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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@@ -1,24 +1,24 @@
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$default-background: #111318;
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$font-color: #ccd4e0;
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@function color-increase-contrast($color, $amount) {
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@return lighten($color, $amount);
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$hover-font-color: #51A2FB;
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$msp-btn-remove-background: #DE0A28;
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$msp-btn-remove-hover-font-color:#F2F4F7;
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$msp-btn-commit-on-font-color: #68BEFD;
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$entity-badge-font-color: #ccd4e0;
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}
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@@ -1,30 +1,30 @@
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// this is complement of the dark theme
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@function compl($color) {
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}
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$default-background: compl(#111318);
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$font-color: compl(#ccd4e0);
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$hover-font-color: compl(#51A2FB);
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$entity-current-font-color: compl(#68BEFD);
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$msp-btn-commit-on-font-color: compl(#68BEFD);
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$entity-badge-font-color: lighten(#ccd4e0,10%);
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$msp-btn-remove-background: #DE0A28;
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$msp-btn-remove-hover-font-color:#F2F4F7;
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// used in LOG
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$log-message: #0CCA5D;
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$log-info: #5E3673;
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$log-error: #FD354B;
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$logo-background: compl(#111318);
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@function color-lower-contrast($color, $amount) {
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@return lighten($color, $amount);
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}
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@function color-increase-contrast($color, $amount) {
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@return darken($color, $amount);
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// this is complement of the dark theme
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@function compl($color) {
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@return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
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}
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+
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$default-background: compl(#111318);
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$font-color: compl(#ccd4e0);
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$hover-font-color: compl(#51A2FB);
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$entity-current-font-color: compl(#68BEFD);
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$msp-btn-commit-on-font-color: compl(#68BEFD);
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$entity-badge-font-color: lighten(#ccd4e0,10%);
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$msp-btn-remove-background: #DE0A28;
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$msp-btn-remove-hover-font-color:#F2F4F7;
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// used in LOG
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$log-message: #0CCA5D;
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$log-info: #5E3673;
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$log-warning: #FCC937;
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$log-error: #FD354B;
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$logo-background: compl(#111318);
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@function color-lower-contrast($color, $amount) {
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}
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@function color-increase-contrast($color, $amount) {
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@return darken($color, $amount);
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}
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@@ -1,2 +1,2 @@
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@import 'colors/dark';
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+
@import 'colors/dark';
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@import 'base/base';
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@@ -1,2 +1,2 @@
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1
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-
@import 'colors/light';
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+
@import 'colors/light';
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@import 'base/base';
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@@ -40,7 +40,7 @@ var StateObjectActions = /** @class */ (function (_super) {
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return null;
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var def = cell.transform.transformer.definition;
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var display = cell.obj ? cell.obj.label : (def.display && def.display.name) || def.name;
|
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return _jsxs("div", __assign({ className: 'msp-state-actions' }, { children: [!this.props.hideHeader && _jsxs("div", __assign({ className: 'msp-section-header' }, { children: [_jsx(Icon, { svg: CodeSvg }
|
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+
return _jsxs("div", __assign({ className: 'msp-state-actions' }, { children: [!this.props.hideHeader && _jsxs("div", __assign({ className: 'msp-section-header' }, { children: [_jsx(Icon, { svg: CodeSvg }), " ", "Actions (".concat(display, ")")] })), actions.map(function (act, i) { return _jsx(ApplyActionControl, { state: state, action: act, nodeRef: ref, initiallyCollapsed: i === 0 ? !_this.props.alwaysExpandFirst && _this.props.initiallyCollapsed : _this.props.initiallyCollapsed }, "".concat(act.id)); })] }));
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return StateObjectActions;
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}(PluginUIComponent));
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@@ -44,7 +44,7 @@ var AnimationControls = /** @class */ (function (_super) {
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return null;
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var isDisabled = anim.state.animationState === 'playing';
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var canApply = (_b = (_a = anim.current.anim).canApply) === null || _b === void 0 ? void 0 : _b.call(_a, this.plugin);
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return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: anim.getParams(), values: anim.state.params, onChange: this.updateParams, isDisabled: isDisabled }
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+
return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: anim.getParams(), values: anim.state.params, onChange: this.updateParams, isDisabled: isDisabled }), _jsx(ParameterControls, { params: anim.current.params, values: anim.current.paramValues, onChange: this.updateCurrentParams, isDisabled: isDisabled }), _jsx("div", __assign({ className: 'msp-flex-row' }, { children: _jsx(Button, __assign({ icon: anim.state.animationState !== 'playing' ? void 0 : PlayArrowSvg, onClick: this.startOrStop, disabled: canApply !== void 0 && canApply.canApply === false }, { children: anim.state.animationState === 'playing' ? 'Stop' : canApply === void 0 || canApply.canApply ? 'Start' : canApply.reason || 'Start' })) }))] });
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return AnimationControls;
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}(PluginUIComponent));
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@@ -27,7 +27,7 @@ var StateTransformParameters = /** @class */ (function (_super) {
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|
return PD.areEqual(this.props.info.params, params, this.props.info.initialValues);
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};
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StateTransformParameters.prototype.render = function () {
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return _jsx(ParameterControls, { params: this.props.info.params, values: this.props.params, onChange: this.onChange, onEnter: this.props.events.onEnter, isDisabled: this.props.isDisabled }
|
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+
return _jsx(ParameterControls, { params: this.props.info.params, values: this.props.params, onChange: this.onChange, onEnter: this.props.events.onEnter, isDisabled: this.props.isDisabled });
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|
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|
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|
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|
return StateTransformParameters;
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|
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|
}(PurePluginUIComponent));
|
|
@@ -151,7 +151,7 @@ var TransformControlBase = /** @class */ (function (_super) {
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if (this.props.autoHideApply && (!canApply || this.canAutoApply(this.state.params)))
|
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return null;
|
|
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|
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return _jsxs("div", __assign({ className: 'msp-transform-apply-wrap' }, { children: [_jsx(IconButton, { svg: RefreshSvg, className: 'msp-transform-default-params', onClick: this.setDefault, disabled: this.state.busy, title: 'Set default params' }
|
|
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+
return _jsxs("div", __assign({ className: 'msp-transform-apply-wrap' }, { children: [_jsx(IconButton, { svg: RefreshSvg, className: 'msp-transform-default-params', onClick: this.setDefault, disabled: this.state.busy, title: 'Set default params' }), _jsx("div", __assign({ className: "msp-transform-apply-wider" }, { children: _jsx(Button, __assign({ icon: canApply ? CheckSvg : void 0, className: "msp-btn-commit msp-btn-commit-".concat(canApply ? 'on' : 'off'), onClick: this.apply, disabled: !canApply }, { children: this.props.applyLabel || this.applyText() })) }))] }));
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|
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|
};
|
|
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|
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var info = this.getInfo();
|
|
@@ -168,18 +168,18 @@ var TransformControlBase = /** @class */ (function (_super) {
|
|
|
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|
if (!isEmpty && !this.state.isCollapsed) {
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|
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|
var _a = this.getSourceAndTarget(), a = _a.a, b = _a.b, bCell = _a.bCell;
|
|
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|
|
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|
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params = _jsxs(_Fragment, { children: [_jsx(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy }
|
|
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|
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params = _jsxs(_Fragment, { children: [_jsx(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy }), applyControl] });
|
|
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}
|
|
173
|
-
var ctrl = _jsxs("div", __assign({ className: wrapClass, style: { marginBottom: this.props.noMargin ? 0 : void 0 } }, { children: [display !== 'none' && !this.props.wrapInExpander && _jsx("div", __assign({ className: 'msp-transform-header' }, { children: _jsxs(Button, __assign({ onClick: this.toggleExpanded, title: display.description }, { children: [!isEmpty && _jsx(Icon, { svg: this.state.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg }
|
|
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|
+
var ctrl = _jsxs("div", __assign({ className: wrapClass, style: { marginBottom: this.props.noMargin ? 0 : void 0 } }, { children: [display !== 'none' && !this.props.wrapInExpander && _jsx("div", __assign({ className: 'msp-transform-header' }, { children: _jsxs(Button, __assign({ onClick: this.toggleExpanded, title: display.description }, { children: [!isEmpty && _jsx(Icon, { svg: this.state.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg }), display.name] })) })), params] }));
|
|
174
174
|
if (isEmpty || !this.props.wrapInExpander)
|
|
175
175
|
return ctrl;
|
|
176
|
-
return _jsx(ExpandGroup, __assign({ header: this.isUpdate() ? "Update ".concat(display === 'none' ? '' : display.name) : "Apply ".concat(display === 'none' ? '' : display.name), headerLeftMargin: this.props.expanderHeaderLeftMargin }, { children: ctrl })
|
|
176
|
+
return _jsx(ExpandGroup, __assign({ header: this.isUpdate() ? "Update ".concat(display === 'none' ? '' : display.name) : "Apply ".concat(display === 'none' ? '' : display.name), headerLeftMargin: this.props.expanderHeaderLeftMargin }, { children: ctrl }));
|
|
177
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|
};
|
|
178
178
|
TransformControlBase.prototype.renderSimple = function () {
|
|
179
179
|
var _a, _b, _c;
|
|
180
180
|
var info = this.getInfo();
|
|
181
181
|
var canApply = this.canApply();
|
|
182
|
-
var apply = _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ icon: (_a = this.props.simpleApply) === null || _a === void 0 ? void 0 : _a.icon, title: (_b = this.props.simpleApply) === null || _b === void 0 ? void 0 : _b.title, disabled: this.state.busy || !canApply, onClick: this.apply, className: 'msp-btn-apply-simple' }, { children: (_c = this.props.simpleApply) === null || _c === void 0 ? void 0 : _c.header })
|
|
182
|
+
var apply = _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ icon: (_a = this.props.simpleApply) === null || _a === void 0 ? void 0 : _a.icon, title: (_b = this.props.simpleApply) === null || _b === void 0 ? void 0 : _b.title, disabled: this.state.busy || !canApply, onClick: this.apply, className: 'msp-btn-apply-simple' }, { children: (_c = this.props.simpleApply) === null || _c === void 0 ? void 0 : _c.header })), !info.isEmpty && _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleExpanded, isSelected: !this.state.isCollapsed, disabled: this.state.busy, style: { flex: '0 0 40px', padding: 0 } })] }));
|
|
183
183
|
if (this.state.isCollapsed)
|
|
184
184
|
return apply;
|
|
185
185
|
var tId = this.getTransformerId();
|
|
@@ -187,7 +187,7 @@ var TransformControlBase = /** @class */ (function (_super) {
|
|
|
187
187
|
? this.plugin.customParamEditors.get(tId)
|
|
188
188
|
: StateTransformParameters;
|
|
189
189
|
var _d = this.getSourceAndTarget(), a = _d.a, b = _d.b, bCell = _d.bCell;
|
|
190
|
-
return _jsxs(_Fragment, { children: [apply, _jsx(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy }
|
|
190
|
+
return _jsxs(_Fragment, { children: [apply, _jsx(ParamEditor, { info: info, a: a, b: b, bCell: bCell, events: this.events, params: this.state.params, isDisabled: this.state.busy })] });
|
|
191
191
|
};
|
|
192
192
|
TransformControlBase.prototype.render = function () {
|
|
193
193
|
// console.log('rendering', ((this.props as any)?.transform?.transformer || (this.props as any)?.action)?.definition.display.name, +new Date)
|
|
@@ -24,7 +24,7 @@ var StateSnapshots = /** @class */ (function (_super) {
|
|
|
24
24
|
}
|
|
25
25
|
StateSnapshots.prototype.render = function () {
|
|
26
26
|
var _a;
|
|
27
|
-
return _jsxs("div", { children: [_jsx(SectionHeader, { icon: SaveOutlinedSvg, title: 'Plugin State' }
|
|
27
|
+
return _jsxs("div", { children: [_jsx(SectionHeader, { icon: SaveOutlinedSvg, title: 'Plugin State' }), _jsx("div", __assign({ style: { marginBottom: '10px' } }, { children: _jsx(ExpandGroup, __assign({ header: 'Save Options', initiallyExpanded: false }, { children: _jsx(LocalStateSnapshotParams, {}) })) })), _jsx(LocalStateSnapshots, {}), _jsx(LocalStateSnapshotList, {}), _jsx(SectionHeader, { title: 'Save as File', accent: 'blue' }), _jsx(StateExportImportControls, {}), ((_a = this.plugin.spec.components) === null || _a === void 0 ? void 0 : _a.remoteState) !== 'none' && _jsx(RemoteStateSnapshots, {})] });
|
|
28
28
|
};
|
|
29
29
|
return StateSnapshots;
|
|
30
30
|
}(PluginUIComponent));
|
|
@@ -55,7 +55,7 @@ var StateExportImportControls = /** @class */ (function (_super) {
|
|
|
55
55
|
return _this;
|
|
56
56
|
}
|
|
57
57
|
StateExportImportControls.prototype.render = function () {
|
|
58
|
-
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ icon: GetAppSvg, onClick: this.downloadToFileJson, title: 'Save the state description. Input data are loaded using the provided sources. Does not work if local files are used as input.' }, { children: "State" })
|
|
58
|
+
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ icon: GetAppSvg, onClick: this.downloadToFileJson, title: 'Save the state description. Input data are loaded using the provided sources. Does not work if local files are used as input.' }, { children: "State" })), _jsx(Button, __assign({ icon: GetAppSvg, onClick: this.downloadToFileZip, title: 'Save the state including the input data.' }, { children: "Session" })), _jsxs("div", __assign({ className: 'msp-btn msp-btn-block msp-btn-action msp-loader-msp-btn-file' }, { children: [_jsx(Icon, { svg: OpenInBrowserSvg, inline: true }), " Open ", _jsx("input", { onChange: this.open, type: 'file', multiple: false, accept: '.molx,.molj' })] }))] })), _jsxs("div", __assign({ className: 'msp-help-text', style: { padding: '10px' } }, { children: [_jsx(Icon, { svg: WarningSvg }), " This is an experimental feature and stored states/sessions might not be openable in a future version."] }))] });
|
|
59
59
|
};
|
|
60
60
|
return StateExportImportControls;
|
|
61
61
|
}(PluginUIComponent));
|
|
@@ -70,7 +70,7 @@ var LocalStateSnapshotParams = /** @class */ (function (_super) {
|
|
|
70
70
|
this.subscribe(this.plugin.state.snapshotParams, function () { return _this.forceUpdate(); });
|
|
71
71
|
};
|
|
72
72
|
LocalStateSnapshotParams.prototype.render = function () {
|
|
73
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-
return _jsx(ParameterControls, { params: PluginState.SnapshotParams, values: this.plugin.state.snapshotParams.value, onChangeValues: this.plugin.state.setSnapshotParams }
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return LocalStateSnapshotParams;
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};
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return _jsxs("div", { children: [_jsx(ParameterControls, { params: LocalStateSnapshots.Params, values: this.state.params, onEnter: this.add, onChangeValues: this.updateParams }), _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(IconButton, { onClick: this.clear, svg: DeleteOutlinedSvg, title: 'Remove All' }), _jsx(Button, __assign({ onClick: this.add, icon: AddSvg, style: { textAlign: 'right' }, commit: true }, { children: "Add" }))] }))] });
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return _jsx("ul", __assign({ style: { listStyle: 'none', marginTop: '10px' }, className: 'msp-state-list' }, { children: this.plugin.managers.snapshot.state.entries.map(function (e) { return _jsxs("li", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ "data-id": e.snapshot.id, onClick: _this.apply, className: 'msp-no-overflow' }, { children: [_jsx("span", __assign({ style: { fontWeight: e.snapshot.id === current ? 'bold' : void 0 } }, { children: e.name || new Date(e.timestamp).toLocaleString() })
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return _jsx("ul", __assign({ style: { listStyle: 'none', marginTop: '10px' }, className: 'msp-state-list' }, { children: this.plugin.managers.snapshot.state.entries.map(function (e) { return _jsxs("li", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ "data-id": e.snapshot.id, onClick: _this.apply, className: 'msp-no-overflow' }, { children: [_jsx("span", __assign({ style: { fontWeight: e.snapshot.id === current ? 'bold' : void 0 } }, { children: e.name || new Date(e.timestamp).toLocaleString() })), " ", _jsx("small", { children: "".concat(e.snapshot.durationInMs ? formatTimespan(e.snapshot.durationInMs, false) + "".concat(e.description ? ', ' : '') : '').concat(e.description ? e.description : '') })] })), _jsx(IconButton, { svg: ArrowUpwardSvg, "data-id": e.snapshot.id, title: 'Move Up', onClick: _this.moveUp, flex: '20px' }), _jsx(IconButton, { svg: ArrowDownwardSvg, "data-id": e.snapshot.id, title: 'Move Down', onClick: _this.moveDown, flex: '20px' }), _jsx(IconButton, { svg: SwapHorizSvg, "data-id": e.snapshot.id, title: 'Replace', onClick: _this.replace, flex: '20px' }), _jsx(IconButton, { svg: DeleteOutlinedSvg, "data-id": e.snapshot.id, title: 'Remove', onClick: _this.remove, flex: '20px' })] }), e.snapshot.id); }) }));
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return _jsxs(_Fragment, { children: [_jsx(SectionHeader, { title: 'Remote States', accent: 'blue' }
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return _jsxs(_Fragment, { children: [_jsx(SectionHeader, { title: 'Remote States', accent: 'blue' }), !this.props.listOnly && _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.Params, values: this.state.params, onEnter: this.upload, onChange: function (p) {
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_this.setState({ params: __assign(__assign({}, _this.state.params), (_a = {}, _a[p.name] = p.value, _a)) });
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}, isDisabled: this.state.isBusy }
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}, isDisabled: this.state.isBusy }), _jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(IconButton, { onClick: this.refresh, disabled: this.state.isBusy, svg: RefreshSvg }), _jsx(Button, __assign({ icon: CloudUploadSvg, onClick: this.upload, disabled: this.state.isBusy, commit: true }, { children: "Upload" }))] }))] }), _jsx(RemoteStateSnapshotList, { entries: this.state.entries, isBusy: this.state.isBusy, serverUrl: this.state.params.options.serverUrl, fetch: this.fetch, remove: this.props.listOnly ? void 0 : this.remove }), this.props.listOnly && _jsxs("div", __assign({ style: { marginTop: '10px' } }, { children: [_jsx(ParameterControls, { params: this.ListOnlyParams, values: this.state.params, onEnter: this.upload, onChange: function (p) {
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}, isDisabled: this.state.isBusy }
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}, isDisabled: this.state.isBusy }), _jsx("div", __assign({ className: 'msp-flex-row' }, { children: _jsx(Button, __assign({ onClick: this.refresh, disabled: this.state.isBusy, icon: RefreshSvg }, { children: "Refresh" })) }))] }))] });
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@@ -339,7 +339,7 @@ var RemoteStateSnapshotList = /** @class */ (function (_super) {
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}
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return _jsx("ul", __assign({ style: { listStyle: 'none', marginTop: '10px' }, className: 'msp-state-list' }, { children: this.props.entries.valueSeq().map(function (e) { return _jsxs("li", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ "data-id": e.id, onClick: _this.props.fetch, disabled: _this.props.isBusy, onContextMenu: _this.open, title: 'Click to download, right-click to open in a new tab.' }, { children: [e.name || new Date(e.timestamp).toLocaleString(), " ", _jsx("small", { children: e.description }
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return _jsx("ul", __assign({ style: { listStyle: 'none', marginTop: '10px' }, className: 'msp-state-list' }, { children: this.props.entries.valueSeq().map(function (e) { return _jsxs("li", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ "data-id": e.id, onClick: _this.props.fetch, disabled: _this.props.isBusy, onContextMenu: _this.open, title: 'Click to download, right-click to open in a new tab.' }, { children: [e.name || new Date(e.timestamp).toLocaleString(), " ", _jsx("small", { children: e.description })] })), !e.isSticky && _this.props.remove && _jsx(IconButton, { svg: DeleteOutlinedSvg, "data-id": e.id, title: 'Remove', onClick: _this.props.remove, disabled: _this.props.isBusy, small: true })] }), e.id); }) }));
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}(PurePluginUIComponent));
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@@ -39,9 +39,9 @@ var StateTree = /** @class */ (function (_super) {
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StateTree.prototype.render = function () {
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var ref = this.props.state.tree.root.ref;
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if (this.state.showActions) {
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return _jsxs("div", __assign({ style: { margin: '10px', cursor: 'default' } }, { children: [_jsx("p", { children: "Nothing to see here yet." }
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+
return _jsxs("div", __assign({ style: { margin: '10px', cursor: 'default' } }, { children: [_jsx("p", { children: "Nothing to see here yet." }), _jsxs("p", { children: ["Structures and Volumes can be loaded from the ", _jsx(Icon, { svg: HomeOutlinedSvg }), " tab."] })] }));
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}
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return _jsx(StateTreeNode, { cell: this.props.state.cells.get(ref), depth: 0 }
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return _jsx(StateTreeNode, { cell: this.props.state.cells.get(ref), depth: 0 });
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};
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return StateTree;
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}(PluginUIComponent));
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@@ -119,12 +119,12 @@ var StateTreeNode = /** @class */ (function (_super) {
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if (!this.state.showLabel) {
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if (children.size === 0)
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return null;
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return _jsx(_Fragment, { children: children.map(function (c) { return _jsx(StateTreeNode, { cell: cell.parent.cells.get(c), depth: _this.props.depth }, c); }) }
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return _jsx(_Fragment, { children: children.map(function (c) { return _jsx(StateTreeNode, { cell: cell.parent.cells.get(c), depth: _this.props.depth }, c); }) });
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}
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var newDepth = this.props.depth + 1;
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return _jsxs(_Fragment, { children: [_jsx(StateTreeNodeLabel, { cell: cell, depth: this.props.depth }
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return _jsxs(_Fragment, { children: [_jsx(StateTreeNodeLabel, { cell: cell, depth: this.props.depth }), children.size === 0
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: _jsx("div", __assign({ style: { display: this.state.isCollapsed ? 'none' : 'block' } }, { children: children.map(function (c) { return _jsx(StateTreeNode, { cell: cell.parent.cells.get(c), depth: newDepth }, c); }) })
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: _jsx("div", __assign({ style: { display: this.state.isCollapsed ? 'none' : 'block' } }, { children: children.map(function (c) { return _jsx(StateTreeNode, { cell: cell.parent.cells.get(c), depth: newDepth }, c); }) }))] });
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};
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return StateTreeNode;
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}(PluginUIComponent));
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@@ -247,7 +247,7 @@ var StateTreeNodeLabel = /** @class */ (function (_super) {
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var d = decoratorChain[i];
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decorators.push(_jsx(UpdateTransformControl, { state: cell.parent, transform: d.transform, noMargin: true, wrapInExpander: true, expanderHeaderLeftMargin: margin }, "".concat(d.transform.transformer.id, "-").concat(i)));
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}
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return _jsx("div", __assign({ className: 'msp-tree-updates-wrapper' }, { children: decorators })
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return _jsx("div", __assign({ className: 'msp-tree-updates-wrapper' }, { children: decorators }));
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};
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@@ -259,31 +259,31 @@ var StateTreeNodeLabel = /** @class */ (function (_super) {
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var label;
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if (cell.status === 'error' || !cell.obj) {
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var name_1 = cell.status === 'error' ? cell.errorText : n.transformer.definition.display.name;
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|
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label = _jsxs(Button, __assign({ className: 'msp-btn-tree-label msp-no-hover-outline', noOverflow: true, title: name_1, onClick: this.state.isCurrent ? this.setCurrentRoot : this.setCurrent, disabled: disabled }, { children: [cell.status === 'error' && _jsxs("b", { children: ["[", cell.status, "]"] }
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|
+
label = _jsxs(Button, __assign({ className: 'msp-btn-tree-label msp-no-hover-outline', noOverflow: true, title: name_1, onClick: this.state.isCurrent ? this.setCurrentRoot : this.setCurrent, disabled: disabled }, { children: [cell.status === 'error' && _jsxs("b", { children: ["[", cell.status, "]"] }), " ", _jsx("span", { children: name_1 })] }));
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}
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else {
|
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var obj = cell.obj;
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|
var title = "".concat(obj.label, " ").concat(obj.description ? obj.description : '');
|
|
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|
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label = _jsxs(Button, __assign({ className: "msp-btn-tree-label msp-type-class-".concat(obj.type.typeClass), noOverflow: true, disabled: disabled, title: title, onClick: this.state.isCurrent ? this.setCurrentRoot : this.setCurrent }, { children: [_jsx("span", { children: obj.label }
|
|
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|
+
label = _jsxs(Button, __assign({ className: "msp-btn-tree-label msp-type-class-".concat(obj.type.typeClass), noOverflow: true, disabled: disabled, title: title, onClick: this.state.isCurrent ? this.setCurrentRoot : this.setCurrent }, { children: [_jsx("span", { children: obj.label }), " ", obj.description ? _jsx("small", { children: obj.description }) : void 0] }));
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|
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|
}
|
|
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|
var children = cell.parent.tree.children.get(this.ref);
|
|
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|
var cellState = cell.state;
|
|
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|
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var expand = _jsx(IconButton, { svg: cellState.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg, flex: '20px', disabled: disabled, onClick: this.toggleExpanded, transparent: true, className: 'msp-no-hover-outline', style: { visibility: children.size > 0 ? 'visible' : 'hidden' } }
|
|
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|
-
var remove = !cell.state.isLocked ? _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, disabled: disabled, small: true, toggleState: false }
|
|
273
|
-
var visibility = _jsx(IconButton, { svg: cellState.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, disabled: disabled, small: true, onClick: this.toggleVisible }
|
|
271
|
+
var expand = _jsx(IconButton, { svg: cellState.isCollapsed ? ArrowRightSvg : ArrowDropDownSvg, flex: '20px', disabled: disabled, onClick: this.toggleExpanded, transparent: true, className: 'msp-no-hover-outline', style: { visibility: children.size > 0 ? 'visible' : 'hidden' } });
|
|
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|
+
var remove = !cell.state.isLocked ? _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, disabled: disabled, small: true, toggleState: false }) : void 0;
|
|
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|
+
var visibility = _jsx(IconButton, { svg: cellState.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, disabled: disabled, small: true, onClick: this.toggleVisible });
|
|
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|
var marginStyle = {
|
|
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|
marginLeft: "".concat(this.props.depth * 8, "px")
|
|
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|
};
|
|
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|
-
var row = _jsxs("div", __assign({ className: "msp-flex-row msp-tree-row".concat(isCurrent ? ' msp-tree-row-current' : ''), onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: marginStyle }, { children: [expand, label, remove, visibility] })
|
|
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|
+
var row = _jsxs("div", __assign({ className: "msp-flex-row msp-tree-row".concat(isCurrent ? ' msp-tree-row-current' : ''), onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: marginStyle }, { children: [expand, label, remove, visibility] }));
|
|
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|
if (!isCurrent)
|
|
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|
return row;
|
|
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|
if (this.state.action === 'apply' && this.state.currentAction) {
|
|
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|
-
return _jsxs("div", __assign({ style: { marginBottom: '1px' } }, { children: [row, _jsx(ControlGroup, __assign({ header: "Apply ".concat(this.state.currentAction.definition.display.name), initialExpanded: true, hideExpander: true, hideOffset: false, onHeaderClick: this.hideApply, topRightIcon: CloseSvg, headerLeftMargin: "".concat(this.props.depth * 8 + 21, "px") }, { children: _jsx(ApplyActionControl, { onApply: this.hideApply, state: this.props.cell.parent, action: this.state.currentAction, nodeRef: this.props.cell.transform.ref, hideHeader: true, noMargin: true }
|
|
281
|
+
return _jsxs("div", __assign({ style: { marginBottom: '1px' } }, { children: [row, _jsx(ControlGroup, __assign({ header: "Apply ".concat(this.state.currentAction.definition.display.name), initialExpanded: true, hideExpander: true, hideOffset: false, onHeaderClick: this.hideApply, topRightIcon: CloseSvg, headerLeftMargin: "".concat(this.props.depth * 8 + 21, "px") }, { children: _jsx(ApplyActionControl, { onApply: this.hideApply, state: this.props.cell.parent, action: this.state.currentAction, nodeRef: this.props.cell.transform.ref, hideHeader: true, noMargin: true }) }))] }));
|
|
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|
}
|
|
283
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|
if (this.state.action === 'options') {
|
|
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|
var actions = this.actions;
|
|
285
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|
var updates = this.updates("".concat(this.props.depth * 8 + 21, "px"));
|
|
286
|
-
return _jsxs("div", __assign({ style: { marginBottom: '1px' } }, { children: [row, updates, actions && _jsx("div", __assign({ style: { marginLeft: "".concat(this.props.depth * 8 + 21, "px"), marginTop: '-1px' } }, { children: _jsx(ActionMenu, { items: actions, onSelect: this.selectAction }
|
|
286
|
+
return _jsxs("div", __assign({ style: { marginBottom: '1px' } }, { children: [row, updates, actions && _jsx("div", __assign({ style: { marginLeft: "".concat(this.props.depth * 8 + 21, "px"), marginTop: '-1px' } }, { children: _jsx(ActionMenu, { items: actions, onSelect: this.selectAction }) }))] }));
|
|
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|
}
|
|
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|
return row;
|
|
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|
};
|
|
@@ -104,7 +104,7 @@ var TransformUpdaterControl = /** @class */ (function (_super) {
|
|
|
104
104
|
if (!cell || (cell.status !== 'ok' && cell.status !== 'error'))
|
|
105
105
|
return null;
|
|
106
106
|
var transform = cell.transform;
|
|
107
|
-
return _jsx(UpdateTransformControl, { state: state, transform: transform, initiallyCollapsed: this.props.initiallyCollapsed, customHeader: this.props.header }
|
|
107
|
+
return _jsx(UpdateTransformControl, { state: state, transform: transform, initiallyCollapsed: this.props.initiallyCollapsed, customHeader: this.props.header });
|
|
108
108
|
};
|
|
109
109
|
return TransformUpdaterControl;
|
|
110
110
|
}(PluginUIComponent));
|
|
@@ -33,7 +33,7 @@ var StructureComponentControls = /** @class */ (function (_super) {
|
|
|
33
33
|
}); });
|
|
34
34
|
};
|
|
35
35
|
StructureComponentControls.prototype.renderControls = function () {
|
|
36
|
-
return _jsxs(_Fragment, { children: [_jsx(ComponentEditorControls, {}
|
|
36
|
+
return _jsxs(_Fragment, { children: [_jsx(ComponentEditorControls, {}), _jsx(ComponentListControls, {}), _jsx(GenericEntryListControls, {})] });
|
|
37
37
|
};
|
|
38
38
|
return StructureComponentControls;
|
|
39
39
|
}(CollapsableControls));
|
|
@@ -96,7 +96,7 @@ var ComponentEditorControls = /** @class */ (function (_super) {
|
|
|
96
96
|
};
|
|
97
97
|
Object.defineProperty(ComponentEditorControls.prototype, "presetControls", {
|
|
98
98
|
get: function () {
|
|
99
|
-
return _jsx(ActionMenu, { items: this.presetActions, onSelect: this.applyPreset }
|
|
99
|
+
return _jsx(ActionMenu, { items: this.presetActions, onSelect: this.applyPreset });
|
|
100
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|
},
|
|
101
101
|
enumerable: false,
|
|
102
102
|
configurable: true
|
|
@@ -114,7 +114,7 @@ var ComponentEditorControls = /** @class */ (function (_super) {
|
|
|
114
114
|
var undoTitle = this.state.canUndo
|
|
115
115
|
? "Undo ".concat(this.plugin.state.data.latestUndoLabel)
|
|
116
116
|
: 'Some mistakes of the past can be undone.';
|
|
117
|
-
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: BookmarksOutlinedSvg, label: 'Preset', title: 'Apply a representation preset for the current structure(s).', toggle: this.togglePreset, isSelected: this.state.action === 'preset', disabled: this.isDisabled }
|
|
117
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+
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: BookmarksOutlinedSvg, label: 'Preset', title: 'Apply a representation preset for the current structure(s).', toggle: this.togglePreset, isSelected: this.state.action === 'preset', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: AddSvg, label: 'Add', title: 'Add a new representation component for a selection.', toggle: this.toggleAdd, isSelected: this.state.action === 'add', disabled: this.isDisabled }), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options that are applied to all applicable representations.', style: { flex: '0 0 40px', padding: 0 }, toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.isDisabled }), _jsx(IconButton, { svg: RestoreSvg, className: 'msp-flex-item', flex: '40px', onClick: this.undo, disabled: !this.state.canUndo || this.isDisabled, title: undoTitle })] })), this.state.action === 'preset' && this.presetControls, this.state.action === 'add' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(AddComponentControls, { onApply: this.hideAction }) })), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ComponentOptionsControls, { isDisabled: this.isDisabled }) }))] });
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AddComponentControls.prototype.render = function () {
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return _jsxs(_Fragment, { children: [_jsx(ParameterControls, { params: this.state.params, values: this.state.values, onChangeValues: this.paramsChanged }), _jsx(Button, __assign({ icon: AddSvg, title: 'Use Selection and optional Representation to create a new Component.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.apply, style: { marginTop: '1px' } }, { children: "Create Component" }))] });
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this.subscribe(this.plugin.managers.structure.component.events.optionsUpdated, function () { return _this.forceUpdate(); });
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return _jsx(ParameterControls, { params: StructureComponentManager.OptionsParams, values: this.plugin.managers.structure.component.state.options, onChangeValues: this.update, isDisabled: this.props.isDisabled });
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@@ -186,7 +186,7 @@ var ComponentListControls = /** @class */ (function (_super) {
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var componentGroups = this.plugin.managers.structure.hierarchy.currentComponentGroups;
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return null;
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return _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: componentGroups.map(function (g) { return _jsx(StructureComponentGroup, { group: g }, g[0].cell.transform.ref); }) })
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return _jsx("div", __assign({ style: { marginTop: '6px' } }, { children: componentGroups.map(function (g) { return _jsx(StructureComponentGroup, { group: g }, g[0].cell.transform.ref); }) }));
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var label = (_a = cell.obj) === null || _a === void 0 ? void 0 : _a.label;
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: reprLabel })
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs(Button, __assign({ noOverflow: true, className: 'msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, _jsx("small", __assign({ className: 'msp-25-lower-contrast-text', style: { float: 'right' } }, { children: reprLabel }))] })), _jsx(IconButton, { svg: cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: "".concat(cell.state.isHidden ? 'Show' : 'Hide', " component"), small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: DeleteOutlinedSvg, toggleState: false, onClick: this.remove, title: 'Remove', small: true, className: 'msp-form-control', flex: true }), _jsx(IconButton, { svg: MoreHorizSvg, onClick: this.toggleAction, title: 'Actions', toggleState: this.state.action === 'action', className: 'msp-form-control', flex: true })] })), this.state.action === 'label' && _jsx("div", __assign({ className: 'msp-control-offset', style: { marginBottom: '6px' } }, { children: _jsx(ControlRow, { label: 'Label', control: _jsxs("div", __assign({ style: { display: 'flex', textAlignLast: 'center' } }, { children: [_jsx(TextInput, { onChange: this.updateLabel, value: label, style: { flex: '1 1 auto', minWidth: 0 }, className: 'msp-form-control', blurOnEnter: true, blurOnEscape: true }), _jsx(IconButton, { svg: CheckSvg, onClick: this.toggleLabel, className: 'msp-form-control msp-control-button-label', flex: true })] })) }) })), this.state.action === 'action' && _jsxs("div", __assign({ className: 'msp-accent-offset' }, { children: [_jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: _jsx(ActionMenu, { items: this.actions, onSelect: this.selectAction, noOffset: true }) })), _jsx("div", __assign({ style: { marginBottom: '6px' } }, { children: component.representations.map(function (r) { return _jsx(StructureRepresentationEntry, { group: _this.props.group, representation: r }, r.cell.transform.ref); }) }))] }))] });
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StructureRepresentationEntry.prototype.render = function () {
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return _jsxs("div", __assign({ className: 'msp-representation-entry' }, { children: [repr.parent && _jsx(ExpandGroup, __assign({ header: "".concat(((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) || '', " Representation"), noOffset: true }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', customUpdate: this.update, noMargin: true }
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return _jsxs("div", __assign({ className: 'msp-representation-entry' }, { children: [repr.parent && _jsx(ExpandGroup, __assign({ header: "".concat(((_a = repr.obj) === null || _a === void 0 ? void 0 : _a.label) || '', " Representation"), noOffset: true }, { children: _jsx(UpdateTransformControl, { state: repr.parent, transform: repr.transform, customHeader: 'none', customUpdate: this.update, noMargin: true }) })), _jsx(IconButton, { svg: DeleteOutlinedSvg, onClick: this.remove, title: 'Remove', small: true, className: 'msp-default-bg', toggleState: false, style: {
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position: 'absolute', top: 0, right: '32px', lineHeight: '24px', height: '24px', textAlign: 'right', width: '44px', paddingRight: '6px', background: 'none'
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} }
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+
} }), _jsx(IconButton, { svg: this.props.representation.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, onClick: this.toggleVisible, title: 'Toggle Visibility', small: true, className: 'msp-default-bg', style: {
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position: 'absolute', top: 0, right: 0, lineHeight: '24px', height: '24px', textAlign: 'right', width: '32px', paddingRight: '6px', background: 'none'
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} }
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+
} })] }));
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}(PurePluginUIComponent));
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@@ -222,7 +222,7 @@ var StructureFocusControls = /** @class */ (function (_super) {
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title += "\nor use '".concat(binding, "' on element");
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}
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}
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label })
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+
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(Button, __assign({ noOverflow: true, onClick: this.focusCamera, title: title, onMouseEnter: this.highlightCurrent, onMouseLeave: this.clearHighlights, disabled: this.isDisabled || !current, style: { textAlignLast: current ? 'left' : void 0 } }, { children: label })), current && _jsx(IconButton, { svg: CancelOutlinedSvg, onClick: this.clear, title: 'Clear', className: 'msp-form-control', flex: true, disabled: this.isDisabled }), _jsx(ToggleButton, { icon: CenterFocusStrongSvg, title: 'Select a focus target to center on an show its surroundings. Hold shift to focus on multiple targets.', toggle: this.toggleAction, isSelected: this.state.showAction, disabled: this.isDisabled, style: { flex: '0 0 40px', padding: 0 } })] })), this.state.showAction && _jsx(ActionMenu, { items: this.actionItems, onSelect: this.selectAction })] });
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return StructureFocusControls;
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}(PluginUIComponent));
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@@ -37,7 +37,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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}
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|
if (refs.length === 0)
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return null;
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return _jsx(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' }
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return _jsx(GenericEntry, { refs: refs, labelMultiple: 'Unit Cells' });
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},
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enumerable: false,
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configurable: true
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@@ -49,7 +49,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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this.plugin.genericRepresentationControls.forEach(function (provider, key) {
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var _a = provider(_this.plugin.managers.structure.hierarchy.selection), refs = _a[0], labelMultiple = _a[1];
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if (refs.length > 0) {
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controls.push(_jsx("div", { children: _jsx(GenericEntry, { refs: refs, labelMultiple: labelMultiple }
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+
controls.push(_jsx("div", { children: _jsx(GenericEntry, { refs: refs, labelMultiple: labelMultiple }) }, key));
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}
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});
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return controls.length > 0 ? controls : null;
|
|
@@ -58,7 +58,7 @@ var GenericEntryListControls = /** @class */ (function (_super) {
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configurable: true
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});
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GenericEntryListControls.prototype.render = function () {
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return _jsx(_Fragment, { children: _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] })
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+
return _jsx(_Fragment, { children: _jsxs("div", __assign({ style: { marginTop: '6px' } }, { children: [this.unitcell, this.customControls] })) });
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};
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return GenericEntryListControls;
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}(PurePluginUIComponent));
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@@ -144,7 +144,7 @@ var GenericEntry = /** @class */ (function (_super) {
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else {
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label = "".concat(refs.length, " ").concat(labelMultiple || 'Objects');
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}
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|
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return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs("button", __assign({ className: 'msp-form-control msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, " ", _jsx("small", { children: description }
|
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+
return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsxs("button", __assign({ className: 'msp-form-control msp-control-button-label', title: "".concat(label, ". Click to focus."), onClick: this.focus, onMouseEnter: this.highlight, onMouseLeave: this.clearHighlight, style: { textAlign: 'left' } }, { children: [label, " ", _jsx("small", { children: description })] })), _jsx(IconButton, { svg: pivot.cell.state.isHidden ? VisibilityOffOutlinedSvg : VisibilityOutlinedSvg, toggleState: false, className: 'msp-form-control', onClick: this.toggleVisibility, title: "".concat(pivot.cell.state.isHidden ? 'Show' : 'Hide'), small: true, flex: true }), refs.length === 1 && _jsx(IconButton, { svg: MoreHorizSvg, className: 'msp-form-control', onClick: this.toggleOptions, title: 'Options', toggleState: this.state.showOptions, flex: true })] })), (refs.length === 1 && this.state.showOptions && pivot.cell.parent) && _jsx(_Fragment, { children: _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(UpdateTransformControl, { state: pivot.cell.parent, transform: pivot.cell.transform, customHeader: 'none', autoHideApply: true }) })) })] });
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};
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return GenericEntry;
|
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|
}(PurePluginUIComponent));
|