molstar 2.3.5 → 2.3.9
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 +176 -176
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +94 -94
- package/build/viewer/molstar.css +1 -2
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +1 -1
- package/lib/apps/docking-viewer/index.js.map +1 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.d.ts +290 -1
- package/lib/apps/viewer/index.html +94 -94
- package/lib/apps/viewer/index.js +91 -5
- package/lib/apps/viewer/index.js.map +1 -1
- package/lib/cli/chem-comp-dict/create-ions.js +1 -1
- package/lib/cli/chem-comp-dict/create-ions.js.map +1 -1
- package/lib/cli/chem-comp-dict/create-table.js +3 -3
- package/lib/cli/chem-comp-dict/create-table.js.map +1 -1
- package/lib/cli/chem-comp-dict/util.js +2 -2
- package/lib/cli/chem-comp-dict/util.js.map +1 -1
- package/lib/cli/cif2bcif/converter.js +2 -2
- package/lib/cli/cif2bcif/converter.js.map +1 -1
- package/lib/cli/cifschema/index.js +12 -12
- package/lib/cli/cifschema/index.js.map +1 -1
- package/lib/cli/cifschema/util/cif-dic.js +19 -19
- package/lib/cli/cifschema/util/cif-dic.js.map +1 -1
- package/lib/cli/cifschema/util/generate.js +21 -21
- package/lib/cli/cifschema/util/generate.js.map +1 -1
- package/lib/cli/cifschema/util/schema.js +1 -1
- package/lib/cli/cifschema/util/schema.js.map +1 -1
- package/lib/cli/lipid-params/index.js +3 -3
- package/lib/cli/lipid-params/index.js.map +1 -1
- package/lib/cli/state-docs/index.js +4 -4
- package/lib/cli/state-docs/index.js.map +1 -1
- package/lib/cli/state-docs/pd-to-md.js +10 -10
- package/lib/cli/state-docs/pd-to-md.js.map +1 -1
- package/lib/cli/structure-info/model.js +18 -18
- package/lib/cli/structure-info/model.js.map +1 -1
- package/lib/cli/structure-info/volume.js +1 -1
- package/lib/cli/structure-info/volume.js.map +1 -1
- package/lib/commonjs/apps/docking-viewer/index.js +1 -1
- package/lib/commonjs/apps/docking-viewer/index.js.map +1 -1
- package/lib/commonjs/apps/viewer/index.d.ts +289 -0
- package/lib/commonjs/apps/viewer/index.js +91 -5
- package/lib/commonjs/apps/viewer/index.js.map +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js.map +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +3 -3
- package/lib/commonjs/cli/chem-comp-dict/create-table.js.map +1 -1
- package/lib/commonjs/cli/chem-comp-dict/util.js +2 -2
- package/lib/commonjs/cli/chem-comp-dict/util.js.map +1 -1
- package/lib/commonjs/cli/cif2bcif/converter.js +2 -2
- package/lib/commonjs/cli/cif2bcif/converter.js.map +1 -1
- package/lib/commonjs/cli/cif2bcif/index.js +0 -0
- package/lib/commonjs/cli/cifschema/index.js +12 -12
- package/lib/commonjs/cli/cifschema/index.js.map +1 -1
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +19 -19
- package/lib/commonjs/cli/cifschema/util/cif-dic.js.map +1 -1
- package/lib/commonjs/cli/cifschema/util/generate.js +21 -21
- package/lib/commonjs/cli/cifschema/util/generate.js.map +1 -1
- package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/cli/cifschema/util/schema.js.map +1 -1
- package/lib/commonjs/cli/lipid-params/index.js +3 -3
- package/lib/commonjs/cli/lipid-params/index.js.map +1 -1
- package/lib/commonjs/cli/state-docs/index.js +4 -4
- package/lib/commonjs/cli/state-docs/index.js.map +1 -1
- package/lib/commonjs/cli/state-docs/pd-to-md.js +10 -10
- package/lib/commonjs/cli/state-docs/pd-to-md.js.map +1 -1
- package/lib/commonjs/cli/structure-info/model.js +18 -18
- package/lib/commonjs/cli/structure-info/model.js.map +1 -1
- package/lib/commonjs/cli/structure-info/volume.js +1 -1
- package/lib/commonjs/cli/structure-info/volume.js.map +1 -1
- package/lib/commonjs/examples/basic-wrapper/superposition.js +3 -3
- package/lib/commonjs/examples/basic-wrapper/superposition.js.map +1 -1
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +2 -2
- package/lib/commonjs/examples/domain-annotation-server/mapping.js.map +1 -1
- package/lib/commonjs/examples/domain-annotation-server/server.js +3 -3
- package/lib/commonjs/examples/domain-annotation-server/server.js.map +1 -1
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +3 -3
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js.map +1 -1
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +1 -1
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js.map +1 -1
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +2 -2
- package/lib/commonjs/examples/proteopedia-wrapper/index.js.map +1 -1
- package/lib/commonjs/examples/task.js +6 -6
- package/lib/commonjs/examples/task.js.map +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js.map +1 -1
- package/lib/commonjs/extensions/anvil/representation.js +1 -1
- package/lib/commonjs/extensions/anvil/representation.js.map +1 -1
- package/lib/commonjs/extensions/cellpack/color/generate.d.ts +1 -1
- package/lib/commonjs/extensions/cellpack/color/generate.js +1 -1
- package/lib/commonjs/extensions/cellpack/color/provided.d.ts +1 -1
- package/lib/commonjs/extensions/cellpack/color/provided.js +1 -1
- package/lib/commonjs/extensions/cellpack/curve.d.ts +2 -2
- package/lib/commonjs/extensions/cellpack/curve.js +2 -2
- package/lib/commonjs/extensions/cellpack/data.d.ts +32 -0
- package/lib/commonjs/extensions/cellpack/index.d.ts +1 -1
- package/lib/commonjs/extensions/cellpack/index.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.d.ts +5 -3
- package/lib/commonjs/extensions/cellpack/model.js +203 -65
- package/lib/commonjs/extensions/cellpack/model.js.map +1 -1
- package/lib/commonjs/extensions/cellpack/preset.d.ts +2 -1
- package/lib/commonjs/extensions/cellpack/preset.js +12 -15
- package/lib/commonjs/extensions/cellpack/preset.js.map +1 -1
- package/lib/commonjs/extensions/cellpack/property.d.ts +1 -1
- package/lib/commonjs/extensions/cellpack/property.js +1 -1
- package/lib/commonjs/extensions/cellpack/representation.d.ts +53 -0
- package/lib/commonjs/extensions/cellpack/representation.js +47 -0
- package/lib/commonjs/extensions/cellpack/representation.js.map +1 -0
- package/lib/commonjs/extensions/cellpack/state.d.ts +16 -5
- package/lib/commonjs/extensions/cellpack/state.js +234 -27
- package/lib/commonjs/extensions/cellpack/state.js.map +1 -1
- package/lib/commonjs/extensions/cellpack/util.d.ts +3 -1
- package/lib/commonjs/extensions/cellpack/util.js +34 -6
- package/lib/commonjs/extensions/cellpack/util.js.map +1 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +7 -7
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js.map +1 -1
- package/lib/commonjs/extensions/g3d/data.js +2 -2
- package/lib/commonjs/extensions/g3d/data.js.map +1 -1
- package/lib/commonjs/extensions/g3d/model.js +2 -2
- package/lib/commonjs/extensions/g3d/model.js.map +1 -1
- package/lib/commonjs/extensions/geo-export/controls.js +2 -2
- package/lib/commonjs/extensions/geo-export/controls.js.map +1 -1
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +1 -1
- package/lib/commonjs/extensions/geo-export/glb-exporter.js.map +1 -1
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +3 -3
- package/lib/commonjs/extensions/geo-export/obj-exporter.js.map +1 -1
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +1 -1
- package/lib/commonjs/extensions/geo-export/stl-exporter.js.map +1 -1
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +5 -5
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js.map +1 -1
- package/lib/commonjs/extensions/mp4-export/controls.js +1 -1
- package/lib/commonjs/extensions/mp4-export/controls.js.map +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js.map +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +4 -4
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +3 -3
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts +12 -12
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +7 -7
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +11 -11
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +2 -2
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js.map +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +15 -0
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +2 -2
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js.map +1 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +4 -4
- package/lib/commonjs/mol-canvas3d/canvas3d.js +3 -3
- package/lib/commonjs/mol-canvas3d/canvas3d.js.map +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +2 -2
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js.map +1 -1
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +2 -2
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/wboit.js.map +1 -1
- package/lib/commonjs/mol-canvas3d/util.js +1 -1
- package/lib/commonjs/mol-canvas3d/util.js.map +1 -1
- package/lib/commonjs/mol-data/db/table.js +1 -1
- package/lib/commonjs/mol-data/db/table.js.map +1 -1
- package/lib/commonjs/mol-data/int/_spec/sorted-ranges.spec.js +1 -1
- package/lib/commonjs/mol-data/int/_spec/sorted-ranges.spec.js.map +1 -1
- package/lib/commonjs/mol-data/int/impl/ordered-set.d.ts +3 -3
- package/lib/commonjs/mol-data/int/impl/sorted-array.js +2 -2
- package/lib/commonjs/mol-data/int/impl/sorted-array.js.map +1 -1
- package/lib/commonjs/mol-data/int/tuple.js +1 -1
- package/lib/commonjs/mol-data/int/tuple.js.map +1 -1
- package/lib/commonjs/mol-data/util/_spec/interval-iterator.spec.js +1 -1
- package/lib/commonjs/mol-data/util/_spec/interval-iterator.spec.js.map +1 -1
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/image/image.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +19 -11
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js.map +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +57 -15
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js.map +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js.map +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +1 -0
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js.map +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text.js.map +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js.map +1 -1
- package/lib/commonjs/mol-gl/_spec/cylinders.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/cylinders.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/cylinders.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/direct-volume.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/direct-volume.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/direct-volume.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/gl.d.ts +9 -0
- package/lib/commonjs/mol-gl/_spec/gl.js +33 -0
- package/lib/commonjs/mol-gl/_spec/gl.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/gl.shim.js +5 -5
- package/lib/commonjs/mol-gl/_spec/gl.shim.js.map +1 -1
- package/lib/commonjs/mol-gl/_spec/image.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/image.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/image.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/lines.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/lines.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/lines.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/mesh.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/mesh.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/mesh.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/points.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/points.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/points.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/renderer.spec.d.ts +7 -1
- package/lib/commonjs/mol-gl/_spec/renderer.spec.js +7 -45
- package/lib/commonjs/mol-gl/_spec/renderer.spec.js.map +1 -1
- package/lib/commonjs/mol-gl/_spec/spheres.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/spheres.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/spheres.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/text.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/text.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/text.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/_spec/texture-mesh.spec.d.ts +6 -0
- package/lib/commonjs/mol-gl/_spec/texture-mesh.spec.js +42 -0
- package/lib/commonjs/mol-gl/_spec/texture-mesh.spec.js.map +1 -0
- package/lib/commonjs/mol-gl/compute/grid3d.js +3 -3
- package/lib/commonjs/mol-gl/compute/grid3d.js.map +1 -1
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +4 -4
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js.map +1 -1
- package/lib/commonjs/mol-gl/renderable/util.js +1 -1
- package/lib/commonjs/mol-gl/renderable/util.js.map +1 -1
- package/lib/commonjs/mol-gl/renderer.d.ts +2 -2
- package/lib/commonjs/mol-gl/scene.js +1 -1
- package/lib/commonjs/mol-gl/scene.js.map +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js.map +1 -1
- package/lib/commonjs/mol-gl/shader-code.js +8 -8
- package/lib/commonjs/mol-gl/shader-code.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/buffer.d.ts +3 -2
- package/lib/commonjs/mol-gl/webgl/buffer.js +5 -5
- package/lib/commonjs/mol-gl/webgl/buffer.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/compat.js +3 -3
- package/lib/commonjs/mol-gl/webgl/compat.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +6 -4
- package/lib/commonjs/mol-gl/webgl/context.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/extensions.js +5 -1
- package/lib/commonjs/mol-gl/webgl/extensions.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/framebuffer.js +1 -1
- package/lib/commonjs/mol-gl/webgl/framebuffer.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/program.js +14 -12
- package/lib/commonjs/mol-gl/webgl/program.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/render-item.d.ts +3 -2
- package/lib/commonjs/mol-gl/webgl/render-item.js +2 -2
- package/lib/commonjs/mol-gl/webgl/render-item.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/shader.js +3 -3
- package/lib/commonjs/mol-gl/webgl/shader.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/state.d.ts +4 -1
- package/lib/commonjs/mol-gl/webgl/state.js +25 -1
- package/lib/commonjs/mol-gl/webgl/state.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/texture.js +2 -2
- package/lib/commonjs/mol-gl/webgl/texture.js.map +1 -1
- package/lib/commonjs/mol-gl/webgl/uniform.js +2 -2
- package/lib/commonjs/mol-gl/webgl/uniform.js.map +1 -1
- package/lib/commonjs/mol-io/common/file-handle.js +1 -1
- package/lib/commonjs/mol-io/common/file-handle.js.map +1 -1
- package/lib/commonjs/mol-io/common/typed-array.js +1 -1
- package/lib/commonjs/mol-io/common/typed-array.js.map +1 -1
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +1 -1
- package/lib/commonjs/mol-io/reader/ccp4/parser.js.map +1 -1
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js.map +1 -1
- package/lib/commonjs/mol-io/reader/cif/data-model.js +7 -7
- package/lib/commonjs/mol-io/reader/cif/data-model.js.map +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts +2 -2
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +12 -12
- package/lib/commonjs/mol-io/reader/cif/schema.js +7 -7
- package/lib/commonjs/mol-io/reader/cif/schema.js.map +1 -1
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/cif/text/parser.js.map +1 -1
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dcd/parser.js.map +1 -1
- package/lib/commonjs/mol-io/reader/ply/schema.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/ply/schema.js +1 -1
- package/lib/commonjs/mol-io/reader/ply/schema.js.map +1 -1
- package/lib/commonjs/mol-io/reader/result.js +1 -1
- package/lib/commonjs/mol-io/reader/result.js.map +1 -1
- package/lib/commonjs/mol-io/writer/cif/encoder/text.js +3 -3
- package/lib/commonjs/mol-io/writer/cif/encoder/text.js.map +1 -1
- package/lib/commonjs/mol-io/writer/cif/encoder.js +5 -5
- package/lib/commonjs/mol-io/writer/cif/encoder.js.map +1 -1
- package/lib/commonjs/mol-io/writer/mol/encoder.js +4 -4
- package/lib/commonjs/mol-io/writer/mol/encoder.js.map +1 -1
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +6 -6
- package/lib/commonjs/mol-io/writer/mol2/encoder.js.map +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js.map +1 -1
- package/lib/commonjs/mol-math/geometry/primitives/axes3d.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/primitives/axes3d.js +9 -2
- package/lib/commonjs/mol-math/geometry/primitives/axes3d.js.map +1 -1
- package/lib/commonjs/mol-math/geometry/spacegroup/construction.js +8 -8
- package/lib/commonjs/mol-math/geometry/spacegroup/construction.js.map +1 -1
- package/lib/commonjs/mol-math/geometry/spacegroup/tables.js +1 -1
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- package/lib/servers/model/server/structure-wrapper.js +6 -6
- package/lib/servers/model/server/structure-wrapper.js.map +1 -1
- package/lib/servers/model/server.js +3 -3
- package/lib/servers/model/server.js.map +1 -1
- package/lib/servers/model/utils/fetch-props-pdbe.js +4 -4
- package/lib/servers/model/utils/fetch-props-pdbe.js.map +1 -1
- package/lib/servers/model/utils/writer.js +2 -2
- package/lib/servers/model/utils/writer.js.map +1 -1
- package/lib/servers/plugin-state/api-schema.js +2 -2
- package/lib/servers/plugin-state/api-schema.js.map +1 -1
- package/lib/servers/plugin-state/index.js +1 -1
- package/lib/servers/plugin-state/index.js.map +1 -1
- package/lib/servers/volume/pack/format/dsn6.js +1 -1
- package/lib/servers/volume/pack/format/dsn6.js.map +1 -1
- package/lib/servers/volume/pack/main.js +4 -4
- package/lib/servers/volume/pack/main.js.map +1 -1
- package/lib/servers/volume/pack/writer.js +1 -1
- package/lib/servers/volume/pack/writer.js.map +1 -1
- package/lib/servers/volume/pack.js +1 -1
- package/lib/servers/volume/pack.js.map +1 -1
- package/lib/servers/volume/server/api.js +7 -7
- package/lib/servers/volume/server/api.js.map +1 -1
- package/lib/servers/volume/server/local-api.js +1 -1
- package/lib/servers/volume/server/local-api.js.map +1 -1
- package/lib/servers/volume/server/query/encode.js +3 -3
- package/lib/servers/volume/server/query/encode.js.map +1 -1
- package/lib/servers/volume/server/query/execute.js +5 -5
- package/lib/servers/volume/server/query/execute.js.map +1 -1
- package/lib/servers/volume/server/version.js +1 -1
- package/lib/servers/volume/server/version.js.map +1 -1
- package/lib/servers/volume/server/web-api.js +7 -7
- package/lib/servers/volume/server/web-api.js.map +1 -1
- package/lib/servers/volume/server/web-schema.js +6 -6
- package/lib/servers/volume/server/web-schema.js.map +1 -1
- package/lib/servers/volume/server.js +2 -2
- package/lib/servers/volume/server.js.map +1 -1
- package/lib/tests/browser/font-atlas.js +1 -1
- package/lib/tests/browser/font-atlas.js.map +1 -1
- package/lib/tests/browser/index.html +36 -36
- package/lib/tests/browser/render-shape.js +1 -1
- package/lib/tests/browser/render-shape.js.map +1 -1
- package/lib/tests/browser/render-structure.js +1 -1
- package/lib/tests/browser/render-structure.js.map +1 -1
- package/lib/tsconfig.commonjs.tsbuildinfo +1 -1
- package/package.json +158 -155
- package/CHANGELOG.md +0 -181
- package/lib/commonjs/mol-gl/shader/chunks/wboit-params.glsl.d.ts +0 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-params.glsl.js +0 -5
- package/lib/commonjs/mol-gl/shader/chunks/wboit-params.glsl.js.map +0 -1
- package/lib/commonjs/mol-model/structure/model/properties/utils/guess-element.d.ts +0 -6
- package/lib/commonjs/mol-model/structure/model/properties/utils/guess-element.js +0 -40
- package/lib/commonjs/mol-model/structure/model/properties/utils/guess-element.js.map +0 -1
- package/lib/commonjs/mol-repr/structure/visual/aromatic-ring-mesh.js +0 -3
- package/lib/commonjs/mol-repr/structure/visual/aromatic-ring-mesh.js.map +0 -1
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone-iterator.d.ts +0 -37
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone-iterator.js +0 -116
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone-iterator.js.map +0 -1
- package/lib/commonjs/mol-script/util/residue-list.d.ts +0 -7
- package/lib/commonjs/mol-script/util/residue-list.js +0 -63
- package/lib/commonjs/mol-script/util/residue-list.js.map +0 -1
- package/lib/mol-gl/shader/chunks/wboit-params.glsl.d.ts +0 -1
- package/lib/mol-gl/shader/chunks/wboit-params.glsl.js +0 -2
- package/lib/mol-gl/shader/chunks/wboit-params.glsl.js.map +0 -1
- package/lib/mol-model/structure/model/properties/utils/guess-element.d.ts +0 -6
- package/lib/mol-model/structure/model/properties/utils/guess-element.js +0 -36
- package/lib/mol-model/structure/model/properties/utils/guess-element.js.map +0 -1
- package/lib/mol-model-formats/structure/mol copy.d.ts +0 -17
- package/lib/mol-model-formats/structure/mol copy.js +0 -86
- package/lib/mol-model-formats/structure/mol copy.js.map +0 -1
- package/lib/mol-repr/structure/visual/aromatic-ring-mesh.d.ts +0 -0
- package/lib/mol-repr/structure/visual/aromatic-ring-mesh.js +0 -3
- package/lib/mol-repr/structure/visual/aromatic-ring-mesh.js.map +0 -1
- package/lib/mol-repr/structure/visual/util/polymer/backbone-iterator.d.ts +0 -37
- package/lib/mol-repr/structure/visual/util/polymer/backbone-iterator.js +0 -112
- package/lib/mol-repr/structure/visual/util/polymer/backbone-iterator.js.map +0 -1
- package/lib/mol-script/util/residue-list.d.ts +0 -7
- package/lib/mol-script/util/residue-list.js +0 -59
- package/lib/mol-script/util/residue-list.js.map +0 -1
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'polymer-id': Provider<{
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}, "uncertainty">;
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}>, "colors">>;
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}>, "generate">>;
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}, "unit-index">;
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uniform: Provider<{
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|
@@ -18,6 +18,7 @@ export declare const DefaultLabelOptions: {
|
|
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18
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|
export declare type LabelOptions = typeof DefaultLabelOptions;
|
|
19
19
|
export declare function lociLabel(loci: Loci, options?: Partial<LabelOptions>): string;
|
|
20
20
|
export declare function structureElementStatsLabel(stats: StructureElement.Stats, options?: Partial<LabelOptions>): string;
|
|
21
|
+
export declare function structureElementLociLabelMany(locis: StructureElement.Loci[], options?: Partial<LabelOptions>): string;
|
|
21
22
|
export declare function bondLabel(bond: Bond.Location, options?: Partial<LabelOptions>): string;
|
|
22
23
|
export declare function bundleLabel(bundle: Loci.Bundle<any>, options?: Partial<LabelOptions>): string;
|
|
23
24
|
export declare function _bundleLabel(bundle: Loci.Bundle<any>, options: LabelOptions): string;
|
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
* @author David Sehnal <david.sehnal@gmail.com>
|
|
7
7
|
*/
|
|
8
8
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
9
|
-
exports.dihedralLabel = exports.angleLabel = exports.distanceLabel = exports.elementLabel = exports._bundleLabel = exports.bundleLabel = exports.bondLabel = exports.structureElementStatsLabel = exports.lociLabel = exports.DefaultLabelOptions = void 0;
|
|
9
|
+
exports.dihedralLabel = exports.angleLabel = exports.distanceLabel = exports.elementLabel = exports._bundleLabel = exports.bundleLabel = exports.bondLabel = exports.structureElementLociLabelMany = exports.structureElementStatsLabel = exports.lociLabel = exports.DefaultLabelOptions = void 0;
|
|
10
10
|
var tslib_1 = require("tslib");
|
|
11
11
|
var structure_1 = require("../mol-model/structure");
|
|
12
12
|
var loci_1 = require("../mol-model/loci");
|
|
@@ -48,8 +48,8 @@ function lociLabel(loci, options) {
|
|
|
48
48
|
return loci.volume.label || 'Volume';
|
|
49
49
|
case 'isosurface-loci':
|
|
50
50
|
return [
|
|
51
|
-
""
|
|
52
|
-
"Isosurface at "
|
|
51
|
+
"".concat(loci.volume.label || 'Volume'),
|
|
52
|
+
"Isosurface at ".concat(volume_1.Volume.IsoValue.toString(loci.isoValue))
|
|
53
53
|
].join(' | ');
|
|
54
54
|
case 'cell-loci':
|
|
55
55
|
var size = int_1.OrderedSet.size(loci.indices);
|
|
@@ -57,21 +57,21 @@ function lociLabel(loci, options) {
|
|
|
57
57
|
var absVal = volume_1.Volume.IsoValue.absolute(loci.volume.grid.cells.data[start]);
|
|
58
58
|
var relVal = volume_1.Volume.IsoValue.toRelative(absVal, loci.volume.grid.stats);
|
|
59
59
|
var label = [
|
|
60
|
-
""
|
|
61
|
-
""
|
|
60
|
+
"".concat(loci.volume.label || 'Volume'),
|
|
61
|
+
"".concat(size === 1 ? "Cell #".concat(start) : "".concat(size, " Cells"))
|
|
62
62
|
];
|
|
63
63
|
if (size === 1) {
|
|
64
|
-
label.push(volume_1.Volume.IsoValue.toString(absVal)
|
|
64
|
+
label.push("".concat(volume_1.Volume.IsoValue.toString(absVal), " (").concat(volume_1.Volume.IsoValue.toString(relVal), ")"));
|
|
65
65
|
}
|
|
66
66
|
return label.join(' | ');
|
|
67
67
|
}
|
|
68
68
|
}
|
|
69
69
|
exports.lociLabel = lociLabel;
|
|
70
70
|
function countLabel(count, label) {
|
|
71
|
-
return count === 1 ? "1 "
|
|
71
|
+
return count === 1 ? "1 ".concat(label) : "".concat(count, " ").concat(label, "s");
|
|
72
72
|
}
|
|
73
73
|
function otherLabel(count, location, granularity, hidePrefix, reverse, condensed) {
|
|
74
|
-
return elementLabel(location, { granularity: granularity, hidePrefix: hidePrefix, reverse: reverse, condensed: condensed })
|
|
74
|
+
return "".concat(elementLabel(location, { granularity: granularity, hidePrefix: hidePrefix, reverse: reverse, condensed: condensed }), " <small>[+ ").concat(countLabel(count - 1, "other ".concat((0, string_1.capitalize)(granularity))), "]</small>");
|
|
75
75
|
}
|
|
76
76
|
/** Gets residue count of the model chain segments the unit is a subset of */
|
|
77
77
|
function getResidueCount(unit) {
|
|
@@ -88,6 +88,16 @@ function structureElementStatsLabel(stats, options) {
|
|
|
88
88
|
return o.htmlStyling ? label : (0, string_1.stripTags)(label);
|
|
89
89
|
}
|
|
90
90
|
exports.structureElementStatsLabel = structureElementStatsLabel;
|
|
91
|
+
function structureElementLociLabelMany(locis, options) {
|
|
92
|
+
if (options === void 0) { options = {}; }
|
|
93
|
+
var stats = structure_1.StructureElement.Stats.create();
|
|
94
|
+
for (var _i = 0, locis_1 = locis; _i < locis_1.length; _i++) {
|
|
95
|
+
var l = locis_1[_i];
|
|
96
|
+
structure_1.StructureElement.Stats.add(stats, stats, structure_1.StructureElement.Stats.ofLoci(l));
|
|
97
|
+
}
|
|
98
|
+
return structureElementStatsLabel(stats, options);
|
|
99
|
+
}
|
|
100
|
+
exports.structureElementLociLabelMany = structureElementLociLabelMany;
|
|
91
101
|
function _structureElementStatsLabel(stats, countsOnly, hidePrefix, condensed, reverse) {
|
|
92
102
|
if (countsOnly === void 0) { countsOnly = false; }
|
|
93
103
|
if (hidePrefix === void 0) { hidePrefix = false; }
|
|
@@ -228,10 +238,10 @@ function _elementLabel(location, granularity, hidePrefix, reverse) {
|
|
|
228
238
|
var entry = location.unit.model.entry;
|
|
229
239
|
if (entry.length > 30)
|
|
230
240
|
entry = entry.substr(0, 27) + '\u2026'; // ellipsis
|
|
231
|
-
label.push("<small>"
|
|
241
|
+
label.push("<small>".concat(entry, "</small>")); // entry
|
|
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242
|
if (granularity !== 'structure') {
|
|
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|
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label.push("<small>Model "
|
|
234
|
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label.push("<small>Instance "
|
|
243
|
+
label.push("<small>Model ".concat(location.unit.model.modelNum, "</small>")); // model
|
|
244
|
+
label.push("<small>Instance ".concat(location.unit.conformation.operator.name, "</small>")); // instance
|
|
235
245
|
}
|
|
236
246
|
}
|
|
237
247
|
if (structure_1.Unit.isAtomic(location.unit)) {
|
|
@@ -260,33 +270,33 @@ function _atomicElementLabel(location, granularity, hideOccupancy) {
|
|
|
260
270
|
var occupancy = structure_1.StructureProperties.atom.occupancy(location);
|
|
261
271
|
var microHetCompIds = structure_1.StructureProperties.residue.microheterogeneityCompIds(location);
|
|
262
272
|
var compId = granularity === 'residue' && microHetCompIds.length > 1 ?
|
|
263
|
-
"("
|
|
273
|
+
"(".concat(microHetCompIds.join('|'), ")") : comp_id;
|
|
264
274
|
var label = [];
|
|
265
275
|
switch (granularity) {
|
|
266
276
|
case 'element':
|
|
267
|
-
label.push("<b>"
|
|
277
|
+
label.push("<b>".concat(atom_id, "</b>").concat(alt_id ? "%".concat(alt_id) : ''));
|
|
268
278
|
case 'conformation':
|
|
269
279
|
if (granularity === 'conformation' && alt_id) {
|
|
270
|
-
label.push("<small>Conformation</small> <b>"
|
|
280
|
+
label.push("<small>Conformation</small> <b>".concat(alt_id, "</b>"));
|
|
271
281
|
}
|
|
272
282
|
case 'residue':
|
|
273
283
|
var seq_id = label_seq_id === auth_seq_id || !has_label_seq_id ? auth_seq_id : label_seq_id;
|
|
274
|
-
label.push("<b>"
|
|
284
|
+
label.push("<b>".concat(compId, " ").concat(seq_id, "</b>").concat(seq_id !== auth_seq_id ? " <small>[auth</small> <b>".concat(auth_seq_id, "</b><small>]</small>") : '', "<b>").concat(ins_code ? ins_code : '', "</b>"));
|
|
275
285
|
case 'chain':
|
|
276
286
|
if (label_asym_id === auth_asym_id) {
|
|
277
|
-
label.push("<b>"
|
|
287
|
+
label.push("<b>".concat(label_asym_id, "</b>"));
|
|
278
288
|
}
|
|
279
289
|
else {
|
|
280
290
|
if (granularity === 'chain' && structure_1.Unit.Traits.is(location.unit.traits, 1 /* MultiChain */)) {
|
|
281
|
-
label.push("<small>[auth</small> <b>"
|
|
291
|
+
label.push("<small>[auth</small> <b>".concat(auth_asym_id, "</b><small>]</small>"));
|
|
282
292
|
}
|
|
283
293
|
else {
|
|
284
|
-
label.push("<b>"
|
|
294
|
+
label.push("<b>".concat(label_asym_id, "</b> <small>[auth</small> <b>").concat(auth_asym_id, "</b><small>]</small>"));
|
|
285
295
|
}
|
|
286
296
|
}
|
|
287
297
|
}
|
|
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298
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if (label.length > 0 && occupancy !== 1 && !hideOccupancy) {
|
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289
|
-
label[0] = label[0]
|
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299
|
+
label[0] = "".concat(label[0], " <small>[occupancy</small> <b>").concat(Math.round(100 * occupancy) / 100, "</b><small>]</small>");
|
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}
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|
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return label.reverse();
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}
|
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@@ -303,13 +313,13 @@ function _coarseElementLabel(location, granularity) {
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var entityIndex = structure_1.StructureProperties.coarse.entityKey(location);
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314
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var seq = location.unit.model.sequence.byEntityKey[entityIndex];
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305
315
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var comp_id = seq.sequence.compId.value(seq_id_begin - 1); // 1-indexed
|
|
306
|
-
label.push("<b>"
|
|
316
|
+
label.push("<b>".concat(comp_id, " ").concat(seq_id_begin, "</b>"));
|
|
307
317
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}
|
|
308
318
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else {
|
|
309
|
-
label.push("<b>"
|
|
319
|
+
label.push("<b>".concat(seq_id_begin, "-").concat(seq_id_end, "</b>"));
|
|
310
320
|
}
|
|
311
321
|
case 'chain':
|
|
312
|
-
label.push("<b>"
|
|
322
|
+
label.push("<b>".concat(asym_id, "</b>"));
|
|
313
323
|
}
|
|
314
324
|
return label.reverse();
|
|
315
325
|
}
|
|
@@ -318,11 +328,11 @@ function distanceLabel(pair, options) {
|
|
|
318
328
|
if (options === void 0) { options = {}; }
|
|
319
329
|
var o = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), { measureOnly: false, unitLabel: '\u212B' }), options);
|
|
320
330
|
var _a = pair.loci.map(function (l) { return loci_1.Loci.getCenter(l); }), cA = _a[0], cB = _a[1];
|
|
321
|
-
var distance = linear_algebra_1.Vec3.distance(cA, cB).toFixed(2)
|
|
331
|
+
var distance = "".concat(linear_algebra_1.Vec3.distance(cA, cB).toFixed(2), " ").concat(o.unitLabel);
|
|
322
332
|
if (o.measureOnly)
|
|
323
333
|
return distance;
|
|
324
334
|
var label = bundleLabel(pair, o);
|
|
325
|
-
return o.condensed ? distance
|
|
335
|
+
return o.condensed ? "".concat(distance, " | ").concat(label) : "Distance ".concat(distance, "</br>").concat(label);
|
|
326
336
|
}
|
|
327
337
|
exports.distanceLabel = distanceLabel;
|
|
328
338
|
function angleLabel(triple, options) {
|
|
@@ -331,22 +341,22 @@ function angleLabel(triple, options) {
|
|
|
331
341
|
var _a = triple.loci.map(function (l) { return loci_1.Loci.getCenter(l); }), cA = _a[0], cB = _a[1], cC = _a[2];
|
|
332
342
|
var vAB = linear_algebra_1.Vec3.sub((0, linear_algebra_1.Vec3)(), cA, cB);
|
|
333
343
|
var vCB = linear_algebra_1.Vec3.sub((0, linear_algebra_1.Vec3)(), cC, cB);
|
|
334
|
-
var angle = (0, misc_1.radToDeg)(linear_algebra_1.Vec3.angle(vAB, vCB)).toFixed(2)
|
|
344
|
+
var angle = "".concat((0, misc_1.radToDeg)(linear_algebra_1.Vec3.angle(vAB, vCB)).toFixed(2), "\u00B0");
|
|
335
345
|
if (o.measureOnly)
|
|
336
346
|
return angle;
|
|
337
347
|
var label = bundleLabel(triple, o);
|
|
338
|
-
return o.condensed ? angle
|
|
348
|
+
return o.condensed ? "".concat(angle, " | ").concat(label) : "Angle ".concat(angle, "</br>").concat(label);
|
|
339
349
|
}
|
|
340
350
|
exports.angleLabel = angleLabel;
|
|
341
351
|
function dihedralLabel(quad, options) {
|
|
342
352
|
if (options === void 0) { options = {}; }
|
|
343
353
|
var o = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultLabelOptions), { measureOnly: false }), options);
|
|
344
354
|
var _a = quad.loci.map(function (l) { return loci_1.Loci.getCenter(l); }), cA = _a[0], cB = _a[1], cC = _a[2], cD = _a[3];
|
|
345
|
-
var dihedral = (0, misc_1.radToDeg)(linear_algebra_1.Vec3.dihedralAngle(cA, cB, cC, cD)).toFixed(2)
|
|
355
|
+
var dihedral = "".concat((0, misc_1.radToDeg)(linear_algebra_1.Vec3.dihedralAngle(cA, cB, cC, cD)).toFixed(2), "\u00B0");
|
|
346
356
|
if (o.measureOnly)
|
|
347
357
|
return dihedral;
|
|
348
358
|
var label = bundleLabel(quad, o);
|
|
349
|
-
return o.condensed ? dihedral
|
|
359
|
+
return o.condensed ? "".concat(dihedral, " | ").concat(label) : "Dihedral ".concat(dihedral, "</br>").concat(label);
|
|
350
360
|
}
|
|
351
361
|
exports.dihedralLabel = dihedralLabel;
|
|
352
362
|
//# sourceMappingURL=label.js.map
|