molstar 3.3.1 → 3.6.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +20 -20
- package/README.md +202 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/build/viewer/molstar.js.LICENSE.txt +12 -14
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/docking-viewer/index.js +1 -1
- package/lib/apps/docking-viewer/viewport.js +1 -1
- package/lib/apps/viewer/app.d.ts +7 -6
- package/lib/apps/viewer/app.js +3 -1
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/cli/chem-comp-dict/create-saccharides.js +67 -0
- package/lib/cli/chem-comp-dict/util.d.ts +20 -20
- package/lib/cli/cif2bcif/converter.js +1 -1
- package/lib/cli/cif2bcif/index.js +4 -4
- package/lib/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/cli/cifschema/util/cif-dic.js +7 -5
- package/lib/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/cli/cifschema/util/generate.js +12 -3
- package/lib/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/apps/docking-viewer/index.js +14 -14
- package/lib/commonjs/apps/docking-viewer/viewport.js +33 -33
- package/lib/commonjs/apps/viewer/app.d.ts +7 -6
- package/lib/commonjs/apps/viewer/app.js +26 -24
- package/lib/commonjs/apps/viewer/index.js +1 -1
- package/lib/commonjs/cli/chem-comp-dict/create-ions.js +6 -6
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts +7 -0
- package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js +69 -0
- package/lib/commonjs/cli/chem-comp-dict/create-table.js +8 -8
- package/lib/commonjs/cli/chem-comp-dict/util.d.ts +20 -20
- package/lib/commonjs/cli/chem-comp-dict/util.js +17 -17
- package/lib/commonjs/cli/cif2bcif/converter.js +9 -9
- package/lib/commonjs/cli/cif2bcif/index.js +12 -12
- package/lib/commonjs/cli/cifschema/index.js +27 -27
- package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/cif-dic.js +8 -6
- package/lib/commonjs/cli/cifschema/util/generate.d.ts +1 -1
- package/lib/commonjs/cli/cifschema/util/generate.js +12 -3
- package/lib/commonjs/cli/cifschema/util/schema.d.ts +3 -3
- package/lib/commonjs/cli/cifschema/util/schema.js +1 -1
- package/lib/commonjs/cli/lipid-params/index.js +9 -9
- package/lib/commonjs/cli/state-docs/index.js +2 -2
- package/lib/commonjs/cli/structure-info/helpers.js +11 -11
- package/lib/commonjs/cli/structure-info/model.js +15 -15
- package/lib/commonjs/cli/structure-info/volume.js +9 -9
- package/lib/commonjs/examples/alpha-orbitals/controls.js +3 -3
- package/lib/commonjs/examples/alpha-orbitals/index.js +12 -12
- package/lib/commonjs/examples/basic-wrapper/controls.js +2 -2
- package/lib/commonjs/examples/basic-wrapper/index.js +23 -23
- package/lib/commonjs/examples/basic-wrapper/superposition.js +8 -8
- package/lib/commonjs/examples/domain-annotation-server/mapping.js +3 -3
- package/lib/commonjs/examples/domain-annotation-server/server.js +6 -6
- package/lib/commonjs/examples/domain-annotation-server/test.js +3 -3
- package/lib/commonjs/examples/lighting/index.js +7 -7
- package/lib/commonjs/examples/proteopedia-wrapper/annotation.js +2 -2
- package/lib/commonjs/examples/proteopedia-wrapper/helpers.js +4 -4
- package/lib/commonjs/examples/proteopedia-wrapper/index.js +27 -27
- package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js +2 -2
- package/lib/commonjs/examples/task.js +15 -15
- package/lib/commonjs/extensions/alpha-orbitals/collocation.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/data-model.js +1 -1
- package/lib/commonjs/extensions/alpha-orbitals/density.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/gpu/compute.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/orbitals.js +2 -2
- package/lib/commonjs/extensions/alpha-orbitals/transforms.js +13 -13
- package/lib/commonjs/extensions/anvil/algorithm.js +13 -13
- package/lib/commonjs/extensions/anvil/behavior.d.ts +1 -0
- package/lib/commonjs/extensions/anvil/behavior.js +14 -14
- package/lib/commonjs/extensions/anvil/prop.js +7 -7
- package/lib/commonjs/extensions/anvil/representation.d.ts +4 -0
- package/lib/commonjs/extensions/anvil/representation.js +5 -5
- package/lib/commonjs/extensions/cellpack/index.js +1 -1
- package/lib/commonjs/extensions/cellpack/model.js +26 -24
- package/lib/commonjs/extensions/cellpack/preset.js +6 -6
- package/lib/commonjs/extensions/cellpack/property.js +3 -3
- package/lib/commonjs/extensions/cellpack/representation.d.ts +1 -0
- package/lib/commonjs/extensions/cellpack/representation.js +2 -2
- package/lib/commonjs/extensions/cellpack/state.js +13 -13
- package/lib/commonjs/extensions/cellpack/util.js +14 -14
- package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js +7 -7
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.d.ts +397 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/color.js +223 -131
- package/lib/commonjs/extensions/dnatco/confal-pyramids/property.js +6 -8
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts +3 -0
- package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.js +2 -2
- package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js +19 -20
- package/lib/commonjs/extensions/g3d/data.js +6 -6
- package/lib/commonjs/extensions/g3d/format.js +14 -14
- package/lib/commonjs/extensions/g3d/model.js +4 -4
- package/lib/commonjs/extensions/geo-export/controls.js +3 -3
- package/lib/commonjs/extensions/geo-export/glb-exporter.js +9 -9
- package/lib/commonjs/extensions/geo-export/index.js +1 -1
- package/lib/commonjs/extensions/geo-export/mesh-exporter.js +12 -12
- package/lib/commonjs/extensions/geo-export/obj-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/stl-exporter.js +7 -7
- package/lib/commonjs/extensions/geo-export/ui.js +7 -7
- package/lib/commonjs/extensions/geo-export/usdz-exporter.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.js +9 -9
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/plddt.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/color/qmean.js +4 -4
- package/lib/commonjs/extensions/model-archive/quality-assessment/prop.js +5 -5
- package/lib/commonjs/extensions/model-export/export.js +4 -4
- package/lib/commonjs/extensions/model-export/index.js +1 -1
- package/lib/commonjs/extensions/model-export/ui.js +5 -5
- package/lib/commonjs/extensions/mp4-export/controls.js +5 -5
- package/lib/commonjs/extensions/mp4-export/encoder.js +4 -4
- package/lib/commonjs/extensions/mp4-export/index.js +1 -1
- package/lib/commonjs/extensions/mp4-export/ui.js +5 -5
- package/lib/commonjs/extensions/pdbe/preferred-assembly.js +2 -2
- package/lib/commonjs/extensions/pdbe/struct-ref-domain.js +2 -2
- package/lib/commonjs/extensions/pdbe/structure-quality-report/behavior.js +1 -1
- package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js +8 -8
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.js +2 -2
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js +9 -9
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts +1 -0
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js +6 -6
- package/lib/commonjs/extensions/rcsb/assembly-symmetry/ui.js +9 -9
- package/lib/commonjs/extensions/rcsb/validation-report/behavior.js +17 -17
- package/lib/commonjs/extensions/rcsb/validation-report/prop.js +15 -15
- package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts +5 -0
- package/lib/commonjs/extensions/rcsb/validation-report/representation.js +3 -3
- package/lib/commonjs/extensions/zenodo/index.d.ts +7 -0
- package/lib/commonjs/extensions/zenodo/index.js +35 -0
- package/lib/commonjs/extensions/zenodo/ui.d.ts +61 -0
- package/lib/commonjs/extensions/zenodo/ui.js +306 -0
- package/lib/commonjs/mol-canvas3d/camera/stereo.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera/util.js +1 -1
- package/lib/commonjs/mol-canvas3d/camera.js +2 -1
- package/lib/commonjs/mol-canvas3d/canvas3d.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/canvas3d.js +14 -14
- package/lib/commonjs/mol-canvas3d/controls/trackball.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/bounding-sphere-helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/camera-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/helper/handle-helper.js +5 -5
- package/lib/commonjs/mol-canvas3d/helper/helper.d.ts +2 -0
- package/lib/commonjs/mol-canvas3d/helper/helper.js +1 -1
- package/lib/commonjs/mol-canvas3d/helper/interaction-events.js +2 -2
- package/lib/commonjs/mol-canvas3d/passes/draw.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/fxaa.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/image.d.ts +1 -0
- package/lib/commonjs/mol-canvas3d/passes/image.js +1 -1
- package/lib/commonjs/mol-canvas3d/passes/marking.js +6 -6
- package/lib/commonjs/mol-canvas3d/passes/multi-sample.js +3 -3
- package/lib/commonjs/mol-canvas3d/passes/postprocessing.js +12 -12
- package/lib/commonjs/mol-canvas3d/passes/smaa.js +9 -9
- package/lib/commonjs/mol-canvas3d/passes/wboit.js +3 -3
- package/lib/commonjs/mol-canvas3d/util.js +2 -2
- package/lib/commonjs/mol-data/db/column.d.ts +10 -3
- package/lib/commonjs/mol-data/db/column.js +40 -18
- package/lib/commonjs/mol-data/db/table.js +1 -1
- package/lib/commonjs/mol-data/db.js +1 -1
- package/lib/commonjs/mol-data/generic.js +3 -3
- package/lib/commonjs/mol-data/index.js +4 -4
- package/lib/commonjs/mol-data/int/interval.js +1 -1
- package/lib/commonjs/mol-data/int/ordered-set.js +1 -1
- package/lib/commonjs/mol-data/int/segmentation.js +1 -1
- package/lib/commonjs/mol-data/int/sorted-array.js +1 -1
- package/lib/commonjs/mol-data/util.js +7 -7
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +4 -2
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js +4 -4
- package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js +3 -3
- package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js +1 -1
- package/lib/commonjs/mol-geo/geometry/image/image.js +3 -3
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/lines/lines.js +3 -3
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js +5 -3
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/mesh/mesh.js +4 -4
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/points/points.js +3 -3
- package/lib/commonjs/mol-geo/geometry/size-data.js +1 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/spheres/spheres.js +4 -4
- package/lib/commonjs/mol-geo/geometry/text/font-atlas.js +1 -1
- package/lib/commonjs/mol-geo/geometry/text/text-builder.js +3 -2
- package/lib/commonjs/mol-geo/geometry/text/text.js +3 -3
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.d.ts +1 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/color-smoothing.js +10 -8
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts +2 -1
- package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js +4 -4
- package/lib/commonjs/mol-geo/primitive/circle.js +1 -1
- package/lib/commonjs/mol-geo/primitive/cylinder.js +1 -1
- package/lib/commonjs/mol-geo/primitive/polyhedron.js +1 -1
- package/lib/commonjs/mol-geo/primitive/prism.js +1 -1
- package/lib/commonjs/mol-geo/primitive/star.js +1 -1
- package/lib/commonjs/mol-geo/primitive/torus.js +1 -1
- package/lib/commonjs/mol-geo/util/marching-cubes/algorithm.js +9 -9
- package/lib/commonjs/mol-gl/compute/grid3d.js +5 -5
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/reduction.js +3 -3
- package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/active-voxels.js +3 -3
- package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js +3 -3
- package/lib/commonjs/mol-gl/compute/util.js +3 -3
- package/lib/commonjs/mol-gl/renderable/cylinders.js +3 -3
- package/lib/commonjs/mol-gl/renderable/direct-volume.js +3 -3
- package/lib/commonjs/mol-gl/renderable/image.js +3 -3
- package/lib/commonjs/mol-gl/renderable/lines.js +3 -3
- package/lib/commonjs/mol-gl/renderable/mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/points.js +3 -3
- package/lib/commonjs/mol-gl/renderable/schema.js +1 -1
- package/lib/commonjs/mol-gl/renderable/spheres.js +3 -3
- package/lib/commonjs/mol-gl/renderable/text.js +3 -3
- package/lib/commonjs/mol-gl/renderable/texture-mesh.js +3 -3
- package/lib/commonjs/mol-gl/renderable/util.js +1 -1
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/chunks/wboit-write.glsl.js +2 -2
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.d.ts +1 -1
- package/lib/commonjs/mol-gl/shader/direct-volume.frag.js +1 -1
- package/lib/commonjs/mol-gl/shader/image.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/image.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/lines.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/points.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.d.ts +2 -2
- package/lib/commonjs/mol-gl/shader/text.frag.js +2 -2
- package/lib/commonjs/mol-gl/shader-code.js +2 -1
- package/lib/commonjs/mol-gl/webgl/buffer.d.ts +2 -2
- package/lib/commonjs/mol-gl/webgl/buffer.js +16 -17
- package/lib/commonjs/mol-gl/webgl/context.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/context.js +5 -5
- package/lib/commonjs/mol-gl/webgl/program.d.ts +1 -1
- package/lib/commonjs/mol-gl/webgl/program.js +10 -4
- package/lib/commonjs/mol-gl/webgl/render-item.js +1 -1
- package/lib/commonjs/mol-gl/webgl/resources.js +2 -2
- package/lib/commonjs/mol-io/common/binary-cif/classifier.js +7 -6
- package/lib/commonjs/mol-io/common/binary-cif/decoder.js +4 -3
- package/lib/commonjs/mol-io/common/binary-cif.js +3 -3
- package/lib/commonjs/mol-io/common/io-buffer.d.ts +206 -0
- package/lib/commonjs/mol-io/common/io-buffer.js +408 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.d.ts +78 -0
- package/lib/commonjs/mol-io/common/netcdf/reader.js +459 -0
- package/lib/commonjs/mol-io/common/typed-array.js +2 -2
- package/lib/commonjs/mol-io/reader/ccp4/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/cif/binary/parser.js +3 -3
- package/lib/commonjs/mol-io/reader/cif/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts +8 -8
- package/lib/commonjs/mol-io/reader/cif/schema/bird.js +12 -11
- package/lib/commonjs/mol-io/reader/cif/schema/ccd-extras.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts +12 -12
- package/lib/commonjs/mol-io/reader/cif/schema/ccd.js +13 -12
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts +5 -5
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.js +4 -4
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +31 -27
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +44 -39
- package/lib/commonjs/mol-io/reader/cif/schema.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema.js +24 -4
- package/lib/commonjs/mol-io/reader/cif/text/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cif.js +1 -1
- package/lib/commonjs/mol-io/reader/common/text/tokenizer.js +4 -4
- package/lib/commonjs/mol-io/reader/csv/data-model.js +1 -1
- package/lib/commonjs/mol-io/reader/csv/parser.js +7 -7
- package/lib/commonjs/mol-io/reader/cube/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dcd/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/dsn6/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/dx/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/gro/parser.js +6 -6
- package/lib/commonjs/mol-io/reader/mol/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/mol2/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/nctraj/parser.d.ts +18 -0
- package/lib/commonjs/mol-io/reader/nctraj/parser.js +101 -0
- package/lib/commonjs/mol-io/reader/obj/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/pdb/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/ply/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/prmtop/parser.d.ts +58 -0
- package/lib/commonjs/mol-io/reader/prmtop/parser.js +172 -0
- package/lib/commonjs/mol-io/reader/psf/parser.js +8 -8
- package/lib/commonjs/mol-io/reader/sdf/parser.js +2 -2
- package/lib/commonjs/mol-io/reader/top/parser.d.ts +37 -0
- package/lib/commonjs/mol-io/reader/top/parser.js +303 -0
- package/lib/commonjs/mol-io/reader/trr/parser.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/trr/parser.js +146 -0
- package/lib/commonjs/mol-io/reader/xtc/parser.js +4 -4
- package/lib/commonjs/mol-io/reader/xyz/parser.js +2 -2
- package/lib/commonjs/mol-io/writer/cif/encoder.js +3 -2
- package/lib/commonjs/mol-io/writer/cif.js +1 -1
- package/lib/commonjs/mol-io/writer/ligand-encoder.js +1 -1
- package/lib/commonjs/mol-io/writer/mol/encoder.js +2 -2
- package/lib/commonjs/mol-io/writer/mol2/encoder.js +1 -1
- package/lib/commonjs/mol-math/geometry/boundary-helper.js +5 -5
- package/lib/commonjs/mol-math/geometry/common.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/common.js +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js +6 -6
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.d.ts +1 -1
- package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js +8 -8
- package/lib/commonjs/mol-math/geometry/gaussian-density.d.ts +2 -2
- package/lib/commonjs/mol-math/geometry/gaussian-density.js +5 -5
- package/lib/commonjs/mol-math/geometry/molecular-surface.d.ts +2 -1
- package/lib/commonjs/mol-math/geometry/molecular-surface.js +10 -10
- package/lib/commonjs/mol-math/geometry/primitives/box3d.js +2 -1
- package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js +13 -7
- package/lib/commonjs/mol-math/geometry.js +8 -8
- package/lib/commonjs/mol-math/graph/inter-unit-graph.js +1 -1
- package/lib/commonjs/mol-math/graph.js +1 -1
- package/lib/commonjs/mol-math/linear-algebra.js +2 -2
- package/lib/commonjs/mol-model/sequence/alignment/alignment.js +1 -1
- package/lib/commonjs/mol-model/sequence/sequence.js +2 -1
- package/lib/commonjs/mol-model/sequence.js +1 -1
- package/lib/commonjs/mol-model/shape.js +1 -1
- package/lib/commonjs/mol-model/structure/coordinates.js +1 -1
- package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js +2 -2
- package/lib/commonjs/mol-model/structure/model/model.js +17 -9
- package/lib/commonjs/mol-model/structure/model/properties/atomic.js +3 -3
- package/lib/commonjs/mol-model/structure/model/properties/coarse.js +2 -2
- package/lib/commonjs/mol-model/structure/model/properties/common.js +1 -1
- package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts +8 -0
- package/lib/commonjs/mol-model/structure/model/types/saccharides.js +11 -0
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left: 0;
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bottom: 0;
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z-index: 1000;
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.msp-task-state {
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> div {
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padding: 0 ($control-spacing);
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@include non-selectable;
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white-space: nowrap;
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> button {
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display: inline-block;
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// .msp-background-tasks .msp-task-state {
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// }
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.msp-toast-container {
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position: relative;
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float: right;
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margin-top: $control-spacing;
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border: 1px solid $border-color;
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display: table;
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.msp-toast-title {
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height: 100%;
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line-height: $row-height;
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padding: 0 $control-spacing;
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background: $default-background;
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font-weight: bold;
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display: table-cell;
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cursor: pointer;
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}
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.msp-toast-message {
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padding: $info-vertical-padding ($control-spacing + $row-height) $info-vertical-padding $control-spacing;
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display: table-cell;
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|
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a {
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text-decoration: none;
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color: $msp-btn-commit-on-font-color;
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font-weight: bold;
|
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&:hover {
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text-decoration: underline;
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color: $msp-btn-commit-on-hover-font-color;
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}
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&:active, &:focus {
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color: $msp-btn-commit-on-font-color;
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outline-offset: 0;
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outline: none;
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}
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}
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}
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.msp-toast-hide {
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position: absolute;
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width: $row-height + $control-spacing;
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right: 0;
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top: 0;
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bottom: 0;
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.msp-btn-icon {
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|
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background: transparent;
|
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|
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position: absolute;
|
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|
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top: 1px;
|
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right: 0;
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left: 0;
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bottom: 0;
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width: 100%;
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text-align: right;
|
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|
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padding-right: math.div($control-spacing, 2);
|
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|
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}
|
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|
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}
|
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|
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}
|
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1
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+
|
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2
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+
@use "sass:math";
|
|
3
|
+
|
|
4
|
+
.msp-toast-container {
|
|
5
|
+
position: relative;
|
|
6
|
+
// bottom: $control-spacing;
|
|
7
|
+
// right: $control-spacing;
|
|
8
|
+
// margin-left: $control-spacing;
|
|
9
|
+
z-index: 1001;
|
|
10
|
+
|
|
11
|
+
.msp-toast-entry {
|
|
12
|
+
color: $font-color;
|
|
13
|
+
background: $control-background;
|
|
14
|
+
position: relative;
|
|
15
|
+
float: right;
|
|
16
|
+
min-height: $row-height;
|
|
17
|
+
margin-top: $control-spacing;
|
|
18
|
+
border: 1px solid $border-color;
|
|
19
|
+
display: table;
|
|
20
|
+
|
|
21
|
+
.msp-toast-title {
|
|
22
|
+
height: 100%;
|
|
23
|
+
line-height: $row-height;
|
|
24
|
+
padding: 0 $control-spacing;
|
|
25
|
+
background: $default-background;
|
|
26
|
+
font-weight: bold;
|
|
27
|
+
display: table-cell;
|
|
28
|
+
|
|
29
|
+
-webkit-user-select: none; /* Chrome/Safari */
|
|
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|
+
-moz-user-select: none; /* Firefox */
|
|
31
|
+
-ms-user-select: none; /* IE10+ */
|
|
32
|
+
|
|
33
|
+
/* Rules below not implemented in browsers yet */
|
|
34
|
+
-o-user-select: none;
|
|
35
|
+
user-select: none;
|
|
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|
+
|
|
37
|
+
font-weight: light;
|
|
38
|
+
|
|
39
|
+
cursor: pointer;
|
|
40
|
+
}
|
|
41
|
+
|
|
42
|
+
.msp-toast-message {
|
|
43
|
+
padding: $info-vertical-padding ($control-spacing + $row-height) $info-vertical-padding $control-spacing;
|
|
44
|
+
display: table-cell;
|
|
45
|
+
|
|
46
|
+
a {
|
|
47
|
+
text-decoration: none;
|
|
48
|
+
color: $msp-btn-commit-on-font-color;
|
|
49
|
+
font-weight: bold;
|
|
50
|
+
|
|
51
|
+
&:hover {
|
|
52
|
+
text-decoration: underline;
|
|
53
|
+
color: $msp-btn-commit-on-hover-font-color;
|
|
54
|
+
}
|
|
55
|
+
|
|
56
|
+
&:active, &:focus {
|
|
57
|
+
color: $msp-btn-commit-on-font-color;
|
|
58
|
+
outline-offset: 0;
|
|
59
|
+
outline: none;
|
|
60
|
+
}
|
|
61
|
+
}
|
|
62
|
+
}
|
|
63
|
+
|
|
64
|
+
.msp-toast-hide {
|
|
65
|
+
position: absolute;
|
|
66
|
+
width: $row-height + $control-spacing;
|
|
67
|
+
right: 0;
|
|
68
|
+
top: 0;
|
|
69
|
+
bottom: 0;
|
|
70
|
+
|
|
71
|
+
.msp-btn-icon {
|
|
72
|
+
background: transparent;
|
|
73
|
+
position: absolute;
|
|
74
|
+
top: 1px;
|
|
75
|
+
right: 0;
|
|
76
|
+
left: 0;
|
|
77
|
+
bottom: 0;
|
|
78
|
+
width: 100%;
|
|
79
|
+
text-align: right;
|
|
80
|
+
padding-right: math.div($control-spacing, 2);
|
|
81
|
+
}
|
|
82
|
+
}
|
|
83
|
+
}
|
|
84
84
|
}
|
|
@@ -1,164 +1,164 @@
|
|
|
1
|
-
.msp-transformer {
|
|
2
|
-
|
|
3
|
-
.msp-entity-badge {
|
|
4
|
-
position: absolute;
|
|
5
|
-
top: 0;
|
|
6
|
-
right: 0;
|
|
7
|
-
height: $row-height;
|
|
8
|
-
line-height: $row-height;
|
|
9
|
-
width: $row-height;
|
|
10
|
-
}
|
|
11
|
-
}
|
|
12
|
-
|
|
13
|
-
.msp-layout-right, .msp-layout-left {
|
|
14
|
-
background: $control-background;
|
|
15
|
-
}
|
|
16
|
-
|
|
17
|
-
.msp-transformer-wrapper {
|
|
18
|
-
position: relative;
|
|
19
|
-
}
|
|
20
|
-
|
|
21
|
-
.msp-transformer-wrapper {
|
|
22
|
-
|
|
23
|
-
.msp-entity-badge {
|
|
24
|
-
left: 0;
|
|
25
|
-
top: 0;
|
|
26
|
-
}
|
|
27
|
-
|
|
28
|
-
&:first-child {
|
|
29
|
-
.msp-panel-description-content {
|
|
30
|
-
top: $row-height + 1;
|
|
31
|
-
}
|
|
32
|
-
}
|
|
33
|
-
|
|
34
|
-
&:not(:first-child) {
|
|
35
|
-
.msp-panel-description-content {
|
|
36
|
-
bottom: $row-height + 1;
|
|
37
|
-
}
|
|
38
|
-
}
|
|
39
|
-
}
|
|
40
|
-
|
|
41
|
-
.msp-transform-wrapper {
|
|
42
|
-
margin-bottom: $control-spacing;
|
|
43
|
-
}
|
|
44
|
-
|
|
45
|
-
.msp-transform-wrapper-collapsed {
|
|
46
|
-
margin-bottom: 1px;
|
|
47
|
-
}
|
|
48
|
-
|
|
49
|
-
.msp-transform-update-wrapper {
|
|
50
|
-
margin-bottom: 1px;
|
|
51
|
-
}
|
|
52
|
-
|
|
53
|
-
.msp-transform-update-wrapper-collapsed {
|
|
54
|
-
margin-bottom: 1px;
|
|
55
|
-
}
|
|
56
|
-
|
|
57
|
-
.msp-transform-update-wrapper, .msp-transform-update-wrapper-collapsed {
|
|
58
|
-
> .msp-transform-header > button {
|
|
59
|
-
text-align: left;
|
|
60
|
-
padding-left: $row-height;
|
|
61
|
-
line-height: 24px;
|
|
62
|
-
background: color-lower-contrast($control-background, 4%); // $control-background; // color-lower-contrast($default-background, 4%);
|
|
63
|
-
// font-weight: bold;
|
|
64
|
-
}
|
|
65
|
-
}
|
|
66
|
-
|
|
67
|
-
.msp-transform-wrapper > .msp-transform-header > button {
|
|
68
|
-
text-align: left;
|
|
69
|
-
background: $default-background; // color-lower-contrast($default-background, 4%);
|
|
70
|
-
font-weight: bold;
|
|
71
|
-
padding-right: 5px;
|
|
72
|
-
}
|
|
73
|
-
|
|
74
|
-
.msp-transform-header {
|
|
75
|
-
position: relative;
|
|
76
|
-
// border-top: 1px solid $entity-color-Behaviour; // TODO: separate color
|
|
77
|
-
|
|
78
|
-
// > button {
|
|
79
|
-
// text-align: left;
|
|
80
|
-
// padding-left: $row-height;
|
|
81
|
-
// background: $control-background; // color-lower-contrast($default-background, 4%);
|
|
82
|
-
// font-weight: bold;
|
|
83
|
-
// }
|
|
84
|
-
|
|
85
|
-
> button > small {
|
|
86
|
-
font-weight: normal;
|
|
87
|
-
float: right;
|
|
88
|
-
}
|
|
89
|
-
|
|
90
|
-
> button {
|
|
91
|
-
> span:first-child {
|
|
92
|
-
margin-right: 10px;
|
|
93
|
-
}
|
|
94
|
-
}
|
|
95
|
-
|
|
96
|
-
> button:hover {
|
|
97
|
-
color: color-lower-contrast($font-color, 15%);
|
|
98
|
-
}
|
|
99
|
-
}
|
|
100
|
-
|
|
101
|
-
.msp-transform-header-brand {
|
|
102
|
-
// padding-left: 42px;
|
|
103
|
-
margin-bottom: -1px;
|
|
104
|
-
svg {
|
|
105
|
-
fill: $font-color;
|
|
106
|
-
stroke: $font-color;
|
|
107
|
-
}
|
|
108
|
-
// > div {
|
|
109
|
-
// position: absolute;
|
|
110
|
-
// height: 32px;
|
|
111
|
-
// line-height: 32px;
|
|
112
|
-
// width: 32px;
|
|
113
|
-
// top: 0;
|
|
114
|
-
// left: 0;
|
|
115
|
-
// text-align: center;
|
|
116
|
-
// color: #eceff3;
|
|
117
|
-
// fill: #eceff3;
|
|
118
|
-
// stroke: #eceff3;
|
|
119
|
-
// font-size: 85%;
|
|
120
|
-
// }
|
|
121
|
-
}
|
|
122
|
-
|
|
123
|
-
.msp-transform-default-params {
|
|
124
|
-
background: $default-background;
|
|
125
|
-
position: absolute;
|
|
126
|
-
left: 0;
|
|
127
|
-
top: 0;
|
|
128
|
-
width: $row-height;
|
|
129
|
-
padding: 0;
|
|
130
|
-
}
|
|
131
|
-
|
|
132
|
-
.msp-transform-default-params:hover {
|
|
133
|
-
background: color-lower-contrast($default-background, 20%);
|
|
134
|
-
}
|
|
135
|
-
|
|
136
|
-
.msp-transform-apply-wrap {
|
|
137
|
-
position: relative;
|
|
138
|
-
margin-top: 1px;
|
|
139
|
-
width: 100%;
|
|
140
|
-
height: $row-height;
|
|
141
|
-
}
|
|
142
|
-
|
|
143
|
-
.msp-transform-refresh {
|
|
144
|
-
width: $control-label-width + $control-spacing - $row-height - 1;
|
|
145
|
-
margin-left: $row-height + 1;
|
|
146
|
-
background: $default-background;
|
|
147
|
-
text-align: right;
|
|
148
|
-
}
|
|
149
|
-
|
|
150
|
-
.msp-transform-apply {
|
|
151
|
-
display: block;
|
|
152
|
-
position: absolute;
|
|
153
|
-
left: $control-label-width + $control-spacing;
|
|
154
|
-
right: 0;
|
|
155
|
-
top: 0;
|
|
156
|
-
}
|
|
157
|
-
|
|
158
|
-
.msp-transform-apply-wider {
|
|
159
|
-
margin-left: $row-height + 1px;
|
|
160
|
-
}
|
|
161
|
-
|
|
162
|
-
.msp-data-beh {
|
|
163
|
-
margin: $control-spacing 0 !important;
|
|
1
|
+
.msp-transformer {
|
|
2
|
+
|
|
3
|
+
.msp-entity-badge {
|
|
4
|
+
position: absolute;
|
|
5
|
+
top: 0;
|
|
6
|
+
right: 0;
|
|
7
|
+
height: $row-height;
|
|
8
|
+
line-height: $row-height;
|
|
9
|
+
width: $row-height;
|
|
10
|
+
}
|
|
11
|
+
}
|
|
12
|
+
|
|
13
|
+
.msp-layout-right, .msp-layout-left {
|
|
14
|
+
background: $control-background;
|
|
15
|
+
}
|
|
16
|
+
|
|
17
|
+
.msp-transformer-wrapper {
|
|
18
|
+
position: relative;
|
|
19
|
+
}
|
|
20
|
+
|
|
21
|
+
.msp-transformer-wrapper {
|
|
22
|
+
|
|
23
|
+
.msp-entity-badge {
|
|
24
|
+
left: 0;
|
|
25
|
+
top: 0;
|
|
26
|
+
}
|
|
27
|
+
|
|
28
|
+
&:first-child {
|
|
29
|
+
.msp-panel-description-content {
|
|
30
|
+
top: $row-height + 1;
|
|
31
|
+
}
|
|
32
|
+
}
|
|
33
|
+
|
|
34
|
+
&:not(:first-child) {
|
|
35
|
+
.msp-panel-description-content {
|
|
36
|
+
bottom: $row-height + 1;
|
|
37
|
+
}
|
|
38
|
+
}
|
|
39
|
+
}
|
|
40
|
+
|
|
41
|
+
.msp-transform-wrapper {
|
|
42
|
+
margin-bottom: $control-spacing;
|
|
43
|
+
}
|
|
44
|
+
|
|
45
|
+
.msp-transform-wrapper-collapsed {
|
|
46
|
+
margin-bottom: 1px;
|
|
47
|
+
}
|
|
48
|
+
|
|
49
|
+
.msp-transform-update-wrapper {
|
|
50
|
+
margin-bottom: 1px;
|
|
51
|
+
}
|
|
52
|
+
|
|
53
|
+
.msp-transform-update-wrapper-collapsed {
|
|
54
|
+
margin-bottom: 1px;
|
|
55
|
+
}
|
|
56
|
+
|
|
57
|
+
.msp-transform-update-wrapper, .msp-transform-update-wrapper-collapsed {
|
|
58
|
+
> .msp-transform-header > button {
|
|
59
|
+
text-align: left;
|
|
60
|
+
padding-left: $row-height;
|
|
61
|
+
line-height: 24px;
|
|
62
|
+
background: color-lower-contrast($control-background, 4%); // $control-background; // color-lower-contrast($default-background, 4%);
|
|
63
|
+
// font-weight: bold;
|
|
64
|
+
}
|
|
65
|
+
}
|
|
66
|
+
|
|
67
|
+
.msp-transform-wrapper > .msp-transform-header > button {
|
|
68
|
+
text-align: left;
|
|
69
|
+
background: $default-background; // color-lower-contrast($default-background, 4%);
|
|
70
|
+
font-weight: bold;
|
|
71
|
+
padding-right: 5px;
|
|
72
|
+
}
|
|
73
|
+
|
|
74
|
+
.msp-transform-header {
|
|
75
|
+
position: relative;
|
|
76
|
+
// border-top: 1px solid $entity-color-Behaviour; // TODO: separate color
|
|
77
|
+
|
|
78
|
+
// > button {
|
|
79
|
+
// text-align: left;
|
|
80
|
+
// padding-left: $row-height;
|
|
81
|
+
// background: $control-background; // color-lower-contrast($default-background, 4%);
|
|
82
|
+
// font-weight: bold;
|
|
83
|
+
// }
|
|
84
|
+
|
|
85
|
+
> button > small {
|
|
86
|
+
font-weight: normal;
|
|
87
|
+
float: right;
|
|
88
|
+
}
|
|
89
|
+
|
|
90
|
+
> button {
|
|
91
|
+
> span:first-child {
|
|
92
|
+
margin-right: 10px;
|
|
93
|
+
}
|
|
94
|
+
}
|
|
95
|
+
|
|
96
|
+
> button:hover {
|
|
97
|
+
color: color-lower-contrast($font-color, 15%);
|
|
98
|
+
}
|
|
99
|
+
}
|
|
100
|
+
|
|
101
|
+
.msp-transform-header-brand {
|
|
102
|
+
// padding-left: 42px;
|
|
103
|
+
margin-bottom: -1px;
|
|
104
|
+
svg {
|
|
105
|
+
fill: $font-color;
|
|
106
|
+
stroke: $font-color;
|
|
107
|
+
}
|
|
108
|
+
// > div {
|
|
109
|
+
// position: absolute;
|
|
110
|
+
// height: 32px;
|
|
111
|
+
// line-height: 32px;
|
|
112
|
+
// width: 32px;
|
|
113
|
+
// top: 0;
|
|
114
|
+
// left: 0;
|
|
115
|
+
// text-align: center;
|
|
116
|
+
// color: #eceff3;
|
|
117
|
+
// fill: #eceff3;
|
|
118
|
+
// stroke: #eceff3;
|
|
119
|
+
// font-size: 85%;
|
|
120
|
+
// }
|
|
121
|
+
}
|
|
122
|
+
|
|
123
|
+
.msp-transform-default-params {
|
|
124
|
+
background: $default-background;
|
|
125
|
+
position: absolute;
|
|
126
|
+
left: 0;
|
|
127
|
+
top: 0;
|
|
128
|
+
width: $row-height;
|
|
129
|
+
padding: 0;
|
|
130
|
+
}
|
|
131
|
+
|
|
132
|
+
.msp-transform-default-params:hover {
|
|
133
|
+
background: color-lower-contrast($default-background, 20%);
|
|
134
|
+
}
|
|
135
|
+
|
|
136
|
+
.msp-transform-apply-wrap {
|
|
137
|
+
position: relative;
|
|
138
|
+
margin-top: 1px;
|
|
139
|
+
width: 100%;
|
|
140
|
+
height: $row-height;
|
|
141
|
+
}
|
|
142
|
+
|
|
143
|
+
.msp-transform-refresh {
|
|
144
|
+
width: $control-label-width + $control-spacing - $row-height - 1;
|
|
145
|
+
margin-left: $row-height + 1;
|
|
146
|
+
background: $default-background;
|
|
147
|
+
text-align: right;
|
|
148
|
+
}
|
|
149
|
+
|
|
150
|
+
.msp-transform-apply {
|
|
151
|
+
display: block;
|
|
152
|
+
position: absolute;
|
|
153
|
+
left: $control-label-width + $control-spacing;
|
|
154
|
+
right: 0;
|
|
155
|
+
top: 0;
|
|
156
|
+
}
|
|
157
|
+
|
|
158
|
+
.msp-transform-apply-wider {
|
|
159
|
+
margin-left: $row-height + 1px;
|
|
160
|
+
}
|
|
161
|
+
|
|
162
|
+
.msp-data-beh {
|
|
163
|
+
margin: $control-spacing 0 !important;
|
|
164
164
|
}
|