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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case 0: return [4 /*yield*/, prop_1.ValidationReportProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, structure.models[0])];
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@@ -411,7 +411,7 @@ exports.ValidationReportRandomCoilIndexPreset = (0, representation_preset_1.Stru
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colorTheme = random_coil_index_1.RandomCoilIndexColorThemeProvider.name;
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return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__assign(tslib_1.__assign({}, params), { theme: { globalName: colorTheme, focus: { name: colorTheme } } }), plugin)];
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}
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return
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return tslib_1.__awaiter(this, void 0, void 0, function () {
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return
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return
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@@ -132,12 +132,12 @@ exports.ValidationReportProvider = custom_model_property_1.CustomModelProperty.c
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isApplicable: function (data) { return ValidationReport.isApplicable(data); },
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obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
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return
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p =
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p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValidationReportParams)), props);
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}
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@@ -241,9 +241,9 @@ exports.ClashesProvider = custom_structure_property_1.CustomStructureProperty.cr
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isApplicable: function (data) { return true; },
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obtain: function (ctx, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
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return
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+
return tslib_1.__generator(this, function (_a) {
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case 0: return [4 /*yield*/, exports.ValidationReportProvider.attach(ctx, data.models[0])];
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|
@@ -389,7 +389,7 @@ function parseValidationReportXml(xml, model) {
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var atomB = index.findAtomOnResidue(rI, getItem(bo, 'atom1'));
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addIndex(idx, atomA, bondOutliers.index);
|
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addIndex(idx, atomB, bondOutliers.index);
|
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|
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|
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|
+
bondOutliers.data.push(tslib_1.__assign({ tag: 'bond-outlier', atomA: atomA, atomB: atomB }, getMolInfo(bo)));
|
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}
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var molAngleOutliers = g.getElementsByTagName('angle-outlier');
|
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|
if (molAngleOutliers.length)
|
|
@@ -403,7 +403,7 @@ function parseValidationReportXml(xml, model) {
|
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|
addIndex(idx, atomA, angleOutliers.index);
|
|
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|
addIndex(idx, atomB, angleOutliers.index);
|
|
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|
addIndex(idx, atomC, angleOutliers.index);
|
|
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|
-
angleOutliers.data.push(
|
|
406
|
+
angleOutliers.data.push(tslib_1.__assign({ tag: 'angle-outlier', atomA: atomA, atomB: atomB, atomC: atomC }, getMolInfo(ao)));
|
|
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|
}
|
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|
var planeOutliers = g.getElementsByTagName('plane-outlier');
|
|
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|
if (planeOutliers.length)
|
|
@@ -427,7 +427,7 @@ function parseValidationReportXml(xml, model) {
|
|
|
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|
var atomB = index.findAtomOnResidue(rI, atoms[1]);
|
|
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|
addIndex(idx, atomA, bondOutliers.index);
|
|
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|
addIndex(idx, atomB, bondOutliers.index);
|
|
430
|
-
bondOutliers.data.push(
|
|
430
|
+
bondOutliers.data.push(tslib_1.__assign({ tag: 'mog-bond-outlier', atomA: atomA, atomB: atomB }, getMogInfo(mbo)));
|
|
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|
}
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|
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var mogAngleOutliers = g.getElementsByTagName('mog-angle-outlier');
|
|
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|
if (mogAngleOutliers.length)
|
|
@@ -442,7 +442,7 @@ function parseValidationReportXml(xml, model) {
|
|
|
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|
addIndex(idx, atomA, angleOutliers.index);
|
|
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|
addIndex(idx, atomB, angleOutliers.index);
|
|
444
444
|
addIndex(idx, atomC, angleOutliers.index);
|
|
445
|
-
angleOutliers.data.push(
|
|
445
|
+
angleOutliers.data.push(tslib_1.__assign({ tag: 'mog-angle-outlier', atomA: atomA, atomB: atomB, atomC: atomC }, getMogInfo(mao)));
|
|
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446
|
}
|
|
447
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|
}
|
|
448
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|
var clashes_1 = g.getElementsByTagName('clash');
|
|
@@ -31,6 +31,7 @@ export declare const IntraUnitClashParams: {
|
|
|
31
31
|
flatShaded: PD.BooleanParam;
|
|
32
32
|
ignoreLight: PD.BooleanParam;
|
|
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33
|
xrayShaded: PD.BooleanParam;
|
|
34
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
34
35
|
bumpFrequency: PD.Numeric;
|
|
35
36
|
bumpAmplitude: PD.Numeric;
|
|
36
37
|
alpha: PD.Numeric;
|
|
@@ -73,6 +74,7 @@ export declare const InterUnitClashParams: {
|
|
|
73
74
|
flatShaded: PD.BooleanParam;
|
|
74
75
|
ignoreLight: PD.BooleanParam;
|
|
75
76
|
xrayShaded: PD.BooleanParam;
|
|
77
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
76
78
|
bumpFrequency: PD.Numeric;
|
|
77
79
|
bumpAmplitude: PD.Numeric;
|
|
78
80
|
alpha: PD.Numeric;
|
|
@@ -116,6 +118,7 @@ export declare const ClashesParams: {
|
|
|
116
118
|
flatShaded: PD.BooleanParam;
|
|
117
119
|
ignoreLight: PD.BooleanParam;
|
|
118
120
|
xrayShaded: PD.BooleanParam;
|
|
121
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
119
122
|
bumpFrequency: PD.Numeric;
|
|
120
123
|
bumpAmplitude: PD.Numeric;
|
|
121
124
|
alpha: PD.Numeric;
|
|
@@ -158,6 +161,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
|
|
|
158
161
|
flatShaded: PD.BooleanParam;
|
|
159
162
|
ignoreLight: PD.BooleanParam;
|
|
160
163
|
xrayShaded: PD.BooleanParam;
|
|
164
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
161
165
|
bumpFrequency: PD.Numeric;
|
|
162
166
|
bumpAmplitude: PD.Numeric;
|
|
163
167
|
alpha: PD.Numeric;
|
|
@@ -201,6 +205,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
|
|
|
201
205
|
flatShaded: PD.BooleanParam;
|
|
202
206
|
ignoreLight: PD.BooleanParam;
|
|
203
207
|
xrayShaded: PD.BooleanParam;
|
|
208
|
+
allowTransparentBackfaces: PD.BooleanParam;
|
|
204
209
|
bumpFrequency: PD.Numeric;
|
|
205
210
|
bumpAmplitude: PD.Numeric;
|
|
206
211
|
alpha: PD.Numeric;
|
|
@@ -55,7 +55,7 @@ function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, me
|
|
|
55
55
|
}
|
|
56
56
|
return m;
|
|
57
57
|
}
|
|
58
|
-
exports.IntraUnitClashParams =
|
|
58
|
+
exports.IntraUnitClashParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
|
|
59
59
|
function IntraUnitClashVisual(materialId) {
|
|
60
60
|
return (0, units_visual_1.UnitsMeshVisual)({
|
|
61
61
|
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitClashParams),
|
|
@@ -156,7 +156,7 @@ function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
|
|
|
156
156
|
}
|
|
157
157
|
return m;
|
|
158
158
|
}
|
|
159
|
-
exports.InterUnitClashParams =
|
|
159
|
+
exports.InterUnitClashParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { linkCap: param_definition_1.ParamDefinition.Boolean(true), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.01 }) });
|
|
160
160
|
function InterUnitClashVisual(materialId) {
|
|
161
161
|
return (0, complex_visual_1.ComplexMeshVisual)({
|
|
162
162
|
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitClashParams),
|
|
@@ -231,7 +231,7 @@ var ClashesVisuals = {
|
|
|
231
231
|
'intra-clash': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit clash cylinder', ctx, getParams, IntraUnitClashVisual); },
|
|
232
232
|
'inter-clash': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit clash cylinder', ctx, getParams, InterUnitClashVisual); },
|
|
233
233
|
};
|
|
234
|
-
exports.ClashesParams =
|
|
234
|
+
exports.ClashesParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, exports.IntraUnitClashParams), exports.InterUnitClashParams), { unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-clash', 'inter-clash'], param_definition_1.ParamDefinition.objectToOptions(ClashesVisuals)) });
|
|
235
235
|
function getClashesParams(ctx, structure) {
|
|
236
236
|
return param_definition_1.ParamDefinition.clone(exports.ClashesParams);
|
|
237
237
|
}
|
|
@@ -0,0 +1,7 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
3
|
+
*
|
|
4
|
+
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
5
|
+
*/
|
|
6
|
+
import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
|
|
7
|
+
export declare const ZenodoImport: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
|
|
@@ -0,0 +1,35 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
/**
|
|
3
|
+
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
4
|
+
*
|
|
5
|
+
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
6
|
+
*/
|
|
7
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
8
|
+
exports.ZenodoImport = void 0;
|
|
9
|
+
var tslib_1 = require("tslib");
|
|
10
|
+
var behavior_1 = require("../../mol-plugin/behavior/behavior");
|
|
11
|
+
var ui_1 = require("./ui");
|
|
12
|
+
exports.ZenodoImport = behavior_1.PluginBehavior.create({
|
|
13
|
+
name: 'extension-zenodo-import',
|
|
14
|
+
category: 'misc',
|
|
15
|
+
display: {
|
|
16
|
+
name: 'Zenodo Export'
|
|
17
|
+
},
|
|
18
|
+
ctor: /** @class */ (function (_super) {
|
|
19
|
+
tslib_1.__extends(class_1, _super);
|
|
20
|
+
function class_1() {
|
|
21
|
+
return _super !== null && _super.apply(this, arguments) || this;
|
|
22
|
+
}
|
|
23
|
+
class_1.prototype.register = function () {
|
|
24
|
+
this.ctx.customImportControls.set('zenodo-import', ui_1.ZenodoImportUI);
|
|
25
|
+
};
|
|
26
|
+
class_1.prototype.update = function () {
|
|
27
|
+
return false;
|
|
28
|
+
};
|
|
29
|
+
class_1.prototype.unregister = function () {
|
|
30
|
+
this.ctx.customImportControls.delete('zenodo-import');
|
|
31
|
+
};
|
|
32
|
+
return class_1;
|
|
33
|
+
}(behavior_1.PluginBehavior.Handler)),
|
|
34
|
+
params: function () { return ({}); }
|
|
35
|
+
});
|
|
@@ -0,0 +1,61 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
3
|
+
*
|
|
4
|
+
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
|
5
|
+
*/
|
|
6
|
+
/// <reference types="react" />
|
|
7
|
+
import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
|
|
8
|
+
import { PluginContext } from '../../mol-plugin/context';
|
|
9
|
+
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
|
10
|
+
declare type ZenodoFile = {
|
|
11
|
+
bucket: string;
|
|
12
|
+
checksum: string;
|
|
13
|
+
key: string;
|
|
14
|
+
links: {
|
|
15
|
+
[key: string]: string;
|
|
16
|
+
self: string;
|
|
17
|
+
};
|
|
18
|
+
size: number;
|
|
19
|
+
type: string;
|
|
20
|
+
};
|
|
21
|
+
declare type ZenodoRecord = {
|
|
22
|
+
id: number;
|
|
23
|
+
conceptdoi: string;
|
|
24
|
+
conceptrecid: string;
|
|
25
|
+
created: string;
|
|
26
|
+
doi: string;
|
|
27
|
+
files: ZenodoFile[];
|
|
28
|
+
revision: number;
|
|
29
|
+
updated: string;
|
|
30
|
+
metadata: {
|
|
31
|
+
title: string;
|
|
32
|
+
};
|
|
33
|
+
};
|
|
34
|
+
interface State {
|
|
35
|
+
busy?: boolean;
|
|
36
|
+
recordValues: PD.Values<typeof ZenodoImportParams>;
|
|
37
|
+
importValues?: PD.Values<ImportParams>;
|
|
38
|
+
importParams?: ImportParams;
|
|
39
|
+
record?: ZenodoRecord;
|
|
40
|
+
files?: ZenodoFile[];
|
|
41
|
+
}
|
|
42
|
+
declare const ZenodoImportParams: {
|
|
43
|
+
record: PD.Text<string>;
|
|
44
|
+
};
|
|
45
|
+
declare function createImportParams(files: ZenodoFile[], plugin: PluginContext): {
|
|
46
|
+
type: PD.Mapped<PD.NamedParams<any, string> | PD.NamedParams<any, number>>;
|
|
47
|
+
};
|
|
48
|
+
declare type ImportParams = ReturnType<typeof createImportParams>;
|
|
49
|
+
export declare class ZenodoImportUI extends CollapsableControls<{}, State> {
|
|
50
|
+
protected defaultState(): State & CollapsableState;
|
|
51
|
+
private recordParamsOnChange;
|
|
52
|
+
private importParamsOnChange;
|
|
53
|
+
private loadRecord;
|
|
54
|
+
private loadFile;
|
|
55
|
+
private clearRecord;
|
|
56
|
+
private renderLoadRecord;
|
|
57
|
+
private renderRecordInfo;
|
|
58
|
+
private renderImportFile;
|
|
59
|
+
protected renderControls(): JSX.Element | null;
|
|
60
|
+
}
|
|
61
|
+
export {};
|