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-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
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- package/lib/mol-model/structure/model/types/saccharides.js +8 -0
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- package/lib/mol-model/structure/structure/carbohydrates/constants.js +6 -9
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- package/lib/mol-model/structure/structure/unit/bonds/inter-compute.d.ts +1 -0
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- 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
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- package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
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- package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
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- package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
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- package/lib/mol-plugin-ui/skin/light.scss +1 -1
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- 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
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- 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
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- 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
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- 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
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- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
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- package/lib/mol-task/util/scheduler.js +7 -7
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- 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
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [header && (this.props.multiselect && this.state.isExpanded ? this.multiselectHeader : this.basicHeader), (0, jsx_runtime_1.jsx)("div",
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [header && (this.props.multiselect && this.state.isExpanded ? this.multiselectHeader : this.basicHeader), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: this.props.noOffset ? void 0 : this.props.noAccent ? 'msp-control-offset' : 'msp-accent-offset' }, { children: (!header || this.state.isExpanded) && items.map(function (x, i) {
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return (0, jsx_runtime_1.jsx)(Action, { item: x, onSelect: onSelect, current: current, multiselect: _this.props.multiselect }, i);
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|
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}) })
|
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}) }))] });
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@@ -221,7 +221,7 @@ var Action = function (_a) {
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return (0, jsx_runtime_1.jsxs)(common_1.Button,
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return (0, jsx_runtime_1.jsxs)(common_1.Button, tslib_1.__assign({ icon: item.icon, noOverflow: true, className: 'msp-action-menu-button', onClick: function (e) { return onSelect(multiselect ? [item] : item, e); }, disabled: item.disabled, style: style, title: item.description }, { children: [isCurrent || item.selected ? (0, jsx_runtime_1.jsx)("b", { children: item.label }) : item.label, item.addOn] }));
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@@ -11,11 +11,11 @@ var jsx_runtime_1 = require("react/jsx-runtime");
|
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|
*/
|
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var color_1 = require("../../mol-util/color");
|
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var string_1 = require("../../mol-util/string");
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var React =
|
|
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var React = tslib_1.__importStar(require("react"));
|
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var common_1 = require("./common");
|
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|
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var CombinedColorControl = /** @class */ (function (_super) {
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|
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+
tslib_1.__extends(CombinedColorControl, _super);
|
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function CombinedColorControl() {
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var _this = _super !== null && _super.apply(this, arguments) || this;
|
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_this.state = {
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|
@@ -65,12 +65,12 @@ var CombinedColorControl = /** @class */ (function (_super) {
|
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|
};
|
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CombinedColorControl.prototype.swatch = function () {
|
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|
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return (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-combined-color-swatch' }, { children: swatches_1.DefaultColorSwatch.map(function (c) { return (0, jsx_runtime_1.jsx)(common_1.Button, { inline: true, "data-color": c[1], onClick: _this.onClickSwatch, style: { background: color_1.Color.toStyle(c[1]) } }, c[1]); }) }));
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};
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|
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CombinedColorControl.prototype.render = function () {
|
|
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var label = this.props.param.label || (0, string_1.camelCaseToWords)(this.props.name);
|
|
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var _a = color_1.Color.toRgb(this.props.value), r = _a[0], g = _a[1], b = _a[2];
|
|
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.ControlRow, { title: this.props.param.description, label: label, control: (0, jsx_runtime_1.jsx)(common_1.Button, { onClick: this.toggleExpanded, inline: true, className: 'msp-combined-color-button', style: { background: color_1.Color.toStyle(this.props.value) } }
|
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+
return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(common_1.ControlRow, { title: this.props.param.description, label: label, control: (0, jsx_runtime_1.jsx)(common_1.Button, { onClick: this.toggleExpanded, inline: true, className: 'msp-combined-color-button', style: { background: color_1.Color.toStyle(this.props.value) } }) }), this.state.isExpanded && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: [this.swatch(), (0, jsx_runtime_1.jsx)(common_1.ControlRow, { label: 'RGB', className: 'msp-control-label-short', control: (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { display: 'flex', textAlignLast: 'center', left: '80px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onR, numeric: true, value: r, delayMs: 250, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }), (0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onG, numeric: true, value: g, delayMs: 250, style: { order: 2, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true }), (0, jsx_runtime_1.jsx)(common_1.TextInput, { onChange: this.onB, numeric: true, value: b, delayMs: 250, style: { order: 3, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', onEnter: this.props.onEnter, blurOnEnter: true, blurOnEscape: true })] })) }), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.onLighten, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control' }, { children: "Lighten" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: this.onDarken, style: { order: 1, flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control' }, { children: "Darken" }))] }))] }))] });
|
|
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};
|
|
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return CombinedColorControl;
|
|
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|
|
@@ -80,8 +80,8 @@ function ColorOptions() {
|
|
|
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if (_colors)
|
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return _colors;
|
|
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_colors = (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: swatches_1.DefaultColorSwatch.map(function (v) {
|
|
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|
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return (0, jsx_runtime_1.jsx)("option",
|
|
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|
-
}) }
|
|
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|
+
return (0, jsx_runtime_1.jsx)("option", tslib_1.__assign({ value: v[1], style: { background: "".concat(color_1.Color.toStyle(v[1])) } }, { children: (0, string_1.stringToWords)(v[0]) }), v[1]);
|
|
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}) });
|
|
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return _colors;
|
|
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|
}
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exports.ColorOptions = ColorOptions;
|
|
@@ -94,6 +94,6 @@ var DefaultColorSwatchMap = (function () {
|
|
|
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|
return map;
|
|
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|
})();
|
|
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function ColorValueOption(color) {
|
|
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|
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return !DefaultColorSwatchMap.has(color) ? (0, jsx_runtime_1.jsx)("option",
|
|
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|
+
return !DefaultColorSwatchMap.has(color) ? (0, jsx_runtime_1.jsx)("option", tslib_1.__assign({ value: color, style: { background: "".concat(color_1.Color.toStyle(color)) } }, { children: color_1.Color.toRgbString(color) }), color_1.Color.toHexString(color)) : null;
|
|
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}
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|
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exports.ColorValueOption = ColorValueOption;
|
|
@@ -8,11 +8,11 @@ var jsx_runtime_1 = require("react/jsx-runtime");
|
|
|
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|
*
|
|
9
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|
* @author David Sehnal <david.sehnal@gmail.com>
|
|
10
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|
*/
|
|
11
|
-
var React =
|
|
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|
+
var React = tslib_1.__importStar(require("react"));
|
|
12
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|
var color_1 = require("../../mol-util/color");
|
|
13
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|
var icons_1 = require("./icons");
|
|
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|
var ControlGroup = /** @class */ (function (_super) {
|
|
15
|
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|
|
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+
tslib_1.__extends(ControlGroup, _super);
|
|
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function ControlGroup() {
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|
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var _this = _super !== null && _super.apply(this, arguments) || this;
|
|
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|
_this.state = { isExpanded: !!_this.props.initialExpanded };
|
|
@@ -31,14 +31,14 @@ var ControlGroup = /** @class */ (function (_super) {
|
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if (this.props.childrenClassName)
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|
groupClassName += ' ' + this.props.childrenClassName;
|
|
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|
// TODO: customize header style (bg color, togle button etc)
|
|
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|
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return (0, jsx_runtime_1.jsxs)("div",
|
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-control-group-wrapper', style: { position: 'relative', marginTop: this.props.noTopMargin ? 0 : void 0 } }, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-group-header', style: { marginLeft: this.props.headerLeftMargin }, title: this.props.title }, { children: (0, jsx_runtime_1.jsxs)(Button, tslib_1.__assign({ onClick: this.headerClicked }, { children: [!this.props.hideExpander && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowRightSvg : icons_1.ArrowDropDownSvg }), this.props.topRightIcon && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.props.topRightIcon, style: { position: 'absolute', right: '2px', top: 0 } }), (0, jsx_runtime_1.jsx)("b", { children: this.props.header })] })) })), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: groupClassName, style: { display: this.state.isExpanded ? 'block' : 'none', maxHeight: this.props.maxHeight, overflow: 'hidden', overflowY: 'auto' } }, { children: this.props.children }))] }));
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exports.ControlGroup = ControlGroup;
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var TextInput = /** @class */ (function (_super) {
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ExpandableControlRow.prototype.render = function () {
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ControlRow, tslib_1.__assign({ label: (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [label, (0, jsx_runtime_1.jsx)("button", tslib_1.__assign({ className: 'msp-btn-link msp-btn-icon msp-control-group-expander', onClick: this.toggleExpanded, title: "".concat(this.state.isExpanded ? 'Less' : 'More', " options"), style: { background: 'transparent', textAlign: 'left', padding: '0' } }, { children: (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.RemoveSvg : icons_1.AddSvg, style: { display: 'inline-block' } }) }))] }), control: pivot }, { children: this.props.colorStripe && (0, jsx_runtime_1.jsx)("div", { className: 'msp-expandable-group-color-stripe', style: { backgroundColor: color_1.Color.toStyle(this.props.colorStripe) } }) })), this.state.isExpanded && (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-offset' }, { children: controls }))] });
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function Button(props) {
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return (0, jsx_runtime_1.jsxs)("button", tslib_1.__assign({ className: className, onClick: props.onClick, title: props.title, disabled: props.disabled, "data-id": props['data-id'], style: style }, { children: [props.svg && (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: props.svg }), props.extraContent] }));
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var className = props.isSelected ? "".concat(props.className || '', " msp-control-current") : props.className;
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return (0, jsx_runtime_1.jsx)(Button, tslib_1.__assign({ icon: this.props.icon, onClick: this.onClick, title: this.props.title, inline: this.props.inline, disabled: props.disabled, style: props.style, className: className }, { children: label && this.props.isSelected ? (0, jsx_runtime_1.jsx)("b", { children: label }) : label }));
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};
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return ToggleButton;
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exports.ToggleButton = ToggleButton;
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var ExpandGroup = /** @class */ (function (_super) {
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function ExpandGroup() {
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var _this = _super !== null && _super.apply(this, arguments) || this;
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_this.state = { isExpanded: !!_this.props.initiallyExpanded };
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@@ -237,10 +237,10 @@ var ExpandGroup = /** @class */ (function (_super) {
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return _this;
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}
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ExpandGroup.prototype.render = function () {
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div",
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-group-header', style: { marginTop: this.props.marginTop !== void 0 ? this.props.marginTop : '1px', marginLeft: this.props.headerLeftMargin } }, { children: (0, jsx_runtime_1.jsxs)("button", tslib_1.__assign({ className: 'msp-btn msp-form-control msp-btn-block', onClick: this.toggleExpanded, style: this.props.headerStyle }, { children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: this.state.isExpanded ? icons_1.ArrowDropDownSvg : icons_1.ArrowRightSvg }), this.props.header] })) })), this.state.isExpanded &&
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(this.props.noOffset
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? this.props.children
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: (0, jsx_runtime_1.jsx)("div",
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: (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: this.props.accent ? 'msp-accent-offset' : 'msp-control-offset' }, { children: this.props.children })))] });
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};
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return ExpandGroup;
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}(React.PureComponent));
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@@ -249,6 +249,6 @@ function ControlRow(props) {
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var className = 'msp-control-row';
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if (props.className)
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className += ' ' + props.className;
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: className }, { children: [(0, jsx_runtime_1.jsx)("span", tslib_1.__assign({ className: 'msp-control-row-label', title: props.title }, { children: props.label })), (0, jsx_runtime_1.jsx)("div", tslib_1.__assign({ className: 'msp-control-row-ctrl' }, { children: props.control })), props.children] }));
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}
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exports.ControlRow = ControlRow;
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