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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]

  • 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

[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
  • 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.