molstar/CHANGELOG.md

Change Log

All notable changes to this project will be documented in this file, following the suggestions of Keep a CHANGELOG. This project adheres to Semantic Versioning for its most widely used - and defacto - public interfaces.

Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.

[Unreleased]

• Fix exported image artifacts on transparent background with emissive, bloom, or antialiasing
• Fix cel-shaded ambient color being stripped to luminance (now uses full RGB, matching the classic lighting path)
• Fix empty transforms default in ShapeFromPly
• Use morton order for spheres in dot visual with lod-levels
• Add Camera.changed event and rotation/translation setter/getter
• Add instanceGranularity: 'auto' as a memory guard
• Honor instanceGranularity in Visual.getLoci
• Add mesoscale representation preset
• Add presets option to ObjectList param definition
• Fix memory leak in State.dispose() not invoking transformer dispose callbacks for live cells
• Fix bugs in ModelServer surroundingLigands endpoint, resulting in omitWater not honored
• Fix Volume and Isosurface getBoundingSphere ignoring instances
• Fix aromatic ring detection not accounting for hybridization
• Add axis param to camera spin/rock animation
• Fix SSAO half/quarter resolution textures for multi-scale
• Non-covalent interactions: water bridge support

[v5.9.0] - 2026-05-03

• Fix edge case when PluginSpec.animations is empty
• Add 8K UHD option to ViewportScreenshotHelper
• Handle MRC files with empty length header fields
• Handle CCD bonds with Deuterium atoms
• [Breaking] ComponentBond.Entry.map now returns ComponentBond.Pairs
• Fix volume slice marking performance regression
• Add GPU procedural animation (wiggle & tumble)
  • Per-vertex wiggle via fbm noise (position & group mode)
  • Per-instance tumble via fbm noise (rotation + translation)
  • Wiggle theme layer for data-driven per-group wiggle
  • enableAnimation Canvas3D param for global toggle
• Add AnimateTime built-in for, e.g., exporting procedural animation
• Add Procedural Animation panels
  • Viewer: structure dynamics & uncertainty
  • Mesoscale Explorer: entity dynamics
• Fix GraphQLClient missing required headers
• [Breaking] Use Record instead of Array for headers (assets & data-source utils)

[v5.8.0] - 2026-04-03

• Dependencies: remove utils.promisify, node-fetch (#1797)
• Fix circular dependency which causes crash in bundlers (#1791)
• Add putty as a mol-view-spec representation.
• Fix detecting sidechain-only structures as coarse-grained (#1420)
• Fix clip-object transform due to missing axis normalization
• Sequence alignment: Fix return type & improve scoring for unknown residues
• Use PDB SEQRES block to show unresolved residues in Sequence toolbar
• Canvas3D debug-helpers
  • [Breaking] Move helpers to an extension as a PluginBehavior (params are no longer part of Canvas3D)
  • Add helpers for clip-object, direct-volume, image, mesh
• Fix StructureComponent node update throwing error when substructure empty
• CSS: Avoid tooltip box flickering when hovering something under it
• Volume slice visual
  • Fix support for volume instances
  • Fix plane mode: ensure normalized & correctly oriented
• MolViewSpec
  • Add VolumeStreamingExtension (molstar_volume_streaming custom property)
  • Fix focusing empty selections
• Avoid re-calculating static model properties for trajectories

[v5.7.0] - 2026-02-28

• Text label improvements
  • Improve label background vertical centering
  • Handle label depth variant for correct transparent background
  • Draw border under text using fragment depth to prevent overlap on adjacent characters
  • Clamp border width to avoid exceeding SDF range
  • Increase font atlas quality (2x font size multiplier)
• TM-align performance improvements (#1745)
• Disable transparent outline close to opaque elements
• Add axis param to trackball spin & rock animation
• Color smoothing fixes (#1747)
  • Use correct instance for non instance-type
  • Never transform for non instance-type
  • Add extra radius to gaussian surface boundingsphere
• MolViewSpec
  • Add MVSData.toMVSX function and mvs-mvsj-to-mvsx.js CLI utility
• [Breaking] Add PQR file format support (#157)
  • Replace isPdbqt with variant param in TrajectoryFromPDB
• Add CustomVolumeProperty (like for models and structures)
• Geometry export
  • Fix missing usePalette support
  • Fix vertex-based coloring for non-mesh geometries
  • Support line-strips
  • Support vertex-based sizing
• Support memory efficient line-strips in Lines geometry,
  • Add StripLinesBuilder
• Add computeFrenetFrames helper
• Streamlines support
  • Add basic calculation method
  • Add custom-volume-property
  • Add representation with lines and tube-mesh visuals
• Fix TextCtrl always moving cursor to end position
• Add vertex and vertexInstance granularity support for size themes
• Add transform and domain parameters to volume-value size theme
• Fix parsing of single charge type_symbols (e.g., N+) in cif-core
• Detect metal-coordination when parsing pdb
• Handle additional elements in guessElementSymbol* (As, Li, Ga)
• Add more element-pair thresholds for bonding (Ag-S, CoSb, Ga-F)
• Add metalCoordination style param (dashed, solid) for bonds
• Fix unitSymmetryGroups for representations with includeParent enabled
• Add convexHull helper
• Add Structure.coordination sites
• Add Polyhedron representation showing coordination sites
• Guard against xr-spatial-tracking blocked in Permissions-Policy

[v5.6.1] - 2026-01-23

• Disable occlusion culling in ImagePass (#1758)
• MolViewSpec
  • Fix MVSAnnotationStructureComponent not updating properly when parent structure changes

[v5.6.0] - 2026-01-18

• Handle Hex codes that are submitted with alpha channels by ignoring the alpha channel (#1746)
• Only show "already registered transformer" warnings in non-production builds
• Fix label_seq_id assignment in PDB parser to use 1-based linear indexing (#1730) if:
  • when insertion codes are present
  • SEQRES records are present
• Viewer app
  • Add action: 'focus' support to Viewer.structureInteractivity
  • Add viewportFocusBehavior: 'secondary-zoom'
• MolViewSpec
  • Validation treats undefined same as missing value
  • Increase default size of carbohydrate representation
  • color_from_uri and color_from_source take selector parameter
  • Add keepCameraOrientation option for loading functions
  • label_from_* and tooltip_from_* take text_format parameter
  • label_from_* take group_by_fields parameter
• Tweak Gaussian Density smoothness default range (less artefacts)
• Support includeParent for Gaussian Surface (disables GPU support)
• Support floodfill before surface extraction (off, interior, exterior)
  • For Isosurface, Molecular Surface, Gaussian Surface
• Fix to_mmCIF writing duplicate categories under certain conditions (#1738)
• Add stable random number generator (PCG)
  • ME grayscale colors; dot offset; SSAO hemisphere vectors
  • Use blue noise for SSAO hemisphere vectors
• Fix SSAO darkening when sampling background/offscreen pixels
• Adding structure wireframe visuals on molecular and gaussian surfaces
• Fix caching of __srcIndexArray__
• Prevent self-occlusion on quaternary amine
• Fix outline postprocessing artifacts (black bands) on membrane layers at grazing view angles in Illustrative mode (#1749)
• Remove fence from Canvas3D.render to not interfer with requestAnimationFrame
• Fix boundingSphere reuse in structure visuals (was triggering extra calculation)
• Use PDB seqres record to deduce entity information
• Add lipid components names used in amber ff

[v5.5.0] - 2025-12-22

• Viewer app
  • Move viewer extensions, options, and presets to a separate file
  • Add molstar.lib export providing access to a wide range of functionality previously not available from the compiled bundle
  • Add Viewer.subscribe method that keeps track of subscribed plugin events and disposes them together with the parent viewer
  • Add Viewer.structureInteractivity that makes it easy to highlight/select elements on the loaded structure
  • Add viewportBackgroundColor and viewportFocusBehavior options
  • Add mvs.html example to showcase the new functionality combined with MolViewSpec
  • Add dark and blue color theme support (import theme/dark.css or theme/blue.css instead of the default molstar.css)
• MolViewSpec extension
  • Add tryGetPrimitivesFromLoci that makes it easier to access primitive element data from hover/click interactions
  • Add getCurrentMVSSnapshot to obtain source data for the currently displayed snapshot
• Add TM-align structure-based protein alignment algorithm
  • New TMAlign namespace in mol-math/linear-algebra/3d/tm-align.ts
  • New tmAlign function in mol-model/structure/structure/util/tm-align.ts
  • Returns TM-score, RMSD, alignment mapping, and transformation matrix
• Molecular Surface
  • Fix "auto" quality params not hidden
  • Fix calculation when probe diameter is smaller then resolution
• Fix webgl1 shader syntax
• Fix program not compiled for sync picking
• Fix missing gl.flush for async picking (needed for Safari)
• Add Residue Charge color scheme (#1722)
• Add dropdown indicator for mapped parameter definitions and adjust "more options" icon
• Fix flipSided for meshes
• [Breaking] Interior coloring
  • Remove global interiorDarkening, interiorColorFlag, interiorColor
  • Add per-geometry interiorColor, interiorSubstance
• Add label/auth_comp_id to StructureProperties.residue
  • Previously, this has been only been present on .atom (since residue name can alter on per-atom basis), but this has been a bit confusing for the general use-case
• Move canvas "checkered background" logic to canvas3d.ts and only apply it when transparentBackground is on
  • This prevents ugly flickering during plugin initialization
• Fix unit hash collision issues (#1721)

[v5.4.2] - 2025-12-07

• Fix postprocessing issues with SSAO and outlines for large structures (#1387)
• Reduce automatic quality on standalone HMD devices

[v5.4.1] - 2025-11-16

• Fix ugly camera clipping in snapshot transitions
• Add viewport button to toggle illumination mode
• Fix bounding sphere computation for 3D text
• Structure bounding sphere includes atom VDW radii / coarse sphere radii
• Relax camera limits to allow focusing any selection with >1 atom
• MolViewSpec
  • Fix appendSnapshots when loading MVSX
  • Fix all-selector color not applying on substructure
  • Fix primitives in root not being transformed with reference structure
  • Color themes do not prefer smoothing (improves performance in animations)
  • Allow canvas background interpolation
• Fix direct-volume not drawn in illumination mode
• Fix default trackball animated spin speed
• Use PluginCommands to set canvas3d props in camera behavior
• Volume improvements
  • Add Volume.periodicity
  • Wrap isosurfaces for periodic volumes
  • Fix dimensions for slices
• Add support for Input Method Editor (IME) to text params input
• Update guessCifVariant to detect density files not generated by the VolumeServer

[v5.3.0] - 2025-11-05

• Update loading message in MVS Stories Viewer
• Add Canvas3D.setAttribs
• Fix normalizeWheel "spin" calculation fallback
• MolViewSpec
  • Add support for "topology" formats (TOP, PRMTOP, PSF)
  • Add support for additional "coordiates" formats (NCTRAJ, DCD, TRR)
  • Fix coarse structure selection
  • Fix missing default param values in primitives_from_uri

[v5.2.0] - 2025-10-31

• Handle transparency updates on ImagePass
• Fix CIF parser edge case when the last token is escaped
• MolViewSpec
  • Fix tooltips persisting across snapshots
  • Fix CIF annotations with no selector columns being ignored
  • Fix trackpad lock when camera up parallel to direction
  • Add clipping support for primitives
  • Support near camera distance

[v5.1.2] - 2025-10-25

• Fix createColorScaleByType when offsets are available
• Get bond orders from non-standard CONECT records in PDB files
• Remove outdated gl_FrontFacing workaround for buggy drivers
• Fix clip objects for direct-volume rendering
• Support "magic window" style AR (via WebXR)
• Fix PluginState.getStateTransitionFrameIndex
• Update GlycamSaccharideNames and Monosaccharides in carbohydrates/constants.ts
• Support custom ref resolvers in State
• Add full-screen mode support to layout manager
  • Add show-toggle-fullscreen URL param option to Viewer app
• MolViewSpec
  • Support accessing Mol* State nodes by MVS-provided ref
  • Add support for DX map format
  • Better support for coarse structures in MVS:
    • Support for MVS annotations on coarse structures (color_from_, tooltip_from_)
    • Support for MVS labels on coarse structures (label, label_from_*)
    • (Other things already worked on coarse structures before: tooltip, color,component, primitives, component_from_, primitives_from_)
  • Tidy up MVS builder:
    • Add sphere and angle methods
    • [Breaking] Rename builder method primitives_from_uri -> primitivesFromUri

[v5.0.0] - 2025-09-28

• [Breaking] Renamed some color schemes ('inferno' -> 'inferno-no-black', 'magma' -> 'magma-no-black', 'turbo' -> 'turbo-no-black', 'rainbow' -> 'simple-rainbow')
• [Breaking] Box3D.nearestIntersectionWithRay -> Ray3D.intersectBox3D
• [Breaking] Plane3D.distanceToSpher3D -> distanceToSphere3D (fix spelling)
• [Breaking] fix typo MarchinCubes -> MarchingCubes
• [Breaking] PluginContext.initViewer/initContainer/mount are now async and have been renamed to include Async postfix
• [Breaking] Add Volume.instances support and a VolumeInstances transform to dynamically assign it
  • This change is breaking because all volume objects require the instances field now.
• [Breaking] Canvas3D.identify now expects Vec2 or Ray3D
• [Breaking] TrackballControlsParams.animate.spin.speed now means "Number of rotations per second" instead of "radians per second"
• [Breaking] PluginStateSnapshotManager.play now accepts an options object instead of a single boolean value
• Update production build to use esbuild
• Emit explicit paths in imports in lib/
• Fix outlines on opaque elements using illumination mode
• Change Representation.Empty to a lazy property to avoid issue with some bundlers
• MolViewSpec extension:
  • Generic color schemes (palette parameter for color_from_* nodes)
  • Annotation field remapping (field_remapping parameter for color_from_* nodes)
  • representation node: support custom property molstar_representation_params
  • Add backbone and line representation types
  • primitives node: support custom property molstar_mesh/label/line_params
  • canvas node: support custom property molstar_postprocessing with the ability to customize outline, depth of field, bloom, shadow, occlusion (SSAO), fog, and background
  • clip node support for structure and volume representations
  • grid_slice representation support for volumes
  • Support tethers and background for primitive labels
  • Support snapshot_key parameter on primitives that enables transition between states via clicking on 3D objects
  • Inline selectors and MVS annotations support instance_id
  • Support matrix on transform params
  • Support surface_type (molecular / gaussian) on for surface representation nodes
  • Add instance node type
  • Add transform.rotation_center property that enables rotating an object around its centroid or a specific point
  • Support transforming and instancing of structures, components, and volumes
  • Use params hash for node version for more performant tree diffs
  • Add Snapshot.animation support that enables animating almost every property in a given tree
  • Add createMVSX helper function
  • Support Mol* trackball animation via animation.custom.molstar_trackball
  • MVSX - use Murmur hash instead of FNV in archive URI
  • Support additional file formats (pdbqt, gro, xyz, mol, sdf, mol2, xtc, lammpstrj)
  • Support loading trajectory coordinates from separate nodes
  • Trigger markdown commands from primitives using molstar_markdown_commands custom extensions
  • Support molstar_on_load_markdown_commands custom state on the root node
  • Print tree validation errors to plugin log
• Added new color schemes, synchronized with D3.js ('inferno', 'magma', 'turbo', 'rainbow', 'sinebow', 'warm', 'cool', 'cubehelix-default', 'category-10', 'observable-10', 'tableau-10')
• Snapshot Markdown improvements
  • Add MarkdownExtensionManager (PluginContext.managers.markdownExtensions)
  • Support custom markdown commands to control the plugin via the [link](!command) pattern
  • Support rendering custom elements via the ![alt](!parameters) pattern
  • Support tables
  • Support loading images and audio from MVSX files
  • Indicate external links with ⤴
  • Audio support
  • Add PluginState.Snapshot.onLoadMarkdownCommands
• Avoid calculating rings for coarse-grained structures
• Fix isosurface compute shader normals when transformation matrix is applied to volume
• Symmetry operator naming for spacegroup symmetry - parenthesize multi-character indices (1_111-1 -> 1_(11)1(-1))
• Add SymmetryOperator.instanceId that corresponds to a canonical operator name (e.g. ASM-1, ASM-X0-1 for assemblies, 1_555, 1_(11)1(-1) for crystals)
• Mol2 Reader
  • Fix column count parsing
  • Add support for substructure
• Fix shader error when clipping flags are set without clip objects present
• Fix wrong group count calculation on geometry update (#1562)
• Fix wrong instance index in calcMeshColorSmoothing
• Add Ray3D object and helpers
• Volume slice representation: add relativeX/Y/Z options for dimension
• Add StructureInstances transform
• mvs-stories app
  • Add story-id URL arg support
  • Add story-session-url URL arg support
  • Add "Download MVS State" link
  • Add "Open in Mol*" link
  • Add "Edit in MolViewStories" link for story states
• Add ray-based picking
  • Render narrow view of scene scene from ray origin & direction to a few pixel sized viewport
  • Cast ray on every input as opposed to the standard "whole screen" picking
  • Can be enabled with new Canvas3dInteractionHelperParams.convertCoordsToRay param
  • Allows to have input methods that are 3D pointers in the scene
  • Add ray: Ray3D property to DragInput, ClickInput, and MoveInput
• Add async, non-blocking picking (only WebGL2)
  • Refactor Canvas3dInteractionHelper internals to use async picking for move events
• Add enable param for post-processing effects. If false, no effects are applied.
• Dot volume representation improvements
  • Add positional perturbation to avoid camera artifacts
  • Fix handling of negative isoValues by considering only volume cells with values lower than isoValue (#1559)
  • Fix volume-value size theme
• Change the parsing of residue names in PDB files from 3-letter to 4-letter.
• Support versioning transform using a hash function in mol-state
• Support for "state snapshot transitions"
  • Add PluginState.Snapshot.transition that enables associating a state snapshot with a list states that can be animated
  • Add AnimateStateSnapshotTransition animation
  • Update the snapshots UI to support this feature
• Use "proper time" in the animation loop to prevent animation skips during blocking operations (e.g., shader complication)
• Add Hsl and (normalized) Rgb color spaces
• Add Color.interpolateHsl
• Add rotationCenter property to TransformParam
• Add Monolayer transparency (exploiting dpoit).
• Add plugin config item ShowReset (shows/hides "Reset Zoom" button)
• Fix transform params not being normalized when used together with param hash version
• Replace immer with mutative
• Fix renderer transparency check
• Add outlines improvements
• VolumeServer & "VolumeCIF": default to P 1 spacegroup
• Fix ColorScale for continuous case without offsets (broke in v4.13.0)
• Experimental: support for custom color themes in Sequence Panel
• Switch files.rcsb.org validation report URL to new endpoint /validation/view
• Improve picking of objects with too many groups, pick whole instance/object
• Add WebXR support
  • Requires immersive AR/VR headset
  • Supplements non-XR: enter/exit XR anytime and see (mostly) the same scene
  • Add Canvas3D.xr for managing XR sessions
  • Add PointerHelper for rendering XR input devices
  • Add XR button to Viewer and Mesoscale Explorer
  • Add XR button to render-structure in tests/browser
• Fix illumination denoising with transparency on transparent background
• Change the to_mmCIF function parameter from structure to structures to support either a single structure or an array of structures
• ModelServer and VolumeServer: add configurable robots.txt
• Adaptive parallel shader compilation
  • Split shader compilation into linking and finalizing
  • Start linking as early as possible and wait with finalizing to avoid blocking main thread
    • Use of KHR_parallel_shader_compile extension when available to check status
  • Add ShaderManager to compile shaders based on Canvas3D params and Scene content
  • Draw Scene only when shaders are ready
• Fix incorrect animation loop handling in the screenshot code

[v4.18.0] - 2025-06-08

• MolViewSpec extension:
  • Support for label_comp_id and auth_comp_id in annotations
  • Geometric primitives - do not render if position refers to empty substructure
  • Primitive arrow - nicer default cap size (relative to tube_radius)
  • Primitive angle_measurement - added vector_radius 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)

[v4.17.0] - 2025-05-22

• 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)

[v4.16.0] - 2025-05-20

• 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

[v4.15.0] - 2025-05-19

• 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

[v4.14.1] - 2025-05-09

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

[v4.14.0] - 2025-05-07

• 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
• Adjust max resolution of surfaces for auto quality (#1501)
• 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)

[v4.13.0] - 2025-04-14

• 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

[v4.12.0] - 2025-02-28

• 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

[v4.11.0] - 2025-01-26

• 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 triangle_colors, line_colors, 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)
• Fix behavior of Vec3.makeRotation(out, a, b) when a ≈ -b

[v4.10.0] - 2024-12-15

• 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

[v4.9.1] - 2024-12-05

• Fix iOS check when running on Node

[v4.9.0] - 2024-12-01

• 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

[v4.8.0] - 2024-10-27

• 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-IHM/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 ma_qa_metric_local_pairwise 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)

[v4.7.1] - 2024-09-30

• 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

[v4.7.0] - 2024-09-29

• 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".

[v4.6.0] - 2024-08-28

• 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-IHM/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

[v4.5.0] - 2024-07-28

• 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

[v4.4.1] - 2024-06-30

• 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

[v4.3.0] - 2024-05-26

• 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

[v4.2.0] - 2024-05-04

• 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] - 2024-03-31

• 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] - 2024-02-19

• 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] - 2024-02-04

• 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] - 2024-02-03

• 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

[v3.44.0] - 2024-01-06

• 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] - 2023-12-04

• 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)
• 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
• 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

[v3.13.0] - 2022-07-24

• 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

[v3.12.1] - 2022-07-20

• Fix plugin behavior dispose logic to correctly unsubscribe observables.

[v3.12.0] - 2022-07-17

• 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)

[v3.11.0] - 2022-07-04

• 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

[v3.10.2] - 2022-06-26

• Fix superfluous shader varying
• Improve use of gl_VertexID when possible

[v3.10.1] - 2022-06-26

• Fix groupCount when updating TextureMesh-based visuals

[v3.10.0] - 2022-06-24

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

[v3.9.1] - 2022-06-19

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

[v3.9.0] - 2022-05-30

• 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

[v3.8.2] - 2022-05-22

• Fix Scene.opacityAverage not taking xray shaded into account

[v3.8.1] - 2022-05-14

• 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

[v3.8.0] - 2022-04-30

• 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

[v3.7.0] - 2022-04-13

• 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.

[v3.6.2] - 2022-04-05

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

[v3.6.1] - 2022-04-03

• Fix React18 related UI regressions.

[v3.6.0] - 2022-04-03

• 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.

[v3.5.0] - 2022-03-25

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

[v3.4.0] - 2022-03-13

• 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

[v3.3.1] - 2022-02-27

• Fix issue with unit boundary reuse (do at visual level instead)
• Add option to ignore ions for inter-unit bond computation

[v3.3.0] - 2022-02-27

• Fix parsing contour-level from emdb v3 header files
• Fix invalid CSS (#376)
• Fix "texture not renderable" & "texture not bound" warnings (#319)
• Fix visual for bonds between two aromatic rings
• Fix visual for delocalized bonds (parsed from mmcif and mol2)
• Fix ring computation algorithm
• Add UnitResonance property with info about delocalized triplets
• Resolve marking in main renderer loop to improve overall performance
• Use throttleTime instead of debounceTime in sequence viewer for better responsiveness
• Change line geometry default scaleFactor to 2 (3 is too big after fixing line rendering)
• Trajectory animation performance improvements
  • Reuse Model.CoarseGrained for coordinate trajectories
  • Avoid calculating InterUnitBonds when Structure.parent ones are empty
  • Reuse unit boundary if sphere has not changed too much
  • Don't show 'inter-bond' and 'element-cross' visuals in line representations of polymerAndLigand preset
• Fix additional mononucleotides detected as polymer components
• Fix and improve canRemap handling in IntraUnitBonds
• Reuse occlusion for secondary passes during multi-sampling
• Check if marking passes are needed before doing them
• Add resolutionScale parameter to allow trading quality of occlusion for performance

[v3.2.0] - 2022-02-17

• Rename "best database mapping" to "SIFTS Mapping"
• Add schema and export support for atom_site.pdbx_sifts_xref_* fields
• Add schema export support for atom_site.pdbx_label_index field
• Add traceOnly parameter to chain/UniProt-based structure alignment
• Store IndexPairBonds as a dynamic property.

[v3.1.0] - 2022-02-06

• Fix xrayShaded & ignoreLight params not working at the same time
• Add ignoreLight to component params
• Tweaks for cleaner default representation style
  • Cartoon: use nucleotide-ring instead of nucleotide-block
  • Focus: use xrayShaded instead of opacity; adjust target size; don't show non-covalent interactions twice
• Fix representation preset side effects (changing post-processing parameters, see #363)
• Add Quick Styles panel (default, illustrative, stylized)
• Fix exported structure missing secondary-structure categories (#364)
• Fix volume streaming error message: distinguish between missing data and server error (#364)

[v3.0.2] - 2022-01-30

• 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

[v3.0.1] - 2022-01-27

• 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)

[v3.0.0] - 2022-01-23

• Assembly handling tweaks:
  • Do not include suffix for "identity assembly operators"
  • Do not include assembly-related categories to export if the structure was composed from an assembly
  • Special case for structAsymMap if Mol* asym id operator mapping is present
• Support for opening ZIP files with multiple entries
• Add Model Export extension
• Bugfix: Automatically treat empty string as "non-present" value in BinaryCIF writer.
• Fix coarse model support in entity-id color theme
• Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
• Add custom colors to "element-symbol", "molecule-type", "residue-name", and "secondary-structure" themes
• Support/bugfixes for atom_site.pdbx_sifts_xref categories
• Improve/fix marking of InteractionsIntraUnitVisual (mark when all contact-feature members are given)

[v3.0.0-dev.10] - 2022-01-17

• Fix getOperatorsForIndex
• Pass animation info (current frame & count) to state animations
  • Fix camera stutter for "camera spin" animation
• Add formal charge parsing support for MOL/SDF files (thanks @ptourlas)
• [Breaking] Cleaner looking MembraneOrientationVisuals defaults
• [Breaking] Add rock animation to trackball controls
  • Add animate to TrackballControlsParams, remove spin and spinSpeed
  • Add animate to SimpleSettingsParams, remove spin
• Add "camera rock" state animation
• Add support for custom colors to "molecule-type" theme
• [Breaking] Add style parameter to "illustrative" color theme
  • Defaults to "entity-id" style instead of "chain-id"
• Add "illustrative" representation preset

[v3.0.0-dev.9] - 2022-01-09

• Add PDBj as a pdb-provider option
• Move Viewer APP to a separate file to allow use without importing light theme & index.html
• Add symmetry support for mol2 files (only spacegroup setting 1)
• Fix mol2 files element symbol assignment
• Improve bond assignment from IndexPairBonds
  • Add key field for mapping to source data
  • Fix assignment of bonds with unphysical length
• Fix label/stats of single atom selection in multi-chain units

[v3.0.0-dev.8] - 2021-12-31

• Add PluginFeatureDetection and disable WBOIT in Safari 15.
• Add disable-wboit Viewer GET param
• Add prefer-webgl1 Viewer GET param
• [Breaking] Refactor direct-volume rendering
  • Remove isosurface render-mode (use GPU MC instead)
  • Move coloring into theme (like for other geometries/renderables)
    • Add direct color type
    • Remove color from transfer-function (now only alpha)
    • Add direct-volume color theme support
    • Add volume-value color theme
• [Breaking] Use size theme in molecular/gaussian surface & label representations
  • This is breaking because it was hardcoded to physical internally but the repr size theme default was uniform (now physical)

[v3.0.0-dev.7] - 2021-12-20

• Reduce number of created programs/shaders
  • Support specifying variants when creating graphics render-items
  • Change double-side shader param from define to uniform
  • Remove dMarkerType shader define (use uMarker as needed)
  • Support to ignore defines depending on the shader variant
  • Combine pickObject/pickInstance/pickGroup shader variants into one
  • Combine markingDepth/markingMask shader variants into one
  • Correctly set shader define flags for overpaint, transparency, substance, clipping
• [Breaking] Add per-object clip rendering properties (variant/objects)
  • SimpleSettingsParams.clipping.variant/objects and RendererParams.clip were removed

[v3.0.0-dev.6] - 2021-12-19

• Enable temporal multi-sampling by default
  • Fix flickering during marking with camera at rest
• Enable aromaticBonds in structure representations by default
• Add PluginConfig.Structure.DefaultRepresentationPreset
• Add ModelArchive support
  • schema extensions (e.g., AlphaFold uses it for the pLDDT score)
  • ModelArchive option in DownloadStructure action
  • model-archive GET parameter for Viewer app
  • Viewer.loadModelArchive method
• Improve support for loading AlphaFold structures
  • Automatic coloring by pLDDT
  • AlphaFold DB option in DownloadStructure action
  • afdb GET parameter for Viewer app
  • Viewer.loadAlphaFoldDb method
• Add QualityAssessment extension (using data from ma_qa_metric_local mmcif category)
  • pLDDT & qmean score: coloring, repr presets, molql symbol, loci labels (including avg for mutli-residue selections)
  • pLDDT: selection query
• Warn about erroneous symmetry operator matrix (instead of throwing an error)
• Added createPluginUI to mol-plugin-ui
  • Support onBeforeUIRender to make sure initial UI works with custom presets and similar features.
• [Breaking] Removed createPlugin and createPluginAsync from mol-plugin-ui
  • Please use createPluginUI instead
• Improve aromatic bonds handling
  • Don't detect aromatic bonds for rings < 5 atoms based on planarity
  • Prefer atoms in aromatic rings as bond reference positions

[v3.0.0-dev.5] - 2021-12-16

• Fix initial camera reset not triggering for some entries.

[v3.0.0-dev.4] - 2021-12-14

• Add bumpiness (per-object and per-group), bumpFrequency & bumpAmplitude (per-object) render parameters (#299)
• Change label representation defaults: Use text border instead of rectangle background
• Add outline color option to renderer
• Fix false positives in Model.isFromPdbArchive
• Add drag and drop support for loading any file, including multiple at once
  • If there are session files (.molx or .molj) among the dropped files, only the first session will be loaded
• Add drag and drop overlay
• Safari 15.1 - 15.3 WebGL 2 support workaround
• [Breaking] Move react and react-dom to peerDependencies. This might break some builds.

[v3.0.0-dev.3] - 2021-12-4

• Fix OBJ and USDZ export

[v3.0.0-dev.2] - 2021-12-1

• Do not include tests and source maps in NPM package

[v3.0.0-dev.0] - 2021-11-28

• Add multiple lights support (with color, intensity, and direction parameters)
• [Breaking] Add per-object material rendering properties
  • SimpleSettingsParams.lighting.renderStyle and RendererParams.style were removed
• Add substance theme with per-group material rendering properties
• StructureComponentManager.Options state saving support
• ParamDefinition.Group.presets support

[v2.4.1] - 2021-11-28

• Fix: allow atoms in aromatic rings to do hydrogen bonds

[v2.4.0] - 2021-11-25

• Fix secondary-structure property handling
  • StructureElement.Property was incorrectly resolving type & key
  • StructureSelectionQuery helpers 'helix' & 'beta' were not ensuring property availability
• Re-enable VAO with better workaround (bind null elements buffer before deleting)
• Add Representation.geometryVersion (increments whenever the geometry of any of its visuals changes)
• Add support for grid-based smoothing of Overpaint and Transparency visual state for surfaces

[v2.3.9] - 2021-11-20

• Workaround: switch off VAO support for now

[v2.3.8] - 2021-11-20

• Fix double canvas context creation (in plugin context)
• Fix unused vertex attribute handling (track which are used, disable the rest)
• Workaround for VAO issue in Chrome 96 (can cause WebGL to crash on geometry updates)

[v2.3.7] - 2021-11-15

• Added ViewerOptions.collapseRightPanel
• Added Viewer.loadTrajectory to support loading "composed" trajectories (e.g. from gro + xtc)
• Fix: handle parent in Structure.remapModel
• Add rounded and square helix profile options to Cartoon representation (in addition to the default elliptical)

[v2.3.6] - 2021-11-8

• Add additional measurement controls: orientation (box, axes, ellipsoid) & plane (best fit)
• Improve aromatic bond visuals (add aromaticScale, aromaticSpacing, aromaticDashCount params)
• [Breaking] Change adjustCylinderLength default to false (set to true for focus representation)
• Fix marker highlight color overriding select color
• CellPack extension update
  • add binary model support
  • add compartment (including membrane) geometry support
  • add latest mycoplasma model example
• Prefer WebGL1 in Safari 15.1.

[v2.3.5] - 2021-10-19

• Fix sequence viewer for PDB files with COMPND record and multichain entities.
• Fix index pair bonds order assignment

[v2.3.4] - 2021-10-12

• Fix pickScale not taken into account in line/point shader
• Add pixel-scale, pick-scale & pick-padding GET params to Viewer app
• Fix selecting bonds not adding their atoms in selection manager
• Add preferAtoms option to SelectLoci/HighlightLoci behaviors
• Make the implicit atoms of bond visuals pickable
  • Add preferAtomPixelPadding to Canvas3dInteractionHelper
• Add points & crosses visuals to Line representation
• Add pickPadding config option (look around in case target pixel is empty)
• Add multipleBonds param to bond visuals with options: off, symmetric, offset
• Fix argparse config in servers.

[v2.3.3] - 2021-10-01

• Fix direct volume shader

[v2.3.2] - 2021-10-01

• Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.

[v2.3.1] - 2021-09-28

• Add Charmm saccharide names
• Treat missing occupancy column as occupancy of 1
• Fix line shader not accounting for aspect ratio
• [Breaking] Fix point repr & shader
  • Was unusable with wboit
  • Replaced pointFilledCircle & pointEdgeBleach params by pointStyle (square, circle, fuzzy)
  • Set pointSizeAttenuation to false by default
  • Set sizeTheme to uniform by default
• Add markerPriority option to Renderer (useful in combination with edges of marking pass)
• Add support support for chem_comp_bond and struct_conn categories (fixes ModelServer behavior where these categories should have been present)
• Model and VolumeServer: fix argparse config

[v2.3.0] - 2021-09-06

• Take include/exclude flags into account when displaying aromatic bonds
• Improve marking performance
  • Avoid unnecessary draw calls/ui updates when marking
  • Check if loci is superset of visual
  • Check if loci overlaps with unit visual
  • Ensure Interval is used for ranges instead of SortedArray
  • Add uniform marker type
  • Special case for reversing previous mark
• Add optional marking pass
  • Outlines visible and hidden parts of highlighted/selected groups
  • Add highlightStrength/selectStrength renderer params

[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)

[v2.2.2] - 2021-08-11

• Fix TransformData issues #133
• Fix mol-script query compiler const expression recognition.

[v2.2.1] - 2021-08-02

• 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

[v2.2.0] - 2021-07-31

• 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.

[v2.1.0] - 2021-07-05

• Add parameter for to display aromatic bonds as dashes next to solid cylinder/line.
• Add backbone representation
• Fix outline in orthographic mode and set default scale to 2.

[v2.0.7] - 2021-06-23

• 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).

[v2.0.6] - 2021-06-01

• 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.

[v2.0.5] - 2021-04-26

• Ability to pass Canvas3DContext to PluginContext.fromCanvas.
• Relative frame support for Canvas3D viewport.
• Fix bug in screenshot copy UI.
• Add ability to select residues from a list of identifiers to the Selection UI.
• Fix SSAO bugs when used with Canvas3D viewport.
• Support for full pausing (no draw) rendering: Canvas3D.pause(true).
• Add MeshBuilder.addMesh.
• Add Torus primitive.
• Lazy volume loading support.
• [Breaking] Viewer.loadVolumeFromUrl signature change.
  • loadVolumeFromUrl(url, format, isBinary, isovalues, entryId) => loadVolumeFromUrl({ url, format, isBinary }, isovalues, { entryId, isLazy })
• Add TextureMesh support to geo-export extension.

[v2.0.4] - 2021-04-20

• [WIP] Mesh export extension
• Structure.eachAtomicHierarchyElement (#161)
• Fixed reading multi-line values in SDF format
• Fixed Measurements UI labels (#166)

[v2.0.3] - 2021-04-09

• Add support for ColorTheme.palette designed for providing gradient-like coloring.
• [Breaking] The zip function is now asynchronous and expects a RuntimeContext. Also added Zip() returning a Task.
• [Breaking] Add CubeGridFormat in alpha-orbitals extension.

[v2.0.2] - 2021-03-29

• Add Canvas3D.getRenderObjects.
• [WIP] Animate state interpolating, including model trajectories
• Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
• Fix VolumeFromDensityServerCif transform label

[v2.0.1] - 2021-03-23

• Exclude tsconfig.commonjs.tsbuildinfo from npm bundle

[v2.0.0] - 2021-03-23

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