molstar 3.3.1 → 3.6.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +20 -20
- package/README.md +202 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/build/viewer/molstar.js.LICENSE.txt +12 -14
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +1 -1
- package/lib/apps/docking-viewer/viewport.js +1 -1
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +3 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
- package/lib/cli/chem-comp-dict/util.d.ts +20 -20
- package/lib/cli/cif2bcif/converter.js +1 -1
- package/lib/cli/cif2bcif/index.js +4 -4
- package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/cli/cifschema/util/cif-dic.js +7 -5
- package/lib/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/cli/cifschema/util/generate.js +12 -3
- package/lib/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/apps/docking-viewer/index.js +14 -14
- package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +26 -24
- package/lib/commonjs/apps/viewer/index.js +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
- package/lib/commonjs/cli/chem-comp-dict/util.d.ts +20 -20
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
- package/lib/commonjs/cli/cif2bcif/index.js +12 -12
- package/lib/commonjs/cli/cifschema/index.js +27 -27
- package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +8 -6
- package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
- package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -9
- package/lib/commonjs/cli/state-docs/index.js +2 -2
- package/lib/commonjs/cli/structure-info/helpers.js +11 -11
- package/lib/commonjs/cli/structure-info/model.js +15 -15
- package/lib/commonjs/cli/structure-info/volume.js +9 -9
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
- package/lib/commonjs/examples/alpha-orbitals/index.js +12 -12
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
- package/lib/commonjs/examples/basic-wrapper/index.js +23 -23
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
- package/lib/commonjs/examples/lighting/index.js +7 -7
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +27 -27
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
- package/lib/commonjs/examples/task.js +15 -15
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
- package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
- package/lib/commonjs/extensions/anvil/behavior.js +14 -14
- package/lib/commonjs/extensions/anvil/prop.js +7 -7
- package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
- package/lib/commonjs/extensions/anvil/representation.js +5 -5
- package/lib/commonjs/extensions/cellpack/index.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.js +26 -24
- package/lib/commonjs/extensions/cellpack/preset.js +6 -6
- package/lib/commonjs/extensions/cellpack/property.js +3 -3
- package/lib/commonjs/extensions/cellpack/representation.d.ts +1 -0
- package/lib/commonjs/extensions/cellpack/representation.js +2 -2
- package/lib/commonjs/extensions/cellpack/state.js +13 -13
- package/lib/commonjs/extensions/cellpack/util.js +14 -14
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
- package/lib/commonjs/extensions/g3d/data.js +6 -6
- package/lib/commonjs/extensions/g3d/format.js +14 -14
- package/lib/commonjs/extensions/g3d/model.js +4 -4
- package/lib/commonjs/extensions/geo-export/controls.js +3 -3
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
- package/lib/commonjs/extensions/geo-export/index.js +1 -1
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/ui.js +7 -7
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
- package/lib/commonjs/extensions/model-export/export.js +4 -4
- package/lib/commonjs/extensions/model-export/index.js +1 -1
- package/lib/commonjs/extensions/model-export/ui.js +5 -5
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
- package/lib/commonjs/extensions/mp4-export/index.js +1 -1
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
- package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
- package/lib/commonjs/extensions/zenodo/index.js +35 -0
- package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
- package/lib/commonjs/extensions/zenodo/ui.js +306 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera.js +2 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
- package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
- package/lib/commonjs/mol-canvas3d/util.js +2 -2
- package/lib/commonjs/mol-data/db/column.d.ts +10 -3
- package/lib/commonjs/mol-data/db/column.js +40 -18
- package/lib/commonjs/mol-data/db/table.js +1 -1
- package/lib/commonjs/mol-data/db.js +1 -1
- package/lib/commonjs/mol-data/generic.js +3 -3
- package/lib/commonjs/mol-data/index.js +4 -4
- package/lib/commonjs/mol-data/int/interval.js +1 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
- package/lib/commonjs/mol-data/int/segmentation.js +1 -1
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
- package/lib/commonjs/mol-data/util.js +7 -7
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +4 -4
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +4 -4
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -4
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
- package/lib/commonjs/mol-gl/compute/util.js +3 -3
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.js +3 -3
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/points.js +3 -3
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
- package/lib/commonjs/mol-gl/renderable/text.js +3 -3
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/util.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader-code.js +2 -1
- package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
- package/lib/commonjs/mol-gl/webgl/buffer.js +16 -17
- package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +5 -5
- package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/program.js +10 -4
- package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
- package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
- package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
- package/lib/commonjs/mol-io/common/typed-array.js +2 -2
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
- package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +8 -8
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +4 -4
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +31 -27
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
- package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema.js +24 -4
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cif.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
- package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
- package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
- package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
- package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
- package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
- package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
- package/lib/commonjs/mol-io/writer/cif.js +1 -1
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol/encoder.js +2 -2
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
- package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/common.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
- package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
- package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
- package/lib/commonjs/mol-math/geometry.js +8 -8
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
- package/lib/commonjs/mol-math/graph.js +1 -1
- package/lib/commonjs/mol-math/linear-algebra.js +2 -2
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
- package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
- package/lib/commonjs/mol-model/sequence.js +1 -1
- package/lib/commonjs/mol-model/shape.js +1 -1
- package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/commonjs/mol-model/structure/model/model.js +17 -9
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
- package/lib/commonjs/mol-model/structure/model/properties/common.js +1 -1
- package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
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- package/lib/mol-model-formats/structure/pdb/to-cif.js +7 -2
- package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/mol-model-formats/structure/pdb.js +5 -3
- package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
- package/lib/mol-model-formats/structure/prmtop.js +144 -0
- package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
- package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
- package/lib/mol-model-formats/structure/property/symmetry.js +11 -1
- package/lib/mol-model-formats/structure/psf.js +3 -1
- package/lib/mol-model-formats/structure/top.d.ts +16 -0
- package/lib/mol-model-formats/structure/top.js +186 -0
- package/lib/mol-model-formats/structure/trr.d.ts +9 -0
- package/lib/mol-model-formats/structure/trr.js +42 -0
- package/lib/mol-model-formats/structure/util.d.ts +2 -2
- package/lib/mol-model-formats/structure/util.js +19 -20
- package/lib/mol-model-formats/structure/xyz.js +2 -2
- package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
- package/lib/mol-model-props/computed/representations/interactions.d.ts +3 -0
- package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js +3 -2
- package/lib/mol-plugin/commands.d.ts +1 -0
- package/lib/mol-plugin/context.d.ts +2 -1
- package/lib/mol-plugin/context.js +4 -3
- package/lib/mol-plugin/spec.js +1 -1
- package/lib/mol-plugin/util/viewport-screenshot.d.ts +3 -0
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-state/actions/file.d.ts +1 -1
- package/lib/mol-plugin-state/actions/file.js +88 -55
- package/lib/mol-plugin-state/actions/structure.d.ts +17 -8
- package/lib/mol-plugin-state/actions/structure.js +174 -4
- package/lib/mol-plugin-state/actions/volume.js +3 -2
- package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
- package/lib/mol-plugin-state/formats/coordinates.js +67 -0
- package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
- package/lib/mol-plugin-state/formats/registry.js +13 -8
- package/lib/mol-plugin-state/formats/topology.d.ts +73 -0
- package/lib/mol-plugin-state/formats/topology.js +84 -0
- package/lib/mol-plugin-state/helpers/structure-component.js +2 -1
- package/lib/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
- package/lib/mol-plugin-state/helpers/structure-selection-query.js +1 -1
- package/lib/mol-plugin-state/manager/snapshots.js +4 -4
- package/lib/mol-plugin-state/objects.d.ts +47 -1
- package/lib/mol-plugin-state/objects.js +17 -1
- package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
- package/lib/mol-plugin-state/transforms/data.js +61 -9
- package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
- package/lib/mol-plugin-state/transforms/model.js +112 -3
- package/lib/mol-plugin-state/transforms/representation.d.ts +6 -0
- package/lib/mol-plugin-ui/base.js +1 -1
- package/lib/mol-plugin-ui/controls/action-menu.js +7 -7
- package/lib/mol-plugin-ui/controls/color.js +3 -3
- package/lib/mol-plugin-ui/controls/common.js +10 -10
- package/lib/mol-plugin-ui/controls/icons.js +70 -70
- package/lib/mol-plugin-ui/controls/legend.js +3 -3
- package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -1
- package/lib/mol-plugin-ui/controls/parameters.js +51 -51
- package/lib/mol-plugin-ui/controls/screenshot.js +2 -2
- package/lib/mol-plugin-ui/controls/slider.js +5 -5
- package/lib/mol-plugin-ui/controls.js +7 -7
- package/lib/mol-plugin-ui/custom/volume.js +4 -4
- package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
- package/lib/mol-plugin-ui/left-panel.js +33 -12
- package/lib/mol-plugin-ui/plugin.js +10 -10
- package/lib/mol-plugin-ui/react18.d.ts +11 -0
- package/lib/mol-plugin-ui/react18.js +34 -0
- package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/mol-plugin-ui/sequence.js +5 -5
- package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
- package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
- package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
- package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
- package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
- package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
- package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
- package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
- package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
- package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
- package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
- package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
- package/lib/mol-plugin-ui/skin/base/components/viewport.scss +128 -128
- package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
- package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
- package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
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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
- package/lib/mol-plugin-ui/state/actions.js +1 -1
- package/lib/mol-plugin-ui/state/animation.js +1 -1
- package/lib/mol-plugin-ui/state/common.js +7 -7
- package/lib/mol-plugin-ui/state/snapshots.js +9 -9
- package/lib/mol-plugin-ui/state/tree.js +14 -14
- package/lib/mol-plugin-ui/state/update-transform.js +1 -1
- package/lib/mol-plugin-ui/structure/components.js +10 -10
- package/lib/mol-plugin-ui/structure/focus.d.ts +1 -1
- package/lib/mol-plugin-ui/structure/focus.js +3 -3
- package/lib/mol-plugin-ui/structure/generic.js +4 -4
- package/lib/mol-plugin-ui/structure/measurements.js +8 -8
- package/lib/mol-plugin-ui/structure/quick-styles.js +2 -2
- package/lib/mol-plugin-ui/structure/selection.js +7 -7
- package/lib/mol-plugin-ui/structure/source.js +4 -4
- package/lib/mol-plugin-ui/structure/superposition.js +8 -8
- package/lib/mol-plugin-ui/structure/volume.js +4 -4
- package/lib/mol-plugin-ui/task.js +5 -5
- package/lib/mol-plugin-ui/toast.js +4 -4
- package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
- package/lib/mol-plugin-ui/viewport/help.js +8 -8
- package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
- package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
- package/lib/mol-plugin-ui/viewport.js +4 -4
- package/lib/mol-repr/shape/loci/angle.d.ts +1 -0
- package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
- package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
- package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
- package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
- package/lib/mol-repr/structure/complex-visual.d.ts +3 -0
- package/lib/mol-repr/structure/params.d.ts +4 -0
- package/lib/mol-repr/structure/registry.d.ts +10 -0
- package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
- package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
- package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
- package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
- package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
- package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
- package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
- package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
- package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
- package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
- package/lib/mol-repr/structure/units-visual.d.ts +4 -0
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/element-sphere.d.ts +2 -0
- package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
- package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
- package/lib/mol-repr/structure/visual/util/common.js +1 -24
- package/lib/mol-repr/util.d.ts +2 -1
- package/lib/mol-repr/util.js +2 -2
- package/lib/mol-repr/volume/isosurface.d.ts +5 -0
- package/lib/mol-repr/volume/registry.d.ts +1 -0
- package/lib/mol-script/language/builder.d.ts +1 -0
- package/lib/mol-script/language/parser.js +7 -4
- package/lib/mol-task/util/scheduler.d.ts +2 -2
- package/lib/mol-task/util/scheduler.js +7 -7
- package/lib/mol-theme/color/hydrophobicity.js +2 -2
- package/lib/mol-util/data-source.js +2 -1
- package/lib/mol-util/file-info.d.ts +1 -3
- package/lib/mol-util/file-info.js +2 -10
- package/lib/mol-util/index.d.ts +1 -0
- package/lib/mol-util/index.js +5 -0
- package/lib/mol-util/zip/deflate.js +2 -1
- package/lib/mol-util/zip/zip.d.ts +7 -1
- package/lib/mol-util/zip/zip.js +5 -1
- package/lib/servers/model/config.d.ts +2 -2
- package/package.json +162 -160
- package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
- package/lib/mol-plugin-state/formats/structure.js +0 -61
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return (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(HelpSection, { header: 'Interface Controls' }), (0, jsx_runtime_1.jsxs)(HelpGroup, tslib_1.__assign({ header: 'Inline Help' }, { children: [(0, jsx_runtime_1.jsx)(HelpText, { children: "Many user interface elements show a little questionmark icon when hovered over. Clicking the icon toggles the display of an inline help text." }), (0, jsx_runtime_1.jsx)(HelpText, { children: "Tooltips may provide additional information on a user interface element and are shown when hovering over it with the mouse." })] })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Selections' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["The viewer allows changing colors and representations for selections of atoms, residues or chains. Selections can be created by", (0, jsx_runtime_1.jsxs)("ul", tslib_1.__assign({ style: { paddingLeft: '20px' } }, { children: [(0, jsx_runtime_1.jsxs)("li", { children: ["picking elements on the 3D canvas or the sequence view using the mouse, e.g. toggle selection using ", selectToggleTriggers, " (for more see help section on ", (0, jsx_runtime_1.jsx)("i", { children: "Mouse Controls" }), ")"] }), (0, jsx_runtime_1.jsxs)("li", { children: ["using the ", (0, jsx_runtime_1.jsx)("i", { children: "Add" }), ", ", (0, jsx_runtime_1.jsx)("i", { children: "Remove" }), " and ", (0, jsx_runtime_1.jsx)("i", { children: "Only" }), " dropdown buttons in the ", (0, jsx_runtime_1.jsx)("i", { children: "Manage Selection" }), " panel which allow modifing the current selection by predefined sets"] })] }))] }) })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Coloring' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["There are two ways to color structures. Every representation (e.g. cartoon or spacefill) has a color theme which can be changed using the dropdown for each representation in the ", (0, jsx_runtime_1.jsx)("i", { children: "Structure Settings" }), " panel. Additionally any selection atoms, residues or chains can by given a custom color. For that, first select the parts of the structure to be colored (see help section on ", (0, jsx_runtime_1.jsx)("i", { children: "Selections" }), ") and, second, choose a color from the color dropdown botton in the ", (0, jsx_runtime_1.jsx)("i", { children: "Selection" }), " row of the ", (0, jsx_runtime_1.jsx)("i", { children: "Change Representation" }), " panel. The theme color can be seen as a base color that is overpainted by the custom color. Custom colors can be removed for a selection with the 'Clear' option in the color dropdown."] }) })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Representations' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["Structures can be shown with many different representations (e.g. cartoon or spacefill). The ", (0, jsx_runtime_1.jsx)("i", { children: "Change Representation" }), " panel offers a collection of predefined styles which can be applied using the ", (0, jsx_runtime_1.jsx)("i", { children: "Preset" }), " dropdown button. Additionally any selection atoms, residues or chains can by shown with a custom representation. For that, first select the parts of the structure to be mofified (see help section on ", (0, jsx_runtime_1.jsx)("i", { children: "Selections" }), ") and, second, choose a representation to hide or show from the ", (0, jsx_runtime_1.jsx)("i", { children: "Show" }), " and ", (0, jsx_runtime_1.jsx)("i", { children: "Hide" }), " dropdown bottons in the ", (0, jsx_runtime_1.jsx)("i", { children: "Selection" }), " row of the ", (0, jsx_runtime_1.jsx)("i", { children: "Change Representation" }), " panel. The ", (0, jsx_runtime_1.jsx)("i", { children: "Everything" }), " row applies the action to the whole structure instead of the current selection."] }) })), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Surroundings' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: ["To show the surroundings of a residue or ligand, click it in the 3D scene or in the sequence widget using ", focusTriggers, "."] }) })), (0, jsx_runtime_1.jsx)(HelpSection, { header: 'How-to Guides' }), (0, jsx_runtime_1.jsx)(HelpGroup, tslib_1.__assign({ header: 'Create an Image' }, { children: (0, jsx_runtime_1.jsxs)(HelpText, { children: [(0, jsx_runtime_1.jsxs)("p", { children: ["Use the ", (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_1.CameraSvg }), " icon in the viewport to bring up the screenshot controls."] }), (0, jsx_runtime_1.jsxs)("p", { children: ["To adjust the size of the image, use the ", (0, jsx_runtime_1.jsx)("i", { children: "Resolution" }), " dropdown."] })] }) })), (0, jsx_runtime_1.jsx)(HelpSection, { header: 'Mouse Controls' }), (0, jsx_runtime_1.jsx)(ViewportHelpContent, {})] });
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case 0: return [4 /*yield*/, ((_a = this.plugin.helpers.viewportScreenshot) === null || _a === void 0 ? void 0 : _a.getImageDataUri())];
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return (0, jsx_runtime_1.jsxs)("div", { children: [this.state.showPreview && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-image-preview' }, { children: [(0, jsx_runtime_1.jsx)(screenshot_1.ScreenshotPreview, { plugin: this.plugin }), (0, jsx_runtime_1.jsx)(CropControls, { plugin: this.plugin })] })), (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-flex-row' }, { children: [!this.state.imageData && (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.CopySvg, onClick: hasClipboardApi ? this.copy : this.copyImg, disabled: this.state.isDisabled }, { children: "Copy" })), this.state.imageData && (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ onClick: function () { return _this.setState({ imageData: void 0 }); }, disabled: this.state.isDisabled }, { children: "Clear" })), (0, jsx_runtime_1.jsx)(common_1.Button, tslib_1.__assign({ icon: icons_1.GetAppSvg, onClick: this.download, disabled: this.state.isDisabled }, { children: "Download" }))] })), this.state.imageData && (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-row msp-copy-image-wrapper' }, { children: [(0, jsx_runtime_1.jsx)("div", { children: "Right click below + Copy Image" }), (0, jsx_runtime_1.jsx)("img", { src: this.state.imageData, style: { width: '100%', height: 32, display: 'block' } })] })), (0, jsx_runtime_1.jsx)(ScreenshotParams, { plugin: this.plugin, isDisabled: this.state.isDisabled }), (0, jsx_runtime_1.jsxs)(common_1.ExpandGroup, tslib_1.__assign({ header: 'State' }, { children: [(0, jsx_runtime_1.jsx)(snapshots_1.StateExportImportControls, { onAction: this.props.close }), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, tslib_1.__assign({ header: 'Save Options', initiallyExpanded: false, noOffset: true }, { children: (0, jsx_runtime_1.jsx)(snapshots_1.LocalStateSnapshotParams, {}) }))] }))] });
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return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ style: { width: '100%', height: '24px', marginTop: '8px' } }, { children: [(0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.CropOrginalSvg, title: 'Auto-crop', inline: true, isSelected: cropParams.auto, style: { background: 'transparent', float: 'left', width: 'auto', height: '24px', lineHeight: '24px' }, toggle: function () { return helper.toggleAutocrop(); }, label: 'Auto-crop ' + (cropParams.auto ? 'On' : 'Off') }), !cropParams.auto && (0, jsx_runtime_1.jsx)(common_1.Button, { icon: icons_1.CropSvg, title: 'Crop', style: { background: 'transparent', float: 'right', height: '24px', lineHeight: '24px', width: '24px', padding: '0' }, onClick: function () { return helper.autocrop(); } }), !cropParams.auto && !helper.isFullFrame && (0, jsx_runtime_1.jsx)(common_1.Button, { icon: icons_1.CropFreeSvg, title: 'Reset Crop', style: { background: 'transparent', float: 'right', height: '24px', lineHeight: '24px', width: '24px', padding: '0' }, onClick: function () { return helper.resetCrop(); } })] }));
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterMappingControl, { mapping: SimpleSettingsMapping }
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return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterMappingControl, { mapping: SimpleSettingsMapping }), (0, jsx_runtime_1.jsx)(help_1.ViewportHelpContent, {})] });
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clipping: param_definition_1.ParamDefinition.Group(
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clipping: param_definition_1.ParamDefinition.Group(tslib_1.__assign({}, canvas3d_1.Canvas3DParams.cameraClipping.params), { pivot: 'radius' }),
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clipping:
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case 0: return [4 /*yield*/, commands_1.PluginCommands.Canvas3D.SetSettings(ctx, { settings: props.canvas })];
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tslib_1.__extends(ViewportControls, _super);
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_this.state =
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@@ -55,7 +55,7 @@ var ViewportControls = /** @class */ (function (_super) {
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_this.setState(tslib_1.__assign(tslib_1.__assign({}, _this.allCollapsedState), (_a = {}, _a[panel] = !_this.state[panel], _a)));
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return (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icon, toggleState: isOn, onClick: onClick, title: title, style: { background: 'transparent' } }
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return mol_task_1.Task.create("Creating or updating '".concat(label, "' representation"), function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
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return
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return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
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return tslib_1.__generator(this, function (_a) {
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@@ -58,6 +58,7 @@ export declare const AngleParams: {
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flipSided: PD.BooleanParam;
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flatShaded: PD.BooleanParam;
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xrayShaded: PD.BooleanParam;
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allowTransparentBackfaces: PD.BooleanParam;
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bumpFrequency: PD.Numeric;
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bumpAmplitude: PD.Numeric;
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lineSizeAttenuation: PD.BooleanParam;
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@@ -31,17 +31,17 @@ var SharedParams = {
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color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
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arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
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};
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var LinesParams =
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var VectorsParams =
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var SectorParams =
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var LinesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }) });
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var VectorsParams = tslib_1.__assign({}, LinesParams);
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var ArcParams = tslib_1.__assign({}, LinesParams);
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var SectorParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { ignoreLight: param_definition_1.ParamDefinition.Boolean(true), sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }) });
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var AngleVisuals = {
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'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
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'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
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'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (
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'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
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'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
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'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
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'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity })); }, modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
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'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
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exports.AngleParams =
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exports.AngleParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, VectorsParams), ArcParams), SectorParams), common_1.LociLabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['vectors', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(AngleVisuals)) });
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|
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function getAngleState() {
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@@ -16,4 +16,4 @@ exports.MeasurementRepresentationCommonTextParams = {
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textColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black, { isEssential: true }),
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textSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
|
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};
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exports.LociLabelTextParams =
|
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|
+
exports.LociLabelTextParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, text_1.Text.Params), exports.MeasurementRepresentationCommonTextParams), { borderWidth: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 0.5, step: 0.01 }) });
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@@ -58,6 +58,7 @@ export declare const DihedralParams: {
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flipSided: PD.BooleanParam;
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flatShaded: PD.BooleanParam;
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xrayShaded: PD.BooleanParam;
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allowTransparentBackfaces: PD.BooleanParam;
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bumpFrequency: PD.Numeric;
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bumpAmplitude: PD.Numeric;
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lineSizeAttenuation: PD.BooleanParam;
|
|
@@ -31,22 +31,22 @@ var SharedParams = {
|
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color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen),
|
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arcScale: param_definition_1.ParamDefinition.Numeric(0.7, { min: 0.01, max: 1, step: 0.01 })
|
|
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|
};
|
|
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|
-
var LinesParams =
|
|
35
|
-
var VectorsParams =
|
|
36
|
-
var ExtendersParams =
|
|
37
|
-
var ArmsParams =
|
|
38
|
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var ArcParams =
|
|
39
|
-
var SectorParams =
|
|
34
|
+
var LinesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.04, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
35
|
+
var VectorsParams = tslib_1.__assign({}, LinesParams);
|
|
36
|
+
var ExtendersParams = tslib_1.__assign({}, LinesParams);
|
|
37
|
+
var ArmsParams = tslib_1.__assign({}, LinesParams);
|
|
38
|
+
var ArcParams = tslib_1.__assign({}, LinesParams);
|
|
39
|
+
var SectorParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams), { ignoreLight: param_definition_1.ParamDefinition.Boolean(true), sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.75, { min: 0, max: 1, step: 0.01 }) });
|
|
40
40
|
var DihedralVisuals = {
|
|
41
|
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'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
42
|
-
'extenders': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
43
|
-
'connector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
44
|
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'arms': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
45
|
-
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
46
|
-
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (
|
|
47
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
41
|
+
'vectors': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getVectorsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
42
|
+
'extenders': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getExtendersShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
43
|
+
'connector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getConnectorShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
44
|
+
'arms': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArmsShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
45
|
+
'arc': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getArcShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
46
|
+
'sector': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getSectorShape, mesh_1.Mesh.Utils, { modifyProps: function (p) { return (tslib_1.__assign(tslib_1.__assign({}, p), { alpha: p.sectorOpacity })); }, modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
47
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
48
48
|
};
|
|
49
|
-
exports.DihedralParams =
|
|
49
|
+
exports.DihedralParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, VectorsParams), ExtendersParams), ArmsParams), ArcParams), SectorParams), common_1.LociLabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['extenders', 'arms', 'sector', 'text'], param_definition_1.ParamDefinition.objectToOptions(DihedralVisuals)) });
|
|
50
50
|
//
|
|
51
51
|
function getDihedralState() {
|
|
52
52
|
return {
|
|
@@ -25,13 +25,13 @@ var geometry_1 = require("../../../mol-math/geometry");
|
|
|
25
25
|
var SharedParams = {
|
|
26
26
|
unitLabel: param_definition_1.ParamDefinition.Text('\u212B', { isEssential: true })
|
|
27
27
|
};
|
|
28
|
-
var LineParams =
|
|
29
|
-
var TextParams =
|
|
28
|
+
var LineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen, { isEssential: true }), linesSize: param_definition_1.ParamDefinition.Numeric(0.075, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0.01, max: 0.2, step: 0.01 }) });
|
|
29
|
+
var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), SharedParams);
|
|
30
30
|
var DistanceVisuals = {
|
|
31
|
-
'lines': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getLinesShape, lines_1.Lines.Utils, { modifyState: function (s) { return (
|
|
32
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
31
|
+
'lines': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getLinesShape, lines_1.Lines.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
|
|
32
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); } }); },
|
|
33
33
|
};
|
|
34
|
-
exports.DistanceParams =
|
|
34
|
+
exports.DistanceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, LineParams), TextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['lines', 'text'], param_definition_1.ParamDefinition.objectToOptions(DistanceVisuals)) });
|
|
35
35
|
//
|
|
36
36
|
function getDistanceState() {
|
|
37
37
|
return {
|
|
@@ -17,11 +17,11 @@ var text_builder_1 = require("../../../mol-geo/geometry/text/text-builder");
|
|
|
17
17
|
var geometry_1 = require("../../../mol-math/geometry");
|
|
18
18
|
var label_1 = require("../../../mol-theme/label");
|
|
19
19
|
var common_1 = require("./common");
|
|
20
|
-
var TextParams =
|
|
20
|
+
var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), { offsetZ: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }) });
|
|
21
21
|
var LabelVisuals = {
|
|
22
|
-
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (
|
|
22
|
+
'text': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, { modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { pickable: false })); } }); },
|
|
23
23
|
};
|
|
24
|
-
exports.LabelParams =
|
|
24
|
+
exports.LabelParams = tslib_1.__assign(tslib_1.__assign({}, TextParams), { scaleByRadius: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['text'], param_definition_1.ParamDefinition.objectToOptions(LabelVisuals)) });
|
|
25
25
|
//
|
|
26
26
|
var tmpSphere = (0, geometry_1.Sphere3D)();
|
|
27
27
|
function label(info, condensed) {
|
|
@@ -19,6 +19,7 @@ export declare const OrientationParams: {
|
|
|
19
19
|
flatShaded: PD.BooleanParam;
|
|
20
20
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ignoreLight: PD.BooleanParam;
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21
21
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xrayShaded: PD.BooleanParam;
|
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22
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
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22
23
|
bumpFrequency: PD.Numeric;
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23
24
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bumpAmplitude: PD.Numeric;
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24
25
|
alpha: PD.Numeric;
|
|
@@ -27,15 +27,15 @@ var SharedParams = {
|
|
|
27
27
|
scaleFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
|
|
28
28
|
radiusScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 10, step: 0.1 })
|
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29
29
|
};
|
|
30
|
-
var AxesParams =
|
|
31
|
-
var BoxParams =
|
|
32
|
-
var EllipsoidParams =
|
|
30
|
+
var AxesParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams);
|
|
31
|
+
var BoxParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams);
|
|
32
|
+
var EllipsoidParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), SharedParams);
|
|
33
33
|
var OrientationVisuals = {
|
|
34
34
|
'axes': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getAxesShape, mesh_1.Mesh.Utils); },
|
|
35
35
|
'box': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getBoxShape, mesh_1.Mesh.Utils); },
|
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36
36
|
'ellipsoid': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getEllipsoidShape, mesh_1.Mesh.Utils); },
|
|
37
37
|
};
|
|
38
|
-
exports.OrientationParams =
|
|
38
|
+
exports.OrientationParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, AxesParams), BoxParams), EllipsoidParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['box'], param_definition_1.ParamDefinition.objectToOptions(OrientationVisuals)) });
|
|
39
39
|
//
|
|
40
40
|
function getAxesName(locis) {
|
|
41
41
|
var label = (0, label_1.structureElementLociLabelMany)(locis, { countsOnly: true });
|
|
@@ -20,11 +20,11 @@ var marker_action_1 = require("../../../mol-util/marker-action");
|
|
|
20
20
|
var plane_1 = require("../../../mol-geo/primitive/plane");
|
|
21
21
|
var structure_1 = require("../../../mol-model/structure");
|
|
22
22
|
var geometry_1 = require("../../../mol-math/geometry");
|
|
23
|
-
var _PlaneParams =
|
|
23
|
+
var _PlaneParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), scaleFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 10, step: 0.1 }) });
|
|
24
24
|
var PlaneVisuals = {
|
|
25
25
|
'plane': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getPlaneShape, mesh_1.Mesh.Utils); },
|
|
26
26
|
};
|
|
27
|
-
exports.PlaneParams =
|
|
27
|
+
exports.PlaneParams = tslib_1.__assign(tslib_1.__assign({}, _PlaneParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['plane'], param_definition_1.ParamDefinition.objectToOptions(PlaneVisuals)) });
|
|
28
28
|
//
|
|
29
29
|
function getPlaneName(locis) {
|
|
30
30
|
var label = (0, label_1.structureElementLociLabelMany)(locis, { countsOnly: true });
|
|
@@ -21,6 +21,7 @@ export declare const UnitcellParams: {
|
|
|
21
21
|
flatShaded: PD.BooleanParam;
|
|
22
22
|
ignoreLight: PD.BooleanParam;
|
|
23
23
|
xrayShaded: PD.BooleanParam;
|
|
24
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
24
25
|
bumpFrequency: PD.Numeric;
|
|
25
26
|
bumpAmplitude: PD.Numeric;
|
|
26
27
|
alpha: PD.Numeric;
|
|
@@ -31,11 +31,11 @@ var CellAttachment = {
|
|
|
31
31
|
corner: 'Corner',
|
|
32
32
|
center: 'Center'
|
|
33
33
|
};
|
|
34
|
-
var CellParams =
|
|
34
|
+
var CellParams = tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { cellColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), cellScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), ref: param_definition_1.ParamDefinition.Select('model', param_definition_1.ParamDefinition.objectToOptions(CellRef), { isEssential: true }), attachment: param_definition_1.ParamDefinition.Select('corner', param_definition_1.ParamDefinition.objectToOptions(CellAttachment), { isEssential: true }) });
|
|
35
35
|
var UnitcellVisuals = {
|
|
36
36
|
'mesh': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getUnitcellShape, mesh_1.Mesh.Utils); },
|
|
37
37
|
};
|
|
38
|
-
exports.UnitcellParams =
|
|
38
|
+
exports.UnitcellParams = tslib_1.__assign({}, CellParams);
|
|
39
39
|
function getUnitcellMesh(data, props, mesh) {
|
|
40
40
|
var state = mesh_builder_1.MeshBuilder.createState(256, 128, mesh);
|
|
41
41
|
var fromFractional = data.symmetry.spacegroup.cell.fromFractional;
|