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v3.43.1
...
safari-deb
| Author | SHA1 | Date | |
|---|---|---|---|
|
1db0ada684 |
@@ -18,7 +18,7 @@
|
||||
],
|
||||
"brace-style": "off",
|
||||
"comma-spacing": "off",
|
||||
"space-infix-ops": "off",
|
||||
"space-infix-ops": "error",
|
||||
"comma-dangle": "off",
|
||||
"eqeqeq": [
|
||||
"error",
|
||||
@@ -55,8 +55,7 @@
|
||||
"block-spacing": "error",
|
||||
"keyword-spacing": "off",
|
||||
"space-before-blocks": "error",
|
||||
"semi-spacing": "error",
|
||||
"no-constant-binary-expression": "error"
|
||||
"semi-spacing": "error"
|
||||
},
|
||||
"overrides": [
|
||||
{
|
||||
@@ -108,7 +107,6 @@
|
||||
"1tbs", { "allowSingleLine": true }
|
||||
],
|
||||
"@typescript-eslint/comma-spacing": "error",
|
||||
"@typescript-eslint/space-infix-ops": "error",
|
||||
"@typescript-eslint/space-before-function-paren": ["error", {
|
||||
"anonymous": "always",
|
||||
"named": "never",
|
||||
|
||||
10
.github/pull_request_template.md
vendored
10
.github/pull_request_template.md
vendored
@@ -1,10 +0,0 @@
|
||||
<!-- Thank you for contributing to Mol* -->
|
||||
|
||||
# Description
|
||||
|
||||
|
||||
## Actions
|
||||
|
||||
- [ ] Added description of changes to the `[Unreleased]` section of `CHANGELOG.md`
|
||||
- [ ] Updated headers of modified files
|
||||
- [ ] Added my name to `package.json`'s `contributors`
|
||||
4
.github/workflows/node.yml
vendored
4
.github/workflows/node.yml
vendored
@@ -1,5 +1,3 @@
|
||||
name: Build
|
||||
|
||||
on:
|
||||
push:
|
||||
pull_request:
|
||||
@@ -17,6 +15,6 @@ jobs:
|
||||
- name: Lint
|
||||
run: npm run lint
|
||||
- name: Test
|
||||
run: npm install --no-save "gl@^6.0.2" && xvfb-run --auto-servernum npm run jest
|
||||
run: npm install --no-save "gl@^5.0.0" && xvfb-run --auto-servernum npm run jest
|
||||
- name: Build
|
||||
run: npm run build
|
||||
|
||||
18
.travis.yml
Normal file
18
.travis.yml
Normal file
@@ -0,0 +1,18 @@
|
||||
language: node_js
|
||||
os: linux
|
||||
sudo: required
|
||||
dist: trusty
|
||||
before_install:
|
||||
- sudo apt-get install -y mesa-utils
|
||||
- sudo apt-get install -y xvfb
|
||||
- sudo apt-get install -y libgl1-mesa-dri
|
||||
- sudo apt-get install -y libglapi-mesa
|
||||
- sudo apt-get install -y libosmesa6
|
||||
- sudo apt-get install -y gcc-4.9
|
||||
- sudo apt-get install -y libstdc++6
|
||||
- sudo apt-get install -y libxi-dev
|
||||
node_js:
|
||||
- "12"
|
||||
- "10"
|
||||
before_script:
|
||||
- export DISPLAY=:99.0; sh -e /etc/init.d/xvfb start
|
||||
1
.vscode/extensions.json
vendored
1
.vscode/extensions.json
vendored
@@ -6,6 +6,7 @@
|
||||
"recommendations": [
|
||||
"dbaeumer.vscode-eslint",
|
||||
"firsttris.vscode-jest-runner",
|
||||
"msjsdiag.debugger-for-chrome",
|
||||
"slevesque.shader",
|
||||
"stpn.vscode-graphql",
|
||||
"wayou.vscode-todo-highlight"
|
||||
|
||||
394
CHANGELOG.md
394
CHANGELOG.md
@@ -6,400 +6,6 @@ Note that since we don't clearly distinguish between a public and private interf
|
||||
|
||||
## [Unreleased]
|
||||
|
||||
## [v3.43.1] - 2023-12-02
|
||||
|
||||
- Fix `react-markdown` dependency
|
||||
|
||||
## [v3.43.0] - 2023-12-02
|
||||
|
||||
- Fix `State.tryGetCellData` (return type & data check)
|
||||
- Don't change camera.target unless flyMode or pointerLock are enabled
|
||||
- Handle empty CIF files
|
||||
- Snapshot improvements:
|
||||
- Add `key` property
|
||||
- Ability to existing snapshot name, key, and description
|
||||
- Support markdown in descriptions (ignores all HTML tags)
|
||||
- Ability to link to snapshots by key from descriptions
|
||||
- Separate UI control showing description of the current snapshot
|
||||
- Do not activate drag overlay for non-file content
|
||||
- Add `structure-element-sphere` visual to `spacefill` representation
|
||||
- Fix missing `await` in `HeadlessPluginContext.saveStateSnapshot`
|
||||
- Added support for providing custom sequence viewers to the plugin spec
|
||||
- MolViewSpec extension (MVS)
|
||||
- Add URL parameters `mvs-url`, `mvs-data`, `mvs-format`
|
||||
- Add drag&drop for `.mvsj` files
|
||||
- Fix `bumpiness` scaling with `ignoreLight` enabled
|
||||
- Add `transforms` & `label` params to `ShapeFromPly`
|
||||
- Optimize `LociSelectManager.selectOnly` to avoid superfluous loci set operations
|
||||
- Dispose of viewer on `unload` event to aid GC
|
||||
|
||||
## [v3.42.0] - 2023-11-05
|
||||
|
||||
- Fix handling of PDB files with insertion codes (#945)
|
||||
- Fix de-/saturate of colors with no hue
|
||||
- Improve `distinctColors` function
|
||||
- Add `sort` and `sampleCountFactor` parameters
|
||||
- Fix clustering issues
|
||||
- Add `clipPrimitive` option to spheres geometry, clipping whole spheres instead of cutting them
|
||||
- Add `DragAndDropManager`
|
||||
- Add `options` support for default bond labels
|
||||
|
||||
## [v3.41.0] - 2023-10-15
|
||||
|
||||
- Add `PluginContext.initialized` promise & support for it in the `Plugin` UI component.
|
||||
- Fix undesired interaction between settings panel and the panel on the right.
|
||||
- Add ability to customize server parameters for `RCSBAssemblySymmetry`.
|
||||
|
||||
## [v3.40.1] - 2023-09-30
|
||||
|
||||
- Do not call `updateFocusRepr` if default `StructureFocusRepresentation` isn't present.
|
||||
- Treat "tap" as a click in `InputObserver`
|
||||
- ModelServer ligand queries: fix atom count reported by SDF/MOL/MOL2 export
|
||||
- CCD extension: Make visuals for aromatic bonds configurable
|
||||
- Add optional `file?: CifFile` to `MmcifFormat.data`
|
||||
- Add support for webgl extensions
|
||||
- `WEBGL_clip_cull_distance`
|
||||
- `EXT_conservative_depth`
|
||||
- `WEBGL_stencil_texturing`
|
||||
- `EXT_clip_control`
|
||||
- Add `MultiSampleParams.reduceFlicker` (to be able to switch it off)
|
||||
- Add `alphaThickness` parameter to adjust alpha of spheres for radius
|
||||
- Ability to hide "right" panel from simplified viewport controls
|
||||
- Add `blockIndex` parameter to TrajectoryFromMmCif
|
||||
- Fix bounding sphere calculation for "element-like" visuals
|
||||
- Fix RCSB PDB validation report URL
|
||||
- Add sharpening postprocessing option
|
||||
- Take pixel-ratio into account for outline scale
|
||||
- Gracefully handle missing HTMLImageElement
|
||||
- Fix pixel-ratio changes not applied to all render passes
|
||||
|
||||
## [v3.39.0] - 2023-09-02
|
||||
|
||||
- Add some elements support for `guessElementSymbolString` function
|
||||
- Faster bounding rectangle calculation for imposter spheres
|
||||
- Allow toggling of hydrogens as part of `LabelTextVisual`
|
||||
|
||||
## [v3.38.3] - 2023-07-29
|
||||
|
||||
- Fix imposter spheres not updating, e.g. in trajectories (broke in v3.38.0)
|
||||
|
||||
## [v3.38.2] - 2023-07-24
|
||||
|
||||
- Don't rely solely on `chem_comp_atom` when detecting CCD files (#877)
|
||||
- Actually support non-physical keys in `Bindings.Trigger.code`
|
||||
|
||||
## [v3.38.1] - 2023-07-22
|
||||
|
||||
- Fix pixel-scale not updated in SSAO pass
|
||||
|
||||
## [v3.38.0] - 2023-07-18
|
||||
|
||||
- Fix display issue with SIFTS mapping
|
||||
- Support non-physical keys in `Bindings.Trigger.code`
|
||||
- Update `getStateSnapshot` to only overwrite current snapshot if it was created automatically
|
||||
- Fix distinct palette's `getSamples` infinite loop
|
||||
- Add 'NH2', 'FOR', 'FMT' to `CommonProteinCaps`
|
||||
- Add `opened` event to `PluginStateSnapshotManager`
|
||||
- Properly switch-off fog
|
||||
- Add `approximate` option for spheres rendering
|
||||
- Reduce `Spheres` memory usage
|
||||
- Derive mapping from VertexID
|
||||
- Pull position and group from texture
|
||||
- Add `Euler` math primitive
|
||||
- Add stride option to element sphere & point visuals
|
||||
- Add `disabledExtensions` field to default viewer's options
|
||||
- Add `LRUCache.remove`
|
||||
- Add 'Chain Instance' and 'Uniform' options for 'Carbon Color' param (in Color Theme: Element Symbol)
|
||||
|
||||
## [v3.37.1] - 2023-06-20
|
||||
|
||||
- Fix issues with wboit/dpoit in large scenes
|
||||
- Fix lines, text, points rendering (broken in v3.37.0)
|
||||
|
||||
## [v3.37.0] - 2023-06-17
|
||||
|
||||
- Add `inverted` option to `xrayShaded` parameter
|
||||
- Model-export extension: Add ability to set a file name for structures
|
||||
- Add `contextHash` to `SizeTheme`
|
||||
- Add mipmap-based blur for image backgrounds
|
||||
|
||||
## [v3.36.1] - 2023-06-11
|
||||
|
||||
- Allow parsing of CCD ligand files
|
||||
- Add dedicated wwPDB CCD extension to align and visualize ideal & model CCD coordinates
|
||||
- Make operators in `IndexPairBonds` a directed property
|
||||
- Remove erroneous bounding-box overlap test in `Structure.eachUnitPair`
|
||||
- Fix `EdgeBuilder.addNextEdge` for loop edges
|
||||
- Optimize inter unit bond compute
|
||||
- Ensure consistent state for volume representation (#210)
|
||||
- Improve SSAO for thin geometry (e.g. lines)
|
||||
- Add snapshot support for structure selections
|
||||
- Add `nucleicProfile` parameter to cartoon representation
|
||||
- Add `cartoon` theme with separate colorings for for mainchain and sidechain visuals
|
||||
|
||||
## [v3.35.0] - 2023-05-14
|
||||
|
||||
- Enable odd dash count (1,3,5)
|
||||
- Add principal axes spec and fix edge cases
|
||||
- Add a uniform color theme for NtC tube that still paints residue and segment dividers in a different color
|
||||
- Mesh exporter improvements
|
||||
- Support points & lines in glTF export
|
||||
- Set alphaMode and doubleSided in glTF export
|
||||
- Fix flipped cylinder caps
|
||||
- Fix bond assignments `struct_conn` records referencing waters
|
||||
- Add StructConn extension providing functions for inspecting struct_conns
|
||||
- Fix `PluginState.setSnapshot` triggering unnecessary state updates
|
||||
- Fix an edge case in the `mol-state`'s `State` when trying to apply a transform to an existing Null object
|
||||
- Add `SbNcbrPartialCharges` extension for coloring and labeling atoms and residues by partial atomic charges
|
||||
- uses custom mmcif categories `_sb_ncbr_partial_atomic_charges_meta` and `_sb_ncbr_partial_atomic_charges` (more info in [README.md](./src/extensions/sb-ncbr/README.md))
|
||||
- Parse HEADER record when reading PDB file
|
||||
- Support `ignoreHydrogens` in interactions representation
|
||||
- Add hydroxyproline (HYP) commonly present in collagen molecules to the list of amino acids
|
||||
- Fix assemblies for Archive PDB files (do not generate unique `label_asym_id` if `REMARK 350` is present)
|
||||
- Add additional functions to `core.math` in `mol-script`
|
||||
- `cantorPairing`, `sortedCantorPairing`, `invertCantorPairing`,
|
||||
- `trunc`, `sign`
|
||||
|
||||
## [v3.34.0] - 2023-04-16
|
||||
|
||||
- Avoid `renderMarkingDepth` for fully transparent renderables
|
||||
- Remove `camera.far` doubling workaround
|
||||
- Add `ModifiersKeys.areNone` helper function
|
||||
- Do not render NtC tube segments unless all required atoms are present in the structure
|
||||
- Fix rendering issues caused by VAO reuse
|
||||
- Add "Zoom All", "Orient Axes", "Reset Axes" buttons to the "Reset Camera" button
|
||||
- Improve trackball move-state handling when key bindings use modifiers
|
||||
- Fix rendering with very small viewport and SSAO enabled
|
||||
- Fix `.getAllLoci` for structure representations with `structure.child`
|
||||
- Fix `readAllLinesAsync` refering to dom length property
|
||||
- Make mol-util/file-info node compatible
|
||||
- Add `eachLocation` to representation/visual interface
|
||||
|
||||
## [v3.33.0] - 2023-04-02
|
||||
|
||||
- Handle resizes of viewer element even when window remains the same size
|
||||
- Throttle canvas resize events
|
||||
- Selection toggle buttons hidden if selection mode is off
|
||||
- Camera focus loci bindings allow reset on click-away to be overridden
|
||||
- Input/controls improvements
|
||||
- Move or fly around the scene using keys
|
||||
- Pointer lock to look around scene
|
||||
- Toggle spin/rock animation using keys
|
||||
- Apply bumpiness as lightness variation with `ignoreLight`
|
||||
- Remove `JSX` reference from `loci-labels.ts`
|
||||
- Fix overpaint/transparency/substance smoothing not updated when geometry changes
|
||||
- Fix camera project/unproject when using offset viewport
|
||||
- Add support for loading all blocks from a mmcif file as a trajectory
|
||||
- Add `Frustum3D` and `Plane3D` math primitives
|
||||
- Include `occupancy` and `B_iso_or_equiv` when creating `Conformation` from `Model`
|
||||
- Remove LazyImports (introduced in v3.31.1)
|
||||
|
||||
## [v3.32.0] - 2023-03-20
|
||||
|
||||
- Avoid rendering of fully transparent renderables
|
||||
- Add occlusion color parameter
|
||||
- Fix issue with outlines and orthographic camera
|
||||
- Reduce over-blurring occlusion at larger view distances
|
||||
- Fix occlusion artefact with non-canvas viewport and pixel-ratio > 1
|
||||
- Update nodejs-shims conditionals to handle polyfilled document object in NodeJS environment.
|
||||
- Ensure marking edges are at least one pixel wide
|
||||
- Add exposure parameter to renderer
|
||||
- Only trigger marking when mouse is directly over canvas
|
||||
- Fix blurry occlusion in screenshots
|
||||
- [Breaking] Add `setFSModule` to `mol-util/data-source` instead of trying to trick WebPack
|
||||
|
||||
## [v3.31.4] - 2023-02-24
|
||||
|
||||
- Allow link cylinder/line `dashCount` set to '0'
|
||||
- Stop animation loop when disposing `PluginContext` (thanks @gfrn for identifying the issue)
|
||||
|
||||
## [v3.31.3] - 2023-02-22
|
||||
|
||||
- Fix impostor bond visuals not correctly updating on `sizeFactor` changes
|
||||
- Fix degenerate case in PCA
|
||||
- Fix near clipping avoidance in impostor shaders
|
||||
- Update `fs` import in `data-source.ts`
|
||||
|
||||
## [v3.31.2] - 2023-02-12
|
||||
|
||||
- Fix exit code of volume pack executable (pack.ts). Now exits with non-0 status when an error happens
|
||||
- Remove pca transform from components ui focus (too distracting)
|
||||
- Fix artefacts with opaque outlines behind transparent objects
|
||||
- Fix polymer trace visual not updating
|
||||
- Fix use of `WEBGL_provoking_vertex`
|
||||
|
||||
## [v3.31.1] - 2023-02-05
|
||||
|
||||
- Improve Component camera focus based on the PCA of the structure and the following rules:
|
||||
- The first residue should be in first quadrant if there is only one chain
|
||||
- The average position of the residues of the first chain should be in the first quadrant if there is more than one chain
|
||||
- Add `HeadlessPluginContext` and `HeadlessScreenshotHelper` to be used in Node.js
|
||||
- Add example `image-renderer`
|
||||
- Fix wrong offset when rendering text with orthographic projection
|
||||
- Update camera/handle helper when `devicePixelRatio` changes
|
||||
- Add various options to customize the axes camera-helper
|
||||
- Fix issue with texture-mesh color smoothing when changing themes
|
||||
- Add fast boundary helper and corresponding unit trait
|
||||
- Add Observable for Canvas3D commits
|
||||
|
||||
## [v3.30.0] - 2023-01-29
|
||||
|
||||
- Improve `Dnatco` extension
|
||||
- Factor out common code in `Dnatco` extension
|
||||
- Add `NtC tube` visual. Applicable for structures with NtC annotation
|
||||
- [Breaking] Rename `DnatcoConfalPyramids` to `DnatcoNtCs`
|
||||
- Improve boundary calculation performance
|
||||
- Add option to create & include images in state snapshots
|
||||
- Fix SSAO artefacts with high bias values
|
||||
- Fix SSAO resolution scale parameter handling
|
||||
- Improve outlines, visually more stable at different view distances
|
||||
|
||||
## [v3.29.0] - 2023-01-15
|
||||
|
||||
- `meshes` extension: Fixed a bug in mesh visualization (show backfaces when opacity < 1)
|
||||
- Add color quick select control to Volume controls
|
||||
- Fix `dropFiles` bug
|
||||
- Fix some cyclic imports and reduce the use of const enums. This should make it easier to use the library with the `isolatedModules: true` TS config.
|
||||
- Fix `dropFiles` bug (#679)
|
||||
- Add `input type='color'` picker to `CombinedColorControl`
|
||||
- Set `ParameterMappingControl` disabled when state is updating
|
||||
- Performance tweaks
|
||||
- Update clip `defines` only when changed
|
||||
- Check for identity in structure/unit areEqual methods
|
||||
- Avoid cloning of structure representation parameters
|
||||
- Make SymmetryOperator.createMapping monomorphic
|
||||
- Improve bonding-sphere calculation
|
||||
- Defer Scene properties calculation (markerAverage, opacityAverage, hasOpaque)
|
||||
- Improve checks in in UnitsRepresentation setVisualState
|
||||
- Add StructureElement.Loci.forEachLocation
|
||||
- Add RepresentationRegistry.clear and ThemeRegistry.clear
|
||||
- Add generic Loci support for overpaint, substance, clipping themes
|
||||
- Add `.getCenter` and `.center` to `Camera`
|
||||
- Add support to dim unmarked groups
|
||||
- Add support for marker edge strength
|
||||
|
||||
## [v3.28.0] - 2022-12-20
|
||||
|
||||
- Show histogram in direct volume control point settings
|
||||
- Add `solidInterior` parameter to sphere/cylinder impostors
|
||||
- [Breaking] Tweak `ignoreHydrogens` non-polar handling (introduced in 3.27.0)
|
||||
- Add `meshes` and `volumes-and-segmentations` extensions
|
||||
- See https://molstarvolseg.ncbr.muni.cz/ for more info
|
||||
- Fix missing support for info in `ParamDefinition.Converted`
|
||||
- Add support for multi-visual volume representations
|
||||
- Improve volume isosurface bounding-sphere
|
||||
- Add basic volume segmentation support to core
|
||||
- Add `Volume.Segment` model
|
||||
- Add `Segmentation` custom volume property
|
||||
- Add `SegmentRepresentation` representation
|
||||
- Add `volume-segment` color theme
|
||||
- Fix GPU marching cubes failing for large meshes with webgl2 (due to use of float16)
|
||||
|
||||
## [v3.27.0] - 2022-12-15
|
||||
|
||||
- Add an `includeTransparent` parameter to hide/show outlines of components that are transparent
|
||||
- Fix 'once' for animations of systems with many frames
|
||||
- Better guard against issue (black fringes) with bumpiness in impostors
|
||||
- Improve impostor shaders
|
||||
- Fix sphere near-clipping with orthographic projection
|
||||
- Fix cylinder near-clipping
|
||||
- Add interior cylinder caps
|
||||
- Add per-pixel object clipping
|
||||
- Fix `QualityAssessment` assignment bug for structures with different auth vs label sequence numbering
|
||||
- Refresh `ApplyActionControl`'s param definition when toggling expanded state
|
||||
- Fix `struct_conn` bond assignment for ions
|
||||
- Ability to show only polar hydrogens
|
||||
|
||||
## [v3.26.0] - 2022-12-04
|
||||
|
||||
- Support for ``powerPreference`` webgl attribute. Add ``PluginConfig.General.PowerPreference`` and ``power-preference`` Viewer GET param.
|
||||
- Excluded common protein caps `NME` and `ACE` from the ligand selection query
|
||||
- Add screen-space shadow post-processing effect
|
||||
- Add "Structure Molecular Surface" visual
|
||||
- Add `external-volume` theme (coloring of arbitrary geometries by user-selected volume)
|
||||
|
||||
## [v3.25.1] - 2022-11-20
|
||||
|
||||
- Fix edge-case in `Structure.eachUnitPair` with single-element units
|
||||
- Fix 'auto' structure-quality for coarse models
|
||||
|
||||
## [v3.25.0] - 2022-11-16
|
||||
|
||||
- Fix handling of gzipped assets (reverts #615)
|
||||
|
||||
## [v3.24.0] - 2022-11-13
|
||||
|
||||
- Make `PluginContext.initContainer` checkered canvas background optional
|
||||
- Store URL of downloaded assets to detect zip/gzip based on extension (#615)
|
||||
- Add optional `operator.key`; can be referenced in `IndexPairBonds`
|
||||
- Add overpaint/transparency/substance theme strength to representations
|
||||
- Fix viewport color for transparent background
|
||||
|
||||
## [v3.23.0] - 2022-10-19
|
||||
|
||||
- Add `PluginContext.initContainer/mount/unmount` methods; these should make it easier to reuse a plugin context with both custom and built-in UI
|
||||
- Add `PluginContext.canvas3dInitialized`
|
||||
- `createPluginUI` now resolves after the 3d canvas has been initialized
|
||||
- Change EM Volume Streaming default from `Whole Structure` to `Auto`
|
||||
|
||||
## [v3.22.0] - 2022-10-17
|
||||
|
||||
- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
|
||||
|
||||
## [v3.21.0] - 2022-10-17
|
||||
|
||||
- Add `VolumeIsosurfaceParams.pickingGranularity` param
|
||||
- Prevent component controls collapsing when option is selected
|
||||
|
||||
## [v3.20.0] - 2022-10-16
|
||||
|
||||
- [Breaking] Rename the ``model-index`` color theme to ``trajectory-index``
|
||||
- Add a new ``model-index`` color theme that uniquely colors each loaded model
|
||||
- Add the new ``model-index`` and ``structure-index`` color themes as an option for the carbon color in the ``element-symbol`` and ``ilustrative`` color themes
|
||||
- Add ``structure-index`` color theme that uniquely colors each root structure
|
||||
- Add ``nearest`` method to ``Lookup3D``
|
||||
- Add mipmap-based blur for skybox backgrounds
|
||||
|
||||
## [v3.19.0] - 2022-10-01
|
||||
|
||||
- Fix "empty textures" error on empty canvas
|
||||
- Optimize BinaryCIF integer packing encoder
|
||||
- Fix dual depth peeling when post-processing is off or when rendering direct-volumes
|
||||
- Add ``cameraClipping.minNear`` parameter
|
||||
- Fix black artifacts on specular highlights with transparent background
|
||||
|
||||
## [v3.18.0] - 2022-09-17
|
||||
|
||||
- Integration of Dual depth peeling - OIT method
|
||||
- Stereo camera improvements
|
||||
- Fix param updates not applied
|
||||
- Better param ranges and description
|
||||
- Add timer.mark for left/right camera
|
||||
|
||||
## [v3.17.0] - 2022-09-11
|
||||
|
||||
- [Fix] Clone ``Canvas3DParams`` when creating a ``Canvas3D`` instance to prevent shared state between multiple instances
|
||||
- Add ``includeResidueTest`` option to ``alignAndSuperposeWithSIFTSMapping``
|
||||
- Add ``parentDisplay`` param for interactions representation.
|
||||
- [Experimental] Add support for PyMOL, VMD, and Jmol atom expressions in selection scripts
|
||||
- Support for ``failIfMajorPerformanceCaveat`` webgl attribute. Add ``PluginConfig.General.AllowMajorPerformanceCaveat`` and ``allow-major-performance-caveat`` Viewer GET param.
|
||||
- Fix handling of PDB TER records (#549)
|
||||
- Add support for getting multiple loci from a representation (``.getAllLoci()``)
|
||||
- Add ``key`` property to intra- and inter-bonds for referencing source data
|
||||
- Fix click event triggered after move
|
||||
|
||||
## [v3.16.0] - 2022-08-25
|
||||
|
||||
- Support ``globalColorParams`` and ``globalSymmetryParams`` in common representation params
|
||||
- Support ``label`` parameter in ``Viewer.loadStructureFromUrl``
|
||||
- Fix ``ViewportHelpContent`` Mouse Controls section
|
||||
|
||||
## [v3.15.0] - 2022-08-23
|
||||
|
||||
- Fix wboit in Safari >=15 (add missing depth renderbuffer to wboit pass)
|
||||
- Add 'Around Camera' option to Volume streaming
|
||||
- Avoid queuing more than one update in Volume streaming
|
||||
|
||||
## [v3.14.0] - 2022-08-20
|
||||
|
||||
- Expose inter-bonds compute params in structure
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
[](./LICENSE)
|
||||
[](https://www.npmjs.com/package/molstar)
|
||||
[](https://github.com/molstar/molstar/actions/workflows/node.yml)
|
||||
[](https://travis-ci.org/molstar/molstar)
|
||||
[](https://gitter.im/molstar/Lobby)
|
||||
|
||||
# Mol*
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 58 KiB |
@@ -1,129 +0,0 @@
|
||||
# Mol* MolViewSpec extension
|
||||
|
||||
**MolViewSpec (MVS)** is a tool for standardized description of reproducible molecular visualizations shareable across software applications.
|
||||
|
||||
MolViewSpec provides a generic description of typical visual scenes that may occur as part of molecular visualizations. A tree format allows the composition of complex scene descriptors by combining reoccurring nodes that serve as building blocks.
|
||||
|
||||
|
||||
## More sources:
|
||||
|
||||
- MolViewSpec home page: https://molstar.org/mol-view-spec/
|
||||
- Python library `molviewspec` for building MolViewSpec views: https://pypi.org/project/molviewspec/
|
||||
- Python library `molviewspec` in action: https://colab.research.google.com/drive/1O2TldXlS01s-YgkD9gy87vWsfCBTYuz9
|
||||
|
||||
|
||||
## MolViewSpec data structure
|
||||
|
||||
MVS is based on a tree format, i.e. a molecular view is described as a tree where individual node types represent common data operations needed to create the view (e.g. download, parse, color). Each node can have parameters that provide additional details for the operation.
|
||||
|
||||
A simple example of a MVS tree showing PDB structure 1cbs:
|
||||
|
||||
|
||||
|
||||
```txt
|
||||
- root {}
|
||||
- download {url: "https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif"}
|
||||
- parse {format: "bcif"}
|
||||
- structure {type: "model"}
|
||||
- component {selector: "polymer"}
|
||||
- representation {type: "cartoon"}
|
||||
- color {color: "green"}
|
||||
- color {selector: {label_asym_id: "A", beg_label_seq_id: 1, end_label_seq_id: 50}, color: "#6688ff"}
|
||||
- label {text: "Protein"}
|
||||
- component {selector: "ligand"}
|
||||
- representation {type: "ball_and_stick"}
|
||||
- color {color: "#cc3399"}
|
||||
- label {text: "Retinoic Acid"}
|
||||
- canvas {background_color: "#ffffee"}
|
||||
- camera {target: [17,21,27], position: [41,34,69], up: [-0.129,0.966,-0.224]}
|
||||
```
|
||||
|
||||
(This is just a human-friendly representation of the tree, not the actual data format!)
|
||||
|
||||
A complete list of supported node types and their parameters is described by the [MVS tree schema](./mvs-tree-schema.md).
|
||||
|
||||
### Encoding
|
||||
|
||||
A MolViewSpec tree can be encoded and stored in `.mvsj` format, which is basically a JSON representation of the tree with additional metadata:
|
||||
|
||||
```json
|
||||
{
|
||||
"metadata": {
|
||||
"title": "Example MolViewSpec - 1cbs with labelled protein and ligand",
|
||||
"version": "1",
|
||||
"timestamp": "2023-11-24T10:38:17.483Z"
|
||||
},
|
||||
"root": {
|
||||
"kind": "root",
|
||||
"children": [
|
||||
{
|
||||
"kind": "download",
|
||||
"params": {"url": "https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif"},
|
||||
"children": [
|
||||
{
|
||||
"kind": "parse",
|
||||
"params": {"format": "bcif"},
|
||||
"children": [
|
||||
...
|
||||
```
|
||||
Complete file: [1cbs.mvsj](../../../examples/mvs/1cbs.mvsj)
|
||||
|
||||
|
||||
## MolViewSpec extension functionality
|
||||
|
||||
Mol* MolViewSpec extension provides functionality for building, validating, and visualizing MVS views.
|
||||
|
||||
### Graphical user interface
|
||||
|
||||
- **Drag&drop support:** The easiest way to load a MVS view into Mol* Viewer is to drag a `.mvsj` file and drop it in a browser window with Mol* Viewer.
|
||||
|
||||
- **Load via menu:** Another way to load a MVS view is to use "Download File" or "Open Files" action, available in the "Home" tab in the left panel. For these actions, the "Format" parameter must be set to "MVSJ" (in the "Miscellaneous" category) or "Auto".
|
||||
|
||||
- **URL parameters:** Mol* Viewer supports `mvs-url`, `mvs-data`, and `mvs-format` URL parameters to specify a MVS view to be loaded when the viewer is initialized.
|
||||
- `mvs-url` specifies the address from which the MVS view should be retrieved.
|
||||
- `mvs-data` specifies the MVS view data directly. Keep in mind that some characters must be escaped to be used in the URL. Also beware that URLs longer than 2000 character may not work in all browsers.
|
||||
- `mvs-format` specifies the format of the MVS view data (from `mvs-url` or `mvs-data`). The only allowed (and default) value is `mvsj`, as this is currently the only supported format.
|
||||
|
||||
Examples of URL parameter usage:
|
||||
|
||||
- https://molstar.org/viewer?mvs-format=mvsj&mvs-url=https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/1cbs.mvsj
|
||||
|
||||
- https://molstar.org/viewer?mvs-format=mvsj&mvs-data=%7B%22metadata%22%3A%7B%22title%22%3A%22Example%20MolViewSpec%20-%201cbs%20with%20labelled%20protein%20and%20ligand%22%2C%22version%22%3A%221%22%2C%22timestamp%22%3A%222023-11-24T10%3A38%3A17.483%22%7D%2C%22root%22%3A%7B%22kind%22%3A%22root%22%2C%22children%22%3A%5B%7B%22kind%22%3A%22download%22%2C%22params%22%3A%7B%22url%22%3A%22https%3A//www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22parse%22%2C%22params%22%3A%7B%22format%22%3A%22bcif%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22structure%22%2C%22params%22%3A%7B%22type%22%3A%22model%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22component%22%2C%22params%22%3A%7B%22selector%22%3A%22polymer%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22representation%22%2C%22params%22%3A%7B%22type%22%3A%22cartoon%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22color%22%2C%22params%22%3A%7B%22color%22%3A%22green%22%7D%7D%2C%7B%22kind%22%3A%22color%22%2C%22params%22%3A%7B%22selector%22%3A%7B%22label_asym_id%22%3A%22A%22%2C%22beg_label_seq_id%22%3A1%2C%22end_label_seq_id%22%3A50%7D%2C%22color%22%3A%22%236688ff%22%7D%7D%5D%7D%2C%7B%22kind%22%3A%22label%22%2C%22params%22%3A%7B%22text%22%3A%22Protein%22%7D%7D%5D%7D%2C%7B%22kind%22%3A%22component%22%2C%22params%22%3A%7B%22selector%22%3A%22ligand%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22representation%22%2C%22params%22%3A%7B%22type%22%3A%22ball_and_stick%22%7D%2C%22children%22%3A%5B%7B%22kind%22%3A%22color%22%2C%22params%22%3A%7B%22color%22%3A%22%23cc3399%22%7D%7D%5D%7D%2C%7B%22kind%22%3A%22label%22%2C%22params%22%3A%7B%22text%22%3A%22Retinoic%20Acid%22%7D%7D%5D%7D%5D%7D%5D%7D%5D%7D%2C%7B%22kind%22%3A%22canvas%22%2C%22params%22%3A%7B%22background_color%22%3A%22%23ffffee%22%7D%7D%2C%7B%22kind%22%3A%22camera%22%2C%22params%22%3A%7B%22target%22%3A%5B17%2C21%2C27%5D%2C%22position%22%3A%5B41%2C34%2C69%5D%2C%22up%22%3A%5B-0.129%2C0.966%2C-0.224%5D%7D%7D%5D%7D%7D
|
||||
|
||||
|
||||
### Programming interface
|
||||
|
||||
Most functions for manipulation of MVS data (including parsing, encoding, validating, and building) are provided by the `MVSData` object (defined in [src/extensions/mvs/mvs-data.ts](../../../src/extensions/mvs/mvs-data.ts)). In TypeScript, `MVSData` is also the type for a MVS view.
|
||||
|
||||
The `loadMVS` function (defined in [src/extensions/mvs/load.ts](../../../src/extensions/mvs/load.ts)) can be used to load MVS view data into Mol* Viewer.
|
||||
|
||||
Example usage:
|
||||
|
||||
```ts
|
||||
// Fetch a MVS, validate, and load
|
||||
const response = await fetch('https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/1cbs.mvsj');
|
||||
const rawData = await response.text();
|
||||
const mvsData: MVSData = MVSData.fromMVSJ(rawData);
|
||||
if (!MVSData.isValid(mvsData)) throw new Error(`Oh no: ${MVSData.validationIssues(mvsData)}`);
|
||||
await loadMVS(this.plugin, mvsData, { replaceExisting: true });
|
||||
console.log('Loaded this:', MVSData.toPrettyString(mvsData));
|
||||
console.log('Loaded this:', MVSData.toMVSJ(mvsData));
|
||||
|
||||
// Build a MVS and load
|
||||
const builder = MVSData.createBuilder();
|
||||
const structure = builder
|
||||
.download({ url: 'https://www.ebi.ac.uk/pdbe/entry-files/download/1og2_updated.cif' })
|
||||
.parse({ format: 'mmcif' })
|
||||
.modelStructure();
|
||||
structure
|
||||
.component({ selector: 'polymer' })
|
||||
.representation({ type: 'cartoon' });
|
||||
structure
|
||||
.component({ selector: 'ligand' })
|
||||
.representation({ type: 'ball_and_stick' })
|
||||
.color({ color: '#aa55ff' as any });
|
||||
const mvsData2: MVSData = builder.getState();
|
||||
await loadMVS(this.plugin, mvsData2, { replaceExisting: false });
|
||||
```
|
||||
|
||||
When using the pre-built Mol* plugin bundle, `MVSData` and `loadMVS` are exposed as `molstar.PluginExtensions.mvs.MVSData` and `molstar.PluginExtensions.mvs.loadMVS`. Furthermore, the `molstar.Viewer` class has `loadMvsFromUrl` and `loadMvsData` methods, providing the same functionality as `mvs-url` and `mvs-data` URL parameters.
|
||||
@@ -1,565 +0,0 @@
|
||||
# MolViewSpec tree schema
|
||||
|
||||
(This documentation was auto-generated by calling `treeSchemaToMarkdown(MVSTreeSchema, MVSDefaults)`)
|
||||
|
||||
- **`root`**
|
||||
|
||||
[Root of the tree must be of this kind]
|
||||
|
||||
Auxiliary node kind that only appears as the tree root.
|
||||
|
||||
Parent: none
|
||||
|
||||
Params: none
|
||||
|
||||
- **`download`**
|
||||
|
||||
This node instructs to retrieve a data resource.
|
||||
|
||||
Parent: `root`
|
||||
|
||||
Params:
|
||||
|
||||
- **`url: `**`string`
|
||||
|
||||
URL of the data resource.
|
||||
|
||||
- **`parse`**
|
||||
|
||||
This node instructs to parse a data resource.
|
||||
|
||||
Parent: `download`
|
||||
|
||||
Params:
|
||||
|
||||
- **`format: `**`"mmcif" | "bcif" | "pdb"`
|
||||
|
||||
Format of the input data resource.
|
||||
|
||||
- **`structure`**
|
||||
|
||||
This node instructs to create a structure from a parsed data resource. "Structure" refers to an internal representation of molecular coordinates without any visual representation.
|
||||
|
||||
Parent: `parse`
|
||||
|
||||
Params:
|
||||
|
||||
- **`type: `**`"model" | "assembly" | "symmetry" | "symmetry_mates"`
|
||||
|
||||
Type of structure to be created (`"model"` for original model coordinates, `"assembly"` for assembly structure, `"symmetry"` for a set of crystal unit cells based on Miller indices, `"symmetry_mates"` for a set of asymmetric units within a radius from the original model).
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read coordinates from (only applies when the input data are from CIF or BinaryCIF). If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read coordinates from (only applies when the input data are from CIF or BinaryCIF and `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`model_index?: `**`Integer`
|
||||
|
||||
0-based index of model in case the input data contain multiple models.
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`assembly_id?: `**`string | null`
|
||||
|
||||
Assembly identifier (only applies when `kind` is `"assembly"`). If `null`, the first assembly is selected.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`radius?: `**`number`
|
||||
|
||||
Distance (in Angstroms) from the original model in which asymmetric units should be included (only applies when `kind` is `"symmetry_mates"`).
|
||||
|
||||
Default: `5`
|
||||
|
||||
- **`ijk_min?: `**`[Integer, Integer, Integer]`
|
||||
|
||||
Miller indices of the bottom-left unit cell to be included (only applies when `kind` is `"symmetry"`).
|
||||
|
||||
Default: `[-1, -1, -1]`
|
||||
|
||||
- **`ijk_max?: `**`[Integer, Integer, Integer]`
|
||||
|
||||
Miller indices of the top-right unit cell to be included (only applies when `kind` is `"symmetry"`).
|
||||
|
||||
Default: `[1, 1, 1]`
|
||||
|
||||
- **`transform`**
|
||||
|
||||
This node instructs to rotate and/or translate structure coordinates.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`rotation?: `**`Array<number>`
|
||||
|
||||
Rotation matrix (3x3 matrix flattened in column major format (j*3+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. The default value is the identity matrix (corresponds to no rotation).
|
||||
|
||||
Default: `[1, 0, 0, 0, 1, 0, 0, 0, 1]`
|
||||
|
||||
- **`translation?: `**`[number, number, number]`
|
||||
|
||||
Translation vector, applied to the structure coordinates after rotation. The default value is the zero vector (corresponds to no translation).
|
||||
|
||||
Default: `[0, 0, 0]`
|
||||
|
||||
- **`component`**
|
||||
|
||||
This node instructs to create a component (i.e. a subset of the parent structure).
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`selector: `**`("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water") | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>>`
|
||||
|
||||
Defines what part of the parent structure should be included in this component.
|
||||
|
||||
Default: `"all"`
|
||||
|
||||
- **`component_from_uri`**
|
||||
|
||||
This node instructs to create a component defined by an external annotation resource.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`uri: `**`string`
|
||||
|
||||
URL of the annotation resource.
|
||||
|
||||
- **`format: `**`"cif" | "bcif" | "json"`
|
||||
|
||||
Format of the annotation resource.
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"` and `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"component"`
|
||||
|
||||
- **`field_values?: `**`Array<string> | null`
|
||||
|
||||
List of component identifiers (i.e. values in the field given by `field_name`) which should be included in this component. If `null`, component identifiers are ignored (all annotation rows are included), and `field_name` field can be dropped from the annotation.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`component_from_source`**
|
||||
|
||||
This node instructs to create a component defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from. If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from. If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"component"`
|
||||
|
||||
- **`field_values?: `**`Array<string> | null`
|
||||
|
||||
List of component identifiers (i.e. values in the field given by `field_name`) which should be included in this component. If `null`, component identifiers are ignored (all annotation rows are included), and `field_name` field can be dropped from the annotation.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`representation`**
|
||||
|
||||
This node instructs to create a visual representation of a component.
|
||||
|
||||
Parent: `component` or `component_from_uri` or `component_from_source`
|
||||
|
||||
Params:
|
||||
|
||||
- **`type: `**`"ball_and_stick" | "cartoon" | "surface"`
|
||||
|
||||
Method of visual representation of the component.
|
||||
|
||||
- **`color`**
|
||||
|
||||
This node instructs to apply color to a visual representation.
|
||||
|
||||
Parent: `representation`
|
||||
|
||||
Params:
|
||||
|
||||
- **`color: `**`HexColor | ("white" | "gray" | "black" | "red" | "orange" | "yellow" | "green" | "cyan" | "blue" | "magenta")`
|
||||
|
||||
Color to apply to the representation. Can be either a color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`).
|
||||
|
||||
- **`selector?: `**`("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water") | Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }> | Array<Partial<{ label_entity_id: string, label_asym_id: string, auth_asym_id: string, label_seq_id: Integer, auth_seq_id: Integer, pdbx_PDB_ins_code: string, beg_label_seq_id: Integer, end_label_seq_id: Integer, beg_auth_seq_id: Integer, end_auth_seq_id: Integer, label_atom_id: string, auth_atom_id: string, type_symbol: string, atom_id: Integer, atom_index: Integer }>>`
|
||||
|
||||
Defines to what part of the representation this color should be applied.
|
||||
|
||||
Default: `"all"`
|
||||
|
||||
- **`color_from_uri`**
|
||||
|
||||
This node instructs to apply colors to a visual representation. The colors are defined by an external annotation resource.
|
||||
|
||||
Parent: `representation`
|
||||
|
||||
Params:
|
||||
|
||||
- **`uri: `**`string`
|
||||
|
||||
URL of the annotation resource.
|
||||
|
||||
- **`format: `**`"cif" | "bcif" | "json"`
|
||||
|
||||
Format of the annotation resource.
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"` and `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"color"`
|
||||
|
||||
- **`color_from_source`**
|
||||
|
||||
This node instructs to apply colors to a visual representation. The colors are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.
|
||||
|
||||
Parent: `representation`
|
||||
|
||||
Params:
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from. If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from. If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"color"`
|
||||
|
||||
- **`label`**
|
||||
|
||||
This node instructs to add a label (textual visual representation) to a component.
|
||||
|
||||
Parent: `component` or `component_from_uri` or `component_from_source`
|
||||
|
||||
Params:
|
||||
|
||||
- **`text: `**`string`
|
||||
|
||||
Content of the shown label.
|
||||
|
||||
- **`label_from_uri`**
|
||||
|
||||
This node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an external annotation resource.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`uri: `**`string`
|
||||
|
||||
URL of the annotation resource.
|
||||
|
||||
- **`format: `**`"cif" | "bcif" | "json"`
|
||||
|
||||
Format of the annotation resource.
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"` and `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"label"`
|
||||
|
||||
- **`label_from_source`**
|
||||
|
||||
This node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from. If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from. If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"label"`
|
||||
|
||||
- **`tooltip`**
|
||||
|
||||
This node instructs to add a tooltip to a component. "Tooltip" is a text which is not a part of the visualization but should be presented to the users when they interact with the component (typically, the tooltip will be shown somewhere on the screen when the user hovers over a visual representation of the component).
|
||||
|
||||
Parent: `component` or `component_from_uri` or `component_from_source`
|
||||
|
||||
Params:
|
||||
|
||||
- **`text: `**`string`
|
||||
|
||||
Content of the shown tooltip.
|
||||
|
||||
- **`tooltip_from_uri`**
|
||||
|
||||
This node instructs to add tooltips to parts of a structure. The tooltips are defined by an external annotation resource.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`uri: `**`string`
|
||||
|
||||
URL of the annotation resource.
|
||||
|
||||
- **`format: `**`"cif" | "bcif" | "json"`
|
||||
|
||||
Format of the annotation resource.
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `format` is `"cif"` or `"bcif"` and `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from (only applies when `format` is `"cif"` or `"bcif"`). If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"tooltip"`
|
||||
|
||||
- **`tooltip_from_source`**
|
||||
|
||||
This node instructs to add tooltips to parts of a structure. The tooltips are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.
|
||||
|
||||
Parent: `structure`
|
||||
|
||||
Params:
|
||||
|
||||
- **`schema: `**`"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"`
|
||||
|
||||
Annotation schema defines what fields in the annotation will be taken into account.
|
||||
|
||||
- **`block_header?: `**`string | null`
|
||||
|
||||
Header of the CIF block to read annotation from. If `null`, block is selected based on `block_index`.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`block_index?: `**`Integer`
|
||||
|
||||
0-based index of the CIF block to read annotation from (only applies when `block_header` is `null`).
|
||||
|
||||
Default: `0`
|
||||
|
||||
- **`category_name?: `**`string | null`
|
||||
|
||||
Name of the CIF category to read annotation from. If `null`, the first category in the block is used.
|
||||
|
||||
Default: `null`
|
||||
|
||||
- **`field_name?: `**`string`
|
||||
|
||||
Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).
|
||||
|
||||
Default: `"tooltip"`
|
||||
|
||||
- **`focus`**
|
||||
|
||||
This node instructs to set the camera focus to a component (zoom in).
|
||||
|
||||
Parent: `component` or `component_from_uri` or `component_from_source`
|
||||
|
||||
Params:
|
||||
|
||||
- **`direction?: `**`[number, number, number]`
|
||||
|
||||
Vector describing the direction of the view (camera position -> focused target).
|
||||
|
||||
Default: `[0, 0, -1]`
|
||||
|
||||
- **`up?: `**`[number, number, number]`
|
||||
|
||||
Vector which will be aligned with the screen Y axis.
|
||||
|
||||
Default: `[0, 1, 0]`
|
||||
|
||||
- **`camera`**
|
||||
|
||||
This node instructs to set the camera position and orientation.
|
||||
|
||||
Parent: `root`
|
||||
|
||||
Params:
|
||||
|
||||
- **`target: `**`[number, number, number]`
|
||||
|
||||
Coordinates of the point in space at which the camera is pointing.
|
||||
|
||||
- **`position: `**`[number, number, number]`
|
||||
|
||||
Coordinates of the camera.
|
||||
|
||||
- **`up?: `**`[number, number, number]`
|
||||
|
||||
Vector which will be aligned with the screen Y axis.
|
||||
|
||||
Default: `[0, 1, 0]`
|
||||
|
||||
- **`canvas`**
|
||||
|
||||
This node sets canvas properties.
|
||||
|
||||
Parent: `root`
|
||||
|
||||
Params:
|
||||
|
||||
- **`background_color: `**`HexColor | ("white" | "gray" | "black" | "red" | "orange" | "yellow" | "green" | "cyan" | "blue" | "magenta")`
|
||||
|
||||
Color of the canvas background. Can be either a color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`).
|
||||
@@ -1,118 +0,0 @@
|
||||
# wwPDB StructConn extension
|
||||
|
||||
The STRUCT_CONN category in the mmCIF file format contains details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on (see more at <https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/struct_conn.html>).
|
||||
|
||||
**wwPDB StructConn extension** in Mol* provides functionality to retrieve and visualize these connections.
|
||||
|
||||
The extension exposes three functions, located in `src/extensions/wwpdb/struct-conn/index.ts`.
|
||||
|
||||
- `getStructConns` - to retrieve struct_conn records from a loaded structure
|
||||
- `inspectStructConn` - to visualize a struct_conn
|
||||
- `clearStructConnInspections` - to remove visulizations created by `inspectStructConn`
|
||||
|
||||
|
||||
## Example 1
|
||||
|
||||
The following example is a minimal HTML using this functionality:
|
||||
|
||||
```html
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="utf-8" />
|
||||
<link rel="icon" href="./favicon.ico" type="image/x-icon">
|
||||
<title>Mol* Viewer</title>
|
||||
<link rel="stylesheet" type="text/css" href="molstar.css" />
|
||||
</head>
|
||||
<body style="margin: 0px;">
|
||||
<div style="position: absolute; width: 100%; height: 10%; padding-block: 10px;">
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'disulf1');">disulf1</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'disulf2');">disulf2</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale1');">covale1</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale2');">covale2</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale3');">covale3</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'covale4');">covale4</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc1');">metalc1</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc2');">metalc2</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc3');">metalc3</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, '5elb', 'metalc4');">metalc4</button>
|
||||
<button onclick="molstar.PluginExtensions.wwPDBStructConn.clearStructConnInspections(molstarViewer.plugin, '5elb');">CLEAR</button>
|
||||
</div>
|
||||
<div id="app" style="position: absolute; top: 10%; width: 100%; height: 90%;"></div>
|
||||
<script type="text/javascript" src="./molstar.js"></script>
|
||||
<script type="text/javascript">
|
||||
var molstarViewer;
|
||||
molstar.Viewer.create('app', { layoutIsExpanded: false }).then(viewer => {
|
||||
molstarViewer = viewer;
|
||||
viewer.loadPdb('5elb');
|
||||
});
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
```
|
||||
|
||||
The PDB ID (`'5elb'`) can be replaced be `undefined`, in which case the functions will apply to the first loaded structure.
|
||||
|
||||
|
||||
## Example 2
|
||||
|
||||
This is a more elaborated example, which automatically loads `5elb` (or any PDB entry given in the URL after `?pdb=`), retrieves the list of struct_conns, and creates a button for each struct_conn.
|
||||
|
||||
Be aware that some of the struct_conns may be present in the deposited model but not in the preferred assembly (default view). The presented example will raise a dialog window with error message in such cases, e.g. `disulf6` in entry `5elb`.
|
||||
|
||||
```html
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="utf-8" />
|
||||
<link rel="icon" href="./favicon.ico" type="image/x-icon">
|
||||
<title>Mol* Viewer - StructConn Extension Demo</title>
|
||||
<link rel="stylesheet" type="text/css" href="molstar.css" />
|
||||
</head>
|
||||
<style>
|
||||
body { margin: 0px; }
|
||||
#app { position: absolute; width: 85%; height: 100%; }
|
||||
#controls { position: absolute; right: 0; width: 15%; height: 100%; display: flex; flex-direction: column; overflow-y: scroll; }
|
||||
h1 { text-align: center; margin: 12px; font-weight: bold; font-size: 120%; }
|
||||
button { margin: 4px; margin-top: 0px; }
|
||||
</style>
|
||||
<body>
|
||||
<div id="app"></div>
|
||||
<div id="controls">
|
||||
<h1 id="pdb-id">Loading...</h1>
|
||||
<button onclick="clearInspections();">CLEAR</button>
|
||||
</div>
|
||||
<script type="text/javascript" src="./molstar.js"></script>
|
||||
<script type="text/javascript">
|
||||
var pdbId = window.location.search.match(/[?&]pdb=(\w+)/i)?.[1]?.toLowerCase() ?? '5elb';
|
||||
var molstarViewer;
|
||||
function inspect(structConnId) {
|
||||
if (molstarViewer?.plugin) {
|
||||
molstar.PluginExtensions.wwPDBStructConn.inspectStructConn(molstarViewer.plugin, pdbId, structConnId).then(nSelectedAtoms => {
|
||||
if (nSelectedAtoms < 2) alert('Some of the interacting atoms were not found :(\n(maybe not present in the viewed assembly)');
|
||||
});
|
||||
}
|
||||
}
|
||||
function clearInspections() {
|
||||
if (molstarViewer?.plugin) {
|
||||
molstar.PluginExtensions.wwPDBStructConn.clearStructConnInspections(molstarViewer.plugin, pdbId);
|
||||
}
|
||||
}
|
||||
molstar.Viewer.create('app', { layoutIsExpanded: false }).then(viewer => {
|
||||
molstarViewer = viewer;
|
||||
return viewer.loadPdb(pdbId);
|
||||
}).then(() => {
|
||||
const structConns = molstar.PluginExtensions.wwPDBStructConn.getStructConns(molstarViewer.plugin, pdbId);
|
||||
const controls = document.getElementById('controls');
|
||||
for (const structConnId in structConns) {
|
||||
const button = document.createElement('button');
|
||||
button.innerText = structConnId;
|
||||
button.addEventListener('click', () => inspect(structConnId));
|
||||
controls.appendChild(button);
|
||||
};
|
||||
document.getElementById('pdb-id').innerHTML = pdbId;
|
||||
});
|
||||
</script>
|
||||
</body>
|
||||
</html>
|
||||
```
|
||||
@@ -26,7 +26,6 @@
|
||||
* Non-standard residues
|
||||
* Protein (1BRR, 5Z6Y)
|
||||
* DNA (5D3G)
|
||||
* Collagen (6JEC)
|
||||
* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
|
||||
* Long linear sugar chain (4HG6)
|
||||
* Anisotropic B-factors/Ellipsoids (1EJG)
|
||||
|
||||
75130
examples/7qpd.fw2.cif
75130
examples/7qpd.fw2.cif
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -1,115 +0,0 @@
|
||||
{
|
||||
"metadata": {
|
||||
"title": "Example MolViewSpec - 1cbs with labelled and zoomed ligand",
|
||||
"version": "1",
|
||||
"timestamp": "2023-11-24T10:45:49.873Z"
|
||||
},
|
||||
"root": {
|
||||
"kind": "root",
|
||||
"children": [
|
||||
{
|
||||
"kind": "download",
|
||||
"params": {
|
||||
"url": "https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "parse",
|
||||
"params": {
|
||||
"format": "bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "structure",
|
||||
"params": {
|
||||
"type": "model"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "polymer"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "cartoon"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"color": "green"
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"selector": {
|
||||
"label_asym_id": "A",
|
||||
"end_label_seq_id": 50
|
||||
},
|
||||
"color": "#6688ff"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "label",
|
||||
"params": {
|
||||
"text": "Protein"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "ligand"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "focus",
|
||||
"params": {
|
||||
"direction": [0.5, 0, -1],
|
||||
"up": [0.365, 0.913, 0.183]
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "ball_and_stick"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"color": "#cc3399"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "label",
|
||||
"params": {
|
||||
"text": "Retinoic Acid"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "canvas",
|
||||
"params": {
|
||||
"background_color": "#ffffee"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
@@ -1,117 +0,0 @@
|
||||
{
|
||||
"metadata": {
|
||||
"title": "Example MolViewSpec - 1cbs with labelled protein and ligand",
|
||||
"version": "1",
|
||||
"timestamp": "2023-11-24T10:38:17.483Z"
|
||||
},
|
||||
"root": {
|
||||
"kind": "root",
|
||||
"children": [
|
||||
{
|
||||
"kind": "download",
|
||||
"params": {
|
||||
"url": "https://www.ebi.ac.uk/pdbe/entry-files/1cbs.bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "parse",
|
||||
"params": {
|
||||
"format": "bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "structure",
|
||||
"params": {
|
||||
"type": "model"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "polymer"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "cartoon"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"color": "green"
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"selector": {
|
||||
"label_asym_id": "A",
|
||||
"beg_label_seq_id": 1,
|
||||
"end_label_seq_id": 50
|
||||
},
|
||||
"color": "#6688ff"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "label",
|
||||
"params": {
|
||||
"text": "Protein"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "ligand"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "ball_and_stick"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"color": "#cc3399"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "label",
|
||||
"params": {
|
||||
"text": "Retinoic Acid"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "canvas",
|
||||
"params": {
|
||||
"background_color": "#ffffee"
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "camera",
|
||||
"params": {
|
||||
"target": [17, 21, 27],
|
||||
"position": [41, 34, 69],
|
||||
"up": [-0.129,0.966,-0.224]
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
@@ -1,67 +0,0 @@
|
||||
{
|
||||
"metadata": {
|
||||
"title": "Example MolViewSpec - 1h9t colored by external annotation",
|
||||
"version": "1",
|
||||
"timestamp": "2023-11-24T10:47:33.182Z"
|
||||
},
|
||||
"root": {
|
||||
"kind": "root",
|
||||
"children": [
|
||||
{
|
||||
"kind": "download",
|
||||
"params": {
|
||||
"url": "https://www.ebi.ac.uk/pdbe/entry-files/1h9t.bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "parse",
|
||||
"params": {
|
||||
"format": "bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "structure",
|
||||
"params": {
|
||||
"type": "model"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "polymer"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "cartoon"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"selector": "all",
|
||||
"color": "white"
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "color_from_uri",
|
||||
"params": {
|
||||
"uri": "/examples/mvs/1h9t_domains.json",
|
||||
"format": "json",
|
||||
"schema": "all_atomic"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
@@ -1,583 +0,0 @@
|
||||
{
|
||||
"metadata": {
|
||||
"title": "Example MolViewSpec - 1h9t colored and labelled by external annotation",
|
||||
"version": "1",
|
||||
"timestamp": "2023-11-24T10:48:28.677Z"
|
||||
},
|
||||
"root": {
|
||||
"kind": "root",
|
||||
"children": [
|
||||
{
|
||||
"kind": "download",
|
||||
"params": {
|
||||
"url": "https://www.ebi.ac.uk/pdbe/entry-files/1h9t.bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "parse",
|
||||
"params": {
|
||||
"format": "bcif"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "structure",
|
||||
"params": {
|
||||
"type": "model"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "protein"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "cartoon"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"selector": "all",
|
||||
"color": "white"
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "color_from_uri",
|
||||
"params": {
|
||||
"uri": "/examples/mvs/1h9t_domains.json",
|
||||
"format": "json",
|
||||
"schema": "all_atomic"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "nucleic"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "ball_and_stick"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color",
|
||||
"params": {
|
||||
"selector": "all",
|
||||
"color": "white"
|
||||
}
|
||||
},
|
||||
{
|
||||
"kind": "color_from_uri",
|
||||
"params": {
|
||||
"uri": "/examples/mvs/1h9t_domains.json",
|
||||
"format": "json",
|
||||
"schema": "all_atomic"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": "ion"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "representation",
|
||||
"params": {
|
||||
"type": "surface"
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "color_from_uri",
|
||||
"params": {
|
||||
"uri": "/examples/mvs/1h9t_domains.json",
|
||||
"format": "json",
|
||||
"schema": "all_atomic"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": {
|
||||
"label_asym_id": "A",
|
||||
"beg_label_seq_id": 9,
|
||||
"end_label_seq_id": 83
|
||||
}
|
||||
},
|
||||
"children": [
|
||||
{
|
||||
"kind": "label",
|
||||
"params": {
|
||||
"text": "DNA-binding"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"kind": "component",
|
||||
"params": {
|
||||
"selector": {
|
||||
"label_asym_id": "B",
|
||||
"beg_label_seq_id": 9,
|
||||
"end_label_seq_id": 83
|
||||
}
|
||||
},
|
||||
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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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||||
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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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||||
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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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||||
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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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|
||||
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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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||||
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|
||||
@@ -1,155 +0,0 @@
|
||||
[
|
||||
{
|
||||
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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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|
||||
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|
||||
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|
||||
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|
||||
{
|
||||
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|
||||
"beg_label_seq_id": 9,
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"beg_label_seq_id": 84,
|
||||
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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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|
||||
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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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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
{
|
||||
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|
||||
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|
||||
"color": "#4400ff",
|
||||
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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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|
||||
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|
||||
},
|
||||
{
|
||||
"label_asym_id": "F",
|
||||
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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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|
||||
{
|
||||
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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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|
||||
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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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|
||||
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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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|
||||
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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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|
||||
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|
||||
"label_asym_id": "A",
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"label_asym_id": "A",
|
||||
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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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|
||||
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|
||||
"color": "#ff0000",
|
||||
"tooltip": "Ligand binding site"
|
||||
},
|
||||
|
||||
{
|
||||
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|
||||
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|
||||
"color": "#ff0000",
|
||||
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|
||||
},
|
||||
{
|
||||
"label_asym_id": "B",
|
||||
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|
||||
"color": "#ff0000",
|
||||
"tooltip": "Ligand binding site"
|
||||
},
|
||||
{
|
||||
"label_asym_id": "B",
|
||||
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|
||||
"color": "#ff0000",
|
||||
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|
||||
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|
||||
{
|
||||
"label_asym_id": "B",
|
||||
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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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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
17028
package-lock.json
generated
17028
package-lock.json
generated
File diff suppressed because it is too large
Load Diff
118
package.json
118
package.json
@@ -1,6 +1,6 @@
|
||||
{
|
||||
"name": "molstar",
|
||||
"version": "3.43.1",
|
||||
"version": "3.14.0",
|
||||
"description": "A comprehensive macromolecular library.",
|
||||
"homepage": "https://github.com/molstar/molstar#readme",
|
||||
"repository": {
|
||||
@@ -13,7 +13,7 @@
|
||||
"scripts": {
|
||||
"lint": "eslint .",
|
||||
"lint-fix": "eslint . --fix",
|
||||
"test": "npm install --no-save \"gl@^6.0.2\" && npm run lint && jest",
|
||||
"test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
|
||||
"jest": "jest",
|
||||
"build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
|
||||
"clean": "node ./scripts/clean.js",
|
||||
@@ -89,96 +89,76 @@
|
||||
"Ludovic Autin <autin@scripps.edu>",
|
||||
"Michal Malý <michal.maly@ibt.cas.cz>",
|
||||
"Jiří Černý <jiri.cerny@ibt.cas.cz>",
|
||||
"Panagiotis Tourlas <panagiot_tourlov@hotmail.com>",
|
||||
"Adam Midlik <midlik@gmail.com>",
|
||||
"Koya Sakuma <koya.sakuma.work@gmail.com>",
|
||||
"Gianluca Tomasello <giagitom@gmail.com>",
|
||||
"Ke Ma <mark.ma@rcsb.org>",
|
||||
"Jason Pattle <jpattle@exscientia.co.uk>",
|
||||
"David Williams <dwilliams@nobiastx.com>",
|
||||
"Zhenyu Zhang <jump2cn@gmail.com>",
|
||||
"Russell Parker <russell@benchling.com>",
|
||||
"Dominik Tichy <tichydominik451@gmail.com>",
|
||||
"Yana Rose <yana.v.rose@gmail.com>",
|
||||
"Yakov Pechersky <ffxen158@gmail.com>"
|
||||
"Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
|
||||
],
|
||||
"license": "MIT",
|
||||
"devDependencies": {
|
||||
"@graphql-codegen/add": "^5.0.0",
|
||||
"@graphql-codegen/cli": "^5.0.0",
|
||||
"@graphql-codegen/time": "^5.0.0",
|
||||
"@graphql-codegen/typescript": "^4.0.1",
|
||||
"@graphql-codegen/typescript-graphql-files-modules": "^3.0.0",
|
||||
"@graphql-codegen/typescript-graphql-request": "^6.0.1",
|
||||
"@graphql-codegen/typescript-operations": "^4.0.1",
|
||||
"@types/cors": "^2.8.17",
|
||||
"@types/gl": "^6.0.5",
|
||||
"@types/jpeg-js": "^0.3.7",
|
||||
"@types/pngjs": "^6.0.4",
|
||||
"@types/jest": "^29.5.10",
|
||||
"@types/react": "^18.2.41",
|
||||
"@types/react-dom": "^18.2.17",
|
||||
"@typescript-eslint/eslint-plugin": "^6.13.1",
|
||||
"@typescript-eslint/parser": "^6.13.1",
|
||||
"@graphql-codegen/add": "^3.2.1",
|
||||
"@graphql-codegen/cli": "^2.11.6",
|
||||
"@graphql-codegen/time": "^3.2.1",
|
||||
"@graphql-codegen/typescript": "^2.7.3",
|
||||
"@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
|
||||
"@graphql-codegen/typescript-graphql-request": "^4.5.3",
|
||||
"@graphql-codegen/typescript-operations": "^2.5.3",
|
||||
"@types/cors": "^2.8.12",
|
||||
"@types/gl": "^4.1.1",
|
||||
"@types/jest": "^28.1.7",
|
||||
"@types/react": "^18.0.17",
|
||||
"@types/react-dom": "^18.0.6",
|
||||
"@typescript-eslint/eslint-plugin": "^5.33.1",
|
||||
"@typescript-eslint/parser": "^5.33.1",
|
||||
"benchmark": "^2.1.4",
|
||||
"concurrently": "^8.2.2",
|
||||
"cpx2": "^6.0.1",
|
||||
"concurrently": "^7.3.0",
|
||||
"cpx2": "^4.2.0",
|
||||
"crypto-browserify": "^3.12.0",
|
||||
"css-loader": "^6.8.1",
|
||||
"eslint": "^8.55.0",
|
||||
"css-loader": "^6.7.1",
|
||||
"eslint": "^8.22.0",
|
||||
"extra-watch-webpack-plugin": "^1.0.3",
|
||||
"file-loader": "^6.2.0",
|
||||
"fs-extra": "^11.2.0",
|
||||
"graphql": "^16.8.1",
|
||||
"fs-extra": "^10.1.0",
|
||||
"graphql": "^16.6.0",
|
||||
"http-server": "^14.1.1",
|
||||
"jest": "^29.7.0",
|
||||
"mini-css-extract-plugin": "^2.7.6",
|
||||
"jest": "^28.1.3",
|
||||
"mini-css-extract-plugin": "^2.6.1",
|
||||
"path-browserify": "^1.0.1",
|
||||
"raw-loader": "^4.0.2",
|
||||
"react": "^18.2.0",
|
||||
"react-dom": "^18.2.0",
|
||||
"sass": "^1.69.5",
|
||||
"sass-loader": "^13.3.2",
|
||||
"simple-git": "^3.21.0",
|
||||
"sass": "^1.54.5",
|
||||
"sass-loader": "^13.0.2",
|
||||
"simple-git": "^3.12.0",
|
||||
"stream-browserify": "^3.0.0",
|
||||
"style-loader": "^3.3.3",
|
||||
"ts-jest": "^29.1.1",
|
||||
"typescript": "^5.3.2",
|
||||
"webpack": "^5.89.0",
|
||||
"webpack-cli": "^5.1.4"
|
||||
"style-loader": "^3.3.1",
|
||||
"ts-jest": "^28.0.8",
|
||||
"typescript": "^4.7.4",
|
||||
"webpack": "^5.74.0",
|
||||
"webpack-cli": "^4.10.0"
|
||||
},
|
||||
"dependencies": {
|
||||
"@types/argparse": "^2.0.14",
|
||||
"@types/benchmark": "^2.1.5",
|
||||
"@types/compression": "1.7.5",
|
||||
"@types/express": "^4.17.21",
|
||||
"@types/node": "^16.18.66",
|
||||
"@types/node-fetch": "^2.6.9",
|
||||
"@types/swagger-ui-dist": "3.30.4",
|
||||
"@types/argparse": "^2.0.10",
|
||||
"@types/benchmark": "^2.1.1",
|
||||
"@types/compression": "1.7.2",
|
||||
"@types/express": "^4.17.13",
|
||||
"@types/node": "^16.11.51",
|
||||
"@types/node-fetch": "^2.6.2",
|
||||
"@types/swagger-ui-dist": "3.30.1",
|
||||
"argparse": "^2.0.1",
|
||||
"body-parser": "^1.20.2",
|
||||
"body-parser": "^1.20.0",
|
||||
"compression": "^1.7.4",
|
||||
"cors": "^2.8.5",
|
||||
"express": "^4.18.2",
|
||||
"express": "^4.18.1",
|
||||
"h264-mp4-encoder": "^1.0.12",
|
||||
"immer": "^9.0.21",
|
||||
"immutable": "^4.3.4",
|
||||
"io-ts": "^2.2.20",
|
||||
"node-fetch": "^2.7.0",
|
||||
"react-markdown": "^9.0.1",
|
||||
"rxjs": "^7.8.1",
|
||||
"swagger-ui-dist": "^5.10.3",
|
||||
"tslib": "^2.6.2",
|
||||
"util.promisify": "^1.1.2",
|
||||
"immer": "^9.0.15",
|
||||
"immutable": "^4.1.0",
|
||||
"node-fetch": "^2.6.7",
|
||||
"rxjs": "^7.5.6",
|
||||
"swagger-ui-dist": "^4.14.0",
|
||||
"tslib": "^2.4.0",
|
||||
"util.promisify": "^1.1.1",
|
||||
"xhr2": "^0.2.1"
|
||||
},
|
||||
"peerDependencies": {
|
||||
"react": "^18.1.0 || ^17.0.2 || ^16.14.0",
|
||||
"react-dom": "^18.1.0 || ^17.0.2 || ^16.14.0"
|
||||
},
|
||||
"optionalDependencies": {
|
||||
"gl": "^6.0.2",
|
||||
"jpeg-js": "^0.4.4",
|
||||
"pngjs": "^6.0.0"
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
@@ -15,7 +15,7 @@ const deployDir = path.resolve(buildDir, 'deploy/');
|
||||
const localPath = path.resolve(deployDir, 'molstar.github.io/');
|
||||
|
||||
const analyticsTag = /<!-- __MOLSTAR_ANALYTICS__ -->/g;
|
||||
const analyticsCode = `<!-- Cloudflare Web Analytics --><script defer src='https://static.cloudflareinsights.com/beacon.min.js' data-cf-beacon='{"token": "c414cbae2d284ea995171a81e4a3e721"}'></script><!-- End Cloudflare Web Analytics --><iframe src="https://web3dsurvey.com/collector-iframe.html" style="width: 1px; height: 1px;"></iframe>`;
|
||||
const analyticsCode = `<!-- Cloudflare Web Analytics --><script defer src='https://static.cloudflareinsights.com/beacon.min.js' data-cf-beacon='{"token": "c414cbae2d284ea995171a81e4a3e721"}'></script><!-- End Cloudflare Web Analytics -->`;
|
||||
|
||||
function log(command, stdout, stderr) {
|
||||
if (command) {
|
||||
|
||||
@@ -58,22 +58,20 @@ class Viewer {
|
||||
}
|
||||
|
||||
static async create(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
|
||||
const o = {
|
||||
...DefaultViewerOptions, ...{
|
||||
layoutIsExpanded: false,
|
||||
layoutShowControls: false,
|
||||
layoutShowRemoteState: false,
|
||||
layoutShowSequence: true,
|
||||
layoutShowLog: false,
|
||||
layoutShowLeftPanel: true,
|
||||
const o = { ...DefaultViewerOptions, ...{
|
||||
layoutIsExpanded: false,
|
||||
layoutShowControls: false,
|
||||
layoutShowRemoteState: false,
|
||||
layoutShowSequence: true,
|
||||
layoutShowLog: false,
|
||||
layoutShowLeftPanel: true,
|
||||
|
||||
viewportShowExpand: true,
|
||||
viewportShowControls: false,
|
||||
viewportShowSettings: false,
|
||||
viewportShowSelectionMode: false,
|
||||
viewportShowAnimation: false,
|
||||
}
|
||||
};
|
||||
viewportShowExpand: true,
|
||||
viewportShowControls: false,
|
||||
viewportShowSettings: false,
|
||||
viewportShowSelectionMode: false,
|
||||
viewportShowAnimation: false,
|
||||
} };
|
||||
const defaultSpec = DefaultPluginUISpec();
|
||||
|
||||
const spec: PluginUISpec = {
|
||||
@@ -137,16 +135,18 @@ class Viewer {
|
||||
}
|
||||
};
|
||||
|
||||
PluginCommands.Canvas3D.SetSettings(plugin, {
|
||||
settings: {
|
||||
renderer: {
|
||||
...plugin.canvas3d!.props.renderer,
|
||||
backgroundColor: ColorNames.white,
|
||||
},
|
||||
camera: {
|
||||
...plugin.canvas3d!.props.camera,
|
||||
helper: { axes: { name: 'off', params: {} } }
|
||||
}
|
||||
plugin.behaviors.canvas3d.initialized.subscribe(v => {
|
||||
if (v) {
|
||||
PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
|
||||
renderer: {
|
||||
...plugin.canvas3d!.props.renderer,
|
||||
backgroundColor: ColorNames.white,
|
||||
},
|
||||
camera: {
|
||||
...plugin.canvas3d!.props.camera,
|
||||
helper: { axes: { name: 'off', params: {} } }
|
||||
}
|
||||
} });
|
||||
}
|
||||
});
|
||||
|
||||
@@ -166,7 +166,7 @@ class Viewer {
|
||||
structures.push({ ref: structureProperties?.ref || structure.ref });
|
||||
}
|
||||
|
||||
// remove current structures from hierarchy as they will be merged
|
||||
// remove current structuresfrom hierarchy as they will be merged
|
||||
// TODO only works with using loadStructuresFromUrlsAndMerge once
|
||||
// need some more API metho to work with the hierarchy
|
||||
this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
@@ -31,8 +31,7 @@ function shinyStyle(plugin: PluginContext) {
|
||||
postprocessing: {
|
||||
...plugin.canvas3d!.props.postprocessing,
|
||||
occlusion: { name: 'off', params: {} },
|
||||
shadow: { name: 'off', params: {} },
|
||||
outline: { name: 'off', params: {} },
|
||||
outline: { name: 'off', params: {} }
|
||||
}
|
||||
} });
|
||||
}
|
||||
@@ -45,21 +44,17 @@ function occlusionStyle(plugin: PluginContext) {
|
||||
postprocessing: {
|
||||
...plugin.canvas3d!.props.postprocessing,
|
||||
occlusion: { name: 'on', params: {
|
||||
blurKernelSize: 15,
|
||||
multiScale: { name: 'off', params: {} },
|
||||
radius: 5,
|
||||
bias: 0.8,
|
||||
blurKernelSize: 15,
|
||||
radius: 5,
|
||||
samples: 32,
|
||||
resolutionScale: 1,
|
||||
color: Color(0x000000),
|
||||
resolutionScale: 1
|
||||
} },
|
||||
outline: { name: 'on', params: {
|
||||
scale: 1.0,
|
||||
threshold: 0.33,
|
||||
color: Color(0x0000),
|
||||
includeTransparent: true,
|
||||
} },
|
||||
shadow: { name: 'off', params: {} },
|
||||
} }
|
||||
}
|
||||
} });
|
||||
}
|
||||
@@ -207,14 +202,14 @@ const InteractionsPreset = StructureRepresentationPresetProvider({
|
||||
const components = {
|
||||
ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
|
||||
surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
|
||||
interactions: await presetStaticComponent(plugin, structureCell, 'ligand'),
|
||||
interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
|
||||
};
|
||||
|
||||
const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
|
||||
const representations = {
|
||||
ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
|
||||
ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
|
||||
interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial, includeParent: true, parentDisplay: 'between' }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
|
||||
interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
|
||||
label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, material: CustomMaterial, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
|
||||
};
|
||||
|
||||
|
||||
@@ -1,48 +1,39 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
|
||||
import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
|
||||
import { Backgrounds } from '../../extensions/backgrounds';
|
||||
import { CellPack } from '../../extensions/cellpack';
|
||||
import { DnatcoNtCs } from '../../extensions/dnatco';
|
||||
import { DnatcoConfalPyramids } from '../../extensions/dnatco';
|
||||
import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
|
||||
import { GeometryExport } from '../../extensions/geo-export';
|
||||
import { MAQualityAssessment, QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
|
||||
import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
|
||||
import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
|
||||
import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
|
||||
import { ModelExport } from '../../extensions/model-export';
|
||||
import { Mp4Export } from '../../extensions/mp4-export';
|
||||
import { MolViewSpec } from '../../extensions/mvs/behavior';
|
||||
import { loadMVS } from '../../extensions/mvs/load';
|
||||
import { MVSData } from '../../extensions/mvs/mvs-data';
|
||||
import { PDBeStructureQualityReport } from '../../extensions/pdbe';
|
||||
import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
|
||||
import { RCSBAssemblySymmetryConfig } from '../../extensions/rcsb/assembly-symmetry/behavior';
|
||||
import { SbNcbrPartialCharges, SbNcbrPartialChargesPreset, SbNcbrPartialChargesPropertyProvider } from '../../extensions/sb-ncbr';
|
||||
import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
|
||||
import { wwPDBChemicalComponentDictionary } from '../../extensions/wwpdb/ccd/behavior';
|
||||
import { wwPDBStructConnExtensionFunctions } from '../../extensions/wwpdb/struct-conn';
|
||||
import { ZenodoImport } from '../../extensions/zenodo';
|
||||
import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
|
||||
import { Volume } from '../../mol-model/volume';
|
||||
import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
|
||||
import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
|
||||
import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
|
||||
import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
|
||||
import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
|
||||
import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
|
||||
import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
|
||||
import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
|
||||
import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
|
||||
import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
|
||||
import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
|
||||
import { PluginStateObject } from '../../mol-plugin-state/objects';
|
||||
import { StateTransforms } from '../../mol-plugin-state/transforms';
|
||||
import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
|
||||
import { PluginUIContext } from '../../mol-plugin-ui/context';
|
||||
import { createPluginUI } from '../../mol-plugin-ui/react18';
|
||||
import { PluginUIContext } from '../../mol-plugin-ui/context';
|
||||
import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
|
||||
import { PluginCommands } from '../../mol-plugin/commands';
|
||||
import { PluginConfig } from '../../mol-plugin/config';
|
||||
@@ -54,19 +45,20 @@ import { Asset } from '../../mol-util/assets';
|
||||
import { Color } from '../../mol-util/color';
|
||||
import '../../mol-util/polyfill';
|
||||
import { ObjectKeys } from '../../mol-util/type-helpers';
|
||||
import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
|
||||
import { Backgrounds } from '../../extensions/backgrounds';
|
||||
|
||||
export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
|
||||
export { consoleStats, setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
|
||||
export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
|
||||
|
||||
const CustomFormats = [
|
||||
['g3d', G3dProvider] as const
|
||||
];
|
||||
|
||||
export const ExtensionMap = {
|
||||
'volseg': PluginSpec.Behavior(Volseg),
|
||||
const Extensions = {
|
||||
'backgrounds': PluginSpec.Behavior(Backgrounds),
|
||||
'cellpack': PluginSpec.Behavior(CellPack),
|
||||
'dnatco-ntcs': PluginSpec.Behavior(DnatcoNtCs),
|
||||
'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
|
||||
'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
|
||||
'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
|
||||
'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
|
||||
@@ -77,15 +69,11 @@ export const ExtensionMap = {
|
||||
'geo-export': PluginSpec.Behavior(GeometryExport),
|
||||
'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
|
||||
'zenodo-import': PluginSpec.Behavior(ZenodoImport),
|
||||
'sb-ncbr-partial-charges': PluginSpec.Behavior(SbNcbrPartialCharges),
|
||||
'wwpdb-chemical-component-dictionary': PluginSpec.Behavior(wwPDBChemicalComponentDictionary),
|
||||
'mvs': PluginSpec.Behavior(MolViewSpec),
|
||||
};
|
||||
|
||||
const DefaultViewerOptions = {
|
||||
customFormats: CustomFormats as [string, DataFormatProvider][],
|
||||
extensions: ObjectKeys(ExtensionMap),
|
||||
disabledExtensions: [] as string[],
|
||||
extensions: ObjectKeys(Extensions),
|
||||
layoutIsExpanded: true,
|
||||
layoutShowControls: true,
|
||||
layoutShowRemoteState: true,
|
||||
@@ -100,10 +88,7 @@ const DefaultViewerOptions = {
|
||||
pickScale: PluginConfig.General.PickScale.defaultValue,
|
||||
pickPadding: PluginConfig.General.PickPadding.defaultValue,
|
||||
enableWboit: PluginConfig.General.EnableWboit.defaultValue,
|
||||
enableDpoit: PluginConfig.General.EnableDpoit.defaultValue,
|
||||
preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
|
||||
allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
|
||||
powerPreference: PluginConfig.General.PowerPreference.defaultValue,
|
||||
|
||||
viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
|
||||
viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
|
||||
@@ -117,10 +102,6 @@ const DefaultViewerOptions = {
|
||||
pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
|
||||
emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
|
||||
saccharideCompIdMapType: 'default' as SaccharideCompIdMapType,
|
||||
volumesAndSegmentationsDefaultServer: VolsegVolumeServerConfig.DefaultServer.defaultValue,
|
||||
rcsbAssemblySymmetryDefaultServerType: RCSBAssemblySymmetryConfig.DefaultServerType.defaultValue,
|
||||
rcsbAssemblySymmetryDefaultServerUrl: RCSBAssemblySymmetryConfig.DefaultServerUrl.defaultValue,
|
||||
rcsbAssemblySymmetryApplyColors: RCSBAssemblySymmetryConfig.ApplyColors.defaultValue,
|
||||
};
|
||||
type ViewerOptions = typeof DefaultViewerOptions;
|
||||
|
||||
@@ -139,13 +120,11 @@ export class Viewer {
|
||||
const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
|
||||
const defaultSpec = DefaultPluginUISpec();
|
||||
|
||||
const disabledExtension = new Set(o.disabledExtensions ?? []);
|
||||
|
||||
const spec: PluginUISpec = {
|
||||
actions: defaultSpec.actions,
|
||||
behaviors: [
|
||||
...defaultSpec.behaviors,
|
||||
...o.extensions.filter(e => !disabledExtension.has(e)).map(e => ExtensionMap[e]),
|
||||
...o.extensions.map(e => Extensions[e]),
|
||||
],
|
||||
animations: [...defaultSpec.animations || []],
|
||||
customParamEditors: defaultSpec.customParamEditors,
|
||||
@@ -179,10 +158,7 @@ export class Viewer {
|
||||
[PluginConfig.General.PickScale, o.pickScale],
|
||||
[PluginConfig.General.PickPadding, o.pickPadding],
|
||||
[PluginConfig.General.EnableWboit, o.enableWboit],
|
||||
[PluginConfig.General.EnableDpoit, o.enableDpoit],
|
||||
[PluginConfig.General.PreferWebGl1, o.preferWebgl1],
|
||||
[PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
|
||||
[PluginConfig.General.PowerPreference, o.powerPreference],
|
||||
[PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
|
||||
[PluginConfig.Viewport.ShowControls, o.viewportShowControls],
|
||||
[PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
|
||||
@@ -197,10 +173,6 @@ export class Viewer {
|
||||
[PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
|
||||
[PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
|
||||
[PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
|
||||
[VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
|
||||
[RCSBAssemblySymmetryConfig.DefaultServerType, o.rcsbAssemblySymmetryDefaultServerType],
|
||||
[RCSBAssemblySymmetryConfig.DefaultServerUrl, o.rcsbAssemblySymmetryDefaultServerUrl],
|
||||
[RCSBAssemblySymmetryConfig.ApplyColors, o.rcsbAssemblySymmetryApplyColors],
|
||||
]
|
||||
};
|
||||
|
||||
@@ -227,7 +199,7 @@ export class Viewer {
|
||||
return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
|
||||
}
|
||||
|
||||
loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions & { label?: string }) {
|
||||
loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
|
||||
const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
|
||||
return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
|
||||
source: {
|
||||
@@ -236,7 +208,6 @@ export class Viewer {
|
||||
url: Asset.Url(url),
|
||||
format: format as any,
|
||||
isBinary,
|
||||
label: options?.label,
|
||||
options: { ...params.source.params.options, representationParams: options?.representationParams as any },
|
||||
}
|
||||
}
|
||||
@@ -470,34 +441,9 @@ export class Viewer {
|
||||
return { model, coords, preset };
|
||||
}
|
||||
|
||||
async loadMvsFromUrl(url: string, format: 'mvsj') {
|
||||
if (format === 'mvsj') {
|
||||
const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'string' }));
|
||||
const mvsData = MVSData.fromMVSJ(data);
|
||||
await loadMVS(this.plugin, mvsData, { sanityChecks: true });
|
||||
} else {
|
||||
throw new Error(`Unknown MolViewSpec format: ${format}`);
|
||||
}
|
||||
// We might add more formats in the future
|
||||
}
|
||||
|
||||
async loadMvsData(data: string, format: 'mvsj') {
|
||||
if (format === 'mvsj') {
|
||||
const mvsData = MVSData.fromMVSJ(data);
|
||||
await loadMVS(this.plugin, mvsData, { sanityChecks: true });
|
||||
} else {
|
||||
throw new Error(`Unknown MolViewSpec format: ${format}`);
|
||||
}
|
||||
// We might add more formats in the future
|
||||
}
|
||||
|
||||
handleResize() {
|
||||
this.plugin.layout.events.updated.next(void 0);
|
||||
}
|
||||
|
||||
dispose() {
|
||||
this.plugin.dispose();
|
||||
}
|
||||
}
|
||||
|
||||
export interface LoadStructureOptions {
|
||||
@@ -546,15 +492,8 @@ export const ViewerAutoPreset = StructureRepresentationPresetProvider({
|
||||
return await QualityAssessmentPLDDTPreset.apply(ref, params, plugin);
|
||||
} else if (!!structure.models.some(m => QualityAssessment.isApplicable(m, 'qmean'))) {
|
||||
return await QualityAssessmentQmeanPreset.apply(ref, params, plugin);
|
||||
} else if (!!structure.models.some(m => SbNcbrPartialChargesPropertyProvider.isApplicable(m))) {
|
||||
return await SbNcbrPartialChargesPreset.apply(ref, params, plugin);
|
||||
} else {
|
||||
return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
|
||||
}
|
||||
}
|
||||
});
|
||||
|
||||
export const PluginExtensions = {
|
||||
wwPDBStructConn: wwPDBStructConnExtensionFunctions,
|
||||
mvs: { MVSData, loadMVS },
|
||||
};
|
||||
});
|
||||
@@ -38,15 +38,6 @@
|
||||
viewer.loadPdb('7bv2');
|
||||
viewer.loadEmdb('EMD-30210', { detail: 6 });
|
||||
// viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
|
||||
// viewer.loadStructureFromUrl('my url', 'pdb', false, {
|
||||
// representationParams: {
|
||||
// theme: {
|
||||
// globalName: 'uniform',
|
||||
// globalColorParams: { value: 0xff0000 }
|
||||
// }
|
||||
// },
|
||||
// label: 'my structure'
|
||||
// });
|
||||
});
|
||||
</script>
|
||||
</body>
|
||||
|
||||
@@ -60,15 +60,9 @@
|
||||
var pickScale = getParam('pick-scale', '[^&]+').trim();
|
||||
var pickPadding = getParam('pick-padding', '[^&]+').trim();
|
||||
var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
|
||||
var enableDpoit = getParam('enable-dpoit', '[^&]+').trim() === '1';
|
||||
var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
|
||||
var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
|
||||
var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
|
||||
|
||||
// console.log('Available extensions: ', Object.keys(molstar.ExtensionMap));
|
||||
|
||||
molstar.Viewer.create('app', {
|
||||
disabledExtensions: [], // anything from Object.keys(molstar.ExtensionMap)
|
||||
layoutShowControls: !hideControls,
|
||||
viewportShowExpand: false,
|
||||
collapseLeftPanel: collapseLeftPanel,
|
||||
@@ -80,11 +74,8 @@
|
||||
pixelScale: parseFloat(pixelScale) || 1,
|
||||
pickScale: parseFloat(pickScale) || 0.25,
|
||||
pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
|
||||
enableWboit: (disableWboit || enableDpoit) ? false : void 0, // use default value if disable-wboit is not set
|
||||
enableDpoit: enableDpoit ? true : void 0,
|
||||
enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
|
||||
preferWebgl1: preferWebgl1,
|
||||
allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
|
||||
powerPreference: powerPreference || 'high-performance',
|
||||
}).then(viewer => {
|
||||
var snapshotId = getParam('snapshot-id', '[^&]+').trim();
|
||||
if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
|
||||
@@ -98,14 +89,6 @@
|
||||
var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
|
||||
if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
|
||||
|
||||
var mvsUrl = getParam('mvs-url', '[^&]+').trim();
|
||||
var mvsData = getParam('mvs-data', '[^&]+').trim();
|
||||
var mvsFormat = getParam('mvs-format', '[^&]+').trim() || 'mvsj';
|
||||
if (mvsUrl && mvsData) console.error('Cannot specify mvs-url and mvs-data URL parameters at the same time. Ignoring both.');
|
||||
else if (mvsUrl) viewer.loadMvsFromUrl(mvsUrl, mvsFormat);
|
||||
else if (mvsData) viewer.loadMvsData(mvsData, mvsFormat);
|
||||
|
||||
|
||||
var pdb = getParam('pdb', '[^&]+').trim();
|
||||
if (pdb) viewer.loadPdb(pdb);
|
||||
|
||||
@@ -120,11 +103,6 @@
|
||||
|
||||
var modelArchive = getParam('model-archive', '[^&]+').trim();
|
||||
if (modelArchive) viewer.loadModelArchive(modelArchive);
|
||||
|
||||
window.addEventListener('unload', () => {
|
||||
// to aid GC
|
||||
viewer.dispose();
|
||||
});
|
||||
});
|
||||
</script>
|
||||
<!-- __MOLSTAR_ANALYTICS__ -->
|
||||
|
||||
@@ -81,5 +81,5 @@ export const DefaultDataOptions: DataOptions = {
|
||||
const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
|
||||
const CCD_PATH = path.join(DATA_DIR, 'components.cif');
|
||||
const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
|
||||
const CCD_URL = 'https://files.wwpdb.org/pub/pdb/data/monomers/components.cif';
|
||||
const PVCD_URL = 'https://files.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
|
||||
const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
|
||||
const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
|
||||
|
||||
@@ -22,7 +22,6 @@ export function getFieldType(type: string, description: string, values?: string[
|
||||
case 'uline':
|
||||
case 'uchar3':
|
||||
case 'uchar1':
|
||||
case 'uchar5':
|
||||
// only force lower-case for enums
|
||||
return values && values.length ? EnumCol(values.map(x => x.toLowerCase()), 'lstr', description) : StrCol(description);
|
||||
case 'aliasname':
|
||||
@@ -62,7 +61,6 @@ export function getFieldType(type: string, description: string, values?: string[
|
||||
case 'symop':
|
||||
case 'exp_data_doi':
|
||||
case 'asym_id':
|
||||
case 'uniprot_ptm_id':
|
||||
return StrCol(description);
|
||||
case 'int':
|
||||
case 'non_negative_int':
|
||||
@@ -73,7 +71,6 @@ export function getFieldType(type: string, description: string, values?: string[
|
||||
case 'ec-type':
|
||||
case 'ucode-alphanum-csv':
|
||||
case 'id_list':
|
||||
case 'entity_id_list':
|
||||
return ListCol('str', ',', description);
|
||||
case 'id_list_spc':
|
||||
return ListCol('str', ' ', description);
|
||||
@@ -91,7 +88,6 @@ export function getFieldType(type: string, description: string, values?: string[
|
||||
case 'Tag':
|
||||
case 'Implied':
|
||||
case 'Word':
|
||||
case 'Uri':
|
||||
return wrapContainer('str', ',', description, container);
|
||||
case 'Real':
|
||||
return wrapContainer('float', ',', description, container);
|
||||
@@ -155,7 +151,7 @@ function getImportFrames(d: Data.CifFrame, imports: Imports) {
|
||||
}
|
||||
|
||||
/** get field from given or linked category */
|
||||
function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField | undefined {
|
||||
function getField(category: string, field: string, d: Data.CifFrame, imports: Imports, ctx: FrameData): Data.CifField|undefined {
|
||||
const { categories, links } = ctx;
|
||||
const cat = d.categories[category];
|
||||
if (cat) {
|
||||
|
||||
@@ -25,7 +25,7 @@ async function readFile(path: string) {
|
||||
}
|
||||
}
|
||||
|
||||
async function parseCif(data: string | Uint8Array) {
|
||||
async function parseCif(data: string|Uint8Array) {
|
||||
const comp = CIF.parse(data);
|
||||
const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
|
||||
if (parsed.isError) throw parsed;
|
||||
|
||||
@@ -38,7 +38,7 @@ function print(volume: Volume) {
|
||||
}
|
||||
|
||||
async function doMesh(volume: Volume, filename: string) {
|
||||
const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, -1, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) })).run();
|
||||
const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) })).run();
|
||||
console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
|
||||
|
||||
// Export the mesh in OBJ format.
|
||||
|
||||
@@ -4,16 +4,16 @@
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import { createRoot } from 'react-dom/client';
|
||||
import * as ReactDOM from 'react-dom';
|
||||
import { AlphaOrbitalsExample } from '.';
|
||||
import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
|
||||
import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
|
||||
import { PluginContextContainer } from '../../mol-plugin-ui/plugin';
|
||||
|
||||
export function mountControls(orbitals: AlphaOrbitalsExample, parent: Element) {
|
||||
createRoot(parent).render(<PluginContextContainer plugin={orbitals.plugin}>
|
||||
ReactDOM.render(<PluginContextContainer plugin={orbitals.plugin}>
|
||||
<Controls orbitals={orbitals} />
|
||||
</PluginContextContainer>);
|
||||
</PluginContextContainer>, parent);
|
||||
}
|
||||
|
||||
function Controls({ orbitals }: { orbitals: AlphaOrbitalsExample }) {
|
||||
|
||||
@@ -25,7 +25,7 @@ import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
|
||||
import './index.html';
|
||||
require('mol-plugin-ui/skin/light.scss');
|
||||
|
||||
import { setDebugMode, setTimingMode, consoleStats } from '../../mol-util/debug';
|
||||
import { setDebugMode, setTimingMode } from '../../mol-util/debug';
|
||||
|
||||
interface DemoInput {
|
||||
moleculeSdf: string,
|
||||
@@ -82,20 +82,24 @@ export class AlphaOrbitalsExample {
|
||||
|
||||
this.plugin.managers.interactivity.setProps({ granularity: 'element' });
|
||||
|
||||
if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
|
||||
PluginCommands.Toast.Show(this.plugin, {
|
||||
title: 'Error',
|
||||
message: `Browser/device does not support required WebGL extension (OES_texture_float).`
|
||||
this.plugin.behaviors.canvas3d.initialized.subscribe(init => {
|
||||
if (!init) return;
|
||||
|
||||
if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
|
||||
PluginCommands.Toast.Show(this.plugin, {
|
||||
title: 'Error',
|
||||
message: `Browser/device does not support required WebGL extension (OES_texture_float).`
|
||||
});
|
||||
return;
|
||||
}
|
||||
|
||||
this.load({
|
||||
moleculeSdf: DemoMoleculeSDF,
|
||||
...DemoOrbitals
|
||||
});
|
||||
return;
|
||||
}
|
||||
|
||||
this.load({
|
||||
moleculeSdf: DemoMoleculeSDF,
|
||||
...DemoOrbitals
|
||||
mountControls(this, document.getElementById('controls')!);
|
||||
});
|
||||
|
||||
mountControls(this, document.getElementById('controls')!);
|
||||
}
|
||||
|
||||
readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
|
||||
@@ -222,5 +226,4 @@ export class AlphaOrbitalsExample {
|
||||
|
||||
(window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();
|
||||
(window as any).AlphaOrbitalsExample.setDebugMode = setDebugMode;
|
||||
(window as any).AlphaOrbitalsExample.setTimingMode = setTimingMode;
|
||||
(window as any).AlphaOrbitalsExample.consoleStats = consoleStats;
|
||||
(window as any).AlphaOrbitalsExample.setTimingMode = setTimingMode;
|
||||
@@ -46,14 +46,6 @@ class BasicWrapper {
|
||||
this.plugin.representation.structure.themes.colorThemeRegistry.add(CustomColorThemeProvider);
|
||||
this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider!);
|
||||
this.plugin.customModelProperties.register(StripedResidues.propertyProvider, true);
|
||||
|
||||
this.plugin.managers.dragAndDrop.addHandler('custom-wrapper', (files) => {
|
||||
if (files.some(f => f.name.toLowerCase().endsWith('.testext'))) {
|
||||
console.log('.testext File dropped');
|
||||
return true;
|
||||
}
|
||||
return false;
|
||||
});
|
||||
}
|
||||
|
||||
async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
|
||||
|
||||
@@ -1,94 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*
|
||||
* Example command-line application generating images of PDB structures
|
||||
* Build: npm install --no-save gl jpeg-js pngjs // these packages are not listed in dependencies for performance reasons
|
||||
* npm run build
|
||||
* Run: node lib/commonjs/examples/image-renderer 1cbs ../outputs_1cbs/
|
||||
*/
|
||||
|
||||
import { ArgumentParser } from 'argparse';
|
||||
import fs from 'fs';
|
||||
import path from 'path';
|
||||
import gl from 'gl';
|
||||
import pngjs from 'pngjs';
|
||||
import jpegjs from 'jpeg-js';
|
||||
|
||||
import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
|
||||
import { ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif } from '../../mol-plugin-state/transforms/model';
|
||||
import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
|
||||
import { HeadlessPluginContext } from '../../mol-plugin/headless-plugin-context';
|
||||
import { DefaultPluginSpec } from '../../mol-plugin/spec';
|
||||
import { ExternalModules, STYLIZED_POSTPROCESSING } from '../../mol-plugin/util/headless-screenshot';
|
||||
import { setFSModule } from '../../mol-util/data-source';
|
||||
|
||||
|
||||
setFSModule(fs);
|
||||
|
||||
interface Args {
|
||||
pdbId: string,
|
||||
outDirectory: string
|
||||
}
|
||||
|
||||
function parseArguments(): Args {
|
||||
const parser = new ArgumentParser({ description: 'Example command-line application generating images of PDB structures' });
|
||||
parser.add_argument('pdbId', { help: 'PDB identifier' });
|
||||
parser.add_argument('outDirectory', { help: 'Directory for outputs' });
|
||||
const args = parser.parse_args();
|
||||
return { ...args };
|
||||
}
|
||||
|
||||
async function main() {
|
||||
const args = parseArguments();
|
||||
const url = `https://www.ebi.ac.uk/pdbe/entry-files/download/${args.pdbId}.bcif`;
|
||||
console.log('PDB ID:', args.pdbId);
|
||||
console.log('Source URL:', url);
|
||||
console.log('Outputs:', args.outDirectory);
|
||||
|
||||
// Create a headless plugin
|
||||
const externalModules: ExternalModules = { gl, pngjs, 'jpeg-js': jpegjs };
|
||||
const plugin = new HeadlessPluginContext(externalModules, DefaultPluginSpec(), { width: 800, height: 800 });
|
||||
await plugin.init();
|
||||
|
||||
// Download and visualize data in the plugin
|
||||
const update = plugin.build();
|
||||
const structure = update.toRoot()
|
||||
.apply(Download, { url, isBinary: true })
|
||||
.apply(ParseCif)
|
||||
.apply(TrajectoryFromMmCif)
|
||||
.apply(ModelFromTrajectory)
|
||||
.apply(StructureFromModel);
|
||||
const polymer = structure.apply(StructureComponent, { type: { name: 'static', params: 'polymer' } });
|
||||
const ligand = structure.apply(StructureComponent, { type: { name: 'static', params: 'ligand' } });
|
||||
polymer.apply(StructureRepresentation3D, {
|
||||
type: { name: 'cartoon', params: { alpha: 1 } },
|
||||
colorTheme: { name: 'sequence-id', params: {} },
|
||||
});
|
||||
ligand.apply(StructureRepresentation3D, {
|
||||
type: { name: 'ball-and-stick', params: { sizeFactor: 1 } },
|
||||
colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'element-symbol', params: {} } } },
|
||||
sizeTheme: { name: 'physical', params: {} },
|
||||
});
|
||||
await update.commit();
|
||||
|
||||
// Export images
|
||||
fs.mkdirSync(args.outDirectory, { recursive: true });
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'basic.png'));
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'basic.jpg'));
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'large.png'), { width: 1600, height: 1200 });
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'large.jpg'), { width: 1600, height: 1200 });
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'stylized.png'), undefined, STYLIZED_POSTPROCESSING);
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'stylized.jpg'), undefined, STYLIZED_POSTPROCESSING);
|
||||
await plugin.saveImage(path.join(args.outDirectory, 'stylized-compressed-jpg.jpg'), undefined, STYLIZED_POSTPROCESSING, undefined, 10);
|
||||
|
||||
// Export state loadable in Mol* Viewer
|
||||
await plugin.saveStateSnapshot(path.join(args.outDirectory, 'molstar-state.molj'));
|
||||
|
||||
// Cleanup
|
||||
await plugin.clear();
|
||||
plugin.dispose();
|
||||
}
|
||||
|
||||
main();
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
@@ -24,31 +24,8 @@ const Canvas3DPresets = {
|
||||
illustrative: {
|
||||
canvas3d: <Preset>{
|
||||
postprocessing: {
|
||||
occlusion: {
|
||||
name: 'on',
|
||||
params: {
|
||||
samples: 32,
|
||||
multiScale: { name: 'off', params: {} },
|
||||
radius: 5,
|
||||
bias: 0.8,
|
||||
blurKernelSize: 15,
|
||||
resolutionScale: 1,
|
||||
color: Color(0x000000),
|
||||
}
|
||||
},
|
||||
outline: {
|
||||
name: 'on',
|
||||
params: {
|
||||
scale: 1,
|
||||
threshold: 0.33,
|
||||
color: Color(0x000000),
|
||||
includeTransparent: true,
|
||||
}
|
||||
},
|
||||
shadow: {
|
||||
name: 'off',
|
||||
params: {}
|
||||
},
|
||||
occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
|
||||
outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000) } }
|
||||
},
|
||||
renderer: {
|
||||
ambientIntensity: 1.0,
|
||||
@@ -59,25 +36,8 @@ const Canvas3DPresets = {
|
||||
occlusion: {
|
||||
canvas3d: <Preset>{
|
||||
postprocessing: {
|
||||
occlusion: {
|
||||
name: 'on',
|
||||
params: {
|
||||
samples: 32,
|
||||
multiScale: { name: 'off', params: {} },
|
||||
radius: 5,
|
||||
bias: 0.8,
|
||||
blurKernelSize: 15,
|
||||
resolutionScale: 1,
|
||||
}
|
||||
},
|
||||
outline: {
|
||||
name: 'off',
|
||||
params: {}
|
||||
},
|
||||
shadow: {
|
||||
name: 'off',
|
||||
params: {}
|
||||
},
|
||||
occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
|
||||
outline: { name: 'off', params: {} }
|
||||
},
|
||||
renderer: {
|
||||
ambientIntensity: 0.4,
|
||||
@@ -90,8 +50,7 @@ const Canvas3DPresets = {
|
||||
canvas3d: <Preset>{
|
||||
postprocessing: {
|
||||
occlusion: { name: 'off', params: {} },
|
||||
outline: { name: 'off', params: {} },
|
||||
shadow: { name: 'off', params: {} },
|
||||
outline: { name: 'off', params: {} }
|
||||
},
|
||||
renderer: {
|
||||
ambientIntensity: 0.4,
|
||||
|
||||
@@ -1,159 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*
|
||||
* Command-line application for rendering images from MolViewSpec files
|
||||
* Build: npm install --no-save gl jpeg-js pngjs // these packages are not listed in Mol* dependencies for performance reasons
|
||||
* npm run build
|
||||
* Run: node lib/commonjs/examples/mvs/mvs-render -i examples/mvs/1cbs.mvsj -o ../outputs/1cbs.png --size 800x600 --molj
|
||||
*/
|
||||
|
||||
import { ArgumentParser } from 'argparse';
|
||||
import fs from 'fs';
|
||||
import gl from 'gl';
|
||||
import jpegjs from 'jpeg-js';
|
||||
import path from 'path';
|
||||
import pngjs from 'pngjs';
|
||||
|
||||
import { Canvas3DParams } from '../../mol-canvas3d/canvas3d';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { HeadlessPluginContext } from '../../mol-plugin/headless-plugin-context';
|
||||
import { DefaultPluginSpec, PluginSpec } from '../../mol-plugin/spec';
|
||||
import { ExternalModules, defaultCanvas3DParams } from '../../mol-plugin/util/headless-screenshot';
|
||||
import { setFSModule } from '../../mol-util/data-source';
|
||||
import { onelinerJsonString } from '../../mol-util/json';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
|
||||
// MolViewSpec must be imported after HeadlessPluginContext
|
||||
import { MolViewSpec } from '../../extensions/mvs/behavior';
|
||||
import { loadMVS } from '../../extensions/mvs/load';
|
||||
import { MVSData } from '../../extensions/mvs/mvs-data';
|
||||
import { dfs } from '../../extensions/mvs/tree/generic/tree-utils';
|
||||
|
||||
|
||||
setFSModule(fs);
|
||||
|
||||
const DEFAULT_SIZE = '800x800';
|
||||
|
||||
/** Command line argument values for `main` */
|
||||
interface Args {
|
||||
input: string[],
|
||||
output: string[],
|
||||
size: { width: number, height: number },
|
||||
molj: boolean,
|
||||
}
|
||||
|
||||
/** Return parsed command line arguments for `main` */
|
||||
function parseArguments(): Args {
|
||||
const parser = new ArgumentParser({ description: 'Command-line application for rendering images from MolViewSpec files' });
|
||||
parser.add_argument('-i', '--input', { required: true, nargs: '+', help: 'Input file(s) in .mvsj format' });
|
||||
parser.add_argument('-o', '--output', { required: true, nargs: '+', help: 'File path(s) for output files (one output path for each input file). Output format is inferred from the file extension (.png or .jpg)' });
|
||||
parser.add_argument('-s', '--size', { help: `Output image resolution, {width}x{height}. Default: ${DEFAULT_SIZE}.`, default: DEFAULT_SIZE });
|
||||
parser.add_argument('-m', '--molj', { action: 'store_true', help: `Save Mol* state (.molj) in addition to rendered images (use the same output file paths but with .molj extension)` });
|
||||
const args = parser.parse_args();
|
||||
try {
|
||||
const parts = args.size.split('x');
|
||||
if (parts.length !== 2) throw new Error('Must contain two x-separated parts');
|
||||
args.size = { width: parseIntStrict(parts[0]), height: parseIntStrict(parts[1]) };
|
||||
} catch {
|
||||
parser.error(`argument: --size: invalid image size string: '${args.size}' (must be two x-separated integers (width and height), e.g. '400x300')`);
|
||||
}
|
||||
if (args.input.length !== args.output.length) {
|
||||
parser.error(`argument: --output: must specify the same number of input and output file paths (specified ${args.input.length} input path${args.input.length !== 1 ? 's' : ''} but ${args.output.length} output path${args.output.length !== 1 ? 's' : ''})`);
|
||||
}
|
||||
return { ...args };
|
||||
}
|
||||
|
||||
/** Main workflow for rendering images from MolViewSpec files */
|
||||
async function main(args: Args): Promise<void> {
|
||||
const plugin = await createHeadlessPlugin(args);
|
||||
|
||||
for (let i = 0; i < args.input.length; i++) {
|
||||
const input = args.input[i];
|
||||
const output = args.output[i];
|
||||
console.log(`Processing ${input} -> ${output}`);
|
||||
|
||||
const data = fs.readFileSync(input, { encoding: 'utf8' });
|
||||
const mvsData = MVSData.fromMVSJ(data);
|
||||
removeLabelNodes(mvsData);
|
||||
|
||||
await loadMVS(plugin, mvsData, { sanityChecks: true, replaceExisting: true });
|
||||
fs.mkdirSync(path.dirname(output), { recursive: true });
|
||||
if (args.molj) {
|
||||
await plugin.saveStateSnapshot(withExtension(output, '.molj'));
|
||||
}
|
||||
await plugin.saveImage(output);
|
||||
checkState(plugin);
|
||||
}
|
||||
await plugin.clear();
|
||||
plugin.dispose();
|
||||
}
|
||||
|
||||
/** Return a new and initiatized HeadlessPlugin */
|
||||
async function createHeadlessPlugin(args: Pick<Args, 'size'>): Promise<HeadlessPluginContext> {
|
||||
const externalModules: ExternalModules = { gl, pngjs, 'jpeg-js': jpegjs };
|
||||
const spec = DefaultPluginSpec();
|
||||
spec.behaviors.push(PluginSpec.Behavior(MolViewSpec));
|
||||
const headlessCanvasOptions = defaultCanvas3DParams();
|
||||
const canvasOptions = {
|
||||
...PD.getDefaultValues(Canvas3DParams),
|
||||
cameraResetDurationMs: headlessCanvasOptions.cameraResetDurationMs,
|
||||
postprocessing: headlessCanvasOptions.postprocessing,
|
||||
};
|
||||
const plugin = new HeadlessPluginContext(externalModules, spec, args.size, { canvas: canvasOptions });
|
||||
try {
|
||||
await plugin.init();
|
||||
} catch (error) {
|
||||
plugin.dispose();
|
||||
throw error;
|
||||
}
|
||||
return plugin;
|
||||
}
|
||||
|
||||
/** Parse integer, fail early. */
|
||||
function parseIntStrict(str: string): number {
|
||||
if (str === '') throw new Error('Is empty string');
|
||||
const result = Number(str);
|
||||
if (isNaN(result)) throw new Error('Is NaN');
|
||||
if (Math.floor(result) !== result) throw new Error('Is not integer');
|
||||
return result;
|
||||
}
|
||||
|
||||
/** Replace the file extension in `filename` by `extension`. If `filename` has no extension, add it. */
|
||||
function withExtension(filename: string, extension: string): string {
|
||||
const oldExtension = path.extname(filename);
|
||||
return filename.slice(0, -oldExtension.length) + extension;
|
||||
}
|
||||
|
||||
/** Remove any label* nodes from the MVS tree (in-place). Print warning if removed at least one node. */
|
||||
function removeLabelNodes(mvsData: MVSData): void {
|
||||
let removedSomething = false;
|
||||
dfs(mvsData.root, node => {
|
||||
const nChildren = node.children?.length ?? 0;
|
||||
node.children = node.children?.filter(c => !c.kind.startsWith('label'));
|
||||
if ((node.children?.length ?? 0) !== nChildren) {
|
||||
removedSomething = true;
|
||||
}
|
||||
});
|
||||
if (removedSomething) {
|
||||
// trying to render labels would fail because `document` is not available in Nodejs
|
||||
console.error('Rendering labels is not yet supported in mvs-render. Skipping any label* nodes.');
|
||||
}
|
||||
}
|
||||
|
||||
/** Check Mol* state, print and throw error if any cell is not OK. */
|
||||
function checkState(plugin: PluginContext): void {
|
||||
const cells = Array.from(plugin.state.data.cells.values());
|
||||
const badCell = cells.find(cell => cell.status !== 'ok');
|
||||
if (badCell) {
|
||||
console.error(`Building Mol* state failed`);
|
||||
console.error(` Transformer: ${badCell.transform.transformer.id}`);
|
||||
console.error(` Params: ${onelinerJsonString(badCell.transform.params)}`);
|
||||
console.error(` Error: ${badCell.errorText}`);
|
||||
console.error(``);
|
||||
throw new Error(`Building Mol* state failed: ${badCell.errorText}`);
|
||||
}
|
||||
}
|
||||
|
||||
main(parseArguments());
|
||||
@@ -1,57 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*
|
||||
* Command-line application for validating MolViewSpec files
|
||||
* Build: npm run build
|
||||
* Run: node lib/commonjs/examples/mvs/mvs-validate examples/mvs/1cbs.mvsj
|
||||
*/
|
||||
|
||||
import { ArgumentParser } from 'argparse';
|
||||
import fs from 'fs';
|
||||
|
||||
import { setFSModule } from '../../mol-util/data-source';
|
||||
import { MVSData } from '../../extensions/mvs/mvs-data';
|
||||
|
||||
|
||||
setFSModule(fs);
|
||||
|
||||
/** Command line argument values for `main` */
|
||||
interface Args {
|
||||
input: string[],
|
||||
no_extra: boolean,
|
||||
}
|
||||
|
||||
/** Return parsed command line arguments for `main` */
|
||||
function parseArguments(): Args {
|
||||
const parser = new ArgumentParser({ description: 'Command-line application for validating MolViewSpec files. Prints validation status (OK/FAILED) to stdout, detailed validation issues to stderr. Exits with a zero exit code if all input files are OK.' });
|
||||
parser.add_argument('input', { nargs: '+', help: 'Input file(s) in .mvsj format' });
|
||||
parser.add_argument('--no-extra', { action: 'store_true', help: 'Treat presence of extra node params as an issue.' });
|
||||
const args = parser.parse_args();
|
||||
return { ...args };
|
||||
}
|
||||
|
||||
/** Main workflow for validating MolViewSpec files. Returns the number of failed input files. */
|
||||
function main(args: Args): number {
|
||||
let nFailed = 0;
|
||||
for (const input of args.input) {
|
||||
const data = fs.readFileSync(input, { encoding: 'utf8' });
|
||||
const mvsData = MVSData.fromMVSJ(data);
|
||||
const issues = MVSData.validationIssues(mvsData, { noExtra: args.no_extra });
|
||||
const status = issues ? 'FAILED' : 'OK';
|
||||
console.log(`${status.padEnd(6)} ${input}`);
|
||||
if (issues) {
|
||||
nFailed++;
|
||||
for (const issue of issues) {
|
||||
console.error(issue);
|
||||
}
|
||||
}
|
||||
}
|
||||
return nFailed;
|
||||
}
|
||||
|
||||
const nFailed = main(parseArguments());
|
||||
if (nFailed > 0) {
|
||||
process.exitCode = 1;
|
||||
}
|
||||
@@ -50,7 +50,7 @@ const _testBasis: Basis = {
|
||||
0.025886090588624934,
|
||||
0.019164790004065606,
|
||||
-0.013539970104105408
|
||||
],
|
||||
] as Vec3,
|
||||
'shells': [
|
||||
{
|
||||
'angularMomentum': [0],
|
||||
@@ -101,7 +101,7 @@ const _testBasis: Basis = {
|
||||
0.5082729578468134,
|
||||
1.6880351220025265,
|
||||
0.4963443067810461
|
||||
],
|
||||
] as Vec3,
|
||||
'shells': [
|
||||
{
|
||||
'angularMomentum': [0],
|
||||
@@ -158,7 +158,7 @@ const _testBasis: Basis = {
|
||||
1.1367367844436005,
|
||||
-0.47018519422670163,
|
||||
-1.356802622574504
|
||||
],
|
||||
] as Vec3,
|
||||
'shells': [
|
||||
{
|
||||
'angularMomentum': [0],
|
||||
|
||||
@@ -53,7 +53,7 @@ export async function sphericalCollocation(
|
||||
L,
|
||||
shell.coefficients[amIndex++],
|
||||
shell.exponents,
|
||||
atom.center as unknown as Vec3,
|
||||
atom.center,
|
||||
cutoffThreshold,
|
||||
alpha
|
||||
);
|
||||
|
||||
@@ -22,7 +22,7 @@ export interface SphericalElectronShell {
|
||||
export interface Basis {
|
||||
atoms: {
|
||||
// in Bohr units!
|
||||
center: [number, number, number];
|
||||
center: Vec3;
|
||||
shells: SphericalElectronShell[];
|
||||
}[];
|
||||
}
|
||||
@@ -78,7 +78,7 @@ export function initCubeGrid(params: CubeGridComputationParams): CubeGridInfo {
|
||||
const count = geometry.length;
|
||||
const box = Box3D.expand(
|
||||
Box3D(),
|
||||
Box3D.fromVec3Array(Box3D(), geometry as unknown as Vec3[]),
|
||||
Box3D.fromVec3Array(Box3D(), geometry),
|
||||
Vec3.create(expand, expand, expand)
|
||||
);
|
||||
const size = Box3D.size(Vec3(), box);
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
@@ -28,12 +28,6 @@ export const Backgrounds = PluginBehavior.create<{ }>({
|
||||
ctor: class extends PluginBehavior.Handler<{ }> {
|
||||
register(): void {
|
||||
this.ctx.config.set(PluginConfig.Background.Styles, [
|
||||
[{
|
||||
variant: {
|
||||
name: 'off',
|
||||
params: {}
|
||||
}
|
||||
}, 'Off'],
|
||||
[{
|
||||
variant: {
|
||||
name: 'radialGradient',
|
||||
@@ -56,7 +50,6 @@ export const Backgrounds = PluginBehavior.create<{ }>({
|
||||
lightness: 0,
|
||||
saturation: 0,
|
||||
opacity: 1,
|
||||
blur: 0,
|
||||
coverage: 'viewport',
|
||||
}
|
||||
}
|
||||
@@ -79,7 +72,6 @@ export const Backgrounds = PluginBehavior.create<{ }>({
|
||||
lightness: 0,
|
||||
saturation: 0,
|
||||
opacity: 1,
|
||||
blur: 0.3,
|
||||
}
|
||||
}
|
||||
}, 'Purple Nebula Skybox'],
|
||||
|
||||
@@ -45,14 +45,8 @@ export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Valu
|
||||
const palette = getPalette(size, { palette: {
|
||||
name: 'generate',
|
||||
params: {
|
||||
hue,
|
||||
chroma: [30, 80],
|
||||
luminance: [15, 85],
|
||||
clusteringStepCount: 50,
|
||||
minSampleCount: 800,
|
||||
maxCount: 75,
|
||||
sampleCountFactor: 5,
|
||||
sort: 'contrast'
|
||||
hue, chroma: [30, 80], luminance: [15, 85],
|
||||
clusteringStepCount: 50, minSampleCount: 800, maxCount: 75
|
||||
}
|
||||
} }, { minLabel: 'Min', maxLabel: 'Max' });
|
||||
legend = palette.legend;
|
||||
|
||||
@@ -52,7 +52,7 @@ export interface Compartment {
|
||||
}
|
||||
|
||||
// Primitives discribing a compartment
|
||||
export enum CompartmentPrimitiveType {
|
||||
export const enum CompartmentPrimitiveType {
|
||||
MetaBall = 0,
|
||||
Sphere = 1,
|
||||
Cube = 2,
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
* @author Ludovic Autin <ludovic.autin@gmail.com>
|
||||
@@ -236,7 +236,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
|
||||
structure = await getCurve(name, getCurveTransforms(ingredient), model);
|
||||
} else {
|
||||
if ((!results || results.length === 0)) return;
|
||||
let bu: string | undefined = source.bu ? source.bu : undefined;
|
||||
let bu: string|undefined = source.bu ? source.bu : undefined;
|
||||
if (bu) {
|
||||
if (bu === 'AU') {
|
||||
bu = undefined;
|
||||
@@ -585,7 +585,7 @@ export const LoadCellPackModel = StateAction.build({
|
||||
... ctx.managers.structure.component.state.options,
|
||||
visualQuality: 'custom',
|
||||
ignoreLight: true,
|
||||
hydrogens: 'hide-all',
|
||||
showHydrogens: false,
|
||||
});
|
||||
ctx.canvas3d?.setProps({
|
||||
multiSample: { mode: 'off' },
|
||||
@@ -600,21 +600,10 @@ export const LoadCellPackModel = StateAction.build({
|
||||
name: 'on',
|
||||
params: {
|
||||
samples: 32,
|
||||
multiScale: { name: 'off', params: {} },
|
||||
radius: 8,
|
||||
bias: 1,
|
||||
blurKernelSize: 15,
|
||||
resolutionScale: 1,
|
||||
color: Color(0x000000),
|
||||
}
|
||||
},
|
||||
shadow: {
|
||||
name: 'on',
|
||||
params: {
|
||||
bias: 0.6,
|
||||
maxDistance: 80,
|
||||
steps: 3,
|
||||
tolerance: 1.0,
|
||||
}
|
||||
},
|
||||
outline: {
|
||||
@@ -623,7 +612,6 @@ export const LoadCellPackModel = StateAction.build({
|
||||
scale: 1,
|
||||
threshold: 0.33,
|
||||
color: ColorNames.black,
|
||||
includeTransparent: true,
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,59 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import { ConfalPyramidsPreset } from './confal-pyramids/behavior';
|
||||
import { ConfalPyramidsColorThemeProvider } from './confal-pyramids/color';
|
||||
import { ConfalPyramidsProvider } from './confal-pyramids/property';
|
||||
import { ConfalPyramidsRepresentationProvider } from './confal-pyramids/representation';
|
||||
import { NtCTubePreset } from './ntc-tube/behavior';
|
||||
import { NtCTubeColorThemeProvider } from './ntc-tube/color';
|
||||
import { NtCTubeProvider } from './ntc-tube/property';
|
||||
import { NtCTubeRepresentationProvider } from './ntc-tube/representation';
|
||||
|
||||
|
||||
export const DnatcoNtCs = PluginBehavior.create<{ autoAttach: boolean, showToolTip: boolean }>({
|
||||
name: 'dnatco-ntcs',
|
||||
category: 'custom-props',
|
||||
display: {
|
||||
name: 'DNATCO NtC Annotations',
|
||||
description: 'DNATCO NtC Annotations',
|
||||
},
|
||||
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showToolTip: boolean }> {
|
||||
register(): void {
|
||||
this.ctx.customModelProperties.register(ConfalPyramidsProvider, this.params.autoAttach);
|
||||
this.ctx.customModelProperties.register(NtCTubeProvider, this.params.autoAttach);
|
||||
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
|
||||
this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.add(NtCTubeColorThemeProvider);
|
||||
this.ctx.representation.structure.registry.add(NtCTubeRepresentationProvider);
|
||||
|
||||
this.ctx.builders.structure.representation.registerPreset(ConfalPyramidsPreset);
|
||||
this.ctx.builders.structure.representation.registerPreset(NtCTubePreset);
|
||||
}
|
||||
|
||||
unregister() {
|
||||
this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
|
||||
this.ctx.customModelProperties.unregister(NtCTubeProvider.descriptor.name);
|
||||
|
||||
this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
|
||||
this.ctx.representation.structure.registry.remove(NtCTubeRepresentationProvider);
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.remove(NtCTubeColorThemeProvider);
|
||||
|
||||
this.ctx.builders.structure.representation.unregisterPreset(ConfalPyramidsPreset);
|
||||
this.ctx.builders.structure.representation.unregisterPreset(NtCTubePreset);
|
||||
}
|
||||
},
|
||||
params: () => ({
|
||||
autoAttach: PD.Boolean(true),
|
||||
showToolTip: PD.Boolean(true)
|
||||
})
|
||||
});
|
||||
|
||||
@@ -1,219 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { Color, ColorMap } from '../../mol-util/color';
|
||||
|
||||
export const DefaultNtCClassColors = {
|
||||
A: 0xFFC1C1,
|
||||
B: 0xC8CFFF,
|
||||
BII: 0x0059DA,
|
||||
miB: 0x3BE8FB,
|
||||
Z: 0x01F60E,
|
||||
IC: 0xFA5CFB,
|
||||
OPN: 0xE90000,
|
||||
SYN: 0xFFFF01,
|
||||
N: 0xF2F2F2,
|
||||
};
|
||||
export const ErrorColor = Color(0xFFA10A);
|
||||
|
||||
export const NtCColors = ColorMap({
|
||||
NANT_Upr: DefaultNtCClassColors.N,
|
||||
NANT_Lwr: DefaultNtCClassColors.N,
|
||||
AA00_Upr: DefaultNtCClassColors.A,
|
||||
AA00_Lwr: DefaultNtCClassColors.A,
|
||||
AA02_Upr: DefaultNtCClassColors.A,
|
||||
AA02_Lwr: DefaultNtCClassColors.A,
|
||||
AA03_Upr: DefaultNtCClassColors.A,
|
||||
AA03_Lwr: DefaultNtCClassColors.A,
|
||||
AA04_Upr: DefaultNtCClassColors.A,
|
||||
AA04_Lwr: DefaultNtCClassColors.A,
|
||||
AA08_Upr: DefaultNtCClassColors.A,
|
||||
AA08_Lwr: DefaultNtCClassColors.A,
|
||||
AA09_Upr: DefaultNtCClassColors.A,
|
||||
AA09_Lwr: DefaultNtCClassColors.A,
|
||||
AA01_Upr: DefaultNtCClassColors.A,
|
||||
AA01_Lwr: DefaultNtCClassColors.A,
|
||||
AA05_Upr: DefaultNtCClassColors.A,
|
||||
AA05_Lwr: DefaultNtCClassColors.A,
|
||||
AA06_Upr: DefaultNtCClassColors.A,
|
||||
AA06_Lwr: DefaultNtCClassColors.A,
|
||||
AA10_Upr: DefaultNtCClassColors.A,
|
||||
AA10_Lwr: DefaultNtCClassColors.A,
|
||||
AA11_Upr: DefaultNtCClassColors.A,
|
||||
AA11_Lwr: DefaultNtCClassColors.A,
|
||||
AA07_Upr: DefaultNtCClassColors.A,
|
||||
AA07_Lwr: DefaultNtCClassColors.A,
|
||||
AA12_Upr: DefaultNtCClassColors.A,
|
||||
AA12_Lwr: DefaultNtCClassColors.A,
|
||||
AA13_Upr: DefaultNtCClassColors.A,
|
||||
AA13_Lwr: DefaultNtCClassColors.A,
|
||||
AB01_Upr: DefaultNtCClassColors.A,
|
||||
AB01_Lwr: DefaultNtCClassColors.B,
|
||||
AB02_Upr: DefaultNtCClassColors.A,
|
||||
AB02_Lwr: DefaultNtCClassColors.B,
|
||||
AB03_Upr: DefaultNtCClassColors.A,
|
||||
AB03_Lwr: DefaultNtCClassColors.B,
|
||||
AB04_Upr: DefaultNtCClassColors.A,
|
||||
AB04_Lwr: DefaultNtCClassColors.B,
|
||||
AB05_Upr: DefaultNtCClassColors.A,
|
||||
AB05_Lwr: DefaultNtCClassColors.B,
|
||||
BA01_Upr: DefaultNtCClassColors.B,
|
||||
BA01_Lwr: DefaultNtCClassColors.A,
|
||||
BA05_Upr: DefaultNtCClassColors.B,
|
||||
BA05_Lwr: DefaultNtCClassColors.A,
|
||||
BA09_Upr: DefaultNtCClassColors.B,
|
||||
BA09_Lwr: DefaultNtCClassColors.A,
|
||||
BA08_Upr: DefaultNtCClassColors.BII,
|
||||
BA08_Lwr: DefaultNtCClassColors.A,
|
||||
BA10_Upr: DefaultNtCClassColors.B,
|
||||
BA10_Lwr: DefaultNtCClassColors.A,
|
||||
BA13_Upr: DefaultNtCClassColors.BII,
|
||||
BA13_Lwr: DefaultNtCClassColors.A,
|
||||
BA16_Upr: DefaultNtCClassColors.BII,
|
||||
BA16_Lwr: DefaultNtCClassColors.A,
|
||||
BA17_Upr: DefaultNtCClassColors.BII,
|
||||
BA17_Lwr: DefaultNtCClassColors.A,
|
||||
BB00_Upr: DefaultNtCClassColors.B,
|
||||
BB00_Lwr: DefaultNtCClassColors.B,
|
||||
BB01_Upr: DefaultNtCClassColors.B,
|
||||
BB01_Lwr: DefaultNtCClassColors.B,
|
||||
BB17_Upr: DefaultNtCClassColors.B,
|
||||
BB17_Lwr: DefaultNtCClassColors.B,
|
||||
BB02_Upr: DefaultNtCClassColors.B,
|
||||
BB02_Lwr: DefaultNtCClassColors.B,
|
||||
BB03_Upr: DefaultNtCClassColors.B,
|
||||
BB03_Lwr: DefaultNtCClassColors.B,
|
||||
BB11_Upr: DefaultNtCClassColors.B,
|
||||
BB11_Lwr: DefaultNtCClassColors.B,
|
||||
BB16_Upr: DefaultNtCClassColors.B,
|
||||
BB16_Lwr: DefaultNtCClassColors.B,
|
||||
BB04_Upr: DefaultNtCClassColors.B,
|
||||
BB04_Lwr: DefaultNtCClassColors.BII,
|
||||
BB05_Upr: DefaultNtCClassColors.B,
|
||||
BB05_Lwr: DefaultNtCClassColors.BII,
|
||||
BB07_Upr: DefaultNtCClassColors.BII,
|
||||
BB07_Lwr: DefaultNtCClassColors.BII,
|
||||
BB08_Upr: DefaultNtCClassColors.BII,
|
||||
BB08_Lwr: DefaultNtCClassColors.BII,
|
||||
BB10_Upr: DefaultNtCClassColors.miB,
|
||||
BB10_Lwr: DefaultNtCClassColors.miB,
|
||||
BB12_Upr: DefaultNtCClassColors.miB,
|
||||
BB12_Lwr: DefaultNtCClassColors.miB,
|
||||
BB13_Upr: DefaultNtCClassColors.miB,
|
||||
BB13_Lwr: DefaultNtCClassColors.miB,
|
||||
BB14_Upr: DefaultNtCClassColors.miB,
|
||||
BB14_Lwr: DefaultNtCClassColors.miB,
|
||||
BB15_Upr: DefaultNtCClassColors.miB,
|
||||
BB15_Lwr: DefaultNtCClassColors.miB,
|
||||
BB20_Upr: DefaultNtCClassColors.miB,
|
||||
BB20_Lwr: DefaultNtCClassColors.miB,
|
||||
IC01_Upr: DefaultNtCClassColors.IC,
|
||||
IC01_Lwr: DefaultNtCClassColors.IC,
|
||||
IC02_Upr: DefaultNtCClassColors.IC,
|
||||
IC02_Lwr: DefaultNtCClassColors.IC,
|
||||
IC03_Upr: DefaultNtCClassColors.IC,
|
||||
IC03_Lwr: DefaultNtCClassColors.IC,
|
||||
IC04_Upr: DefaultNtCClassColors.IC,
|
||||
IC04_Lwr: DefaultNtCClassColors.IC,
|
||||
IC05_Upr: DefaultNtCClassColors.IC,
|
||||
IC05_Lwr: DefaultNtCClassColors.IC,
|
||||
IC06_Upr: DefaultNtCClassColors.IC,
|
||||
IC06_Lwr: DefaultNtCClassColors.IC,
|
||||
IC07_Upr: DefaultNtCClassColors.IC,
|
||||
IC07_Lwr: DefaultNtCClassColors.IC,
|
||||
OP01_Upr: DefaultNtCClassColors.OPN,
|
||||
OP01_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP02_Upr: DefaultNtCClassColors.OPN,
|
||||
OP02_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP03_Upr: DefaultNtCClassColors.OPN,
|
||||
OP03_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP04_Upr: DefaultNtCClassColors.OPN,
|
||||
OP04_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP05_Upr: DefaultNtCClassColors.OPN,
|
||||
OP05_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP06_Upr: DefaultNtCClassColors.OPN,
|
||||
OP06_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP07_Upr: DefaultNtCClassColors.OPN,
|
||||
OP07_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP08_Upr: DefaultNtCClassColors.OPN,
|
||||
OP08_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP09_Upr: DefaultNtCClassColors.OPN,
|
||||
OP09_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP10_Upr: DefaultNtCClassColors.OPN,
|
||||
OP10_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP11_Upr: DefaultNtCClassColors.OPN,
|
||||
OP11_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP12_Upr: DefaultNtCClassColors.OPN,
|
||||
OP12_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP13_Upr: DefaultNtCClassColors.OPN,
|
||||
OP13_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP14_Upr: DefaultNtCClassColors.OPN,
|
||||
OP14_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP15_Upr: DefaultNtCClassColors.OPN,
|
||||
OP15_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP16_Upr: DefaultNtCClassColors.OPN,
|
||||
OP16_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP17_Upr: DefaultNtCClassColors.OPN,
|
||||
OP17_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP18_Upr: DefaultNtCClassColors.OPN,
|
||||
OP18_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP19_Upr: DefaultNtCClassColors.OPN,
|
||||
OP19_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP20_Upr: DefaultNtCClassColors.OPN,
|
||||
OP20_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP21_Upr: DefaultNtCClassColors.OPN,
|
||||
OP21_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP22_Upr: DefaultNtCClassColors.OPN,
|
||||
OP22_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP23_Upr: DefaultNtCClassColors.OPN,
|
||||
OP23_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP24_Upr: DefaultNtCClassColors.OPN,
|
||||
OP24_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP25_Upr: DefaultNtCClassColors.OPN,
|
||||
OP25_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP26_Upr: DefaultNtCClassColors.OPN,
|
||||
OP26_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP27_Upr: DefaultNtCClassColors.OPN,
|
||||
OP27_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP28_Upr: DefaultNtCClassColors.OPN,
|
||||
OP28_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP29_Upr: DefaultNtCClassColors.OPN,
|
||||
OP29_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP30_Upr: DefaultNtCClassColors.OPN,
|
||||
OP30_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP31_Upr: DefaultNtCClassColors.OPN,
|
||||
OP31_Lwr: DefaultNtCClassColors.OPN,
|
||||
OPS1_Upr: DefaultNtCClassColors.OPN,
|
||||
OPS1_Lwr: DefaultNtCClassColors.OPN,
|
||||
OP1S_Upr: DefaultNtCClassColors.OPN,
|
||||
OP1S_Lwr: DefaultNtCClassColors.SYN,
|
||||
AAS1_Upr: DefaultNtCClassColors.SYN,
|
||||
AAS1_Lwr: DefaultNtCClassColors.A,
|
||||
AB1S_Upr: DefaultNtCClassColors.A,
|
||||
AB1S_Lwr: DefaultNtCClassColors.SYN,
|
||||
AB2S_Upr: DefaultNtCClassColors.A,
|
||||
AB2S_Lwr: DefaultNtCClassColors.SYN,
|
||||
BB1S_Upr: DefaultNtCClassColors.B,
|
||||
BB1S_Lwr: DefaultNtCClassColors.SYN,
|
||||
BB2S_Upr: DefaultNtCClassColors.B,
|
||||
BB2S_Lwr: DefaultNtCClassColors.SYN,
|
||||
BBS1_Upr: DefaultNtCClassColors.SYN,
|
||||
BBS1_Lwr: DefaultNtCClassColors.B,
|
||||
ZZ01_Upr: DefaultNtCClassColors.Z,
|
||||
ZZ01_Lwr: DefaultNtCClassColors.Z,
|
||||
ZZ02_Upr: DefaultNtCClassColors.Z,
|
||||
ZZ02_Lwr: DefaultNtCClassColors.Z,
|
||||
ZZ1S_Upr: DefaultNtCClassColors.Z,
|
||||
ZZ1S_Lwr: DefaultNtCClassColors.SYN,
|
||||
ZZ2S_Upr: DefaultNtCClassColors.Z,
|
||||
ZZ2S_Lwr: DefaultNtCClassColors.SYN,
|
||||
ZZS1_Upr: DefaultNtCClassColors.SYN,
|
||||
ZZS1_Lwr: DefaultNtCClassColors.Z,
|
||||
ZZS2_Upr: DefaultNtCClassColors.SYN,
|
||||
ZZS2_Lwr: DefaultNtCClassColors.Z,
|
||||
});
|
||||
|
||||
@@ -6,22 +6,23 @@
|
||||
*/
|
||||
|
||||
import { ConfalPyramidsColorThemeProvider } from './color';
|
||||
import { ConfalPyramidsProvider } from './property';
|
||||
import { ConfalPyramids, ConfalPyramidsProvider } from './property';
|
||||
import { ConfalPyramidsRepresentationProvider } from './representation';
|
||||
import { Dnatco } from '../property';
|
||||
import { DnatcoTypes } from '../types';
|
||||
import { ConfalPyramidsTypes } from './types';
|
||||
import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
|
||||
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
|
||||
import { StateObjectRef } from '../../../mol-state';
|
||||
import { Task } from '../../../mol-task';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
|
||||
export const ConfalPyramidsPreset = StructureRepresentationPresetProvider({
|
||||
export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider({
|
||||
id: 'preset-structure-representation-confal-pyramids',
|
||||
display: {
|
||||
name: 'Confal Pyramids', group: 'Annotation',
|
||||
description: 'Schematic depiction of conformer class and confal value.',
|
||||
},
|
||||
isApplicable(a) {
|
||||
return a.data.models.length >= 1 && a.data.models.some(m => Dnatco.isApplicable(m));
|
||||
return a.data.models.length >= 1 && a.data.models.some(m => ConfalPyramids.isApplicable(m));
|
||||
},
|
||||
params: () => StructureRepresentationPresetProvider.CommonParams,
|
||||
async apply(ref, params, plugin) {
|
||||
@@ -47,7 +48,50 @@ export const ConfalPyramidsPreset = StructureRepresentationPresetProvider({
|
||||
}
|
||||
});
|
||||
|
||||
export function confalPyramidLabel(step: DnatcoTypes.Step) {
|
||||
export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean, showToolTip: boolean }>({
|
||||
name: 'dnatco-confal-pyramids-prop',
|
||||
category: 'custom-props',
|
||||
display: {
|
||||
name: 'Confal Pyramids',
|
||||
description: 'Schematic depiction of conformer class and confal value.',
|
||||
},
|
||||
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showToolTip: boolean }> {
|
||||
private provider = ConfalPyramidsProvider;
|
||||
|
||||
register(): void {
|
||||
this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
|
||||
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
|
||||
this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
|
||||
|
||||
this.ctx.builders.structure.representation.registerPreset(DnatcoConfalPyramidsPreset);
|
||||
}
|
||||
|
||||
update(p: { autoAttach: boolean, showToolTip: boolean }) {
|
||||
const updated = this.params.autoAttach !== p.autoAttach;
|
||||
this.params.autoAttach = p.autoAttach;
|
||||
this.params.showToolTip = p.showToolTip;
|
||||
this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
|
||||
return updated;
|
||||
}
|
||||
|
||||
unregister() {
|
||||
this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
|
||||
|
||||
this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
|
||||
|
||||
this.ctx.builders.structure.representation.unregisterPreset(DnatcoConfalPyramidsPreset);
|
||||
}
|
||||
},
|
||||
params: () => ({
|
||||
autoAttach: PD.Boolean(true),
|
||||
showToolTip: PD.Boolean(true)
|
||||
})
|
||||
});
|
||||
|
||||
export function confalPyramidLabel(halfPyramid: ConfalPyramidsTypes.HalfPyramid) {
|
||||
const { step } = halfPyramid;
|
||||
return `
|
||||
<b>${step.auth_asym_id_1}</b> |
|
||||
<b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
|
||||
|
||||
@@ -5,10 +5,8 @@
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { ErrorColor, NtCColors } from '../color';
|
||||
import { ConfalPyramidsProvider } from './property';
|
||||
import { ConfalPyramids, ConfalPyramidsProvider } from './property';
|
||||
import { ConfalPyramidsTypes as CPT } from './types';
|
||||
import { Dnatco } from '../property';
|
||||
import { Location } from '../../../mol-model/location';
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { ColorTheme } from '../../../mol-theme/color';
|
||||
@@ -21,7 +19,215 @@ import { ObjectKeys } from '../../../mol-util/type-helpers';
|
||||
|
||||
const Description = 'Assigns colors to confal pyramids';
|
||||
|
||||
const PyramidsColors = ColorMap({ ...NtCColors });
|
||||
const DefaultClassColors = {
|
||||
A: 0xFFC1C1,
|
||||
B: 0xC8CFFF,
|
||||
BII: 0x0059DA,
|
||||
miB: 0x3BE8FB,
|
||||
Z: 0x01F60E,
|
||||
IC: 0xFA5CFB,
|
||||
OPN: 0xE90000,
|
||||
SYN: 0xFFFF01,
|
||||
N: 0xF2F2F2,
|
||||
};
|
||||
const ErrorColor = Color(0xFFA10A);
|
||||
|
||||
const PyramidsColors = ColorMap({
|
||||
NANT_Upr: DefaultClassColors.N,
|
||||
NANT_Lwr: DefaultClassColors.N,
|
||||
AA00_Upr: DefaultClassColors.A,
|
||||
AA00_Lwr: DefaultClassColors.A,
|
||||
AA02_Upr: DefaultClassColors.A,
|
||||
AA02_Lwr: DefaultClassColors.A,
|
||||
AA03_Upr: DefaultClassColors.A,
|
||||
AA03_Lwr: DefaultClassColors.A,
|
||||
AA04_Upr: DefaultClassColors.A,
|
||||
AA04_Lwr: DefaultClassColors.A,
|
||||
AA08_Upr: DefaultClassColors.A,
|
||||
AA08_Lwr: DefaultClassColors.A,
|
||||
AA09_Upr: DefaultClassColors.A,
|
||||
AA09_Lwr: DefaultClassColors.A,
|
||||
AA01_Upr: DefaultClassColors.A,
|
||||
AA01_Lwr: DefaultClassColors.A,
|
||||
AA05_Upr: DefaultClassColors.A,
|
||||
AA05_Lwr: DefaultClassColors.A,
|
||||
AA06_Upr: DefaultClassColors.A,
|
||||
AA06_Lwr: DefaultClassColors.A,
|
||||
AA10_Upr: DefaultClassColors.A,
|
||||
AA10_Lwr: DefaultClassColors.A,
|
||||
AA11_Upr: DefaultClassColors.A,
|
||||
AA11_Lwr: DefaultClassColors.A,
|
||||
AA07_Upr: DefaultClassColors.A,
|
||||
AA07_Lwr: DefaultClassColors.A,
|
||||
AA12_Upr: DefaultClassColors.A,
|
||||
AA12_Lwr: DefaultClassColors.A,
|
||||
AA13_Upr: DefaultClassColors.A,
|
||||
AA13_Lwr: DefaultClassColors.A,
|
||||
AB01_Upr: DefaultClassColors.A,
|
||||
AB01_Lwr: DefaultClassColors.B,
|
||||
AB02_Upr: DefaultClassColors.A,
|
||||
AB02_Lwr: DefaultClassColors.B,
|
||||
AB03_Upr: DefaultClassColors.A,
|
||||
AB03_Lwr: DefaultClassColors.B,
|
||||
AB04_Upr: DefaultClassColors.A,
|
||||
AB04_Lwr: DefaultClassColors.B,
|
||||
AB05_Upr: DefaultClassColors.A,
|
||||
AB05_Lwr: DefaultClassColors.B,
|
||||
BA01_Upr: DefaultClassColors.B,
|
||||
BA01_Lwr: DefaultClassColors.A,
|
||||
BA05_Upr: DefaultClassColors.B,
|
||||
BA05_Lwr: DefaultClassColors.A,
|
||||
BA09_Upr: DefaultClassColors.B,
|
||||
BA09_Lwr: DefaultClassColors.A,
|
||||
BA08_Upr: DefaultClassColors.BII,
|
||||
BA08_Lwr: DefaultClassColors.A,
|
||||
BA10_Upr: DefaultClassColors.B,
|
||||
BA10_Lwr: DefaultClassColors.A,
|
||||
BA13_Upr: DefaultClassColors.BII,
|
||||
BA13_Lwr: DefaultClassColors.A,
|
||||
BA16_Upr: DefaultClassColors.BII,
|
||||
BA16_Lwr: DefaultClassColors.A,
|
||||
BA17_Upr: DefaultClassColors.BII,
|
||||
BA17_Lwr: DefaultClassColors.A,
|
||||
BB00_Upr: DefaultClassColors.B,
|
||||
BB00_Lwr: DefaultClassColors.B,
|
||||
BB01_Upr: DefaultClassColors.B,
|
||||
BB01_Lwr: DefaultClassColors.B,
|
||||
BB17_Upr: DefaultClassColors.B,
|
||||
BB17_Lwr: DefaultClassColors.B,
|
||||
BB02_Upr: DefaultClassColors.B,
|
||||
BB02_Lwr: DefaultClassColors.B,
|
||||
BB03_Upr: DefaultClassColors.B,
|
||||
BB03_Lwr: DefaultClassColors.B,
|
||||
BB11_Upr: DefaultClassColors.B,
|
||||
BB11_Lwr: DefaultClassColors.B,
|
||||
BB16_Upr: DefaultClassColors.B,
|
||||
BB16_Lwr: DefaultClassColors.B,
|
||||
BB04_Upr: DefaultClassColors.B,
|
||||
BB04_Lwr: DefaultClassColors.BII,
|
||||
BB05_Upr: DefaultClassColors.B,
|
||||
BB05_Lwr: DefaultClassColors.BII,
|
||||
BB07_Upr: DefaultClassColors.BII,
|
||||
BB07_Lwr: DefaultClassColors.BII,
|
||||
BB08_Upr: DefaultClassColors.BII,
|
||||
BB08_Lwr: DefaultClassColors.BII,
|
||||
BB10_Upr: DefaultClassColors.miB,
|
||||
BB10_Lwr: DefaultClassColors.miB,
|
||||
BB12_Upr: DefaultClassColors.miB,
|
||||
BB12_Lwr: DefaultClassColors.miB,
|
||||
BB13_Upr: DefaultClassColors.miB,
|
||||
BB13_Lwr: DefaultClassColors.miB,
|
||||
BB14_Upr: DefaultClassColors.miB,
|
||||
BB14_Lwr: DefaultClassColors.miB,
|
||||
BB15_Upr: DefaultClassColors.miB,
|
||||
BB15_Lwr: DefaultClassColors.miB,
|
||||
BB20_Upr: DefaultClassColors.miB,
|
||||
BB20_Lwr: DefaultClassColors.miB,
|
||||
IC01_Upr: DefaultClassColors.IC,
|
||||
IC01_Lwr: DefaultClassColors.IC,
|
||||
IC02_Upr: DefaultClassColors.IC,
|
||||
IC02_Lwr: DefaultClassColors.IC,
|
||||
IC03_Upr: DefaultClassColors.IC,
|
||||
IC03_Lwr: DefaultClassColors.IC,
|
||||
IC04_Upr: DefaultClassColors.IC,
|
||||
IC04_Lwr: DefaultClassColors.IC,
|
||||
IC05_Upr: DefaultClassColors.IC,
|
||||
IC05_Lwr: DefaultClassColors.IC,
|
||||
IC06_Upr: DefaultClassColors.IC,
|
||||
IC06_Lwr: DefaultClassColors.IC,
|
||||
IC07_Upr: DefaultClassColors.IC,
|
||||
IC07_Lwr: DefaultClassColors.IC,
|
||||
OP01_Upr: DefaultClassColors.OPN,
|
||||
OP01_Lwr: DefaultClassColors.OPN,
|
||||
OP02_Upr: DefaultClassColors.OPN,
|
||||
OP02_Lwr: DefaultClassColors.OPN,
|
||||
OP03_Upr: DefaultClassColors.OPN,
|
||||
OP03_Lwr: DefaultClassColors.OPN,
|
||||
OP04_Upr: DefaultClassColors.OPN,
|
||||
OP04_Lwr: DefaultClassColors.OPN,
|
||||
OP05_Upr: DefaultClassColors.OPN,
|
||||
OP05_Lwr: DefaultClassColors.OPN,
|
||||
OP06_Upr: DefaultClassColors.OPN,
|
||||
OP06_Lwr: DefaultClassColors.OPN,
|
||||
OP07_Upr: DefaultClassColors.OPN,
|
||||
OP07_Lwr: DefaultClassColors.OPN,
|
||||
OP08_Upr: DefaultClassColors.OPN,
|
||||
OP08_Lwr: DefaultClassColors.OPN,
|
||||
OP09_Upr: DefaultClassColors.OPN,
|
||||
OP09_Lwr: DefaultClassColors.OPN,
|
||||
OP10_Upr: DefaultClassColors.OPN,
|
||||
OP10_Lwr: DefaultClassColors.OPN,
|
||||
OP11_Upr: DefaultClassColors.OPN,
|
||||
OP11_Lwr: DefaultClassColors.OPN,
|
||||
OP12_Upr: DefaultClassColors.OPN,
|
||||
OP12_Lwr: DefaultClassColors.OPN,
|
||||
OP13_Upr: DefaultClassColors.OPN,
|
||||
OP13_Lwr: DefaultClassColors.OPN,
|
||||
OP14_Upr: DefaultClassColors.OPN,
|
||||
OP14_Lwr: DefaultClassColors.OPN,
|
||||
OP15_Upr: DefaultClassColors.OPN,
|
||||
OP15_Lwr: DefaultClassColors.OPN,
|
||||
OP16_Upr: DefaultClassColors.OPN,
|
||||
OP16_Lwr: DefaultClassColors.OPN,
|
||||
OP17_Upr: DefaultClassColors.OPN,
|
||||
OP17_Lwr: DefaultClassColors.OPN,
|
||||
OP18_Upr: DefaultClassColors.OPN,
|
||||
OP18_Lwr: DefaultClassColors.OPN,
|
||||
OP19_Upr: DefaultClassColors.OPN,
|
||||
OP19_Lwr: DefaultClassColors.OPN,
|
||||
OP20_Upr: DefaultClassColors.OPN,
|
||||
OP20_Lwr: DefaultClassColors.OPN,
|
||||
OP21_Upr: DefaultClassColors.OPN,
|
||||
OP21_Lwr: DefaultClassColors.OPN,
|
||||
OP22_Upr: DefaultClassColors.OPN,
|
||||
OP22_Lwr: DefaultClassColors.OPN,
|
||||
OP23_Upr: DefaultClassColors.OPN,
|
||||
OP23_Lwr: DefaultClassColors.OPN,
|
||||
OP24_Upr: DefaultClassColors.OPN,
|
||||
OP24_Lwr: DefaultClassColors.OPN,
|
||||
OP25_Upr: DefaultClassColors.OPN,
|
||||
OP25_Lwr: DefaultClassColors.OPN,
|
||||
OP26_Upr: DefaultClassColors.OPN,
|
||||
OP26_Lwr: DefaultClassColors.OPN,
|
||||
OP27_Upr: DefaultClassColors.OPN,
|
||||
OP27_Lwr: DefaultClassColors.OPN,
|
||||
OP28_Upr: DefaultClassColors.OPN,
|
||||
OP28_Lwr: DefaultClassColors.OPN,
|
||||
OP29_Upr: DefaultClassColors.OPN,
|
||||
OP29_Lwr: DefaultClassColors.OPN,
|
||||
OP30_Upr: DefaultClassColors.OPN,
|
||||
OP30_Lwr: DefaultClassColors.OPN,
|
||||
OP31_Upr: DefaultClassColors.OPN,
|
||||
OP31_Lwr: DefaultClassColors.OPN,
|
||||
OPS1_Upr: DefaultClassColors.OPN,
|
||||
OPS1_Lwr: DefaultClassColors.OPN,
|
||||
OP1S_Upr: DefaultClassColors.OPN,
|
||||
OP1S_Lwr: DefaultClassColors.SYN,
|
||||
AAS1_Upr: DefaultClassColors.SYN,
|
||||
AAS1_Lwr: DefaultClassColors.A,
|
||||
AB1S_Upr: DefaultClassColors.A,
|
||||
AB1S_Lwr: DefaultClassColors.SYN,
|
||||
AB2S_Upr: DefaultClassColors.A,
|
||||
AB2S_Lwr: DefaultClassColors.SYN,
|
||||
BB1S_Upr: DefaultClassColors.B,
|
||||
BB1S_Lwr: DefaultClassColors.SYN,
|
||||
BB2S_Upr: DefaultClassColors.B,
|
||||
BB2S_Lwr: DefaultClassColors.SYN,
|
||||
BBS1_Upr: DefaultClassColors.SYN,
|
||||
BBS1_Lwr: DefaultClassColors.B,
|
||||
ZZ01_Upr: DefaultClassColors.Z,
|
||||
ZZ01_Lwr: DefaultClassColors.Z,
|
||||
ZZ02_Upr: DefaultClassColors.Z,
|
||||
ZZ02_Lwr: DefaultClassColors.Z,
|
||||
ZZ1S_Upr: DefaultClassColors.Z,
|
||||
ZZ1S_Lwr: DefaultClassColors.SYN,
|
||||
ZZ2S_Upr: DefaultClassColors.Z,
|
||||
ZZ2S_Lwr: DefaultClassColors.SYN,
|
||||
ZZS1_Upr: DefaultClassColors.SYN,
|
||||
ZZS1_Lwr: DefaultClassColors.Z,
|
||||
ZZS2_Upr: DefaultClassColors.SYN,
|
||||
ZZS2_Lwr: DefaultClassColors.Z,
|
||||
});
|
||||
type PyramidsColors = typeof PyramidsColors;
|
||||
|
||||
export const ConfalPyramidsColorThemeParams = {
|
||||
@@ -66,7 +272,7 @@ export const ConfalPyramidsColorThemeProvider: ColorTheme.Provider<ConfalPyramid
|
||||
factory: ConfalPyramidsColorTheme,
|
||||
getParams: getConfalPyramidsColorThemeParams,
|
||||
defaultValues: PD.getDefaultValues(ConfalPyramidsColorThemeParams),
|
||||
isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => Dnatco.isApplicable(m)),
|
||||
isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => ConfalPyramids.isApplicable(m)),
|
||||
ensureCustomProperties: {
|
||||
attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ConfalPyramidsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
|
||||
detach: (data) => data.structure && ConfalPyramidsProvider.ref(data.structure.models[0], false)
|
||||
|
||||
@@ -5,18 +5,90 @@
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { Dnatco, DnatcoParams, DnatcoSteps } from '../property';
|
||||
import { ConfalPyramidsTypes as CPT } from './types';
|
||||
import { Column, Table } from '../../../mol-data/db';
|
||||
import { toTable } from '../../../mol-io/reader/cif/schema';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
import { Model } from '../../../mol-model/structure';
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
|
||||
import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
|
||||
|
||||
export const ConfalPyramidsParams = { ...DnatcoParams };
|
||||
export type ConfalPyramids = PropertyWrapper<CPT.Steps | undefined>;
|
||||
|
||||
export namespace ConfalPyramids {
|
||||
export const Schema = {
|
||||
ndb_struct_ntc_step: {
|
||||
id: Column.Schema.int,
|
||||
name: Column.Schema.str,
|
||||
PDB_model_number: Column.Schema.int,
|
||||
label_entity_id_1: Column.Schema.int,
|
||||
label_asym_id_1: Column.Schema.str,
|
||||
label_seq_id_1: Column.Schema.int,
|
||||
label_comp_id_1: Column.Schema.str,
|
||||
label_alt_id_1: Column.Schema.str,
|
||||
label_entity_id_2: Column.Schema.int,
|
||||
label_asym_id_2: Column.Schema.str,
|
||||
label_seq_id_2: Column.Schema.int,
|
||||
label_comp_id_2: Column.Schema.str,
|
||||
label_alt_id_2: Column.Schema.str,
|
||||
auth_asym_id_1: Column.Schema.str,
|
||||
auth_seq_id_1: Column.Schema.int,
|
||||
auth_asym_id_2: Column.Schema.str,
|
||||
auth_seq_id_2: Column.Schema.int,
|
||||
PDB_ins_code_1: Column.Schema.str,
|
||||
PDB_ins_code_2: Column.Schema.str,
|
||||
},
|
||||
ndb_struct_ntc_step_summary: {
|
||||
step_id: Column.Schema.int,
|
||||
assigned_CANA: Column.Schema.str,
|
||||
assigned_NtC: Column.Schema.str,
|
||||
confal_score: Column.Schema.int,
|
||||
euclidean_distance_NtC_ideal: Column.Schema.float,
|
||||
cartesian_rmsd_closest_NtC_representative: Column.Schema.float,
|
||||
closest_CANA: Column.Schema.str,
|
||||
closest_NtC: Column.Schema.str,
|
||||
closest_step_golden: Column.Schema.str
|
||||
}
|
||||
};
|
||||
export type Schema = typeof Schema;
|
||||
|
||||
export async function fromCif(ctx: CustomProperty.Context, model: Model, props: ConfalPyramidsProps): Promise<CustomProperty.Data<ConfalPyramids>> {
|
||||
const info = PropertyWrapper.createInfo();
|
||||
const data = getCifData(model);
|
||||
if (data === undefined) return { value: { info, data: undefined } };
|
||||
|
||||
const fromCif = createPyramidsFromCif(model, data.steps, data.stepsSummary);
|
||||
return { value: { info, data: fromCif } };
|
||||
}
|
||||
|
||||
function getCifData(model: Model) {
|
||||
if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF');
|
||||
if (!hasNdbStructNtcCategories(model)) return undefined;
|
||||
return {
|
||||
steps: toTable(Schema.ndb_struct_ntc_step, model.sourceData.data.frame.categories.ndb_struct_ntc_step),
|
||||
stepsSummary: toTable(Schema.ndb_struct_ntc_step_summary, model.sourceData.data.frame.categories.ndb_struct_ntc_step_summary)
|
||||
};
|
||||
}
|
||||
|
||||
function hasNdbStructNtcCategories(model: Model): boolean {
|
||||
if (!MmcifFormat.is(model.sourceData)) return false;
|
||||
const names = (model.sourceData).data.frame.categoryNames;
|
||||
return names.includes('ndb_struct_ntc_step') && names.includes('ndb_struct_ntc_step_summary');
|
||||
}
|
||||
|
||||
export function isApplicable(model?: Model): boolean {
|
||||
return !!model && hasNdbStructNtcCategories(model);
|
||||
}
|
||||
}
|
||||
|
||||
export const ConfalPyramidsParams = {};
|
||||
export type ConfalPyramidsParams = typeof ConfalPyramidsParams;
|
||||
export type ConfalPyramidsProps = PD.Values<ConfalPyramidsParams>;
|
||||
|
||||
export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramidsParams, DnatcoSteps> = CustomModelProperty.createProvider({
|
||||
export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramidsParams, ConfalPyramids> = CustomModelProperty.createProvider({
|
||||
label: 'Confal Pyramids',
|
||||
descriptor: CustomPropertyDescriptor({
|
||||
name: 'confal_pyramids',
|
||||
@@ -24,9 +96,94 @@ export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramids
|
||||
type: 'static',
|
||||
defaultParams: ConfalPyramidsParams,
|
||||
getParams: (data: Model) => ConfalPyramidsParams,
|
||||
isApplicable: (data: Model) => Dnatco.isApplicable(data),
|
||||
isApplicable: (data: Model) => ConfalPyramids.isApplicable(data),
|
||||
obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<ConfalPyramidsProps>) => {
|
||||
const p = { ...PD.getDefaultValues(ConfalPyramidsParams), ...props };
|
||||
return Dnatco.fromCif(ctx, data, p);
|
||||
return ConfalPyramids.fromCif(ctx, data, p);
|
||||
}
|
||||
});
|
||||
|
||||
type StepsSummaryTable = Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step_summary>;
|
||||
|
||||
function createPyramidsFromCif(
|
||||
model: Model,
|
||||
cifSteps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
|
||||
stepsSummary: StepsSummaryTable
|
||||
): CPT.Steps {
|
||||
const steps = new Array<CPT.Step>();
|
||||
const mapping = new Array<CPT.MappedChains>();
|
||||
|
||||
const {
|
||||
id, PDB_model_number, name,
|
||||
auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
|
||||
auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
|
||||
_rowCount
|
||||
} = cifSteps;
|
||||
|
||||
if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
|
||||
|
||||
for (let i = 0; i < _rowCount; i++) {
|
||||
const {
|
||||
NtC,
|
||||
confal_score,
|
||||
rmsd
|
||||
} = getSummaryData(id.value(i), i, stepsSummary);
|
||||
const modelNum = PDB_model_number.value(i);
|
||||
const chainId = auth_asym_id_1.value(i);
|
||||
const seqId = auth_seq_id_1.value(i);
|
||||
const modelIdx = modelNum - 1;
|
||||
|
||||
if (mapping.length <= modelIdx || !mapping[modelIdx])
|
||||
mapping[modelIdx] = new Map<string, CPT.MappedResidues>();
|
||||
|
||||
const step = {
|
||||
PDB_model_number: modelNum,
|
||||
name: name.value(i),
|
||||
auth_asym_id_1: chainId,
|
||||
auth_seq_id_1: seqId,
|
||||
label_comp_id_1: label_comp_id_1.value(i),
|
||||
label_alt_id_1: label_alt_id_1.value(i),
|
||||
PDB_ins_code_1: PDB_ins_code_1.value(i),
|
||||
auth_asym_id_2: auth_asym_id_2.value(i),
|
||||
auth_seq_id_2: auth_seq_id_2.value(i),
|
||||
label_comp_id_2: label_comp_id_2.value(i),
|
||||
label_alt_id_2: label_alt_id_2.value(i),
|
||||
PDB_ins_code_2: PDB_ins_code_2.value(i),
|
||||
confal_score,
|
||||
NtC,
|
||||
rmsd,
|
||||
};
|
||||
|
||||
steps.push(step);
|
||||
|
||||
const mappedChains = mapping[modelIdx];
|
||||
const residuesOnChain = mappedChains.get(chainId) ?? new Map<number, number[]>();
|
||||
const stepsForResidue = residuesOnChain.get(seqId) ?? [];
|
||||
stepsForResidue.push(steps.length - 1);
|
||||
|
||||
residuesOnChain.set(seqId, stepsForResidue);
|
||||
mappedChains.set(chainId, residuesOnChain);
|
||||
mapping[modelIdx] = mappedChains;
|
||||
}
|
||||
|
||||
return { steps, mapping };
|
||||
}
|
||||
|
||||
function getSummaryData(id: number, i: number, stepsSummary: StepsSummaryTable) {
|
||||
const {
|
||||
step_id,
|
||||
confal_score,
|
||||
assigned_NtC,
|
||||
cartesian_rmsd_closest_NtC_representative,
|
||||
} = stepsSummary;
|
||||
|
||||
// Assume that step_ids in ntc_step_summary are in the same order as steps in ntc_step
|
||||
for (let j = i; j < stepsSummary._rowCount; j++) {
|
||||
if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
|
||||
}
|
||||
// Safety net for cases where the previous assumption is not met
|
||||
for (let j = 0; j < i; j++) {
|
||||
if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
|
||||
}
|
||||
throw new Error('Inconsistent mmCIF data');
|
||||
}
|
||||
|
||||
@@ -5,10 +5,9 @@
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { ConfalPyramidsProvider } from './property';
|
||||
import { ConfalPyramids, ConfalPyramidsProvider } from './property';
|
||||
import { ConfalPyramidsIterator } from './util';
|
||||
import { ConfalPyramidsTypes as CPT } from './types';
|
||||
import { Dnatco } from '../property';
|
||||
import { Interval } from '../../../mol-data/int';
|
||||
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
|
||||
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
|
||||
@@ -88,8 +87,6 @@ function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Str
|
||||
const it = new ConfalPyramidsIterator(structure, unit);
|
||||
while (it.hasNext) {
|
||||
const allPoints = it.move();
|
||||
if (!allPoints)
|
||||
continue;
|
||||
|
||||
for (const points of allPoints) {
|
||||
const { O3, P, OP1, OP2, O5, confalScore } = points;
|
||||
@@ -153,7 +150,9 @@ function getConfalPyramidLoci(pickingId: PickingId, structureGroup: StructureGro
|
||||
if (halfPyramidsCount <= groupId) return EmptyLoci;
|
||||
|
||||
const idx = Math.floor(groupId / 2); // Map groupIndex to a step, see createConfalPyramidsMesh() for full explanation
|
||||
return CPT.Loci(data.steps, [idx]);
|
||||
const step = data.steps[idx];
|
||||
|
||||
return CPT.Loci({ step, isLower: groupId % 2 === 1 }, [{}]);
|
||||
}
|
||||
|
||||
function eachConfalPyramid(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
|
||||
@@ -198,7 +197,7 @@ export const ConfalPyramidsRepresentationProvider = StructureRepresentationProvi
|
||||
defaultValues: PD.getDefaultValues(ConfalPyramidsParams),
|
||||
defaultColorTheme: { name: 'confal-pyramids' },
|
||||
defaultSizeTheme: { name: 'uniform' },
|
||||
isApplicable: (structure: Structure) => structure.models.some(m => Dnatco.isApplicable(m)),
|
||||
isApplicable: (structure: Structure) => structure.models.some(m => ConfalPyramids.isApplicable(m)),
|
||||
ensureCustomProperties: {
|
||||
attach: (ctx: CustomProperty.Context, structure: Structure) => ConfalPyramidsProvider.attach(ctx, structure.model, void 0, true),
|
||||
detach: (data) => ConfalPyramidsProvider.ref(data.model, false),
|
||||
|
||||
@@ -5,29 +5,61 @@
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { DnatcoTypes } from '../types';
|
||||
import { DataLocation } from '../../../mol-model/location';
|
||||
import { DataLoci } from '../../../mol-model/loci';
|
||||
import { confalPyramidLabel } from './behavior';
|
||||
|
||||
export namespace ConfalPyramidsTypes {
|
||||
export interface Location extends DataLocation<DnatcoTypes.HalfStep, {}> {}
|
||||
export const DataTag = 'dnatco-confal-half-pyramid';
|
||||
|
||||
export function Location(step: DnatcoTypes.Step, isLower: boolean) {
|
||||
return DataLocation(DnatcoTypes.DataTag, { step, isLower }, {});
|
||||
export type Step = {
|
||||
PDB_model_number: number,
|
||||
name: string,
|
||||
auth_asym_id_1: string,
|
||||
auth_seq_id_1: number,
|
||||
label_comp_id_1: string,
|
||||
label_alt_id_1: string,
|
||||
PDB_ins_code_1: string,
|
||||
auth_asym_id_2: string,
|
||||
auth_seq_id_2: number,
|
||||
label_comp_id_2: string,
|
||||
label_alt_id_2: string,
|
||||
PDB_ins_code_2: string,
|
||||
confal_score: number,
|
||||
NtC: string,
|
||||
rmsd: number,
|
||||
}
|
||||
|
||||
export type MappedChains = Map<string, MappedResidues>;
|
||||
export type MappedResidues = Map<number, number[]>;
|
||||
|
||||
export interface Steps {
|
||||
steps: Array<Step>,
|
||||
mapping: MappedChains[],
|
||||
}
|
||||
|
||||
export interface HalfPyramid {
|
||||
step: Step,
|
||||
isLower: boolean,
|
||||
}
|
||||
|
||||
export interface Location extends DataLocation<HalfPyramid, {}> {}
|
||||
|
||||
export function Location(step: Step, isLower: boolean) {
|
||||
return DataLocation(DataTag, { step, isLower }, {});
|
||||
}
|
||||
|
||||
export function isLocation(x: any): x is Location {
|
||||
return !!x && x.kind === 'data-location' && x.tag === DnatcoTypes.DataTag;
|
||||
return !!x && x.kind === 'data-location' && x.tag === DataTag;
|
||||
}
|
||||
|
||||
export interface Loci extends DataLoci<DnatcoTypes.Step[], number> {}
|
||||
export interface Loci extends DataLoci<HalfPyramid, {}> {}
|
||||
|
||||
export function Loci(data: DnatcoTypes.Step[], elements: ReadonlyArray<number>): Loci {
|
||||
return DataLoci(DnatcoTypes.DataTag, data, elements, undefined, () => elements[0] !== undefined ? confalPyramidLabel(data[elements[0]]) : '');
|
||||
export function Loci(data: HalfPyramid, elements: ReadonlyArray<{}>): Loci {
|
||||
return DataLoci(DataTag, data, elements, undefined, () => confalPyramidLabel(data));
|
||||
}
|
||||
|
||||
export function isLoci(x: any): x is Loci {
|
||||
return !!x && x.kind === 'data-loci' && x.tag === DnatcoTypes.DataTag;
|
||||
return !!x && x.kind === 'data-loci' && x.tag === DataTag;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,15 +1,16 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { ConfalPyramidsProvider } from './property';
|
||||
import { DnatcoTypes } from '../types';
|
||||
import { DnatcoUtil } from '../util';
|
||||
import { ConfalPyramidsTypes as CPT } from './types';
|
||||
import { Segmentation } from '../../../mol-data/int';
|
||||
import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
|
||||
import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../../mol-model/structure';
|
||||
|
||||
type Residue = Segmentation.Segment<ResidueIndex>;
|
||||
|
||||
export type Pyramid = {
|
||||
O3: ElementIndex,
|
||||
@@ -21,17 +22,31 @@ export type Pyramid = {
|
||||
stepIdx: number,
|
||||
};
|
||||
|
||||
function getPyramid(
|
||||
loc: StructureElement.Location,
|
||||
one: DnatcoUtil.Residue, two: DnatcoUtil.Residue,
|
||||
altIdOne: string, altIdTwo: string,
|
||||
insCodeOne: string, insCodeTwo: string,
|
||||
confalScore: number, stepIdx: number): Pyramid {
|
||||
const O3 = DnatcoUtil.getAtomIndex(loc, one, ['O3\'', 'O3*'], altIdOne, insCodeOne);
|
||||
const P = DnatcoUtil.getAtomIndex(loc, two, ['P'], altIdTwo, insCodeTwo);
|
||||
const OP1 = DnatcoUtil.getAtomIndex(loc, two, ['OP1'], altIdTwo, insCodeTwo);
|
||||
const OP2 = DnatcoUtil.getAtomIndex(loc, two, ['OP2'], altIdTwo, insCodeTwo);
|
||||
const O5 = DnatcoUtil.getAtomIndex(loc, two, ['O5\'', 'O5*'], altIdTwo, insCodeTwo);
|
||||
const EmptyStepIndices = new Array<number>();
|
||||
|
||||
function copyResidue(r?: Residue) {
|
||||
return r ? { index: r.index, start: r.start, end: r.end } : void 0;
|
||||
}
|
||||
|
||||
function getAtomIndex(loc: StructureElement.Location, residue: Residue, names: string[], altId: string): ElementIndex {
|
||||
for (let eI = residue.start; eI < residue.end; eI++) {
|
||||
loc.element = loc.unit.elements[eI];
|
||||
const elName = StructureProperties.atom.label_atom_id(loc);
|
||||
const elAltId = StructureProperties.atom.label_alt_id(loc);
|
||||
|
||||
if (names.includes(elName) && (elAltId === altId || elAltId.length === 0))
|
||||
return loc.element;
|
||||
}
|
||||
|
||||
return -1 as ElementIndex;
|
||||
}
|
||||
|
||||
function getPyramid(loc: StructureElement.Location, one: Residue, two: Residue, altIdOne: string, altIdTwo: string, confalScore: number, stepIdx: number): Pyramid {
|
||||
const O3 = getAtomIndex(loc, one, ['O3\'', 'O3*'], altIdOne);
|
||||
const P = getAtomIndex(loc, two, ['P'], altIdTwo);
|
||||
const OP1 = getAtomIndex(loc, two, ['OP1'], altIdTwo);
|
||||
const OP2 = getAtomIndex(loc, two, ['OP2'], altIdTwo);
|
||||
const O5 = getAtomIndex(loc, two, ['O5\'', 'O5*'], altIdTwo);
|
||||
|
||||
return { O3, P, OP1, OP2, O5, confalScore, stepIdx };
|
||||
}
|
||||
@@ -39,29 +54,39 @@ function getPyramid(
|
||||
export class ConfalPyramidsIterator {
|
||||
private chainIt: Segmentation.SegmentIterator<ChainIndex>;
|
||||
private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
|
||||
private residueOne?: DnatcoUtil.Residue;
|
||||
private residueTwo: DnatcoUtil.Residue;
|
||||
private data?: DnatcoTypes.Steps;
|
||||
private residueOne?: Residue;
|
||||
private residueTwo: Residue;
|
||||
private data?: CPT.Steps;
|
||||
private loc: StructureElement.Location;
|
||||
|
||||
private moveStep() {
|
||||
this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
|
||||
this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
|
||||
private getStepIndices(r: Residue) {
|
||||
this.loc.element = this.loc.unit.elements[r.start];
|
||||
|
||||
// Check for discontinuity
|
||||
if (this.residueTwo.index !== (this.residueOne!.index + 1))
|
||||
return void 0;
|
||||
const modelIdx = StructureProperties.unit.model_num(this.loc) - 1;
|
||||
const chainId = StructureProperties.chain.auth_asym_id(this.loc);
|
||||
const seqId = StructureProperties.residue.auth_seq_id(this.loc);
|
||||
|
||||
const chains = this.data!.mapping[modelIdx];
|
||||
if (!chains) return EmptyStepIndices;
|
||||
const residues = chains.get(chainId);
|
||||
if (!residues) return EmptyStepIndices;
|
||||
return residues.get(seqId) ?? EmptyStepIndices;
|
||||
}
|
||||
|
||||
private moveStep() {
|
||||
this.residueOne = copyResidue(this.residueTwo);
|
||||
this.residueTwo = copyResidue(this.residueIt.move())!;
|
||||
|
||||
return this.toPyramids(this.residueOne!, this.residueTwo);
|
||||
}
|
||||
|
||||
private toPyramids(one: DnatcoUtil.Residue, two: DnatcoUtil.Residue) {
|
||||
const indices = DnatcoUtil.getStepIndices(this.data!, this.loc, one);
|
||||
private toPyramids(one: Residue, two: Residue) {
|
||||
const indices = this.getStepIndices(one);
|
||||
|
||||
const points = [];
|
||||
for (const idx of indices) {
|
||||
const step = this.data!.steps[idx];
|
||||
points.push(getPyramid(this.loc, one, two, step.label_alt_id_1, step.label_alt_id_2, step.PDB_ins_code_1, step.PDB_ins_code_2, step.confal_score, idx));
|
||||
points.push(getPyramid(this.loc, one, two, step.label_alt_id_1, step.label_alt_id_2, step.confal_score, idx));
|
||||
}
|
||||
|
||||
return points;
|
||||
@@ -96,8 +121,6 @@ export class ConfalPyramidsIterator {
|
||||
return this.moveStep();
|
||||
} else {
|
||||
this.residueIt.setSegment(this.chainIt.move());
|
||||
if (this.residueIt.hasNext)
|
||||
this.residueTwo = this.residueIt.move();
|
||||
return this.moveStep();
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
export { DnatcoNtCs } from './behavior';
|
||||
export { DnatcoConfalPyramids } from './confal-pyramids/behavior';
|
||||
|
||||
@@ -1,57 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { NtCTubeColorThemeProvider } from './color';
|
||||
import { NtCTubeProvider } from './property';
|
||||
import { NtCTubeRepresentationProvider } from './representation';
|
||||
import { DnatcoTypes } from '../types';
|
||||
import { Dnatco } from '../property';
|
||||
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
|
||||
import { StateObjectRef } from '../../../mol-state';
|
||||
import { Task } from '../../../mol-task';
|
||||
|
||||
export const NtCTubePreset = StructureRepresentationPresetProvider({
|
||||
id: 'preset-structure-representation-ntc-tube',
|
||||
display: {
|
||||
name: 'NtC Tube', group: 'Annotation',
|
||||
description: 'NtC Tube',
|
||||
},
|
||||
isApplicable(a) {
|
||||
return a.data.models.length >= 1 && a.data.models.some(m => Dnatco.isApplicable(m));
|
||||
},
|
||||
params: () => StructureRepresentationPresetProvider.CommonParams,
|
||||
async apply(ref, params, plugin) {
|
||||
const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
|
||||
const model = structureCell?.obj?.data.model;
|
||||
if (!structureCell || !model) return {};
|
||||
|
||||
await plugin.runTask(Task.create('NtC tube', async runtime => {
|
||||
await NtCTubeProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
|
||||
}));
|
||||
|
||||
const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);
|
||||
|
||||
const tube = await plugin.builders.structure.tryCreateComponentStatic(structureCell, 'nucleic', { label: 'NtC Tube' });
|
||||
const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
|
||||
|
||||
let tubeRepr;
|
||||
if (representations)
|
||||
tubeRepr = builder.buildRepresentation(update, tube, { type: NtCTubeRepresentationProvider, typeParams, color: NtCTubeColorThemeProvider }, { tag: 'ntc-tube' });
|
||||
|
||||
await update.commit({ revertOnError: true });
|
||||
return { components: { ...components, tube }, representations: { ...representations, tubeRepr } };
|
||||
}
|
||||
});
|
||||
|
||||
export function NtCTubeSegmentLabel(step: DnatcoTypes.Step) {
|
||||
return `
|
||||
<b>${step.auth_asym_id_1}</b> |
|
||||
<b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
|
||||
${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
|
||||
<i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
|
||||
`;
|
||||
}
|
||||
@@ -1,99 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { ErrorColor, NtCColors } from '../color';
|
||||
import { NtCTubeProvider } from './property';
|
||||
import { NtCTubeTypes as NTT } from './types';
|
||||
import { Dnatco } from '../property';
|
||||
import { Location } from '../../../mol-model/location';
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { ColorTheme } from '../../../mol-theme/color';
|
||||
import { ThemeDataContext } from '../../../mol-theme/theme';
|
||||
import { Color, ColorMap } from '../../../mol-util/color';
|
||||
import { getColorMapParams } from '../../../mol-util/color/params';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { TableLegend } from '../../../mol-util/legend';
|
||||
import { ObjectKeys } from '../../../mol-util/type-helpers';
|
||||
|
||||
const Description = 'Assigns colors to NtC Tube segments';
|
||||
|
||||
const NtCTubeColors = ColorMap({
|
||||
...NtCColors,
|
||||
residueMarker: Color(0x222222),
|
||||
stepBoundaryMarker: Color(0x656565),
|
||||
});
|
||||
type NtCTubeColors = typeof NtCTubeColors;
|
||||
|
||||
export const NtCTubeColorThemeParams = {
|
||||
colors: PD.MappedStatic('default', {
|
||||
'default': PD.EmptyGroup(),
|
||||
'custom': PD.Group(getColorMapParams(NtCTubeColors)),
|
||||
'uniform': PD.Color(Color(0xEEEEEE)),
|
||||
}),
|
||||
markResidueBoundaries: PD.Boolean(true),
|
||||
markSegmentBoundaries: PD.Boolean(true),
|
||||
};
|
||||
export type NtCTubeColorThemeParams = typeof NtCTubeColorThemeParams;
|
||||
|
||||
export function getNtCTubeColorThemeParams(ctx: ThemeDataContext) {
|
||||
return PD.clone(NtCTubeColorThemeParams);
|
||||
}
|
||||
|
||||
export function NtCTubeColorTheme(ctx: ThemeDataContext, props: PD.Values<NtCTubeColorThemeParams>): ColorTheme<NtCTubeColorThemeParams> {
|
||||
const colorMap = props.colors.name === 'default'
|
||||
? NtCTubeColors
|
||||
: props.colors.name === 'custom'
|
||||
? props.colors.params
|
||||
: ColorMap({
|
||||
...Object.fromEntries(ObjectKeys(NtCTubeColors).map(item => [item, props.colors.params])),
|
||||
residueMarker: NtCTubeColors.residueMarker,
|
||||
stepBoundaryMarker: NtCTubeColors.stepBoundaryMarker
|
||||
}) as NtCTubeColors;
|
||||
|
||||
function color(location: Location, isSecondary: boolean): Color {
|
||||
if (NTT.isLocation(location)) {
|
||||
const { data } = location;
|
||||
const { step, kind } = data;
|
||||
let key;
|
||||
if (kind === 'upper')
|
||||
key = step.NtC + '_Upr' as keyof NtCTubeColors;
|
||||
else if (kind === 'lower')
|
||||
key = step.NtC + '_Lwr' as keyof NtCTubeColors;
|
||||
else if (kind === 'residue-boundary')
|
||||
key = (!props.markResidueBoundaries ? step.NtC + '_Lwr' : 'residueMarker') as keyof NtCTubeColors;
|
||||
else /* segment-boundary */
|
||||
key = (!props.markSegmentBoundaries ? step.NtC + '_Lwr' : 'stepBoundaryMarker') as keyof NtCTubeColors;
|
||||
|
||||
return colorMap[key] ?? ErrorColor;
|
||||
}
|
||||
|
||||
return ErrorColor;
|
||||
}
|
||||
|
||||
return {
|
||||
factory: NtCTubeColorTheme,
|
||||
granularity: 'group',
|
||||
color,
|
||||
props,
|
||||
description: Description,
|
||||
legend: TableLegend(ObjectKeys(colorMap).map(k => [k.replace('_', ' '), colorMap[k]] as [string, Color]).concat([['Error', ErrorColor]])),
|
||||
};
|
||||
}
|
||||
|
||||
export const NtCTubeColorThemeProvider: ColorTheme.Provider<NtCTubeColorThemeParams, 'ntc-tube'> = {
|
||||
name: 'ntc-tube',
|
||||
label: 'NtC Tube',
|
||||
category: ColorTheme.Category.Residue,
|
||||
factory: NtCTubeColorTheme,
|
||||
getParams: getNtCTubeColorThemeParams,
|
||||
defaultValues: PD.getDefaultValues(NtCTubeColorThemeParams),
|
||||
isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => Dnatco.isApplicable(m)),
|
||||
ensureCustomProperties: {
|
||||
attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? NtCTubeProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
|
||||
detach: (data) => data.structure && NtCTubeProvider.ref(data.structure.models[0], false)
|
||||
}
|
||||
};
|
||||
@@ -1,44 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { NtCTubeTypes as NTT } from './types';
|
||||
import { Dnatco, DnatcoParams } from '../property';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
import { Model } from '../../../mol-model/structure';
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
|
||||
import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
|
||||
export const NtCTubeParams = { ...DnatcoParams };
|
||||
export type NtCTubeParams = typeof NtCTubeParams;
|
||||
export type NtCTubeProps = PD.Values<NtCTubeParams>;
|
||||
export type NtCTubeData = PropertyWrapper<NTT.Data | undefined>;
|
||||
|
||||
async function fromCif(ctx: CustomProperty.Context, model: Model, props: NtCTubeProps): Promise<CustomProperty.Data<NtCTubeData>> {
|
||||
const info = PropertyWrapper.createInfo();
|
||||
const data = Dnatco.getCifData(model);
|
||||
if (data === undefined) return { value: { info, data: undefined } };
|
||||
|
||||
const steps = Dnatco.getStepsFromCif(model, data.steps, data.stepsSummary);
|
||||
return { value: { info, data: { data: steps } } };
|
||||
}
|
||||
|
||||
export const NtCTubeProvider: CustomModelProperty.Provider<NtCTubeParams, NtCTubeData> = CustomModelProperty.createProvider({
|
||||
label: 'NtC Tube',
|
||||
descriptor: CustomPropertyDescriptor({
|
||||
name: 'ntc-tube',
|
||||
}),
|
||||
type: 'static',
|
||||
defaultParams: NtCTubeParams,
|
||||
getParams: (data: Model) => NtCTubeParams,
|
||||
isApplicable: (data: Model) => Dnatco.isApplicable(data),
|
||||
obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<NtCTubeProps>) => {
|
||||
const p = { ...PD.getDefaultValues(NtCTubeParams), ...props };
|
||||
return fromCif(ctx, data, p);
|
||||
}
|
||||
});
|
||||
@@ -1,454 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { NtCTubeProvider } from './property';
|
||||
import { NtCTubeSegmentsIterator } from './util';
|
||||
import { NtCTubeTypes as NTT } from './types';
|
||||
import { Dnatco } from '../property';
|
||||
import { DnatcoTypes } from '../types';
|
||||
import { DnatcoUtil } from '../util';
|
||||
import { Interval } from '../../../mol-data/int';
|
||||
import { BaseGeometry, VisualQuality } from '../../../mol-geo/geometry/base';
|
||||
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
|
||||
import { addFixedCountDashedCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
|
||||
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
|
||||
import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
|
||||
import { PickingId } from '../../../mol-geo/geometry/picking';
|
||||
import { CylinderProps } from '../../../mol-geo/primitive/cylinder';
|
||||
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
|
||||
import { Sphere3D } from '../../../mol-math/geometry/primitives/sphere3d';
|
||||
import { Vec3 } from '../../../mol-math/linear-algebra';
|
||||
import { smoothstep } from '../../../mol-math/interpolate';
|
||||
import { NullLocation } from '../../../mol-model/location';
|
||||
import { EmptyLoci, Loci } from '../../../mol-model/loci';
|
||||
import { Structure, StructureElement, Unit } from '../../../mol-model/structure';
|
||||
import { structureUnion } from '../../../mol-model/structure/query/utils/structure-set';
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
|
||||
import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder, UnitsRepresentation } from '../../../mol-repr/structure/representation';
|
||||
import { UnitsMeshParams, UnitsMeshVisual, UnitsVisual } from '../../../mol-repr/structure/units-visual';
|
||||
import { createCurveSegmentState, CurveSegmentState } from '../../../mol-repr/structure/visual/util/polymer';
|
||||
import { getStructureQuality, VisualUpdateState } from '../../../mol-repr/util';
|
||||
import { VisualContext } from '../../../mol-repr/visual';
|
||||
import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
|
||||
import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
|
||||
const v3add = Vec3.add;
|
||||
const v3copy = Vec3.copy;
|
||||
const v3cross = Vec3.cross;
|
||||
const v3fromArray = Vec3.fromArray;
|
||||
const v3matchDirection = Vec3.matchDirection;
|
||||
const v3normalize = Vec3.normalize;
|
||||
const v3orthogonalize = Vec3.orthogonalize;
|
||||
const v3scale = Vec3.scale;
|
||||
const v3slerp = Vec3.slerp;
|
||||
const v3spline = Vec3.spline;
|
||||
const v3sub = Vec3.sub;
|
||||
const v3toArray = Vec3.toArray;
|
||||
|
||||
const NtCTubeMeshParams = {
|
||||
...UnitsMeshParams,
|
||||
linearSegments: PD.Numeric(4, { min: 2, max: 8, step: 1 }, BaseGeometry.CustomQualityParamInfo),
|
||||
radialSegments: PD.Numeric(22, { min: 4, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
|
||||
residueMarkerWidth: PD.Numeric(0.05, { min: 0.01, max: 0.25, step: 0.01 }),
|
||||
segmentBoundaryWidth: PD.Numeric(0.05, { min: 0.01, max: 0.25, step: 0.01 }),
|
||||
};
|
||||
type NtCTubeMeshParams = typeof NtCTubeMeshParams;
|
||||
|
||||
type QualityOptions = Exclude<VisualQuality, 'auto' | 'custom'>;
|
||||
const LinearSegmentCount: Record<QualityOptions, number> = {
|
||||
highest: 6,
|
||||
higher: 6,
|
||||
high: 4,
|
||||
medium: 4,
|
||||
low: 3,
|
||||
lower: 3,
|
||||
lowest: 2,
|
||||
};
|
||||
const RadialSegmentCount: Record<QualityOptions, number> = {
|
||||
highest: 32,
|
||||
higher: 26,
|
||||
high: 22,
|
||||
medium: 18,
|
||||
low: 14,
|
||||
lower: 10,
|
||||
lowest: 6,
|
||||
};
|
||||
|
||||
const _curvePoint = Vec3();
|
||||
const _tanA = Vec3();
|
||||
const _tanB = Vec3();
|
||||
const _firstTangentVec = Vec3();
|
||||
const _lastTangentVec = Vec3();
|
||||
const _firstNormalVec = Vec3();
|
||||
const _lastNormalVec = Vec3();
|
||||
|
||||
const _tmpNormal = Vec3();
|
||||
const _tangentVec = Vec3();
|
||||
const _normalVec = Vec3();
|
||||
const _binormalVec = Vec3();
|
||||
const _prevNormal = Vec3();
|
||||
const _nextNormal = Vec3();
|
||||
|
||||
function interpolatePointsAndTangents(state: CurveSegmentState, p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, tRange: number[]) {
|
||||
const { curvePoints, tangentVectors, linearSegments } = state;
|
||||
const tension = 0.5;
|
||||
const r = tRange[1] - tRange[0];
|
||||
|
||||
for (let j = 0; j <= linearSegments; ++j) {
|
||||
const t = j * r / linearSegments + tRange[0];
|
||||
|
||||
v3spline(_curvePoint, p0, p1, p2, p3, t, tension);
|
||||
v3spline(_tanA, p0, p1, p2, p3, t - 0.01, tension);
|
||||
v3spline(_tanB, p0, p1, p2, p3, t + 0.01, tension);
|
||||
|
||||
v3toArray(_curvePoint, curvePoints, j * 3);
|
||||
v3normalize(_tangentVec, v3sub(_tangentVec, _tanA, _tanB));
|
||||
v3toArray(_tangentVec, tangentVectors, j * 3);
|
||||
}
|
||||
}
|
||||
|
||||
function interpolateNormals(state: CurveSegmentState, firstDirection: Vec3, lastDirection: Vec3) {
|
||||
const { curvePoints, tangentVectors, normalVectors, binormalVectors } = state;
|
||||
|
||||
const n = curvePoints.length / 3;
|
||||
|
||||
v3fromArray(_firstTangentVec, tangentVectors, 0);
|
||||
v3fromArray(_lastTangentVec, tangentVectors, (n - 1) * 3);
|
||||
|
||||
v3orthogonalize(_firstNormalVec, _firstTangentVec, firstDirection);
|
||||
v3orthogonalize(_lastNormalVec, _lastTangentVec, lastDirection);
|
||||
v3matchDirection(_lastNormalVec, _lastNormalVec, _firstNormalVec);
|
||||
|
||||
v3copy(_prevNormal, _firstNormalVec);
|
||||
|
||||
const n1 = n - 1;
|
||||
for (let i = 0; i < n; ++i) {
|
||||
const j = smoothstep(0, n1, i) * n1;
|
||||
const t = i === 0 ? 0 : 1 / (n - j);
|
||||
|
||||
v3fromArray(_tangentVec, tangentVectors, i * 3);
|
||||
|
||||
v3orthogonalize(_normalVec, _tangentVec, v3slerp(_tmpNormal, _prevNormal, _lastNormalVec, t));
|
||||
v3toArray(_normalVec, normalVectors, i * 3);
|
||||
|
||||
v3copy(_prevNormal, _normalVec);
|
||||
|
||||
v3normalize(_binormalVec, v3cross(_binormalVec, _tangentVec, _normalVec));
|
||||
v3toArray(_binormalVec, binormalVectors, i * 3);
|
||||
}
|
||||
|
||||
for (let i = 1; i < n1; ++i) {
|
||||
v3fromArray(_prevNormal, normalVectors, (i - 1) * 3);
|
||||
v3fromArray(_normalVec, normalVectors, i * 3);
|
||||
v3fromArray(_nextNormal, normalVectors, (i + 1) * 3);
|
||||
|
||||
v3scale(_normalVec, v3add(_normalVec, _prevNormal, v3add(_normalVec, _nextNormal, _normalVec)), 1 / 3);
|
||||
v3toArray(_normalVec, normalVectors, i * 3);
|
||||
|
||||
v3fromArray(_tangentVec, tangentVectors, i * 3);
|
||||
v3normalize(_binormalVec, v3cross(_binormalVec, _tangentVec, _normalVec));
|
||||
v3toArray(_binormalVec, binormalVectors, i * 3);
|
||||
}
|
||||
}
|
||||
|
||||
function interpolate(state: CurveSegmentState, p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, firstDir: Vec3, lastDir: Vec3, tRange = [0, 1]) {
|
||||
interpolatePointsAndTangents(state, p0, p1, p2, p3, tRange);
|
||||
interpolateNormals(state, firstDir, lastDir);
|
||||
}
|
||||
|
||||
function createNtCTubeSegmentsIterator(structureGroup: StructureGroup): LocationIterator {
|
||||
const { structure, group } = structureGroup;
|
||||
const instanceCount = group.units.length;
|
||||
|
||||
const data = NtCTubeProvider.get(structure.model)?.value?.data;
|
||||
if (!data) return LocationIterator(0, 1, 1, () => NullLocation);
|
||||
|
||||
const numBlocks = data.data.steps.length * 4;
|
||||
|
||||
const getLocation = (groupId: number, instanceId: number) => {
|
||||
if (groupId > numBlocks) return NullLocation;
|
||||
const stepIdx = Math.floor(groupId / 4);
|
||||
const step = data.data.steps[stepIdx];
|
||||
const r = groupId % 4;
|
||||
const kind =
|
||||
r === 0 ? 'upper' :
|
||||
r === 1 ? 'lower' :
|
||||
r === 2 ? 'residue-boundary' : 'segment-boundary';
|
||||
|
||||
return NTT.Location({ step, kind });
|
||||
};
|
||||
return LocationIterator(totalMeshGroupsCount(data.data.steps) + 1, instanceCount, 1, getLocation);
|
||||
}
|
||||
|
||||
function segmentCount(structure: Structure, props: PD.Values<NtCTubeMeshParams>): { linear: number, radial: number } {
|
||||
const quality = props.quality;
|
||||
|
||||
if (quality === 'custom')
|
||||
return { linear: props.linearSegments, radial: props.radialSegments };
|
||||
else if (quality === 'auto') {
|
||||
const autoQuality = getStructureQuality(structure) as QualityOptions;
|
||||
return { linear: LinearSegmentCount[autoQuality], radial: RadialSegmentCount[autoQuality] };
|
||||
} else
|
||||
return { linear: LinearSegmentCount[quality], radial: RadialSegmentCount[quality] };
|
||||
}
|
||||
|
||||
function stepBoundingSphere(step: DnatcoTypes.Step, struLoci: StructureElement.Loci): Sphere3D | undefined {
|
||||
const one = DnatcoUtil.residueToLoci(step.auth_asym_id_1, step.auth_seq_id_1, step.label_alt_id_1, step.PDB_ins_code_1, struLoci, 'auth');
|
||||
const two = DnatcoUtil.residueToLoci(step.auth_asym_id_2, step.auth_seq_id_2, step.label_alt_id_2, step.PDB_ins_code_2, struLoci, 'auth');
|
||||
|
||||
if (StructureElement.Loci.is(one) && StructureElement.Loci.is(two)) {
|
||||
const union = structureUnion(struLoci.structure, [StructureElement.Loci.toStructure(one), StructureElement.Loci.toStructure(two)]);
|
||||
return union.boundary.sphere;
|
||||
}
|
||||
return void 0;
|
||||
}
|
||||
|
||||
function totalMeshGroupsCount(steps: DnatcoTypes.Step[]) {
|
||||
// Each segment has two blocks, Residue Boundary marker and a Segment Boundary marker
|
||||
return steps.length * 4 - 1; // Subtract one because the last Segment Boundary marker is not drawn
|
||||
}
|
||||
|
||||
function createNtCTubeMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<NtCTubeMeshParams>, mesh?: Mesh) {
|
||||
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
|
||||
|
||||
const prop = NtCTubeProvider.get(structure.model).value;
|
||||
if (prop === undefined || prop.data === undefined) return Mesh.createEmpty(mesh);
|
||||
|
||||
const { data } = prop.data;
|
||||
if (data.steps.length === 0) return Mesh.createEmpty(mesh);
|
||||
|
||||
const MarkerLinearSegmentCount = 2;
|
||||
const segCount = segmentCount(structure, props);
|
||||
const vertexCount = Math.floor((segCount.linear * 4 * data.steps.length / structure.model.atomicHierarchy.chains._rowCount) * segCount.radial);
|
||||
const chunkSize = Math.floor(vertexCount / 3);
|
||||
const diameter = 1.0 * theme.size.props.value;
|
||||
|
||||
const mb = MeshBuilder.createState(vertexCount, chunkSize, mesh);
|
||||
|
||||
const state = createCurveSegmentState(segCount.linear);
|
||||
const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state;
|
||||
for (let idx = 0; idx <= segCount.linear; idx++) {
|
||||
widthValues[idx] = diameter;
|
||||
heightValues[idx] = diameter;
|
||||
}
|
||||
const [normals, binormals] = [binormalVectors, normalVectors]; // Needed so that the tube is not drawn from inside out
|
||||
|
||||
const markerState = createCurveSegmentState(MarkerLinearSegmentCount);
|
||||
const { curvePoints: mCurvePoints, normalVectors: mNormalVectors, binormalVectors: mBinormalVectors, widthValues: mWidthValues, heightValues: mHeightValues } = markerState;
|
||||
for (let idx = 0; idx <= MarkerLinearSegmentCount; idx++) {
|
||||
mWidthValues[idx] = diameter;
|
||||
mHeightValues[idx] = diameter;
|
||||
}
|
||||
const [mNormals, mBinormals] = [mBinormalVectors, mNormalVectors];
|
||||
|
||||
const firstDir = Vec3();
|
||||
const lastDir = Vec3();
|
||||
const markerDir = Vec3();
|
||||
|
||||
const residueMarkerWidth = props.residueMarkerWidth / 2;
|
||||
const it = new NtCTubeSegmentsIterator(structure, unit);
|
||||
while (it.hasNext) {
|
||||
const segment = it.move();
|
||||
if (!segment)
|
||||
continue;
|
||||
|
||||
const { p_1, p0, p1, p2, p3, p4, pP } = segment;
|
||||
const FirstBlockId = segment.stepIdx * 4;
|
||||
const SecondBlockId = FirstBlockId + 1;
|
||||
const ResidueMarkerId = FirstBlockId + 2;
|
||||
const SegmentBoundaryMarkerId = FirstBlockId + 3;
|
||||
|
||||
const { rmShift, rmPos } = calcResidueMarkerShift(p2, p3, pP);
|
||||
|
||||
if (segment.firstInChain) {
|
||||
v3normalize(firstDir, v3sub(firstDir, p2, p1));
|
||||
v3normalize(lastDir, v3sub(lastDir, rmPos, p2));
|
||||
} else {
|
||||
v3copy(firstDir, lastDir);
|
||||
v3normalize(lastDir, v3sub(lastDir, rmPos, p2));
|
||||
}
|
||||
|
||||
// C5' -> O3' block
|
||||
interpolate(state, p0, p1, p2, p3, firstDir, lastDir);
|
||||
mb.currentGroup = FirstBlockId;
|
||||
addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, segment.firstInChain || segment.followsGap, false, 'rounded');
|
||||
|
||||
// O3' -> C5' block
|
||||
v3copy(firstDir, lastDir);
|
||||
v3normalize(markerDir, v3sub(markerDir, p3, rmPos));
|
||||
v3normalize(lastDir, v3sub(lastDir, p4, p3));
|
||||
|
||||
// From O3' to the residue marker
|
||||
interpolate(state, p1, p2, p3, p4, firstDir, markerDir, [0, rmShift - residueMarkerWidth]);
|
||||
mb.currentGroup = SecondBlockId;
|
||||
addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, false, false, 'rounded');
|
||||
|
||||
// Residue marker
|
||||
interpolate(markerState, p1, p2, p3, p4, markerDir, markerDir, [rmShift - residueMarkerWidth, rmShift + residueMarkerWidth]);
|
||||
mb.currentGroup = ResidueMarkerId;
|
||||
addTube(mb, mCurvePoints, mNormals, mBinormals, MarkerLinearSegmentCount, segCount.radial, mWidthValues, mHeightValues, false, false, 'rounded');
|
||||
|
||||
if (segment.capEnd) {
|
||||
// From the residue marker to C5' of the end
|
||||
interpolate(state, p1, p2, p3, p4, markerDir, lastDir, [rmShift + residueMarkerWidth, 1]);
|
||||
mb.currentGroup = SecondBlockId;
|
||||
addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, false, true, 'rounded');
|
||||
} else {
|
||||
// From the residue marker to C5' of the step boundary marker
|
||||
interpolate(state, p1, p2, p3, p4, markerDir, lastDir, [rmShift + residueMarkerWidth, 1 - props.segmentBoundaryWidth]);
|
||||
mb.currentGroup = SecondBlockId;
|
||||
addTube(mb, curvePoints, normals, binormals, segCount.linear, segCount.radial, widthValues, heightValues, false, false, 'rounded');
|
||||
|
||||
// Step boundary marker
|
||||
interpolate(markerState, p1, p2, p3, p4, lastDir, lastDir, [1 - props.segmentBoundaryWidth, 1]);
|
||||
mb.currentGroup = SegmentBoundaryMarkerId;
|
||||
addTube(mb, mCurvePoints, mNormals, mBinormals, MarkerLinearSegmentCount, segCount.radial, mWidthValues, mHeightValues, false, false, 'rounded');
|
||||
}
|
||||
|
||||
if (segment.followsGap) {
|
||||
const cylinderProps: CylinderProps = {
|
||||
radiusTop: diameter / 2, radiusBottom: diameter / 2, topCap: true, bottomCap: true, radialSegments: segCount.radial,
|
||||
};
|
||||
mb.currentGroup = FirstBlockId;
|
||||
addFixedCountDashedCylinder(mb, p_1, p1, 1, 2 * segCount.linear, false, cylinderProps);
|
||||
}
|
||||
}
|
||||
|
||||
const boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1.05);
|
||||
|
||||
const m = MeshBuilder.getMesh(mb);
|
||||
m.setBoundingSphere(boundingSphere);
|
||||
return m;
|
||||
}
|
||||
|
||||
const _rmvCO = Vec3();
|
||||
const _rmvPO = Vec3();
|
||||
const _rmPos = Vec3();
|
||||
const _HalfPi = Math.PI / 2;
|
||||
function calcResidueMarkerShift(pO: Vec3, pC: Vec3, pP: Vec3): { rmShift: number, rmPos: Vec3 } {
|
||||
v3sub(_rmvCO, pC, pO);
|
||||
v3sub(_rmvPO, pP, pO);
|
||||
|
||||
// Project position of P atom on the O3' -> C5' vector
|
||||
const beta = Vec3.angle(_rmvPO, _rmvCO);
|
||||
const alpha = _HalfPi - Math.abs(beta);
|
||||
const lengthMO = Math.cos(alpha) * Vec3.magnitude(_rmvPO);
|
||||
const shift = lengthMO / Vec3.magnitude(_rmvCO);
|
||||
|
||||
v3scale(_rmvCO, _rmvCO, shift);
|
||||
v3add(_rmPos, _rmvCO, pO);
|
||||
|
||||
return { rmShift: shift, rmPos: _rmPos };
|
||||
}
|
||||
|
||||
function getNtCTubeSegmentLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number) {
|
||||
const { groupId, objectId, instanceId } = pickingId;
|
||||
if (objectId !== id) return EmptyLoci;
|
||||
|
||||
const { structure } = structureGroup;
|
||||
|
||||
const unit = structureGroup.group.units[instanceId];
|
||||
if (!Unit.isAtomic(unit)) return EmptyLoci;
|
||||
|
||||
const data = NtCTubeProvider.get(structure.model)?.value?.data ?? undefined;
|
||||
if (!data) return EmptyLoci;
|
||||
|
||||
const MeshGroupsCount = totalMeshGroupsCount(data.data.steps);
|
||||
if (groupId > MeshGroupsCount) return EmptyLoci;
|
||||
|
||||
const stepIdx = Math.floor(groupId / 4);
|
||||
const bs = stepBoundingSphere(data.data.steps[stepIdx], Structure.toStructureElementLoci(structure));
|
||||
|
||||
/*
|
||||
* NOTE 1) Each step is drawn with 4 mesh groups. We need to divide/multiply by 4 to convert between steps and mesh groups.
|
||||
* NOTE 2) Molstar will create a mesh only for the asymmetric unit. When the entire biological assembly
|
||||
* is displayed, Molstar just copies and transforms the mesh. This means that even though the mesh
|
||||
* might be displayed multiple times, groupIds of the individual blocks in the mesh will be the same.
|
||||
* If there are multiple copies of a mesh, Molstar needs to be able to tell which block belongs to which copy of the mesh.
|
||||
* To do that, Molstar adds an offset to groupIds of the copied meshes. Offset is calculated as follows:
|
||||
*
|
||||
* offset = NumberOfBlocks * UnitIndex
|
||||
*
|
||||
* "NumberOfBlocks" is the number of valid Location objects got from LocationIterator *or* the greatest groupId set by
|
||||
* the mesh generator - whichever is smaller.
|
||||
*
|
||||
* UnitIndex is the index of the Unit the mesh belongs to, starting from 0. (See "unitMap" in the Structure object).
|
||||
* We can also get this index from the value "instanceId" of the "pickingId" object.
|
||||
*
|
||||
* If this offset is not applied, picking a piece of one of the copied meshes would actually pick that piece in the original mesh.
|
||||
* This is particularly apparent with highlighting - hovering over items in a copied mesh incorrectly highlights those items in the source mesh.
|
||||
*
|
||||
* Molstar can take advantage of the fact that ElementLoci has a reference to the Unit object attached to it. Since we cannot attach ElementLoci
|
||||
* to a step, we need to calculate the offseted groupId here and pass it as part of the DataLoci.
|
||||
*/
|
||||
const offsetGroupId = stepIdx * 4 + (MeshGroupsCount + 1) * instanceId;
|
||||
return NTT.Loci(data.data.steps, [stepIdx], [offsetGroupId], bs);
|
||||
}
|
||||
|
||||
function eachNtCTubeSegment(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
|
||||
if (NTT.isLoci(loci)) {
|
||||
const offsetGroupId = loci.elements[0];
|
||||
return apply(Interval.ofBounds(offsetGroupId, offsetGroupId + 4));
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
function NtCTubeVisual(materialId: number): UnitsVisual<NtCTubeMeshParams> {
|
||||
return UnitsMeshVisual<NtCTubeMeshParams>({
|
||||
defaultProps: PD.getDefaultValues(NtCTubeMeshParams),
|
||||
createGeometry: createNtCTubeMesh,
|
||||
createLocationIterator: createNtCTubeSegmentsIterator,
|
||||
getLoci: getNtCTubeSegmentLoci,
|
||||
eachLocation: eachNtCTubeSegment,
|
||||
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<NtCTubeMeshParams>, currentProps: PD.Values<NtCTubeMeshParams>) => {
|
||||
state.createGeometry = (
|
||||
newProps.quality !== currentProps.quality ||
|
||||
newProps.residueMarkerWidth !== currentProps.residueMarkerWidth ||
|
||||
newProps.segmentBoundaryWidth !== currentProps.segmentBoundaryWidth ||
|
||||
newProps.doubleSided !== currentProps.doubleSided ||
|
||||
newProps.alpha !== currentProps.alpha ||
|
||||
newProps.linearSegments !== currentProps.linearSegments ||
|
||||
newProps.radialSegments !== currentProps.radialSegments
|
||||
);
|
||||
}
|
||||
}, materialId);
|
||||
|
||||
}
|
||||
const NtCTubeVisuals = {
|
||||
'ntc-tube-symbol': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, NtCTubeMeshParams>) => UnitsRepresentation('NtC Tube Mesh', ctx, getParams, NtCTubeVisual),
|
||||
};
|
||||
|
||||
export const NtCTubeParams = {
|
||||
...NtCTubeMeshParams
|
||||
};
|
||||
export type NtCTubeParams = typeof NtCTubeParams;
|
||||
export function getNtCTubeParams(ctx: ThemeRegistryContext, structure: Structure) {
|
||||
return PD.clone(NtCTubeParams);
|
||||
}
|
||||
|
||||
export type NtCTubeRepresentation = StructureRepresentation<NtCTubeParams>;
|
||||
export function NtCTubeRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, NtCTubeParams>): NtCTubeRepresentation {
|
||||
return Representation.createMulti('NtC Tube', ctx, getParams, StructureRepresentationStateBuilder, NtCTubeVisuals as unknown as Representation.Def<Structure, NtCTubeParams>);
|
||||
}
|
||||
|
||||
export const NtCTubeRepresentationProvider = StructureRepresentationProvider({
|
||||
name: 'ntc-tube',
|
||||
label: 'NtC Tube',
|
||||
description: 'Displays schematic representation of NtC conformers',
|
||||
factory: NtCTubeRepresentation,
|
||||
getParams: getNtCTubeParams,
|
||||
defaultValues: PD.getDefaultValues(NtCTubeParams),
|
||||
defaultColorTheme: { name: 'ntc-tube' },
|
||||
defaultSizeTheme: { name: 'uniform', props: { value: 2.0 } },
|
||||
isApplicable: (structure: Structure) => structure.models.every(m => Dnatco.isApplicable(m)),
|
||||
ensureCustomProperties: {
|
||||
attach: async (ctx: CustomProperty.Context, structure: Structure) => structure.models.forEach(m => NtCTubeProvider.attach(ctx, m, void 0, true)),
|
||||
detach: (data) => data.models.forEach(m => NtCTubeProvider.ref(m, false)),
|
||||
},
|
||||
});
|
||||
@@ -1,51 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { NtCTubeSegmentLabel } from './behavior';
|
||||
import { DnatcoTypes } from '../types';
|
||||
import { Sphere3D } from '../../../mol-math/geometry/primitives/sphere3d';
|
||||
import { DataLocation } from '../../../mol-model/location';
|
||||
import { DataLoci } from '../../../mol-model/loci';
|
||||
|
||||
export namespace NtCTubeTypes {
|
||||
const DataTag = 'dnatco-tube-segment-data';
|
||||
const DummyTag = 'dnatco-tube-dummy';
|
||||
|
||||
export type Data = {
|
||||
data: DnatcoTypes.Steps,
|
||||
}
|
||||
|
||||
export type TubeBlock = {
|
||||
step: DnatcoTypes.Step,
|
||||
kind: 'upper' | 'lower' | 'residue-boundary' | 'segment-boundary';
|
||||
}
|
||||
|
||||
export interface Location extends DataLocation<TubeBlock> {}
|
||||
|
||||
export function Location(payload: TubeBlock) {
|
||||
return DataLocation(DataTag, payload, {});
|
||||
}
|
||||
|
||||
export function isLocation(x: any): x is Location {
|
||||
return !!x && x.kind === 'data-location' && x.tag === DataTag;
|
||||
}
|
||||
|
||||
export interface Loci extends DataLoci<DnatcoTypes.Step[], number> {}
|
||||
export interface DummyLoci extends DataLoci<{}, number> {}
|
||||
|
||||
export function Loci(data: DnatcoTypes.Step[], stepIndices: number[], elements: number[], boundingSphere?: Sphere3D): Loci {
|
||||
return DataLoci(DataTag, data, elements, boundingSphere ? () => boundingSphere : undefined, () => stepIndices[0] !== undefined ? NtCTubeSegmentLabel(data[stepIndices[0]]) : '');
|
||||
}
|
||||
|
||||
export function DummyLoci(): DummyLoci {
|
||||
return DataLoci(DummyTag, {}, [], undefined, () => '');
|
||||
}
|
||||
|
||||
export function isLoci(x: any): x is Loci {
|
||||
return !!x && x.kind === 'data-loci' && x.tag === DataTag;
|
||||
}
|
||||
}
|
||||
@@ -1,214 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { NtCTubeTypes as NTT } from './types';
|
||||
import { NtCTubeProvider } from './property';
|
||||
import { DnatcoUtil } from '../util';
|
||||
import { Segmentation, SortedArray } from '../../../mol-data/int';
|
||||
import { Vec3 } from '../../../mol-math/linear-algebra';
|
||||
import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
|
||||
|
||||
function getAtomPosition(vec: Vec3, loc: StructureElement.Location, residue: DnatcoUtil.Residue, names: string[], altId: string, insCode: string) {
|
||||
const eI = DnatcoUtil.getAtomIndex(loc, residue, names, altId, insCode);
|
||||
if (eI !== -1) {
|
||||
loc.unit.conformation.invariantPosition(eI, vec);
|
||||
return true;
|
||||
}
|
||||
|
||||
return false; // Atom not found
|
||||
}
|
||||
|
||||
const p_1 = Vec3();
|
||||
const p0 = Vec3();
|
||||
const p1 = Vec3();
|
||||
const p2 = Vec3();
|
||||
const p3 = Vec3();
|
||||
const p4 = Vec3();
|
||||
const pP = Vec3();
|
||||
|
||||
const C5PrimeNames = ['C5\'', 'C5*'];
|
||||
const O3PrimeNames = ['O3\'', 'O3*'];
|
||||
const O5PrimeNames = ['O5\'', 'O5*'];
|
||||
const PNames = ['P'];
|
||||
|
||||
function getPoints(
|
||||
loc: StructureElement.Location,
|
||||
r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue,
|
||||
altId0: string, altId1: string, altId2: string,
|
||||
insCode0: string, insCode1: string, insCode2: string,
|
||||
) {
|
||||
if (r0) {
|
||||
if (!getAtomPosition(p_1, loc, r0, C5PrimeNames, altId0, insCode0))
|
||||
return void 0;
|
||||
if (!getAtomPosition(p0, loc, r0, O3PrimeNames, altId0, insCode0))
|
||||
return void 0;
|
||||
} else {
|
||||
if (!getAtomPosition(p0, loc, r1, O5PrimeNames, altId1, insCode1))
|
||||
return void 0;
|
||||
}
|
||||
|
||||
if (!getAtomPosition(p1, loc, r1, C5PrimeNames, altId1, insCode1))
|
||||
return void 0;
|
||||
if (!getAtomPosition(p2, loc, r1, O3PrimeNames, altId1, insCode1))
|
||||
return void 0;
|
||||
|
||||
if (!getAtomPosition(p3, loc, r2, C5PrimeNames, altId2, insCode2))
|
||||
return void 0;
|
||||
if (!getAtomPosition(p4, loc, r2, O3PrimeNames, altId2, insCode2))
|
||||
return void 0;
|
||||
if (!getAtomPosition(pP, loc, r2, PNames, altId2, insCode2))
|
||||
return void 0;
|
||||
|
||||
return { p_1, p0, p1, p2, p3, p4, pP };
|
||||
}
|
||||
|
||||
function hasGapElements(r: DnatcoUtil.Residue, unit: Unit) {
|
||||
for (let xI = r.start; xI < r.end; xI++) {
|
||||
const eI = unit.elements[xI];
|
||||
if (SortedArray.has(unit.gapElements, eI)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
export type NtCTubeSegment = {
|
||||
p_1: Vec3,
|
||||
p0: Vec3,
|
||||
p1: Vec3,
|
||||
p2: Vec3,
|
||||
p3: Vec3,
|
||||
p4: Vec3,
|
||||
pP: Vec3,
|
||||
stepIdx: number,
|
||||
followsGap: boolean,
|
||||
firstInChain: boolean,
|
||||
capEnd: boolean,
|
||||
}
|
||||
|
||||
export class NtCTubeSegmentsIterator {
|
||||
private chainIt: Segmentation.SegmentIterator<ChainIndex>;
|
||||
private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
|
||||
|
||||
/* Second residue of the previous step, may be undefined
|
||||
* if we are at the beginning of a chain or right after a discontinuity */
|
||||
private residuePrev?: DnatcoUtil.Residue;
|
||||
/* First residue of the current step */
|
||||
private residueOne?: DnatcoUtil.Residue;
|
||||
/* Second residue of the current step */
|
||||
private residueTwo: DnatcoUtil.Residue;
|
||||
/* First residue of the next step, may be undefined
|
||||
* if we are at the end of a chain.
|
||||
* Undefined value indicates that the iterator has reached the end.*/
|
||||
private residueNext?: DnatcoUtil.Residue;
|
||||
|
||||
private data?: NTT.Data;
|
||||
private altIdOne = '';
|
||||
private insCodeOne = '';
|
||||
private loc: StructureElement.Location;
|
||||
|
||||
private moveStep() {
|
||||
if (!this.residueNext)
|
||||
return void 0;
|
||||
|
||||
/* Assume discontinuity of the ResidueIndex of the residue that would become residue one (= first residue of the corresponding step)
|
||||
* does not equal to ResidueIndex of what would be residue two (= second residue of the corresponding step). */
|
||||
if (this.residueTwo.index + 1 === this.residueNext.index) {
|
||||
this.residuePrev = DnatcoUtil.copyResidue(this.residueOne);
|
||||
this.residueOne = DnatcoUtil.copyResidue(this.residueTwo);
|
||||
this.residueTwo = DnatcoUtil.copyResidue(this.residueNext)!;
|
||||
this.residueNext = this.residueIt.hasNext ? DnatcoUtil.copyResidue(this.residueIt.move())! : void 0;
|
||||
} else {
|
||||
if (!this.residueIt.hasNext) {
|
||||
this.residueNext = void 0;
|
||||
return void 0;
|
||||
}
|
||||
|
||||
// There is discontinuity, act as if we were at the beginning of a chain
|
||||
this.residuePrev = void 0;
|
||||
this.residueOne = DnatcoUtil.copyResidue(this.residueNext);
|
||||
this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
|
||||
this.residueNext = this.residueIt.hasNext ? DnatcoUtil.copyResidue(this.residueIt.move())! : void 0;
|
||||
}
|
||||
|
||||
return this.toSegment(this.residuePrev, this.residueOne!, this.residueTwo, this.residueNext);
|
||||
}
|
||||
|
||||
private prime() {
|
||||
if (this.residueIt.hasNext)
|
||||
this.residueTwo = DnatcoUtil.copyResidue(this.residueIt.move())!;
|
||||
if (this.residueIt.hasNext)
|
||||
this.residueNext = this.residueIt.move();
|
||||
}
|
||||
|
||||
private toSegment(r0: DnatcoUtil.Residue | undefined, r1: DnatcoUtil.Residue, r2: DnatcoUtil.Residue, r3: DnatcoUtil.Residue | undefined): NtCTubeSegment | undefined {
|
||||
const indices = DnatcoUtil.getStepIndices(this.data!.data, this.loc, r1);
|
||||
if (indices.length === 0)
|
||||
return void 0;
|
||||
|
||||
const stepIdx = indices[0];
|
||||
const step = this.data!.data.steps[stepIdx];
|
||||
|
||||
const altIdPrev = this.altIdOne;
|
||||
const insCodePrev = this.insCodeOne;
|
||||
this.altIdOne = step.label_alt_id_1;
|
||||
this.insCodeOne = step.PDB_ins_code_1;
|
||||
const altIdTwo = step.label_alt_id_2;
|
||||
const insCodeTwo = step.PDB_ins_code_2;
|
||||
const followsGap = !!r0 && hasGapElements(r0, this.loc.unit) && hasGapElements(r1, this.loc.unit);
|
||||
const precedesDiscontinuity = r3 ? r3.index !== r2.index + 1 : false;
|
||||
const points = getPoints(this.loc, r0, r1, r2, altIdPrev, this.altIdOne, altIdTwo, insCodePrev, this.insCodeOne, insCodeTwo);
|
||||
if (!points)
|
||||
return void 0;
|
||||
|
||||
return {
|
||||
...points,
|
||||
stepIdx,
|
||||
followsGap,
|
||||
firstInChain: !r0,
|
||||
capEnd: !this.residueNext || precedesDiscontinuity || hasGapElements(r2, this.loc.unit),
|
||||
};
|
||||
}
|
||||
|
||||
constructor(structure: Structure, unit: Unit.Atomic) {
|
||||
this.chainIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
|
||||
this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
|
||||
|
||||
const prop = NtCTubeProvider.get(unit.model).value;
|
||||
this.data = prop?.data;
|
||||
|
||||
if (this.chainIt.hasNext) {
|
||||
this.residueIt.setSegment(this.chainIt.move());
|
||||
this.prime();
|
||||
}
|
||||
|
||||
this.loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
|
||||
}
|
||||
|
||||
get hasNext() {
|
||||
if (!this.data)
|
||||
return false;
|
||||
return !!this.residueNext
|
||||
? true
|
||||
: this.chainIt.hasNext;
|
||||
}
|
||||
|
||||
move() {
|
||||
if (!!this.residueNext) {
|
||||
return this.moveStep();
|
||||
} else {
|
||||
this.residuePrev = void 0; // Assume discontinuity when we switch chains
|
||||
this.residueNext = void 0;
|
||||
|
||||
this.residueIt.setSegment(this.chainIt.move());
|
||||
this.prime();
|
||||
|
||||
return this.moveStep();
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -1,172 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { DnatcoTypes } from './types';
|
||||
import { Column, Table } from '../../mol-data/db';
|
||||
import { toTable } from '../../mol-io/reader/cif/schema';
|
||||
import { Model } from '../../mol-model/structure';
|
||||
import { CustomProperty } from '../../mol-model-props/common/custom-property';
|
||||
import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
|
||||
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
|
||||
export type DnatcoSteps = PropertyWrapper<DnatcoTypes.Steps | undefined>;
|
||||
|
||||
export const DnatcoParams = {};
|
||||
export type DnatcoParams = typeof DnatcoParams;
|
||||
export type DnatcoProps = PD.Values<DnatcoParams>;
|
||||
|
||||
export namespace Dnatco {
|
||||
export const Schema = {
|
||||
ndb_struct_ntc_step: {
|
||||
id: Column.Schema.int,
|
||||
name: Column.Schema.str,
|
||||
PDB_model_number: Column.Schema.int,
|
||||
label_entity_id_1: Column.Schema.int,
|
||||
label_asym_id_1: Column.Schema.str,
|
||||
label_seq_id_1: Column.Schema.int,
|
||||
label_comp_id_1: Column.Schema.str,
|
||||
label_alt_id_1: Column.Schema.str,
|
||||
label_entity_id_2: Column.Schema.int,
|
||||
label_asym_id_2: Column.Schema.str,
|
||||
label_seq_id_2: Column.Schema.int,
|
||||
label_comp_id_2: Column.Schema.str,
|
||||
label_alt_id_2: Column.Schema.str,
|
||||
auth_asym_id_1: Column.Schema.str,
|
||||
auth_seq_id_1: Column.Schema.int,
|
||||
auth_asym_id_2: Column.Schema.str,
|
||||
auth_seq_id_2: Column.Schema.int,
|
||||
PDB_ins_code_1: Column.Schema.str,
|
||||
PDB_ins_code_2: Column.Schema.str,
|
||||
},
|
||||
ndb_struct_ntc_step_summary: {
|
||||
step_id: Column.Schema.int,
|
||||
assigned_CANA: Column.Schema.str,
|
||||
assigned_NtC: Column.Schema.str,
|
||||
confal_score: Column.Schema.int,
|
||||
euclidean_distance_NtC_ideal: Column.Schema.float,
|
||||
cartesian_rmsd_closest_NtC_representative: Column.Schema.float,
|
||||
closest_CANA: Column.Schema.str,
|
||||
closest_NtC: Column.Schema.str,
|
||||
closest_step_golden: Column.Schema.str
|
||||
}
|
||||
};
|
||||
export type Schema = typeof Schema;
|
||||
|
||||
export function getStepsFromCif(
|
||||
model: Model,
|
||||
cifSteps: Table<typeof Dnatco.Schema.ndb_struct_ntc_step>,
|
||||
stepsSummary: StepsSummaryTable
|
||||
): DnatcoTypes.Steps {
|
||||
const steps = new Array<DnatcoTypes.Step>();
|
||||
const mapping = new Array<DnatcoTypes.MappedChains>();
|
||||
|
||||
const {
|
||||
id, PDB_model_number, name,
|
||||
auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
|
||||
auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
|
||||
_rowCount
|
||||
} = cifSteps;
|
||||
|
||||
if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
|
||||
|
||||
for (let i = 0; i < _rowCount; i++) {
|
||||
const {
|
||||
NtC,
|
||||
confal_score,
|
||||
rmsd
|
||||
} = getSummaryData(id.value(i), i, stepsSummary);
|
||||
const modelNum = PDB_model_number.value(i);
|
||||
const chainId = auth_asym_id_1.value(i);
|
||||
const seqId = auth_seq_id_1.value(i);
|
||||
const modelIdx = modelNum - 1;
|
||||
|
||||
if (mapping.length <= modelIdx || !mapping[modelIdx])
|
||||
mapping[modelIdx] = new Map<string, DnatcoTypes.MappedResidues>();
|
||||
|
||||
const step = {
|
||||
PDB_model_number: modelNum,
|
||||
name: name.value(i),
|
||||
auth_asym_id_1: chainId,
|
||||
auth_seq_id_1: seqId,
|
||||
label_comp_id_1: label_comp_id_1.value(i),
|
||||
label_alt_id_1: label_alt_id_1.value(i),
|
||||
PDB_ins_code_1: PDB_ins_code_1.value(i),
|
||||
auth_asym_id_2: auth_asym_id_2.value(i),
|
||||
auth_seq_id_2: auth_seq_id_2.value(i),
|
||||
label_comp_id_2: label_comp_id_2.value(i),
|
||||
label_alt_id_2: label_alt_id_2.value(i),
|
||||
PDB_ins_code_2: PDB_ins_code_2.value(i),
|
||||
confal_score,
|
||||
NtC,
|
||||
rmsd,
|
||||
};
|
||||
|
||||
steps.push(step);
|
||||
|
||||
const mappedChains = mapping[modelIdx];
|
||||
const residuesOnChain = mappedChains.get(chainId) ?? new Map<number, number[]>();
|
||||
const stepsForResidue = residuesOnChain.get(seqId) ?? [];
|
||||
stepsForResidue.push(steps.length - 1);
|
||||
|
||||
residuesOnChain.set(seqId, stepsForResidue);
|
||||
mappedChains.set(chainId, residuesOnChain);
|
||||
mapping[modelIdx] = mappedChains;
|
||||
}
|
||||
|
||||
return { steps, mapping };
|
||||
}
|
||||
|
||||
export async function fromCif(ctx: CustomProperty.Context, model: Model, props: DnatcoProps): Promise<CustomProperty.Data<DnatcoSteps>> {
|
||||
const info = PropertyWrapper.createInfo();
|
||||
const data = getCifData(model);
|
||||
if (data === undefined) return { value: { info, data: undefined } };
|
||||
|
||||
const fromCif = getStepsFromCif(model, data.steps, data.stepsSummary);
|
||||
return { value: { info, data: fromCif } };
|
||||
}
|
||||
|
||||
export function getCifData(model: Model) {
|
||||
if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF');
|
||||
if (!hasNdbStructNtcCategories(model)) return undefined;
|
||||
return {
|
||||
steps: toTable(Schema.ndb_struct_ntc_step, model.sourceData.data.frame.categories.ndb_struct_ntc_step),
|
||||
stepsSummary: toTable(Schema.ndb_struct_ntc_step_summary, model.sourceData.data.frame.categories.ndb_struct_ntc_step_summary)
|
||||
};
|
||||
}
|
||||
|
||||
function hasNdbStructNtcCategories(model: Model): boolean {
|
||||
if (!MmcifFormat.is(model.sourceData)) return false;
|
||||
const names = (model.sourceData).data.frame.categoryNames;
|
||||
return names.includes('ndb_struct_ntc_step') && names.includes('ndb_struct_ntc_step_summary');
|
||||
}
|
||||
|
||||
export function isApplicable(model?: Model): boolean {
|
||||
return !!model && hasNdbStructNtcCategories(model);
|
||||
}
|
||||
}
|
||||
|
||||
type StepsSummaryTable = Table<typeof Dnatco.Schema.ndb_struct_ntc_step_summary>;
|
||||
|
||||
function getSummaryData(id: number, i: number, stepsSummary: StepsSummaryTable) {
|
||||
const {
|
||||
step_id,
|
||||
confal_score,
|
||||
assigned_NtC,
|
||||
cartesian_rmsd_closest_NtC_representative,
|
||||
} = stepsSummary;
|
||||
|
||||
// Assume that step_ids in ntc_step_summary are in the same order as steps in ntc_step
|
||||
for (let j = i; j < stepsSummary._rowCount; j++) {
|
||||
if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
|
||||
}
|
||||
// Safety net for cases where the previous assumption is not met
|
||||
for (let j = 0; j < i; j++) {
|
||||
if (id === step_id.value(j)) return { NtC: assigned_NtC.value(j), confal_score: confal_score.value(j), rmsd: cartesian_rmsd_closest_NtC_representative.value(j) };
|
||||
}
|
||||
throw new Error('Inconsistent mmCIF data');
|
||||
}
|
||||
@@ -1,41 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
export namespace DnatcoTypes {
|
||||
export const DataTag = 'dnatco-confal-half-step';
|
||||
|
||||
export type Step = {
|
||||
PDB_model_number: number,
|
||||
name: string,
|
||||
auth_asym_id_1: string,
|
||||
auth_seq_id_1: number,
|
||||
label_comp_id_1: string,
|
||||
label_alt_id_1: string,
|
||||
PDB_ins_code_1: string,
|
||||
auth_asym_id_2: string,
|
||||
auth_seq_id_2: number,
|
||||
label_comp_id_2: string,
|
||||
label_alt_id_2: string,
|
||||
PDB_ins_code_2: string,
|
||||
confal_score: number,
|
||||
NtC: string,
|
||||
rmsd: number,
|
||||
}
|
||||
|
||||
export type MappedChains = Map<string, MappedResidues>;
|
||||
export type MappedResidues = Map<number, number[]>;
|
||||
|
||||
export interface Steps {
|
||||
steps: Array<Step>,
|
||||
mapping: MappedChains[],
|
||||
}
|
||||
|
||||
export interface HalfStep {
|
||||
step: Step,
|
||||
isLower: boolean,
|
||||
}
|
||||
}
|
||||
@@ -1,117 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Michal Malý <michal.maly@ibt.cas.cz>
|
||||
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
|
||||
*/
|
||||
|
||||
import { DnatcoTypes } from './types';
|
||||
import { OrderedSet, Segmentation } from '../../mol-data/int';
|
||||
import { EmptyLoci } from '../../mol-model/loci';
|
||||
import { ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
|
||||
|
||||
const EmptyStepIndices = new Array<number>();
|
||||
|
||||
export namespace DnatcoUtil {
|
||||
export type Residue = Segmentation.Segment<ResidueIndex>;
|
||||
|
||||
export function copyResidue(r?: Residue) {
|
||||
return r ? { index: r.index, start: r.start, end: r.end } : void 0;
|
||||
}
|
||||
|
||||
export function getAtomIndex(loc: StructureElement.Location, residue: Residue, names: string[], altId: string, insCode: string): ElementIndex {
|
||||
for (let eI = residue.start; eI < residue.end; eI++) {
|
||||
loc.element = loc.unit.elements[eI];
|
||||
const elName = StructureProperties.atom.label_atom_id(loc);
|
||||
const elAltId = StructureProperties.atom.label_alt_id(loc);
|
||||
const elInsCode = StructureProperties.residue.pdbx_PDB_ins_code(loc);
|
||||
|
||||
if (names.includes(elName) && (elAltId === altId || elAltId.length === 0) && (elInsCode === insCode))
|
||||
return loc.element;
|
||||
}
|
||||
|
||||
return -1 as ElementIndex;
|
||||
}
|
||||
|
||||
export function getStepIndices(data: DnatcoTypes.Steps, loc: StructureElement.Location, r: DnatcoUtil.Residue) {
|
||||
loc.element = loc.unit.elements[r.start];
|
||||
|
||||
const modelIdx = StructureProperties.unit.model_num(loc) - 1;
|
||||
const chainId = StructureProperties.chain.auth_asym_id(loc);
|
||||
const seqId = StructureProperties.residue.auth_seq_id(loc);
|
||||
const insCode = StructureProperties.residue.pdbx_PDB_ins_code(loc);
|
||||
|
||||
const chains = data.mapping[modelIdx];
|
||||
if (!chains) return EmptyStepIndices;
|
||||
const residues = chains.get(chainId);
|
||||
if (!residues) return EmptyStepIndices;
|
||||
const indices = residues.get(seqId);
|
||||
if (!indices) return EmptyStepIndices;
|
||||
|
||||
return insCode !== '' ? indices.filter(idx => data.steps[idx].PDB_ins_code_1 === insCode) : indices;
|
||||
}
|
||||
|
||||
export function residueAltIds(structure: Structure, unit: Unit, residue: Residue) {
|
||||
const altIds = new Array<string>();
|
||||
const loc = StructureElement.Location.create(structure, unit);
|
||||
for (let eI = residue.start; eI < residue.end; eI++) {
|
||||
loc.element = OrderedSet.getAt(unit.elements, eI);
|
||||
const altId = StructureProperties.atom.label_alt_id(loc);
|
||||
if (altId !== '' && !altIds.includes(altId))
|
||||
altIds.push(altId);
|
||||
}
|
||||
|
||||
return altIds;
|
||||
}
|
||||
|
||||
const _loc = StructureElement.Location.create();
|
||||
export function residueToLoci(asymId: string, seqId: number, altId: string | undefined, insCode: string, loci: StructureElement.Loci, source: 'label' | 'auth') {
|
||||
_loc.structure = loci.structure;
|
||||
for (const e of loci.elements) {
|
||||
_loc.unit = e.unit;
|
||||
|
||||
const getAsymId = source === 'label' ? StructureProperties.chain.label_asym_id : StructureProperties.chain.auth_asym_id;
|
||||
const getSeqId = source === 'label' ? StructureProperties.residue.label_seq_id : StructureProperties.residue.auth_seq_id;
|
||||
|
||||
// Walk the entire unit and look for the requested residue
|
||||
const chainIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.chainAtomSegments, e.unit.elements);
|
||||
const residueIt = Segmentation.transientSegments(e.unit.model.atomicHierarchy.residueAtomSegments, e.unit.elements);
|
||||
|
||||
const elemIndex = (idx: number) => OrderedSet.getAt(e.unit.elements, idx);
|
||||
while (chainIt.hasNext) {
|
||||
const chain = chainIt.move();
|
||||
_loc.element = elemIndex(chain.start);
|
||||
const _asymId = getAsymId(_loc);
|
||||
if (_asymId !== asymId)
|
||||
continue; // Wrong chain, skip it
|
||||
|
||||
residueIt.setSegment(chain);
|
||||
while (residueIt.hasNext) {
|
||||
const residue = residueIt.move();
|
||||
_loc.element = elemIndex(residue.start);
|
||||
|
||||
const _seqId = getSeqId(_loc);
|
||||
if (_seqId === seqId) {
|
||||
const _insCode = StructureProperties.residue.pdbx_PDB_ins_code(_loc);
|
||||
if (_insCode !== insCode)
|
||||
continue;
|
||||
if (altId) {
|
||||
const _altIds = residueAltIds(loci.structure, e.unit, residue);
|
||||
if (!_altIds.includes(altId))
|
||||
continue;
|
||||
}
|
||||
|
||||
const start = residue.start as StructureElement.UnitIndex;
|
||||
const end = residue.end as StructureElement.UnitIndex;
|
||||
return StructureElement.Loci(
|
||||
loci.structure,
|
||||
[{ unit: e.unit, indices: OrderedSet.ofBounds(start, end) }]
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return EmptyLoci;
|
||||
}
|
||||
}
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
@@ -13,7 +13,7 @@ import { PLUGIN_VERSION } from '../../mol-plugin/version';
|
||||
import { RuntimeContext } from '../../mol-task';
|
||||
import { Color } from '../../mol-util/color/color';
|
||||
import { fillSerial } from '../../mol-util/array';
|
||||
import { NumberArray, assertUnreachable } from '../../mol-util/type-helpers';
|
||||
import { NumberArray } from '../../mol-util/type-helpers';
|
||||
import { MeshExporter, AddMeshInput, MeshGeoData } from './mesh-exporter';
|
||||
|
||||
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
|
||||
@@ -35,15 +35,6 @@ const BIN_CHUNK_TYPE = 0x004E4942;
|
||||
const JSON_PAD_CHAR = 0x20;
|
||||
const BIN_PAD_CHAR = 0x00;
|
||||
|
||||
function getPrimitiveMode(mode: 'points' | 'lines' | 'triangles'): number {
|
||||
switch (mode) {
|
||||
case 'points': return 0;
|
||||
case 'lines': return 1;
|
||||
case 'triangles': return 4;
|
||||
default: assertUnreachable(mode);
|
||||
}
|
||||
}
|
||||
|
||||
export type GlbData = {
|
||||
glb: Uint8Array
|
||||
}
|
||||
@@ -98,12 +89,12 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
return accessorOffset;
|
||||
}
|
||||
|
||||
private addGeometryBuffers(vertices: Float32Array, normals: Float32Array | undefined, indices: Uint32Array | undefined, vertexCount: number, drawCount: number, isGeoTexture: boolean) {
|
||||
private addGeometryBuffers(vertices: Float32Array, normals: Float32Array, indices: Uint32Array | undefined, vertexCount: number, drawCount: number, isGeoTexture: boolean) {
|
||||
const tmpV = Vec3();
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
|
||||
const vertexArray = new Float32Array(vertexCount * 3);
|
||||
let normalArray: Float32Array | undefined;
|
||||
const normalArray = new Float32Array(vertexCount * 3);
|
||||
let indexArray: Uint32Array | undefined;
|
||||
|
||||
// position
|
||||
@@ -113,35 +104,32 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
}
|
||||
|
||||
// normal
|
||||
if (normals) {
|
||||
normalArray = new Float32Array(vertexCount * 3);
|
||||
for (let i = 0; i < vertexCount; ++i) {
|
||||
v3fromArray(tmpV, normals, i * stride);
|
||||
v3normalize(tmpV, tmpV);
|
||||
v3toArray(tmpV, normalArray, i * 3);
|
||||
}
|
||||
for (let i = 0; i < vertexCount; ++i) {
|
||||
v3fromArray(tmpV, normals, i * stride);
|
||||
v3normalize(tmpV, tmpV);
|
||||
v3toArray(tmpV, normalArray, i * 3);
|
||||
}
|
||||
|
||||
// face
|
||||
if (!isGeoTexture && indices) {
|
||||
indexArray = indices.slice(0, drawCount);
|
||||
if (!isGeoTexture) {
|
||||
indexArray = indices!.slice(0, drawCount);
|
||||
}
|
||||
|
||||
const [vertexMin, vertexMax] = GlbExporter.vec3MinMax(vertexArray);
|
||||
|
||||
let vertexBuffer = vertexArray.buffer;
|
||||
let normalBuffer = normalArray?.buffer;
|
||||
let indexBuffer = (isGeoTexture || !indexArray) ? undefined : indexArray.buffer;
|
||||
let normalBuffer = normalArray.buffer;
|
||||
let indexBuffer = isGeoTexture ? undefined : indexArray!.buffer;
|
||||
if (!IsNativeEndianLittle) {
|
||||
vertexBuffer = flipByteOrder(new Uint8Array(vertexBuffer), 4);
|
||||
if (normalBuffer) normalBuffer = flipByteOrder(new Uint8Array(normalBuffer), 4);
|
||||
normalBuffer = flipByteOrder(new Uint8Array(normalBuffer), 4);
|
||||
if (!isGeoTexture) indexBuffer = flipByteOrder(new Uint8Array(indexBuffer!), 4);
|
||||
}
|
||||
|
||||
return {
|
||||
vertexAccessorIndex: this.addBuffer(vertexBuffer, FLOAT, 'VEC3', vertexCount, ARRAY_BUFFER, vertexMin, vertexMax),
|
||||
normalAccessorIndex: normalBuffer ? this.addBuffer(normalBuffer, FLOAT, 'VEC3', vertexCount, ARRAY_BUFFER) : undefined,
|
||||
indexAccessorIndex: (isGeoTexture || !indexBuffer) ? undefined : this.addBuffer(indexBuffer, UNSIGNED_INT, 'SCALAR', drawCount, ELEMENT_ARRAY_BUFFER)
|
||||
normalAccessorIndex: this.addBuffer(normalBuffer, FLOAT, 'VEC3', vertexCount, ARRAY_BUFFER),
|
||||
indexAccessorIndex: isGeoTexture ? undefined : this.addBuffer(indexBuffer!, UNSIGNED_INT, 'SCALAR', drawCount, ELEMENT_ARRAY_BUFFER)
|
||||
};
|
||||
}
|
||||
|
||||
@@ -170,8 +158,8 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
return this.addBuffer(colorBuffer, UNSIGNED_BYTE, 'VEC4', vertexCount, ARRAY_BUFFER, undefined, undefined, true);
|
||||
}
|
||||
|
||||
private addMaterial(metalness: number, roughness: number, doubleSided: boolean, alpha: boolean) {
|
||||
const hash = `${metalness}|${roughness}|${doubleSided}`;
|
||||
private addMaterial(metalness: number, roughness: number) {
|
||||
const hash = `${metalness}|${roughness}`;
|
||||
if (!this.materialMap.has(hash)) {
|
||||
this.materialMap.set(hash, this.materials.length);
|
||||
this.materials.push({
|
||||
@@ -179,16 +167,14 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
baseColorFactor: [1, 1, 1, 1],
|
||||
metallicFactor: metalness,
|
||||
roughnessFactor: roughness
|
||||
},
|
||||
doubleSided,
|
||||
alphaMode: alpha ? 'BLEND' : 'OPAQUE',
|
||||
}
|
||||
});
|
||||
}
|
||||
return this.materialMap.get(hash)!;
|
||||
}
|
||||
|
||||
protected async addMeshWithColors(input: AddMeshInput) {
|
||||
const { mesh, values, isGeoTexture, mode, webgl, ctx } = input;
|
||||
const { mesh, values, isGeoTexture, webgl, ctx } = input;
|
||||
|
||||
const t = Mat4();
|
||||
|
||||
@@ -200,34 +186,32 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
const instanceCount = values.uInstanceCount.ref.value;
|
||||
const metalness = values.uMetalness.ref.value;
|
||||
const roughness = values.uRoughness.ref.value;
|
||||
const doubleSided = values.uDoubleSided?.ref.value || values.hasReflection.ref.value;
|
||||
const alpha = values.uAlpha.ref.value < 1;
|
||||
|
||||
const material = this.addMaterial(metalness, roughness, doubleSided, alpha);
|
||||
const material = this.addMaterial(metalness, roughness);
|
||||
|
||||
let interpolatedColors: Uint8Array | undefined;
|
||||
if (webgl && mesh && (colorType === 'volume' || colorType === 'volumeInstance')) {
|
||||
if (colorType === 'volume' || colorType === 'volumeInstance') {
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
interpolatedColors = GlbExporter.getInterpolatedColors(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType });
|
||||
interpolatedColors = GlbExporter.getInterpolatedColors(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType });
|
||||
}
|
||||
|
||||
let interpolatedOverpaint: Uint8Array | undefined;
|
||||
if (webgl && mesh && overpaintType === 'volumeInstance') {
|
||||
if (overpaintType === 'volumeInstance') {
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
interpolatedOverpaint = GlbExporter.getInterpolatedOverpaint(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType: overpaintType });
|
||||
interpolatedOverpaint = GlbExporter.getInterpolatedOverpaint(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType: overpaintType });
|
||||
}
|
||||
|
||||
let interpolatedTransparency: Uint8Array | undefined;
|
||||
if (webgl && mesh && transparencyType === 'volumeInstance') {
|
||||
if (transparencyType === 'volumeInstance') {
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
interpolatedTransparency = GlbExporter.getInterpolatedTransparency(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType: transparencyType });
|
||||
interpolatedTransparency = GlbExporter.getInterpolatedTransparency(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType: transparencyType });
|
||||
}
|
||||
|
||||
// instancing
|
||||
const sameGeometryBuffers = mesh !== undefined;
|
||||
const sameColorBuffer = sameGeometryBuffers && colorType !== 'instance' && !colorType.endsWith('Instance') && !dTransparency;
|
||||
let vertexAccessorIndex: number;
|
||||
let normalAccessorIndex: number | undefined;
|
||||
let normalAccessorIndex: number;
|
||||
let indexAccessorIndex: number | undefined;
|
||||
let colorAccessorIndex: number;
|
||||
let meshIndex: number;
|
||||
@@ -251,7 +235,7 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
|
||||
// create a color buffer if needed
|
||||
if (instanceIndex === 0 || !sameColorBuffer) {
|
||||
colorAccessorIndex = this.addColorBuffer({ values, groups, vertexCount, instanceIndex, isGeoTexture, mode }, interpolatedColors, interpolatedOverpaint, interpolatedTransparency);
|
||||
colorAccessorIndex = this.addColorBuffer({ values, groups, vertexCount, instanceIndex, isGeoTexture }, interpolatedColors, interpolatedOverpaint, interpolatedTransparency);
|
||||
}
|
||||
|
||||
// glTF mesh
|
||||
@@ -264,8 +248,7 @@ export class GlbExporter extends MeshExporter<GlbData> {
|
||||
COLOR_0: colorAccessorIndex!
|
||||
},
|
||||
indices: indexAccessorIndex,
|
||||
material,
|
||||
mode: getPrimitiveMode(mode),
|
||||
material
|
||||
}]
|
||||
});
|
||||
}
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
@@ -28,32 +28,24 @@ import { Color } from '../../mol-util/color/color';
|
||||
import { unpackRGBToInt } from '../../mol-util/number-packing';
|
||||
import { RenderObjectExporter, RenderObjectExportData } from './render-object-exporter';
|
||||
import { readAlphaTexture, readTexture } from '../../mol-gl/compute/util';
|
||||
import { assertUnreachable } from '../../mol-util/type-helpers';
|
||||
import { ValueCell } from '../../mol-util/value-cell';
|
||||
|
||||
const GeoExportName = 'geo-export';
|
||||
|
||||
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
|
||||
const v3fromArray = Vec3.fromArray;
|
||||
const v3sub = Vec3.sub;
|
||||
const v3dot = Vec3.dot;
|
||||
const v3unitY = Vec3.unitY;
|
||||
|
||||
type MeshMode = 'points' | 'lines' | 'triangles'
|
||||
|
||||
export interface AddMeshInput {
|
||||
mesh: {
|
||||
vertices: Float32Array
|
||||
normals: Float32Array | undefined
|
||||
normals: Float32Array
|
||||
indices: Uint32Array | undefined
|
||||
groups: Float32Array | Uint8Array
|
||||
vertexCount: number
|
||||
drawCount: number
|
||||
} | undefined
|
||||
meshes: Mesh[] | undefined
|
||||
values: BaseValues & { readonly uDoubleSided?: ValueCell<any> }
|
||||
values: BaseValues
|
||||
isGeoTexture: boolean
|
||||
mode: MeshMode
|
||||
webgl: WebGLContext | undefined
|
||||
ctx: RuntimeContext
|
||||
}
|
||||
@@ -63,8 +55,7 @@ export type MeshGeoData = {
|
||||
groups: Float32Array | Uint8Array,
|
||||
vertexCount: number,
|
||||
instanceIndex: number,
|
||||
isGeoTexture: boolean,
|
||||
mode: MeshMode
|
||||
isGeoTexture: boolean
|
||||
}
|
||||
|
||||
export abstract class MeshExporter<D extends RenderObjectExportData> implements RenderObjectExporter<D> {
|
||||
@@ -231,7 +222,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
}
|
||||
|
||||
protected static getColor(vertexIndex: number, geoData: MeshGeoData, interpolatedColors?: Uint8Array, interpolatedOverpaint?: Uint8Array): Color {
|
||||
const { values, instanceIndex, isGeoTexture, mode, groups } = geoData;
|
||||
const { values, instanceIndex, isGeoTexture, groups, vertexCount } = geoData;
|
||||
const groupCount = values.uGroupCount.ref.value;
|
||||
const colorType = values.dColorType.ref.value;
|
||||
const uColor = values.uColor.ref.value;
|
||||
@@ -240,12 +231,6 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
const dOverpaint = values.dOverpaint.ref.value;
|
||||
const tOverpaint = values.tOverpaint.ref.value.array;
|
||||
|
||||
let vertexCount = geoData.vertexCount;
|
||||
if (mode === 'lines') {
|
||||
vertexIndex *= 2;
|
||||
vertexCount *= 2;
|
||||
}
|
||||
|
||||
let color: Color;
|
||||
switch (colorType) {
|
||||
case 'uniform':
|
||||
@@ -313,18 +298,12 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
}
|
||||
|
||||
protected static getTransparency(vertexIndex: number, geoData: MeshGeoData, interpolatedTransparency?: Uint8Array): number {
|
||||
const { values, instanceIndex, isGeoTexture, mode, groups } = geoData;
|
||||
const { values, instanceIndex, isGeoTexture, groups, vertexCount } = geoData;
|
||||
const groupCount = values.uGroupCount.ref.value;
|
||||
const dTransparency = values.dTransparency.ref.value;
|
||||
const tTransparency = values.tTransparency.ref.value.array;
|
||||
const transparencyType = values.dTransparencyType.ref.value;
|
||||
|
||||
let vertexCount = geoData.vertexCount;
|
||||
if (mode === 'lines') {
|
||||
vertexIndex *= 2;
|
||||
vertexCount *= 2;
|
||||
}
|
||||
|
||||
let transparency: number = 0;
|
||||
if (dTransparency) {
|
||||
switch (transparencyType) {
|
||||
@@ -350,7 +329,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
return transparency;
|
||||
}
|
||||
|
||||
protected abstract addMeshWithColors(input: AddMeshInput): Promise<void>;
|
||||
protected abstract addMeshWithColors(input: AddMeshInput): void;
|
||||
|
||||
private async addMesh(values: MeshValues, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
const aPosition = values.aPosition.ref.value;
|
||||
@@ -370,132 +349,36 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
drawCount = values.drawCount.ref.value;
|
||||
}
|
||||
|
||||
await this.addMeshWithColors({ mesh: { vertices: aPosition, normals: aNormal, indices, groups: aGroup, vertexCount, drawCount }, meshes: undefined, values, isGeoTexture: false, mode: 'triangles', webgl, ctx });
|
||||
await this.addMeshWithColors({ mesh: { vertices: aPosition, normals: aNormal, indices, groups: aGroup, vertexCount, drawCount }, meshes: undefined, values, isGeoTexture: false, webgl, ctx });
|
||||
}
|
||||
|
||||
private async addLines(values: LinesValues, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
const aStart = values.aStart.ref.value;
|
||||
const aEnd = values.aEnd.ref.value;
|
||||
const aGroup = values.aGroup.ref.value;
|
||||
const vertexCount = (values.uVertexCount.ref.value / 4) * 2;
|
||||
const drawCount = values.drawCount.ref.value / (2 * 3);
|
||||
|
||||
if (this.options.linesAsTriangles) {
|
||||
const start = Vec3();
|
||||
const end = Vec3();
|
||||
|
||||
const instanceCount = values.instanceCount.ref.value;
|
||||
const meshes: Mesh[] = [];
|
||||
|
||||
const radialSegments = 6;
|
||||
const topCap = true;
|
||||
const bottomCap = true;
|
||||
|
||||
for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
|
||||
const state = MeshBuilder.createState(512, 256);
|
||||
|
||||
for (let i = 0, il = vertexCount * 2; i < il; i += 4) {
|
||||
v3fromArray(start, aStart, i * 3);
|
||||
v3fromArray(end, aEnd, i * 3);
|
||||
|
||||
const group = aGroup[i];
|
||||
const radius = MeshExporter.getSize(values, instanceIndex, group) * 0.03;
|
||||
|
||||
const cylinderProps = { radiusTop: radius, radiusBottom: radius, topCap, bottomCap, radialSegments };
|
||||
state.currentGroup = aGroup[i];
|
||||
addCylinder(state, start, end, 1, cylinderProps);
|
||||
}
|
||||
|
||||
meshes.push(MeshBuilder.getMesh(state));
|
||||
}
|
||||
|
||||
await this.addMeshWithColors({ mesh: undefined, meshes, values, isGeoTexture: false, mode: 'triangles', webgl, ctx });
|
||||
} else {
|
||||
const n = vertexCount / 2;
|
||||
const vertices = new Float32Array(n * 2 * 3);
|
||||
for (let i = 0; i < n; ++i) {
|
||||
vertices[i * 6] = aStart[i * 4 * 3];
|
||||
vertices[i * 6 + 1] = aStart[i * 4 * 3 + 1];
|
||||
vertices[i * 6 + 2] = aStart[i * 4 * 3 + 2];
|
||||
|
||||
vertices[i * 6 + 3] = aEnd[i * 4 * 3];
|
||||
vertices[i * 6 + 4] = aEnd[i * 4 * 3 + 1];
|
||||
vertices[i * 6 + 5] = aEnd[i * 4 * 3 + 2];
|
||||
}
|
||||
|
||||
await this.addMeshWithColors({ mesh: { vertices, normals: undefined, indices: undefined, groups: aGroup, vertexCount, drawCount }, meshes: undefined, values, isGeoTexture: false, mode: 'lines', webgl, ctx });
|
||||
}
|
||||
// TODO
|
||||
}
|
||||
|
||||
private async addPoints(values: PointsValues, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
const aPosition = values.aPosition.ref.value;
|
||||
const aGroup = values.aGroup.ref.value;
|
||||
const vertexCount = values.uVertexCount.ref.value;
|
||||
const drawCount = values.drawCount.ref.value;
|
||||
|
||||
if (this.options.pointsAsTriangles) {
|
||||
const center = Vec3();
|
||||
|
||||
const instanceCount = values.instanceCount.ref.value;
|
||||
const meshes: Mesh[] = [];
|
||||
|
||||
const detail = 0;
|
||||
|
||||
for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
|
||||
const state = MeshBuilder.createState(512, 256);
|
||||
|
||||
for (let i = 0; i < vertexCount; ++i) {
|
||||
v3fromArray(center, aPosition, i * 3);
|
||||
|
||||
const group = aGroup[i];
|
||||
const radius = MeshExporter.getSize(values, instanceIndex, group) * 0.03;
|
||||
state.currentGroup = group;
|
||||
addSphere(state, center, radius, detail);
|
||||
}
|
||||
|
||||
meshes.push(MeshBuilder.getMesh(state));
|
||||
}
|
||||
|
||||
await this.addMeshWithColors({ mesh: undefined, meshes, values, isGeoTexture: false, mode: 'triangles', webgl, ctx });
|
||||
} else {
|
||||
await this.addMeshWithColors({ mesh: { vertices: aPosition, normals: undefined, indices: undefined, groups: aGroup, vertexCount, drawCount }, meshes: undefined, values, isGeoTexture: false, mode: 'points', webgl, ctx });
|
||||
}
|
||||
// TODO
|
||||
}
|
||||
|
||||
private async addSpheres(values: SpheresValues, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
const center = Vec3();
|
||||
|
||||
const aPosition = values.centerBuffer.ref.value;
|
||||
const aGroup = values.groupBuffer.ref.value;
|
||||
const aPosition = values.aPosition.ref.value;
|
||||
const aGroup = values.aGroup.ref.value;
|
||||
const instanceCount = values.instanceCount.ref.value;
|
||||
const vertexCount = values.uVertexCount.ref.value;
|
||||
const meshes: Mesh[] = [];
|
||||
|
||||
const sphereCount = vertexCount / 6 * instanceCount;
|
||||
const sphereCount = vertexCount / 4 * instanceCount;
|
||||
let detail: number;
|
||||
switch (this.options.primitivesQuality) {
|
||||
case 'auto':
|
||||
if (sphereCount < 2000) detail = 3;
|
||||
else if (sphereCount < 20000) detail = 2;
|
||||
else detail = 1;
|
||||
break;
|
||||
case 'high':
|
||||
detail = 3;
|
||||
break;
|
||||
case 'medium':
|
||||
detail = 2;
|
||||
break;
|
||||
case 'low':
|
||||
detail = 1;
|
||||
break;
|
||||
default:
|
||||
assertUnreachable(this.options.primitivesQuality);
|
||||
}
|
||||
if (sphereCount < 2000) detail = 3;
|
||||
else if (sphereCount < 20000) detail = 2;
|
||||
else detail = 1;
|
||||
|
||||
for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
|
||||
const state = MeshBuilder.createState(512, 256);
|
||||
|
||||
for (let i = 0; i < sphereCount; ++i) {
|
||||
for (let i = 0; i < vertexCount; i += 4) {
|
||||
v3fromArray(center, aPosition, i * 3);
|
||||
|
||||
const group = aGroup[i];
|
||||
@@ -507,13 +390,12 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
meshes.push(MeshBuilder.getMesh(state));
|
||||
}
|
||||
|
||||
await this.addMeshWithColors({ mesh: undefined, meshes, values, isGeoTexture: false, mode: 'triangles', webgl, ctx });
|
||||
await this.addMeshWithColors({ mesh: undefined, meshes, values, isGeoTexture: false, webgl, ctx });
|
||||
}
|
||||
|
||||
private async addCylinders(values: CylindersValues, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
const start = Vec3();
|
||||
const end = Vec3();
|
||||
const dir = Vec3();
|
||||
|
||||
const aStart = values.aStart.ref.value;
|
||||
const aEnd = values.aEnd.ref.value;
|
||||
@@ -526,24 +408,9 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
|
||||
const cylinderCount = vertexCount / 6 * instanceCount;
|
||||
let radialSegments: number;
|
||||
switch (this.options.primitivesQuality) {
|
||||
case 'auto':
|
||||
if (cylinderCount < 2000) radialSegments = 36;
|
||||
else if (cylinderCount < 20000) radialSegments = 24;
|
||||
else radialSegments = 12;
|
||||
break;
|
||||
case 'high':
|
||||
radialSegments = 36;
|
||||
break;
|
||||
case 'medium':
|
||||
radialSegments = 24;
|
||||
break;
|
||||
case 'low':
|
||||
radialSegments = 12;
|
||||
break;
|
||||
default:
|
||||
assertUnreachable(this.options.primitivesQuality);
|
||||
}
|
||||
if (cylinderCount < 2000) radialSegments = 36;
|
||||
else if (cylinderCount < 20000) radialSegments = 24;
|
||||
else radialSegments = 12;
|
||||
|
||||
for (let instanceIndex = 0; instanceIndex < instanceCount; ++instanceIndex) {
|
||||
const state = MeshBuilder.createState(512, 256);
|
||||
@@ -551,17 +418,13 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
for (let i = 0; i < vertexCount; i += 6) {
|
||||
v3fromArray(start, aStart, i * 3);
|
||||
v3fromArray(end, aEnd, i * 3);
|
||||
v3sub(dir, end, start);
|
||||
|
||||
const group = aGroup[i];
|
||||
const radius = MeshExporter.getSize(values, instanceIndex, group) * aScale[i];
|
||||
const cap = aCap[i];
|
||||
let topCap = cap === 1 || cap === 3;
|
||||
let bottomCap = cap >= 2;
|
||||
if (v3dot(v3unitY, dir) > 0) {
|
||||
[bottomCap, topCap] = [topCap, bottomCap];
|
||||
}
|
||||
const cylinderProps = { radiusTop: radius, radiusBottom: radius, topCap, bottomCap, radialSegments };
|
||||
const topCap = cap === 1 || cap === 3;
|
||||
const bottomCap = cap >= 2;
|
||||
const cylinderProps = { radiusTop: radius, radiusBottom: radius, topCap, bottomCap, radialSegments };
|
||||
state.currentGroup = aGroup[i];
|
||||
addCylinder(state, start, end, 1, cylinderProps);
|
||||
}
|
||||
@@ -569,7 +432,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
meshes.push(MeshBuilder.getMesh(state));
|
||||
}
|
||||
|
||||
await this.addMeshWithColors({ mesh: undefined, meshes, values, isGeoTexture: false, mode: 'triangles', webgl, ctx });
|
||||
await this.addMeshWithColors({ mesh: undefined, meshes, values, isGeoTexture: false, webgl, ctx });
|
||||
}
|
||||
|
||||
private async addTextureMesh(values: TextureMeshValues, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
@@ -594,13 +457,11 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
const vertexCount = values.uVertexCount.ref.value;
|
||||
const drawCount = values.drawCount.ref.value;
|
||||
|
||||
await this.addMeshWithColors({ mesh: { vertices, normals, indices: undefined, groups, vertexCount, drawCount }, meshes: undefined, values, isGeoTexture: true, mode: 'triangles', webgl, ctx });
|
||||
await this.addMeshWithColors({ mesh: { vertices, normals, indices: undefined, groups, vertexCount, drawCount }, meshes: undefined, values, isGeoTexture: true, webgl, ctx });
|
||||
}
|
||||
|
||||
add(renderObject: GraphicsRenderObject, webgl: WebGLContext, ctx: RuntimeContext) {
|
||||
if (!renderObject.state.visible && !this.options.includeHidden) return;
|
||||
if (renderObject.values.drawCount.ref.value === 0) return;
|
||||
if (renderObject.values.instanceCount.ref.value === 0) return;
|
||||
if (!renderObject.state.visible) return;
|
||||
|
||||
switch (renderObject.type) {
|
||||
case 'mesh':
|
||||
@@ -618,13 +479,6 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
|
||||
}
|
||||
}
|
||||
|
||||
protected options = {
|
||||
includeHidden: false,
|
||||
linesAsTriangles: false,
|
||||
pointsAsTriangles: false,
|
||||
primitivesQuality: 'auto' as 'auto' | 'high' | 'medium' | 'low',
|
||||
};
|
||||
|
||||
abstract getData(ctx: RuntimeContext): Promise<D>;
|
||||
|
||||
abstract getBlob(ctx: RuntimeContext): Promise<Blob>;
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
@@ -70,8 +70,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
|
||||
}
|
||||
|
||||
protected async addMeshWithColors(input: AddMeshInput) {
|
||||
const { mesh, values, isGeoTexture, mode, webgl, ctx } = input;
|
||||
if (mode !== 'triangles') return;
|
||||
const { mesh, values, isGeoTexture, webgl, ctx } = input;
|
||||
|
||||
const obj = this.obj;
|
||||
const t = Mat4();
|
||||
@@ -87,19 +86,19 @@ export class ObjExporter extends MeshExporter<ObjData> {
|
||||
const instanceCount = values.uInstanceCount.ref.value;
|
||||
|
||||
let interpolatedColors: Uint8Array | undefined;
|
||||
if (webgl && mesh && (colorType === 'volume' || colorType === 'volumeInstance')) {
|
||||
interpolatedColors = ObjExporter.getInterpolatedColors(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType });
|
||||
if (colorType === 'volume' || colorType === 'volumeInstance') {
|
||||
interpolatedColors = ObjExporter.getInterpolatedColors(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType });
|
||||
}
|
||||
|
||||
let interpolatedOverpaint: Uint8Array | undefined;
|
||||
if (webgl && mesh && overpaintType === 'volumeInstance') {
|
||||
interpolatedOverpaint = ObjExporter.getInterpolatedOverpaint(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType: overpaintType });
|
||||
if (overpaintType === 'volumeInstance') {
|
||||
interpolatedOverpaint = ObjExporter.getInterpolatedOverpaint(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType: overpaintType });
|
||||
}
|
||||
|
||||
let interpolatedTransparency: Uint8Array | undefined;
|
||||
if (webgl && mesh && transparencyType === 'volumeInstance') {
|
||||
if (transparencyType === 'volumeInstance') {
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
interpolatedTransparency = ObjExporter.getInterpolatedTransparency(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType: transparencyType });
|
||||
interpolatedTransparency = ObjExporter.getInterpolatedTransparency(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType: transparencyType });
|
||||
}
|
||||
|
||||
await ctx.update({ isIndeterminate: false, current: 0, max: instanceCount });
|
||||
@@ -127,7 +126,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
|
||||
|
||||
// normal
|
||||
for (let i = 0; i < vertexCount; ++i) {
|
||||
v3transformMat3(tmpV, v3fromArray(tmpV, normals!, i * stride), n);
|
||||
v3transformMat3(tmpV, v3fromArray(tmpV, normals, i * stride), n);
|
||||
StringBuilder.writeSafe(obj, 'vn ');
|
||||
StringBuilder.writeFloat(obj, tmpV[0], 100);
|
||||
StringBuilder.whitespace1(obj);
|
||||
@@ -137,7 +136,7 @@ export class ObjExporter extends MeshExporter<ObjData> {
|
||||
StringBuilder.newline(obj);
|
||||
}
|
||||
|
||||
const geoData = { values, groups, vertexCount, instanceIndex, isGeoTexture, mode };
|
||||
const geoData = { values, groups, vertexCount, instanceIndex, isGeoTexture };
|
||||
|
||||
// color
|
||||
const quantizedColors = new Uint8Array(drawCount * 3);
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
|
||||
*/
|
||||
@@ -30,8 +30,7 @@ export class StlExporter extends MeshExporter<StlData> {
|
||||
private centerTransform: Mat4;
|
||||
|
||||
protected async addMeshWithColors(input: AddMeshInput) {
|
||||
const { values, isGeoTexture, mode, ctx } = input;
|
||||
if (mode !== 'triangles') return;
|
||||
const { values, isGeoTexture, ctx } = input;
|
||||
|
||||
const t = Mat4();
|
||||
const tmpV = Vec3();
|
||||
|
||||
@@ -60,8 +60,6 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
|
||||
}
|
||||
|
||||
componentDidMount() {
|
||||
if (!this.plugin.canvas3d) return;
|
||||
|
||||
const merged = merge(
|
||||
this.controls.behaviors.params,
|
||||
this.plugin.canvas3d!.reprCount
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
/**
|
||||
* Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
@@ -61,8 +61,7 @@ def Material "material${materialKey}"
|
||||
}
|
||||
|
||||
protected async addMeshWithColors(input: AddMeshInput) {
|
||||
const { mesh, values, isGeoTexture, mode, webgl, ctx } = input;
|
||||
if (mode !== 'triangles') return;
|
||||
const { mesh, values, isGeoTexture, webgl, ctx } = input;
|
||||
|
||||
const t = Mat4();
|
||||
const n = Mat3();
|
||||
@@ -79,20 +78,20 @@ def Material "material${materialKey}"
|
||||
const roughness = values.uRoughness.ref.value;
|
||||
|
||||
let interpolatedColors: Uint8Array | undefined;
|
||||
if (webgl && mesh && (colorType === 'volume' || colorType === 'volumeInstance')) {
|
||||
interpolatedColors = UsdzExporter.getInterpolatedColors(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType });
|
||||
if (colorType === 'volume' || colorType === 'volumeInstance') {
|
||||
interpolatedColors = UsdzExporter.getInterpolatedColors(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType });
|
||||
}
|
||||
|
||||
let interpolatedOverpaint: Uint8Array | undefined;
|
||||
if (webgl && mesh && overpaintType === 'volumeInstance') {
|
||||
if (overpaintType === 'volumeInstance') {
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
interpolatedOverpaint = UsdzExporter.getInterpolatedOverpaint(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType: overpaintType });
|
||||
interpolatedOverpaint = UsdzExporter.getInterpolatedOverpaint(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType: overpaintType });
|
||||
}
|
||||
|
||||
let interpolatedTransparency: Uint8Array | undefined;
|
||||
if (webgl && mesh && transparencyType === 'volumeInstance') {
|
||||
if (transparencyType === 'volumeInstance') {
|
||||
const stride = isGeoTexture ? 4 : 3;
|
||||
interpolatedTransparency = UsdzExporter.getInterpolatedTransparency(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values, stride, colorType: transparencyType });
|
||||
interpolatedTransparency = UsdzExporter.getInterpolatedTransparency(webgl!, { vertices: mesh!.vertices, vertexCount: mesh!.vertexCount, values, stride, colorType: transparencyType });
|
||||
}
|
||||
|
||||
await ctx.update({ isIndeterminate: false, current: 0, max: instanceCount });
|
||||
@@ -124,7 +123,7 @@ def Material "material${materialKey}"
|
||||
|
||||
// normal
|
||||
for (let i = 0; i < vertexCount; ++i) {
|
||||
v3transformMat3(tmpV, v3fromArray(tmpV, normals!, i * stride), n);
|
||||
v3transformMat3(tmpV, v3fromArray(tmpV, normals, i * stride), n);
|
||||
StringBuilder.writeSafe(normalBuilder, (i === 0) ? '(' : ',(');
|
||||
StringBuilder.writeFloat(normalBuilder, tmpV[0], 100);
|
||||
StringBuilder.writeSafe(normalBuilder, ',');
|
||||
@@ -134,7 +133,7 @@ def Material "material${materialKey}"
|
||||
StringBuilder.writeSafe(normalBuilder, ')');
|
||||
}
|
||||
|
||||
const geoData = { values, groups, vertexCount, instanceIndex, isGeoTexture, mode };
|
||||
const geoData = { values, groups, vertexCount, instanceIndex, isGeoTexture };
|
||||
|
||||
// face
|
||||
for (let i = 0; i < drawCount; ++i) {
|
||||
|
||||
@@ -1,187 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
/** Testing examples for using mesh-extension.ts. */
|
||||
|
||||
import { CIF } from '../../mol-io/reader/cif';
|
||||
import { Volume } from '../../mol-model/volume';
|
||||
import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
|
||||
import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
|
||||
import { PluginStateObject } from '../../mol-plugin-state/objects';
|
||||
import { StateTransforms } from '../../mol-plugin-state/transforms';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { StateObjectSelector } from '../../mol-state';
|
||||
import { Asset } from '../../mol-util/assets';
|
||||
import { Color } from '../../mol-util/color';
|
||||
import { ParamDefinition } from '../../mol-util/param-definition';
|
||||
|
||||
import { createMeshFromUrl } from './mesh-extension';
|
||||
import { MeshServerInfo } from './mesh-streaming/server-info';
|
||||
import { InitMeshStreaming } from './mesh-streaming/transformers';
|
||||
import * as MeshUtils from './mesh-utils';
|
||||
|
||||
|
||||
export const DB_URL = '/db'; // local
|
||||
|
||||
|
||||
export async function runMeshExtensionExamples(plugin: PluginContext, db_url: string = DB_URL) {
|
||||
console.time('TIME MESH EXAMPLES');
|
||||
// await runIsosurfaceExample(plugin, db_url);
|
||||
// await runMolsurfaceExample(plugin);
|
||||
|
||||
// Focused Ion Beam-Scanning Electron Microscopy of mitochondrial reticulum in murine skeletal muscle: https://www.ebi.ac.uk/empiar/EMPIAR-10070/
|
||||
// await runMeshExample(plugin, 'all', db_url);
|
||||
// await runMeshExample(plugin, 'fg', db_url);
|
||||
// await runMultimeshExample(plugin, 'fg', 'worst', db_url);
|
||||
// await runCifMeshExample(plugin);
|
||||
// await runMeshExample2(plugin, 'fg');
|
||||
await runMeshStreamingExample(plugin);
|
||||
|
||||
console.timeEnd('TIME MESH EXAMPLES');
|
||||
}
|
||||
|
||||
/** Example for downloading multiple separate segments, each containing 1 mesh. */
|
||||
export async function runMeshExample(plugin: PluginContext, segments: 'fg' | 'all', db_url: string = DB_URL) {
|
||||
const detail = 2;
|
||||
const segmentIds = (segments === 'all') ?
|
||||
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17] // segment-16 has no detail-2
|
||||
: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17]; // segment-13 and segment-15 are quasi background
|
||||
|
||||
for (const segmentId of segmentIds) {
|
||||
await createMeshFromUrl(plugin, `${db_url}/empiar-10070-mesh-rounded/segment-${segmentId}/detail-${detail}`, segmentId, detail, true, undefined);
|
||||
}
|
||||
}
|
||||
|
||||
/** Example for downloading multiple separate segments, each containing 1 mesh. */
|
||||
export async function runMeshExample2(plugin: PluginContext, segments: 'one' | 'few' | 'fg' | 'all') {
|
||||
const detail = 1;
|
||||
const segmentIds = (segments === 'one') ? [15]
|
||||
: (segments === 'few') ? [1, 4, 7, 10, 16]
|
||||
: (segments === 'all') ? [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17] // segment-16 has no detail-2
|
||||
: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17]; // segment-13 and segment-15 are quasi background
|
||||
|
||||
for (const segmentId of segmentIds) {
|
||||
await createMeshFromUrl(plugin, `http://localhost:9000/v2/empiar/empiar-10070/mesh_bcif/${segmentId}/${detail}`, segmentId, detail, false, undefined);
|
||||
}
|
||||
}
|
||||
|
||||
/** Example for downloading a single segment containing multiple meshes. */
|
||||
export async function runMultimeshExample(plugin: PluginContext, segments: 'fg' | 'all', detailChoice: 'best' | 'worst', db_url: string = DB_URL) {
|
||||
const urlDetail = (detailChoice === 'best') ? '2' : 'worst';
|
||||
const numDetail = (detailChoice === 'best') ? 2 : 1000;
|
||||
await createMeshFromUrl(plugin, `${db_url}/empiar-10070-multimesh-rounded/segments-${segments}/detail-${urlDetail}`, 0, numDetail, false, undefined);
|
||||
}
|
||||
|
||||
export async function runMeshStreamingExample(plugin: PluginContext, source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070', serverUrl?: string, parent?: StateObjectSelector) {
|
||||
const params = ParamDefinition.getDefaultValues(MeshServerInfo.Params);
|
||||
if (serverUrl) params.serverUrl = serverUrl;
|
||||
params.source = source;
|
||||
params.entryId = entryId;
|
||||
await plugin.runTask(plugin.state.data.applyAction(InitMeshStreaming, params, parent?.ref), { useOverlay: false });
|
||||
}
|
||||
|
||||
/** Example for downloading a protein structure and visualizing molecular surface. */
|
||||
export async function runMolsurfaceExample(plugin: PluginContext) {
|
||||
const entryId = 'pdb-7etq';
|
||||
|
||||
// Node "https://www.ebi.ac.uk/pdbe/entry-files/download/7etq.bcif" ("transformer": "ms-plugin.download") -> var data
|
||||
const data = await plugin.builders.data.download({ url: 'https://www.ebi.ac.uk/pdbe/entry-files/download/7etq.bcif', isBinary: true }, { state: { isGhost: false } });
|
||||
console.log('formats:', plugin.dataFormats.list);
|
||||
|
||||
// Node "CIF File" ("transformer": "ms-plugin.parse-cif")
|
||||
// Node "7ETQ 1 model" ("transformer": "ms-plugin.trajectory-from-mmcif") -> var trajectory
|
||||
const parsed = await plugin.dataFormats.get('mmcif')!.parse(plugin, data, { entryId });
|
||||
const trajectory: StateObjectSelector<PluginStateObject.Molecule.Trajectory> = parsed.trajectory;
|
||||
console.log('parsed', parsed);
|
||||
console.log('trajectory', trajectory);
|
||||
|
||||
// Node "Model 1" ("transformer": "ms-plugin.model-from-trajectory") -> var model
|
||||
const model = await plugin.build().to(trajectory).apply(StateTransforms.Model.ModelFromTrajectory).commit();
|
||||
console.log('model:', model);
|
||||
|
||||
// Node "Model 91 elements" ("transformer": "ms-plugin.structure-from-model") -> var structure
|
||||
const structure = await plugin.build().to(model).apply(StateTransforms.Model.StructureFromModel,).commit();
|
||||
console.log('structure:', structure);
|
||||
|
||||
// Node "Molecular Surface" ("transformer": "ms-plugin.structure-representation-3d") -> var repr
|
||||
const reprParams = createStructureRepresentationParams(plugin, undefined, { type: 'molecular-surface' });
|
||||
const repr = await plugin.build().to(structure).apply(StateTransforms.Representation.StructureRepresentation3D, reprParams).commit();
|
||||
console.log('repr:', repr);
|
||||
}
|
||||
|
||||
/** Example for downloading an EMDB density data and visualizing isosurface. */
|
||||
export async function runIsosurfaceExample(plugin: PluginContext, db_url: string = DB_URL) {
|
||||
const entryId = 'emd-1832';
|
||||
const isoLevel = 2.73;
|
||||
|
||||
let root = await plugin.build();
|
||||
const data = await plugin.builders.data.download({ url: `${db_url}/emd-1832-box`, isBinary: true }, { state: { isGhost: false } });
|
||||
const parsed = await plugin.dataFormats.get('dscif')!.parse(plugin, data, { entryId });
|
||||
|
||||
const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[0] ?? parsed.volume;
|
||||
const volumeData = volume.cell!.obj!.data;
|
||||
console.log('data:', data);
|
||||
console.log('parsed:', parsed);
|
||||
console.log('volume:', volume);
|
||||
console.log('volumeData:', volumeData);
|
||||
|
||||
root = await plugin.build();
|
||||
console.log('root:', root);
|
||||
console.log('to:', root.to(volume));
|
||||
console.log('toRoot:', root.toRoot());
|
||||
|
||||
let volumeParams;
|
||||
volumeParams = createVolumeRepresentationParams(plugin, volumeData, {
|
||||
type: 'isosurface',
|
||||
typeParams: {
|
||||
alpha: 0.5,
|
||||
isoValue: Volume.adjustedIsoValue(volumeData, isoLevel, 'relative'),
|
||||
visuals: ['solid'],
|
||||
sizeFactor: 1,
|
||||
},
|
||||
color: 'uniform',
|
||||
colorParams: { value: Color(0x00aaaa) },
|
||||
|
||||
});
|
||||
root.to(volume).apply(StateTransforms.Representation.VolumeRepresentation3D, volumeParams);
|
||||
|
||||
volumeParams = createVolumeRepresentationParams(plugin, volumeData, {
|
||||
type: 'isosurface',
|
||||
typeParams: {
|
||||
alpha: 1.0,
|
||||
isoValue: Volume.adjustedIsoValue(volumeData, isoLevel, 'relative'),
|
||||
visuals: ['wireframe'],
|
||||
sizeFactor: 1,
|
||||
},
|
||||
color: 'uniform',
|
||||
colorParams: { value: Color(0x8800aa) },
|
||||
|
||||
});
|
||||
root.to(volume).apply(StateTransforms.Representation.VolumeRepresentation3D, volumeParams);
|
||||
await root.commit();
|
||||
}
|
||||
|
||||
|
||||
export async function runCifMeshExample(plugin: PluginContext, api: string = 'http://localhost:9000/v2',
|
||||
source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070',
|
||||
segmentId: number = 1, detail: number = 10,
|
||||
) {
|
||||
const url = `${api}/${source}/${entryId}/mesh_bcif/${segmentId}/${detail}`;
|
||||
getMeshFromBcif(plugin, url);
|
||||
}
|
||||
|
||||
async function getMeshFromBcif(plugin: PluginContext, url: string) {
|
||||
const urlAsset = Asset.getUrlAsset(plugin.managers.asset, url);
|
||||
const asset = await plugin.runTask(plugin.managers.asset.resolve(urlAsset, 'binary'));
|
||||
const parsed = await plugin.runTask(CIF.parseBinary(asset.data));
|
||||
if (parsed.isError) {
|
||||
plugin.log.error('VolumeStreaming, parsing CIF: ' + parsed.toString());
|
||||
return;
|
||||
}
|
||||
console.log('blocks:', parsed.result.blocks);
|
||||
const mesh = await MeshUtils.meshFromCif(parsed.result);
|
||||
console.log(mesh);
|
||||
}
|
||||
@@ -1,40 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Column, Database } from '../../mol-data/db';
|
||||
import { CifFrame } from '../../mol-io/reader/cif';
|
||||
import { toDatabase } from '../../mol-io/reader/cif/schema';
|
||||
|
||||
|
||||
const int = Column.Schema.int;
|
||||
const float = Column.Schema.float;
|
||||
|
||||
|
||||
// TODO in future, move to molstar/src/mol-io/reader/cif/schema/mesh.ts
|
||||
export const Mesh_Data_Schema = {
|
||||
mesh: {
|
||||
id: int,
|
||||
},
|
||||
mesh_vertex: {
|
||||
mesh_id: int,
|
||||
vertex_id: int,
|
||||
x: float,
|
||||
y: float,
|
||||
z: float,
|
||||
},
|
||||
/** Table of triangles, 3 rows per triangle */
|
||||
mesh_triangle: {
|
||||
mesh_id: int,
|
||||
/** Indices of vertices within mesh */
|
||||
vertex_id: int,
|
||||
}
|
||||
};
|
||||
export type Mesh_Data_Schema = typeof Mesh_Data_Schema;
|
||||
export interface Mesh_Data_Database extends Database<Mesh_Data_Schema> {}
|
||||
|
||||
|
||||
// TODO in future, move to molstar/src/mol-io/reader/cif.ts: CIF.schema.mesh
|
||||
export const CIF_schema_mesh = (frame: CifFrame) => toDatabase<Mesh_Data_Schema, Mesh_Data_Database>(Mesh_Data_Schema, frame);
|
||||
@@ -1,223 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
/** Defines new types of State tree transformers for dealing with mesh data. */
|
||||
|
||||
|
||||
import { BaseGeometry, VisualQuality, VisualQualityOptions } from '../../mol-geo/geometry/base';
|
||||
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
|
||||
import { CifFile } from '../../mol-io/reader/cif';
|
||||
import { Box3D } from '../../mol-math/geometry';
|
||||
import { Vec3 } from '../../mol-math/linear-algebra';
|
||||
import { Shape } from '../../mol-model/shape';
|
||||
import { ShapeProvider } from '../../mol-model/shape/provider';
|
||||
import { PluginStateObject } from '../../mol-plugin-state/objects';
|
||||
import { StateTransforms } from '../../mol-plugin-state/transforms';
|
||||
import { Download } from '../../mol-plugin-state/transforms/data';
|
||||
import { ShapeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { StateObjectRef, StateObjectSelector, StateTransformer } from '../../mol-state';
|
||||
import { Task } from '../../mol-task';
|
||||
import { Color } from '../../mol-util/color';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import * as MeshUtils from './mesh-utils';
|
||||
|
||||
|
||||
export const BACKGROUND_OPACITY = 0.2;
|
||||
export const FOREROUND_OPACITY = 1;
|
||||
|
||||
export const VolsegTransform: StateTransformer.Builder.Root = StateTransformer.builderFactory('volseg');
|
||||
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
// Parsed data
|
||||
|
||||
/** Data type for `MeshlistStateObject` - list of meshes */
|
||||
export interface MeshlistData {
|
||||
segmentId: number,
|
||||
segmentName: string,
|
||||
detail: number,
|
||||
meshIds: number[],
|
||||
mesh: Mesh,
|
||||
/** Reference to the object which created this meshlist (e.g. `MeshStreaming.Behavior`) */
|
||||
ownerId?: string,
|
||||
}
|
||||
|
||||
export namespace MeshlistData {
|
||||
export function empty(): MeshlistData {
|
||||
return {
|
||||
segmentId: 0,
|
||||
segmentName: 'Empty',
|
||||
detail: 0,
|
||||
meshIds: [],
|
||||
mesh: Mesh.createEmpty(),
|
||||
};
|
||||
};
|
||||
export async function fromCIF(data: CifFile, segmentId: number, segmentName: string, detail: number): Promise<MeshlistData> {
|
||||
const { mesh, meshIds } = await MeshUtils.meshFromCif(data);
|
||||
return {
|
||||
segmentId,
|
||||
segmentName,
|
||||
detail,
|
||||
meshIds,
|
||||
mesh,
|
||||
};
|
||||
}
|
||||
export function stats(meshListData: MeshlistData): string {
|
||||
return `Meshlist "${meshListData.segmentName}" (detail ${meshListData.detail}): ${meshListData.meshIds.length} meshes, ${meshListData.mesh.vertexCount} vertices, ${meshListData.mesh.triangleCount} triangles`;
|
||||
}
|
||||
export function getShape(data: MeshlistData, color: Color): Shape<Mesh> {
|
||||
const mesh = data.mesh;
|
||||
const meshShape: Shape<Mesh> = Shape.create(data.segmentName, data, mesh,
|
||||
() => color,
|
||||
() => 1,
|
||||
// group => `${data.segmentName} | Segment ${data.segmentId} | Detail ${data.detail} | Mesh ${group}`,
|
||||
group => data.segmentName,
|
||||
);
|
||||
return meshShape;
|
||||
}
|
||||
|
||||
export function combineBBoxes(boxes: (Box3D | null)[]): Box3D | null {
|
||||
let result = null;
|
||||
for (const box of boxes) {
|
||||
if (!box) continue;
|
||||
if (result) {
|
||||
Vec3.min(result.min, result.min, box.min);
|
||||
Vec3.max(result.max, result.max, box.max);
|
||||
} else {
|
||||
result = Box3D.zero();
|
||||
Box3D.copy(result, box);
|
||||
}
|
||||
}
|
||||
return result;
|
||||
}
|
||||
export function bbox(data: MeshlistData): Box3D | null {
|
||||
return MeshUtils.bbox(data.mesh);
|
||||
}
|
||||
|
||||
export function allVerticesUsed(data: MeshlistData): boolean {
|
||||
const unusedVertices = new Set();
|
||||
for (let i = 0; i < data.mesh.vertexCount; i++) {
|
||||
unusedVertices.add(i);
|
||||
}
|
||||
for (let i = 0; i < 3 * data.mesh.triangleCount; i++) {
|
||||
const v = data.mesh.vertexBuffer.ref.value[i];
|
||||
unusedVertices.delete(v);
|
||||
}
|
||||
return unusedVertices.size === 0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
// Raw Data -> Parsed data
|
||||
|
||||
export class MeshlistStateObject extends PluginStateObject.Create<MeshlistData>({ name: 'Parsed Meshlist', typeClass: 'Object' }) { }
|
||||
|
||||
export const ParseMeshlistTransformer = VolsegTransform({
|
||||
name: 'meshlist-from-string',
|
||||
from: PluginStateObject.Format.Cif,
|
||||
to: MeshlistStateObject,
|
||||
params: {
|
||||
label: PD.Text(MeshlistStateObject.type.name, { isHidden: true }),
|
||||
segmentId: PD.Numeric(1, {}, { isHidden: true }),
|
||||
segmentName: PD.Text('Segment'),
|
||||
detail: PD.Numeric(1, {}, { isHidden: true }),
|
||||
/** Reference to the object which manages this meshlist (e.g. `MeshStreaming.Behavior`) */
|
||||
ownerId: PD.Text('', { isHidden: true }),
|
||||
}
|
||||
})({
|
||||
apply({ a, params }, globalCtx) { // `a` is the parent node, params are 2nd argument to To.apply(), `globalCtx` is the plugin
|
||||
return Task.create('Create Parsed Meshlist', async ctx => {
|
||||
const meshlistData = await MeshlistData.fromCIF(a.data, params.segmentId, params.segmentName, params.detail);
|
||||
meshlistData.ownerId = params.ownerId;
|
||||
const es = meshlistData.meshIds.length === 1 ? '' : 'es';
|
||||
return new MeshlistStateObject(meshlistData, { label: params.label, description: `${meshlistData.segmentName} (${meshlistData.meshIds.length} mesh${es})` });
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
// Parsed data -> Shape
|
||||
|
||||
/** Data type for PluginStateObject.Shape.Provider */
|
||||
type MeshShapeProvider = ShapeProvider<MeshlistData, Mesh, Mesh.Params>;
|
||||
namespace MeshShapeProvider {
|
||||
export function fromMeshlistData(meshlist: MeshlistData, color?: Color): MeshShapeProvider {
|
||||
const theColor = color ?? MeshUtils.ColorGenerator.next().value;
|
||||
return {
|
||||
label: 'Mesh',
|
||||
data: meshlist,
|
||||
params: meshShapeProviderParams,
|
||||
geometryUtils: Mesh.Utils,
|
||||
getShape: (ctx, data: MeshlistData) => MeshlistData.getShape(data, theColor),
|
||||
};
|
||||
}
|
||||
}
|
||||
|
||||
const meshShapeProviderParams: Mesh.Params = {
|
||||
...Mesh.Params,
|
||||
quality: PD.Select<VisualQuality>('custom', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }), // use 'custom' when wanting to apply doubleSided
|
||||
doubleSided: PD.Boolean(true, BaseGeometry.CustomQualityParamInfo),
|
||||
// set `flatShaded`: true to see the real mesh vertices and triangles
|
||||
transparentBackfaces: PD.Select('on', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory), // 'on' means: show backfaces with correct opacity, even when opacity < 1 (requires doubleSided) ¯\_(ツ)_/¯
|
||||
};
|
||||
|
||||
|
||||
export const MeshShapeTransformer = VolsegTransform({
|
||||
name: 'shape-from-meshlist',
|
||||
display: { name: 'Shape from Meshlist', description: 'Create Shape from Meshlist data' },
|
||||
from: MeshlistStateObject,
|
||||
to: PluginStateObject.Shape.Provider,
|
||||
params: {
|
||||
color: PD.Value<Color | undefined>(undefined), // undefined means random color
|
||||
},
|
||||
})({
|
||||
apply({ a, params }) {
|
||||
const shapeProvider = MeshShapeProvider.fromMeshlistData(a.data, params.color);
|
||||
return new PluginStateObject.Shape.Provider(shapeProvider, { label: PluginStateObject.Shape.Provider.type.name, description: a.description });
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
|
||||
|
||||
/** Download data and create state tree hierarchy down to visual representation. */
|
||||
export async function createMeshFromUrl(plugin: PluginContext, meshDataUrl: string, segmentId: number, detail: number,
|
||||
collapseTree: boolean, color?: Color, parent?: StateObjectSelector | StateObjectRef, transparentIfBboxAbove?: number,
|
||||
name?: string, ownerId?: string) {
|
||||
|
||||
const update = parent ? plugin.build().to(parent) : plugin.build().toRoot();
|
||||
const rawDataNodeRef = update.apply(Download,
|
||||
{ url: meshDataUrl, isBinary: true, label: `Downloaded Data ${segmentId}` },
|
||||
{ state: { isCollapsed: collapseTree } }
|
||||
).ref;
|
||||
const parsedDataNode = await update.to(rawDataNodeRef)
|
||||
.apply(StateTransforms.Data.ParseCif)
|
||||
.apply(ParseMeshlistTransformer,
|
||||
{ label: undefined, segmentId: segmentId, segmentName: name ?? `Segment ${segmentId}`, detail: detail, ownerId: ownerId },
|
||||
{}
|
||||
)
|
||||
.commit();
|
||||
|
||||
let transparent = false;
|
||||
if (transparentIfBboxAbove !== undefined && parsedDataNode.data) {
|
||||
const bbox = MeshlistData.bbox(parsedDataNode.data) || Box3D.zero();
|
||||
transparent = Box3D.volume(bbox) > transparentIfBboxAbove;
|
||||
}
|
||||
|
||||
await plugin.build().to(parsedDataNode)
|
||||
.apply(MeshShapeTransformer, { color: color },)
|
||||
.apply(ShapeRepresentation3D,
|
||||
{ alpha: transparent ? BACKGROUND_OPACITY : FOREROUND_OPACITY },
|
||||
{ tags: ['mesh-segment-visual', `segment-${segmentId}`] }
|
||||
)
|
||||
.commit();
|
||||
|
||||
return rawDataNodeRef;
|
||||
}
|
||||
@@ -1,332 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { distinctUntilChanged, map } from 'rxjs';
|
||||
|
||||
import { CIF } from '../../../mol-io/reader/cif';
|
||||
import { Box3D } from '../../../mol-math/geometry';
|
||||
import { PluginStateObject } from '../../../mol-plugin-state/objects';
|
||||
import { PluginBehavior } from '../../../mol-plugin/behavior';
|
||||
import { PluginCommand } from '../../../mol-plugin/command';
|
||||
import { PluginCommands } from '../../../mol-plugin/commands';
|
||||
import { PluginContext } from '../../../mol-plugin/context';
|
||||
import { UUID } from '../../../mol-util';
|
||||
import { Asset } from '../../../mol-util/assets';
|
||||
import { Color } from '../../../mol-util/color';
|
||||
import { ColorNames } from '../../../mol-util/color/names';
|
||||
import { Choice } from '../../../mol-util/param-choice';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
|
||||
import { MetadataWrapper } from '../../volumes-and-segmentations/volseg-api/utils';
|
||||
|
||||
import { MeshlistData } from '../mesh-extension';
|
||||
import { MeshServerInfo } from './server-info';
|
||||
|
||||
|
||||
const DEFAULT_SEGMENT_NAME = 'Untitled segment';
|
||||
const DEFAULT_SEGMENT_COLOR = ColorNames.lightgray;
|
||||
export const NO_SEGMENT = -1;
|
||||
/** Maximum (worst) detail level available in GUI (TODO set actual maximum possible value) */
|
||||
const MAX_DETAIL = 10;
|
||||
const DEFAULT_DETAIL = 7; // TODO decide a reasonable default
|
||||
/** Segments whose bounding box volume is above this value (relative to the overall bounding box) are considered as background segments */
|
||||
export const BACKGROUND_SEGMENT_VOLUME_THRESHOLD = 0.5;
|
||||
|
||||
|
||||
export class MeshStreaming extends PluginStateObject.CreateBehavior<MeshStreaming.Behavior>({ name: 'Mesh Streaming' }) { }
|
||||
|
||||
export namespace MeshStreaming {
|
||||
|
||||
export namespace Params {
|
||||
export const ViewTypeChoice = new Choice({ off: 'Off', select: 'Select', all: 'All' }, 'select'); // TODO add camera target?
|
||||
export type ViewType = Choice.Values<typeof ViewTypeChoice>;
|
||||
|
||||
export function create(options: MeshServerInfo.Data) {
|
||||
return {
|
||||
view: PD.MappedStatic('select', {
|
||||
'off': PD.Group({}),
|
||||
'select': PD.Group({
|
||||
baseDetail: PD.Numeric(DEFAULT_DETAIL, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for the non-selected segments (lower number = better)' }),
|
||||
focusDetail: PD.Numeric(1, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for the selected segment (lower number = better)' }),
|
||||
selectedSegment: PD.Numeric(NO_SEGMENT, {}, { isHidden: true }),
|
||||
}, { isFlat: true }),
|
||||
'all': PD.Group({
|
||||
detail: PD.Numeric(DEFAULT_DETAIL, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for all segments (lower number = better)' })
|
||||
}, { isFlat: true }),
|
||||
}, { description: '"Off" hides all segments. \n"Select" shows all segments in lower detail, clicked segment in better detail. "All" shows all segment in the same level.' }),
|
||||
};
|
||||
}
|
||||
|
||||
export type Definition = ReturnType<typeof create>
|
||||
export type Values = PD.Values<Definition>
|
||||
|
||||
export function copyValues(params: Values): Values {
|
||||
return {
|
||||
view: {
|
||||
name: params.view.name,
|
||||
params: { ...params.view.params } as any,
|
||||
}
|
||||
};
|
||||
}
|
||||
export function valuesEqual(p: Values, q: Values): boolean {
|
||||
if (p.view.name !== q.view.name) return false;
|
||||
for (const key in p.view.params) {
|
||||
if ((p.view.params as any)[key] !== (q.view.params as any)[key]) return false;
|
||||
}
|
||||
return true;
|
||||
}
|
||||
export function detailsEqual(p: Values, q: Values): boolean {
|
||||
switch (p.view.name) {
|
||||
case 'off':
|
||||
return q.view.name === 'off';
|
||||
case 'select':
|
||||
return q.view.name === 'select' && p.view.params.baseDetail === q.view.params.baseDetail && p.view.params.focusDetail === q.view.params.focusDetail;
|
||||
case 'all':
|
||||
return q.view.name === 'all' && p.view.params.detail === q.view.params.detail;
|
||||
default:
|
||||
throw new Error('Not implemented');
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
export interface VisualInfo {
|
||||
tag: string, // e.g. high-2, low-1 // ? remove if can be omitted
|
||||
segmentId: number, // ? remove if unused
|
||||
segmentName: string, // ? remove if unused
|
||||
detailType: VisualInfo.DetailType, // ? remove if unused
|
||||
detail: number, // ? remove if unused
|
||||
color: Color, // move to MeshlistData?
|
||||
visible: boolean,
|
||||
data?: MeshlistData,
|
||||
}
|
||||
export namespace VisualInfo {
|
||||
export type DetailType = 'low' | 'high';
|
||||
export const DetailTypes: DetailType[] = ['low', 'high'];
|
||||
export function tagFor(segmentId: number, detail: DetailType) {
|
||||
return `${detail}-${segmentId}`;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
export class Behavior extends PluginBehavior.WithSubscribers<Params.Values> {
|
||||
private id: string;
|
||||
private ref: string = '';
|
||||
public parentData: MeshServerInfo.Data;
|
||||
private metadata?: MetadataWrapper;
|
||||
public visuals?: { [tag: string]: VisualInfo };
|
||||
public backgroundSegments: { [segmentId: number]: boolean } = {};
|
||||
private focusObservable = this.plugin.behaviors.interaction.click.pipe( // QUESTION is this OK way to get focused segment?
|
||||
map(evt => evt.current.loci),
|
||||
map(loci => (loci.kind === 'group-loci') ? loci.shape.sourceData as MeshlistData : null),
|
||||
map(data => (data?.ownerId === this.id) ? data : null), // do not process shapes created by others
|
||||
distinctUntilChanged((old, current) => old?.segmentId === current?.segmentId),
|
||||
);
|
||||
private focusSubscription?: PluginCommand.Subscription = undefined;
|
||||
private backgroundSegmentsInitialized = false;
|
||||
|
||||
constructor(plugin: PluginContext, data: MeshServerInfo.Data, params: Params.Values) {
|
||||
super(plugin, params);
|
||||
this.id = UUID.create22();
|
||||
this.parentData = data;
|
||||
}
|
||||
|
||||
register(ref: string): void {
|
||||
this.ref = ref;
|
||||
}
|
||||
|
||||
unregister(): void {
|
||||
if (this.focusSubscription) {
|
||||
this.focusSubscription.unsubscribe();
|
||||
this.focusSubscription = undefined;
|
||||
}
|
||||
// TODO empty cache here (if used)
|
||||
}
|
||||
|
||||
selectSegment(segmentId: number) {
|
||||
if (this.params.view.name === 'select') {
|
||||
if (this.params.view.params.selectedSegment === segmentId) return;
|
||||
const newParams = Params.copyValues(this.params);
|
||||
if (newParams.view.name === 'select') {
|
||||
newParams.view.params.selectedSegment = segmentId;
|
||||
}
|
||||
const state = this.plugin.state.data;
|
||||
const update = state.build().to(this.ref).update(newParams);
|
||||
PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotUpdateCurrent: true } });
|
||||
}
|
||||
}
|
||||
|
||||
async update(params: Params.Values) {
|
||||
const oldParams = this.params;
|
||||
this.params = params;
|
||||
|
||||
if (!this.metadata) {
|
||||
const response = await fetch(this.getMetadataUrl());
|
||||
const rawMetadata = await response.json();
|
||||
this.metadata = new MetadataWrapper(rawMetadata);
|
||||
}
|
||||
|
||||
if (!this.visuals) {
|
||||
this.initVisualInfos();
|
||||
} else if (!Params.detailsEqual(this.params, oldParams)) {
|
||||
this.updateVisualInfoDetails();
|
||||
}
|
||||
|
||||
switch (params.view.name) {
|
||||
case 'off':
|
||||
await this.disableVisuals();
|
||||
break;
|
||||
case 'select':
|
||||
await this.enableVisuals(params.view.params.selectedSegment);
|
||||
break;
|
||||
case 'all':
|
||||
await this.enableVisuals();
|
||||
break;
|
||||
default:
|
||||
throw new Error('Not implemented');
|
||||
}
|
||||
if (params.view.name !== 'off' && !this.backgroundSegmentsInitialized) {
|
||||
this.guessBackgroundSegments();
|
||||
this.backgroundSegmentsInitialized = true;
|
||||
}
|
||||
if (params.view.name === 'select' && !this.focusSubscription) {
|
||||
this.focusSubscription = this.subscribeObservable(this.focusObservable, data => { this.selectSegment(data?.segmentId ?? NO_SEGMENT); });
|
||||
} else if (params.view.name !== 'select' && this.focusSubscription) {
|
||||
this.focusSubscription.unsubscribe();
|
||||
this.focusSubscription = undefined;
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
private getMetadataUrl() {
|
||||
return `${this.parentData.serverUrl}/${this.parentData.source}/${this.parentData.entryId}/metadata`;
|
||||
}
|
||||
|
||||
private getMeshUrl(segment: number, detail: number) {
|
||||
return `${this.parentData.serverUrl}/${this.parentData.source}/${this.parentData.entryId}/mesh_bcif/${segment}/${detail}`;
|
||||
}
|
||||
|
||||
private initVisualInfos() {
|
||||
const visuals: { [tag: string]: VisualInfo } = {};
|
||||
for (const segid of this.metadata!.meshSegmentIds) {
|
||||
const name = this.metadata?.getSegment(segid)?.biological_annotation.name ?? DEFAULT_SEGMENT_NAME;
|
||||
const color = this.metadata?.getSegmentColor(segid) ?? DEFAULT_SEGMENT_COLOR;
|
||||
for (const detailType of VisualInfo.DetailTypes) {
|
||||
const visual: VisualInfo = {
|
||||
tag: VisualInfo.tagFor(segid, detailType),
|
||||
segmentId: segid,
|
||||
segmentName: name,
|
||||
detailType: detailType,
|
||||
detail: -1, // to be set at the end
|
||||
color: color,
|
||||
visible: false,
|
||||
data: undefined,
|
||||
};
|
||||
visuals[visual.tag] = visual;
|
||||
}
|
||||
}
|
||||
this.visuals = visuals;
|
||||
this.updateVisualInfoDetails();
|
||||
}
|
||||
private updateVisualInfoDetails() {
|
||||
let highDetail: number | undefined;
|
||||
let lowDetail: number | undefined;
|
||||
switch (this.params.view.name) {
|
||||
case 'off':
|
||||
lowDetail = undefined;
|
||||
highDetail = undefined;
|
||||
break;
|
||||
case 'select':
|
||||
lowDetail = this.params.view.params.baseDetail;
|
||||
highDetail = this.params.view.params.focusDetail;
|
||||
break;
|
||||
case 'all':
|
||||
lowDetail = this.params.view.params.detail;
|
||||
highDetail = undefined;
|
||||
break;
|
||||
}
|
||||
for (const tag in this.visuals) {
|
||||
const visual = this.visuals[tag];
|
||||
const preferredDetail = (visual.detailType === 'high') ? highDetail : lowDetail;
|
||||
if (preferredDetail !== undefined) {
|
||||
visual.detail = this.metadata!.getSufficientMeshDetail(visual.segmentId, preferredDetail);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private async enableVisuals(highDetailSegment?: number) {
|
||||
for (const tag in this.visuals) {
|
||||
const visual = this.visuals[tag];
|
||||
const requiredDetailType = visual.segmentId === highDetailSegment ? 'high' : 'low';
|
||||
if (visual.detailType === requiredDetailType) {
|
||||
visual.data = await this.getMeshData(visual);
|
||||
visual.visible = true;
|
||||
} else {
|
||||
visual.visible = false;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private async disableVisuals() {
|
||||
for (const tag in this.visuals) {
|
||||
const visual = this.visuals[tag];
|
||||
visual.visible = false;
|
||||
}
|
||||
}
|
||||
|
||||
/** Fetch data in current `visual.detail`, or return already fetched data (if available in the correct detail). */
|
||||
private async getMeshData(visual: VisualInfo): Promise<MeshlistData> {
|
||||
if (visual.data && visual.data.detail === visual.detail) {
|
||||
// Do not recreate
|
||||
return visual.data;
|
||||
}
|
||||
// TODO cache
|
||||
const url = this.getMeshUrl(visual.segmentId, visual.detail);
|
||||
const urlAsset = Asset.getUrlAsset(this.plugin.managers.asset, url);
|
||||
const asset = await this.plugin.runTask(this.plugin.managers.asset.resolve(urlAsset, 'binary'));
|
||||
const parsed = await this.plugin.runTask(CIF.parseBinary(asset.data));
|
||||
if (parsed.isError) {
|
||||
throw new Error(`Failed parsing CIF file from ${url}`);
|
||||
}
|
||||
const meshlistData = await MeshlistData.fromCIF(parsed.result, visual.segmentId, visual.segmentName, visual.detail);
|
||||
meshlistData.ownerId = this.id;
|
||||
// const bbox = MeshlistData.bbox(meshlistData);
|
||||
// const bboxVolume = bbox ? MS.Box3D.volume(bbox) : 0.0;
|
||||
// console.log(`BBox ${visual.segmentId}: ${Math.round(bboxVolume! / 1e6)} M`, bbox); // DEBUG
|
||||
return meshlistData;
|
||||
}
|
||||
|
||||
private async guessBackgroundSegments() {
|
||||
const bboxes: { [segid: number]: Box3D } = {};
|
||||
for (const tag in this.visuals) {
|
||||
const visual = this.visuals[tag];
|
||||
if (visual.detailType === 'low' && visual.data) {
|
||||
const bbox = MeshlistData.bbox(visual.data);
|
||||
if (bbox) {
|
||||
bboxes[visual.segmentId] = bbox;
|
||||
}
|
||||
}
|
||||
}
|
||||
const totalBbox = MeshlistData.combineBBoxes(Object.values(bboxes));
|
||||
const totalVolume = totalBbox ? Box3D.volume(totalBbox) : 0.0;
|
||||
// console.log(`BBox total: ${Math.round(totalVolume! / 1e6)} M`, totalBbox); // DEBUG
|
||||
|
||||
const isBgSegment: { [segid: number]: boolean } = {};
|
||||
for (const segid in bboxes) {
|
||||
const bbox = bboxes[segid];
|
||||
const bboxVolume = Box3D.volume(bbox);
|
||||
isBgSegment[segid] = (bboxVolume > totalVolume * BACKGROUND_SEGMENT_VOLUME_THRESHOLD);
|
||||
// console.log(`BBox ${segid}: ${Math.round(bboxVolume! / 1e6)} M, ${bboxVolume / totalVolume}`, bbox); // DEBUG
|
||||
}
|
||||
this.backgroundSegments = isBgSegment;
|
||||
}
|
||||
|
||||
getDescription() {
|
||||
return Params.ViewTypeChoice.prettyName(this.params.view.name);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,27 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { PluginStateObject } from '../../../mol-plugin-state/objects';
|
||||
import { Choice } from '../../../mol-util/param-choice';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
|
||||
|
||||
export const DEFAULT_MESH_SERVER = 'http://localhost:9000/v2';
|
||||
|
||||
|
||||
export class MeshServerInfo extends PluginStateObject.Create<MeshServerInfo.Data>({ name: 'Volume Server', typeClass: 'Object' }) { }
|
||||
|
||||
export namespace MeshServerInfo {
|
||||
export const MeshSourceChoice = new Choice({ empiar: 'EMPIAR', emdb: 'EMDB' }, 'empiar');
|
||||
export type MeshSource = Choice.Values<typeof MeshSourceChoice>;
|
||||
|
||||
export const Params = {
|
||||
serverUrl: PD.Text(DEFAULT_MESH_SERVER),
|
||||
source: MeshSourceChoice.PDSelect(),
|
||||
entryId: PD.Text(''),
|
||||
};
|
||||
export type Data = PD.Values<typeof Params>;
|
||||
}
|
||||
@@ -1,214 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
|
||||
import { PluginStateObject } from '../../../mol-plugin-state/objects';
|
||||
import { PluginContext } from '../../../mol-plugin/context';
|
||||
import { ShapeRepresentation } from '../../../mol-repr/shape/representation';
|
||||
import { StateAction, StateTransformer } from '../../../mol-state';
|
||||
import { Task } from '../../../mol-task';
|
||||
import { shallowEqualObjects } from '../../../mol-util';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
|
||||
import { BACKGROUND_OPACITY, FOREROUND_OPACITY, MeshlistData, VolsegTransform } from '../mesh-extension';
|
||||
import { MeshStreaming, NO_SEGMENT } from './behavior';
|
||||
import { MeshServerInfo } from './server-info';
|
||||
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
|
||||
export const MeshServerTransformer = VolsegTransform({
|
||||
name: 'mesh-server-info',
|
||||
from: PluginStateObject.Root,
|
||||
to: MeshServerInfo,
|
||||
params: MeshServerInfo.Params,
|
||||
})({
|
||||
apply({ a, params }, plugin: PluginContext) { // `a` is the parent node, `params` are 2nd argument to To.apply()
|
||||
params.serverUrl = params.serverUrl.replace(/\/*$/, ''); // trim trailing slash
|
||||
const description: string = params.entryId;
|
||||
return new MeshServerInfo({ ...params }, { label: 'Mesh Server', description: description });
|
||||
}
|
||||
});
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
|
||||
export const MeshStreamingTransformer = VolsegTransform({
|
||||
name: 'mesh-streaming-from-server-info',
|
||||
display: { name: 'Mesh Streaming' },
|
||||
from: MeshServerInfo,
|
||||
to: MeshStreaming,
|
||||
params: a => MeshStreaming.Params.create(a!.data),
|
||||
})({
|
||||
canAutoUpdate() { return true; },
|
||||
apply({ a, params }, plugin: PluginContext) {
|
||||
return Task.create('Mesh Streaming', async ctx => {
|
||||
const behavior = new MeshStreaming.Behavior(plugin, a.data, params);
|
||||
await behavior.update(params);
|
||||
return new MeshStreaming(behavior, { label: 'Mesh Streaming', description: behavior.getDescription() });
|
||||
});
|
||||
},
|
||||
update({ a, b, oldParams, newParams }) {
|
||||
return Task.create('Update Mesh Streaming', async ctx => {
|
||||
if (a.data.source !== b.data.parentData.source || a.data.entryId !== b.data.parentData.entryId) {
|
||||
return StateTransformer.UpdateResult.Recreate;
|
||||
}
|
||||
b.data.parentData = a.data;
|
||||
await b.data.update(newParams);
|
||||
b.description = b.data.getDescription();
|
||||
return StateTransformer.UpdateResult.Updated;
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
|
||||
interface MeshVisualGroupData {
|
||||
opacity: number,
|
||||
}
|
||||
|
||||
// export type MeshVisualGroupTransformer = typeof MeshVisualGroupTransformer;
|
||||
export const MeshVisualGroupTransformer = VolsegTransform({
|
||||
name: 'mesh-visual-group-from-streaming',
|
||||
display: { name: 'Mesh Visuals for a Segment' },
|
||||
from: MeshStreaming,
|
||||
to: PluginStateObject.Group,
|
||||
params: {
|
||||
/** Shown on the node in GUI */
|
||||
label: PD.Text('', { isHidden: true }),
|
||||
/** Shown on the node in GUI (gray letters) */
|
||||
description: PD.Text(''),
|
||||
segmentId: PD.Numeric(NO_SEGMENT, {}, { isHidden: true }),
|
||||
opacity: PD.Numeric(-1, { min: 0, max: 1, step: 0.01 }),
|
||||
}
|
||||
})({
|
||||
apply({ a, params }, plugin) {
|
||||
trySetAutoOpacity(params, a);
|
||||
return new PluginStateObject.Group({ opacity: params.opacity }, params);
|
||||
},
|
||||
update({ a, b, oldParams, newParams }, plugin) {
|
||||
if (shallowEqualObjects(oldParams, newParams)) {
|
||||
return StateTransformer.UpdateResult.Unchanged;
|
||||
}
|
||||
newParams.label ||= oldParams.label; // Protect against resetting params to invalid defaults
|
||||
if (newParams.segmentId === NO_SEGMENT) newParams.segmentId = oldParams.segmentId; // Protect against resetting params to invalid defaults
|
||||
trySetAutoOpacity(newParams, a);
|
||||
b.label = newParams.label;
|
||||
b.description = newParams.description;
|
||||
(b.data as MeshVisualGroupData).opacity = newParams.opacity;
|
||||
return StateTransformer.UpdateResult.Updated;
|
||||
},
|
||||
canAutoUpdate({ oldParams, newParams }, plugin) {
|
||||
return newParams.description === oldParams.description;
|
||||
},
|
||||
});
|
||||
|
||||
function trySetAutoOpacity(params: StateTransformer.Params<typeof MeshVisualGroupTransformer>, parent: MeshStreaming) {
|
||||
if (params.opacity === -1) {
|
||||
const isBgSegment = parent.data.backgroundSegments[params.segmentId];
|
||||
if (isBgSegment !== undefined) {
|
||||
params.opacity = isBgSegment ? BACKGROUND_OPACITY : FOREROUND_OPACITY;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
|
||||
export const MeshVisualTransformer = VolsegTransform({
|
||||
name: 'mesh-visual-from-streaming',
|
||||
display: { name: 'Mesh Visual from Streaming' },
|
||||
from: MeshStreaming,
|
||||
to: PluginStateObject.Shape.Representation3D,
|
||||
params: {
|
||||
/** Must be set to PluginStateObject reference to self */
|
||||
ref: PD.Text('', { isHidden: true, isEssential: true }), // QUESTION what is isEssential
|
||||
/** Identification of the mesh visual, e.g. 'low-2' */
|
||||
tag: PD.Text('', { isHidden: true, isEssential: true }),
|
||||
/** Opacity of the visual (not to be set directly, but controlled by the opacity of the parent Group, and by VisualInfo.visible) */
|
||||
opacity: PD.Numeric(-1, { min: 0, max: 1, step: 0.01 }, { isHidden: true }),
|
||||
}
|
||||
})({
|
||||
apply({ a, params, spine }, plugin: PluginContext) {
|
||||
return Task.create('Mesh Visual', async ctx => {
|
||||
const visualInfo: MeshStreaming.VisualInfo = a.data.visuals![params.tag];
|
||||
if (!visualInfo) throw new Error(`VisualInfo with tag '${params.tag}' is missing.`);
|
||||
const groupData = spine.getAncestorOfType(PluginStateObject.Group)?.data as MeshVisualGroupData | undefined;
|
||||
params.opacity = visualInfo.visible ? (groupData?.opacity ?? FOREROUND_OPACITY) : 0.0;
|
||||
const props = PD.getDefaultValues(Mesh.Params);
|
||||
props.flatShaded = true; // `flatShaded: true` is to see the real mesh vertices and triangles (default: false)
|
||||
props.alpha = params.opacity;
|
||||
const repr = ShapeRepresentation((ctx, meshlist: MeshlistData) => MeshlistData.getShape(meshlist, visualInfo.color), Mesh.Utils);
|
||||
await repr.createOrUpdate(props, visualInfo.data ?? MeshlistData.empty()).runInContext(ctx);
|
||||
return new PluginStateObject.Shape.Representation3D({ repr, sourceData: visualInfo.data }, { label: 'Mesh Visual', description: params.tag });
|
||||
});
|
||||
},
|
||||
update({ a, b, oldParams, newParams, spine }, plugin: PluginContext) {
|
||||
return Task.create('Update Mesh Visual', async ctx => {
|
||||
newParams.ref ||= oldParams.ref; // Protect against resetting params to invalid defaults
|
||||
newParams.tag ||= oldParams.tag; // Protect against resetting params to invalid defaults
|
||||
const visualInfo: MeshStreaming.VisualInfo = a.data.visuals![newParams.tag];
|
||||
if (!visualInfo) throw new Error(`VisualInfo with tag '${newParams.tag}' is missing.`);
|
||||
const oldData = b.data.sourceData as MeshlistData | undefined;
|
||||
if (visualInfo.data?.detail !== oldData?.detail) {
|
||||
return StateTransformer.UpdateResult.Recreate;
|
||||
}
|
||||
const groupData = spine.getAncestorOfType(PluginStateObject.Group)?.data as MeshVisualGroupData | undefined;
|
||||
const newOpacity = visualInfo.visible ? (groupData?.opacity ?? FOREROUND_OPACITY) : 0.0; // do not store to newParams directly, because oldParams and newParams might point to the same object!
|
||||
if (newOpacity !== oldParams.opacity) {
|
||||
newParams.opacity = newOpacity;
|
||||
await b.data.repr.createOrUpdate({ alpha: newParams.opacity }).runInContext(ctx);
|
||||
return StateTransformer.UpdateResult.Updated;
|
||||
} else {
|
||||
return StateTransformer.UpdateResult.Unchanged;
|
||||
}
|
||||
});
|
||||
},
|
||||
canAutoUpdate(params, globalCtx) {
|
||||
return true;
|
||||
},
|
||||
dispose({ b, params }, plugin) {
|
||||
b?.data.repr.destroy(); // QUESTION is this correct?
|
||||
},
|
||||
});
|
||||
|
||||
// // // // // // // // // // // // // // // // // // // // // // // //
|
||||
|
||||
export const InitMeshStreaming = StateAction.build({
|
||||
display: { name: 'Mesh Streaming' },
|
||||
from: PluginStateObject.Root,
|
||||
params: MeshServerInfo.Params,
|
||||
isApplicable: (a, _, plugin: PluginContext) => true
|
||||
})(function (p, plugin: PluginContext) {
|
||||
return Task.create('Mesh Streaming', async ctx => {
|
||||
const { params } = p;
|
||||
// p.ref
|
||||
const serverNode = await plugin.build().to(p.ref).apply(MeshServerTransformer, params).commit();
|
||||
// const serverNode = await plugin.build().toRoot().apply(MeshServerTransformer, params).commit();
|
||||
const streamingNode = await plugin.build().to(serverNode).apply(MeshStreamingTransformer, {}).commit();
|
||||
const visuals = streamingNode.data?.visuals ?? {};
|
||||
const bgSegments = streamingNode.data?.backgroundSegments ?? {};
|
||||
|
||||
const segmentGroups: { [segid: number]: string } = {};
|
||||
for (const tag in visuals) {
|
||||
const segid = visuals[tag].segmentId;
|
||||
if (!segmentGroups[segid]) {
|
||||
let description = visuals[tag].segmentName;
|
||||
if (bgSegments[segid]) description += ' (background)';
|
||||
const group = await plugin.build().to(streamingNode).apply(MeshVisualGroupTransformer, { label: `Segment ${segid}`, description: description, segmentId: segid }, { state: { isCollapsed: true } }).commit();
|
||||
segmentGroups[segid] = group.ref;
|
||||
}
|
||||
}
|
||||
const visualsUpdate = plugin.build();
|
||||
for (const tag in visuals) {
|
||||
const ref = `${streamingNode.ref}-${tag}`;
|
||||
const segid = visuals[tag].segmentId;
|
||||
visualsUpdate.to(segmentGroups[segid]).apply(MeshVisualTransformer, { ref: ref, tag: tag }, { ref: ref }); // ref - hack to allow the node make itself invisible
|
||||
}
|
||||
await plugin.state.data.updateTree(visualsUpdate).runInContext(ctx); // QUESTION what is really the difference between this and `visualsUpdate.commit()`?
|
||||
});
|
||||
});
|
||||
|
||||
// TODO make available in GUI, in left panel or in right panel like Volume Streaming in src/mol-plugin-ui/structure/volume.tsx?
|
||||
@@ -1,340 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
/** Helper functions for manipulation with mesh data. */
|
||||
|
||||
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
|
||||
import { CIF, CifFile } from '../../mol-io/reader/cif';
|
||||
import { Box3D } from '../../mol-math/geometry';
|
||||
import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
|
||||
import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
|
||||
import { Grid } from '../../mol-model/volume';
|
||||
import { ColorNames } from '../../mol-util/color/names';
|
||||
import { TypedArray } from '../../mol-util/type-helpers';
|
||||
|
||||
import { CIF_schema_mesh } from './mesh-cif-schema';
|
||||
|
||||
|
||||
type MeshModificationParams = {
|
||||
scale?: [number, number, number],
|
||||
shift?: [number, number, number],
|
||||
matrix?: Mat4,
|
||||
group?: number,
|
||||
invertSides?: boolean
|
||||
};
|
||||
|
||||
/** Modify mesh in-place */
|
||||
export function modify(m: Mesh, params: MeshModificationParams) {
|
||||
if (params.scale !== undefined) {
|
||||
const [qx, qy, qz] = params.scale;
|
||||
const vertices = m.vertexBuffer.ref.value;
|
||||
for (let i = 0; i < vertices.length; i += 3) {
|
||||
vertices[i] *= qx;
|
||||
vertices[i + 1] *= qy;
|
||||
vertices[i + 2] *= qz;
|
||||
}
|
||||
}
|
||||
if (params.shift !== undefined) {
|
||||
const [dx, dy, dz] = params.shift;
|
||||
const vertices = m.vertexBuffer.ref.value;
|
||||
for (let i = 0; i < vertices.length; i += 3) {
|
||||
vertices[i] += dx;
|
||||
vertices[i + 1] += dy;
|
||||
vertices[i + 2] += dz;
|
||||
}
|
||||
}
|
||||
if (params.matrix !== undefined) {
|
||||
const r = m.vertexBuffer.ref.value;
|
||||
const matrix = params.matrix;
|
||||
const size = 3 * m.vertexCount;
|
||||
for (let i = 0; i < size; i += 3) {
|
||||
Vec3.transformMat4Offset(r, r, matrix, i, i, 0);
|
||||
}
|
||||
}
|
||||
if (params.group !== undefined) {
|
||||
const groups = m.groupBuffer.ref.value;
|
||||
for (let i = 0; i < groups.length; i++) {
|
||||
groups[i] = params.group;
|
||||
}
|
||||
}
|
||||
if (params.invertSides) {
|
||||
const indices = m.indexBuffer.ref.value;
|
||||
let tmp;
|
||||
for (let i = 0; i < indices.length; i += 3) {
|
||||
tmp = indices[i];
|
||||
indices[i] = indices[i + 1];
|
||||
indices[i + 1] = tmp;
|
||||
}
|
||||
const normals = m.normalBuffer.ref.value;
|
||||
for (let i = 0; i < normals.length; i++) {
|
||||
normals[i] *= -1;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/** Create a copy a mesh, possibly modified */
|
||||
export function copy(m: Mesh, modification?: MeshModificationParams): Mesh {
|
||||
const nVertices = m.vertexCount;
|
||||
const nTriangles = m.triangleCount;
|
||||
const vertices = new Float32Array(m.vertexBuffer.ref.value);
|
||||
const indices = new Uint32Array(m.indexBuffer.ref.value);
|
||||
const normals = new Float32Array(m.normalBuffer.ref.value);
|
||||
const groups = new Float32Array(m.groupBuffer.ref.value);
|
||||
const result = Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
|
||||
if (modification) {
|
||||
modify(result, modification);
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
/** Join more meshes into one */
|
||||
export function concat(...meshes: Mesh[]): Mesh {
|
||||
const nVertices = sum(meshes.map(m => m.vertexCount));
|
||||
const nTriangles = sum(meshes.map(m => m.triangleCount));
|
||||
const vertices = concatArrays(Float32Array, meshes.map(m => m.vertexBuffer.ref.value));
|
||||
const normals = concatArrays(Float32Array, meshes.map(m => m.normalBuffer.ref.value));
|
||||
const groups = concatArrays(Float32Array, meshes.map(m => m.groupBuffer.ref.value));
|
||||
const newIndices = [];
|
||||
let offset = 0;
|
||||
for (const m of meshes) {
|
||||
newIndices.push(m.indexBuffer.ref.value.map(i => i + offset));
|
||||
offset += m.vertexCount;
|
||||
}
|
||||
const indices = concatArrays(Uint32Array, newIndices);
|
||||
return Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
|
||||
}
|
||||
|
||||
/** Return Mesh from CIF data and mesh IDs (group IDs).
|
||||
* Assume the CIF contains coords in grid space,
|
||||
* transform the output mesh to `space` */
|
||||
export async function meshFromCif(data: CifFile, invertSides: boolean | undefined = undefined, outSpace: 'grid' | 'fractional' | 'cartesian' = 'cartesian'): Promise<{ mesh: Mesh, meshIds: number[] }> {
|
||||
const volumeInfoBlock = data.blocks.find(b => b.header === 'VOLUME_INFO');
|
||||
const meshesBlock = data.blocks.find(b => b.header === 'MESHES');
|
||||
if (!volumeInfoBlock || !meshesBlock) throw new Error('Missing VOLUME_INFO or MESHES block in mesh CIF file');
|
||||
const volumeInfoCif = CIF.schema.densityServer(volumeInfoBlock);
|
||||
const meshCif = CIF_schema_mesh(meshesBlock);
|
||||
|
||||
const nVertices = meshCif.mesh_vertex._rowCount;
|
||||
const nTriangles = Math.floor(meshCif.mesh_triangle._rowCount / 3);
|
||||
|
||||
const mesh_id = meshCif.mesh.id.toArray();
|
||||
const vertex_meshId = meshCif.mesh_vertex.mesh_id.toArray();
|
||||
const x = meshCif.mesh_vertex.x.toArray();
|
||||
const y = meshCif.mesh_vertex.y.toArray();
|
||||
const z = meshCif.mesh_vertex.z.toArray();
|
||||
const triangle_meshId = meshCif.mesh_triangle.mesh_id.toArray();
|
||||
const triangle_vertexId = meshCif.mesh_triangle.vertex_id.toArray();
|
||||
|
||||
// Shift indices from within-mesh indices to overall indices
|
||||
const indices = new Uint32Array(3 * nTriangles);
|
||||
const offsets = offsetMap(vertex_meshId);
|
||||
for (let i = 0; i < 3 * nTriangles; i++) {
|
||||
const offset = offsets.get(triangle_meshId[i])!;
|
||||
indices[i] = offset + triangle_vertexId[i];
|
||||
}
|
||||
const vertices = flattenCoords(x, y, z);
|
||||
const normals = new Float32Array(3 * nVertices);
|
||||
const groups = new Float32Array(vertex_meshId);
|
||||
const mesh = Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
|
||||
|
||||
invertSides ??= isInverted(mesh);
|
||||
if (invertSides) {
|
||||
modify(mesh, { invertSides: true }); // Vertex orientation convention is opposite in Volseg API and in MolStar
|
||||
}
|
||||
|
||||
if (outSpace === 'cartesian') {
|
||||
const volume = await volumeFromDensityServerData(volumeInfoCif).run();
|
||||
const gridToCartesian = Grid.getGridToCartesianTransform(volume.grid);
|
||||
modify(mesh, { matrix: gridToCartesian });
|
||||
} else if (outSpace === 'fractional') {
|
||||
const gridSize = volumeInfoCif.volume_data_3d_info.sample_count.value(0);
|
||||
const originFract = volumeInfoCif.volume_data_3d_info.origin.value(0);
|
||||
const dimensionFract = volumeInfoCif.volume_data_3d_info.dimensions.value(0);
|
||||
if (dimensionFract[0] !== 1 || dimensionFract[1] !== 1 || dimensionFract[2] !== 1) throw new Error(`Asserted the fractional dimensions are [1,1,1], but are actually [${dimensionFract}]`);
|
||||
const scale: [number, number, number] = [1 / gridSize[0], 1 / gridSize[1], 1 / gridSize[2]];
|
||||
modify(mesh, { scale: scale, shift: Array.from(originFract) as any });
|
||||
}
|
||||
|
||||
Mesh.computeNormals(mesh); // normals only necessary if flatShaded==false
|
||||
|
||||
// const boxMesh = makeMeshFromBox([[0,0,0], [1,1,1]], 1);
|
||||
// const gridSize = volumeInfoCif.volume_data_3d_info.sample_count.value(0); const boxMesh = makeMeshFromBox([[0,0,0], Array.from(gridSize)] as any, 1);
|
||||
// const cellSize = volumeInfoCif.volume_data_3d_info.spacegroup_cell_size.value(0); const boxMesh = makeMeshFromBox([[0, 0, 0], Array.from(cellSize)] as any, 1);
|
||||
// mesh = concat(mesh, boxMesh); // debug
|
||||
return { mesh: mesh, meshIds: Array.from(mesh_id) };
|
||||
}
|
||||
|
||||
function isInverted(mesh: Mesh): boolean {
|
||||
const vertices = mesh.vertexBuffer.ref.value;
|
||||
const indices = mesh.indexBuffer.ref.value;
|
||||
const center = meshCenter(mesh);
|
||||
const center3 = Vec3.create(3 * center[0], 3 * center[1], 3 * center[2]);
|
||||
|
||||
let dirMetric = 0.0;
|
||||
const [a, b, c, u, v, normal, radius] = [Vec3(), Vec3(), Vec3(), Vec3(), Vec3(), Vec3(), Vec3()];
|
||||
for (let i = 0; i < indices.length; i += 3) {
|
||||
Vec3.fromArray(a, vertices, 3 * indices[i]);
|
||||
Vec3.fromArray(b, vertices, 3 * indices[i + 1]);
|
||||
Vec3.fromArray(c, vertices, 3 * indices[i + 2]);
|
||||
Vec3.sub(u, b, a);
|
||||
Vec3.sub(v, c, b);
|
||||
Vec3.cross(normal, u, v); // direction of the surface
|
||||
Vec3.add(radius, a, b);
|
||||
Vec3.add(radius, radius, c);
|
||||
Vec3.sub(radius, radius, center3); // direction center -> this triangle
|
||||
dirMetric += Vec3.dot(radius, normal);
|
||||
}
|
||||
return dirMetric < 0;
|
||||
}
|
||||
|
||||
function meshCenter(mesh: Mesh) {
|
||||
const vertices = mesh.vertexBuffer.ref.value;
|
||||
const n = vertices.length;
|
||||
let x = 0.0;
|
||||
let y = 0.0;
|
||||
let z = 0.0;
|
||||
for (let i = 0; i < vertices.length; i += 3) {
|
||||
x += vertices[i];
|
||||
y += vertices[i + 1];
|
||||
z += vertices[i + 2];
|
||||
}
|
||||
return Vec3.create(x / n, y / n, z / n);
|
||||
}
|
||||
|
||||
function flattenCoords(x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number>): Float32Array {
|
||||
const n = x.length;
|
||||
const out = new Float32Array(3 * n);
|
||||
for (let i = 0; i < n; i++) {
|
||||
out[3 * i] = x[i];
|
||||
out[3 * i + 1] = y[i];
|
||||
out[3 * i + 2] = z[i];
|
||||
}
|
||||
return out;
|
||||
}
|
||||
|
||||
/** Get mapping of unique values to the position of their first occurrence */
|
||||
function offsetMap(values: ArrayLike<number>) {
|
||||
const result = new Map<number, number>();
|
||||
for (let i = 0; i < values.length; i++) {
|
||||
if (!result.has(values[i])) {
|
||||
result.set(values[i], i);
|
||||
}
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
/** Return bounding box */
|
||||
export function bbox(mesh: Mesh): Box3D | null { // Is there no function for this?
|
||||
const nVertices = mesh.vertexCount;
|
||||
const coords = mesh.vertexBuffer.ref.value;
|
||||
if (nVertices === 0) {
|
||||
return null;
|
||||
}
|
||||
let minX = coords[0], minY = coords[1], minZ = coords[2];
|
||||
let maxX = minX, maxY = minY, maxZ = minZ;
|
||||
for (let i = 0; i < 3 * nVertices; i += 3) {
|
||||
const x = coords[i], y = coords[i + 1], z = coords[i + 2];
|
||||
if (x < minX) minX = x;
|
||||
if (y < minY) minY = y;
|
||||
if (z < minZ) minZ = z;
|
||||
if (x > maxX) maxX = x;
|
||||
if (y > maxY) maxY = y;
|
||||
if (z > maxZ) maxZ = z;
|
||||
}
|
||||
return Box3D.create(Vec3.create(minX, minY, minZ), Vec3.create(maxX, maxY, maxZ));
|
||||
}
|
||||
|
||||
/** Example mesh - 1 triangle */
|
||||
export function fakeFakeMesh1(): Mesh {
|
||||
const nVertices = 3;
|
||||
const nTriangles = 1;
|
||||
const vertices = new Float32Array([0, 0, 0, 1, 0, 0, 0, 1, 0]);
|
||||
const indices = new Uint32Array([0, 1, 2]);
|
||||
const normals = new Float32Array([0, 0, 1]);
|
||||
const groups = new Float32Array([0]);
|
||||
return Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
|
||||
}
|
||||
|
||||
/** Example mesh - irregular tetrahedron */
|
||||
export function fakeMesh4(): Mesh {
|
||||
const nVertices = 4;
|
||||
const nTriangles = 4;
|
||||
const vertices = new Float32Array([0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1]);
|
||||
const indices = new Uint32Array([0, 2, 1, 0, 1, 3, 1, 2, 3, 2, 0, 3]);
|
||||
const normals = new Float32Array([-1, -1, -1, 1, 0, 0, 0, 1, 0, 0, 0, 1]);
|
||||
const groups = new Float32Array([0, 1, 2, 3]);
|
||||
return Mesh.create(vertices, indices, normals, groups, nVertices, nTriangles);
|
||||
}
|
||||
|
||||
/** Return a box-shaped mesh */
|
||||
export function meshFromBox(box: [[number, number, number], [number, number, number]], group: number = 0) {
|
||||
const [[x0, y0, z0], [x1, y1, z1]] = box;
|
||||
const vertices = new Float32Array([
|
||||
x0, y0, z0,
|
||||
x1, y0, z0,
|
||||
x0, y1, z0,
|
||||
x1, y1, z0,
|
||||
x0, y0, z1,
|
||||
x1, y0, z1,
|
||||
x0, y1, z1,
|
||||
x1, y1, z1,
|
||||
]);
|
||||
const indices = new Uint32Array([
|
||||
2, 1, 0, 1, 2, 3,
|
||||
1, 4, 0, 4, 1, 5,
|
||||
3, 5, 1, 5, 3, 7,
|
||||
2, 7, 3, 7, 2, 6,
|
||||
0, 6, 2, 6, 0, 4,
|
||||
4, 7, 6, 7, 4, 5,
|
||||
]);
|
||||
const groups = new Float32Array([group, group, group, group, group, group, group, group]);
|
||||
const normals = new Float32Array(8);
|
||||
const mesh = Mesh.create(vertices, indices, normals, groups, 8, 12);
|
||||
Mesh.computeNormals(mesh); // normals only necessary if flatShaded==false
|
||||
return mesh;
|
||||
}
|
||||
|
||||
function sum(array: number[]): number {
|
||||
return array.reduce((a, b) => a + b, 0);
|
||||
}
|
||||
|
||||
function concatArrays<T extends TypedArray>(t: new (len: number) => T, arrays: T[]): T {
|
||||
const totalLength = arrays.map(a => a.length).reduce((a, b) => a + b, 0);
|
||||
const result: T = new t(totalLength);
|
||||
let offset = 0;
|
||||
for (const array of arrays) {
|
||||
result.set(array, offset);
|
||||
offset += array.length;
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
/** Generate random colors (in a cycle) */
|
||||
export const ColorGenerator = function* () {
|
||||
const colors = shuffleArray(Object.values(ColorNames));
|
||||
let i = 0;
|
||||
while (true) {
|
||||
yield colors[i];
|
||||
i++;
|
||||
if (i >= colors.length) i = 0;
|
||||
}
|
||||
}();
|
||||
function shuffleArray<T>(array: T[]): T[] {
|
||||
// Stealed from https://www.w3docs.com/snippets/javascript/how-to-randomize-shuffle-a-javascript-array.html
|
||||
let curId = array.length;
|
||||
// There remain elements to shuffle
|
||||
while (0 !== curId) {
|
||||
// Pick a remaining element
|
||||
const randId = Math.floor(Math.random() * curId);
|
||||
curId -= 1;
|
||||
// Swap it with the current element.
|
||||
const tmp = array[curId];
|
||||
array[curId] = array[randId];
|
||||
array[randId] = tmp;
|
||||
}
|
||||
return array;
|
||||
}
|
||||
|
||||
@@ -2,7 +2,6 @@
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
*/
|
||||
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
@@ -15,7 +14,6 @@ import { CustomPropSymbol } from '../../../mol-script/language/symbol';
|
||||
import { Type } from '../../../mol-script/language/type';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
|
||||
import { AtomicIndex } from '../../../mol-model/structure/model/properties/atomic';
|
||||
|
||||
export { QualityAssessment };
|
||||
|
||||
@@ -73,28 +71,14 @@ namespace QualityAssessment {
|
||||
localNames.set(ma_qa_metric.id.value(i), name);
|
||||
}
|
||||
|
||||
const residueKey: AtomicIndex.ResidueLabelKey = {
|
||||
label_entity_id: '',
|
||||
label_asym_id: '',
|
||||
label_seq_id: 0,
|
||||
pdbx_PDB_ins_code: undefined,
|
||||
};
|
||||
|
||||
for (let i = 0, il = ma_qa_metric_local._rowCount; i < il; i++) {
|
||||
if (model_id.value(i) !== model.modelNum) continue;
|
||||
|
||||
const labelAsymId = label_asym_id.value(i);
|
||||
const entityIndex = index.findEntity(labelAsymId);
|
||||
|
||||
residueKey.label_entity_id = model.entities.data.id.value(entityIndex);
|
||||
residueKey.label_asym_id = labelAsymId;
|
||||
residueKey.label_seq_id = label_seq_id.value(i);
|
||||
|
||||
const rI = index.findResidueLabel(residueKey);
|
||||
if (rI >= 0) {
|
||||
const name = localNames.get(metric_id.value(i))!;
|
||||
localMetrics.get(name)!.set(rI, metric_value.value(i));
|
||||
}
|
||||
const rI = index.findResidue(model.entities.data.id.value(entityIndex), labelAsymId, label_seq_id.value(i));
|
||||
const name = localNames.get(metric_id.value(i))!;
|
||||
localMetrics.get(name)!.set(rI, metric_value.value(i));
|
||||
}
|
||||
|
||||
return {
|
||||
|
||||
@@ -1,28 +1,17 @@
|
||||
/**
|
||||
* Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author David Sehnal <david.sehnal@gmail.com>
|
||||
* @author Alexander Rose <alexander.rose@weirdbyte.de>
|
||||
*/
|
||||
|
||||
import { utf8ByteCount, utf8Write } from '../../mol-io/common/utf8';
|
||||
import { Structure, to_mmCIF, Unit } from '../../mol-model/structure';
|
||||
import { to_mmCIF, Unit } from '../../mol-model/structure';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { Task } from '../../mol-task';
|
||||
import { getFormattedTime } from '../../mol-util/date';
|
||||
import { download } from '../../mol-util/download';
|
||||
import { zip } from '../../mol-util/zip/zip';
|
||||
|
||||
const ModelExportNameProp = '__ModelExportName__';
|
||||
export const ModelExport = {
|
||||
getStructureName(structure: Structure): string | undefined {
|
||||
return structure.inheritedPropertyData[ModelExportNameProp];
|
||||
},
|
||||
setStructureName(structure: Structure, name: string) {
|
||||
return structure.inheritedPropertyData[ModelExportNameProp] = name;
|
||||
}
|
||||
};
|
||||
|
||||
export async function exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
|
||||
try {
|
||||
await plugin.runTask(_exportHierarchy(plugin, options), { useOverlay: true });
|
||||
@@ -54,21 +43,19 @@ function _exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'b
|
||||
continue;
|
||||
}
|
||||
|
||||
const name = ModelExport.getStructureName(s) || s.model.entryId || 'unnamed';
|
||||
const name = entryMap.has(s.model.entryId)
|
||||
? `${s.model.entryId}_${entryMap.get(s.model.entryId)! + 1}.${format}`
|
||||
: `${s.model.entryId}.${format}`;
|
||||
entryMap.set(s.model.entryId, (entryMap.get(s.model.entryId) ?? 0) + 1);
|
||||
|
||||
const fileName = entryMap.has(name)
|
||||
? `${name}_${entryMap.get(name)! + 1}.${format}`
|
||||
: `${name}.${format}`;
|
||||
entryMap.set(name, (entryMap.get(name) ?? 0) + 1);
|
||||
|
||||
await ctx.update({ message: `Exporting ${name}...`, isIndeterminate: true, canAbort: false });
|
||||
await ctx.update({ message: `Exporting ${s.model.entryId}...`, isIndeterminate: true, canAbort: false });
|
||||
if (s.elementCount > 100000) {
|
||||
// Give UI chance to update, only needed for larger structures.
|
||||
await new Promise(res => setTimeout(res, 50));
|
||||
}
|
||||
|
||||
try {
|
||||
files.push([fileName, to_mmCIF(name, s, format === 'bcif', { copyAllCategories: true })]);
|
||||
files.push([name, to_mmCIF(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
|
||||
} catch (e) {
|
||||
if (format === 'cif' && s.elementCount > 2000000) {
|
||||
plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
|
||||
|
||||
@@ -118,13 +118,11 @@ export class Mp4Controls extends PluginComponent {
|
||||
}
|
||||
|
||||
private init() {
|
||||
if (!this.plugin.canvas3d) return;
|
||||
|
||||
this.subscribe(this.plugin.managers.animation.events.updated.pipe(debounceTime(16)), () => {
|
||||
this.sync();
|
||||
});
|
||||
|
||||
this.subscribe(this.plugin.canvas3d.resized, () => this.syncInfo());
|
||||
this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
|
||||
this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
|
||||
|
||||
this.subscribe(this.plugin.behaviors.state.isBusy, b => this.updateCanApply(b));
|
||||
|
||||
@@ -1 +0,0 @@
|
||||
Find the MVS extension documentation [here](../../../docs/extensions/mvs/README.md).
|
||||
@@ -1,46 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import fs from 'fs';
|
||||
import { MVSData } from '../mvs-data';
|
||||
|
||||
|
||||
describe('MVSData', () => {
|
||||
it('MVSData functions work', async () => {
|
||||
const data = fs.readFileSync('examples/mvs/1cbs.mvsj', { encoding: 'utf8' });
|
||||
const mvsData = MVSData.fromMVSJ(data);
|
||||
expect(mvsData).toBeTruthy();
|
||||
|
||||
expect(MVSData.validationIssues(mvsData)).toEqual(undefined);
|
||||
|
||||
expect(MVSData.isValid(mvsData)).toEqual(true);
|
||||
|
||||
const reencoded = MVSData.toMVSJ(mvsData);
|
||||
expect(reencoded.replace(/\s/g, '')).toEqual(data.replace(/\s/g, ''));
|
||||
|
||||
const prettyString = MVSData.toPrettyString(mvsData);
|
||||
expect(typeof prettyString).toEqual('string');
|
||||
expect(prettyString.length).toBeGreaterThan(0);
|
||||
});
|
||||
|
||||
it('MVSData builder works', async () => {
|
||||
const builder = MVSData.createBuilder();
|
||||
expect(builder).toBeTruthy();
|
||||
|
||||
const mvsData = builder.getState();
|
||||
expect(MVSData.validationIssues(mvsData)).toEqual(undefined);
|
||||
|
||||
builder
|
||||
.download({ url: 'http://example.com' })
|
||||
.parse({ format: 'mmcif' })
|
||||
.assemblyStructure({ assembly_id: '1' })
|
||||
.component({ selector: 'polymer' })
|
||||
.representation()
|
||||
.color({ color: 'green', selector: { label_asym_id: 'A' } });
|
||||
const mvsData2 = builder.getState();
|
||||
expect(MVSData.validationIssues(mvsData2)).toEqual(undefined);
|
||||
});
|
||||
});
|
||||
@@ -1,176 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { CustomModelProperty } from '../../mol-model-props/common/custom-model-property';
|
||||
import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
|
||||
import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
|
||||
import { PluginDragAndDropHandler } from '../../mol-plugin-state/manager/drag-and-drop';
|
||||
import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
|
||||
import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { StructureRepresentationProvider } from '../../mol-repr/structure/representation';
|
||||
import { StateAction } from '../../mol-state';
|
||||
import { ColorTheme } from '../../mol-theme/color';
|
||||
import { ParamDefinition as PD } from '../../mol-util/param-definition';
|
||||
import { MVSAnnotationColorThemeProvider } from './components/annotation-color-theme';
|
||||
import { MVSAnnotationLabelRepresentationProvider } from './components/annotation-label/representation';
|
||||
import { MVSAnnotationsProvider } from './components/annotation-prop';
|
||||
import { MVSAnnotationTooltipsLabelProvider, MVSAnnotationTooltipsProvider } from './components/annotation-tooltips-prop';
|
||||
import { CustomLabelRepresentationProvider } from './components/custom-label/representation';
|
||||
import { CustomTooltipsLabelProvider, CustomTooltipsProvider } from './components/custom-tooltips-prop';
|
||||
import { LoadMvsData, MVSJFormatProvider } from './components/formats';
|
||||
import { makeMultilayerColorThemeProvider } from './components/multilayer-color-theme';
|
||||
import { loadMVS } from './load';
|
||||
import { MVSData } from './mvs-data';
|
||||
|
||||
|
||||
/** Collection of things that can be register/unregistered in a plugin */
|
||||
interface Registrables {
|
||||
customModelProperties?: CustomModelProperty.Provider<any, any>[],
|
||||
customStructureProperties?: CustomStructureProperty.Provider<any, any>[],
|
||||
representations?: StructureRepresentationProvider<any>[],
|
||||
colorThemes?: ColorTheme.Provider[],
|
||||
lociLabels?: LociLabelProvider[],
|
||||
dragAndDropHandlers?: DragAndDropHandler[],
|
||||
dataFormats?: { name: string, provider: DataFormatProvider }[],
|
||||
actions?: StateAction[],
|
||||
}
|
||||
|
||||
|
||||
/** Registers everything needed for loading MolViewSpec files */
|
||||
export const MolViewSpec = PluginBehavior.create<{ autoAttach: boolean }>({
|
||||
name: 'molviewspec',
|
||||
category: 'misc',
|
||||
display: {
|
||||
name: 'MolViewSpec',
|
||||
description: 'MolViewSpec extension',
|
||||
},
|
||||
ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
|
||||
private readonly registrables: Registrables = {
|
||||
customModelProperties: [
|
||||
MVSAnnotationsProvider,
|
||||
],
|
||||
customStructureProperties: [
|
||||
CustomTooltipsProvider,
|
||||
MVSAnnotationTooltipsProvider,
|
||||
],
|
||||
representations: [
|
||||
CustomLabelRepresentationProvider,
|
||||
MVSAnnotationLabelRepresentationProvider,
|
||||
],
|
||||
colorThemes: [
|
||||
MVSAnnotationColorThemeProvider,
|
||||
makeMultilayerColorThemeProvider(this.ctx.representation.structure.themes.colorThemeRegistry),
|
||||
],
|
||||
lociLabels: [
|
||||
CustomTooltipsLabelProvider,
|
||||
MVSAnnotationTooltipsLabelProvider,
|
||||
],
|
||||
dragAndDropHandlers: [
|
||||
MVSDragAndDropHandler,
|
||||
],
|
||||
dataFormats: [
|
||||
{ name: 'MVSJ', provider: MVSJFormatProvider },
|
||||
],
|
||||
actions: [
|
||||
LoadMvsData,
|
||||
]
|
||||
};
|
||||
|
||||
register(): void {
|
||||
for (const prop of this.registrables.customModelProperties ?? []) {
|
||||
this.ctx.customModelProperties.register(prop, this.params.autoAttach);
|
||||
}
|
||||
for (const prop of this.registrables.customStructureProperties ?? []) {
|
||||
this.ctx.customStructureProperties.register(prop, this.params.autoAttach);
|
||||
}
|
||||
for (const repr of this.registrables.representations ?? []) {
|
||||
this.ctx.representation.structure.registry.add(repr);
|
||||
}
|
||||
for (const theme of this.registrables.colorThemes ?? []) {
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.add(theme);
|
||||
}
|
||||
for (const provider of this.registrables.lociLabels ?? []) {
|
||||
this.ctx.managers.lociLabels.addProvider(provider);
|
||||
}
|
||||
for (const handler of this.registrables.dragAndDropHandlers ?? []) {
|
||||
this.ctx.managers.dragAndDrop.addHandler(handler.name, handler.handle);
|
||||
}
|
||||
for (const format of this.registrables.dataFormats ?? []) {
|
||||
this.ctx.dataFormats.add(format.name, format.provider);
|
||||
}
|
||||
for (const action of this.registrables.actions ?? []) {
|
||||
this.ctx.state.data.actions.add(action);
|
||||
}
|
||||
}
|
||||
update(p: { autoAttach: boolean }) {
|
||||
const updated = this.params.autoAttach !== p.autoAttach;
|
||||
this.params.autoAttach = p.autoAttach;
|
||||
for (const prop of this.registrables.customModelProperties ?? []) {
|
||||
this.ctx.customModelProperties.setDefaultAutoAttach(prop.descriptor.name, this.params.autoAttach);
|
||||
}
|
||||
for (const prop of this.registrables.customStructureProperties ?? []) {
|
||||
this.ctx.customStructureProperties.setDefaultAutoAttach(prop.descriptor.name, this.params.autoAttach);
|
||||
}
|
||||
return updated;
|
||||
}
|
||||
unregister() {
|
||||
for (const prop of this.registrables.customModelProperties ?? []) {
|
||||
this.ctx.customModelProperties.unregister(prop.descriptor.name);
|
||||
}
|
||||
for (const prop of this.registrables.customStructureProperties ?? []) {
|
||||
this.ctx.customStructureProperties.unregister(prop.descriptor.name);
|
||||
}
|
||||
for (const repr of this.registrables.representations ?? []) {
|
||||
this.ctx.representation.structure.registry.remove(repr);
|
||||
}
|
||||
for (const theme of this.registrables.colorThemes ?? []) {
|
||||
this.ctx.representation.structure.themes.colorThemeRegistry.remove(theme);
|
||||
}
|
||||
for (const labelProvider of this.registrables.lociLabels ?? []) {
|
||||
this.ctx.managers.lociLabels.removeProvider(labelProvider);
|
||||
}
|
||||
for (const handler of this.registrables.dragAndDropHandlers ?? []) {
|
||||
this.ctx.managers.dragAndDrop.removeHandler(handler.name);
|
||||
}
|
||||
for (const format of this.registrables.dataFormats ?? []) {
|
||||
this.ctx.dataFormats.remove(format.name);
|
||||
}
|
||||
for (const action of this.registrables.actions ?? []) {
|
||||
this.ctx.state.data.actions.remove(action);
|
||||
}
|
||||
}
|
||||
},
|
||||
params: () => ({
|
||||
autoAttach: PD.Boolean(false),
|
||||
})
|
||||
});
|
||||
|
||||
|
||||
/** Registrable method for handling dragged-and-dropped files */
|
||||
interface DragAndDropHandler {
|
||||
name: string,
|
||||
handle: PluginDragAndDropHandler,
|
||||
}
|
||||
|
||||
/** DragAndDropHandler handler for `.mvsj` files */
|
||||
const MVSDragAndDropHandler: DragAndDropHandler = {
|
||||
name: 'mvs-mvsj',
|
||||
/** Load .mvsj files. Delete previous plugin state before loading.
|
||||
* If multiple files are provided, merge their MVS data into one state. */
|
||||
async handle(files: File[], plugin: PluginContext): Promise<boolean> {
|
||||
let applied = false;
|
||||
for (const file of files) {
|
||||
if (file.name.toLowerCase().endsWith('.mvsj')) {
|
||||
const data = await file.text();
|
||||
const mvsData = MVSData.fromMVSJ(data);
|
||||
await loadMVS(plugin, mvsData, { sanityChecks: true, replaceExisting: !applied });
|
||||
applied = true;
|
||||
}
|
||||
}
|
||||
return applied;
|
||||
},
|
||||
};
|
||||
@@ -1,144 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Camera } from '../../mol-canvas3d/camera';
|
||||
import { GraphicsRenderObject } from '../../mol-gl/render-object';
|
||||
import { Sphere3D } from '../../mol-math/geometry';
|
||||
import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
|
||||
import { Vec3 } from '../../mol-math/linear-algebra';
|
||||
import { Loci } from '../../mol-model/loci';
|
||||
import { Structure } from '../../mol-model/structure';
|
||||
import { PluginStateObject } from '../../mol-plugin-state/objects';
|
||||
import { PluginCommands } from '../../mol-plugin/commands';
|
||||
import { PluginContext } from '../../mol-plugin/context';
|
||||
import { StateObjectSelector } from '../../mol-state';
|
||||
import { ColorNames } from '../../mol-util/color/names';
|
||||
|
||||
import { decodeColor } from './helpers/utils';
|
||||
import { ParamsOfKind } from './tree/generic/tree-schema';
|
||||
import { MolstarTree } from './tree/molstar/molstar-tree';
|
||||
import { MVSDefaults } from './tree/mvs/mvs-defaults';
|
||||
|
||||
|
||||
const DefaultFocusOptions = {
|
||||
minRadius: 5,
|
||||
extraRadiusForFocus: 0,
|
||||
extraRadiusForZoomAll: 0,
|
||||
};
|
||||
const DefaultCanvasBackgroundColor = ColorNames.white;
|
||||
|
||||
|
||||
const _tmpVec = Vec3();
|
||||
|
||||
/** Set the camera based on a camera node params. */
|
||||
export async function setCamera(plugin: PluginContext, params: ParamsOfKind<MolstarTree, 'camera'>) {
|
||||
const target = Vec3.create(...params.target);
|
||||
let position = Vec3.create(...params.position);
|
||||
if (plugin.canvas3d) position = fovAdjustedPosition(target, position, plugin.canvas3d.camera.state.mode, plugin.canvas3d.camera.state.fov);
|
||||
const up = Vec3.create(...params.up);
|
||||
Vec3.orthogonalize(up, Vec3.sub(_tmpVec, target, position), up);
|
||||
const snapshot: Partial<Camera.Snapshot> = { target, position, up, radius: 10_000, 'radiusMax': 10_000 };
|
||||
await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
|
||||
}
|
||||
|
||||
/** Focus the camera on the bounding sphere of a (sub)structure (or on the whole scene if `structureNodeSelector` is null).
|
||||
* Orient the camera based on a focus node params. */
|
||||
export async function setFocus(plugin: PluginContext, structureNodeSelector: StateObjectSelector | undefined, params: ParamsOfKind<MolstarTree, 'focus'> = MVSDefaults.focus) {
|
||||
let structure: Structure | undefined = undefined;
|
||||
if (structureNodeSelector) {
|
||||
const cell = plugin.state.data.cells.get(structureNodeSelector.ref);
|
||||
structure = cell?.obj?.data;
|
||||
if (!structure) console.warn('Focus: no structure');
|
||||
if (!(structure instanceof Structure)) {
|
||||
console.warn('Focus: cannot apply to a non-structure node');
|
||||
structure = undefined;
|
||||
}
|
||||
}
|
||||
const boundingSphere = structure ? Loci.getBoundingSphere(Structure.Loci(structure)) : getPluginBoundingSphere(plugin);
|
||||
if (boundingSphere && plugin.canvas3d) {
|
||||
const extraRadius = structure ? DefaultFocusOptions.extraRadiusForFocus : DefaultFocusOptions.extraRadiusForZoomAll;
|
||||
const direction = Vec3.create(...params.direction);
|
||||
const up = Vec3.create(...params.up);
|
||||
Vec3.orthogonalize(up, direction, up);
|
||||
const snapshot = snapshotFromSphereAndDirections(plugin.canvas3d.camera, {
|
||||
center: boundingSphere.center,
|
||||
radius: boundingSphere.radius + extraRadius,
|
||||
up,
|
||||
direction,
|
||||
});
|
||||
await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
|
||||
}
|
||||
}
|
||||
|
||||
/** Return camera snapshot for focusing a sphere with given `center` and `radius`,
|
||||
* while ensuring given view `direction` (aligns with vector position->target)
|
||||
* and `up` (aligns with screen Y axis). */
|
||||
function snapshotFromSphereAndDirections(camera: Camera, options: { center: Vec3, radius: number, direction: Vec3, up: Vec3 }): Partial<Camera.Snapshot> {
|
||||
// This might seem to repeat `plugin.canvas3d.camera.getFocus` but avoid flipping
|
||||
const { center, direction, up } = options;
|
||||
const radius = Math.max(options.radius, DefaultFocusOptions.minRadius);
|
||||
const distance = camera.getTargetDistance(radius);
|
||||
const deltaDirection = Vec3.setMagnitude(_tmpVec, direction, distance);
|
||||
const position = Vec3.sub(Vec3(), center, deltaDirection);
|
||||
return { target: center, position, up, radius };
|
||||
}
|
||||
|
||||
/** Return the distance adjustment ratio for conversion from the "reference camera"
|
||||
* to a camera with an arbitrary field of view `fov`. */
|
||||
function distanceAdjustment(mode: Camera.Mode, fov: number) {
|
||||
if (mode === 'orthographic') return 1 / (2 * Math.tan(fov / 2));
|
||||
else return 1 / (2 * Math.sin(fov / 2));
|
||||
}
|
||||
|
||||
/** Return the position for a camera with an arbitrary field of view `fov`
|
||||
* necessary to just fit into view the same sphere (with center at `target`)
|
||||
* as the "reference camera" placed at `refPosition` would fit, while keeping the camera orientation.
|
||||
* The "reference camera" is a camera which can just fit into view a sphere of radius R with center at distance 2R
|
||||
* (this corresponds to FOV = 2 * asin(1/2) in perspective mode or FOV = 2 * atan(1/2) in orthogonal mode). */
|
||||
function fovAdjustedPosition(target: Vec3, refPosition: Vec3, mode: Camera.Mode, fov: number) {
|
||||
const delta = Vec3.sub(Vec3(), refPosition, target);
|
||||
const adjustment = distanceAdjustment(mode, fov);
|
||||
return Vec3.scaleAndAdd(delta, target, delta, adjustment); // return target + delta * adjustment
|
||||
}
|
||||
|
||||
/** Compute the bounding sphere of the whole scene. */
|
||||
function getPluginBoundingSphere(plugin: PluginContext) {
|
||||
const renderObjects = getRenderObjects(plugin, false);
|
||||
const spheres = renderObjects.map(r => r.values.boundingSphere.ref.value).filter(sphere => sphere.radius > 0);
|
||||
return boundingSphereOfSpheres(spheres);
|
||||
}
|
||||
|
||||
function getRenderObjects(plugin: PluginContext, includeHidden: boolean): GraphicsRenderObject[] {
|
||||
let reprCells = Array.from(plugin.state.data.cells.values()).filter(cell => cell.obj && PluginStateObject.isRepresentation3D(cell.obj));
|
||||
if (!includeHidden) reprCells = reprCells.filter(cell => !cell.state.isHidden);
|
||||
const renderables = reprCells.flatMap(cell => cell.obj!.data.repr.renderObjects);
|
||||
return renderables;
|
||||
}
|
||||
|
||||
let boundaryHelper: BoundaryHelper | undefined = undefined;
|
||||
|
||||
function boundingSphereOfSpheres(spheres: Sphere3D[]): Sphere3D {
|
||||
boundaryHelper ??= new BoundaryHelper('98');
|
||||
boundaryHelper.reset();
|
||||
for (const s of spheres) boundaryHelper.includeSphere(s);
|
||||
boundaryHelper.finishedIncludeStep();
|
||||
for (const s of spheres) boundaryHelper.radiusSphere(s);
|
||||
return boundaryHelper.getSphere();
|
||||
}
|
||||
|
||||
/** Set canvas properties based on a canvas node params. */
|
||||
export function setCanvas(plugin: PluginContext, params: ParamsOfKind<MolstarTree, 'canvas'> | undefined) {
|
||||
const backgroundColor = decodeColor(params?.background_color) ?? DefaultCanvasBackgroundColor;
|
||||
if (backgroundColor !== plugin.canvas3d?.props.renderer.backgroundColor) {
|
||||
plugin.canvas3d?.setProps(old => ({
|
||||
...old,
|
||||
renderer: {
|
||||
...old.renderer,
|
||||
backgroundColor: backgroundColor,
|
||||
}
|
||||
}));
|
||||
}
|
||||
}
|
||||
@@ -1,80 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Location } from '../../../mol-model/location';
|
||||
import { Bond, StructureElement } from '../../../mol-model/structure';
|
||||
import { ColorTheme, LocationColor } from '../../../mol-theme/color';
|
||||
import { ThemeDataContext } from '../../../mol-theme/theme';
|
||||
import { ColorNames } from '../../../mol-util/color/names';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { decodeColor } from '../helpers/utils';
|
||||
import { getMVSAnnotationForStructure } from './annotation-prop';
|
||||
|
||||
|
||||
/** Parameter definition for color theme "MVS Annotation" */
|
||||
export const MVSAnnotationColorThemeParams = {
|
||||
annotationId: PD.Text('', { description: 'Reference to "Annotation" custom model property' }),
|
||||
fieldName: PD.Text('color', { description: 'Annotation field (column) from which to take color values' }),
|
||||
background: PD.Color(ColorNames.gainsboro, { description: 'Color for elements without annotation' }),
|
||||
};
|
||||
export type MVSAnnotationColorThemeParams = typeof MVSAnnotationColorThemeParams
|
||||
|
||||
/** Parameter values for color theme "MVS Annotation" */
|
||||
export type MVSAnnotationColorThemeProps = PD.Values<MVSAnnotationColorThemeParams>
|
||||
|
||||
|
||||
/** Return color theme that assigns colors based on an annotation file.
|
||||
* The annotation file itself is handled by a custom model property (`MVSAnnotationsProvider`),
|
||||
* the color theme then just uses this property. */
|
||||
export function MVSAnnotationColorTheme(ctx: ThemeDataContext, props: MVSAnnotationColorThemeProps): ColorTheme<MVSAnnotationColorThemeParams> {
|
||||
let color: LocationColor = () => props.background;
|
||||
|
||||
if (ctx.structure && !ctx.structure.isEmpty) {
|
||||
const { annotation } = getMVSAnnotationForStructure(ctx.structure, props.annotationId);
|
||||
if (annotation) {
|
||||
const colorForStructureElementLocation = (location: StructureElement.Location) => {
|
||||
// if (annot.getAnnotationForLocation(location)?.color !== annot.getAnnotationForLocation_Reference(location)?.color) throw new Error('AssertionError');
|
||||
return decodeColor(annotation?.getValueForLocation(location, props.fieldName)) ?? props.background;
|
||||
};
|
||||
const auxLocation = StructureElement.Location.create(ctx.structure);
|
||||
|
||||
color = (location: Location) => {
|
||||
if (StructureElement.Location.is(location)) {
|
||||
return colorForStructureElementLocation(location);
|
||||
} else if (Bond.isLocation(location)) {
|
||||
// this will be applied for each bond twice, to get color of each half (a* refers to the adjacent atom, b* to the opposite atom)
|
||||
auxLocation.unit = location.aUnit;
|
||||
auxLocation.element = location.aUnit.elements[location.aIndex];
|
||||
return colorForStructureElementLocation(auxLocation);
|
||||
}
|
||||
return props.background;
|
||||
};
|
||||
} else {
|
||||
console.error(`Annotation source "${props.annotationId}" not present`);
|
||||
}
|
||||
}
|
||||
|
||||
return {
|
||||
factory: MVSAnnotationColorTheme,
|
||||
granularity: 'group',
|
||||
preferSmoothing: true,
|
||||
color: color,
|
||||
props: props,
|
||||
description: 'Assigns colors based on custom MolViewSpec annotation data.',
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
/** A thingy that is needed to register color theme "MVS Annotation" */
|
||||
export const MVSAnnotationColorThemeProvider: ColorTheme.Provider<MVSAnnotationColorThemeParams, 'mvs-annotation'> = {
|
||||
name: 'mvs-annotation',
|
||||
label: 'MVS Annotation',
|
||||
category: ColorTheme.Category.Misc,
|
||||
factory: MVSAnnotationColorTheme,
|
||||
getParams: ctx => MVSAnnotationColorThemeParams,
|
||||
defaultValues: PD.getDefaultValues(MVSAnnotationColorThemeParams),
|
||||
isApplicable: (ctx: ThemeDataContext) => true,
|
||||
};
|
||||
@@ -1,49 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Structure } from '../../../../mol-model/structure';
|
||||
import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../../mol-repr/representation';
|
||||
import { ComplexRepresentation, StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../../../../mol-repr/structure/representation';
|
||||
import { MarkerAction } from '../../../../mol-util/marker-action';
|
||||
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
|
||||
import { MVSAnnotationLabelTextParams, MVSAnnotationLabelTextVisual } from './visual';
|
||||
|
||||
|
||||
/** Components of "MVS Annotation Label" representation */
|
||||
const MVSAnnotationLabelVisuals = {
|
||||
'label-text': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MVSAnnotationLabelTextParams>) => ComplexRepresentation('Label text', ctx, getParams, MVSAnnotationLabelTextVisual),
|
||||
};
|
||||
|
||||
/** Parameter definition for representation type "MVS Annotation Label" */
|
||||
export type MVSAnnotationLabelParams = typeof MVSAnnotationLabelParams
|
||||
export const MVSAnnotationLabelParams = {
|
||||
...MVSAnnotationLabelTextParams,
|
||||
visuals: PD.MultiSelect(['label-text'], PD.objectToOptions(MVSAnnotationLabelVisuals)),
|
||||
};
|
||||
|
||||
/** Parameter values for representation type "MVS Annotation Label" */
|
||||
export type MVSAnnotationLabelProps = PD.ValuesFor<MVSAnnotationLabelParams>
|
||||
|
||||
/** Structure representation type "MVS Annotation Label", allowing showing labels based on "MVS Annotations" custom props */
|
||||
export type MVSAnnotationLabelRepresentation = StructureRepresentation<MVSAnnotationLabelParams>
|
||||
export function MVSAnnotationLabelRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MVSAnnotationLabelParams>): MVSAnnotationLabelRepresentation {
|
||||
const repr = Representation.createMulti('Label', ctx, getParams, StructureRepresentationStateBuilder, MVSAnnotationLabelVisuals as unknown as Representation.Def<Structure, MVSAnnotationLabelParams>);
|
||||
repr.setState({ pickable: false, markerActions: MarkerAction.None });
|
||||
return repr;
|
||||
}
|
||||
|
||||
/** A thingy that is needed to register representation type "MVS Annotation Label", allowing showing labels based on "MVS Annotations" custom props */
|
||||
export const MVSAnnotationLabelRepresentationProvider = StructureRepresentationProvider({
|
||||
name: 'mvs-annotation-label',
|
||||
label: 'MVS Annotation Label',
|
||||
description: 'Displays labels based on annotation custom model property',
|
||||
factory: MVSAnnotationLabelRepresentation,
|
||||
getParams: () => MVSAnnotationLabelParams,
|
||||
defaultValues: PD.getDefaultValues(MVSAnnotationLabelParams),
|
||||
defaultColorTheme: { name: 'uniform' }, // this ain't workin
|
||||
defaultSizeTheme: { name: 'physical' },
|
||||
isApplicable: (structure: Structure) => structure.elementCount > 0,
|
||||
});
|
||||
@@ -1,65 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Text } from '../../../../mol-geo/geometry/text/text';
|
||||
import { TextBuilder } from '../../../../mol-geo/geometry/text/text-builder';
|
||||
import { Structure } from '../../../../mol-model/structure';
|
||||
import { ComplexTextVisual, ComplexVisual } from '../../../../mol-repr/structure/complex-visual';
|
||||
import * as Original from '../../../../mol-repr/structure/visual/label-text';
|
||||
import { ElementIterator, eachSerialElement, getSerialElementLoci } from '../../../../mol-repr/structure/visual/util/element';
|
||||
import { VisualUpdateState } from '../../../../mol-repr/util';
|
||||
import { VisualContext } from '../../../../mol-repr/visual';
|
||||
import { Theme } from '../../../../mol-theme/theme';
|
||||
import { ColorNames } from '../../../../mol-util/color/names';
|
||||
import { omitObjectKeys } from '../../../../mol-util/object';
|
||||
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
|
||||
import { textPropsForSelection } from '../../helpers/label-text';
|
||||
import { groupRows } from '../../helpers/selections';
|
||||
import { getMVSAnnotationForStructure } from '../annotation-prop';
|
||||
|
||||
|
||||
/** Parameter definition for "label-text" visual in "MVS Annotation Label" representation */
|
||||
export type MVSAnnotationLabelTextParams = typeof MVSAnnotationLabelTextParams
|
||||
export const MVSAnnotationLabelTextParams = {
|
||||
annotationId: PD.Text('', { description: 'Reference to "Annotation" custom model property', isEssential: true }),
|
||||
fieldName: PD.Text('label', { description: 'Annotation field (column) from which to take label contents', isEssential: true }),
|
||||
...omitObjectKeys(Original.LabelTextParams, ['level', 'chainScale', 'residueScale', 'elementScale']),
|
||||
borderColor: { ...Original.LabelTextParams.borderColor, defaultValue: ColorNames.black },
|
||||
};
|
||||
|
||||
/** Parameter values for "label-text" visual in "MVS Annotation Label" representation */
|
||||
export type MVSAnnotationLabelTextProps = PD.Values<MVSAnnotationLabelTextParams>
|
||||
|
||||
/** Create "label-text" visual for "MVS Annotation Label" representation */
|
||||
export function MVSAnnotationLabelTextVisual(materialId: number): ComplexVisual<MVSAnnotationLabelTextParams> {
|
||||
return ComplexTextVisual<MVSAnnotationLabelTextParams>({
|
||||
defaultProps: PD.getDefaultValues(MVSAnnotationLabelTextParams),
|
||||
createGeometry: createLabelText,
|
||||
createLocationIterator: ElementIterator.fromStructure,
|
||||
getLoci: getSerialElementLoci,
|
||||
eachLocation: eachSerialElement,
|
||||
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<MVSAnnotationLabelTextParams>, currentProps: PD.Values<MVSAnnotationLabelTextParams>) => {
|
||||
state.createGeometry = newProps.annotationId !== currentProps.annotationId || newProps.fieldName !== currentProps.fieldName;
|
||||
}
|
||||
}, materialId);
|
||||
}
|
||||
|
||||
function createLabelText(ctx: VisualContext, structure: Structure, theme: Theme, props: MVSAnnotationLabelTextProps, text?: Text): Text {
|
||||
const { annotation, model } = getMVSAnnotationForStructure(structure, props.annotationId);
|
||||
const rows = annotation?.getRows() ?? [];
|
||||
const { count, offsets, grouped } = groupRows(rows);
|
||||
const builder = TextBuilder.create(props, count, count / 2, text);
|
||||
for (let iGroup = 0; iGroup < count; iGroup++) {
|
||||
const iFirstRowInGroup = grouped[offsets[iGroup]];
|
||||
const labelText = annotation!.getValueForRow(iFirstRowInGroup, props.fieldName);
|
||||
if (!labelText) continue;
|
||||
const rowsInGroup = grouped.slice(offsets[iGroup], offsets[iGroup + 1]).map(j => rows[j]);
|
||||
const p = textPropsForSelection(structure, theme.size.size, rowsInGroup, model);
|
||||
if (!p) continue;
|
||||
builder.add(labelText, p.center[0], p.center[1], p.center[2], p.depth, p.scale, p.group);
|
||||
}
|
||||
return builder.getText();
|
||||
}
|
||||
@@ -1,383 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Column, Table } from '../../../mol-data/db';
|
||||
import { CIF, CifBlock, CifCategory, CifFile } from '../../../mol-io/reader/cif';
|
||||
import { toTable } from '../../../mol-io/reader/cif/schema';
|
||||
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
|
||||
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
import { Model } from '../../../mol-model/structure';
|
||||
import { Structure, StructureElement } from '../../../mol-model/structure/structure';
|
||||
import { UUID } from '../../../mol-util';
|
||||
import { arrayExtend } from '../../../mol-util/array';
|
||||
import { Asset } from '../../../mol-util/assets';
|
||||
import { Jsonable, canonicalJsonString } from '../../../mol-util/json';
|
||||
import { pickObjectKeys, promiseAllObj } from '../../../mol-util/object';
|
||||
import { Choice } from '../../../mol-util/param-choice';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { AtomRanges } from '../helpers/atom-ranges';
|
||||
import { IndicesAndSortings } from '../helpers/indexing';
|
||||
import { MaybeStringParamDefinition } from '../helpers/param-definition';
|
||||
import { MVSAnnotationRow, MVSAnnotationSchema, getCifAnnotationSchema } from '../helpers/schemas';
|
||||
import { atomQualifies, getAtomRangesForRow } from '../helpers/selections';
|
||||
import { Maybe, safePromise } from '../helpers/utils';
|
||||
|
||||
|
||||
/** Allowed values for the annotation format parameter */
|
||||
const MVSAnnotationFormat = new Choice({ json: 'json', cif: 'cif', bcif: 'bcif' }, 'json');
|
||||
type MVSAnnotationFormat = Choice.Values<typeof MVSAnnotationFormat>
|
||||
const MVSAnnotationFormatTypes = { json: 'string', cif: 'string', bcif: 'binary' } as const satisfies { [format in MVSAnnotationFormat]: 'string' | 'binary' };
|
||||
|
||||
/** Parameter definition for custom model property "MVS Annotations" */
|
||||
export type MVSAnnotationsParams = typeof MVSAnnotationsParams
|
||||
export const MVSAnnotationsParams = {
|
||||
annotations: PD.ObjectList(
|
||||
{
|
||||
source: PD.MappedStatic('source-cif', {
|
||||
'source-cif': PD.EmptyGroup(),
|
||||
'url': PD.Group({
|
||||
url: PD.Text(''),
|
||||
format: MVSAnnotationFormat.PDSelect(),
|
||||
}),
|
||||
}),
|
||||
schema: MVSAnnotationSchema.PDSelect(),
|
||||
cifBlock: PD.MappedStatic('index', {
|
||||
index: PD.Group({ index: PD.Numeric(0, { min: 0, step: 1 }, { description: '0-based index of the block' }) }),
|
||||
header: PD.Group({ header: PD.Text(undefined, { description: 'Block header' }) }),
|
||||
}, { description: 'Specify which CIF block contains annotation data (only relevant when format=cif or format=bcif)' }),
|
||||
cifCategory: MaybeStringParamDefinition(undefined, { description: 'Specify which CIF category contains annotation data (only relevant when format=cif or format=bcif)' }),
|
||||
id: PD.Text('', { description: 'Arbitrary identifier that can be referenced by MVSAnnotationColorTheme' }),
|
||||
},
|
||||
obj => obj.id
|
||||
),
|
||||
};
|
||||
|
||||
/** Parameter values for custom model property "MVS Annotations" */
|
||||
export type MVSAnnotationsProps = PD.Values<MVSAnnotationsParams>
|
||||
|
||||
/** Parameter values for a single annotation within custom model property "MVS Annotations" */
|
||||
export type MVSAnnotationSpec = MVSAnnotationsProps['annotations'][number]
|
||||
|
||||
/** Describes the source of an annotation file */
|
||||
type MVSAnnotationSource = { kind: 'url', url: string, format: MVSAnnotationFormat } | { kind: 'source-cif' }
|
||||
|
||||
/** Data file with one or more (in case of CIF) annotations */
|
||||
type MVSAnnotationFile = { format: 'json', data: Jsonable } | { format: 'cif', data: CifFile }
|
||||
|
||||
/** Data for a single annotation */
|
||||
type MVSAnnotationData = { format: 'json', data: Jsonable } | { format: 'cif', data: CifCategory }
|
||||
|
||||
|
||||
/** Provider for custom model property "Annotations" */
|
||||
export const MVSAnnotationsProvider: CustomModelProperty.Provider<MVSAnnotationsParams, MVSAnnotations> = CustomModelProperty.createProvider({
|
||||
label: 'Annotations',
|
||||
descriptor: CustomPropertyDescriptor({
|
||||
name: 'mvs-annotations',
|
||||
}),
|
||||
type: 'static',
|
||||
defaultParams: MVSAnnotationsParams,
|
||||
getParams: (data: Model) => MVSAnnotationsParams,
|
||||
isApplicable: (data: Model) => true,
|
||||
obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<MVSAnnotationsProps>) => {
|
||||
props = { ...PD.getDefaultValues(MVSAnnotationsParams), ...props };
|
||||
const specs: MVSAnnotationSpec[] = props.annotations ?? [];
|
||||
const annots = await MVSAnnotations.fromSpecs(ctx, specs, data);
|
||||
return { value: annots } satisfies CustomProperty.Data<MVSAnnotations>;
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
/** Represents multiple annotations retrievable by their ID */
|
||||
export class MVSAnnotations {
|
||||
private constructor(private dict: { [id: string]: MVSAnnotation }) { }
|
||||
static async fromSpecs(ctx: CustomProperty.Context, specs: MVSAnnotationSpec[], model?: Model): Promise<MVSAnnotations> {
|
||||
const sources: MVSAnnotationSource[] = specs.map(annotationSourceFromSpec);
|
||||
const files = await getFilesFromSources(ctx, sources, model);
|
||||
const annots: { [id: string]: MVSAnnotation } = {};
|
||||
for (let i = 0; i < specs.length; i++) {
|
||||
const spec = specs[i];
|
||||
try {
|
||||
const file = files[i];
|
||||
if (!file.ok) throw file.error;
|
||||
annots[spec.id] = await MVSAnnotation.fromSpec(ctx, spec, file.value);
|
||||
} catch (err) {
|
||||
console.error(`Failed to obtain annotation (${err}).\nAnnotation specification:`, spec);
|
||||
annots[spec.id] = MVSAnnotation.createEmpty(spec.schema);
|
||||
}
|
||||
}
|
||||
return new MVSAnnotations(annots);
|
||||
}
|
||||
getAnnotation(id: string): MVSAnnotation | undefined {
|
||||
return this.dict[id];
|
||||
}
|
||||
getAllAnnotations(): MVSAnnotation[] {
|
||||
return Object.values(this.dict);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/** Retrieve annotation with given `annotationId` from custom model property "MVS Annotations" and the model from which it comes */
|
||||
export function getMVSAnnotationForStructure(structure: Structure, annotationId: string): { annotation: MVSAnnotation, model: Model } | { annotation: undefined, model: undefined } {
|
||||
const models = structure.isEmpty ? [] : structure.models;
|
||||
for (const model of models) {
|
||||
if (model.customProperties.has(MVSAnnotationsProvider.descriptor)) {
|
||||
const annots = MVSAnnotationsProvider.get(model).value;
|
||||
const annotation = annots?.getAnnotation(annotationId);
|
||||
if (annotation) {
|
||||
return { annotation, model };
|
||||
}
|
||||
}
|
||||
}
|
||||
return { annotation: undefined, model: undefined };
|
||||
}
|
||||
|
||||
/** Main class for processing MVS annotation */
|
||||
export class MVSAnnotation {
|
||||
/** Store mapping `ElementIndex` -> annotation row index for each `Model`, -1 means no row applies */
|
||||
private indexedModels = new Map<UUID, number[]>();
|
||||
private rows: MVSAnnotationRow[] | undefined = undefined;
|
||||
|
||||
constructor(
|
||||
public data: MVSAnnotationData,
|
||||
public schema: MVSAnnotationSchema,
|
||||
) { }
|
||||
|
||||
/** Create a new `MVSAnnotation` based on specification `spec`. Use `file` if provided, otherwise download the file.
|
||||
* Throw error if download fails or problem with data. */
|
||||
static async fromSpec(ctx: CustomProperty.Context, spec: MVSAnnotationSpec, file?: MVSAnnotationFile): Promise<MVSAnnotation> {
|
||||
file ??= await getFileFromSource(ctx, annotationSourceFromSpec(spec));
|
||||
|
||||
let data: MVSAnnotationData;
|
||||
switch (file.format) {
|
||||
case 'json':
|
||||
data = file;
|
||||
break;
|
||||
case 'cif':
|
||||
if (file.data.blocks.length === 0) throw new Error('No block in CIF');
|
||||
const blockSpec = spec.cifBlock;
|
||||
let block: CifBlock;
|
||||
switch (blockSpec.name) {
|
||||
case 'header':
|
||||
const foundBlock = file.data.blocks.find(b => b.header === blockSpec.params.header);
|
||||
if (!foundBlock) throw new Error(`CIF block with header ${blockSpec.params.header} not found`);
|
||||
block = foundBlock;
|
||||
break;
|
||||
case 'index':
|
||||
block = file.data.blocks[blockSpec.params.index];
|
||||
if (!block) throw new Error(`CIF block with index ${blockSpec.params.index} not found`);
|
||||
break;
|
||||
}
|
||||
const categoryName = spec.cifCategory ?? Object.keys(block.categories)[0];
|
||||
if (!categoryName) throw new Error('There are no categories in CIF block');
|
||||
const category = block.categories[categoryName];
|
||||
if (!category) throw new Error(`CIF category ${categoryName} not found`);
|
||||
data = { format: 'cif', data: category };
|
||||
break;
|
||||
}
|
||||
return new MVSAnnotation(data, spec.schema);
|
||||
}
|
||||
|
||||
static createEmpty(schema: MVSAnnotationSchema): MVSAnnotation {
|
||||
return new MVSAnnotation({ format: 'json', data: [] }, schema);
|
||||
}
|
||||
|
||||
/** Reference implementation of `getAnnotationForLocation`, just for checking, DO NOT USE DIRECTLY */
|
||||
getAnnotationForLocation_Reference(loc: StructureElement.Location): MVSAnnotationRow | undefined {
|
||||
const model = loc.unit.model;
|
||||
const iAtom = loc.element;
|
||||
let result: MVSAnnotationRow | undefined = undefined;
|
||||
for (const row of this.getRows()) {
|
||||
if (atomQualifies(model, iAtom, row)) result = row;
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
/** Return value of field `fieldName` assigned to location `loc`, if any */
|
||||
getValueForLocation(loc: StructureElement.Location, fieldName: string): string | undefined {
|
||||
const indexedModel = this.getIndexedModel(loc.unit.model);
|
||||
const iRow = indexedModel[loc.element];
|
||||
return this.getValueForRow(iRow, fieldName);
|
||||
}
|
||||
/** Return value of field `fieldName` assigned to `i`-th annotation row, if any */
|
||||
getValueForRow(i: number, fieldName: string): string | undefined {
|
||||
if (i < 0) return undefined;
|
||||
switch (this.data.format) {
|
||||
case 'json':
|
||||
const value = getValueFromJson(i, fieldName, this.data.data);
|
||||
if (value === undefined || typeof value === 'string') return value;
|
||||
else return `${value}`;
|
||||
case 'cif':
|
||||
return getValueFromCif(i, fieldName, this.data.data);
|
||||
}
|
||||
}
|
||||
|
||||
/** Return cached `ElementIndex` -> `MVSAnnotationRow` mapping for `Model` (or create it if not cached yet) */
|
||||
private getIndexedModel(model: Model): number[] {
|
||||
const key = model.id;
|
||||
if (!this.indexedModels.has(key)) {
|
||||
const result = this.getRowForEachAtom(model);
|
||||
this.indexedModels.set(key, result);
|
||||
}
|
||||
return this.indexedModels.get(key)!;
|
||||
}
|
||||
|
||||
/** Create `ElementIndex` -> `MVSAnnotationRow` mapping for `Model` */
|
||||
private getRowForEachAtom(model: Model): number[] {
|
||||
const indices = IndicesAndSortings.get(model);
|
||||
const nAtoms = model.atomicHierarchy.atoms._rowCount;
|
||||
const result: number[] = Array(nAtoms).fill(-1);
|
||||
const rows = this.getRows();
|
||||
for (let i = 0, nRows = rows.length; i < nRows; i++) {
|
||||
const atomRanges = getAtomRangesForRow(model, rows[i], indices);
|
||||
AtomRanges.foreach(atomRanges, (from, to) => result.fill(i, from, to));
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
/** Parse and return all annotation rows in this annotation */
|
||||
private _getRows(): MVSAnnotationRow[] {
|
||||
switch (this.data.format) {
|
||||
case 'json':
|
||||
return getRowsFromJson(this.data.data, this.schema);
|
||||
case 'cif':
|
||||
return getRowsFromCif(this.data.data, this.schema);
|
||||
}
|
||||
}
|
||||
/** Parse and return all annotation rows in this annotation, or return cached result if available */
|
||||
getRows(): readonly MVSAnnotationRow[] {
|
||||
return this.rows ??= this._getRows();
|
||||
}
|
||||
}
|
||||
|
||||
function getValueFromJson<T>(rowIndex: number, fieldName: string, data: Jsonable): T | undefined {
|
||||
const js = data as any;
|
||||
if (Array.isArray(js)) {
|
||||
const row = js[rowIndex] ?? {};
|
||||
return row[fieldName];
|
||||
} else {
|
||||
const column = js[fieldName] ?? [];
|
||||
return column[rowIndex];
|
||||
}
|
||||
}
|
||||
function getValueFromCif(rowIndex: number, fieldName: string, data: CifCategory): string | undefined {
|
||||
const column = data.getField(fieldName);
|
||||
if (!column) return undefined;
|
||||
if (column.valueKind(rowIndex) !== Column.ValueKind.Present) return undefined;
|
||||
return column.str(rowIndex);
|
||||
}
|
||||
|
||||
function getRowsFromJson(data: Jsonable, schema: MVSAnnotationSchema): MVSAnnotationRow[] {
|
||||
const js = data as any;
|
||||
const cifSchema = getCifAnnotationSchema(schema);
|
||||
if (Array.isArray(js)) {
|
||||
// array of objects
|
||||
return js.map(row => pickObjectKeys(row, Object.keys(cifSchema)));
|
||||
} else {
|
||||
// object of arrays
|
||||
const rows: MVSAnnotationRow[] = [];
|
||||
const keys = Object.keys(js).filter(key => Object.hasOwn(cifSchema, key as any));
|
||||
if (keys.length > 0) {
|
||||
const n = js[keys[0]].length;
|
||||
if (keys.some(key => js[key].length !== n)) throw new Error('FormatError: arrays must have the same length.');
|
||||
for (let i = 0; i < n; i++) {
|
||||
const item: { [key: string]: any } = {};
|
||||
for (const key of keys) {
|
||||
item[key] = js[key][i];
|
||||
}
|
||||
rows.push(item);
|
||||
}
|
||||
}
|
||||
return rows;
|
||||
}
|
||||
}
|
||||
|
||||
function getRowsFromCif(data: CifCategory, schema: MVSAnnotationSchema): MVSAnnotationRow[] {
|
||||
const rows: MVSAnnotationRow[] = [];
|
||||
const cifSchema = getCifAnnotationSchema(schema);
|
||||
const table = toTable(cifSchema, data);
|
||||
arrayExtend(rows, getRowsFromTable(table)); // Avoiding Table.getRows(table) as it replaces . and ? fields by 0 or ''
|
||||
return rows;
|
||||
}
|
||||
|
||||
/** Same as `Table.getRows` but omits `.` and `?` fields (instead of using type defaults) */
|
||||
function getRowsFromTable<S extends Table.Schema>(table: Table<S>): Partial<Table.Row<S>>[] {
|
||||
const rows: Partial<Table.Row<S>>[] = [];
|
||||
const columns = table._columns;
|
||||
const nRows = table._rowCount;
|
||||
const Present = Column.ValueKind.Present;
|
||||
for (let iRow = 0; iRow < nRows; iRow++) {
|
||||
const row: Partial<Table.Row<S>> = {};
|
||||
for (const col of columns) {
|
||||
if (table[col].valueKind(iRow) === Present) {
|
||||
row[col as keyof S] = table[col].value(iRow);
|
||||
}
|
||||
}
|
||||
rows[iRow] = row;
|
||||
}
|
||||
return rows;
|
||||
}
|
||||
|
||||
async function getFileFromSource(ctx: CustomProperty.Context, source: MVSAnnotationSource, model?: Model): Promise<MVSAnnotationFile> {
|
||||
switch (source.kind) {
|
||||
case 'source-cif':
|
||||
return { format: 'cif', data: getSourceFileFromModel(model) };
|
||||
case 'url':
|
||||
const url = Asset.getUrlAsset(ctx.assetManager, source.url);
|
||||
const dataType = MVSAnnotationFormatTypes[source.format];
|
||||
const dataWrapper = await ctx.assetManager.resolve(url, dataType).runInContext(ctx.runtime);
|
||||
const rawData = dataWrapper.data;
|
||||
if (!rawData) throw new Error('Missing data');
|
||||
switch (source.format) {
|
||||
case 'json':
|
||||
const json = JSON.parse(rawData as string) as Jsonable;
|
||||
return { format: 'json', data: json };
|
||||
case 'cif':
|
||||
case 'bcif':
|
||||
const parsed = await CIF.parse(rawData).run();
|
||||
if (parsed.isError) throw new Error(`Failed to parse ${source.format}`);
|
||||
return { format: 'cif', data: parsed.result };
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/** Like `sources.map(s => safePromise(getFileFromSource(ctx, s)))`
|
||||
* but downloads a repeating source only once. */
|
||||
async function getFilesFromSources(ctx: CustomProperty.Context, sources: MVSAnnotationSource[], model?: Model): Promise<Maybe<MVSAnnotationFile>[]> {
|
||||
const promises: { [key: string]: Promise<Maybe<MVSAnnotationFile>> } = {};
|
||||
for (const src of sources) {
|
||||
const key = canonicalJsonString(src);
|
||||
promises[key] ??= safePromise(getFileFromSource(ctx, src, model));
|
||||
}
|
||||
const files = await promiseAllObj(promises);
|
||||
return sources.map(src => files[canonicalJsonString(src)]);
|
||||
}
|
||||
|
||||
function getSourceFileFromModel(model?: Model): CifFile {
|
||||
if (model && MmcifFormat.is(model.sourceData)) {
|
||||
if (model.sourceData.data.file) {
|
||||
return model.sourceData.data.file;
|
||||
} else {
|
||||
const frame = model.sourceData.data.frame;
|
||||
const block = CifBlock(Array.from(frame.categoryNames), frame.categories, frame.header);
|
||||
const file = CifFile([block]);
|
||||
return file;
|
||||
}
|
||||
} else {
|
||||
console.warn('Could not get CifFile from Model, returning empty CifFile');
|
||||
return CifFile([]);
|
||||
}
|
||||
}
|
||||
|
||||
function annotationSourceFromSpec(s: MVSAnnotationSpec): MVSAnnotationSource {
|
||||
switch (s.source.name) {
|
||||
case 'url':
|
||||
return { kind: 'url', ...s.source.params };
|
||||
case 'source-cif':
|
||||
return { kind: 'source-cif' };
|
||||
}
|
||||
}
|
||||
@@ -1,110 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Structure, StructureSelection } from '../../../mol-model/structure';
|
||||
import { StructureQueryHelper } from '../../../mol-plugin-state/helpers/structure-query';
|
||||
import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
|
||||
import { StateObject, StateTransformer } from '../../../mol-state';
|
||||
import { deepEqual } from '../../../mol-util';
|
||||
import { omitObjectKeys } from '../../../mol-util/object';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { rowsToExpression } from '../helpers/selections';
|
||||
import { getMVSAnnotationForStructure } from './annotation-prop';
|
||||
|
||||
|
||||
/** Parameter definition for `MVSAnnotationStructureComponent` transformer */
|
||||
export const MVSAnnotationStructureComponentParams = {
|
||||
annotationId: PD.Text('', { description: 'Reference to "Annotation" custom model property' }),
|
||||
fieldName: PD.Text('component', { description: 'Annotation field (column) from which to take component identifier' }),
|
||||
fieldValues: PD.MappedStatic('all', {
|
||||
all: PD.EmptyGroup(),
|
||||
selected: PD.ObjectList({
|
||||
value: PD.Text(),
|
||||
}, obj => obj.value),
|
||||
}),
|
||||
nullIfEmpty: PD.Optional(PD.Boolean(true, { isHidden: false })),
|
||||
label: PD.Text('', { isHidden: false }),
|
||||
};
|
||||
|
||||
/** Parameter values for `MVSAnnotationStructureComponent` transformer */
|
||||
export type MVSAnnotationStructureComponentProps = PD.ValuesFor<typeof MVSAnnotationStructureComponentParams>
|
||||
|
||||
|
||||
/** Transformer builder for MVS extension */
|
||||
export const MVSTransform = StateTransformer.builderFactory('mvs');
|
||||
|
||||
/** Transformer for creating a structure component based on custom model property "Annotations" */
|
||||
export type MVSAnnotationStructureComponent = typeof MVSAnnotationStructureComponent
|
||||
export const MVSAnnotationStructureComponent = MVSTransform({
|
||||
name: 'mvs-structure-component-from-annotation',
|
||||
display: { name: 'MVS Annotation Component', description: 'A molecular structure component defined by MVS annotation data.' },
|
||||
from: SO.Molecule.Structure,
|
||||
to: SO.Molecule.Structure,
|
||||
params: MVSAnnotationStructureComponentParams,
|
||||
})({
|
||||
apply({ a, params }) {
|
||||
return createMVSAnnotationStructureComponent(a.data, params);
|
||||
},
|
||||
update: ({ a, b, oldParams, newParams }) => {
|
||||
return updateMVSAnnotationStructureComponent(a.data, b, oldParams, newParams);
|
||||
},
|
||||
dispose({ b }) {
|
||||
b?.data.customPropertyDescriptors.dispose();
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
/** Create a substructure based on `MVSAnnotationStructureComponentProps` */
|
||||
export function createMVSAnnotationSubstructure(structure: Structure, params: MVSAnnotationStructureComponentProps): Structure {
|
||||
const { annotation } = getMVSAnnotationForStructure(structure, params.annotationId);
|
||||
if (annotation) {
|
||||
let rows = annotation.getRows();
|
||||
if (params.fieldValues.name === 'selected') {
|
||||
const selectedValues = new Set<string | undefined>(params.fieldValues.params.map(obj => obj.value));
|
||||
rows = rows.filter((row, i) => selectedValues.has(annotation.getValueForRow(i, params.fieldName)));
|
||||
}
|
||||
const expression = rowsToExpression(rows);
|
||||
|
||||
const { selection } = StructureQueryHelper.createAndRun(structure, expression);
|
||||
return StructureSelection.unionStructure(selection);
|
||||
} else {
|
||||
return Structure.Empty;
|
||||
}
|
||||
}
|
||||
|
||||
/** Create a substructure PSO based on `MVSAnnotationStructureComponentProps` */
|
||||
export function createMVSAnnotationStructureComponent(structure: Structure, params: MVSAnnotationStructureComponentProps) {
|
||||
const component = createMVSAnnotationSubstructure(structure, params);
|
||||
|
||||
if (params.nullIfEmpty && component.elementCount === 0) return StateObject.Null;
|
||||
|
||||
let label = params.label;
|
||||
if (label === undefined || label === '') {
|
||||
if (params.fieldValues.name === 'selected' && params.fieldValues.params.length > 0) {
|
||||
const ellipsis = params.fieldValues.params.length > 1 ? '+...' : '';
|
||||
label = `${params.fieldName}: "${params.fieldValues.params[0].value}"${ellipsis}`;
|
||||
} else {
|
||||
label = 'Component from MVS Annotation';
|
||||
}
|
||||
}
|
||||
|
||||
const props = { label, description: Structure.elementDescription(component) };
|
||||
return new SO.Molecule.Structure(component, props);
|
||||
}
|
||||
|
||||
/** Update a substructure PSO based on `MVSAnnotationStructureComponentProps` */
|
||||
export function updateMVSAnnotationStructureComponent(a: Structure, b: SO.Molecule.Structure, oldParams: MVSAnnotationStructureComponentProps, newParams: MVSAnnotationStructureComponentProps) {
|
||||
const change = !deepEqual(newParams, oldParams);
|
||||
const needsRecreate = !deepEqual(omitObjectKeys(newParams, ['label']), omitObjectKeys(oldParams, ['label']));
|
||||
if (!change) {
|
||||
return StateTransformer.UpdateResult.Unchanged;
|
||||
}
|
||||
if (!needsRecreate) {
|
||||
b.label = newParams.label || b.label;
|
||||
return StateTransformer.UpdateResult.Updated;
|
||||
}
|
||||
return StateTransformer.UpdateResult.Recreate;
|
||||
}
|
||||
@@ -1,68 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { CustomStructureProperty } from '../../../mol-model-props/common/custom-structure-property';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
import { Loci } from '../../../mol-model/loci';
|
||||
import { Structure, StructureElement } from '../../../mol-model/structure';
|
||||
import { LociLabelProvider } from '../../../mol-plugin-state/manager/loci-label';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { filterDefined } from '../helpers/utils';
|
||||
import { MVSAnnotationsProvider } from './annotation-prop';
|
||||
|
||||
|
||||
/** Parameter definition for custom structure property "MVSAnnotationTooltips" */
|
||||
export const MVSAnnotationTooltipsParams = {
|
||||
tooltips: PD.ObjectList(
|
||||
{
|
||||
annotationId: PD.Text('', { description: 'Reference to "MVS Annotation" custom model property' }),
|
||||
fieldName: PD.Text('tooltip', { description: 'Annotation field (column) from which to take color values' }),
|
||||
},
|
||||
obj => `${obj.annotationId}:${obj.fieldName}`
|
||||
),
|
||||
};
|
||||
export type MVSAnnotationTooltipsParams = typeof MVSAnnotationTooltipsParams
|
||||
|
||||
/** Values of custom structure property "MVSAnnotationTooltips" (and for its params at the same type) */
|
||||
export type MVSAnnotationTooltipsProps = PD.Values<MVSAnnotationTooltipsParams>
|
||||
|
||||
|
||||
/** Provider for custom structure property "MVSAnnotationTooltips" */
|
||||
export const MVSAnnotationTooltipsProvider: CustomStructureProperty.Provider<MVSAnnotationTooltipsParams, MVSAnnotationTooltipsProps> = CustomStructureProperty.createProvider({
|
||||
label: 'MVS Annotation Tooltips',
|
||||
descriptor: CustomPropertyDescriptor<any, any>({
|
||||
name: 'mvs-annotation-tooltips',
|
||||
}),
|
||||
type: 'local',
|
||||
defaultParams: MVSAnnotationTooltipsParams,
|
||||
getParams: (data: Structure) => MVSAnnotationTooltipsParams,
|
||||
isApplicable: (data: Structure) => data.root === data,
|
||||
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MVSAnnotationTooltipsProps>) => {
|
||||
const fullProps = { ...PD.getDefaultValues(MVSAnnotationTooltipsParams), ...props };
|
||||
return { value: fullProps } satisfies CustomProperty.Data<MVSAnnotationTooltipsProps>;
|
||||
},
|
||||
});
|
||||
|
||||
|
||||
/** Label provider based on data from "MVS Annotation" custom model property */
|
||||
export const MVSAnnotationTooltipsLabelProvider = {
|
||||
label: (loci: Loci): string | undefined => {
|
||||
switch (loci.kind) {
|
||||
case 'element-loci':
|
||||
if (!loci.structure.customPropertyDescriptors.hasReference(MVSAnnotationTooltipsProvider.descriptor)) return undefined;
|
||||
const location = StructureElement.Loci.getFirstLocation(loci);
|
||||
if (!location) return undefined;
|
||||
const tooltipProps = MVSAnnotationTooltipsProvider.get(location.structure).value;
|
||||
if (!tooltipProps || tooltipProps.tooltips.length === 0) return undefined;
|
||||
const annotations = MVSAnnotationsProvider.get(location.unit.model).value;
|
||||
const texts = tooltipProps.tooltips.map(p => annotations?.getAnnotation(p.annotationId)?.getValueForLocation(location, p.fieldName));
|
||||
return filterDefined(texts).join(' | ');
|
||||
default:
|
||||
return undefined;
|
||||
}
|
||||
}
|
||||
} satisfies LociLabelProvider;
|
||||
@@ -1,49 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Structure } from '../../../../mol-model/structure';
|
||||
import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../../mol-repr/representation';
|
||||
import { ComplexRepresentation, StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../../../../mol-repr/structure/representation';
|
||||
import { MarkerAction } from '../../../../mol-util/marker-action';
|
||||
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
|
||||
import { CustomLabelTextParams, CustomLabelTextVisual } from './visual';
|
||||
|
||||
|
||||
/** Components of "Custom Label" representation */
|
||||
const CustomLabelVisuals = {
|
||||
'label-text': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CustomLabelTextParams>) => ComplexRepresentation('Label text', ctx, getParams, CustomLabelTextVisual),
|
||||
};
|
||||
|
||||
/** Parameter definition for representation type "Custom Label" */
|
||||
export type CustomLabelParams = typeof CustomLabelParams
|
||||
export const CustomLabelParams = {
|
||||
...CustomLabelTextParams,
|
||||
visuals: PD.MultiSelect(['label-text'], PD.objectToOptions(CustomLabelVisuals)),
|
||||
};
|
||||
|
||||
/** Parameter values for representation type "Custom Label" */
|
||||
export type CustomLabelProps = PD.ValuesFor<CustomLabelParams>
|
||||
|
||||
/** Structure representation type "Custom Label", allowing user-defined labels at at user-defined positions */
|
||||
export type CustomLabelRepresentation = StructureRepresentation<CustomLabelParams>
|
||||
export function CustomLabelRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CustomLabelParams>): CustomLabelRepresentation {
|
||||
const repr = Representation.createMulti('Label', ctx, getParams, StructureRepresentationStateBuilder, CustomLabelVisuals as unknown as Representation.Def<Structure, CustomLabelParams>);
|
||||
repr.setState({ pickable: false, markerActions: MarkerAction.None });
|
||||
return repr;
|
||||
}
|
||||
|
||||
/** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
|
||||
export const CustomLabelRepresentationProvider = StructureRepresentationProvider({
|
||||
name: 'mvs-custom-label',
|
||||
label: 'Custom Label',
|
||||
description: 'Displays labels with custom text',
|
||||
factory: CustomLabelRepresentation,
|
||||
getParams: () => CustomLabelParams,
|
||||
defaultValues: PD.getDefaultValues(CustomLabelParams),
|
||||
defaultColorTheme: { name: 'uniform' },
|
||||
defaultSizeTheme: { name: 'physical' },
|
||||
isApplicable: (structure: Structure) => structure.elementCount > 0
|
||||
});
|
||||
@@ -1,108 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Text } from '../../../../mol-geo/geometry/text/text';
|
||||
import { TextBuilder } from '../../../../mol-geo/geometry/text/text-builder';
|
||||
import { Structure } from '../../../../mol-model/structure';
|
||||
import { ComplexTextVisual, ComplexVisual } from '../../../../mol-repr/structure/complex-visual';
|
||||
import * as Original from '../../../../mol-repr/structure/visual/label-text';
|
||||
import { ElementIterator, eachSerialElement, getSerialElementLoci } from '../../../../mol-repr/structure/visual/util/element';
|
||||
import { VisualUpdateState } from '../../../../mol-repr/util';
|
||||
import { VisualContext } from '../../../../mol-repr/visual';
|
||||
import { Theme } from '../../../../mol-theme/theme';
|
||||
import { deepEqual } from '../../../../mol-util';
|
||||
import { ColorNames } from '../../../../mol-util/color/names';
|
||||
import { omitObjectKeys } from '../../../../mol-util/object';
|
||||
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
|
||||
import { textPropsForSelection } from '../../helpers/label-text';
|
||||
import { MaybeIntegerParamDefinition, MaybeStringParamDefinition } from '../../helpers/param-definition';
|
||||
|
||||
|
||||
/** Parameter definition for "label-text" visual in "Custom Label" representation */
|
||||
export type CustomLabelTextParams = typeof CustomLabelTextParams
|
||||
export const CustomLabelTextParams = {
|
||||
items: PD.ObjectList(
|
||||
{
|
||||
text: PD.Text('¯\\_(ツ)_/¯'),
|
||||
position: PD.MappedStatic('selection', {
|
||||
x_y_z: PD.Group({
|
||||
x: PD.Numeric(0),
|
||||
y: PD.Numeric(0),
|
||||
z: PD.Numeric(0),
|
||||
scale: PD.Numeric(1, { min: 0, max: 20, step: 0.1 })
|
||||
}),
|
||||
selection: PD.Group({
|
||||
label_entity_id: MaybeStringParamDefinition(),
|
||||
label_asym_id: MaybeStringParamDefinition(),
|
||||
auth_asym_id: MaybeStringParamDefinition(),
|
||||
|
||||
label_seq_id: MaybeIntegerParamDefinition(),
|
||||
auth_seq_id: MaybeIntegerParamDefinition(),
|
||||
pdbx_PDB_ins_code: MaybeStringParamDefinition(),
|
||||
/** Minimum label_seq_id (inclusive) */
|
||||
beg_label_seq_id: MaybeIntegerParamDefinition(undefined, { description: 'Minimum label_seq_id (inclusive)' }),
|
||||
/** Maximum label_seq_id (inclusive) */
|
||||
end_label_seq_id: MaybeIntegerParamDefinition(),
|
||||
/** Minimum auth_seq_id (inclusive) */
|
||||
beg_auth_seq_id: MaybeIntegerParamDefinition(),
|
||||
/** Maximum auth_seq_id (inclusive) */
|
||||
end_auth_seq_id: MaybeIntegerParamDefinition(),
|
||||
|
||||
/** Atom name like 'CA', 'N', 'O'... */
|
||||
label_atom_id: MaybeStringParamDefinition(),
|
||||
/** Atom name like 'CA', 'N', 'O'... */
|
||||
auth_atom_id: MaybeStringParamDefinition(),
|
||||
/** Element symbol like 'H', 'HE', 'LI', 'BE'... */
|
||||
type_symbol: MaybeStringParamDefinition(),
|
||||
/** Unique atom identifier across conformations (_atom_site.id) */
|
||||
atom_id: MaybeIntegerParamDefinition(),
|
||||
/** 0-base index of the atom in the source data */
|
||||
atom_index: MaybeIntegerParamDefinition(),
|
||||
|
||||
}),
|
||||
}),
|
||||
},
|
||||
obj => obj.text,
|
||||
{ isEssential: true }
|
||||
),
|
||||
...omitObjectKeys(Original.LabelTextParams, ['level', 'chainScale', 'residueScale', 'elementScale']),
|
||||
borderColor: { ...Original.LabelTextParams.borderColor, defaultValue: ColorNames.black },
|
||||
};
|
||||
|
||||
/** Parameter values for "label-text" visual in "Custom Label" representation */
|
||||
export type CustomLabelTextProps = PD.Values<CustomLabelTextParams>
|
||||
|
||||
/** Create "label-text" visual for "Custom Label" representation */
|
||||
export function CustomLabelTextVisual(materialId: number): ComplexVisual<CustomLabelTextParams> {
|
||||
return ComplexTextVisual<CustomLabelTextParams>({
|
||||
defaultProps: PD.getDefaultValues(CustomLabelTextParams),
|
||||
createGeometry: createLabelText,
|
||||
createLocationIterator: ElementIterator.fromStructure,
|
||||
getLoci: getSerialElementLoci,
|
||||
eachLocation: eachSerialElement,
|
||||
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CustomLabelTextParams>, currentProps: PD.Values<CustomLabelTextParams>) => {
|
||||
state.createGeometry = !deepEqual(newProps.items, currentProps.items);
|
||||
}
|
||||
}, materialId);
|
||||
}
|
||||
|
||||
function createLabelText(ctx: VisualContext, structure: Structure, theme: Theme, props: CustomLabelTextProps, text?: Text): Text {
|
||||
const count = props.items.length;
|
||||
const builder = TextBuilder.create(props, count, count / 2, text);
|
||||
for (const item of props.items) {
|
||||
switch (item.position.name) {
|
||||
case 'x_y_z':
|
||||
const scale = item.position.params.scale;
|
||||
builder.add(item.text, item.position.params.x, item.position.params.y, item.position.params.z, scale, scale, 0);
|
||||
break;
|
||||
case 'selection':
|
||||
const p = textPropsForSelection(structure, theme.size.size, item.position.params);
|
||||
if (p) builder.add(item.text, p.center[0], p.center[1], p.center[2], p.depth, p.scale, p.group);
|
||||
break;
|
||||
}
|
||||
}
|
||||
return builder.getText();
|
||||
}
|
||||
@@ -1,78 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
|
||||
import { CustomStructureProperty } from '../../../mol-model-props/common/custom-structure-property';
|
||||
import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
|
||||
import { Loci } from '../../../mol-model/loci';
|
||||
import { Structure, StructureElement } from '../../../mol-model/structure';
|
||||
import { LociLabelProvider } from '../../../mol-plugin-state/manager/loci-label';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { filterDefined } from '../helpers/utils';
|
||||
import { ElementSet, Selector, SelectorParams } from './selector';
|
||||
|
||||
|
||||
/** Parameter definition for custom structure property "CustomTooltips" */
|
||||
export type CustomTooltipsParams = typeof CustomTooltipsParams
|
||||
export const CustomTooltipsParams = {
|
||||
tooltips: PD.ObjectList(
|
||||
{
|
||||
text: PD.Text('', { description: 'Text of the tooltip' }),
|
||||
selector: SelectorParams,
|
||||
},
|
||||
obj => obj.text
|
||||
),
|
||||
};
|
||||
|
||||
/** Parameter values of custom structure property "CustomTooltips" */
|
||||
export type CustomTooltipsProps = PD.Values<CustomTooltipsParams>
|
||||
|
||||
/** Values of custom structure property "CustomTooltips" (and for its params at the same type) */
|
||||
export type CustomTooltipsData = { selector: Selector, text: string, elementSet?: ElementSet }[]
|
||||
|
||||
|
||||
/** Provider for custom structure property "CustomTooltips" */
|
||||
export const CustomTooltipsProvider: CustomStructureProperty.Provider<CustomTooltipsParams, CustomTooltipsData> = CustomStructureProperty.createProvider({
|
||||
label: 'Custom Tooltips',
|
||||
descriptor: CustomPropertyDescriptor<any, any>({
|
||||
name: 'mvs-custom-tooltips',
|
||||
}),
|
||||
type: 'local',
|
||||
defaultParams: CustomTooltipsParams,
|
||||
getParams: (data: Structure) => CustomTooltipsParams,
|
||||
isApplicable: (data: Structure) => data.root === data,
|
||||
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<CustomTooltipsProps>) => {
|
||||
const fullProps = { ...PD.getDefaultValues(CustomTooltipsParams), ...props };
|
||||
const value = fullProps.tooltips.map(t => ({
|
||||
selector: t.selector,
|
||||
text: t.text,
|
||||
} satisfies CustomTooltipsData[number]));
|
||||
return { value: value } satisfies CustomProperty.Data<CustomTooltipsData>;
|
||||
},
|
||||
});
|
||||
|
||||
|
||||
/** Label provider based on custom structure property "CustomTooltips" */
|
||||
export const CustomTooltipsLabelProvider = {
|
||||
label: (loci: Loci): string | undefined => {
|
||||
switch (loci.kind) {
|
||||
case 'element-loci':
|
||||
if (!loci.structure.customPropertyDescriptors.hasReference(CustomTooltipsProvider.descriptor)) return undefined;
|
||||
const location = StructureElement.Loci.getFirstLocation(loci);
|
||||
if (!location) return undefined;
|
||||
const tooltipData = CustomTooltipsProvider.get(location.structure).value;
|
||||
if (!tooltipData || tooltipData.length === 0) return undefined;
|
||||
const texts = [];
|
||||
for (const tooltip of tooltipData) {
|
||||
const elements = tooltip.elementSet ??= ElementSet.fromSelector(location.structure, tooltip.selector);
|
||||
if (ElementSet.has(elements, location)) texts.push(tooltip.text);
|
||||
}
|
||||
return filterDefined(texts).join(' | ');
|
||||
default:
|
||||
return undefined;
|
||||
}
|
||||
}
|
||||
} satisfies LociLabelProvider;
|
||||
@@ -1,67 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { DataFormatProvider } from '../../../mol-plugin-state/formats/provider';
|
||||
import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
|
||||
import { PluginContext } from '../../../mol-plugin/context';
|
||||
import { StateAction, StateObjectRef } from '../../../mol-state';
|
||||
import { Task } from '../../../mol-task';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { loadMVS } from '../load';
|
||||
import { MVSData } from '../mvs-data';
|
||||
import { MVSTransform } from './annotation-structure-component';
|
||||
|
||||
|
||||
/** Plugin state object storing `MVSData` */
|
||||
export class Mvs extends SO.Create<MVSData>({ name: 'MVS Data', typeClass: 'Data' }) { }
|
||||
|
||||
/** Transformer for parsing data in MVSJ format */
|
||||
export const ParseMVSJ = MVSTransform({
|
||||
name: 'mvs-parse-mvsj',
|
||||
display: { name: 'MVS Annotation Component', description: 'A molecular structure component defined by MVS annotation data.' },
|
||||
from: SO.Data.String,
|
||||
to: Mvs,
|
||||
})({
|
||||
apply({ a }) {
|
||||
const mvsData = MVSData.fromMVSJ(a.data);
|
||||
return new Mvs(mvsData);
|
||||
},
|
||||
});
|
||||
|
||||
|
||||
/** Params for the `LoadMvsData` action */
|
||||
const LoadMvsDataParams = {
|
||||
replaceExisting: PD.Boolean(false, { description: 'If true, the loaded MVS view will replace the current state; if false, the MVS view will be added to the current state.' }),
|
||||
};
|
||||
|
||||
/** State action which loads a MVS view into Mol* */
|
||||
export const LoadMvsData = StateAction.build({
|
||||
display: { name: 'Load MVS Data' },
|
||||
from: Mvs,
|
||||
params: LoadMvsDataParams,
|
||||
})(({ a, params }, plugin: PluginContext) => Task.create('Load MVS Data', async () => {
|
||||
const mvsData = a.data;
|
||||
await loadMVS(plugin, mvsData, { replaceExisting: params.replaceExisting });
|
||||
}));
|
||||
|
||||
|
||||
/** Data format provider for MVSJ format.
|
||||
* If Visuals:On, it will load the parsed MVS view;
|
||||
* otherwise it will just create a plugin state object with parsed data. */
|
||||
export const MVSJFormatProvider: DataFormatProvider<{}, StateObjectRef<Mvs>, any> = DataFormatProvider({
|
||||
label: 'MVSJ',
|
||||
description: 'MVSJ',
|
||||
category: 'Miscellaneous',
|
||||
stringExtensions: ['mvsj'],
|
||||
parse: async (plugin, data) => {
|
||||
return plugin.state.data.build().to(data).apply(ParseMVSJ).commit();
|
||||
},
|
||||
visuals: async (plugin, data) => {
|
||||
const ref = StateObjectRef.resolveRef(data);
|
||||
const params = PD.getDefaultValues(LoadMvsDataParams);
|
||||
return await plugin.state.data.applyAction(LoadMvsData, params, ref).run();
|
||||
},
|
||||
});
|
||||
@@ -1,147 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Location } from '../../../mol-model/location';
|
||||
import { Bond, Structure, StructureElement } from '../../../mol-model/structure';
|
||||
import { ColorTheme, LocationColor } from '../../../mol-theme/color';
|
||||
import { ThemeDataContext } from '../../../mol-theme/theme';
|
||||
import { Color } from '../../../mol-util/color';
|
||||
import { ColorNames } from '../../../mol-util/color/names';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { stringToWords } from '../../../mol-util/string';
|
||||
import { ElementSet, SelectorParams, isSelectorAll } from './selector';
|
||||
|
||||
|
||||
/** Special value that can be used as color with null-like semantic (i.e. "no color provided").
|
||||
* By some lucky coincidence, Mol* treats -1 as white. */
|
||||
export const NoColor = Color(-1);
|
||||
|
||||
/** Return true if `color` is a real color, false if it is `NoColor`. */
|
||||
function isValidColor(color: Color): boolean {
|
||||
return color >= 0;
|
||||
}
|
||||
|
||||
const DefaultBackgroundColor = ColorNames.white;
|
||||
|
||||
/** Parameter definition for color theme "Multilayer" */
|
||||
export function makeMultilayerColorThemeParams(colorThemeRegistry: ColorTheme.Registry, ctx: ThemeDataContext) {
|
||||
const colorThemeInfo = {
|
||||
help: (value: { name: string, params: {} }) => {
|
||||
const { name, params } = value;
|
||||
const p = colorThemeRegistry.get(name);
|
||||
const ct = p.factory({}, params);
|
||||
return { description: ct.description, legend: ct.legend };
|
||||
}
|
||||
};
|
||||
const nestedThemeTypes = colorThemeRegistry.types.filter(([name, label, category]) => name !== MultilayerColorThemeName && colorThemeRegistry.get(name).isApplicable(ctx)); // Adding 'multilayer' theme itself would cause infinite recursion
|
||||
return {
|
||||
layers: PD.ObjectList(
|
||||
{
|
||||
theme: PD.Mapped<any>(
|
||||
'uniform',
|
||||
nestedThemeTypes,
|
||||
name => PD.Group<any>(colorThemeRegistry.get(name).getParams({ structure: Structure.Empty })),
|
||||
colorThemeInfo),
|
||||
selection: SelectorParams,
|
||||
},
|
||||
obj => stringToWords(obj.theme.name),
|
||||
{ description: 'A list of layers, each defining a color theme. The last listed layer is the top layer (applies first). If the top layer does not provide color for a location or its selection does not cover the location, the underneath layers will apply.' }),
|
||||
background: PD.Color(DefaultBackgroundColor, { description: 'Color for elements where no layer applies' }),
|
||||
};
|
||||
}
|
||||
/** Parameter definition for color theme "Multilayer" */
|
||||
export type MultilayerColorThemeParams = ReturnType<typeof makeMultilayerColorThemeParams>
|
||||
|
||||
/** Parameter values for color theme "Multilayer" */
|
||||
export type MultilayerColorThemeProps = PD.Values<MultilayerColorThemeParams>
|
||||
|
||||
/** Default values for `MultilayerColorThemeProps` */
|
||||
export const DefaultMultilayerColorThemeProps: MultilayerColorThemeProps = { layers: [], background: DefaultBackgroundColor };
|
||||
|
||||
|
||||
/** Return color theme that assigns colors based on a list of nested color themes (layers).
|
||||
* The last layer in the list whose selection covers the given location
|
||||
* and which provides a valid (non-negative) color value will be used.
|
||||
* If a nested theme provider has `ensureCustomProperties` methods, these will not be called automatically
|
||||
* (the caller must ensure that any required custom properties be attached). */
|
||||
function makeMultilayerColorTheme(ctx: ThemeDataContext, props: MultilayerColorThemeProps, colorThemeRegistry: ColorTheme.Registry): ColorTheme<MultilayerColorThemeParams> {
|
||||
const colorLayers: { color: LocationColor, elementSet: ElementSet | undefined }[] = []; // undefined elementSet means 'all'
|
||||
for (let i = props.layers.length - 1; i >= 0; i--) { // iterate from end to get top layer first, bottom layer last
|
||||
const layer = props.layers[i];
|
||||
const themeProvider = colorThemeRegistry.get(layer.theme.name);
|
||||
if (!themeProvider) {
|
||||
console.warn(`Skipping color theme '${layer.theme.name}', cannot find it in registry.`);
|
||||
continue;
|
||||
}
|
||||
if (themeProvider.ensureCustomProperties?.attach) {
|
||||
console.warn(`Multilayer color theme: layer "${themeProvider.name}" has ensureCustomProperties.attach method, but Multilayer color theme does not call it. If the layer does not work, make sure you call ensureCustomProperties.attach somewhere.`);
|
||||
}
|
||||
const theme = themeProvider.factory(ctx, layer.theme.params);
|
||||
switch (theme.granularity) {
|
||||
case 'uniform':
|
||||
case 'instance':
|
||||
case 'group':
|
||||
case 'groupInstance':
|
||||
case 'vertex':
|
||||
case 'vertexInstance':
|
||||
const elementSet = isSelectorAll(layer.selection) ? undefined : ElementSet.fromSelector(ctx.structure, layer.selection); // treating 'all' specially for performance reasons (it's expected to be used most often)
|
||||
colorLayers.push({ color: theme.color, elementSet });
|
||||
break;
|
||||
default:
|
||||
console.warn(`Skipping color theme '${layer.theme.name}', cannot process granularity '${theme.granularity}'`);
|
||||
}
|
||||
};
|
||||
|
||||
function structureElementColor(loc: StructureElement.Location, isSecondary: boolean): Color {
|
||||
for (const layer of colorLayers) {
|
||||
const matches = !layer.elementSet || ElementSet.has(layer.elementSet, loc);
|
||||
if (!matches) continue;
|
||||
const color = layer.color(loc, isSecondary);
|
||||
if (!isValidColor(color)) continue;
|
||||
return color;
|
||||
}
|
||||
return props.background;
|
||||
}
|
||||
const auxLocation = StructureElement.Location.create(ctx.structure);
|
||||
|
||||
const color: LocationColor = (location: Location, isSecondary: boolean) => {
|
||||
if (StructureElement.Location.is(location)) {
|
||||
return structureElementColor(location, isSecondary);
|
||||
} else if (Bond.isLocation(location)) {
|
||||
// this will be applied for each bond twice, to get color of each half (a* refers to the adjacent atom, b* to the opposite atom)
|
||||
auxLocation.unit = location.aUnit;
|
||||
auxLocation.element = location.aUnit.elements[location.aIndex];
|
||||
return structureElementColor(auxLocation, isSecondary);
|
||||
}
|
||||
return props.background;
|
||||
};
|
||||
|
||||
return {
|
||||
factory: (ctx_, props_) => makeMultilayerColorTheme(ctx_, props_, colorThemeRegistry),
|
||||
granularity: 'group',
|
||||
preferSmoothing: true,
|
||||
color: color,
|
||||
props: props,
|
||||
description: 'Combines colors from multiple color themes.',
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
/** Unique name for "Multilayer" color theme */
|
||||
export const MultilayerColorThemeName = 'mvs-multilayer';
|
||||
|
||||
/** A thingy that is needed to register color theme "Multilayer" */
|
||||
export function makeMultilayerColorThemeProvider(colorThemeRegistry: ColorTheme.Registry): ColorTheme.Provider<MultilayerColorThemeParams, typeof MultilayerColorThemeName> {
|
||||
return {
|
||||
name: MultilayerColorThemeName,
|
||||
label: 'Multi-layer',
|
||||
category: ColorTheme.Category.Misc,
|
||||
factory: (ctx, props) => makeMultilayerColorTheme(ctx, props, colorThemeRegistry),
|
||||
getParams: (ctx: ThemeDataContext) => makeMultilayerColorThemeParams(colorThemeRegistry, ctx),
|
||||
defaultValues: DefaultMultilayerColorThemeProps,
|
||||
isApplicable: (ctx: ThemeDataContext) => true,
|
||||
};
|
||||
}
|
||||
@@ -1,81 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { SortedArray } from '../../../mol-data/int';
|
||||
import { ElementIndex, Structure, StructureElement } from '../../../mol-model/structure';
|
||||
import { StaticStructureComponentTypes, createStructureComponent } from '../../../mol-plugin-state/helpers/structure-component';
|
||||
import { PluginStateObject } from '../../../mol-plugin-state/objects';
|
||||
import { MolScriptBuilder } from '../../../mol-script/language/builder';
|
||||
import { Expression } from '../../../mol-script/language/expression';
|
||||
import { UUID } from '../../../mol-util';
|
||||
import { arrayExtend, sortIfNeeded } from '../../../mol-util/array';
|
||||
import { mapArrayToObject, pickObjectKeys } from '../../../mol-util/object';
|
||||
import { Choice } from '../../../mol-util/param-choice';
|
||||
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
|
||||
import { capitalize } from '../../../mol-util/string';
|
||||
import { MVSAnnotationStructureComponentParams, createMVSAnnotationStructureComponent } from './annotation-structure-component';
|
||||
|
||||
|
||||
/** Allowed values for a static selector */
|
||||
export const StaticSelectorChoice = new Choice(mapArrayToObject(StaticStructureComponentTypes, t => capitalize(t)), 'all');
|
||||
export type StaticSelectorChoice = Choice.Values<typeof StaticSelectorChoice>
|
||||
|
||||
|
||||
/** Parameter definition for specifying a part of structure (kinda extension of `StructureComponentParams` from mol-plugin-state/helpers/structure-component) */
|
||||
export const SelectorParams = PD.MappedStatic('static', {
|
||||
static: StaticSelectorChoice.PDSelect(),
|
||||
expression: PD.Value<Expression>(MolScriptBuilder.struct.generator.all),
|
||||
bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty),
|
||||
script: PD.Script({ language: 'mol-script', expression: '(sel.atom.all)' }),
|
||||
annotation: PD.Group(pickObjectKeys(MVSAnnotationStructureComponentParams, ['annotationId', 'fieldName', 'fieldValues'])),
|
||||
}, { description: 'Define a part of the structure where this layer applies (use Static:all to apply to the whole structure)' }
|
||||
);
|
||||
|
||||
/** Parameter values for specifying a part of structure */
|
||||
export type Selector = PD.Values<{ selector: typeof SelectorParams }>['selector']
|
||||
|
||||
/** `Selector` for selecting the whole structure */
|
||||
export const SelectorAll = { name: 'static', params: 'all' } satisfies Selector;
|
||||
|
||||
/** Decide whether a selector is `SelectorAll` */
|
||||
export function isSelectorAll(props: Selector): props is typeof SelectorAll {
|
||||
return props.name === 'static' && props.params === 'all';
|
||||
}
|
||||
|
||||
|
||||
/** Data structure for fast lookup of a structure element location in a substructure */
|
||||
export type ElementSet = { [modelId: UUID]: SortedArray<ElementIndex> }
|
||||
|
||||
export const ElementSet = {
|
||||
/** Create an `ElementSet` from the substructure of `structure` defined by `selector` */
|
||||
fromSelector(structure: Structure | undefined, selector: Selector): ElementSet {
|
||||
if (!structure) return {};
|
||||
const arrays: { [modelId: UUID]: ElementIndex[] } = {};
|
||||
const selection = substructureFromSelector(structure, selector); // using `getAtomRangesForRow` might (might not) be faster here
|
||||
for (const unit of selection.units) {
|
||||
arrayExtend(arrays[unit.model.id] ??= [], unit.elements);
|
||||
}
|
||||
const result: { [modelId: UUID]: SortedArray<ElementIndex> } = {};
|
||||
for (const modelId in arrays) {
|
||||
const array = arrays[modelId as UUID];
|
||||
sortIfNeeded(array, (a, b) => a - b);
|
||||
result[modelId as UUID] = SortedArray.ofSortedArray(array);
|
||||
}
|
||||
return result;
|
||||
},
|
||||
/** Decide if the element set `set` contains structure element location `location` */
|
||||
has(set: ElementSet, location: StructureElement.Location): boolean {
|
||||
const array = set[location.unit.model.id];
|
||||
return array ? SortedArray.has(array, location.element) : false;
|
||||
},
|
||||
};
|
||||
|
||||
function substructureFromSelector(structure: Structure, selector: Selector): Structure {
|
||||
const pso = (selector.name === 'annotation') ?
|
||||
createMVSAnnotationStructureComponent(structure, { ...selector.params, label: '', nullIfEmpty: false })
|
||||
: createStructureComponent(structure, { type: selector, label: '', nullIfEmpty: false }, { source: structure });
|
||||
return PluginStateObject.Molecule.Structure.is(pso) ? pso.data : Structure.Empty;
|
||||
}
|
||||
@@ -1,50 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { AtomRanges } from '../atom-ranges';
|
||||
|
||||
|
||||
describe('union', () => {
|
||||
it('union non-overlapping', async () => {
|
||||
const a = {
|
||||
from: [0, 20, 40, 60, 80],
|
||||
to: [10, 30, 50, 70, 90],
|
||||
} as AtomRanges;
|
||||
const b = {
|
||||
from: [11, 37, 51, 205],
|
||||
to: [15, 39, 55, 210],
|
||||
} as AtomRanges;
|
||||
const c = {
|
||||
from: [-10, 200, 300],
|
||||
to: [-5, 202, 305],
|
||||
} as AtomRanges;
|
||||
const result = {
|
||||
from: [-10, 0, 11, 20, 37, 40, 51, 60, 80, 200, 205, 300],
|
||||
to: [-5, 10, 15, 30, 39, 50, 55, 70, 90, 202, 210, 305],
|
||||
} as AtomRanges;
|
||||
expect(AtomRanges.union([a, b, c])).toEqual(result);
|
||||
});
|
||||
it('union overlapping', async () => {
|
||||
const a = {
|
||||
from: [0, 20, 40, 60, 80],
|
||||
to: [10, 30, 50, 70, 90],
|
||||
} as AtomRanges;
|
||||
const b = {
|
||||
from: [10, 37, 51, 84, 205],
|
||||
to: [15, 40, 55, 88, 220],
|
||||
} as AtomRanges;
|
||||
const c = {
|
||||
from: [-10, 67, 200, 300],
|
||||
to: [5, 80, 210, 305],
|
||||
} as AtomRanges;
|
||||
const result = {
|
||||
from: [-10, 20, 37, 51, 60, 200, 300],
|
||||
to: [15, 30, 50, 55, 90, 220, 305],
|
||||
} as AtomRanges;
|
||||
expect(AtomRanges.union([a, b, c])).toEqual(result);
|
||||
});
|
||||
});
|
||||
|
||||
@@ -1,29 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { range } from '../../../../mol-util/array';
|
||||
import { MVSAnnotationRow } from '../schemas';
|
||||
import { groupRows } from '../selections';
|
||||
|
||||
|
||||
describe('groupRows', () => {
|
||||
it('groupRows', async () => {
|
||||
const rows = [
|
||||
{ label: 'A' }, { label: 'B', group_id: 1 }, { label: 'C', group_id: 'x' }, { label: 'D', group_id: 1 },
|
||||
{ label: 'E' }, { label: 'F' }, { label: 'G', group_id: 'x' }, { label: 'H', group_id: 'x' },
|
||||
] as any as MVSAnnotationRow[];
|
||||
const g = groupRows(rows);
|
||||
const groupedIndices = range(g.count).map(i => g.grouped.slice(g.offsets[i], g.offsets[i + 1]));
|
||||
const groupedRows = groupedIndices.map(group => group.map(j => rows[j]));
|
||||
expect(groupedRows).toEqual([
|
||||
[{ label: 'A' }],
|
||||
[{ label: 'B', group_id: 1 }, { label: 'D', group_id: 1 }],
|
||||
[{ label: 'C', group_id: 'x' }, { label: 'G', group_id: 'x' }, { label: 'H', group_id: 'x' }],
|
||||
[{ label: 'E' }],
|
||||
[{ label: 'F' }],
|
||||
]);
|
||||
});
|
||||
});
|
||||
@@ -1,137 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { SortedArray } from '../../../mol-data/int';
|
||||
import { ElementIndex } from '../../../mol-model/structure';
|
||||
import { arrayExtend, range } from '../../../mol-util/array';
|
||||
|
||||
|
||||
/** Represents a collection of disjoint atom ranges in a model.
|
||||
* The number of ranges is `AtomRanges.count(ranges)`,
|
||||
* the i-th range covers atoms `[ranges.from[i], ranges.to[i])`. */
|
||||
export interface AtomRanges {
|
||||
from: ElementIndex[],
|
||||
to: ElementIndex[],
|
||||
}
|
||||
|
||||
export const AtomRanges = {
|
||||
/** Return the number of disjoined ranges in a `AtomRanges` object */
|
||||
count(ranges: AtomRanges): number {
|
||||
return ranges.from.length;
|
||||
},
|
||||
|
||||
/** Create new `AtomRanges` without any atoms */
|
||||
empty(): AtomRanges {
|
||||
return { from: [], to: [] };
|
||||
},
|
||||
|
||||
/** Create new `AtomRanges` containing a single range of atoms `[from, to)` */
|
||||
single(from: ElementIndex, to: ElementIndex): AtomRanges {
|
||||
return { from: [from], to: [to] };
|
||||
},
|
||||
|
||||
/** Add a range of atoms `[from, to)` to existing `AtomRanges` and return the modified original.
|
||||
* The added range must start after the end of the last existing range
|
||||
* (if it starts just on the next atom, these two ranges will get merged). */
|
||||
add(ranges: AtomRanges, from: ElementIndex, to: ElementIndex): AtomRanges {
|
||||
const n = AtomRanges.count(ranges);
|
||||
if (n > 0) {
|
||||
const lastTo = ranges.to[n - 1];
|
||||
if (from < lastTo) throw new Error('Overlapping ranges not allowed');
|
||||
if (from === lastTo) {
|
||||
ranges.to[n - 1] = to;
|
||||
} else {
|
||||
ranges.from.push(from);
|
||||
ranges.to.push(to);
|
||||
}
|
||||
} else {
|
||||
ranges.from.push(from);
|
||||
ranges.to.push(to);
|
||||
}
|
||||
return ranges;
|
||||
},
|
||||
|
||||
/** Apply function `func` to each range in `ranges` */
|
||||
foreach(ranges: AtomRanges, func: (from: ElementIndex, to: ElementIndex) => any) {
|
||||
const n = AtomRanges.count(ranges);
|
||||
for (let i = 0; i < n; i++) func(ranges.from[i], ranges.to[i]);
|
||||
},
|
||||
|
||||
/** Apply function `func` to each range in `ranges` and return an array with results */
|
||||
map<T>(ranges: AtomRanges, func: (from: ElementIndex, to: ElementIndex) => T): T[] {
|
||||
const n = AtomRanges.count(ranges);
|
||||
const result: T[] = new Array(n);
|
||||
for (let i = 0; i < n; i++) result[i] = func(ranges.from[i], ranges.to[i]);
|
||||
return result;
|
||||
},
|
||||
|
||||
/** Compute the set union of multiple `AtomRanges` objects (as sets of atoms) */
|
||||
union(ranges: AtomRanges[]): AtomRanges {
|
||||
const concat = AtomRanges.empty();
|
||||
for (const r of ranges) {
|
||||
arrayExtend(concat.from, r.from);
|
||||
arrayExtend(concat.to, r.to);
|
||||
}
|
||||
const indices = range(concat.from.length).sort((i, j) => concat.from[i] - concat.from[j]); // sort by start of range
|
||||
const result = AtomRanges.empty();
|
||||
let last = -1;
|
||||
for (const i of indices) {
|
||||
const from = concat.from[i];
|
||||
const to = concat.to[i];
|
||||
if (last >= 0 && from <= result.to[last]) {
|
||||
if (to > result.to[last]) {
|
||||
result.to[last] = to;
|
||||
}
|
||||
} else {
|
||||
result.from.push(from);
|
||||
result.to.push(to);
|
||||
last++;
|
||||
}
|
||||
}
|
||||
return result;
|
||||
},
|
||||
|
||||
/** Return a sorted subset of `atoms` which lie in any of `ranges` (i.e. set intersection of `atoms` and `ranges`).
|
||||
* If `out` is provided, use it to store the result (clear any old contents).
|
||||
* If `outFirstAtomIndex` is provided, fill `outFirstAtomIndex.value` with the index of the first selected atom (if any). */
|
||||
selectAtomsInRanges(atoms: SortedArray<ElementIndex>, ranges: AtomRanges, out?: ElementIndex[], outFirstAtomIndex: { value?: number } = {}): ElementIndex[] {
|
||||
out ??= [];
|
||||
out.length = 0;
|
||||
outFirstAtomIndex.value = undefined;
|
||||
|
||||
const nAtoms = atoms.length;
|
||||
const nRanges = AtomRanges.count(ranges);
|
||||
if (nAtoms <= nRanges) {
|
||||
// Implementation 1 (more efficient when there are fewer atoms)
|
||||
let iRange = SortedArray.findPredecessorIndex(SortedArray.ofSortedArray(ranges.to), atoms[0] + 1);
|
||||
for (let iAtom = 0; iAtom < nAtoms; iAtom++) {
|
||||
const a = atoms[iAtom];
|
||||
while (iRange < nRanges && ranges.to[iRange] <= a) iRange++;
|
||||
const qualifies = iRange < nRanges && ranges.from[iRange] <= a;
|
||||
if (qualifies) {
|
||||
out.push(a);
|
||||
outFirstAtomIndex.value ??= iAtom;
|
||||
}
|
||||
}
|
||||
} else {
|
||||
// Implementation 2 (more efficient when there are fewer ranges)
|
||||
for (let iRange = 0; iRange < nRanges; iRange++) {
|
||||
const from = ranges.from[iRange];
|
||||
const to = ranges.to[iRange];
|
||||
for (let iAtom = SortedArray.findPredecessorIndex(atoms, from); iAtom < nAtoms; iAtom++) {
|
||||
const a = atoms[iAtom];
|
||||
if (a < to) {
|
||||
out.push(a);
|
||||
outFirstAtomIndex.value ??= iAtom;
|
||||
} else {
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return out;
|
||||
},
|
||||
};
|
||||
@@ -1,130 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Column } from '../../../mol-data/db';
|
||||
import { SortedArray } from '../../../mol-data/int';
|
||||
import { ChainIndex, ElementIndex, Model, ResidueIndex } from '../../../mol-model/structure';
|
||||
import { filterInPlace, range, sortIfNeeded } from '../../../mol-util/array';
|
||||
import { Mapping, MultiMap, NumberMap } from './utils';
|
||||
|
||||
|
||||
/** Auxiliary data structure for efficiently finding chains/residues/atoms in a model by their properties */
|
||||
export interface IndicesAndSortings {
|
||||
chainsByLabelEntityId: Mapping<string, readonly ChainIndex[]>,
|
||||
chainsByLabelAsymId: Mapping<string, readonly ChainIndex[]>,
|
||||
chainsByAuthAsymId: Mapping<string, readonly ChainIndex[]>,
|
||||
residuesSortedByLabelSeqId: Mapping<ChainIndex, Sorting<ResidueIndex, number>>,
|
||||
residuesSortedByAuthSeqId: Mapping<ChainIndex, Sorting<ResidueIndex, number>>,
|
||||
residuesByInsCode: Mapping<ChainIndex, Mapping<string, readonly ResidueIndex[]>>,
|
||||
atomsById: Mapping<number, ElementIndex>,
|
||||
atomsByIndex: Mapping<number, ElementIndex>,
|
||||
}
|
||||
|
||||
export const IndicesAndSortings = {
|
||||
/** Get `IndicesAndSortings` for a model (use a cached value or create if not available yet) */
|
||||
get(model: Model): IndicesAndSortings {
|
||||
return model._dynamicPropertyData['indices-and-sortings'] ??= IndicesAndSortings.create(model);
|
||||
},
|
||||
|
||||
/** Create `IndicesAndSortings` for a model */
|
||||
create(model: Model): IndicesAndSortings {
|
||||
const h = model.atomicHierarchy;
|
||||
const nAtoms = h.atoms._rowCount;
|
||||
const nChains = h.chains._rowCount;
|
||||
const { label_entity_id, label_asym_id, auth_asym_id } = h.chains;
|
||||
const { label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = h.residues;
|
||||
const { Present } = Column.ValueKind;
|
||||
|
||||
const chainsByLabelEntityId = new MultiMap<string, ChainIndex>();
|
||||
const chainsByLabelAsymId = new MultiMap<string, ChainIndex>();
|
||||
const chainsByAuthAsymId = new MultiMap<string, ChainIndex>();
|
||||
const residuesSortedByLabelSeqId = new Map<ChainIndex, Sorting<ResidueIndex, number>>();
|
||||
const residuesSortedByAuthSeqId = new Map<ChainIndex, Sorting<ResidueIndex, number>>();
|
||||
const residuesByInsCode = new Map<ChainIndex, MultiMap<string, ResidueIndex>>();
|
||||
const atomsById = new NumberMap<number, ElementIndex>(nAtoms + 1);
|
||||
const atomsByIndex = new NumberMap<number, ElementIndex>(nAtoms);
|
||||
|
||||
for (let iChain = 0 as ChainIndex; iChain < nChains; iChain++) {
|
||||
chainsByLabelEntityId.add(label_entity_id.value(iChain), iChain);
|
||||
chainsByLabelAsymId.add(label_asym_id.value(iChain), iChain);
|
||||
chainsByAuthAsymId.add(auth_asym_id.value(iChain), iChain);
|
||||
|
||||
const iResFrom = h.residueAtomSegments.index[h.chainAtomSegments.offsets[iChain]];
|
||||
const iResTo = h.residueAtomSegments.index[h.chainAtomSegments.offsets[iChain + 1] - 1] + 1;
|
||||
|
||||
const residuesWithLabelSeqId = filterInPlace(range(iResFrom, iResTo) as ResidueIndex[], iRes => label_seq_id.valueKind(iRes) === Present);
|
||||
residuesSortedByLabelSeqId.set(iChain, Sorting.create(residuesWithLabelSeqId, label_seq_id.value));
|
||||
|
||||
const residuesWithAuthSeqId = filterInPlace(range(iResFrom, iResTo) as ResidueIndex[], iRes => auth_seq_id.valueKind(iRes) === Present);
|
||||
residuesSortedByAuthSeqId.set(iChain, Sorting.create(residuesWithAuthSeqId, auth_seq_id.value));
|
||||
|
||||
const residuesHereByInsCode = new MultiMap<string, ResidueIndex>();
|
||||
for (let iRes = iResFrom; iRes < iResTo; iRes++) {
|
||||
if (pdbx_PDB_ins_code.valueKind(iRes) === Present) {
|
||||
residuesHereByInsCode.add(pdbx_PDB_ins_code.value(iRes), iRes);
|
||||
}
|
||||
}
|
||||
residuesByInsCode.set(iChain, residuesHereByInsCode);
|
||||
}
|
||||
|
||||
const atomId = model.atomicConformation.atomId.value;
|
||||
const atomIndex = h.atomSourceIndex.value;
|
||||
for (let iAtom = 0 as ElementIndex; iAtom < nAtoms; iAtom++) {
|
||||
atomsById.set(atomId(iAtom), iAtom);
|
||||
atomsByIndex.set(atomIndex(iAtom), iAtom);
|
||||
}
|
||||
|
||||
return {
|
||||
chainsByLabelEntityId, chainsByLabelAsymId, chainsByAuthAsymId,
|
||||
residuesSortedByLabelSeqId, residuesSortedByAuthSeqId, residuesByInsCode,
|
||||
atomsById, atomsByIndex,
|
||||
};
|
||||
},
|
||||
};
|
||||
|
||||
|
||||
/** Represents a set of things (keys) of type `K`, sorted by some property (value) of type `V` */
|
||||
export interface Sorting<K, V extends number> {
|
||||
/** Keys sorted by their corresponding values */
|
||||
keys: readonly K[],
|
||||
/** Sorted values corresponding to each key (value for `keys[i]` is `values[i]`) */
|
||||
values: SortedArray<V>,
|
||||
}
|
||||
|
||||
export const Sorting = {
|
||||
/** Create a `Sorting` from an array of keys and a function returning their corresponding values.
|
||||
* If two keys have the same value, the smaller key will come first.
|
||||
* This function modifies `keys` - create a copy if you need the original order! */
|
||||
create<K extends number, V extends number>(keys: K[], valueFunction: (k: K) => V): Sorting<K, V> {
|
||||
sortIfNeeded(keys, (a, b) => valueFunction(a) - valueFunction(b) || a - b);
|
||||
const values: SortedArray<V> = SortedArray.ofSortedArray(keys.map(valueFunction));
|
||||
return { keys, values };
|
||||
},
|
||||
|
||||
/** Return a newly allocated array of keys which have value equal to `target`.
|
||||
* The returned keys are sorted by their value. */
|
||||
getKeysWithValue<K, V extends number>(sorting: Sorting<K, V>, target: V): K[] {
|
||||
return Sorting.getKeysWithValueInRange(sorting, target, target);
|
||||
},
|
||||
|
||||
/** Return a newly allocated array of keys which have value within interval `[min, max]` (inclusive).
|
||||
* The returned keys are sorted by their value.
|
||||
* Undefined `min` is interpreted as negative infitity, undefined `max` is interpreted as positive infinity. */
|
||||
getKeysWithValueInRange<K, V extends number>(sorting: Sorting<K, V>, min: V | undefined, max: V | undefined): K[] {
|
||||
const { keys, values } = sorting;
|
||||
if (!keys) return [];
|
||||
const n = keys.length;
|
||||
const from = (min !== undefined) ? SortedArray.findPredecessorIndex(values, min) : 0;
|
||||
let to: number;
|
||||
if (max !== undefined) {
|
||||
to = from;
|
||||
while (to < n && values[to] <= max) to++;
|
||||
} else {
|
||||
to = n;
|
||||
}
|
||||
return keys.slice(from, to);
|
||||
},
|
||||
};
|
||||
@@ -1,87 +0,0 @@
|
||||
/**
|
||||
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
|
||||
*
|
||||
* @author Adam Midlik <midlik@gmail.com>
|
||||
*/
|
||||
|
||||
import { Sphere3D } from '../../../mol-math/geometry';
|
||||
import { BoundaryHelper } from '../../../mol-math/geometry/boundary-helper';
|
||||
import { Vec3 } from '../../../mol-math/linear-algebra';
|
||||
import { ElementIndex, Model, Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
|
||||
import { UUID } from '../../../mol-util';
|
||||
import { arrayExtend } from '../../../mol-util/array';
|
||||
import { AtomRanges } from './atom-ranges';
|
||||
import { IndicesAndSortings } from './indexing';
|
||||
import { MVSAnnotationRow } from './schemas';
|
||||
import { getAtomRangesForRows } from './selections';
|
||||
|
||||
|
||||
/** Properties describing position, size, etc. of a text in 3D */
|
||||
export interface TextProps {
|
||||
/** Anchor point for the text (i.e. the center of the text will appear in front of `center`) */
|
||||
center: Vec3,
|
||||
/** Depth of the text wrt anchor point (i.e. the text will appear in distance `radius` in front of the anchor point) */
|
||||
depth: number,
|
||||
/** Relative text size */
|
||||
scale: number,
|
||||
/** Index of the first atom within structure, to which this text is bound (for coloring and similar purposes) */
|
||||
group: number,
|
||||
}
|
||||
|
||||
const tmpVec = Vec3();
|
||||
const tmpArray: number[] = [];
|
||||
const boundaryHelper = new BoundaryHelper('98');
|
||||
const outAtoms: ElementIndex[] = [];
|
||||
const outFirstAtomIndex: { value?: number } = {};
|
||||
|
||||
/** Return `TextProps` (position, size, etc.) for a text that is to be bound to a substructure of `structure` defined by union of `rows`.
|
||||
* Derives `center` and `depth` from the boundary sphere of the substructure, `scale` from the number of heavy atoms in the substructure. */
|
||||
export function textPropsForSelection(structure: Structure, sizeFunction: (location: StructureElement.Location) => number, rows: MVSAnnotationRow | MVSAnnotationRow[], onlyInModel?: Model): TextProps | undefined {
|
||||
const loc = StructureElement.Location.create(structure);
|
||||
const { units } = structure;
|
||||
const { type_symbol } = StructureProperties.atom;
|
||||
tmpArray.length = 0;
|
||||
let includedAtoms = 0;
|
||||
let includedHeavyAtoms = 0;
|
||||
let group: number | undefined = undefined;
|
||||
let atomSize: number | undefined = undefined;
|
||||
const rangesByModel: { [modelId: UUID]: AtomRanges } = {};
|
||||
for (let iUnit = 0, nUnits = units.length; iUnit < nUnits; iUnit++) {
|
||||
const unit = units[iUnit];
|
||||
if (onlyInModel && unit.model.id !== onlyInModel.id) continue;
|
||||
const ranges = rangesByModel[unit.model.id] ??= getAtomRangesForRows(unit.model, rows, IndicesAndSortings.get(unit.model));
|
||||
const position = unit.conformation.position;
|
||||
loc.unit = unit;
|
||||
AtomRanges.selectAtomsInRanges(unit.elements, ranges, outAtoms, outFirstAtomIndex);
|
||||
for (const atom of outAtoms) {
|
||||
loc.element = atom;
|
||||
position(atom, tmpVec);
|
||||
arrayExtend(tmpArray, tmpVec);
|
||||
group ??= structure.serialMapping.cumulativeUnitElementCount[iUnit] + outFirstAtomIndex.value!;
|
||||
atomSize ??= sizeFunction(loc);
|
||||
includedAtoms++;
|
||||
if (type_symbol(loc) !== 'H') includedHeavyAtoms++;
|
||||
}
|
||||
}
|
||||
if (includedAtoms > 0) {
|
||||
const { center, radius } = (includedAtoms > 1) ? boundarySphere(tmpArray) : { center: Vec3.fromArray(Vec3(), tmpArray, 0), radius: 1.1 * atomSize! };
|
||||
const scale = (includedHeavyAtoms || includedAtoms) ** (1 / 3);
|
||||
return { center, depth: radius, scale, group: group! };
|
||||
}
|
||||
}
|
||||
|
||||
/** Calculate the boundary sphere for a set of points given by their flattened coordinates (`flatCoords.slice(0,3)` is the first point etc.) */
|
||||
function boundarySphere(flatCoords: readonly number[]): Sphere3D {
|
||||
const length = flatCoords.length;
|
||||
boundaryHelper.reset();
|
||||
for (let offset = 0; offset < length; offset += 3) {
|
||||
Vec3.fromArray(tmpVec, flatCoords, offset);
|
||||
boundaryHelper.includePosition(tmpVec);
|
||||
}
|
||||
boundaryHelper.finishedIncludeStep();
|
||||
for (let offset = 0; offset < length; offset += 3) {
|
||||
Vec3.fromArray(tmpVec, flatCoords, offset);
|
||||
boundaryHelper.radiusPosition(tmpVec);
|
||||
}
|
||||
return boundaryHelper.getSphere();
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user