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]

[v3.0.0-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.