Releases | Open Source Science

molstar -

- TypeScript
Published by dsehnal 10 months ago

molstar -

- TypeScript
Published by dsehnal 10 months ago

molstar -

- TypeScript
Published by dsehnal 10 months ago

molstar -

See changelog.md for changes.

- TypeScript
Published by dsehnal 11 months ago

molstar -

MolViewSpec extension:
- Support for labelcompid and authcompid in annotations
- Geometric primitives - do not render if position refers to empty substructure
- Primitive arrow - nicer default cap size (relative to tube_radius)
- Primitive anglemeasurement - added vectorradius param
- Fix MVSX file assets being disposed in multi-snapshot states
Add mol-utils/camera.ts with fovAdjustedPosition and fovNormalizedCameraPosition
Show FOV normalized position in CameraInfo UI and use it in "Copy MVS State"
Support static resources in AssetManager
General:
- Use isolatedModules tsconfig flag
- Fix TurboPack build when using ES6 modules
Support pickingAlphaThreshold when xrayShaded is enabled
Support sampling from arbitrary planes for structure plane and volume slice representations
Refactor SCSS to not use @import (fixes deprecation warnings)

- TypeScript
Published by dsehnal 12 months ago

molstar -

Remove xhr2 dependency for NodeJS, use fetch
Add mvs-stories app included in the molstar NPM package
- Use the app in the corresponding example
Interactions extension: remove salt-bridge interaction kind (since ionic is supported too)

- TypeScript
Published by dsehnal about 1 year ago

molstar - v4.16.0

Load potentially big text files as StringLike to bypass string size limit
MolViewSpec extension:
- Load single-state MVS as if it were multi-state with one state
- Merged loadMVS options keepCamera and keepSnapshotCamera -> keepCamera
- Removed loadMVS option replaceExisting (is now default)
- Added loadMVS option appendSnapshots
Fix camera not being interpolated in MP4 export due to updates in WebGL ContextLost handling

- TypeScript
Published by arose about 1 year ago

molstar - v4.15.0

IHM improvements:
- Disable volume streaming
- Disable validation report visualization
- Enable assembly symmetry for integrative models
Fix transparency rendering with occlusion in NodeJS
mmCIF Support
- Add custom molstar_bond_site category that enables serializing explicit bonds by referencing atom_site.id
- Add includeCategoryNames, keepAtomSiteId, exportExplicitBonds, encoder properties to to_mmCIF exporter
Add support for attachment points property (M APO) to the MOL V2000 parser
Add json-cif extension that should pave way towards structure editing capabilities in Mol*
- JSON-based encoding of the CIF data format
- JSONCifLigandGraph that enables editing of small molecules via modifying atom_site and molstar_bond_site categories
Add ligand-editor example that showcases possible use-cases of the json-cif extension
Breaking (minor): Changed atom_site.id indexing to 1-based in mol-model-formats/structure/mol.ts::getMolModels.
WebGL ContextLost handling
- Fix missing framebuffer & drawbuffer re-attachments
- Fix missing cube texture re-initialization
- Fix missing extensions reset
- Fix timer clearing edge case
- Add reset support for geometry generated on the GPU

- TypeScript
Published by arose about 1 year ago

molstar - v4.14.1

Do not raise error when creating duplicate state transformers and print console warning instead

- TypeScript
Published by arose about 1 year ago

molstar -

Fix Viewer.loadTrajectory when loading a topology file
Fix StructConn.residueCantorPairs to not include identity pairs
Add format selection option to image export UI (PNG, WebP, JPEG)
Add StateBuilder.To.updateState
MVS:
- Support updating transform states
- Add support for is_hidden custom state as an extension
- Add queryMVSRef and createMVSRefMap utility functions
Fix switching representation type in Volume UI
VolumeServer: Avoid grid expansion when requiring unit cell (avoids including an extra layer of cells outside the unit cell query box)

- TypeScript
Published by dsehnal about 1 year ago

molstar -

Support --host option for build-dev.mjs script.
Add Viewer.loadFiles to open supported files
Support installing the viewer as a Progressive Web App (PWA)
ihm-restraints example: show entity labels
Fix element-point visual not using child unit
Ignore renderables with empty draw count
Add experimental support for esbuild for development
- Use npm run dev for faster development builds
Use StructureElement.Bundle instead of expressions to serialize measurement elements
- Fixes measurements not being supported for coarse models
Implementation of ColorScale.createDiscrete (#1458)
Add ColorScale.createDiscrete to the uncertainty color theme
Fix color palette shown in the UI (for non-gradient palettes)
Fix colors description in the UI (when using custom thresholds)
Fix an edge case in the UI when the user deletes all colors from the color list
Add interactions extension and a corresponding example that utilizes it
Add element source index to default atomic granularity hover labels
Add StructureElement.Schema based on corresponding MolViewSpec implementation that allows data-driven selection of structural elements
Add StructureElement.Loci/Bundle.fromExpression/Query/Schema helper functions
Add addLinkCylinderMesh (from createLinkCylinderMesh)
Add Unit.transientCache and Unit.getCopy
Fix ElementBondIterator indices mapping logic for inter-unit bonds
Fix pickPadding and pickScale not updating PickHelper
MolViewSpec extension: support loading extensions when loading multistate files
Do not add bonds for pairs of residues that have a struct_conn entry
Improved ma_qa_metric support
- Parse all local metrics
- Ability to select alternate metrics in the pLDDT/qmean themes
- Do not assume PAE plot is symmetric
Added PluginConfig.Viewport.ShowScreenshotControls to control visibility of screenshot controls
Fix MolViewSpec builder for volumes.
Generalize mvs-kinase-story example to mvs-stories
- Add TATA-binding protein story
- Improve the Kinase story
Fix alpha orbitals example

- TypeScript
Published by dsehnal about 1 year ago

molstar -

Fix PDBj structure data URL
Improve logic when to cull in renderer
Add atom.ihm.has-seq-id and atom.ihm.overlaps-seq-id-range symbol to the query language
MolViewSpec extension:
- Add box, arrow, ellipse, ellipsoid, angle primitives
- Add basic support for volumetric data (map, Volume Server)
- Add support for molstar_color_theme_name custom extension
- Better IH/M support:
- Support coarse components
- Support spacefill representation
- Support carbohydrate representation
- Support for custom.molstar_use_default_coloring property on Color node.
- Use atom.ihm.has-seq-id and atom.ihm.overlaps-seq-id-range for matching label_seq_id locations to support querying coarse elements.
- Add ihm-restraints example
Add mvs-kinase-story example
Remove static uses of ColorTheme and SizeTheme fields. Should resolvent "undefined" errors in certain builds
Add transform property to clip objects
Add support for trimming image geometry to a box
Improve/fix iso-level support of slice representation
Add support for rotating slice representation around an axis
Add default color support for palette based themes
Add plane structure representation
- Can be colored with any structure theme
- Can be colored with the external-volume theme
- Can show atoms as a cutout
- Supports principal axes and bounding box as a reference frame
Add Camera section to "Screenshot / State" controls
Add CoarseIndex for fast lookup of coarse elements

- TypeScript
Published by dsehnal over 1 year ago

molstar - v4.11.0

Fix for tubular helices issue (Fixes #1422)
Volume UI improvements
- Render all volume entries instead of selecting them one-by-one
- Toggle visibility of all volumes
- More accessible iso value control
Support wheel event on sliders
MolViewSpec extension:
- Add validation for discriminated union params
- Primitives: remove trianglecolors, linecolors, have implicit grouping instead; rename many parameters
UI configuration options
- Support removal of independent selection controls in the viewport
- Support custom selection controls
- Support for custom granularity dropdown options
- Support for custom Sequence Viewer mode options
Add external-structure theme that colors any geometry by structure properties
Support float and half-float data type for direct-volume rendering and GPU isosurface extraction
Minor documentation updates
Add support for position-location to volume-value color theme
Add support for color themes to slice representation
Improve/fix palette support in volume color themes
Fix Plane3D.projectPoint
Fix marking related image rendering issues
- Handle pixels without a group
- Take fog into account
MolViewSpec extension: Initial support for customizable representation parameters
Quick Styles section reorganized
UI color improvements (scrollbar contrast, toggle button hover color)
Add overrideWater param for entity-id color theme
Renames PDB-Dev to PDB-IHM and adjusts data source
Fix vertex based themes for spheres shader
Add volume dot representation
Add volume-value size theme
Sequence panel: Mark focused loci (bold+underline)
Change modifier key behavior in Normal Mode (default = select only, Ctrl/Cmd = add to selection, Shift = extend last selected range)
Handle Firefox's limit on vertex ids per draw (#1116)

- TypeScript
Published by arose over 1 year ago

molstar - v4.10.0

Add ModelWithCoordinates decorator transform.
Fix outlines on transparent background using illumination mode (#1364)
Fix transparent depth texture artifacts using illumination mode
Fix marking of consecutive gap elements (#876)
Allow React 19 in dependencies
Fix missing deflate header if CompressionStream is available
Fix is_iOS check for NodeJS
Added PluginCommands.Camera.FocusObject
Plugin state snapshot can have instructions to focus objects (PluginState.Snapshot.camera.focus)
MolViewSpec extension: Support for multi-state files (animations)
Fix units transform data not fully updated when structure child changes
Fix addIndexPairBonds quadratic runtime case
Use adjoint matrix to transform normals in shaders
Fix resize handling in tests/browser

- TypeScript
Published by arose over 1 year ago

molstar - v4.9.1

Fix iOS check when running on Node

- TypeScript
Published by arose over 1 year ago

molstar - v4.9.0

Fix artifacts when using xray shading with high xrayEdgeFalloff values
Enable double rounded capping on tubular helices
Fix single residue tubular helices not showing up
Fix outlines on volume and surface reps that do not disappear (#1326)
Add example glb-export
Membrane orientation: Improve isApplicable check and error handling (#1316)
Fix set fenceSync to null after deleteSync.
Fix operator key-based IndexPairBonds assignment
- Don't add bonds twice
- Add IndexPairs.bySameOperator to avoid looping over all bonds for each unit
Add Structure.intraUnitBondMapping
Add more structure-based visuals to avoid too many (small) render-objects
- structure-intra-bond, structure-ellipsoid-mesh, structure-element-point, structure-element-cross
Upgrade to express v5 (#1311)
Fix occupancy check using wrong index for inter-unit bond computation (@rxht, #1321)
Fix transparent SSAO for image rendering, e.g., volumne slices (#1332)
Fix bonds not shown with ignoreHydrogens on (#1315)
- Better handle mmCIF files with no entities defined by using label_asym_id
- Show bonds in water chains when ignoreHydorgensVariant is non-polar
Add MembraneServer API, generating data to be consumed in the context of MolViewSpec
Fix StructConn.isExhaustive for partial models (e.g., returned by the model server)
Refactor value swapping in molstar-math to fix SWC (Next.js) build (#1345)
Fix transform data not updated when structure child changes
Fix PluginStateSnapshotManager.syncCurrent to work as expected on re-loaded states.
Fix do not compute implicit hydrogens when unit is explicitly protonated (#1257)
ModelServer and VolumeServer: support for input files from Google Cloud Storage (gs://)
Fix color of missing partial charges for SB partial charges extension

- TypeScript
Published by arose over 1 year ago

molstar - v4.8.0

Add SSAO support for transparent geometry
Fix SSAO color not updating
Improve blending of overlapping outlines from transparent & opaque geometries
Default to blended transparency on iOS due to wboit not being supported.
Fix direct-volume with fog off (and on with dpoit) and transparent background on (#1286)
Fix missing pre-multiplied alpha for blended & wboit with no fog (#1284)
Fix backfaces visible using blended transparency on impostors (#1285)
Fix StructureElement.Loci.isSubset() only considers common units (#1292)
Fix Scene.opacityAverage calculation never 1
Fix bloom in illumination mode
Fix findPredecessorIndex bug when repeating values
MolViewSpec: Support for transparency and custom properties
MolViewSpec: MVP Support for geometrical primitives (mesh, lines, line, label, distance measurement)
Mesoscale Explorer: Add support for 4-character PDB IDs (e.g., 8ZZC) in PDB-Dev loader
Fix Sequence View in Safari 18
Improve performance of IndexPairBonds assignment when operator keys are available
ModelArchive QualityAssessment extension:
- Add support for maqametriclocalpairwise mmCIF category
- Add PAE plot component
Add new AlphaFoldDB-PAE example app
Add support for LAMMPS data and dump formats
Remove extra anti-aliasing from text shader (fixes #1208 & #1306)

- TypeScript
Published by arose over 1 year ago

molstar - v4.7.1

Improve resolutionMode (#1279)
- Add auto that picks scaled for mobile devices and native elsewhere
- Add resolution-mode Viewer GET param
- Add PluginConfig.General.ResolutionMode config item

- TypeScript
Published by arose over 1 year ago

molstar - v4.7.0

Add illumination mode
- Path-traced SSGI
- Automatic thickness (estimate)
  - Base thickness as max(backface depth) - min(frontface depth)
  - Per object density factor to adjust thickness
- Progressively trace samples to keep viewport interactive
- Toggle on/off by pressing "G"
- illumination Viewer GET param
Enables dXrayShaded define when rendering depth
Fix handling of PDB files that have chains with same id separated by TER record (#1245)
Sequence Panel: Improve visuals of unmodeled sequence positions (#1248)
Fix no-compression xtc parser (#1258)
Mol2 Reader: Fix mol2 status_bit read error (#1251)
Fix shadows with multiple lights
Fix impostor sphere interior normal when using orthographic projection
Add resolutionMode parameter to Canvas3DContext
- scaled, divides by devicePixelRatio
- native, no changes
Add CustomProperty.Context.errorContext to support reporting errors during loading of custom properties (#1254)
- Use in MolViewSpec extension
Mesoscale Explorer: fix color & style issues
Remove use of deprecated SASS explicit color functions
Allow "Components" section to display nested components created by "Apply Action > Selection".

- TypeScript
Published by arose over 1 year ago

molstar - v4.6.0

Add round-caps option on tubular alpha helices
Fix missing Sequence UI update on state object removal (#1219)
Improved prmtop format support (CTITLE, %COMMENT)
Avoid calculating bonds for water units when ignoreHydrogens is on
Add Water trait to Unit
Improve entity-id coloring for structures with multiple models from the same source (#1221)
Wrap screenshot & image generation in a Task
AlphaFold DB: Add BinaryCIF support when fetching data
PDB-Dev: Add support for 4-character PDB IDs (e.g., 8ZZC)
Fix polymer-gap visual coloring with cartoon theme
Add formal-charge color theme (#328)
Add more coloring options to cartoon theme
Use CompressionStream Browser API when available
Add pdbx_structure_determination_methodology mmcif field and Model helpers
Fix cartoon representation not updated when secondary structure changes
Add Zhang-Skolnick secondary-structure assignment method which handles coarse-grained models (#49)
Calculate bonds for coarse-grained models
VolumeServer: Add health-check endpoint + healthCheckPath config prop to report service health
ModelServer: Add health-check endpoint + healthCheckPath config prop to report service health

- TypeScript
Published by arose almost 2 years ago

molstar - v4.5.0

Separated postprocessing passes
Take into account explicit hydrogens when computing hydrogen bonds
Fix DoF with pixel ratios =! 1
Fix DoF missing transparent depth
Fix trackball pinch zoom and add pan
Fix aromatic link rendering when adjustCylinderLength is true
Change trackball animate spin speed unit to radians per second
Fix mol-plugin-ui/skin/base/components/misc.scss syntax to be in line with latest Sass syntax
Handle missing theme updates
- Fix trajectory-index color-theme not always updated (#896)
- Fix bond cylinders not updated on size-theme change with adjustCylinderLength enabled (#1215)
Use OES_texture_float_linear for SSAO when available

- TypeScript
Published by arose almost 2 years ago

molstar - v4.4.1

Clean solidInterior transparent cylinders
Create a transformer to deflate compressed data
Adjust Quick Styles panel button labels
Improve camera interpolation code (interpolate camera rotation instead of just position)
Mesoscale Explorer
- Add illustrative coloring option
- Press 'C' to toggle between center and zoom & center on click
- Add entities selection description
- Clicking a leaf node in the right panel tree will center each instance in turn
- Add measurement controls to right panel
- Mouse left click on label with snapshot key will load snapshot
- Mouse hover over label with protein name highlight entities with the same name
- Custom ViewportSnapshotDescription with custom MarkdowAnchor
  - # other snapshots with a given key [...](#key)
  - i highlight a protein with a given NAME [...](iNAME)
  - g highlight a group with a given group type and group name [...](ggrouptype.groupname)
  - h URLs with a given link [...](http...)
- Snapshot description panel window size and text can be resized and hidden with new icons
- Add styles controls to right panel
- Add viewport settings to left panel
- Add app info component to left panel with interactive tour and doc link
Fixes SSAO edge artifacts (#1122)
- Add reuseOcclusion parameter to multi-sample pass
- Add blurDepthBias parameter to occlusion pass
- Handle near clip in SSAO blur
Support reading score from B-factor in pLDDT color theme
Add Cel-shading support
- celShaded geometry parameter
- celSteps renderer parameter
Add the ability to customize the Snapshot Description component via PluginUISpec.components.viewport.snapshotDescription
Add doNotDisposeCanvas3DContext option to PluginContext.dispose
Remove support for density data from edmaps.rcsb.org

- TypeScript
Published by arose almost 2 years ago

molstar - v4.3.0

[v4.3.0] - 2023-05-26

Fix State Snapshots export animation (#1140)
Add depth of field (dof) postprocessing effect
Add SbNcbrTunnels extension for for visualizing tunnels in molecular structures from ChannelsDB (more info in tunnels.md)
Fix edge case in minimizing RMSD transform computation

What's Changed

Tunnels extension by @vDusky in https://github.com/molstar/molstar/pull/1105
DOF shader by @corredD in https://github.com/molstar/molstar/pull/1103
fix RMSD minification bug by @dsehnal in https://github.com/molstar/molstar/pull/1138
await the the snapshot setting to avoid rendering while applying snap… by @corredD in https://github.com/molstar/molstar/pull/1140

New Contributors

@vDusky made their first contribution in https://github.com/molstar/molstar/pull/1105

Full Changelog: https://github.com/molstar/molstar/compare/v4.2.0...v4.3.0

- TypeScript
Published by dsehnal about 2 years ago

molstar - v4.2.0

Add emissive material support
Add bloom post-processing
MolViewSpec extension: loadMVS supports keepCamera parameter
Return StateTransform selectors from measurements API (addDistance, addAngle, etc.)
Refactor transparency rendering
- More uniform behavior for blended, wboit, dpoit
- Fix issues with text & image geometry
Fix render-spheres example (#1100)
- Wrong step size in sphere geometry boundingSphere & groupmapping
- Handle empty instanceGrid in renderer & renderable
Fix bond assignment from IndexPairBonds
- Can not always be cached in ElementSetIntraBondCache
- Wrong operator checks in findPairBonds
Fix SSAO artifacts (@corredD, #1082)
Fix bumpiness artifacts (#1107, #1084)

- TypeScript
Published by arose about 2 years ago

molstar - v4.1.0

Add VolumeTransform to translate/rotate a volume like in a structure superposition
Fix BinaryCIF encoder edge cases caused by re-encoding an existing BinaryCIF file
Fix edge-case where width/height in InputObserver are not correct
Fix transparency rendering fallback (#1058)
Fix SSAO broken when OES_texture_float_linear is unavailable
Add normalOffset to external-volume color theme
- This can give results similar to pymol's surfacerampabove_mode=1
Add rotation parameter to skybox background

- TypeScript
Published by arose about 2 years ago

molstar -

Fix BinaryCIF decoder edge cases. Fixes mmCIF model export from data provided by ModelServer.
MolViewSpec extension: support for MVSX file format
Revert "require WEBGLdepthtexture extension" & "remove renderbuffer use"

- TypeScript
Published by dsehnal over 2 years ago

molstar - v4.0.0

Add Mesoscale Explorer app for investigating large systems
[Breaking] Remove cellpack extension (superseded by Mesoscale Explorer app)
[Breaking] Set minimal node.js version to 18
[Breaking] Generalize rcsb/assembly-symmetry/ extension
- Move to assembly-symmetry/
- Remove RCSB specific dependencies and prefixes
[Breaking] Require WEBGL_depth_texture webgl extension
- Remove renderbuffer use
[Breaking] Change build target to ES2018
- Custom builds only require ES6 for dependencies like immer.js
[Breaking] Changed createPluginUI
- The function now takes a single options argument
- The caller must specify a render method that mounts the Mol* react component to DOM
  - A default renderReact18 method is provided, but needs to be imported separately
  - To support React 16 and 17, ReactDOM.render can be passed
Improve SetUtils performance using ES6 features
[Breaking] Reduce memory usage of SymmetryOperator.ArrayMapping
- Requires calling methods from instance
[Breaking] Fix mol-model/structure/model/properties/seconday-structure.ts file name (#938)
[Breaking] Add Canvas3DContext runtime props
- Props: pixelScale, pickScale, transparency (blended, wboit, dpoit)
- Replaces instantiation-time attribs
[Breaking] Change default compile target to ES2018
[Breaking] Add culling & LOD support
- Cull per-object and per-instance
- Cull based on frustum and camera distance
- LOD visibility based on camera distance
- Special LOD mode for spheres with automatic levels
- Occlusion culling (only WebGL2)
  - Hi-Z pass
  - Cull based on previous frame's Hi-Z buffer
Add stochastic/dithered transparency to fade overlapping LODs in and out
Add "Automatic Detail" preset that shows surface/cartoon/ball & stick based on camera distance

- TypeScript
Published by arose over 2 years ago

molstar - v3.45.0

Add color interpolation to impostor cylinders
MolViewSpec components are applicable only when the model has been loaded from MolViewSpec
Add snapshotKey and tooltip params to loci LabelRepresentation
Update FocusLoci behavior to support snapshotKey param
- Clicking a visual with snapshotKey will trigger that snapshot
Render multiline loci label tooltips as Markdown
ParamDefinition.Text updates:
- Support multiline inputs
- Support placeholder parameter
- Support disableInteractiveUpdates to only trigger updates once the control loses focus
Move dependencies related to the headless context from optional deps to optional peer deps

- TypeScript
Published by arose over 2 years ago

molstar - v4.0.0-beta.0

Add Mesoscale Explorer app for investigating large systems
[Breaking] Remove cellpack extension (superseded by Mesoscale Explorer app)
[Breaking] Set minimal node.js version to 18
[Breaking] Generalize rcsb/assembly-symmetry/ extension
- Move to assembly-symmetry/
- Remove RCSB specific dependencies and prefixes
[Breaking] Require WEBGL_depth_texture webgl extension
- Remove renderbuffer use
[Breaking] Change build target to ES2018
- Custom builds only require ES6 for dependencies like immer.js
[Breaking] Changed createPluginUI
- The function now takes a single options argument
- The caller must specify a render method that mounts the Mol* react component to DOM
  - A default renderReact18 method is provided, but needs to be imported separately
  - To support React 16 and 17, ReactDOM.render can be passed
Improve SetUtils performance using ES6 features
[Breaking] Reduce memory usage of SymmetryOperator.ArrayMapping
- Requires calling methods from instance
[Breaking] Fix mol-model/structure/model/properties/seconday-structure.ts file name (#938)
[Breaking] Add Canvas3DContext runtime props
- Props: pixelScale, pickScale, transparency (blended, wboit, dpoit)
- Replaces instantiation-time attribs
[Breaking] Change default compile target to ES2018
[Breaking] Add culling & LOD support
- Cull per-object and per-instance
- Cull based on frustum and camera distance
- LOD visibility based on camera distance
- Special LOD mode for spheres with automatic levels
- Occlusion culling (only WebGL2)
  - Hi-Z pass
  - Cull based on previous frame's Hi-Z buffer
Add stochastic/dithered transparency to fade overlapping LODs in and out
Add "Automatic Detail" preset that shows surface/cartoon/ball & stick based on camera distance

- TypeScript
Published by arose over 2 years ago

molstar - v3.44.0

Add new cartoon visuals to support atomic nucleotide base with sugar
Add thicknessFactor to cartoon representation for scaling nucleotide block/ring/atomic-fill visuals
Use bonds from _struct_conn in mmCIF files that use label_seq_id
Fix measurement label offsetZ default: not needed when scaleByRadius is enbaled
Support for label rendering in HeadlessPluginContext
MolViewSpec extension
- Support all X11 colors
- Support relative URIs
- CLI tools: mvs-validate, mvs-render, mvs-print-schema
- Labels applied in one node
ModelServer SDF/MOL2 ligand export: fix atom indices when additional atoms are present
Avoid showing (and calculating) inter-unit bonds for huge structures
Fixed DragOverlay on WebKit/Safari browsers

- TypeScript
Published by arose over 2 years ago

molstar -

Fix react-markdown dependency

- TypeScript
Published by dsehnal over 2 years ago

molstar - v3.43.0

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

- TypeScript
Published by arose over 2 years ago

molstar - v3.42.0

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

- TypeScript
Published by arose over 2 years ago

molstar - v3.41.0

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.

- TypeScript
Published by arose over 2 years ago

molstar - v3.40.1

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

- TypeScript
Published by arose over 2 years ago

molstar - v3.39.0

Add some elements support for guessElementSymbolString function
Faster bounding rectangle calculation for imposter spheres
Allow toggling of hydrogens as part of LabelTextVisual

- TypeScript
Published by arose over 2 years ago

molstar - v3.38.3

Fix imposter spheres not updating, e.g. in trajectories (broke in v3.38.0)

- TypeScript
Published by arose almost 3 years ago

molstar - v3.38.2

Don't rely solely on chem_comp_atom when detecting CCD files (#877)
Actually support non-physical keys in Bindings.Trigger.code

- TypeScript
Published by arose almost 3 years ago

molstar - v3.38.1

Fix pixel-scale not updated in SSAO pass

- TypeScript
Published by arose almost 3 years ago

molstar - v3.38.0

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)

- TypeScript
Published by arose almost 3 years ago

molstar - v3.37.1

Fix issues with wboit/dpoit in large scenes
Fix lines, text, points rendering (broken in v3.37.0)

- TypeScript
Published by arose almost 3 years ago

molstar - v3.37.0

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

- TypeScript
Published by arose almost 3 years ago

molstar - v3.36.1

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

- TypeScript
Published by arose almost 3 years ago

molstar - v3.35.0

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)
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

- TypeScript
Published by arose about 3 years ago

molstar - v3.34.0

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

- TypeScript
Published by arose about 3 years ago

molstar - v3.33.0

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)

- TypeScript
Published by arose about 3 years ago

molstar -

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

- TypeScript
Published by dsehnal about 3 years ago

molstar -

Allow link cylinder/line dashCount set to '0'
Stop animation loop when disposing PluginContext (thanks @gfrn for identifying the issue)

- TypeScript
Published by dsehnal over 3 years ago

molstar -

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

- TypeScript
Published by dsehnal over 3 years ago

molstar - v3.31.2

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

- TypeScript
Published by arose over 3 years ago

molstar - v3.31.1

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

- TypeScript
Published by arose over 3 years ago

molstar - v3.30.0

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

- TypeScript
Published by arose over 3 years ago

molstar - v3.29.0

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

- TypeScript
Published by arose over 3 years ago

molstar -

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)

- TypeScript
Published by dsehnal over 3 years ago

molstar -

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

- TypeScript
Published by dsehnal over 3 years ago

molstar - v3.26.0

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)

- TypeScript
Published by arose over 3 years ago

molstar - v3.25.1

Fix edge-case in Structure.eachUnitPair with single-element units
Fix 'auto' structure-quality for coarse models

- TypeScript
Published by arose over 3 years ago

molstar - v3.25.0

Fix handling of gzipped assets (reverts #615)

- TypeScript
Published by arose over 3 years ago

molstar - v3.24.0

Make PluginContext.initContainer checkered canvas background optional
Store URL of downloaded assets to detect zip/gzip based on extension
Add optional operator.key; can be referenced in IndexPairBonds
Add overpaint/transparency/substance theme strength to representations
Fix viewport color for transparent background

- TypeScript
Published by arose over 3 years ago

molstar -

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 Whote Structure to Auto

- TypeScript
Published by dsehnal over 3 years ago

molstar - v3.22.0

Replace VolumeIsosurfaceParams.pickingGranularity param with Volume.PickingGranuality

- TypeScript
Published by arose over 3 years ago

molstar - v3.21.0

Add VolumeIsosurfaceParams.pickingGranularity param
Prevent component controls collapsing when option is selected

- TypeScript
Published by arose over 3 years ago

molstar - v3.20.0

[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

- TypeScript
Published by arose over 3 years ago

molstar - v3.19.0

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

- TypeScript
Published by arose over 3 years ago

molstar - v3.18.0

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

- TypeScript
Published by arose over 3 years ago

molstar - v3.17.0

[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

- TypeScript
Published by arose over 3 years ago

molstar -

Support globalColorParams and globalSymmetryParams in common representation params
Support label parameter in Viewer.loadStructureFromUrl
Fix ViewportHelpContent Mouse Controls section

- TypeScript
Published by dsehnal almost 4 years ago

molstar -

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

- TypeScript
Published by dsehnal almost 4 years ago

molstar -

Expose inter-bonds compute params in structure
Improve performance of inter/intra-bonds compute
Fix defaultAttribs handling in Canvas3DContext.fromCanvas
Confal pyramids extension improvements
- Add custom labels to Confal pyramids
- Improve naming of some internal types in Confal pyramids extension coordinate
- Add example mmCIF file with categories necessary to display Confal pyramids
- Change the lookup logic of NtC steps from residues
Add support for download of gzipped files
Don't filter IndexPairBonds by element-based rules in MOL/SDF and MOL2 (without symmetry) models
Fix Glycam Saccharide Names used by default
Fix GPU surfaces rendering in Safari with WebGL2
Add fov (Field of View) Canvas3D parameter
Add sceneRadiusFactor Canvas3D parameter
Add background pass (skybox, image, horizontal/radial gradient)
- Set simple-settings presets via PluginConfig.Background.Styles
- Example presets in new backgrounds extension
- Load skybox/image from URL or File (saved in session)
- Opacity, saturation, lightness controls for skybox/image
- Coverage (viewport or canvas) controls for image/gradient
[Breaking] AssetManager needs to be passed to various graphics related classes
Fix SSAO renderable initialization
Reduce number of webgl state changes
- Add viewport and scissor to state object
- Add hasOpaque to scene object
Handle edge cases where some renderables would not get (correctly) rendered
- Fix text background rendering for opaque text
- Fix helper scenes not shown when rendering directly to draw target
Fix CustomElementProperty coloring not working

- TypeScript
Published by dsehnal almost 4 years ago

molstar - v3.13.0

Fix: only update camera state if manualReset is off (#494)
Improve handling principal axes of points in a plane
Add 'material' annotation support for textures
More effort to avoid using flat qualifier in shaders: add dVaryingGroup
Enable immediateUpdate for iso level in isosurface and volume streaming controls
Add support to download CCD from configurable URL

- TypeScript
Published by arose almost 4 years ago

molstar -

Fix plugin behavior dispose logic to correctly unsubscribe observables.

- TypeScript
Published by dsehnal almost 4 years ago

molstar - v3.12.0

Add colorMarker option to Renderer. This disables the highlight and select marker at a shader level for faster rendering of large scenes in some cases.
Bind shared textures only once per pass, not for each render item
Fix missing 'material' annotation for some uniforms, causing unnecessary uniform updates
Remove use of isnan in impostor shaders, not needed and causing slowdown
Avoid using flat qualifier in shaders, causing slowdown
Improve CellPack's adjustStyle option (disable colorMarker, set component options, enable marking w/o ghost)
Scan all entities when looking for struct_conn entries (fixes issue when the same label_asym_id is used in more than one entity)

- TypeScript
Published by arose almost 4 years ago

molstar - v3.11.0

Add instanceGranularity option for marker, transparency, clipping, overpaint, substance data to save memory
CellPack extension tweaks
- Use instancing to create DNA/RNA curves to save memory
- Enable instanceGranularity by default
- Add adjustStyle option to LoadCellPackModel action (stylized, no multi-sample, no far clipping, chain picking)
Structure Superposition now respects pivot's coordinate system

- TypeScript
Published by arose almost 4 years ago

molstar - v3.10.2

Fix superfluous shader varying
Improve use of gl_VertexID when possible

- TypeScript
Published by arose almost 4 years ago

molstar - v3.10.1

Fix groupCount when updating TextureMesh-based visuals

- TypeScript
Published by arose almost 4 years ago

molstar - v3.10.0

Add support for Glycam saccharide names
Add PluginConfig.Viewport.ShowTrajectoryControls config option

- TypeScript
Published by arose almost 4 years ago

molstar - v3.9.1

Fix missing super.componentWillUnmount() calls (@simeonborko)
Fix missing uGroupCount update for visuals
Fix missing aromatic bond display

- TypeScript
Published by arose almost 4 years ago

molstar - v3.9.0

Improve picking by using drawbuffers (when available) to reduce number of drawcalls
GPU timing support
- Add timing-mode Viewer GET param
- Add support for webgl timer queries
- Add timer marks around GPU render & compute operations
Volume Server CIF: Add check that a data block contains volume data before parsing
Fix Scene.clear not clearing primitives & volumes arrays (@JonStargaryen)
Fix rendering volumes when wboit is switched off and postprocessing is enabled

- TypeScript
Published by arose about 4 years ago

molstar - v3.8.2

Fix Scene.opacityAverage not taking xray shaded into account

- TypeScript
Published by arose about 4 years ago

molstar - v3.8.1

Fix issues with marking camera/handle helper (#433)
Fix issues with array uniforms when running with headless-gl
Fix Polymer Chain Instance coloring
Improve performance of scene marker/opacity average calculation

- TypeScript
Published by arose about 4 years ago

molstar - v3.8.0

Add support for outlines around transparent objects
Improve per-group transparency when wboit is switched off
Improve ColorTheme typing with ColorType generic.
- Defaults to ColorTypeLocation
- Set when using ColorTypeDirect or ColorTypeGrid
Fix case handling of struct_conf mmCIF enumeration field (#425)
Fix allowTransparentBackfaces for per-group transparency
Fix FormatRegistry.isApplicable returning true for unregistered formats
Fix: handle building of GridLookup3D with zero cell size
Fix ignoreLight for direct-volume rendering with webgl1
Fix (non-black) outlines when using transparent background

- TypeScript
Published by arose about 4 years ago

molstar - v3.7.0

Fix xrayShaded for texture-mesh geometries
[Breaking] Change allowTransparentBackfaces to transparentBackfaces with options off, on, opaque. This was only added in 3.6.0, so allowing a breaking change here.
- off: don't show (default)
- on: show with transparency
- opaque: show fully opaque
Add option to disable file drop overlay.

- TypeScript
Published by arose about 4 years ago

molstar - v3.6.2

ModelServer ligand queries: fixes for alternate locations, additional atoms & UNL ligand
React 18 friendly useBehavior hook.

- TypeScript
Published by arose about 4 years ago

molstar - v3.6.1

Fix React18 related UI regressions.

- TypeScript
Published by arose about 4 years ago

molstar -

Check that model and coordinates have same element count when creating a trajectory
Fix aromatic rings assignment: do not mix flags and planarity test
Improve bonds assignment of coarse grained models: check for IndexPairBonds and exhaustive StructConn
Fix unit mapping in bondedAtomicPairs MolScript query
Improve pdb parsing: handle non unique atom and chain names (fixes #156)
Fix volume streaming for entries with multiple contour lists
Add allowTransparentBackfaces parameter to support double-sided rendering of transparent geometries
Fix handling of case insensitive mmCIF enumeration fields (including entity.type)
Fix disable-wboit Viewer GET param
Add support for React 18.
- Used by importing createPluginUI from mol-plugin-ui/react18;
- In Mol* 4.0, React 18 will become the default option.

- TypeScript
Published by dsehnal about 4 years ago

molstar -

Fix issues with bounding-sphere & color-smoothing (mostly for small geometries)
Support BCIF => CIF conversion in cif2bcif CLI tool

- TypeScript
Published by dsehnal about 4 years ago

molstar - v3.4.0

Fix handling of mmcif with empty label_* fields
Improve saccharide detection (compare against list from CCD)
Fix legend label of hydrophobicity color theme
Add LoadTrajectory action
Add CustomImportControls to left panel
Add Zenodo import extension (load structures, trajectories, volumes, and zip files)
Fix loading of some compressed files within sessions
Fix wrong element assignment for atoms with Charmm ion names
Fix handling of empty symmetry cell data
Add support for trr and nctraj coordinates files
Add support for prmtop and top topology files

- TypeScript
Published by arose about 4 years ago

molstar - v3.0.2

Fix color smoothing of elongated structures (by fixing Sphere.expand for spheres with highly directional extrema)
Fix entity label not displayed when multiple instances of the same entity are highlighted
Fix empty elements created in StructureElement.Loci.extendToAllInstances
Measurement options tweaks (allow larger textSize; make customText essential)
Fix visual visibility sync edge case when changing state snapshots

- TypeScript
Published by arose over 4 years ago

molstar - v3.0.1

Fix marking pass not working with transparentBackground
Fix pdbe xray maps url not https
Fix entity-id color theme broken for non-IHM models
Improve/fix marking of InteractionsInterUnitVisual (mark when all contact-feature members are given)
Add missing "entity-id" and "enity-source" options for carbon coloring to "element-symbol" color theme
Fix VolumeServer/query CLI
Support automatic iso-value adjustment for VolumeServer data in Viewer.loadVolumeFromUrl
Emit drag event whenever started within viewport (not only for non-empty loci)

- TypeScript
Published by arose over 4 years ago

molstar - v3.0.0

See https://github.com/molstar/molstar/blob/v3.0.0/CHANGELOG.md

- TypeScript
Published by arose over 4 years ago

molstar -

- TypeScript
Published by arose over 4 years ago

molstar -

- TypeScript
Published by arose over 4 years ago

molstar -

- TypeScript
Published by dsehnal over 4 years ago

molstar -

- TypeScript
Published by dsehnal over 4 years ago

molstar -

[v2.2.3] - 2021-08-25

Add invertCantorPairing helper function
Add Mesh processing helper .smoothEdges
Smooth border of molecular-surface with includeParent enabled
Hide includeParent option from gaussian-surface visuals (not particularly useful)
Improved StructureElement.Loci.size performance (for marking large cellpack models)
Fix new TransformData issues (camera/bounding helper not showing up)
Improve marking performance (avoid superfluous calls to StructureElement.Loci.isWholeStructure)

- TypeScript
Published by dsehnal almost 5 years ago

molstar -

Add surrounding atoms (5 Angstrom) structure selection query
[Breaking] Add maxDistance prop to IndexPairBonds
Fix coordinateSystem not handled in Structure.asParent
Add dynamicBonds to Structure props (force re-calc on model change)
- Expose as optional param in root structure transform helper
Add overpaint support to geometry exporters
InputObserver improvements
- normalize wheel speed across browsers/platforms
- support Safari gestures (used by TrackballControls)
- PinchInput.fractionDelta and use it in TrackballControls

- TypeScript
Published by dsehnal almost 5 years ago

molstar -

Add tubularHelices parameter to Cartoon representation
Add SdfFormat and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
Fix mononucleotides detected as polymer components (#229)
Set default outline scale back to 1
Improved DCD reader cell angle handling (interpret near 0 angles as 90 deg)
Handle more residue/atom names commonly used in force-fields
Add USDZ support to geo-export extension.
Fix includeParent support for multi-instance bond visuals.
Add operator Loci granularity, selecting everything with the same operator name.
Prefer _label_seq_id fields in secondary structure assignment.
Support new EMDB API (https://www.ebi.ac.uk/emdb/api/entry/map/[EMBD-ID]) for EM volume contour levels.
Canvas3D tweaks:
- Update forceDraw logic.
- Ensure the scene is re-rendered when viewport size changes.
- Support noDraw mode in PluginAnimationLoop.

- TypeScript
Published by dsehnal almost 5 years ago

molstar -

Add ability to specify volumeIndex in Viewer.loadVolumeFromUrl to better support Volume Server inputs.
Support in-place reordering for trajectory Frame.x/y/z arrays for better memory efficiency.
Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).

- TypeScript
Published by dsehnal almost 5 years ago

molstar -

Add glTF (GLB) and STL support to geo-export extension.
Protein crosslink improvements
- Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
- Added NOS-bridges query & improved disulfide-bridges query
Fix #178: IndexPairBonds for non-single residue structures (bug due to atom reordering).
Add volumetric color smoothing for MolecularSurface and GaussianSurface representations (#173)
Fix nested 3d grid lookup that caused results being overwritten in non-covalent interactions computation.
Basic implementation of BestDatabaseSequenceMapping (parse from CIF, color theme, superposition).
Add atom id ranges support to Selection UI.

- TypeScript
Published by dsehnal about 5 years ago

molstar -

Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.

- TypeScript
Published by arose about 5 years ago

Recent Releases of molstar

molstar -

molstar -

molstar -

molstar -

molstar -

molstar -

molstar - v4.16.0

molstar - v4.15.0

molstar - v4.14.1

molstar -

molstar -

molstar -

molstar - v4.11.0

molstar - v4.10.0

molstar - v4.9.1

molstar - v4.9.0

molstar - v4.8.0

molstar - v4.7.1

molstar - v4.7.0

molstar - v4.6.0

molstar - v4.5.0

molstar - v4.4.1

molstar - v4.3.0

[v4.3.0] - 2023-05-26

What's Changed

New Contributors

molstar - v4.2.0

molstar - v4.1.0

molstar -

molstar - v4.0.0

molstar - v3.45.0

molstar - v4.0.0-beta.0

molstar - v3.44.0

molstar -

molstar - v3.43.0

molstar - v3.42.0

molstar - v3.41.0

molstar - v3.40.1

molstar - v3.39.0

molstar - v3.38.3

molstar - v3.38.2

molstar - v3.38.1

molstar - v3.38.0

molstar - v3.37.1

molstar - v3.37.0

molstar - v3.36.1

molstar - v3.35.0

molstar - v3.34.0

molstar - v3.33.0

molstar -

molstar -

molstar -

molstar - v3.31.2

molstar - v3.31.1

molstar - v3.30.0

molstar - v3.29.0

molstar -

molstar -

molstar - v3.26.0

molstar - v3.25.1

molstar - v3.25.0

molstar - v3.24.0

molstar -

molstar - v3.22.0

molstar - v3.21.0

molstar - v3.20.0

molstar - v3.19.0

molstar - v3.18.0

molstar - v3.17.0

molstar -

molstar -

molstar -

molstar - v3.13.0

molstar -

molstar - v3.12.0

molstar - v3.11.0

molstar - v3.10.2

molstar - v3.10.1

molstar - v3.10.0