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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@@ -155,6 +158,7 @@ export declare namespace StructureRepresentationRegistry {
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|
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@@ -205,6 +209,7 @@ export declare namespace StructureRepresentationRegistry {
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|
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@@ -266,6 +271,7 @@ export declare namespace StructureRepresentationRegistry {
|
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|
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allowTransparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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}, "gaussian-surface">;
|
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'gaussian-volume': import("./representation").StructureRepresentationProvider<{
|
|
@@ -421,6 +427,7 @@ export declare namespace StructureRepresentationRegistry {
|
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|
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|
xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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allowTransparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
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|
}, "molecular-surface">;
|
|
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|
orientation: import("./representation").StructureRepresentationProvider<{
|
|
@@ -435,6 +442,7 @@ export declare namespace StructureRepresentationRegistry {
|
|
|
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|
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|
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+
allowTransparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
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|
|
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|
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|
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quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -492,6 +500,7 @@ export declare namespace StructureRepresentationRegistry {
|
|
|
492
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|
flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
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|
ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
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|
xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
503
|
+
allowTransparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
495
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|
bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
|
|
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|
alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
|
|
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|
quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -525,6 +534,7 @@ export declare namespace StructureRepresentationRegistry {
|
|
|
525
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|
doubleSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
526
535
|
ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
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536
|
xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
537
|
+
allowTransparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
|
|
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|
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|
|
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|
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|
|
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|
quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -24,7 +24,7 @@ var line_1 = require("./representation/line");
|
|
|
24
24
|
var gaussian_volume_1 = require("./representation/gaussian-volume");
|
|
25
25
|
var backbone_1 = require("./representation/backbone");
|
|
26
26
|
var StructureRepresentationRegistry = /** @class */ (function (_super) {
|
|
27
|
-
|
|
27
|
+
tslib_1.__extends(StructureRepresentationRegistry, _super);
|
|
28
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|
function StructureRepresentationRegistry() {
|
|
29
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|
var _this = _super.call(this) || this;
|
|
30
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|
(0, object_1.objectForEach)(StructureRepresentationRegistry.BuiltIn, function (p, k) {
|
|
@@ -21,6 +21,7 @@ export declare const BackboneParams: {
|
|
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21
21
|
flatShaded: PD.BooleanParam;
|
|
22
22
|
ignoreLight: PD.BooleanParam;
|
|
23
23
|
xrayShaded: PD.BooleanParam;
|
|
24
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
24
25
|
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|
|
25
26
|
alpha: PD.Numeric;
|
|
26
27
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -56,6 +57,7 @@ export declare function getBackboneParams(ctx: ThemeRegistryContext, structure:
|
|
|
56
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|
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|
|
57
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|
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|
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|
|
60
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
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|
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|
|
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alpha: PD.Numeric;
|
|
61
63
|
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|
|
@@ -92,6 +94,7 @@ export declare const BackboneRepresentationProvider: StructureRepresentationProv
|
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|
92
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|
flatShaded: PD.BooleanParam;
|
|
93
95
|
ignoreLight: PD.BooleanParam;
|
|
94
96
|
xrayShaded: PD.BooleanParam;
|
|
97
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
95
98
|
bumpAmplitude: PD.Numeric;
|
|
96
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|
alpha: PD.Numeric;
|
|
97
100
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -20,7 +20,7 @@ var BackboneVisuals = {
|
|
|
20
20
|
'polymer-backbone-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer backbone sphere', ctx, getParams, polymer_backbone_sphere_1.PolymerBackboneSphereVisual); },
|
|
21
21
|
'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
|
|
22
22
|
};
|
|
23
|
-
exports.BackboneParams =
|
|
23
|
+
exports.BackboneParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, polymer_backbone_sphere_1.PolymerBackboneSphereParams), polymer_backbone_cylinder_1.PolymerBackboneCylinderParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 3, step: 0.1 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(BackboneVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
24
24
|
function getBackboneParams(ctx, structure) {
|
|
25
25
|
var params = param_definition_1.ParamDefinition.clone(exports.BackboneParams);
|
|
26
26
|
var hasGaps = false;
|
|
@@ -36,6 +36,7 @@ export declare const BallAndStickParams: {
|
|
|
36
36
|
doubleSided: PD.BooleanParam;
|
|
37
37
|
ignoreLight: PD.BooleanParam;
|
|
38
38
|
xrayShaded: PD.BooleanParam;
|
|
39
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
39
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|
bumpAmplitude: PD.Numeric;
|
|
40
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|
alpha: PD.Numeric;
|
|
41
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|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -88,6 +89,7 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
|
|
|
88
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|
doubleSided: PD.BooleanParam;
|
|
89
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|
ignoreLight: PD.BooleanParam;
|
|
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xrayShaded: PD.BooleanParam;
|
|
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|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
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|
bumpAmplitude: PD.Numeric;
|
|
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|
alpha: PD.Numeric;
|
|
93
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|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -141,6 +143,7 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
|
|
|
141
143
|
doubleSided: PD.BooleanParam;
|
|
142
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|
ignoreLight: PD.BooleanParam;
|
|
143
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|
xrayShaded: PD.BooleanParam;
|
|
146
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
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|
bumpAmplitude: PD.Numeric;
|
|
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|
alpha: PD.Numeric;
|
|
146
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|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -22,7 +22,7 @@ var BallAndStickVisuals = {
|
|
|
22
22
|
'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
|
|
23
23
|
'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
|
|
24
24
|
};
|
|
25
|
-
exports.BallAndStickParams =
|
|
25
|
+
exports.BallAndStickParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
26
26
|
function getBallAndStickParams(ctx, structure) {
|
|
27
27
|
return param_definition_1.ParamDefinition.clone(exports.BallAndStickParams);
|
|
28
28
|
}
|
|
@@ -30,6 +30,7 @@ export declare const CarbohydrateParams: {
|
|
|
30
30
|
flatShaded: PD.BooleanParam;
|
|
31
31
|
ignoreLight: PD.BooleanParam;
|
|
32
32
|
xrayShaded: PD.BooleanParam;
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'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
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exports.CartoonParams =
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exports.CartoonParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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attach: function (ctx, structure) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
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return
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case 0: return [4 /*yield*/, secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure, void 0, true)];
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case 1:
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@@ -36,6 +36,7 @@ export declare const EllipsoidParams: {
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doubleSided: PD.BooleanParam;
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alpha: PD.Numeric;
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@@ -87,6 +88,7 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
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@@ -139,6 +141,7 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
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doubleSided: PD.BooleanParam;
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@@ -21,7 +21,7 @@ var EllipsoidVisuals = {
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'intra-bond': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
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'inter-bond': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
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exports.EllipsoidParams =
|
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+
exports.EllipsoidParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, ellipsoid_mesh_1.EllipsoidMeshParams), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }), linkCap: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(EllipsoidVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
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function getEllipsoidParams(ctx, structure) {
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}
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@@ -47,6 +47,7 @@ export declare const GaussianSurfaceParams: {
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export declare type GaussianSurfaceParams = typeof GaussianSurfaceParams;
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@@ -89,6 +90,7 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
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};
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export declare type GaussianSurfaceRepresentation = StructureRepresentation<GaussianSurfaceParams>;
|
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@@ -132,5 +134,6 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
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}, "gaussian-surface">;
|
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@@ -19,7 +19,7 @@ var GaussianSurfaceVisuals = {
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|
'structure-gaussian-surface-mesh': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Structure-Gaussian surface mesh', ctx, getParams, gaussian_surface_mesh_1.StructureGaussianSurfaceVisual); },
|
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'gaussian-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Gaussian surface wireframe', ctx, getParams, gaussian_surface_wireframe_1.GaussianWireframeVisual); },
|
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};
|
|
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|
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exports.GaussianSurfaceParams =
|
|
22
|
+
exports.GaussianSurfaceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_surface_mesh_1.GaussianSurfaceMeshParams), gaussian_surface_wireframe_1.GaussianWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(GaussianSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
23
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|
function getGaussianSurfaceParams(ctx, structure) {
|
|
24
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|
return param_definition_1.ParamDefinition.clone(exports.GaussianSurfaceParams);
|
|
25
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|
}
|
|
@@ -15,7 +15,7 @@ var GaussianVolumeVisuals = {
|
|
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15
15
|
'gaussian-volume': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Gaussian volume', ctx, getParams, gaussian_density_volume_1.GaussianDensityVolumeVisual); },
|
|
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|
'units-gaussian-volume': function (ctx, getParams) { return (0, representation_1.UnitsRepresentation)('Units-Gaussian volume', ctx, getParams, gaussian_density_volume_1.UnitsGaussianDensityVolumeVisual); }
|
|
17
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|
};
|
|
18
|
-
exports.GaussianVolumeParams =
|
|
18
|
+
exports.GaussianVolumeParams = tslib_1.__assign(tslib_1.__assign({}, gaussian_density_volume_1.GaussianDensityVolumeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-volume'], param_definition_1.ParamDefinition.objectToOptions(GaussianVolumeVisuals)) });
|
|
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function getGaussianVolumeParams(ctx, structure) {
|
|
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|
var p = param_definition_1.ParamDefinition.clone(exports.GaussianVolumeParams);
|
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21
|
p.jumpLength = param_definition_1.ParamDefinition.Numeric(4, { min: 0, max: 20, step: 0.1 });
|
|
@@ -15,7 +15,7 @@ var marker_action_1 = require("../../../mol-util/marker-action");
|
|
|
15
15
|
var LabelVisuals = {
|
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16
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|
'label-text': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Label text', ctx, getParams, label_text_1.LabelTextVisual); },
|
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|
};
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|
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|
-
exports.LabelParams =
|
|
18
|
+
exports.LabelParams = tslib_1.__assign(tslib_1.__assign({}, label_text_1.LabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['label-text'], param_definition_1.ParamDefinition.objectToOptions(LabelVisuals)) });
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|
function getLabelParams(ctx, structure) {
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20
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|
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}
|
|
@@ -23,7 +23,7 @@ var LineVisuals = {
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|
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|
'element-point': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Points', ctx, getParams, element_point_1.ElementPointVisual); },
|
|
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|
'element-cross': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Crosses', ctx, getParams, element_cross_1.ElementCrossVisual); },
|
|
25
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|
};
|
|
26
|
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exports.LineParams =
|
|
26
|
+
exports.LineParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, bond_intra_unit_line_1.IntraUnitBondLineParams), bond_inter_unit_line_1.InterUnitBondLineParams), element_point_1.ElementPointParams), element_cross_1.ElementCrossParams), { multipleBonds: param_definition_1.ParamDefinition.Select('offset', param_definition_1.ParamDefinition.arrayToOptions(['off', 'symmetric', 'offset'])), includeParent: param_definition_1.ParamDefinition.Boolean(false), sizeFactor: param_definition_1.ParamDefinition.Numeric(2, { min: 0.01, max: 10, step: 0.01 }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], param_definition_1.ParamDefinition.objectToOptions(LineVisuals)) });
|
|
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|
function getLineParams(ctx, structure) {
|
|
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|
var params = param_definition_1.ParamDefinition.clone(exports.LineParams);
|
|
29
29
|
params.pointStyle.defaultValue = 'circle';
|
|
@@ -46,6 +46,7 @@ export declare const MolecularSurfaceParams: {
|
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46
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|
flatShaded: PD.BooleanParam;
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|
47
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|
ignoreLight: PD.BooleanParam;
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|
xrayShaded: PD.BooleanParam;
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|
+
allowTransparentBackfaces: PD.BooleanParam;
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|
49
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|
bumpAmplitude: PD.Numeric;
|
|
50
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|
};
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export declare type MolecularSurfaceParams = typeof MolecularSurfaceParams;
|
|
@@ -87,6 +88,7 @@ export declare function getMolecularSurfaceParams(ctx: ThemeRegistryContext, str
|
|
|
87
88
|
flatShaded: PD.BooleanParam;
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|
88
89
|
ignoreLight: PD.BooleanParam;
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89
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|
xrayShaded: PD.BooleanParam;
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91
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
90
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bumpAmplitude: PD.Numeric;
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|
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|
};
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|
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export declare type MolecularSurfaceRepresentation = StructureRepresentation<MolecularSurfaceParams>;
|
|
@@ -129,5 +131,6 @@ export declare const MolecularSurfaceRepresentationProvider: StructureRepresenta
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flatShaded: PD.BooleanParam;
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ignoreLight: PD.BooleanParam;
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+
allowTransparentBackfaces: PD.BooleanParam;
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133
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}, "molecular-surface">;
|
|
@@ -18,7 +18,7 @@ var MolecularSurfaceVisuals = {
|
|
|
18
18
|
'molecular-surface-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Molecular surface mesh', ctx, getParams, molecular_surface_mesh_1.MolecularSurfaceMeshVisual); },
|
|
19
19
|
'molecular-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Molecular surface wireframe', ctx, getParams, molecular_surface_wireframe_1.MolecularSurfaceWireframeVisual); },
|
|
20
20
|
};
|
|
21
|
-
exports.MolecularSurfaceParams =
|
|
21
|
+
exports.MolecularSurfaceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, molecular_surface_mesh_1.MolecularSurfaceMeshParams), molecular_surface_wireframe_1.MolecularSurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['molecular-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(MolecularSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
|
|
22
22
|
function getMolecularSurfaceParams(ctx, structure) {
|
|
23
23
|
return param_definition_1.ParamDefinition.clone(exports.MolecularSurfaceParams);
|
|
24
24
|
}
|
|
@@ -20,6 +20,7 @@ export declare const OrientationParams: {
|
|
|
20
20
|
flatShaded: PD.BooleanParam;
|
|
21
21
|
ignoreLight: PD.BooleanParam;
|
|
22
22
|
xrayShaded: PD.BooleanParam;
|
|
23
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
23
24
|
bumpAmplitude: PD.Numeric;
|
|
24
25
|
alpha: PD.Numeric;
|
|
25
26
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|
|
@@ -52,6 +53,7 @@ export declare function getOrientationParams(ctx: ThemeRegistryContext, structur
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|
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52
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|
flatShaded: PD.BooleanParam;
|
|
53
54
|
ignoreLight: PD.BooleanParam;
|
|
54
55
|
xrayShaded: PD.BooleanParam;
|
|
56
|
+
allowTransparentBackfaces: PD.BooleanParam;
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55
57
|
bumpAmplitude: PD.Numeric;
|
|
56
58
|
alpha: PD.Numeric;
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|
57
59
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
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@@ -85,6 +87,7 @@ export declare const OrientationRepresentationProvider: StructureRepresentationP
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|
|
85
87
|
flatShaded: PD.BooleanParam;
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|
86
88
|
ignoreLight: PD.BooleanParam;
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|
87
89
|
xrayShaded: PD.BooleanParam;
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|
90
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
88
91
|
bumpAmplitude: PD.Numeric;
|
|
89
92
|
alpha: PD.Numeric;
|
|
90
93
|
quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
|