exports.ComplexDirectVolumeVisual = ComplexDirectVolumeVisual;
|
|
315
315
|
// texture-mesh
|
|
316
|
-
exports.ComplexTextureMeshParams =
|
|
316
|
+
exports.ComplexTextureMeshParams = tslib_1.__assign(tslib_1.__assign({}, params_1.StructureTextureMeshParams), params_1.StructureParams);
|
|
317
317
|
function ComplexTextureMeshVisual(builder, materialId) {
|
|
318
|
-
return ComplexVisual(
|
|
318
|
+
return ComplexVisual(tslib_1.__assign(tslib_1.__assign({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
|
|
319
319
|
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
|
|
320
320
|
if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
|
|
321
321
|
state.createGeometry = true;
|
|
@@ -26,11 +26,11 @@ exports.StructureParams = {
|
|
|
26
26
|
unitKinds: getUnitKindsParam(['atomic', 'spheres']),
|
|
27
27
|
includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }),
|
|
28
28
|
};
|
|
29
|
-
exports.StructureMeshParams =
|
|
30
|
-
exports.StructureSpheresParams =
|
|
31
|
-
exports.StructureCylindersParams =
|
|
32
|
-
exports.StructurePointsParams =
|
|
33
|
-
exports.StructureLinesParams =
|
|
34
|
-
exports.StructureTextParams =
|
|
35
|
-
exports.StructureDirectVolumeParams =
|
|
36
|
-
exports.StructureTextureMeshParams =
|
|
29
|
+
exports.StructureMeshParams = tslib_1.__assign({}, mesh_1.Mesh.Params);
|
|
30
|
+
exports.StructureSpheresParams = tslib_1.__assign({}, spheres_1.Spheres.Params);
|
|
31
|
+
exports.StructureCylindersParams = tslib_1.__assign({}, cylinders_1.Cylinders.Params);
|
|
32
|
+
exports.StructurePointsParams = tslib_1.__assign({}, points_1.Points.Params);
|
|
33
|
+
exports.StructureLinesParams = tslib_1.__assign({}, lines_1.Lines.Params);
|
|
34
|
+
exports.StructureTextParams = tslib_1.__assign({}, text_1.Text.Params);
|
|
35
|
+
exports.StructureDirectVolumeParams = tslib_1.__assign({}, direct_volume_1.DirectVolume.Params);
|
|
36
|
+
exports.StructureTextureMeshParams = tslib_1.__assign({}, texture_mesh_1.TextureMesh.Params);
|
|
@@ -24,7 +24,7 @@ var line_1 = require("./representation/line");
|
|
|
24
24
|
var gaussian_volume_1 = require("./representation/gaussian-volume");
|
|
25
25
|
var backbone_1 = require("./representation/backbone");
|
|
26
26
|
var StructureRepresentationRegistry = /** @class */ (function (_super) {
|
|
27
|
-
|
|
27
|
+
tslib_1.__extends(StructureRepresentationRegistry, _super);
|
|
28
28
|
function StructureRepresentationRegistry() {
|
|
29
29
|
var _this = _super.call(this) || this;
|
|
30
30
|
(0, object_1.objectForEach)(StructureRepresentationRegistry.BuiltIn, function (p, k) {
|
|
@@ -20,7 +20,7 @@ var BackboneVisuals = {
|
|
|
20
20
|
'polymer-backbone-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer backbone sphere', ctx, getParams, polymer_backbone_sphere_1.PolymerBackboneSphereVisual); },
|
|
21
21
|
'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
|
|
22
22
|
};
|
|
23
|
-
exports.BackboneParams =
|
|
23
|
+
exports.BackboneParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, polymer_backbone_sphere_1.PolymerBackboneSphereParams), polymer_backbone_cylinder_1.PolymerBackboneCylinderParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 3, step: 0.1 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(BackboneVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
24
24
|
function getBackboneParams(ctx, structure) {
|
|
25
25
|
var params = param_definition_1.ParamDefinition.clone(exports.BackboneParams);
|
|
26
26
|
var hasGaps = false;
|
|
@@ -22,7 +22,7 @@ var BallAndStickVisuals = {
|
|
|
22
22
|
'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
|
|
23
23
|
'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
|
|
24
24
|
};
|
|
25
|
-
exports.BallAndStickParams =
|
|
25
|
+
exports.BallAndStickParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
26
26
|
function getBallAndStickParams(ctx, structure) {
|
|
27
27
|
return param_definition_1.ParamDefinition.clone(exports.BallAndStickParams);
|
|
28
28
|
}
|
|
@@ -21,7 +21,7 @@ var CarbohydrateVisuals = {
|
|
|
21
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'carbohydrate-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate link cylinder', ctx, getParams, carbohydrate_link_cylinder_1.CarbohydrateLinkVisual); },
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'carbohydrate-terminal-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate terminal link cylinder', ctx, getParams, carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkVisual); },
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};
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exports.CarbohydrateParams =
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exports.CarbohydrateParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, carbohydrate_symbol_mesh_1.CarbohydrateSymbolParams), carbohydrate_link_cylinder_1.CarbohydrateLinkParams), carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], param_definition_1.ParamDefinition.objectToOptions(CarbohydrateVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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function getCarbohydrateParams(ctx, structure) {
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return param_definition_1.ParamDefinition.clone(exports.CarbohydrateParams);
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}
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@@ -27,7 +27,7 @@ var CartoonVisuals = {
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'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
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'direction-wedge': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer direction wedge', ctx, getParams, polymer_direction_wedge_1.PolymerDirectionVisual); }
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};
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exports.CartoonParams =
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exports.CartoonParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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function getCartoonParams(ctx, structure) {
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var params = param_definition_1.ParamDefinition.clone(exports.CartoonParams);
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var hasNucleotides = false;
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@@ -61,9 +61,9 @@ exports.CartoonRepresentationProvider = (0, representation_2.StructureRepresenta
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defaultSizeTheme: { name: 'uniform' },
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isApplicable: function (structure) { return structure.polymerResidueCount > 0; },
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ensureCustomProperties: {
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attach: function (ctx, structure) { return
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attach: function (ctx, structure) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
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var _i, _a, m;
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return
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+
return tslib_1.__generator(this, function (_b) {
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switch (_b.label) {
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case 0: return [4 /*yield*/, secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure, void 0, true)];
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case 1:
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@@ -21,7 +21,7 @@ var EllipsoidVisuals = {
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'intra-bond': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
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'inter-bond': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
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};
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exports.EllipsoidParams =
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+
exports.EllipsoidParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, ellipsoid_mesh_1.EllipsoidMeshParams), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }), linkCap: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(EllipsoidVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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function getEllipsoidParams(ctx, structure) {
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return param_definition_1.ParamDefinition.clone(exports.EllipsoidParams);
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}
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@@ -19,7 +19,7 @@ var GaussianSurfaceVisuals = {
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'structure-gaussian-surface-mesh': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Structure-Gaussian surface mesh', ctx, getParams, gaussian_surface_mesh_1.StructureGaussianSurfaceVisual); },
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'gaussian-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Gaussian surface wireframe', ctx, getParams, gaussian_surface_wireframe_1.GaussianWireframeVisual); },
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};
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exports.GaussianSurfaceParams =
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+
exports.GaussianSurfaceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_surface_mesh_1.GaussianSurfaceMeshParams), gaussian_surface_wireframe_1.GaussianWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(GaussianSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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function getGaussianSurfaceParams(ctx, structure) {
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return param_definition_1.ParamDefinition.clone(exports.GaussianSurfaceParams);
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}
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@@ -15,7 +15,7 @@ var GaussianVolumeVisuals = {
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'gaussian-volume': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Gaussian volume', ctx, getParams, gaussian_density_volume_1.GaussianDensityVolumeVisual); },
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'units-gaussian-volume': function (ctx, getParams) { return (0, representation_1.UnitsRepresentation)('Units-Gaussian volume', ctx, getParams, gaussian_density_volume_1.UnitsGaussianDensityVolumeVisual); }
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};
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exports.GaussianVolumeParams =
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+
exports.GaussianVolumeParams = tslib_1.__assign(tslib_1.__assign({}, gaussian_density_volume_1.GaussianDensityVolumeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-volume'], param_definition_1.ParamDefinition.objectToOptions(GaussianVolumeVisuals)) });
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function getGaussianVolumeParams(ctx, structure) {
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var p = param_definition_1.ParamDefinition.clone(exports.GaussianVolumeParams);
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p.jumpLength = param_definition_1.ParamDefinition.Numeric(4, { min: 0, max: 20, step: 0.1 });
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@@ -15,7 +15,7 @@ var marker_action_1 = require("../../../mol-util/marker-action");
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var LabelVisuals = {
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'label-text': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Label text', ctx, getParams, label_text_1.LabelTextVisual); },
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};
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exports.LabelParams =
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+
exports.LabelParams = tslib_1.__assign(tslib_1.__assign({}, label_text_1.LabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['label-text'], param_definition_1.ParamDefinition.objectToOptions(LabelVisuals)) });
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function getLabelParams(ctx, structure) {
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return param_definition_1.ParamDefinition.clone(exports.LabelParams);
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}
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@@ -23,7 +23,7 @@ var LineVisuals = {
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'element-point': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Points', ctx, getParams, element_point_1.ElementPointVisual); },
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'element-cross': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Crosses', ctx, getParams, element_cross_1.ElementCrossVisual); },
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};
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exports.LineParams =
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+
exports.LineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, bond_intra_unit_line_1.IntraUnitBondLineParams), bond_inter_unit_line_1.InterUnitBondLineParams), element_point_1.ElementPointParams), element_cross_1.ElementCrossParams), { multipleBonds: param_definition_1.ParamDefinition.Select('offset', param_definition_1.ParamDefinition.arrayToOptions(['off', 'symmetric', 'offset'])), includeParent: param_definition_1.ParamDefinition.Boolean(false), sizeFactor: param_definition_1.ParamDefinition.Numeric(2, { min: 0.01, max: 10, step: 0.01 }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], param_definition_1.ParamDefinition.objectToOptions(LineVisuals)) });
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function getLineParams(ctx, structure) {
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var params = param_definition_1.ParamDefinition.clone(exports.LineParams);
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params.pointStyle.defaultValue = 'circle';
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