molstar 3.3.1 → 3.6.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +20 -20
- package/README.md +202 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/build/viewer/molstar.js.LICENSE.txt +12 -14
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +1 -1
- package/lib/apps/docking-viewer/viewport.js +1 -1
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +3 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
- package/lib/cli/chem-comp-dict/util.d.ts +20 -20
- package/lib/cli/cif2bcif/converter.js +1 -1
- package/lib/cli/cif2bcif/index.js +4 -4
- package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/cli/cifschema/util/cif-dic.js +7 -5
- package/lib/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/cli/cifschema/util/generate.js +12 -3
- package/lib/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/apps/docking-viewer/index.js +14 -14
- package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +26 -24
- package/lib/commonjs/apps/viewer/index.js +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
- package/lib/commonjs/cli/chem-comp-dict/util.d.ts +20 -20
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
- package/lib/commonjs/cli/cif2bcif/index.js +12 -12
- package/lib/commonjs/cli/cifschema/index.js +27 -27
- package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +8 -6
- package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
- package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -9
- package/lib/commonjs/cli/state-docs/index.js +2 -2
- package/lib/commonjs/cli/structure-info/helpers.js +11 -11
- package/lib/commonjs/cli/structure-info/model.js +15 -15
- package/lib/commonjs/cli/structure-info/volume.js +9 -9
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
- package/lib/commonjs/examples/alpha-orbitals/index.js +12 -12
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
- package/lib/commonjs/examples/basic-wrapper/index.js +23 -23
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
- package/lib/commonjs/examples/lighting/index.js +7 -7
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +27 -27
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
- package/lib/commonjs/examples/task.js +15 -15
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
- package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
- package/lib/commonjs/extensions/anvil/behavior.js +14 -14
- package/lib/commonjs/extensions/anvil/prop.js +7 -7
- package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
- package/lib/commonjs/extensions/anvil/representation.js +5 -5
- package/lib/commonjs/extensions/cellpack/index.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.js +26 -24
- package/lib/commonjs/extensions/cellpack/preset.js +6 -6
- package/lib/commonjs/extensions/cellpack/property.js +3 -3
- package/lib/commonjs/extensions/cellpack/representation.d.ts +1 -0
- package/lib/commonjs/extensions/cellpack/representation.js +2 -2
- package/lib/commonjs/extensions/cellpack/state.js +13 -13
- package/lib/commonjs/extensions/cellpack/util.js +14 -14
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
- package/lib/commonjs/extensions/g3d/data.js +6 -6
- package/lib/commonjs/extensions/g3d/format.js +14 -14
- package/lib/commonjs/extensions/g3d/model.js +4 -4
- package/lib/commonjs/extensions/geo-export/controls.js +3 -3
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
- package/lib/commonjs/extensions/geo-export/index.js +1 -1
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/ui.js +7 -7
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
- package/lib/commonjs/extensions/model-export/export.js +4 -4
- package/lib/commonjs/extensions/model-export/index.js +1 -1
- package/lib/commonjs/extensions/model-export/ui.js +5 -5
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
- package/lib/commonjs/extensions/mp4-export/index.js +1 -1
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
- package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
- package/lib/commonjs/extensions/zenodo/index.js +35 -0
- package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
- package/lib/commonjs/extensions/zenodo/ui.js +306 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera.js +2 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
- package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
- package/lib/commonjs/mol-canvas3d/util.js +2 -2
- package/lib/commonjs/mol-data/db/column.d.ts +10 -3
- package/lib/commonjs/mol-data/db/column.js +40 -18
- package/lib/commonjs/mol-data/db/table.js +1 -1
- package/lib/commonjs/mol-data/db.js +1 -1
- package/lib/commonjs/mol-data/generic.js +3 -3
- package/lib/commonjs/mol-data/index.js +4 -4
- package/lib/commonjs/mol-data/int/interval.js +1 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
- package/lib/commonjs/mol-data/int/segmentation.js +1 -1
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
- package/lib/commonjs/mol-data/util.js +7 -7
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +4 -4
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +4 -4
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -4
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
- package/lib/commonjs/mol-gl/compute/util.js +3 -3
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.js +3 -3
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/points.js +3 -3
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
- package/lib/commonjs/mol-gl/renderable/text.js +3 -3
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/util.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader-code.js +2 -1
- package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
- package/lib/commonjs/mol-gl/webgl/buffer.js +16 -17
- package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +5 -5
- package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/program.js +10 -4
- package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
- package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
- package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
- package/lib/commonjs/mol-io/common/typed-array.js +2 -2
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
- package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +8 -8
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +4 -4
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +31 -27
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
- package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema.js +24 -4
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cif.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
- package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
- package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
- package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
- package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
- package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
- package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
- package/lib/commonjs/mol-io/writer/cif.js +1 -1
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol/encoder.js +2 -2
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
- package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/common.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
- package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
- package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
- package/lib/commonjs/mol-math/geometry.js +8 -8
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
- package/lib/commonjs/mol-math/graph.js +1 -1
- package/lib/commonjs/mol-math/linear-algebra.js +2 -2
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
- package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
- package/lib/commonjs/mol-model/sequence.js +1 -1
- package/lib/commonjs/mol-model/shape.js +1 -1
- package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/commonjs/mol-model/structure/model/model.js +17 -9
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
- package/lib/commonjs/mol-model/structure/model/properties/common.js +1 -1
- package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
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- package/lib/mol-model-formats/structure/pdb/to-cif.js +7 -2
- package/lib/mol-model-formats/structure/pdb.d.ts +1 -1
- package/lib/mol-model-formats/structure/pdb.js +5 -3
- package/lib/mol-model-formats/structure/prmtop.d.ts +16 -0
- package/lib/mol-model-formats/structure/prmtop.js +144 -0
- package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +1 -1
- package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +1 -1
- package/lib/mol-model-formats/structure/property/symmetry.js +11 -1
- package/lib/mol-model-formats/structure/psf.js +3 -1
- package/lib/mol-model-formats/structure/top.d.ts +16 -0
- package/lib/mol-model-formats/structure/top.js +186 -0
- package/lib/mol-model-formats/structure/trr.d.ts +9 -0
- package/lib/mol-model-formats/structure/trr.js +42 -0
- package/lib/mol-model-formats/structure/util.d.ts +2 -2
- package/lib/mol-model-formats/structure/util.js +19 -20
- package/lib/mol-model-formats/structure/xyz.js +2 -2
- package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -0
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -0
- package/lib/mol-model-props/computed/representations/interactions.d.ts +3 -0
- package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -0
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js +3 -2
- package/lib/mol-plugin/commands.d.ts +1 -0
- package/lib/mol-plugin/context.d.ts +2 -1
- package/lib/mol-plugin/context.js +4 -3
- package/lib/mol-plugin/spec.js +1 -1
- package/lib/mol-plugin/util/viewport-screenshot.d.ts +3 -0
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-state/actions/file.d.ts +1 -1
- package/lib/mol-plugin-state/actions/file.js +88 -55
- package/lib/mol-plugin-state/actions/structure.d.ts +17 -8
- package/lib/mol-plugin-state/actions/structure.js +174 -4
- package/lib/mol-plugin-state/actions/volume.js +3 -2
- package/lib/mol-plugin-state/formats/{structure.d.ts → coordinates.d.ts} +34 -18
- package/lib/mol-plugin-state/formats/coordinates.js +67 -0
- package/lib/mol-plugin-state/formats/registry.d.ts +3 -3
- package/lib/mol-plugin-state/formats/registry.js +13 -8
- package/lib/mol-plugin-state/formats/topology.d.ts +73 -0
- package/lib/mol-plugin-state/formats/topology.js +84 -0
- package/lib/mol-plugin-state/helpers/structure-component.js +2 -1
- package/lib/mol-plugin-state/helpers/structure-selection-query.d.ts +1 -1
- package/lib/mol-plugin-state/helpers/structure-selection-query.js +1 -1
- package/lib/mol-plugin-state/manager/snapshots.js +4 -4
- package/lib/mol-plugin-state/objects.d.ts +47 -1
- package/lib/mol-plugin-state/objects.js +17 -1
- package/lib/mol-plugin-state/transforms/data.d.ts +6 -0
- package/lib/mol-plugin-state/transforms/data.js +61 -9
- package/lib/mol-plugin-state/transforms/model.d.ts +14 -2
- package/lib/mol-plugin-state/transforms/model.js +112 -3
- package/lib/mol-plugin-state/transforms/representation.d.ts +6 -0
- package/lib/mol-plugin-ui/base.js +1 -1
- package/lib/mol-plugin-ui/controls/action-menu.js +7 -7
- package/lib/mol-plugin-ui/controls/color.js +3 -3
- package/lib/mol-plugin-ui/controls/common.js +10 -10
- package/lib/mol-plugin-ui/controls/icons.js +70 -70
- package/lib/mol-plugin-ui/controls/legend.js +3 -3
- package/lib/mol-plugin-ui/controls/line-graph/line-graph-component.js +1 -1
- package/lib/mol-plugin-ui/controls/parameters.js +51 -51
- package/lib/mol-plugin-ui/controls/screenshot.js +2 -2
- package/lib/mol-plugin-ui/controls/slider.js +5 -5
- package/lib/mol-plugin-ui/controls.js +7 -7
- package/lib/mol-plugin-ui/custom/volume.js +4 -4
- package/lib/mol-plugin-ui/left-panel.d.ts +8 -1
- package/lib/mol-plugin-ui/left-panel.js +33 -12
- package/lib/mol-plugin-ui/plugin.js +10 -10
- package/lib/mol-plugin-ui/react18.d.ts +11 -0
- package/lib/mol-plugin-ui/react18.js +34 -0
- package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/mol-plugin-ui/sequence.js +5 -5
- package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
- package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
- package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
- package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
- package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
- package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
- package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
- package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
- package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
- package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
- package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
- package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
- package/lib/mol-plugin-ui/skin/base/components/viewport.scss +128 -128
- package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
- package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
- package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
- package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
- package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
- package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
- package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
- package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
- package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
- package/lib/mol-plugin-ui/skin/blue.scss +1 -1
- package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
- package/lib/mol-plugin-ui/skin/dark.scss +1 -1
- package/lib/mol-plugin-ui/skin/light.scss +1 -1
- package/lib/mol-plugin-ui/state/actions.js +1 -1
- package/lib/mol-plugin-ui/state/animation.js +1 -1
- package/lib/mol-plugin-ui/state/common.js +7 -7
- package/lib/mol-plugin-ui/state/snapshots.js +9 -9
- package/lib/mol-plugin-ui/state/tree.js +14 -14
- package/lib/mol-plugin-ui/state/update-transform.js +1 -1
- package/lib/mol-plugin-ui/structure/components.js +10 -10
- package/lib/mol-plugin-ui/structure/focus.d.ts +1 -1
- package/lib/mol-plugin-ui/structure/focus.js +3 -3
- package/lib/mol-plugin-ui/structure/generic.js +4 -4
- package/lib/mol-plugin-ui/structure/measurements.js +8 -8
- package/lib/mol-plugin-ui/structure/quick-styles.js +2 -2
- package/lib/mol-plugin-ui/structure/selection.js +7 -7
- package/lib/mol-plugin-ui/structure/source.js +4 -4
- package/lib/mol-plugin-ui/structure/superposition.js +8 -8
- package/lib/mol-plugin-ui/structure/volume.js +4 -4
- package/lib/mol-plugin-ui/task.js +5 -5
- package/lib/mol-plugin-ui/toast.js +4 -4
- package/lib/mol-plugin-ui/viewport/canvas.js +3 -3
- package/lib/mol-plugin-ui/viewport/help.js +8 -8
- package/lib/mol-plugin-ui/viewport/screenshot.js +3 -3
- package/lib/mol-plugin-ui/viewport/simple-settings.js +1 -1
- package/lib/mol-plugin-ui/viewport.js +4 -4
- package/lib/mol-repr/shape/loci/angle.d.ts +1 -0
- package/lib/mol-repr/shape/loci/dihedral.d.ts +1 -0
- package/lib/mol-repr/shape/loci/orientation.d.ts +1 -0
- package/lib/mol-repr/shape/loci/plane.d.ts +1 -0
- package/lib/mol-repr/shape/model/unitcell.d.ts +1 -0
- package/lib/mol-repr/structure/complex-visual.d.ts +3 -0
- package/lib/mol-repr/structure/params.d.ts +4 -0
- package/lib/mol-repr/structure/registry.d.ts +10 -0
- package/lib/mol-repr/structure/representation/backbone.d.ts +3 -0
- package/lib/mol-repr/structure/representation/ball-and-stick.d.ts +3 -0
- package/lib/mol-repr/structure/representation/carbohydrate.d.ts +3 -0
- package/lib/mol-repr/structure/representation/cartoon.d.ts +3 -0
- package/lib/mol-repr/structure/representation/ellipsoid.d.ts +3 -0
- package/lib/mol-repr/structure/representation/gaussian-surface.d.ts +3 -0
- package/lib/mol-repr/structure/representation/molecular-surface.d.ts +3 -0
- package/lib/mol-repr/structure/representation/orientation.d.ts +3 -0
- package/lib/mol-repr/structure/representation/putty.d.ts +3 -0
- package/lib/mol-repr/structure/representation/spacefill.d.ts +3 -0
- package/lib/mol-repr/structure/units-visual.d.ts +4 -0
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/element-sphere.d.ts +2 -0
- package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/gaussian-density-volume.js +2 -3
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +5 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +10 -10
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js +4 -5
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +4 -4
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
- package/lib/mol-repr/structure/visual/molecular-surface-wireframe.js +5 -5
- package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -0
- package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -0
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -0
- package/lib/mol-repr/structure/visual/util/common.d.ts +1 -3
- package/lib/mol-repr/structure/visual/util/common.js +1 -24
- package/lib/mol-repr/util.d.ts +2 -1
- package/lib/mol-repr/util.js +2 -2
- package/lib/mol-repr/volume/isosurface.d.ts +5 -0
- package/lib/mol-repr/volume/registry.d.ts +1 -0
- package/lib/mol-script/language/builder.d.ts +1 -0
- package/lib/mol-script/language/parser.js +7 -4
- package/lib/mol-task/util/scheduler.d.ts +2 -2
- package/lib/mol-task/util/scheduler.js +7 -7
- package/lib/mol-theme/color/hydrophobicity.js +2 -2
- package/lib/mol-util/data-source.js +2 -1
- package/lib/mol-util/file-info.d.ts +1 -3
- package/lib/mol-util/file-info.js +2 -10
- package/lib/mol-util/index.d.ts +1 -0
- package/lib/mol-util/index.js +5 -0
- package/lib/mol-util/zip/deflate.js +2 -1
- package/lib/mol-util/zip/zip.d.ts +7 -1
- package/lib/mol-util/zip/zip.js +5 -1
- package/lib/servers/model/config.d.ts +2 -2
- package/package.json +162 -160
- package/lib/commonjs/mol-plugin-state/formats/structure.js +0 -64
- package/lib/mol-plugin-state/formats/structure.js +0 -61
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var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
843
|
-
return mol_task_1.Task.create('Volume Representation', function (ctx) { return
|
|
843
|
+
return mol_task_1.Task.create('Volume Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
844
844
|
var oldProvider, props;
|
|
845
845
|
var _a;
|
|
846
|
-
return
|
|
846
|
+
return tslib_1.__generator(this, function (_b) {
|
|
847
847
|
switch (_b.label) {
|
|
848
848
|
case 0:
|
|
849
849
|
if (newParams.type.name !== oldParams.type.name) {
|
|
@@ -851,7 +851,7 @@ var VolumeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
851
851
|
(_a = oldProvider.ensureCustomProperties) === null || _a === void 0 ? void 0 : _a.detach(a.data);
|
|
852
852
|
return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Recreate];
|
|
853
853
|
}
|
|
854
|
-
props =
|
|
854
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams.type.params);
|
|
855
855
|
b.data.repr.setTheme(theme_1.Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
|
|
856
856
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, a.data).runInContext(ctx)];
|
|
857
857
|
case 1:
|
|
@@ -880,12 +880,12 @@ var ShapeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
880
880
|
apply: function (_a, plugin) {
|
|
881
881
|
var _this = this;
|
|
882
882
|
var a = _a.a, params = _a.params;
|
|
883
|
-
return mol_task_1.Task.create('Shape Representation', function (ctx) { return
|
|
883
|
+
return mol_task_1.Task.create('Shape Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
884
884
|
var props, repr;
|
|
885
|
-
return
|
|
885
|
+
return tslib_1.__generator(this, function (_a) {
|
|
886
886
|
switch (_a.label) {
|
|
887
887
|
case 0:
|
|
888
|
-
props =
|
|
888
|
+
props = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(a.data.params)), params);
|
|
889
889
|
repr = (0, representation_1.ShapeRepresentation)(a.data.getShape, a.data.geometryUtils);
|
|
890
890
|
return [4 /*yield*/, repr.createOrUpdate(props, a.data.data).runInContext(ctx)];
|
|
891
891
|
case 1:
|
|
@@ -898,12 +898,12 @@ var ShapeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
898
898
|
update: function (_a, plugin) {
|
|
899
899
|
var _this = this;
|
|
900
900
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
901
|
-
return mol_task_1.Task.create('Shape Representation', function (ctx) { return
|
|
901
|
+
return mol_task_1.Task.create('Shape Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
902
902
|
var props;
|
|
903
|
-
return
|
|
903
|
+
return tslib_1.__generator(this, function (_a) {
|
|
904
904
|
switch (_a.label) {
|
|
905
905
|
case 0:
|
|
906
|
-
props =
|
|
906
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
907
907
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, a.data.data).runInContext(ctx)];
|
|
908
908
|
case 1:
|
|
909
909
|
_a.sent();
|
|
@@ -920,7 +920,7 @@ var ModelUnitcell3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
920
920
|
display: 'Model Unit Cell',
|
|
921
921
|
from: objects_1.PluginStateObject.Molecule.Model,
|
|
922
922
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
923
|
-
params: function () { return (
|
|
923
|
+
params: function () { return (tslib_1.__assign({}, unitcell_1.UnitcellParams)); }
|
|
924
924
|
})({
|
|
925
925
|
isApplicable: function (a) { return !!symmetry_1.ModelSymmetry.Provider.get(a.data); },
|
|
926
926
|
canAutoUpdate: function (_a) {
|
|
@@ -930,17 +930,17 @@ var ModelUnitcell3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
930
930
|
apply: function (_a, plugin) {
|
|
931
931
|
var _this = this;
|
|
932
932
|
var a = _a.a, params = _a.params;
|
|
933
|
-
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return
|
|
933
|
+
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
934
934
|
var symmetry, data, repr;
|
|
935
935
|
var _a;
|
|
936
|
-
return
|
|
936
|
+
return tslib_1.__generator(this, function (_b) {
|
|
937
937
|
switch (_b.label) {
|
|
938
938
|
case 0:
|
|
939
939
|
symmetry = symmetry_1.ModelSymmetry.Provider.get(a.data);
|
|
940
940
|
if (!symmetry)
|
|
941
941
|
return [2 /*return*/, mol_state_1.StateObject.Null];
|
|
942
942
|
data = (0, unitcell_1.getUnitcellData)(a.data, symmetry, params);
|
|
943
|
-
repr = (0, unitcell_1.UnitcellRepresentation)(
|
|
943
|
+
repr = (0, unitcell_1.UnitcellRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return unitcell_1.UnitcellParams; });
|
|
944
944
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
945
945
|
case 1:
|
|
946
946
|
_b.sent();
|
|
@@ -952,15 +952,15 @@ var ModelUnitcell3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
952
952
|
update: function (_a) {
|
|
953
953
|
var _this = this;
|
|
954
954
|
var a = _a.a, b = _a.b, newParams = _a.newParams;
|
|
955
|
-
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return
|
|
955
|
+
return mol_task_1.Task.create('Model Unit Cell', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
956
956
|
var symmetry, props, data;
|
|
957
|
-
return
|
|
957
|
+
return tslib_1.__generator(this, function (_a) {
|
|
958
958
|
switch (_a.label) {
|
|
959
959
|
case 0:
|
|
960
960
|
symmetry = symmetry_1.ModelSymmetry.Provider.get(a.data);
|
|
961
961
|
if (!symmetry)
|
|
962
962
|
return [2 /*return*/, mol_state_1.StateTransformer.UpdateResult.Null];
|
|
963
|
-
props =
|
|
963
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
964
964
|
data = (0, unitcell_1.getUnitcellData)(a.data, symmetry, props);
|
|
965
965
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
966
966
|
case 1:
|
|
@@ -978,7 +978,7 @@ var StructureBoundingBox3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
978
978
|
display: 'Bounding Box',
|
|
979
979
|
from: objects_1.PluginStateObject.Molecule.Structure,
|
|
980
980
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
981
|
-
params:
|
|
981
|
+
params: tslib_1.__assign({ radius: param_definition_1.ParamDefinition.Numeric(0.05, { min: 0.01, max: 4, step: 0.01 }, { isEssential: true }), color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.red, { isEssential: true }) }, mesh_1.Mesh.Params)
|
|
982
982
|
})({
|
|
983
983
|
canAutoUpdate: function () {
|
|
984
984
|
return true;
|
|
@@ -986,9 +986,9 @@ var StructureBoundingBox3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
986
986
|
apply: function (_a, plugin) {
|
|
987
987
|
var _this = this;
|
|
988
988
|
var a = _a.a, params = _a.params;
|
|
989
|
-
return mol_task_1.Task.create('Bounding Box', function (ctx) { return
|
|
989
|
+
return mol_task_1.Task.create('Bounding Box', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
990
990
|
var repr;
|
|
991
|
-
return
|
|
991
|
+
return tslib_1.__generator(this, function (_a) {
|
|
992
992
|
switch (_a.label) {
|
|
993
993
|
case 0:
|
|
994
994
|
repr = (0, representation_1.ShapeRepresentation)(function (_, data, __, shape) {
|
|
@@ -1006,8 +1006,8 @@ var StructureBoundingBox3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1006
1006
|
update: function (_a, plugin) {
|
|
1007
1007
|
var _this = this;
|
|
1008
1008
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1009
|
-
return mol_task_1.Task.create('Bounding Box', function (ctx) { return
|
|
1010
|
-
return
|
|
1009
|
+
return mol_task_1.Task.create('Bounding Box', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1010
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1011
1011
|
switch (_a.label) {
|
|
1012
1012
|
case 0: return [4 /*yield*/, b.data.repr.createOrUpdate(newParams, { box: a.data.boundary.box, radius: newParams.radius, color: newParams.color }).runInContext(ctx)];
|
|
1013
1013
|
case 1:
|
|
@@ -1025,7 +1025,7 @@ var StructureSelectionsDistance3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1025
1025
|
display: '3D Distance',
|
|
1026
1026
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1027
1027
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1028
|
-
params: function () { return (
|
|
1028
|
+
params: function () { return (tslib_1.__assign({}, distance_1.DistanceParams)); }
|
|
1029
1029
|
})({
|
|
1030
1030
|
canAutoUpdate: function (_a) {
|
|
1031
1031
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1034,14 +1034,14 @@ var StructureSelectionsDistance3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1034
1034
|
apply: function (_a, plugin) {
|
|
1035
1035
|
var _this = this;
|
|
1036
1036
|
var a = _a.a, params = _a.params;
|
|
1037
|
-
return mol_task_1.Task.create('Structure Distance', function (ctx) { return
|
|
1037
|
+
return mol_task_1.Task.create('Structure Distance', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1038
1038
|
var data, repr;
|
|
1039
1039
|
var _a;
|
|
1040
|
-
return
|
|
1040
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1041
1041
|
switch (_b.label) {
|
|
1042
1042
|
case 0:
|
|
1043
1043
|
data = (0, helpers_2.getDistanceDataFromStructureSelections)(a.data);
|
|
1044
|
-
repr = (0, distance_1.DistanceRepresentation)(
|
|
1044
|
+
repr = (0, distance_1.DistanceRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return distance_1.DistanceParams; });
|
|
1045
1045
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1046
1046
|
case 1:
|
|
1047
1047
|
_b.sent();
|
|
@@ -1053,12 +1053,12 @@ var StructureSelectionsDistance3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1053
1053
|
update: function (_a, plugin) {
|
|
1054
1054
|
var _this = this;
|
|
1055
1055
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1056
|
-
return mol_task_1.Task.create('Structure Distance', function (ctx) { return
|
|
1056
|
+
return mol_task_1.Task.create('Structure Distance', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1057
1057
|
var props, data;
|
|
1058
|
-
return
|
|
1058
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1059
1059
|
switch (_a.label) {
|
|
1060
1060
|
case 0:
|
|
1061
|
-
props =
|
|
1061
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1062
1062
|
data = (0, helpers_2.getDistanceDataFromStructureSelections)(a.data);
|
|
1063
1063
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1064
1064
|
case 1:
|
|
@@ -1076,7 +1076,7 @@ var StructureSelectionsAngle3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1076
1076
|
display: '3D Angle',
|
|
1077
1077
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1078
1078
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1079
|
-
params: function () { return (
|
|
1079
|
+
params: function () { return (tslib_1.__assign({}, angle_1.AngleParams)); }
|
|
1080
1080
|
})({
|
|
1081
1081
|
canAutoUpdate: function (_a) {
|
|
1082
1082
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1085,14 +1085,14 @@ var StructureSelectionsAngle3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1085
1085
|
apply: function (_a, plugin) {
|
|
1086
1086
|
var _this = this;
|
|
1087
1087
|
var a = _a.a, params = _a.params;
|
|
1088
|
-
return mol_task_1.Task.create('Structure Angle', function (ctx) { return
|
|
1088
|
+
return mol_task_1.Task.create('Structure Angle', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1089
1089
|
var data, repr;
|
|
1090
1090
|
var _a;
|
|
1091
|
-
return
|
|
1091
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1092
1092
|
switch (_b.label) {
|
|
1093
1093
|
case 0:
|
|
1094
1094
|
data = (0, helpers_2.getAngleDataFromStructureSelections)(a.data);
|
|
1095
|
-
repr = (0, angle_1.AngleRepresentation)(
|
|
1095
|
+
repr = (0, angle_1.AngleRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return angle_1.AngleParams; });
|
|
1096
1096
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1097
1097
|
case 1:
|
|
1098
1098
|
_b.sent();
|
|
@@ -1104,12 +1104,12 @@ var StructureSelectionsAngle3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1104
1104
|
update: function (_a, plugin) {
|
|
1105
1105
|
var _this = this;
|
|
1106
1106
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1107
|
-
return mol_task_1.Task.create('Structure Angle', function (ctx) { return
|
|
1107
|
+
return mol_task_1.Task.create('Structure Angle', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1108
1108
|
var props, data;
|
|
1109
|
-
return
|
|
1109
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1110
1110
|
switch (_a.label) {
|
|
1111
1111
|
case 0:
|
|
1112
|
-
props =
|
|
1112
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1113
1113
|
data = (0, helpers_2.getAngleDataFromStructureSelections)(a.data);
|
|
1114
1114
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1115
1115
|
case 1:
|
|
@@ -1127,7 +1127,7 @@ var StructureSelectionsDihedral3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1127
1127
|
display: '3D Dihedral',
|
|
1128
1128
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1129
1129
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1130
|
-
params: function () { return (
|
|
1130
|
+
params: function () { return (tslib_1.__assign({}, dihedral_1.DihedralParams)); }
|
|
1131
1131
|
})({
|
|
1132
1132
|
canAutoUpdate: function (_a) {
|
|
1133
1133
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1136,14 +1136,14 @@ var StructureSelectionsDihedral3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1136
1136
|
apply: function (_a, plugin) {
|
|
1137
1137
|
var _this = this;
|
|
1138
1138
|
var a = _a.a, params = _a.params;
|
|
1139
|
-
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return
|
|
1139
|
+
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1140
1140
|
var data, repr;
|
|
1141
1141
|
var _a;
|
|
1142
|
-
return
|
|
1142
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1143
1143
|
switch (_b.label) {
|
|
1144
1144
|
case 0:
|
|
1145
1145
|
data = (0, helpers_2.getDihedralDataFromStructureSelections)(a.data);
|
|
1146
|
-
repr = (0, dihedral_1.DihedralRepresentation)(
|
|
1146
|
+
repr = (0, dihedral_1.DihedralRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return dihedral_1.DihedralParams; });
|
|
1147
1147
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1148
1148
|
case 1:
|
|
1149
1149
|
_b.sent();
|
|
@@ -1155,12 +1155,12 @@ var StructureSelectionsDihedral3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1155
1155
|
update: function (_a, plugin) {
|
|
1156
1156
|
var _this = this;
|
|
1157
1157
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1158
|
-
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return
|
|
1158
|
+
return mol_task_1.Task.create('Structure Dihedral', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1159
1159
|
var props, data;
|
|
1160
|
-
return
|
|
1160
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1161
1161
|
switch (_a.label) {
|
|
1162
1162
|
case 0:
|
|
1163
|
-
props =
|
|
1163
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1164
1164
|
data = (0, helpers_2.getDihedralDataFromStructureSelections)(a.data);
|
|
1165
1165
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1166
1166
|
case 1:
|
|
@@ -1178,7 +1178,7 @@ var StructureSelectionsLabel3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1178
1178
|
display: '3D Label',
|
|
1179
1179
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1180
1180
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1181
|
-
params: function () { return (
|
|
1181
|
+
params: function () { return (tslib_1.__assign({}, label_1.LabelParams)); }
|
|
1182
1182
|
})({
|
|
1183
1183
|
canAutoUpdate: function (_a) {
|
|
1184
1184
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1187,14 +1187,14 @@ var StructureSelectionsLabel3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1187
1187
|
apply: function (_a, plugin) {
|
|
1188
1188
|
var _this = this;
|
|
1189
1189
|
var a = _a.a, params = _a.params;
|
|
1190
|
-
return mol_task_1.Task.create('Structure Label', function (ctx) { return
|
|
1190
|
+
return mol_task_1.Task.create('Structure Label', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1191
1191
|
var data, repr;
|
|
1192
1192
|
var _a;
|
|
1193
|
-
return
|
|
1193
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1194
1194
|
switch (_b.label) {
|
|
1195
1195
|
case 0:
|
|
1196
1196
|
data = (0, helpers_2.getLabelDataFromStructureSelections)(a.data);
|
|
1197
|
-
repr = (0, label_1.LabelRepresentation)(
|
|
1197
|
+
repr = (0, label_1.LabelRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return label_1.LabelParams; });
|
|
1198
1198
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1199
1199
|
case 1:
|
|
1200
1200
|
_b.sent();
|
|
@@ -1206,12 +1206,12 @@ var StructureSelectionsLabel3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1206
1206
|
update: function (_a, plugin) {
|
|
1207
1207
|
var _this = this;
|
|
1208
1208
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1209
|
-
return mol_task_1.Task.create('Structure Label', function (ctx) { return
|
|
1209
|
+
return mol_task_1.Task.create('Structure Label', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1210
1210
|
var props, data;
|
|
1211
|
-
return
|
|
1211
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1212
1212
|
switch (_a.label) {
|
|
1213
1213
|
case 0:
|
|
1214
|
-
props =
|
|
1214
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1215
1215
|
data = (0, helpers_2.getLabelDataFromStructureSelections)(a.data);
|
|
1216
1216
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1217
1217
|
case 1:
|
|
@@ -1229,7 +1229,7 @@ var StructureSelectionsOrientation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1229
1229
|
display: '3D Orientation',
|
|
1230
1230
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1231
1231
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1232
|
-
params: function () { return (
|
|
1232
|
+
params: function () { return (tslib_1.__assign({}, orientation_1.OrientationParams)); }
|
|
1233
1233
|
})({
|
|
1234
1234
|
canAutoUpdate: function (_a) {
|
|
1235
1235
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1238,14 +1238,14 @@ var StructureSelectionsOrientation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1238
1238
|
apply: function (_a, plugin) {
|
|
1239
1239
|
var _this = this;
|
|
1240
1240
|
var a = _a.a, params = _a.params;
|
|
1241
|
-
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return
|
|
1241
|
+
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1242
1242
|
var data, repr;
|
|
1243
1243
|
var _a;
|
|
1244
|
-
return
|
|
1244
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1245
1245
|
switch (_b.label) {
|
|
1246
1246
|
case 0:
|
|
1247
1247
|
data = (0, helpers_2.getOrientationDataFromStructureSelections)(a.data);
|
|
1248
|
-
repr = (0, orientation_1.OrientationRepresentation)(
|
|
1248
|
+
repr = (0, orientation_1.OrientationRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return orientation_1.OrientationParams; });
|
|
1249
1249
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1250
1250
|
case 1:
|
|
1251
1251
|
_b.sent();
|
|
@@ -1257,12 +1257,12 @@ var StructureSelectionsOrientation3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1257
1257
|
update: function (_a, plugin) {
|
|
1258
1258
|
var _this = this;
|
|
1259
1259
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1260
|
-
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return
|
|
1260
|
+
return mol_task_1.Task.create('Structure Orientation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1261
1261
|
var props, data;
|
|
1262
|
-
return
|
|
1262
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1263
1263
|
switch (_a.label) {
|
|
1264
1264
|
case 0:
|
|
1265
|
-
props =
|
|
1265
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1266
1266
|
data = (0, helpers_2.getOrientationDataFromStructureSelections)(a.data);
|
|
1267
1267
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1268
1268
|
case 1:
|
|
@@ -1280,7 +1280,7 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1280
1280
|
display: '3D Plane',
|
|
1281
1281
|
from: objects_1.PluginStateObject.Molecule.Structure.Selections,
|
|
1282
1282
|
to: objects_1.PluginStateObject.Shape.Representation3D,
|
|
1283
|
-
params: function () { return (
|
|
1283
|
+
params: function () { return (tslib_1.__assign({}, plane_1.PlaneParams)); }
|
|
1284
1284
|
})({
|
|
1285
1285
|
canAutoUpdate: function (_a) {
|
|
1286
1286
|
var oldParams = _a.oldParams, newParams = _a.newParams;
|
|
@@ -1289,14 +1289,14 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1289
1289
|
apply: function (_a, plugin) {
|
|
1290
1290
|
var _this = this;
|
|
1291
1291
|
var a = _a.a, params = _a.params;
|
|
1292
|
-
return mol_task_1.Task.create('Structure Plane', function (ctx) { return
|
|
1292
|
+
return mol_task_1.Task.create('Structure Plane', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1293
1293
|
var data, repr;
|
|
1294
1294
|
var _a;
|
|
1295
|
-
return
|
|
1295
|
+
return tslib_1.__generator(this, function (_b) {
|
|
1296
1296
|
switch (_b.label) {
|
|
1297
1297
|
case 0:
|
|
1298
1298
|
data = (0, helpers_2.getPlaneDataFromStructureSelections)(a.data);
|
|
1299
|
-
repr = (0, plane_1.PlaneRepresentation)(
|
|
1299
|
+
repr = (0, plane_1.PlaneRepresentation)(tslib_1.__assign({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return plane_1.PlaneParams; });
|
|
1300
1300
|
return [4 /*yield*/, repr.createOrUpdate(params, data).runInContext(ctx)];
|
|
1301
1301
|
case 1:
|
|
1302
1302
|
_b.sent();
|
|
@@ -1308,12 +1308,12 @@ var StructureSelectionsPlane3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
1308
1308
|
update: function (_a, plugin) {
|
|
1309
1309
|
var _this = this;
|
|
1310
1310
|
var a = _a.a, b = _a.b, oldParams = _a.oldParams, newParams = _a.newParams;
|
|
1311
|
-
return mol_task_1.Task.create('Structure Plane', function (ctx) { return
|
|
1311
|
+
return mol_task_1.Task.create('Structure Plane', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
1312
1312
|
var props, data;
|
|
1313
|
-
return
|
|
1313
|
+
return tslib_1.__generator(this, function (_a) {
|
|
1314
1314
|
switch (_a.label) {
|
|
1315
1315
|
case 0:
|
|
1316
|
-
props =
|
|
1316
|
+
props = tslib_1.__assign(tslib_1.__assign({}, b.data.repr.props), newParams);
|
|
1317
1317
|
data = (0, helpers_2.getPlaneDataFromStructureSelections)(a.data);
|
|
1318
1318
|
return [4 /*yield*/, b.data.repr.createOrUpdate(props, data).runInContext(ctx)];
|
|
1319
1319
|
case 1:
|
|
@@ -35,8 +35,8 @@ var BoxShape3D = objects_1.PluginStateTransform.BuiltIn({
|
|
|
35
35
|
apply: function (_a) {
|
|
36
36
|
var _this = this;
|
|
37
37
|
var params = _a.params;
|
|
38
|
-
return mol_task_1.Task.create('Shape Representation', function (ctx) { return
|
|
39
|
-
return
|
|
38
|
+
return mol_task_1.Task.create('Shape Representation', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
39
|
+
return tslib_1.__generator(this, function (_a) {
|
|
40
40
|
return [2 /*return*/, new objects_1.PluginStateObject.Shape.Provider({
|
|
41
41
|
label: 'Box',
|
|
42
42
|
data: params,
|
|
@@ -35,11 +35,11 @@ var VolumeFromCcp4 = objects_1.PluginStateTransform.BuiltIn({
|
|
|
35
35
|
apply: function (_a) {
|
|
36
36
|
var _this = this;
|
|
37
37
|
var a = _a.a, params = _a.params;
|
|
38
|
-
return mol_task_1.Task.create('Create volume from CCP4/MRC/MAP', function (ctx) { return
|
|
38
|
+
return mol_task_1.Task.create('Create volume from CCP4/MRC/MAP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
39
39
|
var volume, props;
|
|
40
|
-
return
|
|
40
|
+
return tslib_1.__generator(this, function (_a) {
|
|
41
41
|
switch (_a.label) {
|
|
42
|
-
case 0: return [4 /*yield*/, (0, ccp4_1.volumeFromCcp4)(a.data,
|
|
42
|
+
case 0: return [4 /*yield*/, (0, ccp4_1.volumeFromCcp4)(a.data, tslib_1.__assign(tslib_1.__assign({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
|
|
43
43
|
case 1:
|
|
44
44
|
volume = _a.sent();
|
|
45
45
|
props = { label: volume.label || 'Volume', description: "Volume ".concat(a.data.header.NX, "\u00D7").concat(a.data.header.NX, "\u00D7").concat(a.data.header.NX) };
|
|
@@ -69,11 +69,11 @@ var VolumeFromDsn6 = objects_1.PluginStateTransform.BuiltIn({
|
|
|
69
69
|
apply: function (_a) {
|
|
70
70
|
var _this = this;
|
|
71
71
|
var a = _a.a, params = _a.params;
|
|
72
|
-
return mol_task_1.Task.create('Create volume from DSN6/BRIX', function (ctx) { return
|
|
72
|
+
return mol_task_1.Task.create('Create volume from DSN6/BRIX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
73
73
|
var volume, props;
|
|
74
|
-
return
|
|
74
|
+
return tslib_1.__generator(this, function (_a) {
|
|
75
75
|
switch (_a.label) {
|
|
76
|
-
case 0: return [4 /*yield*/, (0, dsn6_1.volumeFromDsn6)(a.data,
|
|
76
|
+
case 0: return [4 /*yield*/, (0, dsn6_1.volumeFromDsn6)(a.data, tslib_1.__assign(tslib_1.__assign({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
|
|
77
77
|
case 1:
|
|
78
78
|
volume = _a.sent();
|
|
79
79
|
props = { label: volume.label || 'Volume', description: "Volume ".concat(a.data.header.xExtent, "\u00D7").concat(a.data.header.yExtent, "\u00D7").concat(a.data.header.zExtent) };
|
|
@@ -104,11 +104,11 @@ var VolumeFromCube = objects_1.PluginStateTransform.BuiltIn({
|
|
|
104
104
|
apply: function (_a) {
|
|
105
105
|
var _this = this;
|
|
106
106
|
var a = _a.a, params = _a.params;
|
|
107
|
-
return mol_task_1.Task.create('Create volume from Cube', function (ctx) { return
|
|
107
|
+
return mol_task_1.Task.create('Create volume from Cube', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
108
108
|
var volume, props;
|
|
109
|
-
return
|
|
109
|
+
return tslib_1.__generator(this, function (_a) {
|
|
110
110
|
switch (_a.label) {
|
|
111
|
-
case 0: return [4 /*yield*/, (0, cube_1.volumeFromCube)(a.data,
|
|
111
|
+
case 0: return [4 /*yield*/, (0, cube_1.volumeFromCube)(a.data, tslib_1.__assign(tslib_1.__assign({}, params), { label: a.data.name || a.label })).runInContext(ctx)];
|
|
112
112
|
case 1:
|
|
113
113
|
volume = _a.sent();
|
|
114
114
|
props = { label: volume.label || 'Volume', description: "Volume ".concat(a.data.header.dim[0], "\u00D7").concat(a.data.header.dim[1], "\u00D7").concat(a.data.header.dim[2]) };
|
|
@@ -132,9 +132,9 @@ var VolumeFromDx = objects_1.PluginStateTransform.BuiltIn({
|
|
|
132
132
|
apply: function (_a) {
|
|
133
133
|
var _this = this;
|
|
134
134
|
var a = _a.a;
|
|
135
|
-
return mol_task_1.Task.create('Parse DX', function (ctx) { return
|
|
135
|
+
return mol_task_1.Task.create('Parse DX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
136
136
|
var volume, props;
|
|
137
|
-
return
|
|
137
|
+
return tslib_1.__generator(this, function (_a) {
|
|
138
138
|
switch (_a.label) {
|
|
139
139
|
case 0: return [4 /*yield*/, (0, dx_1.volumeFromDx)(a.data, { label: a.data.name || a.label }).runInContext(ctx)];
|
|
140
140
|
case 1:
|
|
@@ -174,10 +174,10 @@ var VolumeFromDensityServerCif = objects_1.PluginStateTransform.BuiltIn({
|
|
|
174
174
|
apply: function (_a) {
|
|
175
175
|
var _this = this;
|
|
176
176
|
var a = _a.a, params = _a.params;
|
|
177
|
-
return mol_task_1.Task.create('Parse density-server CIF', function (ctx) { return
|
|
177
|
+
return mol_task_1.Task.create('Parse density-server CIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
178
178
|
var header, block, densityServerCif, volume, _a, x, y, z, props;
|
|
179
179
|
var _b;
|
|
180
|
-
return
|
|
180
|
+
return tslib_1.__generator(this, function (_c) {
|
|
181
181
|
switch (_c.label) {
|
|
182
182
|
case 0:
|
|
183
183
|
header = params.blockHeader || a.data.blocks[1].header;
|
|
@@ -219,14 +219,14 @@ var AssignColorVolume = objects_1.PluginStateTransform.BuiltIn({
|
|
|
219
219
|
apply: function (_a) {
|
|
220
220
|
var _this = this;
|
|
221
221
|
var a = _a.a, params = _a.params, dependencies = _a.dependencies;
|
|
222
|
-
return mol_task_1.Task.create('Assign Color Volume', function (ctx) { return
|
|
222
|
+
return mol_task_1.Task.create('Assign Color Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
|
223
223
|
var colorVolume, volume, props;
|
|
224
|
-
return
|
|
224
|
+
return tslib_1.__generator(this, function (_a) {
|
|
225
225
|
if (!dependencies || !dependencies[params.ref]) {
|
|
226
226
|
throw new Error('Dependency not available.');
|
|
227
227
|
}
|
|
228
228
|
colorVolume = dependencies[params.ref].data;
|
|
229
|
-
volume =
|
|
229
|
+
volume = tslib_1.__assign(tslib_1.__assign({}, a.data), { colorVolume: colorVolume });
|
|
230
230
|
props = { label: a.label, description: 'Volume + Colors' };
|
|
231
231
|
return [2 /*return*/, new objects_1.PluginStateObject.Volume.Data(volume, props)];
|
|
232
232
|
});
|
|
@@ -7,12 +7,12 @@
|
|
|
7
7
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
8
8
|
exports.StateTransforms = void 0;
|
|
9
9
|
var tslib_1 = require("tslib");
|
|
10
|
-
var Data =
|
|
11
|
-
var Misc =
|
|
12
|
-
var Model =
|
|
13
|
-
var Volume =
|
|
14
|
-
var Representation =
|
|
15
|
-
var Shape =
|
|
10
|
+
var Data = tslib_1.__importStar(require("./transforms/data"));
|
|
11
|
+
var Misc = tslib_1.__importStar(require("./transforms/misc"));
|
|
12
|
+
var Model = tslib_1.__importStar(require("./transforms/model"));
|
|
13
|
+
var Volume = tslib_1.__importStar(require("./transforms/volume"));
|
|
14
|
+
var Representation = tslib_1.__importStar(require("./transforms/representation"));
|
|
15
|
+
var Shape = tslib_1.__importStar(require("./transforms/shape"));
|
|
16
16
|
exports.StateTransforms = {
|
|
17
17
|
Data: Data,
|
|
18
18
|
Misc: Misc,
|