molstar 3.8.2 → 3.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/build/viewer/index.html +4 -1
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/viewer/app.d.ts +1 -1
- package/lib/apps/viewer/app.js +1 -1
- package/lib/apps/viewer/index.html +4 -1
- package/lib/cli/cif2bcif/converter.js +1 -1
- package/lib/commonjs/apps/viewer/app.d.ts +1 -1
- package/lib/commonjs/apps/viewer/app.js +2 -1
- package/lib/commonjs/cli/cif2bcif/converter.js +1 -1
- package/lib/commonjs/examples/alpha-orbitals/index.d.ts +1 -1
- package/lib/commonjs/examples/alpha-orbitals/index.js +4 -1
- package/lib/commonjs/examples/basic-wrapper/custom-theme.js +1 -1
- package/lib/commonjs/examples/proteopedia-wrapper/coloring.js +3 -3
- package/lib/commonjs/extensions/alpha-orbitals/density.d.ts +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/density.js +6 -2
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.d.ts +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +6 -3
- package/lib/commonjs/extensions/anvil/algorithm.js +1 -1
- package/lib/commonjs/extensions/cellpack/color/generate.js +1 -1
- package/lib/commonjs/extensions/cellpack/color/provided.js +1 -1
- package/lib/commonjs/extensions/cellpack/state.js +1 -1
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +1 -1
- package/lib/commonjs/extensions/g3d/model.js +1 -1
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +1 -1
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js +1 -1
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +4 -4
- package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js +2 -2
- package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js +1 -1
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +2 -2
- package/lib/commonjs/mol-canvas3d/canvas3d.js +4 -0
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +7 -7
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +14 -14
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +5 -5
- package/lib/commonjs/mol-canvas3d/passes/draw.js +34 -5
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +5 -0
- package/lib/commonjs/mol-canvas3d/passes/marking.js +5 -0
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +9 -0
- package/lib/commonjs/mol-canvas3d/passes/pick.d.ts +18 -5
- package/lib/commonjs/mol-canvas3d/passes/pick.js +125 -24
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +5 -0
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +4 -0
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +4 -0
- package/lib/commonjs/mol-data/db/column.js +5 -5
- package/lib/commonjs/mol-data/db/table.js +2 -2
- package/lib/commonjs/mol-data/util/array.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +13 -0
- package/lib/commonjs/mol-gl/compute/grid3d.d.ts +2 -2
- package/lib/commonjs/mol-gl/compute/grid3d.js +30 -8
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.d.ts +1 -1
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +6 -1
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.d.ts +1 -1
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +6 -1
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.d.ts +1 -1
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +6 -1
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts +1 -1
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +10 -10
- package/lib/commonjs/mol-gl/renderer.js +77 -32
- package/lib/commonjs/mol-gl/scene.js +2 -0
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
- package/lib/commonjs/mol-gl/shader/cylinders.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/cylinders.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/lines.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/mesh.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/points.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/spheres.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/text.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/text.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader-code.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader-code.js +41 -9
- package/lib/commonjs/mol-gl/webgl/compat.d.ts +34 -1
- package/lib/commonjs/mol-gl/webgl/compat.js +50 -2
- package/lib/commonjs/mol-gl/webgl/context.d.ts +2 -0
- package/lib/commonjs/mol-gl/webgl/context.js +3 -0
- package/lib/commonjs/mol-gl/webgl/extensions.d.ts +3 -2
- package/lib/commonjs/mol-gl/webgl/extensions.js +6 -1
- package/lib/commonjs/mol-gl/webgl/timer.d.ts +22 -0
- package/lib/commonjs/mol-gl/webgl/timer.js +169 -0
- package/lib/commonjs/mol-io/common/binary-cif/array-encoder.js +18 -18
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +16 -16
- package/lib/commonjs/mol-io/common/binary-cif/encoding.js +9 -9
- package/lib/commonjs/mol-io/reader/cif/binary/field.js +3 -3
- package/lib/commonjs/mol-io/reader/cif/data-model.js +14 -14
- package/lib/commonjs/mol-io/reader/cif/schema.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +23 -23
- package/lib/commonjs/mol-io/reader/common/text/column/fixed.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/column/token.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/number-parser.js +6 -6
- package/lib/commonjs/mol-io/reader/csv/parser.js +8 -8
- package/lib/commonjs/mol-io/writer/cif/encoder/binary.js +10 -10
- package/lib/commonjs/mol-io/writer/cif/encoder/text.js +7 -7
- package/lib/commonjs/mol-io/writer/cif/encoder.js +8 -8
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +4 -4
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +13 -2
- package/lib/commonjs/mol-model/sequence/alignment/sequence.js +3 -3
- package/lib/commonjs/mol-model/sequence/sequence.js +9 -9
- package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js +3 -3
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/commonjs/mol-model/structure/export/categories/utils.js +1 -1
- package/lib/commonjs/mol-model/structure/model/model.js +2 -2
- package/lib/commonjs/mol-model/structure/model/properties/custom/indexed.js +6 -6
- package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js +1 -1
- package/lib/commonjs/mol-model/structure/model/types.js +116 -116
- package/lib/commonjs/mol-model/structure/query/context.js +1 -1
- package/lib/commonjs/mol-model/structure/query/queries/generators.js +5 -5
- package/lib/commonjs/mol-model/structure/query/queries/internal.js +4 -4
- package/lib/commonjs/mol-model/structure/query/queries/modifiers.js +4 -4
- package/lib/commonjs/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
- package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js +9 -9
- package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.js +106 -106
- package/lib/commonjs/mol-model/structure/structure/element/loci.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/element/stats.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/properties.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/structure.js +11 -11
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js +5 -5
- package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js +4 -4
- package/lib/commonjs/mol-model/structure/structure/unit/bonds.js +2 -2
- package/lib/commonjs/mol-model/structure/structure/unit/resonance.js +1 -1
- package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js +6 -6
- package/lib/commonjs/mol-model/structure/structure/unit/rings.js +6 -6
- package/lib/commonjs/mol-model/structure/structure/unit.js +16 -16
- package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.js +1 -1
- package/lib/commonjs/mol-model/structure/util.js +4 -4
- package/lib/commonjs/mol-model-formats/structure/basic/atomic.js +2 -2
- package/lib/commonjs/mol-model-formats/structure/basic/parser.js +4 -4
- package/lib/commonjs/mol-model-formats/structure/basic/properties.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/sort.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/basic/util.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/cif-core.js +6 -6
- package/lib/commonjs/mol-model-formats/structure/common/entity.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/cube.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/gro.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/mol.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/mol2.js +4 -4
- package/lib/commonjs/mol-model-formats/structure/prmtop.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js +3 -3
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js +6 -6
- package/lib/commonjs/mol-model-formats/structure/property/secondary-structure.js +8 -8
- package/lib/commonjs/mol-model-formats/structure/psf.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/top.js +1 -1
- package/lib/commonjs/mol-model-formats/structure/xyz.js +1 -1
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +2 -2
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +3 -3
- package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js +2 -2
- package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js +31 -31
- package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js +22 -22
- package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js +32 -32
- package/lib/commonjs/mol-model-props/computed/interactions/charged.js +39 -39
- package/lib/commonjs/mol-model-props/computed/interactions/common.js +34 -34
- package/lib/commonjs/mol-model-props/computed/interactions/contacts-builder.js +1 -1
- package/lib/commonjs/mol-model-props/computed/interactions/contacts.js +1 -1
- package/lib/commonjs/mol-model-props/computed/interactions/halogen-bonds.js +12 -12
- package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js +32 -32
- package/lib/commonjs/mol-model-props/computed/interactions/hydrophobic.js +9 -9
- package/lib/commonjs/mol-model-props/computed/interactions/metal.js +26 -26
- package/lib/commonjs/mol-model-props/computed/interactions/refine.js +20 -20
- package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +2 -2
- package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +2 -2
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bends.js +1 -1
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/bridges.js +12 -12
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/helices.js +6 -6
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/ladders.js +3 -3
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/sheets.js +11 -11
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp/turns.js +3 -3
- package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js +30 -30
- package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js +1 -1
- package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js +10 -10
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js +1 -1
- package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js +3 -3
- package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js +1 -1
- package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js +1 -1
- package/lib/commonjs/mol-plugin/animation-loop.d.ts +2 -1
- package/lib/commonjs/mol-plugin/animation-loop.js +18 -5
- package/lib/commonjs/mol-plugin/behavior/dynamic/camera.js +12 -12
- package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js +7 -7
- package/lib/commonjs/mol-plugin/context.d.ts +2 -2
- package/lib/commonjs/mol-plugin/state.d.ts +1 -14
- package/lib/commonjs/mol-plugin-state/formats/volume.d.ts +12 -11
- package/lib/commonjs/mol-plugin-state/formats/volume.js +20 -13
- package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js +5 -5
- package/lib/commonjs/mol-plugin-state/transforms/representation.js +2 -2
- package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts +1 -1
- package/lib/commonjs/mol-plugin-ui/sequence/polymer.js +1 -1
- package/lib/commonjs/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/commonjs/mol-plugin-ui/structure/focus.js +1 -1
- package/lib/commonjs/mol-plugin-ui/viewport.d.ts +2 -2
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js +10 -10
- package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js +10 -10
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js +12 -12
- package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js +12 -12
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +16 -16
- package/lib/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +1 -1
- package/lib/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -0
- package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +4 -4
- package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
- package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js +2 -2
- package/lib/commonjs/mol-repr/structure/visual/util/bond.js +2 -2
- package/lib/commonjs/mol-repr/structure/visual/util/common.js +3 -3
- package/lib/commonjs/mol-repr/structure/visual/util/link.js +30 -30
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js +6 -6
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js +3 -3
- package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js +20 -20
- package/lib/commonjs/mol-repr/structure/visual/util/polymer.js +6 -6
- package/lib/commonjs/mol-script/language/symbol-table/core.d.ts +2 -2
- package/lib/commonjs/mol-script/runtime/query/table.js +13 -13
- package/lib/commonjs/mol-state/object.d.ts +3 -3
- package/lib/commonjs/mol-task/util/user-timing.js +1 -1
- package/lib/commonjs/mol-theme/clipping.js +19 -19
- package/lib/commonjs/mol-theme/color/atom-id.js +1 -1
- package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js +1 -1
- package/lib/commonjs/mol-theme/color/chain-id.js +4 -4
- package/lib/commonjs/mol-theme/color/element-index.js +1 -1
- package/lib/commonjs/mol-theme/color/element-symbol.js +1 -1
- package/lib/commonjs/mol-theme/color/entity-id.js +4 -4
- package/lib/commonjs/mol-theme/color/entity-source.js +5 -4
- package/lib/commonjs/mol-theme/color/hydrophobicity.js +1 -1
- package/lib/commonjs/mol-theme/color/illustrative.js +1 -1
- package/lib/commonjs/mol-theme/color/model-index.js +1 -1
- package/lib/commonjs/mol-theme/color/molecule-type.js +8 -8
- package/lib/commonjs/mol-theme/color/occupancy.js +1 -1
- package/lib/commonjs/mol-theme/color/operator-hkl.js +1 -1
- package/lib/commonjs/mol-theme/color/operator-name.js +1 -1
- package/lib/commonjs/mol-theme/color/partial-charge.js +1 -1
- package/lib/commonjs/mol-theme/color/polymer-id.js +4 -4
- package/lib/commonjs/mol-theme/color/polymer-index.js +1 -1
- package/lib/commonjs/mol-theme/color/residue-name.js +1 -1
- package/lib/commonjs/mol-theme/color/secondary-structure.js +12 -12
- package/lib/commonjs/mol-theme/color/sequence-id.js +7 -7
- package/lib/commonjs/mol-theme/color/shape-group.js +1 -1
- package/lib/commonjs/mol-theme/color/uncertainty.js +1 -1
- package/lib/commonjs/mol-theme/color/uniform.js +1 -1
- package/lib/commonjs/mol-theme/color/unit-index.js +1 -1
- package/lib/commonjs/mol-theme/color/volume-value.js +1 -1
- package/lib/commonjs/mol-theme/label.js +3 -3
- package/lib/commonjs/mol-util/binding.js +4 -4
- package/lib/commonjs/mol-util/debug.d.ts +6 -1
- package/lib/commonjs/mol-util/debug.js +11 -1
- package/lib/commonjs/mol-util/input/input-observer.js +20 -20
- package/lib/commonjs/mol-util/string-builder.js +1 -1
- package/lib/commonjs/servers/model/preprocess/converter.js +1 -1
- package/lib/commonjs/servers/model/server/query.js +1 -1
- package/lib/commonjs/servers/model/utils/fetch-retry.js +3 -2
- package/lib/commonjs/servers/volume/server/algebra/coordinate.js +6 -6
- package/lib/commonjs/servers/volume/server/query/encode.js +1 -1
- package/lib/examples/alpha-orbitals/index.d.ts +1 -1
- package/lib/examples/alpha-orbitals/index.html +11 -0
- package/lib/examples/alpha-orbitals/index.js +4 -1
- package/lib/examples/basic-wrapper/custom-theme.js +1 -1
- package/lib/examples/proteopedia-wrapper/coloring.js +3 -3
- package/lib/extensions/alpha-orbitals/density.d.ts +1 -1
- package/lib/extensions/alpha-orbitals/density.js +6 -2
- package/lib/extensions/alpha-orbitals/orbitals.d.ts +1 -1
- package/lib/extensions/alpha-orbitals/orbitals.js +6 -3
- package/lib/extensions/anvil/algorithm.js +1 -1
- package/lib/extensions/cellpack/color/generate.js +1 -1
- package/lib/extensions/cellpack/color/provided.js +1 -1
- package/lib/extensions/cellpack/state.js +1 -1
- package/lib/extensions/dnatco/confal-pyramids/color.js +1 -1
- package/lib/extensions/g3d/model.js +1 -1
- package/lib/extensions/model-archive/quality-assessment/color/plddt.js +1 -1
- package/lib/extensions/model-archive/quality-assessment/color/qmean.js +1 -1
- package/lib/extensions/pdbe/structure-quality-report/color.js +1 -1
- package/lib/extensions/rcsb/assembly-symmetry/color.js +4 -4
- package/lib/extensions/rcsb/validation-report/color/density-fit.js +1 -1
- package/lib/extensions/rcsb/validation-report/color/geometry-quality.js +2 -2
- package/lib/extensions/rcsb/validation-report/color/random-coil-index.js +1 -1
- package/lib/extensions/rcsb/validation-report/representation.js +2 -2
- package/lib/mol-canvas3d/canvas3d.js +5 -1
- package/lib/mol-canvas3d/controls/trackball.js +7 -7
- package/lib/mol-canvas3d/helper/camera-helper.js +14 -14
- package/lib/mol-canvas3d/helper/interaction-events.js +5 -5
- package/lib/mol-canvas3d/passes/draw.js +34 -5
- package/lib/mol-canvas3d/passes/fxaa.js +5 -0
- package/lib/mol-canvas3d/passes/marking.js +5 -0
- package/lib/mol-canvas3d/passes/multi-sample.js +9 -0
- package/lib/mol-canvas3d/passes/pick.d.ts +18 -5
- package/lib/mol-canvas3d/passes/pick.js +125 -24
- package/lib/mol-canvas3d/passes/postprocessing.js +5 -0
- package/lib/mol-canvas3d/passes/smaa.js +5 -1
- package/lib/mol-canvas3d/passes/wboit.js +5 -1
- package/lib/mol-data/db/column.js +5 -5
- package/lib/mol-data/db/table.js +2 -2
- package/lib/mol-data/util/array.d.ts +1 -1
- package/lib/mol-geo/geometry/texture-mesh/color-smoothing.js +13 -0
- package/lib/mol-gl/compute/grid3d.d.ts +2 -2
- package/lib/mol-gl/compute/grid3d.js +30 -8
- package/lib/mol-gl/compute/histogram-pyramid/reduction.d.ts +1 -1
- package/lib/mol-gl/compute/histogram-pyramid/reduction.js +6 -1
- package/lib/mol-gl/compute/histogram-pyramid/sum.d.ts +1 -1
- package/lib/mol-gl/compute/histogram-pyramid/sum.js +6 -1
- package/lib/mol-gl/compute/marching-cubes/active-voxels.d.ts +1 -1
- package/lib/mol-gl/compute/marching-cubes/active-voxels.js +6 -1
- package/lib/mol-gl/compute/marching-cubes/isosurface.d.ts +1 -1
- package/lib/mol-gl/compute/marching-cubes/isosurface.js +10 -10
- package/lib/mol-gl/renderer.js +77 -32
- package/lib/mol-gl/scene.js +2 -0
- package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/assign-color-varying.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/assign-material-color.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/assign-material-color.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/color-frag-params.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/color-frag-params.glsl.js +1 -1
- package/lib/mol-gl/shader/chunks/color-vert-params.glsl.d.ts +1 -1
- package/lib/mol-gl/shader/chunks/color-vert-params.glsl.js +1 -1
- package/lib/mol-gl/shader/cylinders.frag.d.ts +1 -1
- package/lib/mol-gl/shader/cylinders.frag.js +1 -1
- package/lib/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/mol-gl/shader/image.frag.d.ts +1 -1
- package/lib/mol-gl/shader/image.frag.js +1 -1
- package/lib/mol-gl/shader/lines.frag.d.ts +1 -1
- package/lib/mol-gl/shader/lines.frag.js +1 -1
- package/lib/mol-gl/shader/mesh.frag.d.ts +1 -1
- package/lib/mol-gl/shader/mesh.frag.js +1 -1
- package/lib/mol-gl/shader/points.frag.d.ts +1 -1
- package/lib/mol-gl/shader/points.frag.js +1 -1
- package/lib/mol-gl/shader/spheres.frag.d.ts +1 -1
- package/lib/mol-gl/shader/spheres.frag.js +1 -1
- package/lib/mol-gl/shader/text.frag.d.ts +1 -1
- package/lib/mol-gl/shader/text.frag.js +1 -1
- package/lib/mol-gl/shader-code.d.ts +1 -1
- package/lib/mol-gl/shader-code.js +41 -9
- package/lib/mol-gl/webgl/compat.d.ts +34 -1
- package/lib/mol-gl/webgl/compat.js +48 -1
- package/lib/mol-gl/webgl/context.d.ts +2 -0
- package/lib/mol-gl/webgl/context.js +3 -0
- package/lib/mol-gl/webgl/extensions.d.ts +3 -2
- package/lib/mol-gl/webgl/extensions.js +7 -2
- package/lib/mol-gl/webgl/timer.d.ts +22 -0
- package/lib/mol-gl/webgl/timer.js +164 -0
- package/lib/mol-io/common/binary-cif/array-encoder.js +18 -18
- package/lib/mol-io/common/binary-cif/decoder.js +16 -16
- package/lib/mol-io/common/binary-cif/encoding.js +9 -9
- package/lib/mol-io/reader/cif/binary/field.js +3 -3
- package/lib/mol-io/reader/cif/data-model.js +14 -14
- package/lib/mol-io/reader/cif/schema.js +1 -1
- package/lib/mol-io/reader/cif/text/parser.js +23 -23
- package/lib/mol-io/reader/common/text/column/fixed.js +1 -1
- package/lib/mol-io/reader/common/text/column/token.js +1 -1
- package/lib/mol-io/reader/common/text/number-parser.js +6 -6
- package/lib/mol-io/reader/csv/parser.js +8 -8
- package/lib/mol-io/writer/cif/encoder/binary.js +10 -10
- package/lib/mol-io/writer/cif/encoder/text.js +7 -7
- package/lib/mol-io/writer/cif/encoder.js +8 -8
- package/lib/mol-io/writer/mol2/encoder.js +4 -4
- package/lib/mol-math/geometry/gaussian-density/gpu.js +13 -2
- package/lib/mol-model/sequence/alignment/sequence.js +3 -3
- package/lib/mol-model/sequence/sequence.js +9 -9
- package/lib/mol-model/structure/export/categories/atom_site_operator_mapping.js +3 -3
- package/lib/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/mol-model/structure/export/categories/utils.js +1 -1
- package/lib/mol-model/structure/model/model.js +2 -2
- package/lib/mol-model/structure/model/properties/custom/indexed.js +6 -6
- package/lib/mol-model/structure/model/properties/utils/atomic-ranges.js +1 -1
- package/lib/mol-model/structure/model/types.js +116 -116
- package/lib/mol-model/structure/query/context.js +1 -1
- package/lib/mol-model/structure/query/queries/generators.js +5 -5
- package/lib/mol-model/structure/query/queries/internal.js +4 -4
- package/lib/mol-model/structure/query/queries/modifiers.js +4 -4
- package/lib/mol-model/structure/query/utils/structure-distance.d.ts +5 -54
- package/lib/mol-model/structure/query/utils/structure-distance.js +9 -9
- package/lib/mol-model/structure/structure/carbohydrates/constants.js +106 -106
- package/lib/mol-model/structure/structure/element/loci.js +5 -5
- package/lib/mol-model/structure/structure/element/stats.js +5 -5
- package/lib/mol-model/structure/structure/properties.js +5 -5
- package/lib/mol-model/structure/structure/structure.js +11 -11
- package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js +5 -5
- package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js +4 -4
- package/lib/mol-model/structure/structure/unit/bonds.js +2 -2
- package/lib/mol-model/structure/structure/unit/resonance.js +1 -1
- package/lib/mol-model/structure/structure/unit/rings/compute.js +6 -6
- package/lib/mol-model/structure/structure/unit/rings.js +6 -6
- package/lib/mol-model/structure/structure/unit.js +16 -16
- package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.js +1 -1
- package/lib/mol-model/structure/util.js +4 -4
- package/lib/mol-model-formats/structure/basic/atomic.js +2 -2
- package/lib/mol-model-formats/structure/basic/parser.js +4 -4
- package/lib/mol-model-formats/structure/basic/properties.js +1 -1
- package/lib/mol-model-formats/structure/basic/sort.js +1 -1
- package/lib/mol-model-formats/structure/basic/util.js +1 -1
- package/lib/mol-model-formats/structure/cif-core.js +6 -6
- package/lib/mol-model-formats/structure/common/entity.js +1 -1
- package/lib/mol-model-formats/structure/cube.js +1 -1
- package/lib/mol-model-formats/structure/gro.js +1 -1
- package/lib/mol-model-formats/structure/mol.js +1 -1
- package/lib/mol-model-formats/structure/mol2.js +4 -4
- package/lib/mol-model-formats/structure/prmtop.js +1 -1
- package/lib/mol-model-formats/structure/property/bonds/chem_comp.js +3 -3
- package/lib/mol-model-formats/structure/property/bonds/index-pair.js +1 -1
- package/lib/mol-model-formats/structure/property/bonds/struct_conn.js +6 -6
- package/lib/mol-model-formats/structure/property/secondary-structure.js +8 -8
- package/lib/mol-model-formats/structure/psf.js +1 -1
- package/lib/mol-model-formats/structure/top.js +1 -1
- package/lib/mol-model-formats/structure/xyz.js +1 -1
- package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js +2 -2
- package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley.js +3 -3
- package/lib/mol-model-props/computed/accessible-surface-area.js +2 -2
- package/lib/mol-model-props/computed/chemistry/functional-group.js +31 -31
- package/lib/mol-model-props/computed/chemistry/geometry.js +22 -22
- package/lib/mol-model-props/computed/chemistry/valence-model.js +32 -32
- package/lib/mol-model-props/computed/interactions/charged.js +39 -39
- package/lib/mol-model-props/computed/interactions/common.js +34 -34
- package/lib/mol-model-props/computed/interactions/contacts-builder.js +1 -1
- package/lib/mol-model-props/computed/interactions/contacts.js +1 -1
- package/lib/mol-model-props/computed/interactions/halogen-bonds.js +12 -12
- package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js +32 -32
- package/lib/mol-model-props/computed/interactions/hydrophobic.js +9 -9
- package/lib/mol-model-props/computed/interactions/metal.js +26 -26
- package/lib/mol-model-props/computed/interactions/refine.js +20 -20
- package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js +2 -2
- package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js +2 -2
- package/lib/mol-model-props/computed/secondary-structure/dssp/bends.js +1 -1
- package/lib/mol-model-props/computed/secondary-structure/dssp/bridges.js +12 -12
- package/lib/mol-model-props/computed/secondary-structure/dssp/helices.js +6 -6
- package/lib/mol-model-props/computed/secondary-structure/dssp/ladders.js +3 -3
- package/lib/mol-model-props/computed/secondary-structure/dssp/sheets.js +11 -11
- package/lib/mol-model-props/computed/secondary-structure/dssp/turns.js +3 -3
- package/lib/mol-model-props/computed/secondary-structure/dssp.js +30 -30
- package/lib/mol-model-props/computed/themes/accessible-surface-area.js +1 -1
- package/lib/mol-model-props/computed/themes/interaction-type.js +10 -10
- package/lib/mol-model-props/integrative/cross-link-restraint/color.js +1 -1
- package/lib/mol-model-props/integrative/cross-link-restraint/format.js +3 -3
- package/lib/mol-model-props/sequence/sifts-mapping.js +1 -1
- package/lib/mol-model-props/sequence/themes/sifts-mapping.js +1 -1
- package/lib/mol-plugin/animation-loop.d.ts +2 -1
- package/lib/mol-plugin/animation-loop.js +18 -5
- package/lib/mol-plugin/behavior/dynamic/camera.js +12 -12
- package/lib/mol-plugin/behavior/dynamic/representation.js +7 -7
- package/lib/mol-plugin/context.d.ts +2 -2
- package/lib/mol-plugin/state.d.ts +1 -14
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-state/formats/volume.d.ts +12 -11
- package/lib/mol-plugin-state/formats/volume.js +20 -13
- package/lib/mol-plugin-state/helpers/structure-selection-query.js +5 -5
- package/lib/mol-plugin-state/transforms/representation.js +2 -2
- package/lib/mol-plugin-ui/controls/parameters.d.ts +1 -1
- package/lib/mol-plugin-ui/sequence/polymer.js +1 -1
- package/lib/mol-plugin-ui/sequence/sequence.js +1 -1
- package/lib/mol-plugin-ui/structure/focus.js +1 -1
- package/lib/mol-plugin-ui/viewport.d.ts +2 -2
- package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js +10 -10
- package/lib/mol-repr/structure/visual/bond-inter-unit-line.js +10 -10
- package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js +12 -12
- package/lib/mol-repr/structure/visual/bond-intra-unit-line.js +12 -12
- package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.js +16 -16
- package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js +1 -1
- package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js +9 -0
- package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.js +4 -4
- package/lib/mol-repr/structure/visual/polymer-direction-wedge.js +1 -1
- package/lib/mol-repr/structure/visual/polymer-trace-mesh.js +2 -2
- package/lib/mol-repr/structure/visual/util/bond.js +2 -2
- package/lib/mol-repr/structure/visual/util/common.js +3 -3
- package/lib/mol-repr/structure/visual/util/link.js +30 -30
- package/lib/mol-repr/structure/visual/util/polymer/backbone.js +6 -6
- package/lib/mol-repr/structure/visual/util/polymer/gap-iterator.js +3 -3
- package/lib/mol-repr/structure/visual/util/polymer/trace-iterator.js +20 -20
- package/lib/mol-repr/structure/visual/util/polymer.js +6 -6
- package/lib/mol-script/language/symbol-table/core.d.ts +2 -2
- package/lib/mol-script/runtime/query/table.js +13 -13
- package/lib/mol-state/object.d.ts +3 -3
- package/lib/mol-task/util/user-timing.js +1 -1
- package/lib/mol-theme/clipping.js +19 -19
- package/lib/mol-theme/color/atom-id.js +1 -1
- package/lib/mol-theme/color/carbohydrate-symbol.js +1 -1
- package/lib/mol-theme/color/chain-id.js +4 -4
- package/lib/mol-theme/color/element-index.js +1 -1
- package/lib/mol-theme/color/element-symbol.js +1 -1
- package/lib/mol-theme/color/entity-id.js +4 -4
- package/lib/mol-theme/color/entity-source.js +5 -4
- package/lib/mol-theme/color/hydrophobicity.js +1 -1
- package/lib/mol-theme/color/illustrative.js +1 -1
- package/lib/mol-theme/color/model-index.js +1 -1
- package/lib/mol-theme/color/molecule-type.js +8 -8
- package/lib/mol-theme/color/occupancy.js +1 -1
- package/lib/mol-theme/color/operator-hkl.js +1 -1
- package/lib/mol-theme/color/operator-name.js +1 -1
- package/lib/mol-theme/color/partial-charge.js +1 -1
- package/lib/mol-theme/color/polymer-id.js +4 -4
- package/lib/mol-theme/color/polymer-index.js +1 -1
- package/lib/mol-theme/color/residue-name.js +1 -1
- package/lib/mol-theme/color/secondary-structure.js +12 -12
- package/lib/mol-theme/color/sequence-id.js +7 -7
- package/lib/mol-theme/color/shape-group.js +1 -1
- package/lib/mol-theme/color/uncertainty.js +1 -1
- package/lib/mol-theme/color/uniform.js +1 -1
- package/lib/mol-theme/color/unit-index.js +1 -1
- package/lib/mol-theme/color/volume-value.js +1 -1
- package/lib/mol-theme/label.js +3 -3
- package/lib/mol-util/binding.js +4 -4
- package/lib/mol-util/debug.d.ts +6 -1
- package/lib/mol-util/debug.js +9 -1
- package/lib/mol-util/input/input-observer.js +20 -20
- package/lib/mol-util/string-builder.js +1 -1
- package/lib/servers/model/preprocess/converter.js +1 -1
- package/lib/servers/model/server/query.js +1 -1
- package/lib/servers/model/utils/fetch-retry.js +3 -2
- package/lib/servers/volume/server/algebra/coordinate.js +6 -6
- package/lib/servers/volume/server/query/encode.js +1 -1
- package/package.json +8 -8
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51
|
-
_b[11 /* Assigned */] = 11 /* Pentagon */,
|
|
40
|
+
_b[0 /* SaccharideType.Hexose */] = 0 /* SaccharideShape.FilledSphere */,
|
|
41
|
+
_b[1 /* SaccharideType.HexNAc */] = 1 /* SaccharideShape.FilledCube */,
|
|
42
|
+
_b[2 /* SaccharideType.Hexosamine */] = 2 /* SaccharideShape.CrossedCube */,
|
|
43
|
+
_b[3 /* SaccharideType.Hexuronate */] = 3 /* SaccharideShape.DividedDiamond */,
|
|
44
|
+
_b[4 /* SaccharideType.Deoxyhexose */] = 4 /* SaccharideShape.FilledCone */,
|
|
45
|
+
_b[5 /* SaccharideType.DeoxyhexNAc */] = 5 /* SaccharideShape.DevidedCone */,
|
|
46
|
+
_b[6 /* SaccharideType.DiDeoxyhexose */] = 6 /* SaccharideShape.FlatBox */,
|
|
47
|
+
_b[7 /* SaccharideType.Pentose */] = 7 /* SaccharideShape.FilledStar */,
|
|
48
|
+
_b[8 /* SaccharideType.Deoxynonulosonate */] = 8 /* SaccharideShape.FilledDiamond */,
|
|
49
|
+
_b[9 /* SaccharideType.DiDeoxynonulosonate */] = 9 /* SaccharideShape.FlatDiamond */,
|
|
50
|
+
_b[10 /* SaccharideType.Unknown */] = 10 /* SaccharideShape.FlatHexagon */,
|
|
51
|
+
_b[11 /* SaccharideType.Assigned */] = 11 /* SaccharideShape.Pentagon */,
|
|
52
52
|
_b);
|
|
53
53
|
export function getSaccharideShape(type, ringMemberCount) {
|
|
54
|
-
if (type === 10 /* Unknown */) {
|
|
54
|
+
if (type === 10 /* SaccharideType.Unknown */) {
|
|
55
55
|
if (ringMemberCount === 4)
|
|
56
|
-
return 12 /* DiamondPrism */;
|
|
56
|
+
return 12 /* SaccharideShape.DiamondPrism */;
|
|
57
57
|
else if (ringMemberCount === 5)
|
|
58
|
-
return 13 /* PentagonalPrism */;
|
|
58
|
+
return 13 /* SaccharideShape.PentagonalPrism */;
|
|
59
59
|
else if (ringMemberCount === 6)
|
|
60
|
-
return 14 /* HexagonalPrism */;
|
|
60
|
+
return 14 /* SaccharideShape.HexagonalPrism */;
|
|
61
61
|
else if (ringMemberCount === 7)
|
|
62
|
-
return 15 /* HeptagonalPrism */;
|
|
62
|
+
return 15 /* SaccharideShape.HeptagonalPrism */;
|
|
63
63
|
else
|
|
64
|
-
return 10 /* FlatHexagon */;
|
|
64
|
+
return 10 /* SaccharideShape.FlatHexagon */;
|
|
65
65
|
}
|
|
66
66
|
else {
|
|
67
67
|
return SaccharideTypeShapeMap[type];
|
|
@@ -71,84 +71,84 @@ export var UnknownSaccharideComponent = {
|
|
|
71
71
|
abbr: 'Unk',
|
|
72
72
|
name: 'Unknown',
|
|
73
73
|
color: SaccharideColors.Secondary,
|
|
74
|
-
type: 10 /* Unknown */
|
|
74
|
+
type: 10 /* SaccharideType.Unknown */
|
|
75
75
|
};
|
|
76
76
|
var Monosaccharides = [
|
|
77
|
-
{ abbr: 'Glc', name: 'Glucose', color: SaccharideColors.Blue, type: 0 /* Hexose */ },
|
|
78
|
-
{ abbr: 'Man', name: 'Mannose', color: SaccharideColors.Green, type: 0 /* Hexose */ },
|
|
79
|
-
{ abbr: 'Gal', name: 'Galactose', color: SaccharideColors.Yellow, type: 0 /* Hexose */ },
|
|
80
|
-
{ abbr: 'Gul', name: 'Gulose', color: SaccharideColors.Orange, type: 0 /* Hexose */ },
|
|
81
|
-
{ abbr: 'Alt', name: 'Altrose', color: SaccharideColors.Pink, type: 0 /* Hexose */ },
|
|
82
|
-
{ abbr: 'All', name: 'Allose', color: SaccharideColors.Purple, type: 0 /* Hexose */ },
|
|
83
|
-
{ abbr: 'Tal', name: 'Talose', color: SaccharideColors.LightBlue, type: 0 /* Hexose */ },
|
|
84
|
-
{ abbr: 'Ido', name: 'Idose', color: SaccharideColors.Brown, type: 0 /* Hexose */ },
|
|
85
|
-
{ abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: SaccharideColors.Blue, type: 1 /* HexNAc */ },
|
|
86
|
-
{ abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: SaccharideColors.Green, type: 1 /* HexNAc */ },
|
|
87
|
-
{ abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: SaccharideColors.Yellow, type: 1 /* HexNAc */ },
|
|
88
|
-
{ abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: SaccharideColors.Orange, type: 1 /* HexNAc */ },
|
|
89
|
-
{ abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: SaccharideColors.Pink, type: 1 /* HexNAc */ },
|
|
90
|
-
{ abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: SaccharideColors.Purple, type: 1 /* HexNAc */ },
|
|
91
|
-
{ abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: SaccharideColors.LightBlue, type: 1 /* HexNAc */ },
|
|
92
|
-
{ abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: SaccharideColors.Brown, type: 1 /* HexNAc */ },
|
|
93
|
-
{ abbr: 'GlcN', name: 'Glucosamine', color: SaccharideColors.Blue, type: 2 /* Hexosamine */ },
|
|
94
|
-
{ abbr: 'ManN', name: 'Mannosamine', color: SaccharideColors.Green, type: 2 /* Hexosamine */ },
|
|
95
|
-
{ abbr: 'GalN', name: 'Galactosamine', color: SaccharideColors.Yellow, type: 2 /* Hexosamine */ },
|
|
96
|
-
{ abbr: 'GulN', name: 'Gulosamine', color: SaccharideColors.Orange, type: 2 /* Hexosamine */ },
|
|
97
|
-
{ abbr: 'AltN', name: 'Altrosamine', color: SaccharideColors.Pink, type: 2 /* Hexosamine */ },
|
|
98
|
-
{ abbr: 'AllN', name: 'Allosamine', color: SaccharideColors.Purple, type: 2 /* Hexosamine */ },
|
|
99
|
-
{ abbr: 'TalN', name: 'Talosamine', color: SaccharideColors.LightBlue, type: 2 /* Hexosamine */ },
|
|
100
|
-
{ abbr: 'IdoN', name: 'Idosamine', color: SaccharideColors.Brown, type: 2 /* Hexosamine */ },
|
|
101
|
-
{ abbr: 'GlcA', name: 'Glucuronic Acid', color: SaccharideColors.Blue, type: 3 /* Hexuronate */ },
|
|
102
|
-
{ abbr: 'ManA', name: 'Mannuronic Acid', color: SaccharideColors.Green, type: 3 /* Hexuronate */ },
|
|
103
|
-
{ abbr: 'GalA', name: 'Galacturonic Acid', color: SaccharideColors.Yellow, type: 3 /* Hexuronate */ },
|
|
104
|
-
{ abbr: 'GulA', name: 'Guluronic Acid', color: SaccharideColors.Orange, type: 3 /* Hexuronate */ },
|
|
105
|
-
{ abbr: 'AltA', name: 'Altruronic Acid', color: SaccharideColors.Pink, type: 3 /* Hexuronate */ },
|
|
106
|
-
{ abbr: 'AllA', name: 'Alluronic Acid', color: SaccharideColors.Purple, type: 3 /* Hexuronate */ },
|
|
107
|
-
{ abbr: 'TalA', name: 'Taluronic Acid', color: SaccharideColors.LightBlue, type: 3 /* Hexuronate */ },
|
|
108
|
-
{ abbr: 'IdoA', name: 'Iduronic Acid', color: SaccharideColors.Brown, type: 3 /* Hexuronate */ },
|
|
109
|
-
{ abbr: 'Qui', name: 'Quinovose', color: SaccharideColors.Blue, type: 4 /* Deoxyhexose */ },
|
|
110
|
-
{ abbr: 'Rha', name: 'Rhamnose', color: SaccharideColors.Green, type: 4 /* Deoxyhexose */ },
|
|
111
|
-
{ abbr: '6dGul', name: '6-Deoxy Gulose', color: SaccharideColors.Orange, type: 4 /* Deoxyhexose */ },
|
|
112
|
-
{ abbr: '6dAlt', name: '6-Deoxy Altrose', color: SaccharideColors.Pink, type: 4 /* Deoxyhexose */ },
|
|
113
|
-
{ abbr: '6dTal', name: '6-Deoxy Talose', color: SaccharideColors.LightBlue, type: 4 /* Deoxyhexose */ },
|
|
114
|
-
{ abbr: 'Fuc', name: 'Fucose', color: SaccharideColors.Red, type: 4 /* Deoxyhexose */ },
|
|
115
|
-
{ abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: SaccharideColors.Blue, type: 5 /* DeoxyhexNAc */ },
|
|
116
|
-
{ abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: SaccharideColors.Green, type: 5 /* DeoxyhexNAc */ },
|
|
117
|
-
{ abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: SaccharideColors.Pink, type: 5 /* DeoxyhexNAc */ },
|
|
118
|
-
{ abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: SaccharideColors.LightBlue, type: 5 /* DeoxyhexNAc */ },
|
|
119
|
-
{ abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: SaccharideColors.Red, type: 5 /* DeoxyhexNAc */ },
|
|
120
|
-
{ abbr: 'Oli', name: 'Olivose', color: SaccharideColors.Blue, type: 6 /* DiDeoxyhexose */ },
|
|
121
|
-
{ abbr: 'Tyv', name: 'Tyvelose', color: SaccharideColors.Green, type: 6 /* DiDeoxyhexose */ },
|
|
122
|
-
{ abbr: 'Abe', name: 'Abequose', color: SaccharideColors.Orange, type: 6 /* DiDeoxyhexose */ },
|
|
123
|
-
{ abbr: 'Par', name: 'Paratose', color: SaccharideColors.Pink, type: 6 /* DiDeoxyhexose */ },
|
|
124
|
-
{ abbr: 'Dig', name: 'Digitoxose', color: SaccharideColors.Purple, type: 6 /* DiDeoxyhexose */ },
|
|
125
|
-
{ abbr: 'Col', name: 'Colitose', color: SaccharideColors.LightBlue, type: 6 /* DiDeoxyhexose */ },
|
|
126
|
-
{ abbr: 'Ara', name: 'Arabinose', color: SaccharideColors.Green, type: 7 /* Pentose */ },
|
|
127
|
-
{ abbr: 'Lyx', name: 'Lyxose', color: SaccharideColors.Yellow, type: 7 /* Pentose */ },
|
|
128
|
-
{ abbr: 'Xyl', name: 'Xylose', color: SaccharideColors.Orange, type: 7 /* Pentose */ },
|
|
129
|
-
{ abbr: 'Rib', name: 'Ribose', color: SaccharideColors.Pink, type: 7 /* Pentose */ },
|
|
130
|
-
{ abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: SaccharideColors.Green, type: 8 /* Deoxynonulosonate */ },
|
|
131
|
-
{ abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: SaccharideColors.Purple, type: 8 /* Deoxynonulosonate */ },
|
|
132
|
-
{ abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: SaccharideColors.LightBlue, type: 8 /* Deoxynonulosonate */ },
|
|
133
|
-
{ abbr: 'Neu', name: 'Neuraminic Acid', color: SaccharideColors.Brown, type: 8 /* Deoxynonulosonate */ },
|
|
134
|
-
{ abbr: 'Sia', name: 'Sialic acid', color: SaccharideColors.Red, type: 8 /* Deoxynonulosonate */ },
|
|
135
|
-
{ abbr: 'Pse', name: 'Pseudaminic Acid', color: SaccharideColors.Green, type: 9 /* DiDeoxynonulosonate */ },
|
|
136
|
-
{ abbr: 'Leg', name: 'Legionaminic Acid', color: SaccharideColors.Yellow, type: 9 /* DiDeoxynonulosonate */ },
|
|
137
|
-
{ abbr: 'Aci', name: 'Acinetaminic Acid', color: SaccharideColors.Pink, type: 9 /* DiDeoxynonulosonate */ },
|
|
138
|
-
{ abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: SaccharideColors.LightBlue, type: 9 /* DiDeoxynonulosonate */ },
|
|
139
|
-
{ abbr: 'Bac', name: 'Bacillosamine', color: SaccharideColors.Blue, type: 10 /* Unknown */ },
|
|
140
|
-
{ abbr: 'LDmanHep', name: 'L-Glycero-D-Manno Heptose', color: SaccharideColors.Green, type: 10 /* Unknown */ },
|
|
141
|
-
{ abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: SaccharideColors.Yellow, type: 10 /* Unknown */ },
|
|
142
|
-
{ abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: SaccharideColors.Orange, type: 10 /* Unknown */ },
|
|
143
|
-
{ abbr: 'DDmanHep', name: 'D-Glycero-D-Manno-Heptose', color: SaccharideColors.Pink, type: 10 /* Unknown */ },
|
|
144
|
-
{ abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: SaccharideColors.Purple, type: 10 /* Unknown */ },
|
|
145
|
-
{ abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: SaccharideColors.LightBlue, type: 10 /* Unknown */ },
|
|
146
|
-
{ abbr: 'Mur', name: 'Muramic Acid', color: SaccharideColors.Brown, type: 10 /* Unknown */ },
|
|
147
|
-
{ abbr: 'Api', name: 'Apicose', color: SaccharideColors.Green, type: 11 /* Assigned */ },
|
|
148
|
-
{ abbr: 'Fru', name: 'Fructose', color: SaccharideColors.Green, type: 11 /* Assigned */ },
|
|
149
|
-
{ abbr: 'Tag', name: 'Tagatose', color: SaccharideColors.Yellow, type: 11 /* Assigned */ },
|
|
150
|
-
{ abbr: 'Sor', name: 'Sorbose', color: SaccharideColors.Orange, type: 11 /* Assigned */ },
|
|
151
|
-
{ abbr: 'Psi', name: 'Psicose', color: SaccharideColors.Pink, type: 11 /* Assigned */ },
|
|
77
|
+
{ abbr: 'Glc', name: 'Glucose', color: SaccharideColors.Blue, type: 0 /* SaccharideType.Hexose */ },
|
|
78
|
+
{ abbr: 'Man', name: 'Mannose', color: SaccharideColors.Green, type: 0 /* SaccharideType.Hexose */ },
|
|
79
|
+
{ abbr: 'Gal', name: 'Galactose', color: SaccharideColors.Yellow, type: 0 /* SaccharideType.Hexose */ },
|
|
80
|
+
{ abbr: 'Gul', name: 'Gulose', color: SaccharideColors.Orange, type: 0 /* SaccharideType.Hexose */ },
|
|
81
|
+
{ abbr: 'Alt', name: 'Altrose', color: SaccharideColors.Pink, type: 0 /* SaccharideType.Hexose */ },
|
|
82
|
+
{ abbr: 'All', name: 'Allose', color: SaccharideColors.Purple, type: 0 /* SaccharideType.Hexose */ },
|
|
83
|
+
{ abbr: 'Tal', name: 'Talose', color: SaccharideColors.LightBlue, type: 0 /* SaccharideType.Hexose */ },
|
|
84
|
+
{ abbr: 'Ido', name: 'Idose', color: SaccharideColors.Brown, type: 0 /* SaccharideType.Hexose */ },
|
|
85
|
+
{ abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: SaccharideColors.Blue, type: 1 /* SaccharideType.HexNAc */ },
|
|
86
|
+
{ abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: SaccharideColors.Green, type: 1 /* SaccharideType.HexNAc */ },
|
|
87
|
+
{ abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: SaccharideColors.Yellow, type: 1 /* SaccharideType.HexNAc */ },
|
|
88
|
+
{ abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: SaccharideColors.Orange, type: 1 /* SaccharideType.HexNAc */ },
|
|
89
|
+
{ abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: SaccharideColors.Pink, type: 1 /* SaccharideType.HexNAc */ },
|
|
90
|
+
{ abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: SaccharideColors.Purple, type: 1 /* SaccharideType.HexNAc */ },
|
|
91
|
+
{ abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: SaccharideColors.LightBlue, type: 1 /* SaccharideType.HexNAc */ },
|
|
92
|
+
{ abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: SaccharideColors.Brown, type: 1 /* SaccharideType.HexNAc */ },
|
|
93
|
+
{ abbr: 'GlcN', name: 'Glucosamine', color: SaccharideColors.Blue, type: 2 /* SaccharideType.Hexosamine */ },
|
|
94
|
+
{ abbr: 'ManN', name: 'Mannosamine', color: SaccharideColors.Green, type: 2 /* SaccharideType.Hexosamine */ },
|
|
95
|
+
{ abbr: 'GalN', name: 'Galactosamine', color: SaccharideColors.Yellow, type: 2 /* SaccharideType.Hexosamine */ },
|
|
96
|
+
{ abbr: 'GulN', name: 'Gulosamine', color: SaccharideColors.Orange, type: 2 /* SaccharideType.Hexosamine */ },
|
|
97
|
+
{ abbr: 'AltN', name: 'Altrosamine', color: SaccharideColors.Pink, type: 2 /* SaccharideType.Hexosamine */ },
|
|
98
|
+
{ abbr: 'AllN', name: 'Allosamine', color: SaccharideColors.Purple, type: 2 /* SaccharideType.Hexosamine */ },
|
|
99
|
+
{ abbr: 'TalN', name: 'Talosamine', color: SaccharideColors.LightBlue, type: 2 /* SaccharideType.Hexosamine */ },
|
|
100
|
+
{ abbr: 'IdoN', name: 'Idosamine', color: SaccharideColors.Brown, type: 2 /* SaccharideType.Hexosamine */ },
|
|
101
|
+
{ abbr: 'GlcA', name: 'Glucuronic Acid', color: SaccharideColors.Blue, type: 3 /* SaccharideType.Hexuronate */ },
|
|
102
|
+
{ abbr: 'ManA', name: 'Mannuronic Acid', color: SaccharideColors.Green, type: 3 /* SaccharideType.Hexuronate */ },
|
|
103
|
+
{ abbr: 'GalA', name: 'Galacturonic Acid', color: SaccharideColors.Yellow, type: 3 /* SaccharideType.Hexuronate */ },
|
|
104
|
+
{ abbr: 'GulA', name: 'Guluronic Acid', color: SaccharideColors.Orange, type: 3 /* SaccharideType.Hexuronate */ },
|
|
105
|
+
{ abbr: 'AltA', name: 'Altruronic Acid', color: SaccharideColors.Pink, type: 3 /* SaccharideType.Hexuronate */ },
|
|
106
|
+
{ abbr: 'AllA', name: 'Alluronic Acid', color: SaccharideColors.Purple, type: 3 /* SaccharideType.Hexuronate */ },
|
|
107
|
+
{ abbr: 'TalA', name: 'Taluronic Acid', color: SaccharideColors.LightBlue, type: 3 /* SaccharideType.Hexuronate */ },
|
|
108
|
+
{ abbr: 'IdoA', name: 'Iduronic Acid', color: SaccharideColors.Brown, type: 3 /* SaccharideType.Hexuronate */ },
|
|
109
|
+
{ abbr: 'Qui', name: 'Quinovose', color: SaccharideColors.Blue, type: 4 /* SaccharideType.Deoxyhexose */ },
|
|
110
|
+
{ abbr: 'Rha', name: 'Rhamnose', color: SaccharideColors.Green, type: 4 /* SaccharideType.Deoxyhexose */ },
|
|
111
|
+
{ abbr: '6dGul', name: '6-Deoxy Gulose', color: SaccharideColors.Orange, type: 4 /* SaccharideType.Deoxyhexose */ },
|
|
112
|
+
{ abbr: '6dAlt', name: '6-Deoxy Altrose', color: SaccharideColors.Pink, type: 4 /* SaccharideType.Deoxyhexose */ },
|
|
113
|
+
{ abbr: '6dTal', name: '6-Deoxy Talose', color: SaccharideColors.LightBlue, type: 4 /* SaccharideType.Deoxyhexose */ },
|
|
114
|
+
{ abbr: 'Fuc', name: 'Fucose', color: SaccharideColors.Red, type: 4 /* SaccharideType.Deoxyhexose */ },
|
|
115
|
+
{ abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: SaccharideColors.Blue, type: 5 /* SaccharideType.DeoxyhexNAc */ },
|
|
116
|
+
{ abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: SaccharideColors.Green, type: 5 /* SaccharideType.DeoxyhexNAc */ },
|
|
117
|
+
{ abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: SaccharideColors.Pink, type: 5 /* SaccharideType.DeoxyhexNAc */ },
|
|
118
|
+
{ abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: SaccharideColors.LightBlue, type: 5 /* SaccharideType.DeoxyhexNAc */ },
|
|
119
|
+
{ abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: SaccharideColors.Red, type: 5 /* SaccharideType.DeoxyhexNAc */ },
|
|
120
|
+
{ abbr: 'Oli', name: 'Olivose', color: SaccharideColors.Blue, type: 6 /* SaccharideType.DiDeoxyhexose */ },
|
|
121
|
+
{ abbr: 'Tyv', name: 'Tyvelose', color: SaccharideColors.Green, type: 6 /* SaccharideType.DiDeoxyhexose */ },
|
|
122
|
+
{ abbr: 'Abe', name: 'Abequose', color: SaccharideColors.Orange, type: 6 /* SaccharideType.DiDeoxyhexose */ },
|
|
123
|
+
{ abbr: 'Par', name: 'Paratose', color: SaccharideColors.Pink, type: 6 /* SaccharideType.DiDeoxyhexose */ },
|
|
124
|
+
{ abbr: 'Dig', name: 'Digitoxose', color: SaccharideColors.Purple, type: 6 /* SaccharideType.DiDeoxyhexose */ },
|
|
125
|
+
{ abbr: 'Col', name: 'Colitose', color: SaccharideColors.LightBlue, type: 6 /* SaccharideType.DiDeoxyhexose */ },
|
|
126
|
+
{ abbr: 'Ara', name: 'Arabinose', color: SaccharideColors.Green, type: 7 /* SaccharideType.Pentose */ },
|
|
127
|
+
{ abbr: 'Lyx', name: 'Lyxose', color: SaccharideColors.Yellow, type: 7 /* SaccharideType.Pentose */ },
|
|
128
|
+
{ abbr: 'Xyl', name: 'Xylose', color: SaccharideColors.Orange, type: 7 /* SaccharideType.Pentose */ },
|
|
129
|
+
{ abbr: 'Rib', name: 'Ribose', color: SaccharideColors.Pink, type: 7 /* SaccharideType.Pentose */ },
|
|
130
|
+
{ abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: SaccharideColors.Green, type: 8 /* SaccharideType.Deoxynonulosonate */ },
|
|
131
|
+
{ abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: SaccharideColors.Purple, type: 8 /* SaccharideType.Deoxynonulosonate */ },
|
|
132
|
+
{ abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: SaccharideColors.LightBlue, type: 8 /* SaccharideType.Deoxynonulosonate */ },
|
|
133
|
+
{ abbr: 'Neu', name: 'Neuraminic Acid', color: SaccharideColors.Brown, type: 8 /* SaccharideType.Deoxynonulosonate */ },
|
|
134
|
+
{ abbr: 'Sia', name: 'Sialic acid', color: SaccharideColors.Red, type: 8 /* SaccharideType.Deoxynonulosonate */ },
|
|
135
|
+
{ abbr: 'Pse', name: 'Pseudaminic Acid', color: SaccharideColors.Green, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
|
|
136
|
+
{ abbr: 'Leg', name: 'Legionaminic Acid', color: SaccharideColors.Yellow, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
|
|
137
|
+
{ abbr: 'Aci', name: 'Acinetaminic Acid', color: SaccharideColors.Pink, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
|
|
138
|
+
{ abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: SaccharideColors.LightBlue, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
|
|
139
|
+
{ abbr: 'Bac', name: 'Bacillosamine', color: SaccharideColors.Blue, type: 10 /* SaccharideType.Unknown */ },
|
|
140
|
+
{ abbr: 'LDmanHep', name: 'L-Glycero-D-Manno Heptose', color: SaccharideColors.Green, type: 10 /* SaccharideType.Unknown */ },
|
|
141
|
+
{ abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: SaccharideColors.Yellow, type: 10 /* SaccharideType.Unknown */ },
|
|
142
|
+
{ abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: SaccharideColors.Orange, type: 10 /* SaccharideType.Unknown */ },
|
|
143
|
+
{ abbr: 'DDmanHep', name: 'D-Glycero-D-Manno-Heptose', color: SaccharideColors.Pink, type: 10 /* SaccharideType.Unknown */ },
|
|
144
|
+
{ abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: SaccharideColors.Purple, type: 10 /* SaccharideType.Unknown */ },
|
|
145
|
+
{ abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: SaccharideColors.LightBlue, type: 10 /* SaccharideType.Unknown */ },
|
|
146
|
+
{ abbr: 'Mur', name: 'Muramic Acid', color: SaccharideColors.Brown, type: 10 /* SaccharideType.Unknown */ },
|
|
147
|
+
{ abbr: 'Api', name: 'Apicose', color: SaccharideColors.Green, type: 11 /* SaccharideType.Assigned */ },
|
|
148
|
+
{ abbr: 'Fru', name: 'Fructose', color: SaccharideColors.Green, type: 11 /* SaccharideType.Assigned */ },
|
|
149
|
+
{ abbr: 'Tag', name: 'Tagatose', color: SaccharideColors.Yellow, type: 11 /* SaccharideType.Assigned */ },
|
|
150
|
+
{ abbr: 'Sor', name: 'Sorbose', color: SaccharideColors.Orange, type: 11 /* SaccharideType.Assigned */ },
|
|
151
|
+
{ abbr: 'Psi', name: 'Psicose', color: SaccharideColors.Pink, type: 11 /* SaccharideType.Assigned */ },
|
|
152
152
|
];
|
|
153
153
|
export var SaccharidesSnfgMap = (function () {
|
|
154
154
|
var map = new Map();
|
|
@@ -278,7 +278,7 @@ export function Loci(structure, elements) {
|
|
|
278
278
|
elements[elements.length] = lociElement;
|
|
279
279
|
continue;
|
|
280
280
|
}
|
|
281
|
-
if (lociElement.unit.kind === 0 /* Atomic */) {
|
|
281
|
+
if (lociElement.unit.kind === 0 /* Unit.Kind.Atomic */) {
|
|
282
282
|
var unitElements = lociElement.unit.elements;
|
|
283
283
|
var h = lociElement.unit.model.atomicHierarchy;
|
|
284
284
|
var label_alt_id = lociElement.unit.model.atomicHierarchy.atoms.label_alt_id;
|
|
@@ -322,9 +322,9 @@ export function Loci(structure, elements) {
|
|
|
322
322
|
Loci.extendToWholeResidues = extendToWholeResidues;
|
|
323
323
|
function getChainSegments(unit) {
|
|
324
324
|
switch (unit.kind) {
|
|
325
|
-
case 0 /* Atomic */: return unit.model.atomicHierarchy.chainAtomSegments;
|
|
326
|
-
case 1 /* Spheres */: return unit.model.coarseHierarchy.spheres.chainElementSegments;
|
|
327
|
-
case 2 /* Gaussians */: return unit.model.coarseHierarchy.gaussians.chainElementSegments;
|
|
325
|
+
case 0 /* Unit.Kind.Atomic */: return unit.model.atomicHierarchy.chainAtomSegments;
|
|
326
|
+
case 1 /* Unit.Kind.Spheres */: return unit.model.coarseHierarchy.spheres.chainElementSegments;
|
|
327
|
+
case 2 /* Unit.Kind.Gaussians */: return unit.model.coarseHierarchy.gaussians.chainElementSegments;
|
|
328
328
|
}
|
|
329
329
|
}
|
|
330
330
|
function isWholeUnit(element) {
|
|
@@ -389,7 +389,7 @@ export function Loci(structure, elements) {
|
|
|
389
389
|
var elements = [];
|
|
390
390
|
for (var i = 0, len = loci.elements.length; i < len; i++) {
|
|
391
391
|
var e = loci.elements[i];
|
|
392
|
-
if (Unit.Traits.is(e.unit.traits, 2 /* Partitioned */)) {
|
|
392
|
+
if (Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */)) {
|
|
393
393
|
var start = i;
|
|
394
394
|
while (i < len && Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
|
|
395
395
|
i++;
|
|
@@ -48,7 +48,7 @@ export var Stats;
|
|
|
48
48
|
}
|
|
49
49
|
}
|
|
50
50
|
else if (size === 1) {
|
|
51
|
-
if (Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
|
|
51
|
+
if (Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
|
|
52
52
|
// handled in `handleUnitChainsSimple`
|
|
53
53
|
return;
|
|
54
54
|
}
|
|
@@ -133,7 +133,7 @@ export var Stats;
|
|
|
133
133
|
if (size === 0)
|
|
134
134
|
return;
|
|
135
135
|
var elements = unit.elements;
|
|
136
|
-
if (!Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
|
|
136
|
+
if (!Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
|
|
137
137
|
if (size === elements.length) {
|
|
138
138
|
stats.chainCount += 1;
|
|
139
139
|
if (stats.chainCount === 1) {
|
|
@@ -207,7 +207,7 @@ export var Stats;
|
|
|
207
207
|
if (size === 0)
|
|
208
208
|
continue;
|
|
209
209
|
var elements = unit.elements;
|
|
210
|
-
if (!Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
|
|
210
|
+
if (!Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
|
|
211
211
|
var eI = elements[OrderedSet.start(indices)];
|
|
212
212
|
addCountHelper(chainCounts, index[eI], elements.length);
|
|
213
213
|
continue;
|
|
@@ -275,7 +275,7 @@ export var Stats;
|
|
|
275
275
|
for (var _i = 0, _b = loci.elements; _i < _b.length; _i++) {
|
|
276
276
|
var e = _b[_i];
|
|
277
277
|
handleElement(stats, loci.structure, e);
|
|
278
|
-
if (!Unit.Traits.is(e.unit.traits, 2 /* Partitioned */)) {
|
|
278
|
+
if (!Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */)) {
|
|
279
279
|
handleUnitChainsSimple(stats, loci.structure, e);
|
|
280
280
|
}
|
|
281
281
|
else {
|
|
@@ -286,7 +286,7 @@ export var Stats;
|
|
|
286
286
|
if (hasPartitions) {
|
|
287
287
|
for (var i = 0, len = loci.elements.length; i < len; i++) {
|
|
288
288
|
var e = loci.elements[i];
|
|
289
|
-
if (!Unit.Traits.is(e.unit.traits, 2 /* Partitioned */))
|
|
289
|
+
if (!Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */))
|
|
290
290
|
continue;
|
|
291
291
|
var start = i;
|
|
292
292
|
while (i < len && Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
|
|
@@ -87,7 +87,7 @@ var residue = {
|
|
|
87
87
|
if (!Unit.isAtomic(l.unit))
|
|
88
88
|
notAtomic();
|
|
89
89
|
var secStruc = (_a = SecondaryStructureProvider.get(l.structure).value) === null || _a === void 0 ? void 0 : _a.get(l.unit.invariantId);
|
|
90
|
-
return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* NA */;
|
|
90
|
+
return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* SecondaryStructureType.Flag.NA */;
|
|
91
91
|
}),
|
|
92
92
|
secondary_structure_key: p(function (l) {
|
|
93
93
|
var _a;
|
|
@@ -121,11 +121,11 @@ var coarse = {
|
|
|
121
121
|
};
|
|
122
122
|
function eK(l) {
|
|
123
123
|
switch (l.unit.kind) {
|
|
124
|
-
case 0 /* Atomic */:
|
|
124
|
+
case 0 /* Unit.Kind.Atomic */:
|
|
125
125
|
return l.unit.model.atomicHierarchy.index.getEntityFromChain(l.unit.chainIndex[l.element]);
|
|
126
|
-
case 1 /* Spheres */:
|
|
126
|
+
case 1 /* Unit.Kind.Spheres */:
|
|
127
127
|
return l.unit.model.coarseHierarchy.spheres.entityKey[l.element];
|
|
128
|
-
case 2 /* Gaussians */:
|
|
128
|
+
case 2 /* Unit.Kind.Gaussians */:
|
|
129
129
|
return l.unit.model.coarseHierarchy.gaussians.entityKey[l.element];
|
|
130
130
|
}
|
|
131
131
|
}
|
|
@@ -148,7 +148,7 @@ var _emptyList = [];
|
|
|
148
148
|
var unit = {
|
|
149
149
|
id: p(function (l) { return l.unit.id; }),
|
|
150
150
|
chainGroupId: p(function (l) { return l.unit.chainGroupId; }),
|
|
151
|
-
multiChain: p(function (l) { return Unit.Traits.is(l.unit.traits, 1 /* MultiChain */); }),
|
|
151
|
+
multiChain: p(function (l) { return Unit.Traits.is(l.unit.traits, 1 /* Unit.Trait.MultiChain */); }),
|
|
152
152
|
object_primitive: p(function (l) { return l.unit.objectPrimitive; }),
|
|
153
153
|
operator_name: p(function (l) { return l.unit.conformation.operator.name; }),
|
|
154
154
|
model_index: p(function (l) { return l.unit.model.modelNum; }),
|
|
@@ -595,7 +595,7 @@ function getEntityIndices(structure) {
|
|
|
595
595
|
var keys = UniqueArray.create();
|
|
596
596
|
for (var _a = 0, units_2 = units; _a < units_2.length; _a++) {
|
|
597
597
|
var unit = units_2[_a];
|
|
598
|
-
var prop = unit.kind === 0 /* Atomic */ ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
|
|
598
|
+
var prop = unit.kind === 0 /* Unit.Kind.Atomic */ ? StructureProperties.entity.key : StructureProperties.coarse.entityKey;
|
|
599
599
|
l.unit = unit;
|
|
600
600
|
var elements = unit.elements;
|
|
601
601
|
var chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
|
|
@@ -921,20 +921,20 @@ function getSerialMapping(structure) {
|
|
|
921
921
|
partitionAtomicUnitByResidue(model, elements, builder, multiChain, operator);
|
|
922
922
|
}
|
|
923
923
|
else {
|
|
924
|
-
builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
|
|
924
|
+
builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, elements, multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */);
|
|
925
925
|
}
|
|
926
926
|
}
|
|
927
927
|
else {
|
|
928
|
-
builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
|
|
928
|
+
builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, elements, multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */);
|
|
929
929
|
}
|
|
930
930
|
}
|
|
931
931
|
var cs = model.coarseHierarchy;
|
|
932
932
|
if (cs.isDefined) {
|
|
933
933
|
if (cs.spheres.count > 0) {
|
|
934
|
-
addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Spheres */);
|
|
934
|
+
addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Unit.Kind.Spheres */);
|
|
935
935
|
}
|
|
936
936
|
if (cs.gaussians.count > 0) {
|
|
937
|
-
addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Gaussians */);
|
|
937
|
+
addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Unit.Kind.Gaussians */);
|
|
938
938
|
}
|
|
939
939
|
}
|
|
940
940
|
return builder.getStructure();
|
|
@@ -953,7 +953,7 @@ function getSerialMapping(structure) {
|
|
|
953
953
|
var position = { x: x, y: y, z: z, indices: indices };
|
|
954
954
|
var lookup = GridLookup3D(position, getBoundary(position), 8192);
|
|
955
955
|
var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
|
|
956
|
-
var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
|
|
956
|
+
var traits = (multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */) | (offset.length > 1 ? 2 /* Unit.Trait.Partitioned */ : 0 /* Unit.Trait.None */);
|
|
957
957
|
builder.beginChainGroup();
|
|
958
958
|
for (var i = 0, _i = offset.length; i < _i; i++) {
|
|
959
959
|
var start = offset[i];
|
|
@@ -961,7 +961,7 @@ function getSerialMapping(structure) {
|
|
|
961
961
|
for (var j = 0, _j = count[i]; j < _j; j++) {
|
|
962
962
|
set[j] = indices[array[start + j]];
|
|
963
963
|
}
|
|
964
|
-
builder.addUnit(0 /* Atomic */, model, operator, SortedArray.ofSortedArray(set), traits);
|
|
964
|
+
builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, SortedArray.ofSortedArray(set), traits);
|
|
965
965
|
}
|
|
966
966
|
builder.endChainGroup();
|
|
967
967
|
}
|
|
@@ -982,7 +982,7 @@ function getSerialMapping(structure) {
|
|
|
982
982
|
var position = { x: x, y: y, z: z, indices: SortedArray.ofSortedArray(startIndices) };
|
|
983
983
|
var lookup = GridLookup3D(position, getBoundary(position), gridCellCount);
|
|
984
984
|
var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
|
|
985
|
-
var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
|
|
985
|
+
var traits = (multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */) | (offset.length > 1 ? 2 /* Unit.Trait.Partitioned */ : 0 /* Unit.Trait.None */);
|
|
986
986
|
builder.beginChainGroup();
|
|
987
987
|
for (var i = 0, _i = offset.length; i < _i; i++) {
|
|
988
988
|
var start = offset[i];
|
|
@@ -993,7 +993,7 @@ function getSerialMapping(structure) {
|
|
|
993
993
|
set[set.length] = l;
|
|
994
994
|
}
|
|
995
995
|
}
|
|
996
|
-
builder.addUnit(0 /* Atomic */, model, operator, SortedArray.ofSortedArray(new Int32Array(set)), traits);
|
|
996
|
+
builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, SortedArray.ofSortedArray(new Int32Array(set)), traits);
|
|
997
997
|
}
|
|
998
998
|
builder.endChainGroup();
|
|
999
999
|
}
|
|
@@ -1001,7 +1001,7 @@ function getSerialMapping(structure) {
|
|
|
1001
1001
|
var chainElementSegments = elements.chainElementSegments;
|
|
1002
1002
|
for (var cI = 0; cI < chainElementSegments.count; cI++) {
|
|
1003
1003
|
var elements_1 = SortedArray.ofBounds(chainElementSegments.offsets[cI], chainElementSegments.offsets[cI + 1]);
|
|
1004
|
-
builder.addUnit(kind, model, SymmetryOperator.Default, elements_1, 0 /* None */);
|
|
1004
|
+
builder.addUnit(kind, model, SymmetryOperator.Default, elements_1, 0 /* Unit.Trait.None */);
|
|
1005
1005
|
}
|
|
1006
1006
|
}
|
|
1007
1007
|
function transform(s, transform) {
|
|
@@ -1278,7 +1278,7 @@ function getSerialMapping(structure) {
|
|
|
1278
1278
|
var l = StructureElement.Location.create(structure);
|
|
1279
1279
|
for (var _b = 0, _c = structure.units; _b < _c.length; _b++) {
|
|
1280
1280
|
var unit = _c[_b];
|
|
1281
|
-
if (unit.kind !== 0 /* Atomic */)
|
|
1281
|
+
if (unit.kind !== 0 /* Unit.Kind.Atomic */)
|
|
1282
1282
|
continue;
|
|
1283
1283
|
l.unit = unit;
|
|
1284
1284
|
var elements = unit.elements;
|
|
@@ -156,7 +156,7 @@ function findPairBonds(unitA, unitB, props, builder) {
|
|
|
156
156
|
var compIdB = label_comp_idB.value(residueIndexB[bI]);
|
|
157
157
|
builder.add(_aI, _bI, {
|
|
158
158
|
order: getInterBondOrderFromTable(compIdA, compIdB, atomIdA, atomIdB),
|
|
159
|
-
flag: (isMetal ? 2 /* MetallicCoordination */ : 1 /* Covalent */) | 32 /* Computed */
|
|
159
|
+
flag: (isMetal ? 2 /* BondType.Flag.MetallicCoordination */ : 1 /* BondType.Flag.Covalent */) | 32 /* BondType.Flag.Computed */
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160
160
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});
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161
161
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}
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162
162
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}
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@@ -185,10 +185,10 @@ function computeInterUnitBonds(structure, props) {
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185
185
|
return findBonds(structure, __assign(__assign({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
|
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186
186
|
var mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
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187
187
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var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
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188
|
-
var notWater = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
|
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189
|
-
(!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
|
|
190
|
-
var notIon = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
|
|
191
|
-
(!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
|
|
188
|
+
var notWater = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* MoleculeType.Water */) &&
|
|
189
|
+
(!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* MoleculeType.Water */));
|
|
190
|
+
var notIon = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* MoleculeType.Ion */) &&
|
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191
|
+
(!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* MoleculeType.Ion */));
|
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192
192
|
return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
|
|
193
193
|
}) }));
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|
194
194
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}
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|
@@ -191,9 +191,9 @@ function findBonds(unit, props) {
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|
191
191
|
order[order.length] = e.order;
|
|
192
192
|
var flag = e.flags;
|
|
193
193
|
if (isMetal) {
|
|
194
|
-
if (flag | 1 /* Covalent */)
|
|
195
|
-
flag ^= 1 /* Covalent */;
|
|
196
|
-
flag |= 2 /* MetallicCoordination */;
|
|
194
|
+
if (flag | 1 /* BondType.Flag.Covalent */)
|
|
195
|
+
flag ^= 1 /* BondType.Flag.Covalent */;
|
|
196
|
+
flag |= 2 /* BondType.Flag.MetallicCoordination */;
|
|
197
197
|
}
|
|
198
198
|
flags[flags.length] = flag;
|
|
199
199
|
}
|
|
@@ -207,7 +207,7 @@ function findBonds(unit, props) {
|
|
|
207
207
|
atomA[atomA.length] = _aI;
|
|
208
208
|
atomB[atomB.length] = _bI;
|
|
209
209
|
order[order.length] = getIntraBondOrderFromTable(compId, atomIdA, label_atom_id.value(bI));
|
|
210
|
-
flags[flags.length] = (isMetal ? 2 /* MetallicCoordination */ : 1 /* Covalent */) | 32 /* Computed */;
|
|
210
|
+
flags[flags.length] = (isMetal ? 2 /* BondType.Flag.MetallicCoordination */ : 1 /* BondType.Flag.Covalent */) | 32 /* BondType.Flag.Computed */;
|
|
211
211
|
var seqIdB = label_seq_id.value(rbI);
|
|
212
212
|
if (seqIdA === seqIdB)
|
|
213
213
|
isDictionaryBased = false;
|
|
@@ -125,14 +125,14 @@ var Bond;
|
|
|
125
125
|
var bonds = location.aUnit.bonds;
|
|
126
126
|
var idx = bonds.getEdgeIndex(location.aIndex, location.bIndex);
|
|
127
127
|
if (idx < 0)
|
|
128
|
-
return BondType.create(0 /* None */);
|
|
128
|
+
return BondType.create(0 /* BondType.Flag.None */);
|
|
129
129
|
return BondType.create(bonds.edgeProps.flags[idx]);
|
|
130
130
|
}
|
|
131
131
|
else {
|
|
132
132
|
var bond = structure.interUnitBonds.getBondFromLocation(location);
|
|
133
133
|
if (bond)
|
|
134
134
|
return BondType.create(bond.props.flag);
|
|
135
|
-
return BondType.create(0 /* None */);
|
|
135
|
+
return BondType.create(0 /* BondType.Flag.None */);
|
|
136
136
|
}
|
|
137
137
|
}
|
|
138
138
|
Bond.getType = getType;
|
|
@@ -37,7 +37,7 @@ function getDelocalizedTriplets(unit) {
|
|
|
37
37
|
var deloBonds = [];
|
|
38
38
|
for (var t = offset[i], _t = offset[i + 1]; t < _t; t++) {
|
|
39
39
|
var f = _flags[t];
|
|
40
|
-
if (!BondType.is(f, 16 /* Aromatic */))
|
|
40
|
+
if (!BondType.is(f, 16 /* BondType.Flag.Aromatic */))
|
|
41
41
|
continue;
|
|
42
42
|
deloBonds.push(b[t]);
|
|
43
43
|
}
|
|
@@ -28,8 +28,8 @@ function State(unit, capacity) {
|
|
|
28
28
|
queue: new Int32Array(capacity),
|
|
29
29
|
pred: new Int32Array(capacity),
|
|
30
30
|
depth: new Int32Array(capacity),
|
|
31
|
-
left: new Int32Array(5 /* MaxDepth */),
|
|
32
|
-
right: new Int32Array(5 /* MaxDepth */),
|
|
31
|
+
left: new Int32Array(5 /* Constants.MaxDepth */),
|
|
32
|
+
right: new Int32Array(5 /* Constants.MaxDepth */),
|
|
33
33
|
color: new Int32Array(capacity),
|
|
34
34
|
currentColor: 0,
|
|
35
35
|
currentAltLoc: '',
|
|
@@ -132,7 +132,7 @@ function addRing(state, a, b, isRingAtom) {
|
|
|
132
132
|
var pred = state.pred, color = state.color, left = state.left, right = state.right;
|
|
133
133
|
var nc = ++state.currentColor;
|
|
134
134
|
var current = a;
|
|
135
|
-
for (var t = 0; t < 5 /* MaxDepth */; t++) {
|
|
135
|
+
for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
|
|
136
136
|
color[current] = nc;
|
|
137
137
|
current = pred[current];
|
|
138
138
|
if (current < 0)
|
|
@@ -141,7 +141,7 @@ function addRing(state, a, b, isRingAtom) {
|
|
|
141
141
|
var leftOffset = 0, rightOffset = 0;
|
|
142
142
|
var found = false, target = 0;
|
|
143
143
|
current = b;
|
|
144
|
-
for (var t = 0; t < 5 /* MaxDepth */; t++) {
|
|
144
|
+
for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
|
|
145
145
|
if (color[current] === nc) {
|
|
146
146
|
target = current;
|
|
147
147
|
found = true;
|
|
@@ -156,7 +156,7 @@ function addRing(state, a, b, isRingAtom) {
|
|
|
156
156
|
return false;
|
|
157
157
|
}
|
|
158
158
|
current = a;
|
|
159
|
-
for (var t = 0; t < 5 /* MaxDepth */; t++) {
|
|
159
|
+
for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
|
|
160
160
|
left[leftOffset++] = current;
|
|
161
161
|
if (target === current)
|
|
162
162
|
break;
|
|
@@ -228,7 +228,7 @@ function findRings(state, from, mark) {
|
|
|
228
228
|
continue;
|
|
229
229
|
}
|
|
230
230
|
var newDepth = Math.min(depth[other], d + 1);
|
|
231
|
-
if (newDepth > 5 /* MaxDepth */)
|
|
231
|
+
if (newDepth > 5 /* Constants.MaxDepth */)
|
|
232
232
|
continue;
|
|
233
233
|
depth[other] = newDepth;
|
|
234
234
|
marked[other] = mark;
|