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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exports.image_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_frag_params\n#include common_clip\n\nuniform vec2 uImageTexDim;\nuniform sampler2D tImageTex;\nuniform sampler2D tGroupTex;\n\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nvarying vec2 vUv;\nvarying float vInstance;\n\n#if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell) || defined(dInterpolation_bspline)\n #define dInterpolation_cubic\n#endif\n\n#if defined(dInterpolation_cubic)\n #if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell)\n #if defined(dInterpolation_catmulrom)\n const float B = 0.0;\n const float C = 0.5;\n #elif defined(dInterpolation_mitchell)\n const float B = 0.333;\n const float C = 0.333;\n #endif\n\n float cubicFilter(float x){\n float f = x;\n if (f < 0.0) {\n f = -f;\n }\n if (f < 1.0) {\n return ((12.0 - 9.0 * B - 6.0 * C) * (f * f * f) +\n (-18.0 + 12.0 * B + 6.0 * C) * (f * f) +\n (6.0 - 2.0 * B)) / 6.0;\n }else if (f >= 1.0 && f < 2.0){\n return ((-B - 6.0 * C) * ( f * f * f)\n + (6.0 * B + 30.0 * C) * (f * f) +\n (-(12.0 * B) - 48.0 * C) * f +\n 8.0 * B + 24.0 * C) / 6.0;\n }else{\n return 0.0;\n }\n }\n #elif defined(dInterpolation_bspline)\n float cubicFilter(float x) {\n float f = x;\n if (f < 0.0) {\n f = -f;\n }\n if (f >= 0.0 && f <= 1.0){\n return (2.0 / 3.0) + (0.5) * (f * f * f) - (f * f);\n } else if (f > 1.0 && f <= 2.0) {\n return 1.0 / 6.0 * pow((2.0 - f), 3.0);\n }\n return 1.0;\n }\n #endif\n\n vec4 biCubic(sampler2D tex, vec2 texCoord) {\n vec2 texelSize = 1.0 / uImageTexDim;\n texCoord -= texelSize / 2.0;\n vec4 nSum = vec4(0.0);\n float nDenom = 0.0;\n vec2 cell = fract(texCoord * uImageTexDim);\n for (float m = -1.0; m <= 2.0; ++m) {\n for (float n = -1.0; n <= 2.0; ++n) {\n vec4 vecData = texture2D(tex, texCoord + texelSize * vec2(m, n));\n float c = cubicFilter(m - cell.x) * cubicFilter(-n + cell.y);\n nSum += vecData * c;\n nDenom += c;\n }\n }\n return nSum / nDenom;\n }\n#endif\n\nvoid main() {\n #include clip_pixel\n\n #if defined(dInterpolation_cubic)\n vec4 imageData = biCubic(tImageTex, vUv);\n #else\n vec4 imageData = texture2D(tImageTex, vUv);\n #endif\n imageData.a = clamp(imageData.a, 0.0, 1.0);\n if (imageData.a > 0.9) imageData.a = 1.0;\n\n float fragmentDepth = gl_FragCoord.z;\n
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exports.image_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_frag_params\n#include common_clip\n\nuniform vec2 uImageTexDim;\nuniform sampler2D tImageTex;\nuniform sampler2D tGroupTex;\n\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nvarying vec2 vUv;\nvarying float vInstance;\n\n#if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell) || defined(dInterpolation_bspline)\n #define dInterpolation_cubic\n#endif\n\n#if defined(dInterpolation_cubic)\n #if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell)\n #if defined(dInterpolation_catmulrom)\n const float B = 0.0;\n const float C = 0.5;\n #elif defined(dInterpolation_mitchell)\n const float B = 0.333;\n const float C = 0.333;\n #endif\n\n float cubicFilter(float x){\n float f = x;\n if (f < 0.0) {\n f = -f;\n }\n if (f < 1.0) {\n return ((12.0 - 9.0 * B - 6.0 * C) * (f * f * f) +\n (-18.0 + 12.0 * B + 6.0 * C) * (f * f) +\n (6.0 - 2.0 * B)) / 6.0;\n }else if (f >= 1.0 && f < 2.0){\n return ((-B - 6.0 * C) * ( f * f * f)\n + (6.0 * B + 30.0 * C) * (f * f) +\n (-(12.0 * B) - 48.0 * C) * f +\n 8.0 * B + 24.0 * C) / 6.0;\n }else{\n return 0.0;\n }\n }\n #elif defined(dInterpolation_bspline)\n float cubicFilter(float x) {\n float f = x;\n if (f < 0.0) {\n f = -f;\n }\n if (f >= 0.0 && f <= 1.0){\n return (2.0 / 3.0) + (0.5) * (f * f * f) - (f * f);\n } else if (f > 1.0 && f <= 2.0) {\n return 1.0 / 6.0 * pow((2.0 - f), 3.0);\n }\n return 1.0;\n }\n #endif\n\n vec4 biCubic(sampler2D tex, vec2 texCoord) {\n vec2 texelSize = 1.0 / uImageTexDim;\n texCoord -= texelSize / 2.0;\n vec4 nSum = vec4(0.0);\n float nDenom = 0.0;\n vec2 cell = fract(texCoord * uImageTexDim);\n for (float m = -1.0; m <= 2.0; ++m) {\n for (float n = -1.0; n <= 2.0; ++n) {\n vec4 vecData = texture2D(tex, texCoord + texelSize * vec2(m, n));\n float c = cubicFilter(m - cell.x) * cubicFilter(-n + cell.y);\n nSum += vecData * c;\n nDenom += c;\n }\n }\n return nSum / nDenom;\n }\n#endif\n\nvoid main() {\n #include clip_pixel\n\n #if defined(dInterpolation_cubic)\n vec4 imageData = biCubic(tImageTex, vUv);\n #else\n vec4 imageData = texture2D(tImageTex, vUv);\n #endif\n imageData.a = clamp(imageData.a, 0.0, 1.0);\n if (imageData.a > 0.9) imageData.a = 1.0;\n\n float fragmentDepth = gl_FragCoord.z;\n\n #if defined(dRenderVariant_pick)\n if (imageData.a < 0.3)\n discard;\n if (uPickType == 1) {\n gl_FragColor = vec4(packIntToRGB(float(uObjectId)), 1.0);\n } else if (uPickType == 2) {\n gl_FragColor = vec4(packIntToRGB(vInstance), 1.0);\n } else {\n gl_FragColor = vec4(texture2D(tGroupTex, vUv).rgb, 1.0);\n }\n #elif defined(dRenderVariant_depth)\n if (imageData.a < 0.05)\n discard;\n gl_FragColor = packDepthToRGBA(gl_FragCoord.z);\n #elif defined(dRenderVariant_marking)\n float marker = uMarker;\n if (uMarker == -1.0) {\n float group = unpackRGBToInt(texture2D(tGroupTex, vUv).rgb);\n marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n }\n if (uMarkingType == 1) {\n if (marker > 0.0 || imageData.a < 0.05)\n discard;\n gl_FragColor = packDepthToRGBA(gl_FragCoord.z);\n } else {\n if (marker == 0.0 || imageData.a < 0.05)\n discard;\n float depthTest = 1.0;\n if (uMarkingDepthTest) {\n depthTest = (fragmentDepth >= getDepth(gl_FragCoord.xy / uDrawingBufferSize)) ? 1.0 : 0.0;\n }\n bool isHighlight = intMod(marker, 2.0) > 0.1;\n gl_FragColor = vec4(0.0, depthTest, isHighlight ? 1.0 : 0.0, 1.0);\n }\n #elif defined(dRenderVariant_color)\n if (imageData.a < 0.05)\n discard;\n gl_FragColor = imageData;\n gl_FragColor.a *= uAlpha;\n\n float marker = uMarker;\n if (uMarker == -1.0) {\n float group = unpackRGBToInt(texture2D(tGroupTex, vUv).rgb);\n marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n }\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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export declare const lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n
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export declare const lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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exports.lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n
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exports.lines_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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export declare const points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n
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export declare const points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dPointStyle_circle)\n float dist = distance(gl_PointCoord, center);\n if (dist > radius) discard;\n #elif defined(dPointStyle_fuzzy)\n float dist = distance(gl_PointCoord, center);\n float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);\n if (fuzzyAlpha < 0.0001) discard;\n #endif\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #if defined(dPointStyle_fuzzy)\n gl_FragColor.a *= fuzzyAlpha;\n #endif\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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/**
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* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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exports.points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n
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exports.points_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nconst vec2 center = vec2(0.5);\nconst float radius = 0.5;\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n #if defined(dPointStyle_circle)\n float dist = distance(gl_PointCoord, center);\n if (dist > radius) discard;\n #elif defined(dPointStyle_fuzzy)\n float dist = distance(gl_PointCoord, center);\n float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);\n if (fuzzyAlpha < 0.0001) discard;\n #endif\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n gl_FragColor = material;\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n gl_FragColor = material;\n\n #if defined(dPointStyle_fuzzy)\n gl_FragColor.a *= fuzzyAlpha;\n #endif\n\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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export declare const text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n
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export declare const text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n if (vTexCoord.x > 1.0) {\n gl_FragColor = vec4(uBackgroundColor, uBackgroundOpacity * material.a);\n } else {\n // retrieve signed distance\n float sdf = texture2D(tFont, vTexCoord).a + uBorderWidth;\n\n // perform adaptive anti-aliasing of the edges\n float w = clamp(smoothness * (abs(dFdx(vTexCoord.x)) + abs(dFdy(vTexCoord.y))), 0.0, 0.5);\n float a = smoothstep(0.5 - w, 0.5 + w, sdf);\n\n // gamma correction for linear attenuation\n a = pow(a, 1.0 / gamma);\n\n if (a < 0.5) discard;\n material.a *= a;\n\n // add border\n float t = 0.5 + uBorderWidth;\n if (uBorderWidth > 0.0 && sdf < t) {\n material.xyz = mix(uBorderColor, material.xyz, smoothstep(t - w, t, sdf));\n }\n\n gl_FragColor = material;\n }\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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exports.text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n
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exports.text_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include common_clip\n\nuniform sampler2D tFont;\n\nuniform vec3 uBorderColor;\nuniform float uBorderWidth;\nuniform vec3 uBackgroundColor;\nuniform float uBackgroundOpacity;\n\nvarying vec2 vTexCoord;\n\nconst float smoothness = 32.0;\nconst float gamma = 2.2;\n\nvoid main2(){\n gl_FragColor = vec4(1.0, 0.0, 0.0, 1.0);\n}\n\nvoid main(){\n #include clip_pixel\n\n float fragmentDepth = gl_FragCoord.z;\n #include assign_material_color\n\n if (vTexCoord.x > 1.0) {\n gl_FragColor = vec4(uBackgroundColor, uBackgroundOpacity * material.a);\n } else {\n // retrieve signed distance\n float sdf = texture2D(tFont, vTexCoord).a + uBorderWidth;\n\n // perform adaptive anti-aliasing of the edges\n float w = clamp(smoothness * (abs(dFdx(vTexCoord.x)) + abs(dFdy(vTexCoord.y))), 0.0, 0.5);\n float a = smoothstep(0.5 - w, 0.5 + w, sdf);\n\n // gamma correction for linear attenuation\n a = pow(a, 1.0 / gamma);\n\n if (a < 0.5) discard;\n material.a *= a;\n\n // add border\n float t = 0.5 + uBorderWidth;\n if (uBorderWidth > 0.0 && sdf < t) {\n material.xyz = mix(uBorderColor, material.xyz, smoothstep(t - w, t, sdf));\n }\n\n gl_FragColor = material;\n }\n\n #if defined(dRenderVariant_pick)\n #include check_picking_alpha\n #elif defined(dRenderVariant_depth)\n gl_FragColor = material;\n #elif defined(dRenderVariant_marking)\n gl_FragColor = material;\n #elif defined(dRenderVariant_color)\n #include apply_marker_color\n #include apply_fog\n #include wboit_write\n #endif\n}\n";
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@@ -167,6 +167,7 @@ var direct_volume_frag_1 = require("./shader/direct-volume.frag");
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exports.DirectVolumeShaderCode = ShaderCode('direct-volume', direct_volume_vert_1.directVolume_vert, direct_volume_frag_1.directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' }, {}, ignoreDefine);
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var image_vert_1 = require("./shader/image.vert");
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var type_helpers_1 = require("../mol-util/type-helpers");
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exports.ImageShaderCode = ShaderCode('image', image_vert_1.image_vert, image_frag_1.image_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
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/**
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exports.createElementsBuffer = exports.createAttributeBuffers = exports.createAttributeBuffer = exports.getAttribType = exports.getBufferType = exports.getDataType = exports.getUsageHint = void 0;
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var tslib_1 = require("tslib");
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var id_factory_1 = require("../../mol-util/id-factory");
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}
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@@ -131,9 +130,9 @@ function getAttribType(gl, kind, itemSize) {
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throw new Error("unknown attribute type for kind '".concat(kind, "' and itemSize '").concat(itemSize, "'"));
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}
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function createAttributeBuffer(gl, state, extensions, array, itemSize, divisor, usageHint) {
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@@ -141,7 +140,7 @@ function createAttributeBuffer(gl, state, extensions, array, itemSize, divisor,
|
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var buffer = createBuffer(gl, array, usageHint, 'attribute');
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|
var _bufferType = buffer._bufferType, _dataType = buffer._dataType, _bpe = buffer._bpe;
|
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return
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return tslib_1.__assign(tslib_1.__assign({}, buffer), { bind: function (location) {
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|
gl.bindBuffer(_bufferType, buffer.getBuffer());
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if (itemSize === 16) {
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for (var i = 0; i < 4; ++i) {
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@@ -172,7 +171,7 @@ exports.createAttributeBuffers = createAttributeBuffers;
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function createElementsBuffer(gl, array, usageHint) {
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172
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173
|
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|
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|
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return
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|
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return tslib_1.__assign(tslib_1.__assign({}, buffer), { bind: function () {
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175
|
gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, buffer.getBuffer());
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} });
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@@ -1,6 +1,6 @@
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/**
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|
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* Copyright (c) 2018-
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|
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* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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4
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*
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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@@ -221,8 +221,8 @@ function createContext(gl, props) {
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221
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}); };
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|
}
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223
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else {
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readPixelsAsync = function (x, y, width, height, buffer) { return
|
|
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|
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return
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|
+
readPixelsAsync = function (x, y, width, height, buffer) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
|
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|
+
return tslib_1.__generator(this, function (_a) {
|
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226
|
readPixels(gl, x, y, width, height, buffer);
|
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227
|
return [2 /*return*/];
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228
|
});
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@@ -233,7 +233,7 @@ function createContext(gl, props) {
|
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gl: gl,
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234
|
isWebGL2: (0, compat_1.isWebGL2)(gl),
|
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235
235
|
get pixelRatio() {
|
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@@ -1,6 +1,6 @@
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"use strict";
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/**
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* Copyright (c) 2018-
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* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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*/
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@@ -11,6 +11,7 @@ var uniform_1 = require("./uniform");
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var buffer_1 = require("./buffer");
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var id_factory_1 = require("../../mol-util/id-factory");
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var debug_1 = require("../../mol-util/debug");
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var compat_1 = require("./compat");
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var getNextProgramId = (0, id_factory_1.idFactory)();
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function getLocations(gl, program, schema) {
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@@ -54,7 +55,7 @@ function checkActiveAttributes(gl, program, schema) {
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}
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var attribType = (0, buffer_1.getAttribType)(gl, spec.kind, spec.itemSize);
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throw new Error("unexpected attribute type for ".concat(name_1));
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var ComputeRenderVariant = { compute: '' };
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exports.ComputeRenderVariants = Object.keys(ComputeRenderVariant);
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function createProgramVariant(ctx, variant, defineValues, shaderCode, schema) {
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defineValues =
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defineValues = tslib_1.__assign(tslib_1.__assign({}, defineValues), { dRenderVariant: mol_util_1.ValueCell.create(variant) });
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Object.defineProperty(schema, 'dRenderVariant', { value: (0, schema_1.DefineSpec)('string') });
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@@ -21,7 +21,7 @@ function defineValueHash(v) {
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typeof v === 'number' ? (v * 10000) : (0, util_1.hashString)(v);
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|
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|
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|
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var wrapped =
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|
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|
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|
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|
} });
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|
return wrapped;
|
|
@@ -40,7 +40,7 @@ function createResources(gl, state, stats, extensions) {
|
|
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|
function wrap(name, resource) {
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|
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|
sets[name].add(resource);
|
|
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|
stats.resourceCounts[name] += 1;
|
|
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|
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return
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|
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|
+
return tslib_1.__assign(tslib_1.__assign({}, resource), { destroy: function () {
|
|
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|
resource.destroy();
|
|
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|
sets[name].delete(resource);
|
|
46
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|
stats.resourceCounts[name] -= 1;
|
|
@@ -9,6 +9,7 @@ exports.classifyFloatArray = exports.classifyIntArray = void 0;
|
|
|
9
9
|
var tslib_1 = require("tslib");
|
|
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10
|
var array_encoder_1 = require("./array-encoder");
|
|
11
11
|
var number_1 = require("../../../mol-util/number");
|
|
12
|
+
var type_helpers_1 = require("../../../mol-util/type-helpers");
|
|
12
13
|
function classifyIntArray(xs) {
|
|
13
14
|
return IntClassifier.classify(xs);
|
|
14
15
|
}
|
|
@@ -59,7 +60,7 @@ var IntClassifier;
|
|
|
59
60
|
for (var i = 0, n = data.length; i < n; i++) {
|
|
60
61
|
incSize(info, size, data[i]);
|
|
61
62
|
}
|
|
62
|
-
return
|
|
63
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'pack' });
|
|
63
64
|
}
|
|
64
65
|
function deltaSize(data, info) {
|
|
65
66
|
var size = SizeInfo();
|
|
@@ -68,7 +69,7 @@ var IntClassifier;
|
|
|
68
69
|
incSizeSigned(size, data[i] - prev);
|
|
69
70
|
prev = data[i];
|
|
70
71
|
}
|
|
71
|
-
return
|
|
72
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'delta' });
|
|
72
73
|
}
|
|
73
74
|
function rleSize(data, info) {
|
|
74
75
|
var size = SizeInfo();
|
|
@@ -85,7 +86,7 @@ var IntClassifier;
|
|
|
85
86
|
}
|
|
86
87
|
incSize(info, size, data[data.length - 1]);
|
|
87
88
|
incSize(info, size, run);
|
|
88
|
-
return
|
|
89
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'rle' });
|
|
89
90
|
}
|
|
90
91
|
function deltaRleSize(data, info) {
|
|
91
92
|
var size = SizeInfo();
|
|
@@ -105,7 +106,7 @@ var IntClassifier;
|
|
|
105
106
|
}
|
|
106
107
|
incSizeSigned(size, prevValue);
|
|
107
108
|
incSizeSigned(size, run);
|
|
108
|
-
return
|
|
109
|
+
return tslib_1.__assign(tslib_1.__assign({}, byteSize(size)), { kind: 'delta-rle' });
|
|
109
110
|
}
|
|
110
111
|
function getSize(data) {
|
|
111
112
|
var info = getInfo(data);
|
|
@@ -124,8 +125,8 @@ var IntClassifier;
|
|
|
124
125
|
case 'rle': return array_encoder_1.ArrayEncoding.by(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
125
126
|
case 'delta': return array_encoder_1.ArrayEncoding.by(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
126
127
|
case 'delta-rle': return array_encoder_1.ArrayEncoding.by(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
128
|
+
default: (0, type_helpers_1.assertUnreachable)(size);
|
|
127
129
|
}
|
|
128
|
-
throw new Error('should not happen :)');
|
|
129
130
|
}
|
|
130
131
|
IntClassifier.classify = classify;
|
|
131
132
|
})(IntClassifier || (IntClassifier = {}));
|
|
@@ -159,8 +160,8 @@ var FloatClassifier;
|
|
|
159
160
|
case 'rle': return fp.and(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
160
161
|
case 'delta': return fp.and(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
161
162
|
case 'delta-rle': return fp.and(array_encoder_1.ArrayEncoding.delta).and(array_encoder_1.ArrayEncoding.runLength).and(array_encoder_1.ArrayEncoding.integerPacking);
|
|
163
|
+
default: (0, type_helpers_1.assertUnreachable)(size);
|
|
162
164
|
}
|
|
163
|
-
throw new Error('should not happen :)');
|
|
164
165
|
}
|
|
165
166
|
FloatClassifier.classify = classify;
|
|
166
167
|
function getMultiplier(mantissaDigits) {
|
|
@@ -8,6 +8,7 @@
|
|
|
8
8
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
9
9
|
exports.decode = void 0;
|
|
10
10
|
var binary_1 = require("../binary");
|
|
11
|
+
var type_helpers_1 = require("../../../mol-util/type-helpers");
|
|
11
12
|
/**
|
|
12
13
|
* Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/
|
|
13
14
|
* by Alexander Rose <alexander.rose@weirdbyte.de>, MIT License, Copyright (c) 2016
|
|
@@ -32,7 +33,7 @@ function decodeStep(data, encoding) {
|
|
|
32
33
|
case 6 /* Uint32 */: return uint32(data);
|
|
33
34
|
case 32 /* Float32 */: return float32(data);
|
|
34
35
|
case 33 /* Float64 */: return float64(data);
|
|
35
|
-
default:
|
|
36
|
+
default: (0, type_helpers_1.assertUnreachable)(encoding.type);
|
|
36
37
|
}
|
|
37
38
|
}
|
|
38
39
|
case 'FixedPoint': return fixedPoint(data, encoding);
|
|
@@ -51,14 +52,14 @@ function getIntArray(type, size) {
|
|
|
51
52
|
case 4 /* Uint8 */: return new Uint8Array(size);
|
|
52
53
|
case 5 /* Uint16 */: return new Uint16Array(size);
|
|
53
54
|
case 6 /* Uint32 */: return new Uint32Array(size);
|
|
54
|
-
default:
|
|
55
|
+
default: (0, type_helpers_1.assertUnreachable)(type);
|
|
55
56
|
}
|
|
56
57
|
}
|
|
57
58
|
function getFloatArray(type, size) {
|
|
58
59
|
switch (type) {
|
|
59
60
|
case 32 /* Float32 */: return new Float32Array(size);
|
|
60
61
|
case 33 /* Float64 */: return new Float64Array(size);
|
|
61
|
-
default:
|
|
62
|
+
default: (0, type_helpers_1.assertUnreachable)(type);
|
|
62
63
|
}
|
|
63
64
|
}
|
|
64
65
|
function int8(data) { return new Int8Array(data.buffer, data.byteOffset); }
|
|
@@ -9,6 +9,6 @@ exports.decode = void 0;
|
|
|
9
9
|
var tslib_1 = require("tslib");
|
|
10
10
|
var decoder_1 = require("./binary-cif/decoder");
|
|
11
11
|
Object.defineProperty(exports, "decode", { enumerable: true, get: function () { return decoder_1.decode; } });
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
12
|
+
tslib_1.__exportStar(require("./binary-cif/encoding"), exports);
|
|
13
|
+
tslib_1.__exportStar(require("./binary-cif/array-encoder"), exports);
|
|
14
|
+
tslib_1.__exportStar(require("./binary-cif/classifier"), exports);
|