molstar 3.0.1 → 3.0.2
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 +194 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/commonjs/apps/docking-viewer/index.js +253 -0
- package/lib/commonjs/apps/docking-viewer/viewport.d.ts +2 -2
- package/lib/commonjs/apps/docking-viewer/viewport.js +326 -0
- package/lib/commonjs/apps/viewer/app.d.ts +3 -3
- package/lib/commonjs/cli/chem-comp-dict/create-ions.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +68 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +282 -0
- package/lib/commonjs/cli/chem-comp-dict/util.d.ts +146 -0
- package/lib/commonjs/cli/chem-comp-dict/util.js +144 -0
- package/lib/commonjs/cli/cif2bcif/converter.d.ts +8 -0
- package/lib/commonjs/cli/cif2bcif/converter.js +187 -0
- package/lib/commonjs/cli/cif2bcif/index.d.ts +8 -0
- package/lib/commonjs/cli/cif2bcif/index.js +81 -0
- package/lib/commonjs/cli/cifschema/index.d.ts +7 -0
- package/lib/commonjs/cli/cifschema/index.js +397 -0
- package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +11 -0
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +456 -0
- package/lib/commonjs/cli/cifschema/util/generate.d.ts +7 -0
- package/lib/commonjs/cli/cifschema/util/generate.js +158 -0
- package/lib/commonjs/cli/cifschema/util/helper.d.ts +10 -0
- package/lib/commonjs/cli/cifschema/util/helper.js +22 -0
- package/lib/commonjs/cli/cifschema/util/schema.d.ts +70 -0
- package/lib/commonjs/cli/cifschema/util/schema.js +64 -0
- package/lib/commonjs/cli/lipid-params/index.d.ts +7 -0
- package/lib/commonjs/cli/lipid-params/index.js +104 -0
- package/lib/commonjs/cli/state-docs/index.js +64 -0
- package/lib/commonjs/cli/state-docs/pd-to-md.js +80 -0
- package/lib/commonjs/cli/structure-info/helpers.d.ts +7 -0
- package/lib/commonjs/cli/structure-info/helpers.js +92 -0
- package/lib/commonjs/cli/structure-info/model.js +336 -0
- package/lib/commonjs/cli/structure-info/volume.js +115 -0
- package/lib/commonjs/examples/alpha-orbitals/controls.js +25 -0
- package/lib/commonjs/examples/alpha-orbitals/example-data.js +60260 -0
- package/lib/commonjs/examples/alpha-orbitals/index.js +230 -0
- package/lib/commonjs/examples/basic-wrapper/coloring.js +31 -0
- package/lib/commonjs/examples/basic-wrapper/controls.js +23 -0
- package/lib/commonjs/examples/basic-wrapper/custom-theme.js +49 -0
- package/lib/commonjs/examples/basic-wrapper/index.js +265 -0
- package/lib/commonjs/examples/basic-wrapper/superposition.js +191 -0
- package/lib/commonjs/examples/domain-annotation-server/mapping.d.ts +6 -0
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +111 -0
- package/lib/commonjs/examples/domain-annotation-server/schemas.d.ts +103 -0
- package/lib/commonjs/examples/domain-annotation-server/schemas.js +73 -0
- package/lib/commonjs/examples/domain-annotation-server/server.d.ts +6 -0
- package/lib/commonjs/examples/domain-annotation-server/server.js +65 -0
- package/lib/commonjs/examples/domain-annotation-server/test.d.ts +6 -0
- package/lib/commonjs/examples/domain-annotation-server/test.js +28 -0
- package/lib/commonjs/examples/lighting/index.js +145 -0
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +88 -0
- package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +97 -0
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +109 -0
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +498 -0
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +19 -0
- package/lib/commonjs/examples/task.d.ts +19 -0
- package/lib/commonjs/examples/task.js +221 -0
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +134 -0
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +69 -0
- package/lib/commonjs/extensions/alpha-orbitals/density.js +113 -0
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +157 -0
- package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.d.ts +7 -0
- package/lib/commonjs/extensions/alpha-orbitals/gpu/shader.frag.js +11 -0
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +121 -0
- package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.d.ts +11 -0
- package/lib/commonjs/extensions/alpha-orbitals/spherical-functions.js +66 -0
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +261 -0
- package/lib/commonjs/extensions/anvil/algorithm.js +578 -0
- package/lib/commonjs/extensions/anvil/behavior.d.ts +2 -2
- package/lib/commonjs/extensions/anvil/behavior.js +209 -0
- package/lib/commonjs/extensions/anvil/prop.js +82 -0
- package/lib/commonjs/extensions/anvil/representation.d.ts +5 -5
- package/lib/commonjs/extensions/anvil/representation.js +118 -0
- package/lib/commonjs/extensions/cellpack/color/generate.js +86 -0
- package/lib/commonjs/extensions/cellpack/color/provided.js +68 -0
- package/lib/commonjs/extensions/cellpack/curve.d.ts +9 -0
- package/lib/commonjs/extensions/cellpack/curve.js +203 -0
- package/lib/commonjs/extensions/cellpack/data.d.ts +107 -0
- package/lib/commonjs/extensions/cellpack/data.js +8 -0
- package/lib/commonjs/extensions/cellpack/index.js +39 -0
- package/lib/commonjs/extensions/cellpack/model.js +903 -0
- package/lib/commonjs/extensions/cellpack/preset.js +109 -0
- package/lib/commonjs/extensions/cellpack/property.js +31 -0
- package/lib/commonjs/extensions/cellpack/representation.d.ts +2 -2
- package/lib/commonjs/extensions/cellpack/representation.js +47 -0
- package/lib/commonjs/extensions/cellpack/state.js +397 -0
- package/lib/commonjs/extensions/cellpack/util.js +181 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts +1 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +121 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +178 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +160 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -3
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +159 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/types.js +27 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +234 -0
- package/lib/commonjs/extensions/dnatco/index.js +12 -0
- package/lib/commonjs/extensions/g3d/data.js +71 -0
- package/lib/commonjs/extensions/g3d/format.js +232 -0
- package/lib/commonjs/extensions/g3d/model.js +215 -0
- package/lib/commonjs/extensions/geo-export/controls.js +109 -0
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +323 -0
- package/lib/commonjs/extensions/geo-export/index.js +36 -0
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +457 -0
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +212 -0
- package/lib/commonjs/extensions/geo-export/render-object-exporter.js +8 -0
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +131 -0
- package/lib/commonjs/extensions/geo-export/ui.js +116 -0
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +222 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts +2 -2
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +236 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +125 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +111 -0
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +130 -0
- package/lib/commonjs/extensions/model-export/export.js +129 -0
- package/lib/commonjs/extensions/model-export/index.js +36 -0
- package/lib/commonjs/extensions/model-export/ui.js +77 -0
- package/lib/commonjs/extensions/mp4-export/controls.js +142 -0
- package/lib/commonjs/extensions/mp4-export/encoder.js +119 -0
- package/lib/commonjs/extensions/mp4-export/index.js +36 -0
- package/lib/commonjs/extensions/mp4-export/ui.js +94 -0
- package/lib/commonjs/extensions/pdbe/index.js +15 -0
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +98 -0
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +128 -0
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +75 -0
- package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +113 -0
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +288 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +5 -5
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +255 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +101 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +220 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +363 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +215 -0
- package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/graphql/symmetry.gql.js +5 -0
- package/lib/commonjs/extensions/rcsb/graphql/types.d.ts +12874 -0
- package/lib/commonjs/extensions/rcsb/graphql/types.js +3 -0
- package/lib/commonjs/extensions/rcsb/index.js +13 -0
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts +3 -3
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +421 -0
- package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +79 -0
- package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +110 -0
- package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +67 -0
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +490 -0
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -5
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +243 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +129 -0
- package/lib/commonjs/mol-canvas3d/camera/transition.js +103 -0
- package/lib/commonjs/mol-canvas3d/camera/util.d.ts +31 -0
- package/lib/commonjs/mol-canvas3d/camera/util.js +94 -0
- package/lib/commonjs/mol-canvas3d/camera.js +334 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +4 -4
- package/lib/commonjs/mol-canvas3d/controls/object.js +49 -0
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +426 -0
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +157 -0
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +217 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -1
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +184 -0
- package/lib/commonjs/mol-canvas3d/helper/helper.js +33 -0
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +94 -0
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +2 -2
- package/lib/commonjs/mol-canvas3d/passes/marking.js +131 -0
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts +2 -2
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +167 -0
- package/lib/commonjs/mol-canvas3d/passes/wboit.d.ts +23 -0
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +115 -0
- package/lib/commonjs/mol-canvas3d/util.d.ts +10 -0
- package/lib/commonjs/mol-canvas3d/util.js +70 -0
- package/lib/commonjs/mol-data/db/column-helpers.d.ts +19 -0
- package/lib/commonjs/mol-data/db/column-helpers.js +44 -0
- package/lib/commonjs/mol-data/db/column.d.ts +135 -0
- package/lib/commonjs/mol-data/db/column.js +425 -0
- package/lib/commonjs/mol-data/db/database.d.ts +25 -0
- package/lib/commonjs/mol-data/db/database.js +40 -0
- package/lib/commonjs/mol-data/db/table.d.ts +57 -0
- package/lib/commonjs/mol-data/db/table.js +302 -0
- package/lib/commonjs/mol-data/db.d.ts +14 -0
- package/lib/commonjs/mol-data/db.js +19 -0
- package/lib/commonjs/mol-data/generic/hash-set.d.ts +12 -0
- package/lib/commonjs/mol-data/generic/hash-set.js +52 -0
- package/lib/commonjs/mol-data/generic/linked-list.d.ts +26 -0
- package/lib/commonjs/mol-data/generic/linked-list.js +95 -0
- package/lib/commonjs/mol-data/generic/unique-array.d.ts +15 -0
- package/lib/commonjs/mol-data/generic/unique-array.js +31 -0
- package/lib/commonjs/mol-data/generic.d.ts +8 -0
- package/lib/commonjs/mol-data/generic.js +12 -0
- package/lib/commonjs/mol-data/index.d.ts +11 -0
- package/lib/commonjs/mol-data/index.js +20 -0
- package/lib/commonjs/mol-data/int/impl/interval.d.ts +30 -0
- package/lib/commonjs/mol-data/int/impl/interval.js +84 -0
- package/lib/commonjs/mol-data/int/impl/ordered-set.d.ts +40 -0
- package/lib/commonjs/mol-data/int/impl/ordered-set.js +423 -0
- package/lib/commonjs/mol-data/int/impl/segmentation.d.ts +41 -0
- package/lib/commonjs/mol-data/int/impl/segmentation.js +109 -0
- package/lib/commonjs/mol-data/int/impl/sorted-array.d.ts +45 -0
- package/lib/commonjs/mol-data/int/impl/sorted-array.js +477 -0
- package/lib/commonjs/mol-data/int/interval.d.ts +53 -0
- package/lib/commonjs/mol-data/int/interval.js +56 -0
- package/lib/commonjs/mol-data/int/linked-index.d.ts +13 -0
- package/lib/commonjs/mol-data/int/linked-index.js +48 -0
- package/lib/commonjs/mol-data/int/map.d.ts +25 -0
- package/lib/commonjs/mol-data/int/map.js +50 -0
- package/lib/commonjs/mol-data/int/ordered-set.d.ts +55 -0
- package/lib/commonjs/mol-data/int/ordered-set.js +80 -0
- package/lib/commonjs/mol-data/int/segmentation.d.ts +32 -0
- package/lib/commonjs/mol-data/int/segmentation.js +22 -0
- package/lib/commonjs/mol-data/int/sorted-array.d.ts +49 -0
- package/lib/commonjs/mol-data/int/sorted-array.js +52 -0
- package/lib/commonjs/mol-data/int/sorted-ranges.d.ts +42 -0
- package/lib/commonjs/mol-data/int/sorted-ranges.js +125 -0
- package/lib/commonjs/mol-data/int/tuple.d.ts +28 -0
- package/lib/commonjs/mol-data/int/tuple.js +86 -0
- package/lib/commonjs/mol-data/int.d.ts +14 -0
- package/lib/commonjs/mol-data/int.js +25 -0
- package/lib/commonjs/mol-data/iterator.d.ts +25 -0
- package/lib/commonjs/mol-data/iterator.js +113 -0
- package/lib/commonjs/mol-data/util/array.d.ts +19 -0
- package/lib/commonjs/mol-data/util/array.js +56 -0
- package/lib/commonjs/mol-data/util/buckets.d.ts +16 -0
- package/lib/commonjs/mol-data/util/buckets.js +81 -0
- package/lib/commonjs/mol-data/util/chunked-array.d.ts +49 -0
- package/lib/commonjs/mol-data/util/chunked-array.js +175 -0
- package/lib/commonjs/mol-data/util/combination.d.ts +17 -0
- package/lib/commonjs/mol-data/util/combination.js +61 -0
- package/lib/commonjs/mol-data/util/equivalence-classes.d.ts +16 -0
- package/lib/commonjs/mol-data/util/equivalence-classes.js +52 -0
- package/lib/commonjs/mol-data/util/grouping.d.ts +23 -0
- package/lib/commonjs/mol-data/util/grouping.js +53 -0
- package/lib/commonjs/mol-data/util/hash-functions.d.ts +26 -0
- package/lib/commonjs/mol-data/util/hash-functions.js +96 -0
- package/lib/commonjs/mol-data/util/interval-iterator.d.ts +19 -0
- package/lib/commonjs/mol-data/util/interval-iterator.js +45 -0
- package/lib/commonjs/mol-data/util/sort.d.ts +12 -0
- package/lib/commonjs/mol-data/util/sort.js +164 -0
- package/lib/commonjs/mol-data/util.d.ts +12 -0
- package/lib/commonjs/mol-data/util.js +16 -0
- package/lib/commonjs/mol-geo/geometry/base.d.ts +5 -5
- package/lib/commonjs/mol-geo/geometry/base.js +152 -0
- package/lib/commonjs/mol-geo/geometry/clipping-data.js +55 -0
- package/lib/commonjs/mol-geo/geometry/color-data.js +235 -0
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders-builder.js +114 -0
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +3 -3
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +197 -0
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +220 -0
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.d.ts +15 -0
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +61 -0
- package/lib/commonjs/mol-geo/geometry/geometry.js +89 -0
- package/lib/commonjs/mol-geo/geometry/image/image.d.ts +3 -3
- package/lib/commonjs/mol-geo/geometry/image/image.js +176 -0
- package/lib/commonjs/mol-geo/geometry/lines/lines-builder.js +110 -0
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +195 -0
- package/lib/commonjs/mol-geo/geometry/marker-data.d.ts +24 -0
- package/lib/commonjs/mol-geo/geometry/marker-data.js +103 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/axes.js +32 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/box.js +100 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/cylinder.js +119 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ellipsoid.js +24 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/ribbon.js +85 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sheet.js +187 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/sphere.js +30 -0
- package/lib/commonjs/mol-geo/geometry/mesh/builder/tube.js +175 -0
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +325 -0
- package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.d.ts +5 -0
- package/lib/commonjs/mol-geo/geometry/mesh/laplacian-smoothing.js +75 -0
- package/lib/commonjs/mol-geo/geometry/mesh/mesh-builder.js +154 -0
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +638 -0
- package/lib/commonjs/mol-geo/geometry/overpaint-data.d.ts +23 -0
- package/lib/commonjs/mol-geo/geometry/overpaint-data.js +68 -0
- package/lib/commonjs/mol-geo/geometry/picking.d.ts +13 -0
- package/lib/commonjs/mol-geo/geometry/picking.js +16 -0
- package/lib/commonjs/mol-geo/geometry/points/points-builder.js +35 -0
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +4 -4
- package/lib/commonjs/mol-geo/geometry/points/points.js +175 -0
- package/lib/commonjs/mol-geo/geometry/size-data.js +123 -0
- package/lib/commonjs/mol-geo/geometry/spheres/spheres-builder.js +58 -0
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +180 -0
- package/lib/commonjs/mol-geo/geometry/substance-data.js +68 -0
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +124 -0
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +284 -0
- package/lib/commonjs/mol-geo/geometry/text/text.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text.js +222 -0
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +70 -0
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +432 -0
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +145 -0
- package/lib/commonjs/mol-geo/geometry/transform-data.d.ts +32 -0
- package/lib/commonjs/mol-geo/geometry/transform-data.js +87 -0
- package/lib/commonjs/mol-geo/geometry/transparency-data.d.ts +24 -0
- package/lib/commonjs/mol-geo/geometry/transparency-data.js +76 -0
- package/lib/commonjs/mol-geo/primitive/box.d.ts +10 -0
- package/lib/commonjs/mol-geo/primitive/box.js +94 -0
- package/lib/commonjs/mol-geo/primitive/cage.d.ts +14 -0
- package/lib/commonjs/mol-geo/primitive/cage.js +33 -0
- package/lib/commonjs/mol-geo/primitive/circle.d.ts +14 -0
- package/lib/commonjs/mol-geo/primitive/circle.js +69 -0
- package/lib/commonjs/mol-geo/primitive/cylinder.d.ts +19 -0
- package/lib/commonjs/mol-geo/primitive/cylinder.js +129 -0
- package/lib/commonjs/mol-geo/primitive/dodecahedron.d.ts +12 -0
- package/lib/commonjs/mol-geo/primitive/dodecahedron.js +67 -0
- package/lib/commonjs/mol-geo/primitive/icosahedron.d.ts +9 -0
- package/lib/commonjs/mol-geo/primitive/icosahedron.js +40 -0
- package/lib/commonjs/mol-geo/primitive/octahedron.d.ts +13 -0
- package/lib/commonjs/mol-geo/primitive/octahedron.js +50 -0
- package/lib/commonjs/mol-geo/primitive/plane.d.ts +9 -0
- package/lib/commonjs/mol-geo/primitive/plane.js +39 -0
- package/lib/commonjs/mol-geo/primitive/polygon.d.ts +10 -0
- package/lib/commonjs/mol-geo/primitive/polygon.js +29 -0
- package/lib/commonjs/mol-geo/primitive/polyhedron.d.ts +12 -0
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +107 -0
- package/lib/commonjs/mol-geo/primitive/primitive.d.ts +24 -0
- package/lib/commonjs/mol-geo/primitive/primitive.js +97 -0
- package/lib/commonjs/mol-geo/primitive/prism.d.ts +29 -0
- package/lib/commonjs/mol-geo/primitive/prism.js +186 -0
- package/lib/commonjs/mol-geo/primitive/pyramid.d.ts +19 -0
- package/lib/commonjs/mol-geo/primitive/pyramid.js +126 -0
- package/lib/commonjs/mol-geo/primitive/sphere.d.ts +10 -0
- package/lib/commonjs/mol-geo/primitive/sphere.js +22 -0
- package/lib/commonjs/mol-geo/primitive/spiked-ball.d.ts +11 -0
- package/lib/commonjs/mol-geo/primitive/spiked-ball.js +61 -0
- package/lib/commonjs/mol-geo/primitive/star.d.ts +14 -0
- package/lib/commonjs/mol-geo/primitive/star.js +49 -0
- package/lib/commonjs/mol-geo/primitive/tetrahedron.d.ts +11 -0
- package/lib/commonjs/mol-geo/primitive/tetrahedron.js +33 -0
- package/lib/commonjs/mol-geo/primitive/torus.d.ts +15 -0
- package/lib/commonjs/mol-geo/primitive/torus.js +64 -0
- package/lib/commonjs/mol-geo/primitive/wedge.d.ts +13 -0
- package/lib/commonjs/mol-geo/primitive/wedge.js +56 -0
- package/lib/commonjs/mol-geo/util/location-iterator.js +91 -0
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +285 -0
- package/lib/commonjs/mol-geo/util/marching-cubes/builder.js +100 -0
- package/lib/commonjs/mol-geo/util/marching-cubes/tables.d.ts +50 -0
- package/lib/commonjs/mol-geo/util/marching-cubes/tables.js +432 -0
- package/lib/commonjs/mol-geo/util.d.ts +36 -0
- package/lib/commonjs/mol-geo/util.js +137 -0
- package/lib/commonjs/mol-gl/commit-queue.js +61 -0
- package/lib/commonjs/mol-gl/compute/grid3d.d.ts +24 -0
- package/lib/commonjs/mol-gl/compute/grid3d.js +188 -0
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.d.ts +16 -0
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +158 -0
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.d.ts +8 -0
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +79 -0
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.d.ts +9 -0
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +84 -0
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +30 -0
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +156 -0
- package/lib/commonjs/mol-gl/compute/marching-cubes/tables.d.ts +8 -0
- package/lib/commonjs/mol-gl/compute/marching-cubes/tables.js +42 -0
- package/lib/commonjs/mol-gl/compute/util.d.ts +39 -0
- package/lib/commonjs/mol-gl/compute/util.js +113 -0
- package/lib/commonjs/mol-gl/object3d.d.ts +16 -0
- package/lib/commonjs/mol-gl/object3d.js +28 -0
- package/lib/commonjs/mol-gl/render-object.js +41 -0
- package/lib/commonjs/mol-gl/renderable/cylinders.d.ts +99 -0
- package/lib/commonjs/mol-gl/renderable/cylinders.js +26 -0
- package/lib/commonjs/mol-gl/renderable/direct-volume.d.ts +104 -0
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +30 -0
- package/lib/commonjs/mol-gl/renderable/image.js +27 -0
- package/lib/commonjs/mol-gl/renderable/lines.d.ts +94 -0
- package/lib/commonjs/mol-gl/renderable/lines.js +26 -0
- package/lib/commonjs/mol-gl/renderable/mesh.d.ts +93 -0
- package/lib/commonjs/mol-gl/renderable/mesh.js +26 -0
- package/lib/commonjs/mol-gl/renderable/points.d.ts +90 -0
- package/lib/commonjs/mol-gl/renderable/points.js +26 -0
- package/lib/commonjs/mol-gl/renderable/schema.d.ts +295 -0
- package/lib/commonjs/mol-gl/renderable/schema.js +203 -0
- package/lib/commonjs/mol-gl/renderable/spheres.d.ts +96 -0
- package/lib/commonjs/mol-gl/renderable/spheres.js +26 -0
- package/lib/commonjs/mol-gl/renderable/text.d.ts +101 -0
- package/lib/commonjs/mol-gl/renderable/text.js +26 -0
- package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts +93 -0
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +26 -0
- package/lib/commonjs/mol-gl/renderable/util.d.ts +41 -0
- package/lib/commonjs/mol-gl/renderable/util.js +181 -0
- package/lib/commonjs/mol-gl/renderable.d.ts +38 -0
- package/lib/commonjs/mol-gl/renderable.js +41 -0
- package/lib/commonjs/mol-gl/scene.d.ts +1 -1
- package/lib/commonjs/mol-gl/scene.js +226 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-fog.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-interior-color.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-light-color.glsl.js +13 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/apply-marker-color.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-clipping-varying.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-group.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-marker-varying.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-position.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-size.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/clip-instance.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/clip-pixel.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/chunks/common-clip.glsl.js +11 -0
- package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/common-frag-params.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/common-vert-params.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/common.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/float-to-rgba.glsl.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/chunks/float-to-rgba.glsl.js +10 -0
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/chunks/light-frag-params.glsl.js +13 -0
- package/lib/commonjs/mol-gl/shader/chunks/matrix-scale.glsl.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/chunks/matrix-scale.glsl.js +10 -0
- package/lib/commonjs/mol-gl/shader/chunks/normal-frag-params.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/normal-frag-params.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/read-from-texture.glsl.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/chunks/read-from-texture.glsl.js +10 -0
- package/lib/commonjs/mol-gl/shader/chunks/rgba-to-float.glsl.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/chunks/rgba-to-float.glsl.js +10 -0
- package/lib/commonjs/mol-gl/shader/chunks/size-vert-params.glsl.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/chunks/size-vert-params.glsl.js +5 -0
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-1d-trilinear.glsl.js +10 -0
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-linear.glsl.js +11 -0
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/chunks/texture3d-from-2d-nearest.glsl.js +11 -0
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +11 -0
- package/lib/commonjs/mol-gl/shader/compose.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/compose.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/accumulate.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/compute/color-smoothing/normalize.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/copy.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/copy.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/cylinders.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/cylinders.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/cylinders.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/depth-merge.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/depth-merge.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +11 -0
- package/lib/commonjs/mol-gl/shader/direct-volume.vert.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/direct-volume.vert.js +11 -0
- package/lib/commonjs/mol-gl/shader/evaluate-wboit.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/evaluate-wboit.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/fxaa.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/fxaa.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/gaussian-density.frag.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/gaussian-density.frag.js +11 -0
- package/lib/commonjs/mol-gl/shader/gaussian-density.vert.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/gaussian-density.vert.js +11 -0
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/reduction.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/sum.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/histogram-pyramid/sum.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/image.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/image.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/image.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/lines.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/lines.vert.d.ts +8 -0
- package/lib/commonjs/mol-gl/shader/lines.vert.js +12 -0
- package/lib/commonjs/mol-gl/shader/marching-cubes/active-voxels.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/marching-cubes/active-voxels.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/marching-cubes/isosurface.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/marking/edge.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/marking/edge.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/marking/overlay.frag.d.ts +1 -0
- package/lib/commonjs/mol-gl/shader/marking/overlay.frag.js +5 -0
- package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/mesh.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/mesh.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/mesh.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/outlines.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/outlines.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/points.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/points.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/points.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/postprocessing.frag.js +11 -0
- package/lib/commonjs/mol-gl/shader/quad.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/quad.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/smaa/blend.frag.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/smaa/blend.frag.js +13 -0
- package/lib/commonjs/mol-gl/shader/smaa/blend.vert.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/smaa/blend.vert.js +13 -0
- package/lib/commonjs/mol-gl/shader/smaa/edges.frag.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/smaa/edges.frag.js +13 -0
- package/lib/commonjs/mol-gl/shader/smaa/edges.vert.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/smaa/edges.vert.js +13 -0
- package/lib/commonjs/mol-gl/shader/smaa/weights.frag.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/smaa/weights.frag.js +13 -0
- package/lib/commonjs/mol-gl/shader/smaa/weights.vert.d.ts +9 -0
- package/lib/commonjs/mol-gl/shader/smaa/weights.vert.js +13 -0
- package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/spheres.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/spheres.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/spheres.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/ssao-blur.frag.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/ssao-blur.frag.js +11 -0
- package/lib/commonjs/mol-gl/shader/ssao.frag.d.ts +7 -0
- package/lib/commonjs/mol-gl/shader/ssao.frag.js +11 -0
- package/lib/commonjs/mol-gl/shader/text.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/text.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader/text.vert.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/text.vert.js +10 -0
- package/lib/commonjs/mol-gl/shader/util/grid3d-template.frag.d.ts +6 -0
- package/lib/commonjs/mol-gl/shader/util/grid3d-template.frag.js +10 -0
- package/lib/commonjs/mol-gl/shader-code.d.ts +47 -0
- package/lib/commonjs/mol-gl/shader-code.js +281 -0
- package/lib/commonjs/mol-gl/webgl/buffer.d.ts +67 -0
- package/lib/commonjs/mol-gl/webgl/buffer.js +180 -0
- package/lib/commonjs/mol-gl/webgl/compat.d.ts +96 -0
- package/lib/commonjs/mol-gl/webgl/compat.js +343 -0
- package/lib/commonjs/mol-gl/webgl/context.d.ts +84 -0
- package/lib/commonjs/mol-gl/webgl/context.js +309 -0
- package/lib/commonjs/mol-gl/webgl/extensions.d.ts +25 -0
- package/lib/commonjs/mol-gl/webgl/extensions.js +102 -0
- package/lib/commonjs/mol-gl/webgl/framebuffer.d.ts +15 -0
- package/lib/commonjs/mol-gl/webgl/framebuffer.js +71 -0
- package/lib/commonjs/mol-gl/webgl/program.d.ts +32 -0
- package/lib/commonjs/mol-gl/webgl/program.js +196 -0
- package/lib/commonjs/mol-gl/webgl/render-item.d.ts +54 -0
- package/lib/commonjs/mol-gl/webgl/render-item.js +335 -0
- package/lib/commonjs/mol-gl/webgl/render-target.d.ts +23 -0
- package/lib/commonjs/mol-gl/webgl/render-target.js +89 -0
- package/lib/commonjs/mol-gl/webgl/renderbuffer.d.ts +20 -0
- package/lib/commonjs/mol-gl/webgl/renderbuffer.js +83 -0
- package/lib/commonjs/mol-gl/webgl/resources.d.ts +38 -0
- package/lib/commonjs/mol-gl/webgl/resources.js +128 -0
- package/lib/commonjs/mol-gl/webgl/shader.d.ts +19 -0
- package/lib/commonjs/mol-gl/webgl/shader.js +50 -0
- package/lib/commonjs/mol-gl/webgl/state.d.ts +60 -0
- package/lib/commonjs/mol-gl/webgl/state.js +147 -0
- package/lib/commonjs/mol-gl/webgl/texture.d.ts +75 -0
- package/lib/commonjs/mol-gl/webgl/texture.js +398 -0
- package/lib/commonjs/mol-gl/webgl/uniform.d.ts +45 -0
- package/lib/commonjs/mol-gl/webgl/uniform.js +112 -0
- package/lib/commonjs/mol-gl/webgl/vertex-array.d.ts +17 -0
- package/lib/commonjs/mol-gl/webgl/vertex-array.js +69 -0
- package/lib/commonjs/mol-io/common/ascii.d.ts +6 -0
- package/lib/commonjs/mol-io/common/ascii.js +15 -0
- package/lib/commonjs/mol-io/common/binary-cif/array-encoder.d.ts +50 -0
- package/lib/commonjs/mol-io/common/binary-cif/array-encoder.js +396 -0
- package/lib/commonjs/mol-io/common/binary-cif/classifier.d.ts +8 -0
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +173 -0
- package/lib/commonjs/mol-io/common/binary-cif/decoder.d.ts +12 -0
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +180 -0
- package/lib/commonjs/mol-io/common/binary-cif/encoding.d.ts +96 -0
- package/lib/commonjs/mol-io/common/binary-cif/encoding.js +47 -0
- package/lib/commonjs/mol-io/common/binary-cif.d.ts +9 -0
- package/lib/commonjs/mol-io/common/binary-cif.js +15 -0
- package/lib/commonjs/mol-io/common/binary.d.ts +9 -0
- package/lib/commonjs/mol-io/common/binary.js +36 -0
- package/lib/commonjs/mol-io/common/file-handle.d.ts +43 -0
- package/lib/commonjs/mol-io/common/file-handle.js +55 -0
- package/lib/commonjs/mol-io/common/msgpack/decode.d.ts +1 -0
- package/lib/commonjs/mol-io/common/msgpack/decode.js +204 -0
- package/lib/commonjs/mol-io/common/msgpack/encode.d.ts +1 -0
- package/lib/commonjs/mol-io/common/msgpack/encode.js +290 -0
- package/lib/commonjs/mol-io/common/simple-buffer.d.ts +48 -0
- package/lib/commonjs/mol-io/common/simple-buffer.js +90 -0
- package/lib/commonjs/mol-io/common/typed-array.d.ts +30 -0
- package/lib/commonjs/mol-io/common/typed-array.js +83 -0
- package/lib/commonjs/mol-io/common/utf8.d.ts +10 -0
- package/lib/commonjs/mol-io/common/utf8.js +131 -0
- package/lib/commonjs/mol-io/reader/ccp4/parser.d.ts +19 -0
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +193 -0
- package/lib/commonjs/mol-io/reader/ccp4/schema.d.ts +118 -0
- package/lib/commonjs/mol-io/reader/ccp4/schema.js +9 -0
- package/lib/commonjs/mol-io/reader/cif/binary/field.d.ts +9 -0
- package/lib/commonjs/mol-io/reader/cif/binary/field.js +54 -0
- package/lib/commonjs/mol-io/reader/cif/binary/parser.d.ts +9 -0
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +73 -0
- package/lib/commonjs/mol-io/reader/cif/data-model.d.ts +85 -0
- package/lib/commonjs/mol-io/reader/cif/data-model.js +307 -0
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +491 -0
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +497 -0
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +12 -0
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.js +18 -0
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +390 -0
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +398 -0
- package/lib/commonjs/mol-io/reader/cif/schema/cif-core.d.ts +684 -0
- package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js +750 -0
- package/lib/commonjs/mol-io/reader/cif/schema/ddl.d.ts +0 -0
- package/lib/commonjs/mol-io/reader/cif/schema/ddl.js +3 -0
- package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts +52 -0
- package/lib/commonjs/mol-io/reader/cif/schema/density-server.js +60 -0
- package/lib/commonjs/mol-io/reader/cif/schema/dic.d.ts +51 -0
- package/lib/commonjs/mol-io/reader/cif/schema/dic.js +63 -0
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +39 -0
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +28 -0
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +5036 -0
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +5046 -0
- package/lib/commonjs/mol-io/reader/cif/schema.d.ts +16 -0
- package/lib/commonjs/mol-io/reader/cif/schema.js +211 -0
- package/lib/commonjs/mol-io/reader/cif/text/parser.d.ts +27 -0
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +732 -0
- package/lib/commonjs/mol-io/reader/cif.d.ts +32 -0
- package/lib/commonjs/mol-io/reader/cif.js +36 -0
- package/lib/commonjs/mol-io/reader/common/binary/column.d.ts +5 -0
- package/lib/commonjs/mol-io/reader/common/binary/column.js +7 -0
- package/lib/commonjs/mol-io/reader/common/text/column/fixed.d.ts +9 -0
- package/lib/commonjs/mol-io/reader/common/text/column/fixed.js +52 -0
- package/lib/commonjs/mol-io/reader/common/text/column/token.d.ts +12 -0
- package/lib/commonjs/mol-io/reader/common/text/column/token.js +63 -0
- package/lib/commonjs/mol-io/reader/common/text/number-parser.d.ts +26 -0
- package/lib/commonjs/mol-io/reader/common/text/number-parser.js +163 -0
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.d.ts +66 -0
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +307 -0
- package/lib/commonjs/mol-io/reader/csv/data-model.d.ts +20 -0
- package/lib/commonjs/mol-io/reader/csv/data-model.js +20 -0
- package/lib/commonjs/mol-io/reader/csv/field.d.ts +7 -0
- package/lib/commonjs/mol-io/reader/csv/field.js +11 -0
- package/lib/commonjs/mol-io/reader/csv/parser.d.ts +16 -0
- package/lib/commonjs/mol-io/reader/csv/parser.js +259 -0
- package/lib/commonjs/mol-io/reader/csv/schema.d.ts +6 -0
- package/lib/commonjs/mol-io/reader/csv/schema.js +11 -0
- package/lib/commonjs/mol-io/reader/cube/parser.d.ts +41 -0
- package/lib/commonjs/mol-io/reader/cube/parser.js +114 -0
- package/lib/commonjs/mol-io/reader/dcd/parser.d.ts +30 -0
- package/lib/commonjs/mol-io/reader/dcd/parser.js +170 -0
- package/lib/commonjs/mol-io/reader/dsn6/parser.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +188 -0
- package/lib/commonjs/mol-io/reader/dsn6/schema.d.ts +43 -0
- package/lib/commonjs/mol-io/reader/dsn6/schema.js +8 -0
- package/lib/commonjs/mol-io/reader/dx/parser.d.ts +24 -0
- package/lib/commonjs/mol-io/reader/dx/parser.js +129 -0
- package/lib/commonjs/mol-io/reader/gro/parser.d.ts +10 -0
- package/lib/commonjs/mol-io/reader/gro/parser.js +173 -0
- package/lib/commonjs/mol-io/reader/mol/parser.d.ts +53 -0
- package/lib/commonjs/mol-io/reader/mol/parser.js +204 -0
- package/lib/commonjs/mol-io/reader/mol2/parser.d.ts +10 -0
- package/lib/commonjs/mol-io/reader/mol2/parser.js +322 -0
- package/lib/commonjs/mol-io/reader/mol2/schema.d.ts +59 -0
- package/lib/commonjs/mol-io/reader/mol2/schema.js +8 -0
- package/lib/commonjs/mol-io/reader/obj/parser.js +35 -0
- package/lib/commonjs/mol-io/reader/pdb/parser.d.ts +10 -0
- package/lib/commonjs/mol-io/reader/pdb/parser.js +35 -0
- package/lib/commonjs/mol-io/reader/pdb/schema.d.ts +12 -0
- package/lib/commonjs/mol-io/reader/pdb/schema.js +9 -0
- package/lib/commonjs/mol-io/reader/ply/parser.d.ts +9 -0
- package/lib/commonjs/mol-io/reader/ply/parser.js +253 -0
- package/lib/commonjs/mol-io/reader/ply/schema.d.ts +52 -0
- package/lib/commonjs/mol-io/reader/ply/schema.js +50 -0
- package/lib/commonjs/mol-io/reader/psf/parser.d.ts +29 -0
- package/lib/commonjs/mol-io/reader/psf/parser.js +282 -0
- package/lib/commonjs/mol-io/reader/result.d.ts +19 -0
- package/lib/commonjs/mol-io/reader/result.js +48 -0
- package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.d.ts +15 -0
- package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js +100 -0
- package/lib/commonjs/mol-io/reader/sdf/parser.d.ts +24 -0
- package/lib/commonjs/mol-io/reader/sdf/parser.js +111 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.d.ts +23 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.js +377 -0
- package/lib/commonjs/mol-io/reader/xyz/parser.d.ts +19 -0
- package/lib/commonjs/mol-io/reader/xyz/parser.js +61 -0
- package/lib/commonjs/mol-io/utils/short-string-pool.d.ts +18 -0
- package/lib/commonjs/mol-io/utils/short-string-pool.js +26 -0
- package/lib/commonjs/mol-io/writer/cif/encoder/binary.d.ts +33 -0
- package/lib/commonjs/mol-io/writer/cif/encoder/binary.js +191 -0
- package/lib/commonjs/mol-io/writer/cif/encoder/text.d.ts +27 -0
- package/lib/commonjs/mol-io/writer/cif/encoder/text.js +257 -0
- package/lib/commonjs/mol-io/writer/cif/encoder/util.d.ts +19 -0
- package/lib/commonjs/mol-io/writer/cif/encoder/util.js +36 -0
- package/lib/commonjs/mol-io/writer/cif/encoder.d.ts +108 -0
- package/lib/commonjs/mol-io/writer/cif/encoder.js +270 -0
- package/lib/commonjs/mol-io/writer/cif.d.ts +46 -0
- package/lib/commonjs/mol-io/writer/cif.js +98 -0
- package/lib/commonjs/mol-io/writer/encoder.d.ts +12 -0
- package/lib/commonjs/mol-io/writer/encoder.js +8 -0
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +127 -0
- package/lib/commonjs/mol-io/writer/mol/encoder.js +125 -0
- package/lib/commonjs/mol-io/writer/mol.js +18 -0
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +328 -0
- package/lib/commonjs/mol-io/writer/mol2.js +18 -0
- package/lib/commonjs/mol-io/writer/sdf.js +18 -0
- package/lib/commonjs/mol-io/writer/writer.d.ts +12 -0
- package/lib/commonjs/mol-io/writer/writer.js +8 -0
- package/lib/commonjs/mol-math/approx.d.ts +37 -0
- package/lib/commonjs/mol-math/approx.js +211 -0
- package/lib/commonjs/mol-math/easing.d.ts +25 -0
- package/lib/commonjs/mol-math/easing.js +91 -0
- package/lib/commonjs/mol-math/geometry/boundary-helper.d.ts +31 -0
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +150 -0
- package/lib/commonjs/mol-math/geometry/boundary.d.ts +13 -0
- package/lib/commonjs/mol-math/geometry/boundary.js +54 -0
- package/lib/commonjs/mol-math/geometry/centroid-helper.d.ts +31 -0
- package/lib/commonjs/mol-math/geometry/centroid-helper.js +114 -0
- package/lib/commonjs/mol-math/geometry/common.d.ts +41 -0
- package/lib/commonjs/mol-math/geometry/common.js +25 -0
- package/lib/commonjs/mol-math/geometry/distance-transform.d.ts +10 -0
- package/lib/commonjs/mol-math/geometry/distance-transform.js +57 -0
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +10 -0
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +139 -0
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +15 -0
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +390 -0
- package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +28 -0
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +52 -0
- package/lib/commonjs/mol-math/geometry/lookup3d/common.d.ts +29 -0
- package/lib/commonjs/mol-math/geometry/lookup3d/common.js +35 -0
- package/lib/commonjs/mol-math/geometry/lookup3d/grid.d.ts +19 -0
- package/lib/commonjs/mol-math/geometry/lookup3d/grid.js +199 -0
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +357 -0
- package/lib/commonjs/mol-math/geometry/primitives/axes3d.d.ts +28 -0
- package/lib/commonjs/mol-math/geometry/primitives/axes3d.js +71 -0
- package/lib/commonjs/mol-math/geometry/primitives/box3d.d.ts +40 -0
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +131 -0
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.d.ts +60 -0
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +269 -0
- package/lib/commonjs/mol-math/geometry/spacegroup/cell.d.ts +17 -0
- package/lib/commonjs/mol-math/geometry/spacegroup/cell.js +40 -0
- package/lib/commonjs/mol-math/geometry/spacegroup/construction.d.ts +50 -0
- package/lib/commonjs/mol-math/geometry/spacegroup/construction.js +169 -0
- package/lib/commonjs/mol-math/geometry/spacegroup/tables.d.ts +371 -0
- package/lib/commonjs/mol-math/geometry/spacegroup/tables.js +1532 -0
- package/lib/commonjs/mol-math/geometry/symmetry-operator.d.ts +76 -0
- package/lib/commonjs/mol-math/geometry/symmetry-operator.js +226 -0
- package/lib/commonjs/mol-math/geometry.d.ts +14 -0
- package/lib/commonjs/mol-math/geometry.js +18 -0
- package/lib/commonjs/mol-math/graph/int-adjacency-graph.d.ts +136 -0
- package/lib/commonjs/mol-math/graph/int-adjacency-graph.js +367 -0
- package/lib/commonjs/mol-math/graph/inter-unit-graph.d.ts +71 -0
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +148 -0
- package/lib/commonjs/mol-math/graph.d.ts +6 -0
- package/lib/commonjs/mol-math/graph.js +10 -0
- package/lib/commonjs/mol-math/histogram.d.ts +15 -0
- package/lib/commonjs/mol-math/histogram.js +35 -0
- package/lib/commonjs/mol-math/interpolate.d.ts +18 -0
- package/lib/commonjs/mol-math/interpolate.js +72 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/common.d.ts +8 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/common.js +26 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/mat3.d.ts +79 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/mat3.js +439 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/mat4.d.ts +150 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/mat4.js +1032 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/minimize-rmsd.d.ts +33 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/minimize-rmsd.js +136 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/quat.d.ts +89 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/quat.js +435 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec2.d.ts +50 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec2.js +159 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec3.d.ts +183 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js +583 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec4.d.ts +63 -0
- package/lib/commonjs/mol-math/linear-algebra/3d/vec4.js +221 -0
- package/lib/commonjs/mol-math/linear-algebra/3d.d.ts +15 -0
- package/lib/commonjs/mol-math/linear-algebra/3d.js +35 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/evd.d.ts +20 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/evd.js +259 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/matrix.d.ts +36 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/matrix.js +111 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/principal-axes.d.ts +21 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/principal-axes.js +134 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/svd.d.ts +11 -0
- package/lib/commonjs/mol-math/linear-algebra/matrix/svd.js +281 -0
- package/lib/commonjs/mol-math/linear-algebra/tensor.d.ts +49 -0
- package/lib/commonjs/mol-math/linear-algebra/tensor.js +325 -0
- package/lib/commonjs/mol-math/linear-algebra.d.ts +7 -0
- package/lib/commonjs/mol-math/linear-algebra.js +11 -0
- package/lib/commonjs/mol-math/misc.d.ts +16 -0
- package/lib/commonjs/mol-math/misc.js +69 -0
- package/lib/commonjs/mol-model/custom-property.js +82 -0
- package/lib/commonjs/mol-model/location.js +23 -0
- package/lib/commonjs/mol-model/loci.d.ts +20 -20
- package/lib/commonjs/mol-model/sequence/alignment/alignment.d.ts +17 -0
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +181 -0
- package/lib/commonjs/mol-model/sequence/alignment/sequence.js +97 -0
- package/lib/commonjs/mol-model/sequence/alignment/substitution-matrix.d.ts +23 -0
- package/lib/commonjs/mol-model/sequence/alignment/substitution-matrix.js +75 -0
- package/lib/commonjs/mol-model/sequence/alignment.d.ts +0 -0
- package/lib/commonjs/mol-model/sequence/alignment.js +2 -0
- package/lib/commonjs/mol-model/sequence/constants.d.ts +10 -0
- package/lib/commonjs/mol-model/sequence/constants.js +73 -0
- package/lib/commonjs/mol-model/sequence/sequence.d.ts +43 -0
- package/lib/commonjs/mol-model/sequence/sequence.js +162 -0
- package/lib/commonjs/mol-model/sequence.d.ts +6 -0
- package/lib/commonjs/mol-model/sequence.js +10 -0
- package/lib/commonjs/mol-model/shape/provider.js +8 -0
- package/lib/commonjs/mol-model/shape/shape.d.ts +1 -1
- package/lib/commonjs/mol-model/shape/shape.js +216 -0
- package/lib/commonjs/mol-model/shape.js +10 -0
- package/lib/commonjs/mol-model/structure/coordinates/coordinates.d.ts +62 -0
- package/lib/commonjs/mol-model/structure/coordinates/coordinates.js +124 -0
- package/lib/commonjs/mol-model/structure/coordinates.d.ts +6 -0
- package/lib/commonjs/mol-model/structure/coordinates.js +10 -0
- package/lib/commonjs/mol-model/structure/export/categories/atom_site.js +160 -0
- package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js +89 -0
- package/lib/commonjs/mol-model/structure/export/categories/misc.js +63 -0
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +102 -0
- package/lib/commonjs/mol-model/structure/export/categories/sequence.js +34 -0
- package/lib/commonjs/mol-model/structure/export/categories/utils.js +110 -0
- package/lib/commonjs/mol-model/structure/export/mmcif.js +247 -0
- package/lib/commonjs/mol-model/structure/model/indexing.d.ts +21 -0
- package/lib/commonjs/mol-model/structure/model/indexing.js +8 -0
- package/lib/commonjs/mol-model/structure/model/model.js +327 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/bonds.d.ts +13 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/bonds.js +93 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/conformation.d.ts +41 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/conformation.js +9 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.d.ts +244 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/hierarchy.js +110 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/measures.d.ts +21 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/measures.js +38 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/types.d.ts +155 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic/types.js +70 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +12 -0
- package/lib/commonjs/mol-model/structure/model/properties/coarse/conformation.d.ts +57 -0
- package/lib/commonjs/mol-model/structure/model/properties/coarse/conformation.js +9 -0
- package/lib/commonjs/mol-model/structure/model/properties/common.d.ts +30 -0
- package/lib/commonjs/mol-model/structure/model/properties/common.js +12 -0
- package/lib/commonjs/mol-model/structure/model/properties/custom/indexed.js +197 -0
- package/lib/commonjs/mol-model/structure/model/properties/global-transform.js +82 -0
- package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.d.ts +47 -0
- package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.js +13 -0
- package/lib/commonjs/mol-model/structure/model/properties/symmetry.js +69 -0
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-derived.js +84 -0
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.d.ts +10 -0
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js +229 -0
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js +117 -0
- package/lib/commonjs/mol-model/structure/model/properties/utils/coarse-keys.js +97 -0
- package/lib/commonjs/mol-model/structure/model/properties/utils/residue-set.js +98 -0
- package/lib/commonjs/mol-model/structure/model/types/ions.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/ions.js +12 -0
- package/lib/commonjs/mol-model/structure/model/types/lipids.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/lipids.js +12 -0
- package/lib/commonjs/mol-model/structure/model/types.d.ts +261 -0
- package/lib/commonjs/mol-model/structure/model/types.js +620 -0
- package/lib/commonjs/mol-model/structure/model/util.js +52 -0
- package/lib/commonjs/mol-model/structure/model.js +20 -0
- package/lib/commonjs/mol-model/structure/query/context.js +135 -0
- package/lib/commonjs/mol-model/structure/query/predicates.js +120 -0
- package/lib/commonjs/mol-model/structure/query/queries/combinators.js +73 -0
- package/lib/commonjs/mol-model/structure/query/queries/filters.js +309 -0
- package/lib/commonjs/mol-model/structure/query/queries/generators.js +351 -0
- package/lib/commonjs/mol-model/structure/query/queries/internal.js +130 -0
- package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +614 -0
- package/lib/commonjs/mol-model/structure/query/query.js +18 -0
- package/lib/commonjs/mol-model/structure/query/selection.js +163 -0
- package/lib/commonjs/mol-model/structure/query/utils/builders.js +86 -0
- package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js +126 -0
- package/lib/commonjs/mol-model/structure/query/utils/structure-set.js +138 -0
- package/lib/commonjs/mol-model/structure/query.js +29 -0
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js +390 -0
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts +64 -0
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +322 -0
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/data.js +19 -0
- package/lib/commonjs/mol-model/structure/structure/element/bundle.js +247 -0
- package/lib/commonjs/mol-model/structure/structure/element/element.js +15 -0
- package/lib/commonjs/mol-model/structure/structure/element/location.js +67 -0
- package/lib/commonjs/mol-model/structure/structure/element/loci.d.ts +1 -1
- package/lib/commonjs/mol-model/structure/structure/element/loci.js +723 -0
- package/lib/commonjs/mol-model/structure/structure/element/stats.js +359 -0
- package/lib/commonjs/mol-model/structure/structure/element/util.js +47 -0
- package/lib/commonjs/mol-model/structure/structure/element.js +13 -0
- package/lib/commonjs/mol-model/structure/structure/properties.d.ts +2 -2
- package/lib/commonjs/mol-model/structure/structure/properties.js +177 -0
- package/lib/commonjs/mol-model/structure/structure/structure.js +1390 -0
- package/lib/commonjs/mol-model/structure/structure/symmetry.js +337 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.d.ts +21 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.js +122 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js +46 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/element-set-intra-bond-cache.js +50 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +199 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +240 -0
- package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +224 -0
- package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js +337 -0
- package/lib/commonjs/mol-model/structure/structure/unit/rings.js +218 -0
- package/lib/commonjs/mol-model/structure/structure/unit.d.ts +4 -4
- package/lib/commonjs/mol-model/structure/structure/unit.js +492 -0
- package/lib/commonjs/mol-model/structure/structure/util/boundary.js +50 -0
- package/lib/commonjs/mol-model/structure/structure/util/lookup3d.js +200 -0
- package/lib/commonjs/mol-model/structure/structure/util/polymer.js +123 -0
- package/lib/commonjs/mol-model/structure/structure/util/principal-axes.js +28 -0
- package/lib/commonjs/mol-model/structure/structure/util/subset-builder.js +115 -0
- package/lib/commonjs/mol-model/structure/structure/util/superposition-db-mapping.js +135 -0
- package/lib/commonjs/mol-model/structure/structure/util/superposition.js +91 -0
- package/lib/commonjs/mol-model/structure/structure/util/unique-subset-builder.js +100 -0
- package/lib/commonjs/mol-model/structure/structure/util/unit-transforms.js +73 -0
- package/lib/commonjs/mol-model/structure/structure.js +24 -0
- package/lib/commonjs/mol-model/structure/topology/topology.d.ts +24 -0
- package/lib/commonjs/mol-model/structure/topology/topology.js +24 -0
- package/lib/commonjs/mol-model/structure/topology.d.ts +6 -0
- package/lib/commonjs/mol-model/structure/topology.js +10 -0
- package/lib/commonjs/mol-model/structure/trajectory.js +22 -0
- package/lib/commonjs/mol-model/structure/util.js +60 -0
- package/lib/commonjs/mol-model/structure.js +16 -0
- package/lib/commonjs/mol-model/volume/grid.d.ts +41 -0
- package/lib/commonjs/mol-model/volume/grid.js +67 -0
- package/lib/commonjs/mol-model-formats/format.d.ts +11 -0
- package/lib/commonjs/mol-model-formats/format.js +9 -0
- package/lib/commonjs/mol-model-formats/shape/ply.d.ts +6 -6
- package/lib/commonjs/mol-model-formats/shape/ply.js +295 -0
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +174 -0
- package/lib/commonjs/mol-model-formats/structure/basic/coarse.js +84 -0
- package/lib/commonjs/mol-model-formats/structure/basic/entities.js +137 -0
- package/lib/commonjs/mol-model-formats/structure/basic/parser.js +245 -0
- package/lib/commonjs/mol-model-formats/structure/basic/properties.js +132 -0
- package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +194 -0
- package/lib/commonjs/mol-model-formats/structure/basic/schema.js +45 -0
- package/lib/commonjs/mol-model-formats/structure/basic/sequence.js +40 -0
- package/lib/commonjs/mol-model-formats/structure/basic/sort.d.ts +13 -0
- package/lib/commonjs/mol-model-formats/structure/basic/sort.js +72 -0
- package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts +8 -0
- package/lib/commonjs/mol-model-formats/structure/basic/util.js +22 -0
- package/lib/commonjs/mol-model-formats/structure/cif-core.js +258 -0
- package/lib/commonjs/mol-model-formats/structure/common/component.d.ts +50 -0
- package/lib/commonjs/mol-model-formats/structure/common/component.js +185 -0
- package/lib/commonjs/mol-model-formats/structure/common/entity.d.ts +40 -0
- package/lib/commonjs/mol-model-formats/structure/common/entity.js +80 -0
- package/lib/commonjs/mol-model-formats/structure/common/property.js +66 -0
- package/lib/commonjs/mol-model-formats/structure/common/util.d.ts +6 -0
- package/lib/commonjs/mol-model-formats/structure/common/util.js +27 -0
- package/lib/commonjs/mol-model-formats/structure/cube.js +78 -0
- package/lib/commonjs/mol-model-formats/structure/dcd.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/dcd.js +67 -0
- package/lib/commonjs/mol-model-formats/structure/gro.js +126 -0
- package/lib/commonjs/mol-model-formats/structure/mmcif.js +93 -0
- package/lib/commonjs/mol-model-formats/structure/mol.js +104 -0
- package/lib/commonjs/mol-model-formats/structure/mol2.js +163 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/anisotropic.d.ts +36 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/anisotropic.js +130 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/assembly.d.ts +10 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/assembly.js +243 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.d.ts +35 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js +145 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/conect.d.ts +11 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/conect.js +75 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/entity.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/entity.js +113 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js +205 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.d.ts +9 -0
- package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js +231 -0
- package/lib/commonjs/mol-model-formats/structure/pdb.js +71 -0
- package/lib/commonjs/mol-model-formats/structure/property/anisotropic.js +72 -0
- package/lib/commonjs/mol-model-formats/structure/property/assembly.js +126 -0
- package/lib/commonjs/mol-model-formats/structure/property/atoms/chem_comp.js +87 -0
- package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +117 -0
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +62 -0
- package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +167 -0
- package/lib/commonjs/mol-model-formats/structure/property/partial-charge.js +18 -0
- package/lib/commonjs/mol-model-formats/structure/property/secondary-structure.js +190 -0
- package/lib/commonjs/mol-model-formats/structure/property/symmetry.js +77 -0
- package/lib/commonjs/mol-model-formats/structure/psf.d.ts +16 -0
- package/lib/commonjs/mol-model-formats/structure/psf.js +123 -0
- package/lib/commonjs/mol-model-formats/structure/sdf.js +27 -0
- package/lib/commonjs/mol-model-formats/structure/util.d.ts +8 -0
- package/lib/commonjs/mol-model-formats/structure/util.js +79 -0
- package/lib/commonjs/mol-model-formats/structure/xtc.d.ts +10 -0
- package/lib/commonjs/mol-model-formats/structure/xtc.js +48 -0
- package/lib/commonjs/mol-model-formats/structure/xyz.js +92 -0
- package/lib/commonjs/mol-model-formats/volume/ccp4.js +96 -0
- package/lib/commonjs/mol-model-formats/volume/cube.js +75 -0
- package/lib/commonjs/mol-model-formats/volume/density-server.js +61 -0
- package/lib/commonjs/mol-model-formats/volume/dsn6.js +67 -0
- package/lib/commonjs/mol-model-formats/volume/dx.js +58 -0
- package/lib/commonjs/mol-model-props/common/custom-element-property.js +110 -0
- package/lib/commonjs/mol-model-props/common/custom-model-property.js +110 -0
- package/lib/commonjs/mol-model-props/common/custom-property.js +70 -0
- package/lib/commonjs/mol-model-props/common/custom-structure-property.js +114 -0
- package/lib/commonjs/mol-model-props/common/wrapper.js +46 -0
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js +101 -0
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.js +46 -0
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +148 -0
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +121 -0
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +63 -0
- package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js +207 -0
- package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js +121 -0
- package/lib/commonjs/mol-model-props/computed/chemistry/util.js +122 -0
- package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +326 -0
- package/lib/commonjs/mol-model-props/computed/helix-orientation/helix-orientation.js +111 -0
- package/lib/commonjs/mol-model-props/computed/helix-orientation.js +29 -0
- package/lib/commonjs/mol-model-props/computed/interactions.js +39 -0
- package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts +3 -3
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/backbone-hbonds.js +125 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bends.js +60 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bridges.js +74 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/common.js +26 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/dihedral-angles.js +51 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/helices.js +64 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/ladders.js +99 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/protein-info.js +37 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/sheets.js +58 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/trace-lookup.js +23 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/turns.js +40 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +212 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/zhang-skolnik.d.ts +0 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure/zhang-skolnik.js +3 -0
- package/lib/commonjs/mol-model-props/computed/secondary-structure.js +119 -0
- package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js +82 -0
- package/lib/commonjs/mol-model-props/computed/valence-model.js +39 -0
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js +68 -0
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js +93 -0
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/property.js +197 -0
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts +4 -4
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js +127 -0
- package/lib/commonjs/mol-model-props/integrative/pair-restraints.js +41 -0
- package/lib/commonjs/mol-model-props/sequence/best-database-mapping.js +88 -0
- package/lib/commonjs/mol-model-props/sequence/themes/best-database-mapping.d.ts +2 -2
- package/lib/commonjs/mol-model-props/sequence/themes/best-database-mapping.js +119 -0
- package/lib/commonjs/mol-plugin/animation-loop.js +75 -0
- package/lib/commonjs/mol-plugin/behavior/behavior.d.ts +1 -1
- package/lib/commonjs/mol-plugin/behavior/behavior.js +179 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +137 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.js +139 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/secondary-structure.js +42 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/computed/valence-model.js +103 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/integrative/cross-link-restraint.js +47 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-mapping.js +70 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/structure-info.js +133 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.js +24 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/representation.d.ts +3 -3
- package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +309 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts +1 -1
- package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js +245 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts +4 -4
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/behavior.js +436 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.js +28 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts +4 -4
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/transformers.js +387 -0
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js +167 -0
- package/lib/commonjs/mol-plugin/behavior/static/camera.js +37 -0
- package/lib/commonjs/mol-plugin/behavior/static/misc.js +31 -0
- package/lib/commonjs/mol-plugin/behavior/static/representation.js +100 -0
- package/lib/commonjs/mol-plugin/behavior/static/state.js +259 -0
- package/lib/commonjs/mol-plugin/behavior.js +29 -0
- package/lib/commonjs/mol-plugin/command.js +106 -0
- package/lib/commonjs/mol-plugin/commands.d.ts +2 -2
- package/lib/commonjs/mol-plugin/commands.js +60 -0
- package/lib/commonjs/mol-plugin/config.d.ts +1 -1
- package/lib/commonjs/mol-plugin/context.js +441 -0
- package/lib/commonjs/mol-plugin/features.d.ts +9 -0
- package/lib/commonjs/mol-plugin/features.js +38 -0
- package/lib/commonjs/mol-plugin/layout.d.ts +4 -4
- package/lib/commonjs/mol-plugin/layout.js +179 -0
- package/lib/commonjs/mol-plugin/state.js +184 -0
- package/lib/commonjs/mol-plugin/util/substructure-parent-helper.js +106 -0
- package/lib/commonjs/mol-plugin/util/task-manager.d.ts +40 -0
- package/lib/commonjs/mol-plugin/util/task-manager.js +144 -0
- package/lib/commonjs/mol-plugin/util/toast.js +85 -0
- package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts +3 -3
- package/lib/commonjs/mol-plugin/util/viewport-screenshot.js +413 -0
- package/lib/commonjs/mol-plugin/version.d.ts +10 -0
- package/lib/commonjs/mol-plugin/version.js +14 -0
- package/lib/commonjs/mol-plugin-state/actions/file.js +189 -0
- package/lib/commonjs/mol-plugin-state/actions/structure.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/actions/structure.js +412 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/assembly-unwind.js +115 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/camera-rock.js +62 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/camera-spin.js +61 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/explode-units.js +86 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.d.ts +2 -2
- package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.js +172 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/spin-structure.js +89 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/state-interpolation.js +81 -0
- package/lib/commonjs/mol-plugin-state/animation/built-in/state-snapshots.js +97 -0
- package/lib/commonjs/mol-plugin-state/animation/helpers.js +88 -0
- package/lib/commonjs/mol-plugin-state/animation/model.js +26 -0
- package/lib/commonjs/mol-plugin-state/builder/data.js +53 -0
- package/lib/commonjs/mol-plugin-state/builder/preset-provider.js +8 -0
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts +11 -11
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.js +291 -0
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts +6 -6
- package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.js +114 -0
- package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts +18 -18
- package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js +529 -0
- package/lib/commonjs/mol-plugin-state/builder/structure/representation.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/builder/structure/representation.js +156 -0
- package/lib/commonjs/mol-plugin-state/builder/structure.js +208 -0
- package/lib/commonjs/mol-plugin-state/component.d.ts +22 -0
- package/lib/commonjs/mol-plugin-state/component.js +83 -0
- package/lib/commonjs/mol-plugin-state/formats/provider.js +33 -0
- package/lib/commonjs/mol-plugin-state/formats/shape.js +45 -0
- package/lib/commonjs/mol-plugin-state/formats/structure.js +65 -0
- package/lib/commonjs/mol-plugin-state/formats/trajectory.js +173 -0
- package/lib/commonjs/mol-plugin-state/formats/volume.d.ts +10 -10
- package/lib/commonjs/mol-plugin-state/helpers/root-structure.d.ts +5 -5
- package/lib/commonjs/mol-plugin-state/helpers/root-structure.js +207 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-clipping.js +101 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-component.d.ts +2 -2
- package/lib/commonjs/mol-plugin-state/helpers/structure-component.js +184 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js +126 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-query.js +53 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-representation-params.js +85 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +723 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js +126 -0
- package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js +124 -0
- package/lib/commonjs/mol-plugin-state/helpers/volume-representation-params.js +85 -0
- package/lib/commonjs/mol-plugin-state/manager/animation.js +304 -0
- package/lib/commonjs/mol-plugin-state/manager/camera.js +138 -0
- package/lib/commonjs/mol-plugin-state/manager/interactivity.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/manager/interactivity.js +268 -0
- package/lib/commonjs/mol-plugin-state/manager/loci-label.js +95 -0
- package/lib/commonjs/mol-plugin-state/manager/snapshots.js +377 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/component.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/manager/structure/component.js +685 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/focus.js +176 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js +256 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.js +351 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/measurement.js +376 -0
- package/lib/commonjs/mol-plugin-state/manager/structure/selection.js +556 -0
- package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy-state.js +133 -0
- package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy.js +146 -0
- package/lib/commonjs/mol-plugin-state/objects.js +270 -0
- package/lib/commonjs/mol-plugin-state/transforms/data.d.ts +1 -1
- package/lib/commonjs/mol-plugin-state/transforms/data.js +606 -0
- package/lib/commonjs/mol-plugin-state/transforms/helpers.js +43 -0
- package/lib/commonjs/mol-plugin-state/transforms/misc.js +57 -0
- package/lib/commonjs/mol-plugin-state/transforms/model.d.ts +7 -7
- package/lib/commonjs/mol-plugin-state/transforms/model.js +1288 -0
- package/lib/commonjs/mol-plugin-state/transforms/representation.d.ts +13 -13
- package/lib/commonjs/mol-plugin-state/transforms/representation.js +1329 -0
- package/lib/commonjs/mol-plugin-state/transforms/shape.js +72 -0
- package/lib/commonjs/mol-plugin-state/transforms/volume.js +237 -0
- package/lib/commonjs/mol-plugin-state/transforms.js +24 -0
- package/lib/commonjs/mol-plugin-ui/base.js +104 -0
- package/lib/commonjs/mol-plugin-ui/context.js +35 -0
- package/lib/commonjs/mol-plugin-ui/controls/action-menu.js +250 -0
- package/lib/commonjs/mol-plugin-ui/controls/color.js +100 -0
- package/lib/commonjs/mol-plugin-ui/controls/common.d.ts +166 -0
- package/lib/commonjs/mol-plugin-ui/controls/common.js +255 -0
- package/lib/commonjs/mol-plugin-ui/controls/icons.d.ts +84 -0
- package/lib/commonjs/mol-plugin-ui/controls/icons.js +223 -0
- package/lib/commonjs/mol-plugin-ui/controls/legend.js +52 -0
- package/lib/commonjs/mol-plugin-ui/controls/line-graph/line-graph-component.d.ts +40 -0
- package/lib/commonjs/mol-plugin-ui/controls/line-graph/line-graph-component.js +311 -0
- package/lib/commonjs/mol-plugin-ui/controls/line-graph/point-component.d.ts +10 -0
- package/lib/commonjs/mol-plugin-ui/controls/line-graph/point-component.js +38 -0
- package/lib/commonjs/mol-plugin-ui/controls/parameters.js +1334 -0
- package/lib/commonjs/mol-plugin-ui/controls/screenshot.js +260 -0
- package/lib/commonjs/mol-plugin-ui/controls/slider.d.ts +147 -0
- package/lib/commonjs/mol-plugin-ui/controls/slider.js +624 -0
- package/lib/commonjs/mol-plugin-ui/controls.js +301 -0
- package/lib/commonjs/mol-plugin-ui/custom/volume.js +253 -0
- package/lib/commonjs/mol-plugin-ui/hooks/use-behavior.d.ts +14 -0
- package/lib/commonjs/mol-plugin-ui/hooks/use-behavior.js +28 -0
- package/lib/commonjs/mol-plugin-ui/index.js +39 -0
- package/lib/commonjs/mol-plugin-ui/left-panel.js +156 -0
- package/lib/commonjs/mol-plugin-ui/plugin.js +256 -0
- package/lib/commonjs/mol-plugin-ui/sequence/chain.js +88 -0
- package/lib/commonjs/mol-plugin-ui/sequence/element.js +89 -0
- package/lib/commonjs/mol-plugin-ui/sequence/hetero.js +106 -0
- package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +132 -0
- package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +282 -0
- package/lib/commonjs/mol-plugin-ui/sequence/wrapper.js +29 -0
- package/lib/commonjs/mol-plugin-ui/sequence.js +387 -0
- package/lib/commonjs/mol-plugin-ui/spec.js +18 -0
- package/lib/commonjs/mol-plugin-ui/state/actions.js +51 -0
- package/lib/commonjs/mol-plugin-ui/state/animation.js +55 -0
- package/lib/commonjs/mol-plugin-ui/state/apply-action.js +59 -0
- package/lib/commonjs/mol-plugin-ui/state/common.js +203 -0
- package/lib/commonjs/mol-plugin-ui/state/snapshots.js +349 -0
- package/lib/commonjs/mol-plugin-ui/state/tree.js +295 -0
- package/lib/commonjs/mol-plugin-ui/state/update-transform.js +115 -0
- package/lib/commonjs/mol-plugin-ui/structure/components.js +367 -0
- package/lib/commonjs/mol-plugin-ui/structure/focus.js +233 -0
- package/lib/commonjs/mol-plugin-ui/structure/generic.js +155 -0
- package/lib/commonjs/mol-plugin-ui/structure/measurements.d.ts +1 -1
- package/lib/commonjs/mol-plugin-ui/structure/measurements.js +334 -0
- package/lib/commonjs/mol-plugin-ui/structure/selection.d.ts +1 -1
- package/lib/commonjs/mol-plugin-ui/structure/selection.js +354 -0
- package/lib/commonjs/mol-plugin-ui/structure/source.js +340 -0
- package/lib/commonjs/mol-plugin-ui/structure/superposition.js +332 -0
- package/lib/commonjs/mol-plugin-ui/structure/volume.js +324 -0
- package/lib/commonjs/mol-plugin-ui/task.js +98 -0
- package/lib/commonjs/mol-plugin-ui/toast.js +57 -0
- package/lib/commonjs/mol-plugin-ui/viewport/canvas.js +58 -0
- package/lib/commonjs/mol-plugin-ui/viewport/help.js +123 -0
- package/lib/commonjs/mol-plugin-ui/viewport/screenshot.js +103 -0
- package/lib/commonjs/mol-plugin-ui/viewport/simple-settings.js +155 -0
- package/lib/commonjs/mol-plugin-ui/viewport.js +83 -0
- package/lib/commonjs/mol-repr/representation.js +383 -0
- package/lib/commonjs/mol-repr/shape/loci/angle.d.ts +2 -2
- package/lib/commonjs/mol-repr/shape/loci/angle.js +176 -0
- package/lib/commonjs/mol-repr/shape/loci/common.d.ts +3 -3
- package/lib/commonjs/mol-repr/shape/loci/common.js +20 -0
- package/lib/commonjs/mol-repr/shape/loci/dihedral.d.ts +2 -2
- package/lib/commonjs/mol-repr/shape/loci/dihedral.js +257 -0
- package/lib/commonjs/mol-repr/shape/loci/distance.d.ts +2 -2
- package/lib/commonjs/mol-repr/shape/loci/distance.js +96 -0
- package/lib/commonjs/mol-repr/shape/loci/label.d.ts +2 -2
- package/lib/commonjs/mol-repr/shape/loci/label.js +65 -0
- package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts +2 -2
- package/lib/commonjs/mol-repr/shape/loci/orientation.js +103 -0
- package/lib/commonjs/mol-repr/shape/loci/plane.d.ts +1 -1
- package/lib/commonjs/mol-repr/shape/loci/plane.js +61 -0
- package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts +1 -1
- package/lib/commonjs/mol-repr/shape/model/unitcell.js +81 -0
- package/lib/commonjs/mol-repr/shape/representation.js +275 -0
- package/lib/commonjs/mol-repr/structure/complex-representation.js +182 -0
- package/lib/commonjs/mol-repr/structure/complex-visual.d.ts +7 -7
- package/lib/commonjs/mol-repr/structure/complex-visual.js +325 -0
- package/lib/commonjs/mol-repr/structure/params.d.ts +10 -10
- package/lib/commonjs/mol-repr/structure/params.js +37 -0
- package/lib/commonjs/mol-repr/structure/registry.d.ts +25 -25
- package/lib/commonjs/mol-repr/structure/registry.js +59 -0
- package/lib/commonjs/mol-repr/structure/representation/backbone.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/backbone.js +52 -0
- package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts +6 -6
- package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js +51 -0
- package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js +46 -0
- package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/cartoon.js +96 -0
- package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts +6 -6
- package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js +50 -0
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts +9 -9
- package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js +42 -0
- package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js +40 -0
- package/lib/commonjs/mol-repr/structure/representation/label.d.ts +9 -9
- package/lib/commonjs/mol-repr/structure/representation/label.js +40 -0
- package/lib/commonjs/mol-repr/structure/representation/line.d.ts +9 -9
- package/lib/commonjs/mol-repr/structure/representation/line.js +54 -0
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.d.ts +9 -9
- package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js +41 -0
- package/lib/commonjs/mol-repr/structure/representation/orientation.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/orientation.js +39 -0
- package/lib/commonjs/mol-repr/structure/representation/point.d.ts +6 -6
- package/lib/commonjs/mol-repr/structure/representation/point.js +38 -0
- package/lib/commonjs/mol-repr/structure/representation/putty.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/putty.js +54 -0
- package/lib/commonjs/mol-repr/structure/representation/spacefill.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/representation/spacefill.js +43 -0
- package/lib/commonjs/mol-repr/structure/representation.js +33 -0
- package/lib/commonjs/mol-repr/structure/units-representation.js +409 -0
- package/lib/commonjs/mol-repr/structure/units-visual.d.ts +10 -10
- package/lib/commonjs/mol-repr/structure/units-visual.js +404 -0
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts +4 -4
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts +4 -4
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.js +113 -0
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +219 -0
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +137 -0
- package/lib/commonjs/mol-repr/structure/visual/element-cross.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/element-cross.js +77 -0
- package/lib/commonjs/mol-repr/structure/visual/element-point.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/element-point.js +64 -0
- package/lib/commonjs/mol-repr/structure/visual/element-sphere.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/element-sphere.js +58 -0
- package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/ellipsoid-mesh.js +102 -0
- package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/gaussian-density-volume.js +133 -0
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts +12 -12
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +379 -0
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js +69 -0
- package/lib/commonjs/mol-repr/structure/visual/label-text.d.ts +3 -3
- package/lib/commonjs/mol-repr/structure/visual/label-text.js +137 -0
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts +4 -4
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js +99 -0
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js +67 -0
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.js +148 -0
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.js +202 -0
- package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +118 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.js +124 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.js +101 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +88 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.js +89 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +191 -0
- package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js +111 -0
- package/lib/commonjs/mol-repr/structure/visual/util/bond.d.ts +6 -6
- package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts +1 -1
- package/lib/commonjs/mol-repr/structure/visual/util/common.js +317 -0
- package/lib/commonjs/mol-repr/structure/visual/util/element.js +251 -0
- package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js +104 -0
- package/lib/commonjs/mol-repr/structure/visual/util/link.js +366 -0
- package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js +53 -0
- package/lib/commonjs/mol-repr/structure/visual/util/nucleotide.js +76 -0
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js +115 -0
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/curve-segment.d.ts +36 -0
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/curve-segment.js +135 -0
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js +66 -0
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +449 -0
- package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +269 -0
- package/lib/commonjs/mol-repr/util.js +185 -0
- package/lib/commonjs/mol-repr/visual.js +316 -0
- package/lib/commonjs/mol-repr/volume/direct-volume.d.ts +6 -6
- package/lib/commonjs/mol-repr/volume/direct-volume.js +142 -0
- package/lib/commonjs/mol-repr/volume/isosurface.d.ts +12 -12
- package/lib/commonjs/mol-repr/volume/isosurface.js +267 -0
- package/lib/commonjs/mol-repr/volume/registry.d.ts +8 -8
- package/lib/commonjs/mol-repr/volume/registry.js +37 -0
- package/lib/commonjs/mol-repr/volume/representation.d.ts +1 -1
- package/lib/commonjs/mol-repr/volume/representation.js +310 -0
- package/lib/commonjs/mol-repr/volume/slice.d.ts +12 -12
- package/lib/commonjs/mol-repr/volume/slice.js +202 -0
- package/lib/commonjs/mol-repr/volume/util.js +168 -0
- package/lib/commonjs/mol-script/compiler.d.ts +0 -0
- package/lib/commonjs/mol-script/compiler.js +80 -0
- package/lib/commonjs/mol-script/language/builder.d.ts +756 -0
- package/lib/commonjs/mol-script/language/builder.js +74 -0
- package/lib/commonjs/mol-script/language/container.d.ts +6 -0
- package/lib/commonjs/mol-script/language/container.js +8 -0
- package/lib/commonjs/mol-script/language/expression-formatter.d.ts +2 -0
- package/lib/commonjs/mol-script/language/expression-formatter.js +130 -0
- package/lib/commonjs/mol-script/language/expression.d.ts +24 -0
- package/lib/commonjs/mol-script/language/expression.js +27 -0
- package/lib/commonjs/mol-script/language/helpers.d.ts +5 -0
- package/lib/commonjs/mol-script/language/helpers.js +57 -0
- package/lib/commonjs/mol-script/language/parser.d.ts +7 -0
- package/lib/commonjs/mol-script/language/parser.js +168 -0
- package/lib/commonjs/mol-script/language/symbol-table/core.d.ts +254 -0
- package/lib/commonjs/mol-script/language/symbol-table/core.js +169 -0
- package/lib/commonjs/mol-script/language/symbol-table/internal.d.ts +22 -0
- package/lib/commonjs/mol-script/language/symbol-table/internal.js +33 -0
- package/lib/commonjs/mol-script/language/symbol-table/structure-query.d.ts +363 -0
- package/lib/commonjs/mol-script/language/symbol-table/structure-query.js +281 -0
- package/lib/commonjs/mol-script/language/symbol-table.d.ts +589 -0
- package/lib/commonjs/mol-script/language/symbol-table.js +25 -0
- package/lib/commonjs/mol-script/language/symbol.d.ts +73 -0
- package/lib/commonjs/mol-script/language/symbol.js +55 -0
- package/lib/commonjs/mol-script/language/type.d.ts +60 -0
- package/lib/commonjs/mol-script/language/type.js +40 -0
- package/lib/commonjs/mol-script/runtime/environment.d.ts +0 -0
- package/lib/commonjs/mol-script/runtime/environment.js +32 -0
- package/lib/commonjs/mol-script/runtime/expression.d.ts +0 -0
- package/lib/commonjs/mol-script/runtime/expression.js +21 -0
- package/lib/commonjs/mol-script/runtime/query/base.js +175 -0
- package/lib/commonjs/mol-script/runtime/query/compiler.js +11 -0
- package/lib/commonjs/mol-script/runtime/query/table.js +429 -0
- package/lib/commonjs/mol-script/runtime/runtime-macro.d.ts +0 -0
- package/lib/commonjs/mol-script/runtime/runtime-macro.js +68 -0
- package/lib/commonjs/mol-script/runtime/symbol.d.ts +0 -0
- package/lib/commonjs/mol-script/runtime/symbol.js +26 -0
- package/lib/commonjs/mol-script/script/mol-script/examples.d.ts +0 -0
- package/lib/commonjs/mol-script/script/mol-script/examples.js +105 -0
- package/lib/commonjs/mol-script/script/mol-script/parser.d.ts +0 -0
- package/lib/commonjs/mol-script/script/mol-script/parser.js +162 -0
- package/lib/commonjs/mol-script/script/mol-script/script-macro.d.ts +10 -0
- package/lib/commonjs/mol-script/script/mol-script/script-macro.js +47 -0
- package/lib/commonjs/mol-script/script/mol-script/symbols.d.ts +27 -0
- package/lib/commonjs/mol-script/script/mol-script/symbols.js +370 -0
- package/lib/commonjs/mol-script/script/parser.d.ts +8 -0
- package/lib/commonjs/mol-script/script/parser.js +9 -0
- package/lib/commonjs/mol-script/script.js +57 -0
- package/lib/commonjs/mol-script/util/id-list.js +89 -0
- package/lib/commonjs/mol-state/action/manager.js +99 -0
- package/lib/commonjs/mol-state/action.js +63 -0
- package/lib/commonjs/mol-state/index.js +17 -0
- package/lib/commonjs/mol-state/object.js +189 -0
- package/lib/commonjs/mol-state/state/builder.js +276 -0
- package/lib/commonjs/mol-state/state/selection.js +377 -0
- package/lib/commonjs/mol-state/state.js +992 -0
- package/lib/commonjs/mol-state/transform.js +199 -0
- package/lib/commonjs/mol-state/transformer.js +119 -0
- package/lib/commonjs/mol-state/tree/immutable.js +176 -0
- package/lib/commonjs/mol-state/tree/spine.js +86 -0
- package/lib/commonjs/mol-state/tree/transient.js +301 -0
- package/lib/commonjs/mol-state/tree.js +13 -0
- package/lib/commonjs/mol-task/execution/observable.d.ts +46 -0
- package/lib/commonjs/mol-task/execution/observable.js +246 -0
- package/lib/commonjs/mol-task/execution/progress.d.ts +22 -0
- package/lib/commonjs/mol-task/execution/progress.js +29 -0
- package/lib/commonjs/mol-task/execution/runtime-context.d.ts +24 -0
- package/lib/commonjs/mol-task/execution/runtime-context.js +15 -0
- package/lib/commonjs/mol-task/execution/synchronous.d.ts +12 -0
- package/lib/commonjs/mol-task/execution/synchronous.js +19 -0
- package/lib/commonjs/mol-task/index.d.ts +12 -0
- package/lib/commonjs/mol-task/index.js +21 -0
- package/lib/commonjs/mol-task/task.d.ts +49 -0
- package/lib/commonjs/mol-task/task.js +83 -0
- package/lib/commonjs/mol-task/util/chunked.d.ts +9 -0
- package/lib/commonjs/mol-task/util/chunked.js +53 -0
- package/lib/commonjs/mol-task/util/multistep.d.ts +10 -0
- package/lib/commonjs/mol-task/util/multistep.js +18 -0
- package/lib/commonjs/mol-task/util/scheduler.d.ts +13 -0
- package/lib/commonjs/mol-task/util/scheduler.js +194 -0
- package/lib/commonjs/mol-task/util/user-timing.d.ts +11 -0
- package/lib/commonjs/mol-task/util/user-timing.js +32 -0
- package/lib/commonjs/mol-theme/clipping.js +185 -0
- package/lib/commonjs/mol-theme/color/atom-id.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/atom-id.js +84 -0
- package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js +70 -0
- package/lib/commonjs/mol-theme/color/chain-id.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/chain-id.js +118 -0
- package/lib/commonjs/mol-theme/color/element-index.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/element-index.js +75 -0
- package/lib/commonjs/mol-theme/color/element-symbol.d.ts +10 -10
- package/lib/commonjs/mol-theme/color/entity-id.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/entity-source.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/entity-source.js +156 -0
- package/lib/commonjs/mol-theme/color/hydrophobicity.js +96 -0
- package/lib/commonjs/mol-theme/color/illustrative.d.ts +6 -6
- package/lib/commonjs/mol-theme/color/model-index.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/model-index.js +71 -0
- package/lib/commonjs/mol-theme/color/molecule-type.js +85 -0
- package/lib/commonjs/mol-theme/color/occupancy.js +66 -0
- package/lib/commonjs/mol-theme/color/operator-hkl.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/operator-hkl.js +114 -0
- package/lib/commonjs/mol-theme/color/operator-name.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/operator-name.js +76 -0
- package/lib/commonjs/mol-theme/color/partial-charge.js +63 -0
- package/lib/commonjs/mol-theme/color/polymer-id.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/polymer-id.js +126 -0
- package/lib/commonjs/mol-theme/color/polymer-index.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/polymer-index.js +86 -0
- package/lib/commonjs/mol-theme/color/residue-name.js +138 -0
- package/lib/commonjs/mol-theme/color/secondary-structure.js +130 -0
- package/lib/commonjs/mol-theme/color/sequence-id.js +111 -0
- package/lib/commonjs/mol-theme/color/shape-group.js +43 -0
- package/lib/commonjs/mol-theme/color/uncertainty.js +70 -0
- package/lib/commonjs/mol-theme/color/uniform.js +43 -0
- package/lib/commonjs/mol-theme/color/unit-index.d.ts +2 -2
- package/lib/commonjs/mol-theme/color/unit-index.js +73 -0
- package/lib/commonjs/mol-theme/color/volume-value.js +57 -0
- package/lib/commonjs/mol-theme/color.d.ts +19 -19
- package/lib/commonjs/mol-theme/label.js +362 -0
- package/lib/commonjs/mol-theme/overpaint.js +132 -0
- package/lib/commonjs/mol-theme/size/physical.js +70 -0
- package/lib/commonjs/mol-theme/size/shape-group.js +42 -0
- package/lib/commonjs/mol-theme/size/uncertainty.js +62 -0
- package/lib/commonjs/mol-theme/size/uniform.js +38 -0
- package/lib/commonjs/mol-theme/size.js +36 -0
- package/lib/commonjs/mol-theme/substance.js +141 -0
- package/lib/commonjs/mol-theme/theme.js +136 -0
- package/lib/commonjs/mol-theme/transparency.js +140 -0
- package/lib/commonjs/mol-util/array.d.ts +37 -0
- package/lib/commonjs/mol-util/array.js +177 -0
- package/lib/commonjs/mol-util/assets.d.ts +58 -0
- package/lib/commonjs/mol-util/assets.js +153 -0
- package/lib/commonjs/mol-util/async-queue.d.ts +14 -0
- package/lib/commonjs/mol-util/async-queue.js +54 -0
- package/lib/commonjs/mol-util/binding.d.ts +32 -0
- package/lib/commonjs/mol-util/binding.js +116 -0
- package/lib/commonjs/mol-util/bit-flags.d.ts +13 -0
- package/lib/commonjs/mol-util/bit-flags.js +20 -0
- package/lib/commonjs/mol-util/clip.d.ts +1 -1
- package/lib/commonjs/mol-util/clip.js +97 -0
- package/lib/commonjs/mol-util/color/color.d.ts +68 -0
- package/lib/commonjs/mol-util/color/color.js +153 -0
- package/lib/commonjs/mol-util/color/distinct.js +146 -0
- package/lib/commonjs/mol-util/color/index.d.ts +7 -0
- package/lib/commonjs/mol-util/color/index.js +15 -0
- package/lib/commonjs/mol-util/color/lists.d.ts +74 -0
- package/lib/commonjs/mol-util/color/lists.js +91 -0
- package/lib/commonjs/mol-util/color/names.d.ts +167 -0
- package/lib/commonjs/mol-util/color/names.js +175 -0
- package/lib/commonjs/mol-util/color/palette.d.ts +3 -3
- package/lib/commonjs/mol-util/color/palette.js +89 -0
- package/lib/commonjs/mol-util/color/params.js +19 -0
- package/lib/commonjs/mol-util/color/scale.d.ts +31 -0
- package/lib/commonjs/mol-util/color/scale.js +84 -0
- package/lib/commonjs/mol-util/color/spaces/hcl.d.ts +46 -0
- package/lib/commonjs/mol-util/color/spaces/hcl.js +106 -0
- package/lib/commonjs/mol-util/color/spaces/lab.d.ts +39 -0
- package/lib/commonjs/mol-util/color/spaces/lab.js +152 -0
- package/lib/commonjs/mol-util/color/swatches.d.ts +8 -0
- package/lib/commonjs/mol-util/color/swatches.js +25 -0
- package/lib/commonjs/mol-util/console-logger.d.ts +13 -0
- package/lib/commonjs/mol-util/console-logger.js +52 -0
- package/lib/commonjs/mol-util/data-source.d.ts +48 -0
- package/lib/commonjs/mol-util/data-source.js +389 -0
- package/lib/commonjs/mol-util/date.d.ts +7 -0
- package/lib/commonjs/mol-util/date.js +24 -0
- package/lib/commonjs/mol-util/debug.d.ts +18 -0
- package/lib/commonjs/mol-util/debug.js +46 -0
- package/lib/commonjs/mol-util/download.d.ts +6 -0
- package/lib/commonjs/mol-util/download.js +74 -0
- package/lib/commonjs/mol-util/file-info.d.ts +20 -0
- package/lib/commonjs/mol-util/file-info.js +54 -0
- package/lib/commonjs/mol-util/graphql-client.d.ts +44 -0
- package/lib/commonjs/mol-util/graphql-client.js +67 -0
- package/lib/commonjs/mol-util/id-factory.d.ts +7 -0
- package/lib/commonjs/mol-util/id-factory.js +21 -0
- package/lib/commonjs/mol-util/image.d.ts +18 -0
- package/lib/commonjs/mol-util/image.js +46 -0
- package/lib/commonjs/mol-util/index.d.ts +29 -0
- package/lib/commonjs/mol-util/index.js +222 -0
- package/lib/commonjs/mol-util/input/event-offset.d.ts +7 -0
- package/lib/commonjs/mol-util/input/event-offset.js +27 -0
- package/lib/commonjs/mol-util/input/input-observer.d.ts +136 -0
- package/lib/commonjs/mol-util/input/input-observer.js +593 -0
- package/lib/commonjs/mol-util/is-little-endian.d.ts +6 -0
- package/lib/commonjs/mol-util/is-little-endian.js +18 -0
- package/lib/commonjs/mol-util/legend.d.ts +20 -0
- package/lib/commonjs/mol-util/legend.js +17 -0
- package/lib/commonjs/mol-util/log-entry.d.ts +18 -0
- package/lib/commonjs/mol-util/log-entry.js +21 -0
- package/lib/commonjs/mol-util/lru-cache.d.ts +21 -0
- package/lib/commonjs/mol-util/lru-cache.js +47 -0
- package/lib/commonjs/mol-util/make-dir.d.ts +6 -0
- package/lib/commonjs/mol-util/make-dir.js +24 -0
- package/lib/commonjs/mol-util/map.d.ts +11 -0
- package/lib/commonjs/mol-util/map.js +36 -0
- package/lib/commonjs/mol-util/marker-action.d.ts +49 -0
- package/lib/commonjs/mol-util/marker-action.js +286 -0
- package/lib/commonjs/mol-util/mask.d.ts +48 -0
- package/lib/commonjs/mol-util/mask.js +191 -0
- package/lib/commonjs/mol-util/material.js +43 -0
- package/lib/commonjs/mol-util/memoize.d.ts +9 -0
- package/lib/commonjs/mol-util/memoize.js +45 -0
- package/lib/commonjs/mol-util/monadic-parser.d.ts +119 -0
- package/lib/commonjs/mol-util/monadic-parser.js +490 -0
- package/lib/commonjs/mol-util/now.d.ts +13 -0
- package/lib/commonjs/mol-util/now.js +47 -0
- package/lib/commonjs/mol-util/number-packing.d.ts +11 -0
- package/lib/commonjs/mol-util/number-packing.js +36 -0
- package/lib/commonjs/mol-util/number.d.ts +26 -0
- package/lib/commonjs/mol-util/number.js +85 -0
- package/lib/commonjs/mol-util/object.d.ts +23 -0
- package/lib/commonjs/mol-util/object.js +127 -0
- package/lib/commonjs/mol-util/param-definition.js +612 -0
- package/lib/commonjs/mol-util/param-mapping.js +26 -0
- package/lib/commonjs/mol-util/performance-monitor.d.ts +14 -0
- package/lib/commonjs/mol-util/performance-monitor.js +73 -0
- package/lib/commonjs/mol-util/polyfill.d.ts +5 -0
- package/lib/commonjs/mol-util/polyfill.js +610 -0
- package/lib/commonjs/mol-util/read.d.ts +11 -0
- package/lib/commonjs/mol-util/read.js +70 -0
- package/lib/commonjs/mol-util/reference-cache.d.ts +28 -0
- package/lib/commonjs/mol-util/reference-cache.js +57 -0
- package/lib/commonjs/mol-util/retry-if.d.ts +11 -0
- package/lib/commonjs/mol-util/retry-if.js +48 -0
- package/lib/commonjs/mol-util/rx-event-helper.d.ts +15 -0
- package/lib/commonjs/mol-util/rx-event-helper.js +48 -0
- package/lib/commonjs/mol-util/set.d.ts +26 -0
- package/lib/commonjs/mol-util/set.js +133 -0
- package/lib/commonjs/mol-util/sleep.d.ts +6 -0
- package/lib/commonjs/mol-util/sleep.js +13 -0
- package/lib/commonjs/mol-util/string-builder.d.ts +38 -0
- package/lib/commonjs/mol-util/string-builder.js +164 -0
- package/lib/commonjs/mol-util/string.d.ts +31 -0
- package/lib/commonjs/mol-util/string.js +110 -0
- package/lib/commonjs/mol-util/type-helpers.d.ts +35 -0
- package/lib/commonjs/mol-util/type-helpers.js +23 -0
- package/lib/commonjs/mol-util/url.d.ts +7 -0
- package/lib/commonjs/mol-util/url.js +21 -0
- package/lib/commonjs/mol-util/uuid.d.ts +16 -0
- package/lib/commonjs/mol-util/uuid.js +40 -0
- package/lib/commonjs/mol-util/value-cell.d.ts +41 -0
- package/lib/commonjs/mol-util/value-cell.js +55 -0
- package/lib/commonjs/mol-util/zip/bin.d.ts +17 -0
- package/lib/commonjs/mol-util/zip/bin.js +122 -0
- package/lib/commonjs/mol-util/zip/checksum.d.ts +10 -0
- package/lib/commonjs/mol-util/zip/checksum.js +52 -0
- package/lib/commonjs/mol-util/zip/deflate.d.ts +10 -0
- package/lib/commonjs/mol-util/zip/deflate.js +404 -0
- package/lib/commonjs/mol-util/zip/huffman.d.ts +17 -0
- package/lib/commonjs/mol-util/zip/huffman.js +112 -0
- package/lib/commonjs/mol-util/zip/inflate.d.ts +10 -0
- package/lib/commonjs/mol-util/zip/inflate.js +232 -0
- package/lib/commonjs/mol-util/zip/util.d.ts +40 -0
- package/lib/commonjs/mol-util/zip/util.js +136 -0
- package/lib/commonjs/mol-util/zip/zip.d.ts +29 -0
- package/lib/commonjs/mol-util/zip/zip.js +376 -0
- package/lib/commonjs/servers/common/file-handle.d.ts +8 -0
- package/lib/commonjs/servers/common/file-handle.js +70 -0
- package/lib/commonjs/servers/common/swagger-ui/index.d.ts +16 -0
- package/lib/commonjs/servers/common/swagger-ui/index.js +31 -0
- package/lib/commonjs/servers/common/swagger-ui/indexTemplate.d.ts +1 -0
- package/lib/commonjs/servers/common/swagger-ui/indexTemplate.js +5 -0
- package/lib/commonjs/servers/common/util.d.ts +7 -0
- package/lib/commonjs/servers/common/util.js +31 -0
- package/lib/commonjs/servers/model/config.js +267 -0
- package/lib/commonjs/servers/model/preprocess/converter.d.ts +8 -0
- package/lib/commonjs/servers/model/preprocess/converter.js +81 -0
- package/lib/commonjs/servers/model/preprocess/master.js +74 -0
- package/lib/commonjs/servers/model/preprocess/parallel.js +124 -0
- package/lib/commonjs/servers/model/preprocess/preprocess.js +102 -0
- package/lib/commonjs/servers/model/preprocess/util.d.ts +8 -0
- package/lib/commonjs/servers/model/preprocess/util.js +20 -0
- package/lib/commonjs/servers/model/preprocess.js +20 -0
- package/lib/commonjs/servers/model/properties/pdbe.js +21 -0
- package/lib/commonjs/servers/model/properties/providers/pdbe.js +126 -0
- package/lib/commonjs/servers/model/properties/providers/wwpdb.js +132 -0
- package/lib/commonjs/servers/model/properties/wwpdb.js +19 -0
- package/lib/commonjs/servers/model/property-provider.js +63 -0
- package/lib/commonjs/servers/model/query/atoms.js +110 -0
- package/lib/commonjs/servers/model/query/schemas.d.ts +10 -0
- package/lib/commonjs/servers/model/query/schemas.js +61 -0
- package/lib/commonjs/servers/model/query.js +80 -0
- package/lib/commonjs/servers/model/server/api-local.js +106 -0
- package/lib/commonjs/servers/model/server/api-schema.js +183 -0
- package/lib/commonjs/servers/model/server/api-web-multiple.js +14 -0
- package/lib/commonjs/servers/model/server/api-web.js +191 -0
- package/lib/commonjs/servers/model/server/api.js +294 -0
- package/lib/commonjs/servers/model/server/cache.js +88 -0
- package/lib/commonjs/servers/model/server/jobs.js +88 -0
- package/lib/commonjs/servers/model/server/query.js +377 -0
- package/lib/commonjs/servers/model/server/structure-wrapper.js +354 -0
- package/lib/commonjs/servers/model/server.js +66 -0
- package/lib/commonjs/servers/model/test.d.ts +0 -0
- package/lib/commonjs/servers/model/test.js +82 -0
- package/lib/commonjs/servers/model/utils/fetch-props-pdbe.d.ts +6 -0
- package/lib/commonjs/servers/model/utils/fetch-props-pdbe.js +118 -0
- package/lib/commonjs/servers/model/utils/fetch-retry.d.ts +7 -0
- package/lib/commonjs/servers/model/utils/fetch-retry.js +43 -0
- package/lib/commonjs/servers/model/utils/tar.d.ts +22 -0
- package/lib/commonjs/servers/model/utils/tar.js +179 -0
- package/lib/commonjs/servers/model/utils/writer.d.ts +77 -0
- package/lib/commonjs/servers/model/utils/writer.js +223 -0
- package/lib/commonjs/servers/model/version.d.ts +6 -0
- package/lib/commonjs/servers/model/version.js +10 -0
- package/lib/commonjs/servers/plugin-state/api-schema.d.ts +107 -0
- package/lib/commonjs/servers/plugin-state/api-schema.js +135 -0
- package/lib/commonjs/servers/plugin-state/config.d.ts +12 -0
- package/lib/commonjs/servers/plugin-state/config.js +25 -0
- package/lib/commonjs/servers/plugin-state/index.d.ts +6 -0
- package/lib/commonjs/servers/plugin-state/index.js +208 -0
- package/lib/commonjs/servers/plugin-state/version.d.ts +1 -0
- package/lib/commonjs/servers/plugin-state/version.js +5 -0
- package/lib/commonjs/servers/volume/common/binary-schema.d.ts +42 -0
- package/lib/commonjs/servers/volume/common/binary-schema.js +176 -0
- package/lib/commonjs/servers/volume/common/data-format.d.ts +53 -0
- package/lib/commonjs/servers/volume/common/data-format.js +70 -0
- package/lib/commonjs/servers/volume/common/file.d.ts +12 -0
- package/lib/commonjs/servers/volume/common/file.js +86 -0
- package/lib/commonjs/servers/volume/config.d.ts +47 -0
- package/lib/commonjs/servers/volume/config.js +197 -0
- package/lib/commonjs/servers/volume/pack/data-model.js +43 -0
- package/lib/commonjs/servers/volume/pack/downsampling.js +168 -0
- package/lib/commonjs/servers/volume/pack/format/ccp4.js +72 -0
- package/lib/commonjs/servers/volume/pack/format/dsn6.js +76 -0
- package/lib/commonjs/servers/volume/pack/format.js +82 -0
- package/lib/commonjs/servers/volume/pack/main.js +186 -0
- package/lib/commonjs/servers/volume/pack/sampling.js +272 -0
- package/lib/commonjs/servers/volume/pack/version.d.ts +1 -0
- package/lib/commonjs/servers/volume/pack/version.js +5 -0
- package/lib/commonjs/servers/volume/pack/writer.js +86 -0
- package/lib/commonjs/servers/volume/pack.js +62 -0
- package/lib/commonjs/servers/volume/query.d.ts +10 -0
- package/lib/commonjs/servers/volume/query.js +79 -0
- package/lib/commonjs/servers/volume/server/algebra/box.d.ts +32 -0
- package/lib/commonjs/servers/volume/server/algebra/box.js +123 -0
- package/lib/commonjs/servers/volume/server/algebra/coordinate.d.ts +65 -0
- package/lib/commonjs/servers/volume/server/algebra/coordinate.js +137 -0
- package/lib/commonjs/servers/volume/server/api.d.ts +20 -0
- package/lib/commonjs/servers/volume/server/api.js +115 -0
- package/lib/commonjs/servers/volume/server/local-api.d.ts +36 -0
- package/lib/commonjs/servers/volume/server/local-api.js +145 -0
- package/lib/commonjs/servers/volume/server/query/compose.d.ts +9 -0
- package/lib/commonjs/servers/volume/server/query/compose.js +124 -0
- package/lib/commonjs/servers/volume/server/query/data-model.d.ts +91 -0
- package/lib/commonjs/servers/volume/server/query/data-model.js +10 -0
- package/lib/commonjs/servers/volume/server/query/encode.d.ts +9 -0
- package/lib/commonjs/servers/volume/server/query/encode.js +162 -0
- package/lib/commonjs/servers/volume/server/query/execute.d.ts +9 -0
- package/lib/commonjs/servers/volume/server/query/execute.js +254 -0
- package/lib/commonjs/servers/volume/server/query/identify.d.ts +11 -0
- package/lib/commonjs/servers/volume/server/query/identify.js +112 -0
- package/lib/commonjs/servers/volume/server/state.d.ts +12 -0
- package/lib/commonjs/servers/volume/server/state.js +16 -0
- package/lib/commonjs/servers/volume/server/version.d.ts +2 -0
- package/lib/commonjs/servers/volume/server/version.js +6 -0
- package/lib/commonjs/servers/volume/server/web-api.d.ts +10 -0
- package/lib/commonjs/servers/volume/server/web-api.js +226 -0
- package/lib/commonjs/servers/volume/server/web-schema.d.ts +245 -0
- package/lib/commonjs/servers/volume/server/web-schema.js +263 -0
- package/lib/commonjs/servers/volume/server.d.ts +10 -0
- package/lib/commonjs/servers/volume/server.js +59 -0
- package/lib/examples/alpha-orbitals/index.html +61 -61
- package/lib/examples/basic-wrapper/index.html +137 -137
- package/lib/examples/lighting/index.html +88 -88
- package/lib/examples/proteopedia-wrapper/index.html +236 -236
- package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/mol-geo/geometry/lines/lines.d.ts +1 -0
- package/lib/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/mol-math/geometry/primitives/sphere3d.d.ts +1 -1
- package/lib/mol-math/geometry/primitives/sphere3d.js +17 -4
- package/lib/mol-model/structure/structure/element/loci.d.ts +1 -1
- package/lib/mol-model/structure/structure/element/loci.js +4 -2
- package/lib/mol-plugin/behavior/dynamic/representation.d.ts +1 -1
- package/lib/mol-plugin/behavior/dynamic/representation.js +11 -6
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +3 -2
- package/lib/mol-plugin/behavior/static/representation.js +1 -1
- package/lib/mol-plugin/version.js +2 -2
- 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 +127 -127
- 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-repr/shape/loci/common.d.ts +1 -1
- package/lib/mol-repr/shape/loci/common.js +3 -3
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts +1 -1
- package/lib/mol-repr/structure/visual/molecular-surface-mesh.js +2 -2
- package/lib/mol-script/language/builder.d.ts +0 -1
- package/lib/mol-state/transform.js +12 -2
- package/package.json +160 -160
|
@@ -0,0 +1,750 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
/**
|
|
3
|
+
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
|
4
|
+
*
|
|
5
|
+
* Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
|
|
6
|
+
*
|
|
7
|
+
* @author molstar/ciftools package
|
|
8
|
+
*/
|
|
9
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
10
|
+
exports.CifCore_Aliases = exports.CifCore_Schema = void 0;
|
|
11
|
+
var db_1 = require("../../../../mol-data/db");
|
|
12
|
+
var Schema = db_1.Column.Schema;
|
|
13
|
+
var float = Schema.float;
|
|
14
|
+
var int = Schema.int;
|
|
15
|
+
var str = Schema.str;
|
|
16
|
+
var Matrix = Schema.Matrix;
|
|
17
|
+
exports.CifCore_Schema = {
|
|
18
|
+
/**
|
|
19
|
+
* The CATEGORY of data items used to describe the parameters of
|
|
20
|
+
* the crystal unit cell and their measurement.
|
|
21
|
+
*/
|
|
22
|
+
cell: {
|
|
23
|
+
/**
|
|
24
|
+
* The angle between the bounding cell axes.
|
|
25
|
+
*/
|
|
26
|
+
angle_alpha: float,
|
|
27
|
+
/**
|
|
28
|
+
* The angle between the bounding cell axes.
|
|
29
|
+
*/
|
|
30
|
+
angle_beta: float,
|
|
31
|
+
/**
|
|
32
|
+
* The angle between the bounding cell axes.
|
|
33
|
+
*/
|
|
34
|
+
angle_gamma: float,
|
|
35
|
+
/**
|
|
36
|
+
* The number of the formula units in the unit cell as specified
|
|
37
|
+
* by _chemical_formula.structural, _chemical_formula.moiety or
|
|
38
|
+
* _chemical_formula.sum.
|
|
39
|
+
*/
|
|
40
|
+
formula_units_z: int,
|
|
41
|
+
/**
|
|
42
|
+
* The length of each cell axis.
|
|
43
|
+
*/
|
|
44
|
+
length_a: float,
|
|
45
|
+
/**
|
|
46
|
+
* The length of each cell axis.
|
|
47
|
+
*/
|
|
48
|
+
length_b: float,
|
|
49
|
+
/**
|
|
50
|
+
* The length of each cell axis.
|
|
51
|
+
*/
|
|
52
|
+
length_c: float,
|
|
53
|
+
/**
|
|
54
|
+
* Volume of the crystal unit cell.
|
|
55
|
+
*/
|
|
56
|
+
volume: float,
|
|
57
|
+
},
|
|
58
|
+
/**
|
|
59
|
+
* The CATEGORY of data items which describe the composition and
|
|
60
|
+
* chemical properties of the compound under study. The formula data
|
|
61
|
+
* items must be consistent with the density, unit-cell and Z values.
|
|
62
|
+
*/
|
|
63
|
+
chemical: {
|
|
64
|
+
/**
|
|
65
|
+
* The temperature at which a crystalline solid changes to a liquid.
|
|
66
|
+
*/
|
|
67
|
+
melting_point: float,
|
|
68
|
+
/**
|
|
69
|
+
* Trivial name by which the compound is commonly known.
|
|
70
|
+
*/
|
|
71
|
+
name_common: str,
|
|
72
|
+
/**
|
|
73
|
+
* IUPAC or Chemical Abstracts full name of compound.
|
|
74
|
+
*/
|
|
75
|
+
name_systematic: str,
|
|
76
|
+
},
|
|
77
|
+
/**
|
|
78
|
+
* The CATEGORY of data items which specify the composition and chemical
|
|
79
|
+
* properties of the compound. The formula data items must agree
|
|
80
|
+
* with those that specify the density, unit-cell and Z values.
|
|
81
|
+
*
|
|
82
|
+
* The following rules apply to the construction of the data items
|
|
83
|
+
* _chemical_formula.analytical, *.structural and *.sum. For the
|
|
84
|
+
* data item *.moiety the formula construction is broken up into
|
|
85
|
+
* residues or moieties, i.e. groups of atoms that form a molecular
|
|
86
|
+
* unit or molecular ion. The rules given below apply within each
|
|
87
|
+
* moiety but different requirements apply to the way that moieties
|
|
88
|
+
* are connected (see _chemical_formula.moiety).
|
|
89
|
+
*
|
|
90
|
+
* 1. Only recognized element symbols may be used.
|
|
91
|
+
*
|
|
92
|
+
* 2. Each element symbol is followed by a 'count' number. A count of
|
|
93
|
+
* '1' may be omitted.
|
|
94
|
+
*
|
|
95
|
+
* 3. A space or parenthesis must separate each cluster of (element
|
|
96
|
+
* symbol + count).
|
|
97
|
+
*
|
|
98
|
+
* 4. Where a group of elements is enclosed in parentheses, the
|
|
99
|
+
* multiplier for the group must follow the closing parentheses.
|
|
100
|
+
* That is, all element and group multipliers are assumed to be
|
|
101
|
+
* printed as subscripted numbers. [An exception to this rule
|
|
102
|
+
* exists for *.moiety formulae where pre- and post-multipliers
|
|
103
|
+
* are permitted for molecular units].
|
|
104
|
+
*
|
|
105
|
+
* 5. Unless the elements are ordered in a manner that corresponds to
|
|
106
|
+
* their chemical structure, as in _chemical_formula.structural,
|
|
107
|
+
* the order of the elements within any group or moiety
|
|
108
|
+
* depends on whether or not carbon is present. If carbon is
|
|
109
|
+
* present, the order should be: C, then H, then the other
|
|
110
|
+
* elements in alphabetical order of their symbol. If carbon is
|
|
111
|
+
* not present, the elements are listed purely in alphabetic order
|
|
112
|
+
* of their symbol. This is the 'Hill' system used by Chemical
|
|
113
|
+
* Abstracts. This ordering is used in _chemical_formula.moiety
|
|
114
|
+
* and _chemical_formula.sum.
|
|
115
|
+
*
|
|
116
|
+
* _chemical_formula.IUPAC '[Mo (C O)4 (C18 H33 P)2]'
|
|
117
|
+
* _chemical_formula.moiety 'C40 H66 Mo O4 P2'
|
|
118
|
+
* _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
|
|
119
|
+
* _chemical_formula.sum 'C40 H66 Mo O4 P2'
|
|
120
|
+
* _chemical_formula.weight 768.81
|
|
121
|
+
*/
|
|
122
|
+
chemical_formula: {
|
|
123
|
+
/**
|
|
124
|
+
* Formula with each discrete bonded residue or ion shown as a
|
|
125
|
+
* separate moiety. See above CHEMICAL_FORMULA for rules
|
|
126
|
+
* for writing chemical formulae. In addition to the general
|
|
127
|
+
* formulae requirements, the following rules apply:
|
|
128
|
+
* 1. Moieties are separated by commas ','.
|
|
129
|
+
* 2. The order of elements within a moiety follows general rule
|
|
130
|
+
* 5 in CHEMICAL_FORMULA.
|
|
131
|
+
* 3. Parentheses are not used within moieties but may surround
|
|
132
|
+
* a moiety. Parentheses may not be nested.
|
|
133
|
+
* 4. Charges should be placed at the end of the moiety. The
|
|
134
|
+
* Singlege '+' or '-' may be preceded by a numerical multiplier
|
|
135
|
+
* and should be separated from the last (element symbol +
|
|
136
|
+
* count) by a space. Pre- or post-multipliers may be used for
|
|
137
|
+
* individual moieties.
|
|
138
|
+
*/
|
|
139
|
+
moiety: str,
|
|
140
|
+
/**
|
|
141
|
+
* Chemical formulae in which all discrete bonded residues and ions are
|
|
142
|
+
* summed over the constituent elements, following the ordering given
|
|
143
|
+
* in rule 5 of the CATEGORY description. Parentheses normally not used.
|
|
144
|
+
*/
|
|
145
|
+
sum: str,
|
|
146
|
+
/**
|
|
147
|
+
* Mass corresponding to the formulae _chemical_formula.structural,
|
|
148
|
+
* *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
|
|
149
|
+
* parameters yield the density given as _exptl_crystal.density_diffrn.
|
|
150
|
+
*/
|
|
151
|
+
weight: float,
|
|
152
|
+
},
|
|
153
|
+
/**
|
|
154
|
+
* The CATEGORY of data items used to specify space group
|
|
155
|
+
* information about the crystal used in the diffraction measurements.
|
|
156
|
+
*
|
|
157
|
+
* Space-group types are identified by their number as listed in
|
|
158
|
+
* International Tables for Crystallography Volume A, or by their
|
|
159
|
+
* Schoenflies symbol. Specific settings of the space groups can
|
|
160
|
+
* be identified by their Hall symbol, by specifying their
|
|
161
|
+
* symmetry operations or generators, or by giving the
|
|
162
|
+
* transformation that relates the specific setting to the
|
|
163
|
+
* reference setting based on International Tables Volume A and
|
|
164
|
+
* stored in this dictionary.
|
|
165
|
+
*
|
|
166
|
+
* The commonly used Hermann-Mauguin symbol determines the
|
|
167
|
+
* space-group type uniquely but several different Hermann-Mauguin
|
|
168
|
+
* symbols may refer to the same space-group type. A
|
|
169
|
+
* Hermann-Mauguin symbol contains information on the choice of
|
|
170
|
+
* the basis, but not on the choice of origin.
|
|
171
|
+
*
|
|
172
|
+
* Ref: International Tables for Crystallography (2002). Volume A,
|
|
173
|
+
* Space-group symmetry, edited by Th. Hahn, 5th ed.
|
|
174
|
+
* Dordrecht: Kluwer Academic Publishers.
|
|
175
|
+
*/
|
|
176
|
+
space_group: {
|
|
177
|
+
/**
|
|
178
|
+
* The name of the system of geometric crystal classes of space
|
|
179
|
+
* groups (crystal system) to which the space group belongs.
|
|
180
|
+
* Note that rhombohedral space groups belong to the
|
|
181
|
+
* trigonal system.
|
|
182
|
+
*/
|
|
183
|
+
crystal_system: str,
|
|
184
|
+
/**
|
|
185
|
+
* The number as assigned in International Tables for Crystallography
|
|
186
|
+
* Vol. A, specifying the proper affine class (i.e. the orientation
|
|
187
|
+
* preserving affine class) of space groups (crystallographic space
|
|
188
|
+
* group type) to which the space group belongs. This number defines
|
|
189
|
+
* the space group type but not the coordinate system expressed.
|
|
190
|
+
*/
|
|
191
|
+
it_number: int,
|
|
192
|
+
/**
|
|
193
|
+
* The full international Hermann-Mauguin space-group symbol as
|
|
194
|
+
* defined in Section 2.2.3 and given as the second item of the
|
|
195
|
+
* second line of each of the space-group tables of Part 7 of
|
|
196
|
+
* International Tables for Crystallography Volume A (2002).
|
|
197
|
+
*
|
|
198
|
+
* Each component of the space-group name is separated by a
|
|
199
|
+
* space or an underscore character. The use of a space is
|
|
200
|
+
* strongly recommended. The underscore is only retained
|
|
201
|
+
* because it was used in old CIFs. It should not be used in
|
|
202
|
+
* new CIFs.
|
|
203
|
+
*
|
|
204
|
+
* Subscripts should appear without special symbols. Bars should
|
|
205
|
+
* be given as negative signs before the numbers to which they
|
|
206
|
+
* apply. The commonly used Hermann-Mauguin symbol determines the
|
|
207
|
+
* space-group type uniquely but a given space-group type may
|
|
208
|
+
* be described by more than one Hermann-Mauguin symbol. The
|
|
209
|
+
* space-group type is best described using
|
|
210
|
+
* _space_group.IT_number or _space_group.name_Schoenflies. The
|
|
211
|
+
* full international Hermann-Mauguin symbol contains information
|
|
212
|
+
* about the choice of basis for monoclinic and orthorhombic
|
|
213
|
+
* space groups but does not give information about the choice
|
|
214
|
+
* of origin. To define the setting uniquely use
|
|
215
|
+
* _space_group.name_Hall, or list the symmetry operations
|
|
216
|
+
* or generators.
|
|
217
|
+
*
|
|
218
|
+
* Ref: International Tables for Crystallography (2002). Volume A,
|
|
219
|
+
* Space-group symmetry, edited by Th. Hahn, 5th ed.
|
|
220
|
+
* Dordrecht: Kluwer Academic Publishers.
|
|
221
|
+
*/
|
|
222
|
+
'name_h-m_full': str,
|
|
223
|
+
},
|
|
224
|
+
/**
|
|
225
|
+
* The CATEGORY of data items used to describe symmetry equivalent sites
|
|
226
|
+
* in the crystal unit cell.
|
|
227
|
+
*/
|
|
228
|
+
space_group_symop: {
|
|
229
|
+
/**
|
|
230
|
+
* A parsable string giving one of the symmetry operations of the
|
|
231
|
+
* space group in algebraic form. If W is a matrix representation
|
|
232
|
+
* of the rotational part of the symmetry operation defined by the
|
|
233
|
+
* positions and signs of x, y and z, and w is a column of
|
|
234
|
+
* translations defined by fractions, an equivalent position
|
|
235
|
+
* X' is generated from a given position X by the equation
|
|
236
|
+
*
|
|
237
|
+
* X' = WX + w
|
|
238
|
+
*
|
|
239
|
+
* (Note: X is used to represent bold_italics_x in International
|
|
240
|
+
* Tables for Crystallography Vol. A, Part 5)
|
|
241
|
+
*
|
|
242
|
+
* When a list of symmetry operations is given, it must contain
|
|
243
|
+
* a complete set of coordinate representatives which generates
|
|
244
|
+
* all the operations of the space group by the addition of
|
|
245
|
+
* all primitive translations of the space group. Such
|
|
246
|
+
* representatives are to be found as the coordinates of
|
|
247
|
+
* the general-equivalent position in International Tables for
|
|
248
|
+
* Crystallography Vol. A (2002), to which it is necessary to
|
|
249
|
+
* add any centring translations shown above the
|
|
250
|
+
* general-equivalent position.
|
|
251
|
+
*
|
|
252
|
+
* That is to say, it is necessary to list explicitly all the
|
|
253
|
+
* symmetry operations required to generate all the atoms in
|
|
254
|
+
* the unit cell defined by the setting used.
|
|
255
|
+
*/
|
|
256
|
+
operation_xyz: str,
|
|
257
|
+
},
|
|
258
|
+
/**
|
|
259
|
+
* The CATEGORY of data items used to specify the geometry bonds in the
|
|
260
|
+
* structural model as derived from the atomic sites.
|
|
261
|
+
*/
|
|
262
|
+
geom_bond: {
|
|
263
|
+
/**
|
|
264
|
+
* This label is a unique identifier for a particular site in the
|
|
265
|
+
* asymmetric unit of the crystal unit cell.
|
|
266
|
+
*/
|
|
267
|
+
atom_site_label_1: str,
|
|
268
|
+
/**
|
|
269
|
+
* This label is a unique identifier for a particular site in the
|
|
270
|
+
* asymmetric unit of the crystal unit cell.
|
|
271
|
+
*/
|
|
272
|
+
atom_site_label_2: str,
|
|
273
|
+
/**
|
|
274
|
+
* Intramolecular bond distance between the sites identified
|
|
275
|
+
* by _geom_bond.id
|
|
276
|
+
*/
|
|
277
|
+
distance: float,
|
|
278
|
+
/**
|
|
279
|
+
* This code signals whether the angle is referred to in a
|
|
280
|
+
* publication or should be placed in a table of significant angles.
|
|
281
|
+
*/
|
|
282
|
+
publ_flag: str,
|
|
283
|
+
/**
|
|
284
|
+
* The set of data items which specify the symmetry operation codes
|
|
285
|
+
* which must be applied to the atom sites involved in the geometry angle.
|
|
286
|
+
*
|
|
287
|
+
* The symmetry code of each atom site as the symmetry-equivalent position
|
|
288
|
+
* number 'n' and the cell translation number 'pqr'. These numbers are
|
|
289
|
+
* combined to form the code 'n pqr' or n_pqr.
|
|
290
|
+
*
|
|
291
|
+
* The character string n_pqr is composed as follows:
|
|
292
|
+
*
|
|
293
|
+
* n refers to the symmetry operation that is applied to the
|
|
294
|
+
* coordinates stored in _atom_site.fract_xyz. It must match a
|
|
295
|
+
* number given in _symmetry_equiv.pos_site_id.
|
|
296
|
+
*
|
|
297
|
+
* p, q and r refer to the translations that are subsequently
|
|
298
|
+
* applied to the symmetry transformed coordinates to generate
|
|
299
|
+
* the atom used in calculating the angle. These translations
|
|
300
|
+
* (x,y,z) are related to (p,q,r) by the relations
|
|
301
|
+
* p = 5 + x
|
|
302
|
+
* q = 5 + y
|
|
303
|
+
* r = 5 + z
|
|
304
|
+
*/
|
|
305
|
+
site_symmetry_1: str,
|
|
306
|
+
/**
|
|
307
|
+
* The set of data items which specify the symmetry operation codes
|
|
308
|
+
* which must be applied to the atom sites involved in the geometry angle.
|
|
309
|
+
*
|
|
310
|
+
* The symmetry code of each atom site as the symmetry-equivalent position
|
|
311
|
+
* number 'n' and the cell translation number 'pqr'. These numbers are
|
|
312
|
+
* combined to form the code 'n pqr' or n_pqr.
|
|
313
|
+
*
|
|
314
|
+
* The character string n_pqr is composed as follows:
|
|
315
|
+
*
|
|
316
|
+
* n refers to the symmetry operation that is applied to the
|
|
317
|
+
* coordinates stored in _atom_site.fract_xyz. It must match a
|
|
318
|
+
* number given in _symmetry_equiv.pos_site_id.
|
|
319
|
+
*
|
|
320
|
+
* p, q and r refer to the translations that are subsequently
|
|
321
|
+
* applied to the symmetry transformed coordinates to generate
|
|
322
|
+
* the atom used in calculating the angle. These translations
|
|
323
|
+
* (x,y,z) are related to (p,q,r) by the relations
|
|
324
|
+
* p = 5 + x
|
|
325
|
+
* q = 5 + y
|
|
326
|
+
* r = 5 + z
|
|
327
|
+
*/
|
|
328
|
+
site_symmetry_2: str,
|
|
329
|
+
/**
|
|
330
|
+
* Bond valence calculated from the bond distance.
|
|
331
|
+
*/
|
|
332
|
+
valence: float,
|
|
333
|
+
},
|
|
334
|
+
/**
|
|
335
|
+
* The CATEGORY of data items used to record details about the
|
|
336
|
+
* creation and subsequent updating of the data block.
|
|
337
|
+
*/
|
|
338
|
+
audit: {
|
|
339
|
+
/**
|
|
340
|
+
* The digital object identifier (DOI) registered to identify
|
|
341
|
+
* the data set publication represented by the current
|
|
342
|
+
* data block. This can be used as a unique identifier for
|
|
343
|
+
* the data block so long as the code used is a valid DOI
|
|
344
|
+
* (i.e. begins with a valid publisher prefix assigned by a
|
|
345
|
+
* Registration Agency and a suffix guaranteed to be unique
|
|
346
|
+
* by the publisher) and has had its metadata deposited
|
|
347
|
+
* with a DOI Registration Agency.
|
|
348
|
+
*
|
|
349
|
+
* A DOI is a unique character string identifying any
|
|
350
|
+
* object of intellectual property. It provides a
|
|
351
|
+
* persistent identifier for an object on a digital network
|
|
352
|
+
* and permits the association of related current data in a
|
|
353
|
+
* structured extensible way. A DOI is an implementation
|
|
354
|
+
* of the Internet concepts of Uniform Resource Name and
|
|
355
|
+
* Universal Resource Locator managed according to the
|
|
356
|
+
* specifications of the International DOI Foundation
|
|
357
|
+
* (see http://www.doi.org).
|
|
358
|
+
*/
|
|
359
|
+
block_doi: str,
|
|
360
|
+
},
|
|
361
|
+
/**
|
|
362
|
+
* The CATEGORY of data items recording database deposition. These data items
|
|
363
|
+
* are assigned by database managers and should only appear in a CIF if they
|
|
364
|
+
* originate from that source.
|
|
365
|
+
*/
|
|
366
|
+
database_code: {
|
|
367
|
+
/**
|
|
368
|
+
* Code assigned by the Crystallography Open Database (COD).
|
|
369
|
+
*/
|
|
370
|
+
cod: str,
|
|
371
|
+
/**
|
|
372
|
+
* Code assigned by the Cambridge Structural Database.
|
|
373
|
+
*/
|
|
374
|
+
csd: str,
|
|
375
|
+
/**
|
|
376
|
+
* Deposition numbers assigned by the Cambridge Crystallographic
|
|
377
|
+
* Data Centre (CCDC) to files containing structural information
|
|
378
|
+
* archived by the CCDC.
|
|
379
|
+
*/
|
|
380
|
+
depnum_ccdc_archive: str,
|
|
381
|
+
/**
|
|
382
|
+
* Deposition numbers assigned by the Fachinformationszentrum
|
|
383
|
+
* Karlsruhe (FIZ) to files containing structural information
|
|
384
|
+
* archived by the Cambridge Crystallographic Data Centre (CCDC).
|
|
385
|
+
*/
|
|
386
|
+
depnum_ccdc_fiz: str,
|
|
387
|
+
/**
|
|
388
|
+
* Code assigned by the Inorganic Crystal Structure Database.
|
|
389
|
+
*/
|
|
390
|
+
icsd: str,
|
|
391
|
+
/**
|
|
392
|
+
* Code assigned in the Metals Data File.
|
|
393
|
+
*/
|
|
394
|
+
mdf: str,
|
|
395
|
+
/**
|
|
396
|
+
* Code assigned by the NBS (NIST) Crystal Data Database.
|
|
397
|
+
*/
|
|
398
|
+
nbs: str,
|
|
399
|
+
},
|
|
400
|
+
/**
|
|
401
|
+
* The CATEGORY of data items used to describe atom site information
|
|
402
|
+
* used in crystallographic structure studies.
|
|
403
|
+
*/
|
|
404
|
+
atom_site: {
|
|
405
|
+
/**
|
|
406
|
+
* Code for type of atomic displacement parameters used for the site.
|
|
407
|
+
*/
|
|
408
|
+
adp_type: str,
|
|
409
|
+
/**
|
|
410
|
+
* A standard code to signal if the site coordinates have been
|
|
411
|
+
* determined from the intensities or calculated from the geometry
|
|
412
|
+
* of surrounding sites, or have been assigned dummy coordinates.
|
|
413
|
+
*/
|
|
414
|
+
calc_flag: str,
|
|
415
|
+
/**
|
|
416
|
+
* A code which identifies a cluster of atoms that show long range
|
|
417
|
+
* positional disorder but are locally ordered. Within each such
|
|
418
|
+
* cluster of atoms, _atom_site.disorder_group is used to identify
|
|
419
|
+
* the sites that are simultaneously occupied. This field is only
|
|
420
|
+
* needed if there is more than one cluster of disordered atoms
|
|
421
|
+
* showing independent local order.
|
|
422
|
+
*/
|
|
423
|
+
disorder_assembly: str,
|
|
424
|
+
/**
|
|
425
|
+
* A code that identifies a group of positionally disordered atom
|
|
426
|
+
* sites that are locally simultaneously occupied. Atoms that are
|
|
427
|
+
* positionally disordered over two or more sites (e.g. the H
|
|
428
|
+
* atoms of a methyl group that exists in two orientations) can
|
|
429
|
+
* be assigned to two or more groups. Sites belonging to the same
|
|
430
|
+
* group are simultaneously occupied, but those belonging to
|
|
431
|
+
* different groups are not. A minus prefix (e.g. "-1") is used to
|
|
432
|
+
* indicate sites disordered about a special position.
|
|
433
|
+
*/
|
|
434
|
+
disorder_group: str,
|
|
435
|
+
/**
|
|
436
|
+
* Atom site coordinates as fractions of the cell length values.
|
|
437
|
+
*/
|
|
438
|
+
fract_x: float,
|
|
439
|
+
/**
|
|
440
|
+
* Atom site coordinates as fractions of the cell length values.
|
|
441
|
+
*/
|
|
442
|
+
fract_y: float,
|
|
443
|
+
/**
|
|
444
|
+
* Atom site coordinates as fractions of the cell length values.
|
|
445
|
+
*/
|
|
446
|
+
fract_z: float,
|
|
447
|
+
/**
|
|
448
|
+
* This label is a unique identifier for a particular site in the
|
|
449
|
+
* asymmetric unit of the crystal unit cell. It is made up of
|
|
450
|
+
* components, _atom_site.label_component_0 to *_6, which may be
|
|
451
|
+
* specified as separate data items. Component 0 usually matches one
|
|
452
|
+
* of the specified _atom_type.symbol codes. This is not mandatory
|
|
453
|
+
* if an _atom_site.type_symbol item is included in the atom site
|
|
454
|
+
* list. The _atom_site.type_symbol always takes precedence over
|
|
455
|
+
* an _atom_site.label in the identification of the atom type. The
|
|
456
|
+
* label components 1 to 6 are optional, and normally only
|
|
457
|
+
* components 0 and 1 are used. Note that components 0 and 1 are
|
|
458
|
+
* concatenated, while all other components, if specified, are
|
|
459
|
+
* separated by an underline character. Underline separators are
|
|
460
|
+
* only used if higher-order components exist. If an intermediate
|
|
461
|
+
* component is not used it may be omitted provided the underline
|
|
462
|
+
* separators are inserted. For example the label 'C233__ggg' is
|
|
463
|
+
* acceptable and represents the components C, 233, '', and ggg.
|
|
464
|
+
* Each label may have a different number of components.
|
|
465
|
+
*/
|
|
466
|
+
label: str,
|
|
467
|
+
/**
|
|
468
|
+
* The fraction of the atom type present at this site.
|
|
469
|
+
* The sum of the occupancies of all the atom types at this site
|
|
470
|
+
* may not significantly exceed 1.0 unless it is a dummy site. The
|
|
471
|
+
* value must lie in the 99.97% Gaussian confidence interval
|
|
472
|
+
* -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
|
|
473
|
+
* correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
|
|
474
|
+
*/
|
|
475
|
+
occupancy: float,
|
|
476
|
+
/**
|
|
477
|
+
* A concatenated series of single-letter codes which indicate the
|
|
478
|
+
* refinement restraints or constraints applied to this site. This
|
|
479
|
+
* item should not be used. It has been replaced by
|
|
480
|
+
* _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
|
|
481
|
+
* retained in this dictionary only to provide compatibility with
|
|
482
|
+
* legacy CIFs.
|
|
483
|
+
*/
|
|
484
|
+
refinement_flags: str,
|
|
485
|
+
/**
|
|
486
|
+
* The number of different sites that are generated by the
|
|
487
|
+
* application of the space-group symmetry to the coordinates
|
|
488
|
+
* given for this site. It is equal to the multiplicity given
|
|
489
|
+
* for this Wyckoff site in International Tables for Cryst.
|
|
490
|
+
* Vol. A (2002). It is equal to the multiplicity of the general
|
|
491
|
+
* position divided by the order of the site symmetry given in
|
|
492
|
+
* _atom_site.site_symmetry_order.
|
|
493
|
+
*/
|
|
494
|
+
site_symmetry_multiplicity: int,
|
|
495
|
+
/**
|
|
496
|
+
* A code to identify the atom specie(s) occupying this site.
|
|
497
|
+
* This code must match a corresponding _atom_type.symbol. The
|
|
498
|
+
* specification of this code is optional if component_0 of the
|
|
499
|
+
* _atom_site.label is used for this purpose. See _atom_type.symbol.
|
|
500
|
+
*/
|
|
501
|
+
type_symbol: str,
|
|
502
|
+
/**
|
|
503
|
+
* Isotropic atomic displacement parameter, or equivalent isotropic
|
|
504
|
+
* atomic displacement parameter, U(equiv), in angstroms squared,
|
|
505
|
+
* calculated from anisotropic atomic displacement parameters.
|
|
506
|
+
*
|
|
507
|
+
* U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
|
|
508
|
+
*
|
|
509
|
+
* a = the real-space cell vectors
|
|
510
|
+
* a* = the reciprocal-space cell lengths
|
|
511
|
+
* Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
|
|
512
|
+
*/
|
|
513
|
+
u_iso_or_equiv: float,
|
|
514
|
+
},
|
|
515
|
+
/**
|
|
516
|
+
* The CATEGORY of data items used to describe the anisotropic
|
|
517
|
+
* thermal parameters of the atomic sites in a crystal structure.
|
|
518
|
+
*/
|
|
519
|
+
atom_site_aniso: {
|
|
520
|
+
/**
|
|
521
|
+
* Anisotropic atomic displacement parameters are usually looped in
|
|
522
|
+
* a separate list. If this is the case, this code must match the
|
|
523
|
+
* _atom_site.label of the associated atom in the atom coordinate
|
|
524
|
+
* list and conform with the same rules described in _atom_site.label.
|
|
525
|
+
*/
|
|
526
|
+
label: str,
|
|
527
|
+
/**
|
|
528
|
+
* These are the standard anisotropic atomic displacement
|
|
529
|
+
* components in angstroms squared which appear in the
|
|
530
|
+
* structure factor term:
|
|
531
|
+
*
|
|
532
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
533
|
+
*
|
|
534
|
+
* h = the Miller indices
|
|
535
|
+
* a* = the reciprocal-space cell lengths
|
|
536
|
+
*
|
|
537
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
538
|
+
*/
|
|
539
|
+
u_11: float,
|
|
540
|
+
/**
|
|
541
|
+
* These are the standard anisotropic atomic displacement
|
|
542
|
+
* components in angstroms squared which appear in the
|
|
543
|
+
* structure factor term:
|
|
544
|
+
*
|
|
545
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
546
|
+
*
|
|
547
|
+
* h = the Miller indices
|
|
548
|
+
* a* = the reciprocal-space cell lengths
|
|
549
|
+
*
|
|
550
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
551
|
+
*/
|
|
552
|
+
u: Matrix(3, 3),
|
|
553
|
+
/**
|
|
554
|
+
* These are the standard anisotropic atomic displacement
|
|
555
|
+
* components in angstroms squared which appear in the
|
|
556
|
+
* structure factor term:
|
|
557
|
+
*
|
|
558
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
559
|
+
*
|
|
560
|
+
* h = the Miller indices
|
|
561
|
+
* a* = the reciprocal-space cell lengths
|
|
562
|
+
*
|
|
563
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
564
|
+
*/
|
|
565
|
+
u_12: float,
|
|
566
|
+
/**
|
|
567
|
+
* These are the standard anisotropic atomic displacement
|
|
568
|
+
* components in angstroms squared which appear in the
|
|
569
|
+
* structure factor term:
|
|
570
|
+
*
|
|
571
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
572
|
+
*
|
|
573
|
+
* h = the Miller indices
|
|
574
|
+
* a* = the reciprocal-space cell lengths
|
|
575
|
+
*
|
|
576
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
577
|
+
*/
|
|
578
|
+
u_13: float,
|
|
579
|
+
/**
|
|
580
|
+
* These are the standard anisotropic atomic displacement
|
|
581
|
+
* components in angstroms squared which appear in the
|
|
582
|
+
* structure factor term:
|
|
583
|
+
*
|
|
584
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
585
|
+
*
|
|
586
|
+
* h = the Miller indices
|
|
587
|
+
* a* = the reciprocal-space cell lengths
|
|
588
|
+
*
|
|
589
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
590
|
+
*/
|
|
591
|
+
u_22: float,
|
|
592
|
+
/**
|
|
593
|
+
* These are the standard anisotropic atomic displacement
|
|
594
|
+
* components in angstroms squared which appear in the
|
|
595
|
+
* structure factor term:
|
|
596
|
+
*
|
|
597
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
598
|
+
*
|
|
599
|
+
* h = the Miller indices
|
|
600
|
+
* a* = the reciprocal-space cell lengths
|
|
601
|
+
*
|
|
602
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
603
|
+
*/
|
|
604
|
+
u_23: float,
|
|
605
|
+
/**
|
|
606
|
+
* These are the standard anisotropic atomic displacement
|
|
607
|
+
* components in angstroms squared which appear in the
|
|
608
|
+
* structure factor term:
|
|
609
|
+
*
|
|
610
|
+
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
|
|
611
|
+
*
|
|
612
|
+
* h = the Miller indices
|
|
613
|
+
* a* = the reciprocal-space cell lengths
|
|
614
|
+
*
|
|
615
|
+
* The unique elements of the real symmetric matrix are entered by row.
|
|
616
|
+
*/
|
|
617
|
+
u_33: float,
|
|
618
|
+
},
|
|
619
|
+
/**
|
|
620
|
+
* The CATEGORY of data items used to describe atomic type information
|
|
621
|
+
* used in crystallographic structure studies.
|
|
622
|
+
*/
|
|
623
|
+
atom_type: {
|
|
624
|
+
/**
|
|
625
|
+
* A description of the atom(s) designated by this atom type. In
|
|
626
|
+
* most cases this will be the element name and oxidation state of
|
|
627
|
+
* a single atom species. For disordered or nonstoichiometric
|
|
628
|
+
* structures it will describe a combination of atom species.
|
|
629
|
+
*/
|
|
630
|
+
description: str,
|
|
631
|
+
/**
|
|
632
|
+
* The identity of the atom specie(s) representing this atom type.
|
|
633
|
+
* Normally this code is the element symbol followed by the charge
|
|
634
|
+
* if there is one. The symbol may be composed of any character except
|
|
635
|
+
* an underline or a blank, with the proviso that digits designate an
|
|
636
|
+
* oxidation state and must be followed by a + or - character.
|
|
637
|
+
*/
|
|
638
|
+
symbol: str,
|
|
639
|
+
},
|
|
640
|
+
/**
|
|
641
|
+
* The CATEGORY of data items used to describe atomic scattering
|
|
642
|
+
* information used in crystallographic structure studies.
|
|
643
|
+
*/
|
|
644
|
+
atom_type_scat: {
|
|
645
|
+
/**
|
|
646
|
+
* The imaginary component of the anomalous dispersion scattering factors
|
|
647
|
+
* for this atom type and radiation by _diffrn_radiation_wavelength.value
|
|
648
|
+
*/
|
|
649
|
+
dispersion_imag: float,
|
|
650
|
+
/**
|
|
651
|
+
* The real component of the anomalous dispersion scattering factors
|
|
652
|
+
* for this atom type and radiation by _diffrn_radiation_wavelength.value
|
|
653
|
+
*/
|
|
654
|
+
dispersion_real: float,
|
|
655
|
+
/**
|
|
656
|
+
* Reference to source of scattering factors used for this atom type.
|
|
657
|
+
*/
|
|
658
|
+
source: str,
|
|
659
|
+
},
|
|
660
|
+
};
|
|
661
|
+
exports.CifCore_Aliases = {
|
|
662
|
+
'cell.formula_units_z': [
|
|
663
|
+
'cell_formula_units_Z',
|
|
664
|
+
],
|
|
665
|
+
'space_group.it_number': [
|
|
666
|
+
'space_group_IT_number',
|
|
667
|
+
'symmetry_Int_Tables_number',
|
|
668
|
+
],
|
|
669
|
+
'space_group.name_h-m_full': [
|
|
670
|
+
'symmetry_space_group_name_H-M',
|
|
671
|
+
],
|
|
672
|
+
'space_group_symop.operation_xyz': [
|
|
673
|
+
'symmetry_equiv_pos_as_xyz',
|
|
674
|
+
],
|
|
675
|
+
'geom_bond.atom_site_label_1': [
|
|
676
|
+
'geom_bond_atom_site_id_1',
|
|
677
|
+
],
|
|
678
|
+
'geom_bond.atom_site_label_2': [
|
|
679
|
+
'geom_bond_atom_site_id_2',
|
|
680
|
+
],
|
|
681
|
+
'geom_bond.distance': [
|
|
682
|
+
'geom_bond_dist',
|
|
683
|
+
],
|
|
684
|
+
'audit.block_doi': [
|
|
685
|
+
'audit_block_DOI',
|
|
686
|
+
],
|
|
687
|
+
'database_code.cod': [
|
|
688
|
+
'database_code_COD',
|
|
689
|
+
],
|
|
690
|
+
'database_code.csd': [
|
|
691
|
+
'database_code_CSD',
|
|
692
|
+
],
|
|
693
|
+
'database_code.depnum_ccdc_archive': [
|
|
694
|
+
'database_code_depnum_CCDC_archive',
|
|
695
|
+
],
|
|
696
|
+
'database_code.depnum_ccdc_fiz': [
|
|
697
|
+
'database_code_depnum_CCDC_fiz',
|
|
698
|
+
],
|
|
699
|
+
'database_code.icsd': [
|
|
700
|
+
'database_code_ICSD',
|
|
701
|
+
],
|
|
702
|
+
'database_code.mdf': [
|
|
703
|
+
'database_code_MDF',
|
|
704
|
+
],
|
|
705
|
+
'database_code.nbs': [
|
|
706
|
+
'database_code_NBS',
|
|
707
|
+
],
|
|
708
|
+
'atom_site.adp_type': [
|
|
709
|
+
'atom_site_ADP_type',
|
|
710
|
+
'atom_site_thermal_displace_type',
|
|
711
|
+
],
|
|
712
|
+
'atom_site.label': [
|
|
713
|
+
'atom_site_id',
|
|
714
|
+
],
|
|
715
|
+
'atom_site.site_symmetry_multiplicity': [
|
|
716
|
+
'atom_site_symmetry_multiplicity',
|
|
717
|
+
],
|
|
718
|
+
'atom_site.u_iso_or_equiv': [
|
|
719
|
+
'atom_site_U_iso_or_equiv',
|
|
720
|
+
],
|
|
721
|
+
'atom_site_aniso.label': [
|
|
722
|
+
'atom_site_anisotrop_id',
|
|
723
|
+
],
|
|
724
|
+
'atom_site_aniso.u_11': [
|
|
725
|
+
'atom_site_aniso_U_11',
|
|
726
|
+
'atom_site_anisotrop_U_11',
|
|
727
|
+
],
|
|
728
|
+
'atom_site_aniso.u_12': [
|
|
729
|
+
'atom_site_aniso_U_12',
|
|
730
|
+
'atom_site_anisotrop_U_12',
|
|
731
|
+
],
|
|
732
|
+
'atom_site_aniso.u_13': [
|
|
733
|
+
'atom_site_aniso_U_13',
|
|
734
|
+
'atom_site_anisotrop_U_13',
|
|
735
|
+
],
|
|
736
|
+
'atom_site_aniso.u_22': [
|
|
737
|
+
'atom_site_aniso_U_22',
|
|
738
|
+
'atom_site_anisotrop_U_22',
|
|
739
|
+
],
|
|
740
|
+
'atom_site_aniso.u_23': [
|
|
741
|
+
'atom_site_aniso_U_23',
|
|
742
|
+
'atom_site_anisotrop_U_23',
|
|
743
|
+
],
|
|
744
|
+
'atom_site_aniso.u_33': [
|
|
745
|
+
'atom_site_aniso_U_33',
|
|
746
|
+
'atom_site_anisotrop_U_33',
|
|
747
|
+
],
|
|
748
|
+
};
|
|
749
|
+
;
|
|
750
|
+
//# sourceMappingURL=cif-core.js.map
|