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]

[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

Added

• Support for ColorTheme.palette designed for providing gradient-like coloring.

Changed

• [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

Added

• Canvas3D.getRenderObjects.
• [WIP] Animate state interpolating, including model trajectories

Changed

• Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.

Fixed

• VolumeFromDensityServerCif transform label

[v2.0.1] - 2021-03-23

Fixed

• 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.