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 #1105
• DOF shader by @corredD in #1103
• fix RMSD minification bug by @dsehnal in #1138
• await the the snapshot setting to avoid rendering while applying snap… by @corredD in #1140

New Contributors

• @vDusky made their first contribution in #1105

Full Changelog: v4.2.0...v4.3.0

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)

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 surface_ramp_above_mode=1
• Add rotation parameter to skybox background

v4.0.1

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

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• [Breaking] Remove cellpack extension (superseded by Mesoscale Explorer app)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

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

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

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

v3.43.1

• Fix react-markdown dependency

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