TmMolStar/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]

[v3.45.0] - 2023-02-03

• 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] - 2023-01-06

• 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.