CHANGELOG.md



To find the state of this project's repository at the time of any of these versions, check out the tags.


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]

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


[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.