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CHANGELOG.md

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1.6.5

  • Added optional "direction cones" to cartoons visualization.

1.6.5

  • Added BGSU RNA Loop Annotation.

1.6.4

  • Updated/fixed carbohydrate selection behaviour.

1.6.3

  • Fixed screenshot support.

1.6.2

  • Increased camera rotation speed.

1.6.1

  • Added "particle coloring" extension.

1.6.0

  • Better show interactions between different components of a molecule.
  • Better default representation of molecules.
  • Added 3D SNFG carbohydrate representation.

1.5.1

  • Support for _struct_conn mmCIF category.
  • Show metallic bonds in balls and sticks models.

1.5.0

  • Support for labels.
  • Default theme changed to light.

1.4.4

  • Updated DensityServer mapping.

1.4.3

  • Updated PDBe Validation Report support to the latest version of the API.

1.4.2

  • Simplified downloading/opening molecule data.
  • PDBe Validation Reports are no longer applied to HET residues.

1.4.1

  • BinaryCIF is now the default format.

1.4.0

  • Updated Density Streaming to work with the new DensityServer.
  • Added examples.

1.3.2

  • Fixed Density Streaming to work on multiple structures at the same time.

1.3.1

  • Automatic detail for molecular surfaces => improved performance for large molecules.
  • Higher automatic detail for small molecules.

1.3.0

  • Updated for "LiteMol 2".

1.2.1

  • Performance updates thanks to rewrite of the Computation/Task API.

1.2.0

  • Support for density streaming vie DensityServer.

1.1.14

  • Support for PDBe EMDB density data.

1.1.13

  • It is now possible to select 'Show: Everything' in the dynamic denisty surface behaviour.
  • Fixed/improved support for CA/P-only models.

1.1.12

  • Help for viewport.
  • Touch slabbing.
  • Mouse wheel now works similar to PyMOL.
  • Basic ValidatorDB support.

1.1.11

  • Added support for popup messages (toasts).
  • Fog no longer affects selected residue, ambience, and dynamic density data.
  • Expandable transform controls no longer collapse when a value changes.

1.1.10

  • Changed how visual interactivity works.
    • Repeatedly clicking on any element clears the selection.
    • Clicking on dynamically created "ambient" residues now shifts the selection.

1.1.9

  • Ability to manually decompress binary AJAX responses.
  • Support for specifying absolute iso values for density data.

1.1.8

  • Added secondary structure (helices and sheets) approximation for cartoons visualization if not present in the input file.
  • Fixed molecule highlight info to show authAsymId instead of asymId for highlighted residues.

1.1.7

  • Support for ?loadFromURL=url and loadFromURLFormat=format query params,

1.1.6

  • Support for ?loadFromPDB=ID URL query to enable loading of default structures.

1.1.5

  • Improved color picker.

1.1.4

  • Fixed bond display between atoms that have no altLoc specified and these that do.

1.1.3

  • Added rainbow coloring for molecules.
  • Coordinate Streaming now uses BinaryCIF.

1.1.2

  • Added support for BinaryCIF.

1.1.1

  • Added basic SDF support.
  • Improved the behaviour of selecting the next node when the current one is removed.

1.1.0

  • This version is the result of refactoring the "format" support in the Core to better support different formats in the future.
  • To support these features, refactored parsing of molecular and desnity data.
    • This introduces a few breaking changes.
    • Most of these changes happen in the Plugin Spec.
    • Outside of the spec, the most notable change change is renaming Bootstrap.Entity.Transformer.Molecule.CreateFromCif to Bootstrap.Entity.Transformer.Molecule.CreateFromMmCif and Bootstrap.Entity.Transformer.Density.ParseCcp4 to Bootstrap.Entity.Transformer.Density.ParseBinary.
    • Refer to changelogs for Core, Bootstrap, and Plugin for more details.
  • Added the ability to download/open/parse old PDB files.

1.0.14

  • Added query flatten and function Fragment.find(query). (for example residuesByName('ALA').flatten(f => f.find(atomsByElement('C')))).

1.0.13

  • Added xs.intersectWith(ys) query.
  • Fixed and issue with ambientResidues/Atoms query when used inside "inside" query.
  • Fixed transparent objects incorrectly being made interactive when updating visibility.
  • Fixed a mouse-scrolling issue that would scroll the entire page is scrolled on top of the plugin.

1.0.12

  • Updated some internals (the way "collapsed" transforms are handled).

1.0.11

  • Added behaviour to unselect elements on repeated click.
  • Added new queries: atomsByElement, atomsByName, atomsById, residuesByName, residuesById, chainsById.

1.0.10

  • Added BRIX density data support.

1.0.9

  • Fixed mouse issues related to scrollbar position.
  • Toggling expand no longer resets scrollbar position to 0.

1.0.8

  • Screenshot support.

1.0.7

  • Fix to overlapping secondary structure elements.

1.0.6

  • Added support for wireframe models of all surfaces.
  • Camera zoom reversed (moving mouse down brings the structure closer).

1.0.5

  • Fix for visibility state not updating in Chrome.
  • Fix for strange behaviour of themes when updating visuals.
  • Fix of assembly generation.
  • Better handling of AJAX errors.
  • Fixed slider issues in chrome.
  • Align label of the header in the "transform panel" to the center + added bottom border.

1.0.4

  • Fixes in assembly/symmetry generation.
  • Tweaks in atom highlight label.
  • Added atom count to molecule model nodes.

1.0.3

  • Added support for sequence annotations.

1.0.2

  • Added support for validation coloring.

1.0.1

  • Fix for non-displaying C-alpha only molecules.

1.0.0

  • Initial release.